Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015195.1 Corchorus capsularis cultivar CVL-1 contig15216, 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: 10604
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30


Found at i:1098 original size:41 final size:41

Alignment explanation


    Indices: 1036--1119  Score: 141
    Period size: 41  Copynumber: 2.0  Consensus size: 41

       1026 CTAAAAGAAT

                            *             *          
       1036 TTGGTCAGATATGTAATAATTTAATAACCATAGATAGGAAA
          1 TTGGTCAGATATGTAAGAATTTAATAACCAGAGATAGGAAA

                                   *                 
       1077 TTGGTCAGATATGTAAGAATTTAGTAACCAGAGATAGGAAA
          1 TTGGTCAGATATGTAAGAATTTAATAACCAGAGATAGGAAA

              
       1118 TT
          1 TT

       1120 CATTGGTTAG


Statistics
Matches: 40,  Mismatches: 3, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  41   40  1.00

ACGTcount: A:0.42, C:0.07, G:0.20, T:0.31


Consensus pattern (41 bp):   
TTGGTCAGATATGTAAGAATTTAATAACCAGAGATAGGAAA

Found at i:7561 original size:4 final size:4

Alignment explanation


    Indices: 7541--7576  Score: 51
    Period size: 4  Copynumber: 9.8  Consensus size: 4

       7531 AAAGATGAGA

                                                            
       7541 AAAG AAA- AAA- AAA- AAAG AAAG AAAG AAAG AAAG AAA
          1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA

       7577 TCAAGCATAT


Statistics
Matches: 31,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   3    9  0.29
   4   22  0.71

ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00


Consensus pattern (4 bp):   
AAAG

Found at i:10477 original size:25 final size:24

Alignment explanation


    Indices: 10442--10499  Score: 82
    Period size: 25  Copynumber: 2.4  Consensus size: 24

      10432 TTCAAACCCT

                               *     
      10442 AAACTTCATTTCTAACAACTTCTTC
          1 AAACTTCATTTCTAACAA-ATCTTC

                  *                 
      10467 AAACTTTATTTCTAACAAATCTTC
          1 AAACTTCATTTCTAACAAATCTTC

                      
      10491 AAA-TTCATT
          1 AAACTTCATT

      10500 ATCCTTCATT


Statistics
Matches: 30,  Mismatches: 3, Indels: 2
        0.86            0.09        0.06

Matches are distributed among these distances:
  23    5  0.17
  24    8  0.27
  25   17  0.57

ACGTcount: A:0.36, C:0.22, G:0.00, T:0.41


Consensus pattern (24 bp):   
AAACTTCATTTCTAACAAATCTTC

Found at i:10539 original size:26 final size:26

Alignment explanation


    Indices: 10510--10577  Score: 109
    Period size: 26  Copynumber: 2.6  Consensus size: 26

      10500 ATCCTTCATT

                                      
      10510 TTAATCATAAACTAATTAAATACTAA
          1 TTAATCATAAACTAATTAAATACTAA

                 *            *       
      10536 TTAATAATAAACTAATTAGATACTAA
          1 TTAATCATAAACTAATTAAATACTAA

                *           
      10562 TTAAACATAAACTAAT
          1 TTAATCATAAACTAAT

      10578 AAACTAAGTA


Statistics
Matches: 38,  Mismatches: 4, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  26   38  1.00

ACGTcount: A:0.54, C:0.10, G:0.01, T:0.34


Consensus pattern (26 bp):   
TTAATCATAAACTAATTAAATACTAA
Done.