Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011102.1 Corchorus olitorius cultivar O-4 contig11135, 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: 8322
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29


Found at i:215 original size:25 final size:25

Alignment explanation


    Indices: 186--235  Score: 100
    Period size: 25  Copynumber: 2.0  Consensus size: 25

        176 GAGAATCTGT

                                     
        186 GTTAAATTGTATCTGAATCATACGC
          1 GTTAAATTGTATCTGAATCATACGC

                                     
        211 GTTAAATTGTATCTGAATCATACGC
          1 GTTAAATTGTATCTGAATCATACGC

        236 AATGGCTTTC


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  25   25  1.00

ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36


Consensus pattern (25 bp):   
GTTAAATTGTATCTGAATCATACGC

Found at i:1552 original size:19 final size:19

Alignment explanation


    Indices: 1523--1565  Score: 79
    Period size: 19  Copynumber: 2.3  Consensus size: 19

       1513 TCAACAAGAA

                               
       1523 GAATA-TCCATAATTGTTG
          1 GAATACTCCATAATTGTTG

                               
       1541 GAATACTCCATAATTGTTG
          1 GAATACTCCATAATTGTTG

                  
       1560 GAATAC
          1 GAATAC

       1566 GTAGTGATGT


Statistics
Matches: 24,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  18    5  0.21
  19   19  0.79

ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35


Consensus pattern (19 bp):   
GAATACTCCATAATTGTTG

Found at i:5172 original size:20 final size:20

Alignment explanation


    Indices: 5147--5190  Score: 88
    Period size: 20  Copynumber: 2.2  Consensus size: 20

       5137 AGTCGATTGA

                                
       5147 CTTTAGTATGGGAATCTCTT
          1 CTTTAGTATGGGAATCTCTT

                                
       5167 CTTTAGTATGGGAATCTCTT
          1 CTTTAGTATGGGAATCTCTT

                
       5187 CTTT
          1 CTTT

       5191 TTTTCATTCC


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   24  1.00

ACGTcount: A:0.18, C:0.16, G:0.18, T:0.48


Consensus pattern (20 bp):   
CTTTAGTATGGGAATCTCTT
Done.