Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023546.1 Corchorus olitorius cultivar O-4 contig23579, 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: 5302
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:489 original size:51 final size:50

Alignment explanation


    Indices: 388--489  Score: 127
    Period size: 51  Copynumber: 2.0  Consensus size: 50

        378 GTTCTTCATA

                                                     * **     
        388 TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCTTTTAGTGT
          1 TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGT

                                            *                    
        438 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTGT
          1 TTTTC-CTTGTTT-AGATCTTGTCTCCGGACAAACAAACACTCGTACA-GTGT

             
        489 T
          1 T

        490 CTTCATTCAG


Statistics
Matches: 45,  Mismatches: 4, Indels: 5
        0.83            0.07        0.09

Matches are distributed among these distances:
  50    7  0.16
  51   37  0.82
  52    1  0.02

ACGTcount: A:0.22, C:0.24, G:0.14, T:0.41


Consensus pattern (50 bp):   
TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGT

Found at i:4721 original size:11 final size:11

Alignment explanation


    Indices: 4688--4739  Score: 63
    Period size: 11  Copynumber: 4.8  Consensus size: 11

       4678 GTTTGGCATC

                 *     
       4688 GTTTTCGTTTT
          1 GTTTTTGTTTT

                        
       4699 -TTTGTT-TTTT
          1 GTTT-TTGTTTT

                       
       4709 GTTTTTGTTTT
          1 GTTTTTGTTTT

                 *     
       4720 GTTTTCGTTTT
          1 GTTTTTGTTTT

                     
       4731 GTTTTTGTT
          1 GTTTTTGTT

       4740 GCGCTGTCAA


Statistics
Matches: 35,  Mismatches: 3, Indels: 6
        0.80            0.07        0.14

Matches are distributed among these distances:
  10    9  0.26
  11   26  0.74

ACGTcount: A:0.00, C:0.04, G:0.17, T:0.79


Consensus pattern (11 bp):   
GTTTTTGTTTT

Found at i:4736 original size:6 final size:6

Alignment explanation


    Indices: 4697--4739  Score: 54
    Period size: 6  Copynumber: 7.3  Consensus size: 6

       4687 CGTTTTCGTT

                                             *                  
       4697 TTTTTG TTTTTTG TTTTTG -TTTTG TTTTCG -TTTTG TTTTTG TT
          1 TTTTTG -TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TT

       4740 GCGCTGTCAA


Statistics
Matches: 32,  Mismatches: 2, Indels: 5
        0.82            0.05        0.13

Matches are distributed among these distances:
   5    9  0.28
   6   17  0.53
   7    6  0.19

ACGTcount: A:0.00, C:0.02, G:0.16, T:0.81


Consensus pattern (6 bp):   
TTTTTG
Done.