Array 1 51-2153 **** Predicted by CRISPRDetect 2.4 *** >NZ_VCQC01000110.1 Salmonella enterica subsp. enterica serovar Typhimurium strain SEN136 TYPHIMURIUM_S12_trimmed_contig_123, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 51 29 100.0 32 ............................. TGCAGAGTTGTATCTTACCCTGTTTACGTTTC 112 29 100.0 32 ............................. TTATCCCAATATATTTCGCTATCAGTTACATC 173 29 100.0 32 ............................. GACTGTTTATACCGGATTCCATGCGTTTTCAG 234 29 100.0 32 ............................. GAATTACTGGCTAACGACGAACTGACAGTTGA 295 29 100.0 32 ............................. CCGGACCTAAACCTGAAAAAACCGACGCCCAA 356 29 100.0 32 ............................. GCTCATTAAATAACTATATAACCCCCGGACTC 417 29 100.0 32 ............................. TTCCAGAACCGTTTGACTTACTGTGGCCATTA 478 29 100.0 32 ............................. GGCTTTGGTGAAGATTTCTGATTTGGTCATTT 539 29 100.0 32 ............................. GATCGGGTGGTGCCGGTGGGCCATGTGGCGCT 600 29 100.0 32 ............................. GCAGCGGTTGAGTAACTCCTCGTCCACGTCGA 661 29 100.0 32 ............................. CTCCAGCGCTCGAATTTATTTGAGGCCACCAC 722 29 100.0 32 ............................. TTTTGATACGTAGTATTCATTACGCCTCCTAG 783 29 100.0 32 ............................. GCGAGGTCAATAAAAAATGGTGTGGCTTTACC 844 29 100.0 32 ............................. CCGGCATCAGCGCCGATCCGTTCATAGTGCCC 905 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 966 29 100.0 32 ............................. CAGATCCTCAACGGTCAGGCTGTTTAGTTCCT 1027 29 100.0 32 ............................. CGGAGGATGGAATATTTCCGAGGCTGGCGATT 1088 29 96.6 32 .............T............... ATGCCGGAACGCTGATGGCGTTTGACATGAGC 1149 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 1210 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 1271 29 100.0 32 ............................. TGACGCTGGTCTATACCGGCAACGAACGCGAC 1332 29 100.0 32 ............................. TTGACGGTGACGTCAGTGCCGAAGGCGAAATA 1393 29 100.0 32 ............................. CCAGCTTACGCTATTTACGACGTTATTGAGCA 1454 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 1515 29 100.0 32 ............................. CCCCGATAGCGACGCTTCTGTAGTCACTGGCA 1576 29 100.0 33 ............................. GTGAGTTCGGTTTTAATTTCGTCGCTAAGCTGC 1638 29 96.6 32 .........................G... CGTCACTTTCTGACATTTTATTCAGTTCGTTA 1699 29 96.6 32 ..........T.................. TCATTTCTGGACGGGGCTGTGTGACGAATACG 1760 29 100.0 32 ............................. TGTCCAATTAACCCAAACTTTGCGCGCTTAAT 1821 29 93.1 32 A............T............... GGATATGTGAAGTTCAGGTAGCCCATTACGCA 1882 29 100.0 32 ............................. TTGATCGAGAGTGCGAAGAGGCAGAACGGGCA 1943 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 2004 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 2065 29 100.0 32 ............................. CGTTCATCGGCAGCGTCACGCAATATGAAGAT 2126 28 82.8 0 ...............A.AA....-.G... | ========== ====== ====== ====== ============================= ================================= ================== 35 29 98.7 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GCCAGCGGGGATAAACCGTTTGCCGATCCCCTTCCAGACCACCCTTTACAG # Right flank : GTTGCATAATCATAATCTGTGTACCAGTAATGGCAGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTAGACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGTCCGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAGCAGTCGAATCATCTGCCATCCCGATATTGCACGTGAACGTTATGCAGCAATGACTTTTCTTGGTATTACCCGAAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTATCGAATGATGTACACGCGTGACCCCCTGCCGATTGG # Questionable array : NO Score: 6.20 # Score Detail : 1:0, 2:3, 3:0, 4:0.94, 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 [0-12] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [35.0-63.3]%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], // Array 1 28711-27967 **** Predicted by CRISPRDetect 2.4 *** >NZ_VCQC01000005.1 Salmonella enterica subsp. enterica serovar Typhimurium strain SEN136 TYPHIMURIUM_S12_trimmed_contig_6, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ========================================================================== ================== 28710 29 100.0 32 ............................. AACCGCTGGCGGGCTGATTGGTCTGCAACCAC 28649 29 100.0 32 ............................. ATATTCGCCGCTTTCCATTTACCGAACGTAAC 28588 29 100.0 32 ............................. CCACGTTCGGCGATGTTGGCCCCATCGGTCCA 28527 29 100.0 33 ............................. AAACGGTAGTGTTTTAAAACCGTTTCGAGGTGC 28465 29 100.0 74 ............................. AATAAGGCGCGGTGCCACCCTCGGCTTTAATTGTGTTCCCCGCGCCGACGCGTTCCAGCGCACGTTACTCGATC 28362 29 100.0 32 ............................. AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 28301 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 28240 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 28179 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 28118 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 28057 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 27996 29 96.6 0 A............................ | A [27969] ========== ====== ====== ====== ============================= ========================================================================== ================== 12 29 99.4 36 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTGCTCGCTGCCGGTGAAATTGAACCACCTCAGCCTGCGCCGGATATGTTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTCGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTGCGTTTGGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : TTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCGT # Questionable array : NO Score: 5.97 # Score Detail : 1:0, 2:3, 3:0, 4:0.97, 5:0, 6:0.25, 7:-0.25, 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: R [3-0] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [50.0-71.7]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0,5.92 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], //