Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015353.1 Corchorus capsularis cultivar CVL-1 contig15374, 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: 5373
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33


Found at i:1623 original size:12 final size:13

Alignment explanation


    Indices: 1582--1626  Score: 74
    Period size: 13  Copynumber: 3.5  Consensus size: 13

       1572 AATTATTGTT

                         
       1582 TGCTTTATTAATC
          1 TGCTTTATTAATC

                        *
       1595 TGCTTTATTAATT
          1 TGCTTTATTAATC

                         
       1608 TGCTTTA-TAATC
          1 TGCTTTATTAATC

                   
       1620 TGCTTTA
          1 TGCTTTA

       1627 GATTTAGATT


Statistics
Matches: 30,  Mismatches: 2, Indels: 1
        0.91            0.06        0.03

Matches are distributed among these distances:
  12   11  0.37
  13   19  0.63

ACGTcount: A:0.22, C:0.13, G:0.09, T:0.56


Consensus pattern (13 bp):   
TGCTTTATTAATC

Found at i:1634 original size:6 final size:6

Alignment explanation


    Indices: 1623--1649  Score: 54
    Period size: 6  Copynumber: 4.5  Consensus size: 6

       1613 TATAATCTGC

                                           
       1623 TTTAGA TTTAGA TTTAGA TTTAGA TTT
          1 TTTAGA TTTAGA TTTAGA TTTAGA TTT

       1650 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:3223 original size:30 final size:30

Alignment explanation


    Indices: 3157--3214  Score: 89
    Period size: 30  Copynumber: 1.9  Consensus size: 30

       3147 TTTATAGGCA

                        *        *        
       3157 GATGTTCCACTATCGCAGGATTTACAAAAT
          1 GATGTTCCACTACCGCAGGATGTACAAAAT

                    *                   
       3187 GATGTTCCTCTACCGCAGGATGTACAAA
          1 GATGTTCCACTACCGCAGGATGTACAAA

       3215 CAGCTGTTCT


Statistics
Matches: 25,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  30   25  1.00

ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28


Consensus pattern (30 bp):   
GATGTTCCACTACCGCAGGATGTACAAAAT

Found at i:4435 original size:21 final size:21

Alignment explanation


    Indices: 4409--4448  Score: 80
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       4399 CAGAAATCTA

                                 
       4409 CTACTTCCTGTGGTACTTCCT
          1 CTACTTCCTGTGGTACTTCCT

                               
       4430 CTACTTCCTGTGGTACTTC
          1 CTACTTCCTGTGGTACTTC

       4449 TTCTCCATCA


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   19  1.00

ACGTcount: A:0.10, C:0.33, G:0.15, T:0.42


Consensus pattern (21 bp):   
CTACTTCCTGTGGTACTTCCT
Done.