Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01002399.1 Corchorus olitorius cultivar O-4 contig02399, 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: 1940
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.38


Found at i:1238 original size:2 final size:2

Alignment explanation


    Indices: 1231--1257  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

       1221 TGCATGAGAC

                                                    
       1231 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 A

       1258 CACCTAATAT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:1575 original size:18 final size:19

Alignment explanation


    Indices: 1536--1575  Score: 55
    Period size: 21  Copynumber: 2.1  Consensus size: 19

       1526 GTGCTCCCGT

                                 
       1536 TGTGATGCTCCCACTTTTCAA
          1 TGTGATGCTCCCA--TTTCAA

                               
       1557 TGTGATGCTCCCA-TTCAA
          1 TGTGATGCTCCCATTTCAA

             
       1575 T
          1 T

       1576 TATGACCATT


Statistics
Matches: 19,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  18    6  0.32
  21   13  0.68

ACGTcount: A:0.20, C:0.28, G:0.15, T:0.38


Consensus pattern (19 bp):   
TGTGATGCTCCCATTTCAA

Found at i:1784 original size:32 final size:34

Alignment explanation


    Indices: 1733--1795  Score: 85
    Period size: 32  Copynumber: 1.9  Consensus size: 34

       1723 GATATCAACT

                                      *       
       1733 ACTTTTTTTACTTGATTTATTATTTTTTTCTCTA
          1 ACTTTTTTTACTTGATTTATTATTTTCTTCTCTA

                          *      *         
       1767 ACTTTTTTTA-TT-TTTTATTCTTTTCTTCT
          1 ACTTTTTTTACTTGATTTATTATTTTCTTCT

       1796 TCGCTTTCTT


Statistics
Matches: 26,  Mismatches: 3, Indels: 2
        0.84            0.10        0.06

Matches are distributed among these distances:
  32   14  0.54
  33    2  0.08
  34   10  0.38

ACGTcount: A:0.14, C:0.13, G:0.02, T:0.71


Consensus pattern (34 bp):   
ACTTTTTTTACTTGATTTATTATTTTCTTCTCTA

Found at i:1807 original size:24 final size:24

Alignment explanation


    Indices: 1780--1828  Score: 71
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       1770 TTTTTTATTT

                    *       *       
       1780 TTTATTCTTTTCTTCTTCGCTTTC
          1 TTTATTCTCTTCTTCTCCGCTTTC

                               *    
       1804 TTTATTCTCTTCTTCTCCGTTTTC
          1 TTTATTCTCTTCTTCTCCGCTTTC

             
       1828 T
          1 T

       1829 GCTTCGTTTT


Statistics
Matches: 22,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  24   22  1.00

ACGTcount: A:0.04, C:0.27, G:0.04, T:0.65


Consensus pattern (24 bp):   
TTTATTCTCTTCTTCTCCGCTTTC
Done.