Array 1 215176-213194 **** Predicted by CRISPRDetect 2.4 *** >NZ_JADDHQ010000003.1 Salmonella enterica subsp. enterica serovar Kentucky strain SGEHI2016-PSU-BS-159SL opera_scaffold_3, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 215175 29 100.0 32 ............................. TTTTTTATAAATCTGGCGAACCTGCACCCCCT 215114 29 100.0 32 ............................. CTCTCAGCCCCTCCGGGGCGCCCCGTGATAAT 215053 29 100.0 32 ............................. CATCCCCCCTCTTTTCCCCGGGTGTTTGTTGG 214992 29 100.0 32 ............................. ACGGTAGGAATATTCACGTTTTTTAAATCGGA 214931 29 100.0 32 ............................. ACGTGACCGCCGAAATGATTGCGGAAATCGCC 214870 29 100.0 32 ............................. CGCGCCCACCGTTCAGCCCTGGAAAAAGCGGC 214809 29 100.0 32 ............................. CCGCCTTCACCCAGCCCGCCGGACATCTGATC 214748 29 100.0 32 ............................. AGGGCTGGCTGACGCGCACCGAGCGCCGCAAC 214687 29 100.0 32 ............................. AAATTTATGAGGAAAATTATGTCAGACAGTAA 214626 29 100.0 32 ............................. AGGAGTTGTTAGGCCAACTGTATAACGATTTA 214565 29 100.0 32 ............................. AGATGACCATCCCACCAAGCAGGCGAAGAAAA 214504 29 100.0 32 ............................. GTGCCGCTGATTTTCGTAACGCCTCAATGTAT 214443 29 100.0 32 ............................. AAAAAACAATGGTTTTACCGTCCGGCTGAACA 214382 29 100.0 32 ............................. CCGATGATCCAGAAAGTCACAAATGCGAGGAG 214321 29 100.0 32 ............................. AGGGGTTCAGGGGCGAGCGGGCGTTAAAGCGC 214260 29 100.0 32 ............................. CAGACCAGGGAGTTTCTGGCCGAACTGGAGAG 214199 29 100.0 32 ............................. ATGTGCGCATTATTGCTAACCATAGAGACTCA 214138 29 100.0 32 ............................. GGCGACGGCACAAAACGCTCAAAACTCATAAC 214077 29 100.0 32 ............................. TGTTGGCTGGTAACCACCGCAGATCGTCACCT 214016 29 100.0 32 ............................. ACCAGGGGGTTTTTTCCACGTATCGCCGCTGC 213955 29 100.0 32 ............................. AACAGTGGTTTTAGGTTGTCGGTGCTGATCCC 213894 29 100.0 32 ............................. CCCTTTATCTTAGCCGCCAGAACCAGAACGCC 213833 29 100.0 32 ............................. GCCCCGATAGCGTCAACTACCAGGGCCTGCAA 213772 29 100.0 32 ............................. AATTCTTTTGCTTGCGCGTCGTTCATATCGAA 213711 29 100.0 32 ............................. GACAATCAGGGGGCGCTGGTTGACAGTATTAA 213650 29 100.0 32 ............................. TTAGTCAGGACGACTTTTACGGCTATGTAGGC 213589 29 100.0 32 ............................. CTATGAGCAACGATATCACCGCACTGGCGCAG 213528 29 100.0 32 ............................. CCGTAATGCTTTTATGTCCTCGCTTCGCTGCG 213467 29 96.6 32 ...................A......... GAGGTAAAACTAACTGGCCGCGTTGTCCGTCA 213406 29 100.0 32 ............................. TACGCCAGAGGAATGGCTTTCAGTGTTTTGGT 213345 29 100.0 32 ............................. ATATTTTGGCAACTCGTCGTACATTATCGCCA 213284 29 100.0 32 ............................. TGATATTTTTGGTTATTTGCGATTTAGTTTTT 213223 29 100.0 0 ............................. | A [213196] ========== ====== ====== ====== ============================= ================================ ================== 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 234911-232808 **** Predicted by CRISPRDetect 2.4 *** >NZ_JADDHQ010000003.1 Salmonella enterica subsp. enterica serovar Kentucky strain SGEHI2016-PSU-BS-159SL opera_scaffold_3, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 234910 29 100.0 32 ............................. AGAAAGATGCGTACGTTCAATGTCGAGCTTTT 234849 29 100.0 32 ............................. ACTGGCTAATCACGGTTAACGCCGTGCCGGTG 234788 29 100.0 32 ............................. CGGCCGGACTGATTTAACGAGGGGAATTTATG 234727 29 100.0 33 ............................. TTTTATCGTCGTAGCCTATTGCTAACTTGACGC 234665 29 100.0 32 ............................. CCGCTGACGCACTGGATCAACCTGACGCAACG 234604 29 100.0 32 ............................. TAATCTTTCAGCGCGTCCTGGCGGTCAACGAG 234543 29 100.0 32 ............................. TTGAGTGCCACGGCCAGAGCGGTAGCCATTAA 234482 29 100.0 32 ............................. AAAACGGGTTTGCGGAAGGCTGGAACGCCTGC 234421 29 100.0 32 ............................. GAGCGGATCCGGGATCGTCAGCACTCTGAACC 234360 29 100.0 32 ............................. CACGATTTTATGTGCCGCGTCGAGGCGTGGGC 234299 29 100.0 32 ............................. GCGACCAAACCATTCGGATTCCGTAGGGGACC 234238 29 100.0 32 ............................. ATTTCTTGCCTATAATTTCCGGTTCGACGCCA 234177 29 100.0 32 ............................. CACAGATCGCGAGTTTGCTGGGTATATCTGAA 234116 29 100.0 32 ............................. GGGAATGGCTGGATCTGGTGTTGGTTATTTGC 234055 29 100.0 32 ............................. CCGCCGCTGTTCTTCTGTGTCTGCTTTTGTCC 233994 29 96.6 32 ...C......................... GCAGTAATCCCGGGTATTCCGAGTTATATGAA 233933 29 100.0 32 ............................. GCGTCAACCAGTTCTGGCATACCCTCCTCTTC 233872 29 100.0 32 ............................. ATTAGCTGATAAATCATCCAACATGTCACTTA 233811 29 100.0 32 ............................. AGTCGCTGGCGGATGTGCGGCGCACCGAAGCC 233750 29 96.6 32 ..G.......................... CACATAACCCGGCGCGATGGCCGATACATCAT 233689 29 96.6 32 ..G.......................... CGAGAGATCATAGACCAATGGACTGAAAGACT 233628 29 96.6 32 ..G.......................... TTGCGCTGTTCTATTGGCGGCAATTCTCTGAA 233567 29 96.6 32 ..G.......................... AGTACGAGGCACTATTCGGCAAGAAACCGCAC 233506 29 96.6 32 ..G.......................... GGGGCATGTGCGAAATTTCGCTCCAGTTTGTT 233445 29 93.1 32 ..G.....................C.... GCTCAAAACTCGGATGGTATAGGCGTGGCGCA 233384 29 96.6 32 ..G.......................... GCAAGCCACAGCGCAAAAGAGGTCTATTCCTG 233323 29 96.6 32 ..G.......................... GCGCTTCCGCCAACTCTCATCCGTGAAACGGT 233262 29 96.6 32 ..G.......................... CGCCATAAACGCGACTCCGTCACACATCCGTA 233201 29 96.6 32 ..G.......................... ACGCGTTAAAACTGCGCTCAATGCAGACGGCC 233140 29 93.1 32 ..G........A................. CGGTTCGCCCGCTGCTCAGTCTCGCCGGAATG 233079 29 96.6 32 ..G.......................... GGGCATGAGTGCTACTGCTTTCAACCCGAAAG 233018 29 96.6 32 ..G.......................... ATAAATTATCGGGAAATCATAATCAGCGCCGC 232957 29 96.6 32 ..G.......................... AAAACCCTCAAATATGCGTAACGGGAGGCTGG 232896 29 96.6 32 ..G.......................... TGCGCCAACGACTGGAATTTTTGCGTGTAGCC 232835 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], //