Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008546.1 Corchorus capsularis cultivar CVL-1 contig08567, 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: 11057
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.31


Found at i:1754 original size:14 final size:15

Alignment explanation


    Indices: 1720--1757  Score: 51
    Period size: 16  Copynumber: 2.5  Consensus size: 15

       1710 AAACCGAAAT

                          *
       1720 TTTCTTTTTTTCTCT
          1 TTTCTTTTTTTCTCC

                            
       1735 TCTTCTTTTTTTC-CC
          1 T-TTCTTTTTTTCTCC

                    
       1750 TTTCTTTT
          1 TTTCTTTT

       1758 CTGTTTTTTG


Statistics
Matches: 21,  Mismatches: 1, Indels: 3
        0.84            0.04        0.12

Matches are distributed among these distances:
  14    7  0.33
  15    3  0.14
  16   11  0.52

ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76


Consensus pattern (15 bp):   
TTTCTTTTTTTCTCC

Found at i:3549 original size:31 final size:31

Alignment explanation


    Indices: 3506--3603  Score: 115
    Period size: 31  Copynumber: 3.2  Consensus size: 31

       3496 AAAAAGCCGT

                   *                   *   
       3506 GCCACATATACCAAAAAGTGACACATGTCAC
          1 GCCACATGTACCAAAAAGTGACACATGGCAC

                                          *
       3537 GCCACATGTACCAAAAAGTGACACATGGCAT
          1 GCCACATGTACCAAAAAGTGACACATGGCAC

                     **      *  *   *     *
       3568 GCCACATGTTTCAAAAATTGGCACGTGGCAT
          1 GCCACATGTACCAAAAAGTGACACATGGCAC

                 
       3599 GCCAC
          1 GCCAC

       3604 GTGCACAAAA


Statistics
Matches: 59,  Mismatches: 8, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  31   59  1.00

ACGTcount: A:0.36, C:0.28, G:0.18, T:0.18


Consensus pattern (31 bp):   
GCCACATGTACCAAAAAGTGACACATGGCAC

Found at i:10385 original size:15 final size:16

Alignment explanation


    Indices: 10354--10390  Score: 58
    Period size: 15  Copynumber: 2.4  Consensus size: 16

      10344 CTACCTACCT

                            
      10354 AACAAATATACAAACA
          1 AACAAATATACAAACA

                        *   
      10370 AACAAAT-TACATACA
          1 AACAAATATACAAACA

                  
      10385 AACAAA
          1 AACAAA

      10391 GTCACATCTT


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  15   13  0.65
  16    7  0.35

ACGTcount: A:0.68, C:0.19, G:0.00, T:0.14


Consensus pattern (16 bp):   
AACAAATATACAAACA
Done.