Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017136.1 Corchorus olitorius cultivar O-4 contig17169, 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: 16708
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30


Found at i:265 original size:13 final size:13

Alignment explanation


    Indices: 247--272  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

        237 ACCAAGCCTA

                         
        247 AAATTAATTATTT
          1 AAATTAATTATTT

                         
        260 AAATTAATTATTT
          1 AAATTAATTATTT

        273 TATTTTTAGA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54


Consensus pattern (13 bp):   
AAATTAATTATTT

Found at i:955 original size:74 final size:74

Alignment explanation


    Indices: 861--1009  Score: 289
    Period size: 74  Copynumber: 2.0  Consensus size: 74

        851 GTCCCACTTT

                                                                             
        861 GAGGATAAAGCTCTCCCAACAATGGTTTTCTCCATTCACAAGACTCTGCTAAACTTTTTTTGGTA
          1 GAGGATAAAGCTCTCCCAACAATGGTTTTCTCCATTCACAAGACTCTGCTAAACTTTTTTTGGTA

                     
        926 TATTTACAA
         66 TATTTACAA

                                                              *              
        935 GAGGATAAAGCTCTCCCAACAATGGTTTTCTCCATTCACAAGACTCTGCTCAACTTTTTTTGGTA
          1 GAGGATAAAGCTCTCCCAACAATGGTTTTCTCCATTCACAAGACTCTGCTAAACTTTTTTTGGTA

                     
       1000 TATTTACAA
         66 TATTTACAA

             
       1009 G
          1 G

       1010 TTAATCTTGT


Statistics
Matches: 74,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
  74   74  1.00

ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35


Consensus pattern (74 bp):   
GAGGATAAAGCTCTCCCAACAATGGTTTTCTCCATTCACAAGACTCTGCTAAACTTTTTTTGGTA
TATTTACAA

Found at i:2959 original size:31 final size:29

Alignment explanation


    Indices: 2924--2986  Score: 81
    Period size: 31  Copynumber: 2.1  Consensus size: 29

       2914 ATTCCATGTA

                             *             
       2924 TCACTCGATACTGATGTGGCATGTACACATG
          1 TCACTCGATACTGATGTAGCATGT-C-CATG

                 *   *                   
       2955 TCACTTGATGCTGATGTAGCATGTCCATG
          1 TCACTCGATACTGATGTAGCATGTCCATG

               
       2984 TCA
          1 TCA

       2987 GCACCGTTAA


Statistics
Matches: 29,  Mismatches: 3, Indels: 2
        0.85            0.09        0.06

Matches are distributed among these distances:
  29    7  0.24
  30    1  0.03
  31   21  0.72

ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32


Consensus pattern (29 bp):   
TCACTCGATACTGATGTAGCATGTCCATG

Found at i:5260 original size:18 final size:18

Alignment explanation


    Indices: 5237--5272  Score: 63
    Period size: 18  Copynumber: 2.0  Consensus size: 18

       5227 TTTTTCACTT

                      *       
       5237 GGAGACATGGCTGGATCA
          1 GGAGACATGGATGGATCA

                              
       5255 GGAGACATGGATGGATCA
          1 GGAGACATGGATGGATCA

       5273 TGGGGATCAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.31, C:0.14, G:0.39, T:0.17


Consensus pattern (18 bp):   
GGAGACATGGATGGATCA

Found at i:13423 original size:107 final size:103

Alignment explanation


    Indices: 13291--13544  Score: 375
    Period size: 107  Copynumber: 2.4  Consensus size: 103

      13281 CAAACAGAGC

                                                             *               
      13291 CTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTCAAAATTAATAATTT
          1 CTAAGTTTAG-CCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATTAATAA--T

                             *                         
      13356 ATTGTTATAGGGTTTTAGAAATAAAATACA-AAACTAATTTCA
         63 ATTGTTATAGGGTTTTAAAAATAAAATACATAAA-TAA-TTCA

                                                                *            
      13398 CTAAGTTTAGCTCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATTAATAATAT
          1 CTAAGTTTAGC-CCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATTAATAATAT

                                      *            
      13463 TGTTATAGGGTTTTAAAAATAAAATATATAAATAATTCA
         65 TGTTATAGGGTTTTAAAAATAAAATACATAAATAATTCA

                        *           ** *               
      13502 CTAAGTTTAGCCTAAATTAAAATTAAAATTTTATTTTAAGGGT
          1 CTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGT

      13545 TAGAAAAATC


Statistics
Matches: 137,  Mismatches: 8, Indels: 8
        0.90            0.05        0.05

Matches are distributed among these distances:
 103   28  0.20
 104   15  0.11
 105   32  0.23
 106    4  0.03
 107   58  0.42

ACGTcount: A:0.41, C:0.07, G:0.09, T:0.42


Consensus pattern (103 bp):   
CTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATTAATAATATT
GTTATAGGGTTTTAAAAATAAAATACATAAATAATTCA

Found at i:16036 original size:2 final size:2

Alignment explanation


    Indices: 16031--16073  Score: 68
    Period size: 2  Copynumber: 21.5  Consensus size: 2

      16021 ACTAAGTGCT

                                           *                         *    
      16031 TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA TA CA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

             
      16073 T
          1 T

      16074 GGGAACGAAT


Statistics
Matches: 37,  Mismatches: 4, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
   2   37  1.00

ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49


Consensus pattern (2 bp):   
TA

Done.