Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021364.1 Corchorus olitorius cultivar O-4 contig21397, 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: 14922
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32


Found at i:925 original size:32 final size:32

Alignment explanation


    Indices: 889--953  Score: 112
    Period size: 32  Copynumber: 2.0  Consensus size: 32

        879 AGGCCATACT

                      *                     
        889 ACTGTTGAATTAATTAAGAATATTGTCCTAAA
          1 ACTGTTGAATAAATTAAGAATATTGTCCTAAA

                                    *       
        921 ACTGTTGAATAAATTAAGAATATTTTCCTAAA
          1 ACTGTTGAATAAATTAAGAATATTGTCCTAAA

             
        953 A
          1 A

        954 GAGTACTATG


Statistics
Matches: 31,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  32   31  1.00

ACGTcount: A:0.43, C:0.09, G:0.11, T:0.37


Consensus pattern (32 bp):   
ACTGTTGAATAAATTAAGAATATTGTCCTAAA

Found at i:1987 original size:3 final size:3

Alignment explanation


    Indices: 1960--2007  Score: 51
    Period size: 3  Copynumber: 15.7  Consensus size: 3

       1950 AATTGGATAC

                  *          *      * *                                 
       1960 AAT AAC AAT AAT AGT AAT GAG AAT AAT AAT AAT AAT AAT AATT AAT
          1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT

              
       2006 AA
          1 AA

       2008 CACTAATGGC


Statistics
Matches: 36,  Mismatches: 8, Indels: 2
        0.78            0.17        0.04

Matches are distributed among these distances:
   3   33  0.92
   4    3  0.08

ACGTcount: A:0.62, C:0.02, G:0.06, T:0.29


Consensus pattern (3 bp):   
AAT

Found at i:4530 original size:30 final size:31

Alignment explanation


    Indices: 4454--4530  Score: 86
    Period size: 29  Copynumber: 2.5  Consensus size: 31

       4444 ATACCGTACA

                                *   *    * 
       4454 GGTCCCTCTACTTACAAAAAGGGATCAATTT
          1 GGTCCCTCTACTTACAAAAACGGACCAATCT

                  *              *    *    
       4485 GGTCCCCCTAC-TACAAAAACTG-CCGATCT
          1 GGTCCCTCTACTTACAAAAACGGACCAATCT

                             
       4514 GGTCCCTCTACTTACAA
          1 GGTCCCTCTACTTACAA

       4531 TTTGGTGTCA


Statistics
Matches: 38,  Mismatches: 7, Indels: 3
        0.79            0.15        0.06

Matches are distributed among these distances:
  29   14  0.37
  30   14  0.37
  31   10  0.26

ACGTcount: A:0.29, C:0.31, G:0.14, T:0.26


Consensus pattern (31 bp):   
GGTCCCTCTACTTACAAAAACGGACCAATCT

Found at i:4895 original size:31 final size:30

Alignment explanation


    Indices: 4823--4899  Score: 102
    Period size: 29  Copynumber: 2.6  Consensus size: 30

       4813 CGACACCAAA

                           *              
       4823 TTGTAAGTAGAGGGAGCAAATTGATAGTTT
          1 TTGTAAGTAGAGGGACCAAATTGATAGTTT

              *                       **   
       4853 TTAT-AGTAGAGGGACCAAATTGATCCTTTT
          1 TTGTAAGTAGAGGGACCAAATTGAT-AGTTT

                             
       4883 TTGTAAGTAGAGGGACC
          1 TTGTAAGTAGAGGGACC

       4900 TGTACCGTAT


Statistics
Matches: 40,  Mismatches: 5, Indels: 3
        0.83            0.10        0.06

Matches are distributed among these distances:
  29   19  0.47
  30    9  0.22
  31   12  0.30

ACGTcount: A:0.31, C:0.09, G:0.27, T:0.32


Consensus pattern (30 bp):   
TTGTAAGTAGAGGGACCAAATTGATAGTTT

Found at i:10402 original size:19 final size:19

Alignment explanation


    Indices: 10362--10401  Score: 55
    Period size: 18  Copynumber: 2.2  Consensus size: 19

      10352 GAAAGCGGGC

                       *    *  
      10362 TTTGAAATGAATTTTGGAT
          1 TTTGAAATGAAATTTGAAT

                               
      10381 TTTG-AATGAAATTTGAAT
          1 TTTGAAATGAAATTTGAAT

               
      10399 TTT
          1 TTT

      10402 TTTGAAGGGA


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  18   15  0.79
  19    4  0.21

ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50


Consensus pattern (19 bp):   
TTTGAAATGAAATTTGAAT

Found at i:12321 original size:21 final size:20

Alignment explanation


    Indices: 12295--12340  Score: 56
    Period size: 20  Copynumber: 2.2  Consensus size: 20

      12285 ATTAACATGA

                     *           
      12295 TTTGACAATTAAAATTTGGGG
          1 TTTGACAA-CAAAATTTGGGG

                  *  *          
      12316 TTTGACCACCAAATTTGGGG
          1 TTTGACAACAAAATTTGGGG

                 
      12336 TTTGA
          1 TTTGA

      12341 TCGTGAAATC


Statistics
Matches: 22,  Mismatches: 3, Indels: 1
        0.85            0.12        0.04

Matches are distributed among these distances:
  20   15  0.68
  21    7  0.32

ACGTcount: A:0.28, C:0.11, G:0.24, T:0.37


Consensus pattern (20 bp):   
TTTGACAACAAAATTTGGGG
Done.