Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012322.1 Corchorus capsularis cultivar CVL-1 contig12343, 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: 6530
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34


Found at i:1213 original size:13 final size:14

Alignment explanation


    Indices: 1189--1230  Score: 75
    Period size: 14  Copynumber: 3.0  Consensus size: 14

       1179 AAGTCTTAAT

                          
       1189 TTTTCTTTTTTTCC
          1 TTTTCTTTTTTTCC

                          
       1203 TTTTCTTTTTTTCC
          1 TTTTCTTTTTTTCC

               *          
       1217 TTTCCTTTTTTTCC
          1 TTTTCTTTTTTTCC

       1231 CTCAAATCTC


Statistics
Matches: 27,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  14   27  1.00

ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76


Consensus pattern (14 bp):   
TTTTCTTTTTTTCC

Found at i:3047 original size:20 final size:20

Alignment explanation


    Indices: 3022--3059  Score: 58
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       3012 ATTGTGTCTT

                   *            
       3022 GACACGATTAACACGTTTAA
          1 GACACGAGTAACACGTTTAA

                     *        
       3042 GACACGAGTGACACGTTT
          1 GACACGAGTAACACGTTT

       3060 TAATTAACGA


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  20   16  1.00

ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24


Consensus pattern (20 bp):   
GACACGAGTAACACGTTTAA

Found at i:3213 original size:14 final size:14

Alignment explanation


    Indices: 3196--3229  Score: 59
    Period size: 14  Copynumber: 2.4  Consensus size: 14

       3186 TATACTCAAT

                 *        
       3196 TATATTTAATTATA
          1 TATATATAATTATA

                          
       3210 TATATATAATTATA
          1 TATATATAATTATA

                  
       3224 TATATA
          1 TATATA

       3230 GTTTATTCAA


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  14   19  1.00

ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53


Consensus pattern (14 bp):   
TATATATAATTATA

Found at i:5536 original size:88 final size:88

Alignment explanation


    Indices: 5384--5625  Score: 301
    Period size: 94  Copynumber: 2.7  Consensus size: 88

       5374 CTGCGACACT

                                           **                     *     *    
       5384 TTTTATTAGACTAATAGAATAA-TATTTTAGGTCATATTTATATAATATTAATGGGAAAAGAAAC
          1 TTTTATTAGACTAATA-AA-AAGTATTTTAGAACATATTTATATAATATTAATGAGAAAACAAAC

                                     
       5448 C-TTTTTTTTGGCCATCAACAAACC
         64 CTTTTTTTTTGGCCATCAACAAACC

                                                                             
       5472 TTTTATTAGACTAATAAAAAGGTATTTTAGAACATATTTATATAATATTAATGAGAAAACAAACC
          1 TTTTATTAGACTAATAAAAA-GTATTTTAGAACATATTTATATAATATTAATGAGAAAACAAACC

                              *      *   
       5537 TTTTATTTTTTTTTGGCCGTCAACAGACC
         65 -----TTTTTTTTTGGCCATCAACAAACC

                            *                                            
       5566 TTTTATTAGACTAATCGAAAAGTATTTTAGATA-ATATTTATATAATATTAATGAGCAAAA
          1 TTTTATTAGACTAAT-AAAAAGTATTTTAGA-ACATATTTATATAATATTAATGAG-AAAA

       5626 AAAAAGGAAA


Statistics
Matches: 136,  Mismatches: 7, Indels: 15
        0.86            0.04        0.09

Matches are distributed among these distances:
  86    2  0.01
  87    2  0.01
  88   55  0.40
  94   68  0.50
  95    9  0.07

ACGTcount: A:0.40, C:0.10, G:0.11, T:0.39


Consensus pattern (88 bp):   
TTTTATTAGACTAATAAAAAGTATTTTAGAACATATTTATATAATATTAATGAGAAAACAAACCT
TTTTTTTTGGCCATCAACAAACC

Done.