Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022121.1 Corchorus olitorius cultivar O-4 contig22154, 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: 6332
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35


Found at i:910 original size:19 final size:18

Alignment explanation


    Indices: 886--921  Score: 54
    Period size: 18  Copynumber: 1.9  Consensus size: 18

        876 TGAAGACCAT

                               
        886 TTGAAGATAATTTGAAGAC
          1 TTGAAGAT-ATTTGAAGAC

                    *        
        905 TTGAAGATTTTTGAAGA
          1 TTGAAGATATTTGAAGA

        922 ATTATTTCAA


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

Matches are distributed among these distances:
  18    8  0.50
  19    8  0.50

ACGTcount: A:0.39, C:0.03, G:0.22, T:0.36


Consensus pattern (18 bp):   
TTGAAGATATTTGAAGAC

Found at i:3074 original size:19 final size:18

Alignment explanation


    Indices: 3041--3076  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       3031 TTGAGATAAT

                              
       3041 TCTTCAATGATCTTCAAA
          1 TCTTCAATGATCTTCAAA

                     *        
       3059 TCTTCAAATTATCTTCAA
          1 TCTTC-AATGATCTTCAA

       3077 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:0.33, C:0.22, G:0.03, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGATCTTCAAA

Found at i:4100 original size:19 final size:18

Alignment explanation


    Indices: 4076--4111  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       4066 TGAAGACTTA

                               
       4076 TTGAAGACAATTTGAAGAT
          1 TTGAAGACAA-TTGAAGAT

                    *        
       4095 TTGAAGACCATTGAAGA
          1 TTGAAGACAATTGAAGA

       4112 ATTATTTCCA


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:0.08, G:0.22, T:0.28


Consensus pattern (18 bp):   
TTGAAGACAATTGAAGAT

Found at i:5724 original size:11 final size:11

Alignment explanation


    Indices: 5708--5733  Score: 52
    Period size: 11  Copynumber: 2.4  Consensus size: 11

       5698 AGATTGTTTA

                       
       5708 TTTTCTTTTTC
          1 TTTTCTTTTTC

                       
       5719 TTTTCTTTTTC
          1 TTTTCTTTTTC

                
       5730 TTTT
          1 TTTT

       5734 TGATTTGCAC


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   15  1.00

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


Consensus pattern (11 bp):   
TTTTCTTTTTC
Done.