Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015218.1 Corchorus capsularis cultivar CVL-1 contig15239, 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: 2322
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:497 original size:32 final size:32

Alignment explanation


    Indices: 456--554  Score: 97
    Period size: 32  Copynumber: 3.3  Consensus size: 32

        446 TATGATAGTT

                                            
        456 TTTGATTGTTGCATGCGAACTTAGGATAAAAA
          1 TTTGATTGTTGCATGCGAACTTAGGATAAAAA

                       **                 **
        488 TTTGATTGTT-TTTG-G-A-TT--GAT--ATG
          1 TTTGATTGTTGCATGCGAACTTAGGATAAAAA

                                             
        512 TTATGATTGTTGCATGCGAACTTAGGATAAAAA
          1 TT-TGATTGTTGCATGCGAACTTAGGATAAAAA

                      
        545 TTTGATTGTT
          1 TTTGATTGTT

        555 TTTGAATTGA


Statistics
Matches: 50,  Mismatches: 8, Indels: 18
        0.66            0.11        0.24

Matches are distributed among these distances:
  24    3  0.06
  25    8  0.16
  26    5  0.10
  27    1  0.02
  28    3  0.06
  29    3  0.06
  30    1  0.02
  31    5  0.10
  32   18  0.36
  33    3  0.06

ACGTcount: A:0.28, C:0.06, G:0.22, T:0.43


Consensus pattern (32 bp):   
TTTGATTGTTGCATGCGAACTTAGGATAAAAA

Found at i:519 original size:57 final size:57

Alignment explanation


    Indices: 458--572  Score: 221
    Period size: 57  Copynumber: 2.0  Consensus size: 57

        448 TGATAGTTTT

                                                        *            
        458 TGATTGTTGCATGCGAACTTAGGATAAAAATTTGATTGTTTTTGGATTGATATGTTA
          1 TGATTGTTGCATGCGAACTTAGGATAAAAATTTGATTGTTTTTGAATTGATATGTTA

                                                                     
        515 TGATTGTTGCATGCGAACTTAGGATAAAAATTTGATTGTTTTTGAATTGATATGTTA
          1 TGATTGTTGCATGCGAACTTAGGATAAAAATTTGATTGTTTTTGAATTGATATGTTA

             
        572 T
          1 T

        573 TCCCCAATTT


Statistics
Matches: 57,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  57   57  1.00

ACGTcount: A:0.29, C:0.05, G:0.22, T:0.44


Consensus pattern (57 bp):   
TGATTGTTGCATGCGAACTTAGGATAAAAATTTGATTGTTTTTGAATTGATATGTTA

Found at i:1507 original size:14 final size:15

Alignment explanation


    Indices: 1479--1507  Score: 51
    Period size: 15  Copynumber: 2.0  Consensus size: 15

       1469 GTGTGAATTC

                           
       1479 AAATTGATCTTTTGA
          1 AAATTGATCTTTTGA

                           
       1494 AAATTGAT-TTTTGA
          1 AAATTGATCTTTTGA

       1508 TTAACTTAAA


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

Matches are distributed among these distances:
  14    6  0.43
  15    8  0.57

ACGTcount: A:0.34, C:0.03, G:0.14, T:0.48


Consensus pattern (15 bp):   
AAATTGATCTTTTGA

Found at i:1828 original size:19 final size:18

Alignment explanation


    Indices: 1804--1839  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       1794 TGAAGATTTC

                               
       1804 TTGAAGATAATTTGAAGAT
          1 TTGAAGATAA-TTGAAGAT

                    *        
       1823 TTGAAGATTATTGAAGA
          1 TTGAAGATAATTGAAGA

       1840 ATCATTTCAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.42, C:0.00, G:0.22, T:0.36


Consensus pattern (18 bp):   
TTGAAGATAATTGAAGAT
Done.