Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001075.1 Corchorus capsularis cultivar CVL-1 contig01075, 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: 16933
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35


Found at i:4497 original size:2 final size:2

Alignment explanation


    Indices: 4490--4517  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

       4480 AAATATGTTC

                                                     
       4490 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       4518 GTAACTTTTG


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:7582 original size:3 final size:3

Alignment explanation


    Indices: 7574--7600  Score: 54
    Period size: 3  Copynumber: 9.0  Consensus size: 3

       7564 AAATCAAATA

                                               
       7574 TAT TAT TAT TAT TAT TAT TAT TAT TAT
          1 TAT TAT TAT TAT TAT TAT TAT TAT TAT

       7601 GCCACTAGCT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   24  1.00

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67


Consensus pattern (3 bp):   
TAT

Found at i:8455 original size:2 final size:2

Alignment explanation


    Indices: 8448--8493  Score: 67
    Period size: 2  Copynumber: 23.0  Consensus size: 2

       8438 TTGAAGCATC

                             *                                             
       8448 AT AT AT AT AT AGC AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                 
       8490 AT AT
          1 AT AT

       8494 TTCACTATGG


Statistics
Matches: 40,  Mismatches: 2, Indels: 4
        0.87            0.04        0.09

Matches are distributed among these distances:
   1    1  0.03
   2   38  0.95
   3    1  0.03

ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:9956 original size:6 final size:6

Alignment explanation


    Indices: 9942--9978  Score: 65
    Period size: 6  Copynumber: 6.2  Consensus size: 6

       9932 CCAAAACTCT

                *                                      
       9942 GCAGCA GCAGAA GCAGAA GCAGAA GCAGAA GCAGAA G
          1 GCAGAA GCAGAA GCAGAA GCAGAA GCAGAA GCAGAA G

       9979 GTTCGAAAAA


Statistics
Matches: 30,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
   6   30  1.00

ACGTcount: A:0.46, C:0.19, G:0.35, T:0.00


Consensus pattern (6 bp):   
GCAGAA

Found at i:10853 original size:14 final size:14

Alignment explanation


    Indices: 10834--10865  Score: 64
    Period size: 14  Copynumber: 2.3  Consensus size: 14

      10824 TGAATATGTG

                          
      10834 TATATATATACATA
          1 TATATATATACATA

                          
      10848 TATATATATACATA
          1 TATATATATACATA

                
      10862 TATA
          1 TATA

      10866 AAAGGACTTT


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   18  1.00

ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44


Consensus pattern (14 bp):   
TATATATATACATA

Found at i:13192 original size:55 final size:55

Alignment explanation


    Indices: 13108--13213  Score: 187
    Period size: 55  Copynumber: 1.9  Consensus size: 55

      13098 AAAAAGAAGA

                                                       *           
      13108 AGGAAGATTTATAGGATAAGCCTTACTAAAATTTAAAATATTATTTTGAGAGGAT
          1 AGGAAGATTTATAGGATAAGCCTTACTAAAATTTAAAATATTACTTTGAGAGGAT

                                                                
      13163 AGGAAGATTTATATGG-TAAGCCTTACTAAAATTTAAAATATTACTTTGAGA
          1 AGGAAGATTTATA-GGATAAGCCTTACTAAAATTTAAAATATTACTTTGAGA

      13214 ACATTTTAAT


Statistics
Matches: 49,  Mismatches: 1, Indels: 2
        0.94            0.02        0.04

Matches are distributed among these distances:
  55   47  0.96
  56    2  0.04

ACGTcount: A:0.42, C:0.07, G:0.17, T:0.35


Consensus pattern (55 bp):   
AGGAAGATTTATAGGATAAGCCTTACTAAAATTTAAAATATTACTTTGAGAGGAT

Done.