Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016039.1 Corchorus olitorius cultivar O-4 contig16072, 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: 6176
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29


Found at i:1399 original size:42 final size:42

Alignment explanation


    Indices: 1295--1401  Score: 108
    Period size: 42  Copynumber: 2.5  Consensus size: 42

       1285 AGCCAACCAA

                           *         **   *       *   
       1295 TACAATCTGTAACGCTTGAAAATGTTTGAATCAATCAACTGG
          1 TACAATCTGTAACGCATGAAAATGTAAGAACCAATCAAATGG

                    * *    *                *          
       1337 TACAATCTATTACGCCTGAAAATGTAAGAACCGA-CAAATGAG
          1 TACAATCTGTAACGCATGAAAATGTAAGAACCAATCAAATG-G

                          *        
       1379 TACAATCTGTAACGAATGAAAAT
          1 TACAATCTGTAACGCATGAAAAT

       1402 CAGCCAGCCA


Statistics
Matches: 52,  Mismatches: 12, Indels: 2
        0.79            0.18        0.03

Matches are distributed among these distances:
  41    5  0.10
  42   47  0.90

ACGTcount: A:0.41, C:0.17, G:0.16, T:0.26


Consensus pattern (42 bp):   
TACAATCTGTAACGCATGAAAATGTAAGAACCAATCAAATGG

Found at i:1467 original size:42 final size:42

Alignment explanation


    Indices: 1420--1527  Score: 119
    Period size: 42  Copynumber: 2.6  Consensus size: 42

       1410 CAGAGCATCG

                    *                             *    
       1420 TGTAACGCTTGAAAATGTTAGAATCAACCAACT-GGTAGAATC
          1 TGTAACGCATGAAAATGTTAGAATCAACCAA-TAGGTAAAATC

                    * *               *      *       *
       1462 TGTAACGCCTAAAAATGTTAGAATCAGCCAATATGTAAAATT
          1 TGTAACGCATGAAAATGTTAGAATCAACCAATAGGTAAAATC

              *  *                  
       1504 TGCAATGCATGAAAATGTTAGAAT
          1 TGTAACGCATGAAAATGTTAGAAT

       1528 ATTAGAAAAG


Statistics
Matches: 55,  Mismatches: 10, Indels: 2
        0.82            0.15        0.03

Matches are distributed among these distances:
  41    1  0.02
  42   54  0.98

ACGTcount: A:0.41, C:0.14, G:0.18, T:0.28


Consensus pattern (42 bp):   
TGTAACGCATGAAAATGTTAGAATCAACCAATAGGTAAAATC

Found at i:1516 original size:118 final size:117

Alignment explanation


    Indices: 1302--1519  Score: 276
    Period size: 118  Copynumber: 1.8  Consensus size: 117

       1292 CAATACAATC

                               *       *                 *      *            
       1302 TGTAACGCTTGAAAATGTTTGAATCAATCAACTGGTACAATCTATTACGCCTGAAAATGTAAGAA
          1 TGTAACGCTTGAAAATGTTAGAATCAACCAACTGGTACAATCTATAACGCCTAAAAATGTAAGAA

             *            *      *                               
       1367 CCGACAAATGAGTACAATCTGTAACGAATGAAAATCAGCCAGCCAGAGCATCG
         66 CAGACAAAT-AGTAAAATCTGCAACGAATGAAAATCAGCCAGCCAGAGCATCG

                                                 *     *                *    
       1420 TGTAACGCTTGAAAATGTTAGAATCAACCAACTGGTAGAATCTGTAACGCCTAAAAATGTTAGAA
          1 TGTAACGCTTGAAAATGTTAGAATCAACCAACTGGTACAATCTATAACGCCTAAAAATGTAAGAA

                  *            *     * *        
       1485 TCAG-CCAATATGTAAAATTTGCAATGCATGAAAAT
         66 -CAGACAAATA-GTAAAATCTGCAACGAATGAAAAT

       1520 GTTAGAATAT


Statistics
Matches: 84,  Mismatches: 14, Indels: 4
        0.82            0.14        0.04

Matches are distributed among these distances:
 117    1  0.01
 118   81  0.96
 119    2  0.02

ACGTcount: A:0.40, C:0.17, G:0.18, T:0.25


Consensus pattern (117 bp):   
TGTAACGCTTGAAAATGTTAGAATCAACCAACTGGTACAATCTATAACGCCTAAAAATGTAAGAA
CAGACAAATAGTAAAATCTGCAACGAATGAAAATCAGCCAGCCAGAGCATCG

Found at i:1814 original size:30 final size:30

Alignment explanation


    Indices: 1752--1825  Score: 98
    Period size: 30  Copynumber: 2.5  Consensus size: 30

       1742 AAATAAAATT

                                       *  
       1752 GTGGCAAAGCCCGTTGAAAACTACAGATCC
          1 GTGGCAAAGCCCGTTGAAAACTACAGAACC

                                            
       1782 GTGGCAAAGCCCGTTGAAAACCCTA-A-AACC
          1 GTGGCAAAGCCCGTTGAAAA--CTACAGAACC

                   *      
       1812 GTGGCAAGGCCCGT
          1 GTGGCAAAGCCCGT

       1826 CGCCAACTGT


Statistics
Matches: 40,  Mismatches: 2, Indels: 4
        0.87            0.04        0.09

Matches are distributed among these distances:
  30   36  0.90
  31    1  0.03
  32    3  0.08

ACGTcount: A:0.31, C:0.28, G:0.26, T:0.15


Consensus pattern (30 bp):   
GTGGCAAAGCCCGTTGAAAACTACAGAACC

Found at i:2575 original size:30 final size:30

Alignment explanation


    Indices: 2541--2597  Score: 71
    Period size: 30  Copynumber: 1.9  Consensus size: 30

       2531 AAAACCCACT

                                *          
       2541 GCAAACCCCATTG-AAAATTGAAAATGCGCG
          1 GCAAACCCCATTGCAAAA-TAAAAATGCGCG

                 *   *                 
       2571 GCAAATCCCTTTGCAAAATAAAAATGC
          1 GCAAACCCCATTGCAAAATAAAAATGC

       2598 AATTTTGATA


Statistics
Matches: 23,  Mismatches: 3, Indels: 2
        0.82            0.11        0.07

Matches are distributed among these distances:
  30   19  0.83
  31    4  0.17

ACGTcount: A:0.42, C:0.23, G:0.16, T:0.19


Consensus pattern (30 bp):   
GCAAACCCCATTGCAAAATAAAAATGCGCG
Done.