Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011949.1 Corchorus capsularis cultivar CVL-1 contig11970, 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: 11563
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34


Found at i:1283 original size:14 final size:14

Alignment explanation


    Indices: 1264--1297  Score: 59
    Period size: 14  Copynumber: 2.4  Consensus size: 14

       1254 GCATATTAAC

                          
       1264 TTTAGTCCATTTAG
          1 TTTAGTCCATTTAG

                          
       1278 TTTAGTCCATTTAG
          1 TTTAGTCCATTTAG

            *     
       1292 ATTAGT
          1 TTTAGT

       1298 ATCATAGTTA


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  14   19  1.00

ACGTcount: A:0.24, C:0.12, G:0.15, T:0.50


Consensus pattern (14 bp):   
TTTAGTCCATTTAG

Found at i:1475 original size:20 final size:20

Alignment explanation


    Indices: 1439--1477  Score: 60
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       1429 AAATACAAAG

                        *       
       1439 CATTTGATTTACGAATTGGA
          1 CATTTGATTTACAAATTGGA

                      *        
       1459 CATTTGATTTTCAAATTGG
          1 CATTTGATTTACAAATTGG

       1478 TGCTCTTTTT


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  20   17  1.00

ACGTcount: A:0.28, C:0.10, G:0.18, T:0.44


Consensus pattern (20 bp):   
CATTTGATTTACAAATTGGA

Found at i:11533 original size:2 final size:2

Alignment explanation


    Indices: 11517--11563  Score: 78
    Period size: 2  Copynumber: 23.5  Consensus size: 2

      11507 AGACACCTGT

                                                                           
      11517 TA TA GTA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                   
      11559 TA TA T
          1 TA TA T


Statistics
Matches: 43,  Mismatches: 0, Indels: 4
        0.91            0.00        0.09

Matches are distributed among these distances:
   1    1  0.02
   2   40  0.93
   3    2  0.05

ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49


Consensus pattern (2 bp):   
TA

Done.