Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011345.1 Corchorus capsularis cultivar CVL-1 contig11366, 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: 8098
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.40


Found at i:135 original size:15 final size:15

Alignment explanation


    Indices: 115--143  Score: 58
    Period size: 15  Copynumber: 1.9  Consensus size: 15

        105 TTATTCCAAA

                           
        115 TTTTATTCTCTTATT
          1 TTTTATTCTCTTATT

                          
        130 TTTTATTCTCTTAT
          1 TTTTATTCTCTTAT

        144 CCAAATTTGA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.14, C:0.14, G:0.00, T:0.72


Consensus pattern (15 bp):   
TTTTATTCTCTTATT

Found at i:164 original size:19 final size:19

Alignment explanation


    Indices: 140--179  Score: 71
    Period size: 19  Copynumber: 2.1  Consensus size: 19

        130 TTTTATTCTC

                               
        140 TTATCCAAATTTGATTTTA
          1 TTATCCAAATTTGATTTTA

                         *     
        159 TTATCCAAATTTGCTTTTA
          1 TTATCCAAATTTGATTTTA

              
        178 TT
          1 TT

        180 CATTTCAAAG


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  19   20  1.00

ACGTcount: A:0.28, C:0.12, G:0.05, T:0.55


Consensus pattern (19 bp):   
TTATCCAAATTTGATTTTA

Found at i:4319 original size:11 final size:11

Alignment explanation


    Indices: 4303--4329  Score: 54
    Period size: 11  Copynumber: 2.5  Consensus size: 11

       4293 GTAACTTATA

                       
       4303 AACTAAGAAAG
          1 AACTAAGAAAG

                       
       4314 AACTAAGAAAG
          1 AACTAAGAAAG

                 
       4325 AACTA
          1 AACTA

       4330 TATATATATA


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   16  1.00

ACGTcount: A:0.63, C:0.11, G:0.15, T:0.11


Consensus pattern (11 bp):   
AACTAAGAAAG

Found at i:4545 original size:79 final size:78

Alignment explanation


    Indices: 4404--4557  Score: 206
    Period size: 79  Copynumber: 2.0  Consensus size: 78

       4394 TTCAGGTAAG

                                                      * *                    
       4404 TTTCTCTTTTTTTTCCTATTGTTTTTGCTTGCTCTCTGTCTGGTTCATAAATTTCTCATTTTTTC
          1 TTTCTCTTTTTTTTCCTATTGTTTTTGCTTGCTCTCTGTCTGATCCATAAATTTCTCATTTTTTC

                         
       4469 CCTAATTCATAAA
         66 CCTAATTCATAAA

                                                *               *            
       4482 TTTCTCTTTTTTTTTCCTATCT-TTTTTGCTTGCTTTTCTGT-TCGATCCATGAATTTCTC-TTT
          1 TTTCTC-TTTTTTTTCCTAT-TGTTTTTGCTTGC-TCTCTGTCT-GATCCATAAATTTCTCATTT

               *          
       4544 TTTTCCTAATTCAT
         62 TTTCCCTAATTCAT

       4558 GTTTTTTTTA


Statistics
Matches: 67,  Mismatches: 5, Indels: 7
        0.85            0.06        0.09

Matches are distributed among these distances:
  78    6  0.09
  79   41  0.61
  80   20  0.30

ACGTcount: A:0.13, C:0.21, G:0.07, T:0.59


Consensus pattern (78 bp):   
TTTCTCTTTTTTTTCCTATTGTTTTTGCTTGCTCTCTGTCTGATCCATAAATTTCTCATTTTTTC
CCTAATTCATAAA
Done.