Tandem Repeats Finder Program written by: Gary Benson Program in Bioinformatics Boston University Version 4.09 Sequence: Scaffold976 Parameters: 2 7 7 80 10 50 1000 Pmatch=0.80,Pindel=0.10 tuple sizes 0,4,5,7 tuple distances 0, 29, 159, 1000 Length: 34493 ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31 Found at i:9337 original size:13 final size:12 Alignment explanation
Indices: 9318--9379 Score: 79 Period size: 13 Copynumber: 4.9 Consensus size: 12 9308 AGACCGTATG 9318 CAATTTTTTTTT 1 CAATTTTTTTTT 9330 CAAATTTTTTTTT 1 C-AATTTTTTTTT 9343 CAATTTTTTTTTCT 1 CAA-TTTTTTTT-T * 9357 CGATTTTTTTTT 1 CAATTTTTTTTT * 9369 CGATTTTTTTT 1 CAATTTTTTTT 9380 AATCTACAAT Statistics Matches: 46, Mismatches: 1, Indels: 6 0.87 0.02 0.11 Matches are distributed among these distances: 12 15 0.33 13 28 0.61 14 3 0.07 ACGTcount: A:0.15, C:0.10, G:0.03, T:0.73 Consensus pattern (12 bp): CAATTTTTTTTT Found at i:9339 original size:12 final size:13 Alignment explanation
Indices: 9319--9379 Score: 72 Period size: 12 Copynumber: 4.8 Consensus size: 13 9309 GACCGTATGC 9319 AATTTTTTTTTCA 1 AATTTTTTTTTCA 9332 AATTTTTTTTTC- 1 AATTTTTTTTTCA * 9344 AATTTTTTTTTCTC 1 AATTTTTTTTTC-A * 9358 GATTTTTTTTTC- 1 AATTTTTTTTTCA * 9370 GATTTTTTTT 1 AATTTTTTTT 9380 AATCTACAAT Statistics Matches: 45, Mismatches: 1, Indels: 5 0.88 0.02 0.10 Matches are distributed among these distances: 12 22 0.49 13 12 0.27 14 11 0.24 ACGTcount: A:0.15, C:0.08, G:0.03, T:0.74 Consensus pattern (13 bp): AATTTTTTTTTCA Found at i:9346 original size:25 final size:26 Alignment explanation
Indices: 9318--9379 Score: 90 Period size: 26 Copynumber: 2.4 Consensus size: 26 9308 AGACCGTATG 9318 CAATTTTTTTTTC-AAATTTTTTTTT 1 CAATTTTTTTTTCTAAATTTTTTTTT ** 9343 CAATTTTTTTTTCTCGATTTTTTTTT 1 CAATTTTTTTTTCTAAATTTTTTTTT * 9369 CGATTTTTTTT 1 CAATTTTTTTT 9380 AATCTACAAT Statistics Matches: 33, Mismatches: 3, Indels: 1 0.89 0.08 0.03 Matches are distributed among these distances: 25 13 0.39 26 20 0.61 ACGTcount: A:0.15, C:0.10, G:0.03, T:0.73 Consensus pattern (26 bp): CAATTTTTTTTTCTAAATTTTTTTTT Found at i:11253 original size:15 final size:15 Alignment explanation
Indices: 11233--11342 Score: 53 Period size: 16 Copynumber: 6.9 Consensus size: 15 11223 TTTTCACTCA 11233 CTTTTTCTTTTTCTT 1 CTTTTTCTTTTTCTT * 11248 CTTTTTCTTTTATCGCT 1 CTTTTTCTTTT-TC-TT * * 11265 CTCTTTTCATTCTCTT 1 CT-TTTTCTTTTTCTT ** 11281 -TTTTTGAATTTTCTT 1 CTTTTT-CTTTTTCTT * 11296 TTTTTTCATTTTTCTT 1 CTTTTTC-TTTTTCTT * * * 11312 TTCTTTTGTATTTTC-G 1 CT-TTTTCT-TTTTCTT 11328 CTCTTTTCTTTTTCT 1 CT-TTTTCTTTTTCT 11343 CTCATTTGAT Statistics Matches: 74, Mismatches: 12, Indels: 17 0.72 0.12 0.17 Matches are distributed among these distances: 14 4 0.05 15 24 0.32 16 25 0.34 17 14 0.19 18 7 0.09 ACGTcount: A:0.05, C:0.19, G:0.04, T:0.72 Consensus pattern (15 bp): CTTTTTCTTTTTCTT Found at i:11299 original size:17 final size:17 Alignment explanation
Indices: 11274--11326 Score: 54 Period size: 17 Copynumber: 3.2 Consensus size: 17 11264 TCTCTTTTCA * 11274 TTCTCTTTTTTTGAATT 1 TTCTTTTTTTTTGAATT * * 11291 TTC-TTTTTTTTCATTT 1 TTCTTTTTTTTTGAATT * * 11307 TTCTTTTCTTTTGTATT 1 TTCTTTTTTTTTGAATT 11324 TTC 1 TTC 11327 GCTCTTTTCT Statistics Matches: 28, Mismatches: 7, Indels: 2 0.76 0.19 0.05 Matches are distributed among these distances: 16 13 0.46 17 15 0.54 ACGTcount: A:0.08, C:0.13, G:0.04, T:0.75 Consensus pattern (17 bp): TTCTTTTTTTTTGAATT Found at i:11300 original size:16 final size:16 Alignment explanation
Indices: 11274--11326 Score: 61 Period size: 16 Copynumber: 3.2 Consensus size: 16 11264 TCTCTTTTCA 11274 TTCTCTTTTTTTGAATT 1 TTCT-TTTTTTTGAATT * * 11291 TTCTTTTTTTTCATTT 1 TTCTTTTTTTTGAATT * 11307 TTCTTTTCTTTTGTATT 1 TTCTTTT-TTTTGAATT 11324 TTC 1 TTC 11327 GCTCTTTTCT Statistics Matches: 30, Mismatches: 5, Indels: 2 0.81 0.14 0.05 Matches are distributed among these distances: 16 17 0.57 17 13 0.43 ACGTcount: A:0.08, C:0.13, G:0.04, T:0.75 Consensus pattern (16 bp): TTCTTTTTTTTGAATT Found at i:13563 original size:18 final size:17 Alignment explanation
Indices: 13529--13573 Score: 54 Period size: 17 Copynumber: 2.6 Consensus size: 17 13519 AGACCGTATG * 13529 CAATTTTTTTTTCTTTT 1 CAATTTTTTTTTATTTT 13546 CAATTTTTTTTTGATTTT 1 CAATTTTTTTTT-ATTTT * * 13564 GACTTTTTTT 1 CAATTTTTTT 13574 ATGTACCTAT Statistics Matches: 24, Mismatches: 3, Indels: 1 0.86 0.11 0.04 Matches are distributed among these distances: 17 12 0.50 18 12 0.50 ACGTcount: A:0.13, C:0.09, G:0.04, T:0.73 Consensus pattern (17 bp): CAATTTTTTTTTATTTT Found at i:13925 original size:22 final size:22 Alignment explanation
Indices: 13874--13939 Score: 80 Period size: 21 Copynumber: 3.0 Consensus size: 22 13864 GGTATTTGGG * * 13874 AATTGGTTCGAAATAGTATGG- 1 AATTGGTACGAAATGGTATGGT 13895 AATTGGTACGAAATGGTATGGT 1 AATTGGTACGAAATGGTATGGT * * 13917 ATTTGGTACGAATTGGTAATGGT 1 AATTGGTACGAAATGGT-ATGGT 13940 TCAAAGAGGT Statistics Matches: 39, Mismatches: 4, Indels: 2 0.87 0.09 0.04 Matches are distributed among these distances: 21 19 0.49 22 15 0.38 23 5 0.13 ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35 Consensus pattern (22 bp): AATTGGTACGAAATGGTATGGT Found at i:18285 original size:18 final size:17 Alignment explanation
Indices: 18250--18284 Score: 61 Period size: 17 Copynumber: 2.1 Consensus size: 17 18240 TTCTTTGTGT * 18250 ATTCAGTATTAAAAAAA 1 ATTCAGAATTAAAAAAA 18267 ATTCAGAATTAAAAAAA 1 ATTCAGAATTAAAAAAA 18284 A 1 A 18285 AAAGAGAGAA Statistics Matches: 17, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 17 17 1.00 ACGTcount: A:0.63, C:0.06, G:0.06, T:0.26 Consensus pattern (17 bp): ATTCAGAATTAAAAAAA Found at i:26861 original size:17 final size:18 Alignment explanation
Indices: 26822--26863 Score: 52 Period size: 17 Copynumber: 2.4 Consensus size: 18 26812 AAGAAGAAAA 26822 ACAAAA-AGATGAGTGAT 1 ACAAAAGAGATGAGTGAT * 26839 AAAAAAGAGA-GAGTGAT 1 ACAAAAGAGATGAGTGAT * 26856 TCAAAAGA 1 ACAAAAGA 26864 AAAAGAAACG Statistics Matches: 21, Mismatches: 3, Indels: 2 0.81 0.12 0.08 Matches are distributed among these distances: 17 18 0.86 18 3 0.14 ACGTcount: A:0.57, C:0.05, G:0.24, T:0.14 Consensus pattern (18 bp): ACAAAAGAGATGAGTGAT Done.