Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010494.1 Corchorus capsularis cultivar CVL-1 contig10515, 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: 9993
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30


Found at i:127 original size:31 final size:31

Alignment explanation


    Indices: 84--158  Score: 132
    Period size: 31  Copynumber: 2.4  Consensus size: 31

         74 AACTAACACC

                *                          
         84 AGGCTCTTATTTGAGCATTTTCGATAACGTT
          1 AGGCCCTTATTTGAGCATTTTCGATAACGTT

                                       *   
        115 AGGCCCTTATTTGAGCATTTTCGATAATGTT
          1 AGGCCCTTATTTGAGCATTTTCGATAACGTT

                         
        146 AGGCCCTTATTTG
          1 AGGCCCTTATTTG

        159 GCCAAATTAA


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

Matches are distributed among these distances:
  31   42  1.00

ACGTcount: A:0.21, C:0.17, G:0.20, T:0.41


Consensus pattern (31 bp):   
AGGCCCTTATTTGAGCATTTTCGATAACGTT

Found at i:216 original size:31 final size:31

Alignment explanation


    Indices: 84--225  Score: 107
    Period size: 31  Copynumber: 4.6  Consensus size: 31

         74 AACTAACACC

                *          *        *      
         84 AGGCTCTTATTTGAGCATTTTCGATAACGTT
          1 AGGCCCTTATTTGAGAATTTTCGAAAACGTT

                           *        *  *   
        115 AGGCCCTTATTTGAGCATTTTCGATAATGTT
          1 AGGCCCTTATTTGAGAATTTTCGAAAACGTT

                                *            *
        146 AGGCCCTTATTTG-GCCAA-ATT--AAAA-GATC
          1 AGGCCCTTATTTGAG--AATTTTCGAAAACG-TT

            *  *                            
        175 GGGTCCTTATTTGAGAATTTT-GACAAACGTT
          1 AGGCCCTTATTTGAGAATTTTCGA-AAACGTT

                                
        206 AGGCCCTTATTTGAGCAATT
          1 AGGCCCTTATTTGAG-AATT

        226 AGCCAAAAAA


Statistics
Matches: 90,  Mismatches: 12, Indels: 17
        0.76            0.10        0.14

Matches are distributed among these distances:
  28    3  0.03
  29   17  0.19
  30    3  0.03
  31   61  0.68
  32    6  0.07

ACGTcount: A:0.26, C:0.17, G:0.20, T:0.37


Consensus pattern (31 bp):   
AGGCCCTTATTTGAGAATTTTCGAAAACGTT

Found at i:1628 original size:42 final size:42

Alignment explanation


    Indices: 1581--1660  Score: 142
    Period size: 42  Copynumber: 1.9  Consensus size: 42

       1571 AACAGGGAAC

                                                      
       1581 TAGAATAGAATAAGATAATATAGTCAATGAATTGTCATGATT
          1 TAGAATAGAATAAGATAATATAGTCAATGAATTGTCATGATT

                            *    *                
       1623 TAGAATAGAATAAGATTATATCGTCAATGAATTGTCAT
          1 TAGAATAGAATAAGATAATATAGTCAATGAATTGTCAT

       1661 TATTCTGTCT


Statistics
Matches: 36,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  42   36  1.00

ACGTcount: A:0.44, C:0.06, G:0.16, T:0.34


Consensus pattern (42 bp):   
TAGAATAGAATAAGATAATATAGTCAATGAATTGTCATGATT

Found at i:1982 original size:2 final size:2

Alignment explanation


    Indices: 1975--2002  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

       1965 GCCAATTGAC

                                                     
       1975 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

       2003 AAGGGGCTAT


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:4179 original size:12 final size:12

Alignment explanation


    Indices: 4162--4188  Score: 54
    Period size: 12  Copynumber: 2.2  Consensus size: 12

       4152 GCAGAATCCA

                        
       4162 TAAGTCTGAACC
          1 TAAGTCTGAACC

                        
       4174 TAAGTCTGAACC
          1 TAAGTCTGAACC

               
       4186 TAA
          1 TAA

       4189 ATTATAATTA


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

Matches are distributed among these distances:
  12   15  1.00

ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26


Consensus pattern (12 bp):   
TAAGTCTGAACC
Done.