Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005276.1 Corchorus capsularis cultivar CVL-1 contig05294, 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: 12420
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.34


Found at i:2433 original size:10 final size:10

Alignment explanation


    Indices: 2411--2449  Score: 60
    Period size: 10  Copynumber: 3.9  Consensus size: 10

       2401 AAATCTCGAT

                  *   
       2411 ATATCCGTAA
          1 ATATCCATAA

                      
       2421 ATATCCATAA
          1 ATATCCATAA

                  *   
       2431 ATATCCGTAA
          1 ATATCCATAA

                     
       2441 ATATCCATA
          1 ATATCCATA

       2450 TTAAATTAAA


Statistics
Matches: 26,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  10   26  1.00

ACGTcount: A:0.44, C:0.21, G:0.05, T:0.31


Consensus pattern (10 bp):   
ATATCCATAA

Found at i:2434 original size:20 final size:20

Alignment explanation


    Indices: 2411--2449  Score: 78
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       2401 AAATCTCGAT

                                
       2411 ATATCCGTAAATATCCATAA
          1 ATATCCGTAAATATCCATAA

                               
       2431 ATATCCGTAAATATCCATA
          1 ATATCCGTAAATATCCATA

       2450 TTAAATTAAA


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

Matches are distributed among these distances:
  20   19  1.00

ACGTcount: A:0.44, C:0.21, G:0.05, T:0.31


Consensus pattern (20 bp):   
ATATCCGTAAATATCCATAA

Found at i:3482 original size:12 final size:12

Alignment explanation


    Indices: 3461--3511  Score: 84
    Period size: 12  Copynumber: 4.2  Consensus size: 12

       3451 GATACCTCGC

                        
       3461 TATATCCGTCGA
          1 TATATCCGTCGA

                 *      
       3473 TATATTCGTCGA
          1 TATATCCGTCGA

                         
       3485 TATATCCGTTCGA
          1 TATATCCG-TCGA

                        
       3498 TATATCCGTCGA
          1 TATATCCGTCGA

              
       3510 TA
          1 TA

       3512 CCTGTATTTA


Statistics
Matches: 36,  Mismatches: 2, Indels: 2
        0.90            0.05        0.05

Matches are distributed among these distances:
  12   24  0.67
  13   12  0.33

ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37


Consensus pattern (12 bp):   
TATATCCGTCGA

Found at i:3502 original size:25 final size:24

Alignment explanation


    Indices: 3461--3511  Score: 84
    Period size: 25  Copynumber: 2.1  Consensus size: 24

       3451 GATACCTCGC

                             *      
       3461 TATATCCGTCGATATATTCGTCGA
          1 TATATCCGTCGATATATCCGTCGA

                                     
       3485 TATATCCGTTCGATATATCCGTCGA
          1 TATATCCG-TCGATATATCCGTCGA

              
       3510 TA
          1 TA

       3512 CCTGTATTTA


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  24    8  0.32
  25   17  0.68

ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37


Consensus pattern (24 bp):   
TATATCCGTCGATATATCCGTCGA

Found at i:11159 original size:15 final size:15

Alignment explanation


    Indices: 11141--11175  Score: 52
    Period size: 15  Copynumber: 2.3  Consensus size: 15

      11131 GAATGGCGCC

                           
      11141 AACAACAATGGTGCA
          1 AACAACAATGGTGCA

                  *       *
      11156 AACAACCATGGTGCG
          1 AACAACAATGGTGCA

                 
      11171 AACAA
          1 AACAA

      11176 TCATCTTGTG


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  15   18  1.00

ACGTcount: A:0.46, C:0.23, G:0.20, T:0.11


Consensus pattern (15 bp):   
AACAACAATGGTGCA
Done.