Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006772.1 Corchorus capsularis cultivar CVL-1 contig06793, 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: 11092
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33


Found at i:8238 original size:11 final size:11

Alignment explanation


    Indices: 8224--8261  Score: 51
    Period size: 11  Copynumber: 3.5  Consensus size: 11

       8214 ATTCATAACA

                       
       8224 AATTTATAATT
          1 AATTTATAATT

                       
       8235 AATTTATAATT
          1 AATTTATAATT

                        
       8246 -ATTTGATAATT
          1 AATTT-ATAATT

            *    
       8257 TATTT
          1 AATTT

       8262 TATATAGGAA


Statistics
Matches: 25,  Mismatches: 0, Indels: 3
        0.89            0.00        0.11

Matches are distributed among these distances:
  10    4  0.16
  11   17  0.68
  12    4  0.16

ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58


Consensus pattern (11 bp):   
AATTTATAATT

Found at i:8410 original size:131 final size:131

Alignment explanation


    Indices: 8240--8503  Score: 519
    Period size: 131  Copynumber: 2.0  Consensus size: 131

       8230 TAATTAATTT

                                                                             
       8240 ATAATTATTTGATAATTTATTTTATATAGGAAAGAGGATGAATGTCTTTTAATTTTTCCAAACTA
          1 ATAATTATTTGATAATTTATTTTATATAGGAAAGAGGATGAATGTCTTTTAATTTTTCCAAACTA

                                                                             
       8305 AAATGAATACAAATATAATAAACAAAAATTAGAAAATTAACTATTGACACTTGTCAAAGAAACCA
         66 AAATGAATACAAATATAATAAACAAAAATTAGAAAATTAACTATTGACACTTGTCAAAGAAACCA

             
       8370 A
        131 A

                                              *                              
       8371 ATAATTATTTGATAATTTATTTTATATAGGAAAGGGGATGAATGTCTTTTAATTTTTCCAAACTA
          1 ATAATTATTTGATAATTTATTTTATATAGGAAAGAGGATGAATGTCTTTTAATTTTTCCAAACTA

                                                                             
       8436 AAATGAATACAAATATAATAAACAAAAATTAGAAAATTAACTATTGACACTTGTCAAAGAAACCA
         66 AAATGAATACAAATATAATAAACAAAAATTAGAAAATTAACTATTGACACTTGTCAAAGAAACCA

             
       8501 A
        131 A

              
       8502 AT
          1 AT

       8504 GCCAAGTGGC


Statistics
Matches: 132,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
 131  132  1.00

ACGTcount: A:0.47, C:0.09, G:0.10, T:0.34


Consensus pattern (131 bp):   
ATAATTATTTGATAATTTATTTTATATAGGAAAGAGGATGAATGTCTTTTAATTTTTCCAAACTA
AAATGAATACAAATATAATAAACAAAAATTAGAAAATTAACTATTGACACTTGTCAAAGAAACCA
A

Found at i:8802 original size:29 final size:28

Alignment explanation


    Indices: 8738--8792  Score: 83
    Period size: 29  Copynumber: 1.9  Consensus size: 28

       8728 AAATTTCCTT

                 *                *      
       8738 AAAATAAAACAAAATCTTATAATTAAGGA
          1 AAAATTAAACAAAATCTTATAAATAA-GA

                                      
       8767 AAAATTAAACAAAATCTTATAAATAA
          1 AAAATTAAACAAAATCTTATAAATAA

       8793 AAAGATATTA


Statistics
Matches: 24,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  29   24  1.00

ACGTcount: A:0.64, C:0.07, G:0.04, T:0.25


Consensus pattern (28 bp):   
AAAATTAAACAAAATCTTATAAATAAGA

Found at i:9867 original size:23 final size:23

Alignment explanation


    Indices: 9837--9883  Score: 94
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       9827 TAATTACCCT

                                   
       9837 TAATAATAATAAGTTCCCATTTA
          1 TAATAATAATAAGTTCCCATTTA

                                   
       9860 TAATAATAATAAGTTCCCATTTA
          1 TAATAATAATAAGTTCCCATTTA

             
       9883 T
          1 T

       9884 TTATTTTTTC


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  23   24  1.00

ACGTcount: A:0.43, C:0.13, G:0.04, T:0.40


Consensus pattern (23 bp):   
TAATAATAATAAGTTCCCATTTA

Found at i:10437 original size:21 final size:23

Alignment explanation


    Indices: 10380--10449  Score: 99
    Period size: 21  Copynumber: 3.0  Consensus size: 23

      10370 TAGTTTAAAG

                                     
      10380 ATGTAAATTAATTGTTCACATTATC
          1 ATGTAAATT-A-TGTTCACATTATC

                                   
      10405 ATGTAAATTATGTTCACATTATC
          1 ATGTAAATTATGTTCACATTATC

                 *                 
      10428 A-G-ATATTATGTTCACATTATC
          1 ATGTAAATTATGTTCACATTATC

             
      10449 A
          1 A

      10450 CTATGTGAGT


Statistics
Matches: 44,  Mismatches: 1, Indels: 4
        0.90            0.02        0.08

Matches are distributed among these distances:
  21   19  0.43
  22    1  0.02
  23   14  0.32
  24    1  0.02
  25    9  0.20

ACGTcount: A:0.36, C:0.13, G:0.09, T:0.43


Consensus pattern (23 bp):   
ATGTAAATTATGTTCACATTATC

Found at i:11004 original size:13 final size:13

Alignment explanation


    Indices: 10986--11010  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

      10976 TTCAATGTTT

                         
      10986 TAAATATTATTTA
          1 TAAATATTATTTA

                        
      10999 TAAATATTATTT
          1 TAAATATTATTT

      11011 GGAATTCCAA


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56


Consensus pattern (13 bp):   
TAAATATTATTTA
Done.