Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008426.1 Corchorus capsularis cultivar CVL-1 contig08447, 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: 9431
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36


Found at i:292 original size:24 final size:27

Alignment explanation


    Indices: 265--317  Score: 76
    Period size: 26  Copynumber: 2.1  Consensus size: 27

        255 TTCTAGTGAT

                                 *     
        265 GAGAAT-AAG-GAAGGAAAA-GAGGAG
          1 GAGAATCAAGAGAAGGAAAATAAGGAG

                                       
        289 GAGAATCAAGAGAAGGAAAATAAGGAG
          1 GAGAATCAAGAGAAGGAAAATAAGGAG

              
        316 GA
          1 GA

        318 ATTTCATCCT


Statistics
Matches: 25,  Mismatches: 1, Indels: 3
        0.86            0.03        0.10

Matches are distributed among these distances:
  24    6  0.24
  25    3  0.12
  26    9  0.36
  27    7  0.28

ACGTcount: A:0.55, C:0.02, G:0.38, T:0.06


Consensus pattern (27 bp):   
GAGAATCAAGAGAAGGAAAATAAGGAG

Found at i:531 original size:22 final size:22

Alignment explanation


    Indices: 506--549  Score: 63
    Period size: 22  Copynumber: 2.0  Consensus size: 22

        496 GGTTTAGTTA

                                   
        506 TTTAGTTTATG-CTTTAATTTTC
          1 TTTAGTTTATGTCTTT-ATTTTC

                *                 
        528 TTTATTTTATGTCTTTATTTTC
          1 TTTAGTTTATGTCTTTATTTTC

        550 AAGTTTCATT


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

Matches are distributed among these distances:
  22   16  0.80
  23    4  0.20

ACGTcount: A:0.16, C:0.09, G:0.07, T:0.68


Consensus pattern (22 bp):   
TTTAGTTTATGTCTTTATTTTC

Found at i:4379 original size:6 final size:6

Alignment explanation


    Indices: 4368--4397  Score: 60
    Period size: 6  Copynumber: 5.0  Consensus size: 6

       4358 CATTGCATGC

                                              
       4368 ATTTGT ATTTGT ATTTGT ATTTGT ATTTGT
          1 ATTTGT ATTTGT ATTTGT ATTTGT ATTTGT

       4398 TCTATTTGGA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   24  1.00

ACGTcount: A:0.17, C:0.00, G:0.17, T:0.67


Consensus pattern (6 bp):   
ATTTGT

Found at i:6250 original size:21 final size:21

Alignment explanation


    Indices: 6224--6268  Score: 63
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       6214 GCACTGGAGT

                   *   * *       
       6224 ACATGGGTCGCGAGGCAAACC
          1 ACATGGGGCGCCAAGCAAACC

                                 
       6245 ACATGGGGCGCCAAGCAAACC
          1 ACATGGGGCGCCAAGCAAACC

               
       6266 ACA
          1 ACA

       6269 CGGGCACCCA


Statistics
Matches: 21,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  21   21  1.00

ACGTcount: A:0.33, C:0.31, G:0.29, T:0.07


Consensus pattern (21 bp):   
ACATGGGGCGCCAAGCAAACC

Found at i:8303 original size:85 final size:83

Alignment explanation


    Indices: 8159--8319  Score: 261
    Period size: 85  Copynumber: 1.9  Consensus size: 83

       8149 AAATTATAAT

                                                                             
       8159 ATATATCTAAGTTATGTAATTAAAATAGTAAAAATGGTAAAAATAAAATAGTTATAAAGAGATTA
          1 ATATATCTAAGTTATGTAATTAAAATAGTAAAAATGGTAAAAATAAAATAGTTATAAAGA-ATTA

                               
       8224 GATTTAATTAAAAATTCTA
         65 GATTTAATTAAAAATTCTA

                           * *                                               
       8243 ATATATCTAAGTTTTTTTTAATTAAAATAGT-AAAATGGTAAAAATAAAATAGTTATAAAGAATT
          1 ATATATCTAAG--TTATGTAATTAAAATAGTAAAAATGGTAAAAATAAAATAGTTATAAAGAATT

             *           
       8307 ATATTTAATTAAA
         64 AGATTTAATTAAA

       8320 TAAAAATGGA


Statistics
Matches: 72,  Mismatches: 3, Indels: 4
        0.91            0.04        0.05

Matches are distributed among these distances:
  84   26  0.36
  85   30  0.42
  86   16  0.22

ACGTcount: A:0.52, C:0.02, G:0.09, T:0.37


Consensus pattern (83 bp):   
ATATATCTAAGTTATGTAATTAAAATAGTAAAAATGGTAAAAATAAAATAGTTATAAAGAATTAG
ATTTAATTAAAAATTCTA

Found at i:9300 original size:24 final size:24

Alignment explanation


    Indices: 9249--9298  Score: 66
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       9239 TTAGTAGAAT

                        *           
       9249 AATTGTAAAAGTTTATTTCTAAAA
          1 AATTGTAAAAGTATATTTCTAAAA

                                      
       9273 AATTGTAAAAGAATATATTT-TAAAA
          1 AATTGTAAAAG--TATATTTCTAAAA

             
       9298 A
          1 A

       9299 TTCTAATATG


Statistics
Matches: 23,  Mismatches: 1, Indels: 3
        0.85            0.04        0.11

Matches are distributed among these distances:
  24   11  0.48
  25    6  0.26
  26    6  0.26

ACGTcount: A:0.52, C:0.02, G:0.08, T:0.38


Consensus pattern (24 bp):   
AATTGTAAAAGTATATTTCTAAAA
Done.