Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018508.1 Corchorus olitorius cultivar O-4 contig18541, 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: 15670
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--34  Score: 68
    Period size: 2  Copynumber: 17.0  Consensus size: 2

                                                              
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

         35 ATTTGGCTAT


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   32  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:4166 original size:6 final size:6

Alignment explanation


    Indices: 4155--4183  Score: 58
    Period size: 6  Copynumber: 4.8  Consensus size: 6

       4145 TCTTTACTCA

                                             
       4155 CCGTCG CCGTCG CCGTCG CCGTCG CCGTC
          1 CCGTCG CCGTCG CCGTCG CCGTCG CCGTC

       4184 TTCGTAGATC


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

Matches are distributed among these distances:
   6   23  1.00

ACGTcount: A:0.00, C:0.52, G:0.31, T:0.17


Consensus pattern (6 bp):   
CCGTCG

Found at i:9764 original size:44 final size:40

Alignment explanation


    Indices: 9708--9794  Score: 104
    Period size: 44  Copynumber: 2.1  Consensus size: 40

       9698 TTTTGTGTGT

                          *                             
       9708 GAGAGGTAGCCCATCTATTTGGGACCTTTGTATGTGTGTTGAGA
          1 GAGAGGTAGCCCATATATTTGGGA-CTTT-TA--TGTGTTGAGA

                             *                       
       9752 GAGAGAGT-GCCCATATGTTTGGGACTTTTATGTGTTGAGA
          1 GAGAG-GTAGCCCATATATTTGGGACTTTTATGTGTTGAGA

               
       9792 GAG
          1 GAG

       9795 TACCCGCGTG


Statistics
Matches: 40,  Mismatches: 2, Indels: 6
        0.83            0.04        0.12

Matches are distributed among these distances:
  40   13  0.32
  42    2  0.05
  43    4  0.10
  44   19  0.47
  45    2  0.05

ACGTcount: A:0.22, C:0.11, G:0.33, T:0.33


Consensus pattern (40 bp):   
GAGAGGTAGCCCATATATTTGGGACTTTTATGTGTTGAGA

Found at i:11773 original size:43 final size:43

Alignment explanation


    Indices: 11712--11797  Score: 120
    Period size: 43  Copynumber: 2.0  Consensus size: 43

      11702 TCATTAGTCG

                      *           **           *       
      11712 ACAATCAAATTAGACTTTTATCTGAGCTGAAATTGGGATGTTA
          1 ACAATCAAATCAGACTTTTATCCAAGCTGAAATTGAGATGTTA

                                                        
      11755 ACAATCAAATCATG-CTTTTATCCAAGCTGAAATTGAGATGTTA
          1 ACAATCAAATCA-GACTTTTATCCAAGCTGAAATTGAGATGTTA

      11798 GGCTTTAATT


Statistics
Matches: 38,  Mismatches: 4, Indels: 2
        0.86            0.09        0.05

Matches are distributed among these distances:
  43   37  0.97
  44    1  0.03

ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34


Consensus pattern (43 bp):   
ACAATCAAATCAGACTTTTATCCAAGCTGAAATTGAGATGTTA

Found at i:13418 original size:25 final size:24

Alignment explanation


    Indices: 13368--13429  Score: 72
    Period size: 25  Copynumber: 2.5  Consensus size: 24

      13358 TTTATCTCAA

                                     
      13368 GCCCTGCGCCACTTTCCTCTCACAG
          1 GCCCTGCGCCACTTT-CTCTCACAG

                                *     
      13393 GCCCTGCGCCACTTT-TACTTATCAG
          1 GCCCTGCGCCACTTTCT-CTCA-CAG

                 *      
      13418 GCCCTACGCCAC
          1 GCCCTGCGCCAC

      13430 CCCCTGCAGC


Statistics
Matches: 33,  Mismatches: 2, Indels: 4
        0.85            0.05        0.10

Matches are distributed among these distances:
  23    1  0.03
  24    3  0.09
  25   29  0.88

ACGTcount: A:0.15, C:0.45, G:0.16, T:0.24


Consensus pattern (24 bp):   
GCCCTGCGCCACTTTCTCTCACAG
Done.