Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024461.1 Corchorus olitorius cultivar O-4 contig24494, 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: 4495
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34


Found at i:354 original size:31 final size:31

Alignment explanation


    Indices: 319--377  Score: 100
    Period size: 31  Copynumber: 1.9  Consensus size: 31

        309 TTCGTTAAAC

                                           
        319 TTTTTCTTTTTAACTCCTTAAAATAATTATT
          1 TTTTTCTTTTTAACTCCTTAAAATAATTATT

                        *  *            
        350 TTTTTCTTTTTAGCTTCTTAAAATAATT
          1 TTTTTCTTTTTAACTCCTTAAAATAATT

        378 TTCTTTCATG


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  31   26  1.00

ACGTcount: A:0.27, C:0.12, G:0.02, T:0.59


Consensus pattern (31 bp):   
TTTTTCTTTTTAACTCCTTAAAATAATTATT

Found at i:2317 original size:64 final size:65

Alignment explanation


    Indices: 2205--2332  Score: 222
    Period size: 64  Copynumber: 2.0  Consensus size: 65

       2195 GAATTCATGG

                                *                                            
       2205 ATTGCTTTGATTAGATTGGTTTTTTTTGTATTTTCCATTCTTCCTATTATTGTTTCTTATAATAA
          1 ATTGCTTTGATTAGATTGGTGTTTTTTGTATTTTCCATTCTTCCTATTATTGTTTCTTATAATAA

                     *                                 *                    
       2270 ATTGCTTTGGTTAGATTGG-GTTTTTTGTATTTTCCATTCTTCTTATTATTGTTTCTTATAATA
          1 ATTGCTTTGATTAGATTGGTGTTTTTTGTATTTTCCATTCTTCCTATTATTGTTTCTTATAATA

       2333 TATATTTTTT


Statistics
Matches: 60,  Mismatches: 3, Indels: 1
        0.94            0.05        0.02

Matches are distributed among these distances:
  64   42  0.70
  65   18  0.30

ACGTcount: A:0.19, C:0.10, G:0.12, T:0.59


Consensus pattern (65 bp):   
ATTGCTTTGATTAGATTGGTGTTTTTTGTATTTTCCATTCTTCCTATTATTGTTTCTTATAATAA

Found at i:2807 original size:89 final size:89

Alignment explanation


    Indices: 2698--2863  Score: 271
    Period size: 90  Copynumber: 1.9  Consensus size: 89

       2688 TTTTATTGTT

                                                     *     *                 
       2698 TAAGTCTCGAATCCAAAGTTTGTAGATA-AAAAAATTTTATTGGGATGAACTCATCTATCATCAA
          1 TAAGTCTCGAATCCAAAGTTTGTAGATAGAAAAAATTTTATCGGGATAAACTCATCTATCATCAA

                                    
       2762 ACAGGATTAGTCTATTATTTTAAG
         66 ACAGGATTAGTCTATTATTTTAAG

                                               *               *             
       2786 TAAGTCTCGAAATCCAAAGTTTGTAGATAGAAAAACTTTTATCGGGATAAATTCATCTATCATCA
          1 TAAGTCTCG-AATCCAAAGTTTGTAGATAGAAAAAATTTTATCGGGATAAACTCATCTATCATCA

                *        
       2851 AACATGATTAGTC
         65 AACAGGATTAGTC

       2864 ATTCTTGAGC


Statistics
Matches: 71,  Mismatches: 5, Indels: 2
        0.91            0.06        0.03

Matches are distributed among these distances:
  88    9  0.13
  89   19  0.27
  90   43  0.61

ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34


Consensus pattern (89 bp):   
TAAGTCTCGAATCCAAAGTTTGTAGATAGAAAAAATTTTATCGGGATAAACTCATCTATCATCAA
ACAGGATTAGTCTATTATTTTAAG

Done.