Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006982.1 Corchorus capsularis cultivar CVL-1 contig07003, 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: 12165
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33


Found at i:1397 original size:10 final size:10

Alignment explanation


    Indices: 1382--1406  Score: 50
    Period size: 10  Copynumber: 2.5  Consensus size: 10

       1372 GTTGCTGCAC

                      
       1382 AATTCCAGAA
          1 AATTCCAGAA

                      
       1392 AATTCCAGAA
          1 AATTCCAGAA

                 
       1402 AATTC
          1 AATTC

       1407 TAGAGTCCTC


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   15  1.00

ACGTcount: A:0.48, C:0.20, G:0.08, T:0.24


Consensus pattern (10 bp):   
AATTCCAGAA

Found at i:2340 original size:6 final size:6

Alignment explanation


    Indices: 2329--2355  Score: 54
    Period size: 6  Copynumber: 4.5  Consensus size: 6

       2319 ATTAATCTGC

                                           
       2329 TTTAGA TTTAGA TTTAGA TTTAGA TTT
          1 TTTAGA TTTAGA TTTAGA TTTAGA TTT

       2356 GCTTTGCTTT


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   21  1.00

ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56


Consensus pattern (6 bp):   
TTTAGA

Found at i:5923 original size:21 final size:20

Alignment explanation


    Indices: 5865--5924  Score: 50
    Period size: 20  Copynumber: 2.9  Consensus size: 20

       5855 GCCGGTGCCG

                              *   
       5865 TGCCGCCTGCCCGGCCCAGCCA
          1 TGCC-CCTGCCCGG-CCATCCA

            *   *                
       5887 GGCCACTG-CCGCGCCATCCA
          1 TGCCCCTGCCCG-GCCATCCA

                              
       5907 TGCCTCCTGCCCGGCCAT
          1 TGCC-CCTGCCCGGCCAT

       5925 GCTCGGCCAT


Statistics
Matches: 30,  Mismatches: 5, Indels: 7
        0.71            0.12        0.17

Matches are distributed among these distances:
  20   12  0.40
  21   12  0.40
  22    6  0.20

ACGTcount: A:0.10, C:0.52, G:0.25, T:0.13


Consensus pattern (20 bp):   
TGCCCCTGCCCGGCCATCCA

Found at i:6831 original size:23 final size:25

Alignment explanation


    Indices: 6792--6838  Score: 71
    Period size: 24  Copynumber: 2.0  Consensus size: 25

       6782 ATATGCTCAT

                                     
       6792 ATTGATCGATTGATTTG-ATTTTTG
          1 ATTGATCGATTGATTTGAATTTTTG

                        *           
       6816 ATTGAT-GATTGCTTTGAATTTTT
          1 ATTGATCGATTGATTTGAATTTTT

       6839 AAGAATGATT


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  23    9  0.43
  24   12  0.57

ACGTcount: A:0.21, C:0.04, G:0.19, T:0.55


Consensus pattern (25 bp):   
ATTGATCGATTGATTTGAATTTTTG

Found at i:10268 original size:10 final size:10

Alignment explanation


    Indices: 10253--10278  Score: 52
    Period size: 10  Copynumber: 2.6  Consensus size: 10

      10243 GAGGACTCTA

                      
      10253 GAATTTTCTG
          1 GAATTTTCTG

                      
      10263 GAATTTTCTG
          1 GAATTTTCTG

                  
      10273 GAATTT
          1 GAATTT

      10279 GGCAGCAACT


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   16  1.00

ACGTcount: A:0.23, C:0.08, G:0.19, T:0.50


Consensus pattern (10 bp):   
GAATTTTCTG

Found at i:11144 original size:6 final size:6

Alignment explanation


    Indices: 11133--11159  Score: 54
    Period size: 6  Copynumber: 4.5  Consensus size: 6

      11123 ATTAATCTGC

                                           
      11133 TTTAGA TTTAGA TTTAGA TTTAGA TTT
          1 TTTAGA TTTAGA TTTAGA TTTAGA TTT

      11160 GCTTTGCTTT


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   21  1.00

ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56


Consensus pattern (6 bp):   
TTTAGA

Done.