Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022072.1 Corchorus olitorius cultivar O-4 contig22105, 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: 21502
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33


Found at i:1664 original size:15 final size:15

Alignment explanation


    Indices: 1646--1759  Score: 106
    Period size: 15  Copynumber: 7.6  Consensus size: 15

       1636 ATCATCTTTA

                 *         
       1646 GTGCCGTCAATTTCG
          1 GTGCCATCAATTTCG

                     *     
       1661 GTGCCATCAGTTTCG
          1 GTGCCATCAATTTCG

                     *   * 
       1676 GTGCCATCAGTTTTG
          1 GTGCCATCAATTTCG

               *     *     
       1691 GTGTCATCAGTTTCG
          1 GTGCCATCAATTTCG

                          * 
       1706 GTGCCATC-ATCTTTG
          1 GTGCCATCAAT-TTCG

                 *         
       1721 GTGCCGTCAATTTCG
          1 GTGCCATCAATTTCG

                 *  *       
       1736 GTGCCGTCGATGTT-G
          1 GTGCCATCAAT-TTCG

                     
       1751 GTGCCATCA
          1 GTGCCATCA

       1760 TCTTCTTCCA


Statistics
Matches: 83,  Mismatches: 13, Indels: 6
        0.81            0.13        0.06

Matches are distributed among these distances:
  14    1  0.01
  15   78  0.94
  16    4  0.05

ACGTcount: A:0.13, C:0.25, G:0.27, T:0.35


Consensus pattern (15 bp):   
GTGCCATCAATTTCG

Found at i:1680 original size:30 final size:31

Alignment explanation


    Indices: 1646--1759  Score: 119
    Period size: 30  Copynumber: 3.8  Consensus size: 31

       1636 ATCATCTTTA

                 *        *                
       1646 GTGCCGTCAAT-TTCGGTGCCATCAGTTTCG
          1 GTGCCATCAATCTTTGGTGCCATCAGTTTCG

                     *         *           
       1676 GTGCCATCAGT-TTTGGTGTCATCAGTTTCG
          1 GTGCCATCAATCTTTGGTGCCATCAGTTTCG

                                 *   *     
       1706 GTGCCATC-ATCTTTGGTGCCGTCAATTTCG
          1 GTGCCATCAATCTTTGGTGCCATCAGTTTCG

                 *  *   *            
       1736 GTGCCGTCGAT-GTTGGTGCCATCA
          1 GTGCCATCAATCTTTGGTGCCATCA

       1760 TCTTCTTCCA


Statistics
Matches: 71,  Mismatches: 11, Indels: 4
        0.83            0.13        0.05

Matches are distributed among these distances:
  29    1  0.01
  30   68  0.96
  31    2  0.03

ACGTcount: A:0.13, C:0.25, G:0.27, T:0.35


Consensus pattern (31 bp):   
GTGCCATCAATCTTTGGTGCCATCAGTTTCG

Found at i:3010 original size:18 final size:18

Alignment explanation


    Indices: 2987--3055  Score: 102
    Period size: 18  Copynumber: 3.8  Consensus size: 18

       2977 AAGTGTGGCA

                              
       2987 ACTTGGTGCGGTGCGACC
          1 ACTTGGTGCGGTGCGACC

                    *         
       3005 ACTTGGTGTGGTGCGACC
          1 ACTTGGTGCGGTGCGACC

             *              **
       3023 ATTTGGTGCGGTGCGAAT
          1 ACTTGGTGCGGTGCGACC

                           
       3041 ACTTGGTGCGGTGCG
          1 ACTTGGTGCGGTGCG

       3056 CTTTGTTGTT


Statistics
Matches: 45,  Mismatches: 6, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  18   45  1.00

ACGTcount: A:0.12, C:0.20, G:0.41, T:0.28


Consensus pattern (18 bp):   
ACTTGGTGCGGTGCGACC

Found at i:3683 original size:49 final size:47

Alignment explanation


    Indices: 3590--3731  Score: 160
    Period size: 49  Copynumber: 3.0  Consensus size: 47

       3580 GAGCGTGCCA

                        *         *        **              
       3590 ATCAATTTTGTCAAAAAATTGATAAAAAGTGTGATGAAAATTAAAAG
          1 ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAATGAAAATTAAAAG

                                                              
       3637 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAA-GTAAAATTAAAAG
          1 ATCAATTTTGTC-TAAAAATTGAGAAAAAG-TGCAATG-AAAATTAAAAG

            *           *         *           *      *    
       3686 TTCAATTTTGTAGTAAAAATTGTGAAAAAGTGCAGTGAAAAGTAAA
          1 ATCAATTTTGT-CTAAAAATTGAGAAAAAGTGCAATGAAAATTAAA

       3732 GGATTGCTTG


Statistics
Matches: 81,  Mismatches: 9, Indels: 9
        0.82            0.09        0.09

Matches are distributed among these distances:
  47   12  0.15
  48   28  0.35
  49   41  0.51

ACGTcount: A:0.49, C:0.05, G:0.16, T:0.30


Consensus pattern (47 bp):   
ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAATGAAAATTAAAAG

Found at i:14941 original size:14 final size:14

Alignment explanation


    Indices: 14913--14945  Score: 50
    Period size: 14  Copynumber: 2.4  Consensus size: 14

      14903 ATCCTAAATC

                          
      14913 TTTTTCCTTTCTTT
          1 TTTTTCCTTTCTTT

                           
      14927 TTTTTACCTTT-TTT
          1 TTTTT-CCTTTCTTT

                 
      14941 TTTTT
          1 TTTTT

      14946 GTTTTTACCA


Statistics
Matches: 18,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  14   13  0.72
  15    5  0.28

ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82


Consensus pattern (14 bp):   
TTTTTCCTTTCTTT

Found at i:15474 original size:6 final size:6

Alignment explanation


    Indices: 15459--15492  Score: 59
    Period size: 6  Copynumber: 5.5  Consensus size: 6

      15449 TCCTTCAAAT

                                                   
      15459 AAAAAGG AAAAAG AAAAAG AAAAAG AAAAAG AAA
          1 AAAAA-G AAAAAG AAAAAG AAAAAG AAAAAG AAA

      15493 TTATGGCTGA


Statistics
Matches: 27,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
   6   22  0.81
   7    5  0.19

ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00


Consensus pattern (6 bp):   
AAAAAG

Done.