Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013933.1 Corchorus olitorius cultivar O-4 contig13966, 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: 14335
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32


Found at i:574 original size:34 final size:34

Alignment explanation


    Indices: 536--631  Score: 129
    Period size: 34  Copynumber: 2.8  Consensus size: 34

        526 AAAAATTGAA

                             **               
        536 TGGGAACTTTCCCAATTTGAAAACTTAAAACCGG
          1 TGGGAACTTTCCCAATTACAAAACTTAAAACCGG

                         *                 *  
        570 TGGGAACTTTCCCGATTACAAAACTTAAAACTGG
          1 TGGGAACTTTCCCAATTACAAAACTTAAAACCGG

                      *     * *         
        604 TGGGAACTTTACCAATAAAAAAACTTAA
          1 TGGGAACTTTCCCAATTACAAAACTTAA

        632 TGATATTCTC


Statistics
Matches: 54,  Mismatches: 8, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  34   54  1.00

ACGTcount: A:0.40, C:0.19, G:0.16, T:0.26


Consensus pattern (34 bp):   
TGGGAACTTTCCCAATTACAAAACTTAAAACCGG

Found at i:4324 original size:13 final size:15

Alignment explanation


    Indices: 4306--4337  Score: 50
    Period size: 13  Copynumber: 2.3  Consensus size: 15

       4296 GACCCAAAAG

                           
       4306 AAAAGAAA-AA-GAA
          1 AAAAGAAAGAAGGAA

                           
       4319 AAAAGAAAGAAGGAA
          1 AAAAGAAAGAAGGAA

                
       4334 AAAA
          1 AAAA

       4338 AGGGAGAAGA


Statistics
Matches: 17,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  13    8  0.47
  14    2  0.12
  15    7  0.41

ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00


Consensus pattern (15 bp):   
AAAAGAAAGAAGGAA

Found at i:4438 original size:46 final size:45

Alignment explanation


    Indices: 4378--4493  Score: 144
    Period size: 46  Copynumber: 2.5  Consensus size: 45

       4368 ACATTTTGAG

                                                          
       4378 AAACTAATAAGGAAATGGGTCTTTAAAAAAGAAATGGACTTTGAAT
          1 AAACTAATAAGGAAATGGG-CTTTAAAAAAGAAATGGACTTTGAAT

             *                    *     ** *              
       4424 -TACTAAATAAGGAAATGGGCTCTAAAATGGTAATGGACTTTGAAT
          1 AAACT-AATAAGGAAATGGGCTTTAAAAAAGAAATGGACTTTGAAT

                     *               
       4469 GAAACTAATGAGGAAATGGGCTTTA
          1 -AAACTAATAAGGAAATGGGCTTTA

       4494 CTAATCTAAC


Statistics
Matches: 59,  Mismatches: 8, Indels: 6
        0.81            0.11        0.08

Matches are distributed among these distances:
  45   25  0.42
  46   31  0.53
  47    3  0.05

ACGTcount: A:0.43, C:0.08, G:0.22, T:0.27


Consensus pattern (45 bp):   
AAACTAATAAGGAAATGGGCTTTAAAAAAGAAATGGACTTTGAAT

Found at i:4982 original size:22 final size:22

Alignment explanation


    Indices: 4957--5006  Score: 66
    Period size: 22  Copynumber: 2.3  Consensus size: 22

       4947 AAAGCCAAGG

                              *    
       4957 GCTTGAGAT-TTGAAAGCGCGGA
          1 GCTTGA-ATGTTGAAAGCACGGA

                  *               
       4979 GCTTGATTGTTGAAAGCACGGA
          1 GCTTGAATGTTGAAAGCACGGA

                  
       5001 GCTTGA
          1 GCTTGA

       5007 TTTGATTTGC


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

Matches are distributed among these distances:
  21    1  0.04
  22   24  0.96

ACGTcount: A:0.26, C:0.14, G:0.34, T:0.26


Consensus pattern (22 bp):   
GCTTGAATGTTGAAAGCACGGA

Found at i:5007 original size:22 final size:22

Alignment explanation


    Indices: 4966--5008  Score: 77
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       4956 GGCTTGAGAT

                    *             
       4966 TTGAAAGCGCGGAGCTTGATTG
          1 TTGAAAGCACGGAGCTTGATTG

                                 
       4988 TTGAAAGCACGGAGCTTGATT
          1 TTGAAAGCACGGAGCTTGATT

       5009 TGATTTGCGC


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  22   20  1.00

ACGTcount: A:0.26, C:0.14, G:0.33, T:0.28


Consensus pattern (22 bp):   
TTGAAAGCACGGAGCTTGATTG

Found at i:13457 original size:7 final size:7

Alignment explanation


    Indices: 13445--13473  Score: 58
    Period size: 7  Copynumber: 4.1  Consensus size: 7

      13435 TTTGTCTCCA

                   
      13445 TCAATAT
          1 TCAATAT

                   
      13452 TCAATAT
          1 TCAATAT

                   
      13459 TCAATAT
          1 TCAATAT

                   
      13466 TCAATAT
          1 TCAATAT

             
      13473 T
          1 T

      13474 TGACTTTTTT


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   22  1.00

ACGTcount: A:0.41, C:0.14, G:0.00, T:0.45


Consensus pattern (7 bp):   
TCAATAT

Found at i:13608 original size:6 final size:6

Alignment explanation


    Indices: 13599--13635  Score: 74
    Period size: 6  Copynumber: 6.2  Consensus size: 6

      13589 TCCCCCGGCC

                                                       
      13599 CCGTAG CCGTAG CCGTAG CCGTAG CCGTAG CCGTAG C
          1 CCGTAG CCGTAG CCGTAG CCGTAG CCGTAG CCGTAG C

      13636 GCAAGTTGAG


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   31  1.00

ACGTcount: A:0.16, C:0.35, G:0.32, T:0.16


Consensus pattern (6 bp):   
CCGTAG

Done.