Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007386.1 Corchorus capsularis cultivar CVL-1 contig07407, 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: 6514
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32


Found at i:86 original size:15 final size:16

Alignment explanation


    Indices: 66--95  Score: 53
    Period size: 15  Copynumber: 1.9  Consensus size: 16

         56 TTCCAAGAAA

                            
         66 AAAAACCC-TAGCAAG
          1 AAAAACCCATAGCAAG

                           
         81 AAAAACCCATAGCAA
          1 AAAAACCCATAGCAA

         96 TTTCCTTTTT


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  15    8  0.57
  16    6  0.43

ACGTcount: A:0.57, C:0.27, G:0.10, T:0.07


Consensus pattern (16 bp):   
AAAAACCCATAGCAAG

Found at i:2952 original size:40 final size:40

Alignment explanation


    Indices: 2892--2968  Score: 111
    Period size: 40  Copynumber: 1.9  Consensus size: 40

       2882 TGAAGATGGC

                       *         *                   
       2892 TAAACATTTACGAATACAAATGT-TATACACTCACGCTGAT
          1 TAAACATTTACAAATACAAATATAT-TACACTCACGCTGAT

                *                                
       2932 TAAATATTTACAAATACAAATATATTACACTCACGCT
          1 TAAACATTTACAAATACAAATATATTACACTCACGCT

       2969 TAAAACACTT


Statistics
Matches: 33,  Mismatches: 3, Indels: 2
        0.87            0.08        0.05

Matches are distributed among these distances:
  40   32  0.97
  41    1  0.03

ACGTcount: A:0.43, C:0.19, G:0.06, T:0.31


Consensus pattern (40 bp):   
TAAACATTTACAAATACAAATATATTACACTCACGCTGAT

Found at i:3219 original size:15 final size:15

Alignment explanation


    Indices: 3176--3223  Score: 53
    Period size: 15  Copynumber: 3.1  Consensus size: 15

       3166 AAGCTTTCAC

                            
       3176 TTTTAATT-AATATTT
          1 TTTTAATTAAATA-TT

                   *         
       3191 ATTATTATTTAAATATT
          1 -TT-TTAATTAAATATT

                           
       3208 TTTTAATTAAATATT
          1 TTTTAATTAAATATT

             
       3223 T
          1 T

       3224 GTGATTTTTT


Statistics
Matches: 28,  Mismatches: 2, Indels: 5
        0.80            0.06        0.14

Matches are distributed among these distances:
  15   13  0.46
  16    4  0.14
  17    7  0.25
  18    4  0.14

ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62


Consensus pattern (15 bp):   
TTTTAATTAAATATT

Found at i:5469 original size:2 final size:2

Alignment explanation


    Indices: 5462--5501  Score: 80
    Period size: 2  Copynumber: 20.0  Consensus size: 2

       5452 CGGTGGAGGA

                                                                       
       5462 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG

       5502 TGGGGAGAGG


Statistics
Matches: 38,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   38  1.00

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


Consensus pattern (2 bp):   
AG

Done.