Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001622.1 Corchorus olitorius cultivar O-4 contig01622, 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: 14831
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34


Found at i:1138 original size:25 final size:25

Alignment explanation


    Indices: 1110--1160  Score: 93
    Period size: 25  Copynumber: 2.0  Consensus size: 25

       1100 TGACAAAAAA

                                 *   
       1110 ATGAATAGTTAATTTAAGAACCACG
          1 ATGAATAGTTAATTTAAGAACAACG

                                     
       1135 ATGAATAGTTAATTTAAGAACAACG
          1 ATGAATAGTTAATTTAAGAACAACG

             
       1160 A
          1 A

       1161 GAAGGTACCT


Statistics
Matches: 25,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  25   25  1.00

ACGTcount: A:0.47, C:0.10, G:0.16, T:0.27


Consensus pattern (25 bp):   
ATGAATAGTTAATTTAAGAACAACG

Found at i:1356 original size:14 final size:14

Alignment explanation


    Indices: 1337--1365  Score: 58
    Period size: 14  Copynumber: 2.1  Consensus size: 14

       1327 CAATCTTATA

                          
       1337 ATAAAAACCTGATT
          1 ATAAAAACCTGATT

                          
       1351 ATAAAAACCTGATT
          1 ATAAAAACCTGATT

             
       1365 A
          1 A

       1366 GTTCATATAC


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

Matches are distributed among these distances:
  14   15  1.00

ACGTcount: A:0.52, C:0.14, G:0.07, T:0.28


Consensus pattern (14 bp):   
ATAAAAACCTGATT

Found at i:2541 original size:2 final size:2

Alignment explanation


    Indices: 2534--2565  Score: 64
    Period size: 2  Copynumber: 16.0  Consensus size: 2

       2524 ATTAAAAGAA

                                                           
       2534 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       2566 GGAGAATAAT


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   30  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:4094 original size:20 final size:18

Alignment explanation


    Indices: 4055--4092  Score: 76
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       4045 AAGTAGATCG

                              
       4055 ATTTTTTTCGTTATATAT
          1 ATTTTTTTCGTTATATAT

                              
       4073 ATTTTTTTCGTTATATAT
          1 ATTTTTTTCGTTATATAT

              
       4091 AT
          1 AT

       4093 ATATATATAA


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:0.24, C:0.05, G:0.05, T:0.66


Consensus pattern (18 bp):   
ATTTTTTTCGTTATATAT

Found at i:5695 original size:14 final size:14

Alignment explanation


    Indices: 5665--5694  Score: 53
    Period size: 14  Copynumber: 2.2  Consensus size: 14

       5655 CTTTCTCCAC

                          
       5665 TTTCTTTTTTTCTT
          1 TTTCTTTTTTTCTT

                          
       5679 TTTCTTTTTTT-TT
          1 TTTCTTTTTTTCTT

               
       5692 TTT
          1 TTT

       5695 TAAAACGCTT


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  13    5  0.31
  14   11  0.69

ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90


Consensus pattern (14 bp):   
TTTCTTTTTTTCTT

Found at i:11075 original size:21 final size:21

Alignment explanation


    Indices: 11051--11100  Score: 91
    Period size: 21  Copynumber: 2.4  Consensus size: 21

      11041 AACAACCCCT

                                 
      11051 ATTTGATCCAATTTGGATTGA
          1 ATTTGATCCAATTTGGATTGA

                                 
      11072 ATTTGATCCAATTTGGATTGA
          1 ATTTGATCCAATTTGGATTGA

               *    
      11093 ATTCGATC
          1 ATTTGATC

      11101 TAAGGAAGCA


Statistics
Matches: 28,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  21   28  1.00

ACGTcount: A:0.28, C:0.12, G:0.18, T:0.42


Consensus pattern (21 bp):   
ATTTGATCCAATTTGGATTGA
Done.