Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006425.1 Corchorus capsularis cultivar CVL-1 contig06446, 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: 22844
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32


Found at i:2076 original size:16 final size:16

Alignment explanation


    Indices: 2055--2090  Score: 56
    Period size: 16  Copynumber: 2.2  Consensus size: 16

       2045 TGGTGTATGC

                             
       2055 ATGAATA-TTCGAATGA
          1 ATGAATACTT-GAATGA

                            
       2071 ATGAATACTTGAATGA
          1 ATGAATACTTGAATGA

                
       2087 ATGA
          1 ATGA

       2091 CCTAAAAAGG


Statistics
Matches: 19,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  16   17  0.89
  17    2  0.11

ACGTcount: A:0.44, C:0.06, G:0.19, T:0.31


Consensus pattern (16 bp):   
ATGAATACTTGAATGA

Found at i:8059 original size:15 final size:16

Alignment explanation


    Indices: 8031--8060  Score: 53
    Period size: 15  Copynumber: 1.9  Consensus size: 16

       8021 TACCTGACAT

                            
       8031 TCTCTTTCTGATTTGG
          1 TCTCTTTCTGATTTGG

                           
       8047 TCTCTTT-TGATTTG
          1 TCTCTTTCTGATTTG

       8061 CATTTGGCTT


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  15    7  0.50
  16    7  0.50

ACGTcount: A:0.07, C:0.17, G:0.17, T:0.60


Consensus pattern (16 bp):   
TCTCTTTCTGATTTGG

Found at i:8962 original size:25 final size:24

Alignment explanation


    Indices: 8906--8968  Score: 74
    Period size: 24  Copynumber: 2.5  Consensus size: 24

       8896 CAACAATACT

                                  *  
       8906 AAATTA-TAAAATGAAAATGCTGTG
          1 AAATTACT-AAATGAAAATGCTATG

                                    
       8930 AAATTACTAAATGAAAATGCTATG
          1 AAATTACTAAATGAAAATGCTATG

            *              
       8954 GAATATACTACAATG
          1 AAAT-TACTA-AATG

       8969 CTAAAAGTGC


Statistics
Matches: 34,  Mismatches: 2, Indels: 4
        0.85            0.05        0.10

Matches are distributed among these distances:
  24   24  0.71
  25    6  0.18
  26    4  0.12

ACGTcount: A:0.49, C:0.08, G:0.14, T:0.29


Consensus pattern (24 bp):   
AAATTACTAAATGAAAATGCTATG

Found at i:9107 original size:27 final size:27

Alignment explanation


    Indices: 9051--9124  Score: 121
    Period size: 27  Copynumber: 2.7  Consensus size: 27

       9041 AGTGGACTCA

                    *              *    
       9051 AAATGACCTAAATGCCCTCTGAATATGC
          1 AAATGACCAAAATGCCC-CTGAACATGC

                                       
       9079 AAATGACCAAAATGCCCCTGAACATGC
          1 AAATGACCAAAATGCCCCTGAACATGC

                               
       9106 AAATGACCAAAATGCCCCT
          1 AAATGACCAAAATGCCCCT

       9125 AGTGCCGAAA


Statistics
Matches: 44,  Mismatches: 2, Indels: 1
        0.94            0.04        0.02

Matches are distributed among these distances:
  27   28  0.64
  28   16  0.36

ACGTcount: A:0.39, C:0.28, G:0.14, T:0.19


Consensus pattern (27 bp):   
AAATGACCAAAATGCCCCTGAACATGC

Found at i:9136 original size:27 final size:27

Alignment explanation


    Indices: 9050--9144  Score: 93
    Period size: 27  Copynumber: 3.5  Consensus size: 27

       9040 AAGTGGACTC

                     *              * * 
       9050 AAAATGACCTAAATGCCCTCTGAATATG
          1 AAAATGACCAAAATGCCC-CTGAACACG

            *                        * 
       9078 CAAATGACCAAAATGCCCCTGAACATG
          1 AAAATGACCAAAATGCCCCTGAACACG

            *                     **    
       9105 CAAATGACCAAAATGCCCCTAGTGC-CG
          1 AAAATGACCAAAATGCCCCT-GAACACG

                         
       9132 AAAATGACCAAAA
          1 AAAATGACCAAAA

       9145 CAACCCTAAT


Statistics
Matches: 59,  Mismatches: 7, Indels: 3
        0.86            0.10        0.04

Matches are distributed among these distances:
  27   41  0.69
  28   18  0.31

ACGTcount: A:0.42, C:0.26, G:0.15, T:0.17


Consensus pattern (27 bp):   
AAAATGACCAAAATGCCCCTGAACACG

Found at i:14481 original size:16 final size:16

Alignment explanation


    Indices: 14446--14487  Score: 59
    Period size: 16  Copynumber: 2.7  Consensus size: 16

      14436 AATCTTCAAT

                           *
      14446 GACTCGAACC-AAAAT
          1 GACTCGAACCTAAAAC

            *               
      14461 TACTCGAACCTAAAAC
          1 GACTCGAACCTAAAAC

                       
      14477 GACTCGAACCT
          1 GACTCGAACCT

      14488 TATCAATCCG


Statistics
Matches: 23,  Mismatches: 3, Indels: 1
        0.85            0.11        0.04

Matches are distributed among these distances:
  15    9  0.39
  16   14  0.61

ACGTcount: A:0.40, C:0.31, G:0.12, T:0.17


Consensus pattern (16 bp):   
GACTCGAACCTAAAAC

Found at i:18428 original size:13 final size:14

Alignment explanation


    Indices: 18410--18438  Score: 51
    Period size: 13  Copynumber: 2.1  Consensus size: 14

      18400 TAAATATTTG

                          
      18410 TTTCCTTTTTA-TT
          1 TTTCCTTTTTACTT

                          
      18423 TTTCCTTTTTACTT
          1 TTTCCTTTTTACTT

              
      18437 TT
          1 TT

      18439 ATACTTGATC


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  13   11  0.73
  14    4  0.27

ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76


Consensus pattern (14 bp):   
TTTCCTTTTTACTT
Done.