Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012515.1 Corchorus capsularis cultivar CVL-1 contig12536, 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: 20493
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34


Found at i:216 original size:59 final size:59

Alignment explanation


    Indices: 119--305  Score: 358
    Period size: 59  Copynumber: 3.2  Consensus size: 59

        109 GCAATGGAGT

                                                                       
        119 AAAAT-TGAAGTATGTTAAAGACAAGAGAATAGAGAGACAATAGAATATGGAGAAGAAG
          1 AAAATATGAAGTATGTTAAAGACAAGAGAATAGAGAGACAATAGAATATGGAGAAGAAG

                                                                       
        177 AAAATATGAAGTATGTTAAAGACAAGAGAATAGAGAGACAATAGAATATGGAGAAGAAG
          1 AAAATATGAAGTATGTTAAAGACAAGAGAATAGAGAGACAATAGAATATGGAGAAGAAG

                            *                                          
        236 AAAATATGAAGTATGTAAAAGACAAGAGAATAGAGAGACAATAGAATATGGAGAAGAAG
          1 AAAATATGAAGTATGTTAAAGACAAGAGAATAGAGAGACAATAGAATATGGAGAAGAAG

                       
        295 AAAATATGAAG
          1 AAAATATGAAG

        306 AATGAGAGAA


Statistics
Matches: 127,  Mismatches: 1, Indels: 1
        0.98            0.01        0.01

Matches are distributed among these distances:
  58    5  0.04
  59  122  0.96

ACGTcount: A:0.55, C:0.03, G:0.25, T:0.17


Consensus pattern (59 bp):   
AAAATATGAAGTATGTTAAAGACAAGAGAATAGAGAGACAATAGAATATGGAGAAGAAG

Found at i:5157 original size:8 final size:8

Alignment explanation


    Indices: 5144--5168  Score: 50
    Period size: 8  Copynumber: 3.1  Consensus size: 8

       5134 TATATGTGTA

                    
       5144 TCTTAGAT
          1 TCTTAGAT

                    
       5152 TCTTAGAT
          1 TCTTAGAT

                    
       5160 TCTTAGAT
          1 TCTTAGAT

             
       5168 T
          1 T

       5169 TTTTTCCCCT


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   8   17  1.00

ACGTcount: A:0.24, C:0.12, G:0.12, T:0.52


Consensus pattern (8 bp):   
TCTTAGAT

Found at i:9362 original size:6 final size:6

Alignment explanation


    Indices: 9351--9382  Score: 57
    Period size: 6  Copynumber: 5.5  Consensus size: 6

       9341 ATTATTCTGC

                                                  
       9351 TTTAGA TTTAGA TTTAGA TTTAGA TTTA-A TTT
          1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT

       9383 GCTTTGCTTT


Statistics
Matches: 26,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
   5    4  0.15
   6   22  0.85

ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56


Consensus pattern (6 bp):   
TTTAGA

Found at i:12723 original size:15 final size:16

Alignment explanation


    Indices: 12688--12730  Score: 52
    Period size: 15  Copynumber: 2.7  Consensus size: 16

      12678 ATCTCAGGGC

                *            
      12688 TTGATTTGTGTGTGTTG
          1 TTGAGTTGT-TGTGTTG

                            
      12705 TTGAGTTGTTGTG-TG
          1 TTGAGTTGTTGTGTTG

                 *     
      12720 TTGAGATGTTG
          1 TTGAGTTGTTG

      12731 AGATGTTGGA


Statistics
Matches: 24,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  15   12  0.50
  16    4  0.17
  17    8  0.33

ACGTcount: A:0.09, C:0.00, G:0.37, T:0.53


Consensus pattern (16 bp):   
TTGAGTTGTTGTGTTG

Found at i:13981 original size:70 final size:70

Alignment explanation


    Indices: 13868--14006  Score: 278
    Period size: 70  Copynumber: 2.0  Consensus size: 70

      13858 ACCTCTTGTG

                                                                             
      13868 AGAGGTCACGAGTTCGAATCCTGGGATGGGCGGGGTGGGATTTGATATAGGAAAGGGCTACCTCC
          1 AGAGGTCACGAGTTCGAATCCTGGGATGGGCGGGGTGGGATTTGATATAGGAAAGGGCTACCTCC

                 
      13933 TATTA
         66 TATTA

                                                                             
      13938 AGAGGTCACGAGTTCGAATCCTGGGATGGGCGGGGTGGGATTTGATATAGGAAAGGGCTACCTCC
          1 AGAGGTCACGAGTTCGAATCCTGGGATGGGCGGGGTGGGATTTGATATAGGAAAGGGCTACCTCC

                
      14003 TATT
         66 TATT

      14007 GTGTAGCCCA


Statistics
Matches: 69,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  70   69  1.00

ACGTcount: A:0.24, C:0.16, G:0.36, T:0.24


Consensus pattern (70 bp):   
AGAGGTCACGAGTTCGAATCCTGGGATGGGCGGGGTGGGATTTGATATAGGAAAGGGCTACCTCC
TATTA

Found at i:17939 original size:3 final size:3

Alignment explanation


    Indices: 17931--17979  Score: 71
    Period size: 3  Copynumber: 16.3  Consensus size: 3

      17921 TTAAGAAAGA

                                                        *     *       *    
      17931 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG GAG AAA AAG AAA AAG
          1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG

             
      17979 A
          1 A

      17980 TGTGTTGTTT


Statistics
Matches: 40,  Mismatches: 6, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
   3   40  1.00

ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00


Consensus pattern (3 bp):   
AAG

Done.