Array 1 1164384-1162023 **** Predicted by CRISPRDetect 2.4 *** >NZ_NYIT01000005.1 Listeria monocytogenes strain CFSAN049216 CFSAN049216_contig_0000005, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ===================================== ================== 1164383 29 100.0 35 ............................. TCATTTAGAAATGAGTGGGAACGGTTTAGTGAAAA 1164319 29 100.0 36 ............................. TTCTTACTCTGTTTCAACATCTAAGGATAAAATCTC 1164254 29 100.0 37 ............................. TCCCCCTTAAGATACAAACTCGATTTGACAGGTGCAG 1164188 29 100.0 36 ............................. TCGTTTATGACCTTATGAAAGAGTTAACACCTCGAC 1164123 29 100.0 36 ............................. CTTCCTACTTTTTGACATAAAAAATAAGCCGAGTTG 1164058 29 100.0 36 ............................. AAGTTCAAAACCTCCCACACCCGCTATGAATAAATT 1163993 29 100.0 37 ............................. GTCTTTGCATTTGATGATGATTACTTTTTTAAAGTCT 1163927 29 100.0 35 ............................. ACGAGTATCAGCGCTAAAAGAGATTGTTAAGCGCC 1163863 29 100.0 37 ............................. AGTATCGCCTTCGCTAGGCGTTTCGGGCGGCGTTTCC 1163797 29 100.0 37 ............................. TGCCGCAAAAACGTTGGGGAACGTTGTTCAAGGTATT 1163731 29 100.0 36 ............................. ACTTTAGAGAAAGAAAAACAAGAAAAAGTAAAACTG 1163666 29 100.0 37 ............................. TTCGTAATTTTACGATTATACTTTTTAGTCAAATTAC 1163600 29 100.0 35 ............................. GTAACAAGTAGTGTTATACCTGCAACAATACCAGC 1163536 29 100.0 36 ............................. GTCCACATCGACAATAAAAAACACATTGTATCACTT 1163471 29 100.0 36 ............................. CTGGTTACTCAACTGGCGACAGTAATACACCTCAAT 1163406 29 100.0 34 ............................. TTTGGATAGGTTGTTTCTGATAAATAGGTTCACG 1163343 29 100.0 34 ............................. AGAAAAAAAACATCTTTCCAATTTGTTGTTTTGC 1163280 29 100.0 37 ............................. ACAAGTGCTAGAACAGAAGTTATAATTTGAACATTAC 1163214 29 100.0 34 ............................. AGAAGCGTTAGCGGCATTGTTCGAAAGTAATTTA 1163151 29 100.0 36 ............................. TTGTTCGACGGCTTAGACAACCATCACGCTTCTTTA 1163086 29 100.0 35 ............................. GCTTTTTTCAACAATTTTATCACCAGATGTCATTA 1163022 29 100.0 37 ............................. AAGAAATCCGGGAAGTTTTGTTCTACAGAGCGAACGG 1162956 29 100.0 36 ............................. GTGTAATTCTTAATTCCGTATTGATTCGCTAGTTTT 1162891 29 100.0 37 ............................. TAATACAAAATATTCATAACTCCTACATCATTATATA 1162825 29 100.0 37 ............................. TTGGATTTTATTAAATACAGAGTCACGGATTGTATTT 1162759 29 100.0 35 ............................. TTAGAGATAACGTTAGCATCCGTGATAACTTAGTT 1162695 29 100.0 34 ............................. ATAAATTATCCGTATGTTCTTGAATTGTTTCTTC 1162632 29 100.0 35 ............................. AAATTTTTTGTTGATAAGCATGCAGGAGCAAACAA 1162568 29 100.0 37 ............................. CAGTGATTATGCTAAGACCTACACAATCGTTATCACT 1162502 29 100.0 35 ............................. GCATTTAATTGCAATAAACTTTGAATTGAGATTAA 1162438 29 100.0 33 ............................. TAAGGTCATATAAGAAAAAATGTATTTTTTCCC 1162376 29 96.6 34 .......................C..... CAAGATATGCTAGAAATGGCGCAAATAGCGCGCG 1162313 29 100.0 36 ............................. GGCTTTCTGGAATTGTTTCGCTGACATCCCTGCCAG 1162248 29 100.0 37 ............................. CAAAACAGAGAACGCGTGTTCATTATCGGACATCTTA 1162182 29 100.0 35 ............................. TTTTGAAATATGAGGACTTAGAAAATGAAAAAAAT 1162118 29 100.0 37 ............................. AAAAACTATGCAATTAGCAAAGTGATTTTATGTAATT 1162052 29 93.1 0 .......................C....C | A [1162027] ========== ====== ====== ====== ============================= ===================================== ================== 37 29 99.7 36 GTTTTAACTACTTATTATGAAATGTAAAT # Left flank : CATTTAAAATTTGGTGGTGAAGATATGTATGTAATTTTAATTTATGATATTTCAATCGAAAATGGTGGAGCAAAAGTCTGGAGAAATGTATTTAAGATTTGTAAAAAGTACTTAACTCATGTTCAAAAATCAGTTTTTGAAGGTGAAATAACTCCAGCGCTTTTAGTTAAGTTAAGGATGGAGTTAGATAAGTATATTCGAGATGATCAAGATTCAGTAATTGTTTTTTCTAGTAGACAACAAAGATGGCTAGAAAAAGAATTTTGGGGATTAACGGATGAAAAGACTTCTAATTTCTTTTGATGTTCTCGGTCTGTCGACCTTTAGTAGTGCGAAAAATAGTGGGGTTCGACAGATTTAGGGAAATCATTGGGGGAGAAAGAGTTTGAAGTTTTTAAGCGAAAATCTGAAGGGATAAGTTATGATTTTTACGTAATTTTTAAGAGGTCGACAAAAATAGTGACCTGAGTTATGATGGGAGTAGGCGTAAAATAGAGCGG # Right flank : GTCTTCTTAAAATTTAAACCCCAAAAATAAAAAAGGCCAGGACCCAAATCCAAGCCTTTTCCCACAACACCTAAACCAACAAAACCGCAACCAACGCCAAAACCGCCGGCAAGCCCTGTTTCACCAAAATCCCCTTAGAAGAAGTCGCTCCGCCAAACAGCGCCGCCACAACTACACAACTCAAAAAGAAAATCTGCACAGTCTCCGCCATTCCTGCCCCCGCGAAAAACAATCCCCACACAAGTCCTGCCGCAAGAAAGCCATTATAAAGCCCTTGATTCGCGAATAGCGTCTGTACTTTCTTATTCGCAAGGAGTTCTTTCTCGACACCAAATGTCTTGGCTGCGAGTTTGGTATTGGCGAAAAACATTTCTAAAATCATTATATAAATATGCTCGATCATTACGATGAAGGTTAAAATAAATGCTAAAATGGCCATAAAAAATCCCTCTTTTCTACTTCGAAGTATAGCATAGCTTGTAAATTTTTCGTAAAAATAG # 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 [4-0] 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 1179993-1179447 **** Predicted by CRISPRDetect 2.4 *** >NZ_NYIT01000005.1 Listeria monocytogenes strain CFSAN049216 CFSAN049216_contig_0000005, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ===================================== ================== 1179992 29 100.0 35 ............................. ACAGATCAAACTCCGGAAGGGTGATTGTAAATGGC 1179928 29 100.0 36 ............................. TGCTCTCTTTTGTGTAAAGCACATCAAGCATGTAGC 1179863 29 100.0 34 ............................. TTTTCTACTCCTGCTTCTAAAATGTCGTTTATAA 1179800 29 100.0 35 ............................. CTAAAACATCCTTCACTGTATCAACTCCTTTCTAT 1179736 29 96.6 36 A............................ AAAATAGGAGGAAATAAATTATGACTATCAAATTAA 1179671 29 100.0 35 ............................. TTTGTTGAATCAACGGATATAGATTTTACAATTTC 1179607 29 100.0 37 ............................. TTGGTTCCTTTGGAAAACAACAATAGCGTGTAGTATT 1179541 29 75.9 36 ......T.C.A.C...CA...T....... GCAGAAGCAGCAAAATAACCAAAAGTAATGACTTTC G [1179517] 1179475 29 79.3 0 ......A..T....AGA......A..... | ========== ====== ====== ====== ============================= ===================================== ================== 9 29 94.6 36 GTTTTAGTTACTTATTGTGAAATGTAAAT # Left flank : GCGTCCGTGCCACTACTTCAGCTGATATTTTACTTGAAAAAGGTGCCGTAGAAGTTATCGCTTGCGCAACCCACTCCGTCATGGCCGGAAACGCAACCGAACGTTTACAAAATTCAAGTATCAAAGAAGTTATCACATCCGACTCCATCGATCTTCCAGAAGACAAGCAATTCGACAAACTAACAACCATTTCTATCGGACGAATCTTAGGCCGCGCAATCGAAGGCGTACAAGAAAACCGCTCGTTGCATCCGTTGTTTTAAAGAATAAGCAGAAAACAGTAACTTAGTAGAGTTGCTGTTTTTTTGTTATCTGTCGACCTCGAGTAGCGTGAAAAATACCGGGGATCGACAGAAAGTTGTAAGTGGTTGGGGTGGAAGAAGTTTGGCGGTATTTGCTTGGGGAAATCTTCCGGATAAGAGGAGATTTTAGATGTTTTTTTGTAGGTCGACAGAAATAGCTCTTTGAGGTAAGATGGGAGTAAGAAGAAAAGTTAGTGG # Right flank : GAAAACCTGTTATACATAGGATTATCTATTTCCGTTATAATTATTCCTTGCAAATAAATTCCAAAAAACAAACCCCTCATTAATTGGGTTTGTTTTTTTGTGAATAATTATAGTCAAACGAGCAATCTGTTAACAATTTAGCAATAAACGCAATAAAAAGCCGTTTTTTCACTATGGATTGTACTATAAAACATAATCTACCTATGCTAAAATTTAAGGGAAGGTAAGCTGAATAATACATATAAGGAGGACTCTACTATTGAAAAAGATTCTAGTGCCCATATTATTGTTAGCAACAATCTTAGCAAGCTGTTCCTCGCCGAATGAAAAAATAACCAAAGACACTAAAATATCCAAGACTAATACAATAAGAGCAGATTACAAAGTTCCAAAAGATATTAAAGAACTTGAGGATGATAGTGCTAATATTGTTAAAGTAAAATTTCTTCAAAATAAAACGATAGGCAAGGATGGTAGTACTATCAGCGAGATAGAAATTT # Questionable array : NO Score: 5.99 # Score Detail : 1:0, 2:3, 3:0, 4:0.73, 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 : GTTTTAGTTACTTATTGTGAAATGTAAAT # 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: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 [14-0] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [75.0-60.0]%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], //