Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01003416.1 Corchorus capsularis cultivar CVL-1 contig03424, 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, 973

Length: 1623
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31


Found at i:118 original size:9 final size:8

Alignment explanation


    Indices: 84--117  Score: 50
    Period size: 8  Copynumber: 4.1  Consensus size: 8

         74 AAATCGGCTA

                    
         84 TGAATTTT
          1 TGAATTTT

                    *
         92 TGAAGTTTC
          1 TGAA-TTTT

                    
        101 TGAATTTT
          1 TGAATTTT

                    
        109 TGAATTTT
          1 TGAATTTT

             
        117 T
          1 T

        118 TTTTTTTCAA


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
   8   16  0.70
   9    7  0.30

ACGTcount: A:0.24, C:0.03, G:0.15, T:0.59


Consensus pattern (8 bp):   
TGAATTTT

Found at i:1310 original size:33 final size:33

Alignment explanation


    Indices: 1273--1382  Score: 132
    Period size: 33  Copynumber: 3.3  Consensus size: 33

       1263 CCAAAACAGA

                  * *                        
       1273 TTTAGTTTTATTGCAAACAACACTCAAATTAGG
          1 TTTAGTATCATTGCAAACAACACTCAAATTAGG

                       * *               **  *
       1306 TTTAGTATCATCGGAAACAACA-TCTAAAACAGA
          1 TTTAGTATCATTGCAAACAACACTC-AAATTAGG

                  *                          
       1339 TTTAGTGTCATTGCAAACAACACTCAAATTAGG
          1 TTTAGTATCATTGCAAACAACACTCAAATTAGG

                       
       1372 TTTAGTATCAT
          1 TTTAGTATCAT

       1383 CAAAACAATC


Statistics
Matches: 61,  Mismatches: 14, Indels: 4
        0.77            0.18        0.05

Matches are distributed among these distances:
  32    2  0.03
  33   57  0.93
  34    2  0.03

ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33


Consensus pattern (33 bp):   
TTTAGTATCATTGCAAACAACACTCAAATTAGG

Found at i:1371 original size:66 final size:66

Alignment explanation


    Indices: 1260--1383  Score: 221
    Period size: 66  Copynumber: 1.9  Consensus size: 66

       1250 TGACAATTAG

                               * *                                           
       1260 CATCCAAAACAGATTTAGTTTTATTGCAAACAACACTCAAATTAGGTTTAGTATCATCGGAAACA
          1 CATCCAAAACAGATTTAGTGTCATTGCAAACAACACTCAAATTAGGTTTAGTATCATCGGAAACA

             
       1325 A
         66 A

                *                                                     
       1326 CATCTAAAACAGATTTAGTGTCATTGCAAACAACACTCAAATTAGGTTTAGTATCATC
          1 CATCCAAAACAGATTTAGTGTCATTGCAAACAACACTCAAATTAGGTTTAGTATCATC

       1384 AAAACAATCA


Statistics
Matches: 55,  Mismatches: 3, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  66   55  1.00

ACGTcount: A:0.40, C:0.19, G:0.12, T:0.30


Consensus pattern (66 bp):   
CATCCAAAACAGATTTAGTGTCATTGCAAACAACACTCAAATTAGGTTTAGTATCATCGGAAACA
A
Done.