Array 1 89102-90056 **** Predicted by CRISPRDetect 2.4 *** >NZ_SERK01000010.1 Clostridioides difficile strain LC5-008-2 NODE_10_length_181327_cov_22.5756, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ======================================= ================== 89102 29 100.0 37 ............................. TCTGAATACGGAACATAAATAGCAACAGCACCAGAAT 89168 29 100.0 36 ............................. GTTATTGCTCCTGTTTCTGCTGAACTTTTCAATTTG 89233 29 100.0 39 ............................. AAGATACTTTAAGATTAGAGGTTAAGTGTGCAAATTATG 89301 29 100.0 38 ............................. AAACTTTACTTTTTAAAGTAACATTTTTTAAAAATAGA 89368 29 100.0 37 ............................. CCATCAACCTTATCAGAAACTTGACCATCCCAATCAT 89434 29 100.0 38 ............................. AAACTTAAAACTTTTTTATTATAAGTATTGATTTTTTA 89501 29 100.0 37 ............................. AAGGTCGTCTAGACCTAATTTTTTCTTTGCATCTTCT 89567 29 100.0 38 ............................. TATGGAAGTATAGATTATACTAGAAATAGGCTGATAGG 89634 29 100.0 36 ............................. CTCTGTGCAAGAGAGTGACTTAGATGTTGAGCTTAA 89699 29 100.0 37 ............................. ATTCTTTTTGAGTGAAGTTTAATTCTTTTCTAAGTGT 89765 29 100.0 37 ............................. GACTCTAGTATTATTTGAGCTAAAGAAATTGAAGCTG 89831 29 100.0 37 ............................. CCACCAACTCTACATAATAGGTCTCCTGCTTTCCATT 89897 29 100.0 36 ............................. AAGTCACACCGCCCTCCACACGACACTATAATAATA 89962 29 93.1 37 .............C.........A..... AGTATAATGTTGAAAAGTTAGAGAGTACAATCAAGAA 90028 29 69.0 0 A.....C.........AAT....AG..TA | ========== ====== ====== ====== ============================= ======================================= ================== 15 29 97.5 37 GTTTTATATTAACTAAGTGGTATGTAAAT # Left flank : TACAATTTATAGAGTGGAGTTCATACAAAAGATTATCCTCCCAATGTATAGAAGGGAGGTGAGTATGTATGGATAATTTTTTACAAGGTGTACTAGCAAGTTTAGTTGCCAGTTTAATAGTTTACTTAAATAGTAAATTATTTAAAAAAGTAAAAAGCCACTCTGGCAGGAGCGACTTTAGTTTTGAACTAAAAATCAAGTTCAAAAAGAATAAACATTAGTATTTGAACTTCACTCTATGTCTAAATAGATTGTAGTTCTTCTTGTTTTTATTATACCACAAATTGGTACAGATATTCAAAAATAATATATTTATGATATAATAAAAATGTAAATAGTTTTGCAGTGAGCGATATTTGTTACAAAGTAGGGCTTAATGCTTGAAATATAAGGTGTTGAGGGCATGTGATAAGCTTTATCATTTGCACTACTCATGGTTCACTGCAAATTTAAGAGAGTTGCACATGTGTAAGCATTGAAAATGCCCAGTTTATTTTGGG # Right flank : AAAACATGTATTTATACTTAAATTCTGTACCTATATAAAAAAGTGAACTCTGTCAACAAAGCACTTTTTTATATAGATAAATTATCATTTTGTTTTAAGATAGAAGATACTAATGATAACTGTTTATCATTAGTATCTGTATGTACATAAAAGTTTAATTTTTTATATAAATTTGCTCTTTAGAAAAATGAGCAGTATCAATAAATATATTGTTTAAATTTTTTCTAGGAACTAGTTGACTAGCTATAAGATTAGCTTCAACTCTTTGATTGTTAGACTATGAAATTAAATTTAAAGGTTCATTCTTGGTCGTATAAATAGCTTTATTATTCGTATGTACTATAACAATTTTTGCCATCTGCTTTTGATAGATAAAGAGCTTTATCAGCTTTAGAAAATAAATCTTTATATAATTTAGTTGAATCATCAGTGAAGGCAATACCAATACTTAATGTTATTTTATGATTGTCCTTTACTTTTATTTTACTTGCATCATTTAA # Questionable array : NO Score: 6.14 # Score Detail : 1:0, 2:3, 3:0, 4:0.88, 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 : GTTTTATATTAACTAAGTGGTATGTAAAT # 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: F [matched GTTTTATATTAACTAAGTGGTATGTAAAG with 100% identity] Score: 4.5/4.5 # Secondary Structural analysis prediction: NA [-0.50,0.00] Score: 0/0.37 # Array degeneracy analysis prediction: F [0-11] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [63.3-75.0]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [4.91,0.27 Confidence: HIGH] # Array family : I-B [Matched known repeat from this family], // Array 1 18315-18851 **** Predicted by CRISPRDetect 2.4 *** >NZ_SERK01000015.1 Clostridioides difficile strain LC5-008-2 NODE_15_length_99520_cov_23.3319, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ===================================== ================== 18315 29 100.0 35 ............................. ACATATGTCGCTTCATCAGCAGGAACAGATAACAG 18379 29 100.0 37 ............................. ATTCTATATATAGAAGGAGCAGGAGACATAAGTATAA 18445 29 100.0 37 ............................. TCTTTTAACTTTTTCAATTCTTCATCTGAATAATTAA 18511 29 100.0 37 ............................. CCTAACAAAGTCCCTTCTCTATCCTTTTTCATATAGC 18577 29 100.0 37 ............................. CTTCTTCGAGTGAACTTTTATATTGTCTTATTTCTTT 18643 29 100.0 37 ............................. AGTTTAGACTTTAGGTTTAAGGGGATATTCAGTTGTT 18709 29 100.0 36 ............................. GTGTCTTTTTCTTTTCAAAACCAACCAATACGAAAT 18774 29 100.0 18 ............................. TTTTCATCTATTGCATTA Deletion [18821] 18821 29 79.3 0 A.G.A...A........C.........G. | AG [18828] ========== ====== ====== ====== ============================= ===================================== ================== 9 29 97.7 34 GTTTTATATTAACTATATGGAATGTAAAT # Left flank : GATAACCATAATAAAAATAGATATCTATTTTTAGATTAAAAATAATATATCATAAATAAAATAATAAGAGGTAGATACAGTTTTAAGGGAATACAAAAGTTTTTAATTAAACTATGCTTGTTCAGATAGATATTTATTTAAGAAAAAAGACTATTAAAAGCAATATACAAGAATGATATATTAGATTGATTAAACAAGCATAAATATTATGTAAAAAACTTTAAGTTATAGAATTTAAATCTAATGTAGATAGATTACGTTTTTTTGCTTTTATTATGGTATAAATTGGTATCAATATTCAAAAGTAATATATTTATGATATAATAAAATCATAGGAATTTTGCAGTGAGCGATATTTGTGAAAAAATTTGGCGTAACAGTTGAAATATAAGGTGTTGAGAGTGCATGATAAGCGTTATCAATTGCACTATTGCTCGTTCACTGCAAATTTAAGAGAGTTGTATACGTGTAAGTATTGAAAATACTAAGTTTATTTTGGT # Right flank : TTTTTATAATTTTCTTTTAATGTGTTATCTTATGATTATCTAGTTATATTAGCATACAAAAATATAATAAAATTACACTATATTATAAAAACAAAAAGGTAGTATAGAAATCCTATTACCTTTTTATTATTAATTTTATCAGTGTTTTATTATAAATAGCTTACATAATTACACATTTTTTCTGATTAAATAATATGATGCTATTGTTATAATAGATACTAATGCTAATGATGTTATTGCAGTATCTAATCTTCTTATTAATAAACTCATTTCTATATATTCAAGTTCTATTAAATATTAATAAAATATTTCTAGTTTAACAGCTTTTTCTCTATCTATATTTCCATACTTTAACTCTAATTTATCTAAAGATTTTTTATTACAATAATTAACTTTATGTTTAATTAAATATCTTATTGTAGCACCTATTACAATTTTCACTCTAACAAGTATAAATATAATATTCCATCCAAAAGTTAAGAGGGGATATCTTTTTTATG # 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 : GTTTTATATTAACTATATGGAATGTAAAT # 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 GTTTTATATTAACTAAGTGGTATGTAAAG with 90% 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 [73.3-80.0]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [4.5,0 Confidence: HIGH] # Array family : I-B [Matched known repeat from this family], // Array 1 4769-6375 **** Predicted by CRISPRDetect 2.4 *** >NZ_SERK01000018.1 Clostridioides difficile strain LC5-008-2 NODE_18_length_37397_cov_18.6069, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ======================================== ================== 4769 29 100.0 36 ............................. TATAAATAAATAAACAAATCATTAGTTTTGAAACGA 4834 29 100.0 36 ............................. GAATTACCAGAATCGACCTCACAAGTTACTTTAAAA 4899 29 100.0 36 ............................. TATGTTTTTAGTTGGTTTTTTAAACTATTTAAAATG 4964 29 100.0 37 ............................. GTGAATTTTGTAGTTTTTGTTGCATCAAACTCTTTTT 5030 29 100.0 37 ............................. AAAAAATGGGCTGATGAAATGGGTATAACAAGAGAAA 5096 29 100.0 37 ............................. TATATAAGCGGAAATAGAATAGAAGTTGATTATGTGC 5162 29 100.0 37 ............................. TGAAAAAGAAGGCTAAAAATGCCTTGGCAATAGCTGG 5228 29 100.0 36 ............................. CTCTTTAGCGCTTCTTCAAGTTGTATTTGTGTATAA 5293 29 100.0 36 ............................. TAGATTGCTTTCAAATTACCTCTTGTATAGCGTCTT 5358 29 100.0 37 ............................. CTTTTTTTATTAGTGAAAGGGGGTGGTTAAAATTAAA 5424 29 100.0 37 ............................. TTGCTCCGCTATGCCTTGCGCTCTCTAATATCGCTTA 5490 29 100.0 37 ............................. CATAAAACTTTTGTGTATTTCTACACTCAAAAAGACT 5556 29 100.0 37 ............................. TCGGCTATATTGTATGTATTGATAGCGCACTTTTTAA 5622 29 100.0 36 ............................. ATTTTAAATTTTCAAAGATAAATTACACTAAGGCGG 5687 29 100.0 37 ............................. TTCCTATTATAATATGTAACTATATCTAACTTTTATA 5753 29 100.0 37 ............................. TGCTCCACGACCTTGTGGTTCCATAGCAACTATATAC 5819 29 100.0 36 ............................. ATTACTAGATGTAACTATCTCAACTTTGTTTAAATC 5884 29 100.0 40 ............................. GGTTTTAAAGACCCAGCAACGATAAAACAATATGTTGCAA 5953 29 100.0 35 ............................. TGAACTTTAATCGGTTTTATACAACAATATAACGC 6017 29 100.0 38 ............................. AATGAAGGTATAATAAAATTAACAGAAGAAACAAGAGA 6084 29 100.0 37 ............................. TCACACATGAGCAATATCGAAACAGGCAAATCTACAG 6150 29 100.0 36 ............................. TTCGTAAAATAACAATTATCTGGAATATGAGAAGTT 6215 29 100.0 37 ............................. CACTCTTAAGTTGTGACCTATCTGATATATGATTAAA 6281 29 100.0 37 ............................. TCAATATCTATATTAAGTTTATTTTTAAAAACATCTT 6347 29 96.6 0 ...............C............. | ========== ====== ====== ====== ============================= ======================================== ================== 25 29 99.9 37 GTTTTATATTAACTATGTGGTATGTAAAT # Left flank : CTATTATTATATATAACTGACATTTAAGTGACATTTAAGAAAAATATAATGCCTACTTACATAAAATGGAATGTTATTTAAAGAGAACTTTGATTATATTTTCAGAAGCTTTTTTATCCATATCGTTTAAAACAAGAAAATATCTATTCATAGTTATTTTTATATTAGTATGTCCTAATCTTTCAGAGATGATTTTTATATTAGTTCCAGCTAGAAGAAGAATTATTAGAATAGATAATATAGTAAGTATTTACAAATATGTAGGTGTTCTTAAATTGATAAATTATTCCATTTTAATTTTATAGTTTGAATTTTATGATATAATAAAAATATATAAATTTTGCAGTGAGCGATATTTTTGATAAAGTAGGGTTTAACAGTTGCAATGTAAGGGATTGAGGGTGTGTGATAAATGTTATCAATTGCACTACTCATGGTTCACTGCAAATTTGAGAGAGTTGTATGTGTGTAAGTACTGAAAATACTTAGTTTATTTTGGG # Right flank : TTTGCAACAAGTATAGGTAAAATACCCCAATAATTTATACAGCATTTTATCCTTTAAAATATAATTATTTTTTAGCATTTGTAGTAAATAATTACCAGATAACATTGACTTTAGTTTTAATGATTAAAATATAAAAGTAGAATAATTATAAAAAGTATTGAAAAATTTATAAATATATATAATAAAACTTAATGACAAGATATTAGATATAAAAAATAATTACCTTATAAATAGATTGAAATTTATGAATATTCATACTATAATTTAAATATAAGGAGATGCCCTTTGAAAATAAAAATTAAAAAATATTTAATGCTACTACAATAGGAACTAGAACTACACTTAATAAATATACAGAAATTAGATTTGGCTCAATATAAAATACAAATATAGAATTTAGGTGTTTTTTATGAAAAAAATTTTATATGCTTTATATAGTTTCATTGTTATTATAGCTAATTTTAGATTAAAAGAAAAAAATTATAACTTTATTTTATTAG # 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 : GTTTTATATTAACTATGTGGTATGTAAAT # 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: F [matched GTTTTATATTAACTAAGTGGTATGTAAAG with 97% identity] Score: 4.5/4.5 # Secondary Structural analysis prediction: NA [-0.50,0.00] Score: 0/0.37 # Array degeneracy analysis prediction: F [0-1] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [68.3-75.0]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [4.91,0 Confidence: HIGH] # Array family : I-B [Matched known repeat from this family], // Array 1 2650-2876 **** Predicted by CRISPRDetect 2.4 *** >NZ_SERK01000024.1 Clostridioides difficile strain LC5-008-2 NODE_24_length_11527_cov_63.9101, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ====================================== ================== 2650 29 100.0 37 ............................. TTATCTGCGTCTTCTGAAATAGCATACTCTTCAAGAG 2716 29 100.0 36 ............................. GTTGTAAGAAGTATCATTCTATTTTTTAATCTTTCT 2781 29 100.0 38 ............................. CTTATTTATAGTTGGGAAAATGGTTATAAATGTGGTAC 2848 29 96.6 0 ............................G | ========== ====== ====== ====== ============================= ====================================== ================== 4 29 99.2 37 GTTTTAGATTAACTATATGGAATGTAAAT # Left flank : ATTATATGTTATAATAATTGTAGCAAGGATAATAATCGAAAGTGCGAAGGGTGATTATTTTCATATTAAACGCCAAATTCCAAATAAGGAAGGAGGTGAAATTATATGATAGTTTTTTTATTAAGCATACTAGCTGGTGTTATATCAGCTTATATTTATGACAAAATAAAAAATCACCCAGACGCCAATAAGGGTGATTTAAAAAAATAATATTTTCACTTAACAACTGAAAATAATCACTCTTTGTAGGAGTAAATTATTTCCTTGCTTTTATTATACCACAAATTGGTACAGATATTCAAAAATAATATTTTTATGATATAATAAAAATGTAGAGATTTTGCAGTGAGCGATATTTGTTACAAAATATGGCTTAACACTTGAAATCTAAGATGTTGAGGGTGTGTGATAAATGTTATCAATTGCACTACTCATGGTTCACTGCAAATTTGAGAGAGATGCGTATGTGTAGGTATTGGAAATGCCAAGTTTATTTTGGG # Right flank : GCAACAAGAACAACAGTTGATTTTACCTTTTCTAGCCAACGTTTTATATTAACTATGTGGAGAAAAACTAAATAAACAAAGAAAGCACTTACAAATATGTAGGTGCTTTTGTTTTACCTTATATTGGAAATTTGTATAAAGATAAATTATAATGATTATATAGATATTTATGAGGGGGATTACGCTATGGGATTATTCAAAAAGAAGGAAAAAGAAAAAGGCATTTGTATAATTTGTGGTAATGAAGGAAATGCTTTAAAAACTGTAGATAATGAGTTTTTATGTGATGAATGTTTTGAAAAATGCAGAGGTGAAATAGCTGTTCTTGGTAAAGGACTAAAAAAACTGACAAGTAAGGAAGTTATGAATGCTGTAGAGTTATGTAGAGATAATTTTGGAAATTTTGTTAAAAACACATTAATACAAATTGTATATTTAGGAGGACATCCTTTATTTAATAGAGAAGAAATGATTTGTCTTTTAATTAGAAGTGACAAGAT # Questionable array : NO Score: 5.82 # Score Detail : 1:0, 2:3, 3:0, 4:0.96, 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 : GTTTTAGATTAACTATATGGAATGTAAAT # 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: NA # Secondary Structural analysis prediction: NA [0.00,0.00] Score: 0/0.37 # Array degeneracy analysis prediction: F [0-1] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [61.7-68.3]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [0.41,0 Confidence: MEDIUM] # Array family : NA // Array 2 5544-5769 **** Predicted by CRISPRDetect 2.4 *** >NZ_SERK01000024.1 Clostridioides difficile strain LC5-008-2 NODE_24_length_11527_cov_63.9101, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ===================================== ================== 5544 29 89.7 37 .AA..........A............... AATGAATTTTGAGAATCTACATAGGATTGAACTACTA 5610 29 96.6 37 A............................ ACTAAATTAGAGGTCGAGAAGGCTATTGAATCAAAAG 5676 29 100.0 36 ............................. TACACATTTTCTCAAATTTGGACTTCAATTAAAAAT 5741 29 86.2 0 ....................AC.TA.... | ========== ====== ====== ====== ============================= ===================================== ================== 4 29 93.1 37 GTTTTATATTAACTATGTGGTATGTAAAT # Left flank : TGAGATTATTAAAAAGATAAAATTAGAAGAAAATGAAGTAAAAGGAGTTTGGGAAACGAATGGTTCTTGGACTGGTACTGTAAATAAATATACAAAGAGTGTAATAGATAAGGTTAGAACTTGGATAGAGGAGAATAATAGACCAGCTAAGATTGAAGGTGAAAAGAAGAATTTTCATGTAGTGTATAAGATTGAGTAAATTTGATTGTATTAAATAGTTTAGTTTATTTTTGGGGGGATTAATACAATGTATGAGAATTTACTTAAGGAGTACAATTTAAAAACTGATGAAGATGTAGAATACTTTGTAAAGTTTGCTACATTATTACATAAATTAAAACAGGACAATGAAGAAAAATTTCAAGAGTATGCAGAGATATTGAGAGGTATTCTTAGAGAACAAGAAGAGAGAAAAAATAAGTAAATAAATAGATAAAGCACTTGGATATTATGATGTTTCAGGTGCTTTGTTTGTAAAAAAATGGTATAATGGAAATAGA # Right flank : TTAAAAATAATCAAAAACACTTACTTGAATAGTAGGTGTTTTTTTATTGAAAGGATGTGATTATAATGTAAAAATTTTACTTATATAGTATAATAATCTTATAAAATTATTGTGCTAGGGGGATTTGTTATGTTTTGTTCGAATTGTGGTGCAGAAATCACAGGCGTAGGCAAGTTTTGTTCAAGTTGTGGGGTTGCTGTAGAAACTGAAATTATTGAAGATAATAATATTAAATCAAATGACCTAATCGTTGATGCAAATGGAATAGAAATAAATATGACTGAAATTTATAGAAAATATAGAAAAGAAAAAGTAAATGCAATAAAAAATGTAATGGAAATAAGTGGTTTGAATATAAAGGAAGCAAAAAAAATAGTGGATTCTTCCTTTGAAGAGTTAAAAATCAATTTTATTGATGATACTATGAGCAATTCAGAAAAGGAAAAAATAATAAATACTCAAAATAGAAAAAATAATATTGAAAAAGCTCAACAAGAATC # Questionable array : NO Score: 3.70 # Score Detail : 1:0, 2:3, 3:0, 4:0.65, 5:-1.5, 6:0.25, 7:0.01, 8:0.6, 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 : GTTTTATATTAACTATGTGGTATGTAAAT # 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:82.14%AT] # Reference repeat match prediction: F [matched GTTTTATATTAACTAAGTGGTATGTAAAG with 97% identity] Score: 4.5/4.5 # Secondary Structural analysis prediction: NA [0.00,0.00] Score: 0/0.37 # Array degeneracy analysis prediction: F [3-4] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [71.7-76.7]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [4.91,0 Confidence: HIGH] # Array family : I-B [Matched known repeat from this family], // Array 1 239865-240024 **** Predicted by CRISPRDetect 2.4 *** >NZ_SERK01000001.1 Clostridioides difficile strain LC5-008-2 NODE_1_length_767587_cov_28.0268, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ===================================== ================== 239865 29 100.0 37 ............................. TTACAAGCCACAAACATAATAGCGCAAGTATAAAGAA 239931 29 100.0 36 ............................. AATGAACTATCTAAACCAAGGTCATAATTTAATTGA 239996 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ===================================== ================== 3 29 100.0 37 GTTTTATATTAACTATATGGAATGTAAAT # Left flank : GGAGTTCATGTATCAAAAAATTATCCTCCCGACGCTAAGAAGGGAGGTGAATATACATGGATAATTTTTTACAAGGCATACTAGCAAGTCTATCTGCTAGCTTAATAGTTTATATAGCTAGCAAACTATTTAGAAAGCGTAAAAAACCACTCAAAGCGGCAACTAAGAGTGGTTGGGAATTTGATTTAAAAATCAGATTCCATAAAACTAAGTAATTTCTAAATTATGAACTCCACTCTACAGCAAAATAGATTGTAGTTCTTCTTGCTTTTATTATATCACAAATTGGTACAGATATTCAAAAATAATATTTTTATGATATAATAAAGTCATAGAAATTTTGCAGTGTTCGATTTTTTGAAGAAATTAAGGCTTAACAGTTGAAATATAAGGCATTGAGGACTTGTGATAAGTGTTATCAATTGCACTACTCATGGTTCACTGCAAATTTGAGAGATTTGTATATGTGTAGGCATTGGAAATACTCAATTTATTTTGGG # Right flank : TTGTATCCAAAAAATTACAATAATCATACGAACTGCTAATATAAGCAGTCAATATATGTGTACATTTATCCATTTTATCTCTAAACATATAAATTATTATCCCCTTAAAAAACTTTCATAAAAACAAAAAGAACAATATCTCTTTGGCAACTGGCTGACATAACTCATAAGATATTTATATAAGTCTTAGTCCCTATAGCTTTGCGTCACTATATTTCTCTAGTTTTGCCGATTTAGTTTTATTCTATAACTAAATAATACAATAGAATTAGTTATTATTCAACAAGATTGTTTGAAAATTGAATAAATTTATAGGTATGAACGTAATTTCACACTTAAAAACAGACTAAATACGTAGAATATATAGAAAAATTTACCTGTAGTTTTTGTGATAAAAAGCTCCTATTATTAATTTAAGCTAGATAAGTTTGAGGAAGTGACATAAATTGAAAGAAGGAATATATTATGTTGAATAAAAAATTACCAGATGCAGAATTAAA # Questionable array : NO Score: 5.67 # Score Detail : 1:0, 2:3, 3:0, 4:1.00, 5:0, 6:0.25, 7:0.02, 8:0.4, 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 : GTTTTATATTAACTATATGGAATGTAAAT # 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 GTTTTATATTAACTAAGTGGTATGTAAAG with 90% 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 [68.3-73.3]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [4.5,0 Confidence: HIGH] # Array family : I-B [Matched known repeat from this family], // Array 2 483709-484328 **** Predicted by CRISPRDetect 2.4 *** >NZ_SERK01000001.1 Clostridioides difficile strain LC5-008-2 NODE_1_length_767587_cov_28.0268, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ====================================== ================== 483709 29 100.0 35 ............................. TTAGTTCCACTATAAAAATAAATCAAAACTAAAAC 483773 29 100.0 36 ............................. AGTTTAGGTTTTATATCTGCTTTATTAGTTTTTCTA 483838 29 100.0 37 ............................. CTAAAATTATGTTGATTTTTTAGTGGAGTTGTGTTAT 483904 29 100.0 37 ............................. GTATTAATTAAACCTAAACAGGTTACAACATCTAACA 483970 29 100.0 37 ............................. GCGCTTAACTTTCTCTTTCACTTCTATTCCTCCATTT 484036 29 100.0 37 ............................. AGAATAGAATCTAACATATATACACCTCCAATTAAGG 484102 29 100.0 37 ............................. CACTAGGACAGGCACTCCACTTCTAAAGCTTATACTT 484168 29 100.0 38 ............................. CTCGAATCAGGATATAACTATTTAAAAGAAAACATAGA 484235 29 100.0 36 ............................. TGCTGTGATTTCACTAATAAAACAATTAATAATTGT 484300 29 86.2 0 ................G....T.CA.... | ========== ====== ====== ====== ============================= ====================================== ================== 10 29 98.6 37 GTTTTAGATTAACTATATGGAATGTAAAT # Left flank : AATAATGTAGATAATGTTGAAAATTTAGAATTCAATGAGTTTGAACTTAAAACCGAAGAAGAAGAGAAGCGAGAACAAGAGAAAATAGAACAAGAAAAAAACAGTTATAATAACTACATTCAAAACAGAGTGGTTGACCCACTAGATAGAATAAAGAAACTAAAAGAGTTGCTAGATTCAGGAGCAATTACATAGGAAGAATATAATAAAAAGAAAAAAGAATTATTAGAATAGATAATATAGTAAGCACTTACAGGTATGTAGGTGCTTTTAAATTTACAAAGTATTCCATTTTAATTTTATAGTTTAGATTTTATGATATAATAAAAATATAGAAGTTTTGCAGTGTGCGATATTTGTTACAAAGTAGGGCTTAATACTTGAAATCTAAGATGTTGAGGGTGCGTGATAAGTGTTATCAATTGCACTATTGCCCGCTCACTGCAATTTTAAGAGTATTGTATATATGTAGGTATTGGAAATGCTAAGTTTATTTTGGG # Right flank : TTAAATAAACAAAGAAAGCACTTACAAATATGTAGGTGCTTTTATTCTGCTCAAAATTGGTTGGTTGGGTAAAATAATTAGAAAAAGTTAGTAAAAACCTATTGACTGTAACTCGTTACAATATTGTTATTAATGTAACGAGTTACAGAAAAGAGGCGAATAAAATAGCAACTAAAAGTAGGGCAGAGTATATGAAAAATCGTCGAAAAGATAAAAGAGGTTTTAGTGTACTTTTAGACAAAGAAAAGTTAGATAAATTTGATGAAGTATTAGAGGAAAAGAATCTAACCAAGAAAGAATGGCTAGAAGAAAAAATCGACGAGGAACTGGAACAAAAGGAATAAAAAATAAGGGTCACTCCCACCGACCAAAGTTTGAGTAACCCCTATGACGTATACTATCGTATATCAATTATAATATATGTCATTCCTTAAAAAAAATCAATTATTAAGGAGTGTAATATTATGAAAAATGAATTAATGATGTTTGAAGGAAAAGAG # Questionable array : NO Score: 6.19 # Score Detail : 1:0, 2:3, 3:0, 4:0.93, 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 : GTTTTAGATTAACTATATGGAATGTAAAT # 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: NA # Secondary Structural analysis prediction: NA [0.00,0.00] Score: 0/0.37 # Array degeneracy analysis prediction: F [0-4] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [71.7-71.7]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [0.41,0 Confidence: MEDIUM] # Array family : NA // Array 1 190341-191354 **** Predicted by CRISPRDetect 2.4 *** >NZ_SERK01000004.1 Clostridioides difficile strain LC5-008-2 NODE_4_length_277624_cov_29.6861, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ====================================== ================== 190341 29 100.0 37 ............................. ATGAACTTCGGAAGGAACCGTACCTTCATAAATTACA 190407 29 100.0 36 ............................. CTAAAATTATGTTGATTTTTTAGTGGAGTTGTGTTA 190472 29 100.0 37 ............................. TAACATATTTTTCCAATAGATTTAGTTTTTTATTTAA 190538 29 100.0 38 ............................. ACGAAAAACTAGTTAAAAACTGCATCAAAGTATTGATA 190605 29 100.0 36 ............................. AACAAACAGCCCAACTGAAATGCCAATCGCAACACA 190670 29 100.0 38 ............................. TAAGTTGGTTGTATATGTATTGAATCTGGTTCTAATGA 190737 29 100.0 38 ............................. ACAAACAAGTGTAGGATAAACTTTCCTTGCCCAGTATA 190804 29 100.0 37 ............................. TAACAAAATTTGCGAGTACACTTATTTCTAATATATC 190870 29 100.0 36 ............................. ATAAGAGTGGTTTAAGAAAATAAGTTATTTTTCAAA 190935 29 100.0 36 ............................. TGACTCGTGCTATTTTTTTTACACGCCTAAGAGGTA 191000 29 100.0 36 ............................. CGAAAAATCTAGGAAAAACTATTGTAAAAGCGTTTA 191065 29 100.0 37 ............................. TTTGATTACATGGGCAGTTTTTTATTATAGAGTGTTA 191131 29 100.0 35 ............................. TATGCTGATGGAACGGGTGTCTTTCGTACTGCTAG 191195 29 100.0 37 ............................. AAAAATCTTATTAAAGATTATTCAAAGTCTTTTGATT 191261 29 100.0 36 ............................. AACAAAAAAGATACATCTGTAACTAATTTTTATACT 191326 29 96.6 0 ............T................ | ========== ====== ====== ====== ============================= ====================================== ================== 16 29 99.8 37 GTTTTATATTAACTAAGTGGTATGTAAAG # Left flank : CTATTAACTTATGAAATATCTGTAAATGAGCAGATATTTCATAAGTTAATATTTATTGTTTACATAAAATATTTGGTAAAAATAAGTAAGTTTTATATGTTATAATAGTTGTAGCAAGAATAATAATCTAAAGTGGCAAGCATGTCAGCTGGTGTTATATCAGTTTATATTTATGATAAAATAAAAATCTCCCAAACGCCAATAAGAATGATTTAAAAAAATAATATTTTCACTTAAAAATAATCACTCTTTATAGGAGTAAATTATTTTCTTGATTTTATTATACTACAAATTGGTACAGATATTTAAAAATAATATATTCATAATATTATAAATAGTTTTGCAGTGAGCGATATTTTTGATAAAATAGGGCTTAACAGTTGAAACATAAGGCATTGAGGGTATATGATAAATATTATCATTTGCACTACTCGTGGTTCACTGCAAATTTGAGAGAATTGTATAGATGTAAGTGTTGGAAATACTCAATTTATTTTGGG # Right flank : GACAGATATAATGTCAAAATAAGGTTAGGACTTTTAAAAGCATAGCCATATCAGTAAAAATTTAATTATCATTTAAAAATAAATTTTTATTTAAAGAATACACATAAATATTTCCAGACTCAACTCTCTTAAACTATTTTCATATCTTTTAGTAGATACCTTTGTTGTTTTTTAATCTTTAGCAACTTGTTCTTGAGTGAACCTCTTATTTTTTCTAAGTTATTTCAAGCTTTTCAAAAAATTCTCTATTTATATTCATCACACATATAATACAATCAATTCAGTTTTAATTGCCAATATTTAGTTTTTCTGTATCTGATAAACCAAGAATATAATCAGTATATAAACCAAAAATTTTAGCAAATATTATTAACCCATCGTCTCTTGTTGGTATTTCACCAGATTCTATTCATAACACTTGTATTTATATTTGTTTTTTCAAGCAATTCTTTTTGAGAACTATTCATATTTTCCCTAGTATATTTAATCCTTTGATTTAC # 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 : GTTTTATATTAACTAAGTGGTATGTAAAG # 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:75.86%AT] # Reference repeat match prediction: F [matched GTTTTATATTAACTAAGTGGTATGTAAAG with 100% identity] Score: 4.5/4.5 # Secondary Structural analysis prediction: NA [-0.50,0.00] Score: 0/0.37 # Array degeneracy analysis prediction: F [0-1] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [70.0-73.3]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [4.91,0 Confidence: HIGH] # Array family : I-B [Matched known repeat from this family], // Array 1 257958-256235 **** Predicted by CRISPRDetect 2.4 *** >NZ_SERK01000002.1 Clostridioides difficile strain LC5-008-2 NODE_2_length_423027_cov_27.023, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ====================================== ================== 257957 29 100.0 36 ............................. GTGATAGATTATGGTGGTTTGTTTAATCCTATCGCA 257892 29 86.2 25 ....................C..T.T.T. TTTATTTTTCATAAAAAAAGATATA AC [257870] Deletion [257839] 257836 29 100.0 36 ............................. GTGATAGATTATGGTGGTTTGTTTAATCCTATCGCA 257771 29 100.0 37 ............................. TGTAAAAAGTTACTATTTCAGTCTCTTTACTCTGCAA 257705 29 100.0 37 ............................. AATTATTTATATTATCTAAAGTAACTTTAATATTATT 257639 29 100.0 38 ............................. TAAAAAGTTTAATATAAATATCTTCAGCCATATGTAAA 257572 29 100.0 38 ............................. TCCAAAACGGACTTGGTGTTAAGAGCTGTATAAGAAAC 257505 29 100.0 37 ............................. ACATTTTCAGCTAAAATTTTAAAAGGTGTATTAGCAA 257439 29 100.0 37 ............................. TTGGTTGATATAGATATTAGTCCTATTATTTCTGCTT 257373 29 100.0 37 ............................. AAATTAGATAATTTATAAGTCAATAAAATAAGTCCAA 257307 29 100.0 37 ............................. AAATTTGTAATATTATATAATCATCCTAAAACAAAAG 257241 29 100.0 36 ............................. TCGAATGCTATAATTTTAATATATAAAATAAATGGA 257176 29 100.0 36 ............................. ATGGATTTTAGTCGTTTTTAAATTTTTCTCGTAATA 257111 29 100.0 38 ............................. ACCATTCATTTATATTTTTATCTGTATCTCTTAGCCAT 257044 29 100.0 34 ............................. TAAGTTTTCTTAAAAAAGTACTTGCTTTAAATAT 256981 29 100.0 36 ............................. TCTTGTGCTCCTTGCGCAATCAAGTTATAAGACTCT 256916 29 100.0 37 ............................. GAAAATAATCTTAATGAAGTAGATTGGAATGAGGTTA 256850 29 100.0 36 ............................. TCTTTTGATTTAGCGTTGTTTGTCCGGAATTTTAAA 256785 29 100.0 37 ............................. TCGGGCTAGAATGTATTTTAAACCCTAGTTCATTGAA 256719 29 100.0 36 ............................. TTTCTAATATCGCTATTTAAACTCAATGCTTCATTT 256654 29 100.0 37 ............................. TCAGAACAAATTAAATATGTTTCGTTTTCCATGTAAG 256588 29 100.0 38 ............................. AGAACTTTTTTATATTAGAAGTACTTGACATGATTGCC 256521 29 100.0 34 ............................. CTTGATAATATTTCAGCATATGATACTGAAGATG 256458 29 100.0 37 ............................. TTGCCAATGTAACATCTTTAGATATTACAGTATCATT 256392 29 89.7 36 ......................GA...G. AGAATATTAGCAATATCAACGAGTATTTAGAAACTT 256327 29 75.9 35 A...........TA...CA....A....A TTGTAGAATCAACAATAGCATATACTAAAACATCC 256263 29 75.9 0 ACC.............A.CA...C..... | ========== ====== ====== ====== ============================= ====================================== ================== 27 29 97.3 36 GTTTTATATTAACTAAGTGGTATGTAAAT # Left flank : CATTTTATAAATGATGAAAGGTACAAAGTTTTAAAGGTGTGGTGGTAAGTATGTTTGTTATTGTTACTTATGATATTGTTGAAGCAAGGTCGTTAAATAGAATTAGAAGGATACTTAGAAAATATTTGACTTGGACGCAAAATTCTGTTTTTGAAGGCAATATTACTGAAGGAAAGTTACATAAATGTATTTCTGAAATAGAAAATATTATTGATAATAGCGAGGATTCAATCTATGTTTATGAGATAAAAAATCCTAATTCAATTAAAAAGAAATGTTATGGGATTGATAAGTATTCTGATGAAATGTTTATATAGGTTTGCAGTGAGCGATATTTATGCTAAAATAGGTGTTAACAGTTGGAATATAAGGGATTGAAGGTGTATGATAATTGTTATCAATTGCACTACTGCTCGCTCACTGCAAATTTTGATGTTTTTATTGAATTATAATTGCTTGATTGAAGTGTTTTCAATGTATTCAAATATACCTATTTTGGG # Right flank : AAAATAAACTTACCTATAAACATTATAAAATCAATACAAAAATGAGGTGAAATAAAATTTATGATAAAGAAATTAAACAATAAAGATATAAATAAAATCATGGAAATATGGGAAAAAAGTACAATCAAAGCACATGACTTTATAAGTAAAGAATACTGGCAAAATAACTATAATACTGTTAAAAACGAATATATACCTATATCAGATACATTTGTATATGATGATGGAGATGAAATAAAAGGATTTATAAGCATAATAGATAAAAGCTTTATAGGAGCTTTATTTATAAAGCCCAAATACCAAAATCTAGGTATCGGAGGTAAACTTTTAGATTATGCAACTAAAAAATATAAAAGTCTAAGCTTAGCAGTATATAAAGATAATAAAAAAGCAGTTGTGTTTTATAATAAAAAAGGTTTTAATATAGTAAAAGAACAAGTAAATGAAGATTCAGGATTTAAAGAGTACATAATGGAATATAGTAAATAATATGATTACAT # Questionable array : NO Score: 6.11 # Score Detail : 1:0, 2:3, 3:0, 4:0.86, 5:0, 6:0.25, 7:-0.00, 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 : GTTTTATATTAACTAAGTGGTATGTAAAT # 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 GTTTTATATTAACTAAGTGGTATGTAAAG with 100% identity] Score: 4.5/4.5 # Secondary Structural analysis prediction: NA [0.00,-0.50] Score: 0/0.37 # Array degeneracy analysis prediction: R [17-8] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [83.3-75.0]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0,4.91 Confidence: HIGH] # Array family : I-B [Matched known repeat from this family], //