Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014927.1 Corchorus capsularis cultivar CVL-1 contig14948, 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: 8491
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.37


Found at i:90 original size:26 final size:26

Alignment explanation


    Indices: 42--93  Score: 68
    Period size: 27  Copynumber: 1.9  Consensus size: 26

         32 AAATTCAATT

                        *  *          
         42 TTTTAAAATTTCTAACATAATATACA
          1 TTTTAAAATTTCAAAAATAATATACA

                                      
         68 TTTTAATAATTTCAAAAATATATATA
          1 TTTTAA-AATTTCAAAAATA-ATATA

         94 TATATATATT


Statistics
Matches: 22,  Mismatches: 2, Indels: 2
        0.85            0.08        0.08

Matches are distributed among these distances:
  26    6  0.27
  27   11  0.50
  28    5  0.23

ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44


Consensus pattern (26 bp):   
TTTTAAAATTTCAAAAATAATATACA

Found at i:4385 original size:54 final size:55

Alignment explanation


    Indices: 4322--4425  Score: 174
    Period size: 54  Copynumber: 1.9  Consensus size: 55

       4312 ACAAATTTAG

                                                   *               
       4322 TTGTCATTTATTTTTAACGTTATGCAAATTAAATTCTAATGTT-TATATACTTAA
          1 TTGTCATTTATTTTTAACGTTATGCAAATTAAATTCTAACGTTATATATACTTAA

                *                   *                         
       4376 TTGTTATTTATTTTTAACGTTATGTAAATTAAATTCTAACGTTATATATA
          1 TTGTCATTTATTTTTAACGTTATGCAAATTAAATTCTAACGTTATATATA

       4426 TATATATTAA


Statistics
Matches: 46,  Mismatches: 3, Indels: 1
        0.92            0.06        0.02

Matches are distributed among these distances:
  54   40  0.87
  55    6  0.13

ACGTcount: A:0.34, C:0.08, G:0.08, T:0.51


Consensus pattern (55 bp):   
TTGTCATTTATTTTTAACGTTATGCAAATTAAATTCTAACGTTATATATACTTAA

Found at i:4460 original size:29 final size:29

Alignment explanation


    Indices: 4403--4484  Score: 98
    Period size: 29  Copynumber: 2.9  Consensus size: 29

       4393 CGTTATGTAA

                                         
       4403 ATTAAATTC-TAACGTTATATATATATAT
          1 ATTAAATTCTTAACGTTATATATATATAT

                         *                 
       4431 ATTAAATTCTTAATGTTATATA-ACGT-TAT
          1 ATTAAATTCTTAACGTTATATATA--TATAT

               *         *           
       4460 ATTTAATTCTTAAGGTTATATATAT
          1 ATTAAATTCTTAACGTTATATATAT

       4485 TAAATTCTTA


Statistics
Matches: 47,  Mismatches: 3, Indels: 8
        0.81            0.05        0.14

Matches are distributed among these distances:
  28   11  0.23
  29   34  0.72
  30    2  0.04

ACGTcount: A:0.39, C:0.06, G:0.06, T:0.49


Consensus pattern (29 bp):   
ATTAAATTCTTAACGTTATATATATATAT

Found at i:4484 original size:23 final size:23

Alignment explanation


    Indices: 4457--4501  Score: 72
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       4447 TATATAACGT

                  *         *      
       4457 TATATTTAATTCTTAAGGTTATA
          1 TATATTAAATTCTTAACGTTATA

                                  
       4480 TATATTAAATTCTTAACGTTAT
          1 TATATTAAATTCTTAACGTTAT

       4502 GTTTAGGGTT


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  23   20  1.00

ACGTcount: A:0.36, C:0.07, G:0.07, T:0.51


Consensus pattern (23 bp):   
TATATTAAATTCTTAACGTTATA

Found at i:5103 original size:2 final size:2

Alignment explanation


    Indices: 5096--5126  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

       5086 TATCCTATCC

                                                          
       5096 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 T

       5127 TCTAATTATA


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Done.