Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023134.1 Corchorus olitorius cultivar O-4 contig23167, 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: 7599
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36


Found at i:2439 original size:22 final size:23

Alignment explanation


    Indices: 2377--2439  Score: 94
    Period size: 22  Copynumber: 2.8  Consensus size: 23

       2367 TTGTTAGTGT

                                   
       2377 GATTATTAAAATTTTAT-ATGGA
          1 GATTATTAAAATTTTATAATGGA

                  *              * 
       2399 GATTATCAAAATTTTATAATGTA
          1 GATTATTAAAATTTTATAATGGA

                               
       2422 G-TTATTAAAATTTTATAA
          1 GATTATTAAAATTTTATAA

       2440 AAAATATTTA


Statistics
Matches: 37,  Mismatches: 3, Indels: 2
        0.88            0.07        0.05

Matches are distributed among these distances:
  22   32  0.86
  23    5  0.14

ACGTcount: A:0.43, C:0.02, G:0.10, T:0.46


Consensus pattern (23 bp):   
GATTATTAAAATTTTATAATGGA

Found at i:3016 original size:20 final size:22

Alignment explanation


    Indices: 2985--3024  Score: 66
    Period size: 20  Copynumber: 1.9  Consensus size: 22

       2975 TGTAAAAATA

                                  
       2985 TTTATAAAAAAATCA-CTTTTT
          1 TTTATAAAAAAATCATCTTTTT

                                
       3006 TTTAT-AAAAAATCATCTTT
          1 TTTATAAAAAAATCATCTTT

       3025 AGTCACTCTT


Statistics
Matches: 18,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  20    9  0.50
  21    9  0.50

ACGTcount: A:0.42, C:0.10, G:0.00, T:0.47


Consensus pattern (22 bp):   
TTTATAAAAAAATCATCTTTTT

Found at i:6495 original size:31 final size:31

Alignment explanation


    Indices: 6455--6516  Score: 97
    Period size: 31  Copynumber: 2.0  Consensus size: 31

       6445 CTATTAATCT

                          *                
       6455 ATAAGCTATTCATGTTGAAATGAAACTGTGC
          1 ATAAGCTATTCATGATGAAATGAAACTGTGC

                *                   *      
       6486 ATAATCTATTCATGATGAAATGAAGCTGTGC
          1 ATAAGCTATTCATGATGAAATGAAACTGTGC

       6517 TGTTGAGGAG


Statistics
Matches: 28,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  31   28  1.00

ACGTcount: A:0.35, C:0.13, G:0.19, T:0.32


Consensus pattern (31 bp):   
ATAAGCTATTCATGATGAAATGAAACTGTGC
Done.