Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015724.1 Corchorus olitorius cultivar O-4 contig15757, 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: 21843
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35


Found at i:533 original size:15 final size:17

Alignment explanation


    Indices: 499--535  Score: 51
    Period size: 15  Copynumber: 2.3  Consensus size: 17

        489 AAACTCTATT

                           * 
        499 TTTTATTTATATACCTA
          1 TTTTATTTATATACCCA

                             
        516 TTTTATTT-T-TACCCA
          1 TTTTATTTATATACCCA

                 
        531 TTTTA
          1 TTTTA

        536 CTAATTTAAT


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  15   10  0.53
  16    1  0.05
  17    8  0.42

ACGTcount: A:0.24, C:0.14, G:0.00, T:0.62


Consensus pattern (17 bp):   
TTTTATTTATATACCCA

Found at i:1339 original size:25 final size:24

Alignment explanation


    Indices: 1288--1344  Score: 80
    Period size: 25  Copynumber: 2.4  Consensus size: 24

       1278 GTCAGTCTTG

                                *   
       1288 AATTT-TTTAATGTTTAATTCTTA
          1 AATTTATTTAATGTTTAATTATTA

                                    *
       1311 AATTTATTTAATGTCTTAATTATTC
          1 AATTTATTTAATGT-TTAATTATTA

                     
       1336 AATTTATTT
          1 AATTTATTT

       1345 TACAATCCAC


Statistics
Matches: 30,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  23    5  0.17
  24    8  0.27
  25   17  0.57

ACGTcount: A:0.32, C:0.05, G:0.04, T:0.60


Consensus pattern (24 bp):   
AATTTATTTAATGTTTAATTATTA

Found at i:2421 original size:3 final size:3

Alignment explanation


    Indices: 2413--2445  Score: 66
    Period size: 3  Copynumber: 11.0  Consensus size: 3

       2403 ATTTTAGGTC

                                                       
       2413 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
          1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT

       2446 TCATGTTTAA


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   30  1.00

ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33


Consensus pattern (3 bp):   
AAT

Found at i:14229 original size:18 final size:18

Alignment explanation


    Indices: 14206--14240  Score: 54
    Period size: 18  Copynumber: 1.9  Consensus size: 18

      14196 TTAAATTTAG

                               
      14206 TATATATAGTAT-TATTAT
          1 TATATATA-TATATATTAT

                             
      14224 TATATATATATATATTA
          1 TATATATATATATATTA

      14241 AAGAAAAAAT


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

Matches are distributed among these distances:
  17    3  0.19
  18   13  0.81

ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54


Consensus pattern (18 bp):   
TATATATATATATATTAT

Found at i:14639 original size:21 final size:21

Alignment explanation


    Indices: 14614--14653  Score: 62
    Period size: 21  Copynumber: 1.9  Consensus size: 21

      14604 GTGTTTTGAA

                                 
      14614 GATCAGAAACAACAAGAATTT
          1 GATCAGAAACAACAAGAATTT

                     *  *      
      14635 GATCAGAAAGAAGAAGAAT
          1 GATCAGAAACAACAAGAAT

      14654 ATCATGGATC


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:0.55, C:0.10, G:0.20, T:0.15


Consensus pattern (21 bp):   
GATCAGAAACAACAAGAATTT
Done.