Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014457.1 Corchorus capsularis cultivar CVL-1 contig14478, 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: 8955
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.30


Found at i:399 original size:23 final size:23

Alignment explanation


    Indices: 373--430  Score: 57
    Period size: 23  Copynumber: 2.6  Consensus size: 23

        363 ATGGCGGCAG

                                    
        373 TATTCT-TATTTAATTATTATTTA
          1 TATTCTATATTTAATTA-TATTTA

                *   *   *          
        396 TATTGTATTTTTTATTATATTTA
          1 TATTCTATATTTAATTATATTTA

                    *    
        419 TATT-TATGTTTA
          1 TATTCTATATTTA

        431 CTTGCTTCCA


Statistics
Matches: 29,  Mismatches: 5, Indels: 3
        0.78            0.14        0.08

Matches are distributed among these distances:
  22    6  0.21
  23   15  0.52
  24    8  0.28

ACGTcount: A:0.28, C:0.02, G:0.03, T:0.67


Consensus pattern (23 bp):   
TATTCTATATTTAATTATATTTA

Found at i:1003 original size:3 final size:3

Alignment explanation


    Indices: 995--1024  Score: 60
    Period size: 3  Copynumber: 10.0  Consensus size: 3

        985 TTTAAGTCCA

                                                   
        995 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
          1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT

       1025 CATTTTAGTA


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   27  1.00

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67


Consensus pattern (3 bp):   
ATT

Found at i:1355 original size:9 final size:9

Alignment explanation


    Indices: 1341--1399  Score: 59
    Period size: 9  Copynumber: 6.7  Consensus size: 9

       1331 AAATATACTT

                     
       1341 ATATATGTA
          1 ATATATGTA

                     
       1350 ATATATGTA
          1 ATATATGTA

                *    
       1359 ATATGT-TA
          1 ATATATGTA

                     *
       1367 TATATAT-TC
          1 -ATATATGTA

                  * *
       1376 ATATATATT
          1 ATATATGTA

                     
       1385 ATATATGTA
          1 ATATATGTA

                  
       1394 ATATAT
          1 ATATAT

       1400 ATGTTATGTA


Statistics
Matches: 42,  Mismatches: 6, Indels: 4
        0.81            0.12        0.08

Matches are distributed among these distances:
   8    8  0.19
   9   34  0.81

ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49


Consensus pattern (9 bp):   
ATATATGTA

Found at i:8930 original size:2 final size:2

Alignment explanation


    Indices: 8923--8951  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

       8913 GTCATTACTC

                                                       
       8923 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       8952 CACA


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Done.