Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015316.1 Corchorus olitorius cultivar O-4 contig15349, 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: 21585
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33


Found at i:1688 original size:17 final size:18

Alignment explanation


    Indices: 1668--1704  Score: 58
    Period size: 17  Copynumber: 2.1  Consensus size: 18

       1658 CTTCTTTTCC

                              
       1668 ATATTATTTTGT-TCTCT
          1 ATATTATTTTGTCTCTCT

                 *            
       1685 ATATTCTTTTGTCTCTCT
          1 ATATTATTTTGTCTCTCT

              
       1703 AT
          1 AT

       1705 TCTCTTCTCT


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

Matches are distributed among these distances:
  17   11  0.61
  18    7  0.39

ACGTcount: A:0.16, C:0.16, G:0.05, T:0.62


Consensus pattern (18 bp):   
ATATTATTTTGTCTCTCT

Found at i:1710 original size:18 final size:17

Alignment explanation


    Indices: 1645--1704  Score: 57
    Period size: 17  Copynumber: 3.5  Consensus size: 17

       1635 ATTTTTCTCA

                 *       *  *
       1645 TTCTCCATATTCTCTTC
          1 TTCTCTATATTCTTTTG

              *  *     *     
       1662 TTTTCCATATTATTTTG
          1 TTCTCTATATTCTTTTG

                             
       1679 TTCTCTATATTCTTTTG
          1 TTCTCTATATTCTTTTG

                     
       1696 TCTCTCTAT
          1 T-TCTCTAT

       1705 TCTCTTCTCT


Statistics
Matches: 35,  Mismatches: 7, Indels: 1
        0.81            0.16        0.02

Matches are distributed among these distances:
  17   28  0.80
  18    7  0.20

ACGTcount: A:0.13, C:0.23, G:0.03, T:0.60


Consensus pattern (17 bp):   
TTCTCTATATTCTTTTG

Found at i:4891 original size:17 final size:17

Alignment explanation


    Indices: 4871--4943  Score: 60
    Period size: 17  Copynumber: 4.4  Consensus size: 17

       4861 TCTCCCATTC

                             
       4871 TCCATATTCTCTTCTTT
          1 TCCATATTCTCTTCTTT

                    * *  *  *
       4888 TCCATATTATTTTGTTC
          1 TCCATATTCTCTTCTTT

              *           *  
       4905 TCTATATTCTCTT-GTT
          1 TCCATATTCTCTTCTTT

                        *     
       4921 TCTC-TATTCTCGTCTTT
          1 TC-CATATTCTCTTCTTT

                  
       4938 TCCATA
          1 TCCATA

       4944 CTTCAATTCT


Statistics
Matches: 41,  Mismatches: 12, Indels: 6
        0.69            0.20        0.10

Matches are distributed among these distances:
  16   12  0.29
  17   29  0.71

ACGTcount: A:0.14, C:0.25, G:0.04, T:0.58


Consensus pattern (17 bp):   
TCCATATTCTCTTCTTT

Found at i:5235 original size:15 final size:15

Alignment explanation


    Indices: 5215--5245  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       5205 CAAATTTCTT

                           
       5215 TTTCTTTATTTTTTC
          1 TTTCTTTATTTTTTC

                   *       
       5230 TTTCTTTTTTTTTTC
          1 TTTCTTTATTTTTTC

             
       5245 T
          1 T

       5246 CTCACCGAAC


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84


Consensus pattern (15 bp):   
TTTCTTTATTTTTTC

Found at i:12613 original size:131 final size:133

Alignment explanation


    Indices: 12455--12700  Score: 370
    Period size: 131  Copynumber: 1.8  Consensus size: 133

      12445 ATAGTTTTAC

                          *    *                       *                     
      12455 TTTTACTCAACTAAGAACTTTATTTTTATTTAATTAAATCTAATATCCTTATAACTATTTTATTT
          1 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAACATCCTTATAACTATTTTATTT

               **  *      *                                                  
      12520 TTATTATTTTACTATTTTAATTAAAAAACTT-AT-ATATATTAGAATTTTTTAAATATACTTTTA
         66 TTACCATATTACTAATTTAATTAAAAAACTTAATAATATATTAGAATTTTTTAAATATACTTTTA

               
      12583 TAG
        131 TAG

                             *                                   *           
      12586 TTTTACTCAACTAAAAAGTCTATTTTTATTTAATTAAATCTAACATCCTTATACCTATTTTATTT
          1 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAACATCCTTATAACTATTTTATTT

                                    *                         
      12651 TTACCATATTACTAATTTAATTAAGAAACTTAGATAGATATATTAGAATT
         66 TTACCATATTACTAATTTAATTAAAAAACTTA-ATA-ATATATTAGAATT

      12701 GTTAAAAATA


Statistics
Matches: 101,  Mismatches: 10, Indels: 4
        0.88            0.09        0.03

Matches are distributed among these distances:
 131   86  0.85
 133    2  0.02
 135   13  0.13

ACGTcount: A:0.37, C:0.10, G:0.03, T:0.49


Consensus pattern (133 bp):   
TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAACATCCTTATAACTATTTTATTT
TTACCATATTACTAATTTAATTAAAAAACTTAATAATATATTAGAATTTTTTAAATATACTTTTA
TAG

Found at i:16710 original size:11 final size:11

Alignment explanation


    Indices: 16681--16710  Score: 51
    Period size: 11  Copynumber: 2.7  Consensus size: 11

      16671 GATTCTACAG

                   *   
      16681 AAGATTTATCA
          1 AAGATTTCTCA

                       
      16692 AAGATTTCTCA
          1 AAGATTTCTCA

                    
      16703 AAGATTTC
          1 AAGATTTC

      16711 AACACCAATG


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  11   18  1.00

ACGTcount: A:0.40, C:0.13, G:0.10, T:0.37


Consensus pattern (11 bp):   
AAGATTTCTCA
Done.