Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007632.1 Corchorus capsularis cultivar CVL-1 contig07653, 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: 36672
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32


Found at i:4969 original size:2 final size:2

Alignment explanation


    Indices: 4964--4990  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

       4954 ACACACACAC

                                                    
       4964 AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT A

       4991 GTATTAAGTA


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:17878 original size:18 final size:16

Alignment explanation


    Indices: 17845--17881  Score: 56
    Period size: 18  Copynumber: 2.2  Consensus size: 16

      17835 TGCTAAAGAT

                            
      17845 TTTAATCTTAAATTAA
          1 TTTAATCTTAAATTAA

                              
      17861 TTTAATACTTATAATTAA
          1 TTTAAT-CTTA-AATTAA

               
      17879 TTT
          1 TTT

      17882 CAATTATTAA


Statistics
Matches: 19,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  16    6  0.32
  17    4  0.21
  18    9  0.47

ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54


Consensus pattern (16 bp):   
TTTAATCTTAAATTAA

Found at i:20475 original size:29 final size:29

Alignment explanation


    Indices: 20435--20490  Score: 94
    Period size: 29  Copynumber: 1.9  Consensus size: 29

      20425 AAATAAATAG

                   *           *         
      20435 AAAATTGTTCAAACAAATAGAAGAAACAA
          1 AAAATTGCTCAAACAAATAAAAGAAACAA

                                       
      20464 AAAATTGCTCAAACAAATAAAAGAAAC
          1 AAAATTGCTCAAACAAATAAAAGAAAC

      20491 TAAATTAGTT


Statistics
Matches: 25,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  29   25  1.00

ACGTcount: A:0.62, C:0.12, G:0.09, T:0.16


Consensus pattern (29 bp):   
AAAATTGCTCAAACAAATAAAAGAAACAA

Found at i:21277 original size:18 final size:18

Alignment explanation


    Indices: 21254--21291  Score: 67
    Period size: 18  Copynumber: 2.1  Consensus size: 18

      21244 CACCAGCTTT

                              
      21254 GGCTTGGCTAGGGCCTTG
          1 GGCTTGGCTAGGGCCTTG

                  *           
      21272 GGCTTGTCTAGGGCCTTG
          1 GGCTTGGCTAGGGCCTTG

              
      21290 GG
          1 GG

      21292 ATGTCCCTTT


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

Matches are distributed among these distances:
  18   19  1.00

ACGTcount: A:0.05, C:0.21, G:0.45, T:0.29


Consensus pattern (18 bp):   
GGCTTGGCTAGGGCCTTG

Found at i:21636 original size:41 final size:41

Alignment explanation


    Indices: 21579--21702  Score: 230
    Period size: 41  Copynumber: 3.0  Consensus size: 41

      21569 CGCGGGTTTC

                               *                     
      21579 TAATGGTTTATGAAGTTATATAGTGAGGAGGTTCATTTTTT
          1 TAATGGTTTATGAAGTTATGTAGTGAGGAGGTTCATTTTTT

                                         *           
      21620 TAATGGTTTATGAAGTTATGTAGTGAGGATGTTCATTTTTT
          1 TAATGGTTTATGAAGTTATGTAGTGAGGAGGTTCATTTTTT

                                                     
      21661 TAATGGTTTATGAAGTTATGTAGTGAGGAGGTTCATTTTTT
          1 TAATGGTTTATGAAGTTATGTAGTGAGGAGGTTCATTTTTT

             
      21702 T
          1 T

      21703 TTCATGACGC


Statistics
Matches: 80,  Mismatches: 3, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  41   80  1.00

ACGTcount: A:0.25, C:0.02, G:0.25, T:0.48


Consensus pattern (41 bp):   
TAATGGTTTATGAAGTTATGTAGTGAGGAGGTTCATTTTTT

Found at i:34338 original size:30 final size:30

Alignment explanation


    Indices: 34302--34364  Score: 126
    Period size: 30  Copynumber: 2.1  Consensus size: 30

      34292 CATAATAATA

                                          
      34302 ACTGATATAAAATATCAAACACTAAAACTT
          1 ACTGATATAAAATATCAAACACTAAAACTT

                                          
      34332 ACTGATATAAAATATCAAACACTAAAACTT
          1 ACTGATATAAAATATCAAACACTAAAACTT

               
      34362 ACT
          1 ACT

      34365 CAAGGTAAGG


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  30   33  1.00

ACGTcount: A:0.52, C:0.17, G:0.03, T:0.27


Consensus pattern (30 bp):   
ACTGATATAAAATATCAAACACTAAAACTT

Done.