Array 1 5606-7098 **** Predicted by CRISPRDetect 2.4 *** >NZ_CDHY01000146.1 Salmonella enterica subsp. enterica serovar Typhimurium strain STM143, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 5606 29 100.0 32 ............................. TTTTGATACGTAGTATTCATTACGCCTCCTAG 5667 29 100.0 32 ............................. GCGAGGTCAATAAAAAATGGTGTGGCTTTACC 5728 29 100.0 32 ............................. CCGGCATCAGCGCCGATCCGTTCATAGTGCCC 5789 29 100.0 32 ............................. AAAAAACAGAAGAACGGCAAGCGGCACCTCAA 5850 29 100.0 32 ............................. CGTCAGCGCGGTATTGAGGCCGGGGACCGCCC 5911 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 5972 29 100.0 32 ............................. CAGATCCTCAACGGTCAGGCTGTTTAGTTCCT 6033 29 100.0 32 ............................. CGGAGGATGGAATATTTCCGAGGCTGGCGATT 6094 29 96.6 32 .............T............... ATGCCGGAACGCTGATGGCGTTTGACATGAGC 6155 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 6216 29 100.0 32 ............................. TGACGCTGGTCTATACCGGCAACGAACGCGAC 6277 29 100.0 32 ............................. TTGACGGTGACGTCAGTGCCGAAGGCGAAATA 6338 29 100.0 32 ............................. CCAGCTTACGCTATTTACGACGTTATTGAGCA 6399 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 6460 29 100.0 32 ............................. CCCCGATAGCGACGCTTCTGTAGTCACTGGCA 6521 29 100.0 33 ............................. GTGAGTTCGGTTTTAATTTCGTCGCTAAGCTGC 6583 29 96.6 32 .........................G... CGTCACTTTCTGACATTTTATTCAGTTCGTTA 6644 29 96.6 32 ..........T.................. TCATTTCTGGACGGGGCTGTGTGACGAATACG 6705 29 100.0 32 ............................. TGTCCAATTAACCCAAACTTTGCGCGCTTAAT 6766 29 93.1 32 A............T............... GGATATGTGAAGTTCAGGTAGCCCATTACGCA 6827 29 100.0 32 ............................. TTGATCGAGAGTGCGAAGAGGCAGAACGGGCA 6888 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 6949 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 7010 29 100.0 32 ............................. CGTTCATCGGCAGCGTCACGCAATATGAAGAT 7071 28 82.8 0 ...............A.AA....-.G... | ========== ====== ====== ====== ============================= ================================= ================== 25 29 98.2 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGTGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTAGAATGTGGTGCTGACAAAAAGTAGTTTATAAACAATTATATCCGTTTAGT # Right flank : GTTGCATAATCATAATCTGTGTACCAGTAATGGCAGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTAGACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGTCCGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAGCAGTCGAATCATCTGCCATCCCGATATTGCACGTGAACGTTATGCAGCAATGACTTTTCTTGGTATTACCCGAAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTATCGAATGATGTACACGCGTGACCCCCTGCCGATTGG # 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 : GTGTTCCCCGCGCCAGCGGGGATAAACCG # 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: F [5,4] Score: 0.37/0.37 # Reference repeat match prediction: F [matched GTGTTCCCCGCGCCAGCGGGGATAAACCG with 100% identity] Score: 4.5/4.5 # Secondary Structural analysis prediction: F [-13.50,-12.00] Score: 0.37/0.37 # Array degeneracy analysis prediction: F [0-10] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [70.0-63.3]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [5.65,0 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 8891-9285 **** Predicted by CRISPRDetect 2.4 *** >NZ_CDHY01000130.1 Salmonella enterica subsp. enterica serovar Typhimurium strain STM143, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 8891 29 96.6 32 ............................T CCCACCGCGCTGATTAACGACGGACTGTTACA 8952 29 100.0 32 ............................. TGAGCAACGACAGTAAATAATTTTTCGTGCTG 9013 29 100.0 32 ............................. AACCGCTGGCGGGCTGATTGGTCTGCAACCAC 9074 29 100.0 32 ............................. CAACCAGGCTGGATCGTAACTCCTATCCCCTC 9135 29 100.0 32 ............................. AAAATGCAGGTGGGGTAACGAATGCGAGATTG 9196 29 100.0 32 ............................. CCATTATTCAACCCTCCAGGCTCGCGCCGGCT 9257 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================ ================== 7 29 99.5 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTGCTCGCTGCCGGTGAAATTGAACCACCTCAGCCTGCGCCGGATATGTTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTCGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTGCGTTTGGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : CCAGTGGGCGTAGCCAGCTCA # 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 : GTGTTCCCCGCGCCAGCGGGGATAAACCG # 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: F [5,4] Score: 0.37/0.37 # Reference repeat match prediction: F [matched GTGTTCCCCGCGCCAGCGGGGATAAACCG with 100% identity] Score: 4.5/4.5 # Secondary Structural analysis prediction: F [-13.50,-12.00] Score: 0.37/0.37 # Array degeneracy analysis prediction: R [1-0] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [71.7-11.7]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [5.51,0.41 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 182-31 **** Predicted by CRISPRDetect 2.4 *** >NZ_CDHY01000039.1 Salmonella enterica subsp. enterica serovar Typhimurium strain STM143, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 181 29 100.0 32 ............................. CAACCAGGCTGGATCGTAACTCCTATCCCCTC 120 29 100.0 32 ............................. AAAATGCAGGTGGGGTAACGAATGCGAGATTG 59 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================ ================== 3 29 100.0 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : ATTCACCAACAACAATATCGCCCTGCAACGGTTTATCCCCGCTGGCGCGGGGAACACCGTTGCGTCAGGTTGATCCAGTGCGTCAGCGGCGGTTTATCCCCGCTGGCGCGGGGAACACTCTCGGTCTCGGTCTCGGTCTCGGTAGTGACGCGGTTTATCCCCGCTGGCGCGGGGAACACACTTCCTTCAGTCTTAACGATAATCCGCAACGCGGTTTATCCCCGCTGGCGCGGGGAACACGCAAAATAGCGATGAGCTGGCTACGCCCACTGGCGGTTTATCCCCGCTGGCGCGGGGAACACAGCCGGCGCGAGCCTGGAGGGTTGAATAATGGCGGTTTATCCCCGCTGGCGCGGGGAACACCAATCTCGCATTCGTTACCCCACCTGCATTTTCGGTTTATCCCCGCTGGCGCGGGGAACACGAGGGGATAGGAGTTACGATCCAGCCTGGTTGCGGTTTATCCCCGCTGGCGCGGGGAACACGTGGTTGCAGACCAC # Right flank : GCCATTATTCAACCCTCCAGGCTCGCGCCGG # Questionable array : NO Score: 5.67 # Score Detail : 1:0, 2:3, 3:0, 4:1.00, 5:0, 6:0.25, 7:0.02, 8:0.4, 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 : GTGTTCCCCGCGCCAGCGGGGATAAACCG # 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: R [4,5] Score: 0.37/0.37 # Reference repeat match prediction: R [matched GTGTTCCCCGCGCCAGCGGGGATAAACCG with 100% identity] Score: 4.5/4.5 # Secondary Structural analysis prediction: R [-12.00,-13.50] Score: 0.37/0.37 # Array degeneracy analysis prediction: NA [0-0] Score: 0/0.41 # AT richness analysis in flanks prediction: R [18.3-35.0]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0,5.51 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 2 197-1978 **** Predicted by CRISPRDetect 2.4 *** >NZ_CDHY01000039.1 Salmonella enterica subsp. enterica serovar Typhimurium strain STM143, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 197 29 100.0 32 ............................. CAACCAGGCTGGATCGTAACTCCTATCCCCTC 258 29 100.0 32 ............................. AAAATGCAGGTGGGGTAACGAATGCGAGATTG 319 29 100.0 32 ............................. CCATTATTCAACCCTCCAGGCTCGCGCCGGCT 380 29 100.0 33 ............................. CCAGTGGGCGTAGCCAGCTCATCGCTATTTTGC 442 29 100.0 32 ............................. CGTTGCGGATTATCGTTAAGACTGAAGGAAGT 503 29 100.0 32 ............................. CGTCACTACCGAGACCGAGACCGAGACCGAGA 564 29 100.0 32 ............................. CCGCTGACGCACTGGATCAACCTGACGCAACG 625 29 100.0 32 ............................. TTGCAGGGCGATATTGTTGTTGGTGAATGGGA 686 29 100.0 32 ............................. CGTCGCGGAAAATTTCGCATTGACGATAAAGA 747 29 100.0 32 ............................. TTACGTGTTTATTCATCTGTTGCATTAGATTC 808 29 96.6 32 ............................T GAGGCGTACAGGCTGTTAGATGAGAAATTACC 869 29 100.0 32 ............................. ACGCCCCGAATGTGTTTGCCTCGCCCGCTGCC 930 29 100.0 32 ............................. ACGCCCCGAATGTGTTTGCCTCGCCCGCTGCC 991 29 100.0 32 ............................. TGGATTATCTGTATTTTACGGAAGTGGGCGCG 1052 29 100.0 32 ............................. GTCGTTCATCAGGCACTACCGGCACTTTCTGG 1113 29 100.0 32 ............................. ATATTCGCCGCTTTCCATTTACCGAACGTAAC 1174 29 100.0 32 ............................. CCACGTTCGGCGATGTTGGCCCCATCGGTCCA 1235 29 100.0 33 ............................. AAACGGTAGTGTTTTAAAACCGTTTCGAGGTGC 1297 29 100.0 32 ............................. AATAAGGCGCGGTGCCACCCTCGGCTTTAATT 1358 29 65.5 13 ..............GA..C.TTCC.G.GC ACGTTACTCGATC Deletion [1400] 1400 29 100.0 32 ............................. AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 1461 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 1522 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 1583 29 100.0 32 ............................. GCACTATTTCGAATGTCTCGACGCCAGATTTA 1644 29 100.0 32 ............................. AACGAATTGAGACTATTAGAGATTATTCGCCT 1705 29 100.0 32 ............................. GCAACCCATTAATTAACTAAGCAGTAATAAAC 1766 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 1827 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 1888 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 1949 29 96.6 0 A............................ | A [1975] ========== ====== ====== ====== ============================= ================================= ================== 30 29 98.5 31 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : CCGGCGCGAGCCTGGAGGGTTGAATAATGGCGGTTTATCCCCGCTGGCGCGGGGAACACCAATCTCGCATTCGTTACCCCACCTGCATTTTCGGTTTATCCCCGCTGGCGCGGGGAACACGAGGGGATAGGAGTTACGATCCAGCCTGGTTGCGGTTTATCCCCGCTGGCGCGGGGAACACGTGGTCTGCAACCACG # Right flank : GTTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCG # Questionable array : NO Score: 6.14 # Score Detail : 1:0, 2:3, 3:0, 4:0.93, 5:0, 6:0.25, 7:-0.04, 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 : GTGTTCCCCGCGCCAGCGGGGATAAACCG # 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: F [5,4] Score: 0.37/0.37 # Reference repeat match prediction: F [matched GTGTTCCCCGCGCCAGCGGGGATAAACCG with 100% identity] Score: 4.5/4.5 # Secondary Structural analysis prediction: F [-13.50,-12.00] Score: 0.37/0.37 # Array degeneracy analysis prediction: F [0-13] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [35.0-48.3]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [5.65,0.27 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], //