Array 1 2077-52 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHKA01000013.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N48677 N48677_contig_13, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 2076 29 100.0 32 ............................. TTTTGATACGTAGTATTCATTACGCCTCCTAG 2015 29 100.0 32 ............................. GCGAGGTCAATAAAAAATGGTGTGGCTTTACC 1954 29 100.0 32 ............................. CCGGCATCAGCGCCGATCCGTTCATAGTGCCC 1893 29 100.0 32 ............................. AAAAAACAGAAGAACGGCAAGCGGCACCTCAA 1832 29 100.0 32 ............................. CGTCAGCGCGGTATTGAGGCCGGGGACCGCCC 1771 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 1710 29 100.0 32 ............................. CAGATCCTCAACGGTCAGGCTGTTTAGTTCCT 1649 29 100.0 32 ............................. CGGAGGATGGAATATTTCCGAGGCTGGCGATT 1588 29 96.6 32 .............T............... ATGCCGGAACGCTGATGGCGTTTGACATGAGC 1527 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 1466 29 100.0 32 ............................. TGACGCTGGTCTATACCGGCAACGAACGCGAC 1405 29 100.0 32 ............................. TTGACGGTGACGTCAGTGCCGAAGGCGAAATA 1344 29 100.0 32 ............................. CCAGCTTACGCTATTTACGACGTTATTGAGCA 1283 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 1222 29 100.0 32 ............................. CCCCGATAGCGACGCTTCTGTAGTCACTGGCA 1161 29 100.0 33 ............................. GTGAGTTCGGTTTTAATTTCGTCGCTAAGCTGC 1099 29 96.6 32 .........................G... CGTCACTTTCTGACATTTTATTCAGTTCGTTA 1038 29 96.6 32 ..........T.................. TCATTTCTGGACGGGGCTGTGTGACGAATACG 977 29 100.0 32 ............................. TGTCCAATTAACCCAAACTTTGCGCGCTTAAT 916 29 93.1 32 A............T............... GGATATGTGAAGTTCAGGTAGCCCATTACGCA 855 29 100.0 32 ............................. TTGATCGAGAGTGCGAAGAGGCAGAACGGGCA 794 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 733 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 672 29 100.0 32 ............................. TTACGTGTTTATTCATCTGTTGCATTAGATTC 611 29 96.6 32 ............................T GAGGCGTACAGGCTGTTAGATGAGAAATTACC 550 29 100.0 32 ............................. ACGCCCCGAATGTGTTTGCCTCGCCCGCTGCC 489 29 100.0 32 ............................. TGGATTATCTGTATTTTACGGAAGTGGGCGCG 428 29 100.0 32 ............................. GTCGTTCATCAGGCACTACCGGCACTTTCTGG 367 29 100.0 32 ............................. ATATTCGCCGCTTTCCATTTACCGAACGTAAC 306 29 100.0 32 ............................. CCACGTTCGGCGATGTTGGCCCCATCGGTCCA 245 29 100.0 33 ............................. AAACGGTAGTGTTTTAAAACCGTTTCGAGGTGC 183 29 100.0 32 ............................. AATAAGGCGCGGTGCCACCCTCGGCTTTAATT 122 29 65.5 13 ..............GA..C.TTCC.G.GC ACGTTACTCGATC Deletion [81] 80 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================= ================== 34 29 98.1 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGTGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTAGAATGTGGTGCTGACAAAAAGTAGTTTATAAACAATTATATCCGTTTAGT # Right flank : GAGCCGTTTCCGCTAAATACCCCCGCAGTGATTGTGTTCCCCGCGCCAGCGG # Questionable array : NO Score: 6.11 # Score Detail : 1:0, 2:3, 3:0, 4:0.90, 5:0, 6:0.25, 7:-0.04, 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 [11-1] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [31.7-70.0]%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 1 161379-160866 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHKA01000014.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N48677 N48677_contig_14, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 161378 24 82.8 32 -----........................ TTCTTGAATATGATTGCGGGTATATGTGGATA 161322 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 161261 29 100.0 32 ............................. GCACTATTTCGAATGTCTCGACGCCAGATTTA 161200 29 100.0 32 ............................. AACGAATTGAGACTATTAGAGATTATTCGCCT 161139 29 100.0 32 ............................. GCAACCCATTAATTAACTAAGCAGTAATAAAC 161078 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 161017 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 160956 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 160895 29 96.6 0 A............................ | A [160868] ========== ====== ====== ====== ============================= ================================ ================== 9 29 97.3 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : TGT # Right flank : TTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCGT # Questionable array : NO Score: 6.12 # Score Detail : 1:0, 2:3, 3:0, 4:0.86, 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 [3-1] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [50.0-5.0]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0.27,5.65 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], //