Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014071.1 Corchorus capsularis cultivar CVL-1 contig14092, 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: 14644
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31


Found at i:1860 original size:33 final size:33

Alignment explanation


    Indices: 1823--1891  Score: 138
    Period size: 33  Copynumber: 2.1  Consensus size: 33

       1813 TAAAATGTTT

                                             
       1823 AAAAATGATATGCTAGTTAAAAAGGAAAGGGAA
          1 AAAAATGATATGCTAGTTAAAAAGGAAAGGGAA

                                             
       1856 AAAAATGATATGCTAGTTAAAAAGGAAAGGGAA
          1 AAAAATGATATGCTAGTTAAAAAGGAAAGGGAA

               
       1889 AAA
          1 AAA

       1892 TAATTAGGGG


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  33   36  1.00

ACGTcount: A:0.57, C:0.03, G:0.23, T:0.17


Consensus pattern (33 bp):   
AAAAATGATATGCTAGTTAAAAAGGAAAGGGAA

Found at i:5972 original size:30 final size:31

Alignment explanation


    Indices: 5938--6001  Score: 103
    Period size: 30  Copynumber: 2.1  Consensus size: 31

       5928 GTTAAGGTTT

                                  *        
       5938 GAACATGACAACAGTA-TTTCACCAAAAAAA
          1 GAACATGACAACAGTAGTTTCAACAAAAAAA

                                *          
       5968 GAACATGACAACAGTAGTTTGAACAAAAAAA
          1 GAACATGACAACAGTAGTTTCAACAAAAAAA

               
       5999 GAA
          1 GAA

       6002 AAGAAAAAAA


Statistics
Matches: 31,  Mismatches: 2, Indels: 1
        0.91            0.06        0.03

Matches are distributed among these distances:
  30   16  0.52
  31   15  0.48

ACGTcount: A:0.55, C:0.16, G:0.14, T:0.16


Consensus pattern (31 bp):   
GAACATGACAACAGTAGTTTCAACAAAAAAA

Found at i:7034 original size:31 final size:31

Alignment explanation


    Indices: 6996--7060  Score: 103
    Period size: 31  Copynumber: 2.1  Consensus size: 31

       6986 AGTAGCGAAT

                                ** *       
       6996 GTGATGTTAAGTATGATGGTTTATAGCTTGA
          1 GTGATGTTAAGTATGATGGTGCACAGCTTGA

                                           
       7027 GTGATGTTAAGTATGATGGTGCACAGCTTGA
          1 GTGATGTTAAGTATGATGGTGCACAGCTTGA

               
       7058 GTG
          1 GTG

       7061 TTCATTCCGA


Statistics
Matches: 31,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  31   31  1.00

ACGTcount: A:0.25, C:0.06, G:0.32, T:0.37


Consensus pattern (31 bp):   
GTGATGTTAAGTATGATGGTGCACAGCTTGA

Found at i:12058 original size:15 final size:16

Alignment explanation


    Indices: 12038--12072  Score: 54
    Period size: 15  Copynumber: 2.2  Consensus size: 16

      12028 TTTTAGCGGC

                            
      12038 AAAAGAAAAAAAAG-A
          1 AAAAGAAAAAAAAGTA

                     *      
      12053 AAAAGAAAATAAAGTA
          1 AAAAGAAAAAAAAGTA

                
      12069 AAAA
          1 AAAA

      12073 CCCATCAACC


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  15   13  0.72
  16    5  0.28

ACGTcount: A:0.83, C:0.00, G:0.11, T:0.06


Consensus pattern (16 bp):   
AAAAGAAAAAAAAGTA

Found at i:13274 original size:12 final size:12

Alignment explanation


    Indices: 13246--13367  Score: 120
    Period size: 12  Copynumber: 10.2  Consensus size: 12

      13236 CTCCAGATCC

                  *     
      13246 AGTTGATGAAAG
          1 AGTTGAAGAAAG

            *   *       
      13258 GGTTCAAGAAAG
          1 AGTTGAAGAAAG

                *      *
      13270 AGTTCAAGAAAC
          1 AGTTGAAGAAAG

            *           
      13282 TGTTGAAGAAAG
          1 AGTTGAAGAAAG

             *          
      13294 AATTGAAGAAAG
          1 AGTTGAAGAAAG

             *          
      13306 ATTTGAAGAAAG
          1 AGTTGAAGAAAG

            *           
      13318 GGTTGAAGAAAG
          1 AGTTGAAGAAAG

                *        
      13330 AGTTCAAGAAATG
          1 AGTTGAAGAAA-G

                        
      13343 -GTTGAAGAAAG
          1 AGTTGAAGAAAG

              *  *      
      13354 AGCTGCAGAAAG
          1 AGTTGAAGAAAG

              
      13366 AG
          1 AG

      13368 ATGGTGAAGA


Statistics
Matches: 90,  Mismatches: 18, Indels: 4
        0.80            0.16        0.04

Matches are distributed among these distances:
  11    1  0.01
  12   88  0.98
  13    1  0.01

ACGTcount: A:0.46, C:0.05, G:0.30, T:0.19


Consensus pattern (12 bp):   
AGTTGAAGAAAG

Done.