Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012164.1 Corchorus olitorius cultivar O-4 contig12197, 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: 7953
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.33


Found at i:620 original size:24 final size:24

Alignment explanation


    Indices: 593--641  Score: 98
    Period size: 24  Copynumber: 2.0  Consensus size: 24

        583 CATGATGTGT

                                    
        593 TTATATCAAAAATAGGGTAGGAAA
          1 TTATATCAAAAATAGGGTAGGAAA

                                    
        617 TTATATCAAAAATAGGGTAGGAAA
          1 TTATATCAAAAATAGGGTAGGAAA

             
        641 T
          1 T

        642 GAAAATTACT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  24   25  1.00

ACGTcount: A:0.49, C:0.04, G:0.20, T:0.27


Consensus pattern (24 bp):   
TTATATCAAAAATAGGGTAGGAAA

Found at i:987 original size:4 final size:4

Alignment explanation


    Indices: 980--1054  Score: 87
    Period size: 4  Copynumber: 18.8  Consensus size: 4

        970 ATATATTACT

                                 *    *                     *    *    *
        980 TCTC TCTC TCTC TCTC TATC TATC TCTC TCTC TCTC TCTA TCTA TCTA
          1 TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC

               *    *                        
       1028 TCTA TCTA TCTC TCTC TCTC TCTC TCT
          1 TCTC TCTC TCTC TCTC TCTC TCTC TCT

       1055 ATATATATAT


Statistics
Matches: 67,  Mismatches: 4, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   4   67  1.00

ACGTcount: A:0.09, C:0.40, G:0.00, T:0.51


Consensus pattern (4 bp):   
TCTC

Found at i:2494 original size:21 final size:20

Alignment explanation


    Indices: 2459--2515  Score: 71
    Period size: 21  Copynumber: 2.9  Consensus size: 20

       2449 TAGTAATCTT

                                
       2459 ATTTA-TAATTTATTAAGCA
          1 ATTTAGTAATTTATTAAGCA

                               * 
       2478 ATTTAGTAATTGTATTAAGTA
          1 ATTTAGTAATT-TATTAAGCA

            *        *       
       2499 TTTTAGTAACTTATTAA
          1 ATTTAGTAATTTATTAA

       2516 ATTTTCATGA


Statistics
Matches: 33,  Mismatches: 3, Indels: 3
        0.85            0.08        0.08

Matches are distributed among these distances:
  19    5  0.15
  20   11  0.33
  21   17  0.52

ACGTcount: A:0.39, C:0.04, G:0.09, T:0.49


Consensus pattern (20 bp):   
ATTTAGTAATTTATTAAGCA

Found at i:3560 original size:23 final size:23

Alignment explanation


    Indices: 3530--3574  Score: 74
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       3520 CATCAACAAT

                                    
       3530 GCCATGGT-TGTTAATCCTACACG
          1 GCCATGGTGT-TTAATCCTACACG

                                  
       3553 GCCATGGTGTTTAATCCTACAC
          1 GCCATGGTGTTTAATCCTACAC

       3575 AAAGAATATT


Statistics
Matches: 21,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  23   20  0.95
  24    1  0.05

ACGTcount: A:0.22, C:0.27, G:0.20, T:0.31


Consensus pattern (23 bp):   
GCCATGGTGTTTAATCCTACACG

Found at i:3650 original size:37 final size:38

Alignment explanation


    Indices: 3603--3684  Score: 139
    Period size: 40  Copynumber: 2.1  Consensus size: 38

       3593 CAGAGAAATT

                                                  
       3603 TTTCAACCTGCAAACTG-AGAAGAATAAAGCATAAAAA
          1 TTTCAACCTGCAAACTGAAGAAGAATAAAGCATAAAAA

                                                    
       3640 TTTCAACCTGCAAACTGATCAGAAGAATAAAGCATAAAAA
          1 TTTCAACCTGCAAACTGA--AGAAGAATAAAGCATAAAAA

                 
       3680 TTTCA
          1 TTTCA

       3685 GAGAACTAAT


Statistics
Matches: 42,  Mismatches: 0, Indels: 3
        0.93            0.00        0.07

Matches are distributed among these distances:
  37   17  0.40
  40   25  0.60

ACGTcount: A:0.49, C:0.17, G:0.12, T:0.22


Consensus pattern (38 bp):   
TTTCAACCTGCAAACTGAAGAAGAATAAAGCATAAAAA

Done.