Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1880

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: 3569
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33


Found at i:1272 original size:13 final size:13

Alignment explanation


    Indices: 1254--1280  Score: 54
    Period size: 13  Copynumber: 2.1  Consensus size: 13

       1244 ACATATTTTT

                         
       1254 TTGTATCGATACA
          1 TTGTATCGATACA

                         
       1267 TTGTATCGATACA
          1 TTGTATCGATACA

             
       1280 T
          1 T

       1281 ATTTTGTGTA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   14  1.00

ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41


Consensus pattern (13 bp):   
TTGTATCGATACA

Found at i:1305 original size:19 final size:19

Alignment explanation


    Indices: 1268--1305  Score: 51
    Period size: 19  Copynumber: 2.0  Consensus size: 19

       1258 ATCGATACAT

                          *    
       1268 TGTATCGATACATATTTTG
          1 TGTATCGATACATAGTTTG

                                
       1287 TGTATCGATTACA-AGTTTG
          1 TGTATCGA-TACATAGTTTG

       1306 GCTACTGCCA


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  19   13  0.76
  20    4  0.24

ACGTcount: A:0.26, C:0.11, G:0.18, T:0.45


Consensus pattern (19 bp):   
TGTATCGATACATAGTTTG

Found at i:2063 original size:33 final size:32

Alignment explanation


    Indices: 2021--2088  Score: 109
    Period size: 33  Copynumber: 2.1  Consensus size: 32

       2011 CGTTACAAGC

                            *                
       2021 CAATGTATCGATACATTTTGTGATGGATCGATA
          1 CAATGTATCGATACATATTGTG-TGGATCGATA

                                    *       
       2054 CAATGTATCGATACATATTGTGTGTATCGATA
          1 CAATGTATCGATACATATTGTGTGGATCGATA

               
       2086 CAA
          1 CAA

       2089 ATTTAGCTAC


Statistics
Matches: 33,  Mismatches: 2, Indels: 1
        0.92            0.06        0.03

Matches are distributed among these distances:
  32   12  0.36
  33   21  0.64

ACGTcount: A:0.32, C:0.13, G:0.19, T:0.35


Consensus pattern (32 bp):   
CAATGTATCGATACATATTGTGTGGATCGATA

Found at i:2146 original size:20 final size:20

Alignment explanation


    Indices: 2121--2173  Score: 72
    Period size: 20  Copynumber: 2.6  Consensus size: 20

       2111 CCAATGACTT

                            *    
       2121 GTATCGATACATTCT-TTCAA
          1 GTATCGATACATT-TAGTCAA

                               *
       2141 GTATCGATACATTTAGTCAT
          1 GTATCGATACATTTAGTCAA

                         
       2161 GTATCGATACATT
          1 GTATCGATACATT

       2174 ATATCGATAC


Statistics
Matches: 30,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  19    1  0.03
  20   29  0.97

ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40


Consensus pattern (20 bp):   
GTATCGATACATTTAGTCAA

Found at i:2779 original size:28 final size:28

Alignment explanation


    Indices: 2739--2795  Score: 114
    Period size: 28  Copynumber: 2.0  Consensus size: 28

       2729 TTTTCTCTCC

                                        
       2739 CCCTTAATAAAATAATTTAACAATTTCG
          1 CCCTTAATAAAATAATTTAACAATTTCG

                                        
       2767 CCCTTAATAAAATAATTTAACAATTTCG
          1 CCCTTAATAAAATAATTTAACAATTTCG

             
       2795 C
          1 C

       2796 ACATTAAAAA


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  28   29  1.00

ACGTcount: A:0.42, C:0.19, G:0.04, T:0.35


Consensus pattern (28 bp):   
CCCTTAATAAAATAATTTAACAATTTCG

Found at i:2806 original size:28 final size:28

Alignment explanation


    Indices: 2742--2811  Score: 106
    Period size: 28  Copynumber: 2.5  Consensus size: 28

       2732 TCTCTCCCCC

                                       *
       2742 TTAATAAAATAATTTAACAATTTCGCCC
          1 TTAATAAAATAATTTAACAATTTCGCCA

                                         
       2770 TTAATAAAATAATTTAACAATTTCGCACA
          1 TTAATAAAATAATTTAACAATTTCGC-CA

                     *    
       2799 TTAA-AAAAAAATT
          1 TTAATAAAATAATT

       2812 CTTTCTCCCC


Statistics
Matches: 39,  Mismatches: 2, Indels: 2
        0.91            0.05        0.05

Matches are distributed among these distances:
  28   34  0.87
  29    5  0.13

ACGTcount: A:0.50, C:0.13, G:0.03, T:0.34


Consensus pattern (28 bp):   
TTAATAAAATAATTTAACAATTTCGCCA
Done.