Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015234.1 Corchorus capsularis cultivar CVL-1 contig15255, 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: 22734
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31


Found at i:2530 original size:53 final size:53

Alignment explanation


    Indices: 2469--2625  Score: 253
    Period size: 53  Copynumber: 3.0  Consensus size: 53

       2459 GGGTTTCCAA

                                                                 
       2469 AATG-AGATGTCTTAAAAACCCACTTAACATATCAATAATTAAAGGGAACCTT
          1 AATGAAGATGTCTTAAAAACCCACTTAACATATCAATAATTAAAGGGAACCTT

                      *        *                            *    
       2521 AATGAAGATGACTTAAAAATCCACTTAACATATCAATAATTAAAGGGATCCTT
          1 AATGAAGATGTCTTAAAAACCCACTTAACATATCAATAATTAAAGGGAACCTT

              *                                     *   *       
       2574 AACGAAGATGTCTTAAAAACCCACTTAACATATCAATAATCAAATGGAACCT
          1 AATGAAGATGTCTTAAAAACCCACTTAACATATCAATAATTAAAGGGAACCT

       2626 CAAATTACTG


Statistics
Matches: 95,  Mismatches: 9, Indels: 1
        0.90            0.09        0.01

Matches are distributed among these distances:
  52    4  0.04
  53   91  0.96

ACGTcount: A:0.45, C:0.18, G:0.11, T:0.26


Consensus pattern (53 bp):   
AATGAAGATGTCTTAAAAACCCACTTAACATATCAATAATTAAAGGGAACCTT

Found at i:9470 original size:19 final size:19

Alignment explanation


    Indices: 9446--9483  Score: 76
    Period size: 19  Copynumber: 2.0  Consensus size: 19

       9436 TGCATAATCA

                               
       9446 TTGTTTTCTTGATTGAAAG
          1 TTGTTTTCTTGATTGAAAG

                               
       9465 TTGTTTTCTTGATTGAAAG
          1 TTGTTTTCTTGATTGAAAG

       9484 CTGCATAATC


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   19  1.00

ACGTcount: A:0.21, C:0.05, G:0.21, T:0.53


Consensus pattern (19 bp):   
TTGTTTTCTTGATTGAAAG

Found at i:10560 original size:5 final size:5

Alignment explanation


    Indices: 10550--10578  Score: 58
    Period size: 5  Copynumber: 5.8  Consensus size: 5

      10540 TCTGGCGCAA

                                              
      10550 AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
          1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAA

      10579 ACGTTATGGT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   5   24  1.00

ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00


Consensus pattern (5 bp):   
AAAAG

Found at i:15650 original size:14 final size:14

Alignment explanation


    Indices: 15631--15657  Score: 54
    Period size: 14  Copynumber: 1.9  Consensus size: 14

      15621 TGTGTGAAAA

                          
      15631 ACTTTGTTCTTAAT
          1 ACTTTGTTCTTAAT

                         
      15645 ACTTTGTTCTTAA
          1 ACTTTGTTCTTAA

      15658 GTGATCTTTA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   13  1.00

ACGTcount: A:0.22, C:0.15, G:0.07, T:0.56


Consensus pattern (14 bp):   
ACTTTGTTCTTAAT

Found at i:18510 original size:20 final size:20

Alignment explanation


    Indices: 18487--18525  Score: 53
    Period size: 20  Copynumber: 1.9  Consensus size: 20

      18477 AATGAATTTC

                                 
      18487 ACAAGAAACCC-AAGCAAATA
          1 ACAA-AAACCCAAAGCAAATA

                *              
      18507 ACAACAACCCAAAGCAAAT
          1 ACAAAAACCCAAAGCAAAT

      18526 GAAAGGAAAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  19    5  0.29
  20   12  0.71

ACGTcount: A:0.59, C:0.28, G:0.08, T:0.05


Consensus pattern (20 bp):   
ACAAAAACCCAAAGCAAATA
Done.