Array 1 14374-15622 **** Predicted by CRISPRDetect 2.4 *** >NZ_VUJC01000011.1 Salmonella enterica subsp. enterica serovar Java strain 159196 contig011, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 14374 29 100.0 32 ............................. ACGCTGGCCGAAAACGGATTTTCAATCCGCAT 14435 29 100.0 32 ............................. TATTCATCTGCTGCCGCCTGGTTTGTTTTATC 14496 29 100.0 32 ............................. GGATCGGCAAACTTGTTTTAACGCCGGACAAC 14557 29 100.0 32 ............................. CCCCTTCTGATCCCCTTTCAATTTCGCGCTTA 14618 29 100.0 32 ............................. TATGATCCGCCATAGAAACAAATACAAAAATG 14679 29 100.0 32 ............................. CTGTTTTGCAACCGCATCCCCGGATTCGGGAT 14740 29 100.0 32 ............................. TTGCCACAACCACAATGGATCAGGAGCAATTA 14801 29 100.0 32 ............................. AATTATCGAAAGGAGTTACTCAGGGGGGAGAC 14862 29 100.0 32 ............................. CAGCGGAAGCGATCAGTGGTCTCGATACGGAA 14923 29 96.6 32 ...................A......... GGCTCAGGTTGATGATTCTCATGAGACACAAT 14984 29 100.0 32 ............................. GGGTGATCATGACGATCCAGAGCATATTGCCC 15045 29 100.0 32 ............................. GATTGAGAGAAGGGCTTGCTTAGCTTCCTTCC 15106 29 96.6 32 ..................A.......... TGGGGCTGTAAGGTCCGTTTAATATCCACTCA 15167 29 100.0 32 ............................. TTCGTTAATTATATTACAATACAAATCATAAC 15228 29 96.6 33 ............................A GCCTTCCGGTACGTCGTCATTTTCAGTCAGCGG 15290 29 96.6 32 ............T................ CAAAATTAATGTCCAGGACCTTATTAAGTTAC 15351 29 96.6 32 ............T................ GAAGGATTACCACCCCGGCAGCGCTCACCCGT 15412 29 100.0 32 ............................. GCGTTAGCGCGTTACATCCGGTTTGAGGCTGA 15473 29 100.0 32 ............................. GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 15534 29 96.6 32 .............T............... CCGGATGAAAACGCCTACCCGGAAGACTACGA 15595 28 82.8 0 ...............A.AA....-.G... | ========== ====== ====== ====== ============================= ================================= ================== 21 29 98.2 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGCGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACATGTATTGCGCGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATTGCCTGATGCTCTATCAATTTTACGGACGGCCTGCCGATGCCGTCTGTGACTTATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCGGATAAATTTTTCCATAGCGATGCATGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGTAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCTATTATGTTGGTGGAATGTGGTGCTGATAAAAAATAGTTTATAAACAATGATATACGTTTAGT # Right flank : GTTGCATAATCATAATCTGTGTACCAGTAATGGCTGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTTCCGGGGAGGCTTTTATACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGCCCGGCCAGGATTAAGCCTGTTGGTCGAGGATGAGTCTACGTCGATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAACAGTCGAATCATCTGCCATCCCGATATTGCGCGCGAACGTTATGCGGCAATGACTTTTCTCGGTATTACCCGAAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTACCGAATGATGTACACGCGTGGCCCCCTGCCGATTGG # 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: 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 [0-7] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [71.7-63.3]%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 30901-32395 **** Predicted by CRISPRDetect 2.4 *** >NZ_VUJC01000011.1 Salmonella enterica subsp. enterica serovar Java strain 159196 contig011, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 30901 29 100.0 32 ............................. GTACGTCGAAGTATGCTGAATTACAGGAAGGC 30962 29 100.0 32 ............................. CCCGCCGTCTGTTTGCGGTTTTGAGCGCCCGA 31023 29 100.0 32 ............................. GCCGGTCGGCGGTATTACTCAATATTTATACG 31084 29 100.0 32 ............................. TTAGCAATAGGCTACGGCGATAAAACTTTTAA 31145 29 100.0 32 ............................. TTTCGAAATTCCTGCTCGATGTCGACCGCCGG 31206 29 100.0 32 ............................. GGATAAAGACGACGTTGAAGAAGCCGAACACG 31267 29 100.0 32 ............................. CTGCTGAGGGCGAATAACAAAATCATCAACCA 31328 29 100.0 32 ............................. CCTTGCTAGTGGGGAAGCGCTACGATTCACGA 31389 29 100.0 32 ............................. GTGAGCGCCGCCTTGGTACTGGCCTTTTGAGT 31450 29 100.0 32 ............................. GGTATGTTTCCGAAGACCTCGGCTGGCCTTTT 31511 29 96.6 33 ............T................ CAACGTTTCACTGTCGAGATAGCTATTGTCCGC 31573 29 100.0 32 ............................. GCAAACGAGTCTGTTTTGCAGACGTGTCTGGA 31634 29 100.0 32 ............................. CCCCGGCCTGATCTCGATCGGTGACGTAGGCA 31695 29 100.0 32 ............................. AATTTGAATGCACTGGTATTAACGACGAATAT 31756 29 100.0 32 ............................. CGCGGTCATACTTCAGGATCTGCTCTGTTGTT 31817 29 100.0 32 ............................. CCATTCTCGTTGTCGGTCATCTAGCGGTTGCG 31878 29 100.0 32 ............................. CCCAGTCAGGGGCGCGATATTGCCGCCGTGTT 31939 29 100.0 32 ............................. TATCGAGCGTTGTTTCGGTGCGGGCCTGAGCT 32000 29 100.0 32 ............................. AGGGCTACCCGGTTGCGCGTATTGATGCCCCG 32061 29 100.0 32 ............................. TTGTGCGGCAACGCCCGTTTTTATCGGTGGAC 32122 29 100.0 32 ............................. ACCGAGAGTGACATTTTCCCACTACTGGCTGG 32183 29 100.0 32 ............................. TTTGCCGCTGCTCGGTGAGGGAGCGTTTCATA 32244 29 100.0 32 ............................. CGCAACTATCCATGCAAATATTTCCATTGCTA 32305 29 100.0 32 ............................. GCAGCACTGGCTGGAGTGGCTGGCGAAAAATC 32366 29 96.6 0 ............T................ | A [32393] ========== ====== ====== ====== ============================= ================================= ================== 25 29 99.7 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTGCTCGCTGCCGGTGAAATTGAACCACCTCAGCCTGCGCCGGATATGTTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTTGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTTAGATTAGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTAGGTAATAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : GTTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTGCCGTTCGGGAAGGATGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACCGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATACCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCAGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATCACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCG # 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: 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 [0-2] 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], //