Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013437.1 Corchorus capsularis cultivar CVL-1 contig13458, 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: 4152
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32


Found at i:985 original size:91 final size:91

Alignment explanation


    Indices: 830--1011  Score: 355
    Period size: 91  Copynumber: 2.0  Consensus size: 91

        820 CTATTTTGGA

                                                                             
        830 TGGAAATTTCAAGGTGTATGACACGCGCCGTTTTCATGGATGTTAAAACTTAAAAGGTTATACTT
          1 TGGAAATTTCAAGGTGTATGACACGCGCCGTTTTCATGGATGTTAAAACTTAAAAGGTTATACTT

                                      
        895 GACACGTGGAATTTATTTAACAGGTG
         66 GACACGTGGAATTTATTTAACAGGTG

                                                                       *     
        921 TGGAAATTTCAAGGTGTATGACACGCGCCGTTTTCATGGATGTTAAAACTTAAAAGGTTGTACTT
          1 TGGAAATTTCAAGGTGTATGACACGCGCCGTTTTCATGGATGTTAAAACTTAAAAGGTTATACTT

                                      
        986 GACACGTGGAATTTATTTAACAGGTG
         66 GACACGTGGAATTTATTTAACAGGTG

       1012 ACTCTCTTAA


Statistics
Matches: 90,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
  91   90  1.00

ACGTcount: A:0.30, C:0.13, G:0.24, T:0.33


Consensus pattern (91 bp):   
TGGAAATTTCAAGGTGTATGACACGCGCCGTTTTCATGGATGTTAAAACTTAAAAGGTTATACTT
GACACGTGGAATTTATTTAACAGGTG

Found at i:1421 original size:107 final size:105

Alignment explanation


    Indices: 1191--1452  Score: 384
    Period size: 107  Copynumber: 2.5  Consensus size: 105

       1181 AATTTTTCTA

                           * **                                              
       1191 ACCCTTAAAATAAAATTTTAATTTTAATTT-GGGCTAAACTTAGTG-AATTAGTTATATATTTTA
          1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTA

                 *     *                      *     
       1254 TTTCTGAAACCCTATAACAATACTATTAATTATGGAATTT
         66 TTTCTAAAACCATATAACAATACTATTAATTATGAAATTT

                *                                                  * *       
       1294 ACCCATAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTA
          1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTA

               *                    *        *        
       1359 TTTTTAAAACCATATAACAATAAATTATTAATTTTGAAATTT
         66 TTTCTAAAACCATATAACAAT--ACTATTAATTATGAAATTT

                                                                
       1401 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTA
          1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTA

       1453 AGGCTAAACT


Statistics
Matches: 142,  Mismatches: 13, Indels: 4
        0.89            0.08        0.03

Matches are distributed among these distances:
 103   26  0.18
 104   15  0.11
 105   34  0.24
 107   67  0.47

ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40


Consensus pattern (105 bp):   
ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTA
TTTCTAAAACCATATAACAATACTATTAATTATGAAATTT

Found at i:3776 original size:30 final size:31

Alignment explanation


    Indices: 3714--3789  Score: 95
    Period size: 30  Copynumber: 2.5  Consensus size: 31

       3704 AAATTTGCAA

                                             
       3714 ATTGACCCCACTTCAAA--GAAAATTTTAAGAT
          1 ATTGACCCCAC-T-AAATTGAAAATTTTAAGAT

                                 *     *   
       3745 ATTGACCCCA-TAAATTGAAAGTTTTAGGAT
          1 ATTGACCCCACTAAATTGAAAATTTTAAGAT

                           
       3775 ATTGACCCCACTAAA
          1 ATTGACCCCACTAAA

       3790 AGATTTGAGT


Statistics
Matches: 40,  Mismatches: 2, Indels: 6
        0.83            0.04        0.12

Matches are distributed among these distances:
  28    3  0.08
  29    1  0.03
  30   22  0.55
  31   14  0.35

ACGTcount: A:0.39, C:0.20, G:0.12, T:0.29


Consensus pattern (31 bp):   
ATTGACCCCACTAAATTGAAAATTTTAAGAT
Done.