Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012405.1 Corchorus olitorius cultivar O-4 contig12438, 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: 12133
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:836 original size:93 final size:93

Alignment explanation


    Indices: 737--926  Score: 299
    Period size: 93  Copynumber: 2.0  Consensus size: 93

        727 TAAACTTTTT

                   *      *                     *                  *         
        737 AATTAAATTAGTAATATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAA
          1 AATTAAAATAGTAAAATGGTAAAAATAAAATAGGTAAAAGGATATTAGATTTAATCAAATAAAAA

              **            *           
        802 TATTGTTTTTAGTTGAGTAAAACTATAA
         66 TAGAGTTTTTAGTTGACTAAAACTATAA

                                             *                             * 
        830 AATTAAAATAGTAAAATGGTAAAAATAAAATAGTTAAAAGGATATTAGATTTAATCAAATAAAGA
          1 AATTAAAATAGTAAAATGGTAAAAATAAAATAGGTAAAAGGATATTAGATTTAATCAAATAAAAA

                                        
        895 TAGAGTTTTTAGTTGACTAAAACTATAA
         66 TAGAGTTTTTAGTTGACTAAAACTATAA

                
        923 AATT
          1 AATT

        927 TTAAACAATG


Statistics
Matches: 88,  Mismatches: 9, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  93   88  1.00

ACGTcount: A:0.51, C:0.02, G:0.13, T:0.34


Consensus pattern (93 bp):   
AATTAAAATAGTAAAATGGTAAAAATAAAATAGGTAAAAGGATATTAGATTTAATCAAATAAAAA
TAGAGTTTTTAGTTGACTAAAACTATAA

Found at i:842 original size:22 final size:22

Alignment explanation


    Indices: 817--873  Score: 62
    Period size: 22  Copynumber: 2.5  Consensus size: 22

        807 TTTTTAGTTG

                            *      
        817 AGTAAAACT-ATAAAATTAAAAT
          1 AGTAAAA-TGATAAAAATAAAAT

                     *            
        839 AGTAAAATGGTAAAAATAAAAT
          1 AGTAAAATGATAAAAATAAAAT

                    *    
        861 AGTTAAAAGGATA
          1 AG-TAAAATGATA

        874 TTAGATTTAA


Statistics
Matches: 29,  Mismatches: 4, Indels: 3
        0.81            0.11        0.08

Matches are distributed among these distances:
  21    1  0.03
  22   20  0.69
  23    8  0.28

ACGTcount: A:0.61, C:0.02, G:0.12, T:0.25


Consensus pattern (22 bp):   
AGTAAAATGATAAAAATAAAAT

Found at i:995 original size:31 final size:31

Alignment explanation


    Indices: 960--1021  Score: 88
    Period size: 31  Copynumber: 2.0  Consensus size: 31

        950 ATATTCGAAA

                   *   *    * *            
        960 AATAAGGGTATGATAGGCGATTCAAAAGTTT
          1 AATAAGGATATAATAGACAATTCAAAAGTTT

                                           
        991 AATAAGGATATAATAGACAATTCAAAAGTTT
          1 AATAAGGATATAATAGACAATTCAAAAGTTT

       1022 TACAAAACTC


Statistics
Matches: 27,  Mismatches: 4, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  31   27  1.00

ACGTcount: A:0.45, C:0.06, G:0.19, T:0.29


Consensus pattern (31 bp):   
AATAAGGATATAATAGACAATTCAAAAGTTT

Found at i:1315 original size:19 final size:18

Alignment explanation


    Indices: 1291--1326  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       1281 TGAAGACTTA

                               
       1291 TTGAAGACAATTTGAAGAT
          1 TTGAAGACAA-TTGAAGAT

                    *        
       1310 TTGAAGACCATTGAAGA
          1 TTGAAGACAATTGAAGA

       1327 ATAATTTCAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28


Consensus pattern (18 bp):   
TTGAAGACAATTGAAGAT

Found at i:1333 original size:30 final size:30

Alignment explanation


    Indices: 1279--1338  Score: 77
    Period size: 30  Copynumber: 2.0  Consensus size: 30

       1269 GAAGTTCATG

                      *              *    
       1279 TTTGAAGACTTATTGAAGACAATTTGAAGA
          1 TTTGAAGACTCATTGAAGACAATTTCAAGA

                                *          
       1309 TTTGAAGAC-CATTGAAGAATAATTTCAAGA
          1 TTTGAAGACTCATTGAAG-ACAATTTCAAGA

       1339 GCAAGAATTG


Statistics
Matches: 26,  Mismatches: 3, Indels: 2
        0.84            0.10        0.06

Matches are distributed among these distances:
  29    7  0.27
  30   19  0.73

ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32


Consensus pattern (30 bp):   
TTTGAAGACTCATTGAAGACAATTTCAAGA

Found at i:2644 original size:22 final size:22

Alignment explanation


    Indices: 2602--2644  Score: 59
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       2592 TTTCTGATTA

                       *   **     
       2602 ATTGTTTTCTTTAATTTTCTTG
          1 ATTGTTTTCTTAAATAGTCTTG

                                 
       2624 ATTGTTTTCTTAAATAGTCTT
          1 ATTGTTTTCTTAAATAGTCTT

       2645 AATTATTAGT


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  22   18  1.00

ACGTcount: A:0.19, C:0.09, G:0.09, T:0.63


Consensus pattern (22 bp):   
ATTGTTTTCTTAAATAGTCTTG

Found at i:2828 original size:2 final size:2

Alignment explanation


    Indices: 2821--2853  Score: 66
    Period size: 2  Copynumber: 16.5  Consensus size: 2

       2811 ACGATCGATC

                                                             
       2821 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       2854 ATAAGATAAG


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   31  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Done.