Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012517.1 Corchorus olitorius cultivar O-4 contig12550, 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: 6366
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31


Found at i:1317 original size:14 final size:15

Alignment explanation


    Indices: 1298--1327  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       1288 CAATCAAAGC

                           
       1298 AATAAT-CAAGGAAA
          1 AATAATGCAAGGAAA

                           
       1312 AATAATGCAAGGAAA
          1 AATAATGCAAGGAAA

             
       1327 A
          1 A

       1328 TTAAAAAGAT


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

Matches are distributed among these distances:
  14    6  0.40
  15    9  0.60

ACGTcount: A:0.63, C:0.07, G:0.17, T:0.13


Consensus pattern (15 bp):   
AATAATGCAAGGAAA

Found at i:1711 original size:21 final size:21

Alignment explanation


    Indices: 1685--1743  Score: 64
    Period size: 21  Copynumber: 2.8  Consensus size: 21

       1675 GGAATGGCGA

                                 
       1685 TGGCACGGGCATGGCCAGTGG
          1 TGGCACGGGCATGGCCAGTGG

                      * **  *    
       1706 TGGCACGGGCTTAACCGGTGG
          1 TGGCACGGGCATGGCCAGTGG

                      *      
       1727 TGGCACGGTGAATGGCC
          1 TGGCACGG-GCATGGCC

       1744 GGTAATGGCT


Statistics
Matches: 29,  Mismatches: 8, Indels: 1
        0.76            0.21        0.03

Matches are distributed among these distances:
  21   25  0.86
  22    4  0.14

ACGTcount: A:0.15, C:0.24, G:0.44, T:0.17


Consensus pattern (21 bp):   
TGGCACGGGCATGGCCAGTGG

Found at i:4849 original size:29 final size:28

Alignment explanation


    Indices: 4816--4898  Score: 107
    Period size: 28  Copynumber: 2.9  Consensus size: 28

       4806 AAGAAAATAT

                   *                     
       4816 ATTTTTTATTTCTAAAAACGCAGAAAC-A
          1 ATTTTTTTTTTCTAAAAACGCA-AAACAA

                       *                  
       4844 ATTTTTTTTTTTTAGAAAACGCAAAACAAA
          1 ATTTTTTTTTTCTA-AAAACGCAAAAC-AA

                                      
       4874 ATTTTTTTTTTC-AAAAACGCAAAAC
          1 ATTTTTTTTTTCTAAAAACGCAAAAC

       4899 TAATAAATTA


Statistics
Matches: 49,  Mismatches: 3, Indels: 6
        0.84            0.05        0.10

Matches are distributed among these distances:
  28   28  0.57
  29    9  0.18
  30   12  0.24

ACGTcount: A:0.42, C:0.13, G:0.06, T:0.39


Consensus pattern (28 bp):   
ATTTTTTTTTTCTAAAAACGCAAAACAA

Found at i:4975 original size:23 final size:23

Alignment explanation


    Indices: 4912--4975  Score: 60
    Period size: 23  Copynumber: 2.8  Consensus size: 23

       4902 TAAATTAAAA

                  *  *             
       4912 ACGCAAGAATTTTTTTTTTTATG
          1 ACGCAAAAAATTTTTTTTTTATG

                          **         
       4935 ACGCAGAAACAA--AATTTTTTATG
          1 ACGCA-AAA-AATTTTTTTTTTATG

                              
       4958 ACGCAAAAAATTTTTTTT
          1 ACGCAAAAAATTTTTTTT

       4976 CCGATGCAAA


Statistics
Matches: 31,  Mismatches: 6, Indels: 8
        0.69            0.13        0.18

Matches are distributed among these distances:
  21    2  0.06
  22    3  0.10
  23   23  0.74
  24    2  0.06
  25    1  0.03

ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42


Consensus pattern (23 bp):   
ACGCAAAAAATTTTTTTTTTATG

Found at i:5367 original size:15 final size:15

Alignment explanation


    Indices: 5347--5384  Score: 58
    Period size: 15  Copynumber: 2.5  Consensus size: 15

       5337 ACAGAGATTG

                           
       5347 ACAGAAAGCAATTAA
          1 ACAGAAAGCAATTAA

                   *       
       5362 ACAGAAATCAATTAA
          1 ACAGAAAGCAATTAA

                    
       5377 ACTAGAAA
          1 AC-AGAAA

       5385 ACATAGCAGA


Statistics
Matches: 21,  Mismatches: 1, Indels: 1
        0.91            0.04        0.04

Matches are distributed among these distances:
  15   16  0.76
  16    5  0.24

ACGTcount: A:0.61, C:0.13, G:0.11, T:0.16


Consensus pattern (15 bp):   
ACAGAAAGCAATTAA
Done.