Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021520.1 Corchorus olitorius cultivar O-4 contig21553, 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: 18791
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35


Found at i:2394 original size:33 final size:33

Alignment explanation


    Indices: 2293--2427  Score: 123
    Period size: 33  Copynumber: 4.1  Consensus size: 33

       2283 TTGTAAAGAG

                    *       *       *      * 
       2293 TGTTTTAGATGTTGTTAGTGATGATACTAAACC
          1 TGTTTTAGGTGTTGTTTGTGATGAAACTAAATC

             **    *                *        
       2326 TAATTTAAGTGTTGTTTGTGATGACACTAAATC
          1 TGTTTTAGGTGTTGTTTGTGATGAAACTAAATC

                                              
       2359 TGTTTTAGGTGTTGTTTGTGATGAAAC-AAATTC
          1 TGTTTTAGGTGTTGTTTGTGATGAAACTAAA-TC

                        * **                   
       2392 TGTTTT-GGATGCTAATTGTGATGAAAAC-AAATC
          1 TGTTTTAGG-TGTTGTTTGTGATG-AAACTAAATC

               
       2425 TGT
          1 TGT

       2428 GTTGGTTGAT


Statistics
Matches: 85,  Mismatches: 14, Indels: 6
        0.81            0.13        0.06

Matches are distributed among these distances:
  32    5  0.06
  33   73  0.86
  34    7  0.08

ACGTcount: A:0.28, C:0.08, G:0.21, T:0.42


Consensus pattern (33 bp):   
TGTTTTAGGTGTTGTTTGTGATGAAACTAAATC

Found at i:4383 original size:21 final size:22

Alignment explanation


    Indices: 4354--4395  Score: 61
    Period size: 21  Copynumber: 2.0  Consensus size: 22

       4344 TTGTTCGAAC

                                   
       4354 TCAACTTGAAGACCA-TTGAAGT
          1 TCAACTTGAAGA-CATTTGAAGT

                                 
       4376 TCAA-TTGAAGACATTTGAAG
          1 TCAACTTGAAGACATTTGAAG

       4396 GTGATTTGGG


Statistics
Matches: 19,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  20    2  0.11
  21   13  0.68
  22    4  0.21

ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29


Consensus pattern (22 bp):   
TCAACTTGAAGACATTTGAAGT

Found at i:4479 original size:21 final size:21

Alignment explanation


    Indices: 4453--4494  Score: 84
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       4443 TAAAATCAGA

                                 
       4453 ACAACTCCTGCCCAGGACTTG
          1 ACAACTCCTGCCCAGGACTTG

                                 
       4474 ACAACTCCTGCCCAGGACTTG
          1 ACAACTCCTGCCCAGGACTTG

       4495 GTCTGTTGAA


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

Matches are distributed among these distances:
  21   21  1.00

ACGTcount: A:0.24, C:0.38, G:0.19, T:0.19


Consensus pattern (21 bp):   
ACAACTCCTGCCCAGGACTTG

Found at i:6257 original size:21 final size:22

Alignment explanation


    Indices: 6224--6265  Score: 59
    Period size: 21  Copynumber: 2.0  Consensus size: 22

       6214 AGAATGGTAT

                           *      
       6224 TTAAAATCTAAACCTTATTTAA
          1 TTAAAATCTAAACCTCATTTAA

                 *               
       6246 TTAAATTC-AAACCTCATTTA
          1 TTAAAATCTAAACCTCATTTA

       6266 CAAAAACTTT


Statistics
Matches: 18,  Mismatches: 2, Indels: 1
        0.86            0.10        0.05

Matches are distributed among these distances:
  21   11  0.61
  22    7  0.39

ACGTcount: A:0.43, C:0.17, G:0.00, T:0.40


Consensus pattern (22 bp):   
TTAAAATCTAAACCTCATTTAA

Found at i:9670 original size:132 final size:134

Alignment explanation


    Indices: 9511--9776  Score: 491
    Period size: 132  Copynumber: 2.0  Consensus size: 134

       9501 AGTCATAAGG

                                                                             
       9511 ATATTATATTTAATTAAATAAAAGCAGAGTTTTTAGTTGAGTAAAACTATAAAAGTCTAAACAAT
          1 ATATTATATTTAATTAAATAAAAGCAGAGTTTTTAGTTGAGTAAAACTATAAAAGTCTAAACAAT

             *                                                          *    
       9576 GGCATTTAAGAAATATATT-AAAAAAAAAGG-TATAACGGGCGATTCAGAAGTTTTACAATAGTA
         66 GACATTTAAGAAATATATTCAAAAAAAAAGGATATAACGGGCGATTCAGAAGTTTTACAAGAGTA

                
       9639 TGTA
        131 TGTA

                                                                             
       9643 ATATTATATTTAATTAAATAAAAGCAGAGTTTTTAGTTGAGTAAAACTATAAAAGTCTAAACAAT
          1 ATATTATATTTAATTAAATAAAAGCAGAGTTTTTAGTTGAGTAAAACTATAAAAGTCTAAACAAT

                                      *                                      
       9708 GACATTTAAGAAATATATTCAAAAAATAAGGATATAACGGGCGATTCAGAAGTTTTACAAGAGTA
         66 GACATTTAAGAAATATATTCAAAAAAAAAGGATATAACGGGCGATTCAGAAGTTTTACAAGAGTA

                
       9773 TGTA
        131 TGTA

       9777 CCTTTTAATA


Statistics
Matches: 129,  Mismatches: 3, Indels: 2
        0.96            0.02        0.01

Matches are distributed among these distances:
 132   83  0.64
 133   10  0.08
 134   36  0.28

ACGTcount: A:0.46, C:0.07, G:0.15, T:0.32


Consensus pattern (134 bp):   
ATATTATATTTAATTAAATAAAAGCAGAGTTTTTAGTTGAGTAAAACTATAAAAGTCTAAACAAT
GACATTTAAGAAATATATTCAAAAAAAAAGGATATAACGGGCGATTCAGAAGTTTTACAAGAGTA
TGTA

Found at i:18571 original size:2 final size:2

Alignment explanation


    Indices: 18564--18589  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

      18554 CATATGAAGC

                                                  
      18564 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

      18590 TCTCAAATGG


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Done.