Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000809.1 Corchorus olitorius cultivar O-4 contig00809, 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: 7391
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35


Found at i:2268 original size:14 final size:15

Alignment explanation


    Indices: 2235--2273  Score: 53
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       2225 ATTCTTTGTT

                   *       
       2235 TTTTCTTCTTTTTCA
          1 TTTTCTTTTTTTTCA

            *              
       2250 ATTTCTTTTTTTTC-
          1 TTTTCTTTTTTTTCA

                      
       2264 TTTTCTTTTT
          1 TTTTCTTTTT

       2274 GGGTAATAAT


Statistics
Matches: 21,  Mismatches: 3, Indels: 1
        0.84            0.12        0.04

Matches are distributed among these distances:
  14    9  0.43
  15   12  0.57

ACGTcount: A:0.05, C:0.15, G:0.00, T:0.79


Consensus pattern (15 bp):   
TTTTCTTTTTTTTCA

Found at i:2552 original size:27 final size:28

Alignment explanation


    Indices: 2498--2553  Score: 69
    Period size: 30  Copynumber: 2.0  Consensus size: 28

       2488 TCTAAATTGA

                               *          
       2498 TATTATTAAAATATACTTTTATTATGCCAT
          1 TATTATTAAAATATA--TTAATTATGCCAT

                                 *     
       2528 TATTATTAAAATATA-TAATTTTGCCA
          1 TATTATTAAAATATATTAATTATGCCA

       2554 ACATGTTTCA


Statistics
Matches: 24,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  27    9  0.38
  30   15  0.62

ACGTcount: A:0.39, C:0.09, G:0.04, T:0.48


Consensus pattern (28 bp):   
TATTATTAAAATATATTAATTATGCCAT

Found at i:3473 original size:2 final size:2

Alignment explanation


    Indices: 3466--3498  Score: 66
    Period size: 2  Copynumber: 16.5  Consensus size: 2

       3456 TACTTATGAA

                                                             
       3466 AT 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 AT A

       3499 GCTTCGTTCA


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   31  1.00

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


Consensus pattern (2 bp):   
AT

Done.