Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_3458

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: 18556
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:11258 original size:23 final size:23

Alignment explanation


    Indices: 11232--11276  Score: 58
    Period size: 23  Copynumber: 2.0  Consensus size: 23

      11222 TTTCTTTTGT

                                     
      11232 TTCTTT-TTCTAAC-TCATTTTTCC
          1 TTCTTTCTTC-AACTTC-TTTTTCC

                                  
      11255 TTCTTTCTTCAACTTCTTTTTC
          1 TTCTTTCTTCAACTTCTTTTTC

      11277 AAATTTCTTT


Statistics
Matches: 20,  Mismatches: 0, Indels: 4
        0.83            0.00        0.17

Matches are distributed among these distances:
  23   15  0.75
  24    5  0.25

ACGTcount: A:0.11, C:0.27, G:0.00, T:0.62


Consensus pattern (23 bp):   
TTCTTTCTTCAACTTCTTTTTCC

Found at i:11294 original size:18 final size:18

Alignment explanation


    Indices: 11268--11306  Score: 51
    Period size: 18  Copynumber: 2.2  Consensus size: 18

      11258 TTTCTTCAAC

                *         *   
      11268 TTCTTTTTCAAATTTCTT
          1 TTCTGTTTCAAATTCCTT

                      *       
      11286 TTCTGTTTCACATTCCTT
          1 TTCTGTTTCAAATTCCTT

               
      11304 TTC
          1 TTC

      11307 ACTCTCAATC


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.13, C:0.23, G:0.03, T:0.62


Consensus pattern (18 bp):   
TTCTGTTTCAAATTCCTT

Found at i:14188 original size:14 final size:14

Alignment explanation


    Indices: 14169--14199  Score: 53
    Period size: 14  Copynumber: 2.2  Consensus size: 14

      14159 TTTGATTGGT

                        * 
      14169 GGAAAATATTTTCC
          1 GGAAAATATTTTAC

                          
      14183 GGAAAATATTTTAC
          1 GGAAAATATTTTAC

               
      14197 GGA
          1 GGA

      14200 TTTTCCAGTG


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

Matches are distributed among these distances:
  14   16  1.00

ACGTcount: A:0.39, C:0.10, G:0.19, T:0.32


Consensus pattern (14 bp):   
GGAAAATATTTTAC

Found at i:16777 original size:27 final size:26

Alignment explanation


    Indices: 16747--16805  Score: 91
    Period size: 27  Copynumber: 2.2  Consensus size: 26

      16737 CATCCTCAAA

                               *      
      16747 CTATAATCTAGATATTAAATTGGTCT
          1 CTATAATCTAGATATTAAACTGGTCT

                          *            
      16773 CCTATAATCTAGATTTTAAACTGGTCT
          1 -CTATAATCTAGATATTAAACTGGTCT

                  
      16800 CTATAA
          1 CTATAA

      16806 ATTTGATATT


Statistics
Matches: 30,  Mismatches: 2, Indels: 1
        0.91            0.06        0.03

Matches are distributed among these distances:
  26    6  0.20
  27   24  0.80

ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41


Consensus pattern (26 bp):   
CTATAATCTAGATATTAAACTGGTCT

Found at i:17179 original size:20 final size:21

Alignment explanation


    Indices: 17146--17186  Score: 66
    Period size: 20  Copynumber: 2.0  Consensus size: 21

      17136 AATATTTTTC

                                 
      17146 AGTAAAATCATTTTACAGAAA
          1 AGTAAAATCATTTTACAGAAA

                          *      
      17167 AGTAAAA-CATTTTCCAGAAA
          1 AGTAAAATCATTTTACAGAAA

      17187 TTATTTTACG


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  20   12  0.63
  21    7  0.37

ACGTcount: A:0.51, C:0.12, G:0.10, T:0.27


Consensus pattern (21 bp):   
AGTAAAATCATTTTACAGAAA
Done.