Array 1 1171959-1169404 **** Predicted by CRISPRDetect 2.4 *** >NZ_JADKMS010000001.1 Listeria monocytogenes strain LM13_10 contig1_denovo_LM13-10, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ===================================== ================== 1171958 29 100.0 36 ............................. AAAGACCTTCGATTTCATTCTCACTTTCCAGTTAAT 1171893 29 100.0 36 ............................. TTTTTTGTAGCGGAGGTGTACAATGCCGAAAGTGAC 1171828 29 100.0 36 ............................. GCTGGTAAATTTGGCGGAACTAATCGTACTGAAATA 1171763 29 100.0 37 ............................. ACATATTAGCCCTTATATAGAAGCCCCGCCCCTACCA 1171697 29 100.0 35 ............................. TATAGTCCCCATATCCATCTGCTATTATCCTCCAC 1171633 29 100.0 36 ............................. CGCTTCACGTTGGTTTTTCGTAGCCCAATTGCTAAA 1171568 29 100.0 37 ............................. ACGTTGGACAACGAGGTGAGTATGATATGACTCAAAT 1171502 29 100.0 36 ............................. GCGGAATGCGAAGTTGTTATATATAACTTATCTCGC 1171437 29 100.0 36 ............................. TCTTAAATGGTGTTTGCACATGTTAAGGGAGTCATG 1171372 29 100.0 35 ............................. GTGCATATCTCCTATATTCATGGCTGTATATGTGT 1171308 29 100.0 36 ............................. GTCCACATCGACAATAAAAAACACATTGTATCACTT 1171243 29 100.0 36 ............................. CTGGTTACTCAACTGGCGACAGTAATACACCTCAAT 1171178 29 100.0 34 ............................. TTTGGATAGGTTGTTTCTGATAAATAGGTTCACG 1171115 29 100.0 37 ............................. AAGTCTACTTGGATTTAGCTCTACACCTGCAACATGA 1171049 29 100.0 34 ............................. AGAAAAAAAACATCTTTCCAATTTGTTGTTTTGC 1170986 29 100.0 36 ............................. CTGGTTACTCAACTGGCGACAGTAATACACCTCAAT 1170921 29 100.0 34 ............................. TTTGGATAGGTTGTTTCTGATAAATAGGTTCACG 1170858 29 100.0 37 ............................. AAGTCTACTTGGATTTAGCTCTACACCTGCAACATGA 1170792 29 100.0 34 ............................. AGAAAAAAAACATCTTTCCAATTTGTTGTTTTGC 1170729 29 100.0 34 ............................. AGAAGCGTTAGCGGCATTGTTCGAAAGTAATTTA 1170666 29 100.0 36 ............................. TTGTTCGACGGCTTAGACAACCATCACGCTTCTTTA 1170601 29 100.0 36 ............................. TATAAAATATTGCCCAATGTGCGGAAGGAGTTTGGA 1170536 29 100.0 36 ............................. CTCATAAGGATTTCGAGGCGGGTTAAACGACATGTA 1170471 29 100.0 35 ............................. GCTTTTTTCAACAATTTTATCACCAGATGTCATTA 1170407 29 100.0 36 ............................. TGAGCAGTGTCACCTGTTTCCGTATCTGCTTTTTTC 1170342 29 100.0 37 ............................. AAGAAATCCGGGAAGTTTTGTTCTACAGAGCGAACGG 1170276 29 100.0 36 ............................. GTCAATAACTAGACGAGCTAACGTTTGTCGCTGTTT 1170211 29 100.0 35 ............................. TGTTATCTCCTGTGATGTAAAATAACCCTTCTATC 1170147 29 100.0 37 ............................. TAATACAAAATATTCATAACTCCTACATCATTATATA 1170081 29 100.0 36 ............................. TTGCAAACCTAACTTATCTTTGTTTTTTTGCTTTTC 1170016 29 100.0 37 ............................. TTGGATTTTATTAAATACAGAGTCACGGATTGTATTT 1169950 29 100.0 36 ............................. GGAACAGGCGCGCGCTGGGATTTAAAAGCAGAAGGC 1169885 29 100.0 36 ............................. CACGTACTTTAATCGGCATCAAACCACCTCGATTTC 1169820 29 96.6 34 .......................C..... CAAGATATGCTAGAAATGGCGCAAATAGCGCGCG 1169757 29 100.0 36 ............................. ACGTTTGCGGTAGTTTTACCGGGCACGGTCAAATAT 1169692 29 100.0 37 ............................. CAAAACAGAGAACGCGTGTTCATTATCGGACATCTTA 1169626 29 100.0 35 ............................. TTTTGAAATATGAGGACTTAGAAAATGAAAAAAAT 1169562 29 100.0 37 ............................. AAAAACTATGCAATTAGCAAAGTGATTTTATGTAATT 1169496 29 96.6 34 .......................A..... TAACGAGCCAATTAAACCATCTTCTTCTAGTAAT 1169433 29 93.1 0 .......................C....C | A [1169408] ========== ====== ====== ====== ============================= ===================================== ================== 40 29 99.7 36 GTTTTAACTACTTATTATGAAATGTAAAT # Left flank : CATTTAAAATTTGGTGGTGAAGATATGTATGTAATTTTAATTTATGATATTTCAATCGAAAATGGTGGAGCAAAAGTCTGGAGAAATGTATTTAAGATTTGTAAAAAGTACTTAACTCATGTTCAAAAATCAGTTTTTGAAGGTGAAATAACTCCAGCGCTTTTAGTTAAGTTAAGGATGGAGTTAGATAAGTATATTCGAGATGATCAAGATTCAGTAATTGTTTTTTCTAGTAGACAACAAAGATGGCTAGAAAAAGAATTTTGGGGATTAACGGATGAAAAGACTTCTAATTTCTTTTGATGTTCTCGGTCTGTCGACCTTTAGTAGTGCGAAAAATAGTGGGGTTCGACAGATTTAGGGAAATCATTGGGGGAGAAAGAGTTTGAAGTTTTTAAGCGAAAATCTGAAGGGATAAGTTATGATTTTTACGTAATTTTTAAGAGGTCGACAAAAATAGTGACCTGAGTTATGATGGGAGTAGGCGTAAAATAGAGCGG # Right flank : GTCTTCTTAAAATTTAAACCCCAAAAATAAAAAAGGCCAGGACCCAAATCCAAGCCTTTTCCTACACTCCTCTAAACCAACAAAACCACAACCAACGCCAAAACCGCCGGCAAGCCCTGTTTCACCAAAATCCCCTTAGAAGAAGTCGCTCCGCCAAACAGCGCCGCCACAACTACACAACTCAAAAAGAAAATCTGCACAGTCTCCGCCATTCCTGCCCCCGCGAAAAACAATCCCCACACAAGTCCTGCCGCAAGAAAGCCATTATAAAGCCCTTGATTCGCGAATAGCGTCTGTACTTTCTTATTCGCAAGTAGTTCCTTCTCCACACCAAATGTCTTGGCTGCGAGTTTGGTATTGGCGAAAAACATTTCTAAAATCATTATATAAATATGCTCGATCATTACGATGAAGGTTAAAATAAATGCTAAAATGGCCATAAAAAATCCCTCTTTTCTACTTCGAAGTATAGCATAGCTTGTAAATTTTTCGTAAAAATA # 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 : GTTTTAACTACTTATTATGAAATGTAAAT # 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: NA [Repeat is AT rich:82.76%AT] # Reference repeat match prediction: R [matched GTTTTAACTACTTATTATGAAATGTAAAT with 100% identity] Score: 4.5/4.5 # Secondary Structural analysis prediction: NA [0.00,0.00] Score: 0/0.37 # Array degeneracy analysis prediction: R [5-0] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [65.0-56.7]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0,4.91 Confidence: HIGH] # Array family : II-A [Matched known repeat from this family], // Array 2 1187502-1187020 **** Predicted by CRISPRDetect 2.4 *** >NZ_JADKMS010000001.1 Listeria monocytogenes strain LM13_10 contig1_denovo_LM13-10, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ===================================== ================== 1187501 29 96.6 35 ................T............ TTGTCATCTGTGGTGTCTTCAACCACTTCTTCTAT 1187437 29 96.6 35 ................T............ TCTGTAAAATCAAAAGTATCATAGAAACAATCTTC 1187373 29 100.0 35 ............................. TTCGCCATGACGAAATCTAGCGCTTGTCCTACTAA 1187309 29 100.0 36 ............................. GGCACAGTCTTCACGATTTCGGGGATGGGGAAAACT 1187244 29 100.0 35 ............................. TAAACAAGTGCTTCTGGCAATACCAACGTTCCATC 1187180 29 93.1 37 T...............A............ TTGGTTCCTTTGGAAAACAACAATAGCGTGTAGTATT 1187114 29 75.9 36 ......T.C.A.C...CA...T....... GCAGAAACAGCAAAATAACCAAAAGTAATGACTTTC G [1187089] 1187048 29 79.3 0 ......A..T....AGA......A..... | ========== ====== ====== ====== ============================= ===================================== ================== 8 29 92.7 36 GTTTTAGTTACTTATTGTGAAATGTAAAT # Left flank : GCGTCCGTGCCACTACTTCAGCTGATATTTTACTTGAAAAAGGTGCCATAGAAGTTATCGCTTGCGCAACCCACTCTGTCATGGCTGGAAACGCAACCGAACGCTTACAAAACTCCAATATCAAAGAAGTCATCACATCCGACTCCATCGATCTTCCAGAAGACAAGCAATTCGACAAACTAACAACCATTTCTATCGGACGAATCTTAGGCCGCGCAATCGAAGGCGTACAAGAAAACCGCTCGTTGCATCCGTTGTTTTAAAGAATAAGCAGAAAACAGTAACTTAGTAGAGTTGCTGTTTTTTTGTTATCTGTCGACCTCGAGTAGCGTGAAAAATACCGGGGATCGACAGAAAGTTGTAAATGGTTGGGGGAAGAGGAATTTGGCGGTATTTGCTTGGGGAAATCTTCCGGATAAGAGGAGATTTTAGATGTTTTTTGGTAGGTCGACAGAAATAGCTCTTTGAGGTAAGATGGGAGTAAGAAGAAAAGTTAGTGG # Right flank : GAAAACCTGTTATACATAGGATTATCTATTTCCGTTATAATTATTCCTTGCAAATAAATTCCAAAAAACAAACCCCTCATTAATTGGGTTTGTTTTTTGTGAATAATTATAGTCAAACGAGCAATCTGTTAACAATTTAGCAATAAACGCAATAAAAAGCCGTTTTTTCACTATGGATTGTACTATAAAACATAATCTACCTATGCTAAAATTTAAGGGAAGGTAAGCTGAATAATACATATAAGGAGGACTCTACTATTGAAAAAGATTCTAGTGCCCATATTATTGTTAGCAACAATCTTAGCAAGCTGTTCCTCGCCGAATGAAAAAATAACCAAAGACACTAAAATATCCAAGACTATTACAATAAGAGCAGATTACAAAGTTCCAAAAGATATTAAAGAACTTGAGGATGATAGTGCTAATATTGTTAAAGTAAAATTTCTTCAAAATAAAACGATAGGCAAGGATGGTAGTACTATTAGCGAGATAGAAATTTT # Questionable array : NO Score: 5.59 # Score Detail : 1:0, 2:3, 3:0, 4:0.64, 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 : GTTTTAGTTACTTATTGTGAAATGTAAAT # Alternate repeat : GTTTTAGTTACTTATTTTGAAATGTAAAT # Directional analysis summary from each method: # Motif ATTGAAA(N) match prediction: NA Score: 0/4.5 # A,T distribution in repeat prediction: NA [Repeat is AT rich:79.31%AT] # Reference repeat match prediction: R [matched GTTTTAGTTACTTATTGTGAAATGTAAAT with 100% identity] Score: 4.5/4.5 # Secondary Structural analysis prediction: R [0.00,-1.20] Score: 0.37/0.37 # Array degeneracy analysis prediction: R [16-0] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [75.0-58.3]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0.27,5.28 Confidence: HIGH] # Array family : II-A [Matched known repeat from this family], // Array 1 6894-5338 **** Predicted by CRISPRDetect 2.4 *** >NZ_JADKMS010000003.1 Listeria monocytogenes strain LM13_10 contig3_denovo_LM13-10, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ==================================== =============================== ================== 6893 36 100.0 30 .................................... TGATTTTATTTGGGAGAAGATAAACAATGA 6827 36 100.0 30 .................................... ATCGCGACAGTGCCTTTTGATACGTTTTTT 6761 36 100.0 30 .................................... ATATAAAAAATAGAAGTTGACAACTTTAAG 6695 36 100.0 30 .................................... TACAAGGAGTTTACTTCCTAACCTGTATAC 6629 36 100.0 30 .................................... AACCTTACGAAAGATAACCGCATTAGCTTG 6563 36 100.0 30 .................................... CGTTTTTCCAAAGTCTGAATGCTCTTTCAT 6497 36 100.0 30 .................................... TAAAATCCGAAACTAGTGGGCTTGCTGTGT 6431 36 100.0 30 .................................... TTGCATAAAAAAAGCCCTAACGTTGAGGTT 6365 36 100.0 30 .................................... AGTTCCTCCTTCTTCAACGCATTCACCATT 6299 36 100.0 30 .................................... AAAGTAAATCGTCTTCCTCCCACTCAAACT 6233 36 100.0 30 .................................... AGCTCAATTAAATATATATGCTGCGGCATC 6167 36 100.0 30 .................................... TCATTTTCTCCTGGAACGTTTCTGTTACCA 6101 36 100.0 30 .................................... GCTATATTAGTCGTTGGATTCAAATGGTTG 6035 36 100.0 30 .................................... TCTGCCATTCATCACTAAATTCACATAAAT 5969 36 100.0 30 .................................... GTGGTGACTGTCTAGTCCGTTCAGCAAAGG 5903 36 100.0 31 .................................... CATAAAGGATGATGAAAAATGACATTAACAA 5836 36 100.0 30 .................................... ATCGAAATCACCTACACCAAGAAAAAAAGC 5770 36 100.0 30 .................................... ATCGAAATCACCTACACCAAGAAAAAAAGC 5704 36 100.0 30 .................................... ATCGAAATCACCTACACCAAGAAAAAAAGC 5638 36 100.0 30 .................................... TCCGACAAGGAAGATCCGTTCCCGACTTTG 5572 36 100.0 30 .................................... CTAAATCACTCGATAACTAGAGTTGCTAAC 5506 36 100.0 30 .................................... AATGGACGGTGCTGTTGTTGTCACTGAAAA 5440 36 100.0 28 .................................... TAATATTCTCCCCCCATCGCTAACAGGG 5376 36 86.1 0 .............A.....C.....A.A.......G | C,A,T [5341,5344,5349] ========== ====== ====== ====== ==================================== =============================== ================== 24 36 99.4 30 GTTTTAGAGCTATGTTATTTTGAATGCTACCAAAAC # Left flank : GACAAATTAACCGCGACGATTAGCGAGTTGATAGGTTACGAATTATTGGAGCATGAACTGGATTTAGAAGAAGATGAAATAACGGTCATTGAATTATTCAAAGCTTTAGGAATAAAAATAGAAACAAAAAGCGATACCGTATTTGAGAAGTTAATTGAAATAGTACAAGTCTATAAATATCTATCTAAAAAGAAATTGTTAGTACTTATTAACGTGTGTTCCTATCTTACAGAGGAAGAACTGCTAGAGTTGAGACGGTATATCTCTTTATATCAAGTCAAAGTACTATTTATTGAACCTAGAAAAATAAAAGGATCTCCGCAAGTTACTTTAGATTCTGATTATTTTTTACATGTGGAAAATAGTGTATAAGGTAACCGCTGTTCTTTGAAAACAAAATAAATTTTATGTAAACCATAAAATAGCATTCAAAATTGAAATCTTGCTATGGATGAATGGCGCGATTACGGAATCTTGGAGGAAAGAAAAAATTCTGCGAG # Right flank : ATAAAATGCATCGCAATTACCAAACCATGGTTAAATTTAAAAAGGAGTTAAACTATCTACATGACACAGTATCACTATCTTGCTTCGAAGTCGCTCTTAGAAAATGATGGGGAAAAGTTCTCTCGTCTTTATATTAGACTTCTTAAATTTGAATTTTGATATGAATGTTGACCAAGACACTAATGAATTGTTTTTCTATTCAATTGATTTGAACTCAGCTTGTAAATGTAAGTAAAGGGAACCTGCCGCTGAAAGGTAATGGGCAAAAAAATTGTTACGAGACTAAAAGTTTAAAAATCTTGTATGATTATATTCTAAATACGAGTAAAGATAATGACACGCTTGAACTATATACTGCTTGGAACAGCGAGGAAGATTTCCTGCTATTGAATAAAACAGAACTGCTGATCTAGAATTTAACTATCGAAAATCTAATTTTAAATGATAGAGAACTATTAATAATTAAAAAAGAAAATCGATATAACTTTTAGCACCATTCG # Questionable array : NO Score: 6.26 # Score Detail : 1:0, 2:3, 3:0, 4:1.00, 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 : GTTTTAGAGCTATGTTATTTTGAATGCTACCAAAAC # 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: NA [Repeat is AT rich:69.44%AT] # Reference repeat match prediction: R [matched GTTTTAGAGCTATGTTATTTTGAATGCTACCAAAAC with 100% identity] Score: 4.5/4.5 # Secondary Structural analysis prediction: R [-0.80,-1.30] Score: 0.37/0.37 # Array degeneracy analysis prediction: NA [0-0] Score: 0/0.41 # AT richness analysis in flanks prediction: NA [63.3-56.7]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0,4.87 Confidence: HIGH] # Array family : II-A/C [Matched known repeat from this family], //