Array 1 455-1 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHJJ01000020.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N47715 N47715_contig_20, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 454 29 100.0 32 ............................. TTTTGATACGTAGTATTCATTACGCCTCCTAG 393 29 100.0 32 ............................. GCGAGGTCAATAAAAAATGGTGTGGCTTTACC 332 29 100.0 32 ............................. CCGGCATCAGCGCCGATCCGTTCATAGTGCCC 271 29 100.0 32 ............................. AAAAAACAGAAGAACGGCAAGCGGCACCTCAA 210 29 100.0 32 ............................. CGTCAGCGCGGTATTGAGGCCGGGGACCGCCC 149 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 88 29 100.0 32 ............................. CAGATCCTCAACGGTCAGGCTGTTTAGTTCCT 27 27 93.1 0 ...........................-- | ========== ====== ====== ====== ============================= ================================ ================== 8 29 99.1 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGTGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTAGAATGTGGTGCTGACAAAAAGTAGTTTATAAACAATTATATCCGTTTAGT # Right flank : C # Questionable array : NO Score: 6.21 # Score Detail : 1:0, 2:3, 3:0, 4:0.95, 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 [1-0] 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], // Array 1 1-577 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHJJ01000021.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N47715 N47715_contig_21, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 1 27 93.1 32 --........................... AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 60 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 121 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 182 29 100.0 32 ............................. GCACTATTTCGAATGTCTCGACGCCAGATTTA 243 29 100.0 32 ............................. AACGAATTGAGACTATTAGAGATTATTCGCCT 304 29 100.0 32 ............................. GCAACCCATTAATTAACTAAGCAGTAATAAAC 365 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 426 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 487 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 548 29 96.6 0 A............................ | A [574] ========== ====== ====== ====== ============================= ================================ ================== 10 29 98.6 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : | # Right flank : GTTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCG # Questionable array : NO Score: 6.19 # Score Detail : 1:0, 2:3, 3:0, 4:0.93, 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 [1-3] 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 1 698-1 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHJJ01000076.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N47715 N47715_contig_76, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 697 27 93.1 32 --........................... CCGCTGACGCACTGGATCAACCTGACGCAACG 638 29 100.0 32 ............................. TTGCAGGGCGATATTGTTGTTGGTGAATGGGA 577 29 100.0 32 ............................. CGTCGCGGAAAATTTCGCATTGACGATAAAGA 516 29 100.0 32 ............................. TTACGTGTTTATTCATCTGTTGCATTAGATTC 455 29 96.6 32 ............................T GAGGCGTACAGGCTGTTAGATGAGAAATTACC 394 29 100.0 32 ............................. ACGCCCCGAATGTGTTTGCCTCGCCCGCTGCC 333 29 100.0 32 ............................. TGGATTATCTGTATTTTACGGAAGTGGGCGCG 272 29 100.0 32 ............................. GTCGTTCATCAGGCACTACCGGCACTTTCTGG 211 29 100.0 32 ............................. ATATTCGCCGCTTTCCATTTACCGAACGTAAC 150 29 100.0 32 ............................. CCACGTTCGGCGATGTTGGCCCCATCGGTCCA 89 29 100.0 33 ............................. AAACGGTAGTGTTTTAAAACCGTTTCGAGGTGC 27 27 93.1 0 ...........................-- | ========== ====== ====== ====== ============================= ================================= ================== 12 29 98.6 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : | # Right flank : C # Questionable array : NO Score: 6.19 # Score Detail : 1:0, 2:3, 3:0, 4:0.93, 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: F [1-2] 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 [0.41,5.24 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 56-327 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHJJ01000083.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N47715 N47715_contig_84, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 56 29 100.0 32 ............................. CAACCAGGCTGGATCGTAACTCCTATCCCCTC 117 29 100.0 32 ............................. AAAATGCAGGTGGGGTAACGAATGCGAGATTG 178 29 100.0 33 ............................. CCAGTGGGCGTAGCCAGCTCATCGCTATTTTGC 240 29 100.0 32 ............................. CGTTGCGGATTATCGTTAAGACTGAAGGAAGT 301 27 93.1 0 ...........................-- | ========== ====== ====== ====== ============================= ================================= ================== 5 29 98.6 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : CCCGCGCCAGCGGGGATAAACCGAACCGCTGGCGGGCTGATTGGTCTGCAACCACG # Right flank : | # Questionable array : NO Score: 5.99 # Score Detail : 1:0, 2:3, 3:0, 4:0.93, 5:0, 6:0.25, 7:0.01, 8:0.8, 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 [0-1] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [30.0-0.0]%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 1-1004 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHJJ01000058.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N47715 N47715_contig_58, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 1 28 93.1 32 -............T............... ATGCCGGAACGCTGATGGCGTTTGACATGAGC 61 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 122 29 100.0 32 ............................. TGACGCTGGTCTATACCGGCAACGAACGCGAC 183 29 100.0 32 ............................. TTGACGGTGACGTCAGTGCCGAAGGCGAAATA 244 29 100.0 32 ............................. CCAGCTTACGCTATTTACGACGTTATTGAGCA 305 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 366 29 100.0 32 ............................. CCCCGATAGCGACGCTTCTGTAGTCACTGGCA 427 29 100.0 33 ............................. GTGAGTTCGGTTTTAATTTCGTCGCTAAGCTGC 489 29 96.6 32 .........................G... CGTCACTTTCTGACATTTTATTCAGTTCGTTA 550 29 96.6 32 ..........T.................. TCATTTCTGGACGGGGCTGTGTGACGAATACG 611 29 100.0 32 ............................. TGTCCAATTAACCCAAACTTTGCGCGCTTAAT 672 29 93.1 32 A............T............... GGATATGTGAAGTTCAGGTAGCCCATTACGCA 733 29 100.0 32 ............................. TTGATCGAGAGTGCGAAGAGGCAGAACGGGCA 794 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 855 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 916 29 100.0 32 ............................. CGTTCATCGGCAGCGTCACGCAATATGAAGAT 977 28 82.8 0 ...............A.AA....-.G... | ========== ====== ====== ====== ============================= ================================= ================== 17 29 97.2 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : | # Right flank : GTTGCATAATCATAATCTGTGTACCAGTAATGGCAGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTAGACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGTCCGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAGCAGTCGAATCATCTGCCATCCCGATATTGCACGTGAACGTTATGCAGCAATGACTTTTCTTGGTATTACCCGAAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTATCGAATGATGTACACGCGTGACCCCCTGCCGATTGG # Questionable array : NO Score: 6.12 # Score Detail : 1:0, 2:3, 3:0, 4:0.86, 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 [4-8] 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], //