Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023915.1 Corchorus olitorius cultivar O-4 contig23948, 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: 42552
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33


Found at i:11521 original size:22 final size:21

Alignment explanation


    Indices: 11496--11549  Score: 60
    Period size: 19  Copynumber: 2.6  Consensus size: 21

      11486 GAAGTTCGTG

                                  
      11496 TTTGAAGACTTATTGAAGATAA
          1 TTTGAAGA-TTATTGAAGATAA

                               * 
      11518 TTTGAAGA-T-TTGAAGATCA
          1 TTTGAAGATTATTGAAGATAA

                          
      11537 -TTGAAGAATTATT
          1 TTTGAAG-ATTATT

      11550 TCGAGAAGTA


Statistics
Matches: 28,  Mismatches: 1, Indels: 7
        0.78            0.03        0.19

Matches are distributed among these distances:
  18    6  0.21
  19   10  0.36
  20    2  0.07
  21    2  0.07
  22    8  0.29

ACGTcount: A:0.39, C:0.04, G:0.19, T:0.39


Consensus pattern (21 bp):   
TTTGAAGATTATTGAAGATAA

Found at i:25196 original size:21 final size:21

Alignment explanation


    Indices: 25172--25214  Score: 77
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      25162 ATAAGAATAT

                  *              
      25172 TCCAAAGGAAGATTTTGGAAA
          1 TCCAAAAGAAGATTTTGGAAA

                                 
      25193 TCCAAAAGAAGATTTTGGAAA
          1 TCCAAAAGAAGATTTTGGAAA

             
      25214 T
          1 T

      25215 TAATAAAATT


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   21  1.00

ACGTcount: A:0.44, C:0.09, G:0.21, T:0.26


Consensus pattern (21 bp):   
TCCAAAAGAAGATTTTGGAAA

Found at i:37638 original size:115 final size:115

Alignment explanation


    Indices: 37436--37667  Score: 437
    Period size: 115  Copynumber: 2.0  Consensus size: 115

      37426 CATCCTTGCG

                                                     *                       
      37436 TTGTCGAAAACTTGTAATCCTTTGTCTCCCCTTTGAAATTTTCTCTCTTGTCATGGTTGAAGATG
          1 TTGTCGAAAACTTGTAATCCTTTGTCTCCCCTTTGAAATTTGCTCTCTTGTCATGGTTGAAGATG

               *                                              
      37501 TTTTACCTAACTCTTTCTTTACCCACTTTTGCACTTCACAAACAAAATCA
         66 TTTCACCTAACTCTTTCTTTACCCACTTTTGCACTTCACAAACAAAATCA

                                                                             
      37551 TTGTCGAAAACTTGTAATCCTTTGTCTCCCCTTTGAAATTTGCTCTCTTGTCATGGTTGAAGATG
          1 TTGTCGAAAACTTGTAATCCTTTGTCTCCCCTTTGAAATTTGCTCTCTTGTCATGGTTGAAGATG

                            *                                 
      37616 TTTCACCTAACTCTTTGTTTACCCACTTTTGCACTTCACAAACAAAATCA
         66 TTTCACCTAACTCTTTCTTTACCCACTTTTGCACTTCACAAACAAAATCA

              
      37666 TT
          1 TT

      37668 AGTCTTCAAA


Statistics
Matches: 114,  Mismatches: 3, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
 115  114  1.00

ACGTcount: A:0.24, C:0.24, G:0.11, T:0.41


Consensus pattern (115 bp):   
TTGTCGAAAACTTGTAATCCTTTGTCTCCCCTTTGAAATTTGCTCTCTTGTCATGGTTGAAGATG
TTTCACCTAACTCTTTCTTTACCCACTTTTGCACTTCACAAACAAAATCA

Found at i:42486 original size:52 final size:52

Alignment explanation


    Indices: 42337--42486  Score: 239
    Period size: 53  Copynumber: 2.9  Consensus size: 52

      42327 ACCTGATGGA

                                             *                  
      42337 AACTTTCCCAATTTG-AAAAGAGTTAAATTGAACACTTTGAAAACTGGTGGG
          1 AACTTTCCCAATTTGAAAAAGAGTTAAATTGAATACTTTGAAAACTGGTGGG

                                          *                      
      42388 AACTTTCCCAATTTGAAAAAAGAGTTAAATCGAATACTTTGAAAACTGGTGGG
          1 AACTTTCCCAATTTG-AAAAAGAGTTAAATTGAATACTTTGAAAACTGGTGGG

                       *           *                *     
      42441 AACTTTCCCAAATTGAAAAAGAGCTAAATTGAATACTTTGGAAACT
          1 AACTTTCCCAATTTGAAAAAGAGTTAAATTGAATACTTTGAAAACT

      42487 TATATGAAAT


Statistics
Matches: 91,  Mismatches: 6, Indels: 3
        0.91            0.06        0.03

Matches are distributed among these distances:
  51   15  0.16
  52   28  0.31
  53   48  0.53

ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29


Consensus pattern (52 bp):   
AACTTTCCCAATTTGAAAAAGAGTTAAATTGAATACTTTGAAAACTGGTGGG
Done.