Array 1 159967-159083 **** Predicted by CRISPRDetect 2.4 *** >NZ_QZFD01000018.1 Salmonella enterica subsp. enterica serovar Schwarzengrund strain MDH-11 MDH11_trimmed_contig_18, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 159966 29 100.0 32 ............................. AAACATCCGATCAAATACTGCGTTCGTTTGAG 159905 29 100.0 32 ............................. CGTATTTTTGAACTGGCCAGCGCCACCGATGC 159844 29 100.0 32 ............................. GGTTACGCGGGCGTCTGTTAAAGAGTCCTCGT 159783 29 100.0 32 ............................. GCCGGGGTTTCCCAGAGGCATTCTGATGAAAG 159722 29 100.0 32 ............................. CGAATGCAGATGCCTCCCGTACTGCCGCCGGA 159661 29 100.0 32 ............................. GATTGGCCCTTAGATAACGGGAGATCAAGCGC 159600 29 100.0 32 ............................. CATAACCTTCGCTACCACACTTGCCGGTACTT 159539 29 100.0 32 ............................. CCTTGAGGTTAGGGGAGTCAGGAAATTGCATT 159478 29 100.0 32 ............................. ACAAAATCGGCGGCCCAATCGCCGGCGCTGAC 159417 29 100.0 32 ............................. GCCTGCCGTCTTTTTATTGAGGTCTGTAAACC 159356 29 96.6 32 ............................T TAATCATTTTGTTTAAATCCCGGATCACCTCC 159295 29 100.0 32 ............................. GAGTTATTGTCACTCGTCAGTGATAATTTTCT 159234 29 100.0 32 ............................. GTGAGCTCGGTTTTAATTTCGTCGCTAAGGTG 159173 29 100.0 32 ............................. CAAAAGGCCGACAGTGTGTACACCTCTAAAAA 159112 29 96.6 0 ............T................ | A [159085] ========== ====== ====== ====== ============================= ================================ ================== 15 29 99.5 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : CTTATTGAAGATGTTCTCGCGGAAGGGGAAATTCAACCGCCGTTACCTCCTGAAGATTCACAACCCATAGCGATCCCTCTTCCTGTTGCGTTGGGAGATTCCGGTCATCGGAGTACCTAACGATGAGTATGCTGGTTGTCGTTACCGAAAATGTTCCTCCTCGTCTGCGGGGGAGGCTGGCCGTCTGGTTACTGGAAATTCGAGCTGGTGTGTATGTTGGTGATGTTTCCGCAAAGATCCGCGAGATGATATGGCAACAGGTTTCCGTTCTGGCAGATGAGGGAAATGTTGTTATGGCGTGGGCGACAAATACAGAATCAGGTTTTGAGTTTCAGACTTTTGGTGAAAATCGACGTATTCCGGTAGATCTTGATGGACTGCGATTGGTGTCGTTTCTACCTGTTGAAAATCAATAATTTAGAGATCTTTAAAAATTAGGAAAAGTTGGTGGTTTTTTTGTGCGCTAAAAAAGTATTTAAATTCAATTGGGTAGATTTAGA # Right flank : TTTCACCAGCTTATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATTCGCCCAGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTGCCGTTCGGGAAGGATGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACCGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATACCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCGT # Questionable array : NO Score: 6.23 # Score Detail : 1:0, 2:3, 3:0, 4:0.97, 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 [3-0] 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 2 177792-176727 **** Predicted by CRISPRDetect 2.4 *** >NZ_QZFD01000018.1 Salmonella enterica subsp. enterica serovar Schwarzengrund strain MDH-11 MDH11_trimmed_contig_18, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 177791 29 100.0 32 ............................. GCTATGTAGCTAACCTATTGATTTTATAAGAA 177730 29 100.0 32 ............................. TGGCGCAGCAACCAGATCCCGCTAACGAACCC 177669 29 100.0 32 ............................. CGTTGCTGGCTATTCGAACTAACCTGATTGTT 177608 29 100.0 32 ............................. GCCTCAGCATTGTCATAACCCCACGCCTGGCA 177547 29 100.0 32 ............................. CGGCTCGACCGGGAGCTTGCCGGCATCGTGGA 177486 29 100.0 32 ............................. GCAACTTCTTATATGTAAAAAACCGTTATGAT 177425 29 100.0 32 ............................. TCCGGGGAAAGAACTCGCCTCGTCCAGCGTCA 177364 29 100.0 32 ............................. CGGCGGCGGACGCCGCTCAGATAGCCAAAACC 177303 29 96.6 32 ..G.......................... TATACAGGATTCTCACACTTTGGTTTGGTCGA 177242 29 96.6 32 ..G.......................... CGTTTTTTTTATTTGTACTATTGTCAGTACCC 177181 29 96.6 32 ..G.......................... CGGAAACAAACAAAGTTTTGCGCGATTCCACC 177120 29 96.6 32 ..G.......................... CACCAGGTAACAATATCGTCCCCGACCTTTAT 177059 29 96.6 32 ..G.......................... GCGAAATTCCCCAGATACCGCGCATCGGCACT 176998 29 93.1 32 ..G.........T................ CAAAATTAATGTCCAGGACCTTATTAAGTTAC 176937 29 93.1 32 ..G.........T................ CTCGGGGATTTTGTGCCACCCAAAACGCTCGC 176876 29 93.1 32 ..G.........T................ GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 176815 29 93.1 32 ..G..........T............... CCGGATGAAAACGCCTACCCGGAAGACTACGA 176754 28 86.2 0 ..G.........T...........G-... | ========== ====== ====== ====== ============================= ================================ ================== 18 29 96.8 32 GTATTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGCTGAGCGATGATAAACCGCGCGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACTTGTATTGCGCGTAACTGGCGTTTGTCGATGCAAACACATAAATATTTAAATATTGCCTGATGCATTACTAATTTTACGGACGGCCTGCCGATGCCGTCTGTGAGTCATCCATTACCTCGCCTTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTAGAATGTGGTGCGGACAAAAAGTAGTTTATAAACAATGACATACGTTTAGT # Right flank : TTGCATAATTATAGTCTGTGTACCAGTAATGGCTGGTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTATACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCATTGAAGGCCCGGCCAGGATTAAGCCTGTTGGTCGAGGATGAGTCTACGTCGATCTTGTTCGATACCGGCCCTGATGACAGTTTTATGCAAAACGCGTCGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAACAGTCGAATCATCTGCCATCCCGATATTGCGCGTGAACGTTATGCGGCAATGACTTTTCTCGGTATTACCCGAAAAATAAAAAAATTGTCATGTGAAGTGGACTATTCACGCTACCGAATGATGTACACGCGTGACCCCCTGCCGATTGGC # 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: R [4,6] Score: 0.37/0.37 # Reference repeat match prediction: R [matched GTATTCCCCGCGCCAGCGGGGATAAACCG 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 [6-0] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [63.3-66.7]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0,5.65 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], //