Array 1 164-1656 **** Predicted by CRISPRDetect 2.4 *** >NZ_CDIX01000127.1 Salmonella enterica subsp. enterica serovar Typhimurium strain STM109, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 164 29 100.0 32 ............................. TTTTGATACGTAGTATTCATTACGCCTCCTAG 225 29 100.0 32 ............................. GCGAGGTCAATAAAAAATGGTGTGGCTTTACC 286 29 100.0 32 ............................. CCGGCATCAGCGCCGATCCGTTCATAGTGCCC 347 29 100.0 32 ............................. AAAAAACAGAAGAACGGCAAGCGGCACCTCAA 408 29 100.0 32 ............................. CGTCAGCGCGGTATTGAGGCCGGGGACCGCCC 469 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 530 29 100.0 32 ............................. CAGATCCTCAACGGTCAGGCTGTTTAGTTCCT 591 29 100.0 32 ............................. CGGAGGATGGAATATTTCCGAGGCTGGCGATT 652 29 96.6 32 .............T............... ATGCCGGAACGCTGATGGCGTTTGACATGAGC 713 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 774 29 100.0 32 ............................. TGACGCTGGTCTATACCGGCAACGAACGCGAC 835 29 100.0 32 ............................. TTGACGGTGACGTCAGTGCCGAAGGCGAAATA 896 29 100.0 32 ............................. CCAGCTTACGCTATTTACGACGTTATTGAGCA 957 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 1018 29 100.0 32 ............................. CCCCGATAGCGACGCTTCTGTAGTCACTGGCA 1079 29 100.0 33 ............................. GTGAGTTCGGTTTTAATTTCGTCGCTAAGCTGC 1141 29 96.6 32 .........................G... CGTCACTTTCTGACATTTTATTCAGTTCGTTA 1202 29 96.6 32 ..........T.................. TCATTTCTGGACGGGGCTGTGTGACGAATACG 1263 29 100.0 32 ............................. TGTCCAATTAACCCAAACTTTGCGCGCTTAAT 1324 29 93.1 32 A............T............... GGATATGTGAAGTTCAGGTAGCCCATTACGCA 1385 29 100.0 32 ............................. TTGATCGAGAGTGCGAAGAGGCAGAACGGGCA 1446 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 1507 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 1568 29 100.0 32 ............................. CGTTCATCGGCAGCGTCACGCAATATGAAGAT 1629 28 82.8 0 ...............A.AA....-.G... | ========== ====== ====== ====== ============================= ================================= ================== 25 29 98.2 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTAGAATGTGGTGCTGACAAAAAGTAGTTTATAAACAATTATATCCGTTTAGTG # 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 1 223-11 **** Predicted by CRISPRDetect 2.4 *** >NZ_CDIX01000054.1 Salmonella enterica subsp. enterica serovar Typhimurium strain STM109, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 222 29 96.6 32 ............................T CCCACCGCGCTGATTAACGACGGACTGTTACA 161 29 100.0 32 ............................. TGAGCAACGACAGTAAATAATTTTTCGTGCTG 100 29 100.0 32 ............................. AACCGCTGGCGGGCTGATTGGTCTGCAACCAC 39 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================ ================== 4 29 99.2 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTGCTCGCTGCCGGTGAAATTGAACCACCTCAGCCTGCGCCGGATATGTTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTCGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTGCGTTTGGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : GCAACCAGGCT # Questionable array : NO Score: 5.82 # Score Detail : 1:0, 2:3, 3:0, 4:0.96, 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 : 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: F [0-1] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [6.7-71.7]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0.41,5.51 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 704-3 **** Predicted by CRISPRDetect 2.4 *** >NZ_CDIX01000037.1 Salmonella enterica subsp. enterica serovar Typhimurium strain STM109, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 703 29 96.6 32 ............................T CCCACCGCGCTGATTAACGACGGACTGTTACA 642 29 100.0 32 ............................. TGAGCAACGACAGTAAATAATTTTTCGTGCTG 581 29 100.0 32 ............................. AACCGCTGGCGGGCTGATTGGTCTGCAACCAC 520 29 100.0 32 ............................. CAACCAGGCTGGATCGTAACTCCTATCCCCTC 459 29 100.0 32 ............................. AAAATGCAGGTGGGGTAACGAATGCGAGATTG 398 29 100.0 32 ............................. CCATTATTCAACCCTCCAGGCTCGCGCCGGCT 337 29 100.0 33 ............................. CCAGTGGGCGTAGCCAGCTCATCGCTATTTTGC 275 29 100.0 32 ............................. CGTTGCGGATTATCGTTAAGACTGAAGGAAGT 214 29 100.0 32 ............................. CGTCACTACCGAGACCGAGACCGAGACCGAGA 153 29 100.0 32 ............................. CCGCTGACGCACTGGATCAACCTGACGCAACG 92 29 100.0 32 ............................. TTGCAGGGCGATATTGTTGTTGGTGAATGGGA 31 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================= ================== 12 29 99.7 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : AGATAATCCACGGTTTATCCCCGCTGGCGCGGGGAACACGGCAGCGGGCGAGGCAAACACATTCGGGGCGTCGGTTTATCCCCGCTGGCGCGGGGAACACGGCAGCGGGCGAGGCAAACACATTCGGGGCGTCGGTTTATCCCCGCTGGCGCGGGGAACACGGTAATTTCTCATCTAACAGCCTGTACGCCTCAGGTTTATCCCCGCTGGCGCGGGGAACACGAATCTAATGCAACAGATGAATAAACACGTAACGGTTTATCCCCGCTGGCGCGGGGAACACTCTTTATCGTCAATGCGAAATTTTCCGCGACGCGGTTTATCCCCGCTGGCGCGGGGAACACTCCCATTCACCAACAACAATATCGCCCTGCAACGGTTTATCCCCGCTGGCGCGGGGAACACCGTTGCGTCAGGTTGATCCAGTGCGTCAGCGGCGGTTTATCCCCGCTGGCGCGGGGAACACTCTCGGTCTCGGTCTCGGTCTCGGTAGTGACGCG # Right flank : GAG # 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 : 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: F [0-1] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [1.7-35.0]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0.41,5.51 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 2 738-2152 **** Predicted by CRISPRDetect 2.4 *** >NZ_CDIX01000037.1 Salmonella enterica subsp. enterica serovar Typhimurium strain STM109, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ========================================================================== ================== 738 29 100.0 32 ............................. CCGCTGACGCACTGGATCAACCTGACGCAACG 799 29 100.0 32 ............................. TTGCAGGGCGATATTGTTGTTGGTGAATGGGA 860 29 100.0 32 ............................. CGTCGCGGAAAATTTCGCATTGACGATAAAGA 921 29 100.0 32 ............................. TTACGTGTTTATTCATCTGTTGCATTAGATTC 982 29 96.6 32 ............................T GAGGCGTACAGGCTGTTAGATGAGAAATTACC 1043 29 100.0 32 ............................. ACGCCCCGAATGTGTTTGCCTCGCCCGCTGCC 1104 29 100.0 32 ............................. ACGCCCCGAATGTGTTTGCCTCGCCCGCTGCC 1165 29 100.0 32 ............................. TGGATTATCTGTATTTTACGGAAGTGGGCGCG 1226 29 100.0 32 ............................. GTCGTTCATCAGGCACTACCGGCACTTTCTGG 1287 29 100.0 32 ............................. ATATTCGCCGCTTTCCATTTACCGAACGTAAC 1348 29 100.0 32 ............................. CCACGTTCGGCGATGTTGGCCCCATCGGTCCA 1409 29 100.0 33 ............................. AAACGGTAGTGTTTTAAAACCGTTTCGAGGTGC 1471 29 100.0 74 ............................. AATAAGGCGCGGTGCCACCCTCGGCTTTAATTGTGTTCCCCGCGCCGACGCGTTCCAGCGCACGTTACTCGATC 1574 29 100.0 32 ............................. AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 1635 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 1696 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 1757 29 100.0 32 ............................. GCACTATTTCGAATGTCTCGACGCCAGATTTA 1818 29 100.0 32 ............................. AACGAATTGAGACTATTAGAGATTATTCGCCT 1879 29 100.0 32 ............................. GCAACCCATTAATTAACTAAGCAGTAATAAAC 1940 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 2001 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 2062 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 2123 29 96.6 0 A............................ | A [2149] ========== ====== ====== ====== ============================= ========================================================================== ================== 23 29 99.6 34 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : TCCGCAACGCGGTTTATCCCCGCTGGCGCGGGGAACACGCAAAATAGCGATGAGCTGGCTACGCCCACTGGCGGTTTATCCCCGCTGGCGCGGGGAACACAGCCGGCGCGAGCCTGGAGGGTTGAATAATGGCGGTTTATCCCCGCTGGCGCGGGGAACACCAATCTCGCATTCGTTACCCCACCTGCATTTTCGGTTTATCCCCGCTGGCGCGGGGAACACGAGGGGATAGGAGTTACGATCCAGCCTGGTTGCGGTTTATCCCCGCTGGCGCGGGGAACACGTGGTTGCAGACCAATCAGCCCGCCAGCGGTTCGGTTTATCCCCGCTGGCGCGGGGAACACCAGCACGAAAAATTATTTACTGTCGTTGCTCACGGTTTATCCCCGCTGGCGCGGGGAACACTGTAACAGTCCGTCGTTAATCAGCGCGGTGGGAGGTTTATCCCCGCTGGCGCGGGGAACACCGCGTCACTACCGAGACCGAGACCGAGACCGAGA # Right flank : GTTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCG # Questionable array : NO Score: 6.12 # Score Detail : 1:0, 2:3, 3:0, 4:0.98, 5:0, 6:0.25, 7:-0.11, 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 [1-3] 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], //