Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023663.1 Corchorus olitorius cultivar O-4 contig23696, 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: 4458
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37


Found at i:504 original size:11 final size:11

Alignment explanation


    Indices: 490--531  Score: 66
    Period size: 12  Copynumber: 3.6  Consensus size: 11

        480 TATTATTTAT

                       
        490 TTTTTTTATTA
          1 TTTTTTTATTA

                       
        501 TTTTTTTATTA
          1 TTTTTTTATTA

                         
        512 TTTTTTTTATTTA
          1 -TTTTTTTA-TTA

                   
        525 TTTTTTT
          1 TTTTTTT

        532 TACACTGGGC


Statistics
Matches: 29,  Mismatches: 0, Indels: 3
        0.91            0.00        0.09

Matches are distributed among these distances:
  11   11  0.38
  12   15  0.52
  13    3  0.10

ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86


Consensus pattern (11 bp):   
TTTTTTTATTA

Found at i:512 original size:23 final size:24

Alignment explanation


    Indices: 486--531  Score: 85
    Period size: 23  Copynumber: 2.0  Consensus size: 24

        476 CATTTATTAT

                                    
        486 TTATTTTTTTTA-TTATTTTTTTA
          1 TTATTTTTTTTATTTATTTTTTTA

                                   
        509 TTATTTTTTTTATTTATTTTTTT
          1 TTATTTTTTTTATTTATTTTTTT

        532 TACACTGGGC


Statistics
Matches: 22,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  23   12  0.55
  24   10  0.45

ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85


Consensus pattern (24 bp):   
TTATTTTTTTTATTTATTTTTTTA

Found at i:519 original size:27 final size:26

Alignment explanation


    Indices: 478--532  Score: 83
    Period size: 27  Copynumber: 2.1  Consensus size: 26

        468 TCTTGGCCCA

                           *           
        478 TTTATTATTTATTTTTTTTATTATTTT
          1 TTTATTATTTATTTTATTTATT-TTTT

                      *               
        505 TTTATTATTTTTTTTATTTATTTTTT
          1 TTTATTATTTATTTTATTTATTTTTT

              
        531 TT
          1 TT

        533 ACACTGGGCC


Statistics
Matches: 26,  Mismatches: 2, Indels: 1
        0.90            0.07        0.03

Matches are distributed among these distances:
  26    6  0.23
  27   20  0.77

ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84


Consensus pattern (26 bp):   
TTTATTATTTATTTTATTTATTTTTT

Found at i:533 original size:13 final size:12

Alignment explanation


    Indices: 486--533  Score: 80
    Period size: 13  Copynumber: 4.0  Consensus size: 12

        476 CATTTATTAT

                        
        486 TTATTTTTTTTA
          1 TTATTTTTTTTA

                        
        498 TTA-TTTTTTTA
          1 TTATTTTTTTTA

                        
        509 TTATTTTTTTTA
          1 TTATTTTTTTTA

                         
        521 TTTATTTTTTTTA
          1 -TTATTTTTTTTA

        534 CACTGGGCCT


Statistics
Matches: 34,  Mismatches: 0, Indels: 3
        0.92            0.00        0.08

Matches are distributed among these distances:
  11   11  0.32
  12   11  0.32
  13   12  0.35

ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83


Consensus pattern (12 bp):   
TTATTTTTTTTA

Found at i:1736 original size:58 final size:58

Alignment explanation


    Indices: 1633--1742  Score: 150
    Period size: 58  Copynumber: 1.9  Consensus size: 58

       1623 ATTAATCAAA

                                       *                              
       1633 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAGGACGTTTTAGGACCAAAGCT
          1 TATCAAGTGACATGTTCTTTATTAGATACATAAAAAAGGACGTTTTAGGACCAAAGCT

                *            *      *     *          *           
       1691 TATCGAGTGACATGTTTTTTTATTGGATACCTAAAAAA-GATGTTTTAGGACC
          1 TATCAAGTGACATG-TTCTTTATTAGATACATAAAAAAGGACGTTTTAGGACC

       1743 GAGGCATGAT


Statistics
Matches: 45,  Mismatches: 6, Indels: 2
        0.85            0.11        0.04

Matches are distributed among these distances:
  58   26  0.58
  59   19  0.42

ACGTcount: A:0.34, C:0.13, G:0.19, T:0.35


Consensus pattern (58 bp):   
TATCAAGTGACATGTTCTTTATTAGATACATAAAAAAGGACGTTTTAGGACCAAAGCT

Found at i:3065 original size:36 final size:36

Alignment explanation


    Indices: 3018--3087  Score: 104
    Period size: 36  Copynumber: 1.9  Consensus size: 36

       3008 TTCAATAACC

                         *     **               
       3018 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
          1 TTACATCTTTTGTAATTTTAATTATCATATTTCTTA

                  *                           
       3054 TTACATTTTTTGTAATTTTAATTATCATATTTCT
          1 TTACATCTTTTGTAATTTTAATTATCATATTTCT

       3088 CCAAAATCTC


Statistics
Matches: 30,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  36   30  1.00

ACGTcount: A:0.23, C:0.10, G:0.07, T:0.60


Consensus pattern (36 bp):   
TTACATCTTTTGTAATTTTAATTATCATATTTCTTA

Found at i:3975 original size:39 final size:40

Alignment explanation


    Indices: 3921--4001  Score: 137
    Period size: 39  Copynumber: 2.0  Consensus size: 40

       3911 ATACCTAATA

                                             *      
       3921 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
          1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC

                                 *                  
       3960 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
          1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC

              
       4000 AT
          1 AT

       4002 AGGAATTAAA


Statistics
Matches: 39,  Mismatches: 2, Indels: 1
        0.93            0.05        0.02

Matches are distributed among these distances:
  39   31  0.79
  40    8  0.21

ACGTcount: A:0.37, C:0.04, G:0.09, T:0.51


Consensus pattern (40 bp):   
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
Done.