Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021448.1 Corchorus olitorius cultivar O-4 contig21481, 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: 5702
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34


Found at i:214 original size:25 final size:24

Alignment explanation


    Indices: 180--226  Score: 85
    Period size: 25  Copynumber: 1.9  Consensus size: 24

        170 ACGTTTGCAC

                                     
        180 AAATACCTAAGAATTTGAATTAAAA
          1 AAATACCTAAGAATTT-AATTAAAA

                                  
        205 AAATACCTAAGAATTTAATTAA
          1 AAATACCTAAGAATTTAATTAA

        227 TGTAAGTATT


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

Matches are distributed among these distances:
  24    6  0.27
  25   16  0.73

ACGTcount: A:0.55, C:0.09, G:0.06, T:0.30


Consensus pattern (24 bp):   
AAATACCTAAGAATTTAATTAAAA

Found at i:2392 original size:17 final size:17

Alignment explanation


    Indices: 2359--2413  Score: 56
    Period size: 17  Copynumber: 3.2  Consensus size: 17

       2349 AACCCATGTA

                 *      *    
       2359 ATCTTTGATCACCGGTG
          1 ATCTTAGATCACTGGTG

                  *    *     
       2376 ATCTTATATCATTGGTG
          1 ATCTTAGATCACTGGTG

              *          *   
       2393 ATTTTAGATCACTAGTG
          1 ATCTTAGATCACTGGTG

                
       2410 ATCT
          1 ATCT

       2414 GGGGTGATCC


Statistics
Matches: 29,  Mismatches: 9, Indels: 0
        0.76            0.24        0.00

Matches are distributed among these distances:
  17   29  1.00

ACGTcount: A:0.24, C:0.16, G:0.18, T:0.42


Consensus pattern (17 bp):   
ATCTTAGATCACTGGTG

Found at i:2969 original size:30 final size:31

Alignment explanation


    Indices: 2926--2989  Score: 96
    Period size: 30  Copynumber: 2.1  Consensus size: 31

       2916 TGTGTTTTTT

                                             
       2926 TTTTTTTACTTTTGAATGT-CAAACAGGGATAA
          1 TTTTTTTA-TTTTGAAT-TACAAACAGGGATAA

                                           
       2958 TTTTTTT-TTTTGAATTACAAACAGGGATAA
          1 TTTTTTTATTTTGAATTACAAACAGGGATAA

              
       2988 TT
          1 TT

       2990 GATAATCTTT


Statistics
Matches: 31,  Mismatches: 0, Indels: 4
        0.89            0.00        0.11

Matches are distributed among these distances:
  29    1  0.03
  30   23  0.74
  32    7  0.23

ACGTcount: A:0.31, C:0.08, G:0.14, T:0.47


Consensus pattern (31 bp):   
TTTTTTTATTTTGAATTACAAACAGGGATAA
Done.