Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011535.1 Corchorus capsularis cultivar CVL-1 contig11556, 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: 25199
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32


Found at i:2214 original size:10 final size:10

Alignment explanation


    Indices: 2199--2223  Score: 50
    Period size: 10  Copynumber: 2.5  Consensus size: 10

       2189 GAGGACTCTA

                      
       2199 GAATTTTCTG
          1 GAATTTTCTG

                      
       2209 GAATTTTCTG
          1 GAATTTTCTG

                 
       2219 GAATT
          1 GAATT

       2224 GTGCAGGAAC


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   15  1.00

ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48


Consensus pattern (10 bp):   
GAATTTTCTG

Found at i:8356 original size:6 final size:6

Alignment explanation


    Indices: 8345--8371  Score: 54
    Period size: 6  Copynumber: 4.5  Consensus size: 6

       8335 AAAGCAAAGC

                                           
       8345 AAATCT AAATCT AAATCT AAATCT AAA
          1 AAATCT AAATCT AAATCT AAATCT AAA

       8372 GCAGATTAAT


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   21  1.00

ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30


Consensus pattern (6 bp):   
AAATCT

Found at i:9314 original size:10 final size:10

Alignment explanation


    Indices: 9299--9323  Score: 50
    Period size: 10  Copynumber: 2.5  Consensus size: 10

       9289 GAGGACTCTA

                      
       9299 GAATTTTCTG
          1 GAATTTTCTG

                      
       9309 GAATTTTCTG
          1 GAATTTTCTG

                 
       9319 GAATT
          1 GAATT

       9324 GTGCAGGAAC


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   15  1.00

ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48


Consensus pattern (10 bp):   
GAATTTTCTG

Found at i:16228 original size:17 final size:17

Alignment explanation


    Indices: 16206--16242  Score: 56
    Period size: 17  Copynumber: 2.2  Consensus size: 17

      16196 GTTATCCAGC

                    *        
      16206 ACCTCATGGTACCTAGT
          1 ACCTCATGCTACCTAGT

                          *  
      16223 ACCTCATGCTACCTGGT
          1 ACCTCATGCTACCTAGT

               
      16240 ACC
          1 ACC

      16243 ATGAGGGGGA


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

Matches are distributed among these distances:
  17   18  1.00

ACGTcount: A:0.22, C:0.35, G:0.16, T:0.27


Consensus pattern (17 bp):   
ACCTCATGCTACCTAGT

Found at i:20198 original size:11 final size:10

Alignment explanation


    Indices: 20180--20213  Score: 50
    Period size: 11  Copynumber: 3.2  Consensus size: 10

      20170 AATTGTCTTC

                      
      20180 AAATCTTCAA
          1 AAATCTTCAA

                       
      20190 AATATCTTCAA
          1 AA-ATCTTCAA

                       
      20201 GAAATCTTCAA
          1 -AAATCTTCAA

              
      20212 AA
          1 AA

      20214 CACGAACTTC


Statistics
Matches: 22,  Mismatches: 0, Indels: 4
        0.85            0.00        0.15

Matches are distributed among these distances:
  10    4  0.18
  11   16  0.73
  12    2  0.09

ACGTcount: A:0.50, C:0.18, G:0.03, T:0.29


Consensus pattern (10 bp):   
AAATCTTCAA
Done.