Array 1 3047414-3046789 **** Predicted by CRISPRDetect 2.4 *** >NZ_KK341218.1 Mycobacterium tuberculosis XDR KZN 605 adJIf-supercont-complete, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ==================================== ======================================== ================== 3047413 36 100.0 35 .................................... GCCCCGTGGATGGCGGATGCGTTGTGCGCGCAAGT 3047342 36 100.0 40 .................................... CCGACGATGGCCAGTAAATCGGCGTGGGTAACCGATCCGG 3047266 36 100.0 35 .................................... CTGACGGCACGGAGCTTTCCGGCTTCTATCAGGTA 3047195 36 100.0 36 .................................... CCTCATGGTGGGACATGGACGAGCGCGACTATCGGG 3047123 36 97.2 37 ......G............................. TGGACGCAGAATCGCACCGGGTGCGGGAGGTGCAGCA 3047050 36 100.0 40 .................................... GCATATCGCCCGCCACACCACAGCCACGCTACTGCTCCAT 3046974 36 97.2 40 ...C................................ ACACCGCCGATGACAGCTATGTCCGAGTGACATCCTCCCA 3046898 36 97.2 38 ..................A................. TTGAACCGCCCTTCGCGCGGTGTTTCGGCCGTGCCCGA 3046824 36 100.0 0 .................................... | ========== ====== ====== ====== ==================================== ======================================== ================== 9 36 99.1 38 GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC # Left flank : NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNATTTTGAGCGCGAACTCGTCCACAGTCCCCCTTTCAG # Right flank : TACGACGACTGGGTCGCCACCGCGTCTGTTGACCGGCATTCAGGATGAGCATGATGGCGGCGTTGACGGTGAGGACGTTTGGTCATGAAATGACCCCGCCGGGAGATGTCCGGCGGGGTCGGTGGTGTTCGGGGTGTCGGTGTGGTGTTCAGTCTGCCGTGACTTCGGCGATGGCGGTGCGGGTGGTGGATTCGTCGACGATGGCCTTGTCGGCGGCGAAGGCGGCGACGAGGGCTTGCAGGGCGAGGTTGTTGACCGCGCGGGGGTAGCCCCGGCTGGTCTGGTGGATCAACCCGATGGCGTCGTCGGAGAACAGGGCATCGTCGCGTCCGGCTAGCTTGAGGTGGTGGCGTAGGTAGCTGCCGGTGTTGGTGTCGGTCATGGGCGGCATGGCATATCGGAGTCCGATGCGCTGGTCAAGCGCGGCGAGCACGCCGAGTTTCATCCGCCGCCGCAGGGTGGGTTGGCCGATGAGCAGGCAGGCGAACGGGCTTGACGAG # Questionable array : NO Score: 6.21 # Score Detail : 1:0, 2:3, 3:0, 4:0.95, 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: NA [38.3-28.3]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0,1.15 Confidence: HIGH] # Array family : NA // Array 2 3051001-3049511 **** Predicted by CRISPRDetect 2.4 *** >NZ_KK341218.1 Mycobacterium tuberculosis XDR KZN 605 adJIf-supercont-complete, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ==================================== ========================================= ================== 3051000 36 100.0 38 .................................... TTAAAACCGTGTTGCACTGCAACCCGGAATTCTTGCAC 3050926 36 100.0 41 .................................... CATAGAGGGTCGCCGGCTCTGGATCACGCTCCCCTAGTCGT 3050849 36 100.0 36 .................................... TTTTTGCCTCATGCTTGGGCGACAGCTTTTGACCAA 3050777 36 100.0 34 .................................... TCGCAAGCGCCGTGCTTCCAGTGATCGCCTTCTA 3050707 36 100.0 39 .................................... AACACCTCAGTAGCACGTCATACGCCGACCAATCATCAG 3050632 36 100.0 35 .................................... TTTTCTGACCACTTGTGCGGGATTAGCGGGCTTAG 3050561 36 100.0 37 .................................... ACCAATGCGTCGTCATTTCCGGCTTCAATTTCAGCCT 3050488 36 100.0 38 .................................... CTGAGGAGAGCGAGTACTCGGGGCTGCCGTCTGCGCTG 3050414 36 100.0 37 .................................... GCGTGAAACCGCCCCCAGCCTCGCCGGGGCCGCCTAG 3050341 36 100.0 35 .................................... ACTCGGAATCCCATGTGCTGACAGCGGATTCGCAT 3050270 36 100.0 37 .................................... CGGGCAGCGTTCGACACCCGCTCTAGTTGACTTCCGG 3050197 36 100.0 41 .................................... CAGGTGAGCAACGGCGGCGGCAACCTGGCGGCCACGGGTCG 3050120 36 100.0 40 .................................... ATGGGATATCTGCTGCCCGCCCGGGGAGATGCTGTCCGAG 3050044 36 100.0 36 .................................... TTCGTCGACCATCATTGCCATTCCCTCTCCCCACGT 3049972 36 100.0 41 .................................... TTGCGCCAACCCTTTCGGTGTGATGCGGATGGTCGGCTCGG 3049895 36 100.0 24 .................................... CTTGAATAACGCGCAGTGAATTTC Deletion [3049836] 3049835 36 94.4 36 .CG................................. ATTCGCACGAGTTCCCGTCAGCGTCGTAAATCGCCA A [3049831] 3049762 36 100.0 36 .................................... ATTCGCACGAGTTCCCGTCAGCGTCGTAAATCGCCA 3049690 36 100.0 36 .................................... CGCATGGACCCGGGCGAGCTGCAGATGGTCCGGGAG 3049618 36 100.0 36 .................................... CGCATGGACCCGGGCGAGCTGCAGATGGTCCGGGAG 3049546 36 100.0 0 .................................... | ========== ====== ====== ====== ==================================== ========================================= ================== 21 36 99.7 37 GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC # Left flank : GGACGGAAACATTTTGAGCGCGAACTCGTCCACAGTCCCCCTTTCAGGTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAACGCCCCGTGGATGGCGGATGCGTTGTGCGCGCAAGTGTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAACCCGACGATGGCCAGTAAATCGGCGTGGGTAACCGATCCGGGTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAACCTGACGGCACGGAGCTTTCCGGCTTCTATCAGGTAGTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAACCCTCATGGTGGGACATGGACGAGCGCGACTATCGGGGTCGTCGGACCCAAAACCCCGAGAGGGGACGGAAACTGGACGCAGAATCGCACCGGGTGCGGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN # Right flank : TCCACATCGATTTCCTTGACCTCGCCAGGAGAGAAGATCACGTCGTCAGACCCAAAACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN # Questionable array : NO Score: 6.23 # 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 : 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: 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 // Array 3 3052037-3051128 **** Predicted by CRISPRDetect 2.4 *** >NZ_KK341218.1 Mycobacterium tuberculosis XDR KZN 605 adJIf-supercont-complete, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ==================================== ======================================== ================== 3052036 36 100.0 38 .................................... CTTCAGCACCACCATCATCCGGCGCCTCAGCTCAGCAT 3051962 36 100.0 38 .................................... CCTTCGACGCCGGATTCGTGATCTCTTCCCGCGGATAG 3051888 36 100.0 36 .................................... TGCCCCGGCGTTTAGCGATCACAACACCAACTAATG 3051816 36 100.0 36 .................................... CAGCGAAATACAGGCTCCACGACACGACCACAACGC 3051744 36 100.0 36 .................................... CAGCGAAATACAGGCTCCACGACACGACCACAACGC 3051672 36 100.0 37 .................................... AGGTTCGCGTCAGACAGGTTCGCGTCGATCAAGTCCG 3051599 36 100.0 37 .................................... TTTTTGAGCGCGAACTCGTCCACAGTCCCCCTTTCAA 3051526 36 100.0 37 .................................... ATTTTGAGCGCGAACTCGTCCACAGTCCCCCTTTCAG 3051453 36 100.0 35 .................................... GCCCCGTGGATGGCGGATGCGTTGTGCGCGCAAGT 3051382 36 100.0 40 .................................... CCGACGATGGCCAGTAAATCGGCGTGGGTAACCGATCCGG 3051306 36 100.0 35 .................................... CTGACGGCACGGAGCTTTCCGGCTTCTATCAGGTA 3051235 36 100.0 36 .................................... CCTCATGGTGGGACATGGACGAGCGCGACTATCGGG 3051163 36 97.2 0 ......G............................. | ========== ====== ====== ====== ==================================== ======================================== ================== 13 36 99.8 37 GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC # Left flank : GGCCACCTCCATGGTCCTCGACGCGATCGAGCAAGCCATCTGGACCCGCCAACAAGAAGGCGTACTCGACCTGAAAGACGTTATCCACCATACGGATAGGGGATCTCAGTACACATCGATCCGGTTCAGCGAGCGGCTCGCCGAGGCAGGCATCCAACCGTCGGTCGGAGCGGTCGGAAGCTCCTATGACAATGCACTAGCCGAGACGATCAACGGCCTATACAAGACCGAGCTGATCAAACCCGGCAAGCCCTGGCGGTCCATCGAGGATGTCGAGTTGGCCACCGCGCGCTGGGTCGACTGGTTCAACCATCGCCGCCTCTACCAGTACTGCGGCGACGTCCCGCCGGTCGAACTCGAGGCTGCCTACTACGCTCAACGCCAGAGACCAGCCGCCGGCTGAGGTCTCAGATCAGAGAGTCTCCGGACTCACCGGGGCGGTTCACCCCGAGAGGGGACGGAAACTCGGGGAGCCGATCAGCGACCACCGCACCCTGTCA # Right flank : TGGACGCAGAATCGCACCGGGTGCGGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAACTTAAAACCGTGTTGCACTGCAACCCGGAATTCTTGCACGTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAACCATAGAGGGTCGCCGGCTCTGGATCACGCTCCCCTAGTCGTGTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAACTTTTTGCCTCATGCTTGGGCGACAGCTTTTGACCAAGTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAACTCGCAAGCGCCGTGCTTCCAGTGATCGCCTTCTAGTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAACAACACCTCAGTAGCACGTCATACGCCGACCAATCATCAGGTCGT # 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 : 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 [1-0] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [13.3-33.3]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0,1.42 Confidence: HIGH] # Array family : NA // Array 4 3055040-3053472 **** Predicted by CRISPRDetect 2.4 *** >NZ_KK341218.1 Mycobacterium tuberculosis XDR KZN 605 adJIf-supercont-complete, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ==================================== ========================================= ================== 3055039 36 100.0 38 .................................... TTAAAACCGTGTTGCACTGCAACCCGGAATTCTTGCAC 3054965 36 100.0 41 .................................... CATAGAGGGTCGCCGGCTCTGGATCACGCTCCCCTAGTCGT 3054888 36 100.0 36 .................................... TTTTTGCCTCATGCTTGGGCGACAGCTTTTGACCAA 3054816 36 100.0 34 .................................... TCGCAAGCGCCGTGCTTCCAGTGATCGCCTTCTA 3054746 36 100.0 39 .................................... AACACCTCAGTAGCACGTCATACGCCGACCAATCATCAG 3054671 36 100.0 35 .................................... TTTTCTGACCACTTGTGCGGGATTAGCGGGCTTAG 3054600 36 100.0 37 .................................... ACCAATGCGTCGTCATTTCCGGCTTCAATTTCAGCCT 3054527 36 100.0 38 .................................... CTGAGGAGAGCGAGTACTCGGGGCTGCCGTCTGCGCTG 3054453 36 100.0 37 .................................... GCGTGAAACCGCCCCCAGCCTCGCCGGGGCCGCCTAG 3054380 36 100.0 35 .................................... ACTCGGAATCCCATGTGCTGACAGCGGATTCGCAT 3054309 36 100.0 37 .................................... CGGGCAGCGTTCGACACCCGCTCTAGTTGACTTCCGG 3054236 36 100.0 41 .................................... CAGGTGAGCAACGGCGGCGGCAACCTGGCGGCCACGGGTCG 3054159 36 100.0 40 .................................... ATGGGATATCTGCTGCCCGCCCGGGGAGATGCTGTCCGAG 3054083 36 100.0 36 .................................... TTCGTCGACCATCATTGCCATTCCCTCTCCCCACGT 3054011 36 100.0 41 .................................... TTGCGCCAACCCTTTCGGTGTGATGCGGATGGTCGGCTCGG 3053934 36 100.0 24 .................................... CTTGAATAACGCGCAGTGAATTTC Deletion [3053875] 3053874 36 94.4 36 .CG................................. ATTCGCACGAGTTCCCGTCAGCGTCGTAAATCGCCA A [3053870] 3053801 36 100.0 37 .................................... CCGGCAACAATCGCGCCGGCCCGCGCGGATGACTCCG 3053728 36 100.0 36 .................................... CGCATGGACCCGGGCGAGCTGCAGATGGTCCGGGAG 3053656 36 100.0 36 .................................... TGGATTGCGCTAACTGGCTTGGCGCTGATCCTGGTG 3053584 36 100.0 41 .................................... TCCACATCGATTTCCTTGACCTCGCCAGGAGAGAAGATCAC 3053507 36 97.2 0 .........................A.......... | ========== ====== ====== ====== ==================================== ========================================= ================== 22 36 99.6 37 GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC # Left flank : TTCAGTACGCCCTCGACTTGCAACTGCAAAGCCTCGTGCGTGTTATCGAAGCCGGGCACCCGTCGCGGCTCGTCGATATCGATATCACCTCCGAGCCATCCGGAGCCTAAATGCCCACTCGCAGCCGTGAGGAGTACTTCAATCTCCCGCTCAAAGTGGACGAGTCCAGCGGCACTATAGGCAAGATGTTCGTCCTCGTAATATACGACATCAGCGACAACCGGCGGCGGGCTTCACTTGCGAAGATCCTGGCCGGGTTTGGCTATCGCGTCCAAGAGTCCGCATTCGAAGCGATGCTGACGAAGGGCCAGCTCGCGAAACTAGTTGCACGTATCGACCGCTTCGCCATCGACTGCGACAACATCCGGATCTATAAGATAAGAGGTGTTGCGGCAGTTACGTTCTACGGAAGGGGACGGCTTGTCAGCGCAGAGGAGTTTGTGTTCTTTTGACATCATCAGCAGGCATTGTTACCACACGCTGGACGAATTGTCCATAGA # Right flank : TCGTCGACGATCGCGTCGATGTCGATGAACCGCCCCGGCATGTCCGGAGACTCCAGTTCTTGGAAAGGATGGGGTCATGTCAGGTGGTTCATCGAGGAGGTACCCGCCGGAGCTGCGTGAGCGGGCGGTGCGGATGGTCGCAGAGATCCGCGGTCAGCACGATTCGGAGTGGGCAGCGATCAGTGAGGTCGCCCGTCTACTTGGTGTTGGCTGCGCGGAGACGGTGCGTAAGTGGGTGCGCCAGGCGCAGGTCGATGCCGGCGCACGGCCCGGGACCACGACCGAAGAATCCGCTGAGCTGAAGCGCTTGCGGCGGGACAACGCCGAATTGCGAAGGGCGAACGCGATTTTAAAGACCGCGTCGGCTTTCTTCGCGGCCGAGCTCGACCGGCCAGCACGCTAATTACCCGGTTCATCGCCGATCATCAGGGCCACCGCGAGGGCCCCGATGGTTTGCGGTGGGGTGTCGAGTCGATCTGCACACAGCTGACCGAGCTGGG # Questionable array : NO Score: 6.22 # 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 : 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 [5-0] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [38.3-55.0]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0,1.42 Confidence: HIGH] # Array family : NA //