Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021611.1 Corchorus olitorius cultivar O-4 contig21644, 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: 10764
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32


Found at i:1613 original size:37 final size:37

Alignment explanation


    Indices: 1563--1639  Score: 154
    Period size: 37  Copynumber: 2.1  Consensus size: 37

       1553 AGGCTTGTAG

                                                 
       1563 TGTAGCAACTTCTTCTTCCACCATCTCAATATTCCCA
          1 TGTAGCAACTTCTTCTTCCACCATCTCAATATTCCCA

                                                 
       1600 TGTAGCAACTTCTTCTTCCACCATCTCAATATTCCCA
          1 TGTAGCAACTTCTTCTTCCACCATCTCAATATTCCCA

               
       1637 TGT
          1 TGT

       1640 TTCTCAAATT


Statistics
Matches: 40,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  37   40  1.00

ACGTcount: A:0.23, C:0.34, G:0.06, T:0.36


Consensus pattern (37 bp):   
TGTAGCAACTTCTTCTTCCACCATCTCAATATTCCCA

Found at i:1921 original size:13 final size:13

Alignment explanation


    Indices: 1899--1930  Score: 57
    Period size: 13  Copynumber: 2.5  Consensus size: 13

       1889 AAGACATTGA

                         
       1899 AATAGT-ATTAAT
          1 AATAGTAATTAAT

                         
       1911 AATAGTAATTAAT
          1 AATAGTAATTAAT

                   
       1924 AATAGTA
          1 AATAGTA

       1931 TTATTACTTT


Statistics
Matches: 19,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  12    6  0.32
  13   13  0.68

ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38


Consensus pattern (13 bp):   
AATAGTAATTAAT

Found at i:6769 original size:51 final size:51

Alignment explanation


    Indices: 6645--6770  Score: 200
    Period size: 51  Copynumber: 2.5  Consensus size: 51

       6635 TTAGTGTTAA

                                                      *        
       6645 AAAAAGATTAAATC-TGGTAAAGTTTGAAATAAAAATGTGATTTTTAGTTC
          1 AAAAAGATTAAATCTTGGTAAAGTTTGAAATAAAAATGTGATCTTTAGTTC

                             *                                *
       6695 AAAAAGATTAAATCTTGCTAAAGTTTGAAATAAAAATGTGATCTTTAGTTT
          1 AAAAAGATTAAATCTTGGTAAAGTTTGAAATAAAAATGTGATCTTTAGTTC

                      *       *      
       6746 AAAAAGATTAGATCTTGGGAAAGTT
          1 AAAAAGATTAAATCTTGGTAAAGTT

       6771 AAGAGCAAAA


Statistics
Matches: 69,  Mismatches: 6, Indels: 1
        0.91            0.08        0.01

Matches are distributed among these distances:
  50   14  0.20
  51   55  0.80

ACGTcount: A:0.44, C:0.05, G:0.17, T:0.35


Consensus pattern (51 bp):   
AAAAAGATTAAATCTTGGTAAAGTTTGAAATAAAAATGTGATCTTTAGTTC

Found at i:7310 original size:59 final size:59

Alignment explanation


    Indices: 7240--7376  Score: 149
    Period size: 59  Copynumber: 2.4  Consensus size: 59

       7230 ATTAAGTTAA

                  *                    **         *       *              
       7240 TTAAGAGTCAAAGAAAG-GTAATCAATGCT-AAGTGGCTTAATTCATGGTAATTGAGTCAG
          1 TTAAGAATCAAAGAAAGAG-AATCAATAATAAAG-GGCATAATTCAGGGTAATTGAGTCAG

                                    *                 *                
       7299 TTAAGAATCAAAGAAAGAGAATCAGTAATAAAGGGCATAATTTAGGGTAATTGAGTCAG
          1 TTAAGAATCAAAGAAAGAGAATCAATAATAAAGGGCATAATTCAGGGTAATTGAGTCAG

                *                 
       7358 TTAAAAAT--AA-AAAGAGAAT
          1 TTAAGAATCAAAGAAAGAGAAT

       7377 TAATTGTTAA


Statistics
Matches: 68,  Mismatches: 8, Indels: 7
        0.82            0.10        0.08

Matches are distributed among these distances:
  56    9  0.13
  57    2  0.03
  59   53  0.78
  60    4  0.06

ACGTcount: A:0.45, C:0.07, G:0.22, T:0.26


Consensus pattern (59 bp):   
TTAAGAATCAAAGAAAGAGAATCAATAATAAAGGGCATAATTCAGGGTAATTGAGTCAG
Done.