Array 1 43171-44786 **** Predicted by CRISPRDetect 2.4 *** >NZ_QJVH01000039.1 Salmonella enterica subsp. enterica strain CDR398A LRAT_56_S56_L001_R1_001__paired__contig_39, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 43171 29 100.0 33 ............................. TCGTACACCAGCGCTTTACCGGAGTGTCCGTGC 43233 29 100.0 32 ............................. ATCAAATATCAGATAACCCCCGTCGGCAAACC 43294 29 100.0 32 ............................. ATCACATTCCTGAAAAATGACTCCCTTAGCGA 43355 29 100.0 32 ............................. GAAGATATTGAAAGCGCCCAATCTTCCCAGCT 43416 29 100.0 32 ............................. TCCAGCATTGACGCGAACCCTGCGCCGCTGGC 43477 29 100.0 32 ............................. GCTGAAATATTGCTATTTCCGAAGGGGCTGAT 43538 29 100.0 32 ............................. TCCCGCCTGAACAAAATCGACCACGTTATTAA 43599 29 100.0 32 ............................. GCTCCCGCGGGCGCTCCTGTTGGCCAGCATCA 43660 29 100.0 32 ............................. CGTCCAATACGAGCTGAGTGCGCACGCCCTTA 43721 29 100.0 32 ............................. CAGATCGACCGCCTGGAGGTTGAGGTGGTTGG 43782 29 100.0 32 ............................. GCGTGGATTGATTCTGATCGCCGTGGGCGGGC 43843 29 100.0 32 ............................. GAAACAGAGATCGCGTCCGATAATGCCGACAT 43904 29 100.0 32 ............................. AGAATATTCAACTCCAGCGGGAAAAAGACGCA 43965 29 100.0 32 ............................. AACTTTCATCAAACTGGATCGAAGGGCCACTT 44026 29 100.0 32 ............................. CCGGTTTTAGCTCGCTGGAAACCTCGCTTTTG 44087 29 100.0 32 ............................. ACGCCGAGGGTGAATATTTAGACCGGGACGCA 44148 29 100.0 32 ............................. GGATCATCAATGTGGGAAGTTATCACAACGGA 44209 29 100.0 33 ............................. CGAAATTCAGCGTCTGGAATGCAAGGATTTTGT 44271 29 100.0 32 ............................. GCTATATCCCCGAATCGTGCGCTACGTGAAAA 44332 29 100.0 32 ............................. ACGAGGTCATTTTCAGCACTCGTCAGGCGCTG 44393 29 100.0 32 ............................. ATGCCCTGTTCGGCAAAATCCCGCCACGCTGG 44454 29 100.0 32 ............................. TAAAACCGGTGCTGGATTTTGATGAAGACGAA 44515 29 100.0 32 ............................. CCATTCAACATCGCACTTAAGAACTTGTGCCA 44576 29 100.0 32 ............................. CGATATTTATCCAGACTGTCGGACAGGGTGGT 44637 29 100.0 32 ............................. CCTCATCGGGAGCCAACGCCGCGAGAATACGC 44698 29 96.6 32 ............................C AGCACAATCATTATTAGATGAACTTTCATCAA 44759 28 82.8 0 ...............A.AA....-.G... | ========== ====== ====== ====== ============================= ================================= ================== 27 29 99.2 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGCGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCGCGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTGGAATGTGGTGCTGATAAAAAACAGTTTATAAACAACAATATACGTTTAGT # Right flank : GTTGCATAATCATAATCTGTGTACCAGTAATGGCTGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTTCCGGGGAGGCTTTTATACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGCCCGACCAGGATTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGTCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATATGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCATGGCTTCCTGATAACAGTCGAATCATCTGCCATCCCGATATTGCGCGCGAACGTTATGCGGCAATGACTTTTCTCGATATTACCCGCAAAATAAAAAAATTGTCGCGTGAGGTGGACTATTCACGCTACCGAATGATGTACACGCGTGACCCCCTGCCGATTGG # Questionable array : NO Score: 6.22 # Score Detail : 1:0, 2:3, 3:0, 4:0.96, 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 61069-62966 **** Predicted by CRISPRDetect 2.4 *** >NZ_QJVH01000039.1 Salmonella enterica subsp. enterica strain CDR398A LRAT_56_S56_L001_R1_001__paired__contig_39, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 61069 29 100.0 32 ............................. GCGGAATACCACTATATAAAGCCCCTCAACCC 61130 29 100.0 32 ............................. ATTTTTACAAAAACTGGCCCCCTGAATTCATC 61191 29 100.0 32 ............................. TTGATTTTAATGGCGGGCGAATTGTATTTAAC 61252 29 100.0 33 ............................. TTTCCTGTAACATTCCGATATATAATTCTCCGC 61314 29 100.0 32 ............................. GCCCAATTGCCGGCGACGGTTTCCATGTCAGC 61375 29 100.0 32 ............................. TGGCGAAACAGGCCAGAGAACGCGAATTGCAG 61436 29 100.0 32 ............................. CGTGTTCGATGTAGGTTTCTTCCTGAAGGCGA 61497 29 100.0 32 ............................. CTACCAGGCCCGTTTGTCTCAACCATGACCAA 61558 29 100.0 32 ............................. TTGGCATGGCTGGCGACGTAGCGAACAAAATC 61619 29 100.0 32 ............................. CATAAATTACTCGATGCGTACCTGTGAAATCT 61680 29 100.0 32 ............................. ATACAGTAGCAAAATAAAAAGGCCGCGTGAGC 61741 29 100.0 32 ............................. CAATGCCGTTTTGCCCGAGTTTTCACCGCCGT 61802 29 100.0 32 ............................. CTCTATTGCCGGGGGTCGAGATGGCCGCCTGC 61863 29 100.0 32 ............................. GTGATCCGCGCCTATGACGCAATGGTAACGAC 61924 29 96.6 32 ............................T GTAGCGCAGGGACTGGCAACGGTGCCGGGCGT 61985 29 100.0 32 ............................. CAGGAGACGGCCAGCCGCACCGGTGGCGGTGC 62046 29 100.0 32 ............................. GGCGTTTTATTCGACCTGAAAAAATGGATCGT 62107 29 96.6 32 .............T............... ACATCTCGCGGACAATAGCGATTTCCACCGTC 62168 29 96.6 32 .............T............... CGTTTCGTTCATTTATTTAGTTTCCTGTTTCG 62229 29 93.1 29 .............T..............C CTTGTTAAATACAGGCGGCGGCGGGGTTG 62287 29 96.6 32 .............T............... AACGGCGACGGGATCGTTTTTTGTGGCGAAAA 62348 29 96.6 32 .............T............... CAGGATTGGATTAATGAAGACGGGTACGAAAT 62409 29 96.6 32 .............T............... AGATTGCAGAATTATATTTCACGCTGGCAGCA 62470 29 96.6 32 .............T............... CTGTTGTTATGCGTTGGATCGTAATAGTTAAC 62531 29 96.6 32 .............T............... CTTGGCAGGGCTGCGCCGCAATGGCAGCAACA 62592 29 96.6 32 .............T............... GTCTTATAAATTGGGCTGATAGTGCCGCTGAT 62653 29 100.0 32 ............................. TACCTGCCGGGACTGGAGTGCAGGTAACCCCA 62714 29 100.0 11 ............................. CGGCCAGCCAT Deletion [62754] 62754 29 72.4 32 T.AAA.AG...TG................ ACAGGGTATATGAGCTTATACGTCATGAACCA 62815 29 100.0 32 ............................. TCGTTGGTGGCGTTCGTCACCTGGCTGTCGGT 62876 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 62937 29 93.1 0 A...........T................ | A [62963] ========== ====== ====== ====== ============================= ================================= ================== 32 29 97.7 31 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTACTCGCTGCCGGTGAAATTAAACCACCTCAGCCTGCGCCGGATATGCTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTTGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTGCGTTTGGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : GTTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCAGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACATCGTGCCAGCTATTGCCGTTCGGGAAGGATGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACCGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATACCATAACGGCGCGCAATCGCTAATGCTCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATCACCAGTAGCGTATTTTTCTTCTCAGCGTCACTCATTCG # Questionable array : NO Score: 6.09 # Score Detail : 1:0, 2:3, 3:0, 4:0.89, 5:0, 6:0.25, 7:-0.05, 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 : GTGTTCCCCGCGCTAGCGGGGATAAACCG # 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 [0-11] 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], //