Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015123.1 Corchorus capsularis cultivar CVL-1 contig15144, 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: 20309
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31


Found at i:1188 original size:2 final size:2

Alignment explanation


    Indices: 1181--1212  Score: 57
    Period size: 2  Copynumber: 16.5  Consensus size: 2

       1171 TGCTTTGTGC

                                                             
       1181 AT AT AT AT A- 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 AT AT AT A

       1213 GAATTAAAAA


Statistics
Matches: 29,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   1    1  0.03
   2   28  0.97

ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47


Consensus pattern (2 bp):   
AT

Found at i:2409 original size:2 final size:2

Alignment explanation


    Indices: 2398--2427  Score: 53
    Period size: 2  Copynumber: 15.5  Consensus size: 2

       2388 TTACTATTAC

                                                          
       2398 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       2428 TAAAAAATCA


Statistics
Matches: 27,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   1    1  0.04
   2   26  0.96

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:8493 original size:18 final size:18

Alignment explanation


    Indices: 8470--8504  Score: 52
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       8460 AATCCAGGCT

                  *  *        
       8470 ACCAAATTCGTCATACCC
          1 ACCAAACTCATCATACCC

                             
       8488 ACCAAACTCATCATACC
          1 ACCAAACTCATCATACC

       8505 TATTCGGATC


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:0.37, C:0.40, G:0.03, T:0.20


Consensus pattern (18 bp):   
ACCAAACTCATCATACCC

Found at i:13639 original size:27 final size:27

Alignment explanation


    Indices: 13608--13659  Score: 86
    Period size: 27  Copynumber: 1.9  Consensus size: 27

      13598 CATGTCATAT

                                       
      13608 TTTGGTTTTAAACATTCCATTGGATTA
          1 TTTGGTTTTAAACATTCCATTGGATTA

                     *       *       
      13635 TTTGGTTTTGAACATTCGATTGGAT
          1 TTTGGTTTTAAACATTCCATTGGAT

      13660 ATTATTTTAG


Statistics
Matches: 23,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  27   23  1.00

ACGTcount: A:0.23, C:0.10, G:0.19, T:0.48


Consensus pattern (27 bp):   
TTTGGTTTTAAACATTCCATTGGATTA
Done.