Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015785.1 Corchorus capsularis cultivar CVL-1 contig15806, 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: 38263
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34


Found at i:8363 original size:2 final size:2

Alignment explanation


    Indices: 8356--8380  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

       8346 TTCTTTATTT

                                                 
       8356 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 T

       8381 TTTAAAATTT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:16389 original size:5 final size:5

Alignment explanation


    Indices: 16375--16407  Score: 57
    Period size: 5  Copynumber: 6.4  Consensus size: 5

      16365 TAAGGGGGAA

                                                   
      16375 AAAAC AAAAAC AAAAC AAAAC AAAAC AAAAC AA
          1 AAAAC -AAAAC AAAAC AAAAC AAAAC AAAAC AA

      16408 CTATACCATA


Statistics
Matches: 27,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
   5   22  0.81
   6    5  0.19

ACGTcount: A:0.82, C:0.18, G:0.00, T:0.00


Consensus pattern (5 bp):   
AAAAC

Found at i:20670 original size:14 final size:15

Alignment explanation


    Indices: 20646--20678  Score: 50
    Period size: 14  Copynumber: 2.3  Consensus size: 15

      20636 GGCTGGTTGT

                       *   
      20646 TTTTGTTTTTGTTTG
          1 TTTTGTTTTTGCTTG

                           
      20661 TTTT-TTTTTGCTTG
          1 TTTTGTTTTTGCTTG

                
      20675 TTTT
          1 TTTT

      20679 AGCGTTAGTT


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  14   13  0.76
  15    4  0.24

ACGTcount: A:0.00, C:0.03, G:0.15, T:0.82


Consensus pattern (15 bp):   
TTTTGTTTTTGCTTG

Found at i:21076 original size:2 final size:2

Alignment explanation


    Indices: 21069--21102  Score: 68
    Period size: 2  Copynumber: 17.0  Consensus size: 2

      21059 ATAGGAAATC

                                                              
      21069 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      21103 TGCAGAAATG


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   32  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:21247 original size:57 final size:58

Alignment explanation


    Indices: 21110--21265  Score: 199
    Period size: 57  Copynumber: 2.6  Consensus size: 58

      21100 TATTGCAGAA

                                             *                            
      21110 ATGATGAGGATAACTTTGCAGAGCACTTATTTTGTTGCAGACATTTTGCAGAGATTCCTTTC
          1 ATGATGAGGATAACTTTGCAGAGCA-TTATTTTCTT-C--ACATTTTGCAGAGATTCCTTTC

               *                                 **                    
      21172 ATGGTGAGGATAACTTTGCAGAGCATTATTTTCTTC-TTTTATTGCAGAGATTCC-TTC
          1 ATGATGAGGATAACTTTGCAGAGCATTATTTTCTTCACATT-TTGCAGAGATTCCTTTC

                                  **             
      21229 ATGATGAGGATAACTTTGCAGAATATTATTTTCTTCA
          1 ATGATGAGGATAACTTTGCAGAGCATTATTTTCTTCA

      21266 ACTTTTGACT


Statistics
Matches: 85,  Mismatches: 7, Indels: 8
        0.85            0.07        0.08

Matches are distributed among these distances:
  57   38  0.45
  58   13  0.15
  60    1  0.01
  61    9  0.11
  62   24  0.28

ACGTcount: A:0.26, C:0.15, G:0.19, T:0.40


Consensus pattern (58 bp):   
ATGATGAGGATAACTTTGCAGAGCATTATTTTCTTCACATTTTGCAGAGATTCCTTTC

Found at i:33018 original size:109 final size:109

Alignment explanation


    Indices: 32822--33097  Score: 439
    Period size: 110  Copynumber: 2.5  Consensus size: 109

      32812 ACTATTATAG

                         *                     *                             
      32822 TTTTATTCTACTAGAAACTCTATTTTTATTCAATTAAATTAAATTTAATATCTTTATAATTACTT
          1 TTTTATTCTACTAAAAACTCTA---TT-TTC-ATTTAATTAAA-TTAATATCTTTATAATTACTT

                                                              
      32887 TATTTTTACCAAAAAATTTGGATATACT-AAAATTTTTTCTAATATACAA
         60 TATTTTTACCAAAAAATTTGGATATACTAAAAATTTTTTCTAATATACAA

                                                                             
      32936 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
          1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAAT-TAATATCTTTATAATTACTTTATTT

                                 *                       
      33001 TTACCAAAAAATTTGGATATATTAAAAATTTTTTCTAATATACAA
         65 TTACCAAAAAATTTGGATATACTAAAAATTTTTTCTAATATACAA

                                                                 
      33046 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATTCAATAT-TTTATA
          1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATT-AATATCTTTATA

      33098 TATATTTTTT


Statistics
Matches: 156,  Mismatches: 3, Indels: 11
        0.92            0.02        0.06

Matches are distributed among these distances:
 108    1  0.01
 109   64  0.41
 110   68  0.44
 111    2  0.01
 114   21  0.13

ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49


Consensus pattern (109 bp):   
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATTAATATCTTTATAATTACTTTATTTT
TACCAAAAAATTTGGATATACTAAAAATTTTTTCTAATATACAA

Done.