Array 1 170656-169161 **** Predicted by CRISPRDetect 2.4 *** >NZ_VUJM01000001.1 Salmonella enterica subsp. enterica serovar Java strain 162829 contig01, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 170655 29 100.0 32 ............................. GTACGTCGAAGTATGCTGAATTACAGGAAGGC 170594 29 100.0 32 ............................. CCCGCCGTCTGTTTGCGGTTTTGAGCGCCCGA 170533 29 100.0 32 ............................. GCCGGTCGGCGGTATTACTCAATATTTATACG 170472 29 100.0 32 ............................. TTAGCAATAGGCTACGGCGATAAAACTTTTAA 170411 29 100.0 32 ............................. TTTCGAAATTCCTGCTCGATGTCGACCGCCGG 170350 29 100.0 32 ............................. GGATAAAGACGACGTTGAAGAAGCCGAACACG 170289 29 100.0 32 ............................. CTGCTGAGGGCGAATAACAAAATCATCAACCA 170228 29 100.0 32 ............................. CCTTGCTAGTGGGGAAGCGCTACGATTCACGA 170167 29 100.0 32 ............................. GTGAGCGCCGCCTTGGTACTGGCCTTTTGAGT 170106 29 100.0 32 ............................. GGTATGTTTCCGAAGACCTCGGCTGGCCTTTT 170045 29 96.6 33 ............T................ CAACGTTTCACTGTCGAGATAGCTATTGTCCGC 169983 29 100.0 32 ............................. GCAAACGAGTCTGTTTTGCAGACGTGTCTGGA 169922 29 100.0 32 ............................. CCCCGGCCTGATCTCGATCGGTGACGTAGGCA 169861 29 100.0 32 ............................. AATTTGAATGCACTGGTATTAACGACGAATAT 169800 29 100.0 32 ............................. CGCGGTCATACTTCAGGATCTGCTCTGTTGTT 169739 29 100.0 32 ............................. CCATTCTCGTTGTCGGTCATCTAGCGGTTGCG 169678 29 100.0 32 ............................. CCCAGTCAGGGGCGCGATATTGCCGCCGTGTT 169617 29 100.0 32 ............................. TATCGAGCGTTGTTTCGGTGCGGGCCTGAGCT 169556 29 100.0 32 ............................. AGGGCTACCCGGTTGCGCGTATTGATGCCCCG 169495 29 100.0 32 ............................. TTGTGCGGCAACGCCCGTTTTTATCGGTGGAC 169434 29 100.0 32 ............................. ACCGAGAGTGACATTTTCCCACTACTGGCTGG 169373 29 100.0 32 ............................. TTTGCCGCTGCTCGGTGAGGGAGCGTTTCATA 169312 29 100.0 32 ............................. CGCAACTATCCATGCAAATATTTCCATTGCTA 169251 29 100.0 32 ............................. GCAGCACTGGCTGGAGTGGCTGGCGAAAAATC 169190 29 96.6 0 ............T................ | A [169163] ========== ====== ====== ====== ============================= ================================= ================== 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 187183-185934 **** Predicted by CRISPRDetect 2.4 *** >NZ_VUJM01000001.1 Salmonella enterica subsp. enterica serovar Java strain 162829 contig01, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 187182 29 100.0 32 ............................. ACGCTGGCCGAAAACGGATTTTCAATCCGCAT 187121 29 100.0 32 ............................. TATTCATCTGCTGCCGCCTGGTTTGTTTTATC 187060 29 100.0 32 ............................. GGATCGGCAAACTTGTTTTAACGCCGGACAAC 186999 29 100.0 32 ............................. CCCCTTCTGATCCCCTTTCAATTTCGCGCTTA 186938 29 100.0 32 ............................. TATGATCCGCCATAGAAACAAATACAAAAATG 186877 29 100.0 32 ............................. CTGTTTTGCAACCGCATCCCCGGATTCGGGAT 186816 29 100.0 32 ............................. TTGCCACAACCACAATGGATCAGGAGCAATTA 186755 29 100.0 32 ............................. AATTATCGAAAGGAGTTACTCAGGGGGGAGAC 186694 29 100.0 32 ............................. CAGCGGAAGCGATCAGTGGTCTCGATACGGAA 186633 29 96.6 32 ...................A......... GGCTCAGGTTGATGATTCTCATGAGACACAAT 186572 29 100.0 32 ............................. GGGTGATCATGACGATCCAGAGCATATTGCCC 186511 29 100.0 32 ............................. GATTGAGAGAAGGGCTTGCTTAGCTTCCTTCC 186450 29 96.6 32 ..................A.......... TGGGGCTGTAAGGTCCGTTTAATATCCACTCA 186389 29 100.0 32 ............................. TTCGTTAATTATATTACAATACAAATCATAAC 186328 29 96.6 33 ............................A GCCTTCCGGTACGTCGTCATTTTCAGTCAGCGG 186266 29 96.6 32 ............T................ CAAAATTAATGTCCAGGACCTTATTAAGTTAC 186205 29 96.6 32 ............T................ GAAGGATTACCACCCCGGCAGCGCTCACCCGT 186144 29 100.0 32 ............................. GCGTTAGCGCGTTACATCCGGTTTGAGGCTGA 186083 29 100.0 32 ............................. GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 186022 29 96.6 32 .............T............... CCGGATGAAAACGCCTACCCGGAAGACTACGA 185961 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], //