Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010267.1 Corchorus capsularis cultivar CVL-1 contig10288, 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: 21427
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34


Found at i:267 original size:4 final size:4

Alignment explanation


    Indices: 260--293  Score: 68
    Period size: 4  Copynumber: 8.5  Consensus size: 4

        250 GACCGACCTC

                                                      
        260 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
          1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT

        294 TTTTGAGAAT


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   30  1.00

ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76


Consensus pattern (4 bp):   
TTAT

Found at i:330 original size:17 final size:16

Alignment explanation


    Indices: 308--341  Score: 50
    Period size: 17  Copynumber: 2.1  Consensus size: 16

        298 GAGAATTTCG

                             
        308 ACCCACCTAATTAATTA
          1 ACCCACCTAATT-ATTA

                    *       
        325 ACCCACCTGATTATTA
          1 ACCCACCTAATTATTA

             
        341 A
          1 A

        342 TTAATCAACC


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  16    5  0.31
  17   11  0.69

ACGTcount: A:0.38, C:0.29, G:0.03, T:0.29


Consensus pattern (16 bp):   
ACCCACCTAATTATTA

Found at i:3457 original size:21 final size:20

Alignment explanation


    Indices: 3427--3482  Score: 51
    Period size: 21  Copynumber: 2.6  Consensus size: 20

       3417 TCTTTTTAAA

                                 
       3427 AATAATCTTATAAGATCTTTT
          1 AATAA-CTTATAAGATCTTTT

                             *    
       3448 AATAAGCTTACT-AGATTTTTT
          1 AATAA-CTTA-TAAGATCTTTT

             *            
       3469 AGTAACTTTATAAG
          1 AATAAC-TTATAAG

       3483 TGTTTTTGAA


Statistics
Matches: 29,  Mismatches: 3, Indels: 6
        0.76            0.08        0.16

Matches are distributed among these distances:
  20    2  0.07
  21   26  0.90
  22    1  0.03

ACGTcount: A:0.38, C:0.09, G:0.09, T:0.45


Consensus pattern (20 bp):   
AATAACTTATAAGATCTTTT

Found at i:4992 original size:27 final size:27

Alignment explanation


    Indices: 4954--5008  Score: 110
    Period size: 27  Copynumber: 2.0  Consensus size: 27

       4944 TGTGTAACAC

                                       
       4954 GTGGCAAAATACTAGTAATAATAAATA
          1 GTGGCAAAATACTAGTAATAATAAATA

                                       
       4981 GTGGCAAAATACTAGTAATAATAAATA
          1 GTGGCAAAATACTAGTAATAATAAATA

             
       5008 G
          1 G

       5009 ATGCCTTAAA


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  27   28  1.00

ACGTcount: A:0.51, C:0.07, G:0.16, T:0.25


Consensus pattern (27 bp):   
GTGGCAAAATACTAGTAATAATAAATA

Found at i:10290 original size:34 final size:34

Alignment explanation


    Indices: 10246--10314  Score: 120
    Period size: 34  Copynumber: 2.0  Consensus size: 34

      10236 AGTAACAGTA

                                              
      10246 CTTCCAGGATTTAACCCAAATTAAATAGGATTTT
          1 CTTCCAGGATTTAACCCAAATTAAATAGGATTTT

                 *                    *       
      10280 CTTCCTGGATTTAACCCAAATTAAATTGGATTTT
          1 CTTCCAGGATTTAACCCAAATTAAATAGGATTTT

             
      10314 C
          1 C

      10315 CTTTTATGTT


Statistics
Matches: 33,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  34   33  1.00

ACGTcount: A:0.32, C:0.19, G:0.12, T:0.38


Consensus pattern (34 bp):   
CTTCCAGGATTTAACCCAAATTAAATAGGATTTT

Found at i:21396 original size:2 final size:2

Alignment explanation


    Indices: 21391--21425  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

      21381 ATGTGTCGAT

                                                                
      21391 TA TA TA TA TA 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 TA TA TA TA TA T

      21426 CA


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Done.