Array 1 1268-66 **** Predicted by CRISPRDetect 2.4 *** >NZ_MMJD01000019.1 Mycobacterium tuberculosis strain 01-R0239 01-R0239_contig19, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ==================================== ========================================= ================== 1267 36 100.0 38 .................................... TTAAAACCGTGTTGCACTGCAACCCGGAATTCTTGCAC 1193 36 100.0 41 .................................... CATAGAGGGTCGCCGGCTCTGGATCACGCTCCCCTAGTCGT 1116 36 100.0 36 .................................... TTTTTGCCTCATGCTTGGGCGACAGCTTTTGACCAA 1044 36 100.0 34 .................................... TCGCAAGCGCCGTGCTTCCAGTGATCGCCTTCTA 974 36 100.0 39 .................................... AACACCTCAGTAGCACGTCATACGCCGACCAATCATCAG 899 36 100.0 35 .................................... TTTTCTGACCACTTGTGCGGGATTAGCGGGCTTAG 828 36 100.0 37 .................................... ACCAATGCGTCGTCATTTCCGGCTTCAATTTCAGCCT 755 36 100.0 38 .................................... CTGAGGAGAGCGAGTACTCGGGGCTGCCGTCTGCGCTG 681 36 100.0 37 .................................... GCGTGAAACCGCCCCCAGCCTCGCCGGGGCCGCCTAG 608 36 100.0 35 .................................... ACTCGGAATCCCATGTGCTGACAGCGGATTCGCAT 537 36 100.0 37 .................................... CGGGCAGCGTTCGACACCCGCTCTAGTTGACTTCCGG 464 36 100.0 41 .................................... CAGGTGAGCAACGGCGGCGGCAACCTGGCGGCCACGGGTCG 387 36 100.0 40 .................................... ATGGGATATCTGCTGCCCGCCCGGGGAGATGCTGTCCGAG 311 36 100.0 36 .................................... TTCGTCGACCATCATTGCCATTCCCTCTCCCCACGT 239 36 100.0 41 .................................... TTGCGCCAACCCTTTCGGTGTGATGCGGATGGTCGGCTCGG 162 36 100.0 25 .................................... CTTGAATAACGCGCAGTGAATTTCG Deletion [102] 101 36 88.9 0 CGGA................................ | ========== ====== ====== ====== ==================================== ========================================= ================== 17 36 99.3 37 GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC # Left flank : TTCAGTACGCCCTCGACTTGCAACTGCAAAGCCTCGTGCGTGTTATCGAAGCCGGGCACCCGTCGCGGCTCGTCGATATCGATATCACCTCCGAGCCATCCGGAGCCTAAATGCCCACTCGCAGCCGTGAGGAGTACTTCAATCTCCCGCTCAAAGTGGACGAGTCCAGCGGCACTATAGGCAAGATGTTCGTCCTCGTAATATACGACATCAGCGACAACCGGCGGCGGGCTTCACTTGCGAAGATCCTGGCCGGGTTTGGCTATCGCGTCCAAGAGTCCGCATTCGAAGCGATGCTGACGAAGGGCCAGCTCGCGAAACTAGTTGCACGTATCGACCGCTTCGCCATCGACTGCGACAACATCCGGATCTATAAGATAAGAGGTGTTGCGGCAGTTACGTTCTACGGAAGGGGACGGCTTGTCAGCGCAGAGGAGTTTGTGTTCTTTTGACATCATCAGCAGGCATTGTTACCACACGCTGGACGAATTGTCCATAGA # Right flank : CATTCGCACGAGTTCCCGTCAGCGTCGTAAATCGCCAGTCGTCAGACCCAAAACCCCGAGAGGGGA # Questionable array : NO Score: 6.20 # Score Detail : 1:0, 2:3, 3:0, 4:0.96, 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 : GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC # 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: R [2,12] Score: 0.37/0.37 # Reference repeat match prediction: NA # Secondary Structural analysis prediction: R [-6.40,-7.70] Score: 0.37/0.37 # Array degeneracy analysis prediction: R [4-0] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [43.3-55.0]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0,1.42 Confidence: HIGH] # Array family : NA // Array 1 423781-422935 **** Predicted by CRISPRDetect 2.4 *** >NZ_MMJD01000017.1 Mycobacterium tuberculosis strain 01-R0239 01-R0239_contig17, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ==================================== ======================================== ================== 423780 36 100.0 38 .................................... TTTATCACTCCCGACCAAATAGGTATCGGCGTGTTCAA 423706 36 100.0 37 .................................... ATTTTGAGCGCGAACTCGTCCACAGTCCCCCTTTCAG 423633 36 100.0 35 .................................... GCCCCGTGGATGGCGGATGCGTTGTGCGCGCAAGT 423562 36 100.0 40 .................................... CCGACGATGGCCAGTAAATCGGCGTGGGTAACCGATCCGG 423486 36 100.0 38 .................................... TAGTACGCCATCTGTGCCTCATACAGGTCCAGTGCCCT 423412 36 100.0 35 .................................... CTGACGGCACGGAGCTTTCCGGCTTCTATCAGGTA 423341 36 100.0 36 .................................... CCTCATGGTGGGACATGGACGAGCGCGACTATCGGG 423269 36 97.2 37 ......G............................. TGGACGCAGAATCGCACCGGGTGCGGGAGGTGCAGCA 423196 36 100.0 40 .................................... GCATATCGCCCGCCACACCACAGCCACGCTACTGCTCCAT 423120 36 97.2 40 ...C................................ ACACCGCCGATGACAGCTATGTCCGAGTGACATCCTCCCA 423044 36 97.2 38 ..................A................. TTGAACCGCCCTTCGCGCGGTGTTTCGGCCGTGCCCGA 422970 36 100.0 0 .................................... | ========== ====== ====== ====== ==================================== ======================================== ================== 12 36 99.3 38 GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC # Left flank : CC # Right flank : TACGACGACTGGGTCGCCACCGCGTCTGTTGACCGGCATTCAGGATGAGCATGATGGCGGCGTTGACGGTGAGGACGTTTGGTCATGAAATGACCCCGCCGGGAGATGTCCGGCGGGGTCGGTGGTGTTCGGGGTGTCGGTGTGGTGTTCAGTCTGCCGTGACTTCGGCGATGGCGGTGCGGGTGGTGGATTCGTCGACGATGGCCTTGTCGGCGGCGAAGGCGGCGACGAGGGCTTGCAGGGCGAGGTTGTTGACCGCGCGGGGGTAGCCCCGGCTGGTCTGGTGGATCAACCCGATGGCGTCGTCGGAGAACAGGGCATCGTCGCGTCCGGCTAGCTTGAGGTGGTGGCGTAGGTAGCTGCCGGTGTTGGTGTCGGTCATGGGCGGCATGGCATATCGGAGTCCGATGCGCTGGTCAAGCGCGGCGAGCACGCCGAGTTTCATCCGCCGCCGCAGGGTGGGTTGGCCGATGAGCAGGCAGGCGAACGGGCTTGACGAG # Questionable array : NO Score: 6.22 # Score Detail : 1:0, 2:3, 3:0, 4:0.96, 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 : GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC # 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: R [2,12] Score: 0.37/0.37 # Reference repeat match prediction: NA # Secondary Structural analysis prediction: R [-6.40,-7.70] Score: 0.37/0.37 # Array degeneracy analysis prediction: R [2-0] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [38.3-0.0]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0.27,1.15 Confidence: MEDIUM] # Array family : NA // Array 1 223-41 **** Predicted by CRISPRDetect 2.4 *** >NZ_MMJD01000018.1 Mycobacterium tuberculosis strain 01-R0239 01-R0239_contig18, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ==================================== ====================================== ================== 222 36 72.2 35 C..AC.G.GG.GGTC..................... TCGGGGAGCCGATCAGCGACCACCGCACCCTGTCA T [209] 150 36 100.0 38 .................................... CTTCAGCACCACCATCATCCGGCGCCTCAGCTCAGCAT 76 36 100.0 0 .................................... | ========== ====== ====== ====== ==================================== ====================================== ================== 3 36 90.7 37 GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC # Left flank : GTTCGCCTACGTGGCCTTTGTCACCGACGCCTACGCTCGCAGGATCCTGGGCTGGCGGGTCGCTTCCACGATGGCCACCTCCATGGTCCTCGACGCGATCGAGCAAGCCATCTGGACCCGCCAACAAGAAGGCGTACTCGACCTGAAAGACGTTATCCACCATACGGATAGGGGATCTCAGTACACATCGATCCGGTTCAGCGAGCGGCTCGCCGAGGCAGGCATCCAACCGTCGGTCGGAGCGGTCGGAAGCTCCTATGACAATGCACTAGCCGAGACGATCAACGGCCTATACAAGACCGAGCTGATCAAACCCGGCAAGCCCTGGCGGTCCATCGAGGATGTCGAGTTGGCCACCGCGCGCTGGGTCGACTGGTTCAACCATCGCCGCCTCTACCAGTACTGCGGCGACGTCCCGCCGGTCGAACTCGAGGCTGCCTACTACGCTCAACGCCAGAGACCAGCCGCCGGCTGAGGTCTCAGATCAGAGAGTCTCCGGA # Right flank : CCCTTCGACGCCGGATTCGTGATCTCTTCCCGCGGATAGGT # Questionable array : NO Score: 4.90 # Score Detail : 1:0, 2:3, 3:0, 4:0.54, 5:0, 6:0.25, 7:0.02, 8:0.4, 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 : GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC # 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: R [2,12] Score: 0.37/0.37 # Reference repeat match prediction: NA # Secondary Structural analysis prediction: R [-6.40,-7.70] Score: 0.37/0.37 # Array degeneracy analysis prediction: F [0-13] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [26.7-36.7]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0.41,1.01 Confidence: MEDIUM] # Array family : NA // Array 2 1804-1544 **** Predicted by CRISPRDetect 2.4 *** >NZ_MMJD01000018.1 Mycobacterium tuberculosis strain 01-R0239 01-R0239_contig18, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ==================================== ======================================== ================== 1803 36 100.0 37 .................................... TTGGAGCGTGTCACCGCAGACGGCACGATTGAGACAA 1730 36 100.0 39 .................................... CCTCAGCTCAGCATCGCTGATGCGGTCCAGCTCGTCCGT 1655 36 100.0 40 .................................... CCAACCTCACCGCCTGCTGGGTGAGACGTGCTCGCCGCGA 1579 35 75.0 0 ...................T..-.CC.CC...C.TG | C [1548] ========== ====== ====== ====== ==================================== ======================================== ================== 4 36 93.8 39 GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC # Left flank : | # Right flank : TCCGGAGACTCCAGTTCTTGGAAAGGATGGGGTCATGTCAGGTGGTTCATCGAGGAGGTACCCGCCGGAGCTGCGTGAGCGGGCGGTGCGGATGGTCGCAGAGATCCGCGGTCAGCACGATTCGGAGTGGGCAGCGATCAGTGAGGTCGCCCGTCTACTTGGTGTTGGCTGCGCGGAGACGGTGCGTAAGTGGGTGCGCCAGGCGCAGGTCGATGCCGGCGCACGGCCCGGGACCACGACCGAAGAATCCGCTGAGCTGAAGCGCTTGCGGCGGGACAACGCCGAATTGCGAAGGGCGAACGCGATTTTAAAGACCGCGTCGGCTTTCTTCGCGGCCGAGCTCGACCGGCCAGCACGCTAATTACCCGGTTCATCGCCGATCATCAGGGCCACCGCGAGGGCCCCGATGGTTTGCGGTGGGGTGTCGAGTCGATCTGCACACAGCTGACCGAGCTGGGTGTGCCGATCGCCCCATCGACCTACTACGACCACATCAACCG # Questionable array : NO Score: 5.55 # Score Detail : 1:0, 2:3, 3:0, 4:0.69, 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 : GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC # 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: R [2,12] Score: 0.37/0.37 # Reference repeat match prediction: NA # Secondary Structural analysis prediction: R [-6.40,-7.70] Score: 0.37/0.37 # Array degeneracy analysis prediction: R [10-0] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [46.7-0.0]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0.27,1.15 Confidence: MEDIUM] # Array family : NA //