Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010665.1 Corchorus capsularis cultivar CVL-1 contig10686, 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: 1976
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.32


Found at i:362 original size:33 final size:33

Alignment explanation


    Indices: 265--369  Score: 140
    Period size: 33  Copynumber: 3.2  Consensus size: 33

        255 TTGCAAAGAG

                                            * 
        265 TGTTTT-AGATGTTGTTTGCGATGATACTAAACC
          1 TGTTTTAAG-TGTTGTTTGCGATGATACTAAATC

             **                *    *        
        298 TAATTTAAGTGTTGTTTGCAATGACACTAAATC
          1 TGTTTTAAGTGTTGTTTGCGATGATACTAAATC

                              *              
        331 TGTTTTAAGTGTTGTTTGTGATGATACTAAATC
          1 TGTTTTAAGTGTTGTTTGCGATGATACTAAATC

                  
        364 TGTTTT
          1 TGTTTT

        370 GGATGCTAAT


Statistics
Matches: 61,  Mismatches: 10, Indels: 2
        0.84            0.14        0.03

Matches are distributed among these distances:
  33   59  0.97
  34    2  0.03

ACGTcount: A:0.26, C:0.10, G:0.19, T:0.46


Consensus pattern (33 bp):   
TGTTTTAAGTGTTGTTTGCGATGATACTAAATC

Found at i:434 original size:33 final size:33

Alignment explanation


    Indices: 387--500  Score: 117
    Period size: 33  Copynumber: 3.5  Consensus size: 33

        377 AATTGTGATG

                *                            
        387 AAAACAATTCTGTTTTGGTTGAACATAGCATTA
          1 AAAATAATTCTGTTTTGGTTGAACATAGCATTA

                     *            *         *
        420 AAAATAATTTTGTTTTGGTTGATCATAGCATTG
          1 AAAATAATTCTGTTTTGGTTGAACATAGCATTA

            *       *              *   *    *
        453 CAAATAATCCTGTTTTGG-T--AGATAACATTG
          1 AAAATAATTCTGTTTTGGTTGAACATAGCATTA

                   *          
        483 AAAATAAATCTGTTTTGG
          1 AAAATAATTCTGTTTTGG

        501 GTGACGAAAA


Statistics
Matches: 68,  Mismatches: 13, Indels: 3
        0.81            0.15        0.04

Matches are distributed among these distances:
  30   23  0.34
  32    1  0.01
  33   44  0.65

ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39


Consensus pattern (33 bp):   
AAAATAATTCTGTTTTGGTTGAACATAGCATTA

Found at i:1165 original size:17 final size:17

Alignment explanation


    Indices: 1143--1176  Score: 59
    Period size: 17  Copynumber: 2.0  Consensus size: 17

       1133 GAATCGGCTA

                             
       1143 TGAATTTTTGAAGTTTC
          1 TGAATTTTTGAAGTTTC

                        *    
       1160 TGAATTTTTGAATTTTC
          1 TGAATTTTTGAAGTTTC

       1177 AAGAAGGGTG


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

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.24, C:0.06, G:0.15, T:0.56


Consensus pattern (17 bp):   
TGAATTTTTGAAGTTTC
Done.