Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010044.1 Corchorus capsularis cultivar CVL-1 contig10065, 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: 20514
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32


Found at i:1000 original size:3 final size:3

Alignment explanation


    Indices: 992--1017  Score: 52
    Period size: 3  Copynumber: 8.7  Consensus size: 3

        982 CTCGAACAGA

                                              
        992 TCT TCT TCT TCT TCT TCT TCT TCT TC
          1 TCT TCT TCT TCT TCT TCT TCT TCT TC

       1018 CATTTCTGCA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   23  1.00

ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65


Consensus pattern (3 bp):   
TCT

Found at i:4698 original size:94 final size:93

Alignment explanation


    Indices: 4588--4764  Score: 250
    Period size: 94  Copynumber: 1.9  Consensus size: 93

       4578 AAAACAATTA

                       *       *                                             
       4588 ACTAGTTTGATTATGAATCGAGTGTAATATTCAAACCAA-AGAACCATAAAGAA-CAATATAAGC
          1 ACTAGTTTGATCATGAATCAAGTGTAATATTCAAACCAATAG-ACCATAAAGAAGCAA-AT-AGC

                 *                         
       4651 CAATTTTGATTCATGCAAACATGTAATATTG
         63 CAATTCTGATTCATGCAAACATGTAATATTG

                              *               *        *          *          
       4682 ACTAGTTTGATCATGAATTAAGTGTAATATTCAAGCCAATAGATCATAAAGAAGGAAATAGCCAA
          1 ACTAGTTTGATCATGAATCAAGTGTAATATTCAAACCAATAGACCATAAAGAAGCAAATAGCCAA

                              
       4747 TTCTGATTCATGCAAACA
         66 TTCTGATTCATGCAAACA

       4765 AGTCCATATT


Statistics
Matches: 74,  Mismatches: 7, Indels: 5
        0.86            0.08        0.06

Matches are distributed among these distances:
  93   23  0.31
  94   47  0.64
  95    4  0.05

ACGTcount: A:0.42, C:0.14, G:0.15, T:0.29


Consensus pattern (93 bp):   
ACTAGTTTGATCATGAATCAAGTGTAATATTCAAACCAATAGACCATAAAGAAGCAAATAGCCAA
TTCTGATTCATGCAAACATGTAATATTG

Found at i:7629 original size:21 final size:19

Alignment explanation


    Indices: 7573--7629  Score: 60
    Period size: 21  Copynumber: 2.8  Consensus size: 19

       7563 GATTTTTCAT

                               
       7573 TATATATTATTGTTTTTGG
          1 TATATATTATTGTTTTTGG

               *        *         
       7592 TAAGATATCTATAGTTTTTCGG
          1 T-ATATAT-TATTGTTTTT-GG

                            
       7614 TATATATTAATTGTTT
          1 TATATATT-ATTGTTT

       7630 CTTACAAGAC


Statistics
Matches: 30,  Mismatches: 4, Indels: 6
        0.75            0.10        0.15

Matches are distributed among these distances:
  19    1  0.03
  20    6  0.20
  21   20  0.67
  22    3  0.10

ACGTcount: A:0.26, C:0.04, G:0.14, T:0.56


Consensus pattern (19 bp):   
TATATATTATTGTTTTTGG

Found at i:8452 original size:28 final size:28

Alignment explanation


    Indices: 8392--8449  Score: 71
    Period size: 28  Copynumber: 2.0  Consensus size: 28

       8382 TTTGTAGCAA

                  *         *    *      
       8392 TTGGACGTTTTGCCCTTAAATTTCAATT
          1 TTGGACATTTTGCCCTGAAATCTCAATT

                                *        
       8420 TTGGACATTTTGCCCATGAACTCTCAATT
          1 TTGGACATTTTGCCC-TGAAATCTCAATT

             
       8449 T
          1 T

       8450 GGAGCCCCGT


Statistics
Matches: 25,  Mismatches: 4, Indels: 1
        0.83            0.13        0.03

Matches are distributed among these distances:
  28   14  0.56
  29   11  0.44

ACGTcount: A:0.22, C:0.21, G:0.14, T:0.43


Consensus pattern (28 bp):   
TTGGACATTTTGCCCTGAAATCTCAATT

Found at i:15565 original size:146 final size:146

Alignment explanation


    Indices: 15183--15571  Score: 748
    Period size: 144  Copynumber: 2.7  Consensus size: 146

      15173 ACTTTAACGT

                        *                                                    
      15183 AACAAGCAACAAAGTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTGTCACGCGGGTGACCCGGG
          1 AACAAGCAACAATGTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTGTCACGCGGGTGACCCGGG

                                                                             
      15248 TTCGATCCCCGGCAACGGCGATTTTTTTTATCCCGTCACTCTGGACATTTAATGCATCGATAAGA
         66 TTCGATCCCCGGCAACGGCGATTTTTTTTATCCCGTCACTCTGGACATTTAATGCATCGATAAGA

                            
      15313 AAGTTTCTTTTAAAGA
        131 AAGTTTCTTTTAAAGA

                                                                             
      15329 AACAAGCAACAATGTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTGTCACGCGGGTGACCCGGG
          1 AACAAGCAACAATGTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTGTCACGCGGGTGACCCGGG

                                                                             
      15394 TTCGATCCCCGGCAACGGCGA--TTTTTTATCCCGTCACTCTGGACATTTAATGCATCGATAAGA
         66 TTCGATCCCCGGCAACGGCGATTTTTTTTATCCCGTCACTCTGGACATTTAATGCATCGATAAGA

                            
      15457 AAGTTTCTTTTAAAGA
        131 AAGTTTCTTTTAAAGA

                                                                             
      15473 AACAAGCAACAATGTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTGTCACGCGGGTGACCCGGG
          1 AACAAGCAACAATGTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTGTCACGCGGGTGACCCGGG

                                               
      15538 TTCGATCCCCGGCAACGGCGATTTTTTTT-TCCCG
         66 TTCGATCCCCGGCAACGGCGATTTTTTTTATCCCG

      15572 ACATCTTGGA


Statistics
Matches: 240,  Mismatches: 1, Indels: 5
        0.98            0.00        0.02

Matches are distributed among these distances:
 144  144  0.60
 145    5  0.02
 146   91  0.38

ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28


Consensus pattern (146 bp):   
AACAAGCAACAATGTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTGTCACGCGGGTGACCCGGG
TTCGATCCCCGGCAACGGCGATTTTTTTTATCCCGTCACTCTGGACATTTAATGCATCGATAAGA
AAGTTTCTTTTAAAGA
Done.