Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019600.1 Corchorus olitorius cultivar O-4 contig19633, 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: 16021
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33


Found at i:930 original size:19 final size:19

Alignment explanation


    Indices: 906--979  Score: 148
    Period size: 19  Copynumber: 3.9  Consensus size: 19

        896 TCATCAACAC

                               
        906 TAATCAAATGATAATGTGT
          1 TAATCAAATGATAATGTGT

                               
        925 TAATCAAATGATAATGTGT
          1 TAATCAAATGATAATGTGT

                               
        944 TAATCAAATGATAATGTGT
          1 TAATCAAATGATAATGTGT

                             
        963 TAATCAAATGATAATGT
          1 TAATCAAATGATAATGT

        980 ACCAATAAAC


Statistics
Matches: 55,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   55  1.00

ACGTcount: A:0.43, C:0.05, G:0.15, T:0.36


Consensus pattern (19 bp):   
TAATCAAATGATAATGTGT

Found at i:1045 original size:31 final size:30

Alignment explanation


    Indices: 1007--1091  Score: 95
    Period size: 31  Copynumber: 2.9  Consensus size: 30

        997 ACAATAATCA

                      *                    
       1007 AATGATAATACACCAATAATTAATTATTACT
          1 AATGATAATAAACCAATAATTAATTATTA-T

                                     *    
       1038 AATGATAATAAACCAATAATT--TTCTTAT
          1 AATGATAATAAACCAATAATTAATTATTAT

             *         *               
       1066 -TTGAATAATATACCAATAATTAATTA
          1 AATG-ATAATAAACCAATAATTAATTA

       1092 CTAAGGCCCA


Statistics
Matches: 46,  Mismatches: 5, Indels: 7
        0.79            0.09        0.12

Matches are distributed among these distances:
  27    2  0.04
  28   17  0.37
  29    5  0.11
  30    2  0.04
  31   20  0.43

ACGTcount: A:0.48, C:0.11, G:0.04, T:0.38


Consensus pattern (30 bp):   
AATGATAATAAACCAATAATTAATTATTAT

Found at i:1572 original size:14 final size:14

Alignment explanation


    Indices: 1553--1579  Score: 54
    Period size: 14  Copynumber: 1.9  Consensus size: 14

       1543 GGATGCCATG

                          
       1553 TATATATATGTATA
          1 TATATATATGTATA

                         
       1567 TATATATATGTAT
          1 TATATATATGTAT

       1580 GTGTGTGTGT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   13  1.00

ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52


Consensus pattern (14 bp):   
TATATATATGTATA

Found at i:2601 original size:17 final size:17

Alignment explanation


    Indices: 2575--2609  Score: 61
    Period size: 17  Copynumber: 2.1  Consensus size: 17

       2565 AAAAAAAAAA

                             
       2575 TTTATCAATGTTGTTTT
          1 TTTATCAATGTTGTTTT

                 *           
       2592 TTTATTAATGTTGTTTT
          1 TTTATCAATGTTGTTTT

             
       2609 T
          1 T

       2610 ATTAAGAGTT


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  17   17  1.00

ACGTcount: A:0.17, C:0.03, G:0.11, T:0.69


Consensus pattern (17 bp):   
TTTATCAATGTTGTTTT

Found at i:2610 original size:15 final size:16

Alignment explanation


    Indices: 2575--2614  Score: 55
    Period size: 17  Copynumber: 2.5  Consensus size: 16

       2565 AAAAAAAAAA

                 *           
       2575 TTTATCAATGTTGTTTT
          1 TTTATTAATGTTG-TTT

                            
       2592 TTTATTAATGTTG-TT
          1 TTTATTAATGTTGTTT

                    
       2607 TTTATTAA
          1 TTTATTAA

       2615 GAGTTATTGT


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

Matches are distributed among these distances:
  15   10  0.45
  17   12  0.55

ACGTcount: A:0.23, C:0.03, G:0.10, T:0.65


Consensus pattern (16 bp):   
TTTATTAATGTTGTTT

Found at i:13319 original size:16 final size:15

Alignment explanation


    Indices: 13281--13322  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

      13271 ACAGAGGTTG

                  *        
      13281 ACAGAATACAATTAA
          1 ACAGAAAACAATTAA

                           
      13296 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
      13311 ACTAGAAAACAA
          1 AC-AGAAAACAA

      13323 AACAAAGTAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   16  0.64
  16    9  0.36

ACGTcount: A:0.64, C:0.14, G:0.07, T:0.14


Consensus pattern (15 bp):   
ACAGAAAACAATTAA
Done.