Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold1312

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: 2059
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30


Found at i:275 original size:59 final size:59

Alignment explanation


    Indices: 184--298  Score: 212
    Period size: 59  Copynumber: 1.9  Consensus size: 59

        174 GGAAGTTAAA

                                                                       
        184 TTTTTTGTCCGTACCGTAGACCAACTAAACAGGCTTGTTTTTCCATCAATACGTGCAGT
          1 TTTTTTGTCCGTACCGTAGACCAACTAAACAGGCTTGTTTTTCCATCAATACGTGCAGT

                                    *                  *            
        243 TTTTTTGTCCGTACCGTAGACCAATTAAACAGGCTTGTTTTTCTATCAATACGTGC
          1 TTTTTTGTCCGTACCGTAGACCAACTAAACAGGCTTGTTTTTCCATCAATACGTGC

        299 GATAATAATA


Statistics
Matches: 54,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  59   54  1.00

ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37


Consensus pattern (59 bp):   
TTTTTTGTCCGTACCGTAGACCAACTAAACAGGCTTGTTTTTCCATCAATACGTGCAGT

Found at i:1049 original size:14 final size:15

Alignment explanation


    Indices: 1030--1060  Score: 55
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       1020 AATAAGTTAG

                           
       1030 ATATT-AACGAATAA
          1 ATATTAAACGAATAA

                           
       1044 ATATTAAACGAATAA
          1 ATATTAAACGAATAA

              
       1059 AT
          1 AT

       1061 TGCTATGAAC


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    5  0.31
  15   11  0.69

ACGTcount: A:0.58, C:0.06, G:0.06, T:0.29


Consensus pattern (15 bp):   
ATATTAAACGAATAA

Found at i:1389 original size:22 final size:23

Alignment explanation


    Indices: 1344--1395  Score: 97
    Period size: 23  Copynumber: 2.3  Consensus size: 23

       1334 TCGCGCGTCA

                                   
       1344 GCTACGGGCTACGGTACCGGACG
          1 GCTACGGGCTACGGTACCGGACG

                                   
       1367 GCTACGGGCTACGGTA-CGGACG
          1 GCTACGGGCTACGGTACCGGACG

                   
       1389 GCTACGG
          1 GCTACGG

       1396 TGCGGACAAA


Statistics
Matches: 29,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
  22   13  0.45
  23   16  0.55

ACGTcount: A:0.17, C:0.29, G:0.40, T:0.13


Consensus pattern (23 bp):   
GCTACGGGCTACGGTACCGGACG

Found at i:1393 original size:15 final size:15

Alignment explanation


    Indices: 1373--1402  Score: 51
    Period size: 15  Copynumber: 2.0  Consensus size: 15

       1363 GACGGCTACG

                           
       1373 GGCTACGGTACGGAC
          1 GGCTACGGTACGGAC

                     *     
       1388 GGCTACGGTGCGGAC
          1 GGCTACGGTACGGAC

       1403 AAATCGTGTG


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.17, C:0.27, G:0.43, T:0.13


Consensus pattern (15 bp):   
GGCTACGGTACGGAC
Done.