Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010040.1 Corchorus capsularis cultivar CVL-1 contig10061, 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: 23068
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:8503 original size:19 final size:21

Alignment explanation


    Indices: 8463--8509  Score: 57
    Period size: 19  Copynumber: 2.4  Consensus size: 21

       8453 GTATTCCATT

                                 
       8463 TTTGTTGTTCTGTTTTATTTA
          1 TTTGTTGTTCTGTTTTATTTA

                                  
       8484 TTTGTT-TT-TGTTTT-TGTTA
          1 TTTGTTGTTCTGTTTTAT-TTA

                    
       8503 TTT-TTGT
          1 TTTGTTGT

       8510 AGAGGGTTAA


Statistics
Matches: 24,  Mismatches: 0, Indels: 6
        0.80            0.00        0.20

Matches are distributed among these distances:
  18    3  0.12
  19   13  0.54
  20    2  0.08
  21    6  0.25

ACGTcount: A:0.06, C:0.02, G:0.15, T:0.77


Consensus pattern (21 bp):   
TTTGTTGTTCTGTTTTATTTA

Found at i:19600 original size:89 final size:89

Alignment explanation


    Indices: 19449--19615  Score: 316
    Period size: 89  Copynumber: 1.9  Consensus size: 89

      19439 ATGTAATGAG

                                                                             
      19449 CAGGTTTTCAATGGAAAATTGGACTAAAAATCAAGTATAACTATGGTGTTTTTCATACAAGACCT
          1 CAGGTTTTCAATGGAAAATTGGACTAAAAATCAAGTATAACTATGGTGTTTTTCATACAAGACCT

                                    
      19514 AAATCATAATGTTCTAATTCGGCC
         66 AAATCATAATGTTCTAATTCGGCC

                                        *          *                         
      19538 CAGGTTTTCAATGGAAAATTGGACTAAAGATCAAGTATAGCTATGGTGTTTTTCATACAAGACCT
          1 CAGGTTTTCAATGGAAAATTGGACTAAAAATCAAGTATAACTATGGTGTTTTTCATACAAGACCT

                         
      19603 AAATCATAATGTT
         66 AAATCATAATGTT

      19616 ATAACTATAA


Statistics
Matches: 76,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  89   76  1.00

ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33


Consensus pattern (89 bp):   
CAGGTTTTCAATGGAAAATTGGACTAAAAATCAAGTATAACTATGGTGTTTTTCATACAAGACCT
AAATCATAATGTTCTAATTCGGCC

Found at i:22700 original size:1 final size:1

Alignment explanation


    Indices: 22694--22726  Score: 66
    Period size: 1  Copynumber: 33.0  Consensus size: 1

      22684 TTGTTGGCGG

                                             
      22694 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

      22727 TAGAGATGTA


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   32  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Done.