Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016143.1 Corchorus capsularis cultivar CVL-1 contig16164, 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: 6159
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33


Found at i:1106 original size:15 final size:15

Alignment explanation


    Indices: 1086--1128  Score: 77
    Period size: 15  Copynumber: 2.9  Consensus size: 15

       1076 CCTTACTAAG

                           
       1086 CCAGAAGATGAGCCA
          1 CCAGAAGATGAGCCA

                           
       1101 CCAGAAGATGAGCCA
          1 CCAGAAGATGAGCCA

             *           
       1116 CAAGAAGATGAGC
          1 CCAGAAGATGAGC

       1129 AACTCGAATA


Statistics
Matches: 27,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  15   27  1.00

ACGTcount: A:0.42, C:0.23, G:0.28, T:0.07


Consensus pattern (15 bp):   
CCAGAAGATGAGCCA

Found at i:4040 original size:11 final size:11

Alignment explanation


    Indices: 4024--4055  Score: 55
    Period size: 11  Copynumber: 2.9  Consensus size: 11

       4014 GAAGTTCGTG

                       
       4024 TTTGAAGATTA
          1 TTTGAAGATTA

                     * 
       4035 TTTGAAGATAA
          1 TTTGAAGATTA

                      
       4046 TTTGAAGATT
          1 TTTGAAGATT

       4056 TGAAGACAAT


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

Matches are distributed among these distances:
  11   19  1.00

ACGTcount: A:0.38, C:0.00, G:0.19, T:0.44


Consensus pattern (11 bp):   
TTTGAAGATTA

Found at i:4058 original size:19 final size:18

Alignment explanation


    Indices: 4034--4071  Score: 58
    Period size: 19  Copynumber: 2.1  Consensus size: 18

       4024 TTTGAAGATT

                     *         
       4034 ATTTGAAGATAATTTGAAG
          1 ATTTGAAGACAA-TTGAAG

                              
       4053 ATTTGAAGACAATTGAAG
          1 ATTTGAAGACAATTGAAG

             
       4071 A
          1 A

       4072 ATTAATTCAA


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  18    7  0.39
  19   11  0.61

ACGTcount: A:0.45, C:0.03, G:0.21, T:0.32


Consensus pattern (18 bp):   
ATTTGAAGACAATTGAAG

Found at i:5429 original size:6 final size:6

Alignment explanation


    Indices: 5418--5460  Score: 79
    Period size: 6  Copynumber: 7.3  Consensus size: 6

       5408 ATAATTGCCA

                                                               
       5418 TAGATT TAGATT TAGATT TAGATT TAGATT TAGATT TA-ATT TA
          1 TAGATT TAGATT TAGATT TAGATT TAGATT TAGATT TAGATT TA

       5461 TTTTGCTTTG


Statistics
Matches: 37,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
   5    5  0.14
   6   32  0.86

ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51


Consensus pattern (6 bp):   
TAGATT

Found at i:5752 original size:55 final size:54

Alignment explanation


    Indices: 5686--5915  Score: 352
    Period size: 55  Copynumber: 4.2  Consensus size: 54

       5676 GACACGATCA

                                                               *   
       5686 TTTACTGATTACTATTACCTTGTCTCTGATTAATCTCTTTTTACTTAATTGTTGG
          1 TTTACTGATTACTATTACCTTGTCTCTGATTAATCTCTTTTTACTTAATT-ATGG

                                                                  *
       5741 TTTACTGATTACTATTACCTTGTCTCTGATTAATCTCTTTTTACTTAATTACTGA
          1 TTTACTGATTACTATTACCTTGTCTCTGATTAATCTCTTTTTACTTAATTA-TGG

                                     *                         *  
       5796 TTTACTGATTACTATTACCTTGTCTTTGATTAATCTCTTTTTACTTAATTACGG
          1 TTTACTGATTACTATTACCTTGTCTCTGATTAATCTCTTTTTACTTAATTATGG

                *                     *                            *
       5850 ATTTGCTGATTACTATTACCTTGTCTTTGATTAATCTCTTTTTACTTAATTACTGA
          1 -TTTACTGATTACTATTACCTTGTCTCTGATTAATCTCTTTTTACTTAATTA-TGG

               *      
       5906 TTTGCTGATT
          1 TTTACTGATT

       5916 TTTACTTTTC


Statistics
Matches: 164,  Mismatches: 8, Indels: 6
        0.92            0.04        0.03

Matches are distributed among these distances:
  54    1  0.01
  55  162  0.99
  56    1  0.01

ACGTcount: A:0.22, C:0.17, G:0.10, T:0.52


Consensus pattern (54 bp):   
TTTACTGATTACTATTACCTTGTCTCTGATTAATCTCTTTTTACTTAATTATGG

Found at i:5881 original size:110 final size:110

Alignment explanation


    Indices: 5685--5915  Score: 392
    Period size: 110  Copynumber: 2.1  Consensus size: 110

       5675 CGACACGATC

                                                                **           
       5685 ATTTACTGATTACTATTACCTTGTCTCTGATTAATCTCTTTTTACTTAATTGTTGGTTTACTGAT
          1 ATTTACTGATTACTATTACCTTGTCTCTGATTAATCTCTTTTTACTTAATTGACGGTTTACTGAT

                                                         
       5750 TACTATTACCTTGTCTCTGATTAATCTCTTTTTACTTAATTACTG
         66 TACTATTACCTTGTCTCTGATTAATCTCTTTTTACTTAATTACTG

                                      *                                 *    
       5795 ATTTACTGATTACTATTACCTTGTCTTTGATTAATCTCTTTTTACTTAATT-ACGGATTTGCTGA
          1 ATTTACTGATTACTATTACCTTGTCTCTGATTAATCTCTTTTTACTTAATTGACGG-TTTACTGA

                             *                            
       5859 TTACTATTACCTTGTCTTTGATTAATCTCTTTTTACTTAATTACTG
         65 TTACTATTACCTTGTCTCTGATTAATCTCTTTTTACTTAATTACTG

                *      
       5905 ATTTGCTGATT
          1 ATTTACTGATT

       5916 TTTACTTTTC


Statistics
Matches: 114,  Mismatches: 6, Indels: 2
        0.93            0.05        0.02

Matches are distributed among these distances:
 109    2  0.02
 110  112  0.98

ACGTcount: A:0.22, C:0.16, G:0.10, T:0.52


Consensus pattern (110 bp):   
ATTTACTGATTACTATTACCTTGTCTCTGATTAATCTCTTTTTACTTAATTGACGGTTTACTGAT
TACTATTACCTTGTCTCTGATTAATCTCTTTTTACTTAATTACTG

Done.