Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007835.1 Corchorus capsularis cultivar CVL-1 contig07856, 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: 3426
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29


Found at i:1820 original size:66 final size:66

Alignment explanation


    Indices: 1714--1847  Score: 241
    Period size: 66  Copynumber: 2.0  Consensus size: 66

       1704 AGATGCTCTA

                                          *              *                   
       1714 ACATTGTGAGAAGGAAATCACACTTATTTTTTTTAGGGAAAATCATACGTATTACGGTAAAAGTA
          1 ACATTGTGAGAAGGAAATCACACTTATTTTCTTTAGGGAAAATCACACGTATTACGGTAAAAGTA

             
       1779 C
         66 C

                                                                   *         
       1780 ACATTGTGAGAAGGAAATCACACTTATTTTCTTTAGGGAAAATCACACGTATTACTGTAAAAGTA
          1 ACATTGTGAGAAGGAAATCACACTTATTTTCTTTAGGGAAAATCACACGTATTACGGTAAAAGTA

             
       1845 C
         66 C

              
       1846 AC
          1 AC

       1848 GGGAGGTCTT


Statistics
Matches: 65,  Mismatches: 3, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  66   65  1.00

ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31


Consensus pattern (66 bp):   
ACATTGTGAGAAGGAAATCACACTTATTTTCTTTAGGGAAAATCACACGTATTACGGTAAAAGTA
C

Found at i:2643 original size:33 final size:32

Alignment explanation


    Indices: 2606--2667  Score: 88
    Period size: 32  Copynumber: 1.9  Consensus size: 32

       2596 AACTCACCAA

                  *                          
       2606 GAAAAACCATAAACCAAAAAGCAAAGAGCAGGT
          1 GAAAAAACATAAACC-AAAAGCAAAGAGCAGGT

                      *  *               
       2639 GAAAAAACATTAATCAAAAGCAAAGAGCA
          1 GAAAAAACATAAACCAAAAGCAAAGAGCA

       2668 AACCCAAAAT


Statistics
Matches: 26,  Mismatches: 3, Indels: 1
        0.87            0.10        0.03

Matches are distributed among these distances:
  32   14  0.54
  33   12  0.46

ACGTcount: A:0.60, C:0.16, G:0.16, T:0.08


Consensus pattern (32 bp):   
GAAAAAACATAAACCAAAAGCAAAGAGCAGGT

Found at i:3023 original size:113 final size:106

Alignment explanation


    Indices: 2826--3102  Score: 295
    Period size: 113  Copynumber: 2.6  Consensus size: 106

       2816 CCTAACCTCA

                    *                      *        *                      * 
       2826 AAACGCCGTCATCTTTAATTTTTCTCTGAGGGAGGCAAATTGGTAAAAAAAGAAGGCTAAAA-TT
          1 AAACGCCGCCATCTTTAA-TTTTCTCTGAGGAAGGCAAATGGGT-AAAAAAGAAGGCTAAAAGAT

                                                             
       2890 TAGCGGCGTCTAGGTACAAGACGCCGCTAAATAGTGGCGTATGAGGTCC
         64 TAGCGGCGTCTAGGTACAAGA-----CTAAATAGTGGCGTATG-GGTCC

                                                                             
       2939 TAAACGCCGCCATCTTTAATTTTCTCTGAGGAAGGCAAATAGGGTAAAAAAGAAGGCTAAAAGAT
          1 -AAACGCCGCCATCTTTAATTTTCTCTGAGGAAGGCAAAT-GGGTAAAAAAGAAGGCTAAAAGAT

                       *   *                   *       
       3004 T-GCGGCGTCTGGGTTCAAGACTAAATAGTGGCGTCTGGGTCC
         64 TAGCGGCGTCTAGGTACAAGACTAAATAGTGGCGTATGGGTCC

                 *                                 *                         
       3046 AAGACACCGCCATC-------TT-TCTGAGGAAGGCGAATTGGGTAAAAAAGAAGGCTAAAAGAT
          1 AA-ACGCCGCCATCTTTAATTTTCTCTGAGGAAGGC-AAATGGGTAAAAAAGAAGGCTAAAAGAT

       3103 AGCCCATCTT


Statistics
Matches: 150,  Mismatches: 9, Indels: 23
        0.82            0.05        0.13

Matches are distributed among these distances:
  99   36  0.24
 100    5  0.03
 106    2  0.01
 107   15  0.10
 108   16  0.11
 113   54  0.36
 114   22  0.15

ACGTcount: A:0.33, C:0.17, G:0.26, T:0.23


Consensus pattern (106 bp):   
AAACGCCGCCATCTTTAATTTTCTCTGAGGAAGGCAAATGGGTAAAAAAGAAGGCTAAAAGATTA
GCGGCGTCTAGGTACAAGACTAAATAGTGGCGTATGGGTCC

Found at i:3131 original size:51 final size:51

Alignment explanation


    Indices: 3055--3156  Score: 204
    Period size: 51  Copynumber: 2.0  Consensus size: 51

       3045 CAAGACACCG

                                                               
       3055 CCATCTTTCTGAGGAAGGCGAATTGGGTAAAAAAGAAGGCTAAAAGATAGC
          1 CCATCTTTCTGAGGAAGGCGAATTGGGTAAAAAAGAAGGCTAAAAGATAGC

                                                               
       3106 CCATCTTTCTGAGGAAGGCGAATTGGGTAAAAAAGAAGGCTAAAAGATAGC
          1 CCATCTTTCTGAGGAAGGCGAATTGGGTAAAAAAGAAGGCTAAAAGATAGC

       3157 GGCGCGGCGT


Statistics
Matches: 51,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  51   51  1.00

ACGTcount: A:0.39, C:0.14, G:0.27, T:0.20


Consensus pattern (51 bp):   
CCATCTTTCTGAGGAAGGCGAATTGGGTAAAAAAGAAGGCTAAAAGATAGC

Found at i:3370 original size:32 final size:31

Alignment explanation


    Indices: 3267--3360  Score: 152
    Period size: 31  Copynumber: 3.0  Consensus size: 31

       3257 AGAAAGCTAA

                *                         *
       3267 AAGATGCCGCTAAATAGTGGCGTCTGGGTCG
          1 AAGACGCCGCTAAATAGTGGCGTCTGGGTCC

                                           
       3298 AAGACGCCGCTAAATAGTGGCGTCTGGGTCC
          1 AAGACGCCGCTAAATAGTGGCGTCTGGGTCC

                                   *        
       3329 AAGACGCCGCTAAATAGTGGCGTATGAGGTCC
          1 AAGACGCCGCTAAATAGTGGCGTCTG-GGTCC

       3361 TACATGCCGC


Statistics
Matches: 59,  Mismatches: 3, Indels: 1
        0.94            0.05        0.02

Matches are distributed among these distances:
  31   54  0.92
  32    5  0.08

ACGTcount: A:0.24, C:0.22, G:0.33, T:0.20


Consensus pattern (31 bp):   
AAGACGCCGCTAAATAGTGGCGTCTGGGTCC
Done.