Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022890.1 Corchorus olitorius cultivar O-4 contig22923, 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: 7654
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31


Found at i:568 original size:15 final size:15

Alignment explanation


    Indices: 538--579  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

        528 TTACTTTGCT

                            
        538 TTGTTTTCTAGTTTAA
          1 TTGTTTTCT-GTTTAA

                           
        554 TTGTTTTCTGTTTAA
          1 TTGTTTTCTGTTTAA

               *       
        569 TTGCTTTCTGT
          1 TTGTTTTCTGT

        580 CAACCTCTGT


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   16  0.64
  16    9  0.36

ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64


Consensus pattern (15 bp):   
TTGTTTTCTGTTTAA

Found at i:3249 original size:29 final size:30

Alignment explanation


    Indices: 3194--3251  Score: 82
    Period size: 31  Copynumber: 1.9  Consensus size: 30

       3184 AAAGTTCAAA

                       *                   
       3194 TAAGGGCCTGACCTTTAGGGAAAAGGTCATT
          1 TAAGGGCCTGAACTTTA-GGAAAAGGTCATT

                  *                     
       3225 TAAGGGTCTGAACTTT-GGAAAAGGTCA
          1 TAAGGGCCTGAACTTTAGGAAAAGGTCA

       3252 AATCAGTGCT


Statistics
Matches: 25,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  29   11  0.44
  31   14  0.56

ACGTcount: A:0.31, C:0.14, G:0.29, T:0.26


Consensus pattern (30 bp):   
TAAGGGCCTGAACTTTAGGAAAAGGTCATT

Found at i:4006 original size:15 final size:17

Alignment explanation


    Indices: 3980--4015  Score: 58
    Period size: 16  Copynumber: 2.2  Consensus size: 17

       3970 ATCTACTTAC

                             
       3980 CAAATCTACAAA-TAAA
          1 CAAATCTACAAATTAAA

                             
       3996 CAAAT-TACAAATTAAA
          1 CAAATCTACAAATTAAA

                
       4012 CAAA
          1 CAAA

       4016 CCATCTACCA


Statistics
Matches: 19,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  15    6  0.32
  16   13  0.68

ACGTcount: A:0.64, C:0.17, G:0.00, T:0.19


Consensus pattern (17 bp):   
CAAATCTACAAATTAAA

Found at i:4017 original size:48 final size:48

Alignment explanation


    Indices: 3960--4053  Score: 145
    Period size: 48  Copynumber: 2.0  Consensus size: 48

       3950 GAAACTATCA

                *           **                               
       3960 TAAATAAACCATCTACTTACCAAAT-CTACAAATAAACAAATTACAAAT
          1 TAAACAAACCATCTACCAACCAAATAC-ACAAATAAACAAATTACAAAT

                                                          
       4008 TAAACAAACCATCTACCAACCAAATACACAAATAAACAAATTACAA
          1 TAAACAAACCATCTACCAACCAAATACACAAATAAACAAATTACAA

       4054 TTACAAACTA


Statistics
Matches: 42,  Mismatches: 3, Indels: 2
        0.89            0.06        0.04

Matches are distributed among these distances:
  48   41  0.98
  49    1  0.02

ACGTcount: A:0.56, C:0.23, G:0.00, T:0.20


Consensus pattern (48 bp):   
TAAACAAACCATCTACCAACCAAATACACAAATAAACAAATTACAAAT

Found at i:4192 original size:42 final size:42

Alignment explanation


    Indices: 4133--4254  Score: 244
    Period size: 42  Copynumber: 2.9  Consensus size: 42

       4123 TAAATCTCTA

                                                      
       4133 TATGCCCAAACATCTAAATGAGAATTCAACTCAAACTAGATT
          1 TATGCCCAAACATCTAAATGAGAATTCAACTCAAACTAGATT

                                                      
       4175 TATGCCCAAACATCTAAATGAGAATTCAACTCAAACTAGATT
          1 TATGCCCAAACATCTAAATGAGAATTCAACTCAAACTAGATT

                                                  
       4217 TATGCCCAAACATCTAAATGAGAATTCAACTCAAACTA
          1 TATGCCCAAACATCTAAATGAGAATTCAACTCAAACTA

       4255 AGAAACTATC


Statistics
Matches: 80,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  42   80  1.00

ACGTcount: A:0.43, C:0.22, G:0.09, T:0.25


Consensus pattern (42 bp):   
TATGCCCAAACATCTAAATGAGAATTCAACTCAAACTAGATT
Done.