Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019446.1 Corchorus olitorius cultivar O-4 contig19479, 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, 903

Length: 1505
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.35

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:403 original size:22 final size:22

Alignment explanation


    Indices: 371--520  Score: 114
    Period size: 22  Copynumber: 6.8  Consensus size: 22

        361 TGAATATTTT

                                  
        371 TATGAAATTTTGATAACTATCC
          1 TATGAAATTTTGATAACTATCC

               *                   
        393 TATTAAATTTTGATAACTA-CAC
          1 TATGAAATTTTGATAACTATC-C

               *               *    
        415 TATAAAATTTTTGATAA-TTTACC
          1 TATGAAA-TTTTGATAACTAT-CC

                     *            *
        438 TATGAAATTGTGATATACT-TCA
          1 TATGAAATTTTGATA-ACTATCC

                   *             * 
        460 TATGAAACTTTGATAACCTA-AC
          1 TATGAAATTTTGATAA-CTATCC

                    *  *            
        482 TATGAAATATTAATAAACCTA-CC
          1 TATGAAATTTTGAT-AA-CTATCC

                             
        505 TATGAAATTTTG-TAAC
          1 TATGAAATTTTGATAAC

        521 CTGCCTATGA


Statistics
Matches: 103,  Mismatches: 16, Indels: 20
        0.74            0.12        0.14

Matches are distributed among these distances:
  20    1  0.01
  21    4  0.04
  22   61  0.59
  23   35  0.34
  24    2  0.02

ACGTcount: A:0.40, C:0.13, G:0.08, T:0.39


Consensus pattern (22 bp):   
TATGAAATTTTGATAACTATCC

Found at i:536 original size:21 final size:21

Alignment explanation


    Indices: 371--543  Score: 100
    Period size: 22  Copynumber: 7.9  Consensus size: 21

        361 TGAATATTTT

                                   
        371 TATGAAATTTTGATAA-CTATCC
          1 TATGAAATTTT-ATAACCTA-CC

               *                   
        393 TATTAAATTTTGATAA-CTACAC
          1 TATGAAATTTT-ATAACCTAC-C

               *             **    
        415 TATAAAATTTTTGATAATTTACC
          1 TATGAAA-TTTT-ATAACCTACC

                       *        * *
        438 TATGAAATTGTGATATA-CTTCA
          1 TATGAAATT-TTATA-ACCTACC

                       *        * 
        460 TATGAAACTTTGATAACCTAAC
          1 TATGAAA-TTTTATAACCTACC

                       *           
        482 TATGAAATATTAATAAACCTACC
          1 TATGAAAT-TTTAT-AACCTACC

                       *      *  
        505 TATGAAATTTTGTAACCTGCC
          1 TATGAAATTTTATAACCTACC

                 **           
        526 TATGATTTTTTATAACCT
          1 TATGAAATTTTATAACCT

        544 TCCTGTAAGA


Statistics
Matches: 123,  Mismatches: 19, Indels: 19
        0.76            0.12        0.12

Matches are distributed among these distances:
  21   25  0.20
  22   60  0.49
  23   35  0.28
  24    3  0.02

ACGTcount: A:0.38, C:0.14, G:0.08, T:0.40


Consensus pattern (21 bp):   
TATGAAATTTTATAACCTACC

Found at i:1389 original size:2 final size:2

Alignment explanation


    Indices: 1382--1411  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

       1372 AAAGCCACAC

                                                        
       1382 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

       1412 ATAATACTCC


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

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


Consensus pattern (2 bp):   
TA

Done.