Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017253.1 Corchorus olitorius cultivar O-4 contig17286, 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: 5662
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32


Found at i:4112 original size:49 final size:47

Alignment explanation


    Indices: 4037--4177  Score: 171
    Period size: 49  Copynumber: 2.9  Consensus size: 47

       4027 AAAGCAATCA

                                                             
       4037 TTTACTTTTTAC-TGCACTTTTTCTCAATTTTTACTACAAAATTGAACT
          1 TTTA-TTTTTACTTGCACTTTTTCTCAATTTTTA-TACAAAATTGAACT

                            *                  *          *  
       4085 TTTATTTTTACTTGCTTCTTTTTCTCAATTTTTAAGACAAAATTGATCT
          1 TTTATTTTTACTTGC-ACTTTTTCTCAATTTTT-ATACAAAATTGAACT

                                   *                      
       4134 TTTAATTTTTA-TTGCACTTTTTATCAATTTTT-TGACAAAATTGA
          1 TTT-ATTTTTACTTGCACTTTTTCTCAATTTTTAT-ACAAAATTGA

       4178 TTGGCACGCT


Statistics
Matches: 82,  Mismatches: 6, Indels: 11
        0.83            0.06        0.11

Matches are distributed among these distances:
  47   17  0.21
  48   22  0.27
  49   35  0.43
  50    8  0.10

ACGTcount: A:0.27, C:0.14, G:0.06, T:0.53


Consensus pattern (47 bp):   
TTTATTTTTACTTGCACTTTTTCTCAATTTTTATACAAAATTGAACT

Found at i:4466 original size:25 final size:26

Alignment explanation


    Indices: 4410--4473  Score: 80
    Period size: 25  Copynumber: 2.5  Consensus size: 26

       4400 ATTTGTAAAT

                                      
       4410 AAAATTTGAAAATTTATCTTTCAAAA
          1 AAAATTTGAAAATTTATCTTTCAAAA

                                 *    
       4436 AAAA-TTGAAAATTTA-C-TTGAAAA
          1 AAAATTTGAAAATTTATCTTTCAAAA

                           
       4459 GAATAATTTGAAAAT
          1 -AA-AATTTGAAAAT

       4474 AATTTTTGTT


Statistics
Matches: 34,  Mismatches: 1, Indels: 6
        0.83            0.02        0.15

Matches are distributed among these distances:
  23    6  0.18
  24    3  0.09
  25   13  0.38
  26   12  0.35

ACGTcount: A:0.53, C:0.05, G:0.08, T:0.34


Consensus pattern (26 bp):   
AAAATTTGAAAATTTATCTTTCAAAA

Found at i:4779 original size:4 final size:4

Alignment explanation


    Indices: 4770--4803  Score: 68
    Period size: 4  Copynumber: 8.5  Consensus size: 4

       4760 ACTTTCGACT

                                                      
       4770 TACA TACA TACA TACA TACA TACA TACA TACA TA
          1 TACA TACA TACA TACA TACA TACA TACA TACA TA

       4804 TATATATATA


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   30  1.00

ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26


Consensus pattern (4 bp):   
TACA

Found at i:4808 original size:2 final size:2

Alignment explanation


    Indices: 4801--4847  Score: 85
    Period size: 2  Copynumber: 23.5  Consensus size: 2

       4791 ACATACATAC

                                          *                               
       4801 AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                   
       4843 AT AT A
          1 AT AT A

       4848 ATCATGTGCT


Statistics
Matches: 43,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
   2   43  1.00

ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49


Consensus pattern (2 bp):   
AT

Done.