Array 1 17016-17576 **** Predicted by CRISPRDetect 2.4 *** >NZ_RRAR01000001.1 Clostridioides difficile strain 17-265-08880 MRSN537878_contig00001, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ======================================= ================== 17016 29 100.0 37 ............................. TTTTTAGATTTAGAAAGTAGATTTGGAGTTGTTACAG 17082 29 100.0 37 ............................. CACAAAAGCAGGTTTAAAAAAATCAAATATTATAGAA 17148 29 100.0 39 ............................. GCGCAAACCAGGCATAAAATCTTTGCTCTGCTATGCCTT 17216 29 100.0 37 ............................. TTTAAAATAAAATATATTTGCCTACCATCAACTGAAG 17282 29 100.0 37 ............................. CTTCAAGAAGATGCTAGTTTAAGTGATATATCAACTA 17348 29 100.0 38 ............................. TATGTAAAAAATAAAATAAATAAAAGTAACACTTTATA 17415 29 96.6 37 .......................A..... AGCAATTCTGATATTTTTATTCTAATCATTTGAAATC 17481 29 100.0 38 ............................. CCATCTTTTGTTGCTTTACATAAATTTATATTACTTAC 17548 29 82.8 0 ........C........CA....A...T. | ========== ====== ====== ====== ============================= ======================================= ================== 9 29 97.7 38 GTTTTATATTAACTATATGGAATGTAAAT # Left flank : AAAATGTTAATGAGATGTATGATAGGGATTTTGGAGATAATATAATAAAAACACTAGCACAGTCTATACAATCTATTTTACCAGATAATGCTGAACTTTATAAACTTGATGGGGACGAAATGGGTATTCTTGTTGATAATGTTGAAGAAAATGAAATTCTAACTCTATATAATCAAATACAGAATATGATTATACACCTTCAACTATGGAGAAAATATGGATTAAATATAACAATTTCTGCTGGTTGTGTAATATATCCAAAACATGGAGATACAGTAAAAGAACTTTATAAGTGTGCTAGTTACTCTTTACAATATGCGAAAGAGCATGGTAAAAACAGGCTTGTTTTTTTCTCCCAAGAAATATTAAAAAATAAACAGTTGAAATATAAGGCGTTGAGAGTGTATGATAAGCGTTATCAATTGCACTATTGCTCGTTCACTGCAAATTTAAGAGAGTTGTATACGTGTAAGTGTTGAAAATACTAAGTTTATTTTGGG # Right flank : TTTCTTTTAATGTGTTATCTTATGATTATCTAGTTATATTAGCATACAAAAATATAATAAAATTACACTATATTATAAAAACAAAAAGGTAGTATAGAAATCCTATTATCTTTTTATTATTAATTTTATCAGTGTTTTATTATAAATAGCTTACATAATTACACATTTTTTCTGATTAAATAATATGATGCTATTGTTATAATAGATACTAATGCTAATGATGTTATTGCAGTATCTAATCTTCTTATTAATAAACTCATTTCTATATATTCAAGTTCTATTAAATATTGATAAAATATTTCTAGTTTAACAGCTTTTTCTCTATCTATATTTCCATACTTTAACTCTAATTTATCTAAAGATTTTTTATTACAATAATTAACTTTATGTTTAATTAAATATCTTATTGTAGCACCTATTACAATTTTCACTCTAACAAGTATAAATATAATATTCCATCCAAAAGTTAAGAGGGGATATCTTTTTTATGATGGGAATGG # Questionable array : NO Score: 6.15 # Score Detail : 1:0, 2:3, 3:0, 4:0.89, 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 108163-108589 **** Predicted by CRISPRDetect 2.4 *** >NZ_RRAR01000001.1 Clostridioides difficile strain 17-265-08880 MRSN537878_contig00001, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ====================================== ================== 108163 29 100.0 37 ............................. GCTGAATCCTCAATTTTAGGGACTGTTCCTGTTACGA 108229 29 100.0 38 ............................. TTTTCTAAATTCTTCTGGTAATGTTTTTACTTTATTAA 108296 29 100.0 37 ............................. TTCATTGACCAAACATTTTGTTTACATCTAATCGAAA 108362 29 100.0 37 ............................. CAAACAAAAGAAGCACAAGAACGACTTAATGATTTGG 108428 29 100.0 37 ............................. GTTTTAGAAAAAGCTTTAAAAAGTTATGAAAACTAAA 108494 29 100.0 38 ............................. TCAGTTTTTCGTTTGATTGGCTCTATCTTTAAAAAAGT 108561 29 89.7 0 .....................C.TA.... | ========== ====== ====== ====== ============================= ====================================== ================== 7 29 98.5 38 GTTTTAGATTAACTATATGGAATGTAAAT # Left flank : ATTATATGTTATAATAATTGTAGCAAGGATAATAATCGAAAGTGCGAAGGGTGATTATTTTCATATTAAACGCCAAATTCCAAATAAGGAAGGAGGTGAAATTATATGATAGGTTTTTTATTAAGCATACTAGCTGGTGTTATATCAGCTTATATTTATGACAAAATAAAAAATCACCCAGACGCCAATAAGGGTGATTTAAAAAAATAATATTTTCACTTAACAACTGAAAATAATCACTCTTTGTAGGAGTAAATTATTTCCTTGCTTTTATTATACCACAAATTGGTACAGATATTCAAAAATAATATTTTTATGATATAATAAAAATGTAGAGATTTTGAAGTGAGCGATATTTGTTACAAAATATGGCTTAACACTTGAAATCTAAGATGTTGAGGGTGCGTGATAAGTGTTATCAATTGCACTATTGCCCGCTCACTGCAATTTTAAGAGTATTGTATATATGTAGGTATTGGAAATGCTAAGTTTATTTTGGG # Right flank : TTAAAAATACTGAAAAACACTTACTTTTATGGTAGGTGCTTTTTTATATTAAAATCTGTGTACTTAATTGAAATATTTGGTAAAATATGTAAGAATTGTATGATATAATAATTGTAGCAAGGAAAATAATAATTGAAAAGTGCTAAGAGTGGTTATTTCCATATTTGAATACCAAATTCCATAACGGAAGGAGGTGTAACAGTATGGTGATAAATTTTTTATTGAGTATACTGGCTGGTGTTATATCAGCCTTCATGTATGAGAAAATAAAAAACCACTCAAAGGCCAATAAGAGTGGTTTAAAAAAGTAATTCTTTAAATCAATTTTGATGGAAATAGCTACTCTTGTATAAAGTAAATTATTTCCTTGCTTTTATTATACCACAAATTGGTACAGATATTCAAAAATAATATTTTTATGATATAATAAAAATGTAGAGATTTTGCAGTGAGCGATATTTGCGATAAATTGAAGTTTAACAGTTGCAATATAAGGTGTT # Questionable array : NO Score: 6.19 # Score Detail : 1:0, 2:3, 3:0, 4:0.93, 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 [0-3] 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 [0.41,0 Confidence: MEDIUM] # Array family : NA // Array 3 109193-109680 **** Predicted by CRISPRDetect 2.4 *** >NZ_RRAR01000001.1 Clostridioides difficile strain 17-265-08880 MRSN537878_contig00001, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ====================================== ================== 109193 29 100.0 37 ............................. AATTGCTCGACTGTTTGTTGATAAACTTCTCTTAAAT 109259 29 100.0 36 ............................. TCATTTGTATTAATTGAAATATAATCTTGTAATTTC 109324 29 96.6 37 ......T...................... AGTCCTCCAAATTTATTTAAGACATCCACGAATTTGT 109390 29 100.0 38 ............................. ATTGATGACTTTAGGAGTAAGCAGAGCTAATGTTACAC 109457 29 100.0 37 ............................. TTCGCAACTTATGATGGTGAAATGATTACATTAACAG 109523 29 86.2 36 ......T.........G...T.......G GGAACATAAGGTAAATCATAAGAAACTCAAACAAGA 109588 29 82.8 35 A.....T.........G...T.......G ATCACTTTTTCTCAAGCTCTTACAATGATGAAAAA 109652 29 79.3 0 A.....T.........G....C.TA.... | ========== ====== ====== ====== ============================= ====================================== ================== 8 29 93.1 37 GTTTTAGATTAACTATATGGAATGTAAAT # Left flank : ATAATAATTGTAGCAAGGAAAATAATAATTGAAAAGTGCTAAGAGTGGTTATTTCCATATTTGAATACCAAATTCCATAACGGAAGGAGGTGTAACAGTATGGTGATAAATTTTTTATTGAGTATACTGGCTGGTGTTATATCAGCCTTCATGTATGAGAAAATAAAAAACCACTCAAAGGCCAATAAGAGTGGTTTAAAAAAGTAATTCTTTAAATCAATTTTGATGGAAATAGCTACTCTTGTATAAAGTAAATTATTTCCTTGCTTTTATTATACCACAAATTGGTACAGATATTCAAAAATAATATTTTTATGATATAATAAAAATGTAGAGATTTTGCAGTGAGCGATATTTGCGATAAATTGAAGTTTAACAGTTGCAATATAAGGTGTTGAGGGTGTATGATAAGTGTTATCAATTGCACTACTTATGATTCACTGCAAATTTGAGAGAGATGCGTATGTGTAGGTATTGGAAATGCTAAGTTTATTTTGGGG # Right flank : TTAAAAACGCTAAAAACACTTACTTAAAAAGTAGGTGTTTTTTATTGAAAGTAGGTGATTATAATGTAAAAATTTTACTAATATAGTATAATATTGTTAAAGAATATAATTTAGGGGGATATTATATTATGAAGAAAAAAGTATGTTTTTTATTTTCTATTCTTATAGTTATCTGTTTAGCTATTGTAGGATGTTCTAATTCAGAAAGTCCAGAGGAGAGTAGTAAAAATAATGAACCAAAAAAAGAAGAAAAAAAGGATAAAGAAGTAGTCATAGGAGAGAAAATTATTTCAGATAAAATGGAAATCACTATTAATAATATTGAATTCTCTTATGATGTTTTACCAAAGGTTAAGGAAAGTTTATATACACATTATCCTGCTGAGTCAGGCAAAGTATATATTGATATTGCTGCTGATATAAAAAATACTCAAAAACAAGAGTTAAATTGTTCAGATTTACTAACTATTGAAGCAAATTATAATGATGGGTATAAATAT # Questionable array : NO Score: 5.89 # Score Detail : 1:0, 2:3, 3:0, 4:0.65, 5:0, 6:0.25, 7:0.01, 8:1, 9:0.98, # 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 [1-15] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [61.7-75.0]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [0.41,0.27 Confidence: LOW] # Array family : NA // Array 1 60651-61538 **** Predicted by CRISPRDetect 2.4 *** >NZ_RRAR01000003.1 Clostridioides difficile strain 17-265-08880 MRSN537878_contig00003, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ======================================= ================== 60651 29 100.0 38 ............................. AATCATGATTCCAATCATCATAACAATTAAATTTACTA 60718 29 100.0 37 ............................. TACTGAAACCCAGCCATATACATATTTACATACTCCA 60784 29 100.0 39 ............................. TCCATTCTTGCATCACTTGCTCCAGTAGTCATAACAACA 60852 29 100.0 37 ............................. TTTTTTGTTTTTGCTTCATCTTTTTTATCTTTATTCA 60918 29 100.0 37 ............................. AAAATTGCTGAAACAATAGTGATAAGAGAAGATGCTG 60984 29 100.0 35 ............................. AGAGTTGAGGTTGAGTTGGAGGATATTATTTAAGG 61048 29 100.0 36 ............................. TTTTTATTCTAAGAAACTTTTCAATTCTAGTTCTTC 61113 29 100.0 37 ............................. TTTGAAAGTTGTAATATAATAGATTAAAAAACTAATT 61179 29 100.0 37 ............................. AACACTTTAAAAACTAATGTATTCAGTATAAGAGATT 61245 29 96.6 37 ...............T............. CTTGTTAATGCAAATAAACAACATAGCACTATTAATA 61311 29 96.6 38 ...............T............. AGGGTTTCTGATAAAATCTTCAAACATGTAAAATATGT 61378 29 93.1 37 ...............T.A........... CTTATACTTAGTTAGAACTATATATCGACACAAATAT 61444 29 86.2 37 .C.............TA......A..... TGCAATTTTTATTCGTTGTCCAATCGCTTTGAAATTT 61510 29 93.1 0 .......G.......T............. | ========== ====== ====== ====== ============================= ======================================= ================== 14 29 97.5 37 GTTTTATATTAACTAAGTGGTATGTAAAT # Left flank : CTATTATTATATATAACTGACATTTAAGTGACATTTAAGAAAAATATAATGCCTACTTACATAAAATGGAATGTTATTTAAAGAGAACTTTGATTATATTTTCAGAAGCTTTTTTATCCATATCGTTTAAAATATGAGAATATCTATTTATAGTTATTTTTATATTAGTATGTCCTAATCTTTCAGAGATGATTTTTATATTAGTTCTAGCTAGAAGAAGAACTATTAGAATAGATAATATAGTAAGTATTTACAAATATGTAGGTGTTCTTAAATTGATAAATTATTCCATTTTAATTTTATAGTTTGAATTTTATGATATAATAAAAATATATAAATTTTGCAGTGAGCGATATTTTTGATAAAGTAGGGTTTAACAGTTGCAATGTAAGGGATTGAGGGTGTATGATAAATGTTATCAATTGCACTACTCATGGTTCACTGCAAATTTGAGAGAGTTGTATGTGTGTAAGTACTGAAAATACTTAGTTTATTTTGGG # Right flank : TTTGCAACAAGTATAGGTAAAATACCCCAATAATTTATACAGCATTTTCTCCTTTAAAATATAATTATTTTTTAGCATTTGTAGTAAATAATTACCAGATAACATTGACTTTAGTTTTAATGATTAAAATATAAAAGTAGAATAATTATAAAAAGTATTGAAAAATTTATAAATATATATAATAAAACCTAATGACAAGATATTAGATATAAAAAATAATTACCTTATAAATAGATTGAAATTTATGAATATTAATACTATAATTTAAATATAAGGAGATGCCCTTTGAAAATAAAAATTAAAAAATATTTAATGCTATTACAATAGGAACTAGAACTACACTTAATAAATATACAGAAATTAGATTTGGCTCAATATAAAATACAAATATAGAATTTAGGTGTTTTTTATGAAAAAATTTTTATATGCTTTATATAGTTTCATTGTTATTATAGCTAATTTTAGATTAAAAGAAAAAAATTATAACTTTATTTTATTAG # Questionable array : NO Score: 6.14 # Score Detail : 1:0, 2:3, 3:0, 4:0.88, 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 [0-8] 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 124578-125857 **** Predicted by CRISPRDetect 2.4 *** >NZ_RRAR01000028.1 Clostridioides difficile strain 17-265-08880 MRSN537878_contig00028, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ====================================== ================== 124578 29 100.0 37 ............................. TTTAAAATTATTTAGTTATACTAAACATTATATTATA 124644 29 100.0 36 ............................. ACAAAGAATACAAGTCCAACCCCTATTAAAAGTATT 124709 29 100.0 37 ............................. GTACAGGAGCAGGAACAGGAAAAAACACCTCTGAAGA 124775 29 100.0 36 ............................. ATTTCTGTCGAGTTGTTCAATCTGATAGTTGGACTT 124840 29 100.0 37 ............................. TAGACTACTTTACAAATAAACTTAACGAGTACAATGA 124906 29 100.0 37 ............................. TTAAAAATAAAGGGTTTAGAGAGTATATGTATAGAGT 124972 29 100.0 36 ............................. ACAACAGGAACATCAACTGGTGGGTCTATTGGAGGG 125037 29 100.0 37 ............................. AGCAAGATACTGCAAATATTTATATACACCAAACATT 125103 29 100.0 36 ............................. GAACATTTAAAACATCAAATACACGTTTAAAATCCC 125168 29 100.0 38 ............................. ACAGTAGGAATAGGGTCTACTGGAGGGTCAACAGGTGG 125235 29 100.0 37 ............................. CTAATAAGACTAATAACATCTGAATTATTTATATTTA 125301 29 100.0 38 ............................. TTGAAATTACTTACATATAGGTCTATTTAATTAATCAT 125368 29 100.0 37 ............................. TTGAAACTTACTACACCAGTTTTAGTAGTTCCAGCTA 125434 29 100.0 37 ............................. ACAGCAGTAGCAACACCCTCTTCAGCAGCAAAACAAG 125500 29 100.0 36 ............................. TATTTATTGCACCTTCACCATCAAGTGCAACATGTT 125565 29 100.0 37 ............................. CTGCAAATTGCTTTGATTCAGTTGAATTTTTAAATAC 125631 29 100.0 36 ............................. AAAGTAAATCCTAGAGCATAACCAATTTTCGTAGGC 125696 29 100.0 38 ............................. TAAACTGTTGGTTCTACTGGTGTTTCTTCTTTATTTAA 125763 29 96.6 37 .......................A..... AGTATAATGTTGAAAAGTTAGAGAGTACAATCAAGAA 125829 29 69.0 0 A.....C.........AAT....AG..TA | ========== ====== ====== ====== ============================= ====================================== ================== 20 29 98.3 37 GTTTTATATTAACTAAGTGGTATGTAAAT # Left flank : TACAATTTATAGAGTGGAGTTCATACAAAAGATTATCCTCCCAATGTATAGAAGGGAGGTGAGTATGTATGGATAATTTTTTACAAGGTGTACTAGCAAGTTTAGTTGCCAGTTTAATAGTTTACTTAAATAGTAAATTATTTAAAAAAGTAAAAAGCCACTCTGGCAGGAGTGACTTTAGTTTTGAACTAAAAATCAAGTTCAAAAAGAATAAACATTAGTATTTGAACTTCACTCTACATCTAAATAGATTGTAGTTCTTCTTATTTTTATTATACCACAAATTGGTACAGATATTCAAAAATAATATATTTATGATATAATAAAAATGTAAATAGTTTTGCAGTGAGCGATATTTGTTACAAAGTAGGGCTTAACGCTTGAAATATAAGGTGTTGAGGGCATGTGATAAGCTTTATCATTTGCACTACTCATGGTTCACTGCAAATTTAAGAGAGTTGCACATGTGTAAGTATTGAAAATGCCCAGTTTATTTTGGG # Right flank : AAAATATGTATTTATACTTAAATTCTGTACCTATATAAAAAAGTGAACTCTGTCAACAAAGCACTTTTTTATATAGATAAATTATCATTTTGTTTTAAGATAGAAGATACTAATGATAACTGTTTATCATTAGTATCTGTATGTACATAAAAGTTTAATTTTTTATATAAATTTGCTCTTTAGAAAAATGAGCAGTATCAATAAATATATTGTCTAAATTTTTTCTAGGAACTAGTTGACTAGCTATAAGATTAGCTTCAACTCTTTGATTGTTAGACTATGAAATTAAATTTAAAGGTTCATTCTTGGTCGTATAAATAGCTTTATTATTCGTATGTACTATAACAATTTTTGCCATCTGCTTTTGATAGATAAAGAGCTTTATCAGCTTTAGAAAATAAATCTTTATATAATTTAGTTGAATCATCAGTGAAGGCAATACCAATACTTAATGTTATTTTATGATTGTCCTTTACTTTTATTTTACTTGCATCATTTAA # 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 : 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 [0-10] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [65.0-76.7]%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 1 107445-107283 **** Predicted by CRISPRDetect 2.4 *** >NZ_RRAR01000006.1 Clostridioides difficile strain 17-265-08880 MRSN537878_contig00006, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ====================================== ================== 107444 29 100.0 37 ............................. CTGAAAATCTCTACAGCTTTGTCTTTTATACTTGCAA 107378 29 100.0 38 ............................. ATTTTAATTGTCTTAGTCTCTTGTATGTTAATTTCATT 107311 29 96.6 0 ............................A | ========== ====== ====== ====== ============================= ====================================== ================== 3 29 98.9 38 GTTTTATATCAACTATGTGGTATGTAAAG # Left flank : TATGCTTTTAATAATATTCATAATACAATCACCTATAATTAAATTTTTATTAATTATATTCTAGCATCAAATATTGAATAAGTCATCTTCTTTAAAATATAATAAATAGTATTTTGCTCAAATTTTCAAATGCTTCTCTGTCCATCTCTTCTAAAAACTGAGAGTAGCTATTCATAGTTATTTTTATATCTGCATGACCTAATCTTTCTGAAATAGTTTTTATATTAGTTCCAGAAAGAAACATTAAAGTTGCATTATTATAGAATTTAAACATAATTAAATGTAAAAATTAATTGAAAATATTAATTATATGTTATGATATAATAAAAATATAGAAATTTTGCAGTGAGCGATATTTGTGACAAATTGAGGTTTAGCAGTTGAAATATAAGGCATTGAGAATATATAATAAGTATTATCAATTGCACTATTGCGCGTTCACTGCAATTTTAAGAGCATTGTATATGTGTAAACATTGGAGATGCTAAGTTTATTTTGGG # Right flank : TTTTTATTACATTAAAAGCAATTCTCCTAAAAACACAAATAATTGTCACAACACACAGTCCTCATATTTTACAAATTGATTCTAAAGAAGAAATAATTGTGTTAGATATGGATGAAAGTGATAATGTATATAAAAAATAGTTAGAACTTGGAGAATACGGGGTATTAGGCTGGACCAATGAAGGTTTATATTTACATTAAGAGCACTCTTTTTATAGGAGTGCTTATTTTTTTGAAATTCATTAGCATATAAACTATCAAGAACATTACTCAATATACCTTATTTACTTCACCAATGATTATCTTACATATATTAACAATAAAAAAAGACTCTAAAAAGAGTCTTTCCCGAAAAATCTATATATTATAATATAGTTATATTTTCTGCTTGAGGACCTCTAGCACCTTTAACTATATCAAAGCTTACTTGTTGACCTTCTTCTAATGATTTAAATCCTGAAGTTTGTATAGCTGAGAAATGAGCAAACACATCATCTCTAC # Questionable array : NO Score: 5.31 # Score Detail : 1:0, 2:3, 3:0, 4:0.95, 5:0, 6:0.25, 7:0.02, 8:0.4, 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 : 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:75.00%AT] # Reference repeat match prediction: R [matched GTTTTATATTAACTAAGTGGTATGTAAAG with 93% identity] Score: 4.5/4.5 # Secondary Structural analysis prediction: R [0.00,-2.30] Score: 0.37/0.37 # Array degeneracy analysis prediction: NA [0-0] Score: 0/0.41 # AT richness analysis in flanks prediction: NA [75.0-68.3]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0,4.87 Confidence: HIGH] # Array family : I-B [Matched known repeat from this family], // Array 1 172777-174645 **** Predicted by CRISPRDetect 2.4 *** >NZ_RRAR01000008.1 Clostridioides difficile strain 17-265-08880 MRSN537878_contig00008, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ======================================== ================== 172777 29 100.0 36 ............................. GCGGGCAAATTAACTTTTATAAGTTCTAGCAAAAGT 172842 29 100.0 37 ............................. TTTCGGCTCTTCTGTAATACTGTTTTTATCTATACTT 172908 29 100.0 37 ............................. AACTTTGTGCTTTTGTTAAATAAATTATCAATATCAG 172974 29 100.0 37 ............................. AATGTTACGGCAACATTCGAGGGCGACAGGATAATAA 173040 29 100.0 36 ............................. TTAAAATTTGGAGATGCGTCAGCTTTTACTAATCTA 173105 29 100.0 37 ............................. TATCTTGCCTGGAAGTTGTGAAACTGGAATTAATACA 173171 29 100.0 37 ............................. TTCCAATTAAATTCAAAACTATCACCTTTTTGACCTT 173237 29 100.0 37 ............................. CCGAAAAAATCACCTATACCGCTGAATCCATTTTTTA 173303 29 100.0 38 ............................. ATCTGTAACTTTTCTTATTATATCGTCTAATTTTTCTT 173370 29 100.0 40 ............................. CATCCTGTACAGTCGTTTCTTGCCATGCGGAACTTCATAT 173439 29 100.0 38 ............................. CCATTCGCAGAACTAGCAATAGGATTAAATAAAGCAGG 173506 29 100.0 37 ............................. TTGGTTGATATAGATATTAGTCCTATTATTTCTGCTT 173572 29 100.0 37 ............................. AAATTAGATAATTTATAAGTCAATAAAATAAGTCCAA 173638 29 100.0 37 ............................. AAATTTGTAATATTATATAATCATCCTAAAACAAAAG 173704 29 100.0 36 ............................. TCGAATGCTATAATTTTAATATATAAAATAAATGGA 173769 29 100.0 36 ............................. ATGGATTTTAGTCGTTTTTAAATTTTTCTCGTAATA 173834 29 100.0 37 ............................. ATGAAGAATTTGCGAAACTAATAAGAAAAGATATTGA 173900 29 100.0 36 ............................. CTTTCTTTATCAAAGTAAGCTAAATTTAGTTCCTCC 173965 29 100.0 36 ............................. CGTCATTACTTTTTATTGCTTCCATTAAATTTGTTC 174030 29 100.0 36 ............................. ATCGCAAGATAGGCTAAATCTATCAAGGAGAGTTGA 174095 29 100.0 37 ............................. GACTCTGCCATCCCTGTAACAAACAGTCTTACCGCAA 174161 29 100.0 36 ............................. TCTTGTGCTCCTTGCGCAATCAAGTTATAAGACTCT 174226 29 100.0 37 ............................. TCAGAACAAATTAAATATGTTTCGTTTTCCATGTAAG 174292 29 100.0 38 ............................. AGAACTTTTTTATATTAGAAGTACTTGACATGATTGCC 174359 29 100.0 34 ............................. CTTGATAATATTTCAGCATATGATACTGAAGATG 174422 29 100.0 37 ............................. TTGCCAATGTAACATCTTTAGATATTACAGTATCATT 174488 29 89.7 36 ......................GA...G. AGAATATTAGCAATATCAACGAGTATTTAGAAACTT 174553 29 75.9 35 A...........TA...CA....A....A TTGTAGAATCAACAATAGCATATACTAAAACATCC 174617 29 75.9 0 ACC.............A.CA...C..... | ========== ====== ====== ====== ============================= ======================================== ================== 29 29 98.0 37 GTTTTATATTAACTAAGTGGTATGTAAAT # Left flank : CATTTTATAAATGATGAAAGGTACAAAGTTTTAAAGGTGTGGTGGTAAGTATGTTTGTTATTGTTACTTATGATATTGTTGAAGCAAGGTCGTTAAATAGAATTAGAAGGATACTTAGAAAATATTTGACTTGGACGCAAAATTCTGTTTTTGAAGGCAATATTACTGAAGGAAAGTTACATAAATGTATTTCTGAAATAGAAAATATTATTGATAATAGCGAGGATTCAATCTATGTTTATGAGATAAAAAATCCTAATTCAATTAAAAAGAAATGTTATGGGATTGATAAGTATTCTGATGAAATGTTTATATAGGTTTGCAGTGAGCGATATTTATGCTAAAATAGGTGTTAACAGTTGGAATATAAGGGATTGAAGGTGTATGATAATTGTTATCAATTGCACTACTGCTCGCTCACTGCAAATTTTGATGTTTTTATTGAATTATAATTGCTTGATTGAAGTGTTTTCAATGTATTCAAATATACCTATTTTGGG # Right flank : TAAAATAAACTTACCTATAAACATTATAAAATCAATACAAAAATGAGGTGAAATAAAATTTATGATAAAGAAATTAAACAATAAAGATATAAATAAAATCATGGAAATATGGGAAAAAAGTACAATCAAAGCACATGACTTTATAAGTAAAGAATACTGGCAAAATAACTATAATACTGTTAAAAACGAATATATACCTATATCAGATACATTTGTATATGATGATGGAGATGAAATAAAAGGATTTATAAGCATAATAGATAAAAGCTTTATAGGAGCTTTATTTATAAAGCCCAAATACCAAAATCTAGGTATCGGAGGTAAACTTTTAGATTATGCAACTAAAAAATATAAAAGTCTAAGCTTAGCAGTATATAAAGATAATAAAAAAGCAGTTGTGTTTTATAATAAAAAAGGTTTTAATATAGTAAAAGAACAAGTAAATGAAGATTCAGGATTTAAAGAGTACATAATGGAATATAGTAAATAATATGATTACA # 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: 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 [0-17] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [75.0-83.3]%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 292793-291972 **** Predicted by CRISPRDetect 2.4 *** >NZ_RRAR01000007.1 Clostridioides difficile strain 17-265-08880 MRSN537878_contig00007, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ====================================== ================== 292792 29 100.0 37 ............................. CTATTTTAACACCTAGCTGTGTCCCATTCCAATTAAA 292726 29 100.0 37 ............................. CCACCTAGTTGAGTTGTTTCTTGATAATATAAGCCAC 292660 29 100.0 37 ............................. TTTTTTAGTAGTAAATCTCCATCTCTACCTGGTACAC 292594 29 100.0 37 ............................. GATTAAATGTTGTAGTTTTTTTGGTATAATCTAACTC 292528 29 100.0 37 ............................. CCAATTCTCTCGCATTTATATATGAACCTTTTAACTG 292462 29 100.0 37 ............................. AAAGAAGGTGGAGAACAATATGCATGGGTAAAGTGGC 292396 29 100.0 37 ............................. GTATTAATTAAACCTAAACAGGTTACAACATCTAACA 292330 29 100.0 37 ............................. GCGCTTAACTTTCTCTTTCACTTCTATTCCTCCATTT 292264 29 100.0 37 ............................. AGAATAGAATCTAACATATATACACCTCCAATTAAGG 292198 29 100.0 37 ............................. CACTAGGACAGGCACTCCACTTCTAAAGCTTATACTT 292132 29 100.0 38 ............................. CTCGAATCAGGATATAACTATTTAAAAGAAAACATAGA 292065 29 100.0 36 ............................. TGCTGTGATTTCACTAATAAAACAATTAATAATTGT 292000 29 86.2 0 ................G....T.CA.... | ========== ====== ====== ====== ============================= ====================================== ================== 13 29 98.9 37 GTTTTAGATTAACTATATGGAATGTAAAT # Left flank : AATAATGTAGATAATGTTGAAAATTTAGAATTCAATGAGTTTGAACTTAAAACCGAAGAAGAAGAGAAGCGAGAACAAGAGAAAATAGAACAAGAAAAAAACAGTTATAATAACTACATTCAAAACAGAGTGGTTGACCCACTAGATAGAATAAAGAAACTAAAAGAGTTGCTAGATTCAGGAGCAATTACATAGGAAGAATATAATAAAAAGAAAAAAGAATTATTAGAATAGATAATATAGTAAGCACTTACAGGTATGTAGGTGCTTTTAAATTTACAAAGTATTCCATTTTAATTTTATAGTTTAGATTTTATGATATAATAAAAATATAGAAGTTTTGCAGTGTGCGATATTTGTTACAAAGTAGGGCTTAATACTTGAAATCTAAGATGTTGAGGGTGCGTGATAAGTGTTATCAATTGCACTATTGCCCGCTCACTGCAATTTTAAGAGTATTGTATATATGTAGGTATTGGAAATGCTAAGTTTATTTTGGG # Right flank : TAAATAAACAAAGAAAGCACTTACAAATATGTAGGTGCTTTTATTCTGCTCAAAATTGGTCGGTTGGGTAAAATAATTAGAAAAAGTTAGTAAAAACCTATTGACTGTAACTCGTTACAATATTGTTATTAATGTAACGAGTTACAGAAAAGAGGTGAATAAAATAGCAACTAAAAGTAGGGCAGAGTATATGAAAAATCGTCGAAAAGATAAAAGAGGTTTTAGTGTACTTTTAGACAAAGAAAAGTTAGATAAATTTGATGAAGTATTAGAGGAAAAGAATCTAACCAAGAAAGAATGGCTAGAAGAAAAAATCGACGAGGAACTGGAACAAAAGGAATAAAAAATAAGGGTCACTCCCACCGACCAAAGTTTGAGTAACCCCTATGACGTATACTATCGTATATCAATTATAGTATATGTCATTCCTTAAAAAAATCAATTATTAAGGAGTGTAATATTATGAAAAATGAATTAATGATGTTTGAAGGAAAAGAGAT # 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: R [4-0] 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 [0,0.41 Confidence: MEDIUM] # Array family : NA // Array 2 540832-539875 **** Predicted by CRISPRDetect 2.4 *** >NZ_RRAR01000007.1 Clostridioides difficile strain 17-265-08880 MRSN537878_contig00007, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ======================================= ================== 540831 29 100.0 37 ............................. ATAAGAGTGGTTTAAGAAAATAAGTTATTTTTCAAAA 540765 29 100.0 37 ............................. GTGGCAGGGTCTAATGGTAAATTATCTATAGAATTTA 540699 29 100.0 37 ............................. AACTTTGTGCTTTTGTTAAATAAATTATCAATATCAG 540633 29 100.0 36 ............................. GGTAATTGGCTAACTGTATTGTAAATATTATTAAAA 540568 29 100.0 36 ............................. CTGTCTATTTTAATCTTGCAAGTTTTTCACTTATGA 540503 29 100.0 37 ............................. AATAAATTTTTAGCGTTGTAAGCTAATCCAGACAGCC 540437 29 100.0 38 ............................. TTTCCTCAACTTTTAGTCTTTCATCAAGCGCTTTTATT 540370 29 100.0 38 ............................. ACTCATTTAAACGATTTGTTTGGAGAAATTTGTTACGT 540303 29 100.0 37 ............................. TCAATTTACCGTTTTTTTCAAATCTCACAACATCAGA 540237 29 100.0 37 ............................. CTATCGGCTTCTTGAAAAGCCTCATCTGCTCTATTTA 540171 29 100.0 37 ............................. TTCATTAAATCCCCAACCGAATTATCTTTCAGCATTT 540105 29 100.0 39 ............................. CATGCTGATAAGAATCTCTATGAACTTCGGAGGGAACCG 540037 29 100.0 37 ............................. TTGGGTATTTTGCTAAAAATAAAGCTATTAAATTAGA 539971 29 96.6 39 .C........................... CGTATTAACACCTGTTCGGCACTATCACAATAAACACAA 539903 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ======================================= ================== 15 29 99.8 37 GTTTTATATTAACTATATGGAATGTAAAT # Left flank : GGAGTTCATGTATCAAAAAATTATCCTCCCGACGCTAAGAAGGGAGGTGAATATACATGGATAATTTTTTACAAGGCATACTAGCAAGTCTATCTGCTAGCTTAATAGTTTATATAGCTAGCAAACTATTTAGAAAGCGTAAAAAACCACTCAAAGCGGCAACTAAGAGTGGTTGGGAATTTGATTTAAAAATCAGATTCCATAAAACTAAGTAATTTCTAAATTATGAACTCCACTCTACAGCAAAATAGATTGTAGTTCTTCTTGCTTTTATTATATCACAAATTGGTACAGATATTCAAAAATAATATTTTTATGATATAATAAAGTCATAGAAATTTTGCAGTGTTCGATTTTTTGAAGAAATTAAGGCTTAACAGTTGAAATATAAGGCATTGAGGACTTGTGATAAGTGTTATCAATTGCACTACTCATGGTTCACTGCAAATTTGAGAGATTTGTATATGTGTAGGCATTGGAAATACTCAATTTATTTTGGG # Right flank : TGTATCCAAAAAATTACAATAATCATACGAACTGCTAATATAAGCAGTCAATATATGTGTACATTTATCCATTTTATCTCTAAACATATAAATTATTATCCCCCTAAAAAACTTTCATAAAAACAAAAAGAACAATATCTCTTTGGCAACTGGCTAACATAACTCATAAGATATTTATATAAGTCTTAGTCCCTATAGCTTTGCGTCACTAGATTTCTCTAGTTTTGCCGATTTAGTTTTATTCTATAACTAAATAATACAATAGAATTAGTTATTATTCAACAAGATTGTTTGAAAATTGAATAAATTTATAGGTATGAACGTAATTTCACACTTAAAAACAGACTAAATACGTAGAATATATAGAAAAATTTACCTGTAGTTTTTGTGATAAAAAGCTCCTATTATTAATTTAAGCTAGATAAGTTTGAGGAAGTGACATAAATTGAAAGAAGGAATATATTATGTTGAATAAAAAATTACCAGATGCAGAATTAAAA # 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 : 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: R [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 [73.3-68.3]%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], //