Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017148.1 Corchorus olitorius cultivar O-4 contig17181, 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: 20012
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33


Found at i:11936 original size:14 final size:14

Alignment explanation


    Indices: 11912--11945  Score: 50
    Period size: 14  Copynumber: 2.4  Consensus size: 14

      11902 TATTTGCCTG

                           
      11912 ATAACATTCCGCAGA
          1 ATAA-ATTCCGCAGA

                      *   
      11927 ATAAATTCCGTAGA
          1 ATAAATTCCGCAGA

                 
      11941 ATAAA
          1 ATAAA

      11946 AAAACAATCA


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  14   14  0.78
  15    4  0.22

ACGTcount: A:0.47, C:0.18, G:0.12, T:0.24


Consensus pattern (14 bp):   
ATAAATTCCGCAGA

Found at i:11953 original size:55 final size:55

Alignment explanation


    Indices: 11892--12004  Score: 226
    Period size: 55  Copynumber: 2.1  Consensus size: 55

      11882 AATTGAAGAT

                                                                   
      11892 AAACAATCAATATTTGCCTGATAACATTCCGCAGAATAAATTCCGTAGAATAAAA
          1 AAACAATCAATATTTGCCTGATAACATTCCGCAGAATAAATTCCGTAGAATAAAA

                                                                   
      11947 AAACAATCAATATTTGCCTGATAACATTCCGCAGAATAAATTCCGTAGAATAAAA
          1 AAACAATCAATATTTGCCTGATAACATTCCGCAGAATAAATTCCGTAGAATAAAA

               
      12002 AAA
          1 AAA

      12005 GGGAATCAAA


Statistics
Matches: 58,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  55   58  1.00

ACGTcount: A:0.47, C:0.18, G:0.11, T:0.25


Consensus pattern (55 bp):   
AAACAATCAATATTTGCCTGATAACATTCCGCAGAATAAATTCCGTAGAATAAAA

Found at i:11991 original size:14 final size:14

Alignment explanation


    Indices: 11967--12000  Score: 50
    Period size: 14  Copynumber: 2.4  Consensus size: 14

      11957 TATTTGCCTG

                           
      11967 ATAACATTCCGCAGA
          1 ATAA-ATTCCGCAGA

                      *   
      11982 ATAAATTCCGTAGA
          1 ATAAATTCCGCAGA

                 
      11996 ATAAA
          1 ATAAA

      12001 AAAAGGGAAT


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  14   14  0.78
  15    4  0.22

ACGTcount: A:0.47, C:0.18, G:0.12, T:0.24


Consensus pattern (14 bp):   
ATAAATTCCGCAGA

Found at i:14956 original size:128 final size:128

Alignment explanation


    Indices: 14728--14982  Score: 483
    Period size: 128  Copynumber: 2.0  Consensus size: 128

      14718 TTCAATTTTT

                                        *                                    
      14728 GAGATAAGAATCATTTTCATTTCTTGAAGAGATTGAGATTACAAACGCACAGGAAGACCCGTACA
          1 GAGATAAGAATCATTTTCATTTCTTGAAAAGATTGAGATTACAAACGCACAGGAAGACCCGTACA

                  *                               *                        
      14793 CCGCTATATGATTAGCTACATTACCGAAACGCTAATCTGGAGCCAACAAACCCCTTCCCCAAG
         66 CCGCTACATGATTAGCTACATTACCGAAACGCTAATCTAGAGCCAACAAACCCCTTCCCCAAG

                                                                             
      14856 GAGATAAGAATCATTTTCATTTCTTGAAAAGATTGAGATTACAAACGCACAGGAAGACCCGTACA
          1 GAGATAAGAATCATTTTCATTTCTTGAAAAGATTGAGATTACAAACGCACAGGAAGACCCGTACA

                                                                          
      14921 CCGCTACATGATTAGCTACATTACCGAAACGCTAATCTAGAGCCAACAAACCCCTTCCCCAA
         66 CCGCTACATGATTAGCTACATTACCGAAACGCTAATCTAGAGCCAACAAACCCCTTCCCCAA

      14983 CAAACAAACC


Statistics
Matches: 124,  Mismatches: 3, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
 128  124  1.00

ACGTcount: A:0.36, C:0.25, G:0.16, T:0.22


Consensus pattern (128 bp):   
GAGATAAGAATCATTTTCATTTCTTGAAAAGATTGAGATTACAAACGCACAGGAAGACCCGTACA
CCGCTACATGATTAGCTACATTACCGAAACGCTAATCTAGAGCCAACAAACCCCTTCCCCAAG
Done.