Array 1 5333-6397 **** Predicted by CRISPRDetect 2.4 *** >NZ_QZEO01000002.1 Salmonella enterica subsp. enterica serovar Schwarzengrund strain MDH-6 MDH6_trimmed_contig_2, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 5333 29 100.0 32 ............................. GCTATGTAGCTAACCTATTGATTTTATAAGAA 5394 29 100.0 32 ............................. TGGCGCAGCAACCAGATCCCGCTAACGAACCC 5455 29 100.0 32 ............................. CGTTGCTGGCTATTCGAACTAACCTGATTGTT 5516 29 100.0 32 ............................. GCCTCAGCATTGTCATAACCCCACGCCTGGCA 5577 29 100.0 32 ............................. CGGCTCGACCGGGAGCTTGCCGGCATCGTGGA 5638 29 100.0 32 ............................. GCAACTTCTTATATGTAAAAAACCGTTATGAT 5699 29 100.0 32 ............................. TCCGGGGAAAGAACTCGCCTCGTCCAGCGTCA 5760 29 100.0 32 ............................. CGGCGGCGGACGCCGCTCAGATAGCCAAAACC 5821 29 96.6 32 ..G.......................... TATACAGGATTCTCACACTTTGGTTTGGTCGA 5882 29 96.6 32 ..G.......................... CGTTTTTTTTATTTGTACTATTGTCAGTACCC 5943 29 96.6 32 ..G.......................... CGGAAACAAACAAAGTTTTGCGCGATTCCACC 6004 29 96.6 32 ..G.......................... CACCAGGTAACAATATCGTCCCCGACCTTTAT 6065 29 96.6 32 ..G.......................... GCGAAATTCCCCAGATACCGCGCATCGGCACT 6126 29 93.1 32 ..G.........T................ CAAAATTAATGTCCAGGACCTTATTAAGTTAC 6187 29 93.1 32 ..G.........T................ CTCGGGGATTTTGTGCCACCCAAAACGCTCGC 6248 29 93.1 32 ..G.........T................ GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 6309 29 93.1 32 ..G..........T............... CCGGATGAAAACGCCTACCCGGAAGACTACGA 6370 28 86.2 0 ..G.........T..........-.G... | ========== ====== ====== ====== ============================= ================================ ================== 18 29 96.8 32 GTATTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGCTGAGCGATGATAAACCGCGCGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACTTGTATTGCGCGTAACTGGCGTTTGTCGATGCAAACACATAAATATTTAAATATTGCCTGATGCATTACTAATTTTACGGACGGCCTGCCGATGCCGTCTGTGAGTCATCCATTACCTCGCCTTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTAGAATGTGGTGCGGACAAAAAGTAGTTTATAAACAATGACATACGTTTAGT # Right flank : GTTGCATAATTATAGTCTGTGTACCAGTAATGGCTGGTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTATACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCATTGAAGGCCCGGCCAGGATTAAGCCTGTTGGTCGAGGATGAGTCTACGTCGATCTTGTTCGATACCGGCCCTGATGACAGTTTTATGCAAAACGCGTCGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAACAGTCGAATCATCTGCCATCCCGATATTGCGCGTGAACGTTATGCGGCAATGACTTTTCTCGGTATTACCCGAAAAATAAAAAAATTGTCATGTGAAGTGGACTATTCACGCTACCGAATGATGTACACGCGTGACCCCCTGCCGATTGG # Questionable array : NO Score: 5.79 # Score Detail : 1:0, 2:3, 3:0, 4:0.84, 5:0, 6:0.25, 7:0.01, 8:1, 9:0.69, # 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], // Array 2 23158-24102 **** Predicted by CRISPRDetect 2.4 *** >NZ_QZEO01000002.1 Salmonella enterica subsp. enterica serovar Schwarzengrund strain MDH-6 MDH6_trimmed_contig_2, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 23158 29 100.0 32 ............................. AAACATCCGATCAAATACTGCGTTCGTTTGAG 23219 29 100.0 32 ............................. CGTATTTTTGAACTGGCCAGCGCCACCGATGC 23280 29 100.0 32 ............................. GGTTACGCGGGCGTCTGTTAAAGAGTCCTCGT 23341 29 100.0 32 ............................. GCCGGGGTTTCCCAGAGGCATTCTGATGAAAG 23402 29 100.0 32 ............................. CGAATGCAGATGCCTCCCGTACTGCCGCCGGA 23463 29 100.0 32 ............................. GATTGGCCCTTAGATAACGGGAGATCAAGCGC 23524 29 100.0 32 ............................. CATAACCTTCGCTACCACACTTGCCGGTACTT 23585 29 100.0 32 ............................. CCTTGAGGTTAGGGGAGTCAGGAAATTGCATT 23646 29 100.0 32 ............................. ACAAAATCGGCGGCCCAATCGCCGGCGCTGAC 23707 29 100.0 32 ............................. GCCTGCCGTCTTTTTATTGAGGTCTGTAAACC 23768 29 96.6 32 ............................T TAATCATTTTGTTTAAATCCCGGATCACCTCC 23829 29 100.0 32 ............................. GAGTTATTGTCACTCGTCAGTGATAATTTTCT 23890 29 100.0 32 ............................. CCCGTTGAAGATCTGGACGCATGGGGCAAAGC 23951 29 100.0 32 ............................. GTGAGCTCGGTTTTAATTTCGTCGCTAAGGTG 24012 29 100.0 32 ............................. CAAAAGGCCGACAGTGTGTACACCTCTAAAAA 24073 29 96.6 0 ............T................ | A [24100] ========== ====== ====== ====== ============================= ================================ ================== 16 29 99.6 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : CTTATTGAAGATGTTCTCGCGGAAGGGGAAATTCAACCGCCGTTACCTCCTGAAGATTCACAACCCATAGCGATCCCTCTTCCTGTTGCGTTGGGAGATTCCGGTCATCGGAGTACCTAACGATGAGTATGCTGGTTGTCGTTACCGAAAATGTTCCTCCTCGTCTGCGGGGGAGGCTGGCCGTCTGGTTACTGGAAATTCGAGCTGGTGTGTATGTTGGTGATGTTTCCGCAAAGATCCGCGAGATGATATGGCAACAGGTTTCCGTTCTGGCAGATGAGGGAAATGTTGTTATGGCGTGGGCGACAAATACAGAATCAGGTTTTGAGTTTCAGACTTTTGGTGAAAATCGACGTATTCCGGTAGATCTTGATGGACTGCGATTGGTGTCGTTTCTACCTGTTGAAAATCAATAATTTAGAGATCTTTAAAAATTAGGAAAAGTTGGTGGTTTTTTTGTGCGCTAAAAAAGTATTTAAATTCAATTGGGTAGATTTAGA # Right flank : GTTTCACCAGCTTATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATTCGCCCAGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTGCCGTTCGGGAAGGATGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACCGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATACCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCG # 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: 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: F [71.7-48.3]%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], //