Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004544.1 Corchorus capsularis cultivar CVL-1 contig04555, 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, 687

Length: 1146
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29

Warning! 2 characters in sequence are not A, C, G, or T


Found at i:291 original size:17 final size:17

Alignment explanation


    Indices: 269--324  Score: 76
    Period size: 17  Copynumber: 3.1  Consensus size: 17

        259 ATAACAAAAC

                             
        269 ATTAGACATTATCTATA
          1 ATTAGACATTATCTATA

                                 
        286 ATTAGACATTATCTATAAAAA
          1 ATTAGACATTATCTAT----A

                             
        307 ATTAGACATTATCTATA
          1 ATTAGACATTATCTATA

             
        324 A
          1 A

        325 AAGGAATCCA


Statistics
Matches: 35,  Mismatches: 0, Indels: 8
        0.81            0.00        0.19

Matches are distributed among these distances:
  17   18  0.51
  21   17  0.49

ACGTcount: A:0.46, C:0.11, G:0.05, T:0.38


Consensus pattern (17 bp):   
ATTAGACATTATCTATA

Found at i:311 original size:21 final size:21

Alignment explanation


    Indices: 264--326  Score: 89
    Period size: 21  Copynumber: 3.2  Consensus size: 21

        254 ACATTATAAC

                *                
        264 AAAACATTAGACATTATCTAT
          1 AAAAAATTAGACATTATCTAT

                                 
        285 ----AATTAGACATTATCTAT
          1 AAAAAATTAGACATTATCTAT

                                 
        302 AAAAAATTAGACATTATCTAT
          1 AAAAAATTAGACATTATCTAT

                
        323 AAAA
          1 AAAA

        327 GGAATCCATG


Statistics
Matches: 37,  Mismatches: 1, Indels: 8
        0.80            0.02        0.17

Matches are distributed among these distances:
  17   16  0.43
  21   21  0.57

ACGTcount: A:0.51, C:0.11, G:0.05, T:0.33


Consensus pattern (21 bp):   
AAAAAATTAGACATTATCTAT

Found at i:384 original size:10 final size:10

Alignment explanation


    Indices: 369--408  Score: 57
    Period size: 10  Copynumber: 4.1  Consensus size: 10

        359 TATGTTTAAT

                      
        369 TACTTATATA
          1 TACTTATATA

                       
        379 TACTTATACT-
          1 TACTTATA-TA

                      
        389 TACTTATATA
          1 TACTTATATA

                      
        399 TA-TTATATA
          1 TACTTATATA

             
        408 T
          1 T

        409 TCAATATAGA


Statistics
Matches: 28,  Mismatches: 0, Indels: 5
        0.85            0.00        0.15

Matches are distributed among these distances:
   9    9  0.32
  10   18  0.64
  11    1  0.04

ACGTcount: A:0.38, C:0.10, G:0.00, T:0.53


Consensus pattern (10 bp):   
TACTTATATA

Found at i:393 original size:20 final size:19

Alignment explanation


    Indices: 368--405  Score: 67
    Period size: 20  Copynumber: 1.9  Consensus size: 19

        358 TTATGTTTAA

                                
        368 TTACTTATATATACTTATAC
          1 TTACTTATATATA-TTATAC

                              
        388 TTACTTATATATATTATA
          1 TTACTTATATATATTATA

        406 TATTCAATAT


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  19    5  0.28
  20   13  0.72

ACGTcount: A:0.37, C:0.11, G:0.00, T:0.53


Consensus pattern (19 bp):   
TTACTTATATATATTATAC
Done.