Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004181.1 Corchorus capsularis cultivar CVL-1 contig04189, 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: 2005
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.36


Found at i:1012 original size:3 final size:3

Alignment explanation


    Indices: 961--994  Score: 52
    Period size: 3  Copynumber: 11.7  Consensus size: 3

        951 ACTACTACTA

                 *                                        
        961 AAT ACT AAT -AT AAT AAT AAT AAT AAT AAT AAT AA
          1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA

        995 AAGTTTGATT


Statistics
Matches: 28,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
   2    2  0.07
   3   26  0.93

ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32


Consensus pattern (3 bp):   
AAT

Found at i:1253 original size:16 final size:16

Alignment explanation


    Indices: 1234--1264  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

       1224 ATATTTCCTT

                            
       1234 TTTTATATTAATTTCC
          1 TTTTATATTAATTTCC

                      *    
       1250 TTTTATATTAGTTTC
          1 TTTTATATTAATTTC

       1265 AAACTTAAAA


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  16   14  1.00

ACGTcount: A:0.23, C:0.10, G:0.03, T:0.65


Consensus pattern (16 bp):   
TTTTATATTAATTTCC

Found at i:1344 original size:2 final size:2

Alignment explanation


    Indices: 1339--1377  Score: 53
    Period size: 2  Copynumber: 20.0  Consensus size: 2

       1329 AGTTTAGACT

                                 *                              *      
       1339 TA TA TA -A TA TA TA AA TA TA TA TA TA TA TA TA TA TT TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       1378 GATTTTTCTG


Statistics
Matches: 32,  Mismatches: 4, Indels: 2
        0.84            0.11        0.05

Matches are distributed among these distances:
   1    1  0.03
   2   31  0.97

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
TA

Done.