Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011415.1 Corchorus olitorius cultivar O-4 contig11448, 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: 35102
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31


Found at i:1727 original size:24 final size:23

Alignment explanation


    Indices: 1700--1754  Score: 74
    Period size: 24  Copynumber: 2.3  Consensus size: 23

       1690 ACGCAGGGAC

                             *      
       1700 AAAACAATTTTTTTTTATGACGCA
          1 AAAACAATTTTTTTTT-CGACGCA

                *                  
       1724 AAAATAATTTTTTTTTCGACGCA
          1 AAAACAATTTTTTTTTCGACGCA

                    
       1747 AAACACAA
          1 AAA-ACAA

       1755 AACTTTTTTT


Statistics
Matches: 27,  Mismatches: 3, Indels: 2
        0.84            0.09        0.06

Matches are distributed among these distances:
  23    9  0.33
  24   18  0.67

ACGTcount: A:0.42, C:0.15, G:0.07, T:0.36


Consensus pattern (23 bp):   
AAAACAATTTTTTTTTCGACGCA

Found at i:1734 original size:23 final size:23

Alignment explanation


    Indices: 1673--1749  Score: 68
    Period size: 23  Copynumber: 3.1  Consensus size: 23

       1663 GAAAATAAAG

                                       
       1673 AAAAT-ATTTTTTTTATGACGCAGGGA
          1 AAAATAATTTTTTTTATGACGC----A

                 *                   
       1699 CAAAACAATTTTTTTTTATGACGCA
          1 -AAAATAA-TTTTTTTTATGACGCA

                                    
       1724 AAAATAATTTTTTTT-TCGACGCA
          1 AAAATAATTTTTTTTAT-GACGCA

               
       1747 AAA
          1 AAA

       1750 CACAAAACTT


Statistics
Matches: 45,  Mismatches: 2, Indels: 10
        0.79            0.04        0.18

Matches are distributed among these distances:
  22    1  0.02
  23   17  0.38
  24    6  0.13
  25    1  0.02
  27    4  0.09
  28    1  0.02
  29   15  0.33

ACGTcount: A:0.38, C:0.12, G:0.12, T:0.39


Consensus pattern (23 bp):   
AAAATAATTTTTTTTATGACGCA

Found at i:2180 original size:15 final size:16

Alignment explanation


    Indices: 2162--2199  Score: 60
    Period size: 16  Copynumber: 2.4  Consensus size: 16

       2152 AGGTTGACAA

                            
       2162 AAAACAATT-AAACAG
          1 AAAACAATTAAAACAG

                         *  
       2177 AAAACAATTAAAATAG
          1 AAAACAATTAAAACAG

                   
       2193 AAAACAA
          1 AAAACAA

       2200 AACAAAGTAA


Statistics
Matches: 21,  Mismatches: 1, Indels: 1
        0.91            0.04        0.04

Matches are distributed among these distances:
  15    9  0.43
  16   12  0.57

ACGTcount: A:0.71, C:0.11, G:0.05, T:0.13


Consensus pattern (16 bp):   
AAAACAATTAAAACAG

Found at i:19952 original size:37 final size:37

Alignment explanation


    Indices: 19906--19981  Score: 134
    Period size: 37  Copynumber: 2.1  Consensus size: 37

      19896 CCATGGCATG

                                                 
      19906 TTAAAATTGAAGGTTTTTGGTAAACTAAGTTCTATAC
          1 TTAAAATTGAAGGTTTTTGGTAAACTAAGTTCTATAC

                *                   *            
      19943 TTAATATTGAAGGTTTTTGGTAAATTAAGTTCTATAC
          1 TTAAAATTGAAGGTTTTTGGTAAACTAAGTTCTATAC

              
      19980 TT
          1 TT

      19982 GCAACTTTTG


Statistics
Matches: 37,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  37   37  1.00

ACGTcount: A:0.33, C:0.07, G:0.16, T:0.45


Consensus pattern (37 bp):   
TTAAAATTGAAGGTTTTTGGTAAACTAAGTTCTATAC

Found at i:25316 original size:19 final size:18

Alignment explanation


    Indices: 25292--25327  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

      25282 TGAAGACTTA

                               
      25292 TTGAAGATAATTTGAAGAT
          1 TTGAAGATAA-TTGAAGAT

                    *        
      25311 TTGAAGATCATTGAAGA
          1 TTGAAGATAATTGAAGA

      25328 ATTATCTCAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33


Consensus pattern (18 bp):   
TTGAAGATAATTGAAGAT
Done.