Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015819.1 Corchorus capsularis cultivar CVL-1 contig15840, 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: 6224
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.33

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:2717 original size:6 final size:5

Alignment explanation


    Indices: 2685--2719  Score: 54
    Period size: 5  Copynumber: 7.0  Consensus size: 5

       2675 TCTGGTCGAA

                                                      
       2685 ATTTT -TTTT ATTTT ATTTT ATTTT ATTTAT ATTTT
          1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTT-T ATTTT

       2720 TCAATATAAC


Statistics
Matches: 28,  Mismatches: 0, Indels: 4
        0.88            0.00        0.12

Matches are distributed among these distances:
   4    4  0.14
   5   19  0.68
   6    5  0.18

ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80


Consensus pattern (5 bp):   
ATTTT

Found at i:2821 original size:8 final size:8

Alignment explanation


    Indices: 2793--2826  Score: 50
    Period size: 8  Copynumber: 4.1  Consensus size: 8

       2783 GAATCGGCTA

                    
       2793 TGAATTTT
          1 TGAATTTT

                    *
       2801 TGAAGTTTC
          1 TGAA-TTTT

                    
       2810 TGAATTTT
          1 TGAATTTT

                    
       2818 TGAATTTT
          1 TGAATTTT

             
       2826 T
          1 T

       2827 CAAGAAGGTG


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
   8   16  0.70
   9    7  0.30

ACGTcount: A:0.24, C:0.03, G:0.15, T:0.59


Consensus pattern (8 bp):   
TGAATTTT

Found at i:3806 original size:33 final size:33

Alignment explanation


    Indices: 3730--3853  Score: 153
    Period size: 33  Copynumber: 3.7  Consensus size: 33

       3720 AAGACAAAGG

                                         *     
       3730 GTCGCGTGGCCGGTTGTGGCCAGG-CATGGCCGA-
          1 GTCGCGTGGCCGGTTGTGGCC-GGACATGTCC-AT

                **           *               
       3763 GTCGTTTGGCCGGTTGTAGCCGGACATGTCCAT
          1 GTCGCGTGGCCGGTTGTGGCCGGACATGTCCAT

                          *                  
       3796 GTCGCGTGGCCGGTGGTGGCCGGACATGTCCAT
          1 GTCGCGTGGCCGGTTGTGGCCGGACATGTCCAT

                                     
       3829 GTCGCGTGGCCGGTCTTGTGGCCGG
          1 GTCGCGTGGCCGG--TTGTGGCCGG

       3854 TGTTGCGCGG


Statistics
Matches: 78,  Mismatches: 9, Indels: 6
        0.84            0.10        0.06

Matches are distributed among these distances:
  32    3  0.04
  33   66  0.85
  35    9  0.12

ACGTcount: A:0.08, C:0.27, G:0.42, T:0.23


Consensus pattern (33 bp):   
GTCGCGTGGCCGGTTGTGGCCGGACATGTCCAT

Found at i:6175 original size:17 final size:18

Alignment explanation


    Indices: 6155--6194  Score: 55
    Period size: 20  Copynumber: 2.2  Consensus size: 18

       6145 AGTTTAGTTA

                              
       6155 ATTTTTCC-TTACTTTTT
          1 ATTTTTCCATTACTTTTT

                                
       6172 ATTTTTCCAAGTTACTTTTT
          1 ATTTTTCC-A-TTACTTTTT

               
       6192 ATT
          1 ATT

       6195 GTTGGATTCT


Statistics
Matches: 20,  Mismatches: 0, Indels: 3
        0.87            0.00        0.13

Matches are distributed among these distances:
  17    8  0.40
  20   12  0.60

ACGTcount: A:0.17, C:0.15, G:0.03, T:0.65


Consensus pattern (18 bp):   
ATTTTTCCATTACTTTTT
Done.