Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016166.1 Corchorus olitorius cultivar O-4 contig16199, 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: 2838
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32


Found at i:1230 original size:29 final size:29

Alignment explanation


    Indices: 1150--1293  Score: 132
    Period size: 29  Copynumber: 5.0  Consensus size: 29

       1140 AAAGGGAACT

                           **             
       1150 TAGAGTATGCAAAAACAACCAAAATGCCCC
          1 TAGAG-ATGCAAAAATGACCAAAATGCCCC

                 *                         
       1180 -AGAACATG-AAAAATGA-CAATAATGCCCC
          1 TAG-AGATGCAAAAATGACCAA-AATGCCCC

                *               *        
       1208 TAGATATGCAAAAATGACCATAATGCCCC
          1 TAGAGATGCAAAAATGACCAAAATGCCCC

                 *   *              *    
       1237 TAGAGGTGCTAAAATGACCAAAATACCCC
          1 TAGAGATGCAAAAATGACCAAAATGCCCC

             *   *   *          *       
       1266 TGGAGGTGCTAAAATGACCACAATGCCC
          1 TAGAGATGCAAAAATGACCAAAATGCCC

       1294 TTGGACGTGA


Statistics
Matches: 96,  Mismatches: 13, Indels: 11
        0.80            0.11        0.09

Matches are distributed among these distances:
  27    3  0.03
  28   18  0.19
  29   72  0.75
  30    3  0.03

ACGTcount: A:0.42, C:0.24, G:0.17, T:0.17


Consensus pattern (29 bp):   
TAGAGATGCAAAAATGACCAAAATGCCCC

Found at i:1632 original size:59 final size:59

Alignment explanation


    Indices: 1559--1940  Score: 669
    Period size: 59  Copynumber: 6.5  Consensus size: 59

       1549 CAGAGACCTC

                               *                                       
       1559 GAACAAGATAAGATTTTGAGTTGAAAACTCTCTAACAGAGACCTCGAACAGGATTTTAA
          1 GAACAAGATAAGATTTTGAATTGAAAACTCTCTAACAGAGACCTCGAACAGGATTTTAA

                 *                                      *              
       1618 GAACATGATAAGATTTTGAATTGAAAACTCTCTAACAGAGACCTTGAACAGGATTTTAA
          1 GAACAAGATAAGATTTTGAATTGAAAACTCTCTAACAGAGACCTCGAACAGGATTTTAA

                                                                       
       1677 GAACAAGATAAGATTTTGAATTGAAAACTCTCTAACAGAGACCTCGAACAGGATTTTAA
          1 GAACAAGATAAGATTTTGAATTGAAAACTCTCTAACAGAGACCTCGAACAGGATTTTAA

                      *             *                                   
       1736 -AAGCAAGATGAGATTTTGAATTGGAAACTCTCTAACAGAGACCTCGAACAGGATTTTAA
          1 GAA-CAAGATAAGATTTTGAATTGAAAACTCTCTAACAGAGACCTCGAACAGGATTTTAA

                                                        *              
       1795 GAACAAGATAAGATTTTGAATTGAAAACTCTCTAACAGAGACCTTGAACAGGATTTTAA
          1 GAACAAGATAAGATTTTGAATTGAAAACTCTCTAACAGAGACCTCGAACAGGATTTTAA

                                                                       
       1854 GAACAAGATAAGATTTTGAATTGAAAACTCTCTAACAGAGACCTCGAACAGGATTTTAA
          1 GAACAAGATAAGATTTTGAATTGAAAACTCTCTAACAGAGACCTCGAACAGGATTTTAA

            *                     *      
       1913 AAACAAGATAAGATTTTG-ATTTAAAACT
          1 GAACAAGATAAGATTTTGAATTGAAAACT

       1941 GAAACTCAAA


Statistics
Matches: 308,  Mismatches: 13, Indels: 5
        0.94            0.04        0.02

Matches are distributed among these distances:
  58   11  0.04
  59  295  0.96
  60    2  0.01

ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27


Consensus pattern (59 bp):   
GAACAAGATAAGATTTTGAATTGAAAACTCTCTAACAGAGACCTCGAACAGGATTTTAA

Found at i:2401 original size:2 final size:2

Alignment explanation


    Indices: 2394--2418  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

       2384 TTGACAGAGA

                                                 
       2394 AC AC AC AC AC AC AC AC AC AC AC AC A
          1 AC AC AC AC AC AC AC AC AC AC AC AC A

       2419 TATATATATA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00


Consensus pattern (2 bp):   
AC

Found at i:2423 original size:2 final size:2

Alignment explanation


    Indices: 2418--2454  Score: 74
    Period size: 2  Copynumber: 18.5  Consensus size: 2

       2408 ACACACACAC

                                                                   
       2418 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       2455 GAAAGAAGAA


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   35  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Done.