Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01002377.1 Corchorus olitorius cultivar O-4 contig02377, 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: 3739
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.36


Found at i:1247 original size:12 final size:12

Alignment explanation


    Indices: 1209--1276  Score: 100
    Period size: 12  Copynumber: 5.6  Consensus size: 12

       1199 TTTAATACGG

                 *      
       1209 ATATCCACGGAT
          1 ATATCGACGGAT

                         
       1221 ATATCGAACGGAT
          1 ATATCG-ACGGAT

                   *    
       1234 ATATCGATGGAT
          1 ATATCGACGGAT

                   *    
       1246 ATATCGATGGAT
          1 ATATCGACGGAT

                        
       1258 ATATCGACGGAT
          1 ATATCGACGGAT

                   
       1270 ATATCGA
          1 ATATCGA

       1277 GGTATCGATG


Statistics
Matches: 52,  Mismatches: 3, Indels: 2
        0.91            0.05        0.04

Matches are distributed among these distances:
  12   40  0.77
  13   12  0.23

ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28


Consensus pattern (12 bp):   
ATATCGACGGAT

Found at i:1675 original size:34 final size:33

Alignment explanation


    Indices: 1623--1691  Score: 102
    Period size: 34  Copynumber: 2.1  Consensus size: 33

       1613 AAACCCAGAT

                       * *                   
       1623 TTAATTGAAACTCTGACTTAATTGAAACAAATA
          1 TTAATTGAAACCCAGACTTAATTGAAACAAATA

                                          *   
       1656 TTAAGTTGAAACCCAGACTTAATTGAAACAGATA
          1 TTAA-TTGAAACCCAGACTTAATTGAAACAAATA

              
       1690 TT
          1 TT

       1692 TTGATAACAA


Statistics
Matches: 32,  Mismatches: 3, Indels: 1
        0.89            0.08        0.03

Matches are distributed among these distances:
  33    4  0.12
  34   28  0.88

ACGTcount: A:0.43, C:0.13, G:0.12, T:0.32


Consensus pattern (33 bp):   
TTAATTGAAACCCAGACTTAATTGAAACAAATA

Found at i:1681 original size:17 final size:17

Alignment explanation


    Indices: 1613--1684  Score: 74
    Period size: 17  Copynumber: 4.2  Consensus size: 17

       1603 GAGATGACCA

                     *       
       1613 AAACCCAGATTTAATTG
          1 AAACCCAGACTTAATTG

                * *          
       1630 AAACTCTGACTTAATTG
          1 AAACCCAGACTTAATTG

                ** *          
       1647 AAACAAATA-TTAAGTTG
          1 AAACCCAGACTTAA-TTG

                             
       1664 AAACCCAGACTTAATTG
          1 AAACCCAGACTTAATTG

                
       1681 AAAC
          1 AAAC

       1685 AGATATTTTG


Statistics
Matches: 43,  Mismatches: 10, Indels: 4
        0.75            0.18        0.07

Matches are distributed among these distances:
  16    4  0.09
  17   35  0.81
  18    4  0.09

ACGTcount: A:0.44, C:0.17, G:0.11, T:0.28


Consensus pattern (17 bp):   
AAACCCAGACTTAATTG

Found at i:2225 original size:10 final size:10

Alignment explanation


    Indices: 2212--2238  Score: 54
    Period size: 10  Copynumber: 2.7  Consensus size: 10

       2202 ATATATCGAG

                      
       2212 ATATCGATAA
          1 ATATCGATAA

                      
       2222 ATATCGATAA
          1 ATATCGATAA

                   
       2232 ATATCGA
          1 ATATCGA

       2239 CAGATACACG


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   17  1.00

ACGTcount: A:0.48, C:0.11, G:0.11, T:0.30


Consensus pattern (10 bp):   
ATATCGATAA

Found at i:3504 original size:2 final size:2

Alignment explanation


    Indices: 3492--3539  Score: 87
    Period size: 2  Copynumber: 24.0  Consensus size: 2

       3482 TAATGGATGC

                  *                                                       
       3492 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                    
       3534 AT AT AT
          1 AT AT AT

       3540 TTGTACAGGA


Statistics
Matches: 44,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
   2   44  1.00

ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50


Consensus pattern (2 bp):   
AT

Done.