Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019924.1 Corchorus olitorius cultivar O-4 contig19957, 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: 6088
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32


Found at i:840 original size:5 final size:5

Alignment explanation


    Indices: 830--866  Score: 58
    Period size: 5  Copynumber: 7.6  Consensus size: 5

        820 AAATGGTTGC

                            *                            
        830 TTTGT TTTGT TTTGG TTTGT TTTGT TTTG- TTTGT TTT
          1 TTTGT TTTGT TTTGT TTTGT TTTGT TTTGT TTTGT TTT

        867 AATGTTTTAC


Statistics
Matches: 29,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
   4    4  0.14
   5   25  0.86

ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78


Consensus pattern (5 bp):   
TTTGT

Found at i:850 original size:15 final size:14

Alignment explanation


    Indices: 830--866  Score: 65
    Period size: 15  Copynumber: 2.6  Consensus size: 14

        820 AAATGGTTGC

                           
        830 TTTGTTTTGTTTTGG
          1 TTTGTTTTGTTTT-G

                          
        845 TTTGTTTTGTTTTG
          1 TTTGTTTTGTTTTG

                    
        859 TTTGTTTT
          1 TTTGTTTT

        867 AATGTTTTAC


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

Matches are distributed among these distances:
  14    9  0.41
  15   13  0.59

ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78


Consensus pattern (14 bp):   
TTTGTTTTGTTTTG

Found at i:2732 original size:19 final size:18

Alignment explanation


    Indices: 2708--2743  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       2698 TGAAGACTTA

                               
       2708 TTGAAGACAATTTGAAGAT
          1 TTGAAGACAA-TTGAAGAT

                    *        
       2727 TTGAAGACCATTGAAGA
          1 TTGAAGACAATTGAAGA

       2744 ATTATTTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28


Consensus pattern (18 bp):   
TTGAAGACAATTGAAGAT

Found at i:4066 original size:22 final size:22

Alignment explanation


    Indices: 4024--4066  Score: 52
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       4014 TTTCTAATTA

                           **     
       4024 ATTGTTTTCTTTAATTTTCTTG
          1 ATTGTTTTCTTTAATAGTCTTG

                                  
       4046 ATTGTTTTC-TTAGATAGTCTT
          1 ATTGTTTTCTTTA-ATAGTCTT

       4067 AATTACTAGT


Statistics
Matches: 18,  Mismatches: 2, Indels: 2
        0.82            0.09        0.09

Matches are distributed among these distances:
  21    3  0.17
  22   15  0.83

ACGTcount: A:0.16, C:0.09, G:0.12, T:0.63


Consensus pattern (22 bp):   
ATTGTTTTCTTTAATAGTCTTG
Done.