Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005188.1 Corchorus capsularis cultivar CVL-1 contig05206, 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: 2531
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.26


Found at i:155 original size:14 final size:14

Alignment explanation


    Indices: 136--229  Score: 56
    Period size: 14  Copynumber: 6.9  Consensus size: 14

        126 AATTAAAGGA

                          
        136 AGTAATCAGTAAAG
          1 AGTAATCAGTAAAG

                   *     *
        150 AGTAATCGGTAAAA
          1 AGTAATCAGTAAAG

                 **    *    
        164 AGTAAAAATGGCAAAG
          1 AGTAATCA--GTAAAG

                         *
        180 AG---T-AGTAAAA
          1 AGTAATCAGTAAAG

                           
        190 AGTAATCAGGTAAA-
          1 AGTAATCA-GTAAAG

                          
        204 AGTAATCAGT-AAG
          1 AGTAATCAGTAAAG

                         
        217 AAGTAATCAGTAA
          1 -AGTAATCAGTAA

        230 GAAGGTCAAA


Statistics
Matches: 60,  Mismatches: 10, Indels: 19
        0.67            0.11        0.21

Matches are distributed among these distances:
  10    6  0.10
  12    3  0.05
  13    3  0.05
  14   36  0.60
  15    6  0.10
  16    6  0.10

ACGTcount: A:0.52, C:0.06, G:0.21, T:0.20


Consensus pattern (14 bp):   
AGTAATCAGTAAAG

Found at i:230 original size:14 final size:14

Alignment explanation


    Indices: 183--233  Score: 77
    Period size: 14  Copynumber: 3.6  Consensus size: 14

        173 GGCAAAGAGT

                 *        
        183 AGTAAAAAGTAATC
          1 AGTAAGAAGTAATC

                           
        197 AGGTAA-AAGTAATC
          1 A-GTAAGAAGTAATC

                          
        211 AGTAAGAAGTAATC
          1 AGTAAGAAGTAATC

                     
        225 AGTAAGAAG
          1 AGTAAGAAG

        234 GTCAAAAATG


Statistics
Matches: 35,  Mismatches: 0, Indels: 4
        0.90            0.00        0.10

Matches are distributed among these distances:
  13    4  0.11
  14   27  0.77
  15    4  0.11

ACGTcount: A:0.53, C:0.06, G:0.22, T:0.20


Consensus pattern (14 bp):   
AGTAAGAAGTAATC

Found at i:284 original size:42 final size:42

Alignment explanation


    Indices: 225--313  Score: 126
    Period size: 42  Copynumber: 2.1  Consensus size: 42

        215 AGAAGTAATC

                                         *   *        *
        225 AGTAAGAAGGTCAAAAATGGTATCA-AGTGAAATATGGTATTG
          1 AGTAAGAAGGTCAAAAATGGTAT-AGAGTAAAAAATGGTATTA

                                 *                    
        267 AGTAAGAAGGTCAAAAATGGTGTAGAGTAAAAAATGGTATTA
          1 AGTAAGAAGGTCAAAAATGGTATAGAGTAAAAAATGGTATTA

                 
        309 AGTAA
          1 AGTAA

        314 AAGAGTAAAG


Statistics
Matches: 42,  Mismatches: 4, Indels: 2
        0.88            0.08        0.04

Matches are distributed among these distances:
  41    1  0.02
  42   41  0.98

ACGTcount: A:0.46, C:0.03, G:0.26, T:0.25


Consensus pattern (42 bp):   
AGTAAGAAGGTCAAAAATGGTATAGAGTAAAAAATGGTATTA

Found at i:2460 original size:25 final size:25

Alignment explanation


    Indices: 2425--2495  Score: 99
    Period size: 25  Copynumber: 2.8  Consensus size: 25

       2415 GAAGTCACCC

                                      
       2425 AGGGGCATTTTGGTCATTTTGAACCT
          1 AGGGGCATTTTGGTCATTTTGAA-CT

                                     
       2451 -GGGGCATTTTGGTCATTTTGAACT
          1 AGGGGCATTTTGGTCATTTTGAACT

                    *   *        
       2475 AGGGGGCACTTTAGTCATTTT
          1 A-GGGGCATTTTGGTCATTTT

       2496 TAGTTCATTA


Statistics
Matches: 41,  Mismatches: 2, Indels: 4
        0.87            0.04        0.09

Matches are distributed among these distances:
  24    2  0.05
  25   22  0.54
  26   17  0.41

ACGTcount: A:0.18, C:0.14, G:0.28, T:0.39


Consensus pattern (25 bp):   
AGGGGCATTTTGGTCATTTTGAACT

Done.