Array 1 3126587-3125782 **** Predicted by CRISPRDetect 2.4 *** >NZ_CP040318.1 Salmonella enterica subsp. enterica serovar Rough O:-:- strain PNCS009887 chromosome, complete genome Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ========================================================================== ================== 3126586 29 100.0 32 ............................. TGAGCAACGACAGTAAATAATTTTTCGTGCTG 3126525 29 100.0 32 ............................. AACCGCTGGCGGGCTGATTGGTCTGCAACCAC 3126464 29 100.0 32 ............................. ATATTCGCCGCTTTCCATTTACCGAACGTAAC 3126403 29 100.0 32 ............................. CCACGTTCGGCGATGTTGGCCCCATCGGTCCA 3126342 29 100.0 33 ............................. AAACGGTAGTGTTTTAAAACCGTTTCGAGGTGC 3126280 29 100.0 74 ............................. AATAAGGCGCGGTGCCACCCTCGGCTTTAATTGTGTTCCCCGCGCCGACGCGTTCCAGCGCACGTTACTCGATC 3126177 29 100.0 32 ............................. AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 3126116 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 3126055 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 3125994 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 3125933 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 3125872 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 3125811 29 96.6 0 A............................ | A [3125784] ========== ====== ====== ====== ============================= ========================================================================== ================== 13 29 99.5 36 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTGCTCGCTGCCGGTGAAATTGAACCACCTCAGCCTGCGCCGGATATGTTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTCGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTGCGTTTGGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : TTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCGT # Questionable array : NO Score: 5.99 # Score Detail : 1:0, 2:3, 3:0, 4:0.97, 5:0, 6:0.25, 7:-0.23, 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 [3-0] 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], // Array 2 3145006-3142719 **** Predicted by CRISPRDetect 2.4 *** >NZ_CP040318.1 Salmonella enterica subsp. enterica serovar Rough O:-:- strain PNCS009887 chromosome, complete genome Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 3145005 29 100.0 32 ............................. TTTGCCGATCCCCTTCCAGACCACCCTTTACA 3144944 29 100.0 32 ............................. TGCAGAGTTGTATCTTACCCTGTTTACGTTTC 3144883 29 100.0 32 ............................. TTATCCCAATATATTTCGCTATCAGTTACATC 3144822 29 100.0 32 ............................. GCTCATTAAATAACTATATAACCCCCGGACTC 3144761 29 100.0 32 ............................. TTCCAGAACCGTTTGACTTACTGTGGCCATTA 3144700 29 100.0 32 ............................. GGCTTTGGTGAAGATTTCTGATTTGGTCATTT 3144639 29 100.0 32 ............................. GATCGGGTGGTGCCGGTGGGCCATGTGGCGCT 3144578 29 100.0 32 ............................. GCAGCGGTTGAGTAACTCCTCGTCCACGTCGA 3144517 29 100.0 32 ............................. CTCCAGCGCTCGAATTTATTTGAGGCCACCAC 3144456 29 100.0 32 ............................. TTTTGATACGTAGTATTCATTACGCCTCCTAG 3144395 29 100.0 32 ............................. GCGAGGTCAATAAAAAATGGTGTGGCTTTACC 3144334 29 100.0 32 ............................. CCGGCATCAGCGCCGATCCGTTCATAGTGCCC 3144273 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 3144212 29 100.0 32 ............................. CAGATCCTCAACGGTCAGGCTGTTTAGTTCCT 3144151 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 3144090 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 3144029 29 100.0 32 ............................. TGACGCTGGTCTATACCGGCAACGAACGCGAC 3143968 29 100.0 32 ............................. TGTCCAATTAACCCAAACTTTGCGCGCTTAAT 3143907 29 93.1 32 A............T............... GGATATGTGAAGTTCAGGTAGCCCATTACGCA 3143846 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 3143785 29 100.0 32 ............................. CCCCGATAGCGACGCTTCTGTAGTCACTGGCA 3143724 29 100.0 33 ............................. GTGAGTTCGGTTTTAATTTCGTCGCTAAGCTGC 3143662 29 96.6 32 .........................G... CGTCACTTTCTGACATTTTATTCAGTTCGTTA 3143601 29 96.6 32 ..........T.................. TCATTTCTGGACGGGGCTGTGTGACGAATACG 3143540 29 100.0 32 ............................. TTGACGGTGACGTCAGTGCCGAAGGCGAAATA 3143479 29 100.0 32 ............................. CCAGCTTACGCTATTTACGACGTTATTGAGCA 3143418 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 3143357 29 100.0 32 ............................. CCCCGATAGCGACGCTTCTGTAGTCACTGGCA 3143296 29 100.0 33 ............................. GTGAGTTCGGTTTTAATTTCGTCGCTAAGCTGC 3143234 29 96.6 32 .........................G... CGTCACTTTCTGACATTTTATTCAGTTCGTTA 3143173 29 96.6 32 ..........T.................. TCATTTCTGGACGGGGCTGTGTGACGAATACG 3143112 29 100.0 32 ............................. TGTCCAATTAACCCAAACTTTGCGCGCTTAAT 3143051 29 93.1 32 A............T............... GGATATGTGAAGTTCAGGTAGCCCATTACGCA 3142990 29 100.0 32 ............................. TTGATCGAGAGTGCGAAGAGGCAGAACGGGCA 3142929 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 3142868 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 3142807 29 100.0 32 ............................. CGTTCATCGGCAGCGTCACGCAATATGAAGAT 3142746 28 82.8 0 ...............A.AA.....G-... | ========== ====== ====== ====== ============================= ================================= ================== 38 29 98.4 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGTGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTAGAATGTGGTGCTGACAAAAAGTAGTTTATAAACAATTATATCCGTTTAGT # Right flank : TTGCATAATCATAATCTGTGTACCAGTAATGGCAGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTAGACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGTCCGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAGCAGTCGAATCATCTGCCATCCCGATATTGCACGTGAACGTTATGCAGCAATGACTTTTCTTGGTATTACCCGAAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTATCGAATGATGTACACGCGTGACCCCCTGCCGATTGGC # Questionable array : NO Score: 6.18 # Score Detail : 1:0, 2:3, 3:0, 4:0.92, 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: 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 [12-0] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [63.3-70.0]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0,5.65 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], //