Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3775

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: 29545
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31


Found at i:2921 original size:23 final size:22

Alignment explanation


    Indices: 2870--2921  Score: 54
    Period size: 23  Copynumber: 2.3  Consensus size: 22

       2860 CCTCGTCTTT

                   *              
       2870 TTCTTTTGTTTCTTTTTCTAAC
          1 TTCTTTTCTTTCTTTTTCTAAC

                                     
       2892 -TCATTTTCTCTTCTTTCTTC-AAC
          1 TTC-TTTTCT-TTCTTT-TTCTAAC

                   
       2915 TTCTTTT
          1 TTCTTTT

       2922 TCAATTTTCT


Statistics
Matches: 25,  Mismatches: 1, Indels: 7
        0.76            0.03        0.21

Matches are distributed among these distances:
  21    2  0.08
  22    5  0.20
  23   13  0.52
  24    5  0.20

ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65


Consensus pattern (22 bp):   
TTCTTTTCTTTCTTTTTCTAAC

Found at i:13965 original size:14 final size:13

Alignment explanation


    Indices: 13929--13954  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

      13919 CGTAGCTTCG

                         
      13929 AAAAAAAAAAGTT
          1 AAAAAAAAAAGTT

                         
      13942 AAAAAAAAAAGTT
          1 AAAAAAAAAAGTT

      13955 TTGAAAAAAA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15


Consensus pattern (13 bp):   
AAAAAAAAAAGTT

Found at i:16259 original size:24 final size:25

Alignment explanation


    Indices: 16232--16285  Score: 60
    Period size: 23  Copynumber: 2.2  Consensus size: 25

      16222 ATGAGTGATA

                    *                 
      16232 AAAAAAGAGA-GAGTGATTCAAAA-G
          1 AAAAAAGAAACGAGTGA-TCAAAATG

                              *      
      16256 -AAAAAGAAACGAGTGATGAAAATG
          1 AAAAAAGAAACGAGTGATCAAAATG

                  
      16280 AAAAAA
          1 AAAAAA

      16286 AGAATTTGTT


Statistics
Matches: 25,  Mismatches: 2, Indels: 5
        0.78            0.06        0.16

Matches are distributed among these distances:
  23   13  0.52
  24    7  0.28
  25    5  0.20

ACGTcount: A:0.63, C:0.04, G:0.22, T:0.11


Consensus pattern (25 bp):   
AAAAAAGAAACGAGTGATCAAAATG

Found at i:22149 original size:23 final size:23

Alignment explanation


    Indices: 22120--22170  Score: 102
    Period size: 23  Copynumber: 2.2  Consensus size: 23

      22110 TTAATAAGTG

                                   
      22120 TTTTAATGTGTTTAATAAACTCA
          1 TTTTAATGTGTTTAATAAACTCA

                                   
      22143 TTTTAATGTGTTTAATAAACTCA
          1 TTTTAATGTGTTTAATAAACTCA

                 
      22166 TTTTA
          1 TTTTA

      22171 TTGCAGGTGA


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  23   28  1.00

ACGTcount: A:0.33, C:0.08, G:0.08, T:0.51


Consensus pattern (23 bp):   
TTTTAATGTGTTTAATAAACTCA

Found at i:23250 original size:15 final size:15

Alignment explanation


    Indices: 23230--23286  Score: 87
    Period size: 15  Copynumber: 3.7  Consensus size: 15

      23220 GATATCAAGT

                           
      23230 TGAAAAAAAATTTCG
          1 TGAAAAAAAATTTCG

                      *    
      23245 TGAAAAAAAAATTCG
          1 TGAAAAAAAATTTCG

                             
      23260 TGAAAAAAAAAATTTCG
          1 TG--AAAAAAAATTTCG

                      
      23277 TGAAAAAAAA
          1 TGAAAAAAAA

      23287 GAAGAAGCTA


Statistics
Matches: 38,  Mismatches: 2, Indels: 4
        0.86            0.05        0.09

Matches are distributed among these distances:
  15   24  0.63
  17   14  0.37

ACGTcount: A:0.61, C:0.05, G:0.12, T:0.21


Consensus pattern (15 bp):   
TGAAAAAAAATTTCG

Found at i:23254 original size:17 final size:17

Alignment explanation


    Indices: 23232--23286  Score: 96
    Period size: 16  Copynumber: 3.4  Consensus size: 17

      23222 TATCAAGTTG

                             
      23232 AAAAAAAATTTCGTG-A
          1 AAAAAAAATTTCGTGAA

                             
      23248 AAAAAAAA-TTCGTGAA
          1 AAAAAAAATTTCGTGAA

                             
      23264 AAAAAAAATTTCGTGAA
          1 AAAAAAAATTTCGTGAA

                  
      23281 AAAAAA
          1 AAAAAA

      23287 GAAGAAGCTA


Statistics
Matches: 37,  Mismatches: 0, Indels: 3
        0.93            0.00        0.08

Matches are distributed among these distances:
  15    6  0.16
  16   17  0.46
  17   14  0.38

ACGTcount: A:0.64, C:0.05, G:0.11, T:0.20


Consensus pattern (17 bp):   
AAAAAAAATTTCGTGAA
Done.