Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01002607.1 Corchorus capsularis cultivar CVL-1 contig02615, 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, 632

Length: 1054
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.38


Found at i:387 original size:13 final size:13

Alignment explanation


    Indices: 371--397  Score: 54
    Period size: 13  Copynumber: 2.1  Consensus size: 13

        361 TTTTTTCCCC

                         
        371 TCTTTTTTTTATT
          1 TCTTTTTTTTATT

                         
        384 TCTTTTTTTTATT
          1 TCTTTTTTTTATT

             
        397 T
          1 T

        398 TATTCCCTTC


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

Matches are distributed among these distances:
  13   14  1.00

ACGTcount: A:0.07, C:0.07, G:0.00, T:0.85


Consensus pattern (13 bp):   
TCTTTTTTTTATT

Found at i:911 original size:19 final size:18

Alignment explanation


    Indices: 887--938  Score: 67
    Period size: 14  Copynumber: 3.1  Consensus size: 18

        877 AGTTCTTTTC

                               
        887 TTTCTATTACTATTAGTAT
          1 TTTCTATT-CTATTAGTAT

                              
        906 TTTCTATTCTA-T--T-T
          1 TTTCTATTCTATTAGTAT

                              
        920 TTTCTATTCTATTAGTAT
          1 TTTCTATTCTATTAGTAT

             
        938 T
          1 T

        939 AGAATTAGTA


Statistics
Matches: 29,  Mismatches: 0, Indels: 9
        0.76            0.00        0.24

Matches are distributed among these distances:
  14   12  0.41
  15    2  0.07
  17    2  0.07
  18    5  0.17
  19    8  0.28

ACGTcount: A:0.21, C:0.12, G:0.04, T:0.63


Consensus pattern (18 bp):   
TTTCTATTCTATTAGTAT

Found at i:940 original size:6 final size:6

Alignment explanation


    Indices: 929--991  Score: 71
    Period size: 6  Copynumber: 11.2  Consensus size: 6

        919 TTTTCTATTC

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

                                  
        974 TATTAG -ATTAG TATTAG T
          1 TATTAG TATTAG TATTAG T

        992 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:956 original size:11 final size:11

Alignment explanation


    Indices: 930--995  Score: 62
    Period size: 11  Copynumber: 5.5  Consensus size: 11

        920 TTTCTATTCT

                       
        930 ATTAGTATTAG
          1 ATTAGTATTAG

                        
        941 AATTAGTATTAG
          1 -ATTAGTATTAG

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

                       
        969 ATTAGTATTAG
          1 ATTAGTATTAG

                       
        980 ATTAGTATTAG
          1 ATTAGTATTAG

                  
        991 -TTAGT
          1 ATTAGT

        996 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:971 original size:39 final size:37

Alignment explanation


    Indices: 921--995  Score: 132
    Period size: 39  Copynumber: 2.0  Consensus size: 37

        911 ATTCTATTTT

                                                   
        921 TTCTATTCTATTAGTATTAGAATTAGTATTAGATTAGTA
          1 TTCTATTCTATTAGTATTAG-ATTAGTATTAG-TTAGTA

                                                
        960 TTCTATTCTATTAGTATTAGATTAGTATTAGTTAGT
          1 TTCTATTCTATTAGTATTAGATTAGTATTAGTTAGT

        996 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.