Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024332.1 Corchorus olitorius cultivar O-4 contig24365, 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: 22126
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.34


Found at i:9952 original size:38 final size:38

Alignment explanation


    Indices: 9883--9974  Score: 114
    Period size: 38  Copynumber: 2.4  Consensus size: 38

       9873 ATTAAAATGG

                    *    *            *     *      
       9883 TAAAAATAAAATGATTATAAAATATTTAATTTGATTAAA
          1 TAAAAATAGAAT-TTTATAAAATATTGAATTTAATTAAA

                                                   
       9922 TAAAAATAG-ATTTTATAAAAATATTGAATTTAATTAAA
          1 TAAAAATAGAATTTTAT-AAAATATTGAATTTAATTAAA

                *          
       9960 TAAATATAGAATTTT
          1 TAAAAATAGAATTTT

       9975 TAGTACAATA


Statistics
Matches: 46,  Mismatches: 5, Indels: 4
        0.84            0.09        0.07

Matches are distributed among these distances:
  37    4  0.09
  38   29  0.63
  39   13  0.28

ACGTcount: A:0.54, C:0.00, G:0.05, T:0.40


Consensus pattern (38 bp):   
TAAAAATAGAATTTTATAAAATATTGAATTTAATTAAA

Found at i:9964 original size:21 final size:21

Alignment explanation


    Indices: 9910--9973  Score: 64
    Period size: 21  Copynumber: 3.2  Consensus size: 21

       9900 TAAAATATTT

                 *          *    
       9910 AATTTGATTAAATAAAAATAG
          1 AATTTAATTAAATAAATATAG

                 *             * 
       9931 -ATTTTA-T-AA-AAATATTG
          1 AATTTAATTAAATAAATATAG

                                 
       9948 AATTTAATTAAATAAATATAG
          1 AATTTAATTAAATAAATATAG

                 
       9969 AATTT
          1 AATTT

       9974 TTAGTACAAT


Statistics
Matches: 34,  Mismatches: 5, Indels: 8
        0.72            0.11        0.17

Matches are distributed among these distances:
  17    6  0.18
  18    7  0.21
  19    2  0.06
  20    7  0.21
  21   12  0.35

ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41


Consensus pattern (21 bp):   
AATTTAATTAAATAAATATAG

Found at i:10156 original size:60 final size:60

Alignment explanation


    Indices: 10051--10166  Score: 169
    Period size: 60  Copynumber: 1.9  Consensus size: 60

      10041 TGTGAACATG

                           *             *  *      *                    
      10051 AAATTAAATAATAGGTTACACAAAGGGAGGTAGCATTCTTACATCCCAAAACTCACCCCC
          1 AAATTAAATAATAGGCTACACAAAGGGAGATAACATTCTCACATCCCAAAACTCACCCCC

                     *                        *     *               
      10111 AAATTAAATGATAGGCTACACAAAGGGAGATAACCTTCTCCCATCCCAAAACTCAC
          1 AAATTAAATAATAGGCTACACAAAGGGAGATAACATTCTCACATCCCAAAACTCAC

      10167 TACTAGACTG


Statistics
Matches: 49,  Mismatches: 7, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  60   49  1.00

ACGTcount: A:0.41, C:0.26, G:0.13, T:0.21


Consensus pattern (60 bp):   
AAATTAAATAATAGGCTACACAAAGGGAGATAACATTCTCACATCCCAAAACTCACCCCC

Found at i:14798 original size:2 final size:2

Alignment explanation


    Indices: 14793--14820  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

      14783 GTGTATATCA

                                                     
      14793 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      14821 TGCAAATGTT


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:22014 original size:29 final size:28

Alignment explanation


    Indices: 21975--22029  Score: 92
    Period size: 29  Copynumber: 1.9  Consensus size: 28

      21965 GCCTTCCCAA

                  *                      
      21975 AAAGTTGGGACCCTTATTTGAGTATTTTT
          1 AAAGTTCGGACCCTTATTTGAG-ATTTTT

                                      
      22004 AAAGTTCGGACCCTTATTTGAGATTT
          1 AAAGTTCGGACCCTTATTTGAGATTT

      22030 AAGGCAAACT


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

Matches are distributed among these distances:
  28    4  0.16
  29   21  0.84

ACGTcount: A:0.25, C:0.13, G:0.20, T:0.42


Consensus pattern (28 bp):   
AAAGTTCGGACCCTTATTTGAGATTTTT
Done.