Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01003854.1 Corchorus capsularis cultivar CVL-1 contig03862, 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: 6035
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33


Found at i:533 original size:16 final size:16

Alignment explanation


    Indices: 512--546  Score: 54
    Period size: 16  Copynumber: 2.2  Consensus size: 16

        502 TTTAGTTGAG

                             
        512 TAAAATAGTAA-AATTA
          1 TAAAATA-TAATAATTA

                            
        528 TAAAATATAATAATTA
          1 TAAAATATAATAATTA

               
        544 TAA
          1 TAA

        547 GGATATTAGA


Statistics
Matches: 18,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  15    3  0.17
  16   15  0.83

ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34


Consensus pattern (16 bp):   
TAAAATATAATAATTA

Found at i:566 original size:78 final size:75

Alignment explanation


    Indices: 436--664  Score: 319
    Period size: 78  Copynumber: 3.1  Consensus size: 75

        426 GTTTTTTAAT

                           *                                                 
        436 TAAAATAGTAAAATGGTAAAATATAAGTA-ATAAGGATATTAGATTTAATTATATAAAAATAGAG
          1 TAAAATAGTAAAAT-ATAAAATATAA-TATATAAGGATATTAGATTTAATTATATAAAAATAGAG

                        
        500 TTTTTAGTTGAG
         64 TTTTTAGTTGAG

                                                                             
        512 TAAAATAGTAAAATTATAAAATATAATAATTATAAGGATATTAGATTTAATTATATAAAAATAGA
          1 TAAAATAGTAAAA-TATAAAATATAAT-A-TATAAGGATATTAGATTTAATTATATAAAAATAGA

                         
        577 GTTTTTAGTTGAG
         63 GTTTTTAGTTGAG

                                                     *         *             
        590 TAAAATAGT-AAA-ATAAAATAGT--TATA-AA-GATATTATATTTAATTAAATAAAAATAGAGT
          1 TAAAATAGTAAAATATAAAATA-TAATATATAAGGATATTAGATTTAATTATATAAAAATAGAGT

                    *  
        649 TTTTAGTTAAG
         65 TTTTAGTTGAG

                 
        660 TAAAA
          1 TAAAA

        665 CTATATAAAA


Statistics
Matches: 144,  Mismatches: 4, Indels: 16
        0.88            0.02        0.10

Matches are distributed among these distances:
  70   44  0.31
  71    2  0.01
  72    2  0.01
  73    1  0.01
  74    1  0.01
  75    9  0.06
  76   25  0.17
  77    4  0.03
  78   56  0.39

ACGTcount: A:0.51, C:0.00, G:0.12, T:0.37


Consensus pattern (75 bp):   
TAAAATAGTAAAATATAAAATATAATATATAAGGATATTAGATTTAATTATATAAAAATAGAGTT
TTTAGTTGAG

Found at i:602 original size:70 final size:70

Alignment explanation


    Indices: 518--674  Score: 226
    Period size: 70  Copynumber: 2.2  Consensus size: 70

        508 TGAGTAAAAT

                             *           *                 *                 
        518 AGTAAAATTATAAAATATAATAATTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT
          1 AGTAAAATTATAAAATAAAATAATTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTT

                *
        583 AGTTG
         66 AGTTA

                                   *              *                          
        588 AGTAAAA-TAGTAAAATAAAATAGTTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTT
          1 AGTAAAATTA-TAAAATAAAATAATTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTT

                  
        652 TAGTTA
         65 TAGTTA

                             
        658 AGTAAAACTATATAAAA
          1 AGTAAAA-T-TATAAAA

        675 ACCTAAACAA


Statistics
Matches: 77,  Mismatches: 6, Indels: 6
        0.87            0.07        0.07

Matches are distributed among these distances:
  69    2  0.03
  70   68  0.88
  72    5  0.06
  73    2  0.03

ACGTcount: A:0.52, C:0.01, G:0.10, T:0.37


Consensus pattern (70 bp):   
AGTAAAATTATAAAATAAAATAATTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTT
AGTTA

Found at i:1288 original size:14 final size:15

Alignment explanation


    Indices: 1269--1302  Score: 52
    Period size: 14  Copynumber: 2.3  Consensus size: 15

       1259 TTTTCTAACT

                  *        
       1269 AAAAATTCAAAA-AA
          1 AAAAATCCAAAAGAA

                           
       1283 AAAAATCCAAAAGAA
          1 AAAAATCCAAAAGAA

                 
       1298 AAAAA
          1 AAAAA

       1303 AAGGAAATAG


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  14   11  0.61
  15    7  0.39

ACGTcount: A:0.79, C:0.09, G:0.03, T:0.09


Consensus pattern (15 bp):   
AAAAATCCAAAAGAA

Found at i:4820 original size:20 final size:21

Alignment explanation


    Indices: 4795--4835  Score: 66
    Period size: 20  Copynumber: 2.0  Consensus size: 21

       4785 TTCCATTAGC

                      *          
       4795 AAATTACTTAGC-CCGTTAAT
          1 AAATTACTTAACACCGTTAAT

                                 
       4815 AAATTACTTAACACCGTTAAT
          1 AAATTACTTAACACCGTTAAT

       4836 TTTACTCACT


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

Matches are distributed among these distances:
  20   11  0.58
  21    8  0.42

ACGTcount: A:0.39, C:0.20, G:0.07, T:0.34


Consensus pattern (21 bp):   
AAATTACTTAACACCGTTAAT

Done.