Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012284.1 Corchorus capsularis cultivar CVL-1 contig12305, 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: 11162
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36


Found at i:120 original size:14 final size:15

Alignment explanation


    Indices: 101--133  Score: 50
    Period size: 14  Copynumber: 2.3  Consensus size: 15

         91 TTTTTACAAC

                           
        101 AAAAAATAATTATT-
          1 AAAAAATAATTATTG

                   *       
        115 AAAAAATGATTATTG
          1 AAAAAATAATTATTG

                
        130 AAAA
          1 AAAA

        134 TATATAATAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  14   13  0.76
  15    4  0.24

ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30


Consensus pattern (15 bp):   
AAAAAATAATTATTG

Found at i:1668 original size:2 final size:2

Alignment explanation


    Indices: 1655--1684  Score: 51
    Period size: 2  Copynumber: 14.5  Consensus size: 2

       1645 GTTAAAAATA

                                                        
       1655 AT AT AT AGT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT A

       1685 GGGTTTAGGA


Statistics
Matches: 27,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   2   25  0.93
   3    2  0.07

ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47


Consensus pattern (2 bp):   
AT

Found at i:1732 original size:31 final size:31

Alignment explanation


    Indices: 1694--1758  Score: 130
    Period size: 31  Copynumber: 2.1  Consensus size: 31

       1684 AGGGTTTAGG

                                           
       1694 AATGACTTGAGTTGGATAGGGTTAAATCTGT
          1 AATGACTTGAGTTGGATAGGGTTAAATCTGT

                                           
       1725 AATGACTTGAGTTGGATAGGGTTAAATCTGT
          1 AATGACTTGAGTTGGATAGGGTTAAATCTGT

               
       1756 AAT
          1 AAT

       1759 CATACTTCAA


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  31   34  1.00

ACGTcount: A:0.31, C:0.06, G:0.28, T:0.35


Consensus pattern (31 bp):   
AATGACTTGAGTTGGATAGGGTTAAATCTGT

Found at i:3180 original size:2 final size:2

Alignment explanation


    Indices: 3173--3204  Score: 64
    Period size: 2  Copynumber: 16.0  Consensus size: 2

       3163 AAGTTGGTAA

                                                           
       3173 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
          1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT

       3205 TTTTGGGGAC


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   30  1.00

ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50


Consensus pattern (2 bp):   
CT

Found at i:3830 original size:15 final size:15

Alignment explanation


    Indices: 3810--3842  Score: 66
    Period size: 15  Copynumber: 2.2  Consensus size: 15

       3800 TTCTTAAAAT

                           
       3810 AGAACTCAGTGTGAC
          1 AGAACTCAGTGTGAC

                           
       3825 AGAACTCAGTGTGAC
          1 AGAACTCAGTGTGAC

               
       3840 AGA
          1 AGA

       3843 TTTAGAGTGC


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   18  1.00

ACGTcount: A:0.36, C:0.18, G:0.27, T:0.18


Consensus pattern (15 bp):   
AGAACTCAGTGTGAC

Found at i:8979 original size:19 final size:20

Alignment explanation


    Indices: 8943--8982  Score: 57
    Period size: 20  Copynumber: 2.1  Consensus size: 20

       8933 TTTCTGAAGA

                      *         
       8943 TTTCTTTTTGTCTATTTTTT
          1 TTTCTTTTTGACTATTTTTT

                                
       8963 TTTCTTTTT-ACT-TTTTTT
          1 TTTCTTTTTGACTATTTTTT

              
       8981 TT
          1 TT

       8983 CTCTCTAATG


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  18    8  0.42
  19    2  0.11
  20    9  0.47

ACGTcount: A:0.05, C:0.10, G:0.03, T:0.82


Consensus pattern (20 bp):   
TTTCTTTTTGACTATTTTTT
Done.