Array 1 241941-241301 **** Predicted by CRISPRDetect 2.4 *** >NZ_CFLD01000001.1 Salmonella enterica subsp. enterica serovar Typhimurium str. DT104 strain CH42 isolate CH42, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 241940 29 100.0 32 ............................. TGAGCAACGACAGTAAATAATTTTTCGTGCTG 241879 29 100.0 32 ............................. AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 241818 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 241757 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 241696 29 100.0 32 ............................. GCACTATTTCGAATGTCTCGACGCCAGATTTA 241635 29 100.0 32 ............................. AACGAATTGAGACTATTAGAGATTATTCGCCT 241574 29 100.0 32 ............................. GCAACCCATTAATTAACTAAGCAGTAATAAAC 241513 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 241452 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 241391 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 241330 29 96.6 0 A............................ | A [241303] ========== ====== ====== ====== ============================= ================================ ================== 11 29 99.4 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTGCTCGCTGCCGGTGAAATTGAACCACCTCAGCCTGCGCCGGATATGTTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTCGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTGCGTTTGGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : TTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCGT # 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: 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], // Array 2 259687-258073 **** Predicted by CRISPRDetect 2.4 *** >NZ_CFLD01000001.1 Salmonella enterica subsp. enterica serovar Typhimurium str. DT104 strain CH42 isolate CH42, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 259686 29 100.0 32 ............................. TTTGCCGATCCCCTTCCAGACCACCCTTTACA 259625 29 100.0 32 ............................. TGCAGAGTTGTATCTTACCCTGTTTACGTTTC 259564 29 100.0 32 ............................. TTATCCCAATATATTTCGCTATCAGTTACATC 259503 29 100.0 32 ............................. GACTGTTTATACCGGATTCCATGCGTTTTCAG 259442 29 100.0 32 ............................. GAATTACTGGCTAACGACGAACTGACAGTTGA 259381 29 100.0 32 ............................. TTCCAGAACCGTTTGACTTACTGTGGCCATTA 259320 29 100.0 32 ............................. GGCTTTGGTGAAGATTTCTGATTTGGTCATTT 259259 29 100.0 32 ............................. GATCGGGTGGTGCCGGTGGGCCATGTGGCGCT 259198 29 100.0 32 ............................. GCAGCGGTTGAGTAACTCCTCGTCCACGTCGA 259137 29 100.0 32 ............................. CTCCAGCGCTCGAATTTATTTGAGGCCACCAC 259076 29 100.0 32 ............................. TTTTGATACGTAGTATTCATTACGCCTCCTAG 259015 29 100.0 32 ............................. GCGAGGTCAATAAAAAATGGTGTGGCTTTACC 258954 29 100.0 32 ............................. CCGGCATCAGCGCCGATCCGTTCATAGTGCCC 258893 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 258832 29 100.0 32 ............................. CAGATCCTCAACGGTCAGGCTGTTTAGTTCCT 258771 29 100.0 32 ............................. CGGAGGATGGAATATTTCCGAGGCTGGCGATT 258710 29 96.6 32 .............T............... ATGCCGGAACGCTGATGGCGTTTGACATGAGC 258649 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 258588 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 258527 29 100.0 32 ............................. TGACGCTGGTCTATACCGGCAACGAACGCGAC 258466 29 100.0 32 ............................. TTGACGGTGACGTCAGTGCCGAAGGCGAAATA 258405 29 100.0 32 ............................. CCAGCTTACGCTATTTACGACGTTATTGAGCA 258344 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 258283 29 96.6 32 ........A.................... CAGGTTATGCGCAAAAATTAATTCATATTATA 258222 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 258161 29 100.0 32 ............................. CGTTCATCGGCAGCGTCACGCAATATGAAGAT 258100 28 82.8 0 ...............A.AA.....G-... | ========== ====== ====== ====== ============================= ================================ ================== 27 29 98.7 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGTGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTAGAATGTGGTGCTGACAAAAAGTAGTTTATAAACAATTATATCCGTTTAGT # Right flank : TTGCATAATCATAATCTGTGTACCAGTAATGGCAGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTAGACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGTCCGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAGCAGTCGAATCATCTGCCATCCCGATATTGCACGTGAACGTTATGCAGCAATGACTTTTCTTGGTATTACCCGAAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTATCGAATGATGTACACGCGTGACCCCCTGCCGATTGGC # 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: 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 [9-0] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [63.3-70.0]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0,5.65 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], //