Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016179.1 Corchorus capsularis cultivar CVL-1 contig16200, 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: 11800
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36


Found at i:1792 original size:19 final size:20

Alignment explanation


    Indices: 1760--1797  Score: 69
    Period size: 19  Copynumber: 1.9  Consensus size: 20

       1750 AGCTGTCAAT

                                
       1760 AGTTTTGTATAATGTTTATG
          1 AGTTTTGTATAATGTTTATG

                               
       1780 AGTTTTG-ATAATGTTTAT
          1 AGTTTTGTATAATGTTTAT

       1798 ATAATTGTTT


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

Matches are distributed among these distances:
  19   11  0.61
  20    7  0.39

ACGTcount: A:0.26, C:0.00, G:0.18, T:0.55


Consensus pattern (20 bp):   
AGTTTTGTATAATGTTTATG

Found at i:3247 original size:25 final size:25

Alignment explanation


    Indices: 3197--3249  Score: 81
    Period size: 25  Copynumber: 2.1  Consensus size: 25

       3187 CAACAAGTTT

                                 *   
       3197 TATTGGTTTTAATGATATTCATATA
          1 TATTGGTTTTAATGATATTCAGATA

                                      
       3222 TATTGGTTTTAATGATA-TCTAGATA
          1 TATTGGTTTTAATGATATTC-AGATA

               
       3247 TAT
          1 TAT

       3250 GTCAATGCCA


Statistics
Matches: 26,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
  24    2  0.08
  25   24  0.92

ACGTcount: A:0.32, C:0.04, G:0.13, T:0.51


Consensus pattern (25 bp):   
TATTGGTTTTAATGATATTCAGATA

Found at i:5820 original size:28 final size:28

Alignment explanation


    Indices: 5780--5839  Score: 120
    Period size: 28  Copynumber: 2.1  Consensus size: 28

       5770 CTAAAGAAAG

                                        
       5780 GATATCATCATCCGCCAGAGAAGTTGCA
          1 GATATCATCATCCGCCAGAGAAGTTGCA

                                        
       5808 GATATCATCATCCGCCAGAGAAGTTGCA
          1 GATATCATCATCCGCCAGAGAAGTTGCA

                
       5836 GATA
          1 GATA

       5840 AAATTCTCAA


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  28   32  1.00

ACGTcount: A:0.33, C:0.23, G:0.22, T:0.22


Consensus pattern (28 bp):   
GATATCATCATCCGCCAGAGAAGTTGCA

Found at i:7682 original size:40 final size:40

Alignment explanation


    Indices: 7638--7722  Score: 107
    Period size: 40  Copynumber: 2.1  Consensus size: 40

       7628 AGATATAGAT

                  *                *               *
       7638 TGCCACGCGCCGTTAACTCGCGATGTGGACGCCACGTGTC
          1 TGCCACACGCCGTTAACTCGCGACGTGGACGCCACGTGTA

                   * **         *                   
       7678 TGCCACATGTTGTTAACTCGTGACGTGGACGCCACGTGTA
          1 TGCCACACGCCGTTAACTCGCGACGTGGACGCCACGTGTA

                 
       7718 TGCCA
          1 TGCCA

       7723 AGGTGTTCAC


Statistics
Matches: 38,  Mismatches: 7, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  40   38  1.00

ACGTcount: A:0.18, C:0.31, G:0.28, T:0.24


Consensus pattern (40 bp):   
TGCCACACGCCGTTAACTCGCGACGTGGACGCCACGTGTA

Found at i:9473 original size:14 final size:14

Alignment explanation


    Indices: 9456--9496  Score: 55
    Period size: 15  Copynumber: 2.8  Consensus size: 14

       9446 CTCTTCATCC

                          
       9456 TTTTCTTTTCTTTT
          1 TTTTCTTTTCTTTT

                *          
       9470 TTTTTTTTCTCTTTT
          1 TTTTCTTT-TCTTTT

                        
       9485 TTTTCTTCTTCT
          1 TTTTCTT-TTCT

       9497 CCTTCCTCTT


Statistics
Matches: 23,  Mismatches: 2, Indels: 3
        0.82            0.07        0.11

Matches are distributed among these distances:
  14    7  0.30
  15   15  0.65
  16    1  0.04

ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83


Consensus pattern (14 bp):   
TTTTCTTTTCTTTT
Done.