Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01003678.1 Corchorus capsularis cultivar CVL-1 contig03686, 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: 17803
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31


Found at i:47 original size:2 final size:2

Alignment explanation


    Indices: 40--70  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

         30 CTAAGACTAG

                                                          
         40 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

         71 TTAGGGGCCG


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:1475 original size:4 final size:4

Alignment explanation


    Indices: 1468--1499  Score: 55
    Period size: 4  Copynumber: 7.8  Consensus size: 4

       1458 ATATATATAT

                                                   
       1468 ATAC ATAC ATAC ATAC ATAC ATAC ACTAC ATA
          1 ATAC ATAC ATAC ATAC ATAC ATAC A-TAC ATA

       1500 TTATTTGAAA


Statistics
Matches: 27,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   4   23  0.85
   5    4  0.15

ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25


Consensus pattern (4 bp):   
ATAC

Found at i:4042 original size:14 final size:14

Alignment explanation


    Indices: 3998--4043  Score: 53
    Period size: 13  Copynumber: 3.4  Consensus size: 14

       3988 ATTGGAATAG

                          
       3998 TAAAATGGTAAAAA
          1 TAAAATGGTAAAAA

                       *   
       4012 T-AAAT-GTACCAAA
          1 TAAAATGGTA-AAAA

                          
       4025 -AAAATGGTAAAAA
          1 TAAAATGGTAAAAA

                  
       4038 TAAAAT
          1 TAAAAT

       4044 AGTTATAAGG


Statistics
Matches: 26,  Mismatches: 2, Indels: 8
        0.72            0.06        0.22

Matches are distributed among these distances:
  12    3  0.12
  13   14  0.54
  14    9  0.35

ACGTcount: A:0.63, C:0.04, G:0.11, T:0.22


Consensus pattern (14 bp):   
TAAAATGGTAAAAA

Found at i:5327 original size:32 final size:32

Alignment explanation


    Indices: 5286--5358  Score: 105
    Period size: 31  Copynumber: 2.3  Consensus size: 32

       5276 AATTGGCCCC

                                *  * *      
       5286 TCCTGAATTTGGGAAGTTTAGGGGGTAAAATG
          1 TCCTGAATTTGGGAAGTTTAAGGAGCAAAATG

                                            
       5318 TCCTGAATTT-GGAAGTTTAAGGAGCAAAATG
          1 TCCTGAATTTGGGAAGTTTAAGGAGCAAAATG

                       
       5349 TCCT-AATTTG
          1 TCCTGAATTTG

       5359 AAATTCAGGG


Statistics
Matches: 37,  Mismatches: 3, Indels: 3
        0.86            0.07        0.07

Matches are distributed among these distances:
  30    5  0.14
  31   22  0.59
  32   10  0.27

ACGTcount: A:0.30, C:0.10, G:0.27, T:0.33


Consensus pattern (32 bp):   
TCCTGAATTTGGGAAGTTTAAGGAGCAAAATG

Found at i:5375 original size:30 final size:31

Alignment explanation


    Indices: 5286--5379  Score: 93
    Period size: 31  Copynumber: 3.0  Consensus size: 31

       5276 AATTGGCCCC

                           *  *      *      
       5286 TCCTGAATTTGGGAAGTTTAGGGGGTAAAATG
          1 TCCTGAATTT-GGAAATTCAGGGGGCAAAATG

                          *  * *  *        
       5318 TCCTGAATTTGGAAGTTTAAGGAGCAAAATG
          1 TCCTGAATTTGGAAATTCAGGGGGCAAAATG

                                            
       5349 TCCT-AATTT-GAAATTCAGGGGGGCAAAATG
          1 TCCTGAATTTGGAAATTCA-GGGGGCAAAATG

             
       5379 T
          1 T

       5380 TCTTGATGCA


Statistics
Matches: 54,  Mismatches: 7, Indels: 4
        0.83            0.11        0.06

Matches are distributed among these distances:
  29    6  0.11
  30   16  0.30
  31   22  0.41
  32   10  0.19

ACGTcount: A:0.32, C:0.10, G:0.29, T:0.30


Consensus pattern (31 bp):   
TCCTGAATTTGGAAATTCAGGGGGCAAAATG

Found at i:16930 original size:1 final size:1

Alignment explanation


    Indices: 16924--16950  Score: 54
    Period size: 1  Copynumber: 27.0  Consensus size: 1

      16914 CATCTGCCAC

                                       
      16924 AAAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAA

      16951 TCAAACCCAT


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   26  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Done.