Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011457.1 Corchorus capsularis cultivar CVL-1 contig11478, 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: 2335
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30


Found at i:656 original size:33 final size:33

Alignment explanation


    Indices: 619--725  Score: 110
    Period size: 33  Copynumber: 3.2  Consensus size: 33

        609 CGCCTAGCGA

                                  *         ** 
        619 TGGCCGGT-TGTGGCCGGACATGTCC-ATGTCGTG
          1 TGGCCGGTGT-TGGCCGGACATCTCCGA-GTCACG

                             *               
        652 TGGCCGGTGTTGGCCGGGCATCTCCGAGTCACG
          1 TGGCCGGTGTTGGCCGGACATCTCCGAGTCACG

                               *     *    * *
        685 TGGCCGGTGTTGGCCGGACTTCTCCAAGTCGCA
          1 TGGCCGGTGTTGGCCGGACATCTCCGAGTCACG

                    
        718 TGGCCGGT
          1 TGGCCGGT

        726 CACTAGTGCT


Statistics
Matches: 63,  Mismatches: 9, Indels: 4
        0.83            0.12        0.05

Matches are distributed among these distances:
  33   61  0.97
  34    2  0.03

ACGTcount: A:0.09, C:0.28, G:0.38, T:0.24


Consensus pattern (33 bp):   
TGGCCGGTGTTGGCCGGACATCTCCGAGTCACG

Found at i:1786 original size:33 final size:33

Alignment explanation


    Indices: 1689--1793  Score: 140
    Period size: 33  Copynumber: 3.2  Consensus size: 33

       1679 TTGAAAAGAA

                                            * 
       1689 TGTTTT-AGATGTTGTTTGCGATGATACTAAACC
          1 TGTTTTAAG-TGTTGTTTGCGATGATACTAAATC

             **                *    *        
       1722 TAATTTAAGTGTTGTTTGCAATGACACTAAATC
          1 TGTTTTAAGTGTTGTTTGCGATGATACTAAATC

                              *              
       1755 TGTTTTAAGTGTTGTTTGTGATGATACTAAATC
          1 TGTTTTAAGTGTTGTTTGCGATGATACTAAATC

                  
       1788 TGTTTT
          1 TGTTTT

       1794 GGATGCTAAT


Statistics
Matches: 61,  Mismatches: 10, Indels: 2
        0.84            0.14        0.03

Matches are distributed among these distances:
  33   59  0.97
  34    2  0.03

ACGTcount: A:0.26, C:0.10, G:0.19, T:0.46


Consensus pattern (33 bp):   
TGTTTTAAGTGTTGTTTGCGATGATACTAAATC

Found at i:1871 original size:30 final size:31

Alignment explanation


    Indices: 1835--1893  Score: 95
    Period size: 30  Copynumber: 1.9  Consensus size: 31

       1825 TTGGTTGAAC

                                            
       1835 ATAGCATTGAAAAT-AATCCTG-TTTGGGTAG
          1 ATAGCATTGAAAATAAAT-CTGTTTTGGGTAG

                                         
       1865 ATAGCATTGAAAATAAATCTGTTTTGGGT
          1 ATAGCATTGAAAATAAATCTGTTTTGGGT

       1894 GACGAAAAAG


Statistics
Matches: 27,  Mismatches: 0, Indels: 3
        0.90            0.00        0.10

Matches are distributed among these distances:
  30   17  0.63
  31   10  0.37

ACGTcount: A:0.34, C:0.08, G:0.22, T:0.36


Consensus pattern (31 bp):   
ATAGCATTGAAAATAAATCTGTTTTGGGTAG
Done.