Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012167.1 Corchorus capsularis cultivar CVL-1 contig12188, 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: 11601
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35


Found at i:3540 original size:11 final size:11

Alignment explanation


    Indices: 3524--3559  Score: 56
    Period size: 11  Copynumber: 3.3  Consensus size: 11

       3514 CCATTATACT

                       
       3524 ATATCTAATTA
          1 ATATCTAATTA

                       
       3535 ATATCTAATTA
          1 ATATCTAATTA

                        
       3546 ATAGT-TAATTA
          1 ATA-TCTAATTA

               
       3557 ATA
          1 ATA

       3560 ATGAATAAAT


Statistics
Matches: 24,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
  11   23  0.96
  12    1  0.04

ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44


Consensus pattern (11 bp):   
ATATCTAATTA

Found at i:7586 original size:32 final size:33

Alignment explanation


    Indices: 7519--7587  Score: 95
    Period size: 33  Copynumber: 2.1  Consensus size: 33

       7509 TTTGCTCAAC

                     *              **       
       7519 TTGTAAAGGTGTGATGAAGGCCCGTGAACTTCA
          1 TTGTAAAGGCGTGATGAAGGCCCGACAACTTCA

                  *                          
       7552 TTGTAACGGCGTGATGAAGGCCC-ACAACTTCA
          1 TTGTAAAGGCGTGATGAAGGCCCGACAACTTCA

                
       7584 TTGT
          1 TTGT

       7588 TTGTAAGAGC


Statistics
Matches: 32,  Mismatches: 4, Indels: 1
        0.86            0.11        0.03

Matches are distributed among these distances:
  32   11  0.34
  33   21  0.66

ACGTcount: A:0.26, C:0.19, G:0.28, T:0.28


Consensus pattern (33 bp):   
TTGTAAAGGCGTGATGAAGGCCCGACAACTTCA

Found at i:9772 original size:1 final size:1

Alignment explanation


    Indices: 9766--9802  Score: 74
    Period size: 1  Copynumber: 37.0  Consensus size: 1

       9756 AGAACCGAGC

                                                 
       9766 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

       9803 CCGGTTTTGG


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:0.00, C:0.00, G:0.00, T:1.00


Consensus pattern (1 bp):   
T

Found at i:10050 original size:34 final size:33

Alignment explanation


    Indices: 9996--10061  Score: 96
    Period size: 34  Copynumber: 2.0  Consensus size: 33

       9986 TCAAGGAAAA

                    *  *   *                  
       9996 TGAGAATTTTTTTTGTAGATAAGATGTTCTTTTT
          1 TGAGAATTATTATTGGAGATAAGATGTT-TTTTT

                                            
      10030 TGAGAATTATTATTGGAGATAAGATGTTTTTT
          1 TGAGAATTATTATTGGAGATAAGATGTTTTTT

      10062 AATGTATATA


Statistics
Matches: 29,  Mismatches: 3, Indels: 1
        0.88            0.09        0.03

Matches are distributed among these distances:
  33    4  0.14
  34   25  0.86

ACGTcount: A:0.27, C:0.02, G:0.20, T:0.52


Consensus pattern (33 bp):   
TGAGAATTATTATTGGAGATAAGATGTTTTTTT
Done.