Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009884.1 Corchorus olitorius cultivar O-4 contig09916, 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: 9020
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33


Found at i:580 original size:11 final size:10

Alignment explanation


    Indices: 564--615  Score: 54
    Period size: 11  Copynumber: 5.1  Consensus size: 10

        554 AAGTTCGTGT

                       
        564 TTGAAGATTTA
          1 TTGAAGA-TTA

                    * 
        575 TTGAAGATAA
          1 TTGAAGATTA

                       
        585 TTTGAAGA-T-
          1 -TTGAAGATTA

                      
        594 TTGAAGATTA
          1 TTGAAGATTA

                       
        604 TTGAAGAATTA
          1 TTGAAG-ATTA

             
        615 T
          1 T

        616 CTAAAGAGGC


Statistics
Matches: 35,  Mismatches: 2, Indels: 8
        0.78            0.04        0.18

Matches are distributed among these distances:
   8    7  0.20
   9    1  0.03
  10    8  0.23
  11   19  0.54

ACGTcount: A:0.40, C:0.00, G:0.19, T:0.40


Consensus pattern (10 bp):   
TTGAAGATTA

Found at i:599 original size:19 final size:18

Alignment explanation


    Indices: 575--610  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

        565 TGAAGATTTA

                               
        575 TTGAAGATAATTTGAAGAT
          1 TTGAAGATAA-TTGAAGAT

                    *        
        594 TTGAAGATTATTGAAGA
          1 TTGAAGATAATTGAAGA

        611 ATTATCTAAA


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:0.42, C:0.00, G:0.22, T:0.36


Consensus pattern (18 bp):   
TTGAAGATAATTGAAGAT

Found at i:6827 original size:19 final size:18

Alignment explanation


    Indices: 6794--6829  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       6784 TTGAGATAAT

                              
       6794 TCTTCAATGATCTTCAAA
          1 TCTTCAATGATCTTCAAA

                     *        
       6812 TCTTCAAATTATCTTCAA
          1 TCTTC-AATGATCTTCAA

       6830 TAAATCTTCA


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:8418 original size:29 final size:31

Alignment explanation


    Indices: 8367--8425  Score: 86
    Period size: 30  Copynumber: 2.0  Consensus size: 31

       8357 GTTTATTAAT

                                           
       8367 GAAACTTGAAAAATAAAGACATAAAATAAAG
          1 GAAACTTGAAAAATAAAGACATAAAATAAAG

                        *            *    
       8398 GAAA-TTGAAAATTAAAG-CATAAATTAAA
          1 GAAACTTGAAAAATAAAGACATAAAATAAA

       8426 TAACTAATCC


Statistics
Matches: 26,  Mismatches: 2, Indels: 2
        0.87            0.07        0.07

Matches are distributed among these distances:
  29   10  0.38
  30   12  0.46
  31    4  0.15

ACGTcount: A:0.63, C:0.05, G:0.12, T:0.20


Consensus pattern (31 bp):   
GAAACTTGAAAAATAAAGACATAAAATAAAG
Done.