Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013522.1 Corchorus olitorius cultivar O-4 contig13555, 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: 21462
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.29


Found at i:527 original size:20 final size:21

Alignment explanation


    Indices: 485--527  Score: 61
    Period size: 21  Copynumber: 2.1  Consensus size: 21

        475 TCCTTTGTTG

                                 
        485 ATGATCTCCAATGGGCTTCAA
          1 ATGATCTCCAATGGGCTTCAA

                     *        *  
        506 ATGATCTCCGAT-GGCTTTAA
          1 ATGATCTCCAATGGGCTTCAA

              
        526 AT
          1 AT

        528 TCTTCAAGAT


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  20    9  0.45
  21   11  0.55

ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33


Consensus pattern (21 bp):   
ATGATCTCCAATGGGCTTCAA

Found at i:4119 original size:13 final size:13

Alignment explanation


    Indices: 4101--4127  Score: 54
    Period size: 13  Copynumber: 2.1  Consensus size: 13

       4091 TTCCCTACTT

                         
       4101 ACTTGAATTCCAA
          1 ACTTGAATTCCAA

                         
       4114 ACTTGAATTCCAA
          1 ACTTGAATTCCAA

             
       4127 A
          1 A

       4128 AAGGAAGGGA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   14  1.00

ACGTcount: A:0.41, C:0.22, G:0.07, T:0.30


Consensus pattern (13 bp):   
ACTTGAATTCCAA

Found at i:10641 original size:52 final size:52

Alignment explanation


    Indices: 10578--10682  Score: 201
    Period size: 52  Copynumber: 2.0  Consensus size: 52

      10568 AACAAGAATT

                                                  *             
      10578 GCAGGACAACTTCGGCCCAGAACTTGTTCAACTTCGGGGCAGAAGTTGTTGC
          1 GCAGGACAACTTCGGCCCAGAACTTGTTCAACTTCGGGACAGAAGTTGTTGC

                                                                
      10630 GCAGGACAACTTCGGCCCAGAACTTGTTCAACTTCGGGACAGAAGTTGTTGC
          1 GCAGGACAACTTCGGCCCAGAACTTGTTCAACTTCGGGACAGAAGTTGTTGC

             
      10682 G
          1 G

      10683 GAAAGAAAAA


Statistics
Matches: 52,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  52   52  1.00

ACGTcount: A:0.24, C:0.25, G:0.29, T:0.23


Consensus pattern (52 bp):   
GCAGGACAACTTCGGCCCAGAACTTGTTCAACTTCGGGACAGAAGTTGTTGC

Found at i:10672 original size:22 final size:22

Alignment explanation


    Indices: 10636--10679  Score: 61
    Period size: 22  Copynumber: 2.0  Consensus size: 22

      10626 TTGCGCAGGA

                      *           
      10636 CAACTTCGGCCCAGAACTTGTT
          1 CAACTTCGGCACAGAACTTGTT

                     *      *     
      10658 CAACTTCGGGACAGAAGTTGTT
          1 CAACTTCGGCACAGAACTTGTT

      10680 GCGGAAAGAA


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  22   19  1.00

ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27


Consensus pattern (22 bp):   
CAACTTCGGCACAGAACTTGTT

Found at i:11170 original size:21 final size:21

Alignment explanation


    Indices: 11144--11277  Score: 200
    Period size: 21  Copynumber: 6.4  Consensus size: 21

      11134 TGCTAGAAGT

                                  
      11144 TCATTGGAGCAA-GTTCCAAGC
          1 TCATTGGAG-AAGGTTCCAAGC

                                  
      11165 TCATTGGAGCAA-GTTCCAAGC
          1 TCATTGGAG-AAGGTTCCAAGC

                                *
      11186 TCATTGGAGAAGGTTCCAAGT
          1 TCATTGGAGAAGGTTCCAAGC

                                *
      11207 TCATTGGAGAAGGTTCCAAGT
          1 TCATTGGAGAAGGTTCCAAGC

                                *
      11228 TCATTGGAGAAGGTTCCAAGA
          1 TCATTGGAGAAGGTTCCAAGC

                           *     
      11249 TCATTGGAGAAGGTTTCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                    
      11270 TCATTGGA
          1 TCATTGGA

      11278 ATTGCCTAAG


Statistics
Matches: 108,  Mismatches: 4, Indels: 2
        0.95            0.04        0.02

Matches are distributed among these distances:
  20    2  0.02
  21  106  0.98

ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27


Consensus pattern (21 bp):   
TCATTGGAGAAGGTTCCAAGC

Found at i:21391 original size:15 final size:15

Alignment explanation


    Indices: 21365--21402  Score: 67
    Period size: 15  Copynumber: 2.5  Consensus size: 15

      21355 TTTGTTTTGT

                            
      21365 TTTCTAGTTTAATTGC
          1 TTTCT-GTTTAATTGC

                           
      21381 TTTCTGTTTAATTGC
          1 TTTCTGTTTAATTGC

                   
      21396 TTTCTGT
          1 TTTCTGT

      21403 CAACCTCTGT


Statistics
Matches: 22,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  15   17  0.77
  16    5  0.23

ACGTcount: A:0.13, C:0.13, G:0.13, T:0.61


Consensus pattern (15 bp):   
TTTCTGTTTAATTGC
Done.