Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005753.1 Corchorus capsularis cultivar CVL-1 contig05771, 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: 24769
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31


Found at i:2170 original size:12 final size:12

Alignment explanation


    Indices: 2119--2151  Score: 66
    Period size: 12  Copynumber: 2.8  Consensus size: 12

       2109 CCGTTTAATA

                        
       2119 ATTATATATATT
          1 ATTATATATATT

                        
       2131 ATTATATATATT
          1 ATTATATATATT

                     
       2143 ATTATATAT
          1 ATTATATAT

       2152 CTAATATTAT


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   21  1.00

ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58


Consensus pattern (12 bp):   
ATTATATATATT

Found at i:2194 original size:14 final size:13

Alignment explanation


    Indices: 2117--2194  Score: 61
    Period size: 12  Copynumber: 5.8  Consensus size: 13

       2107 AACCGTTTAA

                         
       2117 TAATTATATATAT
          1 TAATTATATATAT

                         
       2130 T-ATTATATATAT
          1 TAATTATATATAT

                       * 
       2142 T-ATTATATATCT
          1 TAATTATATATAT

            *              
       2154 AATATTATTATATAT
          1 TA-ATTA-TATATAT

                ** *       
       2169 ATAAAAAAATATATT
          1 -TAATTATATATA-T

                       
       2184 TAATTATATAT
          1 TAATTATATAT

       2195 TAACAAAATG


Statistics
Matches: 50,  Mismatches: 10, Indels: 9
        0.72            0.14        0.13

Matches are distributed among these distances:
  12   22  0.44
  13    1  0.02
  14   17  0.34
  15    9  0.18
  16    1  0.02

ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51


Consensus pattern (13 bp):   
TAATTATATATAT

Found at i:3153 original size:2 final size:2

Alignment explanation


    Indices: 3146--3177  Score: 64
    Period size: 2  Copynumber: 16.0  Consensus size: 2

       3136 ACCTCATGAG

                                                           
       3146 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

       3178 GAATCACGGA


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:4981 original size:2 final size:2

Alignment explanation


    Indices: 4976--5016  Score: 73
    Period size: 2  Copynumber: 20.5  Consensus size: 2

       4966 ACACACACAC

                                    *                                    
       4976 AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       5017 ACTATTTCCC


Statistics
Matches: 37,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
   2   37  1.00

ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49


Consensus pattern (2 bp):   
AT

Found at i:12660 original size:19 final size:18

Alignment explanation


    Indices: 12627--12662  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

      12617 TTGAAAGAAT

                              
      12627 TCTTCAATAATCTTCAAG
          1 TCTTCAATAATCTTCAAG

                     *        
      12645 TCTTCAAATTATCTTCAA
          1 TCTTC-AATAATCTTCAA

      12663 ATAAGTCTTC


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42


Consensus pattern (18 bp):   
TCTTCAATAATCTTCAAG

Found at i:12673 original size:12 final size:12

Alignment explanation


    Indices: 12642--12675  Score: 52
    Period size: 11  Copynumber: 2.9  Consensus size: 12

      12632 AATAATCTTC

                        
      12642 AAGTCTTCAAAT
          1 AAGTCTTCAAAT

            *           
      12654 TA-TCTTCAAAT
          1 AAGTCTTCAAAT

                       
      12665 AAGTCTTCAAA
          1 AAGTCTTCAAA

      12676 CACGAACTTT


Statistics
Matches: 19,  Mismatches: 2, Indels: 2
        0.83            0.09        0.09

Matches are distributed among these distances:
  11   10  0.53
  12    9  0.47

ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35


Consensus pattern (12 bp):   
AAGTCTTCAAAT

Found at i:23068 original size:15 final size:16

Alignment explanation


    Indices: 23036--23069  Score: 52
    Period size: 16  Copynumber: 2.2  Consensus size: 16

      23026 AAAGAAAAAT

                 *          
      23036 TAAAATTAAATCTAAC
          1 TAAAAGTAAATCTAAC

                            
      23052 TAAAAGTAAAT-TAAC
          1 TAAAAGTAAATCTAAC

               
      23067 TAA
          1 TAA

      23070 GAGAGCAATC


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  15    7  0.41
  16   10  0.59

ACGTcount: A:0.59, C:0.09, G:0.03, T:0.29


Consensus pattern (16 bp):   
TAAAAGTAAATCTAAC

Found at i:24381 original size:19 final size:18

Alignment explanation


    Indices: 24348--24383  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

      24338 TTGAAATACT

                              
      24348 TCTTCAATGATCTTCAAA
          1 TCTTCAATGATCTTCAAA

                     *        
      24366 TCTTCAAATTATCTTCAA
          1 TCTTC-AATGATCTTCAA

      24384 GAAATCTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGATCTTCAAA
Done.