Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015889.1 Corchorus olitorius cultivar O-4 contig15922, 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: 2468
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36


Found at i:1523 original size:15 final size:15

Alignment explanation


    Indices: 1490--1531  Score: 57
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       1480 TTACTTTGCT

                          * 
       1490 TTGTTTTCTAGTTTCA
          1 TTGTTTTCT-GTTTAA

                           
       1506 TTGTTTTCTGTTTAA
          1 TTGTTTTCTGTTTAA

               *       
       1521 TTGCTTTCTGT
          1 TTGTTTTCTGT

       1532 CAACCTCTGT


Statistics
Matches: 24,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  15   15  0.62
  16    9  0.38

ACGTcount: A:0.10, C:0.12, G:0.14, T:0.64


Consensus pattern (15 bp):   
TTGTTTTCTGTTTAA

Found at i:1956 original size:22 final size:21

Alignment explanation


    Indices: 1886--1962  Score: 66
    Period size: 24  Copynumber: 3.4  Consensus size: 21

       1876 AAAAATTTGT

                                   
       1886 GTTTTGCGTCGGA-AAAAAAAAA
          1 GTTTTGCGTC--ATAAAAAAAAA

            **                    *
       1908 AATTTGCGTCATAAAAAAAATTT
          1 GTTTTGCGTCATAAAAAAAA--A

                                  
       1931 GTTTCTGCGTCATAAAAAAAAA
          1 GTTT-TGCGTCATAAAAAAAAA

                      
       1953 GTTTTTGCGT
          1 G-TTTTGCGT

       1963 TTTTCTAAAA


Statistics
Matches: 44,  Mismatches: 6, Indels: 10
        0.73            0.10        0.17

Matches are distributed among these distances:
  20    1  0.02
  21    8  0.18
  22   14  0.32
  23    5  0.11
  24   16  0.36

ACGTcount: A:0.40, C:0.10, G:0.17, T:0.32


Consensus pattern (21 bp):   
GTTTTGCGTCATAAAAAAAAA
Done.