Array 1 65415-64497 **** Predicted by CRISPRDetect 2.4 *** >NZ_PQFR01000054.1 Mycobacterium tuberculosis strain UT356 scaffold3, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ==================================== ======================================== ================== 65414 36 97.2 35 T................................... TCGGGGAGCCGATCAGCGACCACCGCACCCTGTCA A [65411] 65342 36 100.0 38 .................................... TTTATCACTCCCGACCAAATAGGTATCGGCGTGTTCAA 65268 36 100.0 37 .................................... ATTTTGAGCGCGAACTCGTCCACAGTCCCCCTTTCAG 65195 36 100.0 35 .................................... GCCCCGTGGATGGCGGATGCGTTGTGCGCGCAAGT 65124 36 100.0 40 .................................... CCGACGATGGCCAGTAAATCGGCGTGGGTAACCGATCCGG 65048 36 100.0 38 .................................... TAGTACGCCATCTGTGCCTCATACAGGTCCAGTGCCCT 64974 36 100.0 35 .................................... CTGACGGCACGGAGCTTTCCGGCTTCTATCAGGTA 64903 36 100.0 36 .................................... CCTCATGGTGGGACATGGACGAGCGCGACTATCGGG 64831 36 97.2 37 ......G............................. TGGACGCAGAATCGCACCGGGTGCGGGAGGTGCAGCA 64758 36 100.0 40 .................................... GCATATCGCCCGCCACACCACAGCCACGCTACTGCTCCAT 64682 36 97.2 40 ...C................................ ACACCGCCGATGACAGCTATGTCCGAGTGACATCCTCCCA 64606 36 97.2 38 ..................A................. TTGAACCGCCCTTCGCGCGGTGTTTCGGCCGTGCCCGA 64532 36 100.0 0 .................................... | ========== ====== ====== ====== ==================================== ======================================== ================== 13 36 99.1 38 GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC # Left flank : GCCGCCGGCTGAGGTCTCAGATCAGAGAGTCTCCGGACTCACCGGGGCG # 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: F [2-2] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [38.3-26.7]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0.68,0.74 Confidence: LOW] # Array family : NA // Array 1 498-97 **** Predicted by CRISPRDetect 2.4 *** >NZ_PQFR01000112.1 Mycobacterium tuberculosis strain UT356 C680, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ==================================== ====================================== ================== 497 36 100.0 38 .................................... CTTCAGCACCACCATCATCCGGCGCCTCAGCTCAGCAT 423 36 100.0 38 .................................... CCTTCGACGCCGGATTCGTGATCTCTTCCCGCGGATAG 349 36 100.0 36 .................................... TGCCCCGGCGTTTAGCGATCACAACACCAACTAATG 277 36 100.0 36 .................................... CAGCGAAATACAGGCTCCACGACACGACCACAACGC 205 36 100.0 37 .................................... TCTTGACGATGCGGTTGCCCCGCGCCCTTTTCCAGCC 132 36 100.0 0 .................................... | ========== ====== ====== ====== ==================================== ====================================== ================== 6 36 100.0 37 GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC # Left flank : CGACCACCGCACCCTGTC # Right flank : CAGGTTCGCGTCAGACAGGTTCGCGTCGATCAAGTCCGGTCGTCTGAACCGCCCCGGCATGTCCGGAGACTCCAGTTCTTGGAAAGGATGGGGTCAT # 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 : 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: NA [0-0] Score: 0/0.41 # AT richness analysis in flanks prediction: F [36.7-10.0]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0.27,0.74 Confidence: MEDIUM] # Array family : NA // Array 1 1905-37 **** Predicted by CRISPRDetect 2.4 *** >NZ_PQFR01000056.1 Mycobacterium tuberculosis strain UT356 scaffold17, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ==================================== ========================================= ================== 1904 36 100.0 38 .................................... TTAAAACCGTGTTGCACTGCAACCCGGAATTCTTGCAC 1830 36 100.0 41 .................................... CATAGAGGGTCGCCGGCTCTGGATCACGCTCCCCTAGTCGT 1753 36 100.0 36 .................................... TTTTTGCCTCATGCTTGGGCGACAGCTTTTGACCAA 1681 36 100.0 34 .................................... TCGCAAGCGCCGTGCTTCCAGTGATCGCCTTCTA 1611 36 100.0 39 .................................... AACACCTCAGTAGCACGTCATACGCCGACCAATCATCAG 1536 36 100.0 35 .................................... TTTTCTGACCACTTGTGCGGGATTAGCGGGCTTAG 1465 36 100.0 37 .................................... ACCAATGCGTCGTCATTTCCGGCTTCAATTTCAGCCT 1392 36 100.0 38 .................................... CTGAGGAGAGCGAGTACTCGGGGCTGCCGTCTGCGCTG 1318 36 100.0 37 .................................... GCGTGAAACCGCCCCCAGCCTCGCCGGGGCCGCCTAG 1245 36 100.0 35 .................................... ACTCGGAATCCCATGTGCTGACAGCGGATTCGCAT 1174 36 100.0 37 .................................... CGGGCAGCGTTCGACACCCGCTCTAGTTGACTTCCGG 1101 36 100.0 41 .................................... CAGGTGAGCAACGGCGGCGGCAACCTGGCGGCCACGGGTCG 1024 36 100.0 40 .................................... ATGGGATATCTGCTGCCCGCCCGGGGAGATGCTGTCCGAG 948 36 100.0 36 .................................... TTCGTCGACCATCATTGCCATTCCCTCTCCCCACGT 876 36 100.0 41 .................................... TTGCGCCAACCCTTTCGGTGTGATGCGGATGGTCGGCTCGG 799 36 100.0 24 .................................... CTTGAATAACGCGCAGTGAATTTC Deletion [740] 739 36 94.4 36 .CG................................. ATTCGCACGAGTTCCCGTCAGCGTCGTAAATCGCCA A [735] 666 36 100.0 37 .................................... CCGGCAACAATCGCGCCGGCCCGCGCGGATGACTCCG 593 36 100.0 36 .................................... CGCATGGACCCGGGCGAGCTGCAGATGGTCCGGGAG 521 36 100.0 36 .................................... TGGATTGCGCTAACTGGCTTGGCGCTGATCCTGGTG 449 36 100.0 41 .................................... TCCACATCGATTTCCTTGACCTCGCCAGGAGAGAAGATCAC 372 36 97.2 40 .........................A.......... TCGTCGACGATCGCGTCGATGTCGATGTCCCAATCGTCGA 296 36 100.0 37 .................................... TTGGAGCGTGTCACCGCAGACGGCACGATTGAGACAA 223 36 100.0 39 .................................... CCTCAGCTCAGCATCGCTGATGCGGTCCAGCTCGTCCGT 148 36 100.0 40 .................................... CCAACCTCACCGCCTGCTGGGTGAGACGTGCTCGCCGCGA 72 35 75.0 0 ...................T..-.CC.CC...C.TG | C [41] ========== ====== ====== ====== ==================================== ========================================= ================== 26 36 98.7 37 GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC # Left flank : TTCAGTACGCCCTCGACTTGCAACTGCAAAGCCTCGTGCGTGTTATCGAAGCCGGGCACCCGTCGCGGCTCGTCGATATCGATATCACCTCCGAGCCATCCGGAGCCTAAATGCCCACTCGCAGCCGTGAGGAGTACTTCAATCTCCCGCTCAAAGTGGACGAGTCCAGCGGCACTATAGGCAAGATGTTCGTCCTCGTAATATACGACATCAGCGACAACCGGCGGCGGGCTTCACTTGCGAAGATCCTGGCCGGGTTTGGCTATCGCGTCCAAGAGTCCGCATTCGAAGCGATGCTGACGAAGGGCCAGCTCGCGAAACTAGTTGCACGTATCGACCGCTTCGCCATCGACTGCGACAACATCCGGATCTATAAGATAAGAGGTGTTGCGGCAGTTACGTTCTACGGAAGGGGACGGCTTGTCAGCGCAGAGGAGTTTGTGTTCTTTTGACATCATCAGCAGGCATTGTTACCACACGCTGGACGAATTGTCCATAGA # Right flank : GTCCGGAGACTCCAGTTCTTGGAAAGGATGGGGTCAT # Questionable array : NO Score: 6.18 # Score Detail : 1:0, 2:3, 3:0, 4:0.94, 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 [11-0] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [28.3-55.0]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0,1.42 Confidence: HIGH] # Array family : NA // Array 1 9742-11609 **** Predicted by CRISPRDetect 2.4 *** >NZ_PQFR01000075.1 Mycobacterium tuberculosis strain UT356 scaffold18, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ==================================== ========================================= ================== 9742 36 100.0 38 .................................... TTAAAACCGTGTTGCACTGCAACCCGGAATTCTTGCAC 9816 36 100.0 41 .................................... CATAGAGGGTCGCCGGCTCTGGATCACGCTCCCCTAGTCGT 9893 36 100.0 36 .................................... TTTTTGCCTCATGCTTGGGCGACAGCTTTTGACCAA 9965 36 100.0 34 .................................... TCGCAAGCGCCGTGCTTCCAGTGATCGCCTTCTA 10035 36 100.0 39 .................................... AACACCTCAGTAGCACGTCATACGCCGACCAATCATCAG 10110 36 100.0 35 .................................... TTTTCTGACCACTTGTGCGGGATTAGCGGGCTTAG 10181 36 100.0 37 .................................... ACCAATGCGTCGTCATTTCCGGCTTCAATTTCAGCCT 10254 36 100.0 38 .................................... CTGAGGAGAGCGAGTACTCGGGGCTGCCGTCTGCGCTG 10328 36 100.0 37 .................................... GCGTGAAACCGCCCCCAGCCTCGCCGGGGCCGCCTAG 10401 36 100.0 35 .................................... ACTCGGAATCCCATGTGCTGACAGCGGATTCGCAT 10472 36 100.0 37 .................................... CGGGCAGCGTTCGACACCCGCTCTAGTTGACTTCCGG 10545 36 100.0 41 .................................... CAGGTGAGCAACGGCGGCGGCAACCTGGCGGCCACGGGTCG 10622 36 100.0 40 .................................... ATGGGATATCTGCTGCCCGCCCGGGGAGATGCTGTCCGAG 10698 36 100.0 36 .................................... TTCGTCGACCATCATTGCCATTCCCTCTCCCCACGT 10770 36 100.0 41 .................................... TTGCGCCAACCCTTTCGGTGTGATGCGGATGGTCGGCTCGG 10847 36 100.0 24 .................................... CTTGAATAACGCGCAGTGAATTTC Deletion [10907] 10907 36 94.4 36 .CG................................. ATTCGCACGAGTTCCCGTCAGCGTCGTAAATCGCCA A [10911] 10980 36 100.0 37 .................................... CCGGCAACAATCGCGCCGGCCCGCGCGGATGACTCCG 11053 36 100.0 36 .................................... CGCATGGACCCGGGCGAGCTGCAGATGGTCCGGGAG 11125 36 100.0 36 .................................... TGGATTGCGCTAACTGGCTTGGCGCTGATCCTGGTG 11197 36 100.0 41 .................................... TCCACATCGATTTCCTTGACCTCGCCAGGAGAGAAGATCAC 11274 36 97.2 40 .........................A.......... TCGTCGACGATCGCGTCGATGTCGATGTCCCAATCGTCGA 11350 36 100.0 37 .................................... TTGGAGCGTGTCACCGCAGACGGCACGATTGAGACAA 11423 36 100.0 39 .................................... CCTCAGCTCAGCATCGCTGATGCGGTCCAGCTCGTCCGT 11498 36 100.0 40 .................................... CCAACCTCACCGCCTGCTGGGTGAGACGTGCTCGCCGCGA 11574 35 75.0 0 ...................T..-.C.CCC...C.TG | C [11598] ========== ====== ====== ====== ==================================== ========================================= ================== 26 36 98.7 37 GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC # Left flank : TTCAGTACGCCCTCGACTTGCAACTGCAAAGCCTCGTGCGTGTTATCGAAGCCGGGCACCCGTCGCGGCTCGTCGATATCGATATCACCTCCGAGCCATCCGGAGCCTAAATGCCCACTCGCAGCCGTGAGGAGTACTTCAATCTCCCGCTCAAAGTGGACGAGTCCAGCGGCACTATAGGCAAGATGTTCGTCCTCGTAATATACGACATCAGCGACAACCGGCGGCGGGCTTCACTTGCGAAGATCCTGGCCGGGTTTGGCTATCGCGTCCAAGAGTCCGCATTCGAAGCGATGCTGACGAAGGGCCAGCTCGCGAAACTAGTTGCACGTATCGACCGCTTCGCCATCGACTGCGACAACATCCGGATCTATAAGATAAGAGGTGTTGCGGCAGTTACGTTCTACGGAAGGGGACGGCTTGTCAGCGCAGAGGAGTTTGTGTTCTTTTGACATCATCAGCAGGCATTGTTACCACACGCTGGACGAATTGTCCATAGA # Right flank : TCCGGAGACTCCAGTTCTTGGAAAGGATGGGGTCAT # Questionable array : NO Score: 6.18 # Score Detail : 1:0, 2:3, 3:0, 4:0.94, 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: F [12,2] Score: 0.37/0.37 # Reference repeat match prediction: NA # Secondary Structural analysis prediction: F [-7.70,-6.40] Score: 0.37/0.37 # Array degeneracy analysis prediction: F [0-15] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [55.0-28.3]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [1.42,0 Confidence: HIGH] # Array family : NA //