Array 1 1217175-1214877 **** Predicted by CRISPRDetect 2.4 *** >NZ_JADKMX010000001.1 Listeria monocytogenes strain LM12_2 contig1_denovo_LM12_2, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ===================================== ================== 1217174 29 100.0 36 ............................. AAAGACCTTCGATTTCATTCTCACTTTCCAGTTAAT 1217109 29 100.0 36 ............................. TTTTTTGTAGCGGAGGTGTACAATGCCGAAAGTGAC 1217044 29 100.0 36 ............................. GCTGGTAAATTTGGCGGAACTAATCGTACTGAAATA 1216979 29 100.0 37 ............................. ACATATTAGCCCTTATATAGAAGCCCCGCCCCTACCA 1216913 29 100.0 35 ............................. TATAGTCCCCATATCCATCTGCTATTATCCTCCAC 1216849 29 100.0 36 ............................. CGCTTCACGTTGGTTTTTCGTAGCCCAATTGCTAAA 1216784 29 100.0 37 ............................. ACGTTGGACAACGAGGTGAGTATGATATGACTCAAAT 1216718 29 100.0 36 ............................. GCGGAATGCGAAGTTGTTATATATAACTTATCTCGC 1216653 29 100.0 36 ............................. TCTTAAATGGTGTTTGCACATGTTAAGGGAGTCATG 1216588 29 100.0 35 ............................. GTGCATATCTCCTATATTCATGGCTGTATATGTGT 1216524 29 100.0 36 ............................. GTCCACATCGACAATAAAAAACACATTGTATCACTT 1216459 29 100.0 36 ............................. CTGGTTACTCAACTGGCGACAGTAATACACCTCAAT 1216394 29 100.0 34 ............................. TTTGGATAGGTTGTTTCTGATAAATAGGTTCACG 1216331 29 100.0 37 ............................. AAGTCTACTTGGATTTAGCTCTACACCTGCAACATGA 1216265 29 100.0 34 ............................. AGAAAAAAAACATCTTTCCAATTTGTTGTTTTGC 1216202 29 100.0 34 ............................. AGAAGCGTTAGCGGCATTGTTCGAAAGTAATTTA 1216139 29 100.0 36 ............................. TTGTTCGACGGCTTAGACAACCATCACGCTTCTTTA 1216074 29 100.0 36 ............................. TATAAAATATTGCCCAATGTGCGGAAGGAGTTTGGA 1216009 29 100.0 36 ............................. CTCATAAGGATTTCGAGGCGGGTTAAACGACATGTA 1215944 29 100.0 35 ............................. GCTTTTTTCAACAATTTTATCACCAGATGTCATTA 1215880 29 100.0 36 ............................. TGAGCAGTGTCACCTGTTTCCGTATCTGCTTTTTTC 1215815 29 100.0 37 ............................. AAGAAATCCGGGAAGTTTTGTTCTACAGAGCGAACGG 1215749 29 100.0 36 ............................. GTCAATAACTAGACGAGCTAACGTTTGTCGCTGTTT 1215684 29 100.0 35 ............................. TGTTATCTCCTGTGATGTAAAATAACCCTTCTATC 1215620 29 100.0 37 ............................. TAATACAAAATATTCATAACTCCTACATCATTATATA 1215554 29 100.0 36 ............................. TTGCAAACCTAACTTATCTTTGTTTTTTTGCTTTTC 1215489 29 100.0 37 ............................. TTGGATTTTATTAAATACAGAGTCACGGATTGTATTT 1215423 29 100.0 36 ............................. GGAACAGGCGCGCGCTGGGATTTAAAAGCAGAAGGC 1215358 29 100.0 36 ............................. CACGTACTTTAATCGGCATCAAACCACCTCGATTTC 1215293 29 96.6 34 .......................C..... CAAGATATGCTAGAAATGGCGCAAATAGCGCGCG 1215230 29 100.0 36 ............................. ACGTTTGCGGTAGTTTTACCGGGCACGGTCAAATAT 1215165 29 100.0 37 ............................. CAAAACAGAGAACGCGTGTTCATTATCGGACATCTTA 1215099 29 100.0 35 ............................. TTTTGAAATATGAGGACTTAGAAAATGAAAAAAAT 1215035 29 100.0 37 ............................. AAAAACTATGCAATTAGCAAAGTGATTTTATGTAATT 1214969 29 96.6 34 .......................A..... TAACGAGCCAATTAAACCATCTTCTTCTAGTAAT 1214906 29 93.1 0 .......................C....C | A [1214881] ========== ====== ====== ====== ============================= ===================================== ================== 36 29 99.6 36 GTTTTAACTACTTATTATGAAATGTAAAT # Left flank : CATTTAAAATTTGGTGGTGAAGATATGTATGTAATTTTAATTTATGATATTTCAATCGAAAATGGTGGAGCAAAAGTCTGGAGAAATGTATTTAAGATTTGTAAAAAGTACTTAACTCATGTTCAAAAATCAGTTTTTGAAGGTGAAATAACTCCAGCGCTTTTAGTTAAGTTAAGGATGGAGTTAGATAAGTATATTCGAGATGATCAAGATTCAGTAATTGTTTTTTCTAGTAGACAACAAAGATGGCTAGAAAAAGAATTTTGGGGATTAACGGATGAAAAGACTTCTAATTTCTTTTGATGTTCTCGGTCTGTCGACCTTTAGTAGTGCGAAAAATAGTGGGGTTCGACAGATTTAGGGAAATCATTGGGGGAGAAAGAGTTTGAAGTTTTTAAGCGAAAATCTGAAGGGATAAGTTATGATTTTTACGTAATTTTTAAGAGGTCGACAAAAATAGTGACCTGAGTTATGATGGGAGTAGGCGTAAAATAGAGCGG # Right flank : GTCTTCTTAAAATTTAAACCCCAAAAATAAAAAAGGCCAGGACCCAAATCCAAGCCTTTTCCTACACTCCTCTAAACCAACAAAACCACAACCAACGCCAAAACCGCCGGCAAGCCCTGTTTCACCAAAATCCCCTTAGAAGAAGTCGCTCCGCCAAACAGCGCCGCCACAACTACACAACTCAAAAAGAAAATCTGCACAGTCTCCGCCATTCCTGCCCCCGCGAAAAACAATCCCCACACAAGTCCTGCCGCAAGAAAGCCATTATAAAGCCCTTGATTCGCGAATAGCGTCTGTACTTTCTTATTCGCAAGTAGTTCCTTCTCCACACCAAATGTCTTGGCTGCGAGTTTGGTATTGGCGAAAAACATTTCTAAAATCATTATATAAATATGCTCGATCATTACGATGAAGGTTAAAATAAATGCTAAAATGGCCATAAAAAATCCCTCTTTTCTACTTCGAAGTATAGCATAGCTTGTAAATTTTTCGTAAAAATA # Questionable array : NO Score: 6.24 # Score Detail : 1:0, 2:3, 3:0, 4:0.98, 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 1232718-1232236 **** Predicted by CRISPRDetect 2.4 *** >NZ_JADKMX010000001.1 Listeria monocytogenes strain LM12_2 contig1_denovo_LM12_2, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ===================================== ================== 1232717 29 96.6 35 ................T............ TTGTCATCTGTGGTGTCTTCAACCACTTCTTCTAT 1232653 29 96.6 35 ................T............ TCTGTAAAATCAAAAGTATCATAGAAACAATCTTC 1232589 29 100.0 35 ............................. TTCGCCATGACGAAATCTAGCGCTTGTCCTACTAA 1232525 29 100.0 36 ............................. GGCACAGTCTTCACGATTTCGGGGATGGGGAAAACT 1232460 29 100.0 35 ............................. TAAACAAGTGCTTCTGGCAATACCAACGTTCCATC 1232396 29 93.1 37 T...............A............ TTGGTTCCTTTGGAAAACAACAATAGCGTGTAGTATT 1232330 29 75.9 36 ......T.C.A.C...CA...T....... GCAGAAACAGCAAAATAACCAAAAGTAATGACTTTC G [1232305] 1232264 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_JADKMX010000003.1 Listeria monocytogenes strain LM12_2 contig3_denovo_LM12_2, 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], //