Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007702.1 Corchorus olitorius cultivar O-4 contig07728, 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: 1923
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.31


Found at i:1452 original size:31 final size:29

Alignment explanation


    Indices: 1349--1430  Score: 103
    Period size: 29  Copynumber: 2.8  Consensus size: 29

       1339 GGCTAAATAA

                            *        *      
       1349 TCAATTCAGGATATAAGGTTTCACGCAAAACG
          1 TCAATTCAGGATATAACG-TT-AC-AAAAACG

                                         
       1381 -CAATTCAGGATATAACGTTACAAAAACG
          1 TCAATTCAGGATATAACGTTACAAAAACG

                  *               
       1409 TCAATTAAGGATATAACGTTAC
          1 TCAATTCAGGATATAACGTTAC

       1431 CTAATCCGAT


Statistics
Matches: 46,  Mismatches: 3, Indels: 5
        0.85            0.06        0.09

Matches are distributed among these distances:
  28    6  0.13
  29   22  0.48
  30    2  0.04
  31   16  0.35

ACGTcount: A:0.41, C:0.17, G:0.16, T:0.26


Consensus pattern (29 bp):   
TCAATTCAGGATATAACGTTACAAAAACG

Found at i:1574 original size:18 final size:18

Alignment explanation


    Indices: 1551--1585  Score: 52
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       1541 TTTGTCAGAA

                       *      
       1551 AATTAAAGAAATATAAAC
          1 AATTAAAGAAAAATAAAC

                   *         
       1569 AATTAAATAAAAATAAA
          1 AATTAAAGAAAAATAAA

       1586 TTAATAAAAA


Statistics
Matches: 15,  Mismatches: 2, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  18   15  1.00

ACGTcount: A:0.71, C:0.03, G:0.03, T:0.23


Consensus pattern (18 bp):   
AATTAAAGAAAAATAAAC

Found at i:1603 original size:16 final size:18

Alignment explanation


    Indices: 1572--1606  Score: 56
    Period size: 16  Copynumber: 2.1  Consensus size: 18

       1562 TATAAACAAT

                              
       1572 TAAATAAAAATAAATTAA
          1 TAAATAAAAATAAATTAA

                              
       1590 TAAA-AAAAAT-AATTAA
          1 TAAATAAAAATAAATTAA

             
       1606 T
          1 T

       1607 TAATTAATTA


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

Matches are distributed among these distances:
  16    7  0.41
  17    6  0.35
  18    4  0.24

ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29


Consensus pattern (18 bp):   
TAAATAAAAATAAATTAA
Done.