Array 1 250366-248871 **** Predicted by CRISPRDetect 2.4 *** >NZ_MYAF01000001.1 Salmonella enterica subsp. enterica serovar Java strain BCW_2759 NODE_1_length_349854_cov_2.00031, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 250365 29 100.0 32 ............................. GTACGTCGAAGTATGCTGAATTACAGGAAGGC 250304 29 100.0 32 ............................. CCCGCCGTCTGTTTGCGGTTTTGAGCGCCCGA 250243 29 100.0 32 ............................. GCCGGTCGGCGGTATTACTCAATATTTATACG 250182 29 100.0 32 ............................. TTAGCAATAGGCTACGGCGATAAAACTTTTAA 250121 29 100.0 32 ............................. TTTCGAAATTCCTGCTCGATGTCGACCGCCGG 250060 29 100.0 32 ............................. GGATAAAGACGACGTTGAAGAAGCCGAACACG 249999 29 100.0 32 ............................. CTGCTGAGGGCGAATAACAAAATCATCAACCA 249938 29 100.0 32 ............................. CCTTGCTAGTGGGGAAGCGCTACGATTCACGA 249877 29 100.0 32 ............................. GTGAGCGCCGCCTTGGTACTGGCCTTTTGAGT 249816 29 100.0 32 ............................. GGTATGTTTCCGAAGACCTCGGCTGGCCTTTT 249755 29 96.6 33 ............T................ CAACGTTTCACTGTCGAGATAGCTATTGTCCGC 249693 29 100.0 32 ............................. GCAAACGAGTCTGTTTTGCAGACGTGTCTGGA 249632 29 100.0 32 ............................. CCCCGGCCTGATCTCGATCGGTGACGTAGGCA 249571 29 100.0 32 ............................. AATTTGAATGCACTGGTATTAACGACGAATAT 249510 29 100.0 32 ............................. CGCGGTCATACTTCAGGATCTGCTCTGTTGTT 249449 29 100.0 32 ............................. CCATTCTCGTTGTCGGTCATCTAGCGGTTGCG 249388 29 100.0 32 ............................. CCCAGTCAGGGGCGCGATATTGCCGCCGTGTT 249327 29 100.0 32 ............................. TATCGAGCGTTGTTTCGGTGCGGGCCTGAGCT 249266 29 100.0 32 ............................. AGGGCTACCCGGTTGCGCGTATTGATGCCCCG 249205 29 100.0 32 ............................. TTGTGCGGCAACGCCCGTTTTTATCGGTGGAC 249144 29 100.0 32 ............................. ACCGAGAGTGACATTTTCCCACTACTGGCTGG 249083 29 100.0 32 ............................. TTTGCCGCTGCTCGGTGAGGGAGCGTTTCATA 249022 29 100.0 32 ............................. CGCAACTATCCATGCAAATATTTCCATTGCTA 248961 29 100.0 32 ............................. GCAGCACTGGCTGGAGTGGCTGGGGAAAAATC 248900 29 96.6 0 ............T................ | A [248873] ========== ====== ====== ====== ============================= ================================= ================== 25 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 266893-265644 **** Predicted by CRISPRDetect 2.4 *** >NZ_MYAF01000001.1 Salmonella enterica subsp. enterica serovar Java strain BCW_2759 NODE_1_length_349854_cov_2.00031, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 266892 29 100.0 32 ............................. ACGCTGGCCGAAAACGGATTTTCAATCCGCAT 266831 29 100.0 32 ............................. TATTCATCTGCTGCCGCCTGGTTTGTTTTATC 266770 29 100.0 32 ............................. GGATCGGCAAACTTGTTTTAACGCCGGACAAC 266709 29 100.0 32 ............................. CCCCTTCTGATCCCCTTTCAATTTCGCGCTTA 266648 29 100.0 32 ............................. TATGATCCGCCATAGAAACAAATACAAAAATG 266587 29 100.0 32 ............................. CTGTTTTGCAACCGCATCCCCGGATTCGGGAT 266526 29 100.0 32 ............................. TTGCCACAACCACAATGGATCAGGAGCAATTA 266465 29 100.0 32 ............................. AATTATCGAAAGGAGTTACTCAGGGGGGAGAC 266404 29 100.0 32 ............................. CAGCGGAAGCGATCAGTGGTCTCGATACGGAA 266343 29 96.6 32 ...................A......... GGCTCAGGTTGATGATTCTCATGAGACACAAT 266282 29 100.0 32 ............................. GGGTGATCATGACGATCCAGAGCATATTGCCC 266221 29 100.0 32 ............................. GATTGAGAGAAGGGCTTGCTTAGCTTCCTTCC 266160 29 96.6 32 ..................A.......... TGGGGCTGTAAGGTCCGTTTAATATCCACTCA 266099 29 100.0 32 ............................. TTCGTTAATTATATTACAATACAAATCATAAC 266038 29 96.6 33 ............................A GCCTTCCGGTACGTCGTCATTTTCAGTCAGCGG 265976 29 96.6 32 ............T................ CAAAATTAATGTCCAGGACCTTATTAAGTTAC 265915 29 96.6 32 ............T................ GAAGGATTACCACCCCGGCAGCGCTCACCCGT 265854 29 100.0 32 ............................. GCGTTAGCGCGTTACATCCGGTTTGAGGCTGA 265793 29 100.0 32 ............................. GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 265732 29 96.6 32 .............T............... CCGGATGAAAACGCCTACCCGGAAGACTACGA 265671 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], //