Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014263.1 Corchorus capsularis cultivar CVL-1 contig14284, 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: 37455
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.30


Found at i:8965 original size:6 final size:6

Alignment explanation


    Indices: 8954--8978  Score: 50
    Period size: 6  Copynumber: 4.2  Consensus size: 6

       8944 AGCAAAAATT

                                         
       8954 TCCCAA TCCCAA TCCCAA TCCCAA T
          1 TCCCAA TCCCAA TCCCAA TCCCAA T

       8979 ATTTCTTGGA


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   19  1.00

ACGTcount: A:0.32, C:0.48, G:0.00, T:0.20


Consensus pattern (6 bp):   
TCCCAA

Found at i:9556 original size:15 final size:15

Alignment explanation


    Indices: 9536--9570  Score: 52
    Period size: 15  Copynumber: 2.3  Consensus size: 15

       9526 AAGCAGTACA

                        *  
       9536 AGAGAAGAAACATAT
          1 AGAGAAGAAACAGAT

                   *       
       9551 AGAGAAGCAACAGAT
          1 AGAGAAGAAACAGAT

                 
       9566 AGAGA
          1 AGAGA

       9571 TTACTATGTA


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  15   18  1.00

ACGTcount: A:0.57, C:0.09, G:0.26, T:0.09


Consensus pattern (15 bp):   
AGAGAAGAAACAGAT

Found at i:34764 original size:68 final size:67

Alignment explanation


    Indices: 34634--34763  Score: 203
    Period size: 68  Copynumber: 2.0  Consensus size: 67

      34624 AGTATCAGAT

                                                                             
      34634 AATGCTACTTTCAAGGAGGGCAAAAAGTTTTTTTTTAAAAAAAAAGGGGATACCTTCATAAGTAA
          1 AATGCTACTTTCAAGGAGGGC-AAAAGTTTTTTTTTAAAAAAAAAGGGGATACCTTCATAAGTAA

               
      34699 GAA
         65 GAA

                                               **                    *       
      34702 AATGCTACTTTCAAGGAGGGC-AAA-TTTTTTTTTTTAAAAAAA-GGGATACCTTCAGAAGTAAG
          1 AATGCTACTTTCAAGGAGGGCAAAAGTTTTTTTTTAAAAAAAAAGGGGATACCTTCATAAGTAAG

      34764 TCCAAACCAA


Statistics
Matches: 59,  Mismatches: 3, Indels: 4
        0.89            0.05        0.06

Matches are distributed among these distances:
  64   19  0.32
  65   16  0.27
  66    3  0.05
  68   21  0.36

ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30


Consensus pattern (67 bp):   
AATGCTACTTTCAAGGAGGGCAAAAGTTTTTTTTTAAAAAAAAAGGGGATACCTTCATAAGTAAG
AA

Found at i:37026 original size:21 final size:21

Alignment explanation


    Indices: 37002--37049  Score: 69
    Period size: 21  Copynumber: 2.3  Consensus size: 21

      36992 CCAAAAAGAT

                  *              
      37002 AAAACTCAAAAGCAAGAATCA
          1 AAAACTAAAAAGCAAGAATCA

                **               
      37023 AAAAAGAAAAAGCAAGAATCA
          1 AAAACTAAAAAGCAAGAATCA

                  
      37044 AAAACT
          1 AAAACT

      37050 TGAAATTACC


Statistics
Matches: 22,  Mismatches: 5, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  21   22  1.00

ACGTcount: A:0.67, C:0.15, G:0.10, T:0.08


Consensus pattern (21 bp):   
AAAACTAAAAAGCAAGAATCA
Done.