Array 1 248900-250515 **** Predicted by CRISPRDetect 2.4 *** >NZ_MXQU01000002.1 Salmonella enterica subsp. enterica serovar Infantis strain BCW_3995 NODE_2_length_256789_cov_3.25731, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 248900 29 100.0 33 ............................. TCGTACACCAGCGCTTTACCGGAGTGTCCGTGC 248962 29 100.0 32 ............................. ATCAAATATCAGATAACCCCCGTCGGCAAACC 249023 29 100.0 32 ............................. ATCACATTCCTGAAAAATGACTCCCTTAGCGA 249084 29 100.0 32 ............................. GAAGATATTGAAAGCGCCCAATCTTCCCAGCT 249145 29 100.0 32 ............................. TCCAGCATTGACGCGAACCCTGCGCCGCTGGC 249206 29 100.0 32 ............................. GCTGAAATATTGCTATTTCCGAAGGGGCTGAT 249267 29 100.0 32 ............................. TCCCGCCTGAACAAAATCGACCACGTTATTAA 249328 29 100.0 32 ............................. GCTCCCGCGGGCGCTCCTGTTGGCCAGCATCA 249389 29 100.0 32 ............................. CGTCCAATACGAGCTGAGTGCGCACGCCCTTA 249450 29 100.0 32 ............................. CAGATCGACCGCCTGGAGGTTGAGGTGGTTGG 249511 29 100.0 32 ............................. GCGTGGATTGATTCTGATCGCCGTGGGCGGGC 249572 29 100.0 32 ............................. GAAACAGAGATCGCGTCCGATAATGCCGACAT 249633 29 100.0 32 ............................. AGAATATTCAACTCCAGCGGGAAAAAGACGCA 249694 29 100.0 32 ............................. AACTTTCATCAAACTGGATCGAAGGGCCACTT 249755 29 100.0 32 ............................. CCGGTTTTAGCTCGCTGGAAACCTCGCTTTTG 249816 29 100.0 32 ............................. ACGCCGAGGGTGAATATTTAGACCGGGACGCA 249877 29 100.0 32 ............................. GGATCATCAATGTGGGAAGTTATCACAACGGA 249938 29 100.0 33 ............................. CGAAATTCAGCGTCTGGAATGCAAGGATTTTGT 250000 29 100.0 32 ............................. GCTATATCCCCGAATCGTGCGCTACGTGAAAA 250061 29 100.0 32 ............................. ACGAGGTCATTTTCAGCACTCGTCAGGCGCTG 250122 29 100.0 32 ............................. ATGCCCTGTTCGGCAAAATCCCGCCACGCTGG 250183 29 100.0 32 ............................. TAAAACCGGTGCTGGATTTTGATGAAGACGAA 250244 29 100.0 32 ............................. CCATTCAACATCGCACTTAAGAACTTGTGCCA 250305 29 100.0 32 ............................. CGATATTTATCCAGACTGTCGGACAGGGTGGT 250366 29 100.0 32 ............................. CCTCATCGGGAGCCAACGCCGCGAGAATACGC 250427 29 96.6 32 ............................C AGCACAATCATTATTAGATGAACTTTCATCAA 250488 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 1 163699-161801 **** Predicted by CRISPRDetect 2.4 *** >NZ_MXQU01000009.1 Salmonella enterica subsp. enterica serovar Infantis strain BCW_3995 NODE_9_length_173784_cov_3.35627, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 163698 29 100.0 32 ............................. GCGGAATACCACTATATAAAGCCCCTCAACCC 163637 29 100.0 32 ............................. ATTTTTACAAAAACTGGCCCCCTGAATTCATC 163576 29 100.0 32 ............................. TTGATTTTAATGGCGGGCGAATTGTATTTAAC 163515 29 100.0 33 ............................. TTTCCTGTAACATTCCGATATATAATTCTCCGC 163453 29 100.0 32 ............................. GCCCAATTGCCGGCGACGGTTTCCATGTCAGC 163392 29 100.0 32 ............................. TGGCGAAACAGGCCAGAGAACGCGAATTGCAG 163331 29 100.0 32 ............................. CGTGTTCGATGTAGGTTTCTTCCTGAAGGCGA 163270 29 100.0 32 ............................. CTACCAGGCCCGTTTGTCTCAACCATGACCAA 163209 29 100.0 32 ............................. TTGGCATGGCTGGCGACGTAGCGAACAAAATC 163148 29 100.0 32 ............................. CATAAATTACTCGATGCGTACCTGTGAAATCT 163087 29 100.0 32 ............................. ATACAGTAGCAAAATAAAAAGGCCGCGTGAGC 163026 29 100.0 32 ............................. CAATGCCGTTTTGCCCGAGTTTTCACCGCCGT 162965 29 100.0 32 ............................. CTCTATTGCCGGGGGTCGAGATGGCCGCCTGC 162904 29 100.0 32 ............................. GTGATCCGCGCCTATGACGCAATGGTAACGAC 162843 29 96.6 32 ............................T GTAGCGCAGGGACTGGCAACGGTGCCGGGCGT 162782 29 100.0 32 ............................. CAGGAGACGGCCAGCCGCACCGGTGGCGGTGC 162721 29 100.0 32 ............................. GGCGTTTTATTCGACCTGAAAAAATGGATCGT 162660 29 96.6 32 .............T............... ACATCTCGCGGACAATAGCGATTTCCACCGTC 162599 29 96.6 32 .............T............... CGTTTCGTTCATTTATTTAGTTTCCTGTTTCG 162538 29 93.1 29 .............T..............C CTTGTTAAATACAGGCGGCGGCGGGGTTG 162480 29 96.6 32 .............T............... AACGGCGACGGGATCGTTTTTTGTGGCGAAAA 162419 29 96.6 32 .............T............... CAGGATTGGATTAATGAAGACGGGTACGAAAT 162358 29 96.6 32 .............T............... AGATTGCAGAATTATATTTCACGCTGGCAGCA 162297 29 96.6 32 .............T............... CTGTTGTTATGCGTTGGATCGTAATAGTTAAC 162236 29 96.6 32 .............T............... CTTGGCAGGGCTGCGCCGCAATGGCAGCAACA 162175 29 96.6 32 .............T............... GTCTTATAAATTGGGCTGATAGTGCCGCTGAT 162114 29 100.0 32 ............................. TACCTGCCGGGACTGGAGTGCAGGTAACCCCA 162053 29 100.0 11 ............................. CGGCCAGCCAT Deletion [162014] 162013 29 72.4 32 T.AAA.AG...TG................ ACAGGGTATATGAGCTTATACGTCATGAACCA 161952 29 100.0 32 ............................. TCGTTGGTGGCGTTCGTCACCTGGCTGTCGGT 161891 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 161830 29 93.1 0 A...........T................ | A [161803] ========== ====== ====== ====== ============================= ================================= ================== 32 29 97.7 31 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTACTCGCTGCCGGTGAAATTAAACCACCTCAGCCTGCGCCGGATATGCTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTTGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTGCGTTTGGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : TTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCAGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACATCGTGCCAGCTATTGCCGTTCGGGAAGGATGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACCGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATACCATAACGGCGCGCAATCGCTAATGCTCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATCACCAGTAGCGTATTTTTCTTCTCAGCGTCACTCATTCGT # 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: 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: 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], //