Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013083.1 Corchorus olitorius cultivar O-4 contig13116, 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: 20246
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.34


Found at i:54 original size:2 final size:2

Alignment explanation


    Indices: 47--81  Score: 61
    Period size: 2  Copynumber: 17.5  Consensus size: 2

         37 AAAAATTCTA

                                                *               
         47 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

         82 AGTTTTTTAA


Statistics
Matches: 31,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   2   31  1.00

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
AT

Found at i:1542 original size:15 final size:16

Alignment explanation


    Indices: 1524--1554  Score: 55
    Period size: 16  Copynumber: 2.0  Consensus size: 16

       1514 TAATTTTCAA

                            
       1524 TAAAAT-AAAATATAT
          1 TAAAATAAAAATATAT

                            
       1539 TAAAATAAAAATATAT
          1 TAAAATAAAAATATAT

       1555 ATTTTTATTC


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  15    6  0.40
  16    9  0.60

ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32


Consensus pattern (16 bp):   
TAAAATAAAAATATAT

Found at i:7882 original size:29 final size:31

Alignment explanation


    Indices: 7849--7911  Score: 103
    Period size: 31  Copynumber: 2.1  Consensus size: 31

       7839 ATCGGAATCG

                                           
       7849 ATTGACCC-AA-TTGCAAGTAGAGGGACTAA
          1 ATTGACCCAAACTTGCAAGTAGAGGGACTAA

                           *               
       7878 ATTGACCCAAACTTGTAAGTAGAGGGACTAA
          1 ATTGACCCAAACTTGCAAGTAGAGGGACTAA

               
       7909 ATT
          1 ATT

       7912 AATCGATTTT


Statistics
Matches: 31,  Mismatches: 1, Indels: 2
        0.91            0.03        0.06

Matches are distributed among these distances:
  29    8  0.26
  30    2  0.06
  31   21  0.68

ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24


Consensus pattern (31 bp):   
ATTGACCCAAACTTGCAAGTAGAGGGACTAA

Found at i:9273 original size:24 final size:25

Alignment explanation


    Indices: 9215--9279  Score: 87
    Period size: 24  Copynumber: 2.6  Consensus size: 25

       9205 CAAAGTTTAC

                         *    *   *  
       9215 TGTTGGATATTTTCTTGTTTTTTTT
          1 TGTTGGATATTTTGTTGTGTTTATT

                 *                   
       9240 TGTTGCATATTTTGTTG-GTTTATT
          1 TGTTGGATATTTTGTTGTGTTTATT

                            
       9264 TGTTGGATATTTTGTT
          1 TGTTGGATATTTTGTT

       9280 TGAAATTTTA


Statistics
Matches: 35,  Mismatches: 5, Indels: 1
        0.85            0.12        0.02

Matches are distributed among these distances:
  24   20  0.57
  25   15  0.43

ACGTcount: A:0.11, C:0.03, G:0.20, T:0.66


Consensus pattern (25 bp):   
TGTTGGATATTTTGTTGTGTTTATT

Found at i:13413 original size:51 final size:50

Alignment explanation


    Indices: 13312--13413  Score: 111
    Period size: 51  Copynumber: 2.0  Consensus size: 50

      13302 GTTCATCAAC

                                                     * **     
      13312 TTTTCCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCTTTTAGTGT
          1 TTTTCCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCGTACAGTGT

                                      *                           
      13362 TTTTCTCTTGTTT-GAATCTTGTCTCCGGAC-ATACAAACACT-GTACACGTGT
          1 TTTTC-CTTGTTTAG-ATCTTGTCTCAGGACAAT-CAAACACTCGTACA-GTGT

             
      13413 T
          1 T

      13414 CTTCATTCAT


Statistics
Matches: 44,  Mismatches: 4, Indels: 7
        0.80            0.07        0.13

Matches are distributed among these distances:
  50   10  0.23
  51   34  0.77

ACGTcount: A:0.22, C:0.22, G:0.15, T:0.42


Consensus pattern (50 bp):   
TTTTCCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCGTACAGTGT

Found at i:14004 original size:40 final size:40

Alignment explanation


    Indices: 13949--14028  Score: 124
    Period size: 40  Copynumber: 2.0  Consensus size: 40

      13939 GCTGTTTTAT

                     *          *              *    
      13949 TTTATAAGTTCTTTTAAGAAGATTCAGTTAAGAAATGAAA
          1 TTTATAAGTGCTTTTAAGAAAATTCAGTTAAGAAAAGAAA

                                    *               
      13989 TTTATAAGTGCTTTTAAGAAAATTTAGTTAAGAAAAGAAA
          1 TTTATAAGTGCTTTTAAGAAAATTCAGTTAAGAAAAGAAA

      14029 GTCATTAGTT


Statistics
Matches: 36,  Mismatches: 4, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  40   36  1.00

ACGTcount: A:0.45, C:0.04, G:0.15, T:0.36


Consensus pattern (40 bp):   
TTTATAAGTGCTTTTAAGAAAATTCAGTTAAGAAAAGAAA

Found at i:16260 original size:22 final size:22

Alignment explanation


    Indices: 16232--16330  Score: 171
    Period size: 22  Copynumber: 4.5  Consensus size: 22

      16222 TGGAAACATT

                             *    
      16232 TTTGCAGAGCATTATTTACCAC
          1 TTTGCAGAGCATTATTTTCCAC

                               *  
      16254 TTTGCAGAGCATTATTTTCTAC
          1 TTTGCAGAGCATTATTTTCCAC

                                  
      16276 TTTGCAGAGCATTATTTTCCAC
          1 TTTGCAGAGCATTATTTTCCAC

               *                  
      16298 TTTTCAGAGCATTATTTTCCAC
          1 TTTGCAGAGCATTATTTTCCAC

                       
      16320 TTTGCAGAGCA
          1 TTTGCAGAGCA

      16331 CTTCTTGTTG


Statistics
Matches: 72,  Mismatches: 5, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  22   72  1.00

ACGTcount: A:0.24, C:0.21, G:0.14, T:0.40


Consensus pattern (22 bp):   
TTTGCAGAGCATTATTTTCCAC

Done.