Array 1 5639-5338 **** Predicted by CRISPRDetect 2.4 *** >NZ_JAHVAU010000011.1 Listeria monocytogenes strain LM2063 contig11_denovo_LM2063, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ==================================== ============================== ================== 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] ========== ====== ====== ====== ==================================== ============================== ================== 5 36 97.2 30 GTTTTAGAGCTATGTTATTTTGAATGCTACCAAAAC # Left flank : GCTACCAAAACATCGAAATCACCTACACCAAGAAAAAAAG # Right flank : ATAAAATGCATCGCAATTACCAAACCATGGTTAAATTTAAAAAGGAGTTAAACTATCTACATGACACAGTATCACTATCTTGCTTCGAAGTCGCTCTTAGAAAATGATGGGGAAAAGTTCTCTCGTCTTTATATTAGACTTCTTAAATTTGAATTTTGATATGAATGTTGACCAAGACACTAATGAATTGTTTTTCTATTCAATTGATTTGAACTCAGCTTGTAAATGTAAGTAAAGGGAACCTGCCGCTGAAAGGTAATGGGCAAAAAAATTGTTACGAGACTAAAAGTTTAAAAATCTTGTATGATTATATTCTAAATACGAGTAAAGATAATGACACGCTTGAACTATATACTGCTTGGAACAGCGAGGAAGATTTCCTGCTATTGAATAAAACAGAACTGCTGATCTAGAATTTAACTATCGAAAATCTAATTTTAAATGATAGAGAACTATTAATAATTAAAAAAGAAAATCGATATAACTTTTAGCACCATTCG # Questionable array : NO Score: 5.86 # Score Detail : 1:0, 2:3, 3:0, 4:1.00, 5:0, 6:0.25, 7:0.01, 8:0.6, 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: F [63.3-41.7]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0.27,4.87 Confidence: HIGH] # Array family : II-A/C [Matched known repeat from this family], // Array 1 1171789-1169491 **** Predicted by CRISPRDetect 2.4 *** >NZ_JAHVAU010000001.1 Listeria monocytogenes strain LM2063 contig1_denovo_LM2063, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ===================================== ================== 1171788 29 100.0 36 ............................. AAAGACCTTCGATTTCATTCTCACTTTCCAGTTAAT 1171723 29 100.0 36 ............................. TTTTTTGTAGCGGAGGTGTACAATGCCGAAAGTGAC 1171658 29 100.0 36 ............................. GCTGGTAAATTTGGCGGAACTAATCGTACTGAAATA 1171593 29 100.0 37 ............................. ACATATTAGCCCTTATATAGAAGCCCCGCCCCTACCA 1171527 29 100.0 35 ............................. TATAGTCCCCATATCCATCTGCTATTATCCTCCAC 1171463 29 100.0 36 ............................. CGCTTCACGTTGGTTTTTCGTAGCCCAATTGCTAAA 1171398 29 100.0 37 ............................. ACGTTGGACAACGAGGTGAGTATGATATGACTCAAAT 1171332 29 100.0 36 ............................. GCGGAATGCGAAGTTGTTATATATAACTTATCTCGC 1171267 29 100.0 36 ............................. TCTTAAATGGTGTTTGCACATGTTAAGGGAGTCATG 1171202 29 100.0 35 ............................. GTGCATATCTCCTATATTCATGGCTGTATATGTGT 1171138 29 100.0 36 ............................. GTCCACATCGACAATAAAAAACACATTGTATCACTT 1171073 29 100.0 36 ............................. CTGGTTACTCAACTGGCGACAGTAATACACCTCAAT 1171008 29 100.0 34 ............................. TTTGGATAGGTTGTTTCTGATAAATAGGTTCACG 1170945 29 100.0 37 ............................. AAGTCTACTTGGATTTAGCTCTACACCTGCAACATGA 1170879 29 100.0 34 ............................. AGAAAAAAAACATCTTTCCAATTTGTTGTTTTGC 1170816 29 100.0 34 ............................. AGAAGCGTTAGCGGCATTGTTCGAAAGTAATTTA 1170753 29 100.0 36 ............................. TTGTTCGACGGCTTAGACAACCATCACGCTTCTTTA 1170688 29 100.0 36 ............................. TATAAAATATTGCCCAATGTGCGGAAGGAGTTTGGA 1170623 29 100.0 36 ............................. CTCATAAGGATTTCGAGGCGGGTTAAACGACATGTA 1170558 29 100.0 35 ............................. GCTTTTTTCAACAATTTTATCACCAGATGTCATTA 1170494 29 100.0 36 ............................. TGAGCAGTGTCACCTGTTTCCGTATCTGCTTTTTTC 1170429 29 100.0 37 ............................. AAGAAATCCGGGAAGTTTTGTTCTACAGAGCGAACGG 1170363 29 100.0 36 ............................. GTCAATAACTAGACGAGCTAACGTTTGTCGCTGTTT 1170298 29 100.0 35 ............................. TGTTATCTCCTGTGATGTAAAATAACCCTTCTATC 1170234 29 100.0 37 ............................. TAATACAAAATATTCATAACTCCTACATCATTATATA 1170168 29 100.0 36 ............................. TTGCAAACCTAACTTATCTTTGTTTTTTTGCTTTTC 1170103 29 100.0 37 ............................. TTGGATTTTATTAAATACAGAGTCACGGATTGTATTT 1170037 29 100.0 36 ............................. GGAACAGGCGCGCGCTGGGATTTAAAAGCAGAAGGC 1169972 29 100.0 36 ............................. CACGTACTTTAATCGGCATCAAACCACCTCGATTTC 1169907 29 96.6 34 .......................C..... CAAGATATGCTAGAAATGGCGCAAATAGCGCGCG 1169844 29 100.0 36 ............................. ACGTTTGCGGTAGTTTTACCGGGCACGGTCAAATAT 1169779 29 100.0 37 ............................. CAAAACAGAGAACGCGTGTTCATTATCGGACATCTTA 1169713 29 100.0 35 ............................. TTTTGAAATATGAGGACTTAGAAAATGAAAAAAAT 1169649 29 100.0 37 ............................. AAAAACTATGCAATTAGCAAAGTGATTTTATGTAATT 1169583 29 96.6 34 .......................A..... TAACGAGCCAATTAAACCATCTTCTTCTAGTAAT 1169520 29 93.1 0 .......................C....C | A [1169495] ========== ====== ====== ====== ============================= ===================================== ================== 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 1187332-1186850 **** Predicted by CRISPRDetect 2.4 *** >NZ_JAHVAU010000001.1 Listeria monocytogenes strain LM2063 contig1_denovo_LM2063, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ===================================== ================== 1187331 29 96.6 35 ................T............ TTGTCATCTGTGGTGTCTTCAACCACTTCTTCTAT 1187267 29 96.6 35 ................T............ TCTGTAAAATCAAAAGTATCATAGAAACAATCTTC 1187203 29 100.0 35 ............................. TTCGCCATGACGAAATCTAGCGCTTGTCCTACTAA 1187139 29 100.0 36 ............................. GGCACAGTCTTCACGATTTCGGGGATGGGGAAAACT 1187074 29 100.0 35 ............................. TAAACAAGTGCTTCTGGCAATACCAACGTTCCATC 1187010 29 93.1 37 T...............A............ TTGGTTCCTTTGGAAAACAACAATAGCGTGTAGTATT 1186944 29 75.9 36 ......T.C.A.C...CA...T....... GCAGAAACAGCAAAATAACCAAAAGTAATGACTTTC G [1186919] 1186878 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 1201-42 **** Predicted by CRISPRDetect 2.4 *** >NZ_JAHVAU010000003.1 Listeria monocytogenes strain LM2063 contig3_denovo_LM2063, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ==================================== =============================== ================== 1200 36 100.0 30 .................................... TGATTTTATTTGGGAGAAGATAAACAATGA 1134 36 100.0 30 .................................... ATCGCGACAGTGCCTTTTGATACGTTTTTT 1068 36 100.0 30 .................................... ATATAAAAAATAGAAGTTGACAACTTTAAG 1002 36 100.0 30 .................................... TACAAGGAGTTTACTTCCTAACCTGTATAC 936 36 100.0 30 .................................... AACCTTACGAAAGATAACCGCATTAGCTTG 870 36 100.0 30 .................................... CGTTTTTCCAAAGTCTGAATGCTCTTTCAT 804 36 100.0 30 .................................... TAAAATCCGAAACTAGTGGGCTTGCTGTGT 738 36 100.0 30 .................................... TTGCATAAAAAAAGCCCTAACGTTGAGGTT 672 36 100.0 30 .................................... AGTTCCTCCTTCTTCAACGCATTCACCATT 606 36 100.0 30 .................................... AAAGTAAATCGTCTTCCTCCCACTCAAACT 540 36 100.0 30 .................................... AGCTCAATTAAATATATATGCTGCGGCATC 474 36 100.0 30 .................................... TCATTTTCTCCTGGAACGTTTCTGTTACCA 408 36 100.0 30 .................................... GCTATATTAGTCGTTGGATTCAAATGGTTG 342 36 100.0 30 .................................... TCTGCCATTCATCACTAAATTCACATAAAT 276 36 100.0 30 .................................... GTGGTGACTGTCTAGTCCGTTCAGCAAAGG 210 36 100.0 31 .................................... CATAAAGGATGATGAAAAATGACATTAACAA 143 36 100.0 30 .................................... ATCGAAATCACCTACACCAAGAAAAAAAGC 77 36 100.0 0 .................................... | ========== ====== ====== ====== ==================================== =============================== ================== 18 36 100.0 30 GTTTTAGAGCTATGTTATTTTGAATGCTACCAAAAC # Left flank : GACAAATTAACCGCGACGATTAGCGAGTTGATAGGTTACGAATTATTGGAGCATGAACTGGATTTAGAAGAAGATGAAATAACGGTCATTGAATTATTCAAAGCTTTAGGAATAAAAATAGAAACAAAAAGCGATACCGTATTTGAGAAGTTAATTGAAATAGTACAAGTCTATAAATATCTATCTAAAAAGAAATTGTTAGTACTTATTAACGTGTGTTCCTATCTTACAGAGGAAGAACTGCTAGAGTTGAGACGGTATATCTCTTTATATCAAGTCAAAGTACTATTTATTGAACCTAGAAAAATAAAAGGATCTCCGCAAGTTACTTTAGATTCTGATTATTTTTTACATGTGGAAAATAGTGTATAAGGTAACCGCTGTTCTTTGAAAACAAAATAAATTTTATGTAAACCATAAAATAGCATTCAAAATTGAAATCTTGCTATGGATGAATGGCGCGATTACGGAATCTTGGAGGAAAGAAAAAATTCTGCGAG # Right flank : CATCGAAATCACCTACACCAAGAAAAAAAGCGTTTTAGAGCT # 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: R [43.3-56.7]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0,5.14 Confidence: HIGH] # Array family : II-A/C [Matched known repeat from this family], //