Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021044.1 Corchorus olitorius cultivar O-4 contig21077, 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: 30053
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33


Found at i:532 original size:15 final size:15

Alignment explanation


    Indices: 512--546  Score: 70
    Period size: 15  Copynumber: 2.3  Consensus size: 15

        502 CCTCCCTAAA

                           
        512 GACATGTTGTACTTT
          1 GACATGTTGTACTTT

                           
        527 GACATGTTGTACTTT
          1 GACATGTTGTACTTT

                 
        542 GACAT
          1 GACAT

        547 CTTCAAAGAG


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   20  1.00

ACGTcount: A:0.23, C:0.14, G:0.20, T:0.43


Consensus pattern (15 bp):   
GACATGTTGTACTTT

Found at i:3486 original size:51 final size:50

Alignment explanation


    Indices: 3393--3488  Score: 158
    Period size: 51  Copynumber: 1.9  Consensus size: 50

       3383 TAATAGTTTT

                                                 *            
       3393 GTTGCTTAATTAGGGTTTAGGATTACATATATTACCTCTTATGCTCAAAA
          1 GTTGCTTAATTAGGGTTTAGGATTACATATATTACCTATTATGCTCAAAA

                                                           
       3443 GTTGCTTAATTTAGGGTTTAGGATTACATATATTGA-CTATTATGCT
          1 GTTGCTTAA-TTAGGGTTTAGGATTACATATATT-ACCTATTATGCT

       3489 TTCAATTTAC


Statistics
Matches: 43,  Mismatches: 1, Indels: 3
        0.91            0.02        0.06

Matches are distributed among these distances:
  50    9  0.21
  51   33  0.77
  52    1  0.02

ACGTcount: A:0.28, C:0.11, G:0.18, T:0.43


Consensus pattern (50 bp):   
GTTGCTTAATTAGGGTTTAGGATTACATATATTACCTATTATGCTCAAAA

Found at i:5775 original size:5 final size:5

Alignment explanation


    Indices: 5765--5793  Score: 58
    Period size: 5  Copynumber: 5.8  Consensus size: 5

       5755 TCTATGTCGG

                                              
       5765 CCCTC CCCTC CCCTC CCCTC CCCTC CCCT
          1 CCCTC CCCTC CCCTC CCCTC CCCTC CCCT

       5794 TTTTTCTCAT


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

Matches are distributed among these distances:
   5   24  1.00

ACGTcount: A:0.00, C:0.79, G:0.00, T:0.21


Consensus pattern (5 bp):   
CCCTC

Found at i:7206 original size:2 final size:2

Alignment explanation


    Indices: 7199--7224  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

       7189 TACTGCTTAG

                                                  
       7199 TC TC TC TC TC TC TC TC TC TC TC TC TC
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC

       7225 CACTTCCTAA


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:0.00, C:0.50, G:0.00, T:0.50


Consensus pattern (2 bp):   
TC

Found at i:7399 original size:15 final size:15

Alignment explanation


    Indices: 7368--7410  Score: 52
    Period size: 15  Copynumber: 2.8  Consensus size: 15

       7358 AAAACCAGAA

                        *  
       7368 TCTCTTTCTCTTCTT
          1 TCTCTTTCTCTTATT

                            
       7383 TCTCATTTCTC-TATT
          1 TCTC-TTTCTCTTATT

                         
       7398 TCTCTCTTCTCTT
          1 TCTCT-TTCTCTT

       7411 TGAGCCTTAA


Statistics
Matches: 24,  Mismatches: 1, Indels: 5
        0.80            0.03        0.17

Matches are distributed among these distances:
  14    1  0.04
  15   16  0.67
  16    7  0.29

ACGTcount: A:0.05, C:0.33, G:0.00, T:0.63


Consensus pattern (15 bp):   
TCTCTTTCTCTTATT

Found at i:26549 original size:21 final size:21

Alignment explanation


    Indices: 26523--26562  Score: 80
    Period size: 21  Copynumber: 1.9  Consensus size: 21

      26513 CATTTATTTT

                                 
      26523 CCTTTTCGGACCTGATCATGA
          1 CCTTTTCGGACCTGATCATGA

                               
      26544 CCTTTTCGGACCTGATCAT
          1 CCTTTTCGGACCTGATCAT

      26563 TTTCATTATT


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   19  1.00

ACGTcount: A:0.17, C:0.30, G:0.17, T:0.35


Consensus pattern (21 bp):   
CCTTTTCGGACCTGATCATGA
Done.