Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005822.1 Corchorus capsularis cultivar CVL-1 contig05840, 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: 19417
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31


Found at i:3656 original size:62 final size:62

Alignment explanation


    Indices: 3538--3658  Score: 181
    Period size: 62  Copynumber: 2.0  Consensus size: 62

       3528 AGTTTTAGTA

                                 *                 *         ***          
       3538 AACTAAAAACTCTATTTTTATTTAATTAAATATAATATCTTTATAACTATTTTATTTTACTC
          1 AACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAACTAAAATATTTTACTC

                                                                        
       3600 AACTAAAAACTCTATTTTTATATAATTAAA-ACTAATATCCTTATAACTAAAATATTTTA
          1 AACTAAAAACTCTATTTTTATATAATTAAATA-TAATATCCTTATAACTAAAATATTTTA

       3659 ACCATTTTAC


Statistics
Matches: 53,  Mismatches: 5, Indels: 2
        0.88            0.08        0.03

Matches are distributed among these distances:
  61    1  0.02
  62   52  0.98

ACGTcount: A:0.43, C:0.12, G:0.00, T:0.45


Consensus pattern (62 bp):   
AACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAACTAAAATATTTTACTC

Found at i:3684 original size:79 final size:78

Alignment explanation


    Indices: 3590--3753  Score: 292
    Period size: 79  Copynumber: 2.1  Consensus size: 78

       3580 ATAACTATTT

                                                                             
       3590 TATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAAACTAATATCCTTATAACTAAAATAT
          1 TATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAAACTAATATCCTTATAACTAAAATAT

                          
       3655 TTTAACCATTTTAC
         66 TTT-ACCATTTTAC

                                                    *                  **    
       3669 TATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTATTATAT
          1 TATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAAACTAATATCCTTATAACTAAAATAT

                         
       3734 TTTACCATTTTAC
         66 TTTACCATTTTAC

                   
       3747 TATTTTA
          1 TATTTTA

       3754 ATTAAAAAAC


Statistics
Matches: 82,  Mismatches: 3, Indels: 1
        0.95            0.03        0.01

Matches are distributed among these distances:
  78   17  0.21
  79   65  0.79

ACGTcount: A:0.39, C:0.15, G:0.00, T:0.46


Consensus pattern (78 bp):   
TATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAAACTAATATCCTTATAACTAAAATAT
TTTACCATTTTAC

Found at i:10423 original size:2 final size:2

Alignment explanation


    Indices: 10416--10444  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

      10406 TCTGGCCACA

                                                       
      10416 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

      10445 AAATAAAATA


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


Consensus pattern (2 bp):   
AT

Found at i:11812 original size:18 final size:18

Alignment explanation


    Indices: 11789--11824  Score: 72
    Period size: 18  Copynumber: 2.0  Consensus size: 18

      11779 GTACCCGTGT

                              
      11789 TCACTGAAGATTTAAAGC
          1 TCACTGAAGATTTAAAGC

                              
      11807 TCACTGAAGATTTAAAGC
          1 TCACTGAAGATTTAAAGC

      11825 CTTCGTTTGA


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.39, C:0.17, G:0.17, T:0.28


Consensus pattern (18 bp):   
TCACTGAAGATTTAAAGC
Done.