Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009311.1 Corchorus capsularis cultivar CVL-1 contig09332, 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: 4593
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34


Found at i:1760 original size:16 final size:17

Alignment explanation


    Indices: 1741--1786  Score: 51
    Period size: 16  Copynumber: 2.7  Consensus size: 17

       1731 AATTCCCTGC

                             
       1741 TTTTATAATTTCA-TTG
          1 TTTTATAATTTCACTTG

                        *     
       1757 TTTT-TAATTTTAACTTG
          1 TTTTATAA-TTTCACTTG

                         
       1774 TTTTGATAATTTC
          1 TTTT-ATAATTTC

       1787 TCAAAATTTC


Statistics
Matches: 24,  Mismatches: 2, Indels: 6
        0.75            0.06        0.19

Matches are distributed among these distances:
  15    3  0.12
  16    8  0.33
  17    7  0.29
  18    3  0.12
  19    3  0.12

ACGTcount: A:0.24, C:0.07, G:0.07, T:0.63


Consensus pattern (17 bp):   
TTTTATAATTTCACTTG

Found at i:2096 original size:17 final size:18

Alignment explanation


    Indices: 2052--2097  Score: 51
    Period size: 17  Copynumber: 2.7  Consensus size: 18

       2042 GAAATTTTGA

                    *         
       2052 GAAATTATCAAAACAAGT
          1 GAAATTATAAAAACAAGT

            *   *             
       2070 TAAAAT-TAAAAACAA-T
          1 GAAATTATAAAAACAAGT

                        
       2086 GAAATTATAAAA
          1 GAAATTATAAAA

       2098 GCAGGGAATT


Statistics
Matches: 22,  Mismatches: 5, Indels: 3
        0.73            0.17        0.10

Matches are distributed among these distances:
  16    5  0.23
  17   13  0.59
  18    4  0.18

ACGTcount: A:0.63, C:0.07, G:0.07, T:0.24


Consensus pattern (18 bp):   
GAAATTATAAAAACAAGT

Found at i:2097 original size:16 final size:17

Alignment explanation


    Indices: 2052--2097  Score: 51
    Period size: 15  Copynumber: 2.7  Consensus size: 17

       2042 GAAATTTTGA

                               
       2052 GAAATTATCAAAACAAGTT
          1 GAAATTAT-AAAACAAG-T

            *                
       2071 AAAATTA-AAAACAA-T
          1 GAAATTATAAAACAAGT

                        
       2086 GAAATTATAAAA
          1 GAAATTATAAAA

       2098 GCAGGGAATT


Statistics
Matches: 24,  Mismatches: 2, Indels: 5
        0.77            0.06        0.16

Matches are distributed among these distances:
  15    7  0.29
  16    4  0.17
  17    7  0.29
  19    6  0.25

ACGTcount: A:0.63, C:0.07, G:0.07, T:0.24


Consensus pattern (17 bp):   
GAAATTATAAAACAAGT

Found at i:3238 original size:12 final size:12

Alignment explanation


    Indices: 3221--3246  Score: 52
    Period size: 12  Copynumber: 2.2  Consensus size: 12

       3211 CAAAATTGAT

                        
       3221 AAAATAAACACC
          1 AAAATAAACACC

                        
       3233 AAAATAAACACC
          1 AAAATAAACACC

              
       3245 AA
          1 AA

       3247 TAATTATGTA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   14  1.00

ACGTcount: A:0.69, C:0.23, G:0.00, T:0.08


Consensus pattern (12 bp):   
AAAATAAACACC
Done.