Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001700.1 Corchorus olitorius cultivar O-4 contig01700, 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: 2111
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33


Found at i:1407 original size:51 final size:52

Alignment explanation


    Indices: 1333--1436  Score: 165
    Period size: 51  Copynumber: 2.0  Consensus size: 52

       1323 TAACAAAAGT

                                      *                         
       1333 ATGTCAATGTCAAGGATGAGGGAGTTTATTCAAATTCATTTTAATAGATTGA
          1 ATGTCAATGTCAAGGATGAGGGAGTTCATTCAAATTCATTTTAATAGATTGA

                      *                          *    *         
       1385 ATGTCAATGTTAA-GATGAGGGAGTTCATTCAAATTCGTTTTCATAGATTGA
          1 ATGTCAATGTCAAGGATGAGGGAGTTCATTCAAATTCATTTTAATAGATTGA

             
       1436 A
          1 A

       1437 GAACCTCTAT


Statistics
Matches: 48,  Mismatches: 4, Indels: 1
        0.91            0.08        0.02

Matches are distributed among these distances:
  51   36  0.75
  52   12  0.25

ACGTcount: A:0.34, C:0.09, G:0.21, T:0.37


Consensus pattern (52 bp):   
ATGTCAATGTCAAGGATGAGGGAGTTCATTCAAATTCATTTTAATAGATTGA

Found at i:1554 original size:17 final size:17

Alignment explanation


    Indices: 1495--1554  Score: 50
    Period size: 17  Copynumber: 3.3  Consensus size: 17

       1485 GGTTAAGTTG

                       *     
       1495 ATAAGTATAGTGAAATA
          1 ATAAGTATAGTAAAATA

                                  
       1512 ATAAG-AGTAGCTATAAAATAA
          1 ATAAGTA-TAG---TAAAAT-A

                       *     
       1533 ATAAGTATAGTCAAATA
          1 ATAAGTATAGTAAAATA

                 
       1550 ATAAG
          1 ATAAG

       1555 AGTAGTCCTA


Statistics
Matches: 35,  Mismatches: 2, Indels: 12
        0.71            0.04        0.24

Matches are distributed among these distances:
  16    1  0.03
  17   14  0.40
  18    5  0.14
  20    5  0.14
  21    9  0.26
  22    1  0.03

ACGTcount: A:0.55, C:0.03, G:0.15, T:0.27


Consensus pattern (17 bp):   
ATAAGTATAGTAAAATA

Found at i:1560 original size:17 final size:17

Alignment explanation


    Indices: 1502--1561  Score: 50
    Period size: 17  Copynumber: 3.3  Consensus size: 17

       1492 TTGATAAGTA

                *            
       1502 TAGTGAAATAATAAGAG
          1 TAGTCAAATAATAAGAG

                   *              
       1519 TAGCTATAAAATAAATAAGTA-
          1 TAG---TCAAAT-AATAAG-AG

                             
       1540 TAGTCAAATAATAAGAG
          1 TAGTCAAATAATAAGAG

                 
       1557 TAGTC
          1 TAGTC

       1562 CTAAAACTAA


Statistics
Matches: 35,  Mismatches: 2, Indels: 12
        0.71            0.04        0.24

Matches are distributed among these distances:
  16    1  0.03
  17   14  0.40
  18    5  0.14
  20    5  0.14
  21    9  0.26
  22    1  0.03

ACGTcount: A:0.52, C:0.05, G:0.17, T:0.27


Consensus pattern (17 bp):   
TAGTCAAATAATAAGAG

Found at i:1567 original size:38 final size:39

Alignment explanation


    Indices: 1495--1572  Score: 115
    Period size: 38  Copynumber: 2.0  Consensus size: 39

       1485 GGTTAAGTTG

                       *                           
       1495 ATAAGTATAGTGAAATAATAAGAGTAGCTATAAAA-TAA
          1 ATAAGTATAGTCAAATAATAAGAGTAGCTATAAAACTAA

                                          *         
       1533 ATAAGTATAGTCAAATAATAAGAGTAG-TCCTAAAACTAA
          1 ATAAGTATAGTCAAATAATAAGAGTAGCT-ATAAAACTAA

             
       1572 A
          1 A

       1573 ATAAAATTGA


Statistics
Matches: 36,  Mismatches: 2, Indels: 3
        0.88            0.05        0.07

Matches are distributed among these distances:
  37    1  0.03
  38   31  0.86
  39    4  0.11

ACGTcount: A:0.54, C:0.06, G:0.14, T:0.26


Consensus pattern (39 bp):   
ATAAGTATAGTCAAATAATAAGAGTAGCTATAAAACTAA
Done.