Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015986.1 Corchorus capsularis cultivar CVL-1 contig16007, 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: 8633
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--35  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

                                                                
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

         36 CTTCATGTAC


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Found at i:239 original size:24 final size:25

Alignment explanation


    Indices: 212--264  Score: 81
    Period size: 27  Copynumber: 2.1  Consensus size: 25

        202 AAGAAAATTC

                                     
        212 AATCTCCA-CCTCATTCCATTAATG
          1 AATCTCCACCCTCATTCCATTAATG

                                       
        236 AATCTCCACCTCCTCATTCCATTAATG
          1 AATCTCCA-C-CCTCATTCCATTAATG

              
        263 AA
          1 AA

        265 GATCATCTTG


Statistics
Matches: 26,  Mismatches: 0, Indels: 3
        0.90            0.00        0.10

Matches are distributed among these distances:
  24    8  0.31
  27   18  0.69

ACGTcount: A:0.30, C:0.34, G:0.04, T:0.32


Consensus pattern (25 bp):   
AATCTCCACCCTCATTCCATTAATG

Found at i:4326 original size:66 final size:66

Alignment explanation


    Indices: 4249--4433  Score: 317
    Period size: 62  Copynumber: 2.9  Consensus size: 66

       4239 GCAGAAGGGA

                                                                             
       4249 TTAAAAATACCAATTATATAAAGAAAACAATTAATCTAAAATTAAGGCTAAACTAAACTAAACTA
          1 TTAAAAATACCAATTATATAAAGAAAACAATTAATCTAAAATTAAGGCTAAACTAAACTAAACTA

             
       4314 G
         66 G

                                                                             
       4315 TTAAAAATACCAA-T-TAT--AGAAAACAATTAATCTAAAATTAAGGCTAAACTAAACTAAACTA
          1 TTAAAAATACCAATTATATAAAGAAAACAATTAATCTAAAATTAAGGCTAAACTAAACTAAACTA

             
       4376 G
         66 G

                                                                *     
       4377 TTAAAAATGA-CAATTATATAAAGAAAACAATTAATCTAAAATTAAGGCTAATCTAAA
          1 TTAAAAAT-ACCAATTATATAAAGAAAACAATTAATCTAAAATTAAGGCTAAACTAAA

       4434 GTGTATTTGA


Statistics
Matches: 113,  Mismatches: 1, Indels: 10
        0.91            0.01        0.08

Matches are distributed among these distances:
  62   56  0.50
  63    2  0.02
  64    6  0.05
  65    1  0.01
  66   48  0.42

ACGTcount: A:0.56, C:0.11, G:0.06, T:0.26


Consensus pattern (66 bp):   
TTAAAAATACCAATTATATAAAGAAAACAATTAATCTAAAATTAAGGCTAAACTAAACTAAACTA
G

Found at i:6709 original size:39 final size:41

Alignment explanation


    Indices: 6663--6760  Score: 112
    Period size: 42  Copynumber: 2.4  Consensus size: 41

       6653 CTTGTGTTGC

                               *  *         *  *      
       6663 ATGTGTTTAGGGACTTTAGTA-TAG-A-TGCCTCTGTGTTAT
          1 ATGTGTTT-GGGACTTTAGAAGGAGAATTGCCCCTATGTTAT

                                                      
       6702 ATGTGTTTGAGGACTTTAGAAGGAGAATTGCCCCTATGTTAT
          1 ATGTGTTTG-GGACTTTAGAAGGAGAATTGCCCCTATGTTAT

                             
       6744 ATGTGTTTGGGGACTTT
          1 ATGTGTTT-GGGACTTT

       6761 GGGGAGAGAG


Statistics
Matches: 50,  Mismatches: 4, Indels: 7
        0.82            0.07        0.11

Matches are distributed among these distances:
  38    1  0.02
  39   18  0.36
  40    2  0.04
  41    1  0.02
  42   27  0.54
  43    1  0.02

ACGTcount: A:0.21, C:0.10, G:0.28, T:0.41


Consensus pattern (41 bp):   
ATGTGTTTGGGACTTTAGAAGGAGAATTGCCCCTATGTTAT
Done.