Array 1 163233-161799 **** Predicted by CRISPRDetect 2.4 *** >NZ_MYAG01000002.1 Salmonella enterica subsp. enterica serovar Java strain BCW_2758 NODE_2_length_411263_cov_3.14564, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 163232 29 100.0 32 ............................. GTACGTCGAAGTATGCTGAATTACAGGAAGGC 163171 29 100.0 32 ............................. GCCGGTCGGCGGTATTACTCAATATTTATACG 163110 29 100.0 32 ............................. TTAGCAATAGGCTACGGCGATAAAACTTTTAA 163049 29 100.0 32 ............................. TTTCGAAATTCCTGCTCGATGTCGACCGCCGG 162988 29 100.0 32 ............................. GGATAAAGACGACGTTGAAGAAGCCGAACACG 162927 29 100.0 32 ............................. CTGCTGAGGGCGAATAACAAAATCATCAACCA 162866 29 100.0 32 ............................. CCTTGCTAGTGGGGAAGCGCTACGATTCACGA 162805 29 100.0 32 ............................. GTGAGCGCCGCCTTGGTACTGGCCTTTTGAGT 162744 29 100.0 32 ............................. GGTATGTTTCCGAAGACCTCGGCTGGCCTTTT 162683 29 96.6 33 ............T................ CAACGTTTCACTGTCGAGATAGCTATTGTCCGC 162621 29 100.0 32 ............................. GCAAACGAGTCTGTTTTGCAGACGTGTCTGGA 162560 29 100.0 32 ............................. CCCCGGCCTGATCTCGATCGGTGACGTAGGCA 162499 29 100.0 32 ............................. AATTTGAATGCACTGGTATTAACGACGAATAT 162438 29 100.0 32 ............................. CGCGGTCATACTTCAGGATCTGCTCTGTTGTT 162377 29 100.0 32 ............................. CCATTCTCGTTGTCGGTCATCTAGCGGTTGCG 162316 29 100.0 32 ............................. CCCAGTCAGGGGCGCGATATTGCCGCCGTGTT 162255 29 100.0 32 ............................. TATCGAGCGTTGTTTCGGTGCGGGCCTGAGCT 162194 29 100.0 32 ............................. AGGGCTACCCGGTTGCGCGTATTGATGCCCCG 162133 29 100.0 32 ............................. TTGTGCGGCAACGCCCGTTTTTATCGGTGGAC 162072 29 100.0 32 ............................. ACCGAGAGTGACATTTTCCCACTACTGGCTGG 162011 29 100.0 32 ............................. TTTGCCGCTGCTCGGTGAGGGAGCGTTTCATA 161950 29 100.0 32 ............................. CGCAACTATCCATGCAAATATTTCCATTGCTA 161889 29 100.0 32 ............................. GCAGCACTGGCTGGAGTGGCTGGCGAAAAATC 161828 29 96.6 0 ............T................ | A [161801] ========== ====== ====== ====== ============================= ================================= ================== 24 29 99.7 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTGCTCGCTGCCGGTGAAATTGAACCACCTCAGCCTGCGCCGGATATGTTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTTGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTTAGATTAGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTAGGTAATAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : TTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTGCCGTTCGGGAAGGATGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACCGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATACCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCAGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATCACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCGT # Questionable array : NO Score: 6.25 # Score Detail : 1:0, 2:3, 3:0, 4:0.99, 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 2 179760-178511 **** Predicted by CRISPRDetect 2.4 *** >NZ_MYAG01000002.1 Salmonella enterica subsp. enterica serovar Java strain BCW_2758 NODE_2_length_411263_cov_3.14564, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 179759 29 100.0 32 ............................. ACGCTGGCCGAAAACGGATTTTCAATCCGCAT 179698 29 100.0 32 ............................. TATTCATCTGCTGCCGCCTGGTTTGTTTTATC 179637 29 100.0 32 ............................. GGATCGGCAAACTTGTTTTAACGCCGGACAAC 179576 29 100.0 32 ............................. CCCCTTCTGATCCCCTTTCAATTTCGCGCTTA 179515 29 100.0 32 ............................. TATGATCCGCCATAGAAACAAATACAAAAATG 179454 29 100.0 32 ............................. CTGTTTTGCAACCGCATCCCCGGATTCGGGAT 179393 29 100.0 32 ............................. TTGCCACAACCACAATGGATCAGGAGCAATTA 179332 29 100.0 32 ............................. AATTATCGAAAGGAGTTACTCAGGGGGGAGAC 179271 29 100.0 32 ............................. CAGCGGAAGCGATCAGTGGTCTCGATACGGAA 179210 29 96.6 32 ...................A......... GGCTCAGGTTGATGATTCTCATGAGACACAAT 179149 29 100.0 32 ............................. GGGTGATCATGACGATCCAGAGCATATTGCCC 179088 29 100.0 32 ............................. GATTGAGAGAAGGGCTTGCTTAGCTTCCTTCC 179027 29 96.6 32 ..................A.......... TGGGGCTGTAAGGTCCGTTTAATATCCACTCA 178966 29 100.0 32 ............................. TTCGTTAATTATATTACAATACAAATCATAAC 178905 29 96.6 33 ............................A GCCTTCCGGTACGTCGTCATTTTCAGTCAGCGG 178843 29 96.6 32 ............T................ CAAAATTAATGTCCAGGACCTTATTAAGTTAC 178782 29 96.6 32 ............T................ GAAGGATTACCACCCCGGCAGCGCTCACCCGT 178721 29 100.0 32 ............................. GCGTTAGCGCGTTACATCCGGTTTGAGGCTGA 178660 29 100.0 32 ............................. GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 178599 29 96.6 32 .............T............... CCGGATGAAAACGCCTACCCGGAAGACTACGA 178538 28 82.8 0 ...............A.AA.....G-... | ========== ====== ====== ====== ============================= ================================= ================== 21 29 98.2 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGCGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACATGTATTGCGCGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATTGCCTGATGCTCTATCAATTTTACGGACGGCCTGCCGATGCCGTCTGTGACTTATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCGGATAAATTTTTCCATAGCGATGCATGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGTAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCTATTATGTTGGTGGAATGTGGTGCTGATAAAAAATAGTTTATAAACAATGATATACGTTTAGT # Right flank : TTGCATAATCATAATCTGTGTACCAGTAATGGCTGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTTCCGGGGAGGCTTTTATACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGCCCGGCCAGGATTAAGCCTGTTGGTCGAGGATGAGTCTACGTCGATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAACAGTCGAATCATCTGCCATCCCGATATTGCGCGCGAACGTTATGCGGCAATGACTTTTCTCGGTATTACCCGAAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTACCGAATGATGTACACGCGTGGCCCCCTGCCGATTGGC # Questionable array : NO Score: 6.17 # Score Detail : 1:0, 2:3, 3:0, 4:0.91, 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 [7-0] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [63.3-71.7]%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], //