Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023289.1 Corchorus olitorius cultivar O-4 contig23322, 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: 23111
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30


Found at i:38 original size:15 final size:15

Alignment explanation


    Indices: 6--39  Score: 50
    Period size: 15  Copynumber: 2.3  Consensus size: 15

          1 GGTCA

                        ** 
          6 TCAACGCCATCCTGC
          1 TCAACGCCATCCACC

                           
         21 TCAACGCCATCCACC
          1 TCAACGCCATCCACC

                
         36 TCAA
          1 TCAA

         40 GCTGCTGAGG


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  15   17  1.00

ACGTcount: A:0.26, C:0.47, G:0.09, T:0.18


Consensus pattern (15 bp):   
TCAACGCCATCCACC

Found at i:1300 original size:21 final size:21

Alignment explanation


    Indices: 1274--1313  Score: 62
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       1264 CAACAAAGAG

                    *    *       
       1274 GGAGATGCTTCCTTCCTCCTA
          1 GGAGATGCCTCCTACCTCCTA

                               
       1295 GGAGATGCCTCCTACCTCC
          1 GGAGATGCCTCCTACCTCC

       1314 CAAGAGGCGT


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.15, C:0.38, G:0.20, T:0.28


Consensus pattern (21 bp):   
GGAGATGCCTCCTACCTCCTA

Found at i:5338 original size:51 final size:50

Alignment explanation


    Indices: 5237--5339  Score: 118
    Period size: 51  Copynumber: 2.0  Consensus size: 50

       5227 GTTCTTCATA

                                           **         *       
       5237 TTTTTCTTGTTTAGATCTTGTCTCAGGACACCCAAACACTCTTTTAGTGT
          1 TTTTTCTTGTTTAGATCTTGTCTCAGGACACAAAAACACTCTATTAGTGT

                                      *     *         *    *    
       5287 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGACATAAAAACACTGTATTCGTGT
          1 TTTT-TCTTGTTT-AGATCTTGTCTCAGGACACAAAAACACTCTATTAGTGT

              
       5338 TT
          1 TT

       5340 CTCTTTCAGA


Statistics
Matches: 44,  Mismatches: 7, Indels: 3
        0.81            0.13        0.06

Matches are distributed among these distances:
  50    4  0.09
  51   39  0.89
  52    1  0.02

ACGTcount: A:0.20, C:0.21, G:0.14, T:0.45


Consensus pattern (50 bp):   
TTTTTCTTGTTTAGATCTTGTCTCAGGACACAAAAACACTCTATTAGTGT

Found at i:17345 original size:18 final size:18

Alignment explanation


    Indices: 17314--17349  Score: 56
    Period size: 19  Copynumber: 2.0  Consensus size: 18

      17304 ATAAAATTTC

                               
      17314 AATAAAAGAAATATATTAA
          1 AATAAAAGAAATAT-TTAA

                              
      17333 AATAAAA-AAATATTTAA
          1 AATAAAAGAAATATTTAA

      17350 TTTTTATTCC


Statistics
Matches: 17,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  17    4  0.24
  18    6  0.35
  19    7  0.41

ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28


Consensus pattern (18 bp):   
AATAAAAGAAATATTTAA

Found at i:17683 original size:64 final size:64

Alignment explanation


    Indices: 17599--17720  Score: 190
    Period size: 64  Copynumber: 1.9  Consensus size: 64

      17589 GACACTTAAC

                *                                            *   *          
      17599 TATCTTGTGCAATAATTCCGTTAGAAAACTTGGATGCCATTAAATAATGGACATTAGAACTATA
          1 TATCCTGTGCAATAATTCCGTTAGAAAACTTGGATGCCATTAAATAATGAACAATAGAACTATA

                       *               *          *                   
      17663 TATCCTGTGCATTAATTCCGTTAGAAAGCTTGGATGCCGTTAAATAATGAACAATAGA
          1 TATCCTGTGCAATAATTCCGTTAGAAAACTTGGATGCCATTAAATAATGAACAATAGA

      17721 CCTCTTTGTT


Statistics
Matches: 52,  Mismatches: 6, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  64   52  1.00

ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32


Consensus pattern (64 bp):   
TATCCTGTGCAATAATTCCGTTAGAAAACTTGGATGCCATTAAATAATGAACAATAGAACTATA

Found at i:21529 original size:21 final size:24

Alignment explanation


    Indices: 21505--21558  Score: 64
    Period size: 23  Copynumber: 2.5  Consensus size: 24

      21495 GTTATTTAAA

                       *            
      21505 TATTATAAAAAGAA-A-TT-AATT
          1 TATTATAAAAACAATATTTCAATT

                                    
      21526 TATTA-AAAAACAATATTTCAATT
          1 TATTATAAAAACAATATTTCAATT

                       
      21549 TATT-TAAAAA
          1 TATTATAAAAA

      21559 ATTGTGATTA


Statistics
Matches: 28,  Mismatches: 1, Indels: 6
        0.80            0.03        0.17

Matches are distributed among these distances:
  20    7  0.25
  21    6  0.21
  22    2  0.07
  23   13  0.46

ACGTcount: A:0.56, C:0.04, G:0.02, T:0.39


Consensus pattern (24 bp):   
TATTATAAAAACAATATTTCAATT
Done.