Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011767.1 Corchorus capsularis cultivar CVL-1 contig11788, 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: 37213
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.34


Found at i:1480 original size:19 final size:21

Alignment explanation


    Indices: 1456--1497  Score: 61
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       1446 CTGGATGATC

                                 
       1456 TATAA-TAT-TATCTATATAA
          1 TATAATTATATATCTATATAA

                         *       
       1475 TATAATTATATATTTATATAA
          1 TATAATTATATATCTATATAA

              
       1496 TA
          1 TA

       1498 ATGTGAATAA


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

Matches are distributed among these distances:
  19    5  0.25
  20    3  0.15
  21   12  0.60

ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50


Consensus pattern (21 bp):   
TATAATTATATATCTATATAA

Found at i:29709 original size:15 final size:15

Alignment explanation


    Indices: 29691--29728  Score: 51
    Period size: 15  Copynumber: 2.6  Consensus size: 15

      29681 TCAAAACATA

                 *         
      29691 ATTTTTTAAAATTTT
          1 ATTTTATAAAATTTT

                    *      
      29706 ATTTTATATAATTTT
          1 ATTTTATAAAATTTT

                     
      29721 -TTTTATAA
          1 ATTTTATAA

      29729 TTAAGGGTCA


Statistics
Matches: 20,  Mismatches: 3, Indels: 1
        0.83            0.12        0.04

Matches are distributed among these distances:
  14    7  0.35
  15   13  0.65

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


Consensus pattern (15 bp):   
ATTTTATAAAATTTT

Found at i:36577 original size:1 final size:1

Alignment explanation


    Indices: 36571--36595  Score: 50
    Period size: 1  Copynumber: 25.0  Consensus size: 1

      36561 TCCAACCTGT

                                     
      36571 AAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAA

      36596 GAAGTTGACT


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

Matches are distributed among these distances:
   1   24  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Found at i:37102 original size:17 final size:17

Alignment explanation


    Indices: 37082--37122  Score: 73
    Period size: 17  Copynumber: 2.4  Consensus size: 17

      37072 CATTTTGATT

                  *          
      37082 AAAAAACTATTTTTTTA
          1 AAAAAAATATTTTTTTA

                             
      37099 AAAAAAATATTTTTTTA
          1 AAAAAAATATTTTTTTA

                   
      37116 AAAAAAA
          1 AAAAAAA

      37123 AAATTGGGTG


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

Matches are distributed among these distances:
  17   23  1.00

ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39


Consensus pattern (17 bp):   
AAAAAAATATTTTTTTA
Done.