Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008877.1 Corchorus capsularis cultivar CVL-1 contig08898, 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: 6118
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.37


Found at i:36 original size:18 final size:17

Alignment explanation


    Indices: 4--42  Score: 60
    Period size: 17  Copynumber: 2.2  Consensus size: 17

          1 TAT

                     *       
          4 ATATTTTTTTAAAAAAA
          1 ATATTTTTTAAAAAAAA

                              
         21 ATATTTTTTAATAAAAAA
          1 ATATTTTTTAA-AAAAAA

                
         39 ATAT
          1 ATAT

         43 GAAGTGGCAG


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

Matches are distributed among these distances:
  17   10  0.50
  18   10  0.50

ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46


Consensus pattern (17 bp):   
ATATTTTTTAAAAAAAA

Found at i:2219 original size:2 final size:2

Alignment explanation


    Indices: 2212--2238  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

       2202 TAACATAAGA

                                                    
       2212 AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT A

       2239 ATCTTCCCTA


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


Consensus pattern (2 bp):   
AT

Found at i:2309 original size:3 final size:3

Alignment explanation


    Indices: 2288--2330  Score: 63
    Period size: 3  Copynumber: 15.0  Consensus size: 3

       2278 TTCAAGCTTT

                  *                                                    
       2288 AAG AAA AAG AA- AA- AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
          1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG

       2331 GTTATCAATT


Statistics
Matches: 37,  Mismatches: 2, Indels: 2
        0.90            0.05        0.05

Matches are distributed among these distances:
   2    4  0.11
   3   33  0.89

ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00


Consensus pattern (3 bp):   
AAG

Found at i:2507 original size:21 final size:21

Alignment explanation


    Indices: 2481--2521  Score: 64
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       2471 GTTTTTCTTT

                  *              
       2481 AAGGTTGTTAAAAAAGTAATA
          1 AAGGTTATTAAAAAAGTAATA

                          *     
       2502 AAGGTTATTAAAAAGGTAAT
          1 AAGGTTATTAAAAAAGTAAT

       2522 TTAGTAACCA


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.51, C:0.00, G:0.20, T:0.29


Consensus pattern (21 bp):   
AAGGTTATTAAAAAAGTAATA

Found at i:2761 original size:21 final size:20

Alignment explanation


    Indices: 2719--2762  Score: 52
    Period size: 21  Copynumber: 2.1  Consensus size: 20

       2709 TATTGTAATC

                             *  
       2719 TAAAATTACTAAAAAAGTTA
          1 TAAAATTACTAAAAAAGCTA

                     *     *     
       2739 TAAAAGTTATTAAAATAGCTA
          1 TAAAA-TTACTAAAAAAGCTA

               
       2760 TAA
          1 TAA

       2763 TTCTTTCCAC


Statistics
Matches: 20,  Mismatches: 3, Indels: 1
        0.83            0.12        0.04

Matches are distributed among these distances:
  20    5  0.25
  21   15  0.75

ACGTcount: A:0.57, C:0.05, G:0.07, T:0.32


Consensus pattern (20 bp):   
TAAAATTACTAAAAAAGCTA
Done.