Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014955.1 Corchorus olitorius cultivar O-4 contig14988, 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: 2972
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.38


Found at i:2682 original size:15 final size:15

Alignment explanation


    Indices: 2662--2690  Score: 58
    Period size: 15  Copynumber: 1.9  Consensus size: 15

       2652 AAAAAAAAAA

                           
       2662 TTTCTTTGCGTTTTT
          1 TTTCTTTGCGTTTTT

                          
       2677 TTTCTTTGCGTTTT
          1 TTTCTTTGCGTTTT

       2691 ATTCTGAAAA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.00, C:0.14, G:0.14, T:0.72


Consensus pattern (15 bp):   
TTTCTTTGCGTTTTT

Found at i:2695 original size:14 final size:15

Alignment explanation


    Indices: 2663--2695  Score: 50
    Period size: 15  Copynumber: 2.3  Consensus size: 15

       2653 AAAAAAAAAT

                          *
       2663 TTCTTTGCGTTTTTT
          1 TTCTTTGCGTTTTTA

                           
       2678 TTCTTTGCG-TTTTA
          1 TTCTTTGCGTTTTTA

                
       2692 TTCT
          1 TTCT

       2696 GAAAAAAAAA


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

Matches are distributed among these distances:
  14    8  0.47
  15    9  0.53

ACGTcount: A:0.03, C:0.15, G:0.12, T:0.70


Consensus pattern (15 bp):   
TTCTTTGCGTTTTTA

Found at i:2714 original size:37 final size:36

Alignment explanation


    Indices: 2673--2743  Score: 110
    Period size: 36  Copynumber: 2.0  Consensus size: 36

       2663 TTCTTTGCGT

                                                  
       2673 TTTTTTTCTTTGCGT-TTT-ATTCTGAAAAAAAAAATA
          1 TTTTTTTCTTTGCGTCTTTAATT-T-AAAAAAAAAATA

                                               
       2709 TTTTTTTCTTTGCGTCTTTAATTTAAAAAAAAAAT
          1 TTTTTTTCTTTGCGTCTTTAATTTAAAAAAAAAAT

       2744 TGCATTGTGT


Statistics
Matches: 33,  Mismatches: 0, Indels: 4
        0.89            0.00        0.11

Matches are distributed among these distances:
  36   26  0.79
  37    4  0.12
  38    3  0.09

ACGTcount: A:0.34, C:0.08, G:0.07, T:0.51


Consensus pattern (36 bp):   
TTTTTTTCTTTGCGTCTTTAATTTAAAAAAAAAATA

Found at i:2813 original size:28 final size:27

Alignment explanation


    Indices: 2769--2822  Score: 81
    Period size: 28  Copynumber: 2.0  Consensus size: 27

       2759 GCGTTTTTGG

                     *                  
       2769 AAAAAAAAATCTGTTTTGTTTTTGTGTC
          1 AAAAAAAAAACTGTTTTG-TTTTGTGTC

                        *             
       2797 AAAAAAAAAACTTTTTTGTTTTGTGT
          1 AAAAAAAAAACTGTTTTGTTTTGTGT

       2823 TTTTGCGTTT


Statistics
Matches: 24,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  27    8  0.33
  28   16  0.67

ACGTcount: A:0.35, C:0.06, G:0.13, T:0.46


Consensus pattern (27 bp):   
AAAAAAAAAACTGTTTTGTTTTGTGTC
Done.