Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020721.1 Corchorus olitorius cultivar O-4 contig20754, 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: 7973
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.35


Found at i:3591 original size:63 final size:63

Alignment explanation


    Indices: 3476--3673  Score: 238
    Period size: 63  Copynumber: 3.1  Consensus size: 63

       3466 GAAACAACAG

                             *           **    *       *           * *      
       3476 GAAGA-ATCCAAAAAGGCGACTGATGAAATCAATCGACTTCAACTGGAGAATGGGAAGCTAAAA
          1 GAAGATATCC-AAAAGGTGACTGATGAAAAGAATCAACTTCAATTGGAGAATGGGGATCTAAAA

             *                   *      *                  *               
       3539 GGAGATATCCAAAAGGTGACTAATGAAAGGAATCAACTTCAATTGGATAATGGGGATCTAAAA
          1 GAAGATATCCAAAAGGTGACTGATGAAAAGAATCAACTTCAATTGGAGAATGGGGATCTAAAA

                        *                    *          *                   
       3602 GAAGATAT-CAAGAGAGTGACTGATGAAAAGAACCAACTTCAATCGGAGAATGGGGATCTAAAA
          1 GAAGATATCCAAAAG-GTGACTGATGAAAAGAATCAACTTCAATTGGAGAATGGGGATCTAAAA

                     
       3665 GAAGATATC
          1 GAAGATATC

       3674 GAAAGTCACC


Statistics
Matches: 115,  Mismatches: 17, Indels: 5
        0.84            0.12        0.04

Matches are distributed among these distances:
  62    5  0.04
  63  106  0.92
  64    4  0.03

ACGTcount: A:0.44, C:0.13, G:0.24, T:0.19


Consensus pattern (63 bp):   
GAAGATATCCAAAAGGTGACTGATGAAAAGAATCAACTTCAATTGGAGAATGGGGATCTAAAA

Found at i:4186 original size:18 final size:18

Alignment explanation


    Indices: 4163--4200  Score: 76
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       4153 CTGTAGTCTT

                              
       4163 TTTGCATACTGCTCTTTG
          1 TTTGCATACTGCTCTTTG

                              
       4181 TTTGCATACTGCTCTTTG
          1 TTTGCATACTGCTCTTTG

              
       4199 TT
          1 TT

       4201 GGTAACAACT


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   20  1.00

ACGTcount: A:0.11, C:0.21, G:0.16, T:0.53


Consensus pattern (18 bp):   
TTTGCATACTGCTCTTTG

Found at i:5011 original size:37 final size:37

Alignment explanation


    Indices: 4970--5052  Score: 139
    Period size: 37  Copynumber: 2.2  Consensus size: 37

       4960 TTTTGGGGCC

                                           *     
       4970 TGTTGGTTTTTACAGATTGTGTCTAATCTTTGTTGGT
          1 TGTTGGTTTTTACAGATTGTGTCTAATCTTTATTGGT

                                    *            
       5007 TGTTGGTTTTTACAGATTGTGTCTGATCTTTATTGGT
          1 TGTTGGTTTTTACAGATTGTGTCTAATCTTTATTGGT

                     
       5044 TGGTTGGTT
          1 T-GTTGGTT

       5053 GTGTAAAATT


Statistics
Matches: 43,  Mismatches: 2, Indels: 1
        0.93            0.04        0.02

Matches are distributed among these distances:
  37   36  0.84
  38    7  0.16

ACGTcount: A:0.12, C:0.07, G:0.27, T:0.54


Consensus pattern (37 bp):   
TGTTGGTTTTTACAGATTGTGTCTAATCTTTATTGGT

Found at i:6990 original size:2 final size:2

Alignment explanation


    Indices: 6985--7010  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

       6975 TATTTAGAAG

                                                  
       6985 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

       7011 ATCAAAGTAA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Done.