Array 1 1-1292 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHJZ01000028.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N48676 N48676_contig_28, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 1 28 96.6 32 -............................ TTGCAGGGCGATATTGTTGTTGGTGAATGGGA 61 29 100.0 32 ............................. CGTCGCGGAAAATTTCGCATTGACGATAAAGA 122 29 100.0 32 ............................. TTACGTGTTTATTCATCTGTTGCATTAGATTC 183 29 96.6 32 ............................T GAGGCGTACAGGCTGTTAGATGAGAAATTACC 244 29 100.0 32 ............................. ACGCCCCGAATGTGTTTGCCTCGCCCGCTGCC 305 29 100.0 32 ............................. TGGATTATCTGTATTTTACGGAAGTGGGCGCG 366 29 100.0 32 ............................. GTCGTTCATCAGGCACTACCGGCACTTTCTGG 427 29 100.0 32 ............................. ATATTCGCCGCTTTCCATTTACCGAACGTAAC 488 29 100.0 32 ............................. CCACGTTCGGCGATGTTGGCCCCATCGGTCCA 549 29 100.0 33 ............................. AAACGGTAGTGTTTTAAAACCGTTTCGAGGTGC 611 29 100.0 32 ............................. AATAAGGCGCGGTGCCACCCTCGGCTTTAATT 672 29 65.5 13 ..............GA..C.TTCC.G.GC ACGTTACTCGATC Deletion [714] 714 29 100.0 32 ............................. AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 775 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 836 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 897 29 100.0 32 ............................. GCACTATTTCGAATGTCTCGACGCCAGATTTA 958 29 100.0 32 ............................. AACGAATTGAGACTATTAGAGATTATTCGCCT 1019 29 100.0 32 ............................. GCAACCCATTAATTAACTAAGCAGTAATAAAC 1080 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 1141 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 1202 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 1263 29 96.6 0 A............................ | A [1289] ========== ====== ====== ====== ============================= ================================= ================== 22 29 97.8 31 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : | # Right flank : GTTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCG # Questionable array : NO Score: 6.07 # Score Detail : 1:0, 2:3, 3:0, 4:0.89, 5:0, 6:0.25, 7:-0.07, 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], // Array 1 1370-1 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHJZ01000069.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N48676 N48676_contig_69, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 1369 28 96.6 32 -............................ GCGAGGTCAATAAAAAATGGTGTGGCTTTACC 1309 29 100.0 32 ............................. CCGGCATCAGCGCCGATCCGTTCATAGTGCCC 1248 29 100.0 32 ............................. AAAAAACAGAAGAACGGCAAGCGGCACCTCAA 1187 29 100.0 32 ............................. CGTCAGCGCGGTATTGAGGCCGGGGACCGCCC 1126 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 1065 29 100.0 32 ............................. CAGATCCTCAACGGTCAGGCTGTTTAGTTCCT 1004 29 100.0 32 ............................. CGGAGGATGGAATATTTCCGAGGCTGGCGATT 943 29 96.6 32 .............T............... ATGCCGGAACGCTGATGGCGTTTGACATGAGC 882 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 821 29 100.0 32 ............................. TGACGCTGGTCTATACCGGCAACGAACGCGAC 760 29 100.0 32 ............................. TTGACGGTGACGTCAGTGCCGAAGGCGAAATA 699 29 100.0 32 ............................. CCAGCTTACGCTATTTACGACGTTATTGAGCA 638 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 577 29 100.0 32 ............................. CCCCGATAGCGACGCTTCTGTAGTCACTGGCA 516 29 100.0 33 ............................. GTGAGTTCGGTTTTAATTTCGTCGCTAAGCTGC 454 29 96.6 32 .........................G... CGTCACTTTCTGACATTTTATTCAGTTCGTTA 393 29 96.6 32 ..........T.................. TCATTTCTGGACGGGGCTGTGTGACGAATACG 332 29 100.0 32 ............................. TGTCCAATTAACCCAAACTTTGCGCGCTTAAT 271 29 93.1 32 A............T............... GGATATGTGAAGTTCAGGTAGCCCATTACGCA 210 29 100.0 32 ............................. TTGATCGAGAGTGCGAAGAGGCAGAACGGGCA 149 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 88 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 27 27 93.1 0 ...........................-- | ========== ====== ====== ====== ============================= ================================= ================== 23 29 98.4 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : | # Right flank : C # Questionable array : NO Score: 6.18 # Score Detail : 1:0, 2:3, 3:0, 4:0.92, 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 [6-2] 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: R [0,5.65 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], //