Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013447.1 Corchorus olitorius cultivar O-4 contig13480, 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: 8549
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35


Found at i:2719 original size:18 final size:18

Alignment explanation


    Indices: 2696--2734  Score: 78
    Period size: 18  Copynumber: 2.2  Consensus size: 18

       2686 ATCAATGACC

                              
       2696 ATTATAACAAATAAACAA
          1 ATTATAACAAATAAACAA

                              
       2714 ATTATAACAAATAAACAA
          1 ATTATAACAAATAAACAA

               
       2732 ATT
          1 ATT

       2735 GATGAGTGCC


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

Matches are distributed among these distances:
  18   21  1.00

ACGTcount: A:0.64, C:0.10, G:0.00, T:0.26


Consensus pattern (18 bp):   
ATTATAACAAATAAACAA

Found at i:2870 original size:112 final size:112

Alignment explanation


    Indices: 2725--2945  Score: 354
    Period size: 112  Copynumber: 2.0  Consensus size: 112

       2715 TTATAACAAA

                      *                                                      
       2725 TAAACAAATTGATGAGTGCCAAATATCCTAAACACATTTAACCATATAATAAAATATAAAAATTG
          1 TAAACAAATTAATGAGTGCCAAATATCCTAAACACATTTAACCATATAATAAAATATAAAAATTG

                *                                          
       2790 AAAATTGAAAGAAAAATATGATATTTTATAATTTCATGATGGATAAT
         66 AAAACTGAAAGAAAAATATGATATTTTATAATTTCATGATGGATAAT

                                       *              *     **               
       2837 TAAACAAATTAAT-ATGTGCCAAATATTCTAAACACATTTAATCATATGGTAAAATATAAAAATT
          1 TAAACAAATTAATGA-GTGCCAAATATCCTAAACACATTTAACCATATAATAAAATATAAAAATT

             *                     *                     
       2901 GTAAACTGAAAGAAAAATATGATTTTTTATAATTTCATGATGGAT
         65 GAAAACTGAAAGAAAAATATGATATTTTATAATTTCATGATGGAT

       2946 TATGTGGATG


Statistics
Matches: 100,  Mismatches: 8, Indels: 2
        0.91            0.07        0.02

Matches are distributed among these distances:
 111    1  0.01
 112   99  0.99

ACGTcount: A:0.48, C:0.09, G:0.10, T:0.33


Consensus pattern (112 bp):   
TAAACAAATTAATGAGTGCCAAATATCCTAAACACATTTAACCATATAATAAAATATAAAAATTG
AAAACTGAAAGAAAAATATGATATTTTATAATTTCATGATGGATAAT

Found at i:3301 original size:33 final size:33

Alignment explanation


    Indices: 3254--3325  Score: 108
    Period size: 33  Copynumber: 2.2  Consensus size: 33

       3244 ATAATTTTAC

                *          **      *         
       3254 AAAACTATCAAAATATTGATAACGAAATGACTA
          1 AAAATTATCAAAATAGCGATAACAAAATGACTA

                                             
       3287 AAAATTATCAAAATAGCGATAACAAAATGACTA
          1 AAAATTATCAAAATAGCGATAACAAAATGACTA

                  
       3320 AAAATT
          1 AAAATT

       3326 CAACCATTAA


Statistics
Matches: 35,  Mismatches: 4, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  33   35  1.00

ACGTcount: A:0.57, C:0.11, G:0.08, T:0.24


Consensus pattern (33 bp):   
AAAATTATCAAAATAGCGATAACAAAATGACTA

Found at i:4222 original size:3 final size:3

Alignment explanation


    Indices: 4216--4244  Score: 51
    Period size: 3  Copynumber: 10.0  Consensus size: 3

       4206 TTATTACATA

                                                   
       4216 TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT
          1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT

       4245 ATATATAGCA


Statistics
Matches: 25,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   2    2  0.08
   3   23  0.92

ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66


Consensus pattern (3 bp):   
TAT

Found at i:4233 original size:14 final size:14

Alignment explanation


    Indices: 4214--4246  Score: 66
    Period size: 14  Copynumber: 2.4  Consensus size: 14

       4204 AATTATTACA

                          
       4214 TATATTATTATTAT
          1 TATATTATTATTAT

                          
       4228 TATATTATTATTAT
          1 TATATTATTATTAT

                 
       4242 TATAT
          1 TATAT

       4247 ATATAGCAAT


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   19  1.00

ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64


Consensus pattern (14 bp):   
TATATTATTATTAT

Found at i:5215 original size:21 final size:20

Alignment explanation


    Indices: 5158--5215  Score: 82
    Period size: 21  Copynumber: 2.9  Consensus size: 20

       5148 CTGGTTAGCA

                                
       5158 ACTGTACAGATGAGATT-AC
          1 ACTGTACAGATGAGATTAAC

                       * *      
       5177 ACTGTACAGATTAAATTAAC
          1 ACTGTACAGATGAGATTAAC

                               
       5197 TACTGTACAGATGAGATTA
          1 -ACTGTACAGATGAGATTA

       5216 TTAGAGCAGC


Statistics
Matches: 33,  Mismatches: 4, Indels: 2
        0.85            0.10        0.05

Matches are distributed among these distances:
  19   15  0.45
  20    2  0.06
  21   16  0.48

ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29


Consensus pattern (20 bp):   
ACTGTACAGATGAGATTAAC
Done.