Array 1 329098-329431 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHDM01000020.1 Salmonella enterica subsp. enterica serovar Kentucky strain CVM N43448 N43448_contig_20, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 329098 29 100.0 32 ............................. CGTGCAGGGGGTTAAATAAAGAACACGCTGAC 329159 29 100.0 32 ............................. CGCTTGGCGGTTATCATGGCCGGTAATGACTC 329220 29 100.0 32 ............................. GACGCTTACATCTCACCGAGAGATTTTGAGGC 329281 29 100.0 32 ............................. CGGGGATTAGCTCTAAAAATATTTTTATTTTG 329342 29 100.0 32 ............................. CAGTATTTCGGCATGGCAAGCCGCAGCGCGAA 329403 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================ ================== 6 29 100.0 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGCGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTAGAATGTGGTGCTGACAAAAAGTAGTTTATAAACAATGATATACGTTTAGT # Right flank : ATAATCGGGATACATTTTGTTGTCCGGGTGGCGTGTTCCCCGCGCCAGC # 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: F [0-1] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [70.0-33.3]%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 1-761 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHDM01000015.1 Salmonella enterica subsp. enterica serovar Kentucky strain CVM N43448 N43448_contig_15, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 1 29 100.0 32 ............................. TCAGAGCCTTTTTGATGAAGTACTACGGCAAC 62 29 100.0 32 ............................. GCGTACAGCCGTATGCCTCAGACTCCCCACGA 123 29 100.0 32 ............................. GGCCGATATACAGTTTTTACTGTGGGATGCGC 184 29 100.0 32 ............................. CGGAAATTCAGGGAACCCCGGAAGCGATTAGA 245 29 100.0 32 ............................. CAGCAGGACGACGACCCGCGCCCCCGCGTCGG 306 29 93.1 32 A...........T................ GATGTAACGTCTCTCACCTGGCCCGGCGTAAC 367 29 89.7 32 A...C.......T................ CGGACATTGTTCGTGAGCGAGCTGTTGTTCGT 428 29 93.1 32 A...........T................ ACGGGTTAGCGCCTGCGGATAATGCCCAGCAC 489 29 89.7 32 A...........T........G....... GTGGCAATGGTATCGCTATACGAAAGCGACGT 550 29 96.6 32 .......T..................... TTCGTGTATTTTGAGTCGTTTACCGTATCTGC 611 29 100.0 32 ............................. CGCGCCGCACGTTCGGTAGCGTGGCTGAGTTA 672 29 100.0 32 ............................. TGGGACATTCTCGCTAGTCACGGTCATGTCAT 733 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================ ================== 13 29 97.1 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : | # Right flank : GCAACAGTGCTGGTGGAATTAAAAACACCGACGTGTTCCCCGCGCCAGC # Questionable array : NO Score: 6.11 # Score Detail : 1:0, 2:3, 3:0, 4:0.85, 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 [-10.50,-8.90] Score: 0.37/0.37 # Array degeneracy analysis prediction: F [0-4] 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: F [5.65,0.27 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 16184-16334 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHDM01000016.1 Salmonella enterica subsp. enterica serovar Kentucky strain CVM N43448 N43448_contig_16, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 16184 29 100.0 32 ............................. CGCCCCTCACCACCGTGGCCGCGTGCCGTTCG 16245 29 100.0 32 ............................. GCAACTATGTTTAACGCGGCCAATAACGATTT 16306 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================ ================== 3 29 100.0 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTGCTCGCTGCCGGTGAAATTGAACCACCTCAGCCTGCGCCGGATATGCTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGTCTGCGGGGACGTCTTGCCGTCTGGTTACTCGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTAGATGGACTTAGATTAGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTAGGTAATAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : ACCGGGTTGCCGTAGGTGCTGGCCCCCTTGATGTGTTCCCCGCGCCAGCG # Questionable array : NO Score: 5.67 # Score Detail : 1:0, 2:3, 3:0, 4:1.00, 5:0, 6:0.25, 7:0.02, 8:0.4, 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 [71.7-25.0]%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 1-719 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHDM01000017.1 Salmonella enterica subsp. enterica serovar Kentucky strain CVM N43448 N43448_contig_17, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================================== ================== 1 29 100.0 32 ............................. ATTTATCCATTAGTCCCATAGCTGAGTCTCTT 62 29 100.0 32 ............................. TCAACGTTACGACCGAACCACACCGATAAGAA 123 29 100.0 32 ............................. GCACGGGTACGCCGAAAATCGGGGGCTATGCC 184 29 100.0 32 ............................. GGGATCGGCGAGTCGTTCGTGTTTGCTATTTC 245 29 100.0 32 ............................. GTCAACGCCAATGACCGGGAATTATCCCGGAA 306 29 100.0 50 ............................. TTTCCGCTCTCTCTCGTCCATCATTCCGCGCCGGCATAACTGACGATCAG 385 29 100.0 32 ............................. CTGGTCCCGCGTGTATACCAGTATTTACCGTG 446 29 100.0 32 ............................. TAAGTTACGCCAGTGCGGGCGTGTTGCTCATC 507 29 100.0 32 ............................. GTCTGACCAGTGGCGTGGGGGGATTGCAATTT 568 29 96.6 32 ..........T.................. GCGTATGAGCGCCCAGCAGCGAACGTGAATCT 629 29 100.0 32 ............................. CCGCTTTGCTGGCAACATTCACCACATAGCAT 690 29 96.6 0 ............T................ | A [717] ========== ====== ====== ====== ============================= ================================================== ================== 12 29 99.4 34 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : | # Right flank : GTTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCAGGCAGCGCCTTGTCTATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTGCCGTTCGGGAAGGATGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACCGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATACCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCAGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCG # Questionable array : NO Score: 6.21 # Score Detail : 1:0, 2:3, 3:0, 4:0.97, 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 [0-3] 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 1 202-51 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHDM01000086.1 Salmonella enterica subsp. enterica serovar Kentucky strain CVM N43448 N43448_contig_87, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 201 29 100.0 32 ............................. CCAGTCTGTATGAGGCTGCGATTGTGTGTTTT 140 29 100.0 32 ............................. CCTGTAAAACTGATTTCAGGCTGGTTAGTGAC 79 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================ ================== 3 29 100.0 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : | # Right flank : GTAACGCCCGGCGGTATAGTCGATTTCGTGCTGGTGTTCCCCGCGCCAGCG # Questionable array : NO Score: 5.67 # Score Detail : 1:0, 2:3, 3:0, 4:1.00, 5:0, 6:0.25, 7:0.02, 8:0.4, 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: NA [0-0] Score: 0/0.41 # AT richness analysis in flanks prediction: F [30.0-0.0]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0.27,5.24 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], //