Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006054.1 Corchorus capsularis cultivar CVL-1 contig06072, 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: 3413
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.32


Found at i:765 original size:1 final size:1

Alignment explanation


    Indices: 759--795  Score: 74
    Period size: 1  Copynumber: 37.0  Consensus size: 1

        749 AGCTACCTGC

                                                 
        759 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

        796 GCCTGATACA


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   36  1.00

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


Consensus pattern (1 bp):   
A

Found at i:1029 original size:2 final size:2

Alignment explanation


    Indices: 1022--1051  Score: 53
    Period size: 2  Copynumber: 15.5  Consensus size: 2

       1012 CCAAACACAT

                                                          
       1022 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       1052 TTAATATAAA


Statistics
Matches: 27,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   1    1  0.04
   2   26  0.96

ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53


Consensus pattern (2 bp):   
TA

Found at i:3215 original size:109 final size:109

Alignment explanation


    Indices: 3014--3304  Score: 458
    Period size: 109  Copynumber: 2.6  Consensus size: 109

       3004 TTATAGTTTC

                     *                     *                                 
       3014 ATTCTACTAGAAACTCTATTTTTATTCAATTAAATTAAATCTAATATCTTTATAATTACTTTATT
          1 ATTCTACTAAAAACTCTA---TT-TTC-ATTTAATTAAATCTAATATCTTTATAATTACTTTATT

                                                             
       3079 TTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAATTTT
         61 TTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAATTTT

                                                                             
       3128 ATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTTTTAC
          1 ATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTTTTAC

                             *                          
       3193 CAAAAAATTTGGATATATTAAAATTTTTTCTAATATACAATTTT
         66 CAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAATTTT

                                                       *          **         
       3237 ATTCTACTAAAAACTCTATTTTCATTTAATTAAAT-TCAATATTTTATATAATTTTTTTATTTTT
          1 ATTCTACTAAAAACTCTATTTTCATTTAATTAAATCT-AATATCTT-TATAATTACTTTATTTTT

                
       3301 ACCA
         64 ACCA

       3305 TTTTAATTTA


Statistics
Matches: 169,  Mismatches: 6, Indels: 8
        0.92            0.03        0.04

Matches are distributed among these distances:
 108    1  0.01
 109  126  0.75
 110   23  0.14
 111    2  0.01
 114   17  0.10

ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49


Consensus pattern (109 bp):   
ATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTTTTAC
CAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAATTTT
Done.