Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014119.1 Corchorus capsularis cultivar CVL-1 contig14140, 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: 7941
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30


Found at i:2215 original size:6 final size:6

Alignment explanation


    Indices: 2206--2238  Score: 66
    Period size: 6  Copynumber: 5.5  Consensus size: 6

       2196 AAAAGCAAGC

                                                  
       2206 AAATCT AAATCT AAATCT AAATCT AAATCT AAA
          1 AAATCT AAATCT AAATCT AAATCT AAATCT AAA

       2239 GCAGATTATA


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   27  1.00

ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30


Consensus pattern (6 bp):   
AAATCT

Found at i:2250 original size:12 final size:13

Alignment explanation


    Indices: 2235--2279  Score: 74
    Period size: 13  Copynumber: 3.5  Consensus size: 13

       2225 AATCTAAATC

                         
       2235 TAAAGCAGATT-A
          1 TAAAGCAGATTAA

                   *     
       2247 TAAAGCAAATTAA
          1 TAAAGCAGATTAA

                         
       2260 TAAAGCAGATTAA
          1 TAAAGCAGATTAA

                   
       2273 TAAAGCA
          1 TAAAGCA

       2280 AACAATAATT


Statistics
Matches: 30,  Mismatches: 2, Indels: 1
        0.91            0.06        0.03

Matches are distributed among these distances:
  12   10  0.33
  13   20  0.67

ACGTcount: A:0.56, C:0.09, G:0.13, T:0.22


Consensus pattern (13 bp):   
TAAAGCAGATTAA

Found at i:2286 original size:25 final size:25

Alignment explanation


    Indices: 2235--2287  Score: 81
    Period size: 25  Copynumber: 2.1  Consensus size: 25

       2225 AATCTAAATC

                                  *  
       2235 TAAAGCAGATTATAAAGCAAATTAA
          1 TAAAGCAGATTATAAAGCAAATCAA

                                      
       2260 TAAAGCAGATTAATAAAGCAAA-CAA
          1 TAAAGCAGATT-ATAAAGCAAATCAA

               
       2285 TAA
          1 TAA

       2288 TTAAAAAGCA


Statistics
Matches: 26,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
  25   16  0.62
  26   10  0.38

ACGTcount: A:0.58, C:0.09, G:0.11, T:0.21


Consensus pattern (25 bp):   
TAAAGCAGATTATAAAGCAAATCAA

Found at i:5572 original size:21 final size:21

Alignment explanation


    Indices: 5523--5576  Score: 56
    Period size: 21  Copynumber: 2.6  Consensus size: 21

       5513 AACACTGGAG

                        *        
       5523 CACATGGGGCGCGAGGCAAAC
          1 CACATGGGGCGCCAGGCAAAC

              **             **  
       5544 CAGGTGGGGCGCCAGGCTTAC
          1 CACATGGGGCGCCAGGCAAAC

                         
       5565 CACAT-GGGCGCC
          1 CACATGGGGCGCC

       5577 CAGCGCTAGT


Statistics
Matches: 26,  Mismatches: 7, Indels: 1
        0.76            0.21        0.03

Matches are distributed among these distances:
  20    7  0.27
  21   19  0.73

ACGTcount: A:0.20, C:0.31, G:0.39, T:0.09


Consensus pattern (21 bp):   
CACATGGGGCGCCAGGCAAAC

Found at i:7807 original size:10 final size:10

Alignment explanation


    Indices: 7792--7817  Score: 52
    Period size: 10  Copynumber: 2.6  Consensus size: 10

       7782 GAGGACTCTA

                      
       7792 GAATTTTCTG
          1 GAATTTTCTG

                      
       7802 GAATTTTCTG
          1 GAATTTTCTG

                  
       7812 GAATTT
          1 GAATTT

       7818 GGCAGCAACT


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   16  1.00

ACGTcount: A:0.23, C:0.08, G:0.19, T:0.50


Consensus pattern (10 bp):   
GAATTTTCTG
Done.