Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006663.1 Corchorus capsularis cultivar CVL-1 contig06684, 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: 23218
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32


Found at i:1225 original size:110 final size:111

Alignment explanation


    Indices: 1109--1331  Score: 376
    Period size: 111  Copynumber: 2.0  Consensus size: 111

       1099 TAGGGTTTCA

                             *                           *                   
       1109 AAGAAACTAGATGTTGGTGATCGTGATCATCAATTGCAAGTCTGCGCCATAACCG-AGAACAAGC
          1 AAGAAACTAGATGTTGGCGATCGTGATCATCAATTGCAAGTCTGCCCCATAACCGAAGAACAAGC

                                                          
       1173 TGGGCTTGTTGATACCCCTCTCCCTGATGATGATGATGATTTCCTG
         66 TGGGCTTGTTGATACCCCTCTCCCTGATGATGATGATGATTTCCTG

                                                               *           * 
       1219 AAGAAACTAGATGTTGGCGATCGTGATCATCAATTGCAAGTCTGCCCCATACCCGAAGAACAATC
          1 AAGAAACTAGATGTTGGCGATCGTGATCATCAATTGCAAGTCTGCCCCATAACCGAAGAACAAGC

                         *     *                       *  
       1284 TGGGCTTGTTGATGCCCCTGTCCCTGATGATGATGATGATTTCGTG
         66 TGGGCTTGTTGATACCCCTCTCCCTGATGATGATGATGATTTCCTG

              
       1330 AA
          1 AA

       1332 TAGCTTATTA


Statistics
Matches: 105,  Mismatches: 7, Indels: 1
        0.93            0.06        0.01

Matches are distributed among these distances:
 110   52  0.50
 111   53  0.50

ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28


Consensus pattern (111 bp):   
AAGAAACTAGATGTTGGCGATCGTGATCATCAATTGCAAGTCTGCCCCATAACCGAAGAACAAGC
TGGGCTTGTTGATACCCCTCTCCCTGATGATGATGATGATTTCCTG

Found at i:12530 original size:25 final size:25

Alignment explanation


    Indices: 12496--12543  Score: 78
    Period size: 25  Copynumber: 1.9  Consensus size: 25

      12486 TTTGTTTGCA

                                     
      12496 AAAAAATTCACCATGTCTTCCATGT
          1 AAAAAATTCACCATGTCTTCCATGT

                *     *            
      12521 AAAATATTCATCATGTCTTCCAT
          1 AAAAAATTCACCATGTCTTCCAT

      12544 TTTAGTAATG


Statistics
Matches: 21,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  25   21  1.00

ACGTcount: A:0.35, C:0.23, G:0.06, T:0.35


Consensus pattern (25 bp):   
AAAAAATTCACCATGTCTTCCATGT

Found at i:16496 original size:38 final size:37

Alignment explanation


    Indices: 16408--16498  Score: 105
    Period size: 38  Copynumber: 2.5  Consensus size: 37

      16398 ATTTAAACCC

                               *                 
      16408 AAATAGGACGTTGG--AGACAGACAAAAAGCAAAATT
          1 AAATAGGACGTTGGAAAGAAAGACAAAAAGCAAAATT

                 ** *         *                    
      16443 AAATACAAGGATTGGAAATAAAGACAAAAAGGCAAAATT
          1 AAATAGGACG-TTGGAAAGAAAGACAAAAA-GCAAAATT

                             
      16482 AAATAGGACGTTGGAAA
          1 AAATAGGACGTTGGAAA

      16499 CAAAAAACCA


Statistics
Matches: 44,  Mismatches: 8, Indels: 5
        0.77            0.14        0.09

Matches are distributed among these distances:
  35    7  0.16
  36    4  0.09
  38   18  0.41
  39   15  0.34

ACGTcount: A:0.54, C:0.09, G:0.22, T:0.15


Consensus pattern (37 bp):   
AAATAGGACGTTGGAAAGAAAGACAAAAAGCAAAATT

Found at i:17748 original size:38 final size:39

Alignment explanation


    Indices: 17673--17748  Score: 136
    Period size: 39  Copynumber: 2.0  Consensus size: 39

      17663 TTTTATAGTA

                                                   
      17673 AGATTAAATTGTATTAGGATGACTCTAAAAAGAAATCTG
          1 AGATTAAATTGTATTAGGATGACTCTAAAAAGAAATCTG

                                          *       
      17712 AGATTAAATTGTATTAGGATGAC-CTAAAAGGAAATCT
          1 AGATTAAATTGTATTAGGATGACTCTAAAAAGAAATCT

      17749 TTATAGTATT


Statistics
Matches: 36,  Mismatches: 1, Indels: 1
        0.95            0.03        0.03

Matches are distributed among these distances:
  38   13  0.36
  39   23  0.64

ACGTcount: A:0.43, C:0.08, G:0.18, T:0.30


Consensus pattern (39 bp):   
AGATTAAATTGTATTAGGATGACTCTAAAAAGAAATCTG
Done.