Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016751.1 Corchorus olitorius cultivar O-4 contig16784, 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: 20461
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31


Found at i:714 original size:49 final size:48

Alignment explanation


    Indices: 642--778  Score: 161
    Period size: 49  Copynumber: 2.8  Consensus size: 48

        632 AATCCTTTAC

                  *                      *                  
        642 TTTTCACTGCACTTTTTCTCAATTTTTATTACAAAATTGAACTTGT-A
          1 TTTTCATTGCACTTTTTCTCAATTTTTATGACAAAATTGAACTTGTAA

                *                          *           *   *   
        689 TTTTTACTTGCATCTTTTTCTCAATTTTTAAAGACAAAATTGATCTTTTAA
          1 TTTTCA-TTGCA-CTTTTTCTCAATTTTT-ATGACAAAATTGAACTTGTAA

                   *         *                      
        740 TTTTCATCGCACTTTTTATCAATTTTT-TGACAAAATTGA
          1 TTTTCATTGCACTTTTTCTCAATTTTTATGACAAAATTGA

        779 TTGGCACGCT


Statistics
Matches: 76,  Mismatches: 10, Indels: 8
        0.81            0.11        0.09

Matches are distributed among these distances:
  47   16  0.21
  48    4  0.05
  49   31  0.41
  50   19  0.25
  51    6  0.08

ACGTcount: A:0.28, C:0.15, G:0.07, T:0.50


Consensus pattern (48 bp):   
TTTTCATTGCACTTTTTCTCAATTTTTATGACAAAATTGAACTTGTAA

Found at i:1726 original size:47 final size:45

Alignment explanation


    Indices: 1672--1815  Score: 164
    Period size: 49  Copynumber: 3.0  Consensus size: 45

       1662 GAGCGTGCTA

                        *         *                        
       1672 ATCAATTTTGTCCAAAAATTGATAAAAAGTGCAATGAAAATTAAAAG
          1 ATCAATTTTGTCTAAAAATTGAGAAAAAGTGC-A-GAAAATTAAAAG

                                                              
       1719 ATCAATTTTGTCTTAAAAATTGAGAAAAAGGGTGCGAGAAAAATT-AAAG
          1 ATCAATTTTGTC-TAAAAATTGAGAAAAA--GTGC-AG-AAAATTAAAAG

                        *      *                   *      
       1768 ATCAATTTTGTAGTAAAAACTGAGAAAAAGTGCAGAAAAGTAAAAG
          1 ATCAATTTTGT-CTAAAAATTGAGAAAAAGTGCAGAAAATTAAAAG

              
       1814 AT
          1 AT

       1816 TGCTTTGAGT


Statistics
Matches: 85,  Mismatches: 6, Indels: 13
        0.82            0.06        0.12

Matches are distributed among these distances:
  45    5  0.06
  46    8  0.09
  47   16  0.19
  48   14  0.16
  49   31  0.36
  50   11  0.13

ACGTcount: A:0.50, C:0.07, G:0.17, T:0.26


Consensus pattern (45 bp):   
ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAGAAAATTAAAAG

Found at i:3107 original size:9 final size:9

Alignment explanation


    Indices: 3077--3115  Score: 53
    Period size: 9  Copynumber: 4.4  Consensus size: 9

       3067 ATAAACACAT

                    *
       3077 ATAATTTCT
          1 ATAATTTCC

            *        
       3086 TTAATTTCC
          1 ATAATTTCC

                     
       3095 -TAATTTCC
          1 ATAATTTCC

                     
       3103 ATAATTTCC
          1 ATAATTTCC

                
       3112 ATAA
          1 ATAA

       3116 GTAAATTGGG


Statistics
Matches: 27,  Mismatches: 2, Indels: 2
        0.87            0.06        0.06

Matches are distributed among these distances:
   8    8  0.30
   9   19  0.70

ACGTcount: A:0.33, C:0.18, G:0.00, T:0.49


Consensus pattern (9 bp):   
ATAATTTCC

Found at i:8599 original size:20 final size:20

Alignment explanation


    Indices: 8558--8600  Score: 59
    Period size: 20  Copynumber: 2.1  Consensus size: 20

       8548 CTCTCACAAG

                        *    *  
       8558 TTTCTAGCCGTTGGAGCTCT
          1 TTTCTAGCCGTTAGAGCACT

                         *      
       8578 TTTCTAGCCGTTATAGCACT
          1 TTTCTAGCCGTTAGAGCACT

               
       8598 TTT
          1 TTT

       8601 TCCACTTTTT


Statistics
Matches: 20,  Mismatches: 3, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  20   20  1.00

ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44


Consensus pattern (20 bp):   
TTTCTAGCCGTTAGAGCACT

Found at i:19579 original size:2 final size:2

Alignment explanation


    Indices: 19572--19606  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

      19562 GAGAATTTTA

                                                                
      19572 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

      19607 CTAGTTAAAG


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Done.