Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010129.1 Corchorus olitorius cultivar O-4 contig10161, 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: 16997
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35


Found at i:3598 original size:2 final size:2

Alignment explanation


    Indices: 3591--3615  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

       3581 CCACATTAAG

                                                 
       3591 TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA T

       3616 CCTAATATCC


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:4574 original size:12 final size:12

Alignment explanation


    Indices: 4557--4584  Score: 56
    Period size: 12  Copynumber: 2.3  Consensus size: 12

       4547 AAAATTACAA

                        
       4557 TAAGCCATTAGC
          1 TAAGCCATTAGC

                        
       4569 TAAGCCATTAGC
          1 TAAGCCATTAGC

                
       4581 TAAG
          1 TAAG

       4585 TCATAATTAA


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   16  1.00

ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25


Consensus pattern (12 bp):   
TAAGCCATTAGC

Found at i:5362 original size:13 final size:13

Alignment explanation


    Indices: 5344--5373  Score: 51
    Period size: 13  Copynumber: 2.3  Consensus size: 13

       5334 AAACTTTATC

                     *   
       5344 AAAATTAAATAAG
          1 AAAATTAAAAAAG

                         
       5357 AAAATTAAAAAAG
          1 AAAATTAAAAAAG

                
       5370 AAAA
          1 AAAA

       5374 GCACACAGAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  13   16  1.00

ACGTcount: A:0.77, C:0.00, G:0.07, T:0.17


Consensus pattern (13 bp):   
AAAATTAAAAAAG

Found at i:14011 original size:16 final size:17

Alignment explanation


    Indices: 13983--14014  Score: 57
    Period size: 16  Copynumber: 1.9  Consensus size: 17

      13973 CTTTTCTAGA

                             
      13983 TTCTTTGTCTTTTTTTT
          1 TTCTTTGTCTTTTTTTT

                            
      14000 TTCTTT-TCTTTTTTT
          1 TTCTTTGTCTTTTTTT

      14015 ATTTATTTAA


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

Matches are distributed among these distances:
  16    9  0.60
  17    6  0.40

ACGTcount: A:0.00, C:0.12, G:0.03, T:0.84


Consensus pattern (17 bp):   
TTCTTTGTCTTTTTTTT

Found at i:15003 original size:6 final size:6

Alignment explanation


    Indices: 14992--15021  Score: 60
    Period size: 6  Copynumber: 5.0  Consensus size: 6

      14982 ATATTTGCCA

                                              
      14992 TCATAT TCATAT TCATAT TCATAT TCATAT
          1 TCATAT TCATAT TCATAT TCATAT TCATAT

      15022 GACAGTGCTA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   24  1.00

ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50


Consensus pattern (6 bp):   
TCATAT

Found at i:16239 original size:23 final size:24

Alignment explanation


    Indices: 16205--16292  Score: 74
    Period size: 23  Copynumber: 3.7  Consensus size: 24

      16195 GACCGTTTAG

                  *                 
      16205 TAATATTTATAATTAAATATATAT
          1 TAATATATATAATTAAATATATAT

              *          *          
      16229 T-TTATATATAA-AAAATA-ATAT
          1 TAATATATATAATTAAATATATAT

                            *       *
      16250 TAAATATATATAATTACATATATAA
          1 T-AATATATATAATTAAATATATAT

                *      *      
      16275 TAATGTATAATTATTAAA
          1 TAATATAT-ATAATTAAA

      16293 CAGTTTAAAC


Statistics
Matches: 49,  Mismatches: 10, Indels: 9
        0.72            0.15        0.13

Matches are distributed among these distances:
  21    5  0.10
  22    5  0.10
  23   17  0.35
  24   11  0.22
  25   11  0.22

ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44


Consensus pattern (24 bp):   
TAATATATATAATTAAATATATAT

Found at i:16249 original size:21 final size:22

Alignment explanation


    Indices: 16219--16259  Score: 57
    Period size: 21  Copynumber: 1.9  Consensus size: 22

      16209 ATTTATAATT

                       **         
      16219 AAATATATATTTTATATATAAA
          1 AAATATATATTAAATATATAAA

                                
      16241 AAATA-ATATTAAATATATA
          1 AAATATATATTAAATATATA

      16260 TAATTACATA


Statistics
Matches: 17,  Mismatches: 2, Indels: 1
        0.85            0.10        0.05

Matches are distributed among these distances:
  21   12  0.71
  22    5  0.29

ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41


Consensus pattern (22 bp):   
AAATATATATTAAATATATAAA
Done.