Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014804.1 Corchorus capsularis cultivar CVL-1 contig14825, 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: 9413
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33


Found at i:2580 original size:31 final size:31

Alignment explanation


    Indices: 2540--2609  Score: 81
    Period size: 31  Copynumber: 2.2  Consensus size: 31

       2530 TTTCCTATGT

                         *                   
       2540 TTTTGGGTAT-TTTATGCTTGATTATGCCTTA-
          1 TTTT-GGTATATTGATG-TTGATTATGCCTTAC

                          *                 
       2571 TGTTTGGTATATTGGTGTTGATTATGCCTTAC
          1 T-TTTGGTATATTGATGTTGATTATGCCTTAC

                   
       2603 TTTTGGT
          1 TTTTGGT

       2610 GTTTATCAAA


Statistics
Matches: 34,  Mismatches: 2, Indels: 6
        0.81            0.05        0.14

Matches are distributed among these distances:
  31   26  0.76
  32    8  0.24

ACGTcount: A:0.14, C:0.09, G:0.23, T:0.54


Consensus pattern (31 bp):   
TTTTGGTATATTGATGTTGATTATGCCTTAC

Found at i:3354 original size:19 final size:19

Alignment explanation


    Indices: 3291--3355  Score: 60
    Period size: 19  Copynumber: 3.4  Consensus size: 19

       3281 CCCTCTTCTC

                                 
       3291 TTTTCTTCTTCGTGTTGTGAG
          1 TTTTCTTCTTCGTGTTGT--G

                     * * *  * *
       3312 TTTTC-TCTCCCTCTTCTC
          1 TTTTCTTCTTCGTGTTGTG

                               
       3330 TTTTCTTCTTCGTGTTGTG
          1 TTTTCTTCTTCGTGTTGTG

                   
       3349 TTTTCTT
          1 TTTTCTT

       3356 AGGTATTTAT


Statistics
Matches: 33,  Mismatches: 10, Indels: 4
        0.70            0.21        0.09

Matches are distributed among these distances:
  18    5  0.15
  19   15  0.45
  20    8  0.24
  21    5  0.15

ACGTcount: A:0.02, C:0.23, G:0.14, T:0.62


Consensus pattern (19 bp):   
TTTTCTTCTTCGTGTTGTG

Found at i:6383 original size:12 final size:11

Alignment explanation


    Indices: 6368--6405  Score: 51
    Period size: 11  Copynumber: 3.5  Consensus size: 11

       6358 CGATATATCG

                        
       6368 AAAAATATCATA
          1 AAAAATAT-ATA

                    *  
       6380 AAAAATATTTA
          1 AAAAATATATA

                       
       6391 AAAAATA-ATA
          1 AAAAATATATA

                 
       6401 AAAAA
          1 AAAAA

       6406 ATTCGACCAG


Statistics
Matches: 24,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  10    7  0.29
  11    9  0.38
  12    8  0.33

ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24


Consensus pattern (11 bp):   
AAAAATATATA
Done.