Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005002.1 Corchorus capsularis cultivar CVL-1 contig05020, 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: 25320
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31


Found at i:663 original size:99 final size:99

Alignment explanation


    Indices: 487--683  Score: 360
    Period size: 99  Copynumber: 2.0  Consensus size: 99

        477 TGGCTACTAG

                                        *                                    
        487 AAGGTAATAAATAATAATATGACGCAAAGTACATCTATGCTCAAGTTTTCTATCAATGGAATGTC
          1 AAGGTAATAAATAATAATATGACGCAAACTACATCTATGCTCAAGTTTTCTATCAATGGAATGTC

                                              
        552 TTACATGTACTCGGGTACAAGAGCCGGTTTTTAC
         66 TTACATGTACTCGGGTACAAGAGCCGGTTTTTAC

                                                                   *         
        586 AAGGTAATAAATAATAATATGACGCAAACTACATCTATGCTCAAGTTTTCTATCACTGGAATGTC
          1 AAGGTAATAAATAATAATATGACGCAAACTACATCTATGCTCAAGTTTTCTATCAATGGAATGTC

                                              
        651 TTACATAG-ACTCGGGTACAAGAGCCGGTTTTTA
         66 TTACAT-GTACTCGGGTACAAGAGCCGGTTTTTA

        684 TATGTATCGA


Statistics
Matches: 95,  Mismatches: 2, Indels: 2
        0.96            0.02        0.02

Matches are distributed among these distances:
  99   94  0.99
 100    1  0.01

ACGTcount: A:0.35, C:0.17, G:0.18, T:0.31


Consensus pattern (99 bp):   
AAGGTAATAAATAATAATATGACGCAAACTACATCTATGCTCAAGTTTTCTATCAATGGAATGTC
TTACATGTACTCGGGTACAAGAGCCGGTTTTTAC

Found at i:4633 original size:16 final size:18

Alignment explanation


    Indices: 4601--4634  Score: 54
    Period size: 16  Copynumber: 2.0  Consensus size: 18

       4591 ACCCGGCCGA

                              
       4601 TTGACCCGGTAGACCCAG
          1 TTGACCCGGTAGACCCAG

                              
       4619 TTGACCC-GT-GACCCAG
          1 TTGACCCGGTAGACCCAG

       4635 CAACCTCGGC


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  16    7  0.44
  17    2  0.12
  18    7  0.44

ACGTcount: A:0.21, C:0.35, G:0.26, T:0.18


Consensus pattern (18 bp):   
TTGACCCGGTAGACCCAG

Found at i:19232 original size:4 final size:4

Alignment explanation


    Indices: 19223--19253  Score: 62
    Period size: 4  Copynumber: 7.8  Consensus size: 4

      19213 ATTTTTCTTT

                                                  
      19223 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
          1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT

      19254 TTTTGCAGAG


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   27  1.00

ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77


Consensus pattern (4 bp):   
TTTA

Found at i:24139 original size:19 final size:18

Alignment explanation


    Indices: 24115--24150  Score: 63
    Period size: 19  Copynumber: 1.9  Consensus size: 18

      24105 TCGTTTTTTT

                               
      24115 TTCAAAAAATTAAAAAAAA
          1 TTCAAAAAA-TAAAAAAAA

                             
      24134 TTCAAAAAATAAAAAAA
          1 TTCAAAAAATAAAAAAA

      24151 TATTTTTTTT


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  18    8  0.47
  19    9  0.53

ACGTcount: A:0.75, C:0.06, G:0.00, T:0.19


Consensus pattern (18 bp):   
TTCAAAAAATAAAAAAAA

Found at i:24262 original size:20 final size:20

Alignment explanation


    Indices: 24224--24262  Score: 53
    Period size: 20  Copynumber: 1.9  Consensus size: 20

      24214 AAAAAAGAAA

                          *     
      24224 TTTTATTTTTCTTCTTTTTC
          1 TTTTATTTTTCTTCCTTTTC

                                
      24244 TTTTATTTTT-TTCCCTTTT
          1 TTTTATTTTTCTT-CCTTTT

      24263 TTTCCGTTTT


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  19    2  0.12
  20   15  0.88

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


Consensus pattern (20 bp):   
TTTTATTTTTCTTCCTTTTC
Done.