Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015978.1 Corchorus capsularis cultivar CVL-1 contig15999, 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: 11418
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35


Found at i:764 original size:3 final size:3

Alignment explanation


    Indices: 758--809  Score: 104
    Period size: 3  Copynumber: 17.3  Consensus size: 3

        748 ATATCTAATC

                                                                           
        758 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
          1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA

                 
        806 TAA T
          1 TAA T

        810 GGCAAGATTG


Statistics
Matches: 49,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   49  1.00

ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35


Consensus pattern (3 bp):   
TAA

Found at i:3292 original size:21 final size:20

Alignment explanation


    Indices: 3259--3302  Score: 52
    Period size: 21  Copynumber: 2.1  Consensus size: 20

       3249 GTGGAAACCA

                 *               
       3259 TTATAGCTATTTTAATAACTT
          1 TTATAACTATTTTAATAA-TT

                    *     *     
       3280 TTATAACTTTTTTAGTAATT
          1 TTATAACTATTTTAATAATT

               
       3300 TTA
          1 TTA

       3303 GATTACAAGA


Statistics
Matches: 20,  Mismatches: 3, Indels: 1
        0.83            0.12        0.04

Matches are distributed among these distances:
  20    5  0.25
  21   15  0.75

ACGTcount: A:0.32, C:0.07, G:0.05, T:0.57


Consensus pattern (20 bp):   
TTATAACTATTTTAATAATT

Found at i:11375 original size:11 final size:11

Alignment explanation


    Indices: 11356--11403  Score: 51
    Period size: 11  Copynumber: 4.3  Consensus size: 11

      11346 TTAGATTTCC

                *      
      11356 TTTTGTCTTTT
          1 TTTTTTCTTTT

                        
      11367 TTTTTTCTTTTT
          1 TTTTTTC-TTTT

                   *   
      11379 TTTTTTCCTTT
          1 TTTTTTCTTTT

              *   *    
      11390 TTCTTTGTTTT
          1 TTTTTTCTTTT

               
      11401 TTT
          1 TTT

      11404 CTTTTCAAGT


Statistics
Matches: 30,  Mismatches: 6, Indels: 2
        0.79            0.16        0.05

Matches are distributed among these distances:
  11   19  0.63
  12   11  0.37

ACGTcount: A:0.00, C:0.10, G:0.04, T:0.85


Consensus pattern (11 bp):   
TTTTTTCTTTT

Found at i:11378 original size:12 final size:12

Alignment explanation


    Indices: 11363--11409  Score: 51
    Period size: 12  Copynumber: 3.9  Consensus size: 12

      11353 TCCTTTTGTC

                        
      11363 TTTTTTTTTTCT
          1 TTTTTTTTTTCT

                         
      11375 TTTTTTTTTTCCT
          1 TTTTTTTTTT-CT

                *   *   
      11388 TTTTCTTTGT-T
          1 TTTTTTTTTTCT

                 *     
      11399 TTTTTCTTTTC
          1 TTTTTTTTTTC

      11410 AAGTCAAAA


Statistics
Matches: 28,  Mismatches: 5, Indels: 4
        0.76            0.14        0.11

Matches are distributed among these distances:
  11    8  0.29
  12   10  0.36
  13   10  0.36

ACGTcount: A:0.00, C:0.13, G:0.02, T:0.85


Consensus pattern (12 bp):   
TTTTTTTTTTCT

Found at i:11389 original size:24 final size:24

Alignment explanation


    Indices: 11364--11409  Score: 67
    Period size: 23  Copynumber: 2.0  Consensus size: 24

      11354 CCTTTTGTCT

                 *   *              
      11364 TTTTTTTTTCTTTTTTT-TTTTCC
          1 TTTTTCTTTGTTTTTTTCTTTTCC

                                   
      11387 TTTTTCTTTGTTTTTTTCTTTTC
          1 TTTTTCTTTGTTTTTTTCTTTTC

      11410 AAGTCAAAA


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  23   15  0.75
  24    5  0.25

ACGTcount: A:0.00, C:0.13, G:0.02, T:0.85


Consensus pattern (24 bp):   
TTTTTCTTTGTTTTTTTCTTTTCC

Found at i:11400 original size:19 final size:18

Alignment explanation


    Indices: 11357--11408  Score: 70
    Period size: 19  Copynumber: 2.9  Consensus size: 18

      11347 TAGATTTCCT

                 *            
      11357 TTTGTCTTTTT-TTTTTC
          1 TTTGTTTTTTTCTTTTTC

               *               
      11374 TTTTTTTTTTTCCTTTTTC
          1 TTTGTTTTTTT-CTTTTTC

                            
      11393 TTTGTTTTTTTCTTTT
          1 TTTGTTTTTTTCTTTT

      11409 CAAGTCAAAA


Statistics
Matches: 30,  Mismatches: 3, Indels: 3
        0.83            0.08        0.08

Matches are distributed among these distances:
  17    9  0.30
  18    5  0.17
  19   16  0.53

ACGTcount: A:0.00, C:0.12, G:0.04, T:0.85


Consensus pattern (18 bp):   
TTTGTTTTTTTCTTTTTC
Done.