Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010080.1 Corchorus olitorius cultivar O-4 contig10112, 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: 12545
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34


Found at i:1966 original size:46 final size:47

Alignment explanation


    Indices: 1884--1977  Score: 154
    Period size: 46  Copynumber: 2.0  Consensus size: 47

       1874 TTAAATAACA

                                 *                           
       1884 TACTTAACAAACTATTGTCTATCAAACAAACAAATAAACGAAACTCACC
          1 TACTTAACAAACTA-T-TCTAACAAACAAACAAATAAACGAAACTCACC

                                                          
       1933 TACTTAACAAACTA-TCTAACAAACAAACAAATAAACGAAACTCAC
          1 TACTTAACAAACTATTCTAACAAACAAACAAATAAACGAAACTCAC

       1978 ATACCGTGAG


Statistics
Matches: 44,  Mismatches: 1, Indels: 3
        0.92            0.02        0.06

Matches are distributed among these distances:
  46   30  0.68
  49   14  0.32

ACGTcount: A:0.52, C:0.24, G:0.03, T:0.20


Consensus pattern (47 bp):   
TACTTAACAAACTATTCTAACAAACAAACAAATAAACGAAACTCACC

Found at i:4645 original size:3 final size:3

Alignment explanation


    Indices: 4631--4661  Score: 53
    Period size: 3  Copynumber: 10.3  Consensus size: 3

       4621 TTTGAGAGAT

                  *                                  
       4631 TAA TAT TAA TAA TAA TAA TAA TAA TAA TAA T
          1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T

       4662 TAACACTACT


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   3   26  1.00

ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39


Consensus pattern (3 bp):   
TAA

Found at i:7295 original size:2 final size:2

Alignment explanation


    Indices: 7288--7314  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

       7278 TAATAAGAAT

                                                    
       7288 TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA T

       7315 TGCCAAGGGA


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:8141 original size:16 final size:16

Alignment explanation


    Indices: 8120--8150  Score: 62
    Period size: 16  Copynumber: 1.9  Consensus size: 16

       8110 CACCGTTAAA

                            
       8120 GTAATGGATAAAAATT
          1 GTAATGGATAAAAATT

                           
       8136 GTAATGGATAAAAAT
          1 GTAATGGATAAAAAT

       8151 CCTCTCCCCC


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

Matches are distributed among these distances:
  16   15  1.00

ACGTcount: A:0.52, C:0.00, G:0.19, T:0.29


Consensus pattern (16 bp):   
GTAATGGATAAAAATT

Found at i:9980 original size:12 final size:13

Alignment explanation


    Indices: 9959--9996  Score: 60
    Period size: 12  Copynumber: 3.0  Consensus size: 13

       9949 TTATATATAG

                         
       9959 TAATATTAATAAT
          1 TAATATTAATAAT

                         
       9972 TAA-ATTAATAAT
          1 TAATATTAATAAT

                 *       
       9984 TAATAATAATAAT
          1 TAATATTAATAAT

       9997 CCAATGAGCC


Statistics
Matches: 23,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  12   12  0.52
  13   11  0.48

ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42


Consensus pattern (13 bp):   
TAATATTAATAAT
Done.