Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016336.1 Corchorus capsularis cultivar CVL-1 contig16357, 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: 21052
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35


Found at i:1657 original size:17 final size:18

Alignment explanation


    Indices: 1622--1670  Score: 57
    Period size: 18  Copynumber: 2.7  Consensus size: 18

       1612 CATAATTTTC

                               
       1622 TTTAAAG-TACAACAAAAT
          1 TTTAAAGATA-AACAAAAT

                              
       1640 TTTAAAGATAAA-AAAAT
          1 TTTAAAGATAAACAAAAT

                          
       1657 TATTAAAAGATAAA
          1 T-TT-AAAGATAAA

       1671 GTTTTAGAAA


Statistics
Matches: 28,  Mismatches: 0, Indels: 5
        0.85            0.00        0.15

Matches are distributed among these distances:
  17    6  0.21
  18   11  0.39
  19   11  0.39

ACGTcount: A:0.61, C:0.04, G:0.06, T:0.29


Consensus pattern (18 bp):   
TTTAAAGATAAACAAAAT

Found at i:5534 original size:20 final size:21

Alignment explanation


    Indices: 5511--5553  Score: 63
    Period size: 20  Copynumber: 2.1  Consensus size: 21

       5501 AGGTATAAAA

                                  
       5511 ATTATTAA-AAATGTTA-TAAT
          1 ATTATTAATAAAT-TTAGTAAT

                                 
       5531 ATTATTAATAAATTTAGTAAT
          1 ATTATTAATAAATTTAGTAAT

              
       5552 AT
          1 AT

       5554 CTTACATTCT


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  20   11  0.52
  21   10  0.48

ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47


Consensus pattern (21 bp):   
ATTATTAATAAATTTAGTAAT

Found at i:7157 original size:2 final size:2

Alignment explanation


    Indices: 7150--7198  Score: 71
    Period size: 2  Copynumber: 24.0  Consensus size: 2

       7140 AGTTTAGACT

                          *                                                
       7150 TA TA TA TA GTG TA 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

            *       
       7193 GA TA TA
          1 TA TA TA

       7199 CATTGTAAAA


Statistics
Matches: 42,  Mismatches: 4, Indels: 2
        0.88            0.08        0.04

Matches are distributed among these distances:
   2   41  0.98
   3    1  0.02

ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47


Consensus pattern (2 bp):   
TA

Found at i:8369 original size:3 final size:3

Alignment explanation


    Indices: 8361--8394  Score: 68
    Period size: 3  Copynumber: 11.3  Consensus size: 3

       8351 TGTGAGTCTT

                                                         
       8361 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T

       8395 GTTAATAATA


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   31  1.00

ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68


Consensus pattern (3 bp):   
TTA

Found at i:11269 original size:14 final size:14

Alignment explanation


    Indices: 11250--11281  Score: 64
    Period size: 14  Copynumber: 2.3  Consensus size: 14

      11240 TGACTAATTC

                          
      11250 GAGTTTTCATGGGT
          1 GAGTTTTCATGGGT

                          
      11264 GAGTTTTCATGGGT
          1 GAGTTTTCATGGGT

                
      11278 GAGT
          1 GAGT

      11282 CTAACAACGA


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   18  1.00

ACGTcount: A:0.16, C:0.06, G:0.38, T:0.41


Consensus pattern (14 bp):   
GAGTTTTCATGGGT

Found at i:11373 original size:3 final size:3

Alignment explanation


    Indices: 11365--11404  Score: 80
    Period size: 3  Copynumber: 13.3  Consensus size: 3

      11355 ACTTGATCAC

                                                                 
      11365 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
          1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T

      11405 TATATATATA


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   37  1.00

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68


Consensus pattern (3 bp):   
TAT

Done.