Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012528.1 Corchorus olitorius cultivar O-4 contig12561, 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: 6623
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35


Found at i:3930 original size:19 final size:18

Alignment explanation


    Indices: 3897--3932  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       3887 TTGAGATAAT

                              
       3897 TCTTCAATGATCTTCAAA
          1 TCTTCAATGATCTTCAAA

                     *        
       3915 TCTTCAAATTATCTTCAA
          1 TCTTC-AATGATCTTCAA

       3933 TAAGTCTTCA


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

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGATCTTCAAA

Found at i:4816 original size:18 final size:18

Alignment explanation


    Indices: 4793--4830  Score: 58
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       4783 CTCCTCTATC

                     *        
       4793 ATGAAAACACTTCTTTTT
          1 ATGAAAACAATTCTTTTT

                        *     
       4811 ATGAAAACAATTTTTTTT
          1 ATGAAAACAATTCTTTTT

              
       4829 AT
          1 AT

       4831 TACCCTTTCA


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.37, C:0.11, G:0.05, T:0.47


Consensus pattern (18 bp):   
ATGAAAACAATTCTTTTT

Found at i:5733 original size:24 final size:24

Alignment explanation


    Indices: 5697--5756  Score: 111
    Period size: 24  Copynumber: 2.5  Consensus size: 24

       5687 AAGGGTGAAG

                    *               
       5697 CTCTTCCTTTTCTTGATTAACCTC
          1 CTCTTCCTCTTCTTGATTAACCTC

                                    
       5721 CTCTTCCTCTTCTTGATTAACCTC
          1 CTCTTCCTCTTCTTGATTAACCTC

                        
       5745 CTCTTCCTCTTC
          1 CTCTTCCTCTTC

       5757 CTTATTCTCA


Statistics
Matches: 35,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  24   35  1.00

ACGTcount: A:0.10, C:0.38, G:0.03, T:0.48


Consensus pattern (24 bp):   
CTCTTCCTCTTCTTGATTAACCTC

Found at i:6545 original size:22 final size:23

Alignment explanation


    Indices: 6496--6550  Score: 69
    Period size: 23  Copynumber: 2.5  Consensus size: 23

       6486 ATGGTCGATG

                                 * 
       6496 GTTTTGCTTCCTTAAATCGACTA
          1 GTTTTGCTTCCTTAAATCGACAA

                           *       
       6519 GTTTTGCTTCCTT-AGTCGACAA
          1 GTTTTGCTTCCTTAAATCGACAA

                 *     
       6541 -TTTTTCTTCC
          1 GTTTTGCTTCC

       6551 ACTTGTCGAC


Statistics
Matches: 29,  Mismatches: 3, Indels: 2
        0.85            0.09        0.06

Matches are distributed among these distances:
  21    9  0.31
  22    7  0.24
  23   13  0.45

ACGTcount: A:0.16, C:0.24, G:0.13, T:0.47


Consensus pattern (23 bp):   
GTTTTGCTTCCTTAAATCGACAA
Done.