Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011476.1 Corchorus olitorius cultivar O-4 contig11509, 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: 5431
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.39


Found at i:2106 original size:105 final size:101

Alignment explanation


    Indices: 1997--2269  Score: 317
    Period size: 105  Copynumber: 2.7  Consensus size: 101

       1987 TATTATAGAA

                                                                             
       1997 TTTTAGAAATAAAATATAAAACTGATTTCACTAAGTTTAACCCCAAATTAAAATTTTATTTATTT
          1 TTTTAGAAATAAAATATAAAACT-ATTTCACTAAGTTTAACCCCAAATTAAAA-TTTATTTATTT

                        *                           
       2062 TAAGGGTAAATTTCAAAATCAATAATTTATTGTTATAGGG
         64 TAAGGGTAAATTCCAAAATCAAT-A-TTATTGTTATAGGG

                            *               *      *                         
       2102 TTTTAGAAATAAAATACAAAACTCATTTCACTGAGTTTAGCCCCAAATT--AA--T-TTT-TTTT
          1 TTTTAGAAATAAAATATAAAACT-ATTTCACTAAGTTTAACCCCAAATTAAAATTTATTTATTTT

                          *   *                  
       2161 AAGGGTAAATTCCATAATTAATATTATTGTTATAGGG
         65 AAGGGTAAATTCCAAAATCAATATTATTGTTATAGGG

                 *            *     *              **               *        
       2198 TTTTACAAATAAAATATATAACTAATTCACTAAGTTT-AGGCCAAATTAAAATTAAAATTTTATT
          1 TTTTAGAAATAAAATATAAAACTATTTCACTAAGTTTAACCCCAAATTAAAATT--TA-TTTATT

                    
       2262 TTAAGGGT
         63 TTAAGGGT

       2270 TAGAAAAATT


Statistics
Matches: 143,  Mismatches: 16, Indels: 20
        0.80            0.09        0.11

Matches are distributed among these distances:
  94    7  0.05
  95   12  0.08
  96   36  0.25
  97    1  0.01
  98   23  0.16
  99    3  0.02
 100    1  0.01
 102    3  0.02
 103   12  0.08
 105   45  0.31

ACGTcount: A:0.41, C:0.10, G:0.10, T:0.40


Consensus pattern (101 bp):   
TTTTAGAAATAAAATATAAAACTATTTCACTAAGTTTAACCCCAAATTAAAATTTATTTATTTTA
AGGGTAAATTCCAAAATCAATATTATTGTTATAGGG

Found at i:5133 original size:3 final size:3

Alignment explanation


    Indices: 5127--5152  Score: 52
    Period size: 3  Copynumber: 8.7  Consensus size: 3

       5117 AGTAAATTCT

                                              
       5127 TTC TTC TTC TTC TTC TTC TTC TTC TT
          1 TTC TTC TTC TTC TTC TTC TTC TTC TT

       5153 GCATCAGAGA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   23  1.00

ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69


Consensus pattern (3 bp):   
TTC

Found at i:5157 original size:107 final size:107

Alignment explanation


    Indices: 5039--5232  Score: 343
    Period size: 107  Copynumber: 1.8  Consensus size: 107

       5029 AAATTGATAA

                                                                *            
       5039 TCTTCTTGCATCAGAGATCGATAACCTTCTTAATTGATTAATATTTAACAACGTTCTTAATAGCC
          1 TCTTCTTGCATCAGAGATCGATAACCTTCTTAATTGATTAATATTTAACAACATTCTTAATAGCC

                    *                                 
       5104 CTGTAGTTTTTTTAGTAAATTCTTTCTTCTTCTTCTTCTTCT
         66 CTGTAGTTATTTTAGTAAATTCTTTCTTCTTCTTCTTCTTCT

                                                      *      **              
       5146 TCTTCTTGCATCAGAGATCGATAACCTTCTTAATTGATTAATGTTTAACTTCATTCTTAATAGCC
          1 TCTTCTTGCATCAGAGATCGATAACCTTCTTAATTGATTAATATTTAACAACATTCTTAATAGCC

                                  
       5211 CTGTAGTTATTTTAGTAAATTC
         66 CTGTAGTTATTTTAGTAAATTC

       5233 AAATAAGAAA


Statistics
Matches: 82,  Mismatches: 5, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
 107   82  1.00

ACGTcount: A:0.25, C:0.19, G:0.10, T:0.46


Consensus pattern (107 bp):   
TCTTCTTGCATCAGAGATCGATAACCTTCTTAATTGATTAATATTTAACAACATTCTTAATAGCC
CTGTAGTTATTTTAGTAAATTCTTTCTTCTTCTTCTTCTTCT
Done.