Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007077.1 Corchorus capsularis cultivar CVL-1 contig07098, 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: 37070
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:5255 original size:28 final size:27

Alignment explanation


    Indices: 5214--5288  Score: 96
    Period size: 27  Copynumber: 2.7  Consensus size: 27

       5204 AAATGGACTC

                               *        
       5214 AAAATGACCAAAATGCCCTTTGAATGCA
          1 AAAATGACCAAAATGCCC-CTGAATGCA

                 *   *    *          * 
       5242 AAAATTACCTAAATACCCCTGAATGTA
          1 AAAATGACCAAAATGCCCCTGAATGCA

                                
       5269 AAAATGACCAAAATGCCCCT
          1 AAAATGACCAAAATGCCCCT

       5289 ATGTGACCCT


Statistics
Matches: 39,  Mismatches: 8, Indels: 1
        0.81            0.17        0.02

Matches are distributed among these distances:
  27   24  0.62
  28   15  0.38

ACGTcount: A:0.44, C:0.24, G:0.11, T:0.21


Consensus pattern (27 bp):   
AAAATGACCAAAATGCCCCTGAATGCA

Found at i:8302 original size:19 final size:18

Alignment explanation


    Indices: 8269--8304  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       8259 TTGAAATAAT

                              
       8269 TCTTCAATGATCTTCAAA
          1 TCTTCAATGATCTTCAAA

                     *        
       8287 TCTTCAAATTATCTTCAA
          1 TCTTC-AATGATCTTCAA

       8305 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

Found at i:13057 original size:14 final size:14

Alignment explanation


    Indices: 13023--13055  Score: 50
    Period size: 14  Copynumber: 2.4  Consensus size: 14

      13013 GCCCCAATCA

                *         
      13023 ATAATATGACATAT
          1 ATAAAATGACATAT

                          
      13037 ATAAAATGACAT-T
          1 ATAAAATGACATAT

                  
      13050 ATAAAA
          1 ATAAAA

      13056 ATAAAGTCAA


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  13    7  0.39
  14   11  0.61

ACGTcount: A:0.58, C:0.06, G:0.06, T:0.30


Consensus pattern (14 bp):   
ATAAAATGACATAT

Found at i:14873 original size:22 final size:20

Alignment explanation


    Indices: 14836--14875  Score: 53
    Period size: 22  Copynumber: 1.9  Consensus size: 20

      14826 TACCAATTTA

                                
      14836 GATCAATTCATGAAATCAAG
          1 GATCAATTCATGAAATCAAG

                         *      
      14856 GATCTAATTGCATTAAATCA
          1 GATC-AATT-CATGAAATCA

      14876 TGATTGAAAT


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  20    4  0.24
  21    4  0.24
  22    9  0.53

ACGTcount: A:0.42, C:0.15, G:0.12, T:0.30


Consensus pattern (20 bp):   
GATCAATTCATGAAATCAAG

Found at i:20325 original size:10 final size:10

Alignment explanation


    Indices: 20310--20334  Score: 50
    Period size: 10  Copynumber: 2.5  Consensus size: 10

      20300 CTTGGTTTAA

                      
      20310 TTTTGTTGAT
          1 TTTTGTTGAT

                      
      20320 TTTTGTTGAT
          1 TTTTGTTGAT

                 
      20330 TTTTG
          1 TTTTG

      20335 ACCATTCTTT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   15  1.00

ACGTcount: A:0.08, C:0.00, G:0.20, T:0.72


Consensus pattern (10 bp):   
TTTTGTTGAT

Found at i:26168 original size:19 final size:18

Alignment explanation


    Indices: 26144--26180  Score: 56
    Period size: 19  Copynumber: 2.0  Consensus size: 18

      26134 TTGAAGATTT

                               
      26144 CTTGAAGATAATTTGAAGA
          1 CTTGAAGATAA-TTGAAGA

                     *        
      26163 CTTGAAGATCATTGAAGA
          1 CTTGAAGATAATTGAAGA

      26181 ATTATTTCAA


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

Matches are distributed among these distances:
  18    7  0.41
  19   10  0.59

ACGTcount: A:0.41, C:0.08, G:0.22, T:0.30


Consensus pattern (18 bp):   
CTTGAAGATAATTGAAGA

Found at i:27697 original size:18 final size:18

Alignment explanation


    Indices: 27674--27719  Score: 65
    Period size: 18  Copynumber: 2.6  Consensus size: 18

      27664 TTTTAATTAA

                              
      27674 TTGTTTTCTTTAATTTTC
          1 TTGTTTTCTTTAATTTTC

                  *          *
      27692 TTGTTTGCTTTAATTTTG
          1 TTGTTTTCTTTAATTTTC

             *        
      27710 TAGTTTTCTT
          1 TTGTTTTCTT

      27720 AGATTTAATT


Statistics
Matches: 24,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  18   24  1.00

ACGTcount: A:0.11, C:0.09, G:0.11, T:0.70


Consensus pattern (18 bp):   
TTGTTTTCTTTAATTTTC
Done.