Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01004295.1 Corchorus olitorius cultivar O-4 contig04308, 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, 711

Length: 1185
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.42


Found at i:223 original size:15 final size:15

Alignment explanation


    Indices: 203--233  Score: 62
    Period size: 15  Copynumber: 2.1  Consensus size: 15

        193 AATTACAATG

                           
        203 ATCATAGTTAATGTT
          1 ATCATAGTTAATGTT

                           
        218 ATCATAGTTAATGTT
          1 ATCATAGTTAATGTT

             
        233 A
          1 A

        234 ATGTTAACTA


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.35, C:0.06, G:0.13, T:0.45


Consensus pattern (15 bp):   
ATCATAGTTAATGTT

Found at i:626 original size:18 final size:18

Alignment explanation


    Indices: 594--638  Score: 72
    Period size: 18  Copynumber: 2.4  Consensus size: 18

        584 AGTGTTTTAA

                      *        
        594 ATTTCTTAAATTTCTTTTC
          1 ATTTC-TAAACTTCTTTTC

                              
        613 ATTTCTAAACTTCTTTTC
          1 ATTTCTAAACTTCTTTTC

                    
        631 ATTTCTAA
          1 ATTTCTAA

        639 GTGTTTTAAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  18   20  0.80
  19    5  0.20

ACGTcount: A:0.24, C:0.18, G:0.00, T:0.58


Consensus pattern (18 bp):   
ATTTCTAAACTTCTTTTC

Found at i:648 original size:27 final size:27

Alignment explanation


    Indices: 575--654  Score: 74
    Period size: 27  Copynumber: 3.0  Consensus size: 27

        565 CTTATCCGTC

                                       
        575 TCATTTCTAAGTGTTTTAAATTTC-TT
          1 TCATTTCTAAGTGTTTTAAATTTCTTT

            **       **  *        *      
        601 AAATTTCT-TTTCATTTCTAAACTTCTTT
          1 TCATTTCTAAGT-GTTT-TAAATTTCTTT

                                      
        629 TCATTTCTAAGTGTTTTAAATTTCTT
          1 TCATTTCTAAGTGTTTTAAATTTCTT

        655 AAATTTATTT


Statistics
Matches: 38,  Mismatches: 12, Indels: 7
        0.67            0.21        0.12

Matches are distributed among these distances:
  25    1  0.03
  26    9  0.24
  27   16  0.42
  28   11  0.29
  29    1  0.03

ACGTcount: A:0.24, C:0.14, G:0.05, T:0.57


Consensus pattern (27 bp):   
TCATTTCTAAGTGTTTTAAATTTCTTT

Found at i:1053 original size:20 final size:21

Alignment explanation


    Indices: 1024--1063  Score: 64
    Period size: 20  Copynumber: 2.0  Consensus size: 21

       1014 GATAGAGCTC

                                 
       1024 TTTTTCTTTTGAATTTTTTTA
          1 TTTTTCTTTTGAATTTTTTTA

                      *         
       1045 TTTTT-TTTTTAATTTTTTT
          1 TTTTTCTTTTGAATTTTTTT

       1064 CATAATGGGT


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  20   13  0.72
  21    5  0.28

ACGTcount: A:0.12, C:0.03, G:0.03, T:0.82


Consensus pattern (21 bp):   
TTTTTCTTTTGAATTTTTTTA
Done.