Array 1 1-1311 **** Predicted by CRISPRDetect 2.4 *** >NZ_LROA01000002.1 Salmonella enterica subsp. enterica serovar Tennessee strain CFSAN001366 CFSAN001366_contig0001, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 1 28 96.6 32 -............................ ACTTGCTTCATTGACATGCCTGCCACTGCTCC 61 29 100.0 32 ............................. GCGCGCCATTGCTGAGGGTAAACCGGCGATTA 122 29 100.0 32 ............................. CCAGCTCAATTTCGCCAACCTTCGCGCTAATG 183 29 100.0 32 ............................. TCCGTCTCCGCCAACGCCTTTAGCCCATCCAG 244 29 100.0 32 ............................. CTCTTTGATCTCTCCGTTTGCCGTTGAGTGGT 305 29 100.0 32 ............................. TTGACCGGACTCGCGGTTATTCAACTAACCGT 366 29 100.0 32 ............................. TAGAATAATTGTGTTTTTGCTACCAATGGTTG 427 29 100.0 32 ............................. AATCTTCAGAGGACTCAGATCCTGATTACGTT 488 29 100.0 32 ............................. CAGGCATAACTACACCTGTCAGGAGCCAATTA 549 29 100.0 32 ............................. TGGTTACGTATACGCCAGATTCAGAAAAGGCC 610 29 100.0 32 ............................. ATTCAAAAATTCAATATGAGGTTGGAAATTTT 671 29 100.0 32 ............................. GTTGTGTGGGTACAGCCGGCCAGCGTCAGCAG 732 29 100.0 32 ............................. TACGAATAAACAGATTTTTGCGATATCTCTGC 793 29 100.0 32 ............................. CAAATGAAAAATGGTTTAAAGGAGGTCTGTAA 854 29 100.0 32 ............................. TTTACCTGGTTCGTCTGGTTCAACTATATCGA 915 29 100.0 32 ............................. ATCGAATGCTTTTGTGTGTTCTGCTGCCACTT 976 29 100.0 32 ............................. GGGGCGTCACCATTTTTGAATTTATCAGCCGC 1037 29 100.0 32 ............................. ACCAGGCTACCCGCGCGGTAGTTCGTCGACAG 1098 29 100.0 32 ............................. AGCAATGATTGAAAAGCTGGCGATAAACAAGG 1159 29 100.0 33 ............................. ATAAATCTAATTTATTTGATTAGTAGTGCTAAA 1221 29 100.0 32 ............................. TCGCACAACGCCTGGATATCCGCCCATCGGCC 1282 29 96.6 0 ............T................ | A [1309] ========== ====== ====== ====== ============================= ================================= ================== 22 29 99.7 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : | # Right flank : GTTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTGCCGTTCGGGAAGGATGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATACCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATCACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCG # 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: 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 [1-2] 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: F [5.65,0 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 378-44 **** Predicted by CRISPRDetect 2.4 *** >NZ_LROA01000012.1 Salmonella enterica subsp. enterica serovar Tennessee strain CFSAN001366 CFSAN001366_contig0011, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 377 29 100.0 32 ............................. CGCTACGAACTCTGGCAGAAGAGAGCGTTTAT 316 29 100.0 32 ............................. AACGCTACCACCCGGCAGTAAAAGAGCCGACG 255 29 100.0 32 ............................. CAGAACAGGAGCACGTTAGCCGCGTTGCTGAA 194 29 100.0 32 ............................. GCATTCTTTCAAACGTTACTTCTGCTCGCGCC 133 29 100.0 32 ............................. TTGTTGCAGGCGGGAGAACGCAGCGCGTACCC 72 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================ ================== 6 29 100.0 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCACCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGCGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAACCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTGGAATGTGGTGCTGATAAAAAGTAGTTTATAAACAATGATATACGTTTAGT # Right flank : GCCTGCCGTCGCCGTCGCCATATCCGGCGCTGTGTGTTCCCCGC # 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: 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: R [20.0-70.0]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0,5.51 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 41-191 **** Predicted by CRISPRDetect 2.4 *** >NZ_LROA01000189.1 Salmonella enterica subsp. enterica serovar Tennessee strain CFSAN001366 CFSAN001366_contig0188, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 41 29 100.0 32 ............................. ATGGAGCGCGGTGGTTACATCGGCGTTCCGGA 102 29 100.0 32 ............................. GTCGGGATCTCGACCTTTTCAATTTCTTCTAT 163 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================ ================== 3 29 100.0 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : ATAAACCGCGATCAGGAAATCAAGGAGAAGCGGGTGCGTAG # Right flank : TTTGCGACATTTATATTAATGATTATAAA # 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: NA [33.3-40.0]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [5.24,0 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 27-785 **** Predicted by CRISPRDetect 2.4 *** >NZ_LROA01000077.1 Salmonella enterica subsp. enterica serovar Tennessee strain CFSAN001366 CFSAN001366_contig0076, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 27 29 100.0 32 ............................. CTACCAGGCCCGTTTGTCTCAACCATGACCAG 88 29 100.0 32 ............................. CCACGACTAACCGGTACTAATCCTGAGTTCAT 149 29 100.0 32 ............................. TATGAGTTTTCAACATCACCAACTAGTCATGT 210 29 100.0 32 ............................. GCCAAACAGGTTGAGATAGGGCTTCATTATGA 271 29 100.0 32 ............................. ATGGAACAGGCCCAGGCTGCGCAGCAGCAACA 332 29 100.0 32 ............................. TCAATAAAATCAATGATAAGCAGTGTCGTTAA 393 29 100.0 32 ............................. AGAATCGCCAGCGGAAAGAGAAGGGGTTAGCG 454 29 100.0 32 ............................. CGGGAGCACGGGTGTTGCAGCATTGCAGGAAG 515 29 100.0 32 ............................. TGCGGCGCGGTAGTTGGCCTACATGATAGCCA 576 29 100.0 31 ............................. GATGATCGTTTTTTCGTTACGTCGCGCAAAT 636 29 100.0 32 ............................. CACCTCAGATGTTTGGGGTGCAATTTGTAATG 697 29 100.0 32 ............................. AGCGGCTAAACCTGCCGGTTATCGCTGAGCAG 758 28 89.7 0 ............T..........-.G... | ========== ====== ====== ====== ============================= ================================ ================== 13 29 99.2 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : CGTATCTTCGATCATACCGGAACGGTG # Right flank : GTTGCATAATCATAATCTGTGTACCAGTAATGGCTGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTTCCGGGGAGGCTTTTATACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGGGCTGGAGCGGATAAATCGTTGAAGGCCCGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAACAGTCGAATCATCTGCCATCCCGATATTGCGCGCGAACGTTATGCGGCAATGACTTTTCTCGGTATTACCCGAAAAATAAAAAAATTGTCGCGTGAGGTGGACTATTCACGCTACCGAATGATGTACACGCGTGACCCCCTGCCGATTGG # Questionable array : NO Score: 6.22 # Score Detail : 1:0, 2:3, 3:0, 4:0.96, 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: R [21.7-63.3]%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 2 17409-17925 **** Predicted by CRISPRDetect 2.4 *** >NZ_LROA01000077.1 Salmonella enterica subsp. enterica serovar Tennessee strain CFSAN001366 CFSAN001366_contig0076, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 17409 29 100.0 32 ............................. GAATTCGTTATTTTTAAACGAAATCATTATCA 17470 29 100.0 32 ............................. AATGCAACTGCAGTATCCTTACGCCCAAAAGC 17531 29 100.0 32 ............................. GCAGCTATCGATGAGATGAATAACGCGATTTA 17592 29 100.0 32 ............................. TACACACCTAGCAATTAATTACGATTTTGTTT 17653 29 100.0 32 ............................. GAGGGTCGGTGCGCGGTATTAAAACACGCTAT 17714 29 100.0 32 ............................. TACACCAAATGGGGGCCAGCAAAGAAAATGCT 17775 29 100.0 32 ............................. TCGTTTATAGCTGAGAACAAGCTGGCGCTGAT 17836 29 100.0 32 ............................. CGCTGGCGCAACGAGTCGTACCTGTACGCCAG 17897 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================ ================== 9 29 100.0 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : CTTATTGAAGATGTTCTCGCGGCAGGGGAAATTCAACCGCCGTTACCTCCTGAAGATTCACAACCCATAGCGATCCCTCTTCCTGTTGCGTTGGGAGATTCCGGTCATCGGAGCACCTAACGATGAGTATGCTGGTTGTCGTTACCGAAAATGTTCCTCCTCGTCTGCGGGGGAGGCTGGCCGTCTGGTTACTGGAAATTCGAGCTGGTGTGTATGTTGGTGATGTTTCCGCAAAGATCCGCGAGATGATATGGCAACAGGTTTCCGTTCTGGCAGATGAGGGAAATGTTGTTATGGCGTGGGCGACAAATACAGAATCAGGTTTTGAGTTTCAGACTTTTGGTGTAAATCGACGTATTCCGGTAGATCTTGATGGACTGCGATTGGTGTCGTTTCTACCTGTTGAAAATCAATAAGTTAGAGATCTTTAAAAATTAGGAAAAGTTGGTGGGTTTTTTGTGCGCTAAAAAAGTATTTAAATTCAATTGGGTAGATTTAGA # Right flank : ATTCGACGCTCAGGCCGTTCTCTTTTAACCGGGTGTTCCCCGCG # 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 [70.0-30.0]%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], //