Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021993.1 Corchorus olitorius cultivar O-4 contig22026, 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: 3249
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29


Found at i:607 original size:16 final size:16

Alignment explanation


    Indices: 583--615  Score: 50
    Period size: 16  Copynumber: 2.1  Consensus size: 16

        573 AGCTTCCTAG

                            
        583 AAAAACTCAAAA-AAA
          1 AAAAACTCAAAAGAAA

                             
        598 AAAAATCTCAAAAGAAA
          1 AAAAA-CTCAAAAGAAA

             
        615 A
          1 A

        616 TTGTTAGTAG


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  15    5  0.31
  16    7  0.44
  17    4  0.25

ACGTcount: A:0.76, C:0.12, G:0.03, T:0.09


Consensus pattern (16 bp):   
AAAAACTCAAAAGAAA

Found at i:739 original size:22 final size:22

Alignment explanation


    Indices: 711--819  Score: 87
    Period size: 22  Copynumber: 4.7  Consensus size: 22

        701 AAGAAAATCC

                                  
        711 TTTTTTTTATGACGCAGAAATT
          1 TTTTTTTTATGACGCAGAAATT

                    *                **
        733 TTTTTTTTTTAGAAAAACGCA-AAAAC
          1 TTTTTTTTAT-G----ACGCAGAAATT

                                **
        759 TTTTTTTTATGACGCAGAAACA
          1 TTTTTTTTATGACGCAGAAATT

                            *      
        781 TTTTTTTTATGACGCAAAAATAT
          1 TTTTTTTTATGACGCAGAAAT-T

                             
        804 TTTTTTTT-TCGACGCA
          1 TTTTTTTTAT-GACGCA

        820 AAACACAAAA


Statistics
Matches: 70,  Mismatches: 9, Indels: 15
        0.74            0.10        0.16

Matches are distributed among these distances:
  21    5  0.07
  22   32  0.46
  23   15  0.21
  25    1  0.01
  26   12  0.17
  27    5  0.07

ACGTcount: A:0.31, C:0.12, G:0.11, T:0.46


Consensus pattern (22 bp):   
TTTTTTTTATGACGCAGAAATT

Found at i:817 original size:23 final size:21

Alignment explanation


    Indices: 749--822  Score: 94
    Period size: 22  Copynumber: 3.4  Consensus size: 21

        739 TTTTAGAAAA

                     *           
        749 ACGCAAAAACTTTTTTTTATG
          1 ACGCAAAAAATTTTTTTTATG

                     *            
        770 ACGCAGAAACATTTTTTTTATG
          1 ACGCA-AAAAATTTTTTTTATG

                               *   
        792 ACGCAAAAATATTTTTTTTTTCG
          1 ACGCAAAAA-ATTTTTTTTAT-G

                    
        815 ACGCAAAA
          1 ACGCAAAA

        823 CACAAAACAA


Statistics
Matches: 46,  Mismatches: 4, Indels: 4
        0.85            0.07        0.07

Matches are distributed among these distances:
  21    8  0.17
  22   29  0.63
  23    9  0.20

ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39


Consensus pattern (21 bp):   
ACGCAAAAAATTTTTTTTATG

Found at i:889 original size:38 final size:38

Alignment explanation


    Indices: 814--888  Score: 118
    Period size: 37  Copynumber: 2.0  Consensus size: 38

        804 TTTTTTTTTC

                                            *     
        814 GACGCAAAACACAAAACAAAAATTTTTTTTTTCAAAAA
          1 GACGCAAAACACAAAACAAAAATTTTTTTTTTAAAAAA

                                                   
        852 GACGC-AAACACAAAAC-AAAATTTTTTTTTTAGAAAAA
          1 GACGCAAAACACAAAACAAAAATTTTTTTTTTA-AAAAA

        889 ACAGAAAACA


Statistics
Matches: 35,  Mismatches: 1, Indels: 3
        0.90            0.03        0.08

Matches are distributed among these distances:
  36   14  0.40
  37   16  0.46
  38    5  0.14

ACGTcount: A:0.52, C:0.15, G:0.07, T:0.27


Consensus pattern (38 bp):   
GACGCAAAACACAAAACAAAAATTTTTTTTTTAAAAAA

Found at i:898 original size:37 final size:37

Alignment explanation


    Indices: 819--902  Score: 111
    Period size: 36  Copynumber: 2.3  Consensus size: 37

        809 TTTTCGACGC

                                             *   
        819 AAAACACAAAACAAAAATTTTTTTTTTCAAAAAGACG
          1 AAAACACAAAACAAAAATTTTTTTTTTCAAAAAAACG

            *                                      
        856 CAAACACAAAAC-AAAATTTTTTTTTT-AGAAAAAACAG
          1 AAAACACAAAACAAAAATTTTTTTTTTCA-AAAAAAC-G

                       
        893 AAAACA-AAAA
          1 AAAACACAAAA

        903 TTAAAAACAC


Statistics
Matches: 42,  Mismatches: 3, Indels: 5
        0.84            0.06        0.10

Matches are distributed among these distances:
  35    1  0.02
  36   24  0.57
  37   17  0.40

ACGTcount: A:0.58, C:0.13, G:0.05, T:0.24


Consensus pattern (37 bp):   
AAAACACAAAACAAAAATTTTTTTTTTCAAAAAAACG

Found at i:1203 original size:15 final size:15

Alignment explanation


    Indices: 1183--1214  Score: 64
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       1173 ACAAAGATTG

                           
       1183 ACAGAAAGCAATTAA
          1 ACAGAAAGCAATTAA

                           
       1198 ACAGAAAGCAATTAA
          1 ACAGAAAGCAATTAA

              
       1213 AC
          1 AC

       1215 TAAAAAACAG


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   17  1.00

ACGTcount: A:0.59, C:0.16, G:0.12, T:0.12


Consensus pattern (15 bp):   
ACAGAAAGCAATTAA
Done.