Array 1 29014-28069 **** Predicted by CRISPRDetect 2.4 *** >NZ_QZFP01000108.1 Salmonella enterica subsp. enterica serovar Schwarzengrund strain MDH-26 MDH26_contig_108, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 29013 29 100.0 32 ............................. AAACATCCGATCAAATACTGCGTTCGTTTGAG 28952 29 100.0 32 ............................. CGTATTTTTGAACTGGCCAGCGCCACCGATGC 28891 29 100.0 32 ............................. GGTTACGCGGGCGTCTGTTAAAGAGTCCTCGT 28830 29 100.0 32 ............................. GCCGGGGTTTCCCAGAGGCATTCTGATGAAAG 28769 29 100.0 32 ............................. CGAATGCAGATGCCTCCCGTACTGCCGCCGGA 28708 29 100.0 32 ............................. GATTGGCCCTTAGATAACGGGAGATCAAGCGC 28647 29 100.0 32 ............................. CATAACCTTCGCTACCACACTTGCCGGTACTT 28586 29 100.0 32 ............................. CCTTGAGGTTAGGGGAGTCAGGAAATTGCATT 28525 29 100.0 32 ............................. ACAAAATCGGCGGCCCAATCGCCGGCGCTGAC 28464 29 100.0 32 ............................. GCCTGCCGTCTTTTTATTGAGGTCTGTAAACC 28403 29 96.6 32 ............................T TAATCATTTTGTTTAAATCCCGGATCACCTCC 28342 29 100.0 32 ............................. GAGTTATTGTCACTCGTCAGTGATAATTTTCT 28281 29 100.0 32 ............................. CCCGTTGAAGATCTGGACGCATGGGGCAAAGC 28220 29 100.0 32 ............................. GTGAGCTCGGTTTTAATTTCGTCGCTAAGGTG 28159 29 100.0 32 ............................. CAAAAGGCCGACAGTGTGTACACCTCTAAAAA 28098 29 96.6 0 ............T................ | A [28071] ========== ====== ====== ====== ============================= ================================ ================== 16 29 99.6 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : CTTATTGAAGATGTTCTCGCGGAAGGGGAAATTCAACCGCCGTTACCTCCTGAAGATTCACAACCCATAGCGATCCCTCTTCCTGTTGCGTTGGGAGATTCCGGTCATCGGAGTACCTAACGATGAGTATGCTGGTTGTCGTTACCGAAAATGTTCCTCCTCGTCTGCGGGGGAGGCTGGCCGTCTGGTTACTGGAAATTCGAGCTGGTGTGTATGTTGGTGATGTTTCCGCAAAGATCCGCGAGATGATATGGCAACAGGTTTCCGTTCTGGCAGATGAGGGAAATGTTGTTATGGCGTGGGCGACAAATACAGAATCAGGTTTTGAGTTTCAGACTTTTGGTGAAAATCGACGTATTCCGGTAGATCTTGATGGACTGCGATTGGTGTCGTTTCTACCTGTTGAAAATCAATAATTTAGAGATCTTTAAAAATTAGGAAAAGTTGGTGGTTTTTTTGTGCGCTAAAAAAGTATTTAAATTCAATTGGGTAGATTTAGA # Right flank : TTTCACCAGCTTATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATTCGCCCAGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTGCCGTTCGGGAAGGATGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACCGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATACCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCGT # Questionable array : NO Score: 6.24 # Score Detail : 1:0, 2:3, 3:0, 4:0.98, 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 [2-0] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [50.0-71.7]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0,5.92 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 107-1110 **** Predicted by CRISPRDetect 2.4 *** >NZ_QZFP01000040.1 Salmonella enterica subsp. enterica serovar Schwarzengrund strain MDH-26 MDH26_contig_40, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 107 29 100.0 32 ............................. TGGCGCAGCAACCAGATCCCGCTAACGAACCC 168 29 100.0 32 ............................. CGTTGCTGGCTATTCGAACTAACCTGATTGTT 229 29 100.0 32 ............................. GCCTCAGCATTGTCATAACCCCACGCCTGGCA 290 29 100.0 32 ............................. CGGCTCGACCGGGAGCTTGCCGGCATCGTGGA 351 29 100.0 32 ............................. GCAACTTCTTATATGTAAAAAACCGTTATGAT 412 29 100.0 32 ............................. TCCGGGGAAAGAACTCGCCTCGTCCAGCGTCA 473 29 100.0 32 ............................. CGGCGGCGGACGCCGCTCAGATAGCCAAAACC 534 29 96.6 32 ..G.......................... TATACAGGATTCTCACACTTTGGTTTGGTCGA 595 29 96.6 32 ..G.......................... CGTTTTTTTTATTTGTACTATTGTCAGTACCC 656 29 96.6 32 ..G.......................... CGGAAACAAACAAAGTTTTGCGCGATTCCACC 717 29 96.6 32 ..G.......................... CACCAGGTAACAATATCGTCCCCGACCTTTAT 778 29 96.6 32 ..G.......................... GCGAAATTCCCCAGATACCGCGCATCGGCACT 839 29 93.1 32 ..G.........T................ CAAAATTAATGTCCAGGACCTTATTAAGTTAC 900 29 93.1 32 ..G.........T................ CTCGGGGATTTTGTGCCACCCAAAACGCTCGC 961 29 93.1 32 ..G.........T................ GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 1022 29 93.1 32 ..G..........T............... CCGGATGAAAACGCCTACCCGGAAGACTACGA 1083 28 86.2 0 ..G.........T..........-.G... | ========== ====== ====== ====== ============================= ================================ ================== 17 29 96.6 32 GTATTCCCCGCGCCAGCGGGGATAAACCG # Left flank : AAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTAGAATGTGGTGCGGACAAAAAGTAGTTTATAAACAATGACATACGTTTAGTG # Right flank : GTTGCATAATTATAGTCTGTGTACCAGTAATGGCTGGTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTATACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCATTGAAGGCCCGGCCAGGATTAAGCCTGTTGGTCGAGGATGAGTCTACGTCGATCTTGTTCGATACCGGCCCTGATGACAGTTTTATGCAAAACGCGTCGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAACAGTCGAATCATCTGCCATCCCGATATTGCGCGTGAACGTTATGCGGCAATGACTTTTCTCGGTATTACCCGAAAAATAAAAAAATTGTCATGTGAAGTGGACTATTCACGCTACCGAATGATGTACACGCGTGACCCCCTGCCGATTGG # Questionable array : NO Score: 5.73 # Score Detail : 1:0, 2:3, 3:0, 4:0.83, 5:0, 6:0.25, 7:0.01, 8:1, 9:0.64, # 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 : GTATTCCCCGCGCCAGCGGGGATAAACCG # Alternate repeat : GTGTTCCCCGCGCCAGCGGGGATAAACCG # Directional analysis summary from each method: # Motif ATTGAAA(N) match prediction: NA Score: 0/4.5 # A,T distribution in repeat prediction: F [6,4] Score: 0.37/0.37 # Reference repeat match prediction: F [matched GTATTCCCCGCGCCAGCGGGGATAAACCG 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 [0-6] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [66.7-63.3]%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], //