Array 1 1348-38 **** Predicted by CRISPRDetect 2.4 *** >NZ_VCXK02000019.1 Salmonella enterica subsp. enterica serovar Typhimurium strain HIY0064 NODE_19_length_99418_cov_34.166077, 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 190399-189594 **** Predicted by CRISPRDetect 2.4 *** >NZ_VCXK02000009.1 Salmonella enterica subsp. enterica serovar Typhimurium strain HIY0064 NODE_9_length_206912_cov_33.566187, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ========================================================================== ================== 190398 29 100.0 32 ............................. TGAGCAACGACAGTAAATAATTTTTCGTGCTG 190337 29 100.0 32 ............................. AACCGCTGGCGGGCTGATTGGTCTGCAACCAC 190276 29 100.0 32 ............................. ATATTCGCCGCTTTCCATTTACCGAACGTAAC 190215 29 100.0 32 ............................. CCACGTTCGGCGATGTTGGCCCCATCGGTCCA 190154 29 100.0 33 ............................. AAACGGTAGTGTTTTAAAACCGTTTCGAGGTGC 190092 29 100.0 74 ............................. AATAAGGCGCGGTGCCACCCTCGGCTTTAATTGTGTTCCCCGCGCCGACGCGTTCCAGCGCACGTTACTCGATC 189989 29 100.0 32 ............................. AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 189928 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 189867 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 189806 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 189745 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 189684 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 189623 29 96.6 0 A............................ | A [189596] ========== ====== ====== ====== ============================= ========================================================================== ================== 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 206864-206531 **** Predicted by CRISPRDetect 2.4 *** >NZ_VCXK02000009.1 Salmonella enterica subsp. enterica serovar Typhimurium strain HIY0064 NODE_9_length_206912_cov_33.566187, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 206863 29 93.1 32 A............T............... GGATATGTGAAGTTCAGGTAGCCCATTACGCA 206802 29 100.0 32 ............................. TTGATCGAGAGTGCGAAGAGGCAGAACGGGCA 206741 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 206680 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 206619 29 100.0 32 ............................. CGTTCATCGGCAGCGTCACGCAATATGAAGAT 206558 28 82.8 0 ...............A.AA.....G-... | ========== ====== ====== ====== ============================= ================================ ================== 6 29 95.4 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : CCAGCGGGGATAAACCGTGTCCAATTAACCCAAACTTTGCGCGCTTAA # Right flank : TTGCATAATCATAATCTGTGTACCAGTAATGGCAGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTAGACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGTCCGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAGCAGTCGAATCATCTGCCATCCCGATATTGCACGTGAACGTTATGCAGCAATGACTTTTCTTGGTATTACCCGAAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTATCGAATGATGTACACGCGTGACCCCCTGCCGATTGGC # Questionable array : NO Score: 6.03 # Score Detail : 1:0, 2:3, 3:0, 4:0.77, 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 [63.3-41.7]%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 1 629-1 **** Predicted by CRISPRDetect 2.4 *** >NZ_VCXK02000055.1 Salmonella enterica subsp. enterica serovar Typhimurium strain HIY0064 NODE_55_length_664_cov_40.111732, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ============================================================================================= ================== 628 29 96.6 32 ..........T.................. TCATTTCTGGACGGGGCTGTGTGACGAATACG 567 29 100.0 32 ............................. TTGACGGTGACGTCAGTGCCGAAGGCGAAATA 506 29 100.0 32 ............................. CCAGCTTACGCTATTTACGACGTTATTGAGCA 445 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 384 29 100.0 32 ............................. CCCCGATAGCGACGCTTCTGTAGTCACTGGCA 323 29 100.0 33 ............................. GTGAGTTCGGTTTTAATTTCGTCGCTAAGCTGC 261 29 96.6 93 .........................G... CGTCACTTTCTGACATTTTATTCAGTTCGTTAGTGTTCCCCGTGCCAGCGGGGATAAACCGTCATTTCTGGACGGGGCTGTGTGACGAATACG 139 29 100.0 93 ............................. TGTCCAATTAACCCAAACTTTGCGCGCTTAATATGTTCCCCGCGCTAGCGGGGATAAACCGGGATATGTGAAGTTCAGGTAGCCCATTACGCA 17 17 58.6 0 .................------------ | ========== ====== ====== ====== ============================= ============================================================================================= ================== 9 29 93.9 48 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GCCGCGTCACTTTCTGACATTTTATTCAGTTCGTT # Right flank : C # Questionable array : NO Score: 4.67 # Score Detail : 1:0, 2:3, 3:0, 4:0.70, 5:0, 6:0.25, 7:-1.28, 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: F [2-3] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [0.0-35.0]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0.41,5.51 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], //