Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015499.1 Corchorus olitorius cultivar O-4 contig15532, 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: 9833
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.34


Found at i:627 original size:11 final size:11

Alignment explanation


    Indices: 585--627  Score: 50
    Period size: 11  Copynumber: 3.9  Consensus size: 11

        575 TAACTATTAC

                       
        585 TTAACCATAGA
          1 TTAACCATAGA

            *          
        596 CTAACCATAGA
          1 TTAACCATAGA

                 *    *
        607 TTAACTATAGC
          1 TTAACCATAGA

              *       
        618 TTGACCATAG
          1 TTAACCATAG

        628 GTTAGTAATA


Statistics
Matches: 26,  Mismatches: 6, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  11   26  1.00

ACGTcount: A:0.40, C:0.21, G:0.12, T:0.28


Consensus pattern (11 bp):   
TTAACCATAGA

Found at i:1836 original size:26 final size:27

Alignment explanation


    Indices: 1800--1850  Score: 86
    Period size: 26  Copynumber: 1.9  Consensus size: 27

       1790 TTTTTTTGAA

                                       
       1800 AAATCCAAATTAAAAAAA-AAACTTAG
          1 AAATCCAAATTAAAAAAATAAACTTAG

                  *                  
       1826 AAATCCCAATTAAAAAAATAAACTT
          1 AAATCCAAATTAAAAAAATAAACTT

       1851 TAAAAGAAAA


Statistics
Matches: 23,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  26   17  0.74
  27    6  0.26

ACGTcount: A:0.63, C:0.14, G:0.02, T:0.22


Consensus pattern (27 bp):   
AAATCCAAATTAAAAAAATAAACTTAG

Found at i:2934 original size:60 final size:60

Alignment explanation


    Indices: 2861--2977  Score: 189
    Period size: 60  Copynumber: 1.9  Consensus size: 60

       2851 TGTAAATATG

                                                  *                     
       2861 ATCACCTGGTTCGAGGGCAACCATTGGTTTCTCGATTGGCTCGAGAACCCTTGGTTTTTC
          1 ATCACCTGGTTCGAGGGCAACCATTGGTTTCTCGATTGACTCGAGAACCCTTGGTTTTTC

                                  *   *            * *               
       2921 ATCACCTGGTTCGAGGGCAACCCTTGTTTTCTCGATTGATTTGAGAACCCTTGGTTT
          1 ATCACCTGGTTCGAGGGCAACCATTGGTTTCTCGATTGACTCGAGAACCCTTGGTTT

       2978 GGGAACCAAG


Statistics
Matches: 52,  Mismatches: 5, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  60   52  1.00

ACGTcount: A:0.17, C:0.24, G:0.24, T:0.35


Consensus pattern (60 bp):   
ATCACCTGGTTCGAGGGCAACCATTGGTTTCTCGATTGACTCGAGAACCCTTGGTTTTTC

Found at i:3029 original size:27 final size:27

Alignment explanation


    Indices: 2990--3071  Score: 155
    Period size: 27  Copynumber: 3.0  Consensus size: 27

       2980 GAACCAAGTT

                    *                  
       2990 GATTGGTTCGAGAACCCTTGTTTTTTC
          1 GATTGGTTTGAGAACCCTTGTTTTTTC

                                       
       3017 GATTGGTTTGAGAACCCTTGTTTTTTC
          1 GATTGGTTTGAGAACCCTTGTTTTTTC

                                       
       3044 GATTGGTTTGAGAACCCTTGTTTTTTC
          1 GATTGGTTTGAGAACCCTTGTTTTTTC

             
       3071 G
          1 G

       3072 GTCATTCTTC


Statistics
Matches: 54,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  27   54  1.00

ACGTcount: A:0.15, C:0.16, G:0.23, T:0.46


Consensus pattern (27 bp):   
GATTGGTTTGAGAACCCTTGTTTTTTC

Found at i:3496 original size:3 final size:3

Alignment explanation


    Indices: 3490--3541  Score: 104
    Period size: 3  Copynumber: 17.3  Consensus size: 3

       3480 AAAGGAGTAG

                                                                           
       3490 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
          1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA

                 
       3538 TAA T
          1 TAA T

       3542 CCATATGATG


Statistics
Matches: 49,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   49  1.00

ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35


Consensus pattern (3 bp):   
TAA

Found at i:7981 original size:13 final size:13

Alignment explanation


    Indices: 7963--7987  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       7953 TTAGAATTCA

                         
       7963 AAATAATATTTAT
          1 AAATAATATTTAT

                        
       7976 AAATAATATTTA
          1 AAATAATATTTA

       7988 AAACATTGAA


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44


Consensus pattern (13 bp):   
AAATAATATTTAT

Found at i:8369 original size:2 final size:2

Alignment explanation


    Indices: 8362--8390  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

       8352 TGTTTAAATA

                                                       
       8362 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       8391 CTAGTTAAAG


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

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


Consensus pattern (2 bp):   
AT

Done.