Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015364.1 Corchorus olitorius cultivar O-4 contig15397, 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: 18124
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.32


Found at i:7709 original size:16 final size:15

Alignment explanation


    Indices: 7670--7725  Score: 51
    Period size: 16  Copynumber: 3.5  Consensus size: 15

       7660 TCAACATCCG

                           
       7670 AACCCGAAAATACCC
          1 AACCCGAAAATACCC

                *     *     
       7685 AAGCTCGAAATTACCC
          1 AA-CCCGAAAATACCC

                             
       7701 TAACCCGAAACA-ACCC
          1 -AACCCGAAA-ATACCC

                     
       7717 AAGCCCGAA
          1 AA-CCCGAA

       7726 TCCGACTTGA


Statistics
Matches: 33,  Mismatches: 4, Indels: 7
        0.75            0.09        0.16

Matches are distributed among these distances:
  15    4  0.12
  16   27  0.82
  17    2  0.06

ACGTcount: A:0.43, C:0.38, G:0.11, T:0.09


Consensus pattern (15 bp):   
AACCCGAAAATACCC

Found at i:8642 original size:31 final size:31

Alignment explanation


    Indices: 8571--8642  Score: 74
    Period size: 31  Copynumber: 2.3  Consensus size: 31

       8561 ATCTATCAGC

                                      *    
       8571 TTTTAATTTGTTCAATTTAAGGCTTGCATTT
          1 TTTTAATTTGTTCAATTTAAGGCTTGAATTT

             ** *       *       *          
       8602 TAATGATTTGTTTAATTTAATGCTT-AATTT
          1 TTTTAATTTGTTCAATTTAAGGCTTGAATTT

                       
       8632 GTTTTAATTTG
          1 -TTTTAATTTG

       8643 CAATAATATA


Statistics
Matches: 31,  Mismatches: 9, Indels: 2
        0.74            0.21        0.05

Matches are distributed among these distances:
  30    4  0.13
  31   27  0.87

ACGTcount: A:0.25, C:0.06, G:0.12, T:0.57


Consensus pattern (31 bp):   
TTTTAATTTGTTCAATTTAAGGCTTGAATTT

Found at i:8929 original size:5 final size:5

Alignment explanation


    Indices: 8897--8950  Score: 58
    Period size: 5  Copynumber: 10.8  Consensus size: 5

       8887 TATTCAATCT

                               *         *                               
       8897 TTATA -TATA TTGATA ATA-A TTATG TTATA TTATA TTATTA TTATA TTATA
          1 TTATA TTATA TT-ATA TTATA TTATA TTATA TTATA TTA-TA TTATA TTATA

                
       8947 TTAT
          1 TTAT

       8951 CAATAAACTT


Statistics
Matches: 41,  Mismatches: 4, Indels: 8
        0.77            0.08        0.15

Matches are distributed among these distances:
   4    7  0.17
   5   25  0.61
   6    9  0.22

ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57


Consensus pattern (5 bp):   
TTATA

Found at i:13274 original size:16 final size:17

Alignment explanation


    Indices: 13240--13276  Score: 58
    Period size: 17  Copynumber: 2.2  Consensus size: 17

      13230 GAAATAAATA

                             
      13240 TTAAATATTTTTAATTT
          1 TTAAATATTTTTAATTT

                              
      13257 TTAATATATTTTT-ATTT
          1 TTAA-ATATTTTTAATTT

               
      13274 TTA
          1 TTA

      13277 TTAAAAAATT


Statistics
Matches: 19,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  17   11  0.58
  18    8  0.42

ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68


Consensus pattern (17 bp):   
TTAAATATTTTTAATTT
Done.