Array 1 247796-245814 **** Predicted by CRISPRDetect 2.4 *** >NZ_JADDHU010000003.1 Salmonella enterica subsp. enterica serovar Kentucky strain SGEHI2016-PSU-BS-099SL opera_scaffold_3, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 247795 29 100.0 32 ............................. TTTTTTATAAATCTGGCGAACCTGCACCCCCT 247734 29 100.0 32 ............................. CTCTCAGCCCCTCCGGGGCGCCCCGTGATAAT 247673 29 100.0 32 ............................. CATCCCCCCTCTTTTCCCCGGGTGTTTGTTGG 247612 29 100.0 32 ............................. ACGGTAGGAATATTCACGTTTTTTAAATCGGA 247551 29 100.0 32 ............................. ACGTGACCGCCGAAATGATTGCGGAAATCGCC 247490 29 100.0 32 ............................. CGCGCCCACCGTTCAGCCCTGGAAAAAGCGGC 247429 29 100.0 32 ............................. CCGCCTTCACCCAGCCCGCCGGACATCTGATC 247368 29 100.0 32 ............................. AGGGCTGGCTGACGCGCACCGAGCGCCGCAAC 247307 29 100.0 32 ............................. AAATTTATGAGGAAAATTATGTCAGACAGTAA 247246 29 100.0 32 ............................. AGGAGTTGTTAGGCCAACTGTATAACGATTTA 247185 29 100.0 32 ............................. AGATGACCATCCCACCAAGCAGGCGAAGAAAA 247124 29 100.0 32 ............................. GTGCCGCTGATTTTCGTAACGCCTCAATGTAT 247063 29 100.0 32 ............................. AAAAAACAATGGTTTTACCGTCCGGCTGAACA 247002 29 100.0 32 ............................. CCGATGATCCAGAAAGTCACAAATGCGAGGAG 246941 29 100.0 32 ............................. AGGGGTTCAGGGGCGAGCGGGCGTTAAAGCGC 246880 29 100.0 32 ............................. CAGACCAGGGAGTTTCTGGCCGAACTGGAGAG 246819 29 100.0 32 ............................. ATGTGCGCATTATTGCTAACCATAGAGACTCA 246758 29 100.0 32 ............................. GGCGACGGCACAAAACGCTCAAAACTCATAAC 246697 29 100.0 32 ............................. TGTTGGCTGGTAACCACCGCAGATCGTCACCT 246636 29 100.0 32 ............................. ACCAGGGGGTTTTTTCCACGTATCGCCGCTGC 246575 29 100.0 32 ............................. AACAGTGGTTTTAGGTTGTCGGTGCTGATCCC 246514 29 100.0 32 ............................. CCCTTTATCTTAGCCGCCAGAACCAGAACGCC 246453 29 100.0 32 ............................. GCCCCGATAGCGTCAACTACCAGGGCCTGCAA 246392 29 100.0 32 ............................. AATTCTTTTGCTTGCGCGTCGTTCATATCGAA 246331 29 100.0 32 ............................. GACAATCAGGGGGCGCTGGTTGACAGTATTAA 246270 29 100.0 32 ............................. TTAGTCAGGACGACTTTTACGGCTATGTAGGC 246209 29 100.0 32 ............................. CTATGAGCAACGATATCACCGCACTGGCGCAG 246148 29 100.0 32 ............................. CCGTAATGCTTTTATGTCCTCGCTTCGCTGCG 246087 29 96.6 32 ...................A......... GAGGTAAAACTAACTGGCCGCGTTGTCCGTCA 246026 29 100.0 32 ............................. TACGCCAGAGGAATGGCTTTCAGTGTTTTGGT 245965 29 100.0 32 ............................. ATATTTTGGCAACTCGTCGTACATTATCGCCA 245904 29 100.0 32 ............................. TGATATTTTTGGTTATTTGCGATTTAGTTTTT 245843 29 100.0 0 ............................. | A [245816] ========== ====== ====== ====== ============================= ================================ ================== 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 267531-265428 **** Predicted by CRISPRDetect 2.4 *** >NZ_JADDHU010000003.1 Salmonella enterica subsp. enterica serovar Kentucky strain SGEHI2016-PSU-BS-099SL opera_scaffold_3, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 267530 29 100.0 32 ............................. AGAAAGATGCGTACGTTCAATGTCGAGCTTTT 267469 29 100.0 32 ............................. ACTGGCTAATCACGGTTAACGCCGTGCCGGTG 267408 29 100.0 32 ............................. CGGCCGGACTGATTTAACGAGGGGAATTTATG 267347 29 100.0 33 ............................. TTTTATCGTCGTAGCCTATTGCTAACTTGACGC 267285 29 100.0 32 ............................. CCGCTGACGCACTGGATCAACCTGACGCAACG 267224 29 100.0 32 ............................. TAATCTTTCAGCGCGTCCTGGCGGTCAACGAG 267163 29 100.0 32 ............................. TTGAGTGCCACGGCCAGAGCGGTAGCCATTAA 267102 29 100.0 32 ............................. AAAACGGGTTTGCGGAAGGCTGGAACGCCTGC 267041 29 100.0 32 ............................. GAGCGGATCCGGGATCGTCAGCACTCTGAACC 266980 29 100.0 32 ............................. CACGATTTTATGTGCCGCGTCGAGGCGTGGGC 266919 29 100.0 32 ............................. GCGACCAAACCATTCGGATTCCGTAGGGGACC 266858 29 100.0 32 ............................. ATTTCTTGCCTATAATTTCCGGTTCGACGCCA 266797 29 100.0 32 ............................. CACAGATCGCGAGTTTGCTGGGTATATCTGAA 266736 29 100.0 32 ............................. GGGAATGGCTGGATCTGGTGTTGGTTATTTGC 266675 29 100.0 32 ............................. CCGCCGCTGTTCTTCTGTGTCTGCTTTTGTCC 266614 29 96.6 32 ...C......................... GCAGTAATCCCGGGTATTCCGAGTTATATGAA 266553 29 100.0 32 ............................. GCGTCAACCAGTTCTGGCATACCCTCCTCTTC 266492 29 100.0 32 ............................. ATTAGCTGATAAATCATCCAACATGTCACTTA 266431 29 100.0 32 ............................. AGTCGCTGGCGGATGTGCGGCGCACCGAAGCC 266370 29 96.6 32 ..G.......................... CACATAACCCGGCGCGATGGCCGATACATCAT 266309 29 96.6 32 ..G.......................... CGAGAGATCATAGACCAATGGACTGAAAGACT 266248 29 96.6 32 ..G.......................... TTGCGCTGTTCTATTGGCGGCAATTCTCTGAA 266187 29 96.6 32 ..G.......................... AGTACGAGGCACTATTCGGCAAGAAACCGCAC 266126 29 96.6 32 ..G.......................... GGGGCATGTGCGAAATTTCGCTCCAGTTTGTT 266065 29 93.1 32 ..G.....................C.... GCTCAAAACTCGGATGGTATAGGCGTGGCGCA 266004 29 96.6 32 ..G.......................... GCAAGCCACAGCGCAAAAGAGGTCTATTCCTG 265943 29 96.6 32 ..G.......................... GCGCTTCCGCCAACTCTCATCCGTGAAACGGT 265882 29 96.6 32 ..G.......................... CGCCATAAACGCGACTCCGTCACACATCCGTA 265821 29 96.6 32 ..G.......................... ACGCGTTAAAACTGCGCTCAATGCAGACGGCC 265760 29 93.1 32 ..G........A................. CGGTTCGCCCGCTGCTCAGTCTCGCCGGAATG 265699 29 96.6 32 ..G.......................... GGGCATGAGTGCTACTGCTTTCAACCCGAAAG 265638 29 96.6 32 ..G.......................... ATAAATTATCGGGAAATCATAATCAGCGCCGC 265577 29 96.6 32 ..G.......................... AAAACCCTCAAATATGCGTAACGGGAGGCTGG 265516 29 96.6 32 ..G.......................... TGCGCCAACGACTGGAATTTTTGCGTGTAGCC 265455 28 79.3 0 ..G............A.AA.....G-... | ========== ====== ====== ====== ============================= ================================= ================== 35 29 97.7 32 GTATTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGCGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACTTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTAGAATGTGGTGCTGATAAAAAGTAGTTTATAAACAATGACATACGTTTAGT # Right flank : TTGCATAATCATAATCTGTGTACCAGTAATGGCAGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTAGACAGGAGAAGGCCATGGCGTTAAGGATCAGAGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGCCCGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAGCAGTCGAATCATCTGCCATCCCGATATTGCACGTGAACGTTATGCAGCAATGACTTTTCTTGGTATTACCCGAAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTATCGAATGATGTACACGCGTGACCCCCTGCCGATTGGC # 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], //