Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008044.1 Corchorus capsularis cultivar CVL-1 contig08065, 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: 19961
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.31


Found at i:1225 original size:16 final size:16

Alignment explanation


    Indices: 1204--1236  Score: 57
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       1194 ATCTGGAAAC

                            
       1204 AAGTGAAGAAACTTCA
          1 AAGTGAAGAAACTTCA

                      *     
       1220 AAGTGAAGAAGCTTCA
          1 AAGTGAAGAAACTTCA

             
       1236 A
          1 A

       1237 GATGAAGACA


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.48, C:0.12, G:0.21, T:0.18


Consensus pattern (16 bp):   
AAGTGAAGAAACTTCA

Found at i:1242 original size:16 final size:16

Alignment explanation


    Indices: 1203--1244  Score: 52
    Period size: 16  Copynumber: 2.7  Consensus size: 16

       1193 AATCTGGAAA

                            
       1203 CAAG-TGAAGAAACTT
          1 CAAGATGAAGAAACTT

                         *   
       1218 CAA-AGTGAAGAAGCTT
          1 CAAGA-TGAAGAAACTT

                       
       1234 CAAGATGAAGA
          1 CAAGATGAAGA

       1245 CACGCATGGC


Statistics
Matches: 23,  Mismatches: 1, Indels: 5
        0.79            0.03        0.17

Matches are distributed among these distances:
  15    3  0.13
  16   19  0.83
  17    1  0.04

ACGTcount: A:0.48, C:0.12, G:0.24, T:0.17


Consensus pattern (16 bp):   
CAAGATGAAGAAACTT

Found at i:2245 original size:43 final size:40

Alignment explanation


    Indices: 2187--2306  Score: 105
    Period size: 43  Copynumber: 2.9  Consensus size: 40

       2177 CCTTGATATA

                  *  *                                
       2187 GATGCCTCTATGTTATAAATGTGCTTGAGGACTTTGAGATAG
          1 GATGCCCCTGTGTTATAAATGTG-TTGAGGACTTTGAGAT-G

              *                * *      *         *   
       2229 AGTTGCCCCTGTGTTATAATTATGTTAGGGGACTTTGATATG
          1 -GATGCCCCTGTGTTATAAATGTGTT-GAGGACTTTGAGATG

                  *         *      *            
       2271 GATGCCTCTGTGTTATGAATGTATTTGAGGACTTTG
          1 GATGCCCCTGTGTTATAAATGT-GTTGAGGACTTTG

       2307 GTTATTGGGT


Statistics
Matches: 61,  Mismatches: 14, Indels: 6
        0.75            0.17        0.07

Matches are distributed among these distances:
  41   26  0.43
  42    5  0.08
  43   30  0.49

ACGTcount: A:0.23, C:0.12, G:0.27, T:0.39


Consensus pattern (40 bp):   
GATGCCCCTGTGTTATAAATGTGTTGAGGACTTTGAGATG

Found at i:2303 original size:41 final size:40

Alignment explanation


    Indices: 2179--2306  Score: 123
    Period size: 41  Copynumber: 3.1  Consensus size: 40

       2169 AAAATTGCCC

                   *         *            **         
       2179 TTGATATAGATGCCTCTATGTTATAAATGTGCTTGAGGACT
          1 TTGATATGGATGCCTCTGTGTTAT-AATGTATTTGAGGACT

                *      *    *                     *     
       2220 TTGAGATAGAGTTGCCCCTGTGTTATAAT-TATGTTAGGGGACT
          1 TTGATAT-G-GATGCCTCTGTGTTATAATGTAT-TT-GAGGACT

                                                     
       2263 TTGATATGGATGCCTCTGTGTTATGAATGTATTTGAGGACT
          1 TTGATATGGATGCCTCTGTGTTAT-AATGTATTTGAGGACT

               
       2304 TTG
          1 TTG

       2307 GTTATTGGGT


Statistics
Matches: 69,  Mismatches: 12, Indels: 12
        0.74            0.13        0.13

Matches are distributed among these distances:
  41   30  0.43
  42   11  0.16
  43   28  0.41

ACGTcount: A:0.23, C:0.11, G:0.26, T:0.40


Consensus pattern (40 bp):   
TTGATATGGATGCCTCTGTGTTATAATGTATTTGAGGACT
Done.