Array 1 1-547 **** Predicted by CRISPRDetect 2.4 *** >NZ_MNCF01000033.1 Listeria monocytogenes strain 2012-0070 _002_R_2014_07_28_Lm-218_trimmed_contig_34, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ===================================== ================== 1 27 93.1 35 --........................... TGTTATCTCCTGTGATGTAAAATAACCCTTCTATC 63 29 100.0 37 ............................. TAATACAAAATATTCATAACTCCTACATCATTATATA 129 29 100.0 36 ............................. TTGCAAACCTAACTTATCTTTGTTTTTTTGCTTTTC 194 29 100.0 36 ............................. ACGTTTGCGGTAGTTTTACCGGGCACGGTCAAATAT 259 29 100.0 37 ............................. CAAAACAGAGAACGCGTGTTCATTATCGGACATCTTA 325 29 100.0 35 ............................. TTTTGAAATATGAGGACTTAGAAAATGAAAAAAAT 389 29 100.0 37 ............................. AAAAACTATGCAATTAGCAAAGTGATTTTATGTAATT 455 29 96.6 34 .......................A..... TAACGAGCCAATTAAACCATCTTCTTCTAGTAAT 518 29 93.1 0 .......................A....C | C [541] ========== ====== ====== ====== ============================= ===================================== ================== 9 29 98.1 36 GTTTTAACTACTTATTATGAAATGTAAAT # Left flank : | # Right flank : CGTCTTCTTAAAATTTAAACCCCAAAAATAAAAAAGGCCAGGACCCAAATCCAAGCCTTTTCCTACACTCCTCTAAACCAACAAAACCACAACCAACGCCAAAACCGCCGGCAAGCCCTGTTTCACCAAAATCCCCTTAGAAGAAGTCGCTCCGCCAAACAGCGCCGCCACAACTACACAACTCAAAAAGAAAATCTGCACAGTCTCCGCCATTCCTGCCCCCGCGAAAAACAATCCCCACACAAGTCCTGCCGCAAGAAAGCCATTATAAAGCCCTTGATTCGCGAATAGCGTCTGTACTTTCTTATTCGCAAGTAGTTCCTTCTCCACACCAAATGTCTTAGCTGCGAGTTTGGTATTGGCGAAAAACATTTCTAAAATCATTATATAAATATGCTCGATCATTACGATGAAGGTTAAAATAAATGCTAAAATGGCCATAAAAAATCCCTCTTTTCTACTTCGAAGTATAGCATAGCTTGTAAATTTTTCGTAAAAAT # Questionable array : NO Score: 6.16 # Score Detail : 1:0, 2:3, 3:0, 4:0.90, 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: F [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: F [1-4] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [0.0-0.0]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [4.91,0 Confidence: HIGH] # Array family : II-A [Matched known repeat from this family], // Array 1 569-154 **** Predicted by CRISPRDetect 2.4 *** >NZ_MNCF01000084.1 Listeria monocytogenes strain 2012-0070 _002_R_2014_07_28_Lm-218_trimmed_contig_103, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ===================================== ================== 568 29 100.0 33 ............................. AAACAGAAATGAAAGATGGTGAAGAAGTCCTTC 506 29 93.1 34 CG........................... TTTTTTAAGGCAAGTGTCATCGTTTCTAATCCGC 443 29 96.6 36 .........................T... CTAGAACAAAAGAAAAATCATGAGGGTATATTTACA 378 28 96.6 35 .................-........... GGTTTTGAATGCTGGTGGTGATAGTCCTAATGAAG 315 29 96.6 37 ................A............ TTGGTTCCTTTGGAAAACAACAATAACGTGTAGTATT A [298] 248 29 75.9 36 ......T.C.A.C...CA...T....... GCAGAAGCAGCAAAATAACCAAAAGTAATGACTTTC G [224] 182 29 79.3 0 ......A..T....AGA......A..... | ========== ====== ====== ====== ============================= ===================================== ================== 7 29 91.2 35 GTTTTAGTTACTTATTTTGAAATGTAAAT # Left flank : AAGAAGAAAAAGTTAGTG # Right flank : TGAAAACCTGTTATACATAGGATTATCTATTTCCGTTATAATTATTCCTTGCAAATAAATTCCAAAAAACAAACCCCTCATTAATTGGGTTTGTTTTTTTGTGAATAATTATAGTCAAACGAGCAATCTGTTAACAATTTAGCAATAAACGCAA # Questionable array : NO Score: 3.66 # Score Detail : 1:0, 2:3, 3:0, 4:0.56, 5:-1.5, 6:0.25, 7:0.01, 8:1, 9:0.34, # 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 : GTTTTAGTTACTTATTTTGAAATGTAAAT # 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:85.19%AT] # Reference repeat match prediction: R [matched GTTTTAGTTACTTATTTTGAAATGTAAAT 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 [14-2] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [75.0-23.3]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0.27,4.91 Confidence: HIGH] # Array family : II-A [Matched known repeat from this family], // Array 1 11791-12205 **** Predicted by CRISPRDetect 2.4 *** >NZ_MNCF01000020.1 Listeria monocytogenes strain 2012-0070 _002_R_2014_07_28_Lm-218_trimmed_contig_20, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ===================================== ================== 11791 29 100.0 35 ............................. AAACAGAAATGAAAGATGGTGAAGAAGTCCTTACC 11855 29 100.0 34 ............................. TTTTTTAAGGCAAGTGTCATCGTTTCTAATCCGC 11918 29 100.0 34 ............................. CTAGAACAAAAGAAAAATCATGAGGGATATTTAC 11981 29 100.0 35 ............................. GGTTTTGAATGCTGGTGGTGATAGTCCTAATGAAG 12045 29 96.6 37 ................A............ TTGGTTCCTTTGGAAAACAACAATAACGTGTAGTATT 12111 29 75.9 36 ......T.C.A.C...CA...T....... GCAGAAGCAGCAAAATAACCAAAAGTAATGACTTTC G [12134] 12177 29 79.3 0 ......A..T....AGA......A..... | ========== ====== ====== ====== ============================= ===================================== ================== 7 29 93.1 35 GTTTTAGTTACTTATTTTGAAATGTAAAT # Left flank : CGTCCGTGCCACTACTTCAGCTGATATTTTACTTGAAAAAGGTGCCGTAGAAGTTATCGCTTGCGCAACCCACTCCGTCATGGCCGGAAACGCAACCGAACGTTTACAAAATTCAAGTATCAAAGAAGTTATCACATCCGACTCCATCGATCTTCCAGAAGACAAGCAATTCGACAAACTAACAACCATCTCCATCGGACGAATCTTAGGCCGCGCAATCGAAGGCGTACAAGAAAACCGCTCGTTGCATCCGTTGTTTTAAAGAATAAGCAGAAAACAGTAACTTAGTAGAGTTGCTGTTTTTTTGTTATCTGTCGACCTCGAGTAGCGTGAAAAATACCGGGGATCGACAGAAAGTTGTAAGTGGTTGGGGTGGAAGAAGTTTGGCGGTATTTGCTTGGGGGAAATCTTCCGGATAAGAGGAGATTTTAGATGTTTTTTGGTAGGTCGACAGAAATAGCTCTTTGAGGTAAGATGGGAGTAAGAAGAAAAGTTAGTGG # Right flank : TGAAAACCTGTTATACATAGGATTATCTATTTCCGTTATAATTATTCCTTGCAAATAAATTCCAAAAAACAAACCCCTCATTAATTGGGTTTGTTTTTTTGTGAATAATTATAGTCAAACGAGCAATCTGTTAACAATTTAGCAATAAACGCAATAAAAAGCCGTTTTTTCACTATGGATTGTACTATAAAACATAATCTACCTATGCTAAAATTTAAGGGAAGGTAAGCTGAATAATACATATAAGGAGGACTCTACTATTGAAAAAGATTCTAGTGCCCATATTATTGTTAGCAACAATCTTAGCAAGCTGTTCCTCGCCGAATGAAAAAATAACCAAAGACACTAAAATATCCAAGACTATTACAATAAGAGCAGATTACAAAGTTCCAAAAGATATTAAAGAACTTGAGGATGATAGTGCTAATATTGTTAAAGTAAAATTTCTTCAAAATAAAACGATAGGCAAGGATGGTAGTACTATCAGCGAGATAGAAATT # Questionable array : NO Score: 5.91 # Score Detail : 1:0, 2:3, 3:0, 4:0.65, 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 : GTTTTAGTTACTTATTTTGAAATGTAAAT # 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: F [matched GTTTTAGTTACTTATTTTGAAATGTAAAT 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: F [0-15] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [58.3-75.0]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [4.91,0.27 Confidence: HIGH] # Array family : II-A [Matched known repeat from this family], // Array 2 27269-28592 **** Predicted by CRISPRDetect 2.4 *** >NZ_MNCF01000020.1 Listeria monocytogenes strain 2012-0070 _002_R_2014_07_28_Lm-218_trimmed_contig_20, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ===================================== ================== 27269 29 100.0 36 ............................. AAAGACCTTCGATTTCATTCTCACTTTCCAGTTAAT 27334 29 100.0 36 ............................. TTTTTTGTAGCGGAGGTGTACAATGCCGAAAGTGAC 27399 29 100.0 36 ............................. GCTGGTAAATTTGGCGGAACTAATCGTACTGAAATA 27464 29 100.0 37 ............................. ACATATTAGCCCTTATATAGAAGCCCCGCCCCTACCA 27530 29 100.0 35 ............................. TATAGTCCCCATATCCATCTGCTATTATCCTCCAC 27594 29 100.0 36 ............................. CGCTTCACGTTGGTTTTTCGTAGCCCAATTGCTAAA 27659 29 100.0 37 ............................. ACGTTGGACAACGAGGTGAGTATGATATGACTCAAAT 27725 29 100.0 36 ............................. GCGGAATGCGAAGTTGTTATATATAACTTATCTCGC 27790 29 100.0 36 ............................. TCTTAAATGGTGTTTGCACATGTTAAGGGAGTCATG 27855 29 100.0 35 ............................. GTGCATATCTCCTATATTCATGGCTGTATATGTGT 27919 29 100.0 36 ............................. CTGGTTACTCAACTGGCGACAGTAATACACCTCAAT 27984 29 100.0 34 ............................. TTTGGATAGGTTGTTTCTGATAAATAGGTTCACG 28047 29 100.0 37 ............................. AAGTCTACTTGGATTTAGCTCTACACCTGCAACATGA 28113 29 100.0 34 ............................. AGAAAAAAAACATCTTTCCAATTTGTTGTTTTGC 28176 29 100.0 34 ............................. AGAAGCGTTAGCGGCATTGTTCGAAAGTAATTTA 28239 29 100.0 36 ............................. TATAAAATATTGCCCAATGTGCGGAAGGAGTTTGGA 28304 29 100.0 36 ............................. CTCATAAGGATTTCGAGGCGGGTTAAACGACATGTA 28369 29 100.0 35 ............................. GCTTTTTTCAACAATTTTATCACCAGATGTCATTA 28433 29 100.0 36 ............................. TGAGCAGTGTCACCTGTTTCCGTATCTGCTTTTTTC 28498 29 100.0 37 ............................. AAGAAATCCGGGAAGTTTTGTTCTACAGAGCGAACGG 28564 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ===================================== ================== 21 29 100.0 36 GTTTTAACTACTTATTATGAAATGTAAAT # Left flank : CATTTAAAATTTGGTGGTGAAGATATGTATGTAATTTTAATTTATGATATTTCAATCGAAAATGGTGGAGCAAAAGTCTGGAGAAATGTATTTAAGATTTGTAAAAAGTACTTAACTCATGTTCAAAAATCAGTTTTTGAAGGTGAAATAACTCCAGCGCTTTTAGTTAAGTTAAGGATGGAGTTAGATAAGTATATTCGAGATGATCAAGATTCAGTAATTGTTTTTTCTAGTAGACAACAAAGATGGCTAGAAAAAGAATTTTGGGGATTAACGGATGAAAAGACTTCTAATTTCTTTTGATGTTCTCGGTCTGTCGACCTTTAGTAGTGCGAAAAATAGTGGGGTTCGACAGATTTAGGGAAATCATTGGGGGAGAAAGAGTTTGAAGTTTTTAAGCGAAAATCTGAAGGGATAAGTTATGATTTTTACGTAATTTTTAAGAGGTCGACAAAAATAGTGACCTGAGTTATGATGGGAGTAGGCGTAAAATAGAGCGG # Right flank : GTCAATAACTAGACGAGCTAACGTTTGTCGCTGTTTGTTTTAACTACTTATTA # 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 : 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: F [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: NA [0-0] Score: 0/0.41 # AT richness analysis in flanks prediction: NA [56.7-58.3]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [4.5,0 Confidence: HIGH] # Array family : II-A [Matched known repeat from this family], //