Array 1 422118-423060 **** Predicted by CRISPRDetect 2.4 *** >NZ_PHIS01000001.1 Salmonella enterica subsp. enterica serovar Typhimurium strain CFSAN068041 CFSAN068041_contig_1, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 422118 29 100.0 32 ............................. TTTTGATACGTAGTATTCATTACGCCTCCTAG 422179 29 100.0 32 ............................. GCGAGGTCAATAAAAAATGGTGTGGCTTTACC 422240 29 100.0 32 ............................. CCGGCATCAGCGCCGATCCGTTCATAGTGCCC 422301 29 100.0 32 ............................. AAAAAACAGAAGAACGGCAAGCGGCACCTCAA 422362 29 100.0 32 ............................. CGTCAGCGCGGTATTGAGGCCGGGGACCGCCC 422423 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 422484 29 100.0 32 ............................. CAGATCCTCAACGGTCAGGCTGTTTAGTTCCT 422545 29 100.0 32 ............................. CGGAGGATGGAATATTTCCGAGGCTGGCGATT 422606 29 96.6 32 .............T............... ATGCCGGAACGCTGATGGCGTTTGACATGAGC 422667 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 422728 29 100.0 32 ............................. TGACGCTGGTCTATACCGGCAACGAACGCGAC 422789 29 100.0 32 ............................. TTGACGGTGACGTCAGTGCCGAAGGCGAAATA 422850 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 422911 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 422972 29 100.0 32 ............................. CGTTCATCGGCAGCGTCACGCAATATGAAGAT 423033 28 82.8 0 ...............A.AA....-.G... | ========== ====== ====== ====== ============================= ================================ ================== 16 29 98.5 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGTGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTAGAATGTGGTGCTGACAAAAAGTAGTTTATAAACAATTATATCCGTTTAGT # Right flank : GTTGCATAATCATAATCTGTGTACCAGTAATGGCAGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTAGACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGTCCGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAGCAGTCGAATCATCTGCCATCCCGATATTGCACGTGAACGTTATGCAGCAATGACTTTTCTTGGTATTACCCGAAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTATCGAATGATGTACACGCGTGACCCCCTGCCGATTGG # 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: 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 [0-6] 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 2 439192-441040 **** Predicted by CRISPRDetect 2.4 *** >NZ_PHIS01000001.1 Salmonella enterica subsp. enterica serovar Typhimurium strain CFSAN068041 CFSAN068041_contig_1, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ========================================================================== ================== 439192 29 96.6 32 ............................T CCCACCGCGCTGATTAACGACGGACTGTTACA 439253 29 100.0 32 ............................. TGAGCAACGACAGTAAATAATTTTTCGTGCTG 439314 29 100.0 32 ............................. AACCGCTGGCGGGCTGATTGGTCTGCAACCAC 439375 29 100.0 32 ............................. CAACCAGGCTGGATCGTAACTCCTATCCCCTC 439436 29 100.0 32 ............................. AAAATGCAGGTGGGGTAACGAATGCGAGATTG 439497 29 100.0 32 ............................. CCATTATTCAACCCTCCAGGCTCGCGCCGGCT 439558 29 100.0 33 ............................. CCAGTGGGCGTAGCCAGCTCATCGCTATTTTGC 439620 29 100.0 32 ............................. CGTTGCGGATTATCGTTAAGACTGAAGGAAGT 439681 29 100.0 38 ............................. CGTCACTACCGAGACCGAGACCGAGACCGAGACCGAGA 439748 29 100.0 32 ............................. CCGCTGACGCACTGGATCAACCTGACGCAACG 439809 29 100.0 32 ............................. TTGCAGGGCGATATTGTTGTTGGTGAATGGGA 439870 29 100.0 32 ............................. CGTCGCGGAAAATTTCGCATTGACGATAAAGA 439931 29 100.0 32 ............................. TTACGTGTTTATTCATCTGTTGCATTAGATTC 439992 29 96.6 32 ............................T GAGGCGTACAGGCTGTTAGATGAGAAATTACC 440053 29 100.0 32 ............................. ACGCCCCGAATGTGTTTGCCTCGCCCGCTGCC 440114 29 100.0 32 ............................. TGGATTATCTGTATTTTACGGAAGTGGGCGCG 440175 29 100.0 32 ............................. ATATTCGCCGCTTTCCATTTACCGAACGTAAC 440236 29 100.0 32 ............................. CCACGTTCGGCGATGTTGGCCCCATCGGTCCA 440297 29 100.0 33 ............................. AAACGGTAGTGTTTTAAAACCGTTTCGAGGTGC 440359 29 100.0 74 ............................. AATAAGGCGCGGTGCCACCCTCGGCTTTAATTGTGTTCCCCGCGCCGACGCGTTCCAGCGCACGTTACTCGATC 440462 29 100.0 32 ............................. AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 440523 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 440584 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 440645 29 100.0 32 ............................. GCACTATTTCGAATGTCTCGACGCCAGATTTA 440706 29 100.0 32 ............................. AACGAATTGAGACTATTAGAGATTATTCGCCT 440767 29 100.0 32 ............................. GCAACCCATTAATTAACTAAGCAGTAATAAAC 440828 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 440889 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 440950 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 441011 29 96.6 0 A............................ | A [441037] ========== ====== ====== ====== ============================= ========================================================================== ================== 30 29 99.5 34 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTGCTCGCTGCCGGTGAAATTGAACCACCTCAGCCTGCGCCGGATATGTTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTCGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTGCGTTTGGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : GTTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCG # Questionable array : NO Score: 6.14 # Score Detail : 1:0, 2:3, 3:0, 4:0.97, 5:0, 6:0.25, 7:-0.08, 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: F [71.7-48.3]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [5.92,0 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], //