Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016054.1 Corchorus capsularis cultivar CVL-1 contig16075, 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: 2298
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29


Found at i:447 original size:21 final size:23

Alignment explanation


    Indices: 421--465  Score: 58
    Period size: 21  Copynumber: 2.0  Consensus size: 23

        411 TCTGACTGAA

                                   
        421 TTGCTAAACACCGCC-C-CATTT
          1 TTGCTAAACACCGCCTCACATTT

                  **               
        442 TTGCTATTCACCGCCTCACATTT
          1 TTGCTAAACACCGCCTCACATTT

             
        465 T
          1 T

        466 ACACTTTTGC


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  21   13  0.65
  22    1  0.05
  23    6  0.30

ACGTcount: A:0.20, C:0.36, G:0.09, T:0.36


Consensus pattern (23 bp):   
TTGCTAAACACCGCCTCACATTT

Found at i:796 original size:32 final size:32

Alignment explanation


    Indices: 760--872  Score: 145
    Period size: 32  Copynumber: 3.5  Consensus size: 32

        750 GTGGCTGTGG

                 *          *     *         
        760 CGCCCTAGGGGTGCGGTTTGCCATGGCAAAGC
          1 CGCCCCAGGGGTGCGGCTTGCCGTGGCAAAGC

                     *       *              
        792 CGCCCCAGGTGTGCGGCCTGCCGTGGCAAAGC
          1 CGCCCCAGGGGTGCGGCTTGCCGTGGCAAAGC

                    **                      
        824 CGCCCCAGCCGTGCGGCTTGCCGTGGCAAAGC
          1 CGCCCCAGGGGTGCGGCTTGCCGTGGCAAAGC

             *         *     
        856 CTCCCCAGGGGGGCGGC
          1 CGCCCCAGGGGTGCGGC

        873 AAGGCCCTGC


Statistics
Matches: 69,  Mismatches: 12, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  32   69  1.00

ACGTcount: A:0.12, C:0.36, G:0.38, T:0.13


Consensus pattern (32 bp):   
CGCCCCAGGGGTGCGGCTTGCCGTGGCAAAGC

Found at i:885 original size:64 final size:64

Alignment explanation


    Indices: 770--890  Score: 154
    Period size: 64  Copynumber: 1.9  Consensus size: 64

        760 CGCCCTAGGG

                  *                        * *     **   *                   
        770 GTGCGGTTTGCCATGGCAAAGCCGCCCCAGGTGTGCGGCCTGCCGTGGCAAAGCCGCCCCAGCC
          1 GTGCGGCTTGCCATGGCAAAGCCGCCCCAGGGGGGCGGCAGGCCCTGGCAAAGCCGCCCCAGCC

                        *          *                                  
        834 GTGCGGCTTGCCGTGGCAAAGCCTCCCCAGGGGGGCGGCAAGGCCCT-GCAAAGCCGC
          1 GTGCGGCTTGCCATGGCAAAGCCGCCCCAGGGGGGCGGC-AGGCCCTGGCAAAGCCGC

        891 ACAAATGGGG


Statistics
Matches: 48,  Mismatches: 8, Indels: 2
        0.83            0.14        0.03

Matches are distributed among these distances:
  64   44  0.92
  65    4  0.08

ACGTcount: A:0.15, C:0.36, G:0.36, T:0.12


Consensus pattern (64 bp):   
GTGCGGCTTGCCATGGCAAAGCCGCCCCAGGGGGGCGGCAGGCCCTGGCAAAGCCGCCCCAGCC

Found at i:1010 original size:32 final size:32

Alignment explanation


    Indices: 928--1010  Score: 80
    Period size: 32  Copynumber: 2.6  Consensus size: 32

        918 CCGCCCTCCT

                 *  *    *                  
        928 GGGCGACTGTGCCGCGGCAAGCCGCACCCTTG
          1 GGGCGGCTATGCCACGGCAAGCCGCACCCTTG

            *            *     *            
        960 TGGCGGCTATGCCTCGGCAGGCCGCACCC-TG
          1 GGGCGGCTATGCCACGGCAAGCCGCACCCTTG

                                 
        991 GGGTCGGCCT-TGCCACGGCA
          1 GGG-CGG-CTATGCCACGGCA

       1011 TGCTGCCCTG


Statistics
Matches: 42,  Mismatches: 7, Indels: 4
        0.79            0.13        0.08

Matches are distributed among these distances:
  31    4  0.10
  32   36  0.86
  33    2  0.05

ACGTcount: A:0.11, C:0.37, G:0.37, T:0.14


Consensus pattern (32 bp):   
GGGCGGCTATGCCACGGCAAGCCGCACCCTTG

Found at i:1189 original size:14 final size:15

Alignment explanation


    Indices: 1172--1204  Score: 50
    Period size: 15  Copynumber: 2.3  Consensus size: 15

       1162 GAAAACAGGG

                      *    
       1172 ATTATGAA-ATAACA
          1 ATTATGAAGAAAACA

                           
       1186 ATTATGAAGAAAACA
          1 ATTATGAAGAAAACA

                
       1201 ATTA
          1 ATTA

       1205 AACTAAAAAT


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  14    8  0.47
  15    9  0.53

ACGTcount: A:0.58, C:0.06, G:0.09, T:0.27


Consensus pattern (15 bp):   
ATTATGAAGAAAACA

Found at i:1239 original size:6 final size:6

Alignment explanation


    Indices: 1228--1253  Score: 52
    Period size: 6  Copynumber: 4.3  Consensus size: 6

       1218 GTAAAGCAAG

                                          
       1228 TCTAAA TCTAAA TCTAAA TCTAAA TC
          1 TCTAAA TCTAAA TCTAAA TCTAAA TC

       1254 AGATTATAAA


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   20  1.00

ACGTcount: A:0.46, C:0.19, G:0.00, T:0.35


Consensus pattern (6 bp):   
TCTAAA

Done.