Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022829.1 Corchorus olitorius cultivar O-4 contig22862, 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: 17227
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.35


Found at i:6385 original size:18 final size:17

Alignment explanation


    Indices: 6358--6393  Score: 63
    Period size: 18  Copynumber: 2.1  Consensus size: 17

       6348 TTTCTCTTCA

                             
       6358 TCTATTTTTCTTCTAGT
          1 TCTATTTTTCTTCTAGT

                              
       6375 TCTAGTTTTTCTTCTAGT
          1 TCTA-TTTTTCTTCTAGT

             
       6393 T
          1 T

       6394 TTTCCTAAGG


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  17    4  0.22
  18   14  0.78

ACGTcount: A:0.11, C:0.17, G:0.08, T:0.64


Consensus pattern (17 bp):   
TCTATTTTTCTTCTAGT

Found at i:12923 original size:87 final size:87

Alignment explanation


    Indices: 12767--12943  Score: 320
    Period size: 87  Copynumber: 2.0  Consensus size: 87

      12757 AACTCGCTGG

                                                                            *
      12767 ATTTGCAAGCAATTTGGGTATGATTTGCTTGCTAAGATCTAAACAATTAGTTTAAATATTATGGG
          1 ATTTGCAAGCAATTTGGGTATGATTTGCTTGCTAAGATCTAAACAATTAGTTTAAATATTATGGA

                                  
      12832 TAAAACGTATTTGTGATGAAGT
         66 TAAAACGTATTTGTGATGAAGT

                                                                             
      12854 ATTTGCAAGCAATTTGGGTATGATTTGCTTGCTAAGATCTAAACAATTAGTTTAAATAATT-TGG
          1 ATTTGCAAGCAATTTGGGTATGATTTGCTTGCTAAGATCTAAACAATTAGTTTAAAT-ATTATGG

                     *             
      12918 ATAAAACGTGTTTGTGATGAAGT
         65 ATAAAACGTATTTGTGATGAAGT

               
      12941 ATT
          1 ATT

      12944 ACTAACTTAT


Statistics
Matches: 87,  Mismatches: 2, Indels: 2
        0.96            0.02        0.02

Matches are distributed among these distances:
  87   84  0.97
  88    3  0.03

ACGTcount: A:0.33, C:0.08, G:0.20, T:0.38


Consensus pattern (87 bp):   
ATTTGCAAGCAATTTGGGTATGATTTGCTTGCTAAGATCTAAACAATTAGTTTAAATATTATGGA
TAAAACGTATTTGTGATGAAGT

Found at i:15843 original size:102 final size:102

Alignment explanation


    Indices: 15667--15872  Score: 349
    Period size: 102  Copynumber: 2.0  Consensus size: 102

      15657 AGGGTGTATT

                                                   *                         
      15667 TTAAAGTTAGTTATGAATCAAACATATTTTTCTATAGTTTAATGCTTTTAATTCAGTTCTGATTG
          1 TTAAAGTTAGTTATGAATCAAACATATTTTTCTATAGTTGAATGCTTTTAATTCAGTTCTGATTG

                                              *  
      15732 ATTATATATGCCTTCAGTTAAAACTATTAAGTGTGTC
         66 ATTATATATGCCTTCAGTTAAAACTATTAAGTGTCTC

                           *                            *                    
      15769 TTAAAGTTAGTTATGGATCAAACATATTTTTCTATAGTTGAATGGTTTTAATTCAGTTCTGATTG
          1 TTAAAGTTAGTTATGAATCAAACATATTTTTCTATAGTTGAATGCTTTTAATTCAGTTCTGATTG

                       *  *      *               
      15834 ATTATATATGCGTTGAGTTAATACTATTAAGTGTCTC
         66 ATTATATATGCCTTCAGTTAAAACTATTAAGTGTCTC

              
      15871 TT
          1 TT

      15873 TGTACAGATT


Statistics
Matches: 97,  Mismatches: 7, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
 102   97  1.00

ACGTcount: A:0.30, C:0.10, G:0.15, T:0.46


Consensus pattern (102 bp):   
TTAAAGTTAGTTATGAATCAAACATATTTTTCTATAGTTGAATGCTTTTAATTCAGTTCTGATTG
ATTATATATGCCTTCAGTTAAAACTATTAAGTGTCTC

Found at i:16284 original size:16 final size:15

Alignment explanation


    Indices: 16263--16293  Score: 53
    Period size: 16  Copynumber: 2.0  Consensus size: 15

      16253 GTGATTAATC

                            
      16263 TTTTTTTCTTTTCTTT
          1 TTTTTTTC-TTTCTTT

                           
      16279 TTTTTTTCTTTCTTT
          1 TTTTTTTCTTTCTTT

      16294 CTCTCTTTTG


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  15    7  0.47
  16    8  0.53

ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87


Consensus pattern (15 bp):   
TTTTTTTCTTTCTTT
Done.