Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016288.1 Corchorus capsularis cultivar CVL-1 contig16309, 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: 13815
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30


Found at i:246 original size:18 final size:17

Alignment explanation


    Indices: 223--258  Score: 63
    Period size: 18  Copynumber: 2.1  Consensus size: 17

        213 CTCAACCTAA

                              
        223 AACTAGAAGAAAAACTAG
          1 AACTAGAAGAAAAA-TAG

                             
        241 AACTAGAAGAAAAATAG
          1 AACTAGAAGAAAAATAG

             
        258 A
          1 A

        259 TGAAGAGAAA


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  17    4  0.22
  18   14  0.78

ACGTcount: A:0.64, C:0.08, G:0.17, T:0.11


Consensus pattern (17 bp):   
AACTAGAAGAAAAATAG

Found at i:889 original size:19 final size:18

Alignment explanation


    Indices: 856--891  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

        846 TTGAAATAAT

                              
        856 TCTTCAATGATCTTCAAA
          1 TCTTCAATGATCTTCAAA

                     *        
        874 TCTTCAAATTATCTTCAA
          1 TCTTC-AATGATCTTCAA

        892 TAAATATTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGATCTTCAAA

Found at i:3134 original size:19 final size:18

Alignment explanation


    Indices: 3100--3137  Score: 58
    Period size: 19  Copynumber: 2.1  Consensus size: 18

       3090 CTTGAAATAT

                              
       3100 TTCTTCAATGATCTTCAA
          1 TTCTTCAATGATCTTCAA

                      *        
       3118 TTCTTCAAATTATCTTCAA
          1 TTCTTC-AATGATCTTCAA

             
       3137 T
          1 T

       3138 AAATCTTTAA


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  18    6  0.33
  19   12  0.67

ACGTcount: A:0.29, C:0.21, G:0.03, T:0.47


Consensus pattern (18 bp):   
TTCTTCAATGATCTTCAA

Found at i:4345 original size:21 final size:19

Alignment explanation


    Indices: 4313--4351  Score: 51
    Period size: 21  Copynumber: 1.9  Consensus size: 19

       4303 CAATCAAGCA

                               
       4313 AATCAAGATTCAAAGCATC
          1 AATCAAGATTCAAAGCATC

                          *     
       4332 AATCATAGCATTCATAGCAT
          1 AATCA-AG-ATTCAAAGCAT

       4352 ATGAGTCATA


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  19    5  0.29
  20    2  0.12
  21   10  0.59

ACGTcount: A:0.44, C:0.21, G:0.10, T:0.26


Consensus pattern (19 bp):   
AATCAAGATTCAAAGCATC

Found at i:7558 original size:18 final size:17

Alignment explanation


    Indices: 7535--7570  Score: 63
    Period size: 18  Copynumber: 2.1  Consensus size: 17

       7525 CTCAACCTAA

                              
       7535 AACTAGAAGAAAAACTAG
          1 AACTAGAAGAAAAA-TAG

                             
       7553 AACTAGAAGAAAAATAG
          1 AACTAGAAGAAAAATAG

             
       7570 A
          1 A

       7571 TGAAGACAAA


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  17    4  0.22
  18   14  0.78

ACGTcount: A:0.64, C:0.08, G:0.17, T:0.11


Consensus pattern (17 bp):   
AACTAGAAGAAAAATAG

Found at i:8201 original size:19 final size:18

Alignment explanation


    Indices: 8168--8203  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       8158 TTGAAATAAT

                              
       8168 TCTTCAATGATCTTCAAA
          1 TCTTCAATGATCTTCAAA

                     *        
       8186 TCTTCAAATTATCTTCAA
          1 TCTTC-AATGATCTTCAA

       8204 TAAATATTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGATCTTCAAA
Done.