Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020766.1 Corchorus olitorius cultivar O-4 contig20799, 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: 32607
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.35


Found at i:10148 original size:1 final size:1

Alignment explanation


    Indices: 10142--10176  Score: 70
    Period size: 1  Copynumber: 35.0  Consensus size: 1

      10132 TCTCTAAATT

                                               
      10142 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

      10177 GAAAGGAGGG


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   34  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Found at i:27410 original size:16 final size:16

Alignment explanation


    Indices: 27391--27438  Score: 55
    Period size: 16  Copynumber: 3.1  Consensus size: 16

      27381 ACCTAGTATG

                            
      27391 TGTACAAAAATTACAT
          1 TGTACAAAAATTACAT

                          * *
      27407 TGTACTAAAAA--AAAG
          1 TGTAC-AAAAATTACAT

                            
      27422 TGTACAAAAATTACAT
          1 TGTACAAAAATTACAT

             
      27438 T
          1 T

      27439 ATCTCATTTT


Statistics
Matches: 25,  Mismatches: 4, Indels: 6
        0.71            0.11        0.17

Matches are distributed among these distances:
  14    5  0.20
  15    7  0.28
  16    8  0.32
  17    5  0.20

ACGTcount: A:0.52, C:0.10, G:0.08, T:0.29


Consensus pattern (16 bp):   
TGTACAAAAATTACAT

Found at i:28807 original size:21 final size:20

Alignment explanation


    Indices: 28781--28819  Score: 60
    Period size: 21  Copynumber: 1.9  Consensus size: 20

      28771 TCTTCTTCTT

                                 
      28781 TTTCTTCTCCTTTTCTCTTTC
          1 TTTCTTCTCCTTTT-TCTTTC

                    *         
      28802 TTTCTTCTTCTTTTTCTT
          1 TTTCTTCTCCTTTTTCTT

      28820 CTATTTTTAC


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  20    4  0.24
  21   13  0.76

ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72


Consensus pattern (20 bp):   
TTTCTTCTCCTTTTTCTTTC

Found at i:28827 original size:12 final size:11

Alignment explanation


    Indices: 28767--28827  Score: 61
    Period size: 12  Copynumber: 5.5  Consensus size: 11

      28757 TCTCAAGATG

                       
      28767 TTTTTCTTCTT
          1 TTTTTCTTCTT

                       *
      28778 CTTTTTCTTCTC
          1 -TTTTTCTTCTT

            *          
      28790 CTTTTC-TCTT
          1 TTTTTCTTCTT

             *         
      28800 TCTTTCTTCTT
          1 TTTTTCTTCTT

                       *
      28811 CTTTTTCTTCTA
          1 -TTTTTCTTCTT

                 
      28823 TTTTT
          1 TTTTT

      28828 ACTATAGAAA


Statistics
Matches: 40,  Mismatches: 7, Indels: 5
        0.77            0.13        0.10

Matches are distributed among these distances:
  10    7  0.17
  11   14  0.35
  12   19  0.47

ACGTcount: A:0.02, C:0.25, G:0.00, T:0.74


Consensus pattern (11 bp):   
TTTTTCTTCTT
Done.