Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold1742

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, 805

Length: 1343
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25


Found at i:1219 original size:21 final size:21

Alignment explanation


    Indices: 1195--1256  Score: 92
    Period size: 20  Copynumber: 3.0  Consensus size: 21

       1185 TGAAATTCCT

                     *           
       1195 TCTCCACCCATAGAAAAAGTG
          1 TCTCCACCCCTAGAAAAAGTG

                                *
       1216 TCTCCACCCCTA-AAAAAGTT
          1 TCTCCACCCCTAGAAAAAGTG

                                 
       1236 TCTCCACCCCT-GAAAAAGTG
          1 TCTCCACCCCTAGAAAAAGTG

             
       1256 T
          1 T

       1257 TTCTCCCCCG


Statistics
Matches: 37,  Mismatches: 3, Indels: 3
        0.86            0.07        0.07

Matches are distributed among these distances:
  20   26  0.70
  21   11  0.30

ACGTcount: A:0.34, C:0.32, G:0.11, T:0.23


Consensus pattern (21 bp):   
TCTCCACCCCTAGAAAAAGTG

Found at i:1258 original size:22 final size:22

Alignment explanation


    Indices: 1194--1262  Score: 83
    Period size: 21  Copynumber: 3.3  Consensus size: 22

       1184 CTGAAATTCC

                      *            
       1194 TTCTCCACCCATAGAAAAAGTG-
          1 TTCTCCACCCCT-GAAAAAGTGT

                               *  
       1216 -TCTCCACCCCT-AAAAA-AGT
          1 TTCTCCACCCCTGAAAAAGTGT

                                  
       1235 TTCTCCACCCCTGAAAAAGTGT
          1 TTCTCCACCCCTGAAAAAGTGT

                  
       1257 TTCTCC
          1 TTCTCC

       1263 CCCGACGAAA


Statistics
Matches: 40,  Mismatches: 3, Indels: 8
        0.78            0.06        0.16

Matches are distributed among these distances:
  18    1  0.03
  19    5  0.12
  20   11  0.28
  21   15  0.38
  22    8  0.20

ACGTcount: A:0.30, C:0.33, G:0.10, T:0.26


Consensus pattern (22 bp):   
TTCTCCACCCCTGAAAAAGTGT

Found at i:1265 original size:20 final size:21

Alignment explanation


    Indices: 1207--1265  Score: 63
    Period size: 20  Copynumber: 3.0  Consensus size: 21

       1197 TCCACCCATA

                      *          
       1207 GAAAAAGTGTCTC-CACCCCT
          1 GAAAAAGTGTTTCTCACCCCT

                   *              
       1227 -AAAAA-AGTTTCTCCACCCCT
          1 GAAAAAGTGTTTCT-CACCCCT

                                
       1247 GAAAAAGTGTTTCTC-CCCC
          1 GAAAAAGTGTTTCTCACCCC

       1266 GACGAAAATT


Statistics
Matches: 32,  Mismatches: 3, Indels: 8
        0.74            0.07        0.19

Matches are distributed among these distances:
  18    4  0.12
  19    5  0.16
  20   11  0.34
  21    6  0.19
  22    6  0.19

ACGTcount: A:0.31, C:0.34, G:0.12, T:0.24


Consensus pattern (21 bp):   
GAAAAAGTGTTTCTCACCCCT
Done.