Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008522.1 Corchorus capsularis cultivar CVL-1 contig08543, 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: 6494
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30


Found at i:5141 original size:30 final size:30

Alignment explanation


    Indices: 5107--5166  Score: 111
    Period size: 30  Copynumber: 2.0  Consensus size: 30

       5097 TGAATCTAAT

                                  *       
       5107 CAATTAGTCAACTTCTCCACGTGTGAATGC
          1 CAATTAGTCAACTTCTCCACGTCTGAATGC

                                          
       5137 CAATTAGTCAACTTCTCCACGTCTGAATGC
          1 CAATTAGTCAACTTCTCCACGTCTGAATGC

       5167 TTGATATTTT


Statistics
Matches: 29,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  30   29  1.00

ACGTcount: A:0.27, C:0.28, G:0.15, T:0.30


Consensus pattern (30 bp):   
CAATTAGTCAACTTCTCCACGTCTGAATGC

Found at i:5408 original size:98 final size:98

Alignment explanation


    Indices: 5239--5435  Score: 394
    Period size: 98  Copynumber: 2.0  Consensus size: 98

       5229 ATTGCTTCTG

                                                                             
       5239 ACCATCGGTACTCACTTTTTATGTCCCGATGTAATTGCTCGTCACCATCGGTACCAATCAAAGCC
          1 ACCATCGGTACTCACTTTTTATGTCCCGATGTAATTGCTCGTCACCATCGGTACCAATCAAAGCC

                                             
       5304 TCTCGATGTTAAGTTGCTTTAGAACTTAGGCAC
         66 TCTCGATGTTAAGTTGCTTTAGAACTTAGGCAC

                                                                             
       5337 ACCATCGGTACTCACTTTTTATGTCCCGATGTAATTGCTCGTCACCATCGGTACCAATCAAAGCC
          1 ACCATCGGTACTCACTTTTTATGTCCCGATGTAATTGCTCGTCACCATCGGTACCAATCAAAGCC

                                             
       5402 TCTCGATGTTAAGTTGCTTTAGAACTTAGGCAC
         66 TCTCGATGTTAAGTTGCTTTAGAACTTAGGCAC

             
       5435 A
          1 A

       5436 GCGTCGGGAG


Statistics
Matches: 99,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  98   99  1.00

ACGTcount: A:0.25, C:0.26, G:0.17, T:0.31


Consensus pattern (98 bp):   
ACCATCGGTACTCACTTTTTATGTCCCGATGTAATTGCTCGTCACCATCGGTACCAATCAAAGCC
TCTCGATGTTAAGTTGCTTTAGAACTTAGGCAC

Found at i:5810 original size:24 final size:24

Alignment explanation


    Indices: 5778--5826  Score: 89
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       5768 CAATGGAACA

                        *           
       5778 TCATGACCATCAGGACCCAAACTC
          1 TCATGACCATCAAGACCCAAACTC

                                    
       5802 TCATGACCATCAAGACCCAAACTC
          1 TCATGACCATCAAGACCCAAACTC

             
       5826 T
          1 T

       5827 TTGTCCCGAT


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  24   24  1.00

ACGTcount: A:0.35, C:0.37, G:0.10, T:0.18


Consensus pattern (24 bp):   
TCATGACCATCAAGACCCAAACTC

Found at i:6232 original size:21 final size:22

Alignment explanation


    Indices: 6207--6252  Score: 67
    Period size: 21  Copynumber: 2.1  Consensus size: 22

       6197 TTCAATGGGG

                   **             
       6207 TTTGCTATTTACCGCCCCC-CT
          1 TTTGCTAAATACCGCCCCCTCT

                                  
       6228 TTTGCTAAATACCGCCCCCTCT
          1 TTTGCTAAATACCGCCCCCTCT

               
       6250 TTT
          1 TTT

       6253 TATAATTTTT


Statistics
Matches: 22,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  21   17  0.77
  22    5  0.23

ACGTcount: A:0.13, C:0.39, G:0.09, T:0.39


Consensus pattern (22 bp):   
TTTGCTAAATACCGCCCCCTCT

Done.