Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013217.1 Corchorus capsularis cultivar CVL-1 contig13238, 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: 21958
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.31


Found at i:1536 original size:30 final size:28

Alignment explanation


    Indices: 1468--1542  Score: 89
    Period size: 28  Copynumber: 2.6  Consensus size: 28

       1458 CCTAAATCAA

                  *                   * 
       1468 TTTAATATAAACAAATCAATTAAACCCT
          1 TTTAATTTAAACAAATCAATTAAACCAT

               *                        
       1496 TTTCATTTAAACAAATCAATTAAA-CAT
          1 TTTAATTTAAACAAATCAATTAAACCAT

                                
       1523 TTCCTAAATTTAAACAAATC
          1 TT--T-AATTTAAACAAATC

       1543 TAATATAACC


Statistics
Matches: 40,  Mismatches: 4, Indels: 4
        0.83            0.08        0.08

Matches are distributed among these distances:
  27    4  0.10
  28   22  0.55
  29    1  0.03
  30   13  0.32

ACGTcount: A:0.48, C:0.17, G:0.00, T:0.35


Consensus pattern (28 bp):   
TTTAATTTAAACAAATCAATTAAACCAT

Found at i:16781 original size:13 final size:11

Alignment explanation


    Indices: 16744--16800  Score: 60
    Period size: 12  Copynumber: 4.8  Consensus size: 11

      16734 TTATGCACCC

                       
      16744 AAAACATTTAT
          1 AAAACATTTAT

                         
      16755 CAAAACATTTTAT
          1 -AAAACA-TTTAT

               *         
      16768 AAAGCATTTATAT
          1 AAAACA-TT-TAT

                  *    
      16781 AAAACAGTTAT
          1 AAAACATTTAT

                     
      16792 AAAACATTT
          1 AAAACATTT

      16801 CCTCAACGGG


Statistics
Matches: 39,  Mismatches: 4, Indels: 5
        0.81            0.08        0.10

Matches are distributed among these distances:
  11   11  0.28
  12   15  0.38
  13   13  0.33

ACGTcount: A:0.51, C:0.11, G:0.04, T:0.35


Consensus pattern (11 bp):   
AAAACATTTAT

Found at i:19892 original size:16 final size:17

Alignment explanation


    Indices: 19868--19902  Score: 54
    Period size: 16  Copynumber: 2.1  Consensus size: 17

      19858 TTTTTTCTCC

                *            
      19868 TACTCATGGT-GTGTTA
          1 TACTAATGGTGGTGTTA

                             
      19884 TACTAATGGTGGTGTTA
          1 TACTAATGGTGGTGTTA

              
      19901 TA
          1 TA

      19903 AAACTTTTTT


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

Matches are distributed among these distances:
  16    9  0.53
  17    8  0.47

ACGTcount: A:0.23, C:0.09, G:0.26, T:0.43


Consensus pattern (17 bp):   
TACTAATGGTGGTGTTA

Done.