Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007602.1 Corchorus capsularis cultivar CVL-1 contig07623, 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: 5853
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35


Found at i:1713 original size:12 final size:12

Alignment explanation


    Indices: 1689--1722  Score: 50
    Period size: 12  Copynumber: 2.8  Consensus size: 12

       1679 CTTTCCCTCC

                         
       1689 TCTTTTCTGTTTT
          1 TCTTTTCT-TTTT

                        
       1702 TCTTTTCTTTTT
          1 TCTTTTCTTTTT

              *      
       1714 TCCTTTCTT
          1 TCTTTTCTT

       1723 CCTCTAACTG


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  12   12  0.60
  13    8  0.40

ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76


Consensus pattern (12 bp):   
TCTTTTCTTTTT

Found at i:2768 original size:20 final size:20

Alignment explanation


    Indices: 2743--2781  Score: 69
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       2733 AAAAAGAGCA

                                
       2743 CCAATTTGCAAATCAAATGT
          1 CCAATTTGCAAATCAAATGT

                    *          
       2763 CCAATTTGTAAATCAAATG
          1 CCAATTTGCAAATCAAATG

       2782 CCTTGTATTT


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:0.41, C:0.18, G:0.10, T:0.31


Consensus pattern (20 bp):   
CCAATTTGCAAATCAAATGT

Found at i:3356 original size:27 final size:27

Alignment explanation


    Indices: 3315--3381  Score: 82
    Period size: 27  Copynumber: 2.5  Consensus size: 27

       3305 AAGTAGACTC

                    * *               * 
       3315 AAAATGACTAGAATGCCCCTGA-ACATG
          1 AAAATGACCAAAATGCCCCTGATAC-CG

            *                          
       3342 CAAATGACCAAAATGCCCCTGATACCG
          1 AAAATGACCAAAATGCCCCTGATACCG

                         
       3369 AAAATGACCAAAA
          1 AAAATGACCAAAA

       3382 CGACCCTATT


Statistics
Matches: 34,  Mismatches: 5, Indels: 2
        0.83            0.12        0.05

Matches are distributed among these distances:
  27   32  0.94
  28    2  0.06

ACGTcount: A:0.45, C:0.25, G:0.15, T:0.15


Consensus pattern (27 bp):   
AAAATGACCAAAATGCCCCTGATACCG

Found at i:5816 original size:2 final size:2

Alignment explanation


    Indices: 5811--5853  Score: 86
    Period size: 2  Copynumber: 21.5  Consensus size: 2

       5801 ACTTTTTTTC

                                                                          
       5811 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG

             
       5853 A
          1 A


Statistics
Matches: 41,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   41  1.00

ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00


Consensus pattern (2 bp):   
AG

Done.