Array 1 1348-38 **** Predicted by CRISPRDetect 2.4 *** >NZ_VCXL02000018.1 Salmonella enterica subsp. enterica serovar Typhimurium strain HIY0061 NODE_18_length_99418_cov_32.041162, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 1347 29 100.0 32 ............................. TTTGCCGATCCCCTTCCAGACCACCCTTTACA 1286 29 100.0 32 ............................. TGCAGAGTTGTATCTTACCCTGTTTACGTTTC 1225 29 100.0 32 ............................. TTATCCCAATATATTTCGCTATCAGTTACATC 1164 29 100.0 32 ............................. GACTGTTTATACCGGATTCCATGCGTTTTCAG 1103 29 100.0 32 ............................. GAATTACTGGCTAACGACGAACTGACAGTTGA 1042 29 100.0 32 ............................. CCGGACCTAAACCTGAAAAAACCGACGCCCAA 981 29 100.0 32 ............................. GCTCATTAAATAACTATATAACCCCCGGACTC 920 29 100.0 32 ............................. TTCCAGAACCGTTTGACTTACTGTGGCCATTA 859 29 100.0 32 ............................. GGCTTTGGTGAAGATTTCTGATTTGGTCATTT 798 29 100.0 32 ............................. GATCGGGTGGTGCCGGTGGGCCATGTGGCGCT 737 29 100.0 32 ............................. GCAGCGGTTGAGTAACTCCTCGTCCACGTCGA 676 29 100.0 32 ............................. CTCCAGCGCTCGAATTTATTTGAGGCCACCAC 615 29 100.0 32 ............................. TTTTGATACGTAGTATTCATTACGCCTCCTAG 554 29 100.0 32 ............................. GCGAGGTCAATAAAAAATGGTGTGGCTTTACC 493 29 100.0 32 ............................. CCGGCATCAGCGCCGATCCGTTCATAGTGCCC 432 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 371 29 100.0 32 ............................. CAGATCCTCAACGGTCAGGCTGTTTAGTTCCT 310 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 249 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 188 29 100.0 32 ............................. TGACGCTGGTCTATACCGGCAACGAACGCGAC 127 29 100.0 32 ............................. TGTCCAATTAACCCAAACTTTGCGCGCTTAAT 66 29 93.1 0 A............T............... | ========== ====== ====== ====== ============================= ================================ ================== 22 29 99.7 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGTGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTAGAATGTGGTGCTGACAAAAAGTAGTTTATAAACAATTATATCCGTTTAGT # Right flank : GGGATATGTGAAGTTCAGGTAGCCCATTACGCAGTGTT # Questionable array : NO Score: 6.25 # Score Detail : 1:0, 2:3, 3:0, 4:0.99, 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 [2-0] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [33.3-70.0]%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 1 617-38 **** Predicted by CRISPRDetect 2.4 *** >NZ_VCXL02000052.1 Salmonella enterica subsp. enterica serovar Typhimurium strain HIY0061 NODE_52_length_652_cov_41.737143, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 616 29 96.6 32 ..........T.................. TCATTTCTGGACGGGGCTGTGTGACGAATACG 555 29 100.0 32 ............................. TTGACGGTGACGTCAGTGCCGAAGGCGAAATA 494 29 100.0 32 ............................. CCAGCTTACGCTATTTACGACGTTATTGAGCA 433 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 372 29 100.0 32 ............................. CCCCGATAGCGACGCTTCTGTAGTCACTGGCA 311 29 100.0 33 ............................. GTGAGTTCGGTTTTAATTTCGTCGCTAAGCTGC 249 29 96.6 32 .........................G... CGTCACTTTCTGACATTTTATTCAGTTCGTTA 188 29 96.6 32 ..........T.................. TCATTTCTGGACGGGGCTGTGTGACGAATACG 127 29 100.0 32 ............................. TGTCCAATTAACCCAAACTTTGCGCGCTTAAT 66 29 93.1 0 A............T............... | ========== ====== ====== ====== ============================= ================================= ================== 10 29 97.6 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GCCGCGTCACTTTCTGACATTTTATTCAGTTCGTT # Right flank : GGGATATGTGAAGTTCAGGTAGCCCATTACGCAGTGTT # Questionable array : NO Score: 6.06 # Score Detail : 1:0, 2:3, 3:0, 4:0.88, 5:0, 6:0.25, 7:0.01, 8:1, 9:0.92, # 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 : GTGTTCCCCGTGCCAGCGGGGATAAACCG # 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: NA [3-3] Score: 0/0.41 # AT richness analysis in flanks prediction: NA [33.3-35.0]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0,5.24 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 260962-260157 **** Predicted by CRISPRDetect 2.4 *** >NZ_VCXL02000005.1 Salmonella enterica subsp. enterica serovar Typhimurium strain HIY0061 NODE_5_length_277487_cov_31.345374, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ========================================================================== ================== 260961 29 100.0 32 ............................. TGAGCAACGACAGTAAATAATTTTTCGTGCTG 260900 29 100.0 32 ............................. AACCGCTGGCGGGCTGATTGGTCTGCAACCAC 260839 29 100.0 32 ............................. ATATTCGCCGCTTTCCATTTACCGAACGTAAC 260778 29 100.0 32 ............................. CCACGTTCGGCGATGTTGGCCCCATCGGTCCA 260717 29 100.0 33 ............................. AAACGGTAGTGTTTTAAAACCGTTTCGAGGTGC 260655 29 100.0 74 ............................. AATAAGGCGCGGTGCCACCCTCGGCTTTAATTGTGTTCCCCGCGCCGACGCGTTCCAGCGCACGTTACTCGATC 260552 29 100.0 32 ............................. AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 260491 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 260430 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 260369 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 260308 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 260247 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 260186 29 96.6 0 A............................ | A [260159] ========== ====== ====== ====== ============================= ========================================================================== ================== 13 29 99.5 36 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTGCTCGCTGCCGGTGAAATTGAACCACCTCAGCCTGCGCCGGATATGTTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTCGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTGCGTTTGGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : TTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCGT # Questionable array : NO Score: 5.99 # Score Detail : 1:0, 2:3, 3:0, 4:0.97, 5:0, 6:0.25, 7:-0.23, 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 [3-0] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [50.0-71.7]%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 2 277488-277094 **** Predicted by CRISPRDetect 2.4 *** >NZ_VCXL02000005.1 Salmonella enterica subsp. enterica serovar Typhimurium strain HIY0061 NODE_5_length_277487_cov_31.345374, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 277487 29 100.0 32 ............................. TGTCCAATTAACCCAAACTTTGCGCGCTTAAT 277426 29 93.1 32 A............T............... GGATATGTGAAGTTCAGGTAGCCCATTACGCA 277365 29 100.0 32 ............................. TTGATCGAGAGTGCGAAGAGGCAGAACGGGCA 277304 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 277243 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 277182 29 100.0 32 ............................. CGTTCATCGGCAGCGTCACGCAATATGAAGAT 277121 28 82.8 0 ...............A.AA.....G-... | ========== ====== ====== ====== ============================= ================================ ================== 7 29 96.1 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : | # Right flank : TTGCATAATCATAATCTGTGTACCAGTAATGGCAGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTAGACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGTCCGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAGCAGTCGAATCATCTGCCATCCCGATATTGCACGTGAACGTTATGCAGCAATGACTTTTCTTGGTATTACCCGAAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTATCGAATGATGTACACGCGTGACCCCCTGCCGATTGGC # Questionable array : NO Score: 6.06 # Score Detail : 1:0, 2:3, 3:0, 4:0.80, 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 [5-2] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [63.3-0.0]%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], //