Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015643.1 Corchorus olitorius cultivar O-4 contig15676, 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: 3839
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32


Found at i:223 original size:19 final size:18

Alignment explanation


    Indices: 190--225  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

        180 TTGAAATTAT

                              
        190 TCTTCAATGGTCTTCAAA
          1 TCTTCAATGGTCTTCAAA

                     *        
        208 TCTTCAAATTGTCTTCAA
          1 TCTTC-AATGGTCTTCAA

        226 TAAGTCTTCA


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:0.28, C:0.22, G:0.08, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGGTCTTCAAA

Found at i:1038 original size:1 final size:1

Alignment explanation


    Indices: 1032--1068  Score: 74
    Period size: 1  Copynumber: 37.0  Consensus size: 1

       1022 CAACAATTGA

                                                 
       1032 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

       1069 ACATGAAATA


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   36  1.00

ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00


Consensus pattern (1 bp):   
T

Found at i:1720 original size:5 final size:5

Alignment explanation


    Indices: 1710--1738  Score: 58
    Period size: 5  Copynumber: 5.8  Consensus size: 5

       1700 AATATTCAAT

                                              
       1710 CAAAG CAAAG CAAAG CAAAG CAAAG CAAA
          1 CAAAG CAAAG CAAAG CAAAG CAAAG CAAA

       1739 ACAAGAAAAA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   5   24  1.00

ACGTcount: A:0.62, C:0.21, G:0.17, T:0.00


Consensus pattern (5 bp):   
CAAAG

Found at i:1982 original size:6 final size:6

Alignment explanation


    Indices: 1971--2010  Score: 62
    Period size: 6  Copynumber: 6.7  Consensus size: 6

       1961 TTGGAATCCT

                                            **            
       1971 AAAAAG AAAAAG AAAAAG AAAAAG AAAACT AAAAAG AAAA
          1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA

       2011 TTAACATGTT


Statistics
Matches: 30,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
   6   30  1.00

ACGTcount: A:0.82, C:0.03, G:0.12, T:0.03


Consensus pattern (6 bp):   
AAAAAG

Done.