Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015195.1 Corchorus olitorius cultivar O-4 contig15228, 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: 8239
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.35


Found at i:42 original size:3 final size:3

Alignment explanation


    Indices: 36--95  Score: 111
    Period size: 3  Copynumber: 20.0  Consensus size: 3

         26 ATAATTAAAA

                                                                           
         36 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
          1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT

                *          
         84 TCT CCT TCT TCT
          1 TCT TCT TCT TCT

         96 CCAGTAAATC


Statistics
Matches: 55,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
   3   55  1.00

ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65


Consensus pattern (3 bp):   
TCT

Found at i:1207 original size:19 final size:19

Alignment explanation


    Indices: 1142--1216  Score: 69
    Period size: 19  Copynumber: 3.5  Consensus size: 19

       1132 TTATTTGTTA

                               
       1142 AAAATTTAAAGAAAATACT
          1 AAAATTTAAAGAAAATACT

                                        
       1161 AAAATATATATAGAAGATGAGTAATACT
          1 -AAA-AT-T-TA-AAGA--A--AATACT

                               
       1189 AAAATTTAAAGAAAATACT
          1 AAAATTTAAAGAAAATACT

                     
       1208 AAAATTTAA
          1 AAAATTTAA

       1217 GTTTTCTTTC


Statistics
Matches: 47,  Mismatches: 0, Indels: 17
        0.73            0.00        0.27

Matches are distributed among these distances:
  19   15  0.32
  20    3  0.06
  21    3  0.06
  22    1  0.02
  23    6  0.13
  24    6  0.13
  25    1  0.02
  26    3  0.06
  27    3  0.06
  28    6  0.13

ACGTcount: A:0.60, C:0.04, G:0.08, T:0.28


Consensus pattern (19 bp):   
AAAATTTAAAGAAAATACT

Found at i:4039 original size:17 final size:18

Alignment explanation


    Indices: 4019--4053  Score: 54
    Period size: 17  Copynumber: 2.0  Consensus size: 18

       4009 ATTTTCAAAT

                 *            
       4019 TTTCCTTGAAA-TTTTCC
          1 TTTCCCTGAAACTTTTCC

                              
       4036 TTTCCCTGAAACTTTTCC
          1 TTTCCCTGAAACTTTTCC

       4054 CACTTCCAAA


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

Matches are distributed among these distances:
  17   10  0.62
  18    6  0.38

ACGTcount: A:0.17, C:0.29, G:0.06, T:0.49


Consensus pattern (18 bp):   
TTTCCCTGAAACTTTTCC

Done.