Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012593.1 Corchorus capsularis cultivar CVL-1 contig12614, 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: 6466
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.38


Found at i:374 original size:21 final size:21

Alignment explanation


    Indices: 348--387  Score: 71
    Period size: 21  Copynumber: 1.9  Consensus size: 21

        338 TTTTCGATTA

                     *           
        348 ATCTCCTCAGGTCTGTTCCTT
          1 ATCTCCTCACGTCTGTTCCTT

                               
        369 ATCTCCTCACGTCTGTTCC
          1 ATCTCCTCACGTCTGTTCC

        388 GTCGTTGCTT


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.10, C:0.38, G:0.12, T:0.40


Consensus pattern (21 bp):   
ATCTCCTCACGTCTGTTCCTT

Found at i:924 original size:35 final size:34

Alignment explanation


    Indices: 872--942  Score: 108
    Period size: 35  Copynumber: 2.1  Consensus size: 34

        862 TAATTCATAG

                                               
        872 GATAATTCAGAATTGCAT-TTTCATTTGTTTTGTA
          1 GATAATTCAGAATTGCATATTT-ATTTGTTTTGTA

                    *                          
        906 GATAATTCTGAAATTGCATATTTATTTGTTTTGTA
          1 GATAATTCAG-AATTGCATATTTATTTGTTTTGTA

              
        941 GA
          1 GA

        943 ATCTTTGGTT


Statistics
Matches: 34,  Mismatches: 1, Indels: 3
        0.89            0.03        0.08

Matches are distributed among these distances:
  34    9  0.26
  35   22  0.65
  36    3  0.09

ACGTcount: A:0.28, C:0.07, G:0.15, T:0.49


Consensus pattern (34 bp):   
GATAATTCAGAATTGCATATTTATTTGTTTTGTA

Found at i:1553 original size:24 final size:24

Alignment explanation


    Indices: 1509--1556  Score: 62
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       1499 GTGTTTTTTT

                      *             
       1509 TTTTTCTCATGATCTTATGATATA
          1 TTTTTCTCATAATCTTATGATATA

                             *       
       1533 TTTTTCTCATCAAT-TTCTGATATA
          1 TTTTTCTCAT-AATCTTATGATATA

       1557 AAAGTTCTGA


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  24   19  0.90
  25    2  0.10

ACGTcount: A:0.25, C:0.15, G:0.06, T:0.54


Consensus pattern (24 bp):   
TTTTTCTCATAATCTTATGATATA

Found at i:6422 original size:2 final size:2

Alignment explanation


    Indices: 6417--6466  Score: 100
    Period size: 2  Copynumber: 25.0  Consensus size: 2

       6407 AGAAATATGA

                                                                          
       6417 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG

                       
       6459 AG AG AG AG
          1 AG AG AG AG


Statistics
Matches: 48,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   48  1.00

ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00


Consensus pattern (2 bp):   
AG

Done.