Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023413.1 Corchorus olitorius cultivar O-4 contig23446, 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: 6732
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33


Found at i:634 original size:16 final size:16

Alignment explanation


    Indices: 613--643  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

        603 TCACTCTTTG

                            
        613 AAAAAAAAATAAAAAT
          1 AAAAAAAAATAAAAAT

                  *        
        629 AAAAAATAATAAAAA
          1 AAAAAAAAATAAAAA

        644 GGTTAGTAAC


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  16   14  1.00

ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13


Consensus pattern (16 bp):   
AAAAAAAAATAAAAAT

Found at i:3471 original size:64 final size:65

Alignment explanation


    Indices: 3352--3477  Score: 164
    Period size: 64  Copynumber: 2.0  Consensus size: 65

       3342 CACAAAAAAG

                         *    *                     **      ***              
       3352 AGAGAGAAAAAATGAAAAGGCTCGCTAAGTTGAAAATCCTTTAAAGAATGGCTTAGGCAAAAGTT
          1 AGAGAGAAAAAATAAAAAAGCTCGCTAAGTTGAAAATCCTGCAAAGAACAACTTAGGCAAAAGTT

                *                                         *               
       3417 AGAGCGAAAAAA-AAAAAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACAACTTAGGCAAAA
          1 AGAGAGAAAAAATAAAAAAGCTCGCTAAGTTGAAAATCCTGCAAAGAACAACTTAGGCAAAA

       3478 CTTATAGCAC


Statistics
Matches: 52,  Mismatches: 9, Indels: 1
        0.84            0.15        0.02

Matches are distributed among these distances:
  64   41  0.79
  65   11  0.21

ACGTcount: A:0.48, C:0.13, G:0.21, T:0.17


Consensus pattern (65 bp):   
AGAGAGAAAAAATAAAAAAGCTCGCTAAGTTGAAAATCCTGCAAAGAACAACTTAGGCAAAAGTT

Found at i:4199 original size:16 final size:16

Alignment explanation


    Indices: 4178--4212  Score: 61
    Period size: 16  Copynumber: 2.2  Consensus size: 16

       4168 ACAATTCAGA

                            
       4178 AAGCAGAAAAGCTCTG
          1 AAGCAGAAAAGCTCTG

                         *  
       4194 AAGCAGAAAAGCTTTG
          1 AAGCAGAAAAGCTCTG

               
       4210 AAG
          1 AAG

       4213 TATTTTCAGT


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  16   18  1.00

ACGTcount: A:0.46, C:0.14, G:0.26, T:0.14


Consensus pattern (16 bp):   
AAGCAGAAAAGCTCTG

Found at i:4569 original size:41 final size:41

Alignment explanation


    Indices: 4307--4589  Score: 354
    Period size: 41  Copynumber: 6.9  Consensus size: 41

       4297 TTTTCGTTTG

                                    *                
       4307 TTCAAGATCAAGTCATCGAGACCCGTGAATTAAATTATCAA
          1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA

              *     **                               
       4348 TTTAAGATTGAGTCATCGAGACCCTTGAATTAAATTATCAA
          1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA

                    **            *                  
       4389 TTCAAGATTGAGTCATCGAGACACTTGAATTAAATTATCAA
          1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA

                    **    *                          
       4430 TTCAAGATTGAGTCTTCGAGACCCTTGAATTAAATTATCAA
          1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA

                   *      *                *        *   
       4471 TTCAAGAACAAGTCTTCGAGACCCTTGAATCGAATTATTAACAA
          1 TTCAAGATCAAGTCATCGAGACCCTTGAAT-TAA--ATTATCAA

                          *  *                       
       4515 TTCAAGATCAAGTCGTCAAGACCCTTGAATTAAATTATCAA
          1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA

                   *                       *    
       4556 TTCAAGAACAAGTCATTC--GACCCTTGAATCAAAT
          1 TTCAAGATCAAGTCA-TCGAGACCCTTGAATTAAAT

       4590 CAAATCAAAC


Statistics
Matches: 217,  Mismatches: 21, Indels: 9
        0.88            0.09        0.04

Matches are distributed among these distances:
  40   15  0.07
  41  162  0.75
  42    4  0.02
  43    2  0.01
  44   34  0.16

ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30


Consensus pattern (41 bp):   
TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
Done.