Array 1 219541-218719 **** Predicted by CRISPRDetect 2.4 *** >NZ_CAAJVF010000003.1 Clostridioides difficile strain lsh25, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ====================================== ================== 219540 29 100.0 37 ............................. ACGAACATACAACATATAAAATATAGATGTTATCATT 219474 29 100.0 38 ............................. ATAGGCAAAATGTAGACTTAGCAGTACAAATCCATTTC 219407 29 100.0 36 ............................. TGTATAGAATTAAGAATTTTTTAAATACTAATTATA 219342 29 100.0 38 ............................. TTCCAAGTGAGTATGTATGAAGAAATAACTTTTTTAAC 219275 29 100.0 37 ............................. GAAGCTGGCAAAACCGAGGTCGGGAAATCGGCAACAT 219209 29 100.0 37 ............................. ACATATGCTTTTAATTCAACTGTTGAAGATGAAATTA 219143 29 100.0 37 ............................. AAATATATATCAGTTAAGCAGAGAAAATACTGGTCTT 219077 29 100.0 36 ............................. GCAATCATTCCGACTAAGTATAATATTGCAAAGTTA 219012 29 100.0 37 ............................. CTTGTACATGTGTCTCATATTAAATTTAGAGTTTATA 218946 29 100.0 37 ............................. ATTTATTTTTCGCTGAATGTGACTATCAACCATTCTC 218880 29 100.0 37 ............................. GTTGTATTACCTCTGTAATTATTTTTTCCAAAATTAC 218814 29 93.1 37 .C..............T............ TGTCCTAACCTAACAATATATTGGTTACCTCCACCTA 218748 29 86.2 0 ...............A......AT.T... | G [218727] ========== ====== ====== ====== ============================= ====================================== ================== 13 29 98.4 37 GTTTTATATTAACTATGTGGTATGTAAAG # Left flank : CTACAATTTATAGAGTGGAGTTCATACAAAAGATAATCCTCCCAACGTATAGAAGGGAGGTGAATATGTATGGATAATTTTTTACAAGGTATATTAGCAAGTTTAGTTGCTAGTTTAATAGTTTACTTAACTAGTAAGTTATTTAAAAAAGTAAAAAGCCACTCTGGCAGGAGTGACTTTAGTTTTGAACTAGAAATCAAGTTCAAAAAGAATAAACATTAGTATTTGAACTTCACTCTACGTCTAAATAGATTGTAGTTCTTCCTGTTTTTATTATACCACAAATTGGTGCAGATATTCAAAAATAATATTTTTATGATATAATAAAGATATAGAAATTTTGCAGTGTTCGATTTTTTGAATAAAATAGGGCTTAAGCATTGAAATATAAGGCGTTGAAGATGTATGATAAGTATTATCATTTGCACCACTGCTCGCTCACTGCAAATTTTAGAGTGTTGCATATGTGTAAGTGTTGGAAATGCTAAGTTTATTTTGGG # Right flank : AAGTTACAATGAGTACAAGAATGTTTCTATTTATTGTAACTTTTTTTATTACAAACTTAAATTTATAGTATATTATAAAAATCATTATAAAAAGATGATTTAATAAAAAAATATAATTAAAAAAATGATTAATAATCTATAAAAATGGAAAAAGCATCCAATATCCTACAAAAATATATTTTTTTATTACAATTACAAGTTTTTATTGCATCTATTTAGCAAAAGTATTATTATGCAAGTAAGATAATTATCAAAGACAATTCTAAATAGTCTGATTTAAAAGTACAATTAAAGGATATAAATAGGAATAATTTATAAATATTACAGAAGATTTATAACTAAAATTACGAATGTAAGTTTGTTATATGGGGTAGTTGTGTGGATGAATCAAATAAATTAATATTAGAATTGAATAATATTTTCTGTGAATTAGAGAGTATTAATAAATATAAGTTTAATGAATATAAAGAAATTGTTAAAAACTTACACAACAAAAAAGA # Questionable array : NO Score: 6.18 # Score Detail : 1:0, 2:3, 3:0, 4:0.92, 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 : GTTTTATATTAACTATGTGGTATGTAAAG # 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:75.86%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: R [7-0] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [80.0-66.7]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0.27,4.91 Confidence: HIGH] # Array family : I-B [Matched known repeat from this family], // Array 2 267293-266401 **** Predicted by CRISPRDetect 2.4 *** >NZ_CAAJVF010000003.1 Clostridioides difficile strain lsh25, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ============================================== ================== 267292 29 100.0 36 ............................. TATATCCAAGTGCATCCGCTGCGTCTTTAGCTGTTT 267227 29 100.0 37 ............................. GAATCAAAATGCAACAGAATTTTGGCAAGAAGTAATA 267161 29 100.0 38 ............................. ATTAACCGATTCGGCAAAAGTATATCAGATAACACAAA 267094 29 100.0 37 ............................. TTTATATCCGTTTTTATTTCTGTATTACTAAGACACC 267028 29 100.0 36 ............................. AAAGAATTAACAATTATAGTAAGTAAAGGTTATCCA 266963 29 100.0 36 ............................. ATAGGCAAAATGTAGACTTAGCAGTACAAATCCATT 266898 29 100.0 37 ............................. CAAATACACAATTCCAGCTGCAAGACCTGCAACCGCA 266832 29 100.0 37 ............................. TCGTTTGCTAGGAAGTTTATCATATTAAAATTGTGTA 266766 29 100.0 37 ............................. AATTGTAATATCTTTGTATACATCTTCATAGAAAACA 266700 29 100.0 36 ............................. AGCGTTTTGTTTACACTTAATAGAAAAAACAGTTCG 266635 29 100.0 36 ............................. GATATTCCTTCTGTTGATATAGATTTTTCGCCACTT 266570 29 100.0 37 ............................. TTGTAGAAAGGTTTCTTATGGGTTGAAAGAGGCTTTT 266504 29 93.1 46 .......................A....G CATAGTCTATTGAACATTTATTAAGAGATAACTTTCGTTTTATATA 266429 29 79.3 0 ...........G...TA.T.A..T..... | ========== ====== ====== ====== ============================= ============================================== ================== 14 29 98.0 37 GTTTTATATTAACTAAGTGGTATGTAAAT # Left flank : GACAGTCAGTTTTTTGTTTATCTGAATAATATTTTACTTAAATTATTAGAGGTCTTTTTGTATATTTCTTCTAAAACATAAGAATATCTATTCATAGTTAGTTTTAAATCTGTATGACAAAATCTTTCAGAAACTATTTTCATATTAGTTCCTACCAAATGTAACAAACTAGCACCTGTATATCTTAAATTATGTATTTTCATTTGTCATTAGGTATTTTTAATACATTATATAACTATGGTTTTATTATGTGAAATCTAAGTTATAAATACTATTGATGATAGAGTAATTGTATACAAAAATATATAATATATTTATGATATAATAAAGATATAGAAATTTTGCAGTGTTCGATTTTTTGAAGAAAATATGTTTAAGCATTGAAATGTAAGGTATTGATAGTGATTGATAAACATTATCATTTGCACTACTGTTCGCTCACTGCAAATTTAAGAGAATTGCATATGTGTGAGTATTGGAAATTCTAAGTTTATTTTAGG # Right flank : ATTTCAATATTGGACAACGGAAGTTTTTTCAGTGAGTAAAGATTGAATCACTTTATATTTATCTTAATTATGTAATAATATAATCATTATCTTATTTCTATTTGTAATTTTTTTAAGTATGTATTGTCCAGTTGTAATTTGTTTTTATTATTTTAAACTTTCAATTCCAAAATTATCTAATATAATTGAATTAACTTACTTTCTTTTTTTATTTTACCTCCTTGTTCTCTAATTAATTTATACATTTTATTTATATTTAAGAATACATACTCTAATTTGATTACATAAAATAAAATGTTTTTCTACTATAAATTAAACTCTTTAAAAAATATGACTCAACTACTTTAATTTTTATTCTGATGATACATTAATTCTAGACATAATAAAACTCTCCTAGCTAGATGATTTTACATGTTTTAACTATTTCCTAAAAAAGTATAGTTTGATAAAAAGAGCATTTTTATATAAGTACCATATTTTTATTGTGGAAGATAATTATT # Questionable array : NO Score: 6.16 # Score Detail : 1:0, 2:3, 3:0, 4:0.90, 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 [8-0] 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 [0,4.91 Confidence: HIGH] # Array family : I-B [Matched known repeat from this family], // Array 1 45209-46159 **** Predicted by CRISPRDetect 2.4 *** >NZ_CAAJVF010000001.1 Clostridioides difficile strain lsh25, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ====================================== ================== 45209 29 100.0 37 ............................. TTTTAAAAAATTTTTATACACCGTTCGCTATTTCTTT 45275 29 100.0 36 ............................. CTGACAAAACTTTATATAAGAGGACTTATTTAATTG 45340 29 100.0 35 ............................. TATAATATCGGTTTTATAGTTGGGTCTATTGCTAG 45404 29 100.0 36 ............................. GTAAGTTCTGTTATTACATGCTGTTGTGCTTGATAT 45469 29 100.0 37 ............................. TATCTTCAAGATGATACATTTTCAGAAGGATGTATTG 45535 29 100.0 37 ............................. TGATTATTATATTATCACAGGAAGGGACAAAATTTTT 45601 29 100.0 36 ............................. CATGATTTAAAACAAATAGAAAAACAGTTAAAAATC 45666 29 100.0 38 ............................. CTATAATACTTTTCTGAAAAACATTCTTTACAAATAGC 45733 29 100.0 36 ............................. TATCAAAGAATATGGATAGTTTTATTTCTTCACTGC 45798 29 100.0 38 ............................. TCTGCTGGAATATTAAAGTTTAGTTTTTGAAGTGTAAA 45865 29 100.0 36 ............................. ATAGGTCCTGCGCTAACTGTTTTAACTCCAAGCATA 45930 29 100.0 37 ............................. TTAAGTAAGTAGAGTATAAACTATACTAAGAGGTCTT 45996 29 100.0 38 ............................. TCTAGTCAAGAGAAAATGTTCAAAATAGCGAAAGTTTT 46063 29 100.0 37 ............................. AGAGAACTTAAAGACAAGCTTCTAAAACAGGCAAAAG 46129 29 86.2 0 A..............A.......T....A | GA [46149] ========== ====== ====== ====== ============================= ====================================== ================== 15 29 99.1 37 GTTTTATATTAACTATGTGGTATGTAAAG # Left flank : AGTGGAGTTCATACAAAAGATTATCCTCCCAACGTATAGAAGGGAGGTGTGTATGTATGGATAATTTTTTACAAAATGTACTAGAAAGACTATTTGTTAGTTTAATAGTTTGTCTAGTTAGCAATTTACTTAAAAAACGTAAAAAACCACTCAAAGCTGGCACTAAGAGTGGTTGGGAATTTGATTTAAAAATCAGATTCCATAAAACTAAGTAATTTTCAAATTACGAACTCCACTCTACTTCCAAATAGATTGTAGTTCTTCTTGCCTTTATTATACCACAAATTGGTACAGATATTCAAAAATAATATTTTTATGATATAATAAAGATATAGAAATTTTGCAGTGTTCGATTTTTTTAATAAAATAAGGCTTAAGCATTGAAATATAAGGTGTTGAAGATGTATGATAAGTGTTATCATTTGCACTACTGCTCGCTCACTGCAAATTTAAGAGAGTTGCATATGTGTGAGTATTGGAAATGCTCAGTTTATTTTGGG # Right flank : AAGTTACAATGAGTAGAAGAAGATTTCTATTTATTGTAACTTTTTTTATTACAAATTTAAAATTATAATATATTATAAAAATTATTATAAAAAGATGATTTAATAAAAAAATATAATTAAAAAGACGATTAATAATCTACAAAAATGGAAAAAATATCCAATATTCTACAAAAATAGATTTTTTTATTACAATTACGAGTTTTTTATTGCATCTATTTACCAAAAGTATTATTATGTAAGTAAGATAATTATCAAAGACAATTCTGAATAGTCGGAAAACATTTCTAGGGATGAAAAGGTATAATTACATAAGTTTTATAAAAAAATATTAGGGATTTTTAACTAAAAATAAGAACATAAGTTCTGATGATAGGGGGGATAATAGTATGGAAGAAGAAATTTGTTATAAACTATTAATTTTTTATGAAGAGCTAGAAAATTTAAAAAAGAAGGATGAAGTGATATATAGCGAATGTAGAGAAGAGCTAGAAATATTACTT # 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 : GTTTTATATTAACTATGTGGTATGTAAAG # 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:75.86%AT] # Reference repeat match prediction: F [matched GTTTTATATTAACTAAGTGGTATGTAAAG with 97% identity] Score: 4.5/4.5 # Secondary Structural analysis prediction: NA [-0.50,0.00] Score: 0/0.37 # Array degeneracy analysis prediction: F [0-6] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [65.0-81.7]%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 81810-82100 **** Predicted by CRISPRDetect 2.4 *** >NZ_CAAJVF010000001.1 Clostridioides difficile strain lsh25, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ====================================== ================== 81810 29 86.2 36 GC.....................T....A GCCATACCTGCGTAATATATCGCATCAGCCACTTCT 81875 29 96.6 36 G............................ ACACGTTGTGTTGATTGTTTTAACTCATCCATATTG 81940 29 96.6 37 ...............T............. AATTAAATAGCTTTTACATTGGCAATACATTCACCCA 82006 29 100.0 38 ............................. CCCATAGAACCAACATATTTAAATGTTTCACCCATTAG 82073 28 86.2 0 ....................-..TC...A | ========== ====== ====== ====== ============================= ====================================== ================== 5 29 93.1 37 ATTTTATATTAACTAAGTGGTATGTAAAG # Left flank : AAGAGGAAATAGAGAAAAAATCCTCAGAGGAGAACAAAGTAAACGTGGAAACGAAAAAACAAACATTAACTGGTAAAGAGCTAAAGAAAAAAGTTGATTCTATAATTTTAGCAGAGTATAAAGGAAATTATTACACAAATGATGTATTAGATACAGATGGTAGCTATGTACTTAGTTTACAAGTTCAAAATGCAAGTTTTGACAATGAAAGCAGTTGTAAGGCATTTACTAAAGACTTAATTAACAAGTTGAAAGAATTTAGAATAGACTCAGCAGAGATATATTTTGTAGGTTCAAGCGGTCAAACAACATATCAAATTAACATAGATGATTTCTTGAAAGTTCAAGATAATATTGATAGTATAGACAATATGGAGTTTTTCTCTTTTAAAGATTTTAAAAATTAGAAACAAAATAGAGACATTTGCTTAAACAACATGTGTCTCTATTCTACCAAATTATGTTATAATAGTACTTAAGAAATATAATTTTATAGCATG # Right flank : ACTAAATAAACAAAGGAAGCACTTGCTTTTTGGTAGGTGCTTTTGTTTTGCTCAAAATATTTTAAATTAATAGACTAAGTTCTTATTTTTAGATAGAATTATATTTGAGTAAAGAATTTAATAGGGGAGAGTATATTATGTGGGGAAAATTTAAAAAATTAAGTTTGTTGAAGAAAATTTTAGTAATATTTTTAATATACCTTATTGTATTTACAGTATCAATGATGATTCATCAAGCGATACGAGATTCAAAAAATAGAAATGAAGTAGATGAAGGAAATATTACAAAAGAAAATATAATTAGTGAAAGAGAAAAAGAAGATATTTATAAACAAGAGATGCAAGCAAAAGTAGACTCTATTATACCAGAAGACTTAAAAGATAAAACAACATATTATGTTAACATATTAAACCCAACAAAAGGTGAGGGATATATAGTTAGTATTCAAGTGGAAAATTCTAGGTTTAATGATGAAAATGAGTGTAGAAACTTTACTAAA # Questionable array : NO Score: 3.72 # Score Detail : 1:0, 2:3, 3:0, 4:0.65, 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 : ATTTTATATTAACTAAGTGGTATGTAAAG # 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:80.77%AT] # Reference repeat match prediction: F [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 [1-3] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [76.7-68.3]%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 84528-85145 **** Predicted by CRISPRDetect 2.4 *** >NZ_CAAJVF010000001.1 Clostridioides difficile strain lsh25, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ===================================== ================== 84528 29 100.0 34 ............................. TTTAATCCAGGTACGGCAATACTTAAAAGTGATT 84591 29 100.0 37 ............................. CCTCATATTTTTCTATTTTAATTTTTTCCATAGAATC 84657 29 100.0 37 ............................. CCCAAATTATCTTTCATAGTTGTAGCAACTTCCATTA 84723 29 100.0 37 ............................. AGCGAAAATGCTTATGACTTAAAAATACCTCCACAAG 84789 29 100.0 36 ............................. CTTGTAGAACAAATCTTCGCAGAGAGGACGATTAAG 84854 29 100.0 37 ............................. TTCAAATACGCAGAAGAAGAAATTATAAGTTTAAATG 84920 29 100.0 37 ............................. AAAAATAAAAAAAGAGGATTATTAGATACTAATTCTA 84986 29 100.0 37 ............................. ACTATTTTGTCAATGTAAAATAATTGATATAAACTAT 85052 29 100.0 36 ............................. AGTGATAGATTAATAGATGATATTTGTAGTACATTC 85117 29 82.8 0 ................G...GC.TA.... | ========== ====== ====== ====== ============================= ===================================== ================== 10 29 98.3 37 GTTTTAGATTAACTATATGGAATGTAAAT # Left flank : TATCATGTGGTTTATAAGATTGAGTAAATTCTATTGTATTAAATAATTTATTTTAGTTTAGTTTTGAGGGGGATTAATACAATGTGTAAAAGTTTGCTTAATGAATATAATTTAAAAACTGATAAAGAGAGAAAAGATTTTATAAAGTTTGTTATACTATCATATAAGTTGGAACAGAATGATAAAGAGAAGTTTTATGAATATGCAGAGATATTGAGAGAAATGCTTAGAGAGCAAGAAGAGAGAGAAAATAAGTAAATAAATAGATAAAGCACTTGAATATTCTACTGTTTCAAGTGCTTTATATGTTAAAAAATGGTATAATAAAAATATAGAAATTTTGCAGTGTTCGATTTTTTGAACAAAATAGGGCTTAAGCATTGAAATGTAAGGTATTGAGAGCATATGATAAGTGTTATCAATTGCACTACTGGTCGCTCACTGCAAATTTAATAGAGTTATATATGTGTGAGTATTGGAAATGCTAAGTTTATTTTGGG # Right flank : TTAAAAATACTAAAAACACTTACTTGAATGGTAGGTGTTTTTTTAATTGAAGTAGGTGATTATAATGTAAAAAGTAACAAATAGGTAAAATATGTAAGAATTATGTGTTATAATAATTTTAGCAAGGAAATTAAAATTGAAAAGCTAAGGGTGATTTTCTCATATAAACGCCAAATTCCAATGTAGGAAGGAGGTGAATTTATATGTTAATTAACTTTTTATTGAGTATAGTAGCTGGTCTTGTATCAGCTTTCATATATGACAAAATAAAAAATCACCCAAACGCCAATAAGGGTGATTTAAAGAAATAACTTTTAAATTCTAATCAATTAGAGAAATTCACCTTTTACAAAGTAAATTTTATCTCCTTGCTATTATTATAGCATAAATTAGAAAAAATATGCAAATAAAGAAAAATGCTTATTAAATTTAATAGGCATTTTTTTATTTTAATACTAAATGAGGAAGTGAATATATGGTAAGAAGACTGCGGTGTAATA # Questionable array : NO Score: 6.17 # Score Detail : 1:0, 2:3, 3:0, 4:0.91, 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 [0-5] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [71.7-75.0]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [0.41,0 Confidence: MEDIUM] # Array family : NA // Array 4 191442-191667 **** Predicted by CRISPRDetect 2.4 *** >NZ_CAAJVF010000001.1 Clostridioides difficile strain lsh25, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ===================================== ================== 191442 29 100.0 37 ............................. TTCGAACGCATCAGTGCTGCTGCTTGTATATTAGTCA 191508 29 100.0 37 ............................. AGTCCTCCAAATTTATTTAAGACATCCACGAATTTGT 191574 29 96.6 36 ............................G CAACAAGAACAGTTGATTTTACCTTTTCTAGCCAAC 191639 29 82.8 0 ......T.........G....T.CA.... | ========== ====== ====== ====== ============================= ===================================== ================== 4 29 94.9 37 GTTTTAGATTAACTATATGGAATGTAAAT # Left flank : ATTATATGTTATAATAATTGTAGCAAGGATAATAATCGAAAGTGCGAAGGGTGATTATTTTCATATTAAACGCCAAATTCCAAATAAGGAAGGAGGTGAAATTATATGATAGGTTTTTTATTAAGCATAATAGCTGGTGTTATATCAGCTTATATTTATGACAAAATAAAAAATCACCCAGACGCCAATAAGGGTGATTTAAAAAAATAATATTTTCACTTAACAACTGAAAATAATCACTCTTTGTAGGAGTAAATTATTTCCTTACTTTTATTATACCACAAATTGGTACAGATATTCAAAAATAATATTTTTATGATATAATAAAAATGTAGAGATTTTGCAGTGTTCGATTTTTGTAATAAAATATGGCTTAACAATTGGAATACAAGGCATTGAGGGTGTGTGATAAATGTTATCAATTGCACTACTCATGGTTCACTGCAAATTTGAGAGAGGTGTGTATGTGTAGGTATTGGAAATGCTAAGTTTATTTTGGG # Right flank : TTAAATAGAAAAAAGAAAGCACTTACTTAAATAGTAGGTGCTTTTGTTATTCTTTGCTAGATAAAGTAACAAGTTCATTAGGTGTACATTCAAGAACAAGACAAAGCTTTTCGAATAAATCTAATTTTATAGAACTTGTTTCATTGTTAGCTAATTTCATCATGTTAGGATAAGCTATACCTACTTCTTTAGCTAACCAATATCTAGTTCGACCTTTGGATTCAAGTAATTTATCAATGTTAAAATACATTTTTTCACCTCTTAAGTATATTATACAACAATTATATAATGTTTGCAATATATAATATGCAAATAATATAATTATATAATGTTGACATTATATAATGTGTACGATATAATATACTTAAGGAATAAAAAATAAGAGCCACTCGCCCCTACCAAGTTTGAGTAACTCTTATTGACATATACTACATGTGCATTAATTATAGTATATGTCATTCCTTAAAAAAAATCAATTAAGGAGTGTATTTTTATGAACA # Questionable array : NO Score: 5.61 # Score Detail : 1:0, 2:3, 3:0, 4:0.75, 5:0, 6:0.25, 7:0.01, 8:0.6, 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 [0-6] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [63.3-73.3]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [0.41,0.27 Confidence: LOW] # Array family : NA // Array 5 322610-323359 **** Predicted by CRISPRDetect 2.4 *** >NZ_CAAJVF010000001.1 Clostridioides difficile strain lsh25, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ====================================== ================== 322610 29 100.0 37 ............................. TATTAAGGGGTACTTTTAAGCTAGTATTTCTATGCTT 322676 29 100.0 37 ............................. CAAAAAGTCGCCAAAATAGCAGCATTAAATAAATTTC 322742 29 100.0 37 ............................. TACAAAACTTATGCTAACTTTAGAAAATATAACTCAT 322808 29 100.0 36 ............................. GCTTATCAACTATTGTTCCTGTTGGGGCTGCCATAG 322873 29 100.0 36 ............................. CAATCTGATAAATCATTCTTGTATATTGATTTTAAC 322938 29 100.0 36 ............................. CAGCGAAACCGAAAACCTTGTCTTTTAGCCAACCGC 323003 29 100.0 35 ............................. ATATGAGGATTTTCTCTAAATGAATGGTGGTTAAG 323067 29 96.6 37 .............C............... CAGTTGACACAATGAGTAAAAGCGAAGCAGAGCAAGC 323133 29 100.0 38 ............................. AATATTCTTCTTCTATCTGTATCTAATCTTAGACCATC 323200 29 100.0 37 ............................. GTAGATTATAAAATGTTGAAATAATAAGGAGGTGTGG 323266 29 100.0 36 ............................. ATTAGTGTGCTAAAAAACACATTAAATTATGATAGA 323331 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ====================================== ================== 12 29 99.7 37 GTTTTATATTAACTATGTGGTATGTAAAT # Left flank : ACTATTATTATATAACTAACATCTAAGTGACATTTAAGAAAAATATGAGATTACTGATATTTTACTGATATAAAACTGAATGTTATTTAAAGAGAGCCTTGATTATATTTTTAGAAGCTTTTTATGCATATTATCTAAAATATGAGAATATCTATTCATAGTTATTTTTATATCAGTATGACCTAATTTTTTAGAGAGAATTTTTATATTAAATCCAGTTAGAAGAAGACTTATTAGAATATCCAATGTAGTAAGCACTAGCAGATATTCTTAAATTGATAAATTACTCCATTTTAATTTTATAGGTTAAATTTTATGATATAATAAAAATATATAAATTTTGCAGTGAGCGATATTTTTGATAAAGTAGGGTTTAACAGTTGCAATGTAAGGCGTTGAGGGTGTATGATAAATGTTATCAATTGCACTACTCATGGTTCACTGCAAATTTAAGAAAGTTGTATGTGTGTAAGTACTGAAAATACTTAGTTTATTTTGGG # Right flank : TTTGCAACAAGTATAGGTAAAATACTCCAATAATTTATATAGCATTTTCTCCTTTAAAATATAATTATTTTTTATCATTTGTAGTAAGTAATTACCAGATAACATTGACTTTAGTCTTATTGATTAAAATATAAAAGTAGAATAATTATAAAAAGTATTGAAAAGTTTATAAATATATAGAATAAAACTTAATGACAAGATACTAGATATAAAAATAATTACCTTATAAATAGATTGAAATTTGTGAATATTCATACTATAATTTAGATATAAGGAGATGCTCTTATAAACTTAAAGGGTTTGTACTACTTGTACTATCAGTATTGATAATATTAAAGAATATATACCATTTGTATTTGTTGAAAAAGATTTTAATAGTAATACAATGTAAAACAACACAAATATCAAAATTTAATATTGATAGAGGTATAAACATTATAAAAATAATTGAAAATAAAAAAATATTTAATCCAACTACAATATAAATTAGAACTACACTT # Questionable array : NO Score: 6.25 # Score Detail : 1:0, 2:3, 3:0, 4:0.99, 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 : GTTTTATATTAACTATGTGGTATGTAAAT # 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 97% identity] Score: 4.5/4.5 # Secondary Structural analysis prediction: NA [-0.50,0.00] Score: 0/0.37 # Array degeneracy analysis prediction: F [0-1] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [71.7-76.7]%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 40349-40577 **** Predicted by CRISPRDetect 2.4 *** >NZ_CAAJVF010000004.1 Clostridioides difficile strain lsh25, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ====================================== ================== 40349 29 100.0 38 ............................. AAATTTGATTTCTACTTAATACATTCTTACTTCCGACT 40416 29 100.0 37 ............................. GAAGTATATAAATATCCAGCCTCTGTAACAAATGCAG 40482 29 100.0 38 ............................. TAGTGTTGGTTCAGGAAAAACTTATACAATGATTACAG 40549 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ====================================== ================== 4 29 100.0 38 GTTTTATATTAACTATATGGAATGTAAAT # Left flank : GGAGTTCATGTATCAAAAAATTATCCTCCCGACGTTAAGAAGGGAGGTGAATATACATGGATAATTTTTTACAAGGCATACTAGCAAGTCTATCTGCTAGCTTAATAGTTTATATAGCTAGCAAACTATTTAGAAAGCGTAAAAAACCACTCAAAGCGGCAACTAAGAGTGGTTGGGAATTTGATTTAAAAATCAGATTCCATAAAACTAAGTAATTTCTAAATTATGAACTCCACTCTACAGCAAAATAGATTGTAGTTCTTCTTGCTTTTATTATATCACAAATTGGTACAGATATTCAAAAATAATATTTTTATGATATAATAAAGTCATAGAAATTTTGCAGTGTTCGATTTTTTGAAGAAATTAAGGCTTAACAGTTGAAATATAAGGCATTGAGGACTTGTGATAAGTGTTATCAATTGCACTACTCATGGTTCACTGCAAATTTGAGAGATTTGTATATGTGTAGGCATTGGAAATACTCAATTTATTTTGGG # Right flank : TTGTATCAAAAAAATTACAATAATCATACGAACTGCTAATATAAGCAGTCAATATATGTGTACATTTATCCATTTTATCTCTAAACATATAAATTATTATCCCCCTAAAAAACTTTCATAAAAACAAAAAGAACAATATCTCTTTGGCAACTGGCTGACATAACTCATAAGATATTTATATAAGTCTTAGTCCCTATAGCTTTGCGTCACTAGATTTCTCTAGTTTTGCCGATTTAGTTTTATTCTATAACTAAATAATACAATAGAATTAGTTATTATTCAACAAGATTGTTTGAAAATTGAATAAATTTATAGGTATGAACGTAATTTCACACTTAAAAACAGACTAAATACGTAGAATATATAGAAAAATTTACCTGTAGTTTTTGTGATAAAAAGCTCCTATTATTAATTTAAGCTAGATAAGTTTGAGGAAGTGACATAAATTGAAAGAAGGAATATATTATGCTAAATAAAAAATTACCAGATGCAGAATTAAA # Questionable array : NO Score: 5.86 # Score Detail : 1:0, 2:3, 3:0, 4:1.00, 5:0, 6:0.25, 7:0.01, 8:0.6, 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:80.00%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: R [1-0] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [68.3-75.0]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [4.5,0.41 Confidence: HIGH] # Array family : I-B [Matched known repeat from this family], //