Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013941.1 Corchorus capsularis cultivar CVL-1 contig13962, 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: 17361
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.30


Found at i:130 original size:2 final size:2

Alignment explanation


    Indices: 123--149  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

        113 TTCTCATTGT

                                                    
        123 TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA T

        150 TCATACGAAC


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:241 original size:30 final size:30

Alignment explanation


    Indices: 207--272  Score: 87
    Period size: 30  Copynumber: 2.2  Consensus size: 30

        197 CATTTTGACC

                                **        
        207 AAAAAAAAAAATGCTTATGATCCTCTTTGA
          1 AAAAAAAAAAATGCTTATGAAACTCTTTGA

                 *   **                   
        237 AAAAAGAAATTTGCTTATGAAACTCTTTGA
          1 AAAAAAAAAAATGCTTATGAAACTCTTTGA

                  
        267 AAAAAA
          1 AAAAAA

        273 TTGATACCGG


Statistics
Matches: 30,  Mismatches: 6, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  30   30  1.00

ACGTcount: A:0.50, C:0.11, G:0.11, T:0.29


Consensus pattern (30 bp):   
AAAAAAAAAAATGCTTATGAAACTCTTTGA

Found at i:520 original size:17 final size:18

Alignment explanation


    Indices: 498--532  Score: 54
    Period size: 17  Copynumber: 2.0  Consensus size: 18

        488 TTTTTTTAAT

                  *           
        498 AATTATTTTAA-TAATTA
          1 AATTATATTAATTAATTA

                              
        515 AATTATATTAATTAATTA
          1 AATTATATTAATTAATTA

        533 TATAAATATA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  17   10  0.62
  18    6  0.38

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (18 bp):   
AATTATATTAATTAATTA

Found at i:3510 original size:30 final size:30

Alignment explanation


    Indices: 3476--3538  Score: 90
    Period size: 30  Copynumber: 2.1  Consensus size: 30

       3466 AAATCCTAAC

                 *         *      *       
       3476 AAATCTTTGGTAATCTTAAGATTCAACAAG
          1 AAATCATTGGTAATCCTAAGATCCAACAAG

                                    *     
       3506 AAATCATTGGTAATCCTAAGATCCGACAAG
          1 AAATCATTGGTAATCCTAAGATCCAACAAG

               
       3536 AAA
          1 AAA

       3539 AATAAGACGA


Statistics
Matches: 29,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  30   29  1.00

ACGTcount: A:0.43, C:0.16, G:0.14, T:0.27


Consensus pattern (30 bp):   
AAATCATTGGTAATCCTAAGATCCAACAAG

Found at i:4039 original size:12 final size:12

Alignment explanation


    Indices: 4022--4050  Score: 58
    Period size: 12  Copynumber: 2.4  Consensus size: 12

       4012 AAGTAGGAGA

                        
       4022 GAGAATGAGTGG
          1 GAGAATGAGTGG

                        
       4034 GAGAATGAGTGG
          1 GAGAATGAGTGG

                 
       4046 GAGAA
          1 GAGAA

       4051 AGAGAATAGG


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

Matches are distributed among these distances:
  12   17  1.00

ACGTcount: A:0.38, C:0.00, G:0.48, T:0.14


Consensus pattern (12 bp):   
GAGAATGAGTGG
Done.