Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015709.1 Corchorus capsularis cultivar CVL-1 contig15730, 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: 9353
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30


Found at i:275 original size:16 final size:16

Alignment explanation


    Indices: 250--281  Score: 55
    Period size: 16  Copynumber: 2.0  Consensus size: 16

        240 GAATTGTTAC

                 *          
        250 GACCCGAACCCGAAAA
          1 GACCCAAACCCGAAAA

                            
        266 GACCCAAACCCGAAAA
          1 GACCCAAACCCGAAAA

        282 CCCGAGGTTC


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  16   15  1.00

ACGTcount: A:0.47, C:0.38, G:0.16, T:0.00


Consensus pattern (16 bp):   
GACCCAAACCCGAAAA

Found at i:369 original size:15 final size:15

Alignment explanation


    Indices: 315--371  Score: 53
    Period size: 15  Copynumber: 3.6  Consensus size: 15

        305 TCCGAACCGT

                          *  
        315 ATGACCCGAAACCGAAA
          1 ATGACCCG-AACC-CAA

             *              
        332 ACGACCC-AACCCAGA
          1 ATGACCCGAACCCA-A

                            
        347 ATTGACCCGAACCCAA
          1 A-TGACCCGAACCCAA

                     
        363 ATGACCCGA
          1 ATGACCCGA

        372 CATTTGAACG


Statistics
Matches: 34,  Mismatches: 3, Indels: 8
        0.76            0.07        0.18

Matches are distributed among these distances:
  14    1  0.03
  15   14  0.41
  16    7  0.21
  17   12  0.35

ACGTcount: A:0.40, C:0.37, G:0.16, T:0.07


Consensus pattern (15 bp):   
ATGACCCGAACCCAA

Found at i:9325 original size:2 final size:2

Alignment explanation


    Indices: 9318--9353  Score: 72
    Period size: 2  Copynumber: 18.0  Consensus size: 2

       9308 CATGTTCATC

                                                                 
       9318 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   34  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Done.