Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015654.1 Corchorus olitorius cultivar O-4 contig15687, 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: 54474
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:11613 original size:21 final size:21

Alignment explanation


    Indices: 11568--11626  Score: 77
    Period size: 21  Copynumber: 2.9  Consensus size: 21

      11558 CTGTTTGGTA

                                *
      11568 ACTGTACAGATGAGATTA--C
          1 ACTGTACAGATGAGATTATGT

                  *    *         
      11587 ACTGTATAGATTAGATTATGT
          1 ACTGTACAGATGAGATTATGT

                               
      11608 ACTGTACAGATGAGATTAT
          1 ACTGTACAGATGAGATTAT

      11627 TAGAACAGCG


Statistics
Matches: 33,  Mismatches: 5, Indels: 2
        0.82            0.12        0.05

Matches are distributed among these distances:
  19   16  0.48
  21   17  0.52

ACGTcount: A:0.36, C:0.10, G:0.20, T:0.34


Consensus pattern (21 bp):   
ACTGTACAGATGAGATTATGT

Found at i:31371 original size:15 final size:15

Alignment explanation


    Indices: 31351--31400  Score: 57
    Period size: 15  Copynumber: 3.2  Consensus size: 15

      31341 AGTACAAAGA

                           
      31351 AAGAGAAGAGCAAGG
          1 AAGAGAAGAGCAAGG

                     *     
      31366 AAGAGAAGAACAA-G
          1 AAGAGAAGAGCAAGG

                              
      31380 AAGAAGAAGAAGCAGAGG
          1 AAG-AGAAG-AGCA-AGG

               
      31398 AAG
          1 AAG

      31401 TTGCTGCCTG


Statistics
Matches: 29,  Mismatches: 2, Indels: 5
        0.81            0.06        0.14

Matches are distributed among these distances:
  14    4  0.14
  15   17  0.59
  16    3  0.10
  17    1  0.03
  18    4  0.14

ACGTcount: A:0.58, C:0.06, G:0.36, T:0.00


Consensus pattern (15 bp):   
AAGAGAAGAGCAAGG

Found at i:35672 original size:2 final size:2

Alignment explanation


    Indices: 35665--35689  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

      35655 GTAAAAGGAT

                                                 
      35665 TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA T

      35690 CCCCTTCTAC


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

Matches are distributed among these distances:
   2   23  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:41648 original size:30 final size:30

Alignment explanation


    Indices: 41592--41649  Score: 73
    Period size: 30  Copynumber: 1.9  Consensus size: 30

      41582 TTTGATTAAG

                             *            
      41592 CATAATTGAGCTTGATCCAATCCAATACCA
          1 CATAATTGAGCTTGATCAAATCCAATACCA

                *            *           
      41622 CATAGTTGAGCTTGACTTAAAT-CAATAC
          1 CATAATTGAGCTTGA-TCAAATCCAATAC

      41650 TATATATTAT


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  30   20  0.83
  31    4  0.17

ACGTcount: A:0.36, C:0.22, G:0.12, T:0.29


Consensus pattern (30 bp):   
CATAATTGAGCTTGATCAAATCCAATACCA

Found at i:50046 original size:35 final size:35

Alignment explanation


    Indices: 50000--50067  Score: 136
    Period size: 35  Copynumber: 1.9  Consensus size: 35

      49990 TGGATACGAT

                                               
      50000 CCACTCCACCAATGAATACCTCTTTTATAAGTTGA
          1 CCACTCCACCAATGAATACCTCTTTTATAAGTTGA

                                             
      50035 CCACTCCACCAATGAATACCTCTTTTATAAGTT
          1 CCACTCCACCAATGAATACCTCTTTTATAAGTT

      50068 CACATTTGAC


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  35   33  1.00

ACGTcount: A:0.31, C:0.29, G:0.07, T:0.32


Consensus pattern (35 bp):   
CCACTCCACCAATGAATACCTCTTTTATAAGTTGA

Found at i:52735 original size:72 final size:72

Alignment explanation


    Indices: 52618--52833  Score: 414
    Period size: 72  Copynumber: 3.0  Consensus size: 72

      52608 AGAAGTAAAT

                                                                             
      52618 TATATTCTTTCATAAATTTCTTCAAAAGTTGAGGCCACCATCACTAACCCACCACCACCACCCAA
          1 TATATTCTTTCATAAATTTCTTCAAAAGTTGAGGCCACCATCACTAACCCACCACCACCACCCAA

                   
      52683 GGGGGTG
         66 GGGGGTG

                                                                             
      52690 TATATTCTTTCATAAATTTCTTCAAAAGTTGAGGCCACCATCACTAACCCACCACCACCACCCAA
          1 TATATTCTTTCATAAATTTCTTCAAAAGTTGAGGCCACCATCACTAACCCACCACCACCACCCAA

                   
      52755 GGGGGTG
         66 GGGGGTG

                                                                *            
      52762 TATATTCTTTCATAAATTTCTTCAAAAGTTGAGGCCACCATCACTAACCCACTACCACCACCCAA
          1 TATATTCTTTCATAAATTTCTTCAAAAGTTGAGGCCACCATCACTAACCCACCACCACCACCCAA

            *      
      52827 CGGGGTG
         66 GGGGGTG

      52834 GTGGAAGGTA


Statistics
Matches: 142,  Mismatches: 2, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
  72  142  1.00

ACGTcount: A:0.31, C:0.31, G:0.13, T:0.25


Consensus pattern (72 bp):   
TATATTCTTTCATAAATTTCTTCAAAAGTTGAGGCCACCATCACTAACCCACCACCACCACCCAA
GGGGGTG
Done.