Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017105.1 Corchorus olitorius cultivar O-4 contig17138, 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: 23228
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32


Found at i:478 original size:24 final size:25

Alignment explanation


    Indices: 446--502  Score: 82
    Period size: 25  Copynumber: 2.4  Consensus size: 25

        436 ATCAGCCTTG

                                 *   
        446 AATTT-TTTAATGT-TTAATTCTTA
          1 AATTTATTTAATGTCTTAATTATTA

                                    *
        469 AATTTATTTAATGTCTTAATTATTC
          1 AATTTATTTAATGTCTTAATTATTA

                     
        494 AATTTATTT
          1 AATTTATTT

        503 TACAATCCAC


Statistics
Matches: 30,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  23    5  0.17
  24    8  0.27
  25   17  0.57

ACGTcount: A:0.32, C:0.05, G:0.04, T:0.60


Consensus pattern (25 bp):   
AATTTATTTAATGTCTTAATTATTA

Found at i:1443 original size:21 final size:22

Alignment explanation


    Indices: 1414--1457  Score: 56
    Period size: 21  Copynumber: 2.0  Consensus size: 22

       1404 GAGTACTTAT

                      *            
       1414 AAATCCAATTGTCA-CACGTATA
          1 AAATCCAATTATCAGC-CGTATA

                                  
       1436 AAAT-CAATTATCAGCCGTATA
          1 AAATCCAATTATCAGCCGTATA

             
       1457 A
          1 A

       1458 GATACAATAA


Statistics
Matches: 20,  Mismatches: 1, Indels: 3
        0.83            0.04        0.12

Matches are distributed among these distances:
  21   15  0.75
  22    5  0.25

ACGTcount: A:0.43, C:0.20, G:0.09, T:0.27


Consensus pattern (22 bp):   
AAATCCAATTATCAGCCGTATA

Found at i:14597 original size:2 final size:2

Alignment explanation


    Indices: 14590--14622  Score: 66
    Period size: 2  Copynumber: 16.5  Consensus size: 2

      14580 AAAATTAATC

                                                             
      14590 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

      14623 TCAAAAATAG


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   31  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:16790 original size:54 final size:54

Alignment explanation


    Indices: 16707--16812  Score: 149
    Period size: 54  Copynumber: 2.0  Consensus size: 54

      16697 TTGAATTTCA

                  *       *                     *   *  *          
      16707 AATTTTGCCCTAATTAATTTTTACATTTTGTCAAGTGTCTTAATTTTTTTGTCG
          1 AATTTTACCCTAATAAATTTTTACATTTTGTCAAGTCTCTAAACTTTTTTGTCG

                                   **                           
      16761 AATTTTACCCTAATAAATTTTTAGGTTTTGTCAAGTCTCTAAACTTTTTTGT
          1 AATTTTACCCTAATAAATTTTTACATTTTGTCAAGTCTCTAAACTTTTTTGT

      16813 TAAAATTATT


Statistics
Matches: 45,  Mismatches: 7, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  54   45  1.00

ACGTcount: A:0.25, C:0.13, G:0.10, T:0.52


Consensus pattern (54 bp):   
AATTTTACCCTAATAAATTTTTACATTTTGTCAAGTCTCTAAACTTTTTTGTCG

Found at i:16828 original size:18 final size:17

Alignment explanation


    Indices: 16805--16842  Score: 51
    Period size: 17  Copynumber: 2.2  Consensus size: 17

      16795 GTCTCTAAAC

                  *           
      16805 TTTTTTGTTA-AAATTAT
          1 TTTTTTTTTACAAA-TAT

                             
      16822 TTTTTTTTTACAAATAT
          1 TTTTTTTTTACAAATAT

                
      16839 TTTT
          1 TTTT

      16843 GTCTAAAACT


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

Matches are distributed among these distances:
  17   16  0.84
  18    3  0.16

ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68


Consensus pattern (17 bp):   
TTTTTTTTTACAAATAT

Found at i:22037 original size:10 final size:10

Alignment explanation


    Indices: 22022--22052  Score: 53
    Period size: 10  Copynumber: 3.1  Consensus size: 10

      22012 GATAACCTTG

                      
      22022 ATAAAAAAAA
          1 ATAAAAAAAA

                      
      22032 ATAAAAAAAA
          1 ATAAAAAAAA

             *        
      22042 ACAAAAAAAA
          1 ATAAAAAAAA

             
      22052 A
          1 A

      22053 CCAGAGATAA


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  10   20  1.00

ACGTcount: A:0.90, C:0.03, G:0.00, T:0.06


Consensus pattern (10 bp):   
ATAAAAAAAA

Done.