Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015436.1 Corchorus capsularis cultivar CVL-1 contig15457, 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: 14366
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33


Found at i:3509 original size:33 final size:33

Alignment explanation


    Indices: 3472--3576  Score: 131
    Period size: 33  Copynumber: 3.2  Consensus size: 33

       3462 ATTAGCATCC

                                *            
       3472 AAAACAGATTTAGTATCATCACAAACAACACTT
          1 AAAACAGATTTAGTATCATCGCAAACAACACTT

                          *    *            *
       3505 AAAACAGATTTAGTGTCATTGCAAACAACACTC
          1 AAAACAGATTTAGTATCATCGCAAACAACACTT

               **  *                          
       3538 AAATTAGGTTTAGTATCATCGCAAACAACA-TCT
          1 AAAACAGATTTAGTATCATCGCAAACAACACT-T

                  
       3571 AAAACA
          1 AAAACA

       3577 CTCTTTACAA


Statistics
Matches: 59,  Mismatches: 12, Indels: 2
        0.81            0.16        0.03

Matches are distributed among these distances:
  32    1  0.02
  33   58  0.98

ACGTcount: A:0.46, C:0.20, G:0.10, T:0.25


Consensus pattern (33 bp):   
AAAACAGATTTAGTATCATCGCAAACAACACTT

Found at i:5113 original size:9 final size:9

Alignment explanation


    Indices: 5099--5132  Score: 52
    Period size: 9  Copynumber: 3.8  Consensus size: 9

       5089 TCTGGTCGAA

                     
       5099 ATTTTTTTT
          1 ATTTTTTTT

                     
       5108 A-TTTTTTT
          1 ATTTTTTTT

                     
       5116 ATTTTTTTT
          1 ATTTTTTTT

                    
       5125 ATATTTTT
          1 AT-TTTTT

       5133 CGATATAACT


Statistics
Matches: 23,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
   8    8  0.35
   9   10  0.43
  10    5  0.22

ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85


Consensus pattern (9 bp):   
ATTTTTTTT

Found at i:5121 original size:17 final size:18

Alignment explanation


    Indices: 5099--5132  Score: 61
    Period size: 17  Copynumber: 1.9  Consensus size: 18

       5089 TCTGGTCGAA

                              
       5099 ATTTTTTTTAT-TTTTTT
          1 ATTTTTTTTATATTTTTT

                             
       5116 ATTTTTTTTATATTTTT
          1 ATTTTTTTTATATTTTT

       5133 CGATATAACT


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  17   11  0.69
  18    5  0.31

ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85


Consensus pattern (18 bp):   
ATTTTTTTTATATTTTTT

Found at i:10379 original size:21 final size:21

Alignment explanation


    Indices: 10340--10379  Score: 55
    Period size: 21  Copynumber: 1.9  Consensus size: 21

      10330 TTGATGTCCA

                   *             
      10340 ATTTTTCTCTTAAGTATTTCG
          1 ATTTTTCCCTTAAGTATTTCG

                                
      10361 ATTTTTCCCTTGAAG-ATTT
          1 ATTTTTCCCTT-AAGTATTT

      10380 TTGGACAGAA


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

Matches are distributed among these distances:
  21   14  0.82
  22    3  0.18

ACGTcount: A:0.20, C:0.15, G:0.10, T:0.55


Consensus pattern (21 bp):   
ATTTTTCCCTTAAGTATTTCG

Found at i:14171 original size:21 final size:20

Alignment explanation


    Indices: 14145--14188  Score: 70
    Period size: 21  Copynumber: 2.1  Consensus size: 20

      14135 CAGAGGGACT

                                 
      14145 GAGAGGCTCAGAGAGAGCAGA
          1 GAGAGGCTCAGAGAGAG-AGA

                         *      
      14166 GAGAGGCTCAGAGGGAGAGA
          1 GAGAGGCTCAGAGAGAGAGA

               
      14186 GAG
          1 GAG

      14189 CTTCAGAGAC


Statistics
Matches: 22,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  20    6  0.27
  21   16  0.73

ACGTcount: A:0.36, C:0.11, G:0.48, T:0.05


Consensus pattern (20 bp):   
GAGAGGCTCAGAGAGAGAGA

Found at i:14194 original size:18 final size:17

Alignment explanation


    Indices: 14129--14196  Score: 57
    Period size: 18  Copynumber: 3.6  Consensus size: 17

      14119 GTGAAAGGCT

                                
      14129 GAGCTTCAGAGGGACTGAGA
          1 GAGC-TCAGAGGGA--GAGA

                                
      14149 G-GCTCAGAGAGAGCAGAGA
          1 GAGCTCAGAG-G-G-AGAGA

                              
      14168 GAGGCTCAGAGGGAGAGA
          1 GA-GCTCAGAGGGAGAGA

                       
      14186 GAGCTTCAGAG
          1 GAGC-TCAGAG

      14197 ACAGGCTCAG


Statistics
Matches: 42,  Mismatches: 0, Indels: 14
        0.75            0.00        0.25

Matches are distributed among these distances:
  17    2  0.05
  18   19  0.45
  19    9  0.21
  20    3  0.07
  21    9  0.21

ACGTcount: A:0.32, C:0.15, G:0.43, T:0.10


Consensus pattern (17 bp):   
GAGCTCAGAGGGAGAGA
Done.