Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011416.1 Corchorus capsularis cultivar CVL-1 contig11437, 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: 31275
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33


Found at i:8976 original size:18 final size:17

Alignment explanation


    Indices: 8949--8982  Score: 50
    Period size: 18  Copynumber: 1.9  Consensus size: 17

       8939 TTTCATAAGT

                      *      
       8949 AAACTAACTATAAGCTA
          1 AAACTAACTACAAGCTA

                             
       8966 AAACATAACTACAAGCT
          1 AAAC-TAACTACAAGCT

       8983 TTACAAGAGA


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  17    4  0.27
  18   11  0.73

ACGTcount: A:0.53, C:0.21, G:0.06, T:0.21


Consensus pattern (17 bp):   
AAACTAACTACAAGCTA

Found at i:21025 original size:6 final size:6

Alignment explanation


    Indices: 21016--21042  Score: 54
    Period size: 6  Copynumber: 4.5  Consensus size: 6

      21006 TGTATGTATT

                                           
      21016 TATGTA TATGTA TATGTA TATGTA TAT
          1 TATGTA TATGTA TATGTA TATGTA TAT

      21043 TCATGTTTTT


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   21  1.00

ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52


Consensus pattern (6 bp):   
TATGTA

Found at i:21547 original size:27 final size:27

Alignment explanation


    Indices: 21517--21574  Score: 89
    Period size: 27  Copynumber: 2.1  Consensus size: 27

      21507 TTTAACACGG

                                       
      21517 TAAACCATCGGGTATTTGGCCTGGTGA
          1 TAAACCATCGGGTATTTGGCCTGGTGA

                ***                    
      21544 TAAAGTGTCGGGTATTTGGCCTGGTGA
          1 TAAACCATCGGGTATTTGGCCTGGTGA

                
      21571 TAAA
          1 TAAA

      21575 GTGCTGAACT


Statistics
Matches: 28,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  27   28  1.00

ACGTcount: A:0.24, C:0.14, G:0.31, T:0.31


Consensus pattern (27 bp):   
TAAACCATCGGGTATTTGGCCTGGTGA

Found at i:21575 original size:27 final size:27

Alignment explanation


    Indices: 21524--21577  Score: 108
    Period size: 27  Copynumber: 2.0  Consensus size: 27

      21514 CGGTAAACCA

                                       
      21524 TCGGGTATTTGGCCTGGTGATAAAGTG
          1 TCGGGTATTTGGCCTGGTGATAAAGTG

                                       
      21551 TCGGGTATTTGGCCTGGTGATAAAGTG
          1 TCGGGTATTTGGCCTGGTGATAAAGTG

      21578 CTGAACTCTT


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  27   27  1.00

ACGTcount: A:0.19, C:0.11, G:0.37, T:0.33


Consensus pattern (27 bp):   
TCGGGTATTTGGCCTGGTGATAAAGTG

Found at i:27857 original size:21 final size:21

Alignment explanation


    Indices: 27833--27876  Score: 54
    Period size: 21  Copynumber: 2.1  Consensus size: 21

      27823 GTATACTAAA

                                  
      27833 TTGCTAAAT-ACCGCCCCATTT
          1 TTGCT-AATCACCGCCCCATTT

                  *         *    
      27854 TTGCTATTCACCGCCCTATTT
          1 TTGCTAATCACCGCCCCATTT

              
      27875 TT
          1 TT

      27877 TACGCTTTTG


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  20    2  0.10
  21   18  0.90

ACGTcount: A:0.18, C:0.32, G:0.09, T:0.41


Consensus pattern (21 bp):   
TTGCTAATCACCGCCCCATTT

Found at i:28227 original size:33 final size:33

Alignment explanation


    Indices: 28183--28269  Score: 122
    Period size: 33  Copynumber: 2.6  Consensus size: 33

      28173 AAAATTGTCT

                 *          *                 
      28183 AGCCGCCCTAGTGGGGCGGCTCCGCCATGGCT-G
          1 AGCCGTCCTAGTGGGGAGGCTCCGCCATGG-TGG

                  *                          
      28216 AGCCGTTCTAGTGGGGAGGCTCCGCCATGGTGG
          1 AGCCGTCCTAGTGGGGAGGCTCCGCCATGGTGG

                       *         
      28249 AGCCGTCCTAGCGGGGAGGCT
          1 AGCCGTCCTAGTGGGGAGGCT

      28270 AGTGTAAAAA


Statistics
Matches: 48,  Mismatches: 5, Indels: 2
        0.87            0.09        0.04

Matches are distributed among these distances:
  32    1  0.02
  33   47  0.98

ACGTcount: A:0.11, C:0.30, G:0.41, T:0.17


Consensus pattern (33 bp):   
AGCCGTCCTAGTGGGGAGGCTCCGCCATGGTGG

Found at i:31251 original size:2 final size:2

Alignment explanation


    Indices: 31244--31274  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

      31234 ATGCATGTAC

                                                          
      31244 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

      31275 G


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Done.