Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017919.1 Corchorus olitorius cultivar O-4 contig17952, 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: 13838
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.27


Found at i:1224 original size:21 final size:20

Alignment explanation


    Indices: 1179--1229  Score: 59
    Period size: 21  Copynumber: 2.5  Consensus size: 20

       1169 TAATTTGTTT

                         *      
       1179 TGTTGGG-CTTTAGATTTGA
          1 TGTTGGGCCTTTAAATTTGA

             *                  *
       1198 TTTTGGGCCTTTAAAGTTTGC
          1 TGTTGGGCCTTTAAA-TTTGA

                       
       1219 TGTTGGGCCTT
          1 TGTTGGGCCTT

       1230 GTGGGTTTTT


Statistics
Matches: 26,  Mismatches: 4, Indels: 2
        0.81            0.12        0.06

Matches are distributed among these distances:
  19    6  0.23
  20    6  0.23
  21   14  0.54

ACGTcount: A:0.12, C:0.12, G:0.29, T:0.47


Consensus pattern (20 bp):   
TGTTGGGCCTTTAAATTTGA

Found at i:1398 original size:23 final size:22

Alignment explanation


    Indices: 1346--1399  Score: 65
    Period size: 23  Copynumber: 2.4  Consensus size: 22

       1336 TTGTTTATTC

                              *   
       1346 TTATGGGCTTGTTTTTTTTCTT
          1 TTATGGGCTTGTTTTTTTACTT

                                    
       1368 TTGATGGGCTTGGTTTTTTTACTT
          1 TT-ATGGGCTT-GTTTTTTTACTT

                     
       1392 ATT-TGGGC
          1 -TTATGGGC

       1400 CTTATGGGCT


Statistics
Matches: 28,  Mismatches: 1, Indels: 5
        0.82            0.03        0.15

Matches are distributed among these distances:
  22    2  0.07
  23   13  0.46
  24   11  0.39
  25    2  0.07

ACGTcount: A:0.07, C:0.09, G:0.24, T:0.59


Consensus pattern (22 bp):   
TTATGGGCTTGTTTTTTTACTT

Found at i:5139 original size:21 final size:21

Alignment explanation


    Indices: 5118--5162  Score: 56
    Period size: 21  Copynumber: 2.2  Consensus size: 21

       5108 AAGAGGTAGA

                         *       
       5118 AAGAAAAGCT-AGGGAAACAG
          1 AAGAAAAGCTGAGAGAAACAG

               *               * 
       5138 AAGCAAAGCTGAGAGAAACCG
          1 AAGAAAAGCTGAGAGAAACAG

                
       5159 AAGA
          1 AAGA

       5163 GGAAGTCAAA


Statistics
Matches: 20,  Mismatches: 4, Indels: 1
        0.80            0.16        0.04

Matches are distributed among these distances:
  20    9  0.45
  21   11  0.55

ACGTcount: A:0.53, C:0.13, G:0.29, T:0.04


Consensus pattern (21 bp):   
AAGAAAAGCTGAGAGAAACAG

Found at i:6425 original size:21 final size:21

Alignment explanation


    Indices: 6401--6446  Score: 58
    Period size: 21  Copynumber: 2.2  Consensus size: 21

       6391 GCGCCGAGAC

                                  
       6401 GAAGAGGCGAAA-CACCAAGAA
          1 GAAGAGGC-AAAGCACCAAGAA

                         *  *    
       6422 GAAGAGGCAAAGCGCCGAGAA
          1 GAAGAGGCAAAGCACCAAGAA

                
       6443 GAAG
          1 GAAG

       6447 CCACAAACGC


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

Matches are distributed among these distances:
  20    3  0.14
  21   19  0.86

ACGTcount: A:0.48, C:0.17, G:0.35, T:0.00


Consensus pattern (21 bp):   
GAAGAGGCAAAGCACCAAGAA

Found at i:6596 original size:21 final size:21

Alignment explanation


    Indices: 6572--6612  Score: 55
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       6562 AAGCTTGAAT

                 *               
       6572 CTGACCGGAGCAAACTCAGGG
          1 CTGACAGGAGCAAACTCAGGG

                    *    *      
       6593 CTGACAGGGGCAAGCTCAGG
          1 CTGACAGGAGCAAACTCAGG

       6613 CCTCACTGGG


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.27, C:0.27, G:0.37, T:0.10


Consensus pattern (21 bp):   
CTGACAGGAGCAAACTCAGGG

Found at i:6623 original size:21 final size:21

Alignment explanation


    Indices: 6581--6623  Score: 50
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       6571 TCTGACCGGA

                       *  *      
       6581 GCAAACTCAGGGCTGACAGGG
          1 GCAAACTCAGGCCTCACAGGG

                *            *   
       6602 GCAAGCTCAGGCCTCACTGGG
          1 GCAAACTCAGGCCTCACAGGG

             
       6623 G
          1 G

       6624 TTGTGACTGA


Statistics
Matches: 18,  Mismatches: 4, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.23, C:0.28, G:0.37, T:0.12


Consensus pattern (21 bp):   
GCAAACTCAGGCCTCACAGGG
Done.