Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012732.1 Corchorus capsularis cultivar CVL-1 contig12753, 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: 22912
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31


Found at i:3423 original size:19 final size:18

Alignment explanation


    Indices: 3390--3425  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       3380 TTGAAATAAT

                              
       3390 TCTTCAATGATCTTCAAA
          1 TCTTCAATGATCTTCAAA

                     *        
       3408 TCTTCAAATTATCTTCAA
          1 TCTTC-AATGATCTTCAA

       3426 GAAATCTTCA


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:12276 original size:16 final size:16

Alignment explanation


    Indices: 12255--12287  Score: 66
    Period size: 16  Copynumber: 2.1  Consensus size: 16

      12245 TTCTCTTCAA

                            
      12255 ATCTTAATGAACTATG
          1 ATCTTAATGAACTATG

                            
      12271 ATCTTAATGAACTATG
          1 ATCTTAATGAACTATG

             
      12287 A
          1 A

      12288 GAAAAACTGG


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

Matches are distributed among these distances:
  16   17  1.00

ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36


Consensus pattern (16 bp):   
ATCTTAATGAACTATG

Found at i:16241 original size:12 final size:13

Alignment explanation


    Indices: 16224--16257  Score: 52
    Period size: 12  Copynumber: 2.7  Consensus size: 13

      16214 AATCTAAATC

                   *     
      16224 TAAAGCAGATTA-
          1 TAAAGCAAATTAT

                         
      16236 TAAAGCAAATTAT
          1 TAAAGCAAATTAT

                     
      16249 TAAAGCAAA
          1 TAAAGCAAA

      16258 CAATAATTAT


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  12   11  0.55
  13    9  0.45

ACGTcount: A:0.56, C:0.09, G:0.12, T:0.24


Consensus pattern (13 bp):   
TAAAGCAAATTAT

Found at i:22070 original size:31 final size:31

Alignment explanation


    Indices: 21991--22099  Score: 87
    Period size: 31  Copynumber: 3.3  Consensus size: 31

      21981 TTAAAAGCAG

                                            * 
      21991 AAACAGGAAATAAA-TTTATTTTTTTTAAAG-GA
          1 AAAC-GGAAA-AAACTTT-TTTTTTTTAAAGAAA

                            *                   
      22023 AAACGGAAAAAGAAAAATTATTTTTTTTTAAAGAAA
          1 AAACGG---AA-AAAACTT-TTTTTTTTTAAAGAAA

              *                     **     
      22059 AATCGGAAAAAACTTTTTTTTTTTTTAGAAA
          1 AAACGGAAAAAACTTTTTTTTTTTAAAGAAA

                      
      22090 AAACGGAAAA
          1 AAACGGAAAA

      22100 TCAAAAACAA


Statistics
Matches: 64,  Mismatches: 6, Indels: 15
        0.75            0.07        0.18

Matches are distributed among these distances:
  31   25  0.39
  32   10  0.16
  33    2  0.03
  34    5  0.08
  35   15  0.23
  36    7  0.11

ACGTcount: A:0.50, C:0.05, G:0.12, T:0.34


Consensus pattern (31 bp):   
AAACGGAAAAAACTTTTTTTTTTTAAAGAAA

Found at i:22409 original size:6 final size:6

Alignment explanation


    Indices: 22398--22424  Score: 54
    Period size: 6  Copynumber: 4.5  Consensus size: 6

      22388 AAAGCAAAGC

                                           
      22398 AAATCT AAATCT AAATCT AAATCT AAA
          1 AAATCT AAATCT AAATCT AAATCT AAA

      22425 GCAGATTATA


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

Matches are distributed among these distances:
   6   21  1.00

ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30


Consensus pattern (6 bp):   
AAATCT

Found at i:22436 original size:12 final size:13

Alignment explanation


    Indices: 22421--22465  Score: 74
    Period size: 13  Copynumber: 3.5  Consensus size: 13

      22411 AATCTAAATC

                         
      22421 TAAAGCAGATT-A
          1 TAAAGCAGATTAA

                   *     
      22433 TAAAGCAAATTAA
          1 TAAAGCAGATTAA

                         
      22446 TAAAGCAGATTAA
          1 TAAAGCAGATTAA

                   
      22459 TAAAGCA
          1 TAAAGCA

      22466 AACAATAATT


Statistics
Matches: 30,  Mismatches: 2, Indels: 1
        0.91            0.06        0.03

Matches are distributed among these distances:
  12   10  0.33
  13   20  0.67

ACGTcount: A:0.56, C:0.09, G:0.13, T:0.22


Consensus pattern (13 bp):   
TAAAGCAGATTAA

Found at i:22472 original size:25 final size:25

Alignment explanation


    Indices: 22421--22473  Score: 81
    Period size: 25  Copynumber: 2.1  Consensus size: 25

      22411 AATCTAAATC

                                  *  
      22421 TAAAGCAGATTATAAAGCAAATTAA
          1 TAAAGCAGATTATAAAGCAAATCAA

                                      
      22446 TAAAGCAGATTAATAAAGCAAA-CAA
          1 TAAAGCAGATT-ATAAAGCAAATCAA

               
      22471 TAA
          1 TAA

      22474 TTATAAAGCA


Statistics
Matches: 26,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
  25   16  0.62
  26   10  0.38

ACGTcount: A:0.58, C:0.09, G:0.11, T:0.21


Consensus pattern (25 bp):   
TAAAGCAGATTATAAAGCAAATCAA
Done.