Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014270.1 Corchorus capsularis cultivar CVL-1 contig14291, 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: 16709
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34


Found at i:1948 original size:21 final size:21

Alignment explanation


    Indices: 1912--1965  Score: 58
    Period size: 21  Copynumber: 2.6  Consensus size: 21

       1902 TAAGCAGCTC

                      *           
       1912 ATGGAGTCAACCGCTCGAA-TA
          1 ATGGAGTCAAACGCTC-AACTA

                       *          
       1933 ATGGAGTCAAATGCTCAACTTA
          1 ATGGAGTCAAACGCTCAAC-TA

                        
       1955 A-GGAGTCAAAC
          1 ATGGAGTCAAAC

       1966 AACTTACTTA


Statistics
Matches: 28,  Mismatches: 3, Indels: 4
        0.80            0.09        0.11

Matches are distributed among these distances:
  20    2  0.07
  21   23  0.82
  22    3  0.11

ACGTcount: A:0.37, C:0.20, G:0.22, T:0.20


Consensus pattern (21 bp):   
ATGGAGTCAAACGCTCAACTA

Found at i:3440 original size:13 final size:13

Alignment explanation


    Indices: 3422--3446  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       3412 CTCTCAGGCA

                         
       3422 TCTCACACACATC
          1 TCTCACACACATC

                        
       3435 TCTCACACACAT
          1 TCTCACACACAT

       3447 TCAACGCTTC


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.32, C:0.44, G:0.00, T:0.24


Consensus pattern (13 bp):   
TCTCACACACATC

Found at i:10108 original size:36 final size:38

Alignment explanation


    Indices: 10043--10121  Score: 135
    Period size: 36  Copynumber: 2.1  Consensus size: 38

      10033 GGAGACCGGT

                                                  
      10043 AAATTCTTGGTTATGTTATATATATATTGGCCAAATTG
          1 AAATTCTTGGTTATGTTATATATATATTGGCCAAATTG

                                          *       
      10081 AAATTCTTGGTTATG-T-TATATATATTGGTCAAATTG
          1 AAATTCTTGGTTATGTTATATATATATTGGCCAAATTG

                 
      10117 AAATT
          1 AAATT

      10122 GTCGATTGAG


Statistics
Matches: 40,  Mismatches: 1, Indels: 2
        0.93            0.02        0.05

Matches are distributed among these distances:
  36   24  0.60
  37    1  0.03
  38   15  0.38

ACGTcount: A:0.33, C:0.06, G:0.15, T:0.46


Consensus pattern (38 bp):   
AAATTCTTGGTTATGTTATATATATATTGGCCAAATTG

Found at i:11170 original size:21 final size:21

Alignment explanation


    Indices: 11142--11181  Score: 55
    Period size: 22  Copynumber: 1.9  Consensus size: 21

      11132 AATTTGTCTG

                         *       
      11142 TAAATATAT-AGTTTTTTTTA
          1 TAAATATATAAGTATTTTTTA

                                
      11162 TAAACTATATAAGTATTTTT
          1 TAAA-TATATAAGTATTTTT

      11182 AGTACAAAGT


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  20    4  0.24
  21    5  0.29
  22    8  0.47

ACGTcount: A:0.38, C:0.03, G:0.05, T:0.55


Consensus pattern (21 bp):   
TAAATATATAAGTATTTTTTA

Found at i:15190 original size:2 final size:2

Alignment explanation


    Indices: 15185--15211  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

      15175 CTAGTGTGTG

                                                    
      15185 TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA T

      15212 TTATTTATTT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:15216 original size:4 final size:4

Alignment explanation


    Indices: 15209--15242  Score: 68
    Period size: 4  Copynumber: 8.5  Consensus size: 4

      15199 TATATATATA

                                                      
      15209 TATT TATT TATT TATT TATT TATT TATT TATT TA
          1 TATT TATT TATT TATT TATT TATT TATT TATT TA

      15243 CAAGTTAATT


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   30  1.00

ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74


Consensus pattern (4 bp):   
TATT

Found at i:15730 original size:14 final size:15

Alignment explanation


    Indices: 15707--15736  Score: 53
    Period size: 14  Copynumber: 2.1  Consensus size: 15

      15697 TACACAAAAC

                           
      15707 AAAACAAAAAACAAA
          1 AAAACAAAAAACAAA

                           
      15722 AAAAC-AAAAACAAA
          1 AAAACAAAAAACAAA

             
      15736 A
          1 A

      15737 CACATATTCT


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14   10  0.67
  15    5  0.33

ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00


Consensus pattern (15 bp):   
AAAACAAAAAACAAA
Done.