Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014725.1 Corchorus olitorius cultivar O-4 contig14758, 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: 82365
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32


Found at i:41449 original size:36 final size:36

Alignment explanation


    Indices: 41409--41623  Score: 274
    Period size: 36  Copynumber: 6.0  Consensus size: 36

      41399 TTGAAGGCAC

                                                
      41409 AGCCCCAGAAGGCCGGCCAGGCCCCATACCATTGCT
          1 AGCCCCAGAAGGCCGGCCAGGCCCCATACCATTGCT

                    *            *            * 
      41445 AGCCCCAGTAGGCCGGCCAGGACCCATACCATTGAT
          1 AGCCCCAGAAGGCCGGCCAGGCCCCATACCATTGCT

                    *            *              
      41481 AGCCCCAGTAGGCCGGCCAGGACCCATACCATTGCT
          1 AGCCCCAGAAGGCCGGCCAGGCCCCATACCATTGCT

                                          *     
      41517 AGCCCCAGAAGGCCGGCCAGGCCCCATACCGTTGCT
          1 AGCCCCAGAAGGCCGGCCAGGCCCCATACCATTGCT

               *             **     **           
      41553 AGCTCCA-ACAGGCCGGGGAGGCCTGATACCATTGCT
          1 AGCCCCAGA-AGGCCGGCCAGGCCCCATACCATTGCT

               *                                 
      41589 AGCGCCA-ACAGGCCGGCCA-GCCCCACTACCATTGC
          1 AGCCCCAGA-AGGCCGGCCAGGCCCCA-TACCATTGC

      41624 CAGGCCGGCC


Statistics
Matches: 159,  Mismatches: 18, Indels: 4
        0.88            0.10        0.02

Matches are distributed among these distances:
  35    5  0.03
  36  154  0.97

ACGTcount: A:0.22, C:0.39, G:0.26, T:0.13


Consensus pattern (36 bp):   
AGCCCCAGAAGGCCGGCCAGGCCCCATACCATTGCT

Found at i:42869 original size:21 final size:21

Alignment explanation


    Indices: 42842--42891  Score: 75
    Period size: 21  Copynumber: 2.4  Consensus size: 21

      42832 TGTCTAGCTT

                                  
      42842 CCTCTTCTTCATACTCCTCACC
          1 CCTCTTCTTCATACTCCTC-CC

                         *       
      42864 CC-CTTCTTCATATTCCTCCC
          1 CCTCTTCTTCATACTCCTCCC

                    
      42884 CCTCTTCT
          1 CCTCTTCT

      42892 CCCTCAACAT


Statistics
Matches: 26,  Mismatches: 1, Indels: 3
        0.87            0.03        0.10

Matches are distributed among these distances:
  20    4  0.15
  21   20  0.77
  22    2  0.08

ACGTcount: A:0.10, C:0.50, G:0.00, T:0.40


Consensus pattern (21 bp):   
CCTCTTCTTCATACTCCTCCC

Found at i:58307 original size:2 final size:2

Alignment explanation


    Indices: 58300--58331  Score: 64
    Period size: 2  Copynumber: 16.0  Consensus size: 2

      58290 AAGTACCTAA

                                                           
      58300 AT AT 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 AT AT

      58332 TAACACTTAT


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   30  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:61154 original size:25 final size:24

Alignment explanation


    Indices: 61104--61155  Score: 68
    Period size: 25  Copynumber: 2.1  Consensus size: 24

      61094 CCTTGAATTT

                          *      *  
      61104 TTTAATGTTTAATTCTTAAATTTA
          1 TTTAATGTTTAATTATTAAATCTA

                              *      
      61128 TTTAATGTCTTAATTATTCAATCTA
          1 TTTAATGT-TTAATTATTAAATCTA

               
      61153 TTT
          1 TTT

      61156 TACAATCCAC


Statistics
Matches: 24,  Mismatches: 3, Indels: 1
        0.86            0.11        0.04

Matches are distributed among these distances:
  24    8  0.33
  25   16  0.67

ACGTcount: A:0.31, C:0.08, G:0.04, T:0.58


Consensus pattern (24 bp):   
TTTAATGTTTAATTATTAAATCTA

Found at i:65010 original size:2 final size:2

Alignment explanation


    Indices: 65003--65029  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

      64993 TCTTTGTGCC

                                                    
      65003 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 T

      65030 TGATGAATTC


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

Matches are distributed among these distances:
   2   25  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:79111 original size:3 final size:3

Alignment explanation


    Indices: 79103--79141  Score: 78
    Period size: 3  Copynumber: 13.0  Consensus size: 3

      79093 CCTTCTCCTC

                                                               
      79103 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
          1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT

      79142 ATACTCATTG


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   36  1.00

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


Consensus pattern (3 bp):   
TAT

Done.