Array 1 3540-4552 **** Predicted by CRISPRDetect 2.4 *** >NZ_RRAG01000001.1 Clostridioides difficile strain 17-246-05417 MRSN510084_contig00001, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ====================================== ================== 3540 29 100.0 37 ............................. AAATCAATCACCACCTCGATTACTCAATTTATAAGTC 3606 29 100.0 36 ............................. TTTTTAAAGAATAGGTTACTTTTAAAGTAGAAAGAT 3671 29 100.0 37 ............................. CGTATTTATTAAGTATGTGTACATTTACTTTTTTTAA 3737 29 100.0 37 ............................. GGTACAAAAAAAAGACTTAGAATTAATAAAATCGAAA 3803 29 100.0 35 ............................. AGAGTTGAGGTTGAGTTGGAGGATATTATTTAAGG 3867 29 100.0 36 ............................. TTTTTATTCTAAGAAACTTTTCAATTCTAGTTCTTC 3932 29 100.0 37 ............................. TTTGAAAGTTGTAATATAATAGATTAAAAAACTAATT 3998 29 100.0 36 ............................. GCTTTTTAGCTTCGTCTACTACTTTATAAGCAAAGC 4063 29 100.0 36 ............................. ATAGTCAAAAGCAACATCATAATCACGTATATTATC 4128 29 100.0 36 ............................. CAACATGTCAGTAATATTGAAACAGGAAATTCGAGT 4193 29 100.0 37 ............................. AACACTTTAAAAACTAATGTATTCAGTATAAGAGATT 4259 29 96.6 37 ...............T............. CTTGTTAATGCAAATAAACAACATAGCACTATTAATA 4325 29 96.6 38 ...............T............. AGGGTTTCTGATAAAATCTTCAAACATGTAAAATATGT 4392 29 93.1 37 ...............T.A........... CTTATACTTAGTTAGAACTATATATCGACACAAATAT 4458 29 86.2 37 .C.............TA......A..... TGCAATTTTTATTCGTTGTCCAATCGCTTTGAAATTT 4524 29 93.1 0 .......G.......T............. | ========== ====== ====== ====== ============================= ====================================== ================== 16 29 97.8 37 GTTTTATATTAACTAAGTGGTATGTAAAT # Left flank : CTATTATTATATATAACTGACATTTAAGTGACATTTAAGAAAAATATAATGCCTACTTACATAAAATGGAATGTTATTTAAAGAGAACTTTGATTATATTTTCAGAAGCTTTTTTATCCATATCGTTTAAAATATGAGAATATCTATTTATAGTTATTTTTATATTAGTATGTCCTAATCTTTCAGAGATGATTTTTATATTAGTTCCAGCTAGAAGAAGAATTATTAGAATAGATAATATAGTAAGTATTTACAAACATGCAGGTGTTCTTAAATTGATAAATTATTCCATTTTAATTTTATAGTTTGAATTTTATGATATAATAAAAATATATAAATTTTGCAGTGAGCGATATTTTTGATAAAGTAGGGTTTAACAGTTGCAATGTAAGGGATTGAGGGTGTATGATAAATGTTATCAATTGCACTACTCATGGTTCACTGCAAATTTGAGAGAGTTGTATGTGTGTAAGTACTGAAAATACTTAGTTTATTTTGGG # Right flank : TTTGCAACAAGTATAGGTAAAATACCCCAATAATTTATACAGCATTTTATCCTTTAAAATATAATTATTTTTTATCATTTGTAGTAAATAATTACCAGATAACATTGACTTTAGTTTTAATGATTAAAATATAAAAGTAGAATAATTATAAAAAGTATTGAAAAATTTATAAATATATATAATAAAACTTAATGACAAGATATTAGATATAAAAAATAATTACCTTATAAATAGATTGAAATTTATGAATATTCATACTATAATTTAAATATAAGGAGATGCCCTTTGAAAATAAAAATTAAAAAATATTTAATGCTATTACAATAGGAACTAGAACTACACTTAATAAATATACAGAAATTAGATTTGGCTCAATATAAAATACAAATATAGAATTTAGGTGTTTTTTATGAAAAAATTTTTATATGCTTTATATAGTTTCATTGTTATTATAGCTAATTTTAGATTAAAAGAAAAAAATTATAACTTTATTTTATTAG # 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 : 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 [68.3-75.0]%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 2 683703-683015 **** Predicted by CRISPRDetect 2.4 *** >NZ_RRAG01000001.1 Clostridioides difficile strain 17-246-05417 MRSN510084_contig00001, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ====================================== ================== 683702 29 100.0 37 ............................. TATAAATAAATAAACGAAAAACATTAACATATATTTT 683636 29 100.0 38 ............................. CCAGCTGTTAACTTATTCTTATAGAGGTATCTAGTACA 683569 29 100.0 36 ............................. AAATCATGTGTAATTATAGAGTTTATATTTATGACA 683504 29 100.0 37 ............................. TTCCAAGCAAGTATATAAGATGAAATATATTCAATTA 683438 29 100.0 37 ............................. CTAATTAAGGGGTGCTTTGACACTATAAATTTAAAGC 683372 29 100.0 37 ............................. TATGGAAGGGTTTAAAAACCTAATAATTACAGCCTTG 683306 29 100.0 37 ............................. GTACTAATTAAACCTAAGCAGGTTACAACATCTAACA 683240 29 96.6 37 ........................C.... TGATAGAATTGAAAGCTACTTCGTCACTTGATAAAGC 683174 29 100.0 37 ............................. GCACTTTGAGAAGTTCCAACTGAACCTACTAACATTG 683108 29 100.0 36 ............................. TGCTGTGATTTCACTAATAAAACAATTAATAATTGT 683043 29 86.2 0 ................G....T.CA.... | ========== ====== ====== ====== ============================= ====================================== ================== 11 29 98.4 37 GTTTTAGATTAACTATATGGAATGTAAAT # Left flank : AATAATGTAGATAATGTTGAAAATTTAGAATTCAATGAGTTTGAACTTAAAACCGAAGAAGAAGAGAAGCGAGAACAAGAGAAAATAGAACAAGAAAAAAACAGTTATAATAACTACATTCAAAACAGAGTGGTTGACCAACTAGATAGAATAAAGAAACTAAAAGAGTTGCTAGATTCAGGAGCAATTACACAGGAAGAATATAATAAAAAGAAAAAAGAATTATTAGAATAGATAATATAGTAAGCACTTACAAGTATGTAGGTGCTTTTAAATTTACAAAGTATTCCATTTTAATTTTATAGTTTAGATTTTATGATATAATAAAAATATAGAAGTTTTGCAGTGTGCGATATTTGTTACAAAGTAGGGCTTAATACTTGAAATCTAAGATGTTGAGGGTGCGTGATAAGTGTTATCAATTGCACTATTGCCCGCTCACTGCAATTTTAAGAGTATTGTATATATGTAGGTATTGGAAATGCTAAGTTTATTTTGGG # Right flank : TAAATAAACAAAGAAAGCACTTACAAATATGTAGCTGCTTTTATTCTGCTCAAAATTGGTCGGTTGGGTAAAATAATTAGAAAAAATTAGTAAAAACCTATTGACTGTAACTCGTTACAATATTGTTATTAATGTAACGAGTTACAGAAAAGAGGTGAATAAAATAGCAACTAAAAGTAGGGCAGAGTATATGAAAAATCGTCGAAAAGATAAAAGAGGTTTTAGTGTACTTTTAGACAAAGAAAAGTTAGATAAATTTGATGAAGTATTAGAGGAAAAGAATCTAACCAAGAAAGAATGGCTAGAAGAAAAAATCGACGAGGAACTGGAACAAAAGGAATAAAAAATAAGGGTCACTCCCACCGACCAAAGTTTGAGTAACCCCTATGACGTATACTATCGTATATCAATTATAGTATATGTCATTCCTTAAAAAAATCAATTATTAAGGAGTGTAATATTATGAAAAATGAATTAATGATGTTTGAAGGAAAAGAGAT # 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 : 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 [5-0] 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 1 108609-109496 **** Predicted by CRISPRDetect 2.4 *** >NZ_RRAG01000024.1 Clostridioides difficile strain 17-246-05417 MRSN510084_contig00024, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ======================================= ================== 108609 29 100.0 37 ............................. TGTATTTGCCTAACGCGATATAGAGCAAAAAATAAAG 108675 29 100.0 37 ............................. CCCCTAGCTTTTATTGTTTGTGGCATCTAGTCGCCAC 108741 29 100.0 37 ............................. GCACTTTGCTATAATTAGCACTTAAAGAGCAACCAGT 108807 29 100.0 36 ............................. TAAAAAACTGTGTTATGTTTTCCCAAATTGTGCTAA 108872 29 100.0 36 ............................. GTTATTGCTCCTGTTTCTGCTGAACTTTTCAATTTG 108937 29 100.0 39 ............................. AAGATACTTTAAGATTAGAGGTTAAGTGTGCAAATTATG 109005 29 100.0 38 ............................. AAACTTTACTTTTTAAAGTAACATTTTTTAAAAATAGA 109072 29 100.0 37 ............................. CCATCAACCTTATCAGAAACTTGACCATCCCAATCAT 109138 29 100.0 38 ............................. AAACTTAAAACTTTTTTATTATAAGTATTGATTTTTTA 109205 29 100.0 37 ............................. GACTCTAGTATTATTTGAGCTAAAGAAATTGAAGCTG 109271 29 100.0 37 ............................. CCACCAACTCTACATAATAGGTCTCCTGCTTTCCATT 109337 29 100.0 36 ............................. AAGTCACACCGCCCTCCACACGACACTATAATAATA 109402 29 93.1 37 .............C.........A..... AGTATAATGTTGAAAAGTTAGAGAGTACAATCAAGAA 109468 29 69.0 0 A.....C.........AAT....AG..TA | ========== ====== ====== ====== ============================= ======================================= ================== 14 29 97.3 37 GTTTTATATTAACTAAGTGGTATGTAAAT # Left flank : TACAATTTATAGAGTGGAGTTCATACAAAAGATTATCCTCCCAATGTATAGAAGGGAGGTGAGTATGTATGGATAATTTTTTACAAGGTGTACTAGCAAGTTTAGTTGCCAGTTTAATAGTTTACTTAAATAGTAAATTATTTAAAAAAGTAAAAAGCCACTCTGGCAGGAGCGACTTTAGTTTTGAACTAAAAATCAAGTTCAAAAAGAATAAACATTAGTATTTGAACTTCACTCTATGTCTAAATAGATTGTAGTTCTTCTTGTTTTTATTATACCACAAATTGGTACAGATATTCAAAAATAATATATTTATGATATAATAAAAATGTAAATAGTTTTGCAGTGAGCGATATTTGTTACAAAGTAGGGCTTAATGCTTGAAATATAAGGTGTTGAGGGCATGTGATAAGCTTTATCATTTGCACTACTCATGGTTCACTGCAAATTTAAGAGAGTTGCACATGTGTAAGCATTGAAAATGCCCAGTTTATTTTGGG # Right flank : AAAACATGTATTTATACTTAAATTCTGTACCTATATAAAAAAGTGAACTCTGTCAACAAAGCACTTTTTTATATAGATAAATTATCATTTTGTTTTAAGATAGAAGATACTAATGATAACTGTTTATCATTAGTATCTGTATGTACATAAAAGTTTAATTTTTTATATAAATTTGCTCTTTAGAAAAATGAGCAGTATCAATAAATATATTGTTTAAATTTTTTCTAGGAACTAGTTGACTAGCTATAAGATTAGCTTCAACTCTTTGATTGTTAGACTATGAAATTAAATTTAAAGGTTCATTCTTGGTCGTATAAATAGCTTTATTATTCGTATGTACTATAACAATTTTTGCCATCTGCTTTTGATAGATAAAGAGCTTTATCAGCTTTAGAAAATAAATCTTTATATAATTTAGTTGAATCATCAGTGAAGGCAATACCAATACTTAATGTTATTTTATGATTGTCCTTTACTTTTATTTTACTCGCATCATTTAA # 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 17792-18482 **** Predicted by CRISPRDetect 2.4 *** >NZ_RRAG01000026.1 Clostridioides difficile strain 17-246-05417 MRSN510084_contig00026, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ====================================== ================== 17792 29 100.0 37 ............................. CATGATAGATTAAAGAAAGCTTTAGAACAAGTTAAAG 17858 29 100.0 36 ............................. GGGAGCTTTGTTTTTGTACATAGCCATCCACAAGTC 17923 29 100.0 38 ............................. TGTAAATGATGATGTTAAAAATATAATAGTTGATGAAG 17990 29 100.0 37 ............................. AGGGGCTTATATATGAATACTTTGCTAATAATAAAGA 18056 29 100.0 37 ............................. TGTGGATTTAAAGATGGAATAGTAACAAAGTATATTA 18122 29 100.0 37 ............................. GCAATATCTCCTCTTGTAATCGCTGAATAAAGATTTC 18188 29 100.0 37 ............................. CTATAACTTTTTCGCCAAAAACGTCTTTTATATCATT 18254 29 100.0 37 ............................. TCCAAAAGAACCTCTTTTTCTGTTTCATCAACTGTGT 18320 29 100.0 38 ............................. TATGTAAAAAATAAAATAAATAAAAGTAACACTTTATA 18387 29 100.0 38 ............................. CCATCTTTTGTTGCTTTACATAAATTTATATTACTTAC 18454 29 82.8 0 ........C........CA....A...T. | ========== ====== ====== ====== ============================= ====================================== ================== 11 29 98.4 37 GTTTTATATTAACTATATGGAATGTAAAT # Left flank : GATAACCATAATAAAAATAGATATCTATTTTTAGATTAAAAATAATATATCATAAATAAAATAATAAGAGGTAGATACAGTTTTAAGGGAATACAAAAGTTTTTAATTAAACTATGCTTGTTCAGATAGATATTTATTTAAGAAAAAAGACTATTAAAAGCAATATACAAAAATGATATATTAGATTGATTAAACAAGCATAAATATTATGTAAAAAACTTTAAGTTATAGAATTTAAATCCAATGTAGATAGATTACGTTTTTTTGCTTTTATTATGGTATAAATTGGTATCAATATTCAAAAGTAATATATTTATGATATAATAAAATTATAGAAATTTTGCAGTGAGCGATATTTGTGAAAAAATTTGGCGTAACAGTTGAAATATAAGGCGTTGAGAGTGTATGATAAGCGTTATCAATTGCACTATTGCTCGTTCACTGCAAATTTAAGAGAGTTGTATACGTGTAAGTGTTGAAAATACTAAGTTTATTTTGGT # Right flank : TTTCTTTTAATGTGTTATCTTATGATTATCTAGTTATATTAGCATACAAAAATATAATAAAATTACACTATATTATAAAAACCAAAAGGTAGTATAGAAATCCTATTACCTTTTTATTATTAATTTTATCAGTGTTTTATTATAAATAGCTTACATAATTACACATTTTTTCTGATTAAATAATATGATGCTATTGTTATAATAGATACTAATGCTAATGATGTTATTGCAGTATCTAATCTTCCTATTAATAAACTCATTTCTATATATTCAAGTTCTATTAAATATTAATAAAATATTTCTAGTTTAACAGCTTTTTCTCTATCTATATTTCCATACTTTAACTCTAATTTATCTAAAGATTTTTTATTACAATAATTAACTTTATGTTTAATTAAATATCTTATTGTAGCACCTATTACAATTTTCACTCTAACAAGCATAAATATAATATTCCATCCAAAAGTTAAGAGGGTATATCTTTTTTTATGATGGGAATG # 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 : 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 [0-5] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [71.7-83.3]%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 109544-109904 **** Predicted by CRISPRDetect 2.4 *** >NZ_RRAG01000026.1 Clostridioides difficile strain 17-246-05417 MRSN510084_contig00026, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ====================================== ================== 109544 29 100.0 38 ............................. TTTTCTAAATTCTTCTGGTAATGTTTTTACTTTATTAA 109611 29 100.0 37 ............................. TTCATTGACCAAACATTTTGTTTACATCTAATCGAAA 109677 29 100.0 37 ............................. CAAACAAAAGAAGCACAAGAACGACTTAATGATTTGG 109743 29 100.0 37 ............................. GTTTTAGAAAAAGCTTTAAAAAGTTATGAAAACTAAA 109809 29 100.0 38 ............................. TCAGTTTTTCGTTTGATTGGCTCTATCTTTAAAAAAGT 109876 29 89.7 0 .....................C.TA.... | ========== ====== ====== ====== ============================= ====================================== ================== 6 29 98.3 38 GTTTTAGATTAACTATATGGAATGTAAAT # Left flank : ATTATATGTTATAATAATTGTAGCAAGGATAATAATCGAAAGTGCGAAGGGTGATTATTTTCATATTAAACGCCAAATTCCAAATAAGGAAGGAGGTGAAATTATATGATAGGTTTTTTATTAAGCATACTAGCTGGTGTTATATCAGCTTATATTTATGACAAAATAAAAAATCACCCAGACGCCAATAAGGGTGATTTAAAAAAATAATATTTTCACTTAACAACTGAAAATAATCACTCTTTGTAGGAGTAAATTATTTCCTTGCTTTTATTATACCACAAATTGGTACAGATATTCAAAAATAATATTTTTATGATATAATAAAAATGTAGAGATTTTGAAGTGAGCGATATTTGTTACAAAATATGGCTTAACACTTGAAATCTAAGATGTTGAGGGTGCGTGATAAGTGTTATCAATTGCACTATTGCCCGCTCACTGCAATTTTAAGAGTATTGTATATATGTAGGTATTGGAAATGCTAAGTTTATTTTGGG # Right flank : TTAAAAATACTGAAAAACACTTACTTTTATGGTAGGTGCTTTTTTATATTAAAATCTGTGTACTTAATTGAAATATTTGGTAAAATATGTAAGAATTGTATGATATAATAATTGTAGCAAGGAAAATAATAATTGAAAAGTGCTAAGAGTGGTTATTTCCATATTTGAATACCAAATTCCATAACGGAAGGAGGTGTAACAGTATGGTGATAAATTTTTTATTGAGTATACTGGCTGGTGTTATATCAGCCTTCATGTATGAGAAAATAAAAAACCACTCAAAGGCCAATAAGAGTGGTTTAAAAAAGTAATTCTTTAAATCAATTTTGATGGAAATAGCTACTCTTGTATAAAGTAAATTATTTCCTTGCTTTTATTATACCACAAATTGGTACAGATATTCAAAAATAATATTTTTATGATATAATAAAAATGTAGAGATTTTGCAGTGAGCGATATTTGCGATAAATTGAAGTTTAACAGTTGCAATATAAGGTGTT # 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 [0-3] 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 110508-110930 **** Predicted by CRISPRDetect 2.4 *** >NZ_RRAG01000026.1 Clostridioides difficile strain 17-246-05417 MRSN510084_contig00026, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ====================================== ================== 110508 29 100.0 37 ............................. AATTGCTCGACTGTTTGTTGATAAACTTCTCTTAAAT 110574 29 100.0 37 ............................. AGTCCTCCAAATTTATTTAAGACATCCACGAATTTGT 110640 29 100.0 38 ............................. ATTGATGACTTTAGGAGTAAGCAGAGCTAATGTTACAC 110707 29 100.0 37 ............................. TTCGCAACTTATGATGGTGAAATGATTACATTAACAG 110773 29 86.2 36 ......T.........G...T.......G GGAACATAAGGTAAATCATAAGAAACTCCAACAAGA 110838 29 82.8 35 A.....T.........G...T.......G ATCACTTTTTCTCAAGCTCTTACAATGATGAAAAA 110902 29 79.3 0 A.....T.........G....C.TA.... | ========== ====== ====== ====== ============================= ====================================== ================== 7 29 92.6 37 GTTTTAGATTAACTATATGGAATGTAAAT # Left flank : ATAATAATTGTAGCAAGGAAAATAATAATTGAAAAGTGCTAAGAGTGGTTATTTCCATATTTGAATACCAAATTCCATAACGGAAGGAGGTGTAACAGTATGGTGATAAATTTTTTATTGAGTATACTGGCTGGTGTTATATCAGCCTTCATGTATGAGAAAATAAAAAACCACTCAAAGGCCAATAAGAGTGGTTTAAAAAAGTAATTCTTTAAATCAATTTTGATGGAAATAGCTACTCTTGTATAAAGTAAATTATTTCCTTGCTTTTATTATACCACAAATTGGTACAGATATTCAAAAATAATATTTTTATGATATAATAAAAATGTAGAGATTTTGCAGTGAGCGATATTTGCGATAAATTGAAGTTTAACAGTTGCAATATAAGGTGTTGAGGGTGTATGATAAGTGTTATCAATTGCACTACTTATGATTCACTGCAAATTTGAGAGAGATGCGTATGTGTAGGTATTGGAAATGCTAAGTTTATTTTGGGG # Right flank : TTAAAAACGCTAAAAACACTTACTTAAAAAGTAGGTGTTTTTTATTGAAAGTAGGTGATTATAATGTAAAAATTTTACTAATATAGTATAATATTGTTAAAGAATATAATTTAGGGGGATATTATATTATGAAGAAAAAAGTATGTTTTTTATTTTCTATTCTTATAGTTATCTGTTTAGCTATTGTAGGATGTTCTAATTCAGAAAGTCCAGAGGAGAGTAGTAAAAATAATGAACCAAAAAAAGAAGAAAAAAAGGATAAAGAAGTAGTCATAGGAGAGAAAATTATTTCAGATAAAATGGAAATCACTATTAATAATATTGAATTCTCTTATGATGTTTTACCAAAGGTTAAGGAAAGTTTATATACACATTATCCTGCTGAGTCAGGCAAAGTATATATTGATATTGCTGCTGATATAAAAAATACTCAAAAACAAGAGTTAAATTGTTCAGATTTACTAACTATTGAAGCAAATTATAATGATGGGTATAAATAT # Questionable array : NO Score: 5.89 # Score Detail : 1:0, 2:3, 3:0, 4:0.63, 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 [0-15] 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 90004-89450 **** Predicted by CRISPRDetect 2.4 *** >NZ_RRAG01000029.1 Clostridioides difficile strain 17-246-05417 MRSN510084_contig00029, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ====================================== ================== 90003 29 100.0 36 ............................. TAACATATTTTTACAATAGATTTAGTTTTTTATTTA 89938 29 100.0 36 ............................. TGTAAAACAAACAATAGAAGAAAGCGTATAGATTTA 89873 29 100.0 38 ............................. ATACGTAACAGCAACAAAACAAGAAAAAGGCAACCATG 89806 29 100.0 37 ............................. AGAATTAACCTAATAATCAAAAAATCACCTCTTTCTT 89740 29 100.0 36 ............................. TAATTTCAATTCCTAACGTAGCTGGTTTAAAATCAA 89675 29 100.0 36 ............................. GTATTAATAATAGAAAAAATCGTACTACTAACTTTA 89610 29 100.0 37 ............................. TCTCTTGTTAGTATTTACACATATTGTAACCTGTTCA 89544 29 100.0 37 ............................. ATAATTAACCGCACAAAAAATTGAAATCGGCAAAATC 89478 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ====================================== ================== 9 29 100.0 37 GTTTTATATTAACTAAGTGGTATGTAAAG # Left flank : CTATTAACTTATGAAATATCTGTAAATGAGCAGATATTTCATAAGTTAATATTTATTGTTTACATAAAATATTTGGTAAAAATAAGTAAGTTTTATATGTTATAATAGTTGTAGCAAGAATAATAATCTAAAGTGGCAAGCATGTCAGCTGGTGTTATATCAGTTTATATTTATGATAAAATAAAAATCTCCCAAACGCCAATAAGAATGATTTAAAAAAATAATATTTTCACTTAAAAATAATCACTCTTTATAGGAGTAAATTATTTTCTTGATTTTATTATACTACAAATTGGTACAGATATTTAAAAATAATATATTCATAATATTATAAATAGTTTTGCAGTGAGCGATATTTTTGATAAAATAGGGCTTAACAGTTGAAACATAAGGCATTGAGGGTATATGATAAATATTATCATTTGCACTACTCGTGGTTCACTGCAAATTTGAGAGAATTGTATAGATGTAAGTGTTGGAAATACTCAATTTATTTTGGG # Right flank : ACAGATATAATATCAAAATAAGGTTAGAACTTTTAAAAGCATAGCCATATCAGTAAAAATTTAATTATCATTTAAAAAATAAATTTTTATTTAAAGAATACACATAAATATTTCCAGACTCAACTCTCTTAAACTATTTTCATATCTTTTAGTAGATACCTTTGTTGTTTTTTAATCTTTAGCAACTTGTTCTTGAGTGAACCTCTTATTTTTTTTAAGTTATTTCAAGCTTTTCAAAAAATTCTCTATTTATATTCATCACACATATAATACAATTAATTCAGTTTTAATTGCCAATATTTAGTTTTTCTGTATCTGATAAACCAAGAATATAATCAGTATATAAACCAAAAATTTTAGCAAATATTATTAACCCATCGTCTCTTGTTGGTCTTTCACCAGACTCTATTCTATTCATAACACTTGTATTTATATTTGTTTTTTCAAGCAATTCTTTTTGAGAACTATTCATATTTTCCCTAATATATTTAATCCTTTGA # Questionable array : NO Score: 6.26 # Score Detail : 1:0, 2:3, 3:0, 4:1.00, 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 : 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:75.86%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: NA [0-0] Score: 0/0.41 # AT richness analysis in flanks prediction: NA [76.7-70.0]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0,4.5 Confidence: HIGH] # Array family : I-B [Matched known repeat from this family], // Array 1 30319-31532 **** Predicted by CRISPRDetect 2.4 *** >NZ_RRAG01000005.1 Clostridioides difficile strain 17-246-05417 MRSN510084_contig00005, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ======================================= ================== 30319 29 100.0 37 ............................. CATTAAATAGCACACCATAAGTTGTTGCATCATTTGC 30385 29 100.0 37 ............................. ATGAAACAGATACTAAATGCTTGGGGTTGGCGATTTG 30451 29 100.0 36 ............................. ATCAGTAACACGAACACGAAGCATTTTATCTTTCAA 30516 29 100.0 36 ............................. TCGTAGATCTTCTCATAATTACAAGAACAATAAGCA 30581 29 100.0 37 ............................. AACAAAATGCTTAATAAAAATTCAAGAAAACTATCTT 30647 29 100.0 37 ............................. GGAAAAATTATAAAAATTTTCAATATAAATACTGGAG 30713 29 100.0 39 ............................. TTAAATAAACTACTATATATCTTTATATCTGCTATTATA 30781 29 100.0 36 ............................. TCGTCATAACAACTCACAGGAATATAAATAGAACTT 30846 29 100.0 37 ............................. TTTTATTATTATAAAGAACTGCACTATTTTTTGATTT 30912 29 100.0 36 ............................. ACTTACATTTAATGGTAGGGTGTGCCGAGCGTTTAG 30977 29 100.0 37 ............................. ATTGTTTCTTTAACGCTTCCCGCGTGAGAGTTCGCAC 31043 29 100.0 37 ............................. TGAAAAGTAGCATGTTCTTTAACAAAAGCATCTAATT 31109 29 100.0 37 ............................. TTAATTTTATAAAAAGCTAAAAATGGGTTTATATATA 31175 29 100.0 37 ............................. ATTGCGATTTCCATTATGGGTGTTTTTTATGTCTGGG 31241 29 100.0 37 ............................. TTTTGTTAAATAACTATTTCTTTTTAAAATATTTCGT 31307 29 100.0 37 ............................. GCAGAAGATTTAGCGACTGTTGTTGCTGAATGGGATG 31373 29 100.0 37 ............................. TACAATTCCAGCGATTTTTAATCAAGCAAAAGCAACT 31439 29 100.0 36 ............................. TCTTCATATTTATTCATGTATTCAATGATAGCATCT 31504 29 89.7 0 .......................GC.G.. | ========== ====== ====== ====== ============================= ======================================= ================== 19 29 99.5 37 GTTTAAATTACACTAAGTTAGTTATAAAT # Left flank : TAAATTAAACTATATTAGTTATAAAATGCCATGCTTATATTATGTGTTTGAATTAAACTAAATTAGTTGAGATATTAAGAATTAAAATTTTAATATAAGTAAGTTATATTAAAATATATAAAAATCATATGATAATATTTATATATTTTAGATAATGAAAAAACTAATTAAGGACATAGACATGTTTTTAATAGTTTGTATTTTGAGTATAAAAAGATATTGATTGTTTAATTGATATCTTTTTATGTTGATGTATTATATCAAAATGTATGTAATAATTCTATTTAGATATGTTTTTAAATTTATTATGTTTTAAAAATAATATTTAGTAGTTTTGGTTTTGCAGTGAGCGAAAAAATTGCATAAGTGGCTGTAAATTAGTGATGGCAAAGATTACAACTGTATTTTTGATTATACCAAAAAACACTACTTAGCGCTCACTGCAAATTATTCATTTTAATAATACTATAAGTATTGGAATTACTGTAGTTTTATTTGGG # Right flank : TATACCAGAAAGTATATATAAAATTATGTGTAAACTATATTGTTATGAGTACAAATAATATTTACCTATTCATTAAAAAACTTAACTAAGAATTTGATTTATATTATTGAAGTATCAATAATTTTGGAAAGTAGAAAATTATACCCCAATAATACCCCAACCACAAAAATAAACAATAAAAAATAACCAAAAAAATCAGTCTAATATCATAACTAAATAGCTATATATCTACATTCACAAAATCAACAAAACAATCAAATAACCACTTATAGACTCCCCTCGTATCCACCATTGAAATCCACGAATACCTATATCCAATTGGATATAGGTATTTTTATACATTTTTAATTTAAATATTATTGATAAATACATTTAAAAAGTGTTAACCTAAAGTGAATAATCTAAATAAAAATACAATACTAGGAGAGGTCATCATTACAATAGCAGCTTGTGATGATGAAAAAGAAATACAAATCGTAATAAAAAATCAAGTTGATAAT # 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 : GTTTAAATTACACTAAGTTAGTTATAAAT # 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: NA # Secondary Structural analysis prediction: NA [0.00,-0.30] Score: 0/0.37 # Array degeneracy analysis prediction: F [0-3] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [76.7-81.7]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [0.41,0 Confidence: MEDIUM] # Array family : NA // Array 2 264292-265761 **** Predicted by CRISPRDetect 2.4 *** >NZ_RRAG01000005.1 Clostridioides difficile strain 17-246-05417 MRSN510084_contig00005, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ====================================== ================== 264292 29 100.0 37 ............................. TCGATAGGTATAGAAGGATTTTCAACTTTAGGAACTG 264358 29 100.0 37 ............................. CCAGCCAAACATCCATATTCACAGTACTTCCTTATAT 264424 29 100.0 36 ............................. TTGTCTGTAACAGCTATATTTTTAGCCTCTTGGTAA 264489 29 100.0 37 ............................. TTGGTTGATATAGATATTAGTCCTATTATTTCTGCTT 264555 29 100.0 37 ............................. AAATTAGATAATTTATAAGTCAATAAAATAAGTCCAA 264621 29 100.0 37 ............................. AAATTTGTAATATTATATAATCATCCTAAAACAAAAG 264687 29 100.0 36 ............................. TCGAATGCTATAATTTTAATATATAAAATAAATGGA 264752 29 100.0 36 ............................. ATGGATTTTAGTCGTTTTTAAATTTTTCTCGTAATA 264817 29 100.0 38 ............................. ACCATTCATTTATATTTTTATCTGTATCTCTTAGCCAT 264884 29 100.0 36 ............................. CGTCATTACTTTTTATTGCTTCCATTAAATTTGTTC 264949 29 100.0 37 ............................. GACTCTGCCATCCCTGTAACAAACAGTCTTACCGCAA 265015 29 100.0 36 ............................. TCTTGTGCTCCTTGCGCAATCAAGTTATAAGACTCT 265080 29 100.0 37 ............................. GAAAATAATCTTAATGAAGTAGATTGGAATGAGGTTA 265146 29 100.0 36 ............................. TCTTTTGATTTAGCGTTGTTTGTCCGGAATTTTAAA 265211 29 100.0 37 ............................. TCGGGCTAGAATGTATTTTAAACCCTAGTTCATTGAA 265277 29 100.0 36 ............................. TTTCTAATATCGCTATTTAAACTCAATGCTTCATTT 265342 29 100.0 37 ............................. TCAGAACAAATTAAATATGTTTCGTTTTCCATGTAAG 265408 29 100.0 38 ............................. AGAACTTTTTTATATTAGAAGTACTTGACATGATTGCC 265475 29 100.0 34 ............................. CTTGATAATATTTCAGCATATGATACTGAAGATG 265538 29 100.0 37 ............................. TTGCCAATGTAACATCTTTAGATATTACAGTATCATT 265604 29 89.7 36 ......................GA...G. AGAATATTAGCAATATCAACGAGTATTTAGAAACTT 265669 29 75.9 35 A...........TA...CA....A....A TTGTAGAATCAACAATAGCATATACTAAAACATCC 265733 29 75.9 0 ACC.............A.CA...C..... | ========== ====== ====== ====== ============================= ====================================== ================== 23 29 97.5 37 GTTTTATATTAACTAAGTGGTATGTAAAT # Left flank : CATTTTATAAATGATGAAAGGTACAAAGTTTTAAAGGTGTGGTGGTAAGTATGTTTGTTATTGTTACTTATGATATTGTTGAAGCAAGGTCGTTAAATAGAATTAGAAGGATACTTAGAAAATATTTGACTTGGACGCAAAATTCTGTTTTTGAAGGCAATATTACTGAAGGAAAGTTACATAAATGTATTTCTGAAATAGAAAATATTATTGATAATAGCGAGGATTCAATCTATGTTTATGAGATAAAAAATCCTAATTCAATTAAAAAGAAATGTTATGGGATTGATAAGTATTCTGATGAAATGTTTATATAGGTTTGCAGTGAGCGATATTTATGCTAAAATAGGTGTTAACAGTTGGAATATAAGGGATTGAAGGTGTATGATAACTGTTATCAATTGCACTACTGCTCGCTCACTGCAAATTTTGATGTTTTTATTGAATTATAATTGCTTGATTGAAGTGTTTTCAATGTATTCAAATATACCTATTTTGGG # Right flank : TAAAATAAACTTACCTATAAACATTATAAAATCAATACAAAAATGAGGTGAAATAAAATTTATGATAAAGAAATTAAACAATAAAGATATAAATAAAATCATGGAAATATGGGAAAAAAGTACAATCAAAGCACATGACTTTATAAGTAAAGAATACTGGCAAAATAACTATAATACTGTTAAAAACGAATATATACCTATATCAGATACATTTGTATATGATGATGGAGATGAAATAAAAGGATTTATAAGCATAATAGATAAAAGCTTTATAGGAGCTTTATTTATAAAGCCCAAATACCAAAATCTAGGTATCGGAGGTAAACTTTTAGATTATGCAACTAAAAAATATAAAAGTCTAAGCTTAGCAGTATATAAAGATAATAAAAAAGCAGTTGTGTTTTATAATAAAAAAGGTTTTAATATAGTAAAAGAACAAGTAAATGAAGATTCAGGATTTAAAGAGTACATAATGGAATATAGTAAATAATATGATTACA # 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 [0-17] 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], //