Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015360.1 Corchorus capsularis cultivar CVL-1 contig15381, 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: 12490
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32


Found at i:6292 original size:19 final size:18

Alignment explanation


    Indices: 6259--6295  Score: 56
    Period size: 19  Copynumber: 2.0  Consensus size: 18

       6249 TTGAAATAAT

                              
       6259 TCTTCAATGATCTTCAAA
          1 TCTTCAATGATCTTCAAA

                     *         
       6277 TCTTCAAATTATCTTCAAA
          1 TCTTC-AATGATCTTCAAA

       6296 AAATCTTCAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  18    5  0.29
  19   12  0.71

ACGTcount: A:0.35, C:0.22, G:0.03, T:0.41


Consensus pattern (18 bp):   
TCTTCAATGATCTTCAAA

Found at i:9018 original size:21 final size:21

Alignment explanation


    Indices: 8975--9027  Score: 61
    Period size: 21  Copynumber: 2.5  Consensus size: 21

       8965 CCGACGCTGG

                  *     *     *  
       8975 CTGTGCGCCCAGGCGCTTTGC
          1 CTGTGCACCCAGCCGCTTGGC

                           *     
       8996 CTGTGCACCCAGCCGGTTGGC
          1 CTGTGCACCCAGCCGCTTGGC

               *       
       9017 CTGGGCACCCA
          1 CTGTGCACCCA

       9028 TGTGCCCTGG


Statistics
Matches: 27,  Mismatches: 5, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  21   27  1.00

ACGTcount: A:0.09, C:0.40, G:0.32, T:0.19


Consensus pattern (21 bp):   
CTGTGCACCCAGCCGCTTGGC

Found at i:9065 original size:12 final size:12

Alignment explanation


    Indices: 9048--9072  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

       9038 GCTATGCGCG

                        
       9048 GACAGCACCCAT
          1 GACAGCACCCAT

                        
       9060 GACAGCACCCAT
          1 GACAGCACCCAT

             
       9072 G
          1 G

       9073 CCATGCTGAT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.32, C:0.40, G:0.20, T:0.08


Consensus pattern (12 bp):   
GACAGCACCCAT

Found at i:9347 original size:17 final size:16

Alignment explanation


    Indices: 9325--9358  Score: 50
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       9315 ACTTTTTCCA

                             
       9325 TCAAATTCATCAATTTT
          1 TCAAATT-ATCAATTTT

                   *        
       9342 TCAAATTTTCAATTTT
          1 TCAAATTATCAATTTT

             
       9358 T
          1 T

       9359 GGGAAAATAG


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  16    9  0.56
  17    7  0.44

ACGTcount: A:0.32, C:0.15, G:0.00, T:0.53


Consensus pattern (16 bp):   
TCAAATTATCAATTTT
Done.