Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008316.1 Corchorus capsularis cultivar CVL-1 contig08337, 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: 26171
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33


Found at i:1760 original size:12 final size:12

Alignment explanation


    Indices: 1743--1771  Score: 58
    Period size: 12  Copynumber: 2.4  Consensus size: 12

       1733 GATCTAACTT

                        
       1743 TTTTTTTTGTTA
          1 TTTTTTTTGTTA

                        
       1755 TTTTTTTTGTTA
          1 TTTTTTTTGTTA

                 
       1767 TTTTT
          1 TTTTT

       1772 AGTTCTACAA


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   17  1.00

ACGTcount: A:0.07, C:0.00, G:0.07, T:0.86


Consensus pattern (12 bp):   
TTTTTTTTGTTA

Found at i:1770 original size:54 final size:55

Alignment explanation


    Indices: 1701--1806  Score: 196
    Period size: 54  Copynumber: 1.9  Consensus size: 55

       1691 GATCTGGCTT

                                                *                  
       1701 TTTTTTTTGTTATTTTTAGTTCTACAATTCTAGATCTAACTTTTT-TTTTTGTTA
          1 TTTTTTTTGTTATTTTTAGTTCTACAATTCTAGATCGAACTTTTTCTTTTTGTTA

                                                                
       1755 TTTTTTTTGTTATTTTTAGTTCTACAATTCTAGATCGAACTTTTTCTTTTTG
          1 TTTTTTTTGTTATTTTTAGTTCTACAATTCTAGATCGAACTTTTTCTTTTTG

       1807 GAAACAACTT


Statistics
Matches: 50,  Mismatches: 1, Indels: 1
        0.96            0.02        0.02

Matches are distributed among these distances:
  54   44  0.88
  55    6  0.12

ACGTcount: A:0.18, C:0.10, G:0.08, T:0.63


Consensus pattern (55 bp):   
TTTTTTTTGTTATTTTTAGTTCTACAATTCTAGATCGAACTTTTTCTTTTTGTTA

Found at i:10033 original size:21 final size:21

Alignment explanation


    Indices: 10001--10045  Score: 56
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       9991 CCCTTCGAGG

                        * *      
      10001 AATCTTTCTCATGCTTTGAAA
          1 AATCTTTCTCATCCCTTGAAA

                                  
      10022 AATCATTT-TCATCCCTTGAAA
          1 AATC-TTTCTCATCCCTTGAAA

               
      10043 AAT
          1 AAT

      10046 AAATAATAAT


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  21   18  0.86
  22    3  0.14

ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40


Consensus pattern (21 bp):   
AATCTTTCTCATCCCTTGAAA

Found at i:10811 original size:42 final size:42

Alignment explanation


    Indices: 10741--10834  Score: 145
    Period size: 42  Copynumber: 2.2  Consensus size: 42

      10731 TTGAGACCTT

                                            *          
      10741 AACAACATCCGATGGGAGATAAAGTAGAACAGCTTGGGGCTGC
          1 AACAACATCCGATGGGAGATAAAGTAGAACAGATTGGGGC-GC

                     *          *                     
      10784 AACAACATCTGAT-GGAGATCAAGTAGAACAGATTGGGGCGC
          1 AACAACATCCGATGGGAGATAAAGTAGAACAGATTGGGGCGC

                      
      10825 AACAACATCC
          1 AACAACATCC

      10835 TTTAAAATTT


Statistics
Matches: 47,  Mismatches: 4, Indels: 2
        0.89            0.08        0.04

Matches are distributed among these distances:
  41   11  0.23
  42   24  0.51
  43   12  0.26

ACGTcount: A:0.37, C:0.20, G:0.27, T:0.16


Consensus pattern (42 bp):   
AACAACATCCGATGGGAGATAAAGTAGAACAGATTGGGGCGC

Found at i:17016 original size:2 final size:2

Alignment explanation


    Indices: 17011--17048  Score: 69
    Period size: 2  Copynumber: 19.5  Consensus size: 2

      17001 GGGGGGGGGG

                                                                      
      17011 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA -A GA G
          1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G

      17049 GGACAAAATT


Statistics
Matches: 35,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   1    1  0.03
   2   34  0.97

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


Consensus pattern (2 bp):   
GA

Done.