Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020228.1 Corchorus olitorius cultivar O-4 contig20261, 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: 9107
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35


Found at i:317 original size:32 final size:32

Alignment explanation


    Indices: 250--344  Score: 160
    Period size: 31  Copynumber: 3.1  Consensus size: 32

        240 ACTAAATACT

                        *                   
        250 AAAAAAATCCCTAATGTTTTTCTTTTGGGAC-
          1 AAAAAAATCCCTTATGTTTTTCTTTTGGGACA

                                            
        281 AAAAAAATCCCTTATGTTTTTCTTTTGGGACA
          1 AAAAAAATCCCTTATGTTTTTCTTTTGGGACA

                                            
        313 AAAAAAATCCCTTATG-TTTT-TTTTGGGACA
          1 AAAAAAATCCCTTATGTTTTTCTTTTGGGACA

              
        343 AA
          1 AA

        345 TTAGTCTCTT


Statistics
Matches: 62,  Mismatches: 1, Indels: 3
        0.94            0.02        0.05

Matches are distributed among these distances:
  30   12  0.19
  31   34  0.55
  32   16  0.26

ACGTcount: A:0.34, C:0.15, G:0.13, T:0.39


Consensus pattern (32 bp):   
AAAAAAATCCCTTATGTTTTTCTTTTGGGACA

Found at i:2314 original size:18 final size:19

Alignment explanation


    Indices: 2280--2318  Score: 62
    Period size: 18  Copynumber: 2.1  Consensus size: 19

       2270 TGAAGATTGC

                               
       2280 TTGAAGATAATTTGAAGAA
          1 TTGAAGATAATTTGAAGAA

                    *          
       2299 TTGAAGATCA-TTGAAGAA
          1 TTGAAGATAATTTGAAGAA

              
       2317 TT
          1 TT

       2319 ATTTCAAGGA


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  18   10  0.53
  19    9  0.47

ACGTcount: A:0.44, C:0.03, G:0.21, T:0.33


Consensus pattern (19 bp):   
TTGAAGATAATTTGAAGAA

Found at i:5984 original size:2 final size:2

Alignment explanation


    Indices: 5977--6007  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

       5967 TTTTAATCTA

                                                          
       5977 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       6008 CTAGTTAAAG


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:8936 original size:36 final size:36

Alignment explanation


    Indices: 8889--8958  Score: 113
    Period size: 36  Copynumber: 1.9  Consensus size: 36

       8879 TTCAATAACC

                         *      *               
       8889 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
          1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA

                  *                           
       8925 TTACATTTTTTGTAATTTTGATTATCATATTTCT
          1 TTACATCTTTTGTAATTTTGATTATCATATTTCT

       8959 CCAAAATCTC


Statistics
Matches: 31,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  36   31  1.00

ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60


Consensus pattern (36 bp):   
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Done.