Array 1 1-1778 **** Predicted by CRISPRDetect 2.4 *** >NZ_JYUY01000116.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N30693 N30693_contig_117, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 1 28 96.6 32 -............................ TGAGCAACGACAGTAAATAATTTTTCGTGCTG 61 29 100.0 32 ............................. AACCGCTGGCGGGCTGATTGGTCTGCAACCAC 122 29 100.0 32 ............................. CAACCAGGCTGGATCGTAACTCCTATCCCCTC 183 29 100.0 32 ............................. AAAATGCAGGTGGGGTAACGAATGCGAGATTG 244 29 100.0 33 ............................. CCAGTGGGCGTAGCCAGCTCATCGCTATTTTGC 306 29 100.0 32 ............................. CGTTGCGGATTATCGTTAAGACTGAAGGAAGT 367 29 100.0 32 ............................. CGTCACTACCGAGACCGAGACCGAGACCGAGA 428 29 100.0 32 ............................. CCGCTGACGCACTGGATCAACCTGACGCAACG 489 29 100.0 32 ............................. TTGCAGGGCGATATTGTTGTTGGTGAATGGGA 550 29 100.0 32 ............................. CGTCGCGGAAAATTTCGCATTGACGATAAAGA 611 29 100.0 32 ............................. TTACGTGTTTATTCATCTGTTGCATTAGATTC 672 29 96.6 32 ............................T GAGGCGTACAGGCTGTTAGATGAGAAATTACC 733 29 100.0 32 ............................. ACGCCCCGAATGTGTTTGCCTCGCCCGCTGCC 794 29 100.0 32 ............................. TGGATTATCTGTATTTTACGGAAGTGGGCGCG 855 29 100.0 32 ............................. GTCGTTCATCAGGCACTACCGGCACTTTCTGG 916 29 100.0 32 ............................. ATATTCGCCGCTTTCCATTTACCGAACGTAAC 977 29 100.0 32 ............................. CCACGTTCGGCGATGTTGGCCCCATCGGTCCA 1038 29 100.0 33 ............................. AAACGGTAGTGTTTTAAAACCGTTTCGAGGTGC 1100 29 100.0 32 ............................. AATAAGGCGCGGTGCCACCCTCGGCTTTAATT 1161 29 65.5 13 ..............GA..C.TTCC.G.GC ACGTTACTCGATC Deletion [1203] 1203 29 100.0 32 ............................. AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 1264 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 1325 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 1386 29 100.0 32 ............................. GCACTATTTCGAATGTCTCGACGCCAGATTTA 1447 29 100.0 32 ............................. AACGAATTGAGACTATTAGAGATTATTCGCCT 1508 29 100.0 32 ............................. GCAACCCATTAATTAACTAAGCAGTAATAAAC 1569 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 1630 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 1691 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 1752 27 89.7 0 A..........................-- | ========== ====== ====== ====== ============================= ================================= ================== 30 29 98.2 31 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : | # Right flank : | # Questionable array : NO Score: 6.12 # Score Detail : 1:0, 2:3, 3:0, 4:0.91, 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: 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 [1-13] 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], // Array 1 5052-3925 **** Predicted by CRISPRDetect 2.4 *** >NZ_JYUY01000112.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N30693 N30693_contig_113, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 5051 29 100.0 32 ............................. CAGATCCTCAACGGTCAGGCTGTTTAGTTCCT 4990 29 100.0 32 ............................. CGGAGGATGGAATATTTCCGAGGCTGGCGATT 4929 29 96.6 32 .............T............... ATGCCGGAACGCTGATGGCGTTTGACATGAGC 4868 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 4807 29 100.0 32 ............................. TGACGCTGGTCTATACCGGCAACGAACGCGAC 4746 29 100.0 32 ............................. TTGACGGTGACGTCAGTGCCGAAGGCGAAATA 4685 29 100.0 32 ............................. CCAGCTTACGCTATTTACGACGTTATTGAGCA 4624 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 4563 29 100.0 32 ............................. CCCCGATAGCGACGCTTCTGTAGTCACTGGCA 4502 29 100.0 33 ............................. GTGAGTTCGGTTTTAATTTCGTCGCTAAGCTGC 4440 29 96.6 32 .........................G... CGTCACTTTCTGACATTTTATTCAGTTCGTTA 4379 29 96.6 32 ..........T.................. TCATTTCTGGACGGGGCTGTGTGACGAATACG 4318 29 100.0 32 ............................. TGTCCAATTAACCCAAACTTTGCGCGCTTAAT 4257 29 93.1 32 A............T............... GGATATGTGAAGTTCAGGTAGCCCATTACGCA 4196 29 100.0 32 ............................. TTGATCGAGAGTGCGAAGAGGCAGAACGGGCA 4135 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 4074 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 4013 29 100.0 32 ............................. CGTTCATCGGCAGCGTCACGCAATATGAAGAT 3952 28 82.8 0 ...............A.AA.....G-... | ========== ====== ====== ====== ============================= ================================= ================== 19 29 97.7 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : CCAGCGGGGATAAACCGAACAGGAACAGGAAAAAAAAGATTTGTCCGG # Right flank : TTGCATAATCATAATCTGTGTACCAGTAATGGCAGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTAGACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGTCCGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAGCAGTCGAATCATCTGCCATCCCGATATTGCACGTGAACGTTATGCAGCAATGACTTTTCTTGGTATTACCCGAAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTATCGAATGATGTACACGCGTGACCCCCTGCCGATTGGC # Questionable array : NO Score: 6.15 # Score Detail : 1:0, 2:3, 3:0, 4:0.89, 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 [8-3] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [63.3-43.3]%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], //