Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017439.1 Corchorus olitorius cultivar O-4 contig17472, 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: 3014
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.35


Found at i:983 original size:11 final size:11

Alignment explanation


    Indices: 967--992  Score: 52
    Period size: 11  Copynumber: 2.4  Consensus size: 11

        957 AGATAATTTC

                       
        967 TTTTCTTCTAG
          1 TTTTCTTCTAG

                       
        978 TTTTCTTCTAG
          1 TTTTCTTCTAG

                
        989 TTTT
          1 TTTT

        993 TAGGCAAAGG


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   15  1.00

ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69


Consensus pattern (11 bp):   
TTTTCTTCTAG

Found at i:2154 original size:23 final size:24

Alignment explanation


    Indices: 2111--2169  Score: 70
    Period size: 23  Copynumber: 2.5  Consensus size: 24

       2101 GCGTCTTTGT

                                     
       2111 GAAAAAAAAAACCTTTGTTTGCGTC
          1 GAAAAAAAAAA-CTTTGTTTGCGTC

                                     
       2136 GAAAAAAAAAA-TATT-TTTGCGTC
          1 GAAAAAAAAAACT-TTGTTTGCGTC

                        
       2159 -ATAAAAAAAAA
          1 GA-AAAAAAAAA

       2170 GAAAATTGTT


Statistics
Matches: 32,  Mismatches: 0, Indels: 6
        0.84            0.00        0.16

Matches are distributed among these distances:
  22    1  0.03
  23   18  0.56
  24    2  0.06
  25   11  0.34

ACGTcount: A:0.53, C:0.10, G:0.12, T:0.25


Consensus pattern (24 bp):   
GAAAAAAAAAACTTTGTTTGCGTC

Found at i:2164 original size:22 final size:22

Alignment explanation


    Indices: 2128--2239  Score: 91
    Period size: 22  Copynumber: 4.7  Consensus size: 22

       2118 AAAACCTTTG

                             *      
       2128 TTTGCGTCGA-AAAAAAAAATATT
          1 TTTGCGTC-ATAAAAAAGAA-ATT

                                        
       2151 TTTGCGTCATAAAAAAAAAGAAAATTGT
          1 TTTGCGTCAT---AAAAAAG-AAA-T-T

                              * *  
       2179 TTCTGCGTCATAAAAAAGGAGTT
          1 TT-TGCGTCATAAAAAAGAAATT

                             * *  
       2202 TTTGCGTCATAAAAAAGGAGTT
          1 TTTGCGTCATAAAAAAGAAATT

                            
       2224 TTTGCGTCATAAAAAA
          1 TTTGCGTCATAAAAAA

       2240 AAGAAAATTT


Statistics
Matches: 78,  Mismatches: 3, Indels: 17
        0.80            0.03        0.17

Matches are distributed among these distances:
  22   37  0.47
  23   11  0.14
  24    1  0.01
  25    1  0.01
  26   14  0.18
  27    3  0.04
  28    3  0.04
  29    8  0.10

ACGTcount: A:0.43, C:0.10, G:0.17, T:0.30


Consensus pattern (22 bp):   
TTTGCGTCATAAAAAAGAAATT

Found at i:2169 original size:29 final size:29

Alignment explanation


    Indices: 2137--2195  Score: 82
    Period size: 29  Copynumber: 2.0  Consensus size: 29

       2127 GTTTGCGTCG

                           *             
       2137 AAAAAAAAAATATTTTTGCGTCATAAAAA
          1 AAAAAAAAAATATTTCTGCGTCATAAAAA

                *    * *                 
       2166 AAAAGAAAATTGTTTCTGCGTCATAAAAA
          1 AAAAAAAAAATATTTCTGCGTCATAAAAA

             
       2195 A
          1 A

       2196 GGAGTTTTTG


Statistics
Matches: 26,  Mismatches: 4, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  29   26  1.00

ACGTcount: A:0.54, C:0.08, G:0.10, T:0.27


Consensus pattern (29 bp):   
AAAAAAAAAATATTTCTGCGTCATAAAAA
Done.