Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001405.1 Corchorus capsularis cultivar CVL-1 contig01405, 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: 1796
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35


Found at i:1669 original size:27 final size:26

Alignment explanation


    Indices: 1608--1700  Score: 120
    Period size: 27  Copynumber: 3.6  Consensus size: 26

       1598 TACCTTCTTA

                           *      *   
       1608 CTTTTTACTGATTACCATTT-TACT-
          1 CTTTTTACTGATTACTATTTCTGCTC

                                       
       1632 C-TTTTACTGATTACTATTTTCTGCTC
          1 CTTTTTACTGATTACTA-TTTCTGCTC

                            *         
       1658 CTTTTTACTGATTACTCTTTCTGCTC
          1 CTTTTTACTGATTACTATTTCTGCTC

                             
       1684 CTTTTTTACTGATTACT
          1 C-TTTTTACTGATTACT

       1701 CTTGCTTTTT


Statistics
Matches: 61,  Mismatches: 3, Indels: 7
        0.86            0.04        0.10

Matches are distributed among these distances:
  23   14  0.23
  24    4  0.07
  25    3  0.05
  26   11  0.18
  27   29  0.48

ACGTcount: A:0.16, C:0.23, G:0.06, T:0.55


Consensus pattern (26 bp):   
CTTTTTACTGATTACTATTTCTGCTC

Found at i:1737 original size:22 final size:22

Alignment explanation


    Indices: 1709--1767  Score: 79
    Period size: 21  Copynumber: 2.8  Consensus size: 22

       1699 CTCTTGCTTT

                                 * 
       1709 TTACTGATTACCT-TTTTACTTC
          1 TTACTGATTACCTATTTTAC-CC

                                  
       1731 TTACTGATTA-CTATTTTACCC
          1 TTACTGATTACCTATTTTACCC

                             
       1752 TTACTGATTA-CTATTT
          1 TTACTGATTACCTATTT

       1768 AGTTTTTTTT


Statistics
Matches: 35,  Mismatches: 1, Indels: 3
        0.90            0.03        0.08

Matches are distributed among these distances:
  21   19  0.54
  22   16  0.46

ACGTcount: A:0.22, C:0.20, G:0.05, T:0.53


Consensus pattern (22 bp):   
TTACTGATTACCTATTTTACCC

Found at i:1756 original size:21 final size:22

Alignment explanation


    Indices: 1570--1767  Score: 102
    Period size: 22  Copynumber: 8.7  Consensus size: 22

       1560 CTTTACTTTG

                                  
       1570 TACTGATTACTATTTTACT-CT
          1 TACTGATTACTATTTTACTCCT

             **           *     ** 
       1591 TGTTGATTACCT-TCTTACTTTT
          1 TACTGATTA-CTATTTTACTCCT

                      *          * 
       1613 TACTGATTACCATTTTACTCTTT
          1 TACTGATTACTATTTTACTC-CT

                              *        
       1636 TACTGATTACTATTTTCTGCTCCTTTT
          1 TACTGATTACTA-TTT-TACTCC---T

                       *     *         
       1663 TACTGATTACTCTTTCTGCTCCTTTTT
          1 TACTGATTACTATTT-TACTCC----T

                         *  *  ** 
       1690 TACTGATTAC--TCTTGCTTTT
          1 TACTGATTACTATTTTACTCCT

                                *  
       1710 TACTGATTACCT-TTTTACTTCT
          1 TACTGATTA-CTATTTTACTCCT

                                  
       1732 TACTGATTACTATTTTAC-CCT
          1 TACTGATTACTATTTTACTCCT

                           
       1753 TACTGATTACTATTT
          1 TACTGATTACTATTT

       1768 AGTTTTTTTT


Statistics
Matches: 144,  Mismatches: 20, Indels: 26
        0.76            0.11        0.14

Matches are distributed among these distances:
  20   10  0.07
  21   34  0.24
  22   38  0.26
  23   13  0.09
  24    7  0.05
  25    6  0.04
  26   10  0.07
  27   26  0.18

ACGTcount: A:0.18, C:0.21, G:0.07, T:0.54


Consensus pattern (22 bp):   
TACTGATTACTATTTTACTCCT
Done.