Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023516.1 Corchorus olitorius cultivar O-4 contig23549, 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: 4808
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34


Found at i:575 original size:6 final size:6

Alignment explanation


    Indices: 564--592  Score: 51
    Period size: 6  Copynumber: 5.0  Consensus size: 6

        554 GGAGCCATGG

                                              
        564 TTTCTT TTTCTT TTTCTT TTT-TT TTTCTT
          1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT

        593 CTTTTAATTT


Statistics
Matches: 22,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
   5    5  0.23
   6   17  0.77

ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86


Consensus pattern (6 bp):   
TTTCTT

Found at i:597 original size:12 final size:11

Alignment explanation


    Indices: 564--597  Score: 50
    Period size: 11  Copynumber: 3.0  Consensus size: 11

        554 GGAGCCATGG

                        
        564 TTTCTTTTTCTT
          1 TTTCTTTTT-TT

                       
        576 TTTCTTTTTTT
          1 TTTCTTTTTTT

                  *    
        587 TTTCTTCTTTT
          1 TTTCTTTTTTT

        598 AATTTTGAAA


Statistics
Matches: 21,  Mismatches: 1, Indels: 1
        0.91            0.04        0.04

Matches are distributed among these distances:
  11   12  0.57
  12    9  0.43

ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85


Consensus pattern (11 bp):   
TTTCTTTTTTT

Found at i:603 original size:14 final size:11

Alignment explanation


    Indices: 564--597  Score: 50
    Period size: 12  Copynumber: 2.9  Consensus size: 11

        554 GGAGCCATGG

                        
        564 TTTCTTTTTCTT
          1 TTTCTTTTT-TT

                       
        576 TTTCTTTTTTT
          1 TTTCTTTTTTT

                       
        587 TTTCTTCTTTT
          1 TTTCTT-TTTT

        598 AATTTTGAAA


Statistics
Matches: 21,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  11    8  0.38
  12   13  0.62

ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85


Consensus pattern (11 bp):   
TTTCTTTTTTT

Found at i:3002 original size:25 final size:26

Alignment explanation


    Indices: 2969--3018  Score: 84
    Period size: 25  Copynumber: 2.0  Consensus size: 26

       2959 ATTTGTTTGT

                       *              
       2969 TTAATTGGTAGGTAG-TATTTAGATG
          1 TTAATTGGTAGATAGTTATTTAGATG

                                     
       2994 TTAATTGGTAGATAGTTATTTAGAT
          1 TTAATTGGTAGATAGTTATTTAGAT

       3019 ATTTGGATAT


Statistics
Matches: 23,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  25   14  0.61
  26    9  0.39

ACGTcount: A:0.30, C:0.00, G:0.24, T:0.46


Consensus pattern (26 bp):   
TTAATTGGTAGATAGTTATTTAGATG

Found at i:3990 original size:16 final size:16

Alignment explanation


    Indices: 3969--4009  Score: 82
    Period size: 16  Copynumber: 2.6  Consensus size: 16

       3959 GAACATTCTC

                            
       3969 CATTTTCTAAGAGTTG
          1 CATTTTCTAAGAGTTG

                            
       3985 CATTTTCTAAGAGTTG
          1 CATTTTCTAAGAGTTG

                     
       4001 CATTTTCTA
          1 CATTTTCTA

       4010 TTCTCTAGAA


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   25  1.00

ACGTcount: A:0.24, C:0.15, G:0.15, T:0.46


Consensus pattern (16 bp):   
CATTTTCTAAGAGTTG
Done.