Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018649.1 Corchorus olitorius cultivar O-4 contig18682, 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: 10860
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30


Found at i:413 original size:48 final size:46

Alignment explanation


    Indices: 338--480  Score: 151
    Period size: 50  Copynumber: 3.0  Consensus size: 46

        328 GAGCGTGCCA

                        *         *                 *      
        338 ATCAATTTTGTCAAAAAATTGATAAAAAGTGCGATGAAAATTAAAAG
          1 ATCAATTTTGTCTAAAAATTGAGAAAAAGTGC-ATGAAAAATAAAAG

                                           *    *             
        385 ATCAATTTTGTCTTAAAAATTGAGAAAAAATATGCAAGTAAAAATAAAAG
          1 ATCAATTTTGTC-TAAAAATTGAG-AAAAA-GTGCATG-AAAAATAAAAG

            *           *                            *    
        435 TTCAATTTTGTAGTAAAAATTGAGAAAAAGTGCAGTGAAAAGTAAA
          1 ATCAATTTTGT-CTAAAAATTGAGAAAAAGTGCA-TGAAAAATAAA

        481 GGGTTGCTTT


Statistics
Matches: 80,  Mismatches: 10, Indels: 11
        0.79            0.10        0.11

Matches are distributed among these distances:
  47   12  0.15
  48   21  0.26
  49   13  0.16
  50   34  0.43

ACGTcount: A:0.51, C:0.06, G:0.15, T:0.28


Consensus pattern (46 bp):   
ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCATGAAAAATAAAAG

Found at i:1765 original size:9 final size:9

Alignment explanation


    Indices: 1745--1782  Score: 60
    Period size: 9  Copynumber: 4.3  Consensus size: 9

       1735 TTAATTCATT

                     
       1745 TAATTTCC-
          1 TAATTTCCA

                     
       1753 TAATTTCCA
          1 TAATTTCCA

                    *
       1762 TAATTTCCC
          1 TAATTTCCA

                     
       1771 TAATTTCCA
          1 TAATTTCCA

               
       1780 TAA
          1 TAA

       1783 GTAATTTGGG


Statistics
Matches: 27,  Mismatches: 2, Indels: 1
        0.90            0.07        0.03

Matches are distributed among these distances:
   8    8  0.30
   9   19  0.70

ACGTcount: A:0.32, C:0.24, G:0.00, T:0.45


Consensus pattern (9 bp):   
TAATTTCCA

Found at i:1774 original size:18 final size:17

Alignment explanation


    Indices: 1745--1782  Score: 67
    Period size: 18  Copynumber: 2.2  Consensus size: 17

       1735 TTAATTCATT

                             
       1745 TAATTTCCTAATTTCCA
          1 TAATTTCCTAATTTCCA

                              
       1762 TAATTTCCCTAATTTCCA
          1 TAATTT-CCTAATTTCCA

               
       1780 TAA
          1 TAA

       1783 GTAATTTGGG


Statistics
Matches: 20,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  17    6  0.30
  18   14  0.70

ACGTcount: A:0.32, C:0.24, G:0.00, T:0.45


Consensus pattern (17 bp):   
TAATTTCCTAATTTCCA

Found at i:9209 original size:15 final size:15

Alignment explanation


    Indices: 9189--9233  Score: 56
    Period size: 15  Copynumber: 2.9  Consensus size: 15

       9179 TTGTTTACAA

                       *   
       9189 AATATATAATAGTAT
          1 AATATATAATAATAT

                            
       9204 AATATA-ATATAATAT
          1 AATATATA-ATAATAT

                           
       9219 AATATAATAATAATA
          1 AATAT-ATAATAATA

       9234 ATAACAGCAC


Statistics
Matches: 26,  Mismatches: 1, Indels: 5
        0.81            0.03        0.16

Matches are distributed among these distances:
  14    1  0.04
  15   17  0.65
  16    7  0.27
  17    1  0.04

ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38


Consensus pattern (15 bp):   
AATATATAATAATAT

Found at i:9211 original size:5 final size:5

Alignment explanation


    Indices: 9201--9233  Score: 57
    Period size: 5  Copynumber: 6.4  Consensus size: 5

       9191 TATATAATAG

                                                   
       9201 TATAA TATAA TATAA TATAA TATAA TAATAA TA
          1 TATAA TATAA TATAA TATAA TATAA T-ATAA TA

       9234 ATAACAGCAC


Statistics
Matches: 27,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   5   22  0.81
   6    5  0.19

ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39


Consensus pattern (5 bp):   
TATAA

Done.