Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014705.1 Corchorus capsularis cultivar CVL-1 contig14726, 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: 7509
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34


Found at i:259 original size:20 final size:19

Alignment explanation


    Indices: 228--265  Score: 58
    Period size: 20  Copynumber: 1.9  Consensus size: 19

        218 ATAATCCCTC

                               
        228 AAAAAAATTAAAGAAAATA
          1 AAAAAAATTAAAGAAAATA

                         *     
        247 AAAAAAATATAAATAAAAT
          1 AAAAAAAT-TAAAGAAAAT

        266 TGTGATGCTT


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  19    8  0.47
  20    9  0.53

ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18


Consensus pattern (19 bp):   
AAAAAAATTAAAGAAAATA

Found at i:2313 original size:13 final size:13

Alignment explanation


    Indices: 2295--2322  Score: 56
    Period size: 13  Copynumber: 2.2  Consensus size: 13

       2285 TTTATGTACC

                         
       2295 TTTTGAAACTTTA
          1 TTTTGAAACTTTA

                         
       2308 TTTTGAAACTTTA
          1 TTTTGAAACTTTA

              
       2321 TT
          1 TT

       2323 AGATTCAATA


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

Matches are distributed among these distances:
  13   15  1.00

ACGTcount: A:0.29, C:0.07, G:0.07, T:0.57


Consensus pattern (13 bp):   
TTTTGAAACTTTA

Found at i:4489 original size:15 final size:15

Alignment explanation


    Indices: 4469--4502  Score: 59
    Period size: 15  Copynumber: 2.3  Consensus size: 15

       4459 TTGCTGGAGC

                           
       4469 TTAAACTATTTGAAT
          1 TTAAACTATTTGAAT

                   *       
       4484 TTAAACTCTTTGAAT
          1 TTAAACTATTTGAAT

                
       4499 TTAA
          1 TTAA

       4503 TCAGAATTTT


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  15   18  1.00

ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47


Consensus pattern (15 bp):   
TTAAACTATTTGAAT

Found at i:6023 original size:12 final size:11

Alignment explanation


    Indices: 5993--6020  Score: 56
    Period size: 11  Copynumber: 2.5  Consensus size: 11

       5983 TTCGCAGTAC

                       
       5993 AAAAAATGAAA
          1 AAAAAATGAAA

                       
       6004 AAAAAATGAAA
          1 AAAAAATGAAA

                  
       6015 AAAAAA
          1 AAAAAA

       6021 ATGTCTACAT


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   17  1.00

ACGTcount: A:0.86, C:0.00, G:0.07, T:0.07


Consensus pattern (11 bp):   
AAAAAATGAAA

Found at i:6212 original size:13 final size:13

Alignment explanation


    Indices: 6182--6224  Score: 63
    Period size: 12  Copynumber: 3.5  Consensus size: 13

       6172 CATCGATACA

                         
       6182 TCGATATATCCG-
          1 TCGATATATCCGT

                         
       6194 TCGATATATCCGT
          1 TCGATATATCCGT

                     *   
       6207 TCGATATATTCGT
          1 TCGATATATCCGT

                  
       6220 T-GATA
          1 TCGATA

       6225 CCTGTATTTA


Statistics
Matches: 29,  Mismatches: 1, Indels: 2
        0.91            0.03        0.06

Matches are distributed among these distances:
  12   16  0.55
  13   13  0.45

ACGTcount: A:0.26, C:0.19, G:0.16, T:0.40


Consensus pattern (13 bp):   
TCGATATATCCGT
Done.