Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010555.1 Corchorus capsularis cultivar CVL-1 contig10576, 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: 26559
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32


Found at i:3637 original size:48 final size:48

Alignment explanation


    Indices: 3565--3851  Score: 346
    Period size: 48  Copynumber: 6.0  Consensus size: 48

       3555 AAACATTAAA

                 *    *         *    **       * *      *    
       3565 GCCTTTCGTCCGGGAAGGGCATTTTTTGAAAAAGTAGGTAAAAAAAGT
          1 GCCTTCCGTCTGGGAAGGGCGTTTTGGGAAAAAGCAAGTAAAATAAGT

                  *         *  **     *          *       *    
       3613 GCCTTCTGTCTGGGAATGGTATTTT-TGAAAATAGCAGGTAAAAAAAAGT
          1 GCCTTCCGTCTGGGAAGGGCGTTTTGGGAAAA-AGCAAGT-AAAATAAGT

                               *                             
       3662 GCCTTCCGTCTGGGAAGGGTGTTTTGGGAAACAA-CAAGTAAAATAAGT
          1 GCCTTCCGTCTGGGAAGGGCGTTTTGGGAAA-AAGCAAGTAAAATAAGT

             *                                          *  *
       3710 GTCTTCCGTCTGGGAAGGGCGTTTTGGGAAAAAGCAAGTAAAATCAGC
          1 GCCTTCCGTCTGGGAAGGGCGTTTTGGGAAAAAGCAAGTAAAATAAGT

                                                            
       3758 GCCTTCCGTCTGGGAAGGGCGTTTTGGGAAAAAGCAAGTAAAATAAGT
          1 GCCTTCCGTCTGGGAAGGGCGTTTTGGGAAAAAGCAAGTAAAATAAGT

             *                                             
       3806 GTCTTCCGTCTGGGAAGGGCGTTTTGGGAAAAA-CAAGTAAAATAAG
          1 GCCTTCCGTCTGGGAAGGGCGTTTTGGGAAAAAGCAAGTAAAATAAG

       3852 AAACAAAATT


Statistics
Matches: 214,  Mismatches: 20, Indels: 11
        0.87            0.08        0.04

Matches are distributed among these distances:
  47   21  0.10
  48  152  0.71
  49   35  0.16
  50    5  0.02
  51    1  0.00

ACGTcount: A:0.32, C:0.14, G:0.29, T:0.25


Consensus pattern (48 bp):   
GCCTTCCGTCTGGGAAGGGCGTTTTGGGAAAAAGCAAGTAAAATAAGT

Found at i:3950 original size:17 final size:17

Alignment explanation


    Indices: 3928--3960  Score: 57
    Period size: 17  Copynumber: 1.9  Consensus size: 17

       3918 CCCTTTTTTA

                      *      
       3928 TTTTAATTTTTTGCTTT
          1 TTTTAATTTTGTGCTTT

                            
       3945 TTTTAATTTTGTGCTT
          1 TTTTAATTTTGTGCTT

       3961 AATTGATTAC


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  17   15  1.00

ACGTcount: A:0.12, C:0.06, G:0.09, T:0.73


Consensus pattern (17 bp):   
TTTTAATTTTGTGCTTT

Found at i:5260 original size:15 final size:16

Alignment explanation


    Indices: 5242--5271  Score: 53
    Period size: 15  Copynumber: 1.9  Consensus size: 16

       5232 CCTTTTGATC

                            
       5242 TTTCTGT-TTTTCTTT
          1 TTTCTGTGTTTTCTTT

                           
       5257 TTTCTGTGTTTTCTT
          1 TTTCTGTGTTTTCTT

       5272 GAACTTTTCC


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  15    7  0.50
  16    7  0.50

ACGTcount: A:0.00, C:0.13, G:0.10, T:0.77


Consensus pattern (16 bp):   
TTTCTGTGTTTTCTTT

Found at i:10708 original size:48 final size:48

Alignment explanation


    Indices: 10633--10742  Score: 168
    Period size: 48  Copynumber: 2.3  Consensus size: 48

      10623 CGGATACATT

                           *                                 
      10633 TTTCAATCCCAAAAGGCAAACCAAAAGTAAACAATTCTTTGCT-TCATG
          1 TTTCAATCCCAAAAGACAAACCAAAAGTAAACAATTCTTTGCTCT-ATG

                               *  *                        *
      10681 TTTCAATCCCAAAAGACAATCCGAAAGTAAACAATTCTTTGCTCTATT
          1 TTTCAATCCCAAAAGACAAACCAAAAGTAAACAATTCTTTGCTCTATG

                          
      10729 TTTCAATCCCAAAA
          1 TTTCAATCCCAAAA

      10743 TGAAAAAAAA


Statistics
Matches: 57,  Mismatches: 4, Indels: 2
        0.90            0.06        0.03

Matches are distributed among these distances:
  48   56  0.98
  49    1  0.02

ACGTcount: A:0.39, C:0.24, G:0.08, T:0.29


Consensus pattern (48 bp):   
TTTCAATCCCAAAAGACAAACCAAAAGTAAACAATTCTTTGCTCTATG

Found at i:11172 original size:18 final size:19

Alignment explanation


    Indices: 11146--11212  Score: 57
    Period size: 18  Copynumber: 3.5  Consensus size: 19

      11136 AAGAACATGG

                *      *       
      11146 AGAAGAAAGGATAAGA-GA
          1 AGAAAAAAGGAAAAGAGGA

                     *      *  
      11164 AGAAAAAAGAAAAAGATGA
          1 AGAAAAAAGGAAAAGAGGA

             *                   
      11183 AAAAAAAACGTGAAAAGAGGA
          1 AGAAAAAA-G-GAAAAGAGGA

                      
      11204 A-AAAAAAGG
          1 AGAAAAAAGG

      11213 GATAGGGCTG


Statistics
Matches: 40,  Mismatches: 6, Indels: 6
        0.77            0.12        0.12

Matches are distributed among these distances:
  18   14  0.35
  19   10  0.25
  20    7  0.17
  21    9  0.22

ACGTcount: A:0.69, C:0.01, G:0.25, T:0.04


Consensus pattern (19 bp):   
AGAAAAAAGGAAAAGAGGA
Done.