Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012432.1 Corchorus capsularis cultivar CVL-1 contig12453, 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: 21943
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31


Found at i:976 original size:2 final size:2

Alignment explanation


    Indices: 969--998  Score: 53
    Period size: 2  Copynumber: 15.5  Consensus size: 2

        959 TATTACTATG

                                                          
        969 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

        999 AGAAACAATA


Statistics
Matches: 27,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   1    1  0.04
   2   26  0.96

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


Consensus pattern (2 bp):   
AT

Found at i:1832 original size:3 final size:3

Alignment explanation


    Indices: 1826--1853  Score: 56
    Period size: 3  Copynumber: 9.3  Consensus size: 3

       1816 GGAAATTGAG

                                                 
       1826 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
          1 GAA GAA GAA GAA GAA GAA GAA GAA GAA G

       1854 TGGAAAGAGA


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   25  1.00

ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00


Consensus pattern (3 bp):   
GAA

Found at i:3035 original size:81 final size:81

Alignment explanation


    Indices: 2897--3060  Score: 238
    Period size: 81  Copynumber: 2.0  Consensus size: 81

       2887 TGTCAAAACT

                        *        *                         *                 
       2897 GATACCACCCAAGACATAGTAGTCAAAGACTCTGTTAGGACCCCGGAGTCCCCCATGCCTTCTTC
          1 GATACCACCCAAAACATAGTAATCAAAGACTCTGTTAGGACCCCGGAATCCCCCATGCCTTCTTC

            *       *       
       2962 TTCAGAGTGTTTGAAG
         66 ATCAGAGTATTTGAAG

                           *        *                  *       **            
       2978 GATACCACCCAAAACGTAGTAATCGAAGACTCTGTTAGGACCCTGGAATCCTTCATGCCTTCTTC
          1 GATACCACCCAAAACATAGTAATCAAAGACTCTGTTAGGACCCCGGAATCCCCCATGCCTTCTTC

                            
       3043 ATCAGAGTATTTGAAG
         66 ATCAGAGTATTTGAAG

              
       3059 GA
          1 GA

       3061 ACTATCTAAT


Statistics
Matches: 73,  Mismatches: 10, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  81   73  1.00

ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26


Consensus pattern (81 bp):   
GATACCACCCAAAACATAGTAATCAAAGACTCTGTTAGGACCCCGGAATCCCCCATGCCTTCTTC
ATCAGAGTATTTGAAG

Found at i:9052 original size:61 final size:61

Alignment explanation


    Indices: 8958--9080  Score: 246
    Period size: 61  Copynumber: 2.0  Consensus size: 61

       8948 AAATTCTTAA

                                                                         
       8958 TTTTTTTTTAATAAACCGTATTTTTTTGTTGCAAGTTTGCAACAAGTAGCAGGCCACATCT
          1 TTTTTTTTTAATAAACCGTATTTTTTTGTTGCAAGTTTGCAACAAGTAGCAGGCCACATCT

                                                                         
       9019 TTTTTTTTTAATAAACCGTATTTTTTTGTTGCAAGTTTGCAACAAGTAGCAGGCCACATCT
          1 TTTTTTTTTAATAAACCGTATTTTTTTGTTGCAAGTTTGCAACAAGTAGCAGGCCACATCT

             
       9080 T
          1 T

       9081 GAGATTCAAT


Statistics
Matches: 62,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  61   62  1.00

ACGTcount: A:0.26, C:0.16, G:0.15, T:0.43


Consensus pattern (61 bp):   
TTTTTTTTTAATAAACCGTATTTTTTTGTTGCAAGTTTGCAACAAGTAGCAGGCCACATCT

Found at i:11241 original size:104 final size:103

Alignment explanation


    Indices: 11062--11269  Score: 371
    Period size: 104  Copynumber: 2.0  Consensus size: 103

      11052 ACAAAGCAAT

                    *         *                                              
      11062 GGGTCACTTAATCCCCAATATTCCTTTTAAGTAACTCCTCAAAATGACAACCATAAGAACTAGTA
          1 GGGTCACTAAATCCCCAAGATTCCTTTTAAGTAACTCCTCAAAATGACAACCATAAGAACTAGTA

                                          *  *    
      11127 CAAAAGAAGAACATTTATGAAATTATGAAAGAATTGAA
         66 CAAAAGAAGAACATTTATGAAATTATGAAAAAACTGAA

                                                                             
      11165 GGGTCACTAAATCCCCAAGATTCCTTTTTAAGTAACTCCTCAAAATGACAACCATAAGAACTAGT
          1 GGGTCACTAAATCCCCAAGATTCC-TTTTAAGTAACTCCTCAAAATGACAACCATAAGAACTAGT

                                                   
      11230 ACAAAAGAAGAACATTTATGAAATTATGAAAAAACTGAA
         65 ACAAAAGAAGAACATTTATGAAATTATGAAAAAACTGAA

             
      11269 G
          1 G

      11270 ATGACCTGGA


Statistics
Matches: 100,  Mismatches: 4, Indels: 1
        0.95            0.04        0.01

Matches are distributed among these distances:
 103   22  0.22
 104   78  0.78

ACGTcount: A:0.44, C:0.18, G:0.13, T:0.25


Consensus pattern (103 bp):   
GGGTCACTAAATCCCCAAGATTCCTTTTAAGTAACTCCTCAAAATGACAACCATAAGAACTAGTA
CAAAAGAAGAACATTTATGAAATTATGAAAAAACTGAA

Found at i:19347 original size:2 final size:2

Alignment explanation


    Indices: 19340--19384  Score: 90
    Period size: 2  Copynumber: 22.5  Consensus size: 2

      19330 GACCAAGAAG

                                                                          
      19340 AT AT AT AT AT 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 AT AT AT AT AT

                
      19382 AT A
          1 AT A

      19385 GCTAGGTTTT


Statistics
Matches: 43,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   43  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Done.