Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01003130.1 Corchorus capsularis cultivar CVL-1 contig03138, 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, 929

Length: 1549
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33


Found at i:502 original size:21 final size:21

Alignment explanation


    Indices: 478--519  Score: 84
    Period size: 21  Copynumber: 2.0  Consensus size: 21

        468 TAAAAAAAAA

                                 
        478 GAAAAATAATGGTCTGCAAAG
          1 GAAAAATAATGGTCTGCAAAG

                                 
        499 GAAAAATAATGGTCTGCAAAG
          1 GAAAAATAATGGTCTGCAAAG

        520 TTATCTCAAT


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   21  1.00

ACGTcount: A:0.48, C:0.10, G:0.24, T:0.19


Consensus pattern (21 bp):   
GAAAAATAATGGTCTGCAAAG

Found at i:781 original size:37 final size:37

Alignment explanation


    Indices: 731--805  Score: 141
    Period size: 37  Copynumber: 2.0  Consensus size: 37

        721 AAAAATTGTC

                                                 
        731 TCCAATCATGTCAATAGTACAAAGTAGAATTATTGAT
          1 TCCAATCATGTCAATAGTACAAAGTAGAATTATTGAT

                  *                              
        768 TCCAATTATGTCAATAGTACAAAGTAGAATTATTGAT
          1 TCCAATCATGTCAATAGTACAAAGTAGAATTATTGAT

             
        805 T
          1 T

        806 GTATTGAAAT


Statistics
Matches: 37,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  37   37  1.00

ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35


Consensus pattern (37 bp):   
TCCAATCATGTCAATAGTACAAAGTAGAATTATTGAT

Found at i:1173 original size:17 final size:17

Alignment explanation


    Indices: 1151--1195  Score: 54
    Period size: 18  Copynumber: 2.6  Consensus size: 17

       1141 TTTTTTTTTG

                             
       1151 TTTGTTTTTTGAGTCAA
          1 TTTGTTTTTTGAGTCAA

                      *      *
       1168 TTTGTTTTATAGAGTCAG
          1 TTTGTTTT-TTGAGTCAA

               *      
       1186 TTTCTTTTTT
          1 TTTGTTTTTT

       1196 AATCCCAGTT


Statistics
Matches: 23,  Mismatches: 4, Indels: 2
        0.79            0.14        0.07

Matches are distributed among these distances:
  17    9  0.39
  18   14  0.61

ACGTcount: A:0.16, C:0.07, G:0.16, T:0.62


Consensus pattern (17 bp):   
TTTGTTTTTTGAGTCAA

Done.