Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016836.1 Corchorus olitorius cultivar O-4 contig16869, 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: 8032
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32


Found at i:153 original size:20 final size:20

Alignment explanation


    Indices: 125--170  Score: 65
    Period size: 20  Copynumber: 2.3  Consensus size: 20

        115 CGGAAGGTAA

                *              *
        125 TGTTCTCAATATTTTATTCT
          1 TGTTTTCAATATTTTATTCC

                      *         
        145 TGTTTTCAATGTTTTATTCC
          1 TGTTTTCAATATTTTATTCC

                  
        165 TGTTTT
          1 TGTTTT

        171 GCCCTTCCCC


Statistics
Matches: 23,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  20   23  1.00

ACGTcount: A:0.15, C:0.13, G:0.09, T:0.63


Consensus pattern (20 bp):   
TGTTTTCAATATTTTATTCC

Found at i:197 original size:68 final size:68

Alignment explanation


    Indices: 13--198  Score: 232
    Period size: 68  Copynumber: 2.8  Consensus size: 68

          3 GAAGGTGTTG

                   *                         *                               
         13 TTTCAATATTTTATTCCTG-TTTGCCCTTCCCGGTCGG-AGGGTGTTGTTCTCAATACTTGATCC
          1 TTTCAATGTTTTATTCCTGTTTTGCCCTTCCCGATCGGAAGGG-GTTGTTCTCAATACTTGATCC

                
         76 CTAT
         65 CTAT

                *            *                        ***           *  *  * *
         80 TTTCGATGTTTTATTCCCGTTTTGCCCTTCCCGATCGGAAGGTAATGTTCTCAATATTTTATTCT
          1 TTTCAATGTTTTATTCCTGTTTTGCCCTTCCCGATCGGAAGGGGTTGTTCTCAATACTTGATCCC

             * 
        145 TGT
         66 TAT

                                            *                  
        148 TTTCAATGTTTTATTCCTGTTTTGCCCTTCCCCATCGGAAGGGGTTGTTCT
          1 TTTCAATGTTTTATTCCTGTTTTGCCCTTCCCGATCGGAAGGGGTTGTTCT

        199 TATTCTCTTC


Statistics
Matches: 99,  Mismatches: 18, Indels: 3
        0.82            0.15        0.03

Matches are distributed among these distances:
  67   16  0.16
  68   80  0.81
  69    3  0.03

ACGTcount: A:0.15, C:0.23, G:0.18, T:0.45


Consensus pattern (68 bp):   
TTTCAATGTTTTATTCCTGTTTTGCCCTTCCCGATCGGAAGGGGTTGTTCTCAATACTTGATCCC
TAT

Found at i:1276 original size:36 final size:36

Alignment explanation


    Indices: 1236--1305  Score: 131
    Period size: 36  Copynumber: 1.9  Consensus size: 36

       1226 AGATGGATAT

                                                
       1236 TTAGCCAATGTCTTGAGACATTGATGAAATAAATGA
          1 TTAGCCAATGTCTTGAGACATTGATGAAATAAATGA

                          *                   
       1272 TTAGCCAATGTCTTTAGACATTGATGAAATAAAT
          1 TTAGCCAATGTCTTGAGACATTGATGAAATAAAT

       1306 TAGAGAAAAT


Statistics
Matches: 33,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  36   33  1.00

ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33


Consensus pattern (36 bp):   
TTAGCCAATGTCTTGAGACATTGATGAAATAAATGA

Found at i:5936 original size:15 final size:15

Alignment explanation


    Indices: 5916--5957  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       5906 ACAGAGGTTG

                           
       5916 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                           
       5931 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                *       
       5946 ACTACAAAACAA
          1 AC-AGAAAACAA

       5958 AACAAAGTAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   17  0.68
  16    8  0.32

ACGTcount: A:0.67, C:0.17, G:0.05, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA

Done.