Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012498.1 Corchorus olitorius cultivar O-4 contig12531, 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: 7700
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35


Found at i:424 original size:27 final size:27

Alignment explanation


    Indices: 368--418  Score: 77
    Period size: 27  Copynumber: 1.9  Consensus size: 27

        358 GAGCGTGTCT

                                 **    
        368 AAAGTCGTTTACATATTTTTTTGACCA
          1 AAAGTCGTTTACATATTTTTTAAACCA

                                     
        395 AAAGTCGTTTACATA-TTTTTAAAC
          1 AAAGTCGTTTACATATTTTTTAAAC

        419 ATAAAAAAGA


Statistics
Matches: 22,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  26    7  0.32
  27   15  0.68

ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43


Consensus pattern (27 bp):   
AAAGTCGTTTACATATTTTTTAAACCA

Found at i:2024 original size:4 final size:4

Alignment explanation


    Indices: 2008--2040  Score: 57
    Period size: 4  Copynumber: 8.2  Consensus size: 4

       1998 TTTCTTTAAT

                   *                                 
       2008 TCTA TCCA TCTA TCTA TCTA TCTA TCTA TCTA T
          1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA T

       2041 ATATATATAA


Statistics
Matches: 27,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   4   27  1.00

ACGTcount: A:0.24, C:0.27, G:0.00, T:0.48


Consensus pattern (4 bp):   
TCTA

Found at i:3893 original size:24 final size:24

Alignment explanation


    Indices: 3841--3887  Score: 85
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       3831 GAAGATGGGG

                    *               
       3841 AAAGTTCTGGAAGGACAGATGATA
          1 AAAGTTCTCGAAGGACAGATGATA

                                   
       3865 AAAGTTCTCGAAGGACAGATGAT
          1 AAAGTTCTCGAAGGACAGATGAT

       3888 TTAAGTGGTG


Statistics
Matches: 22,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  24   22  1.00

ACGTcount: A:0.40, C:0.11, G:0.28, T:0.21


Consensus pattern (24 bp):   
AAAGTTCTCGAAGGACAGATGATA

Found at i:6919 original size:2 final size:2

Alignment explanation


    Indices: 6914--6946  Score: 57
    Period size: 2  Copynumber: 16.0  Consensus size: 2

       6904 TCACACACAC

                                                            
       6914 AT AT AT AT AT AT AT AT AT AT AT AT ACT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT

       6947 TATTTTAGTT


Statistics
Matches: 30,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   2   28  0.93
   3    2  0.07

ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:6989 original size:51 final size:52

Alignment explanation


    Indices: 6933--7036  Score: 201
    Period size: 52  Copynumber: 2.0  Consensus size: 52

       6923 TATATATATA

                                                                
       6933 TATATACTATATATTA-TTTTAGTTACCAGGAAAATTACTAAAAGGCCAAAT
          1 TATATACTATATATTATTTTTAGTTACCAGGAAAATTACTAAAAGGCCAAAT

                                                                
       6984 TATATACTATATATTATTTTTAGTTACCAGGAAAATTACTAAAAGGCCAAAT
          1 TATATACTATATATTATTTTTAGTTACCAGGAAAATTACTAAAAGGCCAAAT

             
       7036 T
          1 T

       7037 GAGAATTAAT


Statistics
Matches: 52,  Mismatches: 0, Indels: 1
        0.98            0.00        0.02

Matches are distributed among these distances:
  51   16  0.31
  52   36  0.69

ACGTcount: A:0.42, C:0.12, G:0.10, T:0.37


Consensus pattern (52 bp):   
TATATACTATATATTATTTTTAGTTACCAGGAAAATTACTAAAAGGCCAAAT

Done.