Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012169.1 Corchorus capsularis cultivar CVL-1 contig12190, 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: 13528
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32


Found at i:5612 original size:18 final size:19

Alignment explanation


    Indices: 5578--5613  Score: 56
    Period size: 19  Copynumber: 1.9  Consensus size: 19

       5568 TTTTGAGTCA

                               
       5578 TTTGAGTCGGTTTAGTTTT
          1 TTTGAGTCGGTTTAGTTTT

                   *          
       5597 TTTGAGTTGG-TTAGTTT
          1 TTTGAGTCGGTTTAGTTT

       5614 GAGTCTGAGT


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.11, C:0.03, G:0.28, T:0.58


Consensus pattern (19 bp):   
TTTGAGTCGGTTTAGTTTT

Found at i:5955 original size:35 final size:35

Alignment explanation


    Indices: 5916--5982  Score: 116
    Period size: 35  Copynumber: 1.9  Consensus size: 35

       5906 ATGAGAAAGG

                  * *                          
       5916 AACAGATAGAGAAGAAGTAATTGATGGAGAGAACT
          1 AACAGAGAAAGAAGAAGTAATTGATGGAGAGAACT

                                            
       5951 AACAGAGAAAGAAGAAGTAATTGATGGAGAGA
          1 AACAGAGAAAGAAGAAGTAATTGATGGAGAGA

       5983 CCTATAAGAA


Statistics
Matches: 30,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  35   30  1.00

ACGTcount: A:0.51, C:0.04, G:0.30, T:0.15


Consensus pattern (35 bp):   
AACAGAGAAAGAAGAAGTAATTGATGGAGAGAACT

Found at i:9195 original size:29 final size:31

Alignment explanation


    Indices: 9163--9221  Score: 86
    Period size: 32  Copynumber: 1.9  Consensus size: 31

       9153 TTTTGACCAC

                            *              
       9163 TGAACTT-CAA-ATCACGACATTTTACCCCA
          1 TGAACTTCCAATATCAAGACATTTTACCCCA

                                          
       9192 TGAACTTCCCAATATCAAGACATTTTACCC
          1 TGAACTT-CCAATATCAAGACATTTTACCC

       9222 TTGATGGAGG


Statistics
Matches: 26,  Mismatches: 1, Indels: 3
        0.87            0.03        0.10

Matches are distributed among these distances:
  29    7  0.27
  31    3  0.12
  32   16  0.62

ACGTcount: A:0.34, C:0.31, G:0.07, T:0.29


Consensus pattern (31 bp):   
TGAACTTCCAATATCAAGACATTTTACCCCA

Found at i:13305 original size:36 final size:36

Alignment explanation


    Indices: 13227--13297  Score: 133
    Period size: 36  Copynumber: 2.0  Consensus size: 36

      13217 CATGAGTGTC

                                      *         
      13227 AAGTGTAATTCCTATGTGGTAATAAATATGGAATTA
          1 AAGTGTAATTCCTATGTGGTAATAAAGATGGAATTA

                                               
      13263 AAGTGTAATTCCTATGTGGTAATAAAGATGGAATT
          1 AAGTGTAATTCCTATGTGGTAATAAAGATGGAATT

      13298 GGAGTGTAGT


Statistics
Matches: 34,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  36   34  1.00

ACGTcount: A:0.38, C:0.06, G:0.21, T:0.35


Consensus pattern (36 bp):   
AAGTGTAATTCCTATGTGGTAATAAAGATGGAATTA

Found at i:13378 original size:2 final size:2

Alignment explanation


    Indices: 13360--13392  Score: 50
    Period size: 2  Copynumber: 17.0  Consensus size: 2

      13350 TGGCTGTTAT

                   *                                          
      13360 TA TA TT TA TA T- 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 TA TA TA

      13393 CTAGTTAAAG


Statistics
Matches: 28,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
   1    1  0.04
   2   27  0.96

ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55


Consensus pattern (2 bp):   
TA

Done.