Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010561.1 Corchorus capsularis cultivar CVL-1 contig10582, 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: 22374
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33


Found at i:8737 original size:13 final size:12

Alignment explanation


    Indices: 8714--8756  Score: 68
    Period size: 12  Copynumber: 3.5  Consensus size: 12

       8704 TTAATACAGG

                        
       8714 TATCGACGGATA
          1 TATCGACGGATA

                         
       8726 TATCGAACGGATA
          1 TATCG-ACGGATA

                      * 
       8739 TATCGACGGACA
          1 TATCGACGGATA

                  
       8751 TATCGA
          1 TATCGA

       8757 GGTATCGATG


Statistics
Matches: 29,  Mismatches: 1, Indels: 2
        0.91            0.03        0.06

Matches are distributed among these distances:
  12   17  0.59
  13   12  0.41

ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23


Consensus pattern (12 bp):   
TATCGACGGATA

Found at i:9849 original size:3 final size:3

Alignment explanation


    Indices: 9841--9870  Score: 53
    Period size: 3  Copynumber: 10.3  Consensus size: 3

       9831 TCATTTCCCC

                                                     
       9841 CAT CAT CAT CAT CAT CAT CAT CAT CA- CAT C
          1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C

       9871 TTCTGTGAGC


Statistics
Matches: 26,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   2    2  0.08
   3   24  0.92

ACGTcount: A:0.33, C:0.37, G:0.00, T:0.30


Consensus pattern (3 bp):   
CAT

Found at i:10164 original size:10 final size:10

Alignment explanation


    Indices: 10149--10174  Score: 52
    Period size: 10  Copynumber: 2.6  Consensus size: 10

      10139 AATTTAATAT

                      
      10149 GGATATTTAC
          1 GGATATTTAC

                      
      10159 GGATATTTAC
          1 GGATATTTAC

                  
      10169 GGATAT
          1 GGATAT

      10175 ATCGAGATTT


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   16  1.00

ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38


Consensus pattern (10 bp):   
GGATATTTAC

Found at i:10398 original size:11 final size:11

Alignment explanation


    Indices: 10384--10413  Score: 51
    Period size: 11  Copynumber: 2.7  Consensus size: 11

      10374 TTTGTTTTTG

                       
      10384 TTTTTGTTTCA
          1 TTTTTGTTTCA

                     * 
      10395 TTTTTGTTTTA
          1 TTTTTGTTTCA

                    
      10406 TTTTTGTT
          1 TTTTTGTT

      10414 ACGTTGTCAA


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

Matches are distributed among these distances:
  11   18  1.00

ACGTcount: A:0.07, C:0.03, G:0.10, T:0.80


Consensus pattern (11 bp):   
TTTTTGTTTCA

Found at i:17597 original size:2 final size:2

Alignment explanation


    Indices: 17590--17617  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

      17580 ATCCTATTTC

                                                     
      17590 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA

      17618 GCCTTCTGGC


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

Matches are distributed among these distances:
   2   26  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:21342 original size:3 final size:3

Alignment explanation


    Indices: 21334--21382  Score: 98
    Period size: 3  Copynumber: 16.3  Consensus size: 3

      21324 ATCGATGTTA

                                                                           
      21334 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
          1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG

             
      21382 A
          1 A

      21383 TGCGCATCCA


Statistics
Matches: 46,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   46  1.00

ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00


Consensus pattern (3 bp):   
AAG

Found at i:21526 original size:5 final size:5

Alignment explanation


    Indices: 21511--21554  Score: 72
    Period size: 5  Copynumber: 9.0  Consensus size: 5

      21501 AGAGAGAGAG

                   *                                             
      21511 AGAAA ATAAA AGAAA AGAAA AGAAA AGAAA AGAAA AG-AA AGAAA
          1 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA

      21555 GTAAACAAAG


Statistics
Matches: 36,  Mismatches: 2, Indels: 2
        0.90            0.05        0.05

Matches are distributed among these distances:
   4    4  0.11
   5   32  0.89

ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02


Consensus pattern (5 bp):   
AGAAA

Found at i:22280 original size:3 final size:3

Alignment explanation


    Indices: 22272--22310  Score: 78
    Period size: 3  Copynumber: 13.0  Consensus size: 3

      22262 ATTTCAATAT

                                                               
      22272 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA

      22311 AATAAAAAAT


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   36  1.00

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67


Consensus pattern (3 bp):   
TTA

Done.