Array 1 97818-98882 **** Predicted by CRISPRDetect 2.4 *** >NZ_QZES01000009.1 Salmonella enterica subsp. enterica serovar Schwarzengrund strain MDH-2 MDH2_trimmed__paired__contig_9, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 97818 29 100.0 32 ............................. GCTATGTAGCTAACCTATTGATTTTATAAGAA 97879 29 100.0 32 ............................. TGGCGCAGCAACCAGATCCCGCTAACGAACCC 97940 29 100.0 32 ............................. CGTTGCTGGCTATTCGAACTAACCTGATTGTT 98001 29 100.0 32 ............................. GCCTCAGCATTGTCATAACCCCACGCCTGGCA 98062 29 100.0 32 ............................. CGGCTCGACCGGGAGCTTGCCGGCATCGTGGA 98123 29 100.0 32 ............................. GCAACTTCTTATATGTAAAAAACCGTTATGAT 98184 29 100.0 32 ............................. TCCGGGGAAAGAACTCGCCTCGTCCAGCGTCA 98245 29 100.0 32 ............................. CGGCGGCGGACGCCGCTCAGATAGCCAAAACC 98306 29 96.6 32 ..G.......................... TATACAGGATTCTCACACTTTGGTTTGGTCGA 98367 29 96.6 32 ..G.......................... CGTTTTTTTTATTTGTACTATTGTCAGTACCC 98428 29 96.6 32 ..G.......................... CGGAAACAAACAAAGTTTTGCGCGATTCCACC 98489 29 96.6 32 ..G.......................... CACCAGGTAACAATATCGTCCCCGACCTTTAT 98550 29 96.6 32 ..G.......................... GCGAAATTCCCCAGATACCGCGCATCGGCACT 98611 29 93.1 32 ..G.........T................ CAAAATTAATGTCCAGGACCTTATTAAGTTAC 98672 29 93.1 32 ..G.........T................ CTCGGGGATTTTGTGCCACCCAAAACGCTCGC 98733 29 93.1 32 ..G.........T................ GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 98794 29 93.1 32 ..G..........T............... CCGGATGAAAACGCCTACCCGGAAGACTACGA 98855 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 115643-116587 **** Predicted by CRISPRDetect 2.4 *** >NZ_QZES01000009.1 Salmonella enterica subsp. enterica serovar Schwarzengrund strain MDH-2 MDH2_trimmed__paired__contig_9, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 115643 29 100.0 32 ............................. AAACATCCGATCAAATACTGCGTTCGTTTGAG 115704 29 100.0 32 ............................. CGTATTTTTGAACTGGCCAGCGCCACCGATGC 115765 29 100.0 32 ............................. GGTTACGCGGGCGTCTGTTAAAGAGTCCTCGT 115826 29 100.0 32 ............................. GCCGGGGTTTCCCAGAGGCATTCTGATGAAAG 115887 29 100.0 32 ............................. CGAATGCAGATGCCTCCCGTACTGCCGCCGGA 115948 29 100.0 32 ............................. GATTGGCCCTTAGATAACGGGAGATCAAGCGC 116009 29 100.0 32 ............................. CATAACCTTCGCTACCACACTTGCCGGTACTT 116070 29 100.0 32 ............................. CCTTGAGGTTAGGGGAGTCAGGAAATTGCATT 116131 29 100.0 32 ............................. ACAAAATCGGCGGCCCAATCGCCGGCGCTGAC 116192 29 100.0 32 ............................. GCCTGCCGTCTTTTTATTGAGGTCTGTAAACC 116253 29 96.6 32 ............................T TAATCATTTTGTTTAAATCCCGGATCACCTCC 116314 29 100.0 32 ............................. GAGTTATTGTCACTCGTCAGTGATAATTTTCT 116375 29 100.0 32 ............................. CCCGTTGAAGATCTGGACGCATGGGGCAAAGC 116436 29 100.0 32 ............................. GTGAGCTCGGTTTTAATTTCGTCGCTAAGGTG 116497 29 100.0 32 ............................. CAAAAGGCCGACAGTGTGTACACCTCTAAAAA 116558 29 96.6 0 ............T................ | A [116585] ========== ====== ====== ====== ============================= ================================ ================== 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], //