Array 1 117875-118764 **** Predicted by CRISPRDetect 2.4 *** >NZ_SEQU01000010.1 Clostridioides difficile strain LC4-009-0 NODE_10_length_209579_cov_49.6282, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ======================================= ================== 117875 29 100.0 38 ............................. AAAAAAGTCTCAATAACACCAGTCGAAGCAGAAAAATC 117942 29 100.0 36 ............................. CATTGTCAACATCATCTAATTTTTTTGTTACTGTAA 118007 29 100.0 37 ............................. TAGATTTTTTCACAAATAAACTTAACGAGTACAATGA 118073 29 100.0 39 ............................. TAGTTTTAAACTTTTTTTCTGGACATATTACAACATCAA 118141 29 100.0 37 ............................. TATCTTTAGCATTATATTTTTTAGTATCAGATGTGTG 118207 29 100.0 38 ............................. ATCTTTTAATTTTTATAACTAACTATTTACAAATTCAA 118274 29 100.0 38 ............................. TCTATCCACCCCCTTTTTTATAAATTTGCATTAAAAAA 118341 29 100.0 37 ............................. AAATTTGTAATATTATATAATCATCCTAAAACAAAAG 118407 29 100.0 38 ............................. AATAATGTTGATAAGACAGCAGAGGAAATAAAAGCTAG 118474 29 100.0 36 ............................. GTTATAGTCTTTTGGATAACTACCCAATTAGGATTT 118539 29 100.0 37 ............................. AAAAATATTATAGATACAAAAAAAGATTCAGAAAACA 118605 29 100.0 36 ............................. AAGTCACACCGCCCTCCACACGACACTATAATAATA 118670 29 93.1 37 .............C.........A..... AGTATAATGTTGAAAAGTTAGAGAGTACAATCAAGAA 118736 29 69.0 0 A.....C.........AAT....AG..TA | ========== ====== ====== ====== ============================= ======================================= ================== 14 29 97.3 37 GTTTTATATTAACTAAGTGGTATGTAAAT # Left flank : TACAATTTATAGAGTGGAGTTCATACAAAAGATTATCCTCCCAATGTATAGAAGGGAGGTGAGTATGTATGGATAATTTTTTACAAGGTGTACTAGCAAGTTTAGTTGCCAGTTTAATAGTTTACTTAAATAGTAAATTATTTAAAAAAGTAAAAAGCCACTCTGGCAGGAGCGACTTTAGTTTTGAACTAAAAATCAAGTTCAAAAAGAATAAACATTAGTATTTGAACTTCACTCTATGTCTAAATAGATTGTAGTTCTTCTTGTTTTTATTATACCACAAATTGGTACAGATATTCAAAAATAATATATTTATGATATAATAAAAATGTAAATAGTTTTGCAGTGAGCGATATTTGTTACAAAGTAGGGCTTAATGCTTGAAATATAAGGTGTTGAGGGCATGTGATAAGCTTTATCATTTGCACTACTCATGGTTCACTGCAAATTTAAGAGAGTTGCACATGTGTAAGCATTGAAAATGCCCAGTTTATTTTGGG # Right flank : AAAACATGTATTTATACTTAAATTCTGTACCTATATAAAAAAGTGAACTCTGTCAACAAAGCACTTTTTTATATAGATAAATTATCATTTTGTTTTAAGATAGAAGATACTAATGATAACTGTTTATCATTAGTATCTGTATGTACATAAAAGTTTAATTTTTTATATAAATTTGCTCTTTAGAAAAATGAGCAGTATCAATAAATATATTGTCTAAATTTTTTCTAGGAACTAGTTGACTAGCTATAAGATTAGCTTCAACTCTTTGATTGTTAGACTATGAAATTAAATTTAAAGGTTCATTCTTGGTCGTATAAATAGCTTTATTATTCGTATGTACTATAACAATTTTTGCCATCTGCTTTTGATAGATAAAGAGCTTTATCAGCTTTAGAAAATAAATCTTTATATAATTTAGTTGAATCATCAGTGAAGGCAATACCAATACTTAATGTTATTTTATGATTGTCCTTTACTTTTATTTTACTCGCATCATTTAA # Questionable array : NO Score: 6.12 # Score Detail : 1:0, 2:3, 3:0, 4:0.86, 5:0, 6:0.25, 7:0.01, 8:1, 9:1, # Score Legend : 1: cas, 2: likely_repeat, 3: motif_match, 4: overall_repeat_identity, 5: one_repeat_cluster, 6: exp_repeat_length, 7: exp_spacer_length, 8: spacer_identity, 9: log(total repeats) - log(total mutated repeats), # Primary repeat : GTTTTATATTAACTAAGTGGTATGTAAAT # Alternate repeat : NA # Directional analysis summary from each method: # Motif ATTGAAA(N) match prediction: NA Score: 0/4.5 # A,T distribution in repeat prediction: NA [Repeat is AT rich:79.31%AT] # Reference repeat match prediction: F [matched GTTTTATATTAACTAAGTGGTATGTAAAG with 100% identity] Score: 4.5/4.5 # Secondary Structural analysis prediction: NA [-0.50,0.00] Score: 0/0.37 # Array degeneracy analysis prediction: F [0-11] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [63.3-75.0]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [4.91,0.27 Confidence: HIGH] # Array family : I-B [Matched known repeat from this family], // Array 1 239569-240064 **** Predicted by CRISPRDetect 2.4 *** >NZ_SEQU01000001.1 Clostridioides difficile strain LC4-009-0 NODE_1_length_481821_cov_51.7422, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ======================================= ================== 239569 29 100.0 38 ............................. AGTATTTCAGCAATTTTACTTTTAATAACTTTATCAGC 239636 29 100.0 37 ............................. TCAATTTACCGTTTTTTTCAAATCTCACAACATCAGA 239702 29 100.0 37 ............................. CTATCGGCTTCTTGAAAAGCCTCATCTGCTCTATTTA 239768 29 96.6 37 ......C...................... TTCATTAAATCCCCAACCGAATTATCTTTCAGCATTT 239834 29 100.0 39 ............................. CATGCTGATAAGAATCTCTATGAACTTCGGAGGGAACCG 239902 29 100.0 37 ............................. TTGGGTATTTTGCTAAAAATAAAGCTATTAAATTAGA 239968 29 96.6 39 .C........................... CGTATTAACACCTGTTCGGCACTATCACAATAAACACAA 240036 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ======================================= ================== 8 29 99.2 38 GTTTTATATTAACTATATGGAATGTAAAT # Left flank : GGAGTTCATGTATCAAAAAATTATCCTCCCGACGCTAAGAAGGGAGGTGAATATACATGGATAATTTTTTACAAGGCATACTAGCAAGTCTATCTGCTAGCTTAATAGTTTATATAGCTAGCAAACTATTTAGAAAGCGTAAAAAACCACTCAAAGCGGCAACTAAGAGTGGTTGGGAATTTGATTTAAAAATCAGATTCCATAAAACTAAGTAATTTCTAAATTATGAACTCCACTCTACAGCAAAATAGATTGTAGTTCTTCTTGCTTTTATTATATCACAAATTGGTACAGATATTCAAAAATAATATTTTTATGATATAATAAAGTCATAGAAATTTTGCAGTGTTCGATTTTTTGAAGAAATTAAGGCTTAACAGTTGAAATATAAGGCATTGAGGACTTGTGATAAGTGTTATCAATTGCACTACTCATGGTTCACTGCAAATTTGAGAGATTTGTATATGTGTAGGCATTGGAAATACTCAATTTATTTTGGG # Right flank : TTGTATCCAAAAAATTACAATAATCATACGAACTGCTAATATAAGCAGTCAATATATGTGTACATTTATCCATTTTATCTCTAAACATATAAATTATTATCCCCCTAAAAAACTTTCATAAAAACAAAAAGAACAATATCTCTTTGGCAACTGGCTAACATAACTCATAAGATATTTATATAAGTCTTAGTCCCTATAGCTTTGCGTCACTAGATTTCTCTAGTTTTGCCGATTTAGTTTTATTCTATAACTAAATAATACAATAGAATTAGTTATTATTCAACAAGATTGTTTGAAAATTGAATAAATTTATAGGTATGAACGTAATTTCACACTTAAAAACAGACTAAATACGTAGAATATATAGAAAAATTTACCTGTAGTTTTTGTGATAAAAAGCTCCTATTATTAATTTAAGCTAGATAAGTTTGAGGAAGTGACATAAATTGAAAGAAGGAATATATTATGTTGAATAAAAAATTACCAGATGCAGAATTAAA # Questionable array : NO Score: 6.22 # Score Detail : 1:0, 2:3, 3:0, 4:0.96, 5:0, 6:0.25, 7:0.01, 8:1, 9:1, # Score Legend : 1: cas, 2: likely_repeat, 3: motif_match, 4: overall_repeat_identity, 5: one_repeat_cluster, 6: exp_repeat_length, 7: exp_spacer_length, 8: spacer_identity, 9: log(total repeats) - log(total mutated repeats), # Primary repeat : GTTTTATATTAACTATATGGAATGTAAAT # Alternate repeat : NA # Directional analysis summary from each method: # Motif ATTGAAA(N) match prediction: NA Score: 0/4.5 # A,T distribution in repeat prediction: NA [Repeat is AT rich:82.76%AT] # Reference repeat match prediction: F [matched GTTTTATATTAACTAAGTGGTATGTAAAG with 90% identity] Score: 4.5/4.5 # Secondary Structural analysis prediction: NA [0.00,0.00] Score: 0/0.37 # Array degeneracy analysis prediction: F [0-1] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [68.3-73.3]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [4.91,0 Confidence: HIGH] # Array family : I-B [Matched known repeat from this family], // Array 1 275633-275146 **** Predicted by CRISPRDetect 2.4 *** >NZ_SEQU01000002.1 Clostridioides difficile strain LC4-009-0 NODE_2_length_475986_cov_56.0294, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ===================================== ================== 275632 29 100.0 37 ............................. TTTTTCATTTTTATTTTTTTAGTTGCATTTTCAACTG 275566 29 100.0 37 ............................. TATTTTTTAGCTTTTTCTCTATATGTACCAATATCAC 275500 29 100.0 36 ............................. TAGAAATACAATTCGGAACTTGTTTCTGTTGAATTT 275435 29 100.0 37 ............................. AGGTTTAAAAACCTCTGTTCTTCCACCATAATACCCA 275369 29 100.0 37 ............................. AGGATAAAGAAAAGACTCACACAAGACACAGTGTCAG 275303 29 86.2 36 .........C............GA...G. AGAATATTAGCAATATCAACGAGTATTTAGAAACTT 275238 29 75.9 35 A...........TA...CA....A....A TTGTAGAATCAACAATAGCATATACTAAAACATCC 275174 29 75.9 0 ACC.............A.CA...C..... | ========== ====== ====== ====== ============================= ===================================== ================== 8 29 92.2 37 GTTTTATATTAACTAAGTGGTATGTAAAT # Left flank : CATTTTATAAATGATGAAAGGTACAAAGTTTTAAAGGTGTGGTGGTAAGTATGTTTGTTATTGTTACTTATGATATTGTTGAAGCAAGGTCGTTAAATAGAATTAGAAGGATACTTAGAAAATATTTGACTTGGACGCAAAATTCTGTTTTTGAAGGCAATATTACTGAAGGAAAGTTACATAAATGTATTTCTGAAATAGAAAATATTATTGATAATAGCGAGGATTCAATCTATGTTTATGAGATAAAAAATCCTAATTCAATTAAAAAGAAATGTTATGGGATTGATAAGTATTCTGATGAAATGTTTATATAGGTTTGCAGTGAGCGATATTTATGCTAAAATAGGTGTTAACAGTTGGAATATAAGGGATTGAAGGTGTATGATAACTGTTATCAATTGCACTACTGCTCGCTCACTGCAAATTTTGATGTTTTTATTGAATTATAATTGCTTGATTGAAGTGTTTTCAATGTATTCAAATATACCTATTTTGGG # Right flank : AAAATACACTTACCTACAAACATTATAAAATCAATACAAAAATGAGGTGAAACAAAATTTATGATAAAGAAATTAAACAGTAAAGATATAAATAAAATCATGGAAATATGGGAAAAAAGTACAATCAAAGCACATGACTTTATAAGTAAAGAATACTGGCAAAATAACTACAATACTGTTAAAAACGAATATATACCTATATCAGATACATTTGTATATGATGATGGAGATGAAATAAAAGGATTTATAAGCATAATAGATAAAAGATTTATAGGAGCTTTATTTATAAAGCCCAAATACCAAAATCTAGGTATCGGAGGTAAACTTTTAGATTATGCAACTAAAAAATATAAAAGTCTAAGCTTAGCAGTATATAAAGATAATAAAAAAGCAGTTGTGTTTTATAATAAAAAAGGTTTTAATATAGTAAAAGAACAAGTAAATGAAGATTCAGGATTTAAAGAGTACATAATGGAATATAGTAAATAATATGATTACAT # Questionable array : NO Score: 5.87 # Score Detail : 1:0, 2:3, 3:0, 4:0.61, 5:0, 6:0.25, 7:0.01, 8:1, 9:1, # Score Legend : 1: cas, 2: likely_repeat, 3: motif_match, 4: overall_repeat_identity, 5: one_repeat_cluster, 6: exp_repeat_length, 7: exp_spacer_length, 8: spacer_identity, 9: log(total repeats) - log(total mutated repeats), # Primary repeat : GTTTTATATTAACTAAGTGGTATGTAAAT # Alternate repeat : NA # Directional analysis summary from each method: # Motif ATTGAAA(N) match prediction: NA Score: 0/4.5 # A,T distribution in repeat prediction: NA [Repeat is AT rich:79.31%AT] # Reference repeat match prediction: R [matched GTTTTATATTAACTAAGTGGTATGTAAAG with 100% identity] Score: 4.5/4.5 # Secondary Structural analysis prediction: NA [0.00,-0.50] Score: 0/0.37 # Array degeneracy analysis prediction: R [18-0] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [78.3-75.0]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0,4.91 Confidence: HIGH] # Array family : I-B [Matched known repeat from this family], // Array 1 10649-9833 **** Predicted by CRISPRDetect 2.4 *** >NZ_SEQU01000022.1 Clostridioides difficile strain LC4-009-0 NODE_22_length_34066_cov_61.5993, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ====================================== ================== 10648 29 86.2 37 .AG..........A.T............. TGACTTTCATATGCTCTTTTATCAGCTTCTGACATAA 10582 29 100.0 37 ............................. ACTGGTAAAACTCTTAATGTATATGTTATTTGTAAAG 10516 29 93.1 36 A..............T............. CAGCTTTTTCTTTTAAGCTACATAACTGATTATACT 10451 29 96.6 36 A............................ TTCATAACTTGATTTGATTCATAACTTGTAGCCATT 10386 29 89.7 38 .........C.....T............T TGTCTTATTTTATTATTAAAGTTTTCTTGTTCATTTGT 10319 29 93.1 37 ...............T.....G....... GAATTAGTAGAGTACAAAAATTTAAAGTCAGAATTTA 10253 29 93.1 37 ..A.........................T TCAAATATAAAAGACTTTACATCTTTGCCATCGATTG 10187 29 93.1 36 .............A.T............. AAGGAACTTTTAAGAAGAATGTTACTTGCAGGAGAA 10122 29 96.6 37 A............................ TCCACATCTGCATCTTTACTTATGTTATTTGTATTGT 10056 29 100.0 37 ............................. TCATTTATCATGTTCAATCTAGCATTCGTACTAGTCA 9990 29 100.0 36 ............................. AATGGAGCTATAGTAGACAGCATTGATACAAATATT 9925 29 96.6 36 A............................ TTTGCAATAGCTTGTTTCATAAGATATACGCATTGA 9860 28 86.2 0 ...............T....-..T....A | ========== ====== ====== ====== ============================= ====================================== ================== 13 29 94.2 37 GTTTTATATTAACTAAGTGGTATGTAAAG # Left flank : TAAGAAGTTAGATATACAAGATAATGAAAAGTTAGTAGTACTAGAGAGTAAAAGAGGTTGGAGTGGAAGTGTCAATAAGTATTCACAGAGTGTAATAGATAAAATAAGACATTGGATAGGTGAAAACAATAAGCCTGCTAAGATACAAGGTGAGAAGAAGAATTTTCATGTGGTTTATAAGATTGAGTAAATTTATAAGATTGTATTAAATAATTTATTTTAGTTTATTTTGGGGGGATTAATACAATGATTGAAGATTTACTTAATGAATATAATTTAAAAACTGATGAAGATGTAGAGTATTTTGTGAAGTTTGCTAATGCATTATATGAACTAAAACAGAATAGTGAAGAAAAATTTCAAGAATATGCAGAGATATTAAGAGGTATTCTTAGAGAACAAGAAGAGAGAAAAAATAAGTAAAATAATATAGATAAAGCACTTGAATATTATGATGTTTCAAGTGCTTTGTTTGTTAAAAAATGATATAATATAGGTAA # Right flank : TTAAAAATAATGAAAAACACTTACTTGAATAGTAGGTGTTTTTTTATTGAAAGGATGTGATAATAATGTAAAAATTTTACTGATATAGTATAATAATCTTATAAAATTATGTAGGGGGTAATATTATGGGATTATTTGGGGGTAAAGAACCATGCAGCATATGTGGAGGAAAGGGTAAAAATAAAGTTTTAGAAAATGAATATTTATGTAATAATTGTTTTATTAATTTCACAATATTTTCTAGAGAAAGATTAAAAGCAACTAGTGCAATGCAAGTATTAGCTGACCATGAAGGGATAAGAAAATTTATAAATTTTTCTAAAACAAATAGAGAACTATTAGCAAAATTTGTTGAGACAAATAGAATTAATAAATTTGTATCCATTGATGAAGATAATAACTTTATTAAAATATCAGATATTCGCAAAGGTGGAGATGTAATAGAGAATGTATATGCAATTGATGAAATTATGCAATTTGAACTTTTAGAAGATGGAGAG # Questionable array : NO Score: 5.34 # Score Detail : 1:0, 2:3, 3:0, 4:0.71, 5:0, 6:0.25, 7:0.01, 8:1, 9:0.37, # Score Legend : 1: cas, 2: likely_repeat, 3: motif_match, 4: overall_repeat_identity, 5: one_repeat_cluster, 6: exp_repeat_length, 7: exp_spacer_length, 8: spacer_identity, 9: log(total repeats) - log(total mutated repeats), # Primary repeat : GTTTTATATTAACTAAGTGGTATGTAAAG # Alternate repeat : NA # Directional analysis summary from each method: # Motif ATTGAAA(N) match prediction: NA Score: 0/4.5 # A,T distribution in repeat prediction: NA [Repeat is AT rich:78.57%AT] # Reference repeat match prediction: R [matched GTTTTATATTAACTAAGTGGTATGTAAAG with 100% identity] Score: 4.5/4.5 # Secondary Structural analysis prediction: NA [0.00,0.00] Score: 0/0.37 # Array degeneracy analysis prediction: F [4-10] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [76.7-76.7]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0.41,4.5 Confidence: HIGH] # Array family : I-B [Matched known repeat from this family], // Array 2 12511-12222 **** Predicted by CRISPRDetect 2.4 *** >NZ_SEQU01000022.1 Clostridioides difficile strain LC4-009-0 NODE_22_length_34066_cov_61.5993, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ===================================== ================== 12510 29 86.2 37 GAA..........A............... AATGAATTTTGAGAATCTACATAGGATTGAACTACTA 12444 29 100.0 37 ............................. ACTAAATTAGAGGTCGAGAAGGCTATTGAATCAAAAG 12378 29 93.1 36 G...........................G GGAACATAAGGTAAATCATAAGAAACTCCAACAAGA 12313 29 96.6 35 ............................G ATCACTTTTTCTCAAGCTCTTACAATGATGAAAAA 12249 28 86.2 0 ....................-..TC...A | ========== ====== ====== ====== ============================= ===================================== ================== 5 29 92.4 36 ATTTTATATTAACTATGTGGTATGTAAAT # Left flank : ATTTCAAGCAGTTAAACAAATTATAAGAAAGCTTGATATTAAAGAAGATGAAATGAAAACAGTACTAGAAACCAACGGTTCTTGGACTGGTACTGTAACCAAATATTCTAATAAGGTTACAGAAAAAGTAAAAGAGTGGTTGAAAGAAAATAATAATCCCATTTCTGTTAAAGGAGACAAGAAAAACTATTATATATTGTATAAAAATAATTAGATTTTAGTTTTGAGTTTGAGGGGGATTAATAAAATGCGTGAAAGTTTACTTAATGAATATAATTTAAAAACTGATGAAGATGTAGAATACTTTGTAAAGTTTGCTACATTATTACATAAATTAAAACAGGACAATGAAGAAAAATTTCAAGAGTATGCAGAGATATTGAGAGGTATTCTTAGAGAACAAGAAGAGAGAAAAAATAAGTAAATAAATAGATAAAGCACTTGGATATTATGATGTTTCAGGTGCTTTGTTTGTAAAAAAATGGTATAATGGAAATAGA # Right flank : TTAAATAAACAAAGAAAGCACTTACAAATATGTAGGTGCTTTTGTTTTGCTCAAATTGGTCGATTGGGTAAAATAATTAGAAAAAATTGGGATAAGTTATTGACTTTTGAGTTCCAAAACTATATAATTTAATTATGGAACTCAAAAGTGAGGTGATAACATGAGTCCTAAAAAAATAGGAAGACCTGTTGTAGGAAGCCCTAAAACTAATGATATTAAGGTTAGAGTAGATGATGAAACTAATGAAAAATTAGATGAATACTGTAAAAAAAATAACCTTACAAAAGCAGAGGCTATAAGACAGGGAATCCATTTACTTTTAGAAAAATAACAAAAATAGAGTGTTCGCCCGACCAAGTTTGAACACTCTATTTAAACCATAAGAAGTAATCTTCTATATGAAATATTTTATCATATAGAGAAACTTCTTTCAAATTAAATTTAGGAGGAGTATGTATGATGAATGATTTACAAATATTTAAAAGTGAAGATTTTGGAGA # Questionable array : NO Score: 3.69 # Score Detail : 1:0, 2:3, 3:0, 4:0.62, 5:-1.5, 6:0.25, 7:0.01, 8:0.8, 9:0.51, # Score Legend : 1: cas, 2: likely_repeat, 3: motif_match, 4: overall_repeat_identity, 5: one_repeat_cluster, 6: exp_repeat_length, 7: exp_spacer_length, 8: spacer_identity, 9: log(total repeats) - log(total mutated repeats), # Primary repeat : ATTTTATATTAACTATGTGGTATGTAAAT # Alternate repeat : NA # Directional analysis summary from each method: # Motif ATTGAAA(N) match prediction: NA Score: 0/4.5 # A,T distribution in repeat prediction: NA [Repeat is AT rich:80.00%AT] # Reference repeat match prediction: R [matched GTTTTATATTAACTAAGTGGTATGTAAAG with 96% identity] Score: 4.5/4.5 # Secondary Structural analysis prediction: NA [0.00,0.00] Score: 0/0.37 # Array degeneracy analysis prediction: R [3-1] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [71.7-71.7]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0,4.91 Confidence: HIGH] # Array family : I-B [Matched known repeat from this family], // Array 3 14758-14134 **** Predicted by CRISPRDetect 2.4 *** >NZ_SEQU01000022.1 Clostridioides difficile strain LC4-009-0 NODE_22_length_34066_cov_61.5993, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ====================================== ================== 14757 29 89.7 37 .AA..........A............... AATGAATTTTGAGAATCTACATAGGATTGAACTACTA 14691 29 96.6 37 A............................ ACTAAATTAGAGGTCGAGAAGGCTATTGAATCAAAAG 14625 29 100.0 38 ............................. GTATACTCAATAAAAAATTTATCACCATACTGTTACAC 14558 29 100.0 37 ............................. GAAGCATTATTTATTTTTTCTTCTATTATATCTATTT 14492 29 100.0 37 ............................. TAGGGAATTAGGAAATGGCTATTCTCCCCCTATATCC 14426 29 89.7 38 ......G.........A...A........ ATTTGAACATTTGTTACAGCATTAGAGATATTAATTGC 14359 29 89.7 36 ......G.........A...A........ CCAACTGAATAAACAATAATTTTATCAATTTCTTTA 14294 29 89.7 37 ......G.........A...A........ CATCATAGTCACGTATATTTTCTTTAAAAGTCAAAGT 14228 29 89.7 37 ......G.........A...A........ TTCGCAACTTATGATGGTGAAATGATTACATTAACAG 14162 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ====================================== ================== 10 29 94.5 37 GTTTTATATTAACTATGTGGTATGTAAAT # Left flank : TGAGATTATTAAAAAGATAAAATTAGAAGAAAATGAAGTAAAAGGAGTTTGGGAAACAAATGGCTCTTGGACTGGGACTGTAAATAAGTATACAGAAAGTGTAATAGATAAGGTTAGAACTTGGATAGAGGAGAATAATAGACCAGCTAAGATTGAAGGTGAAAAGAAGAATTTTCATGTAGTGTATAAGATTGAGTAAATTTGATTGTATTAAATAGTTTAGTTTATTTTTGGGGGGATTAATACAATGTATGAGAATTTACTTAAGGAGTACAATTTAAAAACTGATGAAGATGCAGAATACTTTGTAAAGTTTGCTACATTATTACATAAATTAAAACAGGACAATGAAGAAAAATTTCAAGAGTATGCAGAGATATTGAGAGGTATTCTTAGAGAACAAGAAGAGAGAAAAAATAAGTAAATAAATAGATAAAGCACTTGGATATTATGATGTTTCAGGTGCTTTGTTTGTAAAAAAATGGTATAATGGAAATAGA # Right flank : AAAGCAAAAGATAGGAATGATAATTTTAAAACTCCAGACTTTTATATTAACAATGTGGAGAAAAACTAAATAGAAAAAAGAAGCACTTACTTAAATAGTAGGTGCTTTTGTTATTCTTTGCTAGATAAAGTAACAAGTTCATTAGGTGTACATTCAAGAACAAGACAAAGCTTTTCGAATAAATCTAATTTTATAGAACTTGTTTCATTGTTAGCTAATTTCATCATGTTAGGATAAGCTATACCTACTTCTTTAGCTAACCAATATCTAGTTCGACCTTTGGATTCAAGTAATTTATCAATGTTAAAATACATTTTTTCACCTCTTAAGTATATTATACAACAATTATATAATGTTTGCAATATATAATATGCAAACAATATAATTATATAATGTTGACATTATATAATGTGTACGATATAATATACTTAAGGAATAAAAAATAAGAGCCACTCGCCCCTACCAAGTTTGAGTAACTCTTATTGACATATACTACATAT # Questionable array : NO Score: 5.67 # Score Detail : 1:0, 2:3, 3:0, 4:0.72, 5:0, 6:0.25, 7:0.01, 8:1, 9:0.69, # Score Legend : 1: cas, 2: likely_repeat, 3: motif_match, 4: overall_repeat_identity, 5: one_repeat_cluster, 6: exp_repeat_length, 7: exp_spacer_length, 8: spacer_identity, 9: log(total repeats) - log(total mutated repeats), # Primary repeat : GTTTTATATTAACTATGTGGTATGTAAAT # Alternate repeat : GTTTTAGATTAACTATATGGAATGTAAAT # Directional analysis summary from each method: # Motif ATTGAAA(N) match prediction: NA Score: 0/4.5 # A,T distribution in repeat prediction: NA [Repeat is AT rich:79.31%AT] # Reference repeat match prediction: R [matched GTTTTATATTAACTAAGTGGTATGTAAAG with 97% identity] Score: 4.5/4.5 # Secondary Structural analysis prediction: NA [0.00,-0.50] Score: 0/0.37 # Array degeneracy analysis prediction: F [0-4] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [73.3-71.7]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0.41,4.5 Confidence: HIGH] # Array family : I-B [Matched known repeat from this family], // Array 4 17272-16451 **** Predicted by CRISPRDetect 2.4 *** >NZ_SEQU01000022.1 Clostridioides difficile strain LC4-009-0 NODE_22_length_34066_cov_61.5993, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ====================================== ================== 17271 29 100.0 38 ............................. TAAACGAAATTAAAAATCTAATTGATAGTATTACAAGA 17204 29 100.0 36 ............................. CAAGTGGGCGAAAGATGATTATATACCAGAATCACT 17139 29 100.0 37 ............................. AAAACTGAATAATGCAGGTGAAAAGTTCTTAACAGAG 17073 29 100.0 37 ............................. GGGACAGACTCAACCCTACTATTTACAAGCTTTATAA 17007 29 100.0 37 ............................. AATATATTCTATTATTAAAAGTAATTGTATCGGGTAC 16941 29 100.0 37 ............................. TTTATCAAATACACATACATTTTAATATTTTCTTCAT 16875 29 100.0 38 ............................. TCTAAAAGGTCACATATATTTATTAAATCTGTTGCCTT 16808 29 100.0 38 ............................. CAGCTTTACATATCTATCTATGATTTTTGAATCTCCAT 16741 29 100.0 36 ............................. TCTAATTTAGTTGTTAAAATAAATTCCTTACCAATT 16676 29 100.0 37 ............................. TGAGCTGTTAGATAATATCCTAGCATTTTTATTTTTC 16610 29 100.0 36 ............................. TATGTACCTAGAAATTTAGAAAGTTTTGGAGAAATA 16545 29 100.0 37 ............................. TTCGCAACTTATGATGGTGAAATGATTACATTAACAG 16479 29 89.7 0 ......T.........G...T........ | ========== ====== ====== ====== ============================= ====================================== ================== 13 29 99.2 37 GTTTTAGATTAACTATATGGAATGTAAAT # Left flank : ATGATATAATAATTGTAGCAAGGAAAATAAAATTGAAAAGCTAAGGGTGATTTTCTCATATAAACGCCAAATTCCAATATAGGAAGGAGGTGAATTTATATGTTAATTAACTTTTTATTGAGTATAGTAGCTGGAATTGTTTCAGCTTACATTTACGAGAAAATAAAAAATCACCCAAACGCCAATAAGGGTGATTTAAAGAAATAACTTTTAAATTCTAATCAATTAGAGAAATTCACCTTTTACAAAGTAAATTTTATCTCCTTGCTATTATTATACCACAAATTGGTACAGATATTCAAAAATAATATATTTATGATATAATAAAAATGTAGAGATTTTGCAGTGTTCGATTTTTGTGATAAAATATGGCCTAACACTTGAAATATAATGTATTGAGGACGTATGATAAGTATTATCATTTGCACTACTCATGGTTCACTGCAAATTTGAGAGAGGTGTGTATGTGTAGGTATTGGAAATGCTAAGTTTATTTTGGG # Right flank : AAAGCAAAAGATAGGAATGATAATTTTAAAACTCCAGACTTTTATATTAACAATGTGGAGAAAAACTAAATAGAAGAAAGAAGCACTTATTTTTGGTAGGTGCTTTTGTTTTGCTCAAAATTGGTCGGTTGAGTAAAATAATTAGAAAAAATTAGTAAAAACTCTTGAAAAGTGTCGCGATACAATGTATAATTATATTATCGCGATACAGAAAAGAGGTGAAAATTATTACTGATAGCAGTAGAGCAGATTACTTCAAGCAGAGACGACAGAATAAGAAAACTTTTAGTGTTCTACTAGATAGAGAGAAAGTAGAAAAAATTGAAGAACATTTAAAAAAGCAGAACAAGACTAAAACTATTTGGCTTGAAGAAAAGATTAATGAAGAGTTAGAAAAAGAGGAATAAAAAATAAGAGACGTTCTCCCCGACCAAAGATTGAACATCCCTTATTGACGTATATTATATACACTAACTATAGTATACGTCATTCCTTAAAAA # Questionable array : NO Score: 6.22 # Score Detail : 1:0, 2:3, 3:0, 4:0.96, 5:0, 6:0.25, 7:0.01, 8:1, 9:1, # Score Legend : 1: cas, 2: likely_repeat, 3: motif_match, 4: overall_repeat_identity, 5: one_repeat_cluster, 6: exp_repeat_length, 7: exp_spacer_length, 8: spacer_identity, 9: log(total repeats) - log(total mutated repeats), # Primary repeat : GTTTTAGATTAACTATATGGAATGTAAAT # Alternate repeat : NA # Directional analysis summary from each method: # Motif ATTGAAA(N) match prediction: NA Score: 0/4.5 # A,T distribution in repeat prediction: NA [Repeat is AT rich:79.31%AT] # Reference repeat match prediction: NA # Secondary Structural analysis prediction: NA [0.00,0.00] Score: 0/0.37 # Array degeneracy analysis prediction: R [3-0] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [73.3-63.3]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0.27,0.41 Confidence: LOW] # Array family : NA // Array 1 17838-19713 **** Predicted by CRISPRDetect 2.4 *** >NZ_SEQU01000004.1 Clostridioides difficile strain LC4-009-0 NODE_4_length_297047_cov_47.5365, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ======================================= ================== 17838 29 100.0 37 ............................. GTTACCACCAATAAGTCTAATATCAGTAGCTCCACCA 17904 29 100.0 37 ............................. TTTTTTACACCTCCAAACACAGCTCCTATCAGCTCAG 17970 29 100.0 39 ............................. GAACTTTTAAATATAAATTTTTATATTCTCCAACACTTC 18038 29 100.0 37 ............................. GGTACTGCCTATGACAACAAAGTATATACAGTTAAAG 18104 29 100.0 37 ............................. CCAACTAGGTGAAAGAAGCTTACCCAAAAGTATCACC 18170 29 100.0 38 ............................. TAATTAATGGTGTTATTAAGTCAAATTTTTGATTTTGC 18237 29 100.0 36 ............................. AAACTCAAAACTTTTTTATTATAGGTATTGATTTTT 18302 29 100.0 37 ............................. TAAATATTCATTTCAAGCTCTTTCATAAGCTCATATT 18368 29 100.0 38 ............................. GTAAGTCACTCTTTGCACGAGAGTGGCTTTTTGCTTTT 18435 29 100.0 36 ............................. TTAGACGAGATTGTTTTTATAGATACAGGACTAGAA 18500 29 100.0 36 ............................. GTTTTGAACGGGTATGACTAGTTTAGTTTCGTCAAG 18565 29 100.0 37 ............................. AAATAACAATTATTAGGAATTTGAGAAGTATTATGTG 18631 29 100.0 36 ............................. AATCACGAAAGTATTAACTACTTCTCGAACAGGCAA 18696 29 100.0 37 ............................. TTACTAACAGGAACATCAAAAGGAGGTTTAAAATCCG 18762 29 100.0 38 ............................. TCCCACACGTATAAATCAATTTGGTTTTCTGCTGTCGT 18829 29 100.0 37 ............................. TGCAAAAAAATCGGATAACCTAGTTCCTCTACAACTT 18895 29 100.0 37 ............................. ACGAGTCTAATATATTTTCGCTTCTTTTATTATTCTG 18961 29 100.0 37 ............................. TTTTTAAAGAATAGGTCACTAAAAAATTTTAATTTTG 19027 29 100.0 37 ............................. TGTGGATTTAAAGATGGAATAGTAACAAAGTATATTA 19093 29 100.0 37 ............................. GCAATATCTCCTCTTGTAATCGCTGAATAAAGATTTC 19159 29 100.0 37 ............................. CTATAACTTTTTCGCCAAAAACGTCTTTTATATCATT 19225 29 100.0 37 ............................. TCCAAAAGAACCTCTTTTTCTGTTTCATCAACTGTGT 19291 29 100.0 36 ............................. TTCTTTGAAAAGCATACTTTCTTTATTCTATCTTTA 19356 29 100.0 37 ............................. ATCGTAAATTTTTGTATAGGAGTCATACTTATAAGAG 19422 29 100.0 37 ............................. CAAAATGATTTGAAAATAACAAATATGTCTTTATTAA 19488 29 96.6 36 ............T................ TATAAATAAATAAACAGAAACAAAAATCAAATCTTT 19553 29 100.0 36 ............................. ATCATAAGAACCAGGGATATAGGGAAGGTCATAAGC 19618 29 100.0 38 ............................. CCATCTTTTGTTGCTTTACATAAATTTATATTACTTAC 19685 29 82.8 0 ........C........CA....A...T. | ========== ====== ====== ====== ============================= ======================================= ================== 29 29 99.3 37 GTTTTATATTAACTATATGGAATGTAAAT # Left flank : GATAACCATAATAAAAATAGATATCTATTTTTAGATTAAAAATAATATATCATAAATAAAATAATAAGAGGTAGATACAGTTTTAAGGGAATACAAAAGTTTTTAATTAAACTATGCTTGTTCAGATAGATATTTATTTAAGAAAAAAGACTATTAAAAGCAATATACAAGAATGATATATTAGATTGATTAAACAAGCATAAATATTATGTAAAAAACTTTAAGTTATAGAATTTAAATCTAATGTAGATAGATTACGTTTTTTTGCTTTTATTATGGTATAAATTGGTATCAATATTCAAAAGTAATATATTTATGATATAATAAAATTATAGGAATTTTGCAGTGAGCGATATTTGTGAAAAAATTTGGCGTAACAGTTGAAATATAAGGCGTTGAGAGTGCATGATAAGCGTTATCAATTGCACTATTGCTCGTTCACTGCAAATTTAAGAGAGTTGTATACGTGTAAGTGTTGAAAATACTAAGTTTATTTTGGG # Right flank : TTTCTTTTAATGTGTTATCTTATGATTATCTAGTTATATTAGCATACAAAAATATAATAAAATTACACTATATTATAAAAACCAAAAGGTAGTATAGAAATCCTATTACCTTTTTATTATTAATTTTATCAGTGTTTTATTATAAATAGCTTACATAATTACACATTTTTTCTGATTAAATAATATGATGCTATTGTTATAATAGATACTAATGCTAATGATGTTATTGCAGTATCTAATCTTCCTATTAATAAACTCATTTCTATATATTCAAGTTCTATTAAATATTAATAAAATATTTCTAGTTTAACAGCTTTTTCTCTATCTATATTTCCATACTTTAACTCTAATTTATCTAAAGATTTTTTATTACAATAATTAACTTTATGTTTAATTAAATATCTTATTGTAGCACCTATTACAATTTTCACTCTAACAAGCATAAATATAATATTCCATCCAAAAGTTAAGAGGGTATATCTTTTTTTATGATGGGAATG # Questionable array : NO Score: 6.22 # Score Detail : 1:0, 2:3, 3:0, 4:0.96, 5:0, 6:0.25, 7:0.01, 8:1, 9:1, # Score Legend : 1: cas, 2: likely_repeat, 3: motif_match, 4: overall_repeat_identity, 5: one_repeat_cluster, 6: exp_repeat_length, 7: exp_spacer_length, 8: spacer_identity, 9: log(total repeats) - log(total mutated repeats), # Primary repeat : GTTTTATATTAACTATATGGAATGTAAAT # Alternate repeat : NA # Directional analysis summary from each method: # Motif ATTGAAA(N) match prediction: NA Score: 0/4.5 # A,T distribution in repeat prediction: NA [Repeat is AT rich:82.76%AT] # Reference repeat match prediction: F [matched GTTTTATATTAACTAAGTGGTATGTAAAG with 90% identity] Score: 4.5/4.5 # Secondary Structural analysis prediction: NA [0.00,0.00] Score: 0/0.37 # Array degeneracy analysis prediction: F [0-6] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [70.0-83.3]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [4.91,0.27 Confidence: HIGH] # Array family : I-B [Matched known repeat from this family], // Array 2 100258-100759 **** Predicted by CRISPRDetect 2.4 *** >NZ_SEQU01000004.1 Clostridioides difficile strain LC4-009-0 NODE_4_length_297047_cov_47.5365, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ===================================================================================================================== ================== 100258 29 93.1 35 ...............T............T TTGCAGAAATATAATTTTATTGTTCTAAATTTAAT 100322 29 96.6 37 ............................T GTTAGTGACTATTCTAGAATGCAACAAGAAACAACAG 100388 29 100.0 36 ............................. TTTCTTTAATACTTTCCCATAACTTGCCTAAAAAAA 100453 29 100.0 37 ............................. CCAAGTTGAAAATTTAGAATCTATGTCTTTACACCAT 100519 29 93.1 37 .................CA.......... ATGGGAGCATTAACTTTAGCATTTGGAGCATTAGCAG 100585 28 82.8 117 ...............T....-.CT....T TTTGAACAAATACAGAAAACACTTATTTAAATAGTAAGTGTTTTTGTTGTGCTTAAATTTAATCAGTTATGTGAAATTATTATGGAATAATATTACAAATAATTAATGAAAAAATTA 100730 29 69.0 0 T..A.......TA...T..AA...A...T | A [100752] ========== ====== ====== ====== ============================= ===================================================================================================================== ================== 7 29 90.7 50 GTATTATATTAACTAAGTGGTATGTAAAG # Left flank : TGTAAAGAAGCTGTATTTGTAACTGAGGGAATTGAATATCAAGTGGCAGATGGTGATGGAAATGTGCTACAAACTTATCCAGTAGACGATTCAACTAGAATGCAACAAGAAACAACAGCAGGTACTAAATCAAAGGGAACAACAGCGTTTGCTATAACATCAGACTCAAATGCTGTAAAAATAATTGTAAAAGATAAAGTAAATAATAAGGTCATGGGAGAAATAAATGCTACTTTAGAATAAAAATAGTATTAGAGAAAAGAAAAAAGTTAACAGGTAAAATATTCTAAATGAATAGAATAAATTAATGTTAATTTATGATATAATGATAATATAGATATTTTGCAGTGTACGATTTTTTATATAAATTGGATGTAATCATTGAAATTACTACAATATAAGCATGTTTTGTGGTGTGTGAAAAACACTACTGGTTACTCACTGCAATTTTAATATGGTTTTATATGTGCAAGAACTGGAAGTGCTCAATTTATTTTGGG # Right flank : TACATTTAATTTATAGTGAAGGAGAATGTTATGGCATTATTTGGGGATAAAGTTGATAAAGAAGATAAAAAGAAATTAAAAGAGCAAGAAGAAATACAAAAATTCATGAATAAGTATCAATTACAAGATTTAAATGAAAAAGATTTAACTATTTTAAGAAGAATAGCGGATGATTTATTTGCAACTGGACTTATAAAAACAGGATTAGCATTGAGTTTTACAAAAATAGAAGAACAAACTAAAATAAATTATCTTAGTGCTTTAGTTGAGCAAAACTGGATGATAATTAGACAATTATCTCAATTGAATAGCAATATAGAAAAACTTGTAGAAGATAAAAAATAATGGACTGAAAATAATAATACAGAAAACACTTACTTAAATAGTAGGTGTTTTTTTATATGAAATTTTGAGGGAGGGAGGGAAAAATATGTCCTTAGAATTAGGAACAGCAGTAGGTTATCTAGATTTAGATGGAGGGAAGTTTTTTAAAGCTCTTG # Questionable array : NO Score: 3.98 # Score Detail : 1:0, 2:3, 3:0, 4:0.54, 5:0, 6:0.25, 7:-1.37, 8:1, 9:0.56, # Score Legend : 1: cas, 2: likely_repeat, 3: motif_match, 4: overall_repeat_identity, 5: one_repeat_cluster, 6: exp_repeat_length, 7: exp_spacer_length, 8: spacer_identity, 9: log(total repeats) - log(total mutated repeats), # Primary repeat : GTATTATATTAACTAAGTGGTATGTAAAG # Alternate repeat : NA # Directional analysis summary from each method: # Motif ATTGAAA(N) match prediction: NA Score: 0/4.5 # A,T distribution in repeat prediction: NA [Repeat is AT rich:78.57%AT] # Reference repeat match prediction: F [matched GTTTTATATTAACTAAGTGGTATGTAAAG with 100% identity] Score: 4.5/4.5 # Secondary Structural analysis prediction: NA [-0.20,0.00] Score: 0/0.37 # Array degeneracy analysis prediction: F [1-15] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [68.3-73.3]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [4.91,0 Confidence: HIGH] # Array family : I-B [Matched known repeat from this family], // Array 3 235622-236956 **** Predicted by CRISPRDetect 2.4 *** >NZ_SEQU01000004.1 Clostridioides difficile strain LC4-009-0 NODE_4_length_297047_cov_47.5365, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ====================================== ================== 235622 29 100.0 35 ............................. AAACCTGGATTAGCTTTTATCCAACATTCTTCTCT 235686 29 100.0 35 ............................. GCTACTAGACCAGCTACCACTAACAGTACGAATGA 235750 29 100.0 36 ............................. ATAGTATAAACACTTTCAACCGTCCTTGAAAGTGTT 235815 29 100.0 37 ............................. TTACTTAGAAACAAATATATTGTTATTAACATACCAA 235881 29 100.0 38 ............................. TTAAGAGCATCTTCTATACCTATTTTAAAGTTTACTGG 235948 29 100.0 37 ............................. TTGCTATCTGAGTATTAATTTCTTCTATTTCTTGCCT 236014 29 100.0 37 ............................. ATTATAATATGTAACTATATCTAACTTTTATATTATC 236080 29 100.0 37 ............................. GTATGTCTTTTAAAGTTGCTAATACAACTGTTGGGTC 236146 29 100.0 36 ............................. TGAATATCACTACACCAAATTTTTAGACATTCAAAC 236211 29 100.0 37 ............................. TAATTAGTGGTGTTATAAGACTCATTTTTTGATTTTA 236277 29 100.0 37 ............................. TTGACTTACTATGTATTACTTCTAAGTTACTTATATC 236343 29 100.0 38 ............................. CAAGATATTTTTAATAAAATTTCTGAGCGAACTGTTTT 236410 29 100.0 36 ............................. AAAAATAGAACAAATTATGGAAAAATACTAGTAAAT 236475 29 100.0 37 ............................. TCTCATCACAACACTATATACATAGTAAATTAACATA 236541 29 100.0 35 ............................. GCATGTTAAAGTGGCTAATTGGAACTATGATTACA 236605 29 100.0 32 ............................. AGTCCAGACCCTAATCCTCCTGTTGACCCAGA 236666 29 100.0 36 ............................. ATAGTCAAAAGCAACATCATAATCACGTATATTATC 236731 29 100.0 36 ............................. CAACATGTCAGTAATATTGAAACAGGAAATTCGAGT 236796 29 100.0 37 ............................. AACACTTTAAAAACTAATGTATTCAGTATAAGAGATT 236862 29 93.1 37 ...............T.A........... CTTGTTAATGCAAATAAACAACATAGCACTATTAATA 236928 29 96.6 0 ...............T............. | ========== ====== ====== ====== ============================= ====================================== ================== 21 29 99.5 36 GTTTTATATTAACTAAGTGGTATGTAAAT # Left flank : CTATTATTATATATAACTGACATTTAAGTGACATTTAAGAAAAATATAATGCCTACTTACATAAAATGGAATGTTATTTAAAGAGAACTTTGATTATATTTTCAGAAGTTTTTTTATCCATATCGTTTAAAACAAGAAAATATCTATTCATAGTTATTTTTATATTAGTATGTCCTAATCTTTCAGAGATGATTTTTATATTAGTTCTAGCTAGAAGAAGAACTATTAGAATAGATAATATAGTAAGTATTTACAAATATGTAGGTGTTCTTAAATTGATAAATTATTCCATTTTAATTTTATAGTTTGAATTTTATGATATAATAAAAATATATAAATTTTGCAGTGAGCGATATTTTTGATAAAGTAGGGTTTAACAGTTGCAATGTAAGGGATTGAGGGTGTATGATAAATGTTATCAATTGCACTACTCATGGTTCACTGCAAATTTGAGAGAGTTGTATGTGTGTAAGTACTGAAAATACTTAGTTTATTTTGGG # Right flank : TTTGCAACAAGTATAGGTAAAATACCCCAATAATTTATACAGCATTTTCTCCTTTAAAATATAATTATTTTTTAGCATTTGTAGTAAATAATTACCAGATAATATTGACTTTAGTTTTAATGATTAAAATATAAAAGTAGAATAATTATAAAAAGTATTGAAAAATTTATAAATATATATAATAAAACTTAATGACAAGATATTAGATATAAAAAATAATTACCTTATAAATAGATTGAAATTTATGAATATTCATACTATAATTTAAATATAAGGAGATGCCCTTTGAAAATAAAAATTAAAAAATATTTAATGCTATTACAATAGGAACTAGAACTACACTTAATAAATATACAGAAATTAGATTTGGCTCAATATAAAATACAAATATAGAATTTAGGTGTTTTTTATGAAAAAATTTTTATATGCTTTATATAGTTTCATTGTTATTATAGCTAATTTTAGATTAAAAGAAAAAAATTATAACTTTATTTTATTAG # Questionable array : NO Score: 6.23 # Score Detail : 1:0, 2:3, 3:0, 4:0.97, 5:0, 6:0.25, 7:0.01, 8:1, 9:1, # Score Legend : 1: cas, 2: likely_repeat, 3: motif_match, 4: overall_repeat_identity, 5: one_repeat_cluster, 6: exp_repeat_length, 7: exp_spacer_length, 8: spacer_identity, 9: log(total repeats) - log(total mutated repeats), # Primary repeat : GTTTTATATTAACTAAGTGGTATGTAAAT # Alternate repeat : NA # Directional analysis summary from each method: # Motif ATTGAAA(N) match prediction: NA Score: 0/4.5 # A,T distribution in repeat prediction: NA [Repeat is AT rich:79.31%AT] # Reference repeat match prediction: F [matched GTTTTATATTAACTAAGTGGTATGTAAAG with 100% identity] Score: 4.5/4.5 # Secondary Structural analysis prediction: NA [-0.50,0.00] Score: 0/0.37 # Array degeneracy analysis prediction: F [0-3] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [68.3-73.3]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [4.91,0 Confidence: HIGH] # Array family : I-B [Matched known repeat from this family], // Array 1 2939-3751 **** Predicted by CRISPRDetect 2.4 *** >NZ_SEQU01000006.1 Clostridioides difficile strain LC4-009-0 NODE_6_length_260416_cov_49.1045, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ====================================== ================== 2939 29 100.0 36 ............................. GAAATTAGTTGAACTATTGCTTGATATTCCATATAC 3004 29 100.0 37 ............................. CAATAAACCCAAAAACATTTAAAGAATACATGTTTAA 3070 29 100.0 36 ............................. TGCTTACGAATGGTTGGAATTACATCTATTGCTAAC 3135 29 100.0 38 ............................. CAATATGATTTTGCATTAGATTTTAGTGAAGGATTAGC 3202 29 100.0 35 ............................. TTTCTTTAAAACAGACATCAATTTCGTTATATCTG 3266 29 100.0 36 ............................. TTAGAATCAAAAGCACTTAATCCTAGTTCTTTCATA 3331 29 100.0 37 ............................. AGCTTTTTAGCTTCGTCTACTACTTTATAAGCAAAGC 3397 29 100.0 37 ............................. AAAAGTTGCACGCCTATTTGATTTTTCAATACATTAT 3463 29 100.0 36 ............................. GACAAAGCGACTATTACTATCTCAGGTGATAAAAAT 3528 29 100.0 36 ............................. GATGAACAATAAAACAATCATCTAAAGACGAAGAAA 3593 29 100.0 36 ............................. GTTCCTGTTGTGTTTTTTACTAATCCCATTTTATAT 3658 29 100.0 36 ............................. TGCTGTGATTTCACTAATAAAACAATTAATAATTGT 3723 29 86.2 0 ................G....T.CA.... | ========== ====== ====== ====== ============================= ====================================== ================== 13 29 98.9 36 GTTTTAGATTAACTATATGGAATGTAAAT # Left flank : AATAATGTAGATAATGTTGAAAATTTAGAATTCAATGAGTTTGAACTTAAAACCGAAGAAGAAGAGAAGCGAGAACAAGAGAAAATAGAACAAGAAAAAAACAGTTATAATAACTACATTCAAAACAGAGTGGTTGACCCACTAGATAGAATAAAGAAACTAAAAGAGTTGCTAGATTCAGGAGCAATTACACAGGAAGAATATAATAAAAAGAAAAAAGAATTATTAGAATAGATAATATAGTAAGCACTTACAAGTATGTAGGTGCTTTTAAATTTACAAAGTATTCCATTTTAATTTTATAGTTTAGATTTTATGATATAATAAAAATATAGAAGTTTTGCAGTGTGCGATATTTGTTACAAAGTAGGGCTTAATACTTGAAATCTAAGATGTTGAGGGTGCGTGATAAGTGTTATCAATTGCACTATTGCCCGCTCACTGCAATTTTAAGAGTATTGTATATATGTAGGTATTGGAAATGCTAAGTTTATTTTGGG # Right flank : TTAAATAAACAAAGAAAGCACTTACAAATATGTAGGTGCTTTTATTCTGCTCAAAATTGGTCGGTTGGGTAAAATCATTAGAAAAAATTAGTAAAAACCTCTTTTCTGTAACTCGTTACAATATTATTATTAATGTAACGAGTTACAGAAAAGAGGTGAATAAAATAGCAACTAAAAGTAGGGCAGAGTATATGAAAAATTGTCGAAAAGATAAAAGAGGTTTTAGTGTACTTTTAGACAAAGAAAAGTTAGATAAATTTGATGAAGTATTAGAGGAAAAGAATCTAACCAAGAAAGAATGGCTAGAAGAAAAAATCGACGAGGAACTGGAACAAAAGGAATAAAAAATAAGGGTCACTCCCACCGACCAAAGTTTGAGTAACCCCTATGATGTATACTATCGTATATCAATTATAATATATGTCATTCCTTAAAAAAATCAATTATTAAGGAGTGTAATATTATGAAAAATGAATTAATGATGTTTGAAGGAAAAGAGA # Questionable array : NO Score: 6.21 # Score Detail : 1:0, 2:3, 3:0, 4:0.95, 5:0, 6:0.25, 7:0.01, 8:1, 9:1, # Score Legend : 1: cas, 2: likely_repeat, 3: motif_match, 4: overall_repeat_identity, 5: one_repeat_cluster, 6: exp_repeat_length, 7: exp_spacer_length, 8: spacer_identity, 9: log(total repeats) - log(total mutated repeats), # Primary repeat : GTTTTAGATTAACTATATGGAATGTAAAT # Alternate repeat : NA # Directional analysis summary from each method: # Motif ATTGAAA(N) match prediction: NA Score: 0/4.5 # A,T distribution in repeat prediction: NA [Repeat is AT rich:79.31%AT] # Reference repeat match prediction: NA # Secondary Structural analysis prediction: NA [0.00,0.00] Score: 0/0.37 # Array degeneracy analysis prediction: F [0-4] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [71.7-71.7]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [0.41,0 Confidence: MEDIUM] # Array family : NA // Array 1 1186-895 **** Predicted by CRISPRDetect 2.4 *** >NZ_SEQU01000016.1 Clostridioides difficile strain LC4-009-0 NODE_16_length_115584_cov_48.3925, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ===================================== ================== 1185 29 100.0 36 ............................. CATAAGCACTCAAAGGATTTGAAATATAAGAATAGG 1120 29 100.0 37 ............................. AGTATTCCTTCTATTAAATTAGATTGGACTCCAATTA 1054 29 100.0 36 ............................. TCATAAATATTCATTTTTTCTCTCCTTATTATTAAA 989 29 100.0 37 ............................. AGAGGCAACTAATTGCTTATGAGTCTGCTAGTCTTAA 923 29 96.6 0 ............................A | ========== ====== ====== ====== ============================= ===================================== ================== 5 29 99.3 37 GTTTTATATCAACTATGTGGTATGTAAAG # Left flank : TATGCTTTTAATAATATTCATAATACAATCACCTATAATTAAATTTTTATTAATTATATTCTAGCATCAAATATTGAATAAGTCATCTTCTTTAAAATATAATAAATAGTATTTTGCTCAAATTTTCAAATGCTTCTCTGTCCATCTCTTCTAAAAACTGAGAGTAGCTATTCATAGTTATTTTTATATCTGCATGACCTAATCTTTCTGAAATAGTTTTTATATTAGTTCCAGAAAGAAACATTAAAGTTGCATTATTATAGAATTTAAACATAATTAAATGTAAAAATTAATTGAAAATATTAATTATATGTTATGATATAATAAAAATATAGAAATTTTGCAGTGAGCGATATTTGTGACAAATTGAGGTTTAGCAGTTGAAATATAAGGCATTGAGAATATATAATAAGTATTATCAATTGCACTATTGCGCGTTCACTGCAATTTTAAGAGCATTGTATATGTGTAAACATTGGAGATGCTAAGTTTATTTTGGG # Right flank : TTTTTATTACATTAAAAACAATTCTCCCAAAAACACAAATAATTGTCACAACACACAGTCCTCATATTTTACAAATTGATTCTAAAGAAGAAATGATTGTGTTAGATATGGCTGAAAGTGATAATGTATATAAAAAAGAGTTAGAACTTGGAGAATACGGGGTATTAGGCTGGACCAATGAAGGTTTATATTTACATTAAGAGCACTCTTTTTATAGGAGTGCTTATTTTTTTGAAATTCATTAGCATATAAACTATCAAGAACATTACTCAATATACCTTATTTACTTCACCAATGATTATCTTACATATATTAACAATAAAAAAAGACTCTAAAAAGAGTCTTTCCCGAAAAATCTATATATTATAATATAGTTATATTTTCTGCTTGAGGACCTCTAGCACCTTTAACTATATCAAAGCTTACTTGTTGACCTTCTTCTAATGATTTAAATCCTGAAGTTTGTATAGCTGAGAAATGAGCAAACACATCATCTCTAC # Questionable array : NO Score: 6.02 # Score Detail : 1:0, 2:3, 3:0, 4:0.96, 5:0, 6:0.25, 7:0.01, 8:0.8, 9:1, # Score Legend : 1: cas, 2: likely_repeat, 3: motif_match, 4: overall_repeat_identity, 5: one_repeat_cluster, 6: exp_repeat_length, 7: exp_spacer_length, 8: spacer_identity, 9: log(total repeats) - log(total mutated repeats), # Primary repeat : GTTTTATATCAACTATGTGGTATGTAAAG # Alternate repeat : NA # Directional analysis summary from each method: # Motif ATTGAAA(N) match prediction: NA Score: 0/4.5 # A,T distribution in repeat prediction: NA [Repeat is AT rich:72.41%AT] # Reference repeat match prediction: R [matched GTTTTATATTAACTAAGTGGTATGTAAAG with 94% identity] Score: 4.5/4.5 # Secondary Structural analysis prediction: R [0.00,-2.60] Score: 0.37/0.37 # Array degeneracy analysis prediction: R [1-0] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [73.3-68.3]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0,5.28 Confidence: HIGH] # Array family : I-B [Matched known repeat from this family], //