Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024389.1 Corchorus olitorius cultivar O-4 contig24422, 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: 1900
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.34


Found at i:319 original size:9 final size:9

Alignment explanation


    Indices: 307--331  Score: 50
    Period size: 9  Copynumber: 2.8  Consensus size: 9

        297 AAAAATATCA

                     
        307 AAAAAAAAT
          1 AAAAAAAAT

                     
        316 AAAAAAAAT
          1 AAAAAAAAT

                   
        325 AAAAAAA
          1 AAAAAAA

        332 GTTTCGACCA


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   9   16  1.00

ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08


Consensus pattern (9 bp):   
AAAAAAAAT

Found at i:1151 original size:15 final size:15

Alignment explanation


    Indices: 1131--1162  Score: 64
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       1121 CCTTGGGGGT

                           
       1131 TCAAAATCAACAAGC
          1 TCAAAATCAACAAGC

                           
       1146 TCAAAATCAACAAGC
          1 TCAAAATCAACAAGC

              
       1161 TC
          1 TC

       1163 CACTTAGTTT


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

Matches are distributed among these distances:
  15   17  1.00

ACGTcount: A:0.50, C:0.28, G:0.06, T:0.16


Consensus pattern (15 bp):   
TCAAAATCAACAAGC

Found at i:1796 original size:33 final size:33

Alignment explanation


    Indices: 1754--1889  Score: 150
    Period size: 33  Copynumber: 4.1  Consensus size: 33

       1744 CTGAACCTAA

                            *       *        
       1754 TTTGAGTGTTGTTTGCAATGACACGAAATCTGT
          1 TTTGAGTGTTGTTTGCGATGACACTAAATCTGT

                                 *      *  **
       1787 TTTGAGTGTTGTTTGCGATGATACTAAACCTAA
          1 TTTGAGTGTTGTTTGCGATGACACTAAATCTGT

                           *             *   
       1820 TTTGAGTGTTGTTTGTGATGACACTAAATTTGT
          1 TTTGAGTGTTGTTTGCGATGACACTAAATCTGT

                            *     *            
       1853 TTT-AGGTGTTGTTTGTGATGAAAC-AAATTCTGT
          1 TTTGA-GTGTTGTTTGCGATGACACTAAA-TCTGT

                
       1886 TTTG
          1 TTTG

       1890 GATGCTAATT


Statistics
Matches: 86,  Mismatches: 14, Indels: 5
        0.82            0.13        0.05

Matches are distributed among these distances:
  32    4  0.05
  33   82  0.95

ACGTcount: A:0.24, C:0.09, G:0.24, T:0.44


Consensus pattern (33 bp):   
TTTGAGTGTTGTTTGCGATGACACTAAATCTGT

Found at i:1824 original size:66 final size:66

Alignment explanation


    Indices: 1747--1873  Score: 193
    Period size: 66  Copynumber: 1.9  Consensus size: 66

       1737 AGTAATTCTG

                                                                             
       1747 AACCTAATTTGAGTGTTGTTTGCAATGACACGAAATCTGTTTT-GAGTGTTGTTTGCGATGATAC
          1 AACCTAATTTGAGTGTTGTTTGCAATGACACGAAATCTGTTTTAG-GTGTTGTTTGCGATGATAC

              
       1811 TA
         65 TA

                                  **       *    *                  *     
       1813 AACCTAATTTGAGTGTTGTTTGTGATGACACTAAATTTGTTTTAGGTGTTGTTTGTGATGA
          1 AACCTAATTTGAGTGTTGTTTGCAATGACACGAAATCTGTTTTAGGTGTTGTTTGCGATGA

       1874 AACAAATTCT


Statistics
Matches: 55,  Mismatches: 5, Indels: 2
        0.89            0.08        0.03

Matches are distributed among these distances:
  66   54  0.98
  67    1  0.02

ACGTcount: A:0.24, C:0.09, G:0.24, T:0.43


Consensus pattern (66 bp):   
AACCTAATTTGAGTGTTGTTTGCAATGACACGAAATCTGTTTTAGGTGTTGTTTGCGATGATACT
A
Done.