Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013155.1 Corchorus olitorius cultivar O-4 contig13188, 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: 3221
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36


Found at i:28 original size:19 final size:19

Alignment explanation


    Indices: 4--41  Score: 76
    Period size: 19  Copynumber: 2.0  Consensus size: 19

          1 ACC

                               
          4 TATTTATCTATTATTCTCT
          1 TATTTATCTATTATTCTCT

                               
         23 TATTTATCTATTATTCTCT
          1 TATTTATCTATTATTCTCT

         42 GTATCTATTT


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   19  1.00

ACGTcount: A:0.21, C:0.16, G:0.00, T:0.63


Consensus pattern (19 bp):   
TATTTATCTATTATTCTCT

Found at i:46 original size:16 final size:17

Alignment explanation


    Indices: 8--50  Score: 52
    Period size: 19  Copynumber: 2.5  Consensus size: 17

          1 ACCTATT

                              *
          8 TATCTATTATTCTCTTATT
          1 TATCTATTATTCTC-T-TG

                             
         27 TATCTATTATTCTC-TG
          1 TATCTATTATTCTCTTG

                    
         43 TATCTATT
          1 TATCTATT

         51 TATCAATTTA


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

Matches are distributed among these distances:
  16    9  0.39
  19   14  0.61

ACGTcount: A:0.21, C:0.16, G:0.02, T:0.60


Consensus pattern (17 bp):   
TATCTATTATTCTCTTG

Found at i:51 original size:24 final size:23

Alignment explanation


    Indices: 3--79  Score: 74
    Period size: 24  Copynumber: 3.4  Consensus size: 23

          1 AC

                                   
          3 CTATTTATCTATTATTCTC---T
          1 CTATTTATCTATTATTCTCTTAT

                                    
         23 -TATTTATCTATTATTCTCTGTAT
          1 CTATTTATCTATTATTCTCT-TAT

                     *              *
         46 CTATTTATCAATT-TATCTCTATAC
          1 CTATTTATCTATTAT-TCTCT-TAT

                      
         70 CTATTTATCT
          1 CTATTTATCT

         80 TTTTTATTAT


Statistics
Matches: 47,  Mismatches: 4, Indels: 8
        0.80            0.07        0.14

Matches are distributed among these distances:
  19   18  0.38
  23    2  0.04
  24   27  0.57

ACGTcount: A:0.23, C:0.18, G:0.01, T:0.57


Consensus pattern (23 bp):   
CTATTTATCTATTATTCTCTTAT

Found at i:3182 original size:2 final size:2

Alignment explanation


    Indices: 3171--3215  Score: 83
    Period size: 2  Copynumber: 23.0  Consensus size: 2

       3161 TTAAGTCTTT

                                                                          
       3171 TA TA TA -A 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 TA TA TA TA

                 
       3212 TA TA
          1 TA TA

       3216 GTAGGT


Statistics
Matches: 42,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   1    1  0.02
   2   41  0.98

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
TA

Done.