Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015769.1 Corchorus capsularis cultivar CVL-1 contig15790, 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: 10164
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35


Found at i:594 original size:11 final size:11

Alignment explanation


    Indices: 578--612  Score: 70
    Period size: 11  Copynumber: 3.2  Consensus size: 11

        568 AGGACTTGCA

                       
        578 AAAGGTAAAAG
          1 AAAGGTAAAAG

                       
        589 AAAGGTAAAAG
          1 AAAGGTAAAAG

                       
        600 AAAGGTAAAAG
          1 AAAGGTAAAAG

              
        611 AA
          1 AA

        613 CTACTACCTT


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

Matches are distributed among these distances:
  11   24  1.00

ACGTcount: A:0.66, C:0.00, G:0.26, T:0.09


Consensus pattern (11 bp):   
AAAGGTAAAAG

Found at i:4204 original size:25 final size:25

Alignment explanation


    Indices: 4157--4205  Score: 64
    Period size: 25  Copynumber: 2.0  Consensus size: 25

       4147 ATACCTTCGT

                 *           *       
       4157 TTTTCCTTTTACTTTCTTTTTTCAA
          1 TTTTCATTTTACTTTCTATTTTCAA

                                     
       4182 TTTTCATTTTCACTTTC-ATTTTCA
          1 TTTTCATTTT-ACTTTCTATTTTCA

       4206 TCATTTTTTT


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  25   15  0.71
  26    6  0.29

ACGTcount: A:0.14, C:0.20, G:0.00, T:0.65


Consensus pattern (25 bp):   
TTTTCATTTTACTTTCTATTTTCAA

Found at i:4553 original size:15 final size:16

Alignment explanation


    Indices: 4531--4576  Score: 58
    Period size: 15  Copynumber: 2.9  Consensus size: 16

       4521 CATGAAAACA

                            
       4531 ATTTTTTTTTGAAATC
          1 ATTTTTTTTTGAAATC

                    **      
       4547 A-TTTTTTGAGAAATC
          1 ATTTTTTTTTGAAATC

                           
       4562 ATTATTTTTTTGAAA
          1 ATT-TTTTTTTGAAA

       4577 AATCTTTTTT


Statistics
Matches: 24,  Mismatches: 4, Indels: 3
        0.77            0.13        0.10

Matches are distributed among these distances:
  15   13  0.54
  16    2  0.08
  17    9  0.38

ACGTcount: A:0.30, C:0.04, G:0.09, T:0.57


Consensus pattern (16 bp):   
ATTTTTTTTTGAAATC

Found at i:8526 original size:12 final size:13

Alignment explanation


    Indices: 8503--8545  Score: 54
    Period size: 12  Copynumber: 3.3  Consensus size: 13

       8493 AATAATTTTC

                         
       8503 TTTAATTTTCTTG
          1 TTTAATTTTCTTG

                          
       8516 TTTAA-TTTCTTAG
          1 TTTAATTTTCTT-G

                          
       8529 -TTAATTTTACTTG
          1 TTTAATTTT-CTTG

                
       8542 TTTA
          1 TTTA

       8546 TTTGATTTAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 7
        0.79            0.00        0.21

Matches are distributed among these distances:
  12   10  0.38
  13   10  0.38
  14    6  0.23

ACGTcount: A:0.21, C:0.07, G:0.07, T:0.65


Consensus pattern (13 bp):   
TTTAATTTTCTTG
Done.