Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023434.1 Corchorus olitorius cultivar O-4 contig23467, 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: 2002
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--27  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

                                                    
          1 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 T

         28 GACACGATTA


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:633 original size:15 final size:15

Alignment explanation


    Indices: 595--633  Score: 69
    Period size: 15  Copynumber: 2.6  Consensus size: 15

        585 TATTGTCTTT

                    *      
        595 AATCTCACAATAGCC
          1 AATCTCACCATAGCC

                           
        610 AATCTCACCATAGCC
          1 AATCTCACCATAGCC

                     
        625 AATCTCACC
          1 AATCTCACC

        634 GCTACACCGA


Statistics
Matches: 23,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  15   23  1.00

ACGTcount: A:0.36, C:0.38, G:0.05, T:0.21


Consensus pattern (15 bp):   
AATCTCACCATAGCC

Found at i:1513 original size:20 final size:21

Alignment explanation


    Indices: 1488--1528  Score: 66
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       1478 CCACCGTAGA

                                 
       1488 CTCCA-TTCCCCACTTTTGCT
          1 CTCCATTTCCCCACTTTTGCT

                     *           
       1508 CTCCATTTCTCCACTTTTGCT
          1 CTCCATTTCCCCACTTTTGCT

       1529 TTCATTTTTG


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  20    5  0.26
  21   14  0.74

ACGTcount: A:0.10, C:0.41, G:0.05, T:0.44


Consensus pattern (21 bp):   
CTCCATTTCCCCACTTTTGCT

Found at i:1696 original size:28 final size:28

Alignment explanation


    Indices: 1649--1725  Score: 120
    Period size: 28  Copynumber: 2.8  Consensus size: 28

       1639 TCTGTTTTAC

                        *  *             
       1649 TTGTTGAATTGGGATGATTTTGTGTG-TT
          1 TTGTTGAATTGGAATAATTTTGTG-GATT

                                        
       1677 TTGTTGAATTGGAATAATTTTGTGGATT
          1 TTGTTGAATTGGAATAATTTTGTGGATT

                                 
       1705 TTGTTGAATTGGAATAATTTT
          1 TTGTTGAATTGGAATAATTTT

       1726 TTGGGTGCAT


Statistics
Matches: 46,  Mismatches: 2, Indels: 2
        0.92            0.04        0.04

Matches are distributed among these distances:
  27    1  0.02
  28   45  0.98

ACGTcount: A:0.22, C:0.00, G:0.26, T:0.52


Consensus pattern (28 bp):   
TTGTTGAATTGGAATAATTTTGTGGATT
Done.