Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001629.1 Corchorus capsularis cultivar CVL-1 contig01629, 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: 3579
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40


Found at i:1756 original size:49 final size:48

Alignment explanation


    Indices: 1674--1777  Score: 165
    Period size: 49  Copynumber: 2.1  Consensus size: 48

       1664 GTAAGTAATG

                                        *                     
       1674 AAGTATTATGTATATATATATTAAAAATTAAAAAATTAAAATTTTTTATT
          1 AAGTATTATG-ATATATATATTAAAAATAAAAAAATT-AAATTTTTTATT

                                                             
       1724 AAAGTATTATG-TATATATATTAAAAATAAAAAAATTAAATTTTTTATT
          1 -AAGTATTATGATATATATATTAAAAATAAAAAAATTAAATTTTTTATT

                  
       1772 AAGTAT
          1 AAGTAT

       1778 AAAAAATTAA


Statistics
Matches: 52,  Mismatches: 1, Indels: 4
        0.91            0.02        0.07

Matches are distributed among these distances:
  47    6  0.12
  48   12  0.23
  49   24  0.46
  51   10  0.19

ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44


Consensus pattern (48 bp):   
AAGTATTATGATATATATATTAAAAATAAAAAAATTAAATTTTTTATT

Found at i:1771 original size:27 final size:26

Alignment explanation


    Indices: 1741--1794  Score: 72
    Period size: 26  Copynumber: 2.0  Consensus size: 26

       1731 TATGTATATA

                                       
       1741 TATTAAAAATAAAAAAATTAAATTTTT
          1 TATTAAAAAT-AAAAAATTAAATTTTT

                  **            *     
       1768 TATTAAGTATAAAAAATTAATTTTTT
          1 TATTAAAAATAAAAAATTAAATTTTT

             
       1794 T
          1 T

       1795 CATTGAAGTT


Statistics
Matches: 24,  Mismatches: 3, Indels: 1
        0.86            0.11        0.04

Matches are distributed among these distances:
  26   16  0.67
  27    8  0.33

ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46


Consensus pattern (26 bp):   
TATTAAAAATAAAAAATTAAATTTTT

Found at i:1792 original size:26 final size:29

Alignment explanation


    Indices: 1752--1808  Score: 84
    Period size: 26  Copynumber: 2.1  Consensus size: 29

       1742 ATTAAAAATA

                                         
       1752 AAAAAATTAAATTTTTT-ATT-AAG-TAT
          1 AAAAAATTAAATTTTTTCATTGAAGTTAT

                      *                  
       1778 AAAAAATTAATTTTTTTCATTGAAGTTAT
          1 AAAAAATTAAATTTTTTCATTGAAGTTAT

              
       1807 AA
          1 AA

       1809 CCTCTATAGT


Statistics
Matches: 27,  Mismatches: 1, Indels: 3
        0.87            0.03        0.10

Matches are distributed among these distances:
  26   16  0.59
  27    3  0.11
  28    3  0.11
  29    5  0.19

ACGTcount: A:0.47, C:0.02, G:0.05, T:0.46


Consensus pattern (29 bp):   
AAAAAATTAAATTTTTTCATTGAAGTTAT

Found at i:2141 original size:20 final size:21

Alignment explanation


    Indices: 2116--2156  Score: 57
    Period size: 20  Copynumber: 2.0  Consensus size: 21

       2106 TGATATAAGA

                                 
       2116 GTATAGCATTTTCA-TAATCT
          1 GTATAGCATTTTCAGTAATCT

                  **             
       2136 GTATAGTTTTTTCAGTAATCT
          1 GTATAGCATTTTCAGTAATCT

       2157 TATGTAAGAA


Statistics
Matches: 18,  Mismatches: 2, Indels: 1
        0.86            0.10        0.05

Matches are distributed among these distances:
  20   12  0.67
  21    6  0.33

ACGTcount: A:0.27, C:0.12, G:0.12, T:0.49


Consensus pattern (21 bp):   
GTATAGCATTTTCAGTAATCT

Found at i:2624 original size:13 final size:13

Alignment explanation


    Indices: 2606--2635  Score: 60
    Period size: 13  Copynumber: 2.3  Consensus size: 13

       2596 TACTCAAATG

                         
       2606 TGATTACTTAATT
          1 TGATTACTTAATT

                         
       2619 TGATTACTTAATT
          1 TGATTACTTAATT

                
       2632 TGAT
          1 TGAT

       2636 ATTATGAAAG


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   17  1.00

ACGTcount: A:0.30, C:0.07, G:0.10, T:0.53


Consensus pattern (13 bp):   
TGATTACTTAATT
Done.