Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010799.1 Corchorus capsularis cultivar CVL-1 contig10820, whole genome shotgun sequence

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: 3867
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26


Found at i:1936 original size:62 final size:62

Alignment explanation


    Indices: 1860--2120  Score: 402
    Period size: 62  Copynumber: 4.2  Consensus size: 62

       1850 AGTCCATGGA

                    *                                        *    *       
       1860 TCTGAAGATAGTTCCTAAAAGATATTTGAGAGTGAATCTGAAGACAGTTAACGAGGATAGGT
          1 TCTGAAGACAGTTCCTAAAAGATATTTGAGAGTGAATCTGAAGACAGTTCACGAAGATAGGT

                               *       *                  *               
       1922 TCTGAAGACAGTTCCTAAATGATATTTTAGAGTGAATCTGAAGACAATTCACGAAGATAGGT
          1 TCTGAAGACAGTTCCTAAAAGATATTTGAGAGTGAATCTGAAGACAGTTCACGAAGATAGGT

                    *                                                     
       1984 TCTGAAGATAGTTCCTAAAAGATATTTGAGAGTGAATCTGAAGACAGTTCACGAAGATAGGT
          1 TCTGAAGACAGTTCCTAAAAGATATTTGAGAGTGAATCTGAAGACAGTTCACGAAGATAGGT

                                       *                        *           
       2046 TCTGAAGACAGTTCCTAAAAGATATTTTAGAGTGAATCT-AAGGACAGTTCATGAAGA-AGGAT
          1 TCTGAAGACAGTTCCTAAAAGATATTTGAGAGTGAATCTGAA-GACAGTTCACGAAGATAGG-T

                          
       2108 T-TGAAGACAGTTC
          1 TCTGAAGACAGTTC

       2121 TTATGAAGTT


Statistics
Matches: 184,  Mismatches: 13, Indels: 5
        0.91            0.06        0.02

Matches are distributed among these distances:
  61   17  0.09
  62  167  0.91

ACGTcount: A:0.37, C:0.11, G:0.23, T:0.28


Consensus pattern (62 bp):   
TCTGAAGACAGTTCCTAAAAGATATTTGAGAGTGAATCTGAAGACAGTTCACGAAGATAGGT

Found at i:2033 original size:36 final size:35

Alignment explanation


    Indices: 1984--2095  Score: 93
    Period size: 36  Copynumber: 3.4  Consensus size: 35

       1974 GAAGATAGGT

                    *                           
       1984 TCTGAAGATAGTTCCTAAAAGATATTTGAGAGTGAA
          1 TCTGAAGACAGTTCCTAAAAGATATTT-AGAGTGAA

                              *                 
       2020 TCTGAAGACAGTT-C-ACGAAG--A--TAG-GT---
          1 TCTGAAGACAGTTCCTA-AAAGATATTTAGAGTGAA

                                                
       2046 TCTGAAGACAGTTCCTAAAAGATATTTTAGAGTGAA
          1 TCTGAAGACAGTTCCTAAAAGATA-TTTAGAGTGAA

                           
       2082 TCT-AAGGACAGTTC
          1 TCTGAA-GACAGTTC

       2096 ATGAAGAAGG


Statistics
Matches: 60,  Mismatches: 3, Indels: 26
        0.67            0.03        0.29

Matches are distributed among these distances:
  26   13  0.22
  27    4  0.07
  28    1  0.02
  29    3  0.05
  30    2  0.03
  31    1  0.02
  32    3  0.05
  33    3  0.05
  34    1  0.02
  35    6  0.10
  36   23  0.38

ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29


Consensus pattern (35 bp):   
TCTGAAGACAGTTCCTAAAAGATATTTAGAGTGAA

Done.