Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015507.1 Corchorus capsularis cultivar CVL-1 contig15528, 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: 13655
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.31


Found at i:1224 original size:23 final size:24

Alignment explanation


    Indices: 1184--1229  Score: 67
    Period size: 25  Copynumber: 1.9  Consensus size: 24

       1174 TTTAAACCCT

                                     
       1184 AATTTTTTTTTAAAAGAAAAAACAC
          1 AATTTTTTTTT-AAAGAAAAAACAC

                        *         
       1209 AATTTTTTTTT-TAGAAAAAAC
          1 AATTTTTTTTTAAAGAAAAAAC

       1230 GTAAAAAGAA


Statistics
Matches: 20,  Mismatches: 1, Indels: 2
        0.87            0.04        0.09

Matches are distributed among these distances:
  23    9  0.45
  25   11  0.55

ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41


Consensus pattern (24 bp):   
AATTTTTTTTTAAAGAAAAAACAC

Found at i:2846 original size:11 final size:10

Alignment explanation


    Indices: 2830--2882  Score: 56
    Period size: 11  Copynumber: 5.2  Consensus size: 10

       2820 TGCTTCTTGA

                       
       2830 AATAATTCTTC
          1 AATAA-TCTTC

                      
       2841 AATAATCTTC
          1 AATAATCTTC

                      
       2851 -A-AATCTTC
          1 AATAATCTTC

              *        
       2859 AAAATATCTTC
          1 AATA-ATCTTC

                       
       2870 AATAAATCTTC
          1 AAT-AATCTTC

              
       2881 AA
          1 AA

       2883 ACACGAACTT


Statistics
Matches: 37,  Mismatches: 1, Indels: 8
        0.80            0.02        0.17

Matches are distributed among these distances:
   8    7  0.19
   9    2  0.05
  10    6  0.16
  11   21  0.57
  12    1  0.03

ACGTcount: A:0.43, C:0.19, G:0.00, T:0.38


Consensus pattern (10 bp):   
AATAATCTTC

Found at i:2869 original size:19 final size:18

Alignment explanation


    Indices: 2836--2871  Score: 54
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       2826 TTGAAATAAT

                   *          
       2836 TCTTCAATAATCTTCAAA
          1 TCTTCAAAAATCTTCAAA

                              
       2854 TCTTCAAAATATCTTCAA
          1 TCTTCAAAA-ATCTTCAA

       2872 TAAATCTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    8  0.50
  19    8  0.50

ACGTcount: A:0.39, C:0.22, G:0.00, T:0.39


Consensus pattern (18 bp):   
TCTTCAAAAATCTTCAAA

Found at i:11925 original size:20 final size:22

Alignment explanation


    Indices: 11876--11926  Score: 61
    Period size: 20  Copynumber: 2.4  Consensus size: 22

      11866 CAAATTATGC

                                  
      11876 ATGTTTTTATAGCTATTTTTAT
          1 ATGTTTTTATAGCTATTTTTAT

              **                  
      11898 ATACTTTT-T-GCTATTTTTAT
          1 ATGTTTTTATAGCTATTTTTAT

            *        
      11918 GTGTTTTTA
          1 ATGTTTTTA

      11927 CCCTATTTTG


Statistics
Matches: 23,  Mismatches: 5, Indels: 3
        0.74            0.16        0.10

Matches are distributed among these distances:
  20   16  0.70
  21    1  0.04
  22    6  0.26

ACGTcount: A:0.20, C:0.06, G:0.10, T:0.65


Consensus pattern (22 bp):   
ATGTTTTTATAGCTATTTTTAT

Found at i:13441 original size:13 final size:13

Alignment explanation


    Indices: 13423--13457  Score: 61
    Period size: 13  Copynumber: 2.7  Consensus size: 13

      13413 TTAATTATTG

                         
      13423 TTTGCTTTATTAA
          1 TTTGCTTTATTAA

                         
      13436 TTTGCTTTATTAA
          1 TTTGCTTTATTAA

             *       
      13449 TCTGCTTTA
          1 TTTGCTTTA

      13458 GATTTAGATT


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  13   21  1.00

ACGTcount: A:0.20, C:0.11, G:0.09, T:0.60


Consensus pattern (13 bp):   
TTTGCTTTATTAA

Found at i:13465 original size:6 final size:6

Alignment explanation


    Indices: 13454--13480  Score: 54
    Period size: 6  Copynumber: 4.5  Consensus size: 6

      13444 ATTAATCTGC

                                           
      13454 TTTAGA TTTAGA TTTAGA TTTAGA TTT
          1 TTTAGA TTTAGA TTTAGA TTTAGA TTT

      13481 GCTTTGCTTT


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   21  1.00

ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56


Consensus pattern (6 bp):   
TTTAGA

Done.