Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016484.1 Corchorus capsularis cultivar CVL-1 contig16505, 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: 7816
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34


Found at i:621 original size:30 final size:30

Alignment explanation


    Indices: 585--643  Score: 102
    Period size: 30  Copynumber: 2.0  Consensus size: 30

        575 CAAGGGGGAG

                                           
        585 GGAATGATGCGCCCAAGG-CTTATCATGGAA
          1 GGAATGATGCG-CCAAGGACTTATCATGGAA

                                         
        615 GGAATGATGCGCCAAGGACTTATCATGGA
          1 GGAATGATGCGCCAAGGACTTATCATGGA

        644 CTTGAAGACA


Statistics
Matches: 28,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
  29    6  0.21
  30   22  0.79

ACGTcount: A:0.31, C:0.19, G:0.31, T:0.20


Consensus pattern (30 bp):   
GGAATGATGCGCCAAGGACTTATCATGGAA

Found at i:4221 original size:100 final size:100

Alignment explanation


    Indices: 4045--4243  Score: 317
    Period size: 100  Copynumber: 2.0  Consensus size: 100

       4035 ACTTATTACG

                                                             *               
       4045 TGAGTATATATGAAAGTAAAATAATTTTAAGGGGTTATCAGTATTACTATAAAACACAGGGCACT
          1 TGAGTATATATGAAAGTAAAATAATTTTAAGGGGTTATCAGTATTACTACAAAACACAGGGCACT

                                               
       4110 CAATACATGAGTGAATATGAAAATAAAATAATTTT
         66 CAATACATGAGTGAATATGAAAATAAAATAATTTT

                                                    *     *   * *     *      
       4145 TGAGTATATATGAAAGTAAAATAATTTTAAGGGGTTATCATTATTATTACGAGACACATGGCACT
          1 TGAGTATATATGAAAGTAAAATAATTTTAAGGGGTTATCAGTATTACTACAAAACACAGGGCACT

              *  **                           
       4210 CATTATGTGAGTGAATATGAAAATAAAATAATTT
         66 CAATACATGAGTGAATATGAAAATAAAATAATTT

       4244 AAATGTGGTA


Statistics
Matches: 90,  Mismatches: 9, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
 100   90  1.00

ACGTcount: A:0.43, C:0.08, G:0.17, T:0.33


Consensus pattern (100 bp):   
TGAGTATATATGAAAGTAAAATAATTTTAAGGGGTTATCAGTATTACTACAAAACACAGGGCACT
CAATACATGAGTGAATATGAAAATAAAATAATTTT

Found at i:5029 original size:2 final size:2

Alignment explanation


    Indices: 5022--5060  Score: 78
    Period size: 2  Copynumber: 19.5  Consensus size: 2

       5012 CTCAGGACTT

                                                                      
       5022 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
          1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C

       5061 TTCAAACTCA


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   37  1.00

ACGTcount: A:0.49, C:0.51, G:0.00, T:0.00


Consensus pattern (2 bp):   
CA

Found at i:5305 original size:2 final size:2

Alignment explanation


    Indices: 5287--5328  Score: 57
    Period size: 2  Copynumber: 20.5  Consensus size: 2

       5277 TTATAATTAG

                  *        *                                              
       5287 TA TA GA TA TA GA TA TA TA TA TA TA TA TA TA TA TA CTA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA T

       5329 TATTTTTAAC


Statistics
Matches: 35,  Mismatches: 4, Indels: 2
        0.85            0.10        0.05

Matches are distributed among these distances:
   2   33  0.94
   3    2  0.06

ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45


Consensus pattern (2 bp):   
TA

Found at i:6877 original size:3 final size:3

Alignment explanation


    Indices: 6869--6893  Score: 50
    Period size: 3  Copynumber: 8.3  Consensus size: 3

       6859 GTTAGTTTAG

                                             
       6869 ATT ATT ATT ATT ATT ATT ATT ATT A
          1 ATT ATT ATT ATT ATT ATT ATT ATT A

       6894 CAAGACACAG


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   22  1.00

ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64


Consensus pattern (3 bp):   
ATT

Found at i:7256 original size:53 final size:53

Alignment explanation


    Indices: 7176--7282  Score: 187
    Period size: 53  Copynumber: 2.0  Consensus size: 53

       7166 GCTGTTTTAT

                      * *                                        
       7176 TTTATAAATTCTTTTAAGAAAATTCAGTTAAAAAATCAAATTTTGTTGTGAAA
          1 TTTATAAATTATCTTAAGAAAATTCAGTTAAAAAATCAAATTTTGTTGTGAAA

                                           *                     
       7229 TTTATAAATTATCTTAAGAAAATTCAGTTAAGAAATCAAATTTTGTTGTGAAA
          1 TTTATAAATTATCTTAAGAAAATTCAGTTAAAAAATCAAATTTTGTTGTGAAA

             
       7282 T
          1 T

       7283 GATAACAAAA


Statistics
Matches: 51,  Mismatches: 3, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  53   51  1.00

ACGTcount: A:0.43, C:0.06, G:0.10, T:0.41


Consensus pattern (53 bp):   
TTTATAAATTATCTTAAGAAAATTCAGTTAAAAAATCAAATTTTGTTGTGAAA
Done.