Array 1 5358-6729 **** Predicted by CRISPRDetect 2.4 *** >NZ_VCQE01000235.1 Salmonella enterica subsp. enterica serovar Typhimurium strain SEN82 TYPHIMURIUM_S15_trimmed_contig_249, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 5358 29 100.0 32 ............................. GCGAGGTCAATAAAAAATGGTGTGGCTTTACC 5419 29 100.0 32 ............................. CCGGCATCAGCGCCGATCCGTTCATAGTGCCC 5480 29 100.0 32 ............................. AAAAAACAGAAGAACGGCAAGCGGCACCTCAA 5541 29 100.0 32 ............................. CGTCAGCGCGGTATTGAGGCCGGGGACCGCCC 5602 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 5663 29 100.0 32 ............................. CAGATCCTCAACGGTCAGGCTGTTTAGTTCCT 5724 29 100.0 32 ............................. CGGAGGATGGAATATTTCCGAGGCTGGCGATT 5785 29 96.6 32 .............T............... ATGCCGGAACGCTGATGGCGTTTGACATGAGC 5846 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 5907 29 100.0 32 ............................. TGACGCTGGTCTATACCGGCAACGAACGCGAC 5968 29 100.0 32 ............................. TTGACGGTGACGTCAGTGCCGAAGGCGAAATA 6029 29 100.0 32 ............................. CCAGCTTACGCTATTTACGACGTTATTGAGCA 6090 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 6151 29 100.0 32 ............................. CCCCGATAGCGACGCTTCTGTAGTCACTGGCA 6212 29 100.0 33 ............................. GTGAGTTCGGTTTTAATTTCGTCGCTAAGCTGC 6274 29 96.6 32 .........................G... CGTCACTTTCTGACATTTTATTCAGTTCGTTA 6335 29 96.6 32 ..........T.................. TCATTTCTGGACGGGGCTGTGTGACGAATACG 6396 29 100.0 32 ............................. TGTCCAATTAACCCAAACTTTGCGCGCTTAAT 6457 29 93.1 32 A............T............... GGATATGTGAAGTTCAGGTAGCCCATTACGCA 6518 29 100.0 32 ............................. TTGATCGAGAGTGCGAAGAGGCAGAACGGGCA 6579 29 100.0 32 ............................. CGTCAACGCGGGATTGAGTCCGGGGACCGCCC 6640 29 79.3 32 ...G..G............ATC...T... CGCAGGAACGAGAAACAAAAGCCTTATCCGGT 6701 29 79.3 0 .....AG..A........C..C......C | ========== ====== ====== ====== ============================= ================================= ================== 23 29 97.2 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGTGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTAGAATGTGGTGCTGACAAAAAGTAGTTTATAAACAATTATATCCGTTTAGT # Right flank : CCGGTCCACAACGGCCGGGCGGTTTTGTTCCTGTGTTCCCCGCGCCAGCGGGGCTGAA # Questionable array : NO Score: 6.12 # Score Detail : 1:0, 2:3, 3:0, 4:0.86, 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 [1-16] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [70.0-30.0]%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], // Array 1 9-1179 **** Predicted by CRISPRDetect 2.4 *** >NZ_VCQE01000084.1 Salmonella enterica subsp. enterica serovar Typhimurium strain SEN82 TYPHIMURIUM_S15_trimmed_contig_88, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 9 29 100.0 32 ............................. TTACGTGTTTATTCATCTGTTGCATTAGATTC 70 29 96.6 32 ............................T GAGGCGTACAGGCTGTTAGATGAGAAATTACC 131 29 100.0 32 ............................. ACGCCCCGAATGTGTTTGCCTCGCCCGCTGCC 192 29 100.0 32 ............................. TGGATTATCTGTATTTTACGGAAGTGGGCGCG 253 29 100.0 32 ............................. GTCGTTCATCAGGCACTACCGGCACTTTCTGG 314 29 100.0 32 ............................. ATATTCGCCGCTTTCCATTTACCGAACGTAAC 375 29 100.0 32 ............................. CCACGTTCGGCGATGTTGGCCCCATCGGTCCA 436 29 100.0 33 ............................. AAACGGTAGTGTTTTAAAACCGTTTCGAGGTGC 498 29 100.0 32 ............................. AATAAGGCGCGGTGCCACCCTCGGCTTTAATT 559 29 65.5 13 ..............GA..C.TTCC.G.GC ACGTTACTCGATC Deletion [601] 601 29 100.0 32 ............................. AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 662 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 723 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 784 29 100.0 32 ............................. GCACTATTTCGAATGTCTCGACGCCAGATTTA 845 29 100.0 32 ............................. AACGAATTGAGACTATTAGAGATTATTCGCCT 906 29 100.0 32 ............................. GCAACCCATTAATTAACTAAGCAGTAATAAAC 967 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 1028 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 1089 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 1150 29 96.6 0 A............................ | A [1176] ========== ====== ====== ====== ============================= ================================= ================== 20 29 97.8 31 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GATAAAGAG # Right flank : GTTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCG # Questionable array : NO Score: 6.07 # Score Detail : 1:0, 2:3, 3:0, 4:0.89, 5:0, 6:0.25, 7:-0.07, 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: R [10.0-48.3]%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], //