Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011971.1 Corchorus capsularis cultivar CVL-1 contig11992, 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: 29167
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32


Found at i:1300 original size:6 final size:6

Alignment explanation


    Indices: 1291--1319  Score: 58
    Period size: 6  Copynumber: 4.8  Consensus size: 6

       1281 TTGATTTTCC

                                             
       1291 CCCATG CCCATG CCCATG CCCATG CCCAT
          1 CCCATG CCCATG CCCATG CCCATG CCCAT

       1320 CGGATAAAAC


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   23  1.00

ACGTcount: A:0.17, C:0.52, G:0.14, T:0.17


Consensus pattern (6 bp):   
CCCATG

Found at i:2982 original size:29 final size:29

Alignment explanation


    Indices: 2949--3006  Score: 73
    Period size: 29  Copynumber: 2.0  Consensus size: 29

       2939 TTTTATATTT

                                          
       2949 TTTATAATAAAGAGAAAAGAAA-AAAGAAA
          1 TTTATAATAAAGAG-AAAGAAAGAAAGAAA

                 **  *                   
       2978 TTTATTGTAGAGAGAAAGAAAGAAAGAAA
          1 TTTATAATAAAGAGAAAGAAAGAAAGAAA

       3007 GAAAGAAAGA


Statistics
Matches: 25,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  28    7  0.28
  29   18  0.72

ACGTcount: A:0.62, C:0.00, G:0.19, T:0.19


Consensus pattern (29 bp):   
TTTATAATAAAGAGAAAGAAAGAAAGAAA

Found at i:3027 original size:4 final size:4

Alignment explanation


    Indices: 2990--3016  Score: 54
    Period size: 4  Copynumber: 6.8  Consensus size: 4

       2980 TATTGTAGAG

                                             
       2990 AGAA AGAA AGAA AGAA AGAA AGAA AGA
          1 AGAA AGAA AGAA AGAA AGAA AGAA AGA

       3017 GGGAAGAAAG


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   23  1.00

ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00


Consensus pattern (4 bp):   
AGAA

Found at i:7219 original size:15 final size:16

Alignment explanation


    Indices: 7199--7228  Score: 53
    Period size: 15  Copynumber: 1.9  Consensus size: 16

       7189 GTGTTCTGGC

                            
       7199 TATATGGTT-CAAAAA
          1 TATATGGTTGCAAAAA

                           
       7214 TATATGGTTGCAAAA
          1 TATATGGTTGCAAAA

       7229 TCTTGAGAGA


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  15    9  0.64
  16    5  0.36

ACGTcount: A:0.43, C:0.07, G:0.17, T:0.33


Consensus pattern (16 bp):   
TATATGGTTGCAAAAA

Found at i:9349 original size:1 final size:1

Alignment explanation


    Indices: 9343--9367  Score: 50
    Period size: 1  Copynumber: 25.0  Consensus size: 1

       9333 TTAAAATGAG

                                     
       9343 TTTTTTTTTTTTTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTT

       9368 CGCTTTTAAT


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

Matches are distributed among these distances:
   1   24  1.00

ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00


Consensus pattern (1 bp):   
T

Found at i:16204 original size:6 final size:6

Alignment explanation


    Indices: 16171--16200  Score: 51
    Period size: 6  Copynumber: 5.0  Consensus size: 6

      16161 AGGATAGCGG

                                        *     
      16171 CAGGGA CAGGGA CAGGGA CAGGGA AAGGGA
          1 CAGGGA CAGGGA CAGGGA CAGGGA CAGGGA

      16201 AAGGCTGGTC


Statistics
Matches: 23,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
   6   23  1.00

ACGTcount: A:0.37, C:0.13, G:0.50, T:0.00


Consensus pattern (6 bp):   
CAGGGA

Found at i:19435 original size:21 final size:21

Alignment explanation


    Indices: 19394--19436  Score: 59
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      19384 GTTGCGTTTG

                           **    
      19394 CAGACAGTGATAATTTTAAAC
          1 CAGACAGTGATAATTCCAAAC

                       *         
      19415 CAGACAGTGATTATTCCAAAC
          1 CAGACAGTGATAATTCCAAAC

             
      19436 C
          1 C

      19437 TGGCAAGGCA


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  21   19  1.00

ACGTcount: A:0.40, C:0.21, G:0.14, T:0.26


Consensus pattern (21 bp):   
CAGACAGTGATAATTCCAAAC

Found at i:28874 original size:21 final size:21

Alignment explanation


    Indices: 28848--28892  Score: 56
    Period size: 21  Copynumber: 2.1  Consensus size: 21

      28838 TCTTTCTGGA

                                  
      28848 TTGCTAAACACCGTCCC-ATTT
          1 TTGCTAAACACCG-CCCAATTT

                  **             
      28869 TTGCTATTCACCGCCCAATTT
          1 TTGCTAAACACCGCCCAATTT

               
      28890 TTG
          1 TTG

      28893 ACGTTTTTTT


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

Matches are distributed among these distances:
  20    3  0.14
  21   18  0.86

ACGTcount: A:0.20, C:0.31, G:0.11, T:0.38


Consensus pattern (21 bp):   
TTGCTAAACACCGCCCAATTT
Done.