Array 1 107787-106069 **** Predicted by CRISPRDetect 2.4 *** >NZ_LRXY01000030.1 Salmonella enterica strain 04 Contig_30, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ==================================== ================== 107786 29 100.0 36 ............................. TTTCCTGTCACCTTCCGTTATTTCGTTGCTCTGCTA 107721 29 100.0 32 ............................. GCCCAATTGCCGGCGACGGTTTCCATGTCAGC 107660 29 100.0 32 ............................. TGGCGAAACAGGCCAGAGAACGCGAATTGCAG 107599 29 100.0 32 ............................. CGTGTTCGATGTAGGTTTCTTCCTGAAGGCGA 107538 29 100.0 32 ............................. CTACCAGGCCCGTTTGTCTCAACCATGACCAA 107477 29 100.0 32 ............................. TTGGCATGGCTGGCGACGTAGCGAACAAAATC 107416 29 100.0 32 ............................. CATAAATTACTCGATGCGTACCTGTGAAATCT 107355 29 100.0 32 ............................. ATACAGTAGCAAAATAAAAAGGCCGCGTGAGC 107294 29 100.0 32 ............................. CAATGCCGTTTTGCCCGAGTTTTCACCGCCGT 107233 29 100.0 32 ............................. CTCTATTGCCGGGGGTCGAGATGGCCGCCTGC 107172 29 100.0 32 ............................. GTGATCCGCGCCTATGACGCAATGGTAACGAC 107111 29 96.6 32 ............................T GTAGCGCAGGGACTGGCAACGGTGCCGGGCGT 107050 29 100.0 32 ............................. CAGGAGACGGCCAGCCGCACCGGTGGCGGTGC 106989 29 100.0 32 ............................. GGCGTTTTATTCGACCTGAAAAAATGGATCGT 106928 29 96.6 32 .............T............... ACATCTCGCGGACAATAGCGATTTCCACCGTC 106867 29 96.6 32 .............T............... CGTTTCGTTCATTTATTTAGTTTCCTGTTTCG 106806 29 93.1 29 .............T..............C CTTGTTAAATACAGGCGGCGGCGGGGTTG 106748 29 96.6 32 .............T............... AACGGCGACGGGATCGTTTTTTGTGGCGAAAA 106687 29 96.6 32 .............T............... CAGGATTGGATTAATGAAGACGGGTACGAAAT 106626 29 96.6 32 .............T............... AGATTGCAGAATTATATTTCACGCTGGCAGCA 106565 29 96.6 32 .............T............... CTGTTGTTATGCGTTGGATCGTAATAGTTAAC 106504 29 96.6 32 .............T............... CTTGGCAGGGCTGCGCCGCAATGGCAGCAACA 106443 29 96.6 32 .............T............... GTCTTATAAATTGGGCTGATAGTGCCGCTGAT 106382 29 100.0 32 ............................. TACCTGCCGGGACTGGAGTGCAGGTAACCCCA 106321 29 100.0 11 ............................. CGGCCAGCCAT Deletion [106282] 106281 29 72.4 32 T.AAA.AG...TG................ ACAGGGTATATGAGCTTATACGTCATGAACCA 106220 29 100.0 32 ............................. TCGTTGGTGGCGTTCGTCACCTGGCTGTCGGT 106159 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 106098 29 93.1 0 A...........T................ | A [106071] ========== ====== ====== ====== ============================= ==================================== ================== 29 29 97.5 31 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : AAACCA # Right flank : TTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCAGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACATCGTGCCAGCTATTGCCGTTCGGGAAGGATGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACCGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATACCATAACGGCGCGCAATCGCTAATGCTCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATCACCAGTAGCGTATTTTTCTTCTCAGCGTCACTCATTCGT # Questionable array : NO Score: 6.05 # Score Detail : 1:0, 2:3, 3:0, 4:0.88, 5:0, 6:0.25, 7:-0.05, 8:1, 9:0.97, # 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 : GTGTTCCCCGCGCTAGCGGGGATAAACCG # 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 [11-0] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [50.0-8.3]%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 12292-13663 **** Predicted by CRISPRDetect 2.4 *** >NZ_LRXY01000007.1 Salmonella enterica strain 04 Contig_7, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 12292 29 100.0 33 ............................. TCGTACACCAGCGCTTTACCGGAGTGTCCGTGC 12354 29 100.0 32 ............................. GCTGAAATATTGCTATTTCCGAAGGGGCTGAT 12415 29 100.0 32 ............................. TCCCGCCTGAACAAAATCGACCACGTTATTAA 12476 29 100.0 32 ............................. GCTCCCGCGGGCGCTCCTGTTGGCCAGCATCA 12537 29 100.0 32 ............................. CGTCCAATACGAGCTGAGTGCGCACGCCCTTA 12598 29 100.0 32 ............................. CAGATCGACCGCCTGGAGGTTGAGGTGGTTGG 12659 29 100.0 32 ............................. GCGTGGATTGATTCTGATCGCCGTGGGCGGGC 12720 29 100.0 32 ............................. GAAACAGAGATCGCGTCCGATAATGCCGACAT 12781 29 100.0 32 ............................. AGAATATTCAACTCCAGCGGGAAAAAGACGCA 12842 29 100.0 32 ............................. AACTTTCATCAAACTGGATCGAAGGGCCACTT 12903 29 100.0 32 ............................. CCGGTTTTAGCTCGCTGGAAACCTCGCTTTTG 12964 29 100.0 32 ............................. ACGCCGAGGGTGAATATTTAGACCGGGACGCA 13025 29 100.0 32 ............................. GGATCATCAATGTGGGAAGTTATCACAACGGA 13086 29 100.0 33 ............................. CGAAATTCAGCGTCTGGAATGCAAGGATTTTGT 13148 29 100.0 32 ............................. GCTATATCCCCGAATCGTGCGCTACGTGAAAA 13209 29 100.0 32 ............................. ACGAGGTCATTTTCAGCACTCGTCAGGCGCTG 13270 29 100.0 32 ............................. ATGCCCTGTTCGGCAAAATCCCGCCACGCTGG 13331 29 100.0 32 ............................. TAAAACCGGTGCTGGATTTTGATGAAGACGAA 13392 29 100.0 32 ............................. CCATTCAACATCGCACTTAAGAACTTGTGCCA 13453 29 100.0 32 ............................. CGATATTTATCCAGACTGTCGGACAGGGTGGT 13514 29 100.0 32 ............................. CCTCATCGGGAGCCAACGCCGCGAGAATACGC 13575 29 96.6 32 ............................C AGCACAATCATTATTAGATGAACTTTCATCAA 13636 28 82.8 0 ...............A.AA....-.G... | ========== ====== ====== ====== ============================= ================================= ================== 23 29 99.1 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGCGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCGCGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTGGAATGTGGTGCTGATAAAAAACAGTTTATAAACAACAATATACGTTTAGT # Right flank : GTTGCATAATCATAATCTGTGTACCAGTAATGGCTGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTTCCGGGGAGGCTTTTATACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGCCCGACCAGGATTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGTCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATATGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCATGGCTTCCTGATAACAGTCGAATCATCTGCCATCCCGATATTGCGCGCGAACGTTATGCGGCAATGACTTTTCTCGATATTACCCGCAAAATAAAAAAATTGTCGCGTGAGGTGGACTATTCACGCTACCGAATGATGTACACGCGTGACCCCCTGCCGATTGG # Questionable array : NO Score: 6.21 # Score Detail : 1:0, 2:3, 3:0, 4:0.95, 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 29946-30156 **** Predicted by CRISPRDetect 2.4 *** >NZ_LRXY01000007.1 Salmonella enterica strain 04 Contig_7, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 29946 29 100.0 32 ............................. GCGGAATACCACTATATAAAGCCCCTCAACCC 30007 29 100.0 32 ............................. ATTTTTACAAAAACTGGCCCCCTGAATTCATC 30068 29 100.0 32 ............................. TTGATTTTAATGGCGGGCGAATTGTATTTAAC 30129 28 96.6 0 ............................- | ========== ====== ====== ====== ============================= ================================ ================== 4 29 99.2 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTACTCGCTGCCGGTGAAATTAAACCACCTCAGCCTGCGCCGGATATGCTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTTGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTGCGTTTGGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : | # Questionable array : NO Score: 5.82 # Score Detail : 1:0, 2:3, 3:0, 4:0.96, 5:0, 6:0.25, 7:0.01, 8:0.6, 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: NA [0-0] Score: 0/0.41 # AT richness analysis in flanks prediction: F [71.7-0.0]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [5.51,0 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], //