Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007836.1 Corchorus capsularis cultivar CVL-1 contig07857, 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: 28445
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32


Found at i:17223 original size:21 final size:21

Alignment explanation


    Indices: 17197--17237  Score: 73
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      17187 TGGAGTTGTG

                                 
      17197 AGATTAAACACTGTACAGATC
          1 AGATTAAACACTGTACAGATC

                  *             
      17218 AGATTAGACACTGTACAGAT
          1 AGATTAAACACTGTACAGAT

      17238 GAGAATATAA


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   19  1.00

ACGTcount: A:0.41, C:0.17, G:0.17, T:0.24


Consensus pattern (21 bp):   
AGATTAAACACTGTACAGATC

Found at i:19317 original size:16 final size:17

Alignment explanation


    Indices: 19280--19317  Score: 51
    Period size: 16  Copynumber: 2.3  Consensus size: 17

      19270 TTCTTCTACG

                             
      19280 TTTTCTCTCTCTTCCTA
          1 TTTTCTCTCTCTTCCTA

            *            *   
      19297 ATTTCT-TCTCTTGCTA
          1 TTTTCTCTCTCTTCCTA

                 
      19313 TTTTC
          1 TTTTC

      19318 CTCAAATCTT


Statistics
Matches: 18,  Mismatches: 3, Indels: 1
        0.82            0.14        0.05

Matches are distributed among these distances:
  16   13  0.72
  17    5  0.28

ACGTcount: A:0.08, C:0.29, G:0.03, T:0.61


Consensus pattern (17 bp):   
TTTTCTCTCTCTTCCTA

Found at i:26555 original size:30 final size:30

Alignment explanation


    Indices: 26521--26577  Score: 105
    Period size: 30  Copynumber: 1.9  Consensus size: 30

      26511 AATCCTTTAA

                                          
      26521 AACCTTCAAACTAAAATCTTTACTTCAAAC
          1 AACCTTCAAACTAAAATCTTTACTTCAAAC

                        *              
      26551 AACCTTCAAACTTAAATCTTTACTTCA
          1 AACCTTCAAACTAAAATCTTTACTTCA

      26578 TTTACCTTAA


Statistics
Matches: 26,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  30   26  1.00

ACGTcount: A:0.40, C:0.26, G:0.00, T:0.33


Consensus pattern (30 bp):   
AACCTTCAAACTAAAATCTTTACTTCAAAC

Found at i:27190 original size:17 final size:17

Alignment explanation


    Indices: 27168--27205  Score: 76
    Period size: 17  Copynumber: 2.2  Consensus size: 17

      27158 TGTAAGTTGC

                             
      27168 TTAAAACTTGTTTAGGA
          1 TTAAAACTTGTTTAGGA

                             
      27185 TTAAAACTTGTTTAGGA
          1 TTAAAACTTGTTTAGGA

                
      27202 TTAA
          1 TTAA

      27206 GCAAATCGAA


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

Matches are distributed among these distances:
  17   21  1.00

ACGTcount: A:0.37, C:0.05, G:0.16, T:0.42


Consensus pattern (17 bp):   
TTAAAACTTGTTTAGGA

Found at i:27424 original size:9 final size:9

Alignment explanation


    Indices: 27410--27436  Score: 54
    Period size: 9  Copynumber: 3.0  Consensus size: 9

      27400 ATATGTATAG

                     
      27410 ATAACATTT
          1 ATAACATTT

                     
      27419 ATAACATTT
          1 ATAACATTT

                     
      27428 ATAACATTT
          1 ATAACATTT

      27437 GTATTTGTAA


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   9   18  1.00

ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44


Consensus pattern (9 bp):   
ATAACATTT
Done.