Array 1 1006049-1007234 **** Predicted by CRISPRDetect 2.4 *** >NZ_CP025243.1 Salmonella enterica subsp. enterica serovar Newport str. CDC 2012K-0663 isolate USDA-ARS-USMARC-1936 chromosome, complete genome Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 1006049 29 100.0 32 ............................. TGCTGGCGGCAAAAGAACTCGCTAAATGGGAA 1006110 29 100.0 32 ............................. CAGTGCGGCAGCGCGCAATCGAGACACGCCAT 1006171 29 100.0 32 ............................. CACAAAACGCCAGTGGCATGGTACAACCCGTA 1006232 29 100.0 32 ............................. GCGTGACCATGTTTAACTCTAAATCAGGCCGT 1006293 29 96.6 32 ........A.................... TCATGCTTTCGACTAAATACTACCGCGACAAC 1006354 29 100.0 32 ............................. AAAATAACAACATTATCAGTGTGAAAAGTCTC 1006415 29 100.0 32 ............................. AGATATGAAAAACGTAAAAATTTACACCGCCA 1006476 29 100.0 32 ............................. CAATAGGACAGCCATTCGAGCGCCCAGAGTTT 1006537 29 100.0 32 ............................. GTCAGTATGCACTGCTTGATAAAGTCAGGCCA 1006598 29 100.0 32 ............................. AACTAACGTCTATAGCTAAATGTAGAGAAAAC 1006659 29 100.0 32 ............................. CAGTTTGGAGTCAATGTTATTTCTTCAGGTCA 1006720 29 100.0 32 ............................. TCTCGCTGGTTGCTCCAACTCCTGATATGCCG 1006781 29 100.0 32 ............................. TAAAAATCTTCTTTCATATAACCGTAAGGGTT 1006842 29 100.0 32 ............................. AGGGTTTTGTCACCTCAACGGTCGGGAGTGCA 1006903 29 100.0 32 ............................. GTGCAACAGTTTCTTACCGCAAGCAGTTTGAA 1006964 29 100.0 32 ............................. ATCATCGGGATTCATTTTGTTGTCCGGGTGGC 1007025 29 100.0 32 ............................. CGGTGCTCTATGTCTAAAAATAAAAGCGGTTC 1007086 29 93.1 32 ........T...................C AGCACAATCATTATTAGATGAACTTTCATCAA 1007147 28 96.6 32 ............-................ GGGATCGCGCTGGCGGTCGCATCCGTTGCCGT 1007207 28 82.8 0 ...............A.AA....-.G... | ========== ====== ====== ====== ============================= ================================ ================== 20 29 98.5 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGCGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACTTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCTCTATCAATTTTACGGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTAGAATGTAATGCTGATAAAAAGTAGTTTATAAACAATGATATCCGTTTAGT # Right flank : GTTGCATAATCATAATCTGTGTACCAGTAATGGCAGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTATACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGCCCGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAACAGTCGAATCATCTGCCATCCCGATATTGCGCGCGAACGTTATGCGGCAATGACTTTTCTCGGTATTACCCGAAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTACCGAATGATGTACACGCGTGGCCCCCTGCCGATTGG # 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 [1-8] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [73.3-63.3]%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 2 1023904-1025519 **** Predicted by CRISPRDetect 2.4 *** >NZ_CP025243.1 Salmonella enterica subsp. enterica serovar Newport str. CDC 2012K-0663 isolate USDA-ARS-USMARC-1936 chromosome, complete genome Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 1023904 29 100.0 32 ............................. CTGGAACGGCAGTATTTAAAAGGGGTTATTGA 1023965 29 100.0 32 ............................. TGGGCGCCCGGATTGTTTGCGTGCGGCGACGG 1024026 29 100.0 32 ............................. TTGATTTACCCGCCACTTATTCCCCATTGCAT 1024087 29 96.6 32 ..........................T.. GGACTATCAAACCATCTATGATGCCAATTTTA 1024148 29 100.0 32 ............................. CGCGGGGCTGGTATTCGATACAGACCCGGCTA 1024209 29 100.0 32 ............................. GGAATAAAAATGAATTTGAGTCAACTCTATAA 1024270 29 100.0 32 ............................. CGTTAGGCTGCGGTTGGGCACCGAAGAAAAAA 1024331 29 100.0 32 ............................. ATTATCCCGGAAATCGTGATCAACTACGCAGG 1024392 29 100.0 32 ............................. ATTGTTATTGCGGTAACGGATAATTTATCATT 1024453 29 100.0 32 ............................. CCTGGCGATCGCATTTGGGTGCGGGAAACATT 1024514 29 100.0 32 ............................. CCGAATATGGTGATAATGTTGCACCTTCGCTC 1024575 29 100.0 32 ............................. GACTCGGCCTGTTTTTTGATTTTGACAATCAG 1024636 29 100.0 32 ............................. CCAATAACCGACGAGGGCAAACGCCGTGCGCG 1024697 29 100.0 32 ............................. AGGACTGAGGGAATAGGGACCGTAATTGTAAA 1024758 29 100.0 32 ............................. ACAATGTTGCGTCTAATTCTCATTAATTAAAA 1024819 29 100.0 32 ............................. CAGACGAAAATCAGCCCGCATATTCCGACACA 1024880 29 100.0 32 ............................. AACAGTGGTTTTAGGTTGTCGGTGCTGATCCC 1024941 29 100.0 32 ............................. ATTAAACAACAGGATTTTGCAATTACTGTTGG 1025002 29 100.0 32 ............................. CAGACGGCAGCAGCGTGAAACACGTCAGTATT 1025063 29 100.0 32 ............................. TCAGCTGTTCCATACTCACCCCCTGTGCAATC 1025124 29 100.0 32 ............................. GCGATGTATGCCGCGACGATCGAGAGCGAACT 1025185 29 100.0 32 ............................. CAGCAGATGAAAAATATTTACAGATTGGTAAA 1025246 29 100.0 32 ............................. AAAAAATCCCGCTGACAATATTTTGCCACCTC 1025307 29 100.0 32 ............................. CCGGAAAACTATCTCTATCGCAGGCTGGATAT 1025368 29 100.0 32 ............................. TTCCAAAGGTACTCCCATATCTCCAGCCAACG 1025429 29 100.0 32 ............................. TAAGTTACGCCAGTGCGGGCGTGTTGCTCATC 1025490 29 100.0 0 ............................. | A [1025517] ========== ====== ====== ====== ============================= ================================ ================== 27 29 99.9 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : CTTATTGAAGATGTTCTCGCGGCAGGGGAAATTCAACCGCCGTTACCTCCTGAAGATTCACAACCCATAGCGATCCCTCTTCCTGTTGCGTTGGGAGATTCCGGTCATCGGAGTACCTAACGATGAGTATGCTGGTTGTCGTTACCGAAAATGTTCCTCCTCGTCTGCGGGGGAGGCTGGTCGTCTGGTTACTGGAAATTCGAGCTGGTGTGTATGTTGGTGATGTTTCCGCAAAGATCCGCGAGATGATATGGCAACAGGTTTCCGTTCTGGCAGATGAGGGAAATGTTGTTATGGCGTGGGCGACAAATACAGAATCAGGTTTTGAGTTTCAGACTTTTGGTGTAAATCGACGTATTCCGGTAGATCTTGATGGACTGCGATTGGTGTCGTTTCTACCTGTTGAAAATCAATAAGTTATAGATCTTTAAAAATTAGGAAAAGTTGGTGGGTTTTTTGTGCGCTAAAAAAGTATTTAAATTCAATTGGGTAGATTTAGG # Right flank : GTTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATTCGCCCAGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTGCCGTTCGGGAAGGATGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACCGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATACCATAACGGCGCGCAATCGCTAATGCTCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATCACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCG # 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 [1-1] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [68.3-48.3]%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], //