Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2726

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: 17072
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.33


Found at i:11013 original size:15 final size:15

Alignment explanation


    Indices: 10993--11038  Score: 58
    Period size: 15  Copynumber: 2.9  Consensus size: 15

      10983 CTGTTTCTGT

                           
      10993 TTCTTTCTTTCTTTC
          1 TTCTTTCTTTCTTTC

                            
      11008 TTCTTTCTCTTC-TTC
          1 TTCTTTCT-TTCTTTC

                            
      11023 TTCTTTGCATTTCTTT
          1 TTCTTT-C-TTTCTTT

      11039 AGCCAAGTTT


Statistics
Matches: 27,  Mismatches: 0, Indels: 6
        0.82            0.00        0.18

Matches are distributed among these distances:
  15   17  0.63
  16    7  0.26
  17    3  0.11

ACGTcount: A:0.02, C:0.26, G:0.02, T:0.70


Consensus pattern (15 bp):   
TTCTTTCTTTCTTTC

Found at i:11621 original size:24 final size:24

Alignment explanation


    Indices: 11594--11642  Score: 71
    Period size: 24  Copynumber: 2.0  Consensus size: 24

      11584 TTGAACAGCT

                *      *            
      11594 ACATTATTTCAGCTTCAAGCTTCA
          1 ACATCATTTCAACTTCAAGCTTCA

                            *       
      11618 ACATCATTTCAACTTCTAGCTTCA
          1 ACATCATTTCAACTTCAAGCTTCA

             
      11642 A
          1 A

      11643 TTTGTTTACC


Statistics
Matches: 22,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  24   22  1.00

ACGTcount: A:0.31, C:0.27, G:0.06, T:0.37


Consensus pattern (24 bp):   
ACATCATTTCAACTTCAAGCTTCA

Found at i:16288 original size:16 final size:17

Alignment explanation


    Indices: 16256--16289  Score: 52
    Period size: 16  Copynumber: 2.1  Consensus size: 17

      16246 TATCATTTTG

                        *    
      16256 TAAAAGATATTTTATTT
          1 TAAAAGATATTTAATTT

                             
      16273 TAAAAG-TATTTAATTT
          1 TAAAAGATATTTAATTT

             
      16289 T
          1 T

      16290 TAAATTACAC


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  16   10  0.62
  17    6  0.38

ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53


Consensus pattern (17 bp):   
TAAAAGATATTTAATTT

Found at i:16290 original size:17 final size:18

Alignment explanation


    Indices: 16250--16293  Score: 56
    Period size: 17  Copynumber: 2.5  Consensus size: 18

      16240 TATTTTTATC

                              *
      16250 ATTTTGTAAAAGATATTTT
          1 ATTTT-TAAAAGATATTTA

                              
      16269 A-TTTTAAAAG-TATTTA
          1 ATTTTTAAAAGATATTTA

                     
      16285 ATTTTTAAA
          1 ATTTTTAAA

      16294 TTACACACCG


Statistics
Matches: 23,  Mismatches: 1, Indels: 4
        0.82            0.04        0.14

Matches are distributed among these distances:
  16    6  0.26
  17   13  0.57
  18    3  0.13
  19    1  0.04

ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52


Consensus pattern (18 bp):   
ATTTTTAAAAGATATTTA
Done.