Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000694.1 Corchorus olitorius cultivar O-4 contig00694, 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, 745

Length: 1243
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32


Found at i:204 original size:22 final size:23

Alignment explanation


    Indices: 171--221  Score: 63
    Period size: 22  Copynumber: 2.3  Consensus size: 23

        161 CTATAGTATC

                             *     
        171 AAAAAAT-T-ATAGGGAGATTA-
          1 AAAAAATCTCATAGGGAAATTAT

             *                     
        191 ACAAAATCTCATAGGGAAATTAT
          1 AAAAAATCTCATAGGGAAATTAT

                    
        214 AAAAAATC
          1 AAAAAATC

        222 ATAGGAAGGT


Statistics
Matches: 25,  Mismatches: 3, Indels: 3
        0.81            0.10        0.10

Matches are distributed among these distances:
  20    6  0.24
  21    1  0.04
  22   11  0.44
  23    7  0.28

ACGTcount: A:0.55, C:0.08, G:0.14, T:0.24


Consensus pattern (23 bp):   
AAAAAATCTCATAGGGAAATTAT

Found at i:234 original size:21 final size:21

Alignment explanation


    Indices: 210--250  Score: 64
    Period size: 21  Copynumber: 2.0  Consensus size: 21

        200 CATAGGGAAA

                                 
        210 TTATAAAAAATCATAGGAAGG
          1 TTATAAAAAATCATAGGAAGG

                    **          
        231 TTATAAAATTTCATAGGAAG
          1 TTATAAAAAATCATAGGAAG

        251 ATAAAATTTC


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.49, C:0.05, G:0.17, T:0.29


Consensus pattern (21 bp):   
TTATAAAAAATCATAGGAAGG

Found at i:283 original size:22 final size:22

Alignment explanation


    Indices: 179--372  Score: 147
    Period size: 22  Copynumber: 9.1  Consensus size: 22

        169 TCAAAAAATT

                 *      *      *  
        179 ATAGGGAGATTAACAAAATCTC
          1 ATAGGTAGATTATCAAAATTTC

                 * *          **  
        201 ATAGGGAAATTAT-AAAAAATC
          1 ATAGGTAGATTATCAAAATTTC

                 *  *             
        222 ATAGGAAGGTTAT-AAAATTTC
          1 ATAGGTAGATTATCAAAATTTC

                      *           
        243 ATAGG-A-A-GAT-AAAATTTC
          1 ATAGGTAGATTATCAAAATTTC

                *             *   
        261 ATAGTTAGATTATCAAAAATTC
          1 ATAGGTAGATTATCAAAATTTC

                     *      *      
        283 ATATGG-AGTTTATCACAATTTC
          1 ATA-GGTAGATTATCAAAATTTC

                                  
        305 ATAGGTA-ATTATCAAAATTTC
          1 ATAGGTAGATTATCAAAATTTC

                          *       *
        326 ATAGCGT-GATTATTAAAATTTA
          1 ATAG-GTAGATTATCAAAATTTC

                                   
        348 ATAGGGTAG-TTATCAAAATTTC
          1 ATA-GGTAGATTATCAAAATTTC

               
        370 ATA
          1 ATA

        373 AAAATATTCT


Statistics
Matches: 138,  Mismatches: 24, Indels: 20
        0.76            0.13        0.11

Matches are distributed among these distances:
  18   14  0.10
  19    1  0.01
  20    2  0.01
  21   47  0.34
  22   71  0.51
  23    3  0.02

ACGTcount: A:0.44, C:0.08, G:0.14, T:0.34


Consensus pattern (22 bp):   
ATAGGTAGATTATCAAAATTTC

Found at i:328 original size:65 final size:62

Alignment explanation


    Indices: 230--372  Score: 157
    Period size: 65  Copynumber: 2.3  Consensus size: 62

        220 TCATAGGAAG

                                                 *                *   *    
        230 GTTAT-AAAATTTCATAGGAAGATAAAATTTCATAG-TTAGATTATCAAAAATTCATATGG-A
          1 GTTATCAAAATTTCATAGGAAGATAAAATTTCATAGCGT-GATTATCAAAAATTAATAGGGTA

                    *               *                        *    *          
        290 GTTTATCACAATTTCATAGGTAATTATCAAAATTTCATAGCGTGATTATTAAAATTTAATAGGGT
          1 G-TTATCAAAATTTCATAGG-AA-GAT-AAAATTTCATAGCGTGATTATCAAAAATTAATAGGGT

             
        355 A
         62 A

                             
        356 GTTATCAAAATTTCATA
          1 GTTATCAAAATTTCATA

        373 AAAATATTCT


Statistics
Matches: 68,  Mismatches: 8, Indels: 9
        0.80            0.09        0.11

Matches are distributed among these distances:
  60    1  0.01
  61    4  0.06
  62   12  0.18
  63    2  0.03
  64    2  0.03
  65   44  0.65
  66    3  0.04

ACGTcount: A:0.41, C:0.08, G:0.13, T:0.38


Consensus pattern (62 bp):   
GTTATCAAAATTTCATAGGAAGATAAAATTTCATAGCGTGATTATCAAAAATTAATAGGGTA
Done.