Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013125.1 Corchorus capsularis cultivar CVL-1 contig13146, 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: 17290
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32


Found at i:537 original size:6 final size:6

Alignment explanation


    Indices: 528--556  Score: 58
    Period size: 6  Copynumber: 4.8  Consensus size: 6

        518 ATTTGCTTTT

                                             
        528 GATTTA GATTTA GATTTA GATTTA GATTT
          1 GATTTA GATTTA GATTTA GATTTA GATTT

        557 GCTTTGCTTT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   23  1.00

ACGTcount: A:0.31, C:0.00, G:0.17, T:0.52


Consensus pattern (6 bp):   
GATTTA

Found at i:927 original size:34 final size:34

Alignment explanation


    Indices: 847--927  Score: 110
    Period size: 34  Copynumber: 2.4  Consensus size: 34

        837 ATTAGTTTTT

                  *         *                 
        847 GTTTTTGTTTTTTCCGTTTTTTCTAAAAAAAAAA
          1 GTTTTTCTTTTTTCCGATTTTTCTAAAAAAAAAA

                   *                          
        881 GTTTTTCCTTTTTCCGATTTTTCTAAAAAAAAAA
          1 GTTTTTCTTTTTTCCGATTTTTCTAAAAAAAAAA

                   *      
        915 -TTTGTTTTTTTTT
          1 GTTT-TTCTTTTTT

        928 GCGTCGAAAG


Statistics
Matches: 41,  Mismatches: 5, Indels: 2
        0.85            0.10        0.04

Matches are distributed among these distances:
  33    3  0.07
  34   38  0.93

ACGTcount: A:0.26, C:0.10, G:0.07, T:0.57


Consensus pattern (34 bp):   
GTTTTTCTTTTTTCCGATTTTTCTAAAAAAAAAA

Found at i:3144 original size:55 final size:55

Alignment explanation


    Indices: 3079--3189  Score: 222
    Period size: 55  Copynumber: 2.0  Consensus size: 55

       3069 AATACTGATG

                                                                   
       3079 TTATTCTGCAATTAGCTGACGGATCTTTGGTTTATCCCAAAGGTGTTTTAAAGAA
          1 TTATTCTGCAATTAGCTGACGGATCTTTGGTTTATCCCAAAGGTGTTTTAAAGAA

                                                                   
       3134 TTATTCTGCAATTAGCTGACGGATCTTTGGTTTATCCCAAAGGTGTTTTAAAGAA
          1 TTATTCTGCAATTAGCTGACGGATCTTTGGTTTATCCCAAAGGTGTTTTAAAGAA

             
       3189 T
          1 T

       3190 ATCTTAATTA


Statistics
Matches: 56,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  55   56  1.00

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


Consensus pattern (55 bp):   
TTATTCTGCAATTAGCTGACGGATCTTTGGTTTATCCCAAAGGTGTTTTAAAGAA

Found at i:11010 original size:111 final size:111

Alignment explanation


    Indices: 10816--11037  Score: 365
    Period size: 111  Copynumber: 2.0  Consensus size: 111

      10806 TCTTGAAGAT

                      *     *                 *   * *                *       
      10816 CACCTTGCAAGAAGGCCTTATTCACATCAAGTTGTTGCCGGGGCCAACCATTAGTGATAGCAAGG
          1 CACCTTGCAAAAAGGCATTATTCACATCAAGTTGCTGCAGAGGCCAACCATTAGTGAGAGCAAGG

                                                          
      10881 CAGAGCACCAATCTAATTGTAACAGGTTTTACCACAGGGCTAAATG
         66 CAGAGCACCAATCTAATTGTAACAGGTTTTACCACAGGGCTAAATG

                                                                             
      10927 CACCTTGCAAAAAGGCATTATTCACATCAAGTTGCTGCAGAGGCCAACCATTAGTGAGAGCAAGG
          1 CACCTTGCAAAAAGGCATTATTCACATCAAGTTGCTGCAGAGGCCAACCATTAGTGAGAGCAAGG

                                   *                       
      10992 CAGAG-AGCCAATCTAATTGTAATAGGTTTTACCACAGGGCTAAATG
         66 CAGAGCA-CCAATCTAATTGTAACAGGTTTTACCACAGGGCTAAATG

      11038 TTTCTACAAA


Statistics
Matches: 103,  Mismatches: 7, Indels: 2
        0.92            0.06        0.02

Matches are distributed among these distances:
 110    1  0.01
 111  102  0.99

ACGTcount: A:0.32, C:0.22, G:0.23, T:0.23


Consensus pattern (111 bp):   
CACCTTGCAAAAAGGCATTATTCACATCAAGTTGCTGCAGAGGCCAACCATTAGTGAGAGCAAGG
CAGAGCACCAATCTAATTGTAACAGGTTTTACCACAGGGCTAAATG
Done.