Array 1 215239-213257 **** Predicted by CRISPRDetect 2.4 *** >NZ_JAHQJI010000003.1 Salmonella enterica subsp. enterica serovar Kentucky strain K2011/14 NODE_3_length_749808_cov_33.269472, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 215238 29 100.0 32 ............................. TTTTTTATAAATCTGGCGAACCTGCACCCCCT 215177 29 100.0 32 ............................. CTCTCAGCCCCTCCGGGGCGCCCCGTGATAAT 215116 29 100.0 32 ............................. CATCCCCCCTCTTTTCCCCGGGTGTTTGTTGG 215055 29 100.0 32 ............................. ACGGTAGGAATATTCACGTTTTTTAAATCGGA 214994 29 100.0 32 ............................. ACGTGACCGCCGAAATGATTGCGGAAATCGCC 214933 29 100.0 32 ............................. CGCGCCCACCGTTCAGCCCTGGAAAAAGCGGC 214872 29 100.0 32 ............................. CCGCCTTCACCCAGCCCGCCGGACATCTGATC 214811 29 100.0 32 ............................. AGGGCTGGCTGACGCGCACCGAGCGCCGCAAC 214750 29 100.0 32 ............................. AAATTTATGAGGAAAATTATGTCAGACAGTAA 214689 29 100.0 32 ............................. AGGAGTTGTTAGGCCAACTGTATAACGATTTA 214628 29 100.0 32 ............................. AGATGACCATCCCACCAAGCAGGCGAAGAAAA 214567 29 100.0 32 ............................. GTGCCGCTGATTTTCGTAACGCCTCAATGTAT 214506 29 100.0 32 ............................. AAAAAACAATGGTTTTACCGTCCGGCTGAACA 214445 29 100.0 32 ............................. CCGATGATCCAGAAAGTCACAAATGCGAGGAG 214384 29 100.0 32 ............................. AGGGGTTCAGGGGCGAGCGGGCGTTAAAGCGC 214323 29 100.0 32 ............................. CAGACCAGGGAGTTTCTGGCCGAACTGGAGAG 214262 29 100.0 32 ............................. ATGTGCGCATTATTGCTAACCATAGAGACTCA 214201 29 100.0 32 ............................. GGCGACGGCACAAAACGCTCAAAACTCATAAC 214140 29 100.0 32 ............................. TGTTGGCTGGTAACCACCGCAGATCGTCACCT 214079 29 100.0 32 ............................. ACCAGGGGGTTTTTTCCACGTATCGCCGCTGC 214018 29 100.0 32 ............................. AACAGTGGTTTTAGGTTGTCGGTGCTGATCCC 213957 29 100.0 32 ............................. CCCTTTATCTTAGCCGCCAGAACCAGAACGCC 213896 29 100.0 32 ............................. GCCCCGATAGCGTCAACTACCAGGGCCTGCAA 213835 29 100.0 32 ............................. AATTCTTTTGCTTGCGCGTCGTTCATATCGAA 213774 29 100.0 32 ............................. GACAATCAGGGGGCGCTGGTTGACAGTATTAA 213713 29 100.0 32 ............................. TTAGTCAGGACGACTTTTACGGCTATGTAGGC 213652 29 100.0 32 ............................. CTATGAGCAACGATATCACCGCACTGGCGCAG 213591 29 100.0 32 ............................. CCGTAATGCTTTTATGTCCTCGCTTCGCTGCG 213530 29 96.6 32 ...................A......... GAGGTAAAACTAACTGGCCGCGTTGTCCGTCA 213469 29 100.0 32 ............................. TACGCCAGAGGAATGGCTTTCAGTGTTTTGGT 213408 29 100.0 32 ............................. ATATTTTGGCAACTCGTCGTACATTATCGCCA 213347 29 100.0 32 ............................. TGATATTTTTGGTTATTTGCGATTTAGTTTTT 213286 29 100.0 0 ............................. | A [213259] ========== ====== ====== ====== ============================= ================================ ================== 33 29 99.9 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : CTTATTGAAGATGTTCTCGCGGCAGGGGAAATTCAACCGCCGTTACCTCCTGAAGATTCACAACCCATAGCGATCCCTCTTCCTGTTGCGTTGGGAGATTCCGGTCATCGGAGTACCTAACGATGAGTATGCTGGTTGTCGTTACCGAAAATGTTCCTCCTCGTCTGCGGGGGAGGCTGGCCGTCTGGTTACTGGAAATTCGAGCTGGTGTGTATGTTGGTGATGTTTCCGCAAAGATCCGCGAGATGATATGGCAACAGGTTTCCGTTCTGGCAGATGAGGGAAATGTTGTTATGGCGTGGGCGACAAATACAGAATCAGGTTTTGAGTTTCAGACTTTTGGTGTAAATCGACGTATTCCGGTAGATCTTGATGGACTGCGATTGGTGTCGTTTCTACCTGTTGAAAATCAATAAGTTATAGATCTTTAAAAATTAGGAAAAGTTGGTGGGTTTTTTGTGCGCTAAAAAAGTATTTAAATTCAATTGGGTAGATTTAGA # Right flank : TTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCTCAGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTGCCGTTCGGGAAGGATGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACCGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATACCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCAGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATCACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCGT # Questionable array : NO Score: 6.26 # Score Detail : 1:0, 2:3, 3:0, 4:1.00, 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 [2-0] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [50.0-70.0]%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 234974-232871 **** Predicted by CRISPRDetect 2.4 *** >NZ_JAHQJI010000003.1 Salmonella enterica subsp. enterica serovar Kentucky strain K2011/14 NODE_3_length_749808_cov_33.269472, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 234973 29 100.0 32 ............................. AGAAAGATGCGTACGTTCAATGTCGAGCTTTT 234912 29 100.0 32 ............................. ACTGGCTAATCACGGTTAACGCCGTGCCGGTG 234851 29 100.0 32 ............................. CGGCCGGACTGATTTAACGAGGGGAATTTATG 234790 29 100.0 33 ............................. TTTTATCGTCGTAGCCTATTGCTAACTTGACGC 234728 29 100.0 32 ............................. CCGCTGACGCACTGGATCAACCTGACGCAACG 234667 29 100.0 32 ............................. TAATCTTTCAGCGCGTCCTGGCGGTCAACGAG 234606 29 100.0 32 ............................. TTGAGTGCCACGGCCAGAGCGGTAGCCATTAA 234545 29 100.0 32 ............................. AAAACGGGTTTGCGGAAGGCTGGAACGCCTGC 234484 29 100.0 32 ............................. GAGCGGATCCGGGATCGTCAGCACTCTGAACC 234423 29 100.0 32 ............................. CACGATTTTATGTGCCGCGTCGAGGCGTGGGC 234362 29 100.0 32 ............................. GCGACCAAACCATTCGGATTCCGTAGGGGACC 234301 29 100.0 32 ............................. ATTTCTTGCCTATAATTTCCGGTTCGACGCCA 234240 29 100.0 32 ............................. CACAGATCGCGAGTTTGCTGGGTATATCTGAA 234179 29 100.0 32 ............................. GGGAATGGCTGGATCTGGTGTTGGTTATTTGC 234118 29 100.0 32 ............................. CCGCCGCTGTTCTTCTGTGTCTGCTTTTGTCC 234057 29 96.6 32 ...C......................... GCAGTAATCCCGGGTATTCCGAGTTATATGAA 233996 29 100.0 32 ............................. GCGTCAACCAGTTCTGGCATACCCTCCTCTTC 233935 29 100.0 32 ............................. ATTAGCTGATAAATCATCCAACATGTCACTTA 233874 29 100.0 32 ............................. AGTCGCTGGCGGATGTGCGGCGCACCGAAGCC 233813 29 96.6 32 ..G.......................... CACATAACCCGGCGCGATGGCCGATACATCAT 233752 29 96.6 32 ..G.......................... CGAGAGATCATAGACCAATGGACTGAAAGACT 233691 29 96.6 32 ..G.......................... TTGCGCTGTTCTATTGGCGGCAATTCTCTGAA 233630 29 96.6 32 ..G.......................... AGTACGAGGCACTATTCGGCAAGAAACCGCAC 233569 29 96.6 32 ..G.......................... GGGGCATGTGCGAAATTTCGCTCCAGTTTGTT 233508 29 93.1 32 ..G.....................C.... GCTCAAAACTCGGATGGTATAGGCGTGGCGCA 233447 29 96.6 32 ..G.......................... GCAAGCCACAGCGCAAAAGAGGTCTATTCCTG 233386 29 96.6 32 ..G.......................... GCGCTTCCGCCAACTCTCATCCGTGAAACGGT 233325 29 96.6 32 ..G.......................... CGCCATAAACGCGACTCCGTCACACATCCGTA 233264 29 96.6 32 ..G.......................... ACGCGTTAAAACTGCGCTCAATGCAGACGGCC 233203 29 93.1 32 ..G........A................. CGGTTCGCCCGCTGCTCAGTCTCGCCGGAATG 233142 29 96.6 32 ..G.......................... GGGCATGAGTGCTACTGCTTTCAACCCGAAAG 233081 29 96.6 32 ..G.......................... ATAAATTATCGGGAAATCATAATCAGCGCCGC 233020 29 96.6 32 ..G.......................... AAAACCCTCAAATATGCGTAACGGGAGGCTGG 232959 29 96.6 32 ..G.......................... TGCGCCAACGACTGGAATTTTTGCGTGTAGCC 232898 28 79.3 0 ..G............A.AA.....G-... | ========== ====== ====== ====== ============================= ================================= ================== 35 29 97.7 32 GTATTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGCGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACTTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTAGAATGTGGTGCTGATAAAAAGTAGTTTATAAACAATGACATACGTTTAGT # Right flank : TTGCATAATCATAATCTGTGTACCAGTAATGGCAGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTAGACAGGAGAAGGCCATGGCGCTAAGGATCAGAGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGCCCGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAGCAGTCGAATCATCTGCCATCCCGATATTGCACGTGAACGTTATGCAGCAATGACTTTTCTTGGTATTACCCGAAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTATCGAATGATGTACACGCGTGACCCCCTGCCGATTGGC # Questionable array : NO Score: 5.93 # Score Detail : 1:0, 2:3, 3:0, 4:0.89, 5:0, 6:0.25, 7:0.01, 8:1, 9:0.78, # 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 : GTATTCCCCGCGCCAGCGGGGATAAACCG # Alternate repeat : GTGTTCCCCGCGCCAGCGGGGATAAACCG # Directional analysis summary from each method: # Motif ATTGAAA(N) match prediction: NA Score: 0/4.5 # A,T distribution in repeat prediction: R [4,6] Score: 0.37/0.37 # Reference repeat match prediction: R [matched GTATTCCCCGCGCCAGCGGGGATAAACCG 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 [10-0] 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], //