Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021741.1 Corchorus olitorius cultivar O-4 contig21774, 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: 25554
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32


Found at i:16205 original size:304 final size:303

Alignment explanation


    Indices: 15656--16235  Score: 806
    Period size: 304  Copynumber: 1.9  Consensus size: 303

      15646 TCTCAAGCAG

                                 *                        *              *   
      15656 AAGAAGATGGAGAAATGTCGATGACTAAGGCACAAGTGTTCCACGTTTTTGTACTCTTCTTTACA
          1 AAGAAGATGGAGAAATGTCGACGACTAAGGCACAAGTGTTCCAC-TATTTGTACTCTTCTTCACA

                               *        * * *                                
      15721 ATTGCTGACTCACTTAAGTTTTTATATATAGGGTCTTCAAGAGTCTTCTTAACAAATGCATCGTG
         65 ATTGCTGACTCACTTAAGTCTTTATATAAACGATCTTCAAGAGTCTTCTTAACAAATGCATCGTG

                               *                                     * *     
      15786 ACAAACTTTACCCAATACCTTGAGTTCACCGCAACACTTCTTAGTGACAGCTCCGGTTTTGAATA
        130 ACAAACTTTACCCAATACCATGAGTTCACCGCAACACTTCTTAGTGACAGCTCCGGTATAGAATA

              *          *       * *       *           *        *            
      15851 TACTTGTGAAAACTTCCCTGGCACAGTGCAGTTCCATTTTTGTTTTGCAATTGTTTTCCTTAATA
        195 TAATTGTGAAAACCTCCCTGGAAAAGTGCAGCTCCATTTTTGTCTTGCAATTATTTTCCTTAATA

               *                                        
      15916 ATCTAGTCGGGGTTTTTCGCAGGTGAAATGACTCCGCTTACATA
        260 ATCAAGTCGGGGTTTTTCGCAGGTGAAATGACTCCGCTTACATA

                      * *                     *                            * 
      15960 AAGAAGATGGTGCAATGTCGACGACTAAGGCACATGTGTTCCA-TATTTGAATACTCTTCTTCGC
          1 AAGAAGATGGAGAAATGTCGACGACTAAGGCACAAGTGTTCCACTATTTG--TACTCTTCTTCAC

                 *      *                                        *      *    
      16024 AATTGTTGACTCGCTTAAGTCTTTATATAAACGATCTTCAAGAGTCTTCTTAATAAATGCTTCGT
         64 AATTGCTGACTCACTTAAGTCTTTATATAAACGATCTTCAAGAGTCTTCTTAACAAATGCATCGT

                         *         *                   *                     
      16089 GACAAACTTTACCGAATACCATGTGTTCACCGCAACACTTCTTTGTGACAGCTCCGGTATAGAAT
        129 GACAAACTTTACCCAATACCATGAGTTCACCGCAACACTTCTTAGTGACAGCTCCGGTATAGAAT

                  *                                                     *    
      16154 ATAATTTTGAAAACCTCCCTGGAAAAG-GCCAGGCT-CATTTTTGTCTTGCAATTATTTTGCTTA
        194 ATAATTGTGAAAACCTCCCTGGAAAAGTG-CA-GCTCCATTTTTGTCTTGCAATTATTTTCCTTA

                       *       
      16217 ATAATCAAGTCTGGGTTTT
        257 ATAATCAAGTCGGGGTTTT

      16236 CTGCAACTAA


Statistics
Matches: 240,  Mismatches: 32, Indels: 8
        0.86            0.11        0.03

Matches are distributed among these distances:
 302    5  0.02
 303    1  0.00
 304  232  0.97
 305    2  0.01

ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35


Consensus pattern (303 bp):   
AAGAAGATGGAGAAATGTCGACGACTAAGGCACAAGTGTTCCACTATTTGTACTCTTCTTCACAA
TTGCTGACTCACTTAAGTCTTTATATAAACGATCTTCAAGAGTCTTCTTAACAAATGCATCGTGA
CAAACTTTACCCAATACCATGAGTTCACCGCAACACTTCTTAGTGACAGCTCCGGTATAGAATAT
AATTGTGAAAACCTCCCTGGAAAAGTGCAGCTCCATTTTTGTCTTGCAATTATTTTCCTTAATAA
TCAAGTCGGGGTTTTTCGCAGGTGAAATGACTCCGCTTACATA

Found at i:19256 original size:41 final size:41

Alignment explanation


    Indices: 19179--19273  Score: 109
    Period size: 41  Copynumber: 2.3  Consensus size: 41

      19169 AGACAAATAA

                *     *         *   *      *       * 
      19179 GGACCAAATTTAATCAAATAGTAACTAAAATCCTAAATCGG
          1 GGACTAAATTGAATCAAATAATAAATAAAATACTAAATCAG

                             *        *           *  
      19220 GGACTAAATTGAATCAATTAATAAATGAAATACTAAATTAG
          1 GGACTAAATTGAATCAAATAATAAATAAAATACTAAATCAG

                         
      19261 GGACTAAATTGAA
          1 GGACTAAATTGAA

      19274 CACGGAAACA


Statistics
Matches: 45,  Mismatches: 9, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  41   45  1.00

ACGTcount: A:0.48, C:0.12, G:0.14, T:0.26


Consensus pattern (41 bp):   
GGACTAAATTGAATCAAATAATAAATAAAATACTAAATCAG

Found at i:21919 original size:15 final size:15

Alignment explanation


    Indices: 21896--21926  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

      21886 TACCTATGTC

                           
      21896 ATGTAATGTGAAGAA
          1 ATGTAATGTGAAGAA

                *          
      21911 ATGTTATGTGAAGAA
          1 ATGTAATGTGAAGAA

             
      21926 A
          1 A

      21927 AATCAAAAGC


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

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.45, C:0.00, G:0.26, T:0.29


Consensus pattern (15 bp):   
ATGTAATGTGAAGAA

Found at i:22140 original size:66 final size:66

Alignment explanation


    Indices: 22065--22202  Score: 249
    Period size: 66  Copynumber: 2.1  Consensus size: 66

      22055 ATAATGGGAA

                                                                     *       
      22065 AATGAAAATAGATGGGATCTACTTAAAAATGAACATGAAGATGTCAATTGAAAACTATACGAAAT
          1 AATGAAAATAGATGGGATCTACTTAAAAATGAACATGAAGATGTCAATTGAAAACTAGACGAAAT

             
      22130 T
         66 T

                                                                        *    
      22131 AATGAAAATAGATGGGATCTACTTAAAAATGAACATGAAGATGTCAATTGAAAACTAGACTAAAT
          1 AATGAAAATAGATGGGATCTACTTAAAAATGAACATGAAGATGTCAATTGAAAACTAGACGAAAT

             
      22196 T
         66 T

             *    
      22197 ACTGAA
          1 AATGAA

      22203 TGAAACTAAG


Statistics
Matches: 69,  Mismatches: 3, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  66   69  1.00

ACGTcount: A:0.49, C:0.09, G:0.17, T:0.25


Consensus pattern (66 bp):   
AATGAAAATAGATGGGATCTACTTAAAAATGAACATGAAGATGTCAATTGAAAACTAGACGAAAT
T

Found at i:22480 original size:2 final size:2

Alignment explanation


    Indices: 22475--22504  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

      22465 GTCTACACAC

                                                        
      22475 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      22505 CTTTAATGTG


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Done.