Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019142.1 Corchorus olitorius cultivar O-4 contig19175, 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: 7488
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28


Found at i:1399 original size:51 final size:50

Alignment explanation


    Indices: 1298--1400  Score: 120
    Period size: 51  Copynumber: 2.0  Consensus size: 50

       1288 GTTCTTCATA

                                            *         *       
       1298 TTTTTCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCTTTTAGTGT
          1 TTTTTCTTGTTTAGATCTTGTCTCAGGACAATAAAACACTCTATTAGTGT

                                      *                *    *    
       1348 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGAC-ATAAAAACACTGTATTCGTGT
          1 TTTT-TCTTGTTT-AGATCTTGTCTCAGGACAAT-AAAACACTCTATTAGTGT

              
       1399 TT
          1 TT

       1401 CTCTTTCAGA


Statistics
Matches: 45,  Mismatches: 5, Indels: 5
        0.82            0.09        0.09

Matches are distributed among these distances:
  50    6  0.13
  51   38  0.84
  52    1  0.02

ACGTcount: A:0.21, C:0.19, G:0.14, T:0.46


Consensus pattern (50 bp):   
TTTTTCTTGTTTAGATCTTGTCTCAGGACAATAAAACACTCTATTAGTGT

Found at i:2128 original size:23 final size:23

Alignment explanation


    Indices: 2093--2138  Score: 58
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       2083 CGCCTCCAGG

                          **       
       2093 GTTTAATTTCTTTACTTTTTTTC
          1 GTTTAATTTCTTTAAGTTTTTTC

                                    
       2116 GTTT-ATTTACTTTAAGTTTTTTC
          1 GTTTAATTT-CTTTAAGTTTTTTC

       2139 TTTTCTACAC


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

Matches are distributed among these distances:
  22    4  0.20
  23   16  0.80

ACGTcount: A:0.15, C:0.11, G:0.07, T:0.67


Consensus pattern (23 bp):   
GTTTAATTTCTTTAAGTTTTTTC
Done.