Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022044.1 Corchorus olitorius cultivar O-4 contig22077, 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: 17785
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:365 original size:34 final size:34

Alignment explanation


    Indices: 327--546  Score: 226
    Period size: 34  Copynumber: 6.1  Consensus size: 34

        317 AAGAATTTCG

                                              
        327 TCAGGTTTAAGTTTTCAAATTGGGAAAGTTCCCA
          1 TCAGGTTTAAGTTTTCAAATTGGGAAAGTTCCCA

                                                
        361 TCAGGGTTT-AGTTTTCAAAATTGGGAAAGTTCCCA
          1 TCA-GGTTTAAGTTTTC-AAATTGGGAAAGTTCCCA

                         *                         *   
        396 TCGAGTTTTTTTTTTTTAAGTTTTCAAATTGGGAAAGTTACCA
          1 TC-AG--------GTTTAAGTTTTCAAATTGGGAAAGTTCCCA

                    *  *                      
        439 TCAGGTTTTAGCTTTCAAATTGGGAAAGTTCCCA
          1 TCAGGTTTAAGTTTTCAAATTGGGAAAGTTCCCA

                  *                             
        473 TCGAGTTTTTAAGTTTTCAAATTGGGAAAGTTCCCA
          1 TC-AG-GTTTAAGTTTTCAAATTGGGAAAGTTCCCA

            * *     *         *                
        509 CCGGGTTTTAGTTTTCAATTTAGGGAAAGTTCCCA
          1 TCAGGTTTAAGTTTTCAAATT-GGGAAAGTTCCCA

               
        544 TCA
          1 TCA

        547 TTTTCAGCTT


Statistics
Matches: 155,  Mismatches: 16, Indels: 29
        0.77            0.08        0.14

Matches are distributed among these distances:
  34   52  0.34
  35   43  0.28
  36   29  0.19
  42    2  0.01
  43   22  0.14
  44    7  0.05

ACGTcount: A:0.27, C:0.15, G:0.20, T:0.39


Consensus pattern (34 bp):   
TCAGGTTTAAGTTTTCAAATTGGGAAAGTTCCCA

Found at i:487 original size:70 final size:71

Alignment explanation


    Indices: 408--545  Score: 224
    Period size: 70  Copynumber: 2.0  Consensus size: 71

        398 GAGTTTTTTT

                                           *                                 
        408 TTTTTAAGTTTTCAAATTGGGAAAGTTACCATCAGGTTTTAGCTTTCAAATT-GGGAAAGTTCCC
          1 TTTTTAAGTTTTCAAATTGGGAAAGTTACCACCAGGTTTTAGCTTTCAAATTAGGGAAAGTTCCC

                  
        472 ATCGAG
         66 ATCGAG

                                       *     *        *      *               
        478 TTTTTAAGTTTTCAAATTGGGAAAGTTCCCACCGGGTTTTAGTTTTCAATTTAGGGAAAGTTCCC
          1 TTTTTAAGTTTTCAAATTGGGAAAGTTACCACCAGGTTTTAGCTTTCAAATTAGGGAAAGTTCCC

               
        543 ATC
         66 ATC

        546 ATTTTCAGCT


Statistics
Matches: 62,  Mismatches: 5, Indels: 1
        0.91            0.07        0.01

Matches are distributed among these distances:
  70   47  0.76
  71   15  0.24

ACGTcount: A:0.27, C:0.15, G:0.20, T:0.38


Consensus pattern (71 bp):   
TTTTTAAGTTTTCAAATTGGGAAAGTTACCACCAGGTTTTAGCTTTCAAATTAGGGAAAGTTCCC
ATCGAG

Found at i:6320 original size:22 final size:21

Alignment explanation


    Indices: 6295--6348  Score: 60
    Period size: 19  Copynumber: 2.6  Consensus size: 21

       6285 GAAGTTCGTG

                                  
       6295 TTTGAAGACTTATTGAAGATAA
          1 TTTGAAGA-TTATTGAAGATAA

                               * 
       6317 TTTGAAGA-T-TTGAAGATCA
          1 TTTGAAGATTATTGAAGATAA

                          
       6336 -TTGAAGAATTATT
          1 TTTGAAG-ATTATT

       6349 TCGAGAAGCA


Statistics
Matches: 28,  Mismatches: 1, Indels: 7
        0.78            0.03        0.19

Matches are distributed among these distances:
  18    6  0.21
  19   10  0.36
  20    2  0.07
  21    2  0.07
  22    8  0.29

ACGTcount: A:0.39, C:0.04, G:0.19, T:0.39


Consensus pattern (21 bp):   
TTTGAAGATTATTGAAGATAA

Found at i:10038 original size:15 final size:15

Alignment explanation


    Indices: 10001--10040  Score: 62
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       9991 CACCGAATGA

                   *       
      10001 TGTTTCTACAACGGT
          1 TGTTTCTGCAACGGT

            *              
      10016 CGTTTCTGCAACGGT
          1 TGTTTCTGCAACGGT

                      
      10031 TGTTTCTGCA
          1 TGTTTCTGCA

      10041 CCACTTTTAT


Statistics
Matches: 22,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  15   22  1.00

ACGTcount: A:0.15, C:0.23, G:0.23, T:0.40


Consensus pattern (15 bp):   
TGTTTCTGCAACGGT

Found at i:14254 original size:5 final size:5

Alignment explanation


    Indices: 14244--14287  Score: 70
    Period size: 5  Copynumber: 8.4  Consensus size: 5

      14234 TCCTTCTACC

                                                                
      14244 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATATAT ATATAT AT
          1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT-TAT AT-TAT AT

      14288 ATGAAATTCC


Statistics
Matches: 38,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
   5   27  0.71
   6   11  0.29

ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57


Consensus pattern (5 bp):   
ATTAT

Found at i:14278 original size:2 final size:2

Alignment explanation


    Indices: 14246--14289  Score: 53
    Period size: 2  Copynumber: 24.5  Consensus size: 2

      14236 CTTCTACCAT

                                                                          
      14246 TA TA T- TA TA T- TA TA T- TA TA T- TA TA T- TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                      
      14283 TA TA TA T
          1 TA TA TA T

      14290 GAAATTCCTC


Statistics
Matches: 37,  Mismatches: 0, Indels: 10
        0.79            0.00        0.21

Matches are distributed among these distances:
   1    5  0.14
   2   32  0.86

ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57


Consensus pattern (2 bp):   
TA

Done.