Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009100.1 Corchorus capsularis cultivar CVL-1 contig09121, 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: 40654
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31


Found at i:4686 original size:15 final size:14

Alignment explanation


    Indices: 4652--4682  Score: 53
    Period size: 14  Copynumber: 2.2  Consensus size: 14

       4642 TAGTTTTTAG

                    *     
       4652 TTTAATTGCTTTCT
          1 TTTAATTGATTTCT

                          
       4666 TTTAATTGATTTCT
          1 TTTAATTGATTTCT

               
       4680 TTT
          1 TTT

       4683 TAATCCCCTG


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  14   16  1.00

ACGTcount: A:0.16, C:0.10, G:0.06, T:0.68


Consensus pattern (14 bp):   
TTTAATTGATTTCT

Found at i:8071 original size:39 final size:39

Alignment explanation


    Indices: 8028--8107  Score: 151
    Period size: 39  Copynumber: 2.1  Consensus size: 39

       8018 TTTTGTTGAT

                                            *      
       8028 GACAAAACACTCCTTGAATTGAAGTGTTAACTTATAAGA
          1 GACAAAACACTCCTTGAATTGAAGTGTTAACTGATAAGA

                                                   
       8067 GACAAAACACTCCTTGAATTGAAGTGTTAACTGATAAGA
          1 GACAAAACACTCCTTGAATTGAAGTGTTAACTGATAAGA

              
       8106 GA
          1 GA

       8108 TAATATATAG


Statistics
Matches: 40,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  39   40  1.00

ACGTcount: A:0.41, C:0.15, G:0.17, T:0.26


Consensus pattern (39 bp):   
GACAAAACACTCCTTGAATTGAAGTGTTAACTGATAAGA

Found at i:9250 original size:16 final size:16

Alignment explanation


    Indices: 9229--9264  Score: 63
    Period size: 16  Copynumber: 2.2  Consensus size: 16

       9219 AGCATATTTC

                            
       9229 ATTTAGTAGAAGTTGA
          1 ATTTAGTAGAAGTTGA

                           *
       9245 ATTTAGTAGAAGTTGC
          1 ATTTAGTAGAAGTTGA

                
       9261 ATTT
          1 ATTT

       9265 GCATAAAAAA


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  16   19  1.00

ACGTcount: A:0.33, C:0.03, G:0.22, T:0.42


Consensus pattern (16 bp):   
ATTTAGTAGAAGTTGA

Found at i:29650 original size:2 final size:2

Alignment explanation


    Indices: 29645--29673  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

      29635 CTTAAAAAAC

                                                       
      29645 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

      29674 TGTTAAAGCC


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:30008 original size:47 final size:49

Alignment explanation


    Indices: 29939--30038  Score: 168
    Period size: 47  Copynumber: 2.1  Consensus size: 49

      29929 ACGGCACAGG

                                                             
      29939 TAATCAAGCTTGATTTGGTGGTTTTG-TTTTTTTTATT-ATTTATGAGT
          1 TAATCAAGCTTGATTTGGTGGTTTTGTTTTTTTTTATTCATTTATGAGT

                                                *             
      29986 TAATCAAGCTTGATTTGGTGGTTTTGTTTTTTTTTTTTTCATTTATGAGT
          1 TAATCAAGCTTGATTTGGTGGTTTTG-TTTTTTTTTATTCATTTATGAGT

               
      30036 TAA
          1 TAA

      30039 CGGGGTAATC


Statistics
Matches: 49,  Mismatches: 1, Indels: 3
        0.92            0.02        0.06

Matches are distributed among these distances:
  47   26  0.53
  49   10  0.20
  50   13  0.27

ACGTcount: A:0.19, C:0.05, G:0.18, T:0.58


Consensus pattern (49 bp):   
TAATCAAGCTTGATTTGGTGGTTTTGTTTTTTTTTATTCATTTATGAGT

Found at i:30653 original size:2 final size:2

Alignment explanation


    Indices: 30646--30683  Score: 67
    Period size: 2  Copynumber: 19.0  Consensus size: 2

      30636 CTATCCCCAC

                                                         *          
      30646 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      30684 TTCAGACAAA


Statistics
Matches: 34,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   2   34  1.00

ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53


Consensus pattern (2 bp):   
AT

Found at i:39250 original size:2 final size:2

Alignment explanation


    Indices: 39239--39268  Score: 53
    Period size: 2  Copynumber: 15.5  Consensus size: 2

      39229 TTATAACTTT

                                                          
      39239 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

      39269 TTGGTATCAC


Statistics
Matches: 27,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   1    1  0.04
   2   26  0.96

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


Consensus pattern (2 bp):   
TA

Done.