Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011289.1 Corchorus capsularis cultivar CVL-1 contig11310, 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: 3079
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29


Found at i:2393 original size:18 final size:18

Alignment explanation


    Indices: 2382--2418  Score: 58
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       2372 AAAAAAACAC

                              
       2382 AAAAA-ACGAAAAACAAA
          1 AAAAATACGAAAAACAAA

                          *   
       2399 AAAAATACGAAAAATAAA
          1 AAAAATACGAAAAACAAA

              
       2417 AA
          1 AA

       2419 CAAAACTAAA


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  17    5  0.28
  18   13  0.72

ACGTcount: A:0.81, C:0.08, G:0.05, T:0.05


Consensus pattern (18 bp):   
AAAAATACGAAAAACAAA

Found at i:2399 original size:25 final size:24

Alignment explanation


    Indices: 2371--2423  Score: 70
    Period size: 25  Copynumber: 2.2  Consensus size: 24

       2361 CTGCAAAATT

                                     
       2371 AAAAAAAACACAAAAAACGAAAAAC
          1 AAAAAAAACACAAAAAA-GAAAAAC

                    *  *     *      
       2396 AAAAAAAATACGAAAAATAAAAAC
          1 AAAAAAAACACAAAAAAGAAAAAC

                
       2420 AAAA
          1 AAAA

       2424 CTAAAGGAAA


Statistics
Matches: 25,  Mismatches: 3, Indels: 1
        0.86            0.10        0.03

Matches are distributed among these distances:
  24   10  0.40
  25   15  0.60

ACGTcount: A:0.81, C:0.11, G:0.04, T:0.04


Consensus pattern (24 bp):   
AAAAAAAACACAAAAAAGAAAAAC

Found at i:2403 original size:16 final size:17

Alignment explanation


    Indices: 2374--2418  Score: 56
    Period size: 17  Copynumber: 2.6  Consensus size: 17

       2364 CAAAATTAAA

                   *         
       2374 AAAAACACAAAAA-ACG
          1 AAAAACAAAAAAATACG

                              
       2390 AAAAACAAAAAAAATACG
          1 AAAAAC-AAAAAAATACG

                 *     
       2408 AAAAATAAAAA
          1 AAAAACAAAAA

       2419 CAAAACTAAA


Statistics
Matches: 25,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  16    6  0.24
  17   11  0.44
  18    8  0.32

ACGTcount: A:0.80, C:0.11, G:0.04, T:0.04


Consensus pattern (17 bp):   
AAAAACAAAAAAATACG
Done.