Array 1 4233799-4235291 **** Predicted by CRISPRDetect 2.4 *** >NZ_OU015323.1 Salmonella enterica subsp. enterica serovar Typhimurium strain AUSMDU00004549 isolate AUSMDU00004549 chromosome C1, complete sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 4233799 29 100.0 32 ............................. TTTTGATACGTAGTATTCATTACGCCTCCTAG 4233860 29 100.0 32 ............................. GCGAGGTCAATAAAAAATGGTGTGGCTTTACC 4233921 29 100.0 32 ............................. CCGGCATCAGCGCCGATCCGTTCATAGTGCCC 4233982 29 100.0 32 ............................. AAAAAACAGAAGAACGGCAAGCGGCACCTCAA 4234043 29 100.0 32 ............................. CGTCAGCGCGGTATTGAGGCCGGGGACCGCCC 4234104 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 4234165 29 100.0 32 ............................. CAGATCCTCAACGGTCAGGCTGTTTAGTTCCT 4234226 29 100.0 32 ............................. CGGAGGATGGAATATTTCCGAGGCTGGCGATT 4234287 29 96.6 32 .............T............... ATGCCGGAACGCTGATGGCGTTTGACATGAGC 4234348 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 4234409 29 100.0 32 ............................. TGACGCTGGTCTATACCGGCAACGAACGCGAC 4234470 29 100.0 32 ............................. TTGACGGTGACGTCAGTGCCGAAGGCGAAATA 4234531 29 100.0 32 ............................. CCAGCTTACGCTATTTACGACGTTATTGAGCA 4234592 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 4234653 29 100.0 32 ............................. CCCCGATAGCGACGCTTCTGTAGTCACTGGCA 4234714 29 100.0 33 ............................. GTGAGTTCGGTTTTAATTTCGTCGCTAAGCTGC 4234776 29 96.6 32 .........................G... CGTCACTTTCTGACATTTTATTCAGTTCGTTA 4234837 29 96.6 32 ..........T.................. TCATTTCTGGACGGGGCTGTGTGACGAATACG 4234898 29 100.0 32 ............................. TGTCCAATTAACCCAAACTTTGCGCGCTTAAT 4234959 29 93.1 32 A............T............... GGATATGTGAAGTTCAGGTAGCCCATTACGCA 4235020 29 100.0 32 ............................. TTGATCGAGAGTGCGAAGAGGCAGAACGGGCA 4235081 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 4235142 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 4235203 29 100.0 32 ............................. CGTTCATCGGCAGCGTCACGCAATATGAAGAT 4235264 28 82.8 0 ...............A.AA....-.G... | ========== ====== ====== ====== ============================= ================================= ================== 25 29 98.2 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGTGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTAGAATGTGGTGCTGACAAAAAGTAGTTTATAAACAATTATATCCGTTTAGT # Right flank : GTTGCATAATCATAATCTGTGTACCAGTAATGGCAGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTAGACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGTCCGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAGCAGTCGAATCATCTGCCATCCCGATATTGCACGTGAACGTTATGCAGCAATGACTTTTCTTGGTATTACCCGAAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTATCGAATGATGTACACGCGTGACCCCCTGCCGATTGG # 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: 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 [0-10] 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 4251423-4253387 **** Predicted by CRISPRDetect 2.4 *** >NZ_OU015323.1 Salmonella enterica subsp. enterica serovar Typhimurium strain AUSMDU00004549 isolate AUSMDU00004549 chromosome C1, complete sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 4251423 29 96.6 32 ............................T CCCACCGCGCTGATTAACGACGGACTGTTACA 4251484 29 100.0 32 ............................. TGAGCAACGACAGTAAATAATTTTTCGTGCTG 4251545 29 100.0 32 ............................. AACCGCTGGCGGGCTGATTGGTCTGCAACCAC 4251606 29 100.0 32 ............................. CAACCAGGCTGGATCGTAACTCCTATCCCCTC 4251667 29 100.0 32 ............................. AAAATGCAGGTGGGGTAACGAATGCGAGATTG 4251728 29 100.0 32 ............................. CCATTATTCAACCCTCCAGGCTCGCGCCGGCT 4251789 29 100.0 33 ............................. CCAGTGGGCGTAGCCAGCTCATCGCTATTTTGC 4251851 29 100.0 32 ............................. CGTTGCGGATTATCGTTAAGACTGAAGGAAGT 4251912 29 100.0 32 ............................. CGTCACTACCGAGACCGAGACCGAGACCGAGA 4251973 29 100.0 32 ............................. CCGCTGACGCACTGGATCAACCTGACGCAACG 4252034 29 96.6 32 ..........................A.. TTGCAGGGCGATATTGTTGTTGGTGAATGGGA 4252095 29 100.0 32 ............................. CGTCGCGGAAAATTTCGCATTGACGATAAAGA 4252156 29 100.0 32 ............................. TTACGTGTTTATTCATCTGTTGCATTAGATTC 4252217 29 96.6 32 ............................T GAGGCGTACAGGCTGTTAGATGAGAAATTACC 4252278 29 100.0 32 ............................. ACGCCCCGAATGTGTTTGCCTCGCCCGCTGCC 4252339 29 100.0 32 ............................. ACGCCCCGAATGTGTTTGCCTCGCCCGCTGCC 4252400 29 100.0 32 ............................. TGGATTATCTGTATTTTACGGAAGTGGGCGCG 4252461 29 100.0 32 ............................. GTCGTTCATCAGGCACTACCGGCACTTTCTGG 4252522 29 100.0 32 ............................. ATATTCGCCGCTTTCCATTTACCGAACGTAAC 4252583 29 100.0 32 ............................. CCACGTTCGGCGATGTTGGCCCCATCGGTCCA 4252644 29 100.0 33 ............................. AAACGGTAGTGTTTTAAAACCGTTTCGAGGTGC 4252706 29 100.0 32 ............................. AATAAGGCGCGGTGCCACCCTCGGCTTTAATT 4252767 29 65.5 13 ..............GA..C.TTCC.G.GC ACGTTACTCGATC Deletion [4252809] 4252809 29 100.0 32 ............................. AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 4252870 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 4252931 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 4252992 29 100.0 32 ............................. GCACTATTTCGAATGTCTCGACGCCAGATTTA 4253053 29 100.0 32 ............................. AACGAATTGAGACTATTAGAGATTATTCGCCT 4253114 29 100.0 32 ............................. GCAACCCATTAATTAACTAAGCAGTAATAAAC 4253175 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 4253236 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 4253297 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 4253358 29 96.6 0 A............................ | A [4253384] ========== ====== ====== ====== ============================= ================================= ================== 33 29 98.4 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTGCTCGCTGCCGGTGAAATTGAACCACCTCAGCCTGCGCCGGATATGTTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTCGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTGCGTTTGGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : GTTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCG # Questionable array : NO Score: 6.13 # Score Detail : 1:0, 2:3, 3:0, 4:0.92, 5:0, 6:0.25, 7:-0.04, 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 [2-13] 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], //