Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014551.1 Corchorus olitorius cultivar O-4 contig14584, 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: 6978
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34


Found at i:1352 original size:51 final size:51

Alignment explanation


    Indices: 1256--1352  Score: 117
    Period size: 51  Copynumber: 1.9  Consensus size: 51

       1246 TCATATTTTC

                                                * **           
       1256 CTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCTTTTAGTGTTTCTCT
          1 CTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGTTTCTCT

                                    * *                     
       1307 CTTGTTTCA-ATCTTGTCTCCGGATATACAAACACT-GTACACGTGTT
          1 CTTGTTT-AGATCTTGTCTCCGGACAAACAAACACTCGTACA-GTGTT

       1353 CTTCATTCAG


Statistics
Matches: 39,  Mismatches: 5, Indels: 4
        0.81            0.10        0.08

Matches are distributed among these distances:
  50    2  0.05
  51   36  0.92
  52    1  0.03

ACGTcount: A:0.23, C:0.24, G:0.14, T:0.39


Consensus pattern (51 bp):   
CTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGTTTCTCT

Found at i:2396 original size:3 final size:3

Alignment explanation


    Indices: 2388--2462  Score: 150
    Period size: 3  Copynumber: 25.0  Consensus size: 3

       2378 ACCATGTATA

                                                                           
       2388 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
          1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT

                                               
       2436 TAT TAT TAT TAT TAT TAT TAT TAT TAT
          1 TAT TAT TAT TAT TAT TAT TAT TAT TAT

       2463 ATATAACCCA


Statistics
Matches: 72,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   72  1.00

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67


Consensus pattern (3 bp):   
TAT

Found at i:2849 original size:11 final size:11

Alignment explanation


    Indices: 2825--2859  Score: 52
    Period size: 11  Copynumber: 3.2  Consensus size: 11

       2815 TTGACAGCGC

                       
       2825 AACAAAAACAA
          1 AACAAAAACAA

               *     * 
       2836 AACGAAAACGA
          1 AACAAAAACAA

                       
       2847 AACAAAAACAA
          1 AACAAAAACAA

              
       2858 AA
          1 AA

       2860 AACAGAAAAA


Statistics
Matches: 20,  Mismatches: 4, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  11   20  1.00

ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00


Consensus pattern (11 bp):   
AACAAAAACAA

Found at i:4311 original size:11 final size:11

Alignment explanation


    Indices: 4295--4319  Score: 50
    Period size: 11  Copynumber: 2.3  Consensus size: 11

       4285 CATAGGCTTT

                       
       4295 CTAAATATGGG
          1 CTAAATATGGG

                       
       4306 CTAAATATGGG
          1 CTAAATATGGG

               
       4317 CTA
          1 CTA

       4320 GAGACTGAAT


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

Matches are distributed among these distances:
  11   14  1.00

ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28


Consensus pattern (11 bp):   
CTAAATATGGG

Found at i:5054 original size:16 final size:16

Alignment explanation


    Indices: 5033--5063  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

       5023 AGAAATTGAT

                  *         
       5033 AACATATCAAAAGTAC
          1 AACATAACAAAAGTAC

                           
       5049 AACATAACAAAAGTA
          1 AACATAACAAAAGTA

       5064 AAATAAAAAC


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  16   14  1.00

ACGTcount: A:0.61, C:0.16, G:0.06, T:0.16


Consensus pattern (16 bp):   
AACATAACAAAAGTAC
Done.