Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020170.1 Corchorus olitorius cultivar O-4 contig20203, 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: 11539
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33


Found at i:3701 original size:33 final size:33

Alignment explanation


    Indices: 3659--3725  Score: 134
    Period size: 33  Copynumber: 2.0  Consensus size: 33

       3649 TTTCTGAGCT

                                             
       3659 ATTGTTCTCATGAGATTGGGACTTCTCCAAATC
          1 ATTGTTCTCATGAGATTGGGACTTCTCCAAATC

                                             
       3692 ATTGTTCTCATGAGATTGGGACTTCTCCAAATC
          1 ATTGTTCTCATGAGATTGGGACTTCTCCAAATC

             
       3725 A
          1 A

       3726 AATTTCATAG


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

Matches are distributed among these distances:
  33   34  1.00

ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36


Consensus pattern (33 bp):   
ATTGTTCTCATGAGATTGGGACTTCTCCAAATC

Found at i:8283 original size:5 final size:5

Alignment explanation


    Indices: 8267--8306  Score: 57
    Period size: 5  Copynumber: 8.4  Consensus size: 5

       8257 ACATACTTTT

                    *                                         
       8267 TAATA TAGTA TAATA TAATA T-A-A TAATA TAATA TAATA TA
          1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TA

       8307 GATTATATAT


Statistics
Matches: 31,  Mismatches: 2, Indels: 4
        0.84            0.05        0.11

Matches are distributed among these distances:
   3    2  0.06
   4    2  0.06
   5   27  0.87

ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40


Consensus pattern (5 bp):   
TAATA

Found at i:8294 original size:13 final size:13

Alignment explanation


    Indices: 8276--8304  Score: 58
    Period size: 13  Copynumber: 2.2  Consensus size: 13

       8266 TTAATATAGT

                         
       8276 ATAATATAATATA
          1 ATAATATAATATA

                         
       8289 ATAATATAATATA
          1 ATAATATAATATA

               
       8302 ATA
          1 ATA

       8305 TAGATTATAT


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

Matches are distributed among these distances:
  13   16  1.00

ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38


Consensus pattern (13 bp):   
ATAATATAATATA

Found at i:10462 original size:11 final size:11

Alignment explanation


    Indices: 10442--10479  Score: 53
    Period size: 10  Copynumber: 3.6  Consensus size: 11

      10432 AATCTTACTC

                       
      10442 TATA-ATAACA
          1 TATATATAACA

                       
      10452 TATATATAACA
          1 TATATATAACA

                     * 
      10463 TATATAT-ATA
          1 TATATATAACA

                   
      10473 TATATAT
          1 TATATAT

      10480 TATATCATAA


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

Matches are distributed among these distances:
  10   13  0.50
  11   13  0.50

ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42


Consensus pattern (11 bp):   
TATATATAACA
Done.