Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016089.1 Corchorus olitorius cultivar O-4 contig16122, 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: 14948
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37


Found at i:2568 original size:18 final size:18

Alignment explanation


    Indices: 2545--2579  Score: 54
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       2535 AAAAAACTTA

                               
       2545 TTATTAT-TCTTATTATTT
          1 TTATTATAT-TTATTATTT

                             
       2563 TTATTATATTTATTATT
          1 TTATTATATTTATTATT

       2580 CAATGTTTAC


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  18   15  0.94
  19    1  0.06

ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71


Consensus pattern (18 bp):   
TTATTATATTTATTATTT

Found at i:4307 original size:20 final size:20

Alignment explanation


    Indices: 4282--4325  Score: 63
    Period size: 20  Copynumber: 2.2  Consensus size: 20

       4272 TTTATGACAG

                                 
       4282 TTTTTTTAAAT-GGATAGTTT
          1 TTTTTTTAAATAGG-TAGTTT

                     *          
       4302 TTTTTTTAAGTAGGTAGTTT
          1 TTTTTTTAAATAGGTAGTTT

                
       4322 TTTT
          1 TTTT

       4326 AAATGATATA


Statistics
Matches: 22,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  20   20  0.91
  21    2  0.09

ACGTcount: A:0.20, C:0.00, G:0.16, T:0.64


Consensus pattern (20 bp):   
TTTTTTTAAATAGGTAGTTT

Found at i:7818 original size:15 final size:15

Alignment explanation


    Indices: 7798--7827  Score: 51
    Period size: 15  Copynumber: 2.0  Consensus size: 15

       7788 GCAATACAAA

                  *        
       7798 TTCAGTGCTTAATTT
          1 TTCAGTACTTAATTT

                           
       7813 TTCAGTACTTAATTT
          1 TTCAGTACTTAATTT

       7828 AACAAACAGA


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.23, C:0.13, G:0.10, T:0.53


Consensus pattern (15 bp):   
TTCAGTACTTAATTT

Found at i:11589 original size:58 final size:58

Alignment explanation


    Indices: 11494--11608  Score: 162
    Period size: 58  Copynumber: 2.0  Consensus size: 58

      11484 ATTAATCAAA

                                                          *           
      11494 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTCGGACCAAGGCT
          1 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACCAAGGCT

                *            *                                    *    
      11552 TATCGAGTGACATGTTTTTTTATTAGATGTC-T-AAAAAAGACGTTTTAGGACCGAGGC
          1 TATCAAGTGACATG-TTCTTTATTAGATG-CATAAAAAAAGACGTTTTAGGACCAAGGC

      11609 ATGATGCTAT


Statistics
Matches: 51,  Mismatches: 4, Indels: 4
        0.86            0.07        0.07

Matches are distributed among these distances:
  58   36  0.71
  59   14  0.27
  60    1  0.02

ACGTcount: A:0.32, C:0.14, G:0.21, T:0.33


Consensus pattern (58 bp):   
TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACCAAGGCT

Found at i:13753 original size:2 final size:2

Alignment explanation


    Indices: 13746--13781  Score: 54
    Period size: 2  Copynumber: 18.0  Consensus size: 2

      13736 ACATTACTAT

                                        *     *                  
      13746 TA TA TA TA TA TA TA TA TA TC TA TC TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

      13782 GAACTATACC


Statistics
Matches: 30,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
   2   30  1.00

ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:14003 original size:25 final size:24

Alignment explanation


    Indices: 13969--14015  Score: 76
    Period size: 25  Copynumber: 1.9  Consensus size: 24

      13959 ACGTTTGCAC

                      *              
      13969 AAATACCTAAGAATTTGAATTAAAA
          1 AAATACCTAAAAATTT-AATTAAAA

                                  
      13994 AAATACCTAAAAATTTAATTAA
          1 AAATACCTAAAAATTTAATTAA

      14016 TGTAAGTATT


Statistics
Matches: 21,  Mismatches: 1, Indels: 1
        0.91            0.04        0.04

Matches are distributed among these distances:
  24    6  0.29
  25   15  0.71

ACGTcount: A:0.57, C:0.09, G:0.04, T:0.30


Consensus pattern (24 bp):   
AAATACCTAAAAATTTAATTAAAA
Done.