Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009627.1 Corchorus olitorius cultivar O-4 contig09659, 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: 3469
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36


Found at i:592 original size:18 final size:17

Alignment explanation


    Indices: 569--606  Score: 58
    Period size: 18  Copynumber: 2.2  Consensus size: 17

        559 CTGCCATGTC

                        *     
        569 ATATTTTTTTATTAAAAA
          1 ATATTTTTTTA-AAAAAA

                             
        587 ATATTTTTTTAAAAAAA
          1 ATATTTTTTTAAAAAAA

               
        604 ATA
          1 ATA

        607 ATTAGTTAGG


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  17    8  0.42
  18   11  0.58

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


Consensus pattern (17 bp):   
ATATTTTTTTAAAAAAA

Found at i:768 original size:16 final size:18

Alignment explanation


    Indices: 739--777  Score: 55
    Period size: 17  Copynumber: 2.3  Consensus size: 18

        729 AAAAAAATCA

                     *        
        739 TTTTTCTTCTTTTCT-TT
          1 TTTTTCTTCATTTCTATT

                              
        756 TTTTTCTT-ATTTCTATT
          1 TTTTTCTTCATTTCTATT

                 
        773 TTTTT
          1 TTTTT

        778 ATATCATTTT


Statistics
Matches: 20,  Mismatches: 1, Indels: 2
        0.87            0.04        0.09

Matches are distributed among these distances:
  16    5  0.25
  17   15  0.75

ACGTcount: A:0.05, C:0.13, G:0.00, T:0.82


Consensus pattern (18 bp):   
TTTTTCTTCATTTCTATT

Found at i:1144 original size:2 final size:2

Alignment explanation


    Indices: 1137--1167  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

       1127 TTTGATTTAC

                                                          
       1137 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       1168 TAGTTTAAAC


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:1509 original size:30 final size:31

Alignment explanation


    Indices: 1473--1538  Score: 82
    Period size: 31  Copynumber: 2.2  Consensus size: 31

       1463 TGCAAATGGA

                                            
       1473 TCCCTGAAG-TGAACTT-AGTGAGCAATTGAG
          1 TCCCTGAAGTTG-ACTTAAGTGAGCAATTGAG

                         *    *          * 
       1503 TCCCTGAAGTTGAGTTAATTGAGCAATTGGG
          1 TCCCTGAAGTTGACTTAAGTGAGCAATTGAG

                 
       1534 TCCCT
          1 TCCCT

       1539 CACCAAAATT


Statistics
Matches: 31,  Mismatches: 3, Indels: 3
        0.84            0.08        0.08

Matches are distributed among these distances:
  30   12  0.39
  31   19  0.61

ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30


Consensus pattern (31 bp):   
TCCCTGAAGTTGACTTAAGTGAGCAATTGAG

Found at i:1572 original size:21 final size:20

Alignment explanation


    Indices: 1546--1584  Score: 69
    Period size: 21  Copynumber: 1.9  Consensus size: 20

       1536 CCTCACCAAA

                                 
       1546 ATTTTTTTAAAGAAATTATAT
          1 ATTTTTTTAAA-AAATTATAT

                              
       1567 ATTTTTTTAAAAAATTAT
          1 ATTTTTTTAAAAAATTAT

       1585 TTTTTTAATA


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  20    7  0.39
  21   11  0.61

ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54


Consensus pattern (20 bp):   
ATTTTTTTAAAAAATTATAT

Found at i:1587 original size:16 final size:17

Alignment explanation


    Indices: 1566--1597  Score: 57
    Period size: 16  Copynumber: 1.9  Consensus size: 17

       1556 AGAAATTATA

                             
       1566 TATTTTTTTAA-AAAAT
          1 TATTTTTTTAATAAAAT

                            
       1582 TATTTTTTTAATAAAA
          1 TATTTTTTTAATAAAA

       1598 AATATGACGT


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  16   11  0.73
  17    4  0.27

ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56


Consensus pattern (17 bp):   
TATTTTTTTAATAAAAT

Found at i:2124 original size:43 final size:43

Alignment explanation


    Indices: 2061--2142  Score: 110
    Period size: 43  Copynumber: 1.9  Consensus size: 43

       2051 CCAATTCGGC

                        *                              
       2061 AAAGTTTATCGTGGAAAGATTGAGGACTATGACATTATTGTCA
          1 AAAGTTTATCGTCGAAAGATTGAGGACTATGACATTATTGTCA

                     *     *      *     * *        
       2104 AAAGTTTATTGTCGAGAGATTGGGGACTTTTACATTATT
          1 AAAGTTTATCGTCGAAAGATTGAGGACTATGACATTATT

       2143 ACCACACTAT


Statistics
Matches: 33,  Mismatches: 6, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  43   33  1.00

ACGTcount: A:0.32, C:0.09, G:0.23, T:0.37


Consensus pattern (43 bp):   
AAAGTTTATCGTCGAAAGATTGAGGACTATGACATTATTGTCA
Done.