Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014787.1 Corchorus capsularis cultivar CVL-1 contig14808, 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: 9774
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35


Found at i:1254 original size:16 final size:16

Alignment explanation


    Indices: 1235--1321  Score: 77
    Period size: 16  Copynumber: 5.2  Consensus size: 16

       1225 AACCCGTCCA

                  *         
       1235 ACCCGAGACCCGAATG
          1 ACCCGAAACCCGAATG

                *               
       1251 ACCCAAAACCCGTATAATAG
          1 ACCCGAAACCCG---AAT-G

                      *    *
       1271 ACCCGAAACCTGAATA
          1 ACCCGAAACCCGAATG

               *        *   
       1287 ACCTG-AACCCGGATG
          1 ACCCGAAACCCGAATG

                            
       1302 ACCCGAAACCCGAATG
          1 ACCCGAAACCCGAATG

                
       1318 ACCC
          1 ACCC

       1322 AAGAGAACTA


Statistics
Matches: 55,  Mismatches: 11, Indels: 10
        0.72            0.14        0.13

Matches are distributed among these distances:
  15   11  0.20
  16   27  0.49
  17    3  0.05
  19    3  0.05
  20   11  0.20

ACGTcount: A:0.37, C:0.36, G:0.17, T:0.10


Consensus pattern (16 bp):   
ACCCGAAACCCGAATG

Found at i:6257 original size:70 final size:71

Alignment explanation


    Indices: 6177--6407  Score: 306
    Period size: 70  Copynumber: 3.2  Consensus size: 71

       6167 TTTTTTTAAC

                                                                   *         
       6177 TAAAA-TAGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATTGAGTTTTTA
          1 TAAAACTAGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTTA

                  
       6241 GTTGAG
         66 GTTGAG

                   *                                                         
       6247 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
          1 T-AAA-ACT---A--GTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA

                         
       6312 GTTTTTAGTTGAG
         59 GTTTTTAGTTGAG

                     *      *    *      *       *         *                  
       6325 TAAAA-TAGGAAAATAAAATAATTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTTTA
          1 TAAAACTAGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTTA

                  
       6389 GTTGAG
         66 GTTGAG

                          
       6395 TAAAACTA-TAAAA
          1 TAAAACTAGTAAAA

       6408 ACCTAAACAA


Statistics
Matches: 144,  Mismatches: 8, Indels: 18
        0.85            0.05        0.11

Matches are distributed among these distances:
  70   67  0.47
  71    5  0.03
  72    2  0.01
  73    1  0.01
  75    1  0.01
  76    2  0.01
  77    3  0.02
  78   63  0.44

ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37


Consensus pattern (71 bp):   
TAAAACTAGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTTA
GTTGAG

Found at i:6266 original size:78 final size:77

Alignment explanation


    Indices: 6177--6407  Score: 334
    Period size: 78  Copynumber: 3.1  Consensus size: 77

       6167 TTTTTTTAAC

                                                                  *          
       6177 TAAAATAGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATTGAGTTTTTAG
          1 TAAAAT-GTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTTAG

                         
       6242 TTGAGTAAAATAG
         65 TTGAGTAAAATAG

                                                                             
       6255 TAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTTAG
          1 TAAAAT-GTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTTAG

                         
       6320 TTGAGTAAAATAG
         65 TTGAGTAAAATAG

            *                         *       *         *                    
       6333 GAAAA--T-AAA-AT-A-A-TTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTTTAGT
          1 TAAAATGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTTAGT

                         
       6391 TGAGTAAAACTA-
         66 TGAGTAAAA-TAG

                 
       6403 TAAAA
          1 TAAAA

       6408 ACCTAAACAA


Statistics
Matches: 145,  Mismatches: 7, Indels: 10
        0.90            0.04        0.06

Matches are distributed among these distances:
  70   55  0.38
  71    3  0.02
  72    1  0.01
  73    2  0.01
  74    3  0.02
  75    1  0.01
  78   80  0.55

ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37


Consensus pattern (77 bp):   
TAAAATGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTTAGT
TGAGTAAAATAG

Found at i:7488 original size:6 final size:6

Alignment explanation


    Indices: 7462--7520  Score: 55
    Period size: 6  Copynumber: 9.5  Consensus size: 6

       7452 TAACCTTAAG

                        *                          *       *      *  
       7462 AAAGGA AAACGAA AAAGGGA AAAGGA AAAGGA AAGGGA AAAAGA AAATGA
          1 AAAGGA AAA-GGA AAA-GGA AAAGGA AAAGGA AAAGGA AAAGGA AAAGGA

               *      
       7512 AAATGA AAA
          1 AAAGGA AAA

       7521 ACCTTACATT


Statistics
Matches: 45,  Mismatches: 7, Indels: 2
        0.83            0.13        0.04

Matches are distributed among these distances:
   6   35  0.78
   7   10  0.22

ACGTcount: A:0.68, C:0.02, G:0.27, T:0.03


Consensus pattern (6 bp):   
AAAGGA

Done.