Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001898.1 Corchorus capsularis cultivar CVL-1 contig01900, 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: 2787
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--29  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

                                                       
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T

         30 ATATATATAT


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52


Consensus pattern (2 bp):   
TC

Found at i:34 original size:2 final size:2

Alignment explanation


    Indices: 29--54  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

         19 TCTCTCTCTC

                                                  
         29 TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA

         55 ATGTAGCCAG


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:1017 original size:3 final size:3

Alignment explanation


    Indices: 1009--1061  Score: 106
    Period size: 3  Copynumber: 17.7  Consensus size: 3

        999 AAAAATATTA

                                                                           
       1009 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
          1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT

                  
       1057 AAT AA
          1 AAT AA

       1062 AAAAATTAAA


Statistics
Matches: 50,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   50  1.00

ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32


Consensus pattern (3 bp):   
AAT

Found at i:1776 original size:13 final size:13

Alignment explanation


    Indices: 1758--1782  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       1748 AAATAAATAA

                         
       1758 ATAAATAAAAATT
          1 ATAAATAAAAATT

                        
       1771 ATAAATAAAAAT
          1 ATAAATAAAAAT

       1783 ATTTATGAGA


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

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


Consensus pattern (13 bp):   
ATAAATAAAAATT

Found at i:2448 original size:21 final size:21

Alignment explanation


    Indices: 2424--2467  Score: 54
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       2414 TCAAACTGGA

                                  
       2424 TTGCTAAATAT-CGTCCCATTT
          1 TTGCT-AATATCCGTCCCATTT

                  * *            
       2445 TTGCTATTCTCCGTCCCATTT
          1 TTGCTAATATCCGTCCCATTT

              
       2466 TT
          1 TT

       2468 TACGTTTTTT


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  20    3  0.15
  21   17  0.85

ACGTcount: A:0.16, C:0.27, G:0.09, T:0.48


Consensus pattern (21 bp):   
TTGCTAATATCCGTCCCATTT
Done.