Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001830.1 Corchorus capsularis cultivar CVL-1 contig01831, 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: 2757
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.37


Found at i:993 original size:26 final size:26

Alignment explanation


    Indices: 958--1023  Score: 107
    Period size: 26  Copynumber: 2.6  Consensus size: 26

        948 ATTAATTTCT

                                      
        958 TGAA-GCACCTTGTTAACTCAACTGA
          1 TGAATGCACCTTGTTAACTCAACTGA

                                  *   
        983 TGAATGCACCTTGTTAACTCAATTGA
          1 TGAATGCACCTTGTTAACTCAACTGA

                      *    
       1009 TGAATGCACCGTGTT
          1 TGAATGCACCTTGTT

       1024 TGGACTGTGA


Statistics
Matches: 38,  Mismatches: 2, Indels: 1
        0.93            0.05        0.02

Matches are distributed among these distances:
  25    4  0.11
  26   34  0.89

ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32


Consensus pattern (26 bp):   
TGAATGCACCTTGTTAACTCAACTGA

Found at i:1323 original size:28 final size:29

Alignment explanation


    Indices: 1292--1350  Score: 77
    Period size: 29  Copynumber: 2.1  Consensus size: 29

       1282 AAACTTTATA

                                          
       1292 TTTTGAT-ACTTAAAAAT-AAAATTTATGG
          1 TTTTGATCACTTAAAAATAAAAATTT-TGG

                     *      *            
       1320 TTTTGATCATTTAAAATTAAAAATTTTGG
          1 TTTTGATCACTTAAAAATAAAAATTTTGG

              
       1349 TT
          1 TT

       1351 ACTCAAACCT


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

Matches are distributed among these distances:
  28    7  0.26
  29   13  0.48
  30    7  0.26

ACGTcount: A:0.39, C:0.03, G:0.10, T:0.47


Consensus pattern (29 bp):   
TTTTGATCACTTAAAAATAAAAATTTTGG

Found at i:1579 original size:20 final size:21

Alignment explanation


    Indices: 1531--1584  Score: 65
    Period size: 20  Copynumber: 2.6  Consensus size: 21

       1521 GAAGAAGATT

                                  
       1531 AATTCGTTATTTTTTAAAAAGA
          1 AATTCGTT-TTTTTTAAAAAGA

              *            **    
       1553 AAATCGTTTTTTTTAGGAA-A
          1 AATTCGTTTTTTTTAAAAAGA

                        
       1573 AATTCGTTTTTT
          1 AATTCGTTTTTT

       1585 GTTTTTTGGT


Statistics
Matches: 28,  Mismatches: 4, Indels: 2
        0.82            0.12        0.06

Matches are distributed among these distances:
  20   12  0.43
  21    9  0.32
  22    7  0.25

ACGTcount: A:0.33, C:0.06, G:0.11, T:0.50


Consensus pattern (21 bp):   
AATTCGTTTTTTTTAAAAAGA
Done.