Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020086.1 Corchorus olitorius cultivar O-4 contig20119, 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: 19823
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32


Found at i:941 original size:15 final size:15

Alignment explanation


    Indices: 903--991  Score: 76
    Period size: 15  Copynumber: 5.9  Consensus size: 15

        893 TAGTAAACAC

                           
        903 TTTCGGTGCCATC-A
          1 TTTCGGTGCCATCAA

                **     *    
        917 TCTTTAGTGCCGTCAA
          1 T-TTCGGTGCCATCAA

                          *
        933 TTTCGGTGCCATCAG
          1 TTTCGGTGCCATCAA

                           
        948 TTTCGGTGCCATC-A
          1 TTTCGGTGCCATCAA

                       *  * 
        962 TCTTCGGTGCCGTCGA
          1 T-TTCGGTGCCATCAA

                           
        978 TGTT-GGTGCCATCA
          1 T-TTCGGTGCCATCA

        992 TCTTCTTCCA


Statistics
Matches: 59,  Mismatches: 12, Indels: 7
        0.76            0.15        0.09

Matches are distributed among these distances:
  14    2  0.03
  15   51  0.86
  16    6  0.10

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


Consensus pattern (15 bp):   
TTTCGGTGCCATCAA

Found at i:972 original size:45 final size:45

Alignment explanation


    Indices: 903--991  Score: 135
    Period size: 45  Copynumber: 2.0  Consensus size: 45

        893 TAGTAAACAC

                              *                           
        903 TTTCGGTGCCATCATCTTTAGTGCCGTCAAT-TTCGGTGCCATCAG
          1 TTTCGGTGCCATCATCTTCAGTGCCGTCAATGTT-GGTGCCATCAG

                               *        *               
        948 TTTCGGTGCCATCATCTTCGGTGCCGTCGATGTTGGTGCCATCA
          1 TTTCGGTGCCATCATCTTCAGTGCCGTCAATGTTGGTGCCATCA

        992 TCTTCTTCCA


Statistics
Matches: 40,  Mismatches: 3, Indels: 2
        0.89            0.07        0.04

Matches are distributed among these distances:
  45   38  0.95
  46    2  0.05

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


Consensus pattern (45 bp):   
TTTCGGTGCCATCATCTTCAGTGCCGTCAATGTTGGTGCCATCAG

Found at i:2250 original size:18 final size:18

Alignment explanation


    Indices: 2227--2274  Score: 60
    Period size: 18  Copynumber: 2.7  Consensus size: 18

       2217 AACTTGGTGC

                        *     
       2227 GGTGCGGTGCGACCACTG
          1 GGTGCGGTGCGAACACTG

                  *      *   *
       2245 GGTGCGATGCGAATACTT
          1 GGTGCGGTGCGAACACTG

                        
       2263 GGTGCGGTGCGA
          1 GGTGCGGTGCGA

       2275 TTTGTTGTTG


Statistics
Matches: 25,  Mismatches: 5, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  18   25  1.00

ACGTcount: A:0.15, C:0.21, G:0.44, T:0.21


Consensus pattern (18 bp):   
GGTGCGGTGCGAACACTG

Found at i:2916 original size:50 final size:48

Alignment explanation


    Indices: 2810--2956  Score: 181
    Period size: 50  Copynumber: 3.0  Consensus size: 48

       2800 GAGCGTGCCA

                        *         *             *    *      
       2810 ATCAATTTTGTCAAAAAATTGATAAAAAGTGCAA-TGAAAATTAAAAG
          1 ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAAGTAAAAAATAAAAG

                                                              
       2857 ATCAATTTTGTCTTAAAAATTGAGAAAAAGGTGCAAGTAAAAAATAAAAG
          1 ATCAATTTTGTC-TAAAAATTGAGAAAAA-GTGCAAGTAAAAAATAAAAG

            *           *  *                          *      
       2907 TTCAATTTTGTAGTATAAATTGAGAAAAAGTGC-AGTAAAAAGTAAAAG
          1 ATCAATTTTGT-CTAAAAATTGAGAAAAAGTGCAAGTAAAAAATAAAAG

              
       2955 AT
          1 AT

       2957 TGCTTGGAGT


Statistics
Matches: 87,  Mismatches: 9, Indels: 7
        0.84            0.09        0.07

Matches are distributed among these distances:
  47   12  0.14
  48   29  0.33
  49   10  0.11
  50   36  0.41

ACGTcount: A:0.51, C:0.05, G:0.16, T:0.28


Consensus pattern (48 bp):   
ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAAGTAAAAAATAAAAG

Found at i:19792 original size:2 final size:2

Alignment explanation


    Indices: 19785--19818  Score: 61
    Period size: 2  Copynumber: 17.5  Consensus size: 2

      19775 TTGATGGTCA

                                                                
      19785 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

      19819 AATTA


Statistics
Matches: 31,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   1    1  0.03
   2   30  0.97

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


Consensus pattern (2 bp):   
AT

Done.