Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024029.1 Corchorus olitorius cultivar O-4 contig24062, 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: 6981
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37


Found at i:1182 original size:18 final size:20

Alignment explanation


    Indices: 1155--1194  Score: 57
    Period size: 19  Copynumber: 2.1  Consensus size: 20

       1145 TTGAGTAGAC

                        *       
       1155 TTTAACTTTC-TGTTGGGCT
          1 TTTAACTTTCTTATTGGGCT

                                
       1174 TTTAA-TTTCTTATTGGGCT
          1 TTTAACTTTCTTATTGGGCT

              
       1193 TT
          1 TT

       1195 GCTAAGCTAT


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

Matches are distributed among these distances:
  18    4  0.21
  19   15  0.79

ACGTcount: A:0.12, C:0.12, G:0.17, T:0.57


Consensus pattern (20 bp):   
TTTAACTTTCTTATTGGGCT

Found at i:2138 original size:35 final size:35

Alignment explanation


    Indices: 2099--2176  Score: 104
    Period size: 34  Copynumber: 2.3  Consensus size: 35

       2089 GAGAATATCA

                      * *  *                   
       2099 TTAAGTTTTTTTTATTGGAAAAGTTCCCACCAGTT
          1 TTAAGTTTTTGTAATCGGAAAAGTTCCCACCAGTT

                              *            *   
       2134 TTAAG-TTTTGTAATCGGGAAAGTTCCCACCGGTT
          1 TTAAGTTTTTGTAATCGGAAAAGTTCCCACCAGTT

                     
       2168 TTAAGTTTT
          1 TTAAGTTTT

       2177 CAAATTGGGA


Statistics
Matches: 37,  Mismatches: 5, Indels: 2
        0.84            0.11        0.05

Matches are distributed among these distances:
  34   29  0.78
  35    8  0.22

ACGTcount: A:0.24, C:0.14, G:0.18, T:0.44


Consensus pattern (35 bp):   
TTAAGTTTTTGTAATCGGAAAAGTTCCCACCAGTT

Found at i:2161 original size:34 final size:34

Alignment explanation


    Indices: 2118--2195  Score: 120
    Period size: 34  Copynumber: 2.3  Consensus size: 34

       2108 TTTTATTGGA

                                     **       
       2118 AAAGTTCCCACCAGTTTTAAGTTTTGTAATCGGG
          1 AAAGTTCCCACCAGTTTTAAGTTTTCAAATCGGG

                        *                 *   
       2152 AAAGTTCCCACCGGTTTTAAGTTTTCAAATTGGG
          1 AAAGTTCCCACCAGTTTTAAGTTTTCAAATCGGG

                      
       2186 AAAGTTCCCA
          1 AAAGTTCCCA

       2196 TTCAATTTTT


Statistics
Matches: 40,  Mismatches: 4, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  34   40  1.00

ACGTcount: A:0.28, C:0.19, G:0.19, T:0.33


Consensus pattern (34 bp):   
AAAGTTCCCACCAGTTTTAAGTTTTCAAATCGGG

Found at i:6436 original size:19 final size:20

Alignment explanation


    Indices: 6412--6454  Score: 79
    Period size: 19  Copynumber: 2.2  Consensus size: 20

       6402 GAATGTGTCC

                                
       6412 TAGGTTTGCCTATAAATA-G
          1 TAGGTTTGCCTATAAATAGG

                                
       6431 TAGGTTTGCCTATAAATAGG
          1 TAGGTTTGCCTATAAATAGG

                
       6451 TAGG
          1 TAGG

       6455 ATTATTTCAG


Statistics
Matches: 23,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  19   18  0.78
  20    5  0.22

ACGTcount: A:0.30, C:0.09, G:0.26, T:0.35


Consensus pattern (20 bp):   
TAGGTTTGCCTATAAATAGG
Done.