Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006510.1 Corchorus capsularis cultivar CVL-1 contig06531, 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: 19372
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35


Found at i:4078 original size:22 final size:23

Alignment explanation


    Indices: 4050--4093  Score: 72
    Period size: 22  Copynumber: 2.0  Consensus size: 23

       4040 ATAACCTATC

                                   
       4050 TTCATTCAAATAT-ATTTGTAAT
          1 TTCATTCAAATATAATTTGTAAT

                       *          
       4072 TTCATTCAAATTTAATTTGTAA
          1 TTCATTCAAATATAATTTGTAA

       4094 AGTTGTTGTA


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  22   12  0.60
  23    8  0.40

ACGTcount: A:0.36, C:0.09, G:0.05, T:0.50


Consensus pattern (23 bp):   
TTCATTCAAATATAATTTGTAAT

Found at i:18540 original size:59 final size:59

Alignment explanation


    Indices: 18443--18560  Score: 227
    Period size: 59  Copynumber: 2.0  Consensus size: 59

      18433 ATTTTTATTT

                                             *                         
      18443 CGATTATTTGCGTTTAACAAACTTGTAAACTAATGTTTTGGACTGAATTGACCCAAATC
          1 CGATTATTTGCGTTTAACAAACTTGTAAACTAACGTTTTGGACTGAATTGACCCAAATC

                                                                       
      18502 CGATTATTTGCGTTTAACAAACTTGTAAACTAACGTTTTGGACTGAATTGACCCAAATC
          1 CGATTATTTGCGTTTAACAAACTTGTAAACTAACGTTTTGGACTGAATTGACCCAAATC

      18561 GAAAAGTTCA


Statistics
Matches: 58,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  59   58  1.00

ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35


Consensus pattern (59 bp):   
CGATTATTTGCGTTTAACAAACTTGTAAACTAACGTTTTGGACTGAATTGACCCAAATC

Found at i:19117 original size:2 final size:2

Alignment explanation


    Indices: 19110--19143  Score: 61
    Period size: 2  Copynumber: 17.5  Consensus size: 2

      19100 TCACATAGGC

                                                                
      19110 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

      19144 TAGGTAAAGT


Statistics
Matches: 31,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   1    1  0.03
   2   30  0.97

ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53


Consensus pattern (2 bp):   
TA

Done.