Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013282.1 Corchorus olitorius cultivar O-4 contig13315, 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: 21585
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34


Found at i:6455 original size:26 final size:26

Alignment explanation


    Indices: 6408--6459  Score: 68
    Period size: 26  Copynumber: 2.0  Consensus size: 26

       6398 TTTTTCTTTT

                          *           
       6408 ATTTTTGCGTTTTTGAAAAAAAAAAG
          1 ATTTTTGCGTTTTTAAAAAAAAAAAG

                  *      *            
       6434 ATTTTTTCGTTTTAAAATAAAAAAAA
          1 ATTTTTGCGTTTTTAAA-AAAAAAAA

       6460 AAATTATGCT


Statistics
Matches: 22,  Mismatches: 3, Indels: 1
        0.85            0.12        0.04

Matches are distributed among these distances:
  26   14  0.64
  27    8  0.36

ACGTcount: A:0.46, C:0.04, G:0.10, T:0.40


Consensus pattern (26 bp):   
ATTTTTGCGTTTTTAAAAAAAAAAAG

Found at i:7537 original size:21 final size:22

Alignment explanation


    Indices: 7511--7552  Score: 59
    Period size: 21  Copynumber: 2.0  Consensus size: 22

       7501 GATCTTTATA

                  *               
       7511 ATGACTTATGCTATG-ATTGCC
          1 ATGACTAATGCTATGAATTGCC

                        *        
       7532 ATGACTAATGCTTTGAATTGC
          1 ATGACTAATGCTATGAATTGC

       7553 TTGAATTACT


Statistics
Matches: 18,  Mismatches: 2, Indels: 1
        0.86            0.10        0.05

Matches are distributed among these distances:
  21   13  0.72
  22    5  0.28

ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38


Consensus pattern (22 bp):   
ATGACTAATGCTATGAATTGCC

Found at i:9412 original size:21 final size:21

Alignment explanation


    Indices: 9382--9436  Score: 58
    Period size: 21  Copynumber: 2.6  Consensus size: 21

       9372 ATTGCCATAG

                *           *     
       9382 TTTAGATTTAATTTACTTTGC-
          1 TTTATATTTAATTTA-ATTGCT

                 *    *          
       9403 TTTATTTTTAGTTTAATTGCT
          1 TTTATATTTAATTTAATTGCT

                         
       9424 TTTATATTTAATT
          1 TTTATATTTAATT

       9437 GTTTTAATCC


Statistics
Matches: 27,  Mismatches: 6, Indels: 2
        0.77            0.17        0.06

Matches are distributed among these distances:
  20    4  0.15
  21   23  0.85

ACGTcount: A:0.24, C:0.05, G:0.07, T:0.64


Consensus pattern (21 bp):   
TTTATATTTAATTTAATTGCT

Found at i:12979 original size:32 final size:32

Alignment explanation


    Indices: 12936--12998  Score: 83
    Period size: 32  Copynumber: 2.0  Consensus size: 32

      12926 AGTAAGACAT

                          *          *       
      12936 TTAGCGGCGTTTT-TTGTTAGAAACGCCACTAA
          1 TTAGCGGCGTTTTACT-TTAGAAACACCACTAA

                *                          
      12968 TTAGTGGCGTTTTACTTTAGAAACACCACTA
          1 TTAGCGGCGTTTTACTTTAGAAACACCACTA

      12999 CTATATTAGT


Statistics
Matches: 27,  Mismatches: 3, Indels: 2
        0.84            0.09        0.06

Matches are distributed among these distances:
  32   26  0.96
  33    1  0.04

ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35


Consensus pattern (32 bp):   
TTAGCGGCGTTTTACTTTAGAAACACCACTAA
Done.