Array 1 90940-92311 **** Predicted by CRISPRDetect 2.4 *** >NZ_LINM01000003.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N46861 N46861_contig_3, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 90940 29 100.0 32 ............................. TTTTGATACGTAGTATTCATTACGCCTCCTAG 91001 29 100.0 32 ............................. GCGAGGTCAATAAAAAATGGTGTGGCTTTACC 91062 29 100.0 32 ............................. CCGGCATCAGCGCCGATCCGTTCATAGTGCCC 91123 29 100.0 32 ............................. AAAAAACAGAAGAACGGCAAGCGGCACCTCAA 91184 29 100.0 32 ............................. CGTCAGCGCGGTATTGAGGCCGGGGACCGCCC 91245 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 91306 29 100.0 32 ............................. CAGATCCTCAACGGTCAGGCTGTTTAGTTCCT 91367 29 100.0 32 ............................. CGGAGGATGGAATATTTCCGAGGCTGGCGATT 91428 29 96.6 32 .............T............... ATGCCGGAACGCTGATGGCGTTTGACATGAGC 91489 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 91550 29 100.0 32 ............................. TGACGCTGGTCTATACCGGCAACGAACGCGAC 91611 29 100.0 32 ............................. TTGACGGTGACGTCAGTGCCGAAGGCGAAATA 91672 29 100.0 32 ............................. CCAGCTTACGCTATTTACGACGTTATTGAGCA 91733 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 91794 29 100.0 32 ............................. CCCCGATAGCGACGCTTCTGTAGTCACTGGCA 91855 29 100.0 33 ............................. GTGAGTTCGGTTTTAATTTCGTCGCTAAGCTGC 91917 29 96.6 32 .........................G... CGTCACTTTCTGACATTTTATTCAGTTCGTTA 91978 29 96.6 32 ..........T.................. TCATTTCTGGACGGGGCTGTGTGACGAATACG 92039 29 100.0 32 ............................. TGTCCAATTAACCCAAACTTTGCGCGCTTAAT 92100 29 93.1 32 A............T............... GGATATGTGAAGTTCAGGTAGCCCATTACGCA 92161 29 100.0 32 ............................. TTGATCGAGAGTGCGAAGAGGCAGAACGGGCA 92222 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 92283 29 96.6 0 .................A........... | ========== ====== ====== ====== ============================= ================================= ================== 23 29 98.8 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGTGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTAGAATGTGGTGCTGACAAAAAGTAGTTTATAAACAATTATATCCGTTTAGT # Right flank : GACGAGTTCTGGAAATGGTTAGCTGATAAAGAGTGTTCCCCGCG # Questionable array : NO Score: 6.20 # Score Detail : 1:0, 2:3, 3:0, 4:0.94, 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 [0-5] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [70.0-36.7]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [5.92,0 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 215049-214836 **** Predicted by CRISPRDetect 2.4 *** >NZ_LINM01000012.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N46861 N46861_contig_12, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 215048 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 214987 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 214926 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 214865 29 93.1 0 A........A................... | A [214838] ========== ====== ====== ====== ============================= ================================ ================== 4 29 97.4 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : | # Right flank : TTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCGT # Questionable array : NO Score: 5.73 # Score Detail : 1:0, 2:3, 3:0, 4:0.87, 5:0, 6:0.25, 7:0.01, 8:0.6, 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 [50.0-0.0]%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], // Array 1 16209-16848 **** Predicted by CRISPRDetect 2.4 *** >NZ_LINM01000060.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N46861 N46861_contig_60, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 16209 29 100.0 32 ............................. TGAGCAACGACAGTAAATAATTTTTCGTGCTG 16270 29 100.0 32 ............................. AACCGCTGGCGGGCTGATTGGTCTGCAACCAC 16331 29 100.0 32 ............................. CAACCAGGCTGGATCGTAACTCCTATCCCCTC 16392 29 100.0 32 ............................. AAAATGCAGGTGGGGTAACGAATGCGAGATTG 16453 29 100.0 33 ............................. CCAGTGGGCGTAGCCAGCTCATCGCTATTTTGC 16515 29 100.0 32 ............................. CGTTGCGGATTATCGTTAAGACTGAAGGAAGT 16576 29 100.0 32 ............................. CGTCACTACCGAGACCGAGACCGAGACCGAGA 16637 29 100.0 32 ............................. CCGCTGACGCACTGGATCAACCTGACGCAACG 16698 29 100.0 32 ............................. TTGCAGGGCGATATTGTTGTTGGTGAATGGGA 16759 29 100.0 32 ............................. CGTCGCGGAAAATTTCGCATTGACGATAAAGA 16820 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================= ================== 11 29 100.0 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTGCTCGCTGCCGGTGAAATTGAACCACCTCAGCCTGCGCCGGATATGTTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTCGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTGCGTTTGGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : TTACGTGTTTATTCATCTGTTGCATTAGATTCGTGTTCCCCGCGCCAGCG # 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: 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: NA [0-0] Score: 0/0.41 # AT richness analysis in flanks prediction: F [71.7-43.3]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [5.51,0 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 1-682 **** Predicted by CRISPRDetect 2.4 *** >NZ_LINM01000062.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N46861 N46861_contig_62, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 1 29 100.0 32 ............................. GTCGTTCATCAGGCACTACCGGCACTTTCTGG 62 29 100.0 32 ............................. ATATTCGCCGCTTTCCATTTACCGAACGTAAC 123 29 100.0 32 ............................. CCACGTTCGGCGATGTTGGCCCCATCGGTCCA 184 29 100.0 33 ............................. AAACGGTAGTGTTTTAAAACCGTTTCGAGGTGC 246 29 100.0 32 ............................. AATAAGGCGCGGTGCCACCCTCGGCTTTAATT 307 29 65.5 13 ..............GA..C.TTCC.G.GC ACGTTACTCGATC Deletion [349] 349 29 100.0 32 ............................. AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 410 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 471 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 532 29 100.0 32 ............................. GCACTATTTCGAATGTCTCGACGCCAGATTTA 593 29 100.0 32 ............................. AACGAATTGAGACTATTAGAGATTATTCGCCT 654 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================= ================== 12 29 97.1 30 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : | # Right flank : GCAACCCATTAATTAACTAAGCAGTAATAAACGTGTTCCCCGCGCCAGC # Questionable array : NO Score: 5.96 # Score Detail : 1:0, 2:3, 3:0, 4:0.85, 5:0, 6:0.25, 7:-0.14, 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: NA [0-0] Score: 0/0.41 # AT richness analysis in flanks prediction: R [0.0-43.3]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [5.24,0.27 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], //