Array 1 3068937-3066972 **** Predicted by CRISPRDetect 2.4 *** >NZ_CP019649.1 Salmonella enterica subsp. enterica serovar Typhimurium var. monophasic 4,5,12:i:- strain TW-Stm6 chromosome, complete genome Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ========================================================================== ================== 3068936 29 96.6 32 ............................T CCCACCGCGCTGATTAACGACGGACTGTTACA 3068875 29 100.0 32 ............................. TGAGCAACGACAGTAAATAATTTTTCGTGCTG 3068814 29 100.0 32 ............................. AACCGCTGGCGGGCTGATTGGTCTGCAACCAC 3068753 29 100.0 32 ............................. CAACCAGGCTGGATCGTAACTCCTATCCCCTC 3068692 29 100.0 32 ............................. AAAATGCAGGTGGGGTAACGAATGCGAGATTG 3068631 29 100.0 32 ............................. CCATTATTCAACCCTCCAGGCTCGCGCCGGCT 3068570 29 100.0 33 ............................. CCAGTGGGCGTAGCCAGCTCATCGCTATTTTGC 3068508 29 100.0 32 ............................. CGTTGCGGATTATCGTTAAGACTGAAGGAAGT 3068447 29 100.0 32 ............................. CGTCACTACCGAGACCGAGACCGAGACCGAGA 3068386 29 100.0 32 ............................. CCGCTGACGCACTGGATCAACCTGACGCAACG 3068325 29 100.0 32 ............................. TTGCAGGGCGATATTGTTGTTGGTGAATGGGA 3068264 29 100.0 32 ............................. CGTCGCGGAAAATTTCGCATTGACGATAAAGA 3068203 29 100.0 32 ............................. TTACGTGTTTATTCATCTGTTGCATTAGATTC 3068142 29 96.6 32 ............................T GAGGCGTACAGGCTGTTAGATGAGAAATTACC 3068081 29 100.0 32 ............................. ACGCCCCGAATGTGTTTGCCTCGCCCGCTGCC 3068020 29 100.0 32 ............................. ACGCCCCGAATGTGTTTGCCTCGCCCGCTGCC 3067959 29 100.0 32 ............................. TGGATTATCTGTATTTTACGGAAGTGGGCGCG 3067898 29 100.0 32 ............................. GTCGTTCATCAGGCACTACCGGCACTTTCTGG 3067837 29 100.0 32 ............................. ATATTCGCCGCTTTCCATTTACCGAACGTAAC 3067776 29 100.0 32 ............................. CCACGTTCGGCGATGTTGGCCCCATCGGTCCA 3067715 29 100.0 33 ............................. AAACGGTAGTGTTTTAAAACCGTTTCGAGGTGC 3067653 29 100.0 74 ............................. AATAAGGCGCGGTGCCACCCTCGGCTTTAATTGTGTTCCCCGCGCCGACGCGTTCCAGCGCACGTTACTCGATC 3067550 29 100.0 32 ............................. AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 3067489 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 3067428 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 3067367 29 100.0 32 ............................. GCACTATTTCGAATGTCTCGACGCCAGATTTA 3067306 29 100.0 32 ............................. AACGAATTGAGACTATTAGAGATTATTCGCCT 3067245 29 100.0 32 ............................. GCAACCCATTAATTAACTAAGCAGTAATAAAC 3067184 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 3067123 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 3067062 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 3067001 29 96.6 0 A............................ | A [3066974] ========== ====== ====== ====== ============================= ========================================================================== ================== 32 29 99.6 33 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTGCTCGCTGCCGGTGAAATTGAACCACCTCAGCCTGCGCCGGATATGTTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTCGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTGCGTTTGGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : TTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCGT # Questionable array : NO Score: 6.15 # Score Detail : 1:0, 2:3, 3:0, 4:0.98, 5:0, 6:0.25, 7:-0.08, 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 2 3086378-3085068 **** Predicted by CRISPRDetect 2.4 *** >NZ_CP019649.1 Salmonella enterica subsp. enterica serovar Typhimurium var. monophasic 4,5,12:i:- strain TW-Stm6 chromosome, complete genome Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 3086377 29 100.0 32 ............................. TTTTGATACGTAGTATTCATTACGCCTCCTAG 3086316 29 100.0 32 ............................. GCGAGGTCAATAAAAAATGGTGTGGCTTTACC 3086255 29 100.0 32 ............................. CCGGCATCAGCGCCGATCCGTTCATAGTGCCC 3086194 29 100.0 32 ............................. AAAAAACAGAAGAACGGCAAGCGGCACCTCAA 3086133 29 100.0 32 ............................. CGTCAGCGCGGTATTGAGGCCGGGGACCGCCC 3086072 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 3086011 29 100.0 32 ............................. CAGATCCTCAACGGTCAGGCTGTTTAGTTCCT 3085950 29 100.0 32 ............................. CGGAGGATGGAATATTTCCGAGGCTGGCGATT 3085889 29 96.6 32 .............T............... ATGCCGGAACGCTGATGGCGTTTGACATGAGC 3085828 29 100.0 32 ............................. CCAGCTTACGCTATTTACGACGTTATTGAGCA 3085767 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 3085706 29 100.0 32 ............................. CCCCGATAGCGACGCTTCTGTAGTCACTGGCA 3085645 29 100.0 33 ............................. GTGAGTTCGGTTTTAATTTCGTCGCTAAGCTGC 3085583 29 96.6 32 .........................G... CGTCACTTTCTGACATTTTATTCAGTTCGTTA 3085522 29 96.6 32 ..........T.................. TCATTTCTGGACGGGGCTGTGTGACGAATACG 3085461 29 100.0 32 ............................. TGTCCAATTAACCCAAACTTTGCGCGCTTAAT 3085400 29 93.1 32 A............T............... GGATATGTGAAGTTCAGGTAGCCCATTACGCA 3085339 29 100.0 32 ............................. TTGATCGAGAGTGCGAAGAGGCAGAACGGGCA 3085278 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 3085217 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 3085156 29 100.0 32 ............................. CGTTCATCGGCAGCGTCACGCAATATGAAGAT 3085095 28 82.8 0 ...............A.AA.....G-... | ========== ====== ====== ====== ============================= ================================= ================== 22 29 98.0 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGTGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTAGAATGTGGTGCTGACAAAAAGTAGTTTATAAACAATTATATCCGTTTAGT # Right flank : TTGCATAATCATAATCTGTGTACCAGTAATGGCAGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTAGACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGTCCGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAGCAGTCGAATCATCTGCCATCCCGATATTGCACGTGAACGTTATGCAGCAATGACTTTTCTTGGTATTACCCGAAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTATCGAATGATGTACACGCGTGACCCCCTGCCGATTGGC # Questionable array : NO Score: 6.16 # Score Detail : 1:0, 2:3, 3:0, 4:0.90, 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 [8-1] 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], //