Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012681.1 Corchorus capsularis cultivar CVL-1 contig12702, 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: 5484
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32


Found at i:829 original size:31 final size:28

Alignment explanation


    Indices: 794--865  Score: 72
    Period size: 31  Copynumber: 2.4  Consensus size: 28

        784 TAAATTATTG

                                           
        794 CAAATTAAAACAAATTAAGCATTAAATTAAA
          1 CAAATTAAAAC-AA--AAGCATTAAATTAAA

                          *     *          
        825 CAAATAATTAAAACGAAAGCCTTAAATTAAA
          1 C--A-AATTAAAACAAAAGCATTAAATTAAA

                      
        856 CAAATTAAAA
          1 CAAATTAAAA

        866 GCTGATAGAC


Statistics
Matches: 36,  Mismatches: 2, Indels: 9
        0.77            0.04        0.19

Matches are distributed among these distances:
  28    8  0.22
  29    1  0.03
  31   16  0.44
  33    2  0.06
  34    9  0.25

ACGTcount: A:0.61, C:0.11, G:0.04, T:0.24


Consensus pattern (28 bp):   
CAAATTAAAACAAAAGCATTAAATTAAA

Found at i:1303 original size:12 final size:12

Alignment explanation


    Indices: 1282--1329  Score: 53
    Period size: 12  Copynumber: 4.1  Consensus size: 12

       1272 AAATTAAAGT

                 *      
       1282 TCGGGTTCGGGC
          1 TCGGGCTCGGGC

                      * 
       1294 TCGGGCTCGGTC
          1 TCGGGCTCGGGC

                       *
       1306 TCGGG-TCGGGT
          1 TCGGGCTCGGGC

                    *   
       1317 TCGGGCTCAGGC
          1 TCGGGCTCGGGC

             
       1329 T
          1 T

       1330 GCCTCGGGTT


Statistics
Matches: 29,  Mismatches: 6, Indels: 2
        0.78            0.16        0.05

Matches are distributed among these distances:
  11    9  0.31
  12   20  0.69

ACGTcount: A:0.02, C:0.27, G:0.46, T:0.25


Consensus pattern (12 bp):   
TCGGGCTCGGGC

Found at i:1324 original size:29 final size:28

Alignment explanation


    Indices: 1280--1345  Score: 89
    Period size: 29  Copynumber: 2.3  Consensus size: 28

       1270 TCAAATTAAA

                            *       *     
       1280 GTTCGGGTTCGGGCTCGGGCTCGGTCTCGG
          1 GTTCGGGTTCGGGCTCAGGCT--GCCTCGG

                                        
       1310 G-TCGGGTTCGGGCTCAGGCTGCCTCGG
          1 GTTCGGGTTCGGGCTCAGGCTGCCTCGG

                     
       1337 GTTCGGGTT
          1 GTTCGGGTT

       1346 TTTTCGGGCT


Statistics
Matches: 33,  Mismatches: 2, Indels: 4
        0.85            0.05        0.10

Matches are distributed among these distances:
  27    7  0.21
  28    7  0.21
  29   18  0.55
  30    1  0.03

ACGTcount: A:0.02, C:0.26, G:0.45, T:0.27


Consensus pattern (28 bp):   
GTTCGGGTTCGGGCTCAGGCTGCCTCGG

Found at i:1352 original size:16 final size:16

Alignment explanation


    Indices: 1333--1375  Score: 59
    Period size: 16  Copynumber: 2.7  Consensus size: 16

       1323 TCAGGCTGCC

                        **  
       1333 TCGGGTTCGGGTTTTT
          1 TCGGGTTCGGGTAATT

                 *          
       1349 TCGGGCTCGGGTAATT
          1 TCGGGTTCGGGTAATT

                       
       1365 TCGGGTTCGGG
          1 TCGGGTTCGGG

       1376 GTCGGGCGGG


Statistics
Matches: 23,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  16   23  1.00

ACGTcount: A:0.05, C:0.16, G:0.42, T:0.37


Consensus pattern (16 bp):   
TCGGGTTCGGGTAATT
Done.