Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2648

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: 21909
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29


Found at i:1383 original size:28 final size:27

Alignment explanation


    Indices: 1316--1388  Score: 94
    Period size: 27  Copynumber: 2.7  Consensus size: 27

       1306 CTTCACAATC

                 *                    *
       1316 GGGGACACTCCAACCCCGTTAATCATC
          1 GGGGATACTCCAACCCCGTTAATCATA

                                  *      
       1343 GGGGATACTCCAACCCCGTTATTTC-TGA
          1 GGGGATACTCCAACCCCGTTA-ATCAT-A

                              
       1371 GGGGATACTCCAACCCCG
          1 GGGGATACTCCAACCCCG

       1389 ACTTTATTTT


Statistics
Matches: 41,  Mismatches: 3, Indels: 3
        0.87            0.06        0.06

Matches are distributed among these distances:
  27   21  0.51
  28   20  0.49

ACGTcount: A:0.23, C:0.34, G:0.22, T:0.21


Consensus pattern (27 bp):   
GGGGATACTCCAACCCCGTTAATCATA

Found at i:1433 original size:51 final size:51

Alignment explanation


    Indices: 1371--1541  Score: 198
    Period size: 51  Copynumber: 3.3  Consensus size: 51

       1361 TTATTTCTGA

                               *               * *             
       1371 GGGGATACTCCAACCCCGACTTTATTTTCAAAATATCGATTTTTCATAATC
          1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC

                              *           *  *          *  *     
       1422 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAATC
          1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTT-TTC-ATAATC

                         **            *                   *    
       1475 GGGGATACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
          1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAATACCAATTTTTCATAATC

             *             
       1527 GAGGATACTCCAACC
          1 GGGGATACTCCAACC

       1542 TCGTTATTTC


Statistics
Matches: 97,  Mismatches: 20, Indels: 5
        0.80            0.16        0.04

Matches are distributed among these distances:
  51   36  0.37
  52   18  0.19
  53   32  0.33
  54   11  0.11

ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33


Consensus pattern (51 bp):   
GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC

Found at i:1560 original size:28 final size:28

Alignment explanation


    Indices: 1524--1605  Score: 96
    Period size: 28  Copynumber: 2.9  Consensus size: 28

       1514 ATTTTTCACA

                *                       
       1524 ATCGAGGATACTCCAACCTCGTTATTTC
          1 ATCGGGGATACTCCAACCTCGTTATTTC

                              *     *   
       1552 ATCGGGGATACTCCAACCCCGTTACTTC
          1 ATCGGGGATACTCCAACCTCGTTATTTC

                      *                 
       1580 --CGAGGGAACACTCCAACCTCGTTATT
          1 ATCG-GGG-ATACTCCAACCTCGTTATT

       1606 ATCTCCAAAA


Statistics
Matches: 46,  Mismatches: 6, Indels: 4
        0.82            0.11        0.07

Matches are distributed among these distances:
  26    2  0.04
  27    3  0.07
  28   41  0.89

ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27


Consensus pattern (28 bp):   
ATCGGGGATACTCCAACCTCGTTATTTC

Found at i:15225 original size:1 final size:1

Alignment explanation


    Indices: 15219--15309  Score: 74
    Period size: 1  Copynumber: 91.0  Consensus size: 1

      15209 AAATCTTCAC

                        *          *     **          *    *       *     **   
      15219 TTTTTTTTTTTTGTTTTTTTTTTCTTTTTCCTTTTTTTTTTGTTTTGTTTTTTTCTTTTTCCTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

                   *    *       *     
      15284 TTTTTTTGTTTTGTTTTTTTCTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTT

      15310 CCAATTGCCA


Statistics
Matches: 70,  Mismatches: 20, Indels: 0
        0.78            0.22        0.00

Matches are distributed among these distances:
   1   70  1.00

ACGTcount: A:0.00, C:0.08, G:0.05, T:0.87


Consensus pattern (1 bp):   
T

Found at i:15256 original size:31 final size:31

Alignment explanation


    Indices: 15221--15311  Score: 168
    Period size: 31  Copynumber: 3.0  Consensus size: 31

      15211 ATCTTCACTT

                                           
      15221 TTTTTTTTTTG-TTT-TTTTTTTCTTTTTCC
          1 TTTTTTTTTTGTTTTGTTTTTTTCTTTTTCC

                                           
      15250 TTTTTTTTTTGTTTTGTTTTTTTCTTTTTCC
          1 TTTTTTTTTTGTTTTGTTTTTTTCTTTTTCC

                                           
      15281 TTTTTTTTTTGTTTTGTTTTTTTCTTTTTCC
          1 TTTTTTTTTTGTTTTGTTTTTTTCTTTTTCC

      15312 AATTGCCATG


Statistics
Matches: 60,  Mismatches: 0, Indels: 2
        0.97            0.00        0.03

Matches are distributed among these distances:
  29   11  0.18
  30    3  0.05
  31   46  0.77

ACGTcount: A:0.00, C:0.10, G:0.05, T:0.85


Consensus pattern (31 bp):   
TTTTTTTTTTGTTTTGTTTTTTTCTTTTTCC
Done.