Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012793.1 Corchorus olitorius cultivar O-4 contig12826, 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: 31079
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30


Found at i:2615 original size:21 final size:21

Alignment explanation


    Indices: 2589--2628  Score: 64
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       2579 TTCAGCCCCA

                                  
       2589 ACCGGCCAGTG-CCGTGCCACG
          1 ACCGGCCA-TGCCCGTGCCACG

                               
       2610 ACCGGCCATGCCCGTGCCA
          1 ACCGGCCATGCCCGTGCCA

       2629 TCACCATTCC


Statistics
Matches: 18,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  20    2  0.11
  21   16  0.89

ACGTcount: A:0.15, C:0.45, G:0.30, T:0.10


Consensus pattern (21 bp):   
ACCGGCCATGCCCGTGCCACG

Found at i:6474 original size:19 final size:20

Alignment explanation


    Indices: 6446--6487  Score: 59
    Period size: 19  Copynumber: 2.1  Consensus size: 20

       6436 TTGAAGGGTG

                 *              
       6446 TTTGTGATTTT-TATTTAAT
          1 TTTGTAATTTTATATTTAAT

                         *      
       6465 TTTGTAATTTTATTTTTAAT
          1 TTTGTAATTTTATATTTAAT

               
       6485 TTT
          1 TTT

       6488 AGGAATTAAA


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  19   10  0.50
  20   10  0.50

ACGTcount: A:0.21, C:0.00, G:0.07, T:0.71


Consensus pattern (20 bp):   
TTTGTAATTTTATATTTAAT

Found at i:7182 original size:5 final size:5

Alignment explanation


    Indices: 7172--7197  Score: 52
    Period size: 5  Copynumber: 5.2  Consensus size: 5

       7162 ATTTGGATCT

                                           
       7172 AATTA AATTA AATTA AATTA AATTA A
          1 AATTA AATTA AATTA AATTA AATTA A

       7198 TATAAATTGT


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   5   21  1.00

ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38


Consensus pattern (5 bp):   
AATTA

Found at i:12463 original size:22 final size:21

Alignment explanation


    Indices: 12435--12488  Score: 60
    Period size: 19  Copynumber: 2.6  Consensus size: 21

      12425 GAAGTTCGTG

                                  
      12435 TTTGAAGACTTATTGAAGATAA
          1 TTTGAAGA-TTATTGAAGATAA

                               * 
      12457 TTTGAAGA-T-TTGAAGATCA
          1 TTTGAAGATTATTGAAGATAA

                          
      12476 -TTGAAGAATTATT
          1 TTTGAAG-ATTATT

      12489 TCAAGAAGCA


Statistics
Matches: 28,  Mismatches: 1, Indels: 7
        0.78            0.03        0.19

Matches are distributed among these distances:
  18    6  0.21
  19   10  0.36
  20    2  0.07
  21    2  0.07
  22    8  0.29

ACGTcount: A:0.39, C:0.04, G:0.19, T:0.39


Consensus pattern (21 bp):   
TTTGAAGATTATTGAAGATAA

Found at i:18811 original size:24 final size:24

Alignment explanation


    Indices: 18758--18812  Score: 58
    Period size: 24  Copynumber: 2.3  Consensus size: 24

      18748 GGCAACCCAA

                            *       
      18758 TAATTTTAATTTCCTATTTATTTT
          1 TAATTTTAATTTCCTAATTATTTT

            **            *          
      18782 CCATTTTAAGTTT-TTAATTATTTT
          1 TAATTTTAA-TTTCCTAATTATTTT

                   
      18806 TAATTTT
          1 TAATTTT

      18813 TAATCACTAA


Statistics
Matches: 24,  Mismatches: 6, Indels: 2
        0.75            0.19        0.06

Matches are distributed among these distances:
  24   21  0.88
  25    3  0.12

ACGTcount: A:0.25, C:0.07, G:0.02, T:0.65


Consensus pattern (24 bp):   
TAATTTTAATTTCCTAATTATTTT

Found at i:20747 original size:15 final size:16

Alignment explanation


    Indices: 20723--20756  Score: 52
    Period size: 15  Copynumber: 2.2  Consensus size: 16

      20713 TTGAAGAAAG

                         *  
      20723 TTTTTCGAAAAATTAA
          1 TTTTTCGAAAAATAAA

                            
      20739 TTTTT-GAAAAATAAA
          1 TTTTTCGAAAAATAAA

               
      20754 TTT
          1 TTT

      20757 CAAATTTTTA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  15   12  0.71
  16    5  0.29

ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47


Consensus pattern (16 bp):   
TTTTTCGAAAAATAAA

Found at i:26559 original size:14 final size:15

Alignment explanation


    Indices: 26535--26563  Score: 51
    Period size: 14  Copynumber: 2.0  Consensus size: 15

      26525 AACTAAATGT

                           
      26535 TAAACGAAAAAGAAA
          1 TAAACGAAAAAGAAA

                           
      26550 TAAA-GAAAAAGAAA
          1 TAAACGAAAAAGAAA

      26564 AACTAACTAT


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  14   10  0.71
  15    4  0.29

ACGTcount: A:0.76, C:0.03, G:0.14, T:0.07


Consensus pattern (15 bp):   
TAAACGAAAAAGAAA
Done.