Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013051.1 Corchorus olitorius cultivar O-4 contig13084, 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: 16951
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.35


Found at i:7749 original size:6 final size:5

Alignment explanation


    Indices: 7707--7748  Score: 57
    Period size: 5  Copynumber: 7.8  Consensus size: 5

       7697 TTAAATAACC

                                                             
       7707 TTTTG TTTTG TTTTG CTTTTG TTGTTG TTGTTG TTTTG TTTT
          1 TTTTG TTTTG TTTTG -TTTTG TT-TTG TT-TTG TTTTG TTTT

       7749 TCTTGGTCAT


Statistics
Matches: 35,  Mismatches: 0, Indels: 4
        0.90            0.00        0.10

Matches are distributed among these distances:
   5   19  0.54
   6   16  0.46

ACGTcount: A:0.00, C:0.02, G:0.21, T:0.76


Consensus pattern (5 bp):   
TTTTG

Found at i:9254 original size:3 final size:3

Alignment explanation


    Indices: 9230--9284  Score: 71
    Period size: 3  Copynumber: 18.7  Consensus size: 3

       9220 ATATAACATT

                                                                         
       9230 TTG TT- TTG TT- TTG CTT- TTG TTG TTG TTAG TTG TTG TTG TTG TTG
          1 TTG TTG TTG TTG TTG -TTG TTG TTG TTG TT-G TTG TTG TTG TTG TTG

                          
       9274 TTG TTG TTG TT
          1 TTG TTG TTG TT

       9285 TTTTCATGGT


Statistics
Matches: 47,  Mismatches: 0, Indels: 10
        0.82            0.00        0.18

Matches are distributed among these distances:
   2    6  0.13
   3   36  0.77
   4    5  0.11

ACGTcount: A:0.02, C:0.02, G:0.27, T:0.69


Consensus pattern (3 bp):   
TTG

Found at i:12379 original size:17 final size:17

Alignment explanation


    Indices: 12339--12383  Score: 56
    Period size: 18  Copynumber: 2.6  Consensus size: 17

      12329 ATAACCTTTA

                         *   
      12339 GTTTTGTTTTGTTTTGT
          1 GTTTTGTTTTGTTGTGT

                               
      12356 GTTTTTGTTGTTGTTGT-T
          1 G-TTTTGTT-TTGTTGTGT

                      
      12374 GTTTTGTTTT
          1 GTTTTGTTTT

      12384 TTCATGGTCA


Statistics
Matches: 25,  Mismatches: 1, Indels: 5
        0.81            0.03        0.16

Matches are distributed among these distances:
  16    2  0.08
  17    8  0.32
  18    9  0.36
  19    6  0.24

ACGTcount: A:0.00, C:0.00, G:0.24, T:0.76


Consensus pattern (17 bp):   
GTTTTGTTTTGTTGTGT

Found at i:13293 original size:19 final size:18

Alignment explanation


    Indices: 13269--13304  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

      13259 TGAAGACTTA

                               
      13269 TTGAAGACAATTTGAAGAT
          1 TTGAAGACAA-TTGAAGAT

                    *        
      13288 TTGAAGACCATTGAAGA
          1 TTGAAGACAATTGAAGA

      13305 ATAATTTCAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28


Consensus pattern (18 bp):   
TTGAAGACAATTGAAGAT

Found at i:13311 original size:30 final size:30

Alignment explanation


    Indices: 13258--13316  Score: 75
    Period size: 30  Copynumber: 2.0  Consensus size: 30

      13248 AATTTCGTGC

                     *              *     
      13258 TTGAAGACTTATTGAAGACAATTTGAAGAT
          1 TTGAAGACTCATTGAAGACAATTTCAAGAT

                               *          
      13288 TTGAAGAC-CATTGAAGAATAATTTCAAGA
          1 TTGAAGACTCATTGAAG-ACAATTTCAAGA

      13317 GCAAGAATTG


Statistics
Matches: 25,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  29    7  0.28
  30   18  0.72

ACGTcount: A:0.42, C:0.08, G:0.19, T:0.31


Consensus pattern (30 bp):   
TTGAAGACTCATTGAAGACAATTTCAAGAT

Found at i:15953 original size:2 final size:2

Alignment explanation


    Indices: 15924--15999  Score: 64
    Period size: 2  Copynumber: 43.0  Consensus size: 2

      15914 TACTAATTTG

                              *                                           
      15924 TA TA TA -A TA TA AA T- TA T- TA TA T- TA TA TA TA T- TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                           *                                              
      15961 TA TA -A TA TA AA T- TA T- TA TA T- TA TA TA TA TA T- TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

              
      15998 TA
          1 TA

      16000 AAAATAAAAA


Statistics
Matches: 60,  Mismatches: 4, Indels: 20
        0.71            0.05        0.24

Matches are distributed among these distances:
   1   10  0.17
   2   50  0.83

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Found at i:15966 original size:35 final size:35

Alignment explanation


    Indices: 15924--16000  Score: 138
    Period size: 35  Copynumber: 2.2  Consensus size: 35

      15914 TACTAATTTG

                                                
      15924 TATATAATATAAATTATTATATTATATATAT-TATA
          1 TATATAATATAAATTATTATATTATATATATAT-TA

                                               
      15959 TATATAATATAAATTATTATATTATATATATATTA
          1 TATATAATATAAATTATTATATTATATATATATTA

                   
      15994 TATATAA
          1 TATATAA

      16001 AAATAAAAAT


Statistics
Matches: 41,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
  35   40  0.98
  36    1  0.02

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (35 bp):   
TATATAATATAAATTATTATATTATATATATATTA
Done.