Array 1 1171969-1169414 **** Predicted by CRISPRDetect 2.4 *** >NZ_JADKMQ010000001.1 Listeria monocytogenes strain LM13_52 contig1_denovo_LM13_52, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ===================================== ================== 1171968 29 100.0 36 ............................. AAAGACCTTCGATTTCATTCTCACTTTCCAGTTAAT 1171903 29 100.0 36 ............................. TTTTTTGTAGCGGAGGTGTACAATGCCGAAAGTGAC 1171838 29 100.0 36 ............................. GCTGGTAAATTTGGCGGAACTAATCGTACTGAAATA 1171773 29 100.0 37 ............................. ACATATTAGCCCTTATATAGAAGCCCCGCCCCTACCA 1171707 29 100.0 35 ............................. TATAGTCCCCATATCCATCTGCTATTATCCTCCAC 1171643 29 100.0 36 ............................. CGCTTCACGTTGGTTTTTCGTAGCCCAATTGCTAAA 1171578 29 100.0 37 ............................. ACGTTGGACAACGAGGTGAGTATGATATGACTCAAAT 1171512 29 100.0 36 ............................. GCGGAATGCGAAGTTGTTATATATAACTTATCTCGC 1171447 29 100.0 36 ............................. TCTTAAATGGTGTTTGCACATGTTAAGGGAGTCATG 1171382 29 100.0 35 ............................. GTGCATATCTCCTATATTCATGGCTGTATATGTGT 1171318 29 100.0 36 ............................. GTCCACATCGACAATAAAAAACACATTGTATCACTT 1171253 29 100.0 36 ............................. CTGGTTACTCAACTGGCGACAGTAATACACCTCAAT 1171188 29 100.0 34 ............................. TTTGGATAGGTTGTTTCTGATAAATAGGTTCACG 1171125 29 100.0 37 ............................. AAGTCTACTTGGATTTAGCTCTACACCTGCAACATGA 1171059 29 100.0 34 ............................. AGAAAAAAAACATCTTTCCAATTTGTTGTTTTGC 1170996 29 100.0 36 ............................. CTGGTTACTCAACTGGCGACAGTAATACACCTCAAT 1170931 29 100.0 34 ............................. TTTGGATAGGTTGTTTCTGATAAATAGGTTCACG 1170868 29 100.0 37 ............................. AAGTCTACTTGGATTTAGCTCTACACCTGCAACATGA 1170802 29 100.0 34 ............................. AGAAAAAAAACATCTTTCCAATTTGTTGTTTTGC 1170739 29 100.0 34 ............................. AGAAGCGTTAGCGGCATTGTTCGAAAGTAATTTA 1170676 29 100.0 36 ............................. TTGTTCGACGGCTTAGACAACCATCACGCTTCTTTA 1170611 29 100.0 36 ............................. TATAAAATATTGCCCAATGTGCGGAAGGAGTTTGGA 1170546 29 100.0 36 ............................. CTCATAAGGATTTCGAGGCGGGTTAAACGACATGTA 1170481 29 100.0 35 ............................. GCTTTTTTCAACAATTTTATCACCAGATGTCATTA 1170417 29 100.0 36 ............................. TGAGCAGTGTCACCTGTTTCCGTATCTGCTTTTTTC 1170352 29 100.0 37 ............................. AAGAAATCCGGGAAGTTTTGTTCTACAGAGCGAACGG 1170286 29 100.0 36 ............................. GTCAATAACTAGACGAGCTAACGTTTGTCGCTGTTT 1170221 29 100.0 35 ............................. TGTTATCTCCTGTGATGTAAAATAACCCTTCTATC 1170157 29 100.0 37 ............................. TAATACAAAATATTCATAACTCCTACATCATTATATA 1170091 29 100.0 36 ............................. TTGCAAACCTAACTTATCTTTGTTTTTTTGCTTTTC 1170026 29 100.0 37 ............................. TTGGATTTTATTAAATACAGAGTCACGGATTGTATTT 1169960 29 100.0 36 ............................. GGAACAGGCGCGCGCTGGGATTTAAAAGCAGAAGGC 1169895 29 100.0 36 ............................. CACGTACTTTAATCGGCATCAAACCACCTCGATTTC 1169830 29 96.6 34 .......................C..... CAAGATATGCTAGAAATGGCGCAAATAGCGCGCG 1169767 29 100.0 36 ............................. ACGTTTGCGGTAGTTTTACCGGGCACGGTCAAATAT 1169702 29 100.0 37 ............................. CAAAACAGAGAACGCGTGTTCATTATCGGACATCTTA 1169636 29 100.0 35 ............................. TTTTGAAATATGAGGACTTAGAAAATGAAAAAAAT 1169572 29 100.0 37 ............................. AAAAACTATGCAATTAGCAAAGTGATTTTATGTAATT 1169506 29 96.6 34 .......................A..... TAACGAGCCAATTAAACCATCTTCTTCTAGTAAT 1169443 29 93.1 0 .......................C....C | A [1169418] ========== ====== ====== ====== ============================= ===================================== ================== 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 1187512-1187030 **** Predicted by CRISPRDetect 2.4 *** >NZ_JADKMQ010000001.1 Listeria monocytogenes strain LM13_52 contig1_denovo_LM13_52, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ===================================== ================== 1187511 29 96.6 35 ................T............ TTGTCATCTGTGGTGTCTTCAACCACTTCTTCTAT 1187447 29 96.6 35 ................T............ TCTGTAAAATCAAAAGTATCATAGAAACAATCTTC 1187383 29 100.0 35 ............................. TTCGCCATGACGAAATCTAGCGCTTGTCCTACTAA 1187319 29 100.0 36 ............................. GGCACAGTCTTCACGATTTCGGGGATGGGGAAAACT 1187254 29 100.0 35 ............................. TAAACAAGTGCTTCTGGCAATACCAACGTTCCATC 1187190 29 93.1 37 T...............A............ TTGGTTCCTTTGGAAAACAACAATAGCGTGTAGTATT 1187124 29 75.9 36 ......T.C.A.C...CA...T....... GCAGAAACAGCAAAATAACCAAAAGTAATGACTTTC G [1187099] 1187058 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 6960-5338 **** Predicted by CRISPRDetect 2.4 *** >NZ_JADKMQ010000003.1 Listeria monocytogenes strain LM13_52 contig3_denovo_LM13_52, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ==================================== =============================== ================== 6959 36 100.0 30 .................................... TGATTTTATTTGGGAGAAGATAAACAATGA 6893 36 100.0 30 .................................... ATCGCGACAGTGCCTTTTGATACGTTTTTT 6827 36 100.0 30 .................................... ATATAAAAAATAGAAGTTGACAACTTTAAG 6761 36 100.0 30 .................................... TACAAGGAGTTTACTTCCTAACCTGTATAC 6695 36 100.0 30 .................................... AACCTTACGAAAGATAACCGCATTAGCTTG 6629 36 100.0 30 .................................... CGTTTTTCCAAAGTCTGAATGCTCTTTCAT 6563 36 100.0 30 .................................... TAAAATCCGAAACTAGTGGGCTTGCTGTGT 6497 36 100.0 30 .................................... TTGCATAAAAAAAGCCCTAACGTTGAGGTT 6431 36 100.0 30 .................................... AGTTCCTCCTTCTTCAACGCATTCACCATT 6365 36 100.0 30 .................................... AAAGTAAATCGTCTTCCTCCCACTCAAACT 6299 36 100.0 30 .................................... AGCTCAATTAAATATATATGCTGCGGCATC 6233 36 100.0 30 .................................... TCATTTTCTCCTGGAACGTTTCTGTTACCA 6167 36 100.0 30 .................................... GCTATATTAGTCGTTGGATTCAAATGGTTG 6101 36 100.0 30 .................................... TCTGCCATTCATCACTAAATTCACATAAAT 6035 36 100.0 30 .................................... GTGGTGACTGTCTAGTCCGTTCAGCAAAGG 5969 36 100.0 31 .................................... CATAAAGGATGATGAAAAATGACATTAACAA 5902 36 100.0 30 .................................... ATCGAAATCACCTACACCAAGAAAAAAAGC 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] ========== ====== ====== ====== ==================================== =============================== ================== 25 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], //