Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01002561.1 Corchorus capsularis cultivar CVL-1 contig02569, 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, 612

Length: 1021
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:527 original size:18 final size:18

Alignment explanation


    Indices: 504--554  Score: 74
    Period size: 18  Copynumber: 3.1  Consensus size: 18

        494 AGTTCTTTTC

                              
        504 TTTCTATTCTATTAGTAT
          1 TTTCTATTCTATTAGTAT

                              
        522 TTTCTATTCTA-T--T-T
          1 TTTCTATTCTATTAGTAT

                              
        536 TTTCTATTCTATTAGTAT
          1 TTTCTATTCTATTAGTAT

             
        554 T
          1 T

        555 AGAATTAGTA


Statistics
Matches: 29,  Mismatches: 0, Indels: 8
        0.78            0.00        0.22

Matches are distributed among these distances:
  14   12  0.41
  15    2  0.07
  17    2  0.07
  18   13  0.45

ACGTcount: A:0.20, C:0.12, G:0.04, T:0.65


Consensus pattern (18 bp):   
TTTCTATTCTATTAGTAT

Found at i:540 original size:14 final size:14

Alignment explanation


    Indices: 521--548  Score: 56
    Period size: 14  Copynumber: 2.0  Consensus size: 14

        511 TCTATTAGTA

                          
        521 TTTTCTATTCTATT
          1 TTTTCTATTCTATT

                          
        535 TTTTCTATTCTATT
          1 TTTTCTATTCTATT

        549 AGTATTAGAA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   14  1.00

ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71


Consensus pattern (14 bp):   
TTTTCTATTCTATT

Found at i:556 original size:6 final size:6

Alignment explanation


    Indices: 545--607  Score: 71
    Period size: 6  Copynumber: 11.2  Consensus size: 6

        535 TTTTCTATTC

                          *                         *      *       
        545 TATTAG TATTAG AATTAG TATTAG -ATTAG TATT-C TATT-C TATTAG
          1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG

                                  
        590 TATTAG -ATTAG TATTAG T
          1 TATTAG TATTAG TATTAG T

        608 TAGTGATCCC


Statistics
Matches: 50,  Mismatches: 4, Indels: 6
        0.83            0.07        0.10

Matches are distributed among these distances:
   5   19  0.38
   6   31  0.62

ACGTcount: A:0.33, C:0.03, G:0.14, T:0.49


Consensus pattern (6 bp):   
TATTAG

Found at i:572 original size:11 final size:11

Alignment explanation


    Indices: 546--611  Score: 62
    Period size: 11  Copynumber: 5.5  Consensus size: 11

        536 TTTCTATTCT

                       
        546 ATTAGTATTAG
          1 ATTAGTATTAG

                        
        557 AATTAGTATTAG
          1 -ATTAGTATTAG

                           *
        569 ATTAGTATTCTATTCT
          1 ATTAGTA-T-TA---G

                       
        585 ATTAGTATTAG
          1 ATTAGTATTAG

                       
        596 ATTAGTATTAG
          1 ATTAGTATTAG

                  
        607 -TTAGT
          1 ATTAGT

        612 GATCCCGGCT


Statistics
Matches: 47,  Mismatches: 2, Indels: 12
        0.77            0.03        0.20

Matches are distributed among these distances:
  10    5  0.11
  11   18  0.38
  12   12  0.26
  13    2  0.04
  14    2  0.04
  15    1  0.02
  16    7  0.15

ACGTcount: A:0.33, C:0.03, G:0.15, T:0.48


Consensus pattern (11 bp):   
ATTAGTATTAG

Found at i:582 original size:39 final size:37

Alignment explanation


    Indices: 537--611  Score: 132
    Period size: 39  Copynumber: 2.0  Consensus size: 37

        527 ATTCTATTTT

                                                   
        537 TTCTATTCTATTAGTATTAGAATTAGTATTAGATTAGTA
          1 TTCTATTCTATTAGTATTAG-ATTAGTATTAG-TTAGTA

                                                
        576 TTCTATTCTATTAGTATTAGATTAGTATTAGTTAGT
          1 TTCTATTCTATTAGTATTAGATTAGTATTAGTTAGT

        612 GATCCCGGCT


Statistics
Matches: 36,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
  37    5  0.14
  38   11  0.31
  39   20  0.56

ACGTcount: A:0.31, C:0.05, G:0.13, T:0.51


Consensus pattern (37 bp):   
TTCTATTCTATTAGTATTAGATTAGTATTAGTTAGTA
Done.