Array 1 1133-2914 **** Predicted by CRISPRDetect 2.4 *** >NZ_JYTW01000022.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N29343 N29343_contig_22, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 1133 29 100.0 32 ............................. TGAGCAACGACAGTAAATAATTTTTCGTGCTG 1194 29 100.0 32 ............................. AACCGCTGGCGGGCTGATTGGTCTGCAACCAC 1255 29 100.0 32 ............................. CAACCAGGCTGGATCGTAACTCCTATCCCCTC 1316 29 100.0 32 ............................. AAAATGCAGGTGGGGTAACGAATGCGAGATTG 1377 29 100.0 33 ............................. CCAGTGGGCGTAGCCAGCTCATCGCTATTTTGC 1439 29 100.0 32 ............................. CGTTGCGGATTATCGTTAAGACTGAAGGAAGT 1500 29 100.0 32 ............................. CGTCACTACCGAGACCGAGACCGAGACCGAGA 1561 29 100.0 32 ............................. CCGCTGACGCACTGGATCAACCTGACGCAACG 1622 29 100.0 32 ............................. TTGCAGGGCGATATTGTTGTTGGTGAATGGGA 1683 29 100.0 32 ............................. CGTCGCGGAAAATTTCGCATTGACGATAAAGA 1744 29 100.0 32 ............................. TTACGTGTTTATTCATCTGTTGCATTAGATTC 1805 29 96.6 32 ............................T GAGGCGTACAGGCTGTTAGATGAGAAATTACC 1866 29 100.0 32 ............................. ACGCCCCGAATGTGTTTGCCTCGCCCGCTGCC 1927 29 100.0 32 ............................. TGGATTATCTGTATTTTACGGAAGTGGGCGCG 1988 29 100.0 32 ............................. GTCGTTCATCAGGCACTACCGGCACTTTCTGG 2049 29 100.0 32 ............................. ATATTCGCCGCTTTCCATTTACCGAACGTAAC 2110 29 100.0 32 ............................. CCACGTTCGGCGATGTTGGCCCCATCGGTCCA 2171 29 100.0 33 ............................. AAACGGTAGTGTTTTAAAACCGTTTCGAGGTGC 2233 29 100.0 32 ............................. AATAAGGCGCGGTGCCACCCTCGGCTTTAATT 2294 29 65.5 13 ..............GA..C.TTCC.G.GC ACGTTACTCGATC Deletion [2336] 2336 29 100.0 32 ............................. AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 2397 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 2458 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 2519 29 100.0 32 ............................. GCACTATTTCGAATGTCTCGACGCCAGATTTA 2580 29 100.0 32 ............................. AACGAATTGAGACTATTAGAGATTATTCGCCT 2641 29 100.0 32 ............................. GCAACCCATTAATTAACTAAGCAGTAATAAAC 2702 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 2763 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 2824 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 2885 29 96.6 0 A............................ | A [2911] ========== ====== ====== ====== ============================= ================================= ================== 30 29 98.5 31 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTGCTCGCTGCCGGTGAAATTGAACCACCTCAGCCTGCGCCGGATATGTTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTCGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTGCGTTTGGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : GTTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCG # Questionable array : NO Score: 6.14 # Score Detail : 1:0, 2:3, 3:0, 4:0.93, 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 [0-13] 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], // Array 1 90934-92426 **** Predicted by CRISPRDetect 2.4 *** >NZ_JYTW01000008.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N29343 N29343_contig_8, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 90934 29 100.0 32 ............................. TTTTGATACGTAGTATTCATTACGCCTCCTAG 90995 29 100.0 32 ............................. GCGAGGTCAATAAAAAATGGTGTGGCTTTACC 91056 29 100.0 32 ............................. CCGGCATCAGCGCCGATCCGTTCATAGTGCCC 91117 29 100.0 32 ............................. AAAAAACAGAAGAACGGCAAGCGGCACCTCAA 91178 29 100.0 32 ............................. CGTCAGCGCGGTATTGAGGCCGGGGACCGCCC 91239 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 91300 29 100.0 32 ............................. CAGATCCTCAACGGTCAGGCTGTTTAGTTCCT 91361 29 100.0 32 ............................. CGGAGGATGGAATATTTCCGAGGCTGGCGATT 91422 29 96.6 32 .............T............... ATGCCGGAACGCTGATGGCGTTTGACATGAGC 91483 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 91544 29 100.0 32 ............................. TGACGCTGGTCTATACCGGCAACGAACGCGAC 91605 29 100.0 32 ............................. TTGACGGTGACGTCAGTGCCGAAGGCGAAATA 91666 29 100.0 32 ............................. CCAGCTTACGCTATTTACGACGTTATTGAGCA 91727 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 91788 29 100.0 32 ............................. CCCCGATAGCGACGCTTCTGTAGTCACTGGCA 91849 29 100.0 33 ............................. GTGAGTTCGGTTTTAATTTCGTCGCTAAGCTGC 91911 29 96.6 32 .........................G... CGTCACTTTCTGACATTTTATTCAGTTCGTTA 91972 29 96.6 32 ..........T.................. TCATTTCTGGACGGGGCTGTGTGACGAATACG 92033 29 100.0 32 ............................. TGTCCAATTAACCCAAACTTTGCGCGCTTAAT 92094 29 93.1 32 A............T............... GGATATGTGAAGTTCAGGTAGCCCATTACGCA 92155 29 100.0 32 ............................. TTGATCGAGAGTGCGAAGAGGCAGAACGGGCA 92216 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 92277 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 92338 29 100.0 32 ............................. CGTTCATCGGCAGCGTCACGCAATATGAAGAT 92399 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], //