Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009795.1 Corchorus capsularis cultivar CVL-1 contig09816, 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: 4135
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33


Found at i:1587 original size:28 final size:29

Alignment explanation


    Indices: 1529--1603  Score: 98
    Period size: 29  Copynumber: 2.6  Consensus size: 29

       1519 GTAGATTAAG

                         *                
       1529 AATGACCAAAATACCCCCCTAAATGC-AAA
          1 AATGACCAAAAT-GCCCCCTAAATGCAAAA

                                *   **   
       1558 AATGACCAAAATGCCCCCTAGATGTGAAA
          1 AATGACCAAAATGCCCCCTAAATGCAAAA

                             
       1587 AATGACCAAAATGCCCC
          1 AATGACCAAAATGCCCC

       1604 TGGATGACTC


Statistics
Matches: 42,  Mismatches: 3, Indels: 2
        0.89            0.06        0.04

Matches are distributed among these distances:
  28   10  0.24
  29   32  0.76

ACGTcount: A:0.44, C:0.29, G:0.12, T:0.15


Consensus pattern (29 bp):   
AATGACCAAAATGCCCCCTAAATGCAAAA

Found at i:1917 original size:45 final size:45

Alignment explanation


    Indices: 1849--2033  Score: 264
    Period size: 45  Copynumber: 4.1  Consensus size: 45

       1839 GTCTGTGGTC

                        *      *                         
       1849 GATAACTGCTG-GAACTGAAAAAGACCTGTTCTGAGGTCAACTTT
          1 GATAACTGCTGAAAACTGAGAAAGACCTGTTCTGAGGTCAACTTT

                                           *         *   
       1893 GATAACTGCTGAAAACTGAGAAAGACCTGTTATGAGGTCAATTTT
          1 GATAACTGCTGAAAACTGAGAAAGACCTGTTCTGAGGTCAACTTT

                      *                                  
       1938 GATAACTGCTAAAAACTGAGAAAGACCTGTTCTGAGGTCAACTTT
          1 GATAACTGCTGAAAACTGAGAAAGACCTGTTCTGAGGTCAACTTT

                    * *                     *  *    *     
       1983 GATAACTTACCGAAAACTGAGAAAGACCTGTTTTGGGGTCGACTTT
          1 GATAAC-TGCTGAAAACTGAGAAAGACCTGTTCTGAGGTCAACTTT

                 
       2029 GATAA
          1 GATAA

       2034 TCTTATTGAA


Statistics
Matches: 126,  Mismatches: 13, Indels: 2
        0.89            0.09        0.01

Matches are distributed among these distances:
  44   11  0.09
  45   77  0.61
  46   38  0.30

ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28


Consensus pattern (45 bp):   
GATAACTGCTGAAAACTGAGAAAGACCTGTTCTGAGGTCAACTTT

Found at i:3633 original size:105 final size:105

Alignment explanation


    Indices: 3504--3692  Score: 301
    Period size: 105  Copynumber: 1.8  Consensus size: 105

       3494 AAATGACTAA

                                              *                    *         
       3504 ATTTGAAAAACTCTTTTGAAACCAATTTTAT-CCGAAAACCTTTTGAGAAAAACCCTTATTCTTT
          1 ATTTGAAAAACTCTTTTGAAACCAATTTTATCCCAAAAACC-TTTGAGAAAAA-CATTATTCTTT

                    *                                 
       3568 TGCAAAAATAATTTTTATTTTTTAAAATAGGCATGCACTTGC
         64 TGCAAAAACAATTTTTATTTTTTAAAATAGGCATGCACTTGC

                                                                    *        
       3610 ATTTGAAAAACT-TTTTGAAACCAATTTTATCCCAAAAACCTTTGAGAAAAACATTTTTCTTTTG
          1 ATTTGAAAAACTCTTTTGAAACCAATTTTATCCCAAAAACCTTTGAGAAAAACATTATTCTTTTG

              *                
       3674 CACAAACAATTTTTATTTT
         66 CAAAAACAATTTTTATTTT

       3693 AGGAACAATC


Statistics
Matches: 77,  Mismatches: 5, Indels: 4
        0.90            0.06        0.05

Matches are distributed among these distances:
 104   28  0.36
 105   29  0.38
 106   20  0.26

ACGTcount: A:0.37, C:0.16, G:0.08, T:0.40


Consensus pattern (105 bp):   
ATTTGAAAAACTCTTTTGAAACCAATTTTATCCCAAAAACCTTTGAGAAAAACATTATTCTTTTG
CAAAAACAATTTTTATTTTTTAAAATAGGCATGCACTTGC
Done.