Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005220.1 Corchorus capsularis cultivar CVL-1 contig05238, 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: 4343
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33


Found at i:2358 original size:29 final size:29

Alignment explanation


    Indices: 2326--2394  Score: 84
    Period size: 31  Copynumber: 2.3  Consensus size: 29

       2316 CTTTTGTGCG

                           *  *       *  
       2326 CATGGCATGCCACGTGTCGCTTTTTGGTA
          1 CATGGCATGCCACGTATCACTTTTTGATA

                                           
       2355 CATGTGGCATGCCACGTATCACTTTTTGATA
          1 CA--TGGCATGCCACGTATCACTTTTTGATA

                *    
       2386 CATGACATG
          1 CATGGCATG

       2395 TCACTTTTTG


Statistics
Matches: 34,  Mismatches: 4, Indels: 4
        0.81            0.10        0.10

Matches are distributed among these distances:
  29    8  0.24
  31   26  0.76

ACGTcount: A:0.20, C:0.23, G:0.23, T:0.33


Consensus pattern (29 bp):   
CATGGCATGCCACGTATCACTTTTTGATA

Found at i:2366 original size:31 final size:31

Alignment explanation


    Indices: 2328--2389  Score: 97
    Period size: 31  Copynumber: 2.0  Consensus size: 31

       2318 TTTGTGCGCA

                         *  *       *      
       2328 TGGCATGCCACGTGTCGCTTTTTGGTACATG
          1 TGGCATGCCACGTATCACTTTTTGATACATG

                                           
       2359 TGGCATGCCACGTATCACTTTTTGATACATG
          1 TGGCATGCCACGTATCACTTTTTGATACATG

       2390 ACATGTCACT


Statistics
Matches: 28,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  31   28  1.00

ACGTcount: A:0.18, C:0.23, G:0.24, T:0.35


Consensus pattern (31 bp):   
TGGCATGCCACGTATCACTTTTTGATACATG

Found at i:2398 original size:22 final size:24

Alignment explanation


    Indices: 2373--2427  Score: 69
    Period size: 24  Copynumber: 2.4  Consensus size: 24

       2363 ATGCCACGTA

                         *          
       2373 TCACTTTTT-G-ATACATGACATG
          1 TCACTTTTTGGCACACATGACATG

                            *    *  
       2395 TCACTTTTTGGCACACGTGACGTG
          1 TCACTTTTTGGCACACATGACATG

                     
       2419 TCACTTTTT
          1 TCACTTTTT

       2428 TATCCACGTG


Statistics
Matches: 28,  Mismatches: 3, Indels: 2
        0.85            0.09        0.06

Matches are distributed among these distances:
  22    9  0.32
  23    1  0.04
  24   18  0.64

ACGTcount: A:0.20, C:0.22, G:0.16, T:0.42


Consensus pattern (24 bp):   
TCACTTTTTGGCACACATGACATG

Found at i:2459 original size:31 final size:31

Alignment explanation


    Indices: 2421--2479  Score: 100
    Period size: 31  Copynumber: 1.9  Consensus size: 31

       2411 GTGACGTGTC

                              **           
       2421 ACTTTTTTATCCACGTGGTGTGCCACGTATT
          1 ACTTTTTTATCCACGTGGCATGCCACGTATT

                                        
       2452 ACTTTTTTATCCACGTGGCATGCCACGT
          1 ACTTTTTTATCCACGTGGCATGCCACGT

       2480 CGAATACCGT


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  31   26  1.00

ACGTcount: A:0.17, C:0.25, G:0.19, T:0.39


Consensus pattern (31 bp):   
ACTTTTTTATCCACGTGGCATGCCACGTATT
Done.