Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020895.1 Corchorus olitorius cultivar O-4 contig20928, 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: 9205
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34


Found at i:1800 original size:2 final size:2

Alignment explanation


    Indices: 1793--1826  Score: 68
    Period size: 2  Copynumber: 17.0  Consensus size: 2

       1783 ACATCCAAAT

                                                              
       1793 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       1827 ATTTGCACCA


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   32  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:2151 original size:125 final size:126

Alignment explanation


    Indices: 1928--2171  Score: 411
    Period size: 125  Copynumber: 1.9  Consensus size: 126

       1918 ATTAGATGGT

                                        *                                    
       1928 AGAAAATTTCTAAATTAAGAAAATATTGGAACAAGACTTTGAAGCGCCAAACTTTCTCAAATACA
          1 AGAAAATTTCTAAATTAAGAAAATATTGAAACAAGACTTTGAAGCGCCAAACTTTCTCAAATACA

                       *                                                 
       1993 ATATTGCCTAATTATTTTAGACAAGTCGTATTTGGGATACAACAAAGCCACTTGAATATAA
         66 ATATTGCCTAACTATTTTAGACAAGTCGTATTTGGGATACAACAAAGCCACTTGAATATAA

                 *                                       *     *             
       2054 AGAAATTTTCTAAATTAAGAAAATATTGAAACAAGACTTTG-AGATGCCAAGC-TTCTCAAATAC
          1 AGAAAATTTCTAAATTAAGAAAATATTGAAACAAGACTTTGAAG-CGCCAAACTTTCTCAAATAC

                       *                                           
       2117 AATATTGCCTAGCTATTTTAGACAAGTCGTATTTGGGATACAACAAAGCCACTTG
         65 AATATTGCCTAACTATTTTAGACAAGTCGTATTTGGGATACAACAAAGCCACTTG

       2172 GGAACAATCA


Statistics
Matches: 111,  Mismatches: 6, Indels: 3
        0.93            0.05        0.03

Matches are distributed among these distances:
 125   66  0.59
 126   45  0.41

ACGTcount: A:0.41, C:0.16, G:0.14, T:0.30


Consensus pattern (126 bp):   
AGAAAATTTCTAAATTAAGAAAATATTGAAACAAGACTTTGAAGCGCCAAACTTTCTCAAATACA
ATATTGCCTAACTATTTTAGACAAGTCGTATTTGGGATACAACAAAGCCACTTGAATATAA

Found at i:4141 original size:25 final size:26

Alignment explanation


    Indices: 4084--4135  Score: 70
    Period size: 26  Copynumber: 2.0  Consensus size: 26

       4074 TTTCTTACAA

                *                     
       4084 AAATAATAGAAATAAACATTAGATAT
          1 AAATCATAGAAATAAACATTAGATAT

                         *       *    
       4110 AAATCATAGAAATGAAC-TTATATAT
          1 AAATCATAGAAATAAACATTAGATAT

             
       4135 A
          1 A

       4136 TCTCATTGAT


Statistics
Matches: 23,  Mismatches: 3, Indels: 1
        0.85            0.11        0.04

Matches are distributed among these distances:
  25    8  0.35
  26   15  0.65

ACGTcount: A:0.58, C:0.06, G:0.08, T:0.29


Consensus pattern (26 bp):   
AAATCATAGAAATAAACATTAGATAT

Found at i:8380 original size:13 final size:13

Alignment explanation


    Indices: 8350--8402  Score: 60
    Period size: 12  Copynumber: 4.4  Consensus size: 13

       8340 CCCGTTGAGG

                         
       8350 AAATG-TTT-TAT
          1 AAATGCTTTATAT

              *          
       8361 AACTGCTTTATAT
          1 AAATGCTTTATAT

                         
       8374 AAATGCTTTATA-
          1 AAATGCTTTATAT

                 *       
       8386 AAATGTTTTA-AT
          1 AAATGCTTTATAT

                 
       8398 AAATG
          1 AAATG

       8403 TTTTGGGTGC


Statistics
Matches: 36,  Mismatches: 3, Indels: 5
        0.82            0.07        0.11

Matches are distributed among these distances:
  11    5  0.14
  12   17  0.47
  13   14  0.39

ACGTcount: A:0.40, C:0.06, G:0.09, T:0.45


Consensus pattern (13 bp):   
AAATGCTTTATAT

Done.