Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015396.1 Corchorus capsularis cultivar CVL-1 contig15417, 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: 22794
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32


Found at i:830 original size:26 final size:26

Alignment explanation


    Indices: 788--838  Score: 84
    Period size: 26  Copynumber: 2.0  Consensus size: 26

        778 ACCAACATGA

                                      
        788 TTCTAATGTAAACTAATAGGATATGG
          1 TTCTAATGTAAACTAATAGGATATGG

                     *  *            
        814 TTCTAATGTGAATTAATAGGATATG
          1 TTCTAATGTAAACTAATAGGATATG

        839 ATGTGATATG


Statistics
Matches: 23,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  26   23  1.00

ACGTcount: A:0.37, C:0.06, G:0.20, T:0.37


Consensus pattern (26 bp):   
TTCTAATGTAAACTAATAGGATATGG

Found at i:4480 original size:12 final size:12

Alignment explanation


    Indices: 4452--4495  Score: 63
    Period size: 12  Copynumber: 3.7  Consensus size: 12

       4442 GTTTGTTATG

                       * 
       4452 AGTTGAGTTAAAT
          1 AGTT-AGTTAATT

                        
       4465 -GTTAGTTAATT
          1 AGTTAGTTAATT

                        
       4476 AGTTAGTTAATT
          1 AGTTAGTTAATT

                    
       4488 AGTTAGTT
          1 AGTTAGTT

       4496 TTAGTTTTGT


Statistics
Matches: 29,  Mismatches: 1, Indels: 3
        0.88            0.03        0.09

Matches are distributed among these distances:
  11    7  0.24
  12   22  0.76

ACGTcount: A:0.32, C:0.00, G:0.20, T:0.48


Consensus pattern (12 bp):   
AGTTAGTTAATT

Found at i:15926 original size:14 final size:15

Alignment explanation


    Indices: 15909--15940  Score: 57
    Period size: 15  Copynumber: 2.2  Consensus size: 15

      15899 TGTGAGAATA

                           
      15909 GAGTGGTG-AATTGT
          1 GAGTGGTGCAATTGT

                           
      15923 GAGTGGTGCAATTGT
          1 GAGTGGTGCAATTGT

               
      15938 GAG
          1 GAG

      15941 GTTTAAGCAA


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    8  0.47
  15    9  0.53

ACGTcount: A:0.22, C:0.03, G:0.44, T:0.31


Consensus pattern (15 bp):   
GAGTGGTGCAATTGT

Found at i:16961 original size:27 final size:27

Alignment explanation


    Indices: 16923--17003  Score: 153
    Period size: 27  Copynumber: 3.0  Consensus size: 27

      16913 TTATTTCAAA

                                       
      16923 AGAAAAACTAATTTGGAATCACTATAT
          1 AGAAAAACTAATTTGGAATCACTATAT

                                       
      16950 AGAAAAACTAATTTGGAATCACTATAT
          1 AGAAAAACTAATTTGGAATCACTATAT

                                  *    
      16977 AGAAAAACTAATTTGGAATCACCATAT
          1 AGAAAAACTAATTTGGAATCACTATAT

      17004 TGTAGACACA


Statistics
Matches: 53,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  27   53  1.00

ACGTcount: A:0.48, C:0.12, G:0.11, T:0.28


Consensus pattern (27 bp):   
AGAAAAACTAATTTGGAATCACTATAT

Found at i:17154 original size:22 final size:22

Alignment explanation


    Indices: 17129--17174  Score: 83
    Period size: 22  Copynumber: 2.1  Consensus size: 22

      17119 AGCCGAATCA

                                  
      17129 TTTCCTCTCTTTAGAATAATTC
          1 TTTCCTCTCTTTAGAATAATTC

                    *             
      17151 TTTCCTCTTTTTAGAATAATTC
          1 TTTCCTCTCTTTAGAATAATTC

              
      17173 TT
          1 TT

      17175 GAGTTCCTTT


Statistics
Matches: 23,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  22   23  1.00

ACGTcount: A:0.22, C:0.20, G:0.04, T:0.54


Consensus pattern (22 bp):   
TTTCCTCTCTTTAGAATAATTC

Found at i:17271 original size:25 final size:25

Alignment explanation


    Indices: 17238--17290  Score: 88
    Period size: 25  Copynumber: 2.1  Consensus size: 25

      17228 TTATGTGGCC

                                  *  
      17238 TTTTATTTCACTTTTAGTCTTTTGG
          1 TTTTATTTCACTTTTAGTCTTTGGG

                *                    
      17263 TTTTCTTTCACTTTTAGTCTTTGGG
          1 TTTTATTTCACTTTTAGTCTTTGGG

               
      17288 TTT
          1 TTT

      17291 CTTGATTGAT


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  25   26  1.00

ACGTcount: A:0.09, C:0.13, G:0.13, T:0.64


Consensus pattern (25 bp):   
TTTTATTTCACTTTTAGTCTTTGGG

Found at i:21439 original size:18 final size:18

Alignment explanation


    Indices: 21375--21439  Score: 51
    Period size: 18  Copynumber: 3.3  Consensus size: 18

      21365 AATGGATCGA

                              
      21375 ATGGCCGGTTGTGGCCGG
          1 ATGGCCGGTTGTGGCCGG

                             *       
      21393 ATGGCGCATGCGTTG-GCCCGTTCG
          1 ATGGC-C--G-GTTGTGGCCG---G

                              
      21417 ATGGCCGGTTGTGGCCGG
          1 ATGGCCGGTTGTGGCCGG

                 
      21435 ATGGC
          1 ATGGC

      21440 TTGTGCGATG


Statistics
Matches: 37,  Mismatches: 2, Indels: 16
        0.67            0.04        0.29

Matches are distributed among these distances:
  18   11  0.30
  19    1  0.03
  20    4  0.11
  21   10  0.27
  22    4  0.11
  23    1  0.03
  24    6  0.16

ACGTcount: A:0.08, C:0.25, G:0.45, T:0.23


Consensus pattern (18 bp):   
ATGGCCGGTTGTGGCCGG
Done.