Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013381.1 Corchorus olitorius cultivar O-4 contig13414, 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: 26146
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32


Found at i:1397 original size:16 final size:16

Alignment explanation


    Indices: 1376--1408  Score: 66
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       1366 GAGCAAATAG

                            
       1376 CTAAAATTCTTGATCC
          1 CTAAAATTCTTGATCC

                            
       1392 CTAAAATTCTTGATCC
          1 CTAAAATTCTTGATCC

             
       1408 C
          1 C

       1409 GAAGGAATCT


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

Matches are distributed among these distances:
  16   17  1.00

ACGTcount: A:0.30, C:0.27, G:0.06, T:0.36


Consensus pattern (16 bp):   
CTAAAATTCTTGATCC

Found at i:1539 original size:32 final size:32

Alignment explanation


    Indices: 1498--1563  Score: 132
    Period size: 32  Copynumber: 2.1  Consensus size: 32

       1488 AAAACCCTAG

                                            
       1498 ATTTAGTTTTGGGGAAAGAATCAAACATCCTC
          1 ATTTAGTTTTGGGGAAAGAATCAAACATCCTC

                                            
       1530 ATTTAGTTTTGGGGAAAGAATCAAACATCCTC
          1 ATTTAGTTTTGGGGAAAGAATCAAACATCCTC

              
       1562 AT
          1 AT

       1564 CCTTGATGAT


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  32   34  1.00

ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32


Consensus pattern (32 bp):   
ATTTAGTTTTGGGGAAAGAATCAAACATCCTC

Found at i:2950 original size:19 final size:19

Alignment explanation


    Indices: 2926--2964  Score: 78
    Period size: 19  Copynumber: 2.1  Consensus size: 19

       2916 CAACACTGCG

                               
       2926 AGTCGTATTGTCCATAGCT
          1 AGTCGTATTGTCCATAGCT

                               
       2945 AGTCGTATTGTCCATAGCT
          1 AGTCGTATTGTCCATAGCT

             
       2964 A
          1 A

       2965 ATTAGTCAAA


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   20  1.00

ACGTcount: A:0.23, C:0.21, G:0.21, T:0.36


Consensus pattern (19 bp):   
AGTCGTATTGTCCATAGCT

Found at i:9502 original size:14 final size:14

Alignment explanation


    Indices: 9460--9502  Score: 50
    Period size: 14  Copynumber: 2.9  Consensus size: 14

       9450 AGAAACGAAA

                          * 
       9460 AAAGAAAATAAAACCG
          1 AAAGAAAA-AAAA-AG

                  *       
       9476 AAAGAAGAAAAAAG
          1 AAAGAAAAAAAAAG

                         
       9490 AAAGAAAAAAAAA
          1 AAAGAAAAAAAAA

       9503 AGCGAGCAAA


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  14   13  0.54
  15    4  0.17
  16    7  0.29

ACGTcount: A:0.79, C:0.05, G:0.14, T:0.02


Consensus pattern (14 bp):   
AAAGAAAAAAAAAG

Found at i:17609 original size:6 final size:6

Alignment explanation


    Indices: 17586--17627  Score: 50
    Period size: 6  Copynumber: 7.0  Consensus size: 6

      17576 ACCTTGCCTC

                        *                        *           
      17586 TCTTTT TGCTTCT TCTTTT TC-TTT TCTTTT TTTTTT TCTTTT
          1 TCTTTT T-CTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT

      17628 GGTTTGAGAA


Statistics
Matches: 30,  Mismatches: 4, Indels: 4
        0.79            0.11        0.11

Matches are distributed among these distances:
   5    5  0.17
   6   20  0.67
   7    5  0.17

ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81


Consensus pattern (6 bp):   
TCTTTT

Found at i:21990 original size:1 final size:1

Alignment explanation


    Indices: 21984--22009  Score: 52
    Period size: 1  Copynumber: 26.0  Consensus size: 1

      21974 GAATAAATAG

                                      
      21984 TTTTTTTTTTTTTTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTT

      22010 ATAATACAAT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   25  1.00

ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00


Consensus pattern (1 bp):   
T

Done.