Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016022.1 Corchorus olitorius cultivar O-4 contig16055, 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: 10451
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32


Found at i:282 original size:15 final size:16

Alignment explanation


    Indices: 249--288  Score: 55
    Period size: 15  Copynumber: 2.6  Consensus size: 16

        239 TTACTTTGCT

                            
        249 TTGTTTTCTAGTATAA
          1 TTGTTTTCTAGTATAA

                        *   
        265 TTGTTTTCT-GTTTAA
          1 TTGTTTTCTAGTATAA

               *     
        280 TTGCTTTCT
          1 TTGTTTTCT

        289 TTCAACCTCT


Statistics
Matches: 22,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  15   13  0.59
  16    9  0.41

ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62


Consensus pattern (16 bp):   
TTGTTTTCTAGTATAA

Found at i:2426 original size:49 final size:48

Alignment explanation


    Indices: 2385--2486  Score: 177
    Period size: 49  Copynumber: 2.1  Consensus size: 48

       2375 TTTTTAATCT

                             *                               
       2385 ACTACACATTAACTTGTTGTTTACTTTTGTTTTGTATAATTTGATTTGC
          1 ACTACACATTAACTTGTAGTTTACTTTTGTTTTGTATAATTT-ATTTGC

                                                             
       2434 ACTACACATTAACTTGTAGTTTACTTTTGTTTTGTATAATTTGATTTGC
          1 ACTACACATTAACTTGTAGTTTACTTTTGTTTTGTATAATTT-ATTTGC

                
       2483 ACTA
          1 ACTA

       2487 ATTAATTTTT


Statistics
Matches: 52,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  49   52  1.00

ACGTcount: A:0.25, C:0.13, G:0.12, T:0.51


Consensus pattern (48 bp):   
ACTACACATTAACTTGTAGTTTACTTTTGTTTTGTATAATTTATTTGC

Found at i:4262 original size:22 final size:22

Alignment explanation


    Indices: 4234--4276  Score: 68
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       4224 TTTTCCGCAA

                      *     *     
       4234 CAAGTCCTGGGCAGGAGTTGTC
          1 CAAGTCCTGGACAGGACTTGTC

                                 
       4256 CAAGTCCTGGACAGGACTTGT
          1 CAAGTCCTGGACAGGACTTGT

       4277 TCTGAATTTT


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  22   19  1.00

ACGTcount: A:0.21, C:0.23, G:0.33, T:0.23


Consensus pattern (22 bp):   
CAAGTCCTGGACAGGACTTGTC

Found at i:4337 original size:50 final size:48

Alignment explanation


    Indices: 4258--4376  Score: 166
    Period size: 50  Copynumber: 2.4  Consensus size: 48

       4248 GAGTTGTCCA

                          *                                  
       4258 AGTCCTGGACAGGACTTGTTCTGAATTTTCTTCCGTCTTTCAACAGACC
          1 AGTCCTGG-CAGGAGTTGTTCTGAATTTTCTTCCGTCTTTCAACAGACC

                                     *                        
       4307 GAGTCCTGAGCAGGAGTTGTTCTGATTTTTCTTCCGTCTTTCAACAGACC
          1 -AGTCCTG-GCAGGAGTTGTTCTGAATTTTCTTCCGTCTTTCAACAGACC

                *               
       4357 AGGTTCTGGGCAGGAGTTGT
          1 A-GTCCT-GGCAGGAGTTGT

       4377 CAAGTCCTGG


Statistics
Matches: 63,  Mismatches: 3, Indels: 6
        0.88            0.04        0.08

Matches are distributed among these distances:
  49    1  0.02
  50   60  0.95
  51    2  0.03

ACGTcount: A:0.18, C:0.23, G:0.24, T:0.34


Consensus pattern (48 bp):   
AGTCCTGGCAGGAGTTGTTCTGAATTTTCTTCCGTCTTTCAACAGACC

Found at i:6521 original size:33 final size:32

Alignment explanation


    Indices: 6451--6588  Score: 116
    Period size: 33  Copynumber: 4.2  Consensus size: 32

       6441 ATGATCAACC

                                    ** *      
       6451 AAAACAGATTTGTTTTCATCACAATTAGCATCC-
          1 AAAACAGATTTG-TTTCATCACAAACAACA-CCT

                                             
       6484 AAAACAGAATTTGTTTCATCACAAACAACACCT
          1 AAAACAG-ATTTGTTTCATCACAAACAACACCT

                          *                * 
       6517 AAAACAGATTTAGTGTCATCACAAACAACACTT
          1 AAAACAGATTT-GTTTCATCACAAACAACACCT

               **  *      *       *  *    *  
       6550 AAATTAGGTTTAGTATCATCACTAATAACATCT
          1 AAAACAGATTT-GTTTCATCACAAACAACACCT

                  
       6583 AAAACA
          1 AAAACA

       6589 CTCTTTGCAA


Statistics
Matches: 87,  Mismatches: 15, Indels: 6
        0.81            0.14        0.06

Matches are distributed among these distances:
  32    6  0.07
  33   76  0.87
  34    5  0.06

ACGTcount: A:0.43, C:0.20, G:0.08, T:0.28


Consensus pattern (32 bp):   
AAAACAGATTTGTTTCATCACAAACAACACCT
Done.