Array 1 5493-6557 **** Predicted by CRISPRDetect 2.4 *** >NZ_QZEQ01000018.1 Salmonella enterica subsp. enterica serovar Schwarzengrund strain MDH-4 MDH4_trimmed__paired__contig_18, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 5493 29 100.0 32 ............................. GCTATGTAGCTAACCTATTGATTTTATAAGAA 5554 29 100.0 32 ............................. TGGCGCAGCAACCAGATCCCGCTAACGAACCC 5615 29 100.0 32 ............................. CGTTGCTGGCTATTCGAACTAACCTGATTGTT 5676 29 100.0 32 ............................. GCCTCAGCATTGTCATAACCCCACGCCTGGCA 5737 29 100.0 32 ............................. CGGCTCGACCGGGAGCTTGCCGGCATCGTGGA 5798 29 100.0 32 ............................. GCAACTTCTTATATGTAAAAAACCGTTATGAT 5859 29 100.0 32 ............................. TCCGGGGAAAGAACTCGCCTCGTCCAGCGTCA 5920 29 100.0 32 ............................. CGGCGGCGGACGCCGCTCAGATAGCCAAAACC 5981 29 96.6 32 ..G.......................... TATACAGGATTCTCACACTTTGGTTTGGTCGA 6042 29 96.6 32 ..G.......................... CGTTTTTTTTATTTGTACTATTGTCAGTACCC 6103 29 96.6 32 ..G.......................... CGGAAACAAACAAAGTTTTGCGCGATTCCACC 6164 29 96.6 32 ..G.......................... CACCAGGTAACAATATCGTCCCCGACCTTTAT 6225 29 96.6 32 ..G.......................... GCGAAATTCCCCAGATACCGCGCATCGGCACT 6286 29 93.1 32 ..G.........T................ CAAAATTAATGTCCAGGACCTTATTAAGTTAC 6347 29 93.1 32 ..G.........T................ CTCGGGGATTTTGTGCCACCCAAAACGCTCGC 6408 29 93.1 32 ..G.........T................ GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 6469 29 93.1 32 ..G..........T............... CCGGATGAAAACGCCTACCCGGAAGACTACGA 6530 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 23318-24262 **** Predicted by CRISPRDetect 2.4 *** >NZ_QZEQ01000018.1 Salmonella enterica subsp. enterica serovar Schwarzengrund strain MDH-4 MDH4_trimmed__paired__contig_18, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 23318 29 100.0 32 ............................. AAACATCCGATCAAATACTGCGTTCGTTTGAG 23379 29 100.0 32 ............................. CGTATTTTTGAACTGGCCAGCGCCACCGATGC 23440 29 100.0 32 ............................. GGTTACGCGGGCGTCTGTTAAAGAGTCCTCGT 23501 29 100.0 32 ............................. GCCGGGGTTTCCCAGAGGCATTCTGATGAAAG 23562 29 100.0 32 ............................. CGAATGCAGATGCCTCCCGTACTGCCGCCGGA 23623 29 100.0 32 ............................. GATTGGCCCTTAGATAACGGGAGATCAAGCGC 23684 29 100.0 32 ............................. CATAACCTTCGCTACCACACTTGCCGGTACTT 23745 29 100.0 32 ............................. CCTTGAGGTTAGGGGAGTCAGGAAATTGCATT 23806 29 100.0 32 ............................. ACAAAATCGGCGGCCCAATCGCCGGCGCTGAC 23867 29 100.0 32 ............................. GCCTGCCGTCTTTTTATTGAGGTCTGTAAACC 23928 29 96.6 32 ............................T TAATCATTTTGTTTAAATCCCGGATCACCTCC 23989 29 100.0 32 ............................. GAGTTATTGTCACTCGTCAGTGATAATTTTCT 24050 29 100.0 32 ............................. CCCGTTGAAGATCTGGACGCATGGGGCAAAGC 24111 29 100.0 32 ............................. GTGAGCTCGGTTTTAATTTCGTCGCTAAGGTG 24172 29 100.0 32 ............................. CAAAAGGCCGACAGTGTGTACACCTCTAAAAA 24233 29 96.6 0 ............T................ | A [24260] ========== ====== ====== ====== ============================= ================================ ================== 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], //