Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021657.1 Corchorus olitorius cultivar O-4 contig21690, 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: 11203
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32


Found at i:423 original size:15 final size:15

Alignment explanation


    Indices: 393--434  Score: 75
    Period size: 15  Copynumber: 2.7  Consensus size: 15

        383 TTACTTTGTT

                            
        393 TTGTTTTCTAGTTTAA
          1 TTGTTTTCT-GTTTAA

                           
        409 TTGTTTTCTGTTTAA
          1 TTGTTTTCTGTTTAA

                       
        424 TTGTTTTCTGT
          1 TTGTTTTCTGT

        435 CAACCTCTGT


Statistics
Matches: 26,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  15   17  0.65
  16    9  0.35

ACGTcount: A:0.12, C:0.07, G:0.14, T:0.67


Consensus pattern (15 bp):   
TTGTTTTCTGTTTAA

Found at i:7080 original size:49 final size:47

Alignment explanation


    Indices: 7002--7142  Score: 162
    Period size: 49  Copynumber: 2.9  Consensus size: 47

       6992 AAAGCAATCC

                                     *                       
       7002 TTTACTTTTTAC-TGCACTTTTTCTTAATTTTTACTACAAAATTGAACT
          1 TTTA-TTTTTACTTGCACTTTTTCTCAATTTTTA-TACAAAATTGAACT

                                               *          *  
       7050 TTTATTTTTACTTGCATCTTTTTCTCAATTTTTAAGACAAAATTGATCT
          1 TTTATTTTTACTTGCA-CTTTTTCTCAATTTTT-ATACAAAATTGAACT

                *                  *                      
       7099 TTTAATTTT-CATTGCACTTTTTATCAATTTTT-TGACAAAATTGA
          1 TTTATTTTTAC-TTGCACTTTTTCTCAATTTTTAT-ACAAAATTGA

       7143 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   24  0.29
  49   40  0.49
  50    1  0.01

ACGTcount: A:0.28, C:0.14, G:0.06, T:0.52


Consensus pattern (47 bp):   
TTTATTTTTACTTGCACTTTTTCTCAATTTTTATACAAAATTGAACT

Found at i:10249 original size:11 final size:11

Alignment explanation


    Indices: 10233--10258  Score: 52
    Period size: 11  Copynumber: 2.4  Consensus size: 11

      10223 AGATAATTTC

                       
      10233 TTTTCTTCTAG
          1 TTTTCTTCTAG

                       
      10244 TTTTCTTCTAG
          1 TTTTCTTCTAG

                
      10255 TTTT
          1 TTTT

      10259 TAGGCAAAGG


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   15  1.00

ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69


Consensus pattern (11 bp):   
TTTTCTTCTAG

Found at i:11031 original size:15 final size:16

Alignment explanation


    Indices: 11001--11040  Score: 55
    Period size: 15  Copynumber: 2.6  Consensus size: 16

      10991 TTACTCTGCT

                            
      11001 TTGTTTTCTAGTTTAA
          1 TTGTTTTCTAGTTTAA

                     *      
      11017 TTGTTTT-TTGTTTAA
          1 TTGTTTTCTAGTTTAA

               *     
      11032 TTGCTTTCT
          1 TTGTTTTCT

      11041 GTCAATCTCT


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  15   13  0.62
  16    8  0.38

ACGTcount: A:0.12, C:0.07, G:0.12, T:0.68


Consensus pattern (16 bp):   
TTGTTTTCTAGTTTAA
Done.