Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024073.1 Corchorus olitorius cultivar O-4 contig24106, 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: 16064
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32


Found at i:2840 original size:21 final size:21

Alignment explanation


    Indices: 2782--2843  Score: 58
    Period size: 21  Copynumber: 3.0  Consensus size: 21

       2772 AAAGCAGGCA

                    *            
       2782 TGGCCGGTGGTGACTCGGTGC
          1 TGGCCGGTTGTGACTCGGTGC

                 *                  
       2803 TGGCATGAGTTG-G-CTCGGATG-
          1 TGGC-CG-GTTGTGACTCGG-TGC

                                
       2824 TGGCCGGTTGTGACTCGGTG
          1 TGGCCGGTTGTGACTCGGTG

       2844 GTCACTGGTC


Statistics
Matches: 33,  Mismatches: 3, Indels: 11
        0.70            0.06        0.23

Matches are distributed among these distances:
  19    4  0.12
  20    4  0.12
  21   18  0.55
  22    4  0.12
  23    3  0.09

ACGTcount: A:0.08, C:0.19, G:0.45, T:0.27


Consensus pattern (21 bp):   
TGGCCGGTTGTGACTCGGTGC

Found at i:7540 original size:19 final size:18

Alignment explanation


    Indices: 7503--7542  Score: 53
    Period size: 18  Copynumber: 2.2  Consensus size: 18

       7493 TTCTTGAAAT

                        *     
       7503 AATTCTTCAAAGGTCTTC
          1 AATTCTTCAAAGATCTTC

                        *      
       7521 AATTCTTCAAATTATCTTC
          1 AATTCTTCAAA-GATCTTC

               
       7540 AAT
          1 AAT

       7543 AAATCTTCAA


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  18   11  0.58
  19    8  0.42

ACGTcount: A:0.33, C:0.20, G:0.05, T:0.42


Consensus pattern (18 bp):   
AATTCTTCAAAGATCTTC

Found at i:9438 original size:18 final size:19

Alignment explanation


    Indices: 9415--9454  Score: 55
    Period size: 19  Copynumber: 2.2  Consensus size: 19

       9405 TTCTTGAAAT

                               
       9415 AATTCTTCAA-TGGTCTTC
          1 AATTCTTCAATTGGTCTTC

                   *    *      
       9433 AATTCTTGAATTTGTCTTC
          1 AATTCTTCAATTGGTCTTC

               
       9452 AAT
          1 AAT

       9455 AAATCTTCAA


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  18    9  0.47
  19   10  0.53

ACGTcount: A:0.25, C:0.17, G:0.10, T:0.47


Consensus pattern (19 bp):   
AATTCTTCAATTGGTCTTC

Found at i:10352 original size:17 final size:17

Alignment explanation


    Indices: 10319--10351  Score: 50
    Period size: 17  Copynumber: 2.0  Consensus size: 17

      10309 CTCCTCTATC

                             
      10319 ATGAAAACACTTTTTTT
          1 ATGAAAACACTTTTTTT

                   *         
      10336 ATGAAAAGA-TTTTTTT
          1 ATGAAAACACTTTTTTT

      10352 TTTAAAACTA


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  16    7  0.47
  17    8  0.53

ACGTcount: A:0.36, C:0.06, G:0.09, T:0.48


Consensus pattern (17 bp):   
ATGAAAACACTTTTTTT

Found at i:12004 original size:18 final size:19

Alignment explanation


    Indices: 11981--12017  Score: 67
    Period size: 18  Copynumber: 2.0  Consensus size: 19

      11971 CACCCTAGCC

                               
      11981 CTAAAACTAGAAGA-AAAA
          1 CTAAAACTAGAAGAGAAAA

                               
      11999 CTAAAACTAGAAGAGAAAA
          1 CTAAAACTAGAAGAGAAAA

      12018 AGAAGAAGAG


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  18   14  0.78
  19    4  0.22

ACGTcount: A:0.65, C:0.11, G:0.14, T:0.11


Consensus pattern (19 bp):   
CTAAAACTAGAAGAGAAAA
Done.