Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017457.1 Corchorus olitorius cultivar O-4 contig17490, 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, 888

Length: 1481
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33


Found at i:203 original size:21 final size:20

Alignment explanation


    Indices: 162--211  Score: 64
    Period size: 21  Copynumber: 2.5  Consensus size: 20

        152 GATTATGTAA

                           **   
        162 ATGCAAAATGTGAAATTAAT
          1 ATGCAAAATGTGAAACGAAT

                          *      
        182 ATGCGAAAATGTGATACGAAT
          1 ATGC-AAAATGTGAAACGAAT

                     
        203 ATGCAAAAT
          1 ATGCAAAAT

        212 AACATAACAA


Statistics
Matches: 26,  Mismatches: 3, Indels: 2
        0.84            0.10        0.06

Matches are distributed among these distances:
  20    9  0.35
  21   17  0.65

ACGTcount: A:0.48, C:0.08, G:0.18, T:0.26


Consensus pattern (20 bp):   
ATGCAAAATGTGAAACGAAT

Found at i:664 original size:52 final size:50

Alignment explanation


    Indices: 600--830  Score: 345
    Period size: 50  Copynumber: 4.5  Consensus size: 50

        590 CGATCAATTT

                   *     *   *        *                         
        600 CTTTGAATTGTCTTCCACTCTAATATATTAAAAGGACCGTCTTCCGCTTATC
          1 CTTTGAACTGTCTACCAAT-TAA-ATCTTAAAAGGACCGTCTTCCGCTTATC

                                *      *                      
        652 CTTTGAACTGTCTACCAATTCAATCTTGAAAGGACCGTCTTCCGCTTATC
          1 CTTTGAACTGTCTACCAATTAAATCTTAAAAGGACCGTCTTCCGCTTATC

                                *                               
        702 CTTTGAACTGTCTACCAATTCAATCTTATAAAAGGACCGTCTTCCGCTTATC
          1 CTTTGAACTGTCTACCAATTAAATC-T-TAAAAGGACCGTCTTCCGCTTATC

                                *                             
        754 CTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
          1 CTTTGAACTGTCTACCAATTAAATCTTAAAAGGACCGTCTTCCGCTTATC

                                *      
        804 CTTTGAACTGTCTACCAATTCAATCTT
          1 CTTTGAACTGTCTACCAATTAAATCTT

        831 GATATCTGGT


Statistics
Matches: 170,  Mismatches: 7, Indels: 6
        0.93            0.04        0.03

Matches are distributed among these distances:
  50  102  0.60
  51    4  0.02
  52   64  0.38

ACGTcount: A:0.26, C:0.27, G:0.12, T:0.36


Consensus pattern (50 bp):   
CTTTGAACTGTCTACCAATTAAATCTTAAAAGGACCGTCTTCCGCTTATC

Found at i:776 original size:102 final size:102

Alignment explanation


    Indices: 628--830  Score: 397
    Period size: 102  Copynumber: 2.0  Consensus size: 102

        618 TCTAATATAT

                                                               *             
        628 TAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTGAAAGGACCGTCTT
          1 TAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTT

                                                 
        693 CCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTA
         66 CCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTA

                                                                             
        730 TAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTT
          1 TAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTT

                                                
        795 CCGCTTATCCTTTGAACTGTCTACCAATTCAATCTT
         66 CCGCTTATCCTTTGAACTGTCTACCAATTCAATCTT

        831 GATATCTGGT


Statistics
Matches: 100,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
 102  100  1.00

ACGTcount: A:0.26, C:0.28, G:0.12, T:0.34


Consensus pattern (102 bp):   
TAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTT
CCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTA

Found at i:852 original size:50 final size:50

Alignment explanation


    Indices: 627--830  Score: 381
    Period size: 50  Copynumber: 4.0  Consensus size: 50

        617 CTCTAATATA

                                                              
        627 TTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATC
          1 TTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATC

              *                                               
        677 TTGAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATC
          1 TTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATC

                                                                
        727 TTATAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATC
          1 -T-TAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATC

                                                              
        779 TTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATC
          1 TTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATC

              
        829 TT
          1 TT

        831 GATATCTGGT


Statistics
Matches: 150,  Mismatches: 2, Indels: 4
        0.96            0.01        0.03

Matches are distributed among these distances:
  50  100  0.67
  51    2  0.01
  52   48  0.32

ACGTcount: A:0.25, C:0.27, G:0.12, T:0.35


Consensus pattern (50 bp):   
TTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATC
Done.