Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005035.1 Corchorus capsularis cultivar CVL-1 contig05053, 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: 11041
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34


Found at i:2984 original size:42 final size:44

Alignment explanation


    Indices: 2933--3026  Score: 122
    Period size: 45  Copynumber: 2.2  Consensus size: 44

       2923 AGTGCACTAT

                                     *                  
       2933 CTAA-ATTCTACTCC-A-TCTCTAGGTAATTAATCAAAATAAAA
          1 CTAATATTCTACTCCTACTCTCTAGATAATTAATCAAAATAAAA

                                        *      *        *
       2974 CTAATATTCTACTCCTACGTCTCTAGATTATTAATTAAAATAAAG
          1 CTAATATTCTACTCCTAC-TCTCTAGATAATTAATCAAAATAAAA

                    
       3019 CTAATATT
          1 CTAATATT

       3027 AATTGTTGTT


Statistics
Matches: 45,  Mismatches: 4, Indels: 4
        0.85            0.08        0.08

Matches are distributed among these distances:
  41    4  0.09
  42   10  0.22
  43    1  0.02
  45   30  0.67

ACGTcount: A:0.40, C:0.18, G:0.05, T:0.36


Consensus pattern (44 bp):   
CTAATATTCTACTCCTACTCTCTAGATAATTAATCAAAATAAAA

Found at i:4303 original size:12 final size:13

Alignment explanation


    Indices: 4279--4309  Score: 55
    Period size: 12  Copynumber: 2.5  Consensus size: 13

       4269 TGCTACATGA

                         
       4279 CCCTCCAATTTGT
          1 CCCTCCAATTTGT

                         
       4292 CCCTCC-ATTTGT
          1 CCCTCCAATTTGT

                  
       4304 CCCTCC
          1 CCCTCC

       4310 TGACGTGTCA


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  12   12  0.67
  13    6  0.33

ACGTcount: A:0.10, C:0.48, G:0.06, T:0.35


Consensus pattern (13 bp):   
CCCTCCAATTTGT

Found at i:7453 original size:17 final size:17

Alignment explanation


    Indices: 7433--7465  Score: 57
    Period size: 17  Copynumber: 1.9  Consensus size: 17

       7423 GCAGCCTATC

                             
       7433 ACCTCATACCACCTAGT
          1 ACCTCATACCACCTAGT

                     *      
       7450 ACCTCATACTACCTAG
          1 ACCTCATACCACCTAG

       7466 GTATCATGAG


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  17   15  1.00

ACGTcount: A:0.30, C:0.39, G:0.06, T:0.24


Consensus pattern (17 bp):   
ACCTCATACCACCTAGT

Found at i:7639 original size:20 final size:20

Alignment explanation


    Indices: 7614--7652  Score: 69
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       7604 AGAAGAGTTC

                     *          
       7614 GCCTTCCTCGGCAAGTAAAT
          1 GCCTTCCTCAGCAAGTAAAT

                               
       7634 GCCTTCCTCAGCAAGTAAA
          1 GCCTTCCTCAGCAAGTAAA

       7653 GCCCGCCAGT


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  20   18  1.00

ACGTcount: A:0.28, C:0.31, G:0.18, T:0.23


Consensus pattern (20 bp):   
GCCTTCCTCAGCAAGTAAAT
Done.