Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1995

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: 24249
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31


Found at i:9317 original size:30 final size:30

Alignment explanation

Indices: 9283--9379 Score: 99 Period size: 30 Copynumber: 3.2 Consensus size: 30 9273 TAAACTAAAA 9283 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT 1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT * * * * * * 9313 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT 1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT * 9343 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T 1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT 9372 ATGAGCTA 1 -TGAGCTA 9380 GGAGTGAGCT Statistics Matches: 51, Mismatches: 13, Indels: 6 0.73 0.19 0.09 Matches are distributed among these distances: 29 3 0.06 30 45 0.88 31 3 0.06 ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28 Consensus pattern (30 bp): TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT Found at i:11602 original size:5 final size:5 Alignment explanation

Indices: 11592--11664 Score: 53 Period size: 5 Copynumber: 14.0 Consensus size: 5 11582 CTCTTGCCTC * * 11592 TCTTT TCTTT T-TATT TCATTT TCTTT T-TCT TCTCTT GCTTTT TCTTTT 1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCT-TT TC-TTT TC-TTT 11640 TCTTT TCTTT TCTTT T-TTT CTCTTT 1 TCTTT TCTTT TCTTT TCTTT -TCTTT 11665 ACAAGAATGT Statistics Matches: 56, Mismatches: 4, Indels: 15 0.75 0.05 0.20 Matches are distributed among these distances: 4 7 0.12 5 29 0.52 6 18 0.32 7 2 0.04 ACGTcount: A:0.03, C:0.19, G:0.01, T:0.77 Consensus pattern (5 bp): TCTTT Found at i:11621 original size:6 final size:6 Alignment explanation

Indices: 11605--11656 Score: 54 Period size: 6 Copynumber: 8.5 Consensus size: 6 11595 TTTCTTTTTA * 11605 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT 1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT 11654 TTT 1 TTT 11657 TTCTCTTTAC Statistics Matches: 41, Mismatches: 1, Indels: 8 0.82 0.02 0.16 Matches are distributed among these distances: 5 10 0.24 6 22 0.54 7 3 0.07 8 3 0.07 9 3 0.07 ACGTcount: A:0.02, C:0.19, G:0.02, T:0.77 Consensus pattern (6 bp): TTTCTT Found at i:11651 original size:37 final size:36 Alignment explanation

Indices: 11594--11663 Score: 106 Period size: 37 Copynumber: 1.9 Consensus size: 36 11584 CTTGCCTCTC 11594 TTTTCTTTTTATTTCATTTTCTTTTTCTTCTCTTGCT 1 TTTTCTTTTTATTTCATTTTCTTTTT-TTCTCTTGCT * 11631 TTTTCTTTTTCTTTTC-TTTTCTTTTTTTCTCTT 1 TTTTCTTTTT-ATTTCATTTTCTTTTTTTCTCTT 11664 TACAAGAATG Statistics Matches: 31, Mismatches: 1, Indels: 3 0.89 0.03 0.09 Matches are distributed among these distances: 36 7 0.23 37 20 0.65 38 4 0.13 ACGTcount: A:0.03, C:0.19, G:0.01, T:0.77 Consensus pattern (36 bp): TTTTCTTTTTATTTCATTTTCTTTTTTTCTCTTGCT Found at i:12535 original size:10 final size:10 Alignment explanation

Indices: 12520--12560 Score: 64 Period size: 10 Copynumber: 3.9 Consensus size: 10 12510 ATATACTTCG 12520 ATTTTTTTTA 1 ATTTTTTTTA 12530 ATTTTTTTTCA 1 ATTTTTTTT-A 12541 ATTTTTTTTTA 1 A-TTTTTTTTA 12552 ATTTTTTTT 1 ATTTTTTTT 12561 TTCGAATTTC Statistics Matches: 29, Mismatches: 0, Indels: 4 0.88 0.00 0.12 Matches are distributed among these distances: 10 17 0.59 11 4 0.14 12 8 0.28 ACGTcount: A:0.17, C:0.02, G:0.00, T:0.80 Consensus pattern (10 bp): ATTTTTTTTA Found at i:12537 original size:11 final size:11 Alignment explanation

Indices: 12521--12561 Score: 73 Period size: 11 Copynumber: 3.7 Consensus size: 11 12511 TATACTTCGA 12521 TTTTTTTTAAT 1 TTTTTTTTAAT * 12532 TTTTTTTCAAT 1 TTTTTTTTAAT 12543 TTTTTTTTAAT 1 TTTTTTTTAAT 12554 TTTTTTTT 1 TTTTTTTT 12562 TCGAATTTCC Statistics Matches: 28, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 11 28 1.00 ACGTcount: A:0.15, C:0.02, G:0.00, T:0.83 Consensus pattern (11 bp): TTTTTTTTAAT Found at i:14296 original size:30 final size:30 Alignment explanation

Indices: 14262--14358 Score: 108 Period size: 30 Copynumber: 3.2 Consensus size: 30 14252 AAAACTAAAA 14262 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT 1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT * * * * * * 14292 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT 1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT 14322 TGAGCTAAGCTTTAGCTCGTGAGCTAAA-T 1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT 14351 ATGAGCTA 1 -TGAGCTA 14359 GGAGTGAGCT Statistics Matches: 52, Mismatches: 12, Indels: 6 0.74 0.17 0.09 Matches are distributed among these distances: 29 4 0.08 30 45 0.87 31 3 0.06 ACGTcount: A:0.29, C:0.18, G:0.26, T:0.28 Consensus pattern (30 bp): TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT Found at i:17335 original size:21 final size:23 Alignment explanation

Indices: 17290--17336 Score: 62 Period size: 23 Copynumber: 2.1 Consensus size: 23 17280 TCACCTGCAA * * 17290 TAAACACATTAAAATGAGTTTAT 1 TAAACACATTAAAATCAGCTTAT 17313 TAAACACATTAAAA-CA-CTTAT 1 TAAACACATTAAAATCAGCTTAT 17334 TAA 1 TAA 17337 TCATAACACA Statistics Matches: 22, Mismatches: 2, Indels: 2 0.85 0.08 0.08 Matches are distributed among these distances: 21 7 0.32 22 1 0.05 23 14 0.64 ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32 Consensus pattern (23 bp): TAAACACATTAAAATCAGCTTAT Done.