Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009044.1 Corchorus olitorius cultivar O-4 contig09072, 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, 916

Length: 1527
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30


Found at i:475 original size:21 final size:21

Alignment explanation


    Indices: 461--582  Score: 192
    Period size: 21  Copynumber: 5.8  Consensus size: 21

        451 ATTGGAACAA

                                  
        461 GTTCCAAGCTCATTGGAGCAA-
          1 GTTCCAAGCTCATTGGAG-AAG

                                 
        482 GTTCCAAGCTCATTGGAGAAG
          1 GTTCCAAGCTCATTGGAGAAG

                    *            
        503 GTTCCAAGTTCATTGGAGAAG
          1 GTTCCAAGCTCATTGGAGAAG

                    *            
        524 GTTCCAAGTTCATTGGAGAAG
          1 GTTCCAAGCTCATTGGAGAAG

                    *            
        545 GTTCCAAGATCATTGGAGAAG
          1 GTTCCAAGCTCATTGGAGAAG

               *             
        566 GTTTCAAGCTCATTGGA
          1 GTTCCAAGCTCATTGGA

        583 ATTGCCTAAG


Statistics
Matches: 96,  Mismatches: 4, Indels: 2
        0.94            0.04        0.02

Matches are distributed among these distances:
  20    2  0.02
  21   94  0.98

ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27


Consensus pattern (21 bp):   
GTTCCAAGCTCATTGGAGAAG

Found at i:549 original size:63 final size:63

Alignment explanation


    Indices: 445--583  Score: 201
    Period size: 63  Copynumber: 2.2  Consensus size: 63

        435 AAGATGCTAG

                                                         *                 
        445 AAGTTCATTGGAACAAGTTCCAAGCTCATTGGAGCAAGTTCCAAGCTCATTGGAGAAGGTTCC
          1 AAGTTCATTGGAACAAGTTCCAAGCTCATTGGAGCAAGTTCCAAGATCATTGGAGAAGGTTCC

                            *        *                                     * 
        508 AAGTTCATTGGAGA-AGGTTCCAAGTTCATTGGAG-AAGGTTCCAAGATCATTGGAGAAGGTTTC
          1 AAGTTCATTGGA-ACAAGTTCCAAGCTCATTGGAGCAA-GTTCCAAGATCATTGGAGAAGGTTCC

               *         
        571 AAGCTCATTGGAA
          1 AAGTTCATTGGAA

        584 TTGCCTAAGA


Statistics
Matches: 69,  Mismatches: 5, Indels: 5
        0.87            0.06        0.06

Matches are distributed among these distances:
  62    3  0.04
  63   65  0.94
  64    1  0.01

ACGTcount: A:0.31, C:0.17, G:0.26, T:0.27


Consensus pattern (63 bp):   
AAGTTCATTGGAACAAGTTCCAAGCTCATTGGAGCAAGTTCCAAGATCATTGGAGAAGGTTCC

Found at i:1221 original size:20 final size:21

Alignment explanation


    Indices: 1198--1240  Score: 61
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       1188 ATCTTGAAGA

                                 
       1198 ATTTAAAG-CCATCGGAGATC
          1 ATTTAAAGCCCATCGGAGATC

                *        *       
       1218 ATTTGAAGCCCATTGGAGATC
          1 ATTTAAAGCCCATCGGAGATC

              
       1239 AT
          1 AT

       1241 CAACAAAGGA


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  20    7  0.35
  21   13  0.65

ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28


Consensus pattern (21 bp):   
ATTTAAAGCCCATCGGAGATC

Done.