Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001179.1 Corchorus capsularis cultivar CVL-1 contig01179, 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: 11497
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34


Found at i:1452 original size:2 final size:2

Alignment explanation


    Indices: 1447--1475  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

       1437 TAATAGTGTG

                                                       
       1447 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       1476 CTCAAAGCTG


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:8043 original size:3 final size:3

Alignment explanation


    Indices: 8035--8066  Score: 64
    Period size: 3  Copynumber: 10.7  Consensus size: 3

       8025 TTATATATAT

                                                      
       8035 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
          1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT

       8067 TATTGAGTTG


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   29  1.00

ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34


Consensus pattern (3 bp):   
ATA

Found at i:8592 original size:3 final size:3

Alignment explanation


    Indices: 8584--8610  Score: 54
    Period size: 3  Copynumber: 9.0  Consensus size: 3

       8574 TTCCAAAATG

                                               
       8584 TAA TAA TAA TAA TAA TAA TAA TAA TAA
          1 TAA TAA TAA TAA TAA TAA TAA TAA TAA

       8611 AAACTTGTAC


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   24  1.00

ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33


Consensus pattern (3 bp):   
TAA

Found at i:10007 original size:29 final size:30

Alignment explanation


    Indices: 9945--10007  Score: 85
    Period size: 29  Copynumber: 2.2  Consensus size: 30

       9935 GTTTTGCCTC

                           *  *      *    
       9945 TTGAATTTCAATTTTGGATATTTTGTCCCA
          1 TTGAATTTCAATTTTAGACATTTTGACCCA

                                          
       9975 -TGAATTTCAATTTTAGACATTTT-ACCCA
          1 TTGAATTTCAATTTTAGACATTTTGACCCA

                 
      10003 TTGAA
          1 TTGAA

      10008 CTCACAGTTT


Statistics
Matches: 29,  Mismatches: 3, Indels: 3
        0.83            0.09        0.09

Matches are distributed among these distances:
  28    4  0.14
  29   25  0.86

ACGTcount: A:0.29, C:0.14, G:0.11, T:0.46


Consensus pattern (30 bp):   
TTGAATTTCAATTTTAGACATTTTGACCCA
Done.