Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017146.1 Corchorus olitorius cultivar O-4 contig17179, 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: 6526
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.32


Found at i:161 original size:30 final size:29

Alignment explanation


    Indices: 120--176  Score: 89
    Period size: 30  Copynumber: 1.9  Consensus size: 29

        110 GTTTATTAAT

                                           
        120 GAAACTTGAAAATTAAAGACATAAGATAAAG
          1 GAAACTTGAAAATTAAAG-CATAA-ATAAAG

                                       
        151 GAAA-TTGAAAATTAAAGCATAAATAA
          1 GAAACTTGAAAATTAAAGCATAAATAA

        177 CTAATCCTAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 3
        0.90            0.00        0.10

Matches are distributed among these distances:
  28    4  0.15
  29    5  0.19
  30   13  0.50
  31    4  0.15

ACGTcount: A:0.60, C:0.05, G:0.14, T:0.21


Consensus pattern (29 bp):   
GAAACTTGAAAATTAAAGCATAAATAAAG

Found at i:1210 original size:23 final size:23

Alignment explanation


    Indices: 1183--1255  Score: 89
    Period size: 22  Copynumber: 3.3  Consensus size: 23

       1173 GTCGAATTGC

                                   
       1183 TCTTCTCTTTAGTCGA-TAATTT
          1 TCTTCTCTTTAGTCGACTAATTT

                                   *
       1205 TGCTTC-CTTTAGTCGACTAA-TC
          1 T-CTTCTCTTTAGTCGACTAATTT

            *                *     
       1227 CCTTCTCTTTAGTCGACAAATTT
          1 TCTTCTCTTTAGTCGACTAATTT

                  
       1250 TCTTCT
          1 TCTTCT

       1256 TGAAGTCGAC


Statistics
Matches: 42,  Mismatches: 5, Indels: 7
        0.78            0.09        0.13

Matches are distributed among these distances:
  21    4  0.10
  22   25  0.60
  23   13  0.31

ACGTcount: A:0.18, C:0.25, G:0.10, T:0.48


Consensus pattern (23 bp):   
TCTTCTCTTTAGTCGACTAATTT

Found at i:2053 original size:3 final size:3

Alignment explanation


    Indices: 2045--2073  Score: 58
    Period size: 3  Copynumber: 9.7  Consensus size: 3

       2035 ATTAGTGTAA

                                                  
       2045 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
          1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA

       2074 ATTTAAAATT


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   26  1.00

ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31


Consensus pattern (3 bp):   
AAT

Done.