Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014863.1 Corchorus capsularis cultivar CVL-1 contig14884, 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: 4344
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.35


Found at i:1550 original size:10 final size:10

Alignment explanation


    Indices: 1535--1559  Score: 50
    Period size: 10  Copynumber: 2.5  Consensus size: 10

       1525 GTTGCTGCAC

                      
       1535 AATTCCAGAA
          1 AATTCCAGAA

                      
       1545 AATTCCAGAA
          1 AATTCCAGAA

                 
       1555 AATTC
          1 AATTC

       1560 TAGAGTCCTC


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   15  1.00

ACGTcount: A:0.48, C:0.20, G:0.08, T:0.24


Consensus pattern (10 bp):   
AATTCCAGAA

Found at i:2147 original size:13 final size:12

Alignment explanation


    Indices: 2129--2162  Score: 50
    Period size: 12  Copynumber: 2.8  Consensus size: 12

       2119 AGTTTGATTG

                         
       2129 TTTGCTTTATTAA
          1 TTTGCTTTA-TAA

                        
       2142 TTTGCTTTATAA
          1 TTTGCTTTATAA

             *       
       2154 TCTGCTTTA
          1 TTTGCTTTA

       2163 GATTTAGATT


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

Matches are distributed among these distances:
  12   11  0.55
  13    9  0.45

ACGTcount: A:0.21, C:0.12, G:0.09, T:0.59


Consensus pattern (12 bp):   
TTTGCTTTATAA

Found at i:2529 original size:18 final size:17

Alignment explanation


    Indices: 2502--2537  Score: 54
    Period size: 18  Copynumber: 2.1  Consensus size: 17

       2492 TTTCTCTTTA

                             
       2502 TCTATTTTTCTTCCAGT
          1 TCTATTTTTCTTCCAGT

                          *   
       2519 TCTAGTTTTTCTTCTAGT
          1 TCTA-TTTTTCTTCCAGT

             
       2537 T
          1 T

       2538 TTAGGTTGAG


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  17    4  0.24
  18   13  0.76

ACGTcount: A:0.11, C:0.19, G:0.08, T:0.61


Consensus pattern (17 bp):   
TCTATTTTTCTTCCAGT

Found at i:3313 original size:24 final size:26

Alignment explanation


    Indices: 3266--3313  Score: 64
    Period size: 24  Copynumber: 1.9  Consensus size: 26

       3256 TTGCCATAGA

                               *      
       3266 TTTAGATTTAATATACTTTGCTTTTT
          1 TTTAGATTTAATATACTTTCCTTTTT

                          *         
       3292 TTTAG-TTTAAT-TGCTTTCCTTT
          1 TTTAGATTTAATATACTTTCCTTT

       3314 AATTGATAAT


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  24    9  0.45
  25    6  0.30
  26    5  0.25

ACGTcount: A:0.19, C:0.10, G:0.08, T:0.62


Consensus pattern (26 bp):   
TTTAGATTTAATATACTTTCCTTTTT
Done.