Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024044.1 Corchorus olitorius cultivar O-4 contig24077, 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: 9416
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.29


Found at i:1090 original size:15 final size:17

Alignment explanation


    Indices: 1070--1102  Score: 52
    Period size: 15  Copynumber: 2.1  Consensus size: 17

       1060 AGCTTCCTAG

                             
       1070 AAAAACT-AAAA-AAAA
          1 AAAAACTCAAAAGAAAA

                             
       1085 AAAAACTCAAAAGAAAA
          1 AAAAACTCAAAAGAAAA

             
       1102 A
          1 A

       1103 TTGTTAGTAG


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

Matches are distributed among these distances:
  15    7  0.44
  16    4  0.25
  17    5  0.31

ACGTcount: A:0.82, C:0.09, G:0.03, T:0.06


Consensus pattern (17 bp):   
AAAAACTCAAAAGAAAA

Found at i:1617 original size:15 final size:16

Alignment explanation


    Indices: 1593--1632  Score: 55
    Period size: 15  Copynumber: 2.6  Consensus size: 16

       1583 AGAGGTTGAA

                 *          
       1593 AGAAAGCAATTAAAC-
          1 AGAAAACAATTAAACT

                        *   
       1608 AGAAAACAATTATACT
          1 AGAAAACAATTAAACT

                     
       1624 AGAAAACAA
          1 AGAAAACAA

       1633 AACAAAGTAA


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

Matches are distributed among these distances:
  15   13  0.59
  16    9  0.41

ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15


Consensus pattern (16 bp):   
AGAAAACAATTAAACT

Found at i:3043 original size:20 final size:20

Alignment explanation


    Indices: 3018--3078  Score: 59
    Period size: 20  Copynumber: 2.9  Consensus size: 20

       3008 AATCTTCAAT

                                
       3018 GTCTTCAAATCTCCAAATAA
          1 GTCTTCAAATCTCCAAATAA

                           *    * *
       3038 GTCTTCAATGAGTCTTCAAACAC
          1 GTCTTCAA--A-TCTCCAAATAA

                  *           
       3061 GTCTTCGAATCTCCAAAT
          1 GTCTTCAAATCTCCAAAT

       3079 CTATGCTCAA


Statistics
Matches: 32,  Mismatches: 6, Indels: 6
        0.73            0.14        0.14

Matches are distributed among these distances:
  20   15  0.47
  21    1  0.03
  22    1  0.03
  23   15  0.47

ACGTcount: A:0.33, C:0.26, G:0.10, T:0.31


Consensus pattern (20 bp):   
GTCTTCAAATCTCCAAATAA

Found at i:9193 original size:30 final size:28

Alignment explanation


    Indices: 9150--9206  Score: 87
    Period size: 30  Copynumber: 2.0  Consensus size: 28

       9140 TTAGGATTAG

                                  *     
       9150 TTATTTATGCTTTAATTTTCAATTTTCT
          1 TTATTTATGCTTTAATTTTCAAGTTTCT

                                         
       9178 TTATCTTATGTCTTTAATTTTCAAGTTTC
          1 TTAT-TTATG-CTTTAATTTTCAAGTTTC

       9207 ATTAATAAAC


Statistics
Matches: 26,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
  28    4  0.15
  29    5  0.19
  30   17  0.65

ACGTcount: A:0.21, C:0.12, G:0.05, T:0.61


Consensus pattern (28 bp):   
TTATTTATGCTTTAATTTTCAAGTTTCT
Done.