Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008196.1 Corchorus capsularis cultivar CVL-1 contig08217, 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: 6466
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35


Found at i:3534 original size:8 final size:7

Alignment explanation


    Indices: 3508--3532  Score: 50
    Period size: 7  Copynumber: 3.6  Consensus size: 7

       3498 TTCAATTCCC

                   
       3508 TTTTCTT
          1 TTTTCTT

                   
       3515 TTTTCTT
          1 TTTTCTT

                   
       3522 TTTTCTT
          1 TTTTCTT

                
       3529 TTTT
          1 TTTT

       3533 TCCATCTAGG


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   18  1.00

ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88


Consensus pattern (7 bp):   
TTTTCTT

Found at i:4392 original size:21 final size:20

Alignment explanation


    Indices: 4355--4393  Score: 60
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       4345 GATTATTTGT

                       *        
       4355 TTGTCCTTTTTCAAAATTTA
          1 TTGTCCTTTTTAAAAATTTA

                               
       4375 TTGTCCTTTTTAACAAATT
          1 TTGTCCTTTTTAA-AAATT

       4394 AAATTTTCAA


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

Matches are distributed among these distances:
  20   12  0.71
  21    5  0.29

ACGTcount: A:0.26, C:0.15, G:0.05, T:0.54


Consensus pattern (20 bp):   
TTGTCCTTTTTAAAAATTTA

Found at i:4622 original size:12 final size:12

Alignment explanation


    Indices: 4599--4631  Score: 59
    Period size: 12  Copynumber: 2.8  Consensus size: 12

       4589 ATTGAGTTCT

                        
       4599 TAAATA-AATTA
          1 TAAATATAATTA

                        
       4610 TAAATATAATTA
          1 TAAATATAATTA

                      
       4622 TAAATATAAT
          1 TAAATATAAT

       4632 AATATACTCC


Statistics
Matches: 21,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  11    6  0.29
  12   15  0.71

ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39


Consensus pattern (12 bp):   
TAAATATAATTA

Found at i:4783 original size:59 final size:59

Alignment explanation


    Indices: 4691--4808  Score: 227
    Period size: 59  Copynumber: 2.0  Consensus size: 59

       4681 GTGTCTGGAC

                                                                       
       4691 CGTGAGGTCCTAGGTTCAAGTCTCACGGAATGTGAGTTTAGTTAGTAATTTGGTTTATT
          1 CGTGAGGTCCTAGGTTCAAGTCTCACGGAATGTGAGTTTAGTTAGTAATTTGGTTTATT

                                                       *               
       4750 CGTGAGGTCCTAGGTTCAAGTCTCACGGAATGTGAGTTTAGTTTGTAATTTGGTTTATT
          1 CGTGAGGTCCTAGGTTCAAGTCTCACGGAATGTGAGTTTAGTTAGTAATTTGGTTTATT

       4809 TGTGTATTTG


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:0.21, C:0.12, G:0.27, T:0.40


Consensus pattern (59 bp):   
CGTGAGGTCCTAGGTTCAAGTCTCACGGAATGTGAGTTTAGTTAGTAATTTGGTTTATT
Done.