Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005424.1 Corchorus capsularis cultivar CVL-1 contig05442, 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: 20339
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34


Found at i:8373 original size:42 final size:43

Alignment explanation


    Indices: 8303--8385  Score: 125
    Period size: 42  Copynumber: 2.0  Consensus size: 43

       8293 CGCGTTTGGC

                                                       
       8303 TTATCGTGTCTCGTGTCTGAATCATGTC-AGACACGATTAAGA
          1 TTATCGTGTCTCGTGTCTGAATCATGTCAAGACACGATTAAGA

                     *              *                 
       8345 TTATCGTGTTTCGTGTC-GTAATCGTGTCAAGACACGATTAA
          1 TTATCGTGTCTCGTGTCTG-AATCATGTCAAGACACGATTAA

       8386 CACGTTTAAG


Statistics
Matches: 37,  Mismatches: 2, Indels: 3
        0.88            0.05        0.07

Matches are distributed among these distances:
  41    1  0.03
  42   24  0.65
  43   12  0.32

ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35


Consensus pattern (43 bp):   
TTATCGTGTCTCGTGTCTGAATCATGTCAAGACACGATTAAGA

Found at i:8398 original size:20 final size:21

Alignment explanation


    Indices: 8373--8415  Score: 61
    Period size: 20  Copynumber: 2.1  Consensus size: 21

       8363 TAATCGTGTC

                     *           
       8373 AAGACACGATTAACACG-TTT
          1 AAGACACGAGTAACACGCTTT

                       *         
       8393 AAGACACGAGTGACACGCTTT
          1 AAGACACGAGTAACACGCTTT

              
       8414 AA
          1 AA

       8416 TTAACGGGTT


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  20   15  0.75
  21    5  0.25

ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21


Consensus pattern (21 bp):   
AAGACACGAGTAACACGCTTT

Found at i:8572 original size:14 final size:14

Alignment explanation


    Indices: 8549--8582  Score: 59
    Period size: 14  Copynumber: 2.4  Consensus size: 14

       8539 TATATTCAAT

                 *        
       8549 TATATTTAATTATA
          1 TATATATAATTATA

                          
       8563 TATATATAATTATA
          1 TATATATAATTATA

                  
       8577 TATATA
          1 TATATA

       8583 GTTTAGTTAA


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  14   19  1.00

ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53


Consensus pattern (14 bp):   
TATATATAATTATA

Found at i:8810 original size:12 final size:12

Alignment explanation


    Indices: 8793--8824  Score: 64
    Period size: 12  Copynumber: 2.7  Consensus size: 12

       8783 TACCCTATGT

                        
       8793 AAACACGACACG
          1 AAACACGACACG

                        
       8805 AAACACGACACG
          1 AAACACGACACG

                    
       8817 AAACACGA
          1 AAACACGA

       8825 ATTGCCAGGT


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   20  1.00

ACGTcount: A:0.53, C:0.31, G:0.16, T:0.00


Consensus pattern (12 bp):   
AAACACGACACG
Done.