Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000405.1 Corchorus olitorius cultivar O-4 contig00405, 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: 5761
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34


Found at i:115 original size:29 final size:28

Alignment explanation


    Indices: 76--131  Score: 94
    Period size: 29  Copynumber: 2.0  Consensus size: 28

         66 GTTATTCCAC

                  *                      
         76 GTTCTTTAGCGTTCTTGAAAATTAGAAAT
          1 GTTCTTGAGCGTTCTTG-AAATTAGAAAT

                                       
        105 GTTCTTGAGCGTTCTTGAAATTAGAAA
          1 GTTCTTGAGCGTTCTTGAAATTAGAAA

        132 GTTTGAAGAA


Statistics
Matches: 26,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  28   10  0.38
  29   16  0.62

ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39


Consensus pattern (28 bp):   
GTTCTTGAGCGTTCTTGAAATTAGAAAT

Found at i:5561 original size:11 final size:11

Alignment explanation


    Indices: 5537--5571  Score: 52
    Period size: 11  Copynumber: 3.2  Consensus size: 11

       5527 TTGACAGCTT

                       
       5537 AACAAAAACAA
          1 AACAAAAACAA

               *     * 
       5548 AACGAAAACGA
          1 AACAAAAACAA

                       
       5559 AACAAAAACAA
          1 AACAAAAACAA

              
       5570 AA
          1 AA

       5572 AATAGAAAAA


Statistics
Matches: 20,  Mismatches: 4, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  11   20  1.00

ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00


Consensus pattern (11 bp):   
AACAAAAACAA

Found at i:5683 original size:2 final size:2

Alignment explanation


    Indices: 5676--5734  Score: 76
    Period size: 2  Copynumber: 32.5  Consensus size: 2

       5666 CTCATGTAAT

                                                                          
       5676 TA TA TA TA TA TA TA -A TA TA -A TA TA TA TA TA -A TA TA -A T-
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                                              
       5713 TA TA TA TA -A TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA T

       5735 TATCTCATGC


Statistics
Matches: 51,  Mismatches: 0, Indels: 12
        0.81            0.00        0.19

Matches are distributed among these distances:
   1    6  0.12
   2   45  0.88

ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47


Consensus pattern (2 bp):   
TA

Found at i:5704 original size:11 final size:11

Alignment explanation


    Indices: 5679--5731  Score: 76
    Period size: 11  Copynumber: 5.0  Consensus size: 11

       5669 ATGTAATTAT

                       
       5679 ATATATATATA
          1 ATATATATATA

                       
       5690 ATATA-ATAT-
          1 ATATATATATA

                        
       5699 ATATATAATATA
          1 ATATAT-ATATA

                       
       5711 AT-TATATATA
          1 ATATATATATA

                       
       5721 ATATATATATA
          1 ATATATATATA

       5732 TATTATCTCA


Statistics
Matches: 38,  Mismatches: 0, Indels: 8
        0.83            0.00        0.17

Matches are distributed among these distances:
   9    5  0.13
  10   11  0.29
  11   20  0.53
  12    2  0.05

ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45


Consensus pattern (11 bp):   
ATATATATATA

Found at i:5751 original size:26 final size:23

Alignment explanation


    Indices: 5672--5760  Score: 85
    Period size: 26  Copynumber: 3.7  Consensus size: 23

       5662 TTATCTCATG

                                   
       5672 TAATTATATATATATA-TA-ATA
          1 TAATTATATATATATATTATATA

                                      
       5693 TAATATATATATAATATAATTATATA
          1 TAAT-TATATAT-ATAT-ATTATATA

                                *   
       5719 TAA-TATATATATATATTATCTCA
          1 TAATTATATATATATATTATAT-A

                      *        
       5742 TGCAATTATAAATATATAT
          1 T--AATTATATATATATAT

       5761 A


Statistics
Matches: 57,  Mismatches: 2, Indels: 13
        0.79            0.03        0.18

Matches are distributed among these distances:
  21    4  0.07
  22   13  0.23
  23   10  0.18
  24    8  0.14
  25    4  0.07
  26   18  0.32

ACGTcount: A:0.49, C:0.03, G:0.01, T:0.46


Consensus pattern (23 bp):   
TAATTATATATATATATTATATA
Done.