Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001330.1 Corchorus capsularis cultivar CVL-1 contig01330, 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: 9458
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.32


Found at i:1064 original size:15 final size:15

Alignment explanation


    Indices: 1039--1076  Score: 67
    Period size: 15  Copynumber: 2.5  Consensus size: 15

       1029 AAATTTCCTT

                            
       1039 ACCCGAAAATAACCGA
          1 ACCC-AAAATAACCGA

                           
       1055 ACCCAAAATAACCGA
          1 ACCCAAAATAACCGA

                   
       1070 ACCCAAA
          1 ACCCAAA

       1077 TCCAACCCGA


Statistics
Matches: 22,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  15   18  0.82
  16    4  0.18

ACGTcount: A:0.53, C:0.34, G:0.08, T:0.05


Consensus pattern (15 bp):   
ACCCAAAATAACCGA

Found at i:4992 original size:25 final size:26

Alignment explanation


    Indices: 4962--5014  Score: 72
    Period size: 27  Copynumber: 2.0  Consensus size: 26

       4952 ATATAATTAA

                     *                
       4962 AAGATT-ACTACAATATATGGGTCTT
          1 AAGATTAACGACAATATATGGGTCTT

                        *              
       4987 AAGATTAAACGATAATATATGGGTCTT
          1 AAGATT-AACGACAATATATGGGTCTT

             
       5014 A
          1 A

       5015 CCCATATAAG


Statistics
Matches: 24,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  25    6  0.25
  27   18  0.75

ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34


Consensus pattern (26 bp):   
AAGATTAACGACAATATATGGGTCTT

Found at i:6956 original size:14 final size:14

Alignment explanation


    Indices: 6939--6981  Score: 56
    Period size: 14  Copynumber: 3.3  Consensus size: 14

       6929 CCTCTGCTTC

                          
       6939 TTTTTATCTGTCGT
          1 TTTTTATCTGTCGT

                   *      
       6953 TTTTT-TGT-TC-T
          1 TTTTTATCTGTCGT

                          
       6964 TTTTTATCTGTCGT
          1 TTTTTATCTGTCGT

                
       6978 TTTT
          1 TTTT

       6982 GGACATAAAT


Statistics
Matches: 24,  Mismatches: 2, Indels: 6
        0.75            0.06        0.19

Matches are distributed among these distances:
  11    6  0.25
  12    4  0.17
  13    4  0.17
  14   10  0.42

ACGTcount: A:0.05, C:0.12, G:0.12, T:0.72


Consensus pattern (14 bp):   
TTTTTATCTGTCGT

Found at i:7089 original size:24 final size:24

Alignment explanation


    Indices: 7043--7089  Score: 67
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       7033 TTACAGTCTT

                            ***     
       7043 AAATGATGTAGAGTGTGCCAAAAA
          1 AAATGATGTAGAGTGTAAAAAAAA

                                   
       7067 AAATGATGTAGAGTGTAAAAAAA
          1 AAATGATGTAGAGTGTAAAAAAA

       7090 TAGGTGGAGT


Statistics
Matches: 20,  Mismatches: 3, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  24   20  1.00

ACGTcount: A:0.51, C:0.04, G:0.23, T:0.21


Consensus pattern (24 bp):   
AAATGATGTAGAGTGTAAAAAAAA
Done.