Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001888.1 Corchorus olitorius cultivar O-4 contig01888, 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, 663

Length: 1106
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.34


Found at i:140 original size:2 final size:2

Alignment explanation


    Indices: 133--164  Score: 55
    Period size: 2  Copynumber: 16.0  Consensus size: 2

        123 TAGCAAGTTA

                                                 *         
        133 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

        165 TAATCAATAC


Statistics
Matches: 28,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   2   28  1.00

ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47


Consensus pattern (2 bp):   
AT

Found at i:209 original size:77 final size:76

Alignment explanation


    Indices: 76--241  Score: 287
    Period size: 77  Copynumber: 2.2  Consensus size: 76

         66 TTAATATTAG

                              *                      *       *               
         76 TATATAATATATTAATCACTACATTACTTAGAAGCAGACATTATAGCTAGCAAGTTAATATATAT
          1 TATATAATATATTAATCAATACATTACTTAGAAGCAGACATGATAGCTAACAAGTTAATATATAT

                       
        141 ATATATATATA
         66 ATATATATATA

                                                                             
        152 TATATACATATATTAATCAATACATTACTTAGAAGCAGACATGATAGCTAACAAGTTAATATATA
          1 TATATA-ATATATTAATCAATACATTACTTAGAAGCAGACATGATAGCTAACAAGTTAATATATA

                        
        217 TATATATATATA
         65 TATATATATATA

                         
        229 TATATATATATAT
          1 TATATA-ATATAT

        242 AATATATTAA


Statistics
Matches: 85,  Mismatches: 4, Indels: 1
        0.94            0.04        0.01

Matches are distributed among these distances:
  76    6  0.07
  77   79  0.93

ACGTcount: A:0.46, C:0.10, G:0.07, T:0.37


Consensus pattern (76 bp):   
TATATAATATATTAATCAATACATTACTTAGAAGCAGACATGATAGCTAACAAGTTAATATATAT
ATATATATATA

Found at i:217 original size:2 final size:2

Alignment explanation


    Indices: 210--248  Score: 71
    Period size: 2  Copynumber: 20.0  Consensus size: 2

        200 TAACAAGTTA

                                                                       
        210 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

        249 TAATCACTAT


Statistics
Matches: 36,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   1    1  0.03
   2   35  0.97

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


Consensus pattern (2 bp):   
AT

Found at i:321 original size:35 final size:35

Alignment explanation


    Indices: 275--343  Score: 120
    Period size: 35  Copynumber: 2.0  Consensus size: 35

        265 TAGAAGCATA

                                       *       
        275 CATTATCCTGCTAGAGAATGAAGCAAATTTTAATG
          1 CATTATCCTGCTAGAGAATGAAGCAAAATTTAATG

                        *                     
        310 CATTATCCTGCTGGAGAATGAAGCAAAATTTAAT
          1 CATTATCCTGCTAGAGAATGAAGCAAAATTTAAT

        344 CTACTCAATA


Statistics
Matches: 32,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  35   32  1.00

ACGTcount: A:0.38, C:0.14, G:0.17, T:0.30


Consensus pattern (35 bp):   
CATTATCCTGCTAGAGAATGAAGCAAAATTTAATG

Found at i:360 original size:20 final size:20

Alignment explanation


    Indices: 335--375  Score: 73
    Period size: 20  Copynumber: 2.0  Consensus size: 20

        325 GAATGAAGCA

                                
        335 AAATTTAATCTACTCAATAG
          1 AAATTTAATCTACTCAATAG

                           *    
        355 AAATTTAATCTACTCTATAG
          1 AAATTTAATCTACTCAATAG

             
        375 A
          1 A

        376 TCGAATATCT


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  20   20  1.00

ACGTcount: A:0.44, C:0.15, G:0.05, T:0.37


Consensus pattern (20 bp):   
AAATTTAATCTACTCAATAG

Found at i:887 original size:18 final size:19

Alignment explanation


    Indices: 848--887  Score: 55
    Period size: 21  Copynumber: 2.1  Consensus size: 19

        838 GTGCTCCCGT

                                 
        848 TGTGATGCTCCCACTTTTCAA
          1 TGTGATGCTCCCA--TTTCAA

                               
        869 TGTGATGCTCCCA-TTCAA
          1 TGTGATGCTCCCATTTCAA

             
        887 T
          1 T

        888 TCTGACCATT


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

Matches are distributed among these distances:
  18    6  0.32
  21   13  0.68

ACGTcount: A:0.20, C:0.28, G:0.15, T:0.38


Consensus pattern (19 bp):   
TGTGATGCTCCCATTTCAA
Done.