Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009681.1 Corchorus olitorius cultivar O-4 contig09713, 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: 4558
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32


Found at i:879 original size:21 final size:23

Alignment explanation


    Indices: 839--1008  Score: 85
    Period size: 22  Copynumber: 7.8  Consensus size: 23

        829 AAATCTGATA

                 *          *      
        839 GAAAGATTATCAAAA-ATCATAG
          1 GAAAGGTTATCAAAATTTCATAG

                                   
        861 G-AAGGTTA-CAAAATTTCATAG
          1 GAAAGGTTATCAAAATTTCATAG

                 *    *            
        882 GAAAGTTTATTAAAATTTCATA-
          1 GAAAGGTTATCAAAATTTCATAG

             **  *        *    *    
        904 GTTAGATTATCAAATTTTCTTATG
          1 GAAAGGTTATCAAAATTTCATA-G

                 *      *     *    
        928 G--AGTTTATCACAATTTTATAG
          1 GAAAGGTTATCAAAATTTCATAG

             *            *         
        949 GTAA--TTATCAAATTTTCATATG
          1 GAAAGGTTATCAAAATTTCATA-G

               *              *    
        971 G--TGGTTATCAAAATTTAATAG
          1 GAAAGGTTATCAAAATTTCATAG

                               
        992 GATAA--TTATCAAAATTT
          1 GA-AAGGTTATCAAAATTT

       1009 TATAAAAATA


Statistics
Matches: 113,  Mismatches: 22, Indels: 26
        0.70            0.14        0.16

Matches are distributed among these distances:
  20    5  0.04
  21   30  0.27
  22   65  0.58
  23   12  0.11
  24    1  0.01

ACGTcount: A:0.41, C:0.08, G:0.13, T:0.39


Consensus pattern (23 bp):   
GAAAGGTTATCAAAATTTCATAG

Found at i:964 original size:43 final size:43

Alignment explanation


    Indices: 885--1009  Score: 151
    Period size: 43  Copynumber: 2.8  Consensus size: 43

        875 TTCATAGGAA

                   *       *    *                 *     
        885 AGTTTATTAAAATTTCATAGTTAGATTATCAAATTTTCTTATGG
          1 AGTTTATCAAAATTTAATAGGTA-ATTATCAAATTTTCATATGG

                     *     *                           
        929 AGTTTATCACAATTTTATAGGTAATTATCAAATTTTCATATGG
          1 AGTTTATCAAAATTTAATAGGTAATTATCAAATTTTCATATGG

            * *                                   
        972 TGGTTATCAAAATTTAATAGGATAATTATCAAAATTTT
          1 AGTTTATCAAAATTTAATAGG-TAATTATC-AAATTTT

       1010 ATAAAAATAT


Statistics
Matches: 70,  Mismatches: 9, Indels: 3
        0.85            0.11        0.04

Matches are distributed among these distances:
  43   36  0.51
  44   27  0.39
  45    7  0.10

ACGTcount: A:0.37, C:0.07, G:0.11, T:0.45


Consensus pattern (43 bp):   
AGTTTATCAAAATTTAATAGGTAATTATCAAATTTTCATATGG

Found at i:2224 original size:17 final size:17

Alignment explanation


    Indices: 2202--2234  Score: 50
    Period size: 17  Copynumber: 1.9  Consensus size: 17

       2192 TTTTATGGAT

                              
       2202 ATTTAT-ATTATTAATTA
          1 ATTTATAATT-TTAATTA

                            
       2219 ATTTATAATTTTAATT
          1 ATTTATAATTTTAATT

       2235 GATGTAATGA


Statistics
Matches: 15,  Mismatches: 0, Indels: 2
        0.88            0.00        0.12

Matches are distributed among these distances:
  17   12  0.80
  18    3  0.20

ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61


Consensus pattern (17 bp):   
ATTTATAATTTTAATTA

Found at i:3323 original size:22 final size:22

Alignment explanation


    Indices: 3298--3344  Score: 60
    Period size: 22  Copynumber: 2.1  Consensus size: 22

       3288 TTTTTAGTTG

                            *      
       3298 AGTAAAACT-ATAAAAGTAAAAT
          1 AGTAAAA-TGATAAAAATAAAAT

                     *            
       3320 AGTAAAATGGTAAAAATAAAAT
          1 AGTAAAATGATAAAAATAAAAT

               
       3342 AGT
          1 AGT

       3345 TATAAGGATA


Statistics
Matches: 22,  Mismatches: 2, Indels: 2
        0.85            0.08        0.08

Matches are distributed among these distances:
  21    1  0.05
  22   21  0.95

ACGTcount: A:0.62, C:0.02, G:0.13, T:0.23


Consensus pattern (22 bp):   
AGTAAAATGATAAAAATAAAAT

Found at i:3362 original size:93 final size:94

Alignment explanation


    Indices: 3221--3405  Score: 282
    Period size: 93  Copynumber: 2.0  Consensus size: 94

       3211 TTTCTCAAAA

                      *                                *                     
       3221 AAAAAAGTAATATCGTAAAAATAAAAATAGGTATAAAGATATTTGATTTAATTAAATAAAAATAG
          1 AAAAAAGTAAAATCGTAAAAATAAAAATAGGTATAAAGATATTAGATTTAATTAAATAAAAATAG

                         *               
       3286 AGTTTTTAGTTGAGTAAAACTATAAAAGT
         66 AGTTTTTAGTTGACTAAAACTATAAAAGT

                *        *                *     *             *      *       
       3315 AAAATAGTAAAATGGTAAAAAT-AAAATAGTTATAAGGATATTAGATTTATTTAAATGAAAATAG
          1 AAAAAAGTAAAATCGTAAAAATAAAAATAGGTATAAAGATATTAGATTTAATTAAATAAAAATAG

                                       
       3379 AGTTTTTAGTTGACTAAAACTATAAAA
         66 AGTTTTTAGTTGACTAAAACTATAAAA

       3406 ATTTAAACAA


Statistics
Matches: 82,  Mismatches: 9, Indels: 1
        0.89            0.10        0.01

Matches are distributed among these distances:
  93   63  0.77
  94   19  0.23

ACGTcount: A:0.52, C:0.02, G:0.13, T:0.32


Consensus pattern (94 bp):   
AAAAAAGTAAAATCGTAAAAATAAAAATAGGTATAAAGATATTAGATTTAATTAAATAAAAATAG
AGTTTTTAGTTGACTAAAACTATAAAAGT
Done.