Array 1 19628-18151 **** Predicted by CRISPRDetect 2.4 *** >NZ_AYVJ01000210.1 Salmonella enterica subsp. enterica serovar Typhimurium var. Copenhagen str. 0084 isolate CFSAN001284 NODE_93_length_20508_cov_17.895554, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ========================================================================== ================== 19627 29 100.0 32 ............................. TGAGCAACGACAGTAAATAATTTTTCGTGCTG 19566 29 100.0 33 ............................. CCAGTGGGCGTAGCCAGCTCATCGCTATTTTGC 19504 29 100.0 32 ............................. CGTTGCGGATTATCGTTAAGACTGAAGGAAGT 19443 29 100.0 32 ............................. TTGCAGGGCGATATTGTTGTTGGTGAATGGGA 19382 29 100.0 32 ............................. CGTCGCGGAAAATTTCGCATTGACGATAAAGA 19321 29 100.0 32 ............................. TTACGTGTTTATTCATCTGTTGCATTAGATTC 19260 29 96.6 32 ............................T GAGGCGTACAGGCTGTTAGATGAGAAATTACC 19199 29 100.0 32 ............................. ACGCCCCGAATGTGTTTGCCTCGCCCGCTGCC 19138 29 100.0 32 ............................. TGGATTATCTGTATTTTACGGAAGTGGGCGCG 19077 29 100.0 32 ............................. GTCGTTCATCAGGCACTACCGGCACTTTCTGG 19016 29 100.0 32 ............................. ATATTCGCCGCTTTCCATTTACCGAACGTAAC 18955 29 100.0 32 ............................. CCACGTTCGGCGATGTTGGCCCCATCGGTCCA 18894 29 100.0 33 ............................. AAACGGTAGTGTTTTAAAACCGTTTCGAGGTGC 18832 29 100.0 74 ............................. AATAAGGCGCGGTGCCACCCTCGGCTTTAATTGTGTTCCCCGCGCCGACGCGTTCCAGCGCACGTTACTCGATC 18729 29 100.0 32 ............................. AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 18668 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 18607 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 18546 29 100.0 32 ............................. GCACTATTTCGAATGTCTCGACGCCAGATTTA 18485 29 100.0 32 ............................. AACGAATTGAGACTATTAGAGATTATTCGCCT 18424 29 100.0 32 ............................. GCAACCCATTAATTAACTAAGCAGTAATAAAC 18363 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 18302 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 18241 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 18180 29 96.6 0 A............................ | A [18153] ========== ====== ====== ====== ============================= ========================================================================== ================== 24 29 99.6 34 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTGCTCGCTGCCGGTGAAATTGAACCACCTCAGCCTGCGCCGGATATGTTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTCGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTGCGTTTGGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : TTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCGT # Questionable array : NO Score: 6.12 # Score Detail : 1:0, 2:3, 3:0, 4:0.98, 5:0, 6:0.25, 7:-0.11, 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: 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 [3-1] 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], // Array 1 88366-90285 **** Predicted by CRISPRDetect 2.4 *** >NZ_AYVJ01000044.1 Salmonella enterica subsp. enterica serovar Typhimurium var. Copenhagen str. 0084 isolate CFSAN001284 NODE_13_length_102578_cov_18.579910, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 88366 29 100.0 32 ............................. TTTGCCGATCCCCTTCCAGACCACCCTTTACA 88427 29 100.0 32 ............................. TGCAGAGTTGTATCTTACCCTGTTTACGTTTC 88488 29 100.0 32 ............................. TTATCCCAATATATTTCGCTATCAGTTACATC 88549 29 100.0 32 ............................. GCTCATTAAATAACTATATAACCCCCGGACTC 88610 29 100.0 32 ............................. TTCCAGAACCGTTTGACTTACTGTGGCCATTA 88671 29 100.0 32 ............................. GATCGGGTGGTGCCGGTGGGCCATGTGGCGCT 88732 29 100.0 32 ............................. GCAGCGGTTGAGTAACTCCTCGTCCACGTCGA 88793 29 100.0 32 ............................. CTCCAGCGCTCGAATTTATTTGAGGCCACCAC 88854 29 100.0 32 ............................. TTTTGATACGTAGTATTCATTACGCCTCCTAG 88915 29 100.0 32 ............................. GCGAGGTCAATAAAAAATGGTGTGGCTTTACC 88976 29 100.0 32 ............................. CCGGCATCAGCGCCGATCCGTTCATAGTGCCC 89037 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 89098 29 100.0 32 ............................. CAGATCCTCAACGGTCAGGCTGTTTAGTTCCT 89159 29 100.0 32 ............................. CGGAGGATGGAATATTTCCGAGGCTGGCGATT 89220 29 96.6 32 .............T............... ATGCCGGAACGCTGATGGCGTTTGACATGAGC 89281 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 89342 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 89403 29 100.0 32 ............................. TGACGCTGGTCTATACCGGCAACGAACGCGAC 89464 29 100.0 32 ............................. TTGACGGTGACGTCAGTGCCGAAGGCGAAATA 89525 29 100.0 32 ............................. CCAGCTTACGCTATTTACGACGTTATTGAGCA 89586 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 89647 29 100.0 32 ............................. CCCCGATAGAGACGCTTCTGTAGTCACTGGCA 89708 29 100.0 33 ............................. GTGAGTTCGGTTTTAATTTCGTCGCTAAGCTGC 89770 29 96.6 32 .........................G... CGTCACTTTCTGACATTTTATTCAGTTCGTTA 89831 29 96.6 32 ..........T.................. TCATTTCTGGACGGGGCTGTGTGACGAATACG 89892 29 100.0 32 ............................. TGTCCAATTAACCCAAACTTTGCGCGCTTAAT 89953 29 93.1 32 A............T............... GGATATGTGAAGTTCAGGTAGCCCATTACGCA 90014 29 100.0 32 ............................. TTGATCGAGAGTGCGAAGAGGCAGAACGGGCA 90075 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 90136 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 90197 29 100.0 32 ............................. CGTTCATCGGCAGCGTCACGCAATATGAAGAT 90258 28 82.8 0 ...............A.AA....-.G... | ========== ====== ====== ====== ============================= ================================= ================== 32 29 98.6 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGTGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTAGAATGTGGTGCTGACAAAAAGTAGTTTATAAACAATTATATCCGTTTAGT # Right flank : GTTGCATAATCATAATCTGTGTACCAGTAATGGCAGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTAGACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGTCCGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAGCAGTCGAATCATCTGCCATCCCGATATTGCACGTGAACGTTATGCAGCAATGACTTTTCTTGGTATTACCCGAAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTATCGAATGATGTACACGCGTGACCCCCTGCCGATTGG # Questionable array : NO Score: 6.19 # Score Detail : 1:0, 2:3, 3:0, 4:0.93, 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 [0-12] 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], //