Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020537.1 Corchorus olitorius cultivar O-4 contig20570, 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: 19968
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32


Found at i:9365 original size:41 final size:41

Alignment explanation


    Indices: 9313--9573  Score: 432
    Period size: 41  Copynumber: 6.4  Consensus size: 41

       9303 TTCTAAAACT

                  *      *            *  *    *      
       9313 AGGGACCAAATTGAATCAAATAGTAACTAAAATCCTAAATC
          1 AGGGACTAAATTGCATCAAATAGTAAATAGAATCTTAAATC

              *                        *             
       9354 AGTGACTAAATTGCATCAAATAGTAAAGAGAATCTTAAATC
          1 AGGGACTAAATTGCATCAAATAGTAAATAGAATCTTAAATC

                                                *    
       9395 AGGGACTAAATTGCATCAAATAGTAAATAGAATCTTGAATC
          1 AGGGACTAAATTGCATCAAATAGTAAATAGAATCTTAAATC

                                      *              
       9436 AGGGACTAAATTGCATCAAATAGTAATTAGAATCTTAAATC
          1 AGGGACTAAATTGCATCAAATAGTAAATAGAATCTTAAATC

                                      *              
       9477 AGGGACTAAATTGCATCAAATAGTAATTAGAATCTTAAATC
          1 AGGGACTAAATTGCATCAAATAGTAAATAGAATCTTAAATC

                                                     
       9518 AGGGACTAAATTGCATCAAATAGTAAATAGAATCTTAAATC
          1 AGGGACTAAATTGCATCAAATAGTAAATAGAATCTTAAATC

                           
       9559 AGGGACTAAATTGCA
          1 AGGGACTAAATTGCA

       9574 GAGATAAAAA


Statistics
Matches: 207,  Mismatches: 13, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  41  207  1.00

ACGTcount: A:0.45, C:0.13, G:0.15, T:0.26


Consensus pattern (41 bp):   
AGGGACTAAATTGCATCAAATAGTAAATAGAATCTTAAATC

Found at i:11995 original size:58 final size:61

Alignment explanation


    Indices: 11930--12048  Score: 217
    Period size: 61  Copynumber: 2.0  Consensus size: 61

      11920 CATACGTATA

                                                                         
      11930 TTCTAAATGCAACT-A-AAAAACATTTTTGCAAATGAC-AACTAATGTTAAATTGATGGAG
          1 TTCTAAATGCAACTAATAAAAACATTTTTGCAAATGACAAACTAATGTTAAATTGATGGAG

                                                                         
      11988 TTCTAAATGCAACTAATAAAAACATTTTTGCAAATGACAAACTAATGTTAAATTGATGGAG
          1 TTCTAAATGCAACTAATAAAAACATTTTTGCAAATGACAAACTAATGTTAAATTGATGGAG

      12049 GATTGCTAAA


Statistics
Matches: 58,  Mismatches: 0, Indels: 3
        0.95            0.00        0.05

Matches are distributed among these distances:
  58   14  0.24
  59    1  0.02
  60   21  0.36
  61   22  0.38

ACGTcount: A:0.44, C:0.12, G:0.13, T:0.31


Consensus pattern (61 bp):   
TTCTAAATGCAACTAATAAAAACATTTTTGCAAATGACAAACTAATGTTAAATTGATGGAG

Found at i:17237 original size:3 final size:3

Alignment explanation


    Indices: 17231--17282  Score: 104
    Period size: 3  Copynumber: 17.3  Consensus size: 3

      17221 TTAAAAAAAT

                                                                           
      17231 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
          1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA

                 
      17279 ATA A
          1 ATA A

      17283 GGTTAGTAAC


Statistics
Matches: 49,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   49  1.00

ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33


Consensus pattern (3 bp):   
ATA

Done.