Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018988.1 Corchorus olitorius cultivar O-4 contig19021, 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: 23812
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--131  Score: 262
    Period size: 2  Copynumber: 65.5  Consensus size: 2

                                                                          
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                                                                          
         43 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                                                                          
         85 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                   
        127 TA TA T
          1 TA TA T

        132 TATTATTATT


Statistics
Matches: 129,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2  129  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:137 original size:3 final size:3

Alignment explanation


    Indices: 129--170  Score: 84
    Period size: 3  Copynumber: 14.0  Consensus size: 3

        119 TATATATATA

                                                                   
        129 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
          1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT

        171 ACACTCCTTC


Statistics
Matches: 39,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   39  1.00

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67


Consensus pattern (3 bp):   
TAT

Found at i:1050 original size:21 final size:22

Alignment explanation


    Indices: 1017--1060  Score: 56
    Period size: 21  Copynumber: 2.0  Consensus size: 22

       1007 GAGAATAACG

                                    
       1017 AAAAAATCAATATTGAAAT-GAAA
          1 AAAAAAT-AATATT-AAATAGAAA

                                  
       1040 AAAAAAT-ATATTAAATAGAAA
          1 AAAAAATAATATTAAATAGAAA

       1061 CCAAATTGAT


Statistics
Matches: 20,  Mismatches: 0, Indels: 4
        0.83            0.00        0.17

Matches are distributed among these distances:
  20    4  0.20
  21    9  0.45
  23    7  0.35

ACGTcount: A:0.68, C:0.02, G:0.07, T:0.23


Consensus pattern (22 bp):   
AAAAAATAATATTAAATAGAAA

Found at i:22995 original size:21 final size:21

Alignment explanation


    Indices: 22952--22995  Score: 54
    Period size: 21  Copynumber: 2.1  Consensus size: 21

      22942 CCAATTTAGG

                     *     *     
      22952 TTTAGATTTCAATTTCTTGTT
          1 TTTAGATTTAAATTTATTGTT

                                  
      22973 TTTAGATTTAAGATTTATT-TT
          1 TTTAGATTTAA-ATTTATTGTT

              
      22994 TT
          1 TT

      22996 ATGCATCTTA


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  21   14  0.70
  22    6  0.30

ACGTcount: A:0.23, C:0.05, G:0.09, T:0.64


Consensus pattern (21 bp):   
TTTAGATTTAAATTTATTGTT
Done.