Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012273.1 Corchorus olitorius cultivar O-4 contig12306, 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: 20051
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.32

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:3059 original size:11 final size:10

Alignment explanation


    Indices: 3043--3089  Score: 53
    Period size: 11  Copynumber: 4.7  Consensus size: 10

       3033 AAGTTCGTGT

                       
       3043 TTGAAGACTCA
          1 TTGAAGA-TCA

                    * 
       3054 TTGAAGATAA
          1 TTGAAGATCA

                       
       3064 TTTGAAGAT--
          1 -TTGAAGATCA

                      
       3073 TTGAAGATCA
          1 TTGAAGATCA

                   
       3083 TTGAAGA
          1 TTGAAGA

       3090 ATTATTTCAA


Statistics
Matches: 32,  Mismatches: 1, Indels: 7
        0.80            0.03        0.17

Matches are distributed among these distances:
   8    8  0.25
  10    9  0.28
  11   15  0.47

ACGTcount: A:0.40, C:0.06, G:0.21, T:0.32


Consensus pattern (10 bp):   
TTGAAGATCA

Found at i:3078 original size:19 final size:18

Alignment explanation


    Indices: 3054--3089  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       3044 TGAAGACTCA

                               
       3054 TTGAAGATAATTTGAAGAT
          1 TTGAAGATAA-TTGAAGAT

                    *        
       3073 TTGAAGATCATTGAAGA
          1 TTGAAGATAATTGAAGA

       3090 ATTATTTCAA


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

Found at i:4964 original size:29 final size:29

Alignment explanation


    Indices: 4907--4987  Score: 92
    Period size: 29  Copynumber: 2.8  Consensus size: 29

       4897 TAAAGCTTTG

                *                  **     
       4907 ACACGAGTGCA-AACCCACACTCAAAACAA
          1 ACACAAGTGCACAACCCACACT-TGAACAA

            * *      *                   
       4936 TCCCAAGTGTACAACCCACACTTGAACAA
          1 ACACAAGTGCACAACCCACACTTGAACAA

                                   
       4965 ACACAAGTGCACAACCCACACTT
          1 ACACAAGTGCACAACCCACACTT

       4988 AAAAAAAAAT


Statistics
Matches: 42,  Mismatches: 9, Indels: 2
        0.79            0.17        0.04

Matches are distributed among these distances:
  29   32  0.76
  30   10  0.24

ACGTcount: A:0.42, C:0.36, G:0.10, T:0.12


Consensus pattern (29 bp):   
ACACAAGTGCACAACCCACACTTGAACAA
Done.