Array 1 3016976-3015499 **** Predicted by CRISPRDetect 2.4 *** >NZ_CP039716.1 Salmonella enterica subsp. enterica serovar 1,4,[5],12:i:- strain PNCS000211 chromosome, complete genome Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ========================================================================== ================== 3016975 29 100.0 32 ............................. TGAGCAACGACAGTAAATAATTTTTCGTGCTG 3016914 29 100.0 33 ............................. CCAGTGGGCGTAGCCAGCTCATCGCTATTTTGC 3016852 29 100.0 32 ............................. CGTTGCGGATTATCGTTAAGACTGAAGGAAGT 3016791 29 100.0 32 ............................. TTGCAGGGCGATATTGTTGTTGGTGAATGGGA 3016730 29 100.0 32 ............................. CGTCGCGGAAAATTTCGCATTGACGATAAAGA 3016669 29 100.0 32 ............................. TTACGTGTTTATTCATCTGTTGCATTAGATTC 3016608 29 96.6 32 ............................T GAGGCGTACAGGCTGTTAGATGAGAAATTACC 3016547 29 100.0 32 ............................. ACGCCCCGAATGTGTTTGCCTCGCCCGCTGCC 3016486 29 100.0 32 ............................. TGGATTATCTGTATTTTACGGAAGTGGGCGCG 3016425 29 100.0 32 ............................. GTCGTTCATCAGGCACTACCGGCACTTTCTGG 3016364 29 100.0 32 ............................. ATATTCGCCGCTTTCCATTTACCGAACGTAAC 3016303 29 100.0 32 ............................. CCACGTTCGGCGATGTTGGCCCCATCGGTCCA 3016242 29 100.0 33 ............................. AAACGGTAGTGTTTTAAAACCGTTTCGAGGTGC 3016180 29 100.0 74 ............................. AATAAGGCGCGGTGCCACCCTCGGCTTTAATTGTGTTCCCCGCGCCGACGCGTTCCAGCGCACGTTACTCGATC 3016077 29 100.0 32 ............................. AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 3016016 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 3015955 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 3015894 29 100.0 32 ............................. GCACTATTTCGAATGTCTCGACGCCAGATTTA 3015833 29 100.0 32 ............................. AACGAATTGAGACTATTAGAGATTATTCGCCT 3015772 29 100.0 32 ............................. GCAACCCATTAATTAACTAAGCAGTAATAAAC 3015711 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 3015650 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 3015589 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 3015528 29 96.6 0 A............................ | A [3015501] ========== ====== ====== ====== ============================= ========================================================================== ================== 24 29 99.6 34 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTGCTCGCTGCCGGTGAAATTGAACCACCTCAGCCTGCGCCGGATATGTTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTCGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTGCGTTTGGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : TTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCGT # Questionable array : NO Score: 6.12 # Score Detail : 1:0, 2:3, 3:0, 4:0.98, 5:0, 6:0.25, 7:-0.11, 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 [3-1] 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 3034723-3033108 **** Predicted by CRISPRDetect 2.4 *** >NZ_CP039716.1 Salmonella enterica subsp. enterica serovar 1,4,[5],12:i:- strain PNCS000211 chromosome, complete genome Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 3034722 29 100.0 32 ............................. TTTGCCGATCCCCTTCCAGACCACCCTTTACA 3034661 29 100.0 32 ............................. TGCAGAGTTGTATCTTACCCTGTTTACGTTTC 3034600 29 100.0 32 ............................. CTCCAGCGCTCGAATTTATTTGAGGCCACCAC 3034539 29 100.0 32 ............................. TTTTGATACGTAGTATTCATTACGCCTCCTAG 3034478 29 100.0 32 ............................. GCGAGGTCAATAAAAAATGGTGTGGCTTTACC 3034417 29 100.0 32 ............................. CCGGCATCAGCGCCGATCCGTTCATAGTGCCC 3034356 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 3034295 29 100.0 32 ............................. CAGATCCTCAACGGTCAGGCTGTTTAGTTCCT 3034234 29 100.0 32 ............................. CGGAGGATGGAATATTTCCGAGGCTGGCGATT 3034173 29 96.6 32 .............T............... ATGCCGGAACGCTGATGGCGTTTGACATGAGC 3034112 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 3034051 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 3033990 29 100.0 32 ............................. TGACGCTGGTCTATACCGGCAACGAACGCGAC 3033929 29 100.0 32 ............................. TTGACGGTGACGTCAGTGCCGAAGGCGAAATA 3033868 29 100.0 32 ............................. CCAGCTTACGCTATTTACGACGTTATTGAGCA 3033807 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 3033746 29 100.0 32 ............................. CCCCGATAGAGACGCTTCTGTAGTCACTGGCA 3033685 29 100.0 33 ............................. GTGAGTTCGGTTTTAATTTCGTCGCTAAGCTGC 3033623 29 96.6 32 .........................G... CGTCACTTTCTGACATTTTATTCAGTTCGTTA 3033562 29 96.6 32 ..........T.................. TCATTTCTGGACGGGGCTGTGTGACGAATACG 3033501 29 100.0 32 ............................. TGTCCAATTAACCCAAACTTTGCGCGCTTAAT 3033440 29 93.1 32 A............T............... GGATATGTGAAGTTCAGGTAGCCCATTACGCA 3033379 29 100.0 32 ............................. TTGATCGAGAGTGCGAAGAGGCAGAACGGGCA 3033318 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 3033257 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 3033196 29 100.0 32 ............................. CGTTCATCGGCAGCGTCACGCAATATGAAGAT 3033135 28 82.8 0 ...............A.AA.....G-... | ========== ====== ====== ====== ============================= ================================= ================== 27 29 98.3 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGTGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTAGAATGTGGTGCTGACAAAAAGTAGTTTATAAACAATTATATCCGTTTAGT # Right flank : TTGCATAATCATAATCTGTGTACCAGTAATGGCAGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTAGACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGTCCGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAGCAGTCGAATCATCTGCCATCCCGATATTGCACGTGAACGTTATGCAGCAATGACTTTTCTTGGTATTACCCGAAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTATCGAATGATGTACACGCGTGACCCCCTGCCGATTGGC # Questionable array : NO Score: 6.17 # Score Detail : 1:0, 2:3, 3:0, 4:0.91, 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 [10-1] 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], //