Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005512.1 Corchorus capsularis cultivar CVL-1 contig05530, 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: 7996
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35


Found at i:82 original size:51 final size:51

Alignment explanation


    Indices: 2--102  Score: 184
    Period size: 51  Copynumber: 2.0  Consensus size: 51

          1 C

                                                               
          2 ACAAGTTCAATCACTTAATTCAAAACTCTCATTTTTATTTACAAATTACTT
          1 ACAAGTTCAATCACTTAATTCAAAACTCTCATTTTTATTTACAAATTACTT

                         *          *                         
         53 ACAAGTTCAATCATTTAATTCAAAGCTCTCATTTTTATTTACAAATTACT
          1 ACAAGTTCAATCACTTAATTCAAAACTCTCATTTTTATTTACAAATTACT

        103 CAAAAGTTTA


Statistics
Matches: 48,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  51   48  1.00

ACGTcount: A:0.37, C:0.19, G:0.03, T:0.42


Consensus pattern (51 bp):   
ACAAGTTCAATCACTTAATTCAAAACTCTCATTTTTATTTACAAATTACTT

Found at i:495 original size:16 final size:16

Alignment explanation


    Indices: 476--514  Score: 53
    Period size: 16  Copynumber: 2.4  Consensus size: 16

        466 TCCTCTTCTC

                             
        476 TTTTCCTC-CTTTTGTT
          1 TTTTCCTCTCTTTT-TT

                *           
        492 TTTTTCTCTCTTTTTT
          1 TTTTCCTCTCTTTTTT

                   
        508 TTTTCCT
          1 TTTTCCT

        515 TTTTGCTGAC


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  16   15  0.75
  17    5  0.25

ACGTcount: A:0.00, C:0.23, G:0.03, T:0.74


Consensus pattern (16 bp):   
TTTTCCTCTCTTTTTT

Found at i:2268 original size:20 final size:20

Alignment explanation


    Indices: 2243--2281  Score: 62
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       2233 AAAAAGAGCA

                                 
       2243 CCAATTTGC-AAATCAAATGT
          1 CCAATTT-CTAAATCAAATGT

                               
       2263 CCAATTTCTAAATCAAATG
          1 CCAATTTCTAAATCAAATG

       2282 CCTTGTATTT


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

Matches are distributed among these distances:
  19    1  0.06
  20   17  0.94

ACGTcount: A:0.41, C:0.21, G:0.08, T:0.31


Consensus pattern (20 bp):   
CCAATTTCTAAATCAAATGT

Found at i:2371 original size:14 final size:14

Alignment explanation


    Indices: 2352--2385  Score: 68
    Period size: 14  Copynumber: 2.4  Consensus size: 14

       2342 GTATGAAAGT

                          
       2352 AAGTATGTAATGCA
          1 AAGTATGTAATGCA

                          
       2366 AAGTATGTAATGCA
          1 AAGTATGTAATGCA

                  
       2380 AAGTAT
          1 AAGTAT

       2386 TATGCTACAT


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   20  1.00

ACGTcount: A:0.44, C:0.06, G:0.21, T:0.29


Consensus pattern (14 bp):   
AAGTATGTAATGCA

Found at i:3963 original size:2 final size:2

Alignment explanation


    Indices: 3956--3991  Score: 72
    Period size: 2  Copynumber: 18.0  Consensus size: 2

       3946 AGACACATAG

                                                                 
       3956 TA 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 TA

       3992 CACACTAGTA


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   34  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:5855 original size:17 final size:17

Alignment explanation


    Indices: 5833--5866  Score: 68
    Period size: 17  Copynumber: 2.0  Consensus size: 17

       5823 TTAGTCATAA

                             
       5833 TACGAATGAAATTATCC
          1 TACGAATGAAATTATCC

                             
       5850 TACGAATGAAATTATCC
          1 TACGAATGAAATTATCC

       5867 CTAATTATAC


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   17  1.00

ACGTcount: A:0.41, C:0.18, G:0.12, T:0.29


Consensus pattern (17 bp):   
TACGAATGAAATTATCC

Found at i:6408 original size:10 final size:10

Alignment explanation


    Indices: 6374--6409  Score: 56
    Period size: 10  Copynumber: 3.6  Consensus size: 10

       6364 TTTGGTGTAC

                      
       6374 TATAATTATA
          1 TATAATTATA

                       
       6384 TAT-ATATATA
          1 TATAAT-TATA

                      
       6394 TATAATTATA
          1 TATAATTATA

                  
       6404 TATAAT
          1 TATAAT

       6410 AAATATGCTC


Statistics
Matches: 24,  Mismatches: 0, Indels: 4
        0.86            0.00        0.14

Matches are distributed among these distances:
   9    2  0.08
  10   20  0.83
  11    2  0.08

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


Consensus pattern (10 bp):   
TATAATTATA
Done.