Array 1 5424-6916 **** Predicted by CRISPRDetect 2.4 *** >NZ_CDJL01000120.1 Salmonella enterica subsp. enterica serovar Typhimurium strain STM16, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 5424 29 100.0 32 ............................. TTTTGATACGTAGTATTCATTACGCCTCCTAG 5485 29 100.0 32 ............................. GCGAGGTCAATAAAAAATGGTGTGGCTTTACC 5546 29 100.0 32 ............................. CCGGCATCAGCGCCGATCCGTTCATAGTGCCC 5607 29 100.0 32 ............................. AAAAAACAGAAGAACGGCAAGCGGCACCTCAA 5668 29 100.0 32 ............................. CGTCAGCGCGGTATTGAGGCCGGGGACCGCCC 5729 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 5790 29 100.0 32 ............................. CAGATCCTCAACGGTCAGGCTGTTTAGTTCCT 5851 29 100.0 32 ............................. CGGAGGATGGAATATTTCCGAGGCTGGCGATT 5912 29 96.6 32 .............T............... ATGCCGGAACGCTGATGGCGTTTGACATGAGC 5973 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 6034 29 100.0 32 ............................. TGACGCTGGTCTATACCGGCAACGAACGCGAC 6095 29 100.0 32 ............................. TTGACGGTGACGTCAGTGCCGAAGGCGAAATA 6156 29 100.0 32 ............................. CCAGCTTACGCTATTTACGACGTTATTGAGCA 6217 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 6278 29 100.0 32 ............................. CCCCGATAGCGACGCTTCTGTAGTCACTGGCA 6339 29 100.0 33 ............................. GTGAGTTCGGTTTTAATTTCGTCGCTAAGCTGC 6401 29 96.6 32 .........................G... CGTCACTTTCTGACATTTTATTCAGTTCGTTA 6462 29 96.6 32 ..........T.................. TCATTTCTGGACGGGGCTGTGTGACGAATACG 6523 29 100.0 32 ............................. TGTCCAATTAACCCAAACTTTGCGCGCTTAAT 6584 29 93.1 32 A............T............... GGATATGTGAAGTTCAGGTAGCCCATTACGCA 6645 29 100.0 32 ............................. TTGATCGAGAGTGCGAAGAGGCAGAACGGGCA 6706 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 6767 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 6828 29 100.0 32 ............................. CGTTCATCGGCAGCGTCACGCAATATGAAGAT 6889 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 8675-9008 **** Predicted by CRISPRDetect 2.4 *** >NZ_CDJL01000138.1 Salmonella enterica subsp. enterica serovar Typhimurium strain STM16, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 8675 29 96.6 32 ............................T CCCACCGCGCTGATTAACGACGGACTGTTACA 8736 29 100.0 32 ............................. TGAGCAACGACAGTAAATAATTTTTCGTGCTG 8797 29 100.0 32 ............................. AACCGCTGGCGGGCTGATTGGTCTGCAACCAC 8858 29 100.0 32 ............................. CAACCAGGCTGGATCGTAACTCCTATCCCCTC 8919 29 100.0 32 ............................. AAAATGCAGGTGGGGTAACGAATGCGAGATTG 8980 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================ ================== 6 29 99.4 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTGCTCGCTGCCGGTGAAATTGAACCACCTCAGCCTGCGCCGGATATGTTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTCGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTGCGTTTGGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : CCATTATTCAACCCTCCAGGCTCGCGCCGGCTGTGTT # 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 [71.7-25.0]%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 1 233-20 **** Predicted by CRISPRDetect 2.4 *** >NZ_CDJL01000031.1 Salmonella enterica subsp. enterica serovar Typhimurium strain STM16, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 232 29 100.0 32 ............................. AAAATGCAGGTGGGGTAACGAATGCGAGATTG 171 29 100.0 32 ............................. CCATTATTCAACCCTCCAGGCTCGCGCCGGCT 110 29 100.0 33 ............................. CCAGTGGGCGTAGCCAGCTCATCGCTATTTTGC 48 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================= ================== 4 29 100.0 33 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : TGCGTCAGGTTGATCCAGTGCGTCAGCGGCGGTTTATCCCCGCTGGCGCGGGGAACACTCTCGGTCTCGGTCTCGGTCTCGGTAGTGACGCGGTTTATCCCCGCTGGCGCGGGGAACACACTTCCTTCAGTCTTAACGATAATCCGCAACGCGGTTTATCCCCGCTGGCGCGGGGAACACGCAAAATAGCGATGAGCTGGCTACGCCCACTGGCGGTTTATCCCCGCTGGCGCGGGGAACACAGCCGGCGCGAGCCTGGAGGGTTGAATAATGGCGGTTTATCCCCGCTGGCGCGGGGAACACCAATCTCGCATTCGTTACCCCACCTGCATTTTCGGTTTATCCCCGCTGGCGCGGGGAACACGAGGGGATAGGAGTTACGATCCAGCCTGGTTGCGGTTTATCCCCGCTGGCGCGGGGAACACGTGGTTGCAGACCAATCAGCCCGCCAGCGGTTCGGTTWAWCCSCAACCAGGCTGGATCGTAACTCCTATCCCCTC # Right flank : GCGTTGCGGATTATCGTTAA # Questionable array : NO Score: 5.86 # Score Detail : 1:0, 2:3, 3:0, 4:1.00, 5:0, 6:0.25, 7:0.01, 8:0.6, 9:1, # Score Legend : 1: cas, 2: likely_repeat, 3: motif_match, 4: overall_repeat_identity, 5: one_repeat_cluster, 6: exp_repeat_length, 7: exp_spacer_length, 8: spacer_identity, 9: log(total repeats) - log(total mutated repeats), # Primary repeat : 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 [18.3-36.7]%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 2 308-2071 **** Predicted by CRISPRDetect 2.4 *** >NZ_CDJL01000031.1 Salmonella enterica subsp. enterica serovar Typhimurium strain STM16, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= =========================================================================== ================== 308 29 100.0 32 ............................. CAACCAGGCTGGATCGTAACTCCTATCCCCTC 369 29 100.0 32 ............................. AAAATGCAGGTGGGGTAACGAATGCGAGATTG 430 29 100.0 32 ............................. CCATTATTCAACCCTCCAGGCTCGCGCCGGCT 491 29 100.0 33 ............................. CCAGTGGGCGTAGCCAGCTCATCGCTATTTTGC 553 29 100.0 32 ............................. CGTTGCGGATTATCGTTAAGACTGAAGGAAGT 614 29 100.0 32 ............................. CGTCACTACCGAGACCGAGACCGAGACCGAGA 675 29 100.0 32 ............................. CCGCTGACGCACTGGATCAACCTGACGCAACG 736 29 100.0 32 ............................. TTGCAGGGCGATATTGTTGTTGGTGAATGGGA 797 29 100.0 32 ............................. CGTCGCGGAAAATTTCGCATTGACGATAAAGA 858 29 100.0 32 ............................. TTACGTGTTTATTCATCTGTTGCATTAGATTC 919 29 96.6 32 ............................T GAGGCGTACAGGCTGTTAGATGAGAAATTACC 980 29 100.0 32 ............................. ACGCCCCGAATGTGTTTGCCTCGCCCGCTGCC 1041 29 100.0 32 ............................. ACGCCCCGAATGTGTTTGCCTCGCCCGCTGCC 1102 29 100.0 75 ............................. TGGATTATCTGTATTTTACGGAAGTGGGCGCGGGGATAAACCGGTCGTTCATCAGGCACTACCGGCACTTTCTGG 1206 29 100.0 32 ............................. ATATTCGCCGCTTTCCATTTACCGAACGTAAC 1267 29 100.0 32 ............................. CCACGTTCGGCGATGTTGGCCCCATCGGTCCA 1328 29 100.0 33 ............................. AAACGGTAGTGTTTTAAAACCGTTTCGAGGTGC 1390 29 100.0 32 ............................. AATAAGGCGCGGTGCCACCCTCGGCTTTAATT 1451 29 65.5 13 ..............GA..C.TTCC.G.GC ACGTTACTCGATC Deletion [1493] 1493 29 100.0 32 ............................. AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 1554 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 1615 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 1676 29 100.0 32 ............................. GCACTATTTCGAATGTCTCGACGCCAGATTTA 1737 29 100.0 32 ............................. AACGAATTGAGACTATTAGAGATTATTCGCCT 1798 29 100.0 32 ............................. GCAACCCATTAATTAACTAAGCAGTAATAAAC 1859 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 1920 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 1981 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 2042 29 96.6 0 A............................ | A [2068] ========== ====== ====== ====== ============================= =========================================================================== ================== 29 29 98.5 33 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : TTAACGATAATCCGCAACGCGGTTTATCCCCGCTGGCGCGGGGAACACGCAAAATAGCGATGAGCTGGCTACGCCCACTGGCGGTTTATCCCCGCTGGCGCGGGGAACACAGCCGGCGCGAGCCTGGAGGGTTGAATAATGGCGGTTTATCCCCGCTGGCGCGGGGAACACCAATCTCGCATTCGTTACCCCACCTGCATTTTCGGTTTATCCCCGCTGGCGCGGGGAACACGAGGGGATAGGAGTTACGATCCAGCCTGGTTGSGGWTWAACCGAACCGCTGGCGGGCTGATTGGTCTGCAACCACG # Right flank : GTTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCG # Questionable array : NO Score: 6.03 # Score Detail : 1:0, 2:3, 3:0, 4:0.93, 5:0, 6:0.25, 7:-0.15, 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 [36.7-48.3]%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], //