Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001345.1 Corchorus capsularis cultivar CVL-1 contig01345, 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, 657

Length: 1096
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32


Found at i:305 original size:32 final size:32

Alignment explanation


    Indices: 242--324  Score: 96
    Period size: 32  Copynumber: 2.6  Consensus size: 32

        232 CCATGGGCTG

                *                * *        
        242 GCCGCCCAAAATGGGCGGCCTTCCATAGGCAA
          1 GCCGACCAAAATGGGCGGCCTGCAATAGGCAA

               *                             
        274 GCCTACCAAAATGGGCGGCCTGCTAAT-GGCAA
          1 GCCGACCAAAATGGGCGGCCTGC-AATAGGCAA

                     **        
        306 GCCGACCAACTTGGGCGGC
          1 GCCGACCAAAATGGGCGGC

        325 AAACCAGATT


Statistics
Matches: 43,  Mismatches: 7, Indels: 2
        0.83            0.13        0.04

Matches are distributed among these distances:
  32   41  0.95
  33    2  0.05

ACGTcount: A:0.24, C:0.33, G:0.30, T:0.13


Consensus pattern (32 bp):   
GCCGACCAAAATGGGCGGCCTGCAATAGGCAA

Found at i:382 original size:15 final size:15

Alignment explanation


    Indices: 364--401  Score: 51
    Period size: 15  Copynumber: 2.5  Consensus size: 15

        354 AATTAGTTTT

                            
        364 TTAATTTTTTTAAT-A
          1 TTAATTTTTTT-ATGA

                   *       
        379 TTAATTTGTTTATGA
          1 TTAATTTTTTTATGA

                    
        394 TTAATTTT
          1 TTAATTTT

        402 AATTAGTTAC


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  14    2  0.10
  15   18  0.90

ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66


Consensus pattern (15 bp):   
TTAATTTTTTTATGA

Found at i:439 original size:15 final size:15

Alignment explanation


    Indices: 415--478  Score: 66
    Period size: 15  Copynumber: 4.6  Consensus size: 15

        405 TAGTTACTTA

                           
        415 GTTT-ATTAGTTTAT
          1 GTTTAATTAGTTTAT

                           
        429 GTTTAATTAGTTTAT
          1 GTTTAATTAGTTTAT

            **             
        444 AATTAATTAG--TA-
          1 GTTTAATTAGTTTAT

                           
        456 -TTTAATTAGTTTAT
          1 GTTTAATTAGTTTAT

             *       
        470 GATTAATTA
          1 GTTTAATTA

        479 ATTAATGATA


Statistics
Matches: 41,  Mismatches: 4, Indels: 9
        0.76            0.07        0.17

Matches are distributed among these distances:
  11    8  0.20
  13    4  0.10
  14    4  0.10
  15   25  0.61

ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56


Consensus pattern (15 bp):   
GTTTAATTAGTTTAT
Done.