Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005210.1 Corchorus capsularis cultivar CVL-1 contig05228, 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: 3297
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.27


Found at i:1424 original size:33 final size:32

Alignment explanation


    Indices: 1381--1459  Score: 131
    Period size: 33  Copynumber: 2.4  Consensus size: 32

       1371 ACAAAGGATC

                                             
       1381 GTGTGGCCGGGCAAGGCCGAGTCAAGTGGCCGG
          1 GTGTGGCCGGGCAAGGCCGAGTCAAGTGGCC-G

                 *                          
       1414 GTGTGACCGGGCAAGGCCGAGTCAAGTGGCCG
          1 GTGTGGCCGGGCAAGGCCGAGTCAAGTGGCCG

                          
       1446 GTGATGGCCGGGCA
          1 GTG-TGGCCGGGCA

       1460 TCTCCATGTC


Statistics
Matches: 43,  Mismatches: 2, Indels: 2
        0.91            0.04        0.04

Matches are distributed among these distances:
  32    4  0.09
  33   39  0.91

ACGTcount: A:0.16, C:0.24, G:0.47, T:0.13


Consensus pattern (32 bp):   
GTGTGGCCGGGCAAGGCCGAGTCAAGTGGCCG

Found at i:1477 original size:33 final size:33

Alignment explanation


    Indices: 1440--1513  Score: 105
    Period size: 33  Copynumber: 2.2  Consensus size: 33

       1430 CCGAGTCAAG

                                       *      
       1440 TGGCCGGTGATGGC-CGGGCATCTCCATGTCGCA
          1 TGGCCGGTG-TGGCGCGGGCATCTCCAAGTCGCA

                      *                     *
       1473 TGGCCGGTGTTGCGCGGGCATCTCCAAGTCGCG
          1 TGGCCGGTGTGGCGCGGGCATCTCCAAGTCGCA

                    
       1506 TGGCCGGT
          1 TGGCCGGT

       1514 CACTCGCGCC


Statistics
Matches: 37,  Mismatches: 3, Indels: 2
        0.88            0.07        0.05

Matches are distributed among these distances:
  32    3  0.08
  33   34  0.92

ACGTcount: A:0.09, C:0.30, G:0.39, T:0.22


Consensus pattern (33 bp):   
TGGCCGGTGTGGCGCGGGCATCTCCAAGTCGCA

Found at i:1977 original size:22 final size:22

Alignment explanation


    Indices: 1950--1992  Score: 86
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       1940 CCCAGGGCGT

                                  
       1950 TGCTCTCAGGCCCCAGGTTGCC
          1 TGCTCTCAGGCCCCAGGTTGCC

                                 
       1972 TGCTCTCAGGCCCCAGGTTGC
          1 TGCTCTCAGGCCCCAGGTTGC

       1993 TCTCAGGCTT


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  22   21  1.00

ACGTcount: A:0.09, C:0.40, G:0.28, T:0.23


Consensus pattern (22 bp):   
TGCTCTCAGGCCCCAGGTTGCC

Found at i:1995 original size:18 final size:18

Alignment explanation


    Indices: 1948--2000  Score: 70
    Period size: 22  Copynumber: 2.7  Consensus size: 18

       1938 CGCCCAGGGC

                              
       1948 GTTGCTCTCAGGCCCCAG
          1 GTTGCTCTCAGGCCCCAG

                                  
       1966 GTTGCCTGCTCTCAGGCCCCAG
          1 G-T---TGCTCTCAGGCCCCAG

                         
       1988 GTTGCTCTCAGGC
          1 GTTGCTCTCAGGC

       2001 TTCAATCACG


Statistics
Matches: 31,  Mismatches: 0, Indels: 8
        0.79            0.00        0.21

Matches are distributed among these distances:
  18   12  0.39
  19    1  0.03
  21    1  0.03
  22   17  0.55

ACGTcount: A:0.09, C:0.38, G:0.28, T:0.25


Consensus pattern (18 bp):   
GTTGCTCTCAGGCCCCAG
Done.