Array 1 457970-459194 **** Predicted by CRISPRDetect 2.4 *** >NZ_NYCJ01000002.1 Listeria monocytogenes strain CFSAN044797 CFSAN044797_contig_0000002, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ==================================== ============================== ================== 457970 36 100.0 30 .................................... TGATTTTATTTGGGAGAAGATAAACAATGA 458036 36 100.0 30 .................................... ATCGCGACAGTGCCTTTTGATACGTTTTTT 458102 36 100.0 30 .................................... ATATAAAAAATAGAAGTTGACAACTTTAAG 458168 36 100.0 30 .................................... TACAAGGAGTTTACTTCCTAACCTGTATAC 458234 36 100.0 30 .................................... AACCTTACGAAAGATAACCGCATTAGCTTG 458300 36 100.0 30 .................................... CGTTTTTCCAAAGTCTGAATGCTCTTTCAT 458366 36 100.0 30 .................................... TAAAATCCGAAACTAGTGGGCTTGCTGTGT 458432 36 100.0 30 .................................... TTGCATAAAAAAAGCCCTAACGTTGAGGTT 458498 36 100.0 30 .................................... AGTTCCTCCTTCTTCAACGCATTCACCATT 458564 36 100.0 30 .................................... AAAGTAAATCGTCTTCCTCCCACTCAAACT 458630 36 100.0 30 .................................... AGCTCAATTAAATATATATGCTGCGGCATC 458696 36 100.0 30 .................................... TCATTTTCTCCTGGAACGTTTCTGTTACCA 458762 36 100.0 30 .................................... GCTATATTAGTCGTTGGATTCAAATGGTTG 458828 36 100.0 30 .................................... TCTGCCATTCATCACTAAATTCACATAAAT 458894 36 100.0 30 .................................... GTGGTGACTGTCTAGTCCGTTCAGAAAAGG 458960 36 100.0 30 .................................... CTAAATCACTCGATAACTAGAGTTGCTAAC 459026 36 100.0 30 .................................... AATGGACGGTGCTGTTGTTGTCACTGAAAA 459092 36 100.0 28 .................................... TAATATTCTCCCCCCATCGCTAACAGGG 459156 36 86.1 0 .............A.....C.....T.A.......G | A,A,C [459181,459187,459190] ========== ====== ====== ====== ==================================== ============================== ================== 19 36 99.3 30 GTTTTAGAGCTATGTTATTTTGAATGCTACCAAAAC # Left flank : GACAAATTAACCGCGACGATTAGCGAGTTGATAGGTTACGAATTATTGGAGCATGAACTGGATTTAGAAGAAGATGAAATAACGGTCATTGAATTATTCAAAGCTTTAGGAATAAAAATAGAAACAAAAAGCGATACCGTATTTGAGAAGTTAATTGAAATAGTACAAGTCTATAAATATCTATCTAAAAAGAAATTGTTAGTACTTATTAACGTGTGTTCCTATCTTACAGAGGAAGAACTGCTAGAGTTGAGACGGTATATCTCTTTATATCAAGTCAAAGTACTATTTATTGAACCTAGAAAAATAAAAGGATCTCCGCAAGTTACTTTAGATTCTGATTATTTTTTACATGTGGAAAATAGTGTATAAGGTAACCGCTGTTCTTTGAAAACAAAATAAATTTTATGTAAACCATAAAATAGCATTCAAAATTGAAATCTTGCTATGGATGAATGGCGCGATTACGGAATCTTGGAGGAAAGAAAAAATTCTGCGAG # Right flank : GATAAAATGCATCGCAATTACCAAACCATGGTTAAATTTAAAAAGGAGTTAAACTATCTACATGACACAGTATCACTATCTTGCTTCGAAGTCGCTCTTAGAAAATGATGGGGAAAAGTTCTCTCGTCTTTATATTAGACTTCTTAAATTTGAATTTTGATATGAATGTTGACCAAGACACTAATGAATTGTTTTTCTATTCAATTGATTTGAACTCAGCTTGTAAATGTAAGTAAAGGGAACCTGCCGCTGAAAGGTAATGGGCAAAAAAATTGTTACGAGACTAAAAGTTTAAAAATCTTGTATGATTATATTCTAAATACGAGTAAAGATAATGACACGCTTGAACTATATACTGCTTGGAACAGCGAGGAAGATTTCCTGCTATTGAATAAAACAGAACTGCTGATCTAGAATTTAACTATCGAAAATCTAATTTTAAATGATAGAGAACTATTAATAATTAAAAAAGAAAATCGATATAACTTTTAGCACCATTC # 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: F [matched GTTTTAGAGCTATGTTATTTTGAATGCTACCAAAAC with 100% identity] Score: 4.5/4.5 # Secondary Structural analysis prediction: F [-1.30,-0.80] Score: 0.37/0.37 # Array degeneracy analysis prediction: NA [0-0] Score: 0/0.41 # AT richness analysis in flanks prediction: NA [56.7-63.3]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [4.87,0 Confidence: HIGH] # Array family : II-A/C [Matched known repeat from this family], // Array 1 156954-154656 **** Predicted by CRISPRDetect 2.4 *** >NZ_NYCJ01000010.1 Listeria monocytogenes strain CFSAN044797 CFSAN044797_contig_0000010, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ===================================== ================== 156953 29 100.0 36 ............................. AAAGACCTTCGATTTCATTCTCACTTTCCAGTTAAT 156888 29 100.0 36 ............................. TTTTTTGTAGCGGAGGTGTACAATGCCGAAAGTGAC 156823 29 100.0 36 ............................. GCTGGTAAATTTGGCGGAACTAATCGTACTGAAATA 156758 29 100.0 37 ............................. ACATATTAGCCCTTATATAGAAGCCCCGCCCCTACCA 156692 29 100.0 35 ............................. TATAGTCCCCATATCCATCTGCTATTATCCTCCAC 156628 29 100.0 36 ............................. CGCTTCACGTTGGTTTTTCGTAGCCCAATTGCTAAA 156563 29 100.0 37 ............................. ACGTTGGACAACGAGGTGAGTATGATATGACTCAAAT 156497 29 100.0 36 ............................. GCGGAATGCGAAGTTGTTATATATAACTTATCTCGC 156432 29 100.0 36 ............................. TCTTAAATGGTGTTTGCACATGTTAAGGGAGTCATG 156367 29 100.0 35 ............................. GTGCATATCTCCTATATTCATGGCTGTATATGTGT 156303 29 100.0 36 ............................. GTCCACATCGACAATAAAAAACACATTGTATCACTT 156238 29 100.0 36 ............................. CTGGTTACTCAACTGGCGACAGTAATACACCTCAAT 156173 29 100.0 34 ............................. TTTGGATAGGTTGTTTCTGATAAATAGGTTCACG 156110 29 100.0 37 ............................. AAGTCTACTTGGATTTAGCTCTACACCTGCAACATGA 156044 29 100.0 34 ............................. AGAAAAAAAACATCTTTCCAATTTGTTGTTTTGC 155981 29 100.0 34 ............................. AGAAGCGTTAGCGGCATTGTTCGAAAGTAATTTA 155918 29 100.0 36 ............................. TTGTTCGACGGCTTAGACAACCATCACGCTTCTTTA 155853 29 100.0 36 ............................. TATAAAATATTGCCCAATGTGCGGAAGGAGTTTGGA 155788 29 100.0 36 ............................. CTCATAAGGATTTCGAGGCGGGTTAAACGACATGTA 155723 29 100.0 35 ............................. GCTTTTTTCAACAATTTTATCACCAGATGTCATTA 155659 29 100.0 36 ............................. TGAGCAGTGTCACCTGTTTCCGTATCTGCTTTTTTC 155594 29 100.0 37 ............................. AAGAAATCCGGGAAGTTTTGTTCTACAGAGCGAACGG 155528 29 100.0 36 ............................. GTCAATAACTAGACGAGCTAACGTTTGTCGCTGTTT 155463 29 100.0 35 ............................. TGTTATCTCCTGTGATGTAAAATAACCCTTCTATC 155399 29 100.0 37 ............................. TAATACAAAATATTCATAACTCCTACATCATTATATA 155333 29 100.0 36 ............................. TTGCAAACCTAACTTATCTTTGTTTTTTTGCTTTTC 155268 29 100.0 37 ............................. TTGGATTTTATTAAATACAGAGTCACGGATTGTATTT 155202 29 100.0 36 ............................. GGAACAGGCGCGCGCTGGGATTTAAAAGCAGAAGGC 155137 29 100.0 36 ............................. CACGTACTTTAATCGGCATCAAACCACCTCGATTTC 155072 29 96.6 34 .......................C..... CAAGATATGCTAGAAATGGCGCAAATAGCGCGCG 155009 29 100.0 36 ............................. ACGTTTGCGGTAGTTTTACCGGGCACGGTCAAATAT 154944 29 100.0 37 ............................. CAAAACAGAGAACGCGTGTTCATTATCGGACATCTTA 154878 29 100.0 35 ............................. TTTTGAAATATGAGGACTTAGAAAATGAAAAAAAT 154814 29 100.0 37 ............................. AAAAACTATGCAATTAGCAAAGTGATTTTATGTAATT 154748 29 96.6 34 .......................A..... TAACGAGCCAATTAAACCATCTTCTTCTAGTAAT 154685 29 93.1 0 .......................C....C | A [154660] ========== ====== ====== ====== ============================= ===================================== ================== 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 172497-172015 **** Predicted by CRISPRDetect 2.4 *** >NZ_NYCJ01000010.1 Listeria monocytogenes strain CFSAN044797 CFSAN044797_contig_0000010, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ===================================== ================== 172496 29 96.6 35 ................T............ TTGTCATCTGTGGTGTCTTCAACCACTTCTTCTAT 172432 29 96.6 35 ................T............ TCTGTAAAATCAAAAGTATCATAGAAACAATCTTC 172368 29 100.0 35 ............................. TTCGCCATGACGAAATCTAGCGCTTGTCCTACTAA 172304 29 100.0 36 ............................. GGCACAGTCTTCACGATTTCGGGGATGGGGAAAACT 172239 29 100.0 35 ............................. TAAACAAGTGCTTCTGGCAATACCAACGTTCCATC 172175 29 93.1 37 T...............A............ TTGGTTCCTTTGGAAAACAACAATAGCGTGTAGTATT 172109 29 75.9 36 ......T.C.A.C...CA...T....... GCAGAAACAGCAAAATAACCAAAAGTAATGACTTTC G [172084] 172043 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], //