Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012003.1 Corchorus olitorius cultivar O-4 contig12036, 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: 22677
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:1380 original size:26 final size:26

Alignment explanation


    Indices: 1351--1402  Score: 68
    Period size: 26  Copynumber: 2.0  Consensus size: 26

       1341 TTTTCTCAAA

                   *                  
       1351 CTATTTTCTTGATCTCAAGTTTAATT
          1 CTATTTTATTGATCTCAAGTTTAATT

                       * *  *         
       1377 CTATTTTATTGTTTTCTAGTTTAATT
          1 CTATTTTATTGATCTCAAGTTTAATT

       1403 TGCCTATTTC


Statistics
Matches: 22,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  26   22  1.00

ACGTcount: A:0.21, C:0.12, G:0.08, T:0.60


Consensus pattern (26 bp):   
CTATTTTATTGATCTCAAGTTTAATT

Found at i:10907 original size:22 final size:20

Alignment explanation


    Indices: 10862--10907  Score: 56
    Period size: 20  Copynumber: 2.2  Consensus size: 20

      10852 CCCGGGCCAT

                               *
      10862 GGCCTGGTGCGCGCTGGCTT
          1 GGCCTGGTGCGCGCTGGCTA

                  *               
      10882 GGCCTGTTGCGCGGCATGGCTA
          1 GGCCTGGTGCGC-GC-TGGCTA

                
      10904 GGCC
          1 GGCC

      10908 ATGCCTGGGC


Statistics
Matches: 22,  Mismatches: 2, Indels: 2
        0.85            0.08        0.08

Matches are distributed among these distances:
  20   11  0.50
  21    2  0.09
  22    9  0.41

ACGTcount: A:0.04, C:0.30, G:0.43, T:0.22


Consensus pattern (20 bp):   
GGCCTGGTGCGCGCTGGCTA

Found at i:15681 original size:26 final size:26

Alignment explanation


    Indices: 15652--15703  Score: 70
    Period size: 26  Copynumber: 2.0  Consensus size: 26

      15642 TTTTCTTAAA

                   *                   
      15652 CTATTTTCTT-AATCTCTAGTTTAATT
          1 CTATTTTATTGAAT-TCTAGTTTAATT

                       *              
      15678 CTATTTTATTGTATTCTAGTTTAATT
          1 CTATTTTATTGAATTCTAGTTTAATT

      15704 TGTCTATTTT


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
  26   21  0.91
  27    2  0.09

ACGTcount: A:0.23, C:0.12, G:0.06, T:0.60


Consensus pattern (26 bp):   
CTATTTTATTGAATTCTAGTTTAATT

Found at i:16884 original size:21 final size:21

Alignment explanation


    Indices: 16845--16893  Score: 55
    Period size: 21  Copynumber: 2.3  Consensus size: 21

      16835 TCAATGCTTT

                         **       
      16845 AGGAATGCAAGAGGGATTTCAA
          1 AGGAA-GCAAGAGCCATTTCAA

                               * 
      16867 AGGAAGCAAGAGCCATTTCCA
          1 AGGAAGCAAGAGCCATTTCAA

                   
      16888 A-GAAGC
          1 AGGAAGC

      16894 TACAATTCTT


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  20    5  0.21
  21   14  0.58
  22    5  0.21

ACGTcount: A:0.41, C:0.16, G:0.29, T:0.14


Consensus pattern (21 bp):   
AGGAAGCAAGAGCCATTTCAA

Found at i:18701 original size:21 final size:21

Alignment explanation


    Indices: 18677--18717  Score: 57
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      18667 TTACCTTTGT

                                  
      18677 TCAT-AAATTCACTCACTTTAA
          1 TCATCAAATTCACT-ACTTTAA

                   *            
      18698 TCATCAATTTCACTACTTTA
          1 TCATCAAATTCACTACTTTA

      18718 TCACTTACAA


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  21   10  0.56
  22    8  0.44

ACGTcount: A:0.34, C:0.24, G:0.00, T:0.41


Consensus pattern (21 bp):   
TCATCAAATTCACTACTTTAA
Done.