Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017463.1 Corchorus olitorius cultivar O-4 contig17496, 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: 7390
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31


Found at i:385 original size:22 final size:21

Alignment explanation


    Indices: 333--386  Score: 60
    Period size: 19  Copynumber: 2.6  Consensus size: 21

        323 GCTTCTTGGA

                                  
        333 AATAATTCTTC-AATGATCTTC
          1 AATAA-TCTTCAAATGATCTTC

                          *      
        354 -A-AATCTTCAAATTATCTTC
          1 AATAATCTTCAAATGATCTTC

                          
        373 AATAAGTCTTCAAA
          1 AATAA-TCTTCAAA

        387 CAAGAACTTC


Statistics
Matches: 28,  Mismatches: 1, Indels: 7
        0.78            0.03        0.19

Matches are distributed among these distances:
  18    5  0.18
  19   11  0.39
  20    2  0.07
  21    2  0.07
  22    8  0.29

ACGTcount: A:0.39, C:0.19, G:0.04, T:0.39


Consensus pattern (21 bp):   
AATAATCTTCAAATGATCTTC

Found at i:1070 original size:22 final size:22

Alignment explanation


    Indices: 1045--1090  Score: 92
    Period size: 22  Copynumber: 2.1  Consensus size: 22

       1035 TCCCATTTTT

                                  
       1045 GAGGCTACTAGCACTCTAGAAG
          1 GAGGCTACTAGCACTCTAGAAG

                                  
       1067 GAGGCTACTAGCACTCTAGAAG
          1 GAGGCTACTAGCACTCTAGAAG

              
       1089 GA
          1 GA

       1091 CTCCTTATTT


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

Matches are distributed among these distances:
  22   24  1.00

ACGTcount: A:0.33, C:0.22, G:0.28, T:0.17


Consensus pattern (22 bp):   
GAGGCTACTAGCACTCTAGAAG

Found at i:5178 original size:6 final size:6

Alignment explanation


    Indices: 5167--5202  Score: 72
    Period size: 6  Copynumber: 6.0  Consensus size: 6

       5157 AATCGAATAT

                                                     
       5167 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA
          1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA

       5203 TAATACACAA


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   30  1.00

ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00


Consensus pattern (6 bp):   
AGAAAA

Found at i:6768 original size:19 final size:18

Alignment explanation


    Indices: 6735--6770  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       6725 TGGAAATAAT

                              
       6735 TCTTCAATGATCTTCAAA
          1 TCTTCAATGATCTTCAAA

                     *        
       6753 TCTTCAAATTATCTTCAA
          1 TCTTC-AATGATCTTCAA

       6771 TAAGTCTCCA


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
Done.