Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021390.1 Corchorus olitorius cultivar O-4 contig21423, 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: 2605
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34


Found at i:1746 original size:27 final size:25

Alignment explanation


    Indices: 1697--1752  Score: 69
    Period size: 27  Copynumber: 2.1  Consensus size: 25

       1687 TTTCCATGAT

                                       
       1697 TTTAATAATGGAATAATTAAAATATTA
          1 TTTAATAATGGAAT-ATTAAAATA-TA

                                       
       1724 TTTAATAATGGTAAT-TTAGAAATATA
          1 TTTAATAATGG-AATATTA-AAATATA

               
       1750 TTT
          1 TTT

       1753 GAAAAAAAGG


Statistics
Matches: 27,  Mismatches: 0, Indels: 5
        0.84            0.00        0.16

Matches are distributed among these distances:
  26    8  0.30
  27   16  0.59
  28    3  0.11

ACGTcount: A:0.46, C:0.00, G:0.09, T:0.45


Consensus pattern (25 bp):   
TTTAATAATGGAATATTAAAATATA

Found at i:2263 original size:31 final size:31

Alignment explanation


    Indices: 2228--2328  Score: 109
    Period size: 31  Copynumber: 3.3  Consensus size: 31

       2218 AAGTACTTAA

                     *                     
       2228 TTAGTCCCTGTACTATTGAAAAAAGATCAAT
          1 TTAGTCCCTCTACTATTGAAAAAAGATCAAT

                 *    *           ***       
       2259 TTAGTTCCTCCA-TCA-TGAAATCTG-TCAAT
          1 TTAGTCCCTCTACT-ATTGAAAAAAGATCAAT

                                   *       
       2288 TTAGTCCCTCTACTATTGAAAAACGATCAAT
          1 TTAGTCCCTCTACTATTGAAAAAAGATCAAT

                      
       2319 TTAGTCCCTC
          1 TTAGTCCCTC

       2329 CGTGAAACAG


Statistics
Matches: 55,  Mismatches: 11, Indels: 8
        0.74            0.15        0.11

Matches are distributed among these distances:
  29   16  0.29
  30   14  0.25
  31   25  0.45

ACGTcount: A:0.32, C:0.23, G:0.11, T:0.35


Consensus pattern (31 bp):   
TTAGTCCCTCTACTATTGAAAAAAGATCAAT
Done.