Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000654.1 Corchorus capsularis cultivar CVL-1 contig00654, 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, 908

Length: 1514
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30


Found at i:746 original size:13 final size:13

Alignment explanation


    Indices: 728--837  Score: 87
    Period size: 13  Copynumber: 8.1  Consensus size: 13

        718 CAATATCTAA

                         
        728 AAACTGATTTCAG
          1 AAACTGATTTCAG

                    *     
        741 AAACTGAAATT-AG
          1 AAACTG-ATTTCAG

              *               
        754 AATCTGATTTCATTTCAG
          1 AAACTGA--T--T-TCAG

                         
        772 AAACTGATTTCAG
          1 AAACTGATTTCAG

             **          
        785 ATTCTGATTTCAG
          1 AAACTGATTTCAG

                         
        798 AAACTGATTTCAG
          1 AAACTGATTTCAG

            **        *  
        811 TGACTGATTTTAG
          1 AAACTGATTTCAG

                   *     
        824 AAACTGAATTCAG
          1 AAACTGATTTCAG

             
        837 A
          1 A

        838 TTCTGAAATT


Statistics
Matches: 75,  Mismatches: 15, Indels: 14
        0.72            0.14        0.13

Matches are distributed among these distances:
  12    1  0.01
  13   59  0.79
  14    4  0.05
  16    2  0.03
  17    1  0.01
  18    8  0.11

ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35


Consensus pattern (13 bp):   
AAACTGATTTCAG

Found at i:769 original size:31 final size:31

Alignment explanation


    Indices: 734--796  Score: 92
    Period size: 31  Copynumber: 2.0  Consensus size: 31

        724 CTAAAAACTG

                                            
        734 ATTTCAGAAACTGAAATT-AGAATCTGATTTC
          1 ATTTCAGAAACTG-AATTCAGAATCTGATTTC

                          *      *         
        765 ATTTCAGAAACTGATTTCAGATTCTGATTTC
          1 ATTTCAGAAACTGAATTCAGAATCTGATTTC

             
        796 A
          1 A

        797 GAAACTGATT


Statistics
Matches: 29,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  30    3  0.10
  31   26  0.90

ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38


Consensus pattern (31 bp):   
ATTTCAGAAACTGAATTCAGAATCTGATTTC

Found at i:798 original size:26 final size:26

Alignment explanation


    Indices: 765--903  Score: 140
    Period size: 26  Copynumber: 5.3  Consensus size: 26

        755 ATCTGATTTC

                          *           
        765 ATTTCAGAAACTGATTTCAGATTCTG
          1 ATTTCAGAAACTGAATTCAGATTCTG

                          *        *   
        791 ATTTCAGAAACTGATTTCAG-TGACTG
          1 ATTTCAGAAACTGAATTCAGAT-TCTG

                *                     
        817 ATTTTAGAAACTGAATTCAGATTCTG
          1 ATTTCAGAAACTGAATTCAGATTCTG

              *             *        *   
        843 AAATT-AGAAACTGAAATCAGACTGACTG
          1 -ATTTCAGAAACTGAATTCAGA-T-TCTG

                            *          
        871 ATTTCA-AAATCTGAAATCAGATTCTG
          1 ATTTCAGAAA-CTGAATTCAGATTCTG

                   
        897 ATTTCAG
          1 ATTTCAG

        904 TCTCACTTCA


Statistics
Matches: 96,  Mismatches: 9, Indels: 15
        0.80            0.08        0.12

Matches are distributed among these distances:
  25    1  0.01
  26   68  0.71
  27   12  0.12
  28   15  0.16

ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34


Consensus pattern (26 bp):   
ATTTCAGAAACTGAATTCAGATTCTG

Found at i:852 original size:52 final size:54

Alignment explanation


    Indices: 765--897  Score: 166
    Period size: 52  Copynumber: 2.5  Consensus size: 54

        755 ATCTGATTTC

                          *             *            **           
        765 ATTTCAGAAACTGATTTCAGATTCTG-ATTTCAGAAACTGATTTCAG-TGACTG
          1 ATTTCAGAAACTGAATTCAGATTCTGAAATTCAGAAACTGAAATCAGATGACTG

                *                                                  
        817 ATTTTAGAAACTGAATTCAGATTCTGAAATT-AGAAACTGAAATCAGACTGACTG
          1 ATTTCAGAAACTGAATTCAGATTCTGAAATTCAGAAACTGAAATCAGA-TGACTG

                            *           
        871 ATTTCA-AAATCTGAAATCAGATTCTGA
          1 ATTTCAGAAA-CTGAATTCAGATTCTGA

        898 TTTCAGTCTC


Statistics
Matches: 70,  Mismatches: 7, Indels: 6
        0.84            0.08        0.07

Matches are distributed among these distances:
  52   37  0.53
  53    6  0.09
  54   27  0.39

ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33


Consensus pattern (54 bp):   
ATTTCAGAAACTGAATTCAGATTCTGAAATTCAGAAACTGAAATCAGATGACTG

Found at i:992 original size:25 final size:23

Alignment explanation


    Indices: 927--981  Score: 110
    Period size: 23  Copynumber: 2.4  Consensus size: 23

        917 AACAATAAGA

                                   
        927 AAAAAACAGCAAGTTTGAGGGGG
          1 AAAAAACAGCAAGTTTGAGGGGG

                                   
        950 AAAAAACAGCAAGTTTGAGGGGG
          1 AAAAAACAGCAAGTTTGAGGGGG

                     
        973 AAAAAACAG
          1 AAAAAACAG

        982 AATTTGTTTG


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  23   32  1.00

ACGTcount: A:0.49, C:0.09, G:0.31, T:0.11


Consensus pattern (23 bp):   
AAAAAACAGCAAGTTTGAGGGGG
Done.