Array 1 7-1621 **** Predicted by CRISPRDetect 2.4 *** >NZ_JYXD01000025.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N38858 N38858_contig_25, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 7 29 100.0 32 ............................. TTTGCCGATCCCCTTCCAGACCACCCTTTACA 68 29 100.0 32 ............................. TGCAGAGTTGTATCTTACCCTGTTTACGTTTC 129 29 100.0 32 ............................. CTCCAGCGCTCGAATTTATTTGAGGCCACCAC 190 29 100.0 32 ............................. TTTTGATACGTAGTATTCATTACGCCTCCTAG 251 29 100.0 32 ............................. GCGAGGTCAATAAAAAATGGTGTGGCTTTACC 312 29 100.0 32 ............................. CCGGCATCAGCGCCGATCCGTTCATAGTGCCC 373 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 434 29 100.0 32 ............................. CAGATCCTCAACGGTCAGGCTGTTTAGTTCCT 495 29 100.0 32 ............................. CGGAGGATGGAATATTTCCGAGGCTGGCGATT 556 29 96.6 32 .............T............... ATGCCGGAACGCTGATGGCGTTTGACATGAGC 617 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 678 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 739 29 100.0 32 ............................. TGACGCTGGTCTATACCGGCAACGAACGCGAC 800 29 100.0 32 ............................. TTGACGGTGACGTCAGTGCCGAAGGCGAAATA 861 29 100.0 32 ............................. CCAGCTTACGCTATTTACGACGTTATTGAGCA 922 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 983 29 100.0 32 ............................. CCCCGATAGAGACGCTTCTGTAGTCACTGGCA 1044 29 100.0 33 ............................. GTGAGTTCGGTTTTAATTTCGTCGCTAAGCTGC 1106 29 96.6 32 .........................G... CGTCACTTTCTGACATTTTATTCAGTTCGTTA 1167 29 96.6 32 ..........T.................. TCATTTCTGGACGGGGCTGTGTGACGAATACG 1228 29 100.0 32 ............................. TGTCCAATTAACCCAAACTTTGCGCGCTTAAT 1289 29 93.1 32 A............T............... GGATATGTGAAGTTCAGGTAGCCCATTACGCA 1350 29 100.0 32 ............................. TTGATCGAGAGTGCGAAGAGGCAGAACGGGCA 1411 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 1472 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 1533 29 100.0 32 ............................. CGTTCATCGGCAGCGTCACGCAATATGAAGAT 1594 28 82.8 0 ...............A.AA....-.G... | ========== ====== ====== ====== ============================= ================================= ================== 27 29 98.3 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : TTTAGTG # Right flank : GTTGCATAATCATAATCTGTGTACCAGTAATGGCAGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTAGACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGTCCGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAGCAGTCGAATCATCTGCCATCCCGATATTGCACGTGAACGTTATGCAGCAATGACTTTTCTTGGTATTACCCGAAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTATCGAATGATGTACACGCGTGACCCCCTGCCGATTGG # Questionable array : NO Score: 6.17 # Score Detail : 1:0, 2:3, 3:0, 4:0.91, 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: F [5,4] Score: 0.37/0.37 # Reference repeat match prediction: F [matched GTGTTCCCCGCGCCAGCGGGGATAAACCG with 100% identity] Score: 4.5/4.5 # Secondary Structural analysis prediction: F [-13.50,-12.00] Score: 0.37/0.37 # Array degeneracy analysis prediction: F [0-10] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [8.3-63.3]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [5.65,0.27 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 1-1353 **** Predicted by CRISPRDetect 2.4 *** >NZ_JYXD01000042.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N38858 N38858_contig_42, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 1 28 96.6 32 -............................ CGTTGCGGATTATCGTTAAGACTGAAGGAAGT 61 29 100.0 32 ............................. TTGCAGGGCGATATTGTTGTTGGTGAATGGGA 122 29 100.0 32 ............................. CGTCGCGGAAAATTTCGCATTGACGATAAAGA 183 29 100.0 32 ............................. TTACGTGTTTATTCATCTGTTGCATTAGATTC 244 29 96.6 32 ............................T GAGGCGTACAGGCTGTTAGATGAGAAATTACC 305 29 100.0 32 ............................. ACGCCCCGAATGTGTTTGCCTCGCCCGCTGCC 366 29 100.0 32 ............................. TGGATTATCTGTATTTTACGGAAGTGGGCGCG 427 29 100.0 32 ............................. GTCGTTCATCAGGCACTACCGGCACTTTCTGG 488 29 100.0 32 ............................. ATATTCGCCGCTTTCCATTTACCGAACGTAAC 549 29 100.0 32 ............................. CCACGTTCGGCGATGTTGGCCCCATCGGTCCA 610 29 100.0 33 ............................. AAACGGTAGTGTTTTAAAACCGTTTCGAGGTGC 672 29 100.0 32 ............................. AATAAGGCGCGGTGCCACCCTCGGCTTTAATT 733 29 65.5 13 ..............GA..C.TTCC.G.GC ACGTTACTCGATC Deletion [775] 775 29 100.0 32 ............................. AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 836 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 897 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 958 29 100.0 32 ............................. GCACTATTTCGAATGTCTCGACGCCAGATTTA 1019 29 100.0 32 ............................. AACGAATTGAGACTATTAGAGATTATTCGCCT 1080 29 100.0 32 ............................. GCAACCCATTAATTAACTAAGCAGTAATAAAC 1141 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 1202 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 1263 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 1324 29 96.6 0 A............................ | A [1350] ========== ====== ====== ====== ============================= ================================= ================== 23 29 97.9 31 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : | # Right flank : GTTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCG # Questionable array : NO Score: 6.09 # Score Detail : 1:0, 2:3, 3:0, 4:0.90, 5:0, 6:0.25, 7:-0.06, 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: F [5,4] Score: 0.37/0.37 # Reference repeat match prediction: F [matched GTGTTCCCCGCGCCAGCGGGGATAAACCG with 100% identity] Score: 4.5/4.5 # Secondary Structural analysis prediction: F [-13.50,-12.00] Score: 0.37/0.37 # Array degeneracy analysis prediction: F [2-3] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [0.0-0.0]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [5.65,0 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], //