Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013964.1 Corchorus capsularis cultivar CVL-1 contig13985, 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: 10427
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32


Found at i:479 original size:41 final size:41

Alignment explanation


    Indices: 416--500  Score: 120
    Period size: 41  Copynumber: 2.1  Consensus size: 41

        406 TATGAAACCC

                     *              *                
        416 AAACCCTAACAAACAATATAAACCCTAGGTGAGAT-AAAAG
          1 AAACCCTAAAAAACAATATAAACCATAGGTGAGATAAAAAG

                                                       
        456 AAACCCTCAAAAAAC-ATATTAAACCATAGGTGAGATAAAAAG
          1 AAACCCT-AAAAAACAATA-TAAACCATAGGTGAGATAAAAAG

               
        498 AAA
          1 AAA

        501 AAACATGAAC


Statistics
Matches: 40,  Mismatches: 2, Indels: 4
        0.87            0.04        0.09

Matches are distributed among these distances:
  40   10  0.25
  41   22  0.55
  42    8  0.20

ACGTcount: A:0.55, C:0.18, G:0.12, T:0.15


Consensus pattern (41 bp):   
AAACCCTAAAAAACAATATAAACCATAGGTGAGATAAAAAG

Found at i:5747 original size:17 final size:17

Alignment explanation


    Indices: 5725--5758  Score: 52
    Period size: 17  Copynumber: 2.0  Consensus size: 17

       5715 ACTTTTTCCA

                              
       5725 TCAAATTCATCAA-TTTT
          1 TCAAATT-ATCAAGTTTT

                             
       5742 TCAAATTATCAAGTTTT
          1 TCAAATTATCAAGTTTT

       5759 GGGAAAGTGG


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  16    5  0.31
  17   11  0.69

ACGTcount: A:0.35, C:0.15, G:0.03, T:0.47


Consensus pattern (17 bp):   
TCAAATTATCAAGTTTT

Found at i:5758 original size:16 final size:17

Alignment explanation


    Indices: 5725--5758  Score: 52
    Period size: 16  Copynumber: 2.1  Consensus size: 17

       5715 ACTTTTTCCA

                         *   
       5725 TCAAATTCATCAATTTT
          1 TCAAATTCATCAAGTTT

                             
       5742 TCAAATT-ATCAAGTTT
          1 TCAAATTCATCAAGTTT

             
       5758 T
          1 T

       5759 GGGAAAGTGG


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  16    9  0.56
  17    7  0.44

ACGTcount: A:0.35, C:0.15, G:0.03, T:0.47


Consensus pattern (17 bp):   
TCAAATTCATCAAGTTT
Done.