Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1314

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: 36072
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31


Found at i:2641 original size:23 final size:23

Alignment explanation

Indices: 2615--2659 Score: 74 Period size: 23 Copynumber: 2.0 Consensus size: 23 2605 AGTGGAAGGA 2615 GCCAATTGGGAGACAA-ACTATTT 1 GCCAATTGGG-GACAAGACTATTT 2638 GCCAATTGGGGACAAGACTATT 1 GCCAATTGGGGACAAGACTATT 2660 GGTATAGAGC Statistics Matches: 21, Mismatches: 0, Indels: 2 0.91 0.00 0.09 Matches are distributed among these distances: 22 5 0.24 23 16 0.76 ACGTcount: A:0.33, C:0.18, G:0.24, T:0.24 Consensus pattern (23 bp): GCCAATTGGGGACAAGACTATTT Found at i:17225 original size:21 final size:21 Alignment explanation

Indices: 17199--17239 Score: 64 Period size: 21 Copynumber: 2.0 Consensus size: 21 17189 TCAGACGCAA * * 17199 TACTCCACAGCAGGTGGAGTG 1 TACTCCAAAACAGGTGGAGTG 17220 TACTCCAAAACAGGTGGAGT 1 TACTCCAAAACAGGTGGAGT 17240 TTGAGCAGAT Statistics Matches: 18, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 21 18 1.00 ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20 Consensus pattern (21 bp): TACTCCAAAACAGGTGGAGTG Found at i:19175 original size:16 final size:16 Alignment explanation

Indices: 19142--19175 Score: 50 Period size: 16 Copynumber: 2.1 Consensus size: 16 19132 GGAGATTGTT * * 19142 AACATTAATGGGAGAC 1 AACATTAATGGCAAAC 19158 AACATTAATGGCAAAC 1 AACATTAATGGCAAAC 19174 AA 1 AA 19176 TACAAAGTGG Statistics Matches: 16, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 16 16 1.00 ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18 Consensus pattern (16 bp): AACATTAATGGCAAAC Found at i:32558 original size:21 final size:21 Alignment explanation

Indices: 32532--32577 Score: 83 Period size: 21 Copynumber: 2.2 Consensus size: 21 32522 TCGATCCTGT * 32532 TCCTCATAAATAAAGTTTAAA 1 TCCTCATAAACAAAGTTTAAA 32553 TCCTCATAAACAAAGTTTAAA 1 TCCTCATAAACAAAGTTTAAA 32574 TCCT 1 TCCT 32578 TATAGATGAA Statistics Matches: 24, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 21 24 1.00 ACGTcount: A:0.43, C:0.20, G:0.04, T:0.33 Consensus pattern (21 bp): TCCTCATAAACAAAGTTTAAA Done.