Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024091.1 Corchorus olitorius cultivar O-4 contig24124, 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: 7908
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36


Found at i:2404 original size:23 final size:23

Alignment explanation


    Indices: 2374--2419  Score: 76
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       2364 TCATCAACAA

                                    
       2374 TGCCATGGT-TGTTAATCCTACAC
          1 TGCCATGGTGT-TTAATCCTACAC

                                   
       2397 TGCCATGGTGTTTAATCCTACAC
          1 TGCCATGGTGTTTAATCCTACAC

       2420 AAAGAATATT


Statistics
Matches: 22,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
  23   21  0.95
  24    1  0.05

ACGTcount: A:0.22, C:0.26, G:0.17, T:0.35


Consensus pattern (23 bp):   
TGCCATGGTGTTTAATCCTACAC

Found at i:2493 original size:37 final size:38

Alignment explanation


    Indices: 2448--2529  Score: 139
    Period size: 40  Copynumber: 2.1  Consensus size: 38

       2438 CAGAAAAATT

                                                  
       2448 TTTCAACCTGCAAACTG-AGAAGAATAAAGCATAAAAA
          1 TTTCAACCTGCAAACTGAAGAAGAATAAAGCATAAAAA

                                                    
       2485 TTTCAACCTGCAAACTGATCAGAAGAATAAAGCATAAAAA
          1 TTTCAACCTGCAAACTGA--AGAAGAATAAAGCATAAAAA

                 
       2525 TTTCA
          1 TTTCA

       2530 GAGAACTAAT


Statistics
Matches: 42,  Mismatches: 0, Indels: 3
        0.93            0.00        0.07

Matches are distributed among these distances:
  37   17  0.40
  40   25  0.60

ACGTcount: A:0.49, C:0.17, G:0.12, T:0.22


Consensus pattern (38 bp):   
TTTCAACCTGCAAACTGAAGAAGAATAAAGCATAAAAA

Found at i:5478 original size:2 final size:2

Alignment explanation


    Indices: 5471--5501  Score: 55
    Period size: 2  Copynumber: 16.0  Consensus size: 2

       5461 TGTTATCAAA

                                                           
       5471 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       5502 GATTTGAGTT


Statistics
Matches: 28,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   1    1  0.04
   2   27  0.96

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


Consensus pattern (2 bp):   
AT

Found at i:7045 original size:21 final size:21

Alignment explanation


    Indices: 7019--7110  Score: 159
    Period size: 21  Copynumber: 4.4  Consensus size: 21

       7009 TGTTAGGAGA

                                  
       7019 TCATTGGAGCAA-GTTCCAAGC
          1 TCATTGGAG-AAGGTTCCAAGC

                                 
       7040 TCATTGGAGAAGGTTCCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                                 
       7061 TCATTGGAGAAGGTTCCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                           *     
       7082 TCATTGGAGAAGGTTTCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                    
       7103 TCATTGGA
          1 TCATTGGA

       7111 ATTGCCTAAG


Statistics
Matches: 69,  Mismatches: 1, Indels: 2
        0.96            0.01        0.03

Matches are distributed among these distances:
  20    2  0.03
  21   67  0.97

ACGTcount: A:0.28, C:0.18, G:0.27, T:0.26


Consensus pattern (21 bp):   
TCATTGGAGAAGGTTCCAAGC

Done.