Array 1 1008109-1009294 **** Predicted by CRISPRDetect 2.4 *** >NZ_CP025241.1 Salmonella enterica subsp. enterica serovar Newport str. USDA-ARS-USMARC-1929 chromosome, complete genome Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 1008109 29 100.0 32 ............................. TGCTGGCGGCAAAAGAACTCGCTAAATGGGAA 1008170 29 100.0 32 ............................. CAGTGCGGCAGCGCGCAATCGAGACACGCCAT 1008231 29 100.0 32 ............................. CACAAAACGCCAGTGGCATGGTACAACCCGTA 1008292 29 100.0 32 ............................. GCGTGACCATGTTTAACTCTAAATCAGGCCGT 1008353 29 96.6 32 ........A.................... TCATGCTTTCGACTAAATACTACCGCGACAAC 1008414 29 100.0 32 ............................. AAAATAACAACATTATCAGTGTGAAAAGTCTC 1008475 29 100.0 32 ............................. AGATATGAAAAACGTAAAAATTTACACCGCCA 1008536 29 100.0 32 ............................. CAATAGGACAGCCATTCGAGCGCCCAGAGTTT 1008597 29 100.0 32 ............................. GTCAGTATGCACTGCTTGATAAAGTCAGGCCA 1008658 29 100.0 32 ............................. AACTAACGTCTATAGCTAAATGTAGAGAAAAC 1008719 29 100.0 32 ............................. CAGTTTGGAGTCAATGTTATTTCTTCAGGTCA 1008780 29 100.0 32 ............................. TCTCGCTGGTTGCTCCAACTCCTGATATGCCG 1008841 29 100.0 32 ............................. TAAAAATCTTCTTTCATATAACCGTAAGGGTT 1008902 29 100.0 32 ............................. AGGGTTTTGTCACCTCAACGGTCGGGAGTGCA 1008963 29 100.0 32 ............................. GTGCAACAGTTTCTTACCGCAAGCAGTTTGAA 1009024 29 100.0 32 ............................. ATCATCGGGATTCATTTTGTTGTCCGGGTGGC 1009085 29 100.0 32 ............................. CGGTGCTCTATGTCTAAAAATAAAAGCGGTTC 1009146 29 93.1 32 ........T...................C AGCACAATCATTATTAGATGAACTTTCATCAA 1009207 28 96.6 32 ............-................ GGGATCGCGCTGGCGGTCGCATCCGTTGCCGT 1009267 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 1025964-1027579 **** Predicted by CRISPRDetect 2.4 *** >NZ_CP025241.1 Salmonella enterica subsp. enterica serovar Newport str. USDA-ARS-USMARC-1929 chromosome, complete genome Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 1025964 29 100.0 32 ............................. CTGGAACGGCAGTATTTAAAAGGGGTTATTGA 1026025 29 100.0 32 ............................. TGGGCGCCCGGATTGTTTGCGTGCGGCGACGG 1026086 29 100.0 32 ............................. TTGATTTACCCGCCACTTATTCCCCATTGCAT 1026147 29 96.6 32 ..........................T.. GGACTATCAAACCATCTATGATGCCAATTTTA 1026208 29 100.0 32 ............................. CGCGGGGCTGGTATTCGATACAGACCCGGCTA 1026269 29 100.0 32 ............................. GGAATAAAAATGAATTTGAGTCAACTCTATAA 1026330 29 100.0 32 ............................. CGTTAGGCTGCGGTTGGGCACCGAAGAAAAAA 1026391 29 100.0 32 ............................. ATTATCCCGGAAATCGTGATCAACTACGCAGG 1026452 29 100.0 32 ............................. ATTGTTATTGCGGTAACGGATAATTTATCATT 1026513 29 100.0 32 ............................. CCTGGCGATCGCATTTGGGTGCGGGAAACATT 1026574 29 100.0 32 ............................. CCGAATATGGTGATAATGTTGCACCTTCGCTC 1026635 29 100.0 32 ............................. GACTCGGCCTGTTTTTTGATTTTGACAATCAG 1026696 29 100.0 32 ............................. CCAATAACCGACGAGGGCAAACGCCGTGCGCG 1026757 29 100.0 32 ............................. AGGACTGAGGGAATAGGGACCGTAATTGTAAA 1026818 29 100.0 32 ............................. ACAATGTTGCGTCTAATTCTCATTAATTAAAA 1026879 29 100.0 32 ............................. CAGACGAAAATCAGCCCGCATATTCCGACACA 1026940 29 100.0 32 ............................. AACAGTGGTTTTAGGTTGTCGGTGCTGATCCC 1027001 29 100.0 32 ............................. ATTAAACAACAGGATTTTGCAATTACTGTTGG 1027062 29 100.0 32 ............................. CAGACGGCAGCAGCGTGAAACACGTCAGTATT 1027123 29 100.0 32 ............................. TCAGCTGTTCCATACTCACCCCCTGTGCAATC 1027184 29 100.0 32 ............................. GCGATGTATGCCGCGACGATCGAGAGCGAACT 1027245 29 100.0 32 ............................. CAGCAGATGAAAAATATTTACAGATTGGTAAA 1027306 29 100.0 32 ............................. AAAAAATCCCGCTGACAATATTTTGCCACCTC 1027367 29 100.0 32 ............................. CCGGAAAACTATCTCTATCGCAGGCTGGATAT 1027428 29 100.0 32 ............................. TTCCAAAGGTACTCCCATATCTCCAGCCAACG 1027489 29 100.0 32 ............................. TAAGTTACGCCAGTGCGGGCGTGTTGCTCATC 1027550 29 100.0 0 ............................. | A [1027577] ========== ====== ====== ====== ============================= ================================ ================== 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], //