Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016225.1 Corchorus olitorius cultivar O-4 contig16258, 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: 25491
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31


Found at i:647 original size:7 final size:6

Alignment explanation


    Indices: 616--646  Score: 53
    Period size: 6  Copynumber: 5.0  Consensus size: 6

        606 AAGTAACCGG

                                               
        616 ATTTTT AATTTTT ATTTTT ATTTTT ATTTTT
          1 ATTTTT -ATTTTT ATTTTT ATTTTT ATTTTT

        647 TTCCCACTCT


Statistics
Matches: 24,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
   6   18  0.75
   7    6  0.25

ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81


Consensus pattern (6 bp):   
ATTTTT

Found at i:18833 original size:50 final size:51

Alignment explanation


    Indices: 18741--18838  Score: 114
    Period size: 50  Copynumber: 1.9  Consensus size: 51

      18731 ACTTTGTTAG

                                      *       *                
      18741 TTTGTTTATTTAGTCATTTCATTAGTTATGTTTATTTATGTTT-TTTATAA
          1 TTTGTTTATTTAGTCATTTCATTAGTGATGTTTAGTTATGTTTATTTATAA

                       *                                       
      18791 TTTGTTTATTTGGTCATTTCTCATTA-TAGATG-TTAGTT-TGTTTATTTA
          1 TTTGTTTATTTAGTCA-TT-TCATTAGT-GATGTTTAGTTATGTTTATTTA

      18839 ATCATTTCAT


Statistics
Matches: 41,  Mismatches: 3, Indels: 7
        0.80            0.06        0.14

Matches are distributed among these distances:
  50   20  0.49
  51   12  0.29
  52    9  0.22

ACGTcount: A:0.20, C:0.05, G:0.12, T:0.62


Consensus pattern (51 bp):   
TTTGTTTATTTAGTCATTTCATTAGTGATGTTTAGTTATGTTTATTTATAA

Found at i:18844 original size:36 final size:36

Alignment explanation


    Indices: 18791--18900  Score: 123
    Period size: 40  Copynumber: 2.9  Consensus size: 36

      18781 TTTTTTATAA

                        *                       
      18791 TTTGTTTATTTGGTCATTTCTCATTATAGATGTTAG
          1 TTTGTTTATTTGATCATTTCTCATTATAGATGTTAG

                       *          *         *        
      18827 TTTGTTTATTTAATCATTTCATTAGTTATATTTAT-TATAG
          1 TTTGTTTATTTGATCATTTC-TCA-TTATA--GATGT-TAG

                          *                   
      18867 TTTGTTTATTTGATTATTTCTCATTATAGATGTT
          1 TTTGTTTATTTGATCATTTCTCATTATAGATGTT

      18901 TAAGTATGTA


Statistics
Matches: 60,  Mismatches: 8, Indels: 12
        0.75            0.10        0.15

Matches are distributed among these distances:
  36   21  0.35
  37    3  0.05
  38   10  0.17
  39    3  0.05
  40   23  0.38

ACGTcount: A:0.23, C:0.06, G:0.12, T:0.59


Consensus pattern (36 bp):   
TTTGTTTATTTGATCATTTCTCATTATAGATGTTAG

Found at i:21741 original size:61 final size:61

Alignment explanation


    Indices: 21642--21764  Score: 228
    Period size: 61  Copynumber: 2.0  Consensus size: 61

      21632 GACACGGTTA

                                             *                           
      21642 AAAATGACAGATATTGGGGACAAGAGGGAGTACTATATAAACACGATATAGGAAAGTAAGT
          1 AAAATGACAGATATTGGGGACAAGAGGGAGTACCATATAAACACGATATAGGAAAGTAAGT

                                                                 *       
      21703 AAAATGACAGATATTGGGGACAAGAGGGAGTACCATATAAACACGATATAGGAGAGTAAGT
          1 AAAATGACAGATATTGGGGACAAGAGGGAGTACCATATAAACACGATATAGGAAAGTAAGT

             
      21764 A
          1 A

      21765 CCTGAAGGTC


Statistics
Matches: 60,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  61   60  1.00

ACGTcount: A:0.46, C:0.09, G:0.27, T:0.19


Consensus pattern (61 bp):   
AAAATGACAGATATTGGGGACAAGAGGGAGTACCATATAAACACGATATAGGAAAGTAAGT

Found at i:22853 original size:1 final size:1

Alignment explanation


    Indices: 22847--22879  Score: 66
    Period size: 1  Copynumber: 33.0  Consensus size: 1

      22837 TGGGTCAAGG

                                             
      22847 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

      22880 CAGAATTAAA


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   32  1.00

ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00


Consensus pattern (1 bp):   
T

Found at i:23841 original size:25 final size:24

Alignment explanation


    Indices: 23813--23869  Score: 71
    Period size: 25  Copynumber: 2.4  Consensus size: 24

      23803 GTGGATTGTA

                        *       *    
      23813 AAATAAATTGAATAATTAAGTCATT
          1 AAATAAATTGAAGAATTAA-ACATT

                     *              
      23838 AAATAAATTTAAGAATTAAACATT
          1 AAATAAATTGAAGAATTAAACATT

                     
      23862 AAA-AAATT
          1 AAATAAATT

      23870 CAAGGCTGAC


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

Matches are distributed among these distances:
  23    5  0.17
  24    7  0.24
  25   17  0.59

ACGTcount: A:0.58, C:0.04, G:0.05, T:0.33


Consensus pattern (24 bp):   
AAATAAATTGAAGAATTAAACATT

Found at i:24876 original size:32 final size:32

Alignment explanation


    Indices: 24835--24895  Score: 113
    Period size: 32  Copynumber: 1.9  Consensus size: 32

      24825 GACATTTAAG

                                 *          
      24835 AAATATATTCGAAAAATAAGGGTATAATAGAC
          1 AAATATATTCGAAAAATAAGGATATAATAGAC

                                         
      24867 AAATATATTCGAAAAATAAGGATATAATA
          1 AAATATATTCGAAAAATAAGGATATAATA

      24896 AGTGATTCAA


Statistics
Matches: 28,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  32   28  1.00

ACGTcount: A:0.56, C:0.05, G:0.13, T:0.26


Consensus pattern (32 bp):   
AAATATATTCGAAAAATAAGGATATAATAGAC
Done.