Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006626.1 Corchorus olitorius cultivar O-4 contig06651, 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, 736

Length: 1228
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37


Found at i:377 original size:3 final size:3

Alignment explanation


    Indices: 369--415  Score: 94
    Period size: 3  Copynumber: 15.7  Consensus size: 3

        359 ATTTATTTAT

                                                                          
        369 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT

        416 TTCCTCCTAA


Statistics
Matches: 44,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   44  1.00

ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68


Consensus pattern (3 bp):   
TTA

Found at i:443 original size:26 final size:27

Alignment explanation


    Indices: 414--477  Score: 67
    Period size: 26  Copynumber: 2.4  Consensus size: 27

        404 ATTATTATTA

                                       
        414 TTTTCCTCCTAATTCTCTT-ATTTTCC
          1 TTTTCCTCCTAATTCTCTTCATTTTCC

                 *    **    *   *      
        440 TTTTCTTCCTTTTTCTTTTCTTTTTCC
          1 TTTTCCTCCTAATTCTCTTCATTTTCC

                       
        467 TTCTTCCTCCT
          1 TT-TTCCTCCT

        478 TATATTATAA


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

Matches are distributed among these distances:
  26   15  0.50
  27    8  0.27
  28    7  0.23

ACGTcount: A:0.05, C:0.31, G:0.00, T:0.64


Consensus pattern (27 bp):   
TTTTCCTCCTAATTCTCTTCATTTTCC

Found at i:540 original size:27 final size:28

Alignment explanation


    Indices: 488--540  Score: 65
    Period size: 28  Copynumber: 1.9  Consensus size: 28

        478 TATATTATAA

                                **      
        488 TTGGGCCTAGCTCCATATTTTTTTTAAG
          1 TTGGGCCTAGCTCCATATTTCCTTTAAG

                                       
        516 TTGGGCCTAGC-CCAT-TCTTCCTTTA
          1 TTGGGCCTAGCTCCATAT-TTCCTTTA

        541 TTTAATTAAT


Statistics
Matches: 22,  Mismatches: 2, Indels: 3
        0.81            0.07        0.11

Matches are distributed among these distances:
  26    1  0.05
  27   10  0.45
  28   11  0.50

ACGTcount: A:0.15, C:0.25, G:0.17, T:0.43


Consensus pattern (28 bp):   
TTGGGCCTAGCTCCATATTTCCTTTAAG
Done.