Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012160.1 Corchorus capsularis cultivar CVL-1 contig12181, 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: 8149
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35


Found at i:2520 original size:13 final size:14

Alignment explanation


    Indices: 2501--2537  Score: 67
    Period size: 13  Copynumber: 2.7  Consensus size: 14

       2491 TGTCCTTATT

                          
       2501 GTTTTTTTTAAGCC
          1 GTTTTTTTTAAGCC

                          
       2515 -TTTTTTTTAAGCC
          1 GTTTTTTTTAAGCC

                      
       2528 GTTTTTTTTA
          1 GTTTTTTTTA

       2538 TTATACCATG


Statistics
Matches: 22,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
  13   13  0.59
  14    9  0.41

ACGTcount: A:0.14, C:0.11, G:0.11, T:0.65


Consensus pattern (14 bp):   
GTTTTTTTTAAGCC

Found at i:3551 original size:25 final size:25

Alignment explanation


    Indices: 3517--3567  Score: 102
    Period size: 25  Copynumber: 2.0  Consensus size: 25

       3507 GAATTAATTT

                                     
       3517 CAGTATCCCCAAAGTGATATACTTC
          1 CAGTATCCCCAAAGTGATATACTTC

                                     
       3542 CAGTATCCCCAAAGTGATATACTTC
          1 CAGTATCCCCAAAGTGATATACTTC

             
       3567 C
          1 C

       3568 TACAAAATGA


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  25   26  1.00

ACGTcount: A:0.31, C:0.29, G:0.12, T:0.27


Consensus pattern (25 bp):   
CAGTATCCCCAAAGTGATATACTTC

Found at i:7255 original size:6 final size:6

Alignment explanation


    Indices: 7237--7267  Score: 53
    Period size: 6  Copynumber: 5.0  Consensus size: 6

       7227 ATTAATTTGC

                                               
       7237 TTTAGA TTTTAGA TTTAGA TTTAGA TTTAGA
          1 TTTAGA -TTTAGA TTTAGA TTTAGA TTTAGA

       7268 ATTGCTTTGC


Statistics
Matches: 24,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
   6   18  0.75
   7    6  0.25

ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52


Consensus pattern (6 bp):   
TTTAGA

Found at i:7539 original size:32 final size:32

Alignment explanation


    Indices: 7503--7563  Score: 104
    Period size: 32  Copynumber: 1.9  Consensus size: 32

       7493 GAAACTGGTA

                    *                       
       7503 ATCAACTTGATTCAGTGTAATTAAGTAAAGTG
          1 ATCAACTTAATTCAGTGTAATTAAGTAAAGTG

                              *          
       7535 ATCAACTTAATTCAGTGTTATTAAGTAAA
          1 ATCAACTTAATTCAGTGTAATTAAGTAAA

       7564 TTCAGTGATT


Statistics
Matches: 27,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  32   27  1.00

ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36


Consensus pattern (32 bp):   
ATCAACTTAATTCAGTGTAATTAAGTAAAGTG
Done.