Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012201.1 Corchorus capsularis cultivar CVL-1 contig12222, 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: 8037
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34


Found at i:2875 original size:33 final size:33

Alignment explanation


    Indices: 2835--2919  Score: 111
    Period size: 33  Copynumber: 2.6  Consensus size: 33

       2825 CCTGGCCAGA

                             *                 
       2835 GGGTTATAGTA-TCT-GGAAAACGGCCCTGCTAAC
          1 GGGTTATAGTAGT-TAGCAAAA-GGCCCTGCTAAC

                             **              
       2868 GGGTTATAGTAGTTAGCTTAAGGCCCTGCTAAC
          1 GGGTTATAGTAGTTAGCAAAAGGCCCTGCTAAC

                               
       2901 GGGTTATAGTAGTTAGCAA
          1 GGGTTATAGTAGTTAGCAA

       2920 TATGTCGATA


Statistics
Matches: 45,  Mismatches: 5, Indels: 4
        0.83            0.09        0.07

Matches are distributed among these distances:
  33   41  0.91
  34    4  0.09

ACGTcount: A:0.27, C:0.16, G:0.28, T:0.28


Consensus pattern (33 bp):   
GGGTTATAGTAGTTAGCAAAAGGCCCTGCTAAC

Found at i:6107 original size:50 final size:51

Alignment explanation


    Indices: 6045--6144  Score: 175
    Period size: 50  Copynumber: 2.0  Consensus size: 51

       6035 TTATAGAGAT

                   *            *                              
       6045 TTATTCTGATTGTAATGAGATTTCACATGTACTCACT-AAAAAAAAAAAAG
          1 TTATTCTAATTGTAATGAGAATTCACATGTACTCACTCAAAAAAAAAAAAG

                                                              
       6095 TTATTCTAATTGTAATGAGAATTCACATGTACTCACTCAAAAAAAAAAAA
          1 TTATTCTAATTGTAATGAGAATTCACATGTACTCACTCAAAAAAAAAAAA

       6145 AAGAGCCACT


Statistics
Matches: 47,  Mismatches: 2, Indels: 1
        0.94            0.04        0.02

Matches are distributed among these distances:
  50   35  0.74
  51   12  0.26

ACGTcount: A:0.46, C:0.13, G:0.10, T:0.31


Consensus pattern (51 bp):   
TTATTCTAATTGTAATGAGAATTCACATGTACTCACTCAAAAAAAAAAAAG

Found at i:6394 original size:109 final size:109

Alignment explanation


    Indices: 6203--6421  Score: 411
    Period size: 109  Copynumber: 2.0  Consensus size: 109

       6193 CCTCTCTTTC

                                                                             
       6203 TCCCCTTCCTCTCTAATTTCACCATTATTTGTCAGTCCGGTCCCACAAATCTTTAGATTTGTTTG
          1 TCCCCTTCCTCTCTAATTTCACCATTATTTGTCAGTCCGGTCCCACAAATCTTTAGATTTGTTTG

                                                        
       6268 GGTTAATAGTCCAAGATCTTTGGGCTTTTAGTACGTTGAGTCAG
         66 GGTTAATAGTCCAAGATCTTTGGGCTTTTAGTACGTTGAGTCAG

                           *   *   *                                         
       6312 TCCCCTTCCTCTCTAGTTTTACCGTTATTTGTCAGTCCGGTCCCACAAATCTTTAGATTTGTTTG
          1 TCCCCTTCCTCTCTAATTTCACCATTATTTGTCAGTCCGGTCCCACAAATCTTTAGATTTGTTTG

                                                        
       6377 GGTTAATAGTCCAAGATCTTTGGGCTTTTAGTACGTTGAGTCAG
         66 GGTTAATAGTCCAAGATCTTTGGGCTTTTAGTACGTTGAGTCAG

             
       6421 T
          1 T

       6422 TTTTGGAGTC


Statistics
Matches: 107,  Mismatches: 3, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
 109  107  1.00

ACGTcount: A:0.19, C:0.22, G:0.18, T:0.40


Consensus pattern (109 bp):   
TCCCCTTCCTCTCTAATTTCACCATTATTTGTCAGTCCGGTCCCACAAATCTTTAGATTTGTTTG
GGTTAATAGTCCAAGATCTTTGGGCTTTTAGTACGTTGAGTCAG
Done.