Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013190.1 Corchorus capsularis cultivar CVL-1 contig13211, 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: 9055
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.32


Found at i:6916 original size:39 final size:38

Alignment explanation


    Indices: 6862--6939  Score: 111
    Period size: 39  Copynumber: 2.0  Consensus size: 38

       6852 CTGATACCAA

                                       **          
       6862 TTGATACGAATCTAGTTGTATATCGGTGTAAATCCACCT
          1 TTGATACGAATCTAGTTGTA-ATCGGTCCAAATCCACCT

                  *               *               
       6901 TTGATATGAATCTAGTTGTAATTGGTCCAAATCCACCT
          1 TTGATACGAATCTAGTTGTAATCGGTCCAAATCCACCT

             
       6939 T
          1 T

       6940 AGAGACTCGC


Statistics
Matches: 35,  Mismatches: 4, Indels: 1
        0.88            0.10        0.03

Matches are distributed among these distances:
  38   16  0.46
  39   19  0.54

ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37


Consensus pattern (38 bp):   
TTGATACGAATCTAGTTGTAATCGGTCCAAATCCACCT

Found at i:7547 original size:9 final size:9

Alignment explanation


    Indices: 7514--7547  Score: 50
    Period size: 9  Copynumber: 3.8  Consensus size: 9

       7504 AGTTATATTG

                 *   
       7514 AAAAATATA
          1 AAAAAAATA

                    *
       7523 AAAAAAATC
          1 AAAAAAATA

                     
       7532 AAAAAAATA
          1 AAAAAAATA

                   
       7541 AAAAAAA
          1 AAAAAAA

       7548 ATTCGACAAG


Statistics
Matches: 22,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
   9   22  1.00

ACGTcount: A:0.85, C:0.03, G:0.00, T:0.12


Consensus pattern (9 bp):   
AAAAAAATA

Found at i:9034 original size:32 final size:32

Alignment explanation


    Indices: 8993--9055  Score: 83
    Period size: 32  Copynumber: 2.0  Consensus size: 32

       8983 TCCTGATTTG

                            *                
       8993 AGTGTTGTTGCAATGACACTAAATTCTGTTTTA
          1 AGTGTTGTTGCAATGAAACTAAATT-TGTTTTA

                      **                   
       9026 AGTG-TGTTGTGATGAAACTAAATTTGTTTT
          1 AGTGTTGTTGCAATGAAACTAAATTTGTTTT


Statistics
Matches: 27,  Mismatches: 3, Indels: 2
        0.84            0.09        0.06

Matches are distributed among these distances:
  31    6  0.22
  32   17  0.63
  33    4  0.15

ACGTcount: A:0.27, C:0.08, G:0.21, T:0.44


Consensus pattern (32 bp):   
AGTGTTGTTGCAATGAAACTAAATTTGTTTTA
Done.