Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018549.1 Corchorus olitorius cultivar O-4 contig18582, 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: 10142
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37


Found at i:1270 original size:18 final size:18

Alignment explanation


    Indices: 1247--1315  Score: 75
    Period size: 18  Copynumber: 3.8  Consensus size: 18

       1237 TACAAAATAT

                              
       1247 TGTTCCACTGCCGCAGGA
          1 TGTTCCACTGCCGCAGGA

                     ***    * 
       1265 TGTTCCACTATTGCAGAA
          1 TGTTCCACTGCCGCAGGA

                   *  *       
       1283 TGTTCCATTGTCGCAGGA
          1 TGTTCCACTGCCGCAGGA

                  *        
       1301 TGTTCCGCTGCCGCA
          1 TGTTCCACTGCCGCA

       1316 ATCCTCAGAT


Statistics
Matches: 40,  Mismatches: 11, Indels: 0
        0.78            0.22        0.00

Matches are distributed among these distances:
  18   40  1.00

ACGTcount: A:0.17, C:0.29, G:0.25, T:0.29


Consensus pattern (18 bp):   
TGTTCCACTGCCGCAGGA

Found at i:3095 original size:17 final size:17

Alignment explanation


    Indices: 3073--3105  Score: 57
    Period size: 17  Copynumber: 1.9  Consensus size: 17

       3063 TTTGTAAAGT

                             
       3073 TTGTTACACTAGATAGG
          1 TTGTTACACTAGATAGG

                  *         
       3090 TTGTTATACTAGATAG
          1 TTGTTACACTAGATAG

       3106 CTCTATGTAT


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

Matches are distributed among these distances:
  17   15  1.00

ACGTcount: A:0.30, C:0.09, G:0.21, T:0.39


Consensus pattern (17 bp):   
TTGTTACACTAGATAGG

Found at i:3662 original size:15 final size:15

Alignment explanation


    Indices: 3643--3680  Score: 53
    Period size: 14  Copynumber: 2.7  Consensus size: 15

       3633 TCAAAACATA

                           
       3643 ATTTTT-TAAAATTT
          1 ATTTTTATAAAATTT

                     *     
       3657 ATTTTTATATAATTT
          1 ATTTTTATAAAATTT

                      
       3672 A-TTTTATAA
          1 ATTTTTATAA

       3681 TTAAAGGTCA


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  14   13  0.62
  15    8  0.38

ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63


Consensus pattern (15 bp):   
ATTTTTATAAAATTT

Found at i:4477 original size:20 final size:20

Alignment explanation


    Indices: 4454--4492  Score: 51
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       4444 TTTAAGTATT

                 *     *        
       4454 TAATTTTAATTTTTTTGATG
          1 TAATTATAATTGTTTTGATG

                   *           
       4474 TAATTATGATTGTTTTGAT
          1 TAATTATAATTGTTTTGAT

       4493 TATGAACAAG


Statistics
Matches: 16,  Mismatches: 3, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  20   16  1.00

ACGTcount: A:0.26, C:0.00, G:0.13, T:0.62


Consensus pattern (20 bp):   
TAATTATAATTGTTTTGATG
Done.