Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016182.1 Corchorus capsularis cultivar CVL-1 contig16203, 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: 17108
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.29


Found at i:351 original size:2 final size:2

Alignment explanation


    Indices: 344--376  Score: 57
    Period size: 2  Copynumber: 16.0  Consensus size: 2

        334 ATCAGTACAA

                                                            
        344 AT AT AT AT AGT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT

        377 TTAGGCCATG


Statistics
Matches: 30,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   2   28  0.93
   3    2  0.07

ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:412 original size:11 final size:11

Alignment explanation


    Indices: 396--426  Score: 53
    Period size: 11  Copynumber: 2.8  Consensus size: 11

        386 GTCTCTGATT

                       
        396 TATACTATATA
          1 TATACTATATA

                       
        407 TATACTATATA
          1 TATACTATATA

                *    
        418 TATAATATA
          1 TATACTATA

        427 ATAGACTTTC


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  11   19  1.00

ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45


Consensus pattern (11 bp):   
TATACTATATA

Found at i:8545 original size:1 final size:1

Alignment explanation


    Indices: 8508--8534  Score: 54
    Period size: 1  Copynumber: 27.0  Consensus size: 1

       8498 CATGAATTTT

                                       
       8508 AAAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAA

       8535 GACATCAAAA


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

Found at i:9485 original size:65 final size:65

Alignment explanation


    Indices: 9372--9501  Score: 244
    Period size: 65  Copynumber: 2.0  Consensus size: 65

       9362 CGAATTTAAG

                                                                             
       9372 TCTTATAAATGAAAAAAATAAAATAAAAAAACATTATTTTGATGGAACTTTCCTCCATAGTTGAA
          1 TCTTATAAATGAAAAAAATAAAATAAAAAAACATTATTTTGATGGAACTTTCCTCCATAG-TGAA

             
       9437 C
         65 C

                                                                             
       9438 TCTTATAAATGAAAAAAATAAAAT-AAAAAACATTATTTTGATGGAACTTTCCTCCATAGTGAAC
          1 TCTTATAAATGAAAAAAATAAAATAAAAAAACATTATTTTGATGGAACTTTCCTCCATAGTGAAC

       9502 CGAAACTTTA


Statistics
Matches: 64,  Mismatches: 0, Indels: 2
        0.97            0.00        0.03

Matches are distributed among these distances:
  64    5  0.08
  65   35  0.55
  66   24  0.38

ACGTcount: A:0.47, C:0.12, G:0.09, T:0.32


Consensus pattern (65 bp):   
TCTTATAAATGAAAAAAATAAAATAAAAAAACATTATTTTGATGGAACTTTCCTCCATAGTGAAC
Done.