Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010538.1 Corchorus capsularis cultivar CVL-1 contig10559, 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: 41750
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.32


Found at i:10985 original size:3 final size:3

Alignment explanation


    Indices: 10977--11017  Score: 82
    Period size: 3  Copynumber: 13.7  Consensus size: 3

      10967 TAGTTCCTAC

                                                                  
      10977 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
          1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT

      11018 ATATAGAGTT


Statistics
Matches: 38,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   38  1.00

ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66


Consensus pattern (3 bp):   
ATT

Found at i:33483 original size:40 final size:40

Alignment explanation


    Indices: 33428--33507  Score: 160
    Period size: 40  Copynumber: 2.0  Consensus size: 40

      33418 ATCCAGAAAC

                                                    
      33428 TACAAAGCTCGTGTTTCTTCGATTATATACTCACCTAAGA
          1 TACAAAGCTCGTGTTTCTTCGATTATATACTCACCTAAGA

                                                    
      33468 TACAAAGCTCGTGTTTCTTCGATTATATACTCACCTAAGA
          1 TACAAAGCTCGTGTTTCTTCGATTATATACTCACCTAAGA

      33508 ATTTTAGGTT


Statistics
Matches: 40,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  40   40  1.00

ACGTcount: A:0.30, C:0.23, G:0.12, T:0.35


Consensus pattern (40 bp):   
TACAAAGCTCGTGTTTCTTCGATTATATACTCACCTAAGA

Found at i:33542 original size:41 final size:42

Alignment explanation


    Indices: 33485--33570  Score: 149
    Period size: 41  Copynumber: 2.1  Consensus size: 42

      33475 CTCGTGTTTC

                                                       
      33485 TTCGATTATATACTCACCTAAGAATTTTA-GGTT-TTTTTCTT
          1 TTCGATTATATACTCACCTAAGAA-TTTAGGGTTCTTTTTCTT

                                                      
      33526 TTCGATTATATACTCACCTAAGAATTTAGGGTTCTTTTTCTT
          1 TTCGATTATATACTCACCTAAGAATTTAGGGTTCTTTTTCTT

               
      33568 TTC
          1 TTC

      33571 TTTTTTTCCT


Statistics
Matches: 43,  Mismatches: 0, Indels: 3
        0.93            0.00        0.07

Matches are distributed among these distances:
  40    4  0.09
  41   28  0.65
  42   11  0.26

ACGTcount: A:0.23, C:0.16, G:0.10, T:0.50


Consensus pattern (42 bp):   
TTCGATTATATACTCACCTAAGAATTTAGGGTTCTTTTTCTT

Found at i:38339 original size:77 final size:77

Alignment explanation


    Indices: 38212--38365  Score: 263
    Period size: 77  Copynumber: 2.0  Consensus size: 77

      38202 GGATTAGAAG

                                                        *           *        
      38212 GTCTGCTAAACCAATCTCGTTCTCCATATATCTTAAATATTGTTGGTTGCTTTTTATGTGCATCT
          1 GTCTGCTAAACCAATCTCGTTCTCCATATATCTTAAATATTGTTAGTTGCTTTTTACGTGCATCT

                        
      38277 TGATCATTTGTT
         66 TGATCATTTGTT

                                                *                  *     *   
      38289 GTCTGCTAAACCAATCTCGTTCTCCATATATCTTAAGTATTGTTAGTTGCTTTTTCCGTGCTTCT
          1 GTCTGCTAAACCAATCTCGTTCTCCATATATCTTAAATATTGTTAGTTGCTTTTTACGTGCATCT

                        
      38354 TGATCATTTGTT
         66 TGATCATTTGTT

      38366 CCTTTGGCTT


Statistics
Matches: 72,  Mismatches: 5, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  77   72  1.00

ACGTcount: A:0.19, C:0.19, G:0.14, T:0.47


Consensus pattern (77 bp):   
GTCTGCTAAACCAATCTCGTTCTCCATATATCTTAAATATTGTTAGTTGCTTTTTACGTGCATCT
TGATCATTTGTT

Found at i:38668 original size:3 final size:3

Alignment explanation


    Indices: 38660--38688  Score: 58
    Period size: 3  Copynumber: 9.7  Consensus size: 3

      38650 ATTTTGACTT

                                                  
      38660 ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
          1 ATC ATC ATC ATC ATC ATC ATC ATC ATC AT

      38689 TCTCTCTCTC


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   26  1.00

ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34


Consensus pattern (3 bp):   
ATC

Done.