Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022263.1 Corchorus olitorius cultivar O-4 contig22296, 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: 2848
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28


Found at i:793 original size:22 final size:21

Alignment explanation


    Indices: 752--793  Score: 59
    Period size: 21  Copynumber: 2.0  Consensus size: 21

        742 AAATTCCCAT

                                  
        752 TGAAAAAAGGGAAAAGAAAAAA
          1 TGAAAAAA-GGAAAAGAAAAAA

                                 
        774 TGAAAAAA-GAATAAGAAAAA
          1 TGAAAAAAGGAA-AAGAAAAA

        794 GGCACTTGGA


Statistics
Matches: 19,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  20    3  0.16
  21    8  0.42
  22    8  0.42

ACGTcount: A:0.74, C:0.00, G:0.19, T:0.07


Consensus pattern (21 bp):   
TGAAAAAAGGAAAAGAAAAAA

Found at i:1259 original size:13 final size:15

Alignment explanation


    Indices: 1224--1263  Score: 57
    Period size: 13  Copynumber: 2.7  Consensus size: 15

       1214 AAAAAAAAAA

                            
       1224 AACAACAACAAACAGC
          1 AACAACAA-AAACAGC

                           
       1240 AACAACAAAAACAG-
          1 AACAACAAAAACAGC

                       
       1254 AA-AACAAAAA
          1 AACAACAAAAA

       1264 AAGTGAAAAT


Statistics
Matches: 24,  Mismatches: 0, Indels: 3
        0.89            0.00        0.11

Matches are distributed among these distances:
  13    8  0.33
  14    2  0.08
  15    6  0.25
  16    8  0.33

ACGTcount: A:0.72, C:0.23, G:0.05, T:0.00


Consensus pattern (15 bp):   
AACAACAAAAACAGC

Found at i:1259 original size:16 final size:16

Alignment explanation


    Indices: 1222--1265  Score: 56
    Period size: 16  Copynumber: 2.8  Consensus size: 16

       1212 AAAAAAAAAA

                             
       1222 AAAACAACAACAAACAG
          1 AAAACAACAA-AAACAG

             *              
       1239 -CAACAACAAAAACAG
          1 AAAACAACAAAAACAG

                         
       1254 AAAACAA-AAAAA
          1 AAAACAACAAAAA

       1266 GTGAAAATTG


Statistics
Matches: 24,  Mismatches: 2, Indels: 4
        0.80            0.07        0.13

Matches are distributed among these distances:
  15   11  0.46
  16   13  0.54

ACGTcount: A:0.75, C:0.20, G:0.05, T:0.00


Consensus pattern (16 bp):   
AAAACAACAAAAACAG

Found at i:1299 original size:19 final size:20

Alignment explanation


    Indices: 1263--1304  Score: 52
    Period size: 19  Copynumber: 2.1  Consensus size: 20

       1253 GAAAACAAAA

                                
       1263 AAAGTGAAAATTGAAAA-TG
          1 AAAGTGAAAATTGAAAATTG

                  *              
       1282 AAAGTGGAAATT-ATAAATTG
          1 AAAGTGAAAATTGA-AAATTG

               
       1302 AAA
          1 AAA

       1305 AAAGTATAAG


Statistics
Matches: 20,  Mismatches: 1, Indels: 3
        0.83            0.04        0.12

Matches are distributed among these distances:
  18    1  0.05
  19   14  0.70
  20    5  0.25

ACGTcount: A:0.57, C:0.00, G:0.19, T:0.24


Consensus pattern (20 bp):   
AAAGTGAAAATTGAAAATTG

Found at i:1652 original size:14 final size:14

Alignment explanation


    Indices: 1633--1660  Score: 56
    Period size: 14  Copynumber: 2.0  Consensus size: 14

       1623 AAAGGGGGTG

                          
       1633 AATGAAAAAATGAA
          1 AATGAAAAAATGAA

                          
       1647 AATGAAAAAATGAA
          1 AATGAAAAAATGAA

       1661 GAGAAGAAGC


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

Matches are distributed among these distances:
  14   14  1.00

ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14


Consensus pattern (14 bp):   
AATGAAAAAATGAA

Found at i:1875 original size:19 final size:19

Alignment explanation


    Indices: 1851--1890  Score: 80
    Period size: 19  Copynumber: 2.1  Consensus size: 19

       1841 CCAAAAGGAG

                               
       1851 CCAATTCATTGAGTTCATA
          1 CCAATTCATTGAGTTCATA

                               
       1870 CCAATTCATTGAGTTCATA
          1 CCAATTCATTGAGTTCATA

              
       1889 CC
          1 CC

       1891 CCTGACGTTT


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   21  1.00

ACGTcount: A:0.30, C:0.25, G:0.10, T:0.35


Consensus pattern (19 bp):   
CCAATTCATTGAGTTCATA
Done.