Array 1 9257-7156 **** Predicted by CRISPRDetect 2.4 *** >NZ_VCQD01000230.1 Salmonella enterica subsp. enterica serovar Typhimurium strain SEN74 TYPHIMURIUM_S14_trimmed_contig_249, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 9256 27 93.1 32 --........................... TTTGCCGATCCCCTTCCAGACCACCCTTTACA 9197 29 100.0 32 ............................. TTATCCCAATATATTTCGCTATCAGTTACATC 9136 29 100.0 32 ............................. GACTGTTTATACCGGATTCCATGCGTTTTCAG 9075 29 100.0 32 ............................. GAATTACTGGCTAACGACGAACTGACAGTTGA 9014 29 100.0 32 ............................. CCGGACCTAAACCTGAAAAAACCGACGCCCAA 8953 29 100.0 32 ............................. GCTCATTAAATAACTATATAACCCCCGGACTC 8892 29 100.0 32 ............................. TTCCAGAACCGTTTGACTTACTGTGGCCATTA 8831 29 100.0 32 ............................. GGCTTTGGTGAAGATTTCTGATTTGGTCATTT 8770 29 100.0 32 ............................. GATCGGGTGGTGCCGGTGGGCCATGTGGCGCT 8709 29 100.0 32 ............................. GCAGCGGTTGAGTAACTCCTCGTCCACGTCGA 8648 29 100.0 32 ............................. CTCCAGCGCTCGAATTTATTTGAGGCCACCAC 8587 29 100.0 32 ............................. TTTTGATACGTAGTATTCATTACGCCTCCTAG 8526 29 100.0 32 ............................. GCGAGGTCAATAAAAAATGGTGTGGCTTTACC 8465 29 100.0 32 ............................. CCGGCATCAGCGCCGATCCGTTCATAGTGCCC 8404 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 8343 29 100.0 32 ............................. CAGATCCTCAACGGTCAGGCTGTTTAGTTCCT 8282 29 100.0 32 ............................. CGGAGGATGGAATATTTCCGAGGCTGGCGATT 8221 29 96.6 32 .............T............... ATGCCGGAACGCTGATGGCGTTTGACATGAGC 8160 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 8099 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 8038 29 100.0 32 ............................. TGACGCTGGTCTATACCGGCAACGAACGCGAC 7977 29 100.0 32 ............................. TTGACGGTGACGTCAGTGCCGAAGGCGAAATA 7916 29 100.0 32 ............................. CCAGCTTACGCTATTTACGACGTTATTGAGCA 7855 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 7794 29 100.0 32 ............................. CCCCGATAGCGACGCTTCTGTAGTCACTGGCA 7733 29 100.0 33 ............................. GTGAGTTCGGTTTTAATTTCGTCGCTAAGCTGC 7671 29 96.6 32 .........................G... CGTCACTTTCTGACATTTTATTCAGTTCGTTA 7610 29 96.6 32 ..........T.................. TCATTTCTGGACGGGGCTGTGTGACGAATACG 7549 29 100.0 32 ............................. TGTCCAATTAACCCAAACTTTGCGCGCTTAAT 7488 29 93.1 32 A............T............... GGATATGTGAAGTTCAGGTAGCCCATTACGCA 7427 29 100.0 32 ............................. TTGATCGAGAGTGCGAAGAGGCAGAACGGGCA 7366 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 7305 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 7244 29 100.0 32 ............................. CGTTCATCGGCAGCGTCACGCAATATGAAGAT 7183 28 82.8 0 ...............A.AA.....G-... | ========== ====== ====== ====== ============================= ================================= ================== 35 29 98.5 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : | # Right flank : TTGCATAATCATAATCTGTGTACCAGTAATGGCAGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTAGACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGTCCGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAGCAGTCGAATCATCTGCCATCCCGATATTGCACGTGAACGTTATGCAGCAATGACTTTTCTTGGTATTACCCGAAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTATCGAATGATGTACACGCGTGACCCCCTGCCGATTGGC # Questionable array : NO Score: 6.19 # Score Detail : 1:0, 2:3, 3:0, 4:0.93, 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: R [12-1] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [63.3-0.0]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0.27,5.65 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 28708-27903 **** Predicted by CRISPRDetect 2.4 *** >NZ_VCQD01000069.1 Salmonella enterica subsp. enterica serovar Typhimurium strain SEN74 TYPHIMURIUM_S14_trimmed_contig_74, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ========================================================================== ================== 28707 29 100.0 32 ............................. TGAGCAACGACAGTAAATAATTTTTCGTGCTG 28646 29 100.0 32 ............................. AACCGCTGGCGGGCTGATTGGTCTGCAACCAC 28585 29 100.0 32 ............................. ATATTCGCCGCTTTCCATTTACCGAACGTAAC 28524 29 100.0 32 ............................. CCACGTTCGGCGATGTTGGCCCCATCGGTCCA 28463 29 100.0 33 ............................. AAACGGTAGTGTTTTAAAACCGTTTCGAGGTGC 28401 29 100.0 74 ............................. AATAAGGCGCGGTGCCACCCTCGGCTTTAATTGTGTTCCCCGCGCCGACGCGTTCCAGCGCACGTTACTCGATC 28298 29 100.0 32 ............................. AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 28237 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 28176 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 28115 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 28054 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 27993 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 27932 29 96.6 0 A............................ | A [27905] ========== ====== ====== ====== ============================= ========================================================================== ================== 13 29 99.5 36 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTGCTCGCTGCCGGTGAAATTGAACCACCTCAGCCTGCGCCGGATATGTTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTCGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTGCGTTTGGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : TTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCGT # Questionable array : NO Score: 5.99 # Score Detail : 1:0, 2:3, 3:0, 4:0.97, 5:0, 6:0.25, 7:-0.23, 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], //