Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017824.1 Corchorus olitorius cultivar O-4 contig17857, 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: 8015
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32


Found at i:372 original size:20 final size:22

Alignment explanation


    Indices: 344--384  Score: 59
    Period size: 21  Copynumber: 2.0  Consensus size: 22

        334 TCACAAGGAG

                                  
        344 GTTATCAAAA-ATCATAGGAAA
          1 GTTATCAAAATATCATAGGAAA

                       *         
        365 GTTA-CAAAATTTCATAGGAA
          1 GTTATCAAAATATCATAGGAA

        385 GATTTACTAA


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

Matches are distributed among these distances:
  20    5  0.28
  21   13  0.72

ACGTcount: A:0.49, C:0.10, G:0.15, T:0.27


Consensus pattern (22 bp):   
GTTATCAAAATATCATAGGAAA

Found at i:479 original size:22 final size:22

Alignment explanation


    Indices: 344--513  Score: 108
    Period size: 22  Copynumber: 7.8  Consensus size: 22

        334 TCACAAGGAG

                       *        * 
        344 GTTATCAAAA-ATCATAGGAAA
          1 GTTATCAAAATTTCATAGGATA

                                  
        365 GTTA-CAAAATTTCATAGGA-A
          1 GTTATCAAAATTTCATAGGATA

                                      
        385 GATT-TACTAAAATTTCATA--ATTA
          1 G-TTAT-C-AAAATTTCATAGGA-TA

                      *             
        408 GGTTATCAAAGTTTCATATGG--A
          1 -GTTATCAAAATTTCATA-GGATA

                  * *     *         
        430 GTTTATTACAATTTTATAGGCA-A
          1 G-TTATCAAAATTTCATAGG-ATA

            *                     *
        453 TTTATCAAAATTTCATAGCG-TG
          1 GTTATCAAAATTTCATAG-GATA

                         *        
        475 GTTATCAAAATTTAATAGGATA
          1 GTTATCAAAATTTCATAGGATA

                             
        497 GTTATCAAAATTTCATA
          1 GTTATCAAAATTTCATA

        514 AAGATATTTA


Statistics
Matches: 116,  Mismatches: 15, Indels: 35
        0.70            0.09        0.21

Matches are distributed among these distances:
  20    7  0.06
  21   19  0.16
  22   71  0.61
  23   17  0.15
  24    2  0.02

ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37


Consensus pattern (22 bp):   
GTTATCAAAATTTCATAGGATA

Found at i:509 original size:66 final size:66

Alignment explanation


    Indices: 314--513  Score: 171
    Period size: 66  Copynumber: 3.0  Consensus size: 66

        304 TCAAAAAATT

                 *     *        *   *   *             *                      
        314 ATAGGGAGATTAAC-AAAATCTCACAAGGAGGTTATCAAAA-ATCATAGGAAAGTTA-CAAAATT
          1 ATAGGAAGATTTACTAAAATTTCATAAGTAGGTTATCAAAATTTCATAGG-AAGTTATCAAAATT

              
        376 TC
         65 TC

                                       *            *                  * *   
        378 ATAGGAAGATTTACTAAAATTTCATAATTAGGTTATCAAAGTTTCATATGG-AGTTTATTACAAT
          1 ATAGGAAGATTTACTAAAATTTCATAAGTAGGTTATCAAAATTTCATA-GGAAG-TTATCAAAAT

              *
        442 TTT
         64 TTC

                 *                      *                 *                  
        445 ATAGGCA-ATTTA-TCAAAATTTCATAGCGT-GGTTATCAAAATTTAATAGGATAGTTATCAAAA
          1 ATAGGAAGATTTACT-AAAATTTCATA-AGTAGGTTATCAAAATTTCATAGGA-AGTTATCAAAA

                
        507 TTTC
         63 TTTC

               
        511 ATA
          1 ATA

        514 AAGATATTTA


Statistics
Matches: 108,  Mismatches: 19, Indels: 16
        0.76            0.13        0.11

Matches are distributed among these distances:
  64   12  0.11
  65   26  0.24
  66   53  0.49
  67   17  0.16

ACGTcount: A:0.41, C:0.10, G:0.14, T:0.34


Consensus pattern (66 bp):   
ATAGGAAGATTTACTAAAATTTCATAAGTAGGTTATCAAAATTTCATAGGAAGTTATCAAAATTT
C

Found at i:6312 original size:42 final size:43

Alignment explanation


    Indices: 6260--6354  Score: 140
    Period size: 45  Copynumber: 2.2  Consensus size: 43

       6250 AGTGCATTAC

                                    *            *     
       6260 CTAA-ATTATA-CTCCATCTCTAGGTAATTCATCAAATTAAAG
          1 CTAATATTATACCTCCATCTCTAGATAATTCATCAAAATAAAG

                                                         
       6301 CTAATATTATACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
          1 CTAATATTATA--CCTCCATCTCTAGATAATTCATCAAAATAAAG

                     
       6346 CTAATATTA
          1 CTAATATTA

       6355 ATTGTTGCTT


Statistics
Matches: 48,  Mismatches: 2, Indels: 4
        0.89            0.04        0.07

Matches are distributed among these distances:
  41    4  0.08
  42    6  0.12
  45   38  0.79

ACGTcount: A:0.40, C:0.20, G:0.05, T:0.35


Consensus pattern (43 bp):   
CTAATATTATACCTCCATCTCTAGATAATTCATCAAAATAAAG
Done.