Array 1 50-1723 **** Predicted by CRISPRDetect 2.4 *** >NZ_LRNY01000016.1 Salmonella enterica subsp. enterica serovar Tennessee strain CFSAN001376 CFSAN001376_contig0015, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 50 29 100.0 27 ............................. TCCTACACGGACCGCCCGCCCGACCAG 106 29 100.0 33 ............................. CCGAACGCGTCAACGGGGAGTGATCGAGAATCT 168 29 100.0 32 ............................. CGATCAGGAAATCAAGGAGAAGCGGGTGCGTA 229 29 100.0 32 ............................. ATGGAGCGCGGTGGTTACATCGGCGTTCCGGA 290 29 100.0 32 ............................. GTCGGGATCTCGACCTTTTCAATTTCTTCTAT 351 29 100.0 32 ............................. TTTGCGACATTTATATTAATGATTATAAATAT 412 29 100.0 32 ............................. ACTTGCTTCATTGACATGCCTGCCACTGCTCC 473 29 100.0 32 ............................. GCGCGCCATTGCTGAGGGTAAACCGGCGATTA 534 29 100.0 32 ............................. CCAGCTCAATTTCGCCAACCTTCGCGCTAATG 595 29 100.0 32 ............................. TCCGTCTCCGCCAACGCCTTTAGCCCATCCAG 656 29 100.0 32 ............................. CTCTTTGATCTCTCCGTTTGCCGTTGAGTGGT 717 29 100.0 32 ............................. TTGACCGGACTCGCGGTTATTCAACTAACCGT 778 29 100.0 32 ............................. TAGAATAATTGTGTTTTTGCTACCAATGGTTG 839 29 100.0 32 ............................. AATCTTCAGAGGACTCAGATCCTGATTACGTT 900 29 100.0 32 ............................. CAGGCATAACTACACCTGTCAGGAGCCAATTA 961 29 100.0 32 ............................. TGGTTACGTATACGCCAGATTCAGAAAAGGCC 1022 29 100.0 32 ............................. ATTCAAAAATTCAATATGAGGTTGGAAATTTT 1083 29 100.0 32 ............................. GTTGTGTGGGTACAGCCGGCCAGCGTCAGCAG 1144 29 100.0 32 ............................. TACGAATAAACAGATTTTTGCGATATCTCTGC 1205 29 100.0 32 ............................. CAAATGAAAAATGGTTTAAAGGAGGTCTGTAA 1266 29 100.0 32 ............................. TTTACCTGGTTCGTCTGGTTCAACTATATCGA 1327 29 100.0 32 ............................. ATCGAATGCTTTTGTGTGTTCTGCTGCCACTT 1388 29 100.0 32 ............................. GGGGCGTCACCATTTTTGAATTTATCAGCCGC 1449 29 100.0 32 ............................. ACCAGGCTACCCGCGCGGTAGTTCGTCGACAG 1510 29 100.0 32 ............................. AGCAATGATTGAAAAGCTGGCGATAAACAAGG 1571 29 100.0 33 ............................. ATAAATCTAATTTATTTGATTAGTAGTGCTAAA 1633 29 100.0 32 ............................. TCGCACAACGCCTGGATATCCGCCCATCGGCC 1694 29 96.6 0 ............T................ | A [1721] ========== ====== ====== ====== ============================= ================================= ================== 28 29 99.9 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : CAGCGGGGATAAAACCGCTGGCTAATCTGCGTGTTGATGTTGTCCATGCG # Right flank : GTTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTGCCGTTCGGGAAGGATGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATACCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATCACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCG # 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 [0-2] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [38.3-48.3]%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 1 1-334 **** Predicted by CRISPRDetect 2.4 *** >NZ_LRNY01000219.1 Salmonella enterica subsp. enterica serovar Tennessee strain CFSAN001376 CFSAN001376_contig0218, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 1 29 100.0 32 ............................. TACACACCTAGCAATTAATTACGATTTTGTTT 62 29 100.0 32 ............................. GAGGGTCGGTGCGCGGTATTAAAACACGCTAT 123 29 100.0 32 ............................. TACACCAAATGGGGGCCAGCAAAGAAAATGCT 184 29 100.0 32 ............................. TCGTTTATAGCTGAGAACAAGCTGGCGCTGAT 245 29 100.0 32 ............................. CGCTGGCGCAACGAGTCGTACCTGTACGCCAG 306 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================ ================== 6 29 100.0 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : | # Right flank : ATTCGACGCTCAGGCCGTTCTCTTTTAACCGG # 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: R [0.0-25.0]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [5.24,0.27 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 184-33 **** Predicted by CRISPRDetect 2.4 *** >NZ_LRNY01000037.1 Salmonella enterica subsp. enterica serovar Tennessee strain CFSAN001376 CFSAN001376_contig0036, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 183 29 100.0 32 ............................. GAATTCGTTATTTTTAAACGAAATCATTATCA 122 29 100.0 32 ............................. AATGCAACTGCAGTATCCTTACGCCCAAAAGC 61 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================ ================== 3 29 100.0 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : CTTATTGAAGATGTTCTCGCGGCAGGGGAAATTCAACCGCCGTTACCTCCTGAAGATTCACAACCCATAGCGATCCCTCTTCCTGTTGCGTTGGGAGATTCCGGTCATCGGAGCACCTAACGATGAGTATGCTGGTTGTCGTTACCGAAAATGTTCCTCCTCGTCTGCGGGGGAGGCTGGCCGTCTGGTTACTGGAAATTCGAGCTGGTGTGTATGTTGGTGATGTTTCCGCAAAGATCCGCGAGATGATATGGCAACAGGTTTCCGTTCTGGCAGATGAGGGAAATGTTGTTATGGCGTGGGCGACAAATACAGAATCAGGTTTTGAGTTTCAGACTTTTGGTGTAAATCGACGTATTCCGGTAGATCTTGATGGACTGCGATTGGTGTCGTTTCTACCTGTTGAAAATCAATAAGTTAGAGATCTTTAAAAATTAGGAAAAGTTGGTGGGTTTTTTGTGCGCTAAAAAAGTATTTAAATTCAATTGGGTAGATTTAGA # Right flank : GGCAGCTATCGATGAGATGAATAACGCGATTTA # 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: R [31.7-70.0]%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 2 18116-16807 **** Predicted by CRISPRDetect 2.4 *** >NZ_LRNY01000037.1 Salmonella enterica subsp. enterica serovar Tennessee strain CFSAN001376 CFSAN001376_contig0036, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 18115 29 100.0 32 ............................. CGCTACGAACTCTGGCAGAAGAGAGCGTTTAT 18054 29 100.0 32 ............................. AACGCTACCACCCGGCAGTAAAAGAGCCGACG 17993 29 100.0 32 ............................. CAGAACAGGAGCACGTTAGCCGCGTTGCTGAA 17932 29 100.0 32 ............................. GCATTCTTTCAAACGTTACTTCTGCTCGCGCC 17871 29 100.0 32 ............................. TTGTTGCAGGCGGGAGAACGCAGCGCGTACCC 17810 29 100.0 32 ............................. CCTGCCGTCGCCGTCGCCATATCCGGCGCTGT 17749 29 100.0 32 ............................. GGCCACTTATCAGCAAACCGGGCATCCAGAAC 17688 29 100.0 32 ............................. CGAGTCAACAGCGGTAGCCATTGCAGGCATTT 17627 29 100.0 32 ............................. GTTTGCCGTATCTTCGATCATACCGGAACGGT 17566 29 100.0 32 ............................. CTACCAGGCCCGTTTGTCTCAACCATGACCAG 17505 29 100.0 32 ............................. CCACGACTAACCGGTACTAATCCTGAGTTCAT 17444 29 100.0 32 ............................. TATGAGTTTTCAACATCACCAACTAGTCATGT 17383 29 100.0 32 ............................. GCCAAACAGGTTGAGATAGGGCTTCATTATGA 17322 29 100.0 32 ............................. ATGGAACAGGCCCAGGCTGCGCAGCAGCAACA 17261 29 100.0 32 ............................. TCAATAAAATCAATGATAAGCAGTGTCGTTAA 17200 29 100.0 32 ............................. AGAATCGCCAGCGGAAAGAGAAGGGGTTAGCG 17139 29 100.0 32 ............................. CGGGAGCACGGGTGTTGCAGCATTGCAGGAAG 17078 29 100.0 32 ............................. TGCGGCGCGGTAGTTGGCCTACATGATAGCCA 17017 29 100.0 32 ............................. GATGATCGTTTTTTTCGTTACGTCGCGCAAAT 16956 29 100.0 32 ............................. CACCTCAGATGTTTGGGGTGCAATTTGTAATG 16895 29 100.0 32 ............................. AGCGGCTAAACCTGCCGGTTATCGCTGAGCAG 16834 28 89.7 0 ............T...........G-... | ========== ====== ====== ====== ============================= ================================ ================== 22 29 99.5 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCACCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGCGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAACCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTGGAATGTGGTGCTGATAAAAAGTAGTTTATAAACAATGATATACGTTTAGT # Right flank : TTGCATAATCATAATCTGTGTACCAGTAATGGCTGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTTCCGGGGAGGCTTTTATACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGGGCTGGAGCGGATAAATCGTTGAAGGCCCGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAACAGTCGAATCATCTGCCATCCCGATATTGCGCGCGAACGTTATGCGGCAATGACTTTTCTCGGTATTACCCGAAAAATAAAAAAATTGTCGCGTGAGGTGGACTATTCACGCTACCGAATGATGTACACGCGTGACCCCCTGCCGATTGGC # Questionable array : NO Score: 6.23 # 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: 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: NA [63.3-70.0]%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], //