Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014326.1 Corchorus capsularis cultivar CVL-1 contig14347, 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: 12758
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.31


Found at i:83 original size:17 final size:17

Alignment explanation


    Indices: 63--101  Score: 60
    Period size: 17  Copynumber: 2.3  Consensus size: 17

         53 TATTTAATGA

                   *         
         63 TTTTTCCTTTTTTCCTT
          1 TTTTTCCGTTTTTCCTT

                          *  
         80 TTTTTCCGTTTTTCGTT
          1 TTTTTCCGTTTTTCCTT

                 
         97 TTTTT
          1 TTTTT

        102 TAAAAAGAAA


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  17   20  1.00

ACGTcount: A:0.00, C:0.18, G:0.05, T:0.77


Consensus pattern (17 bp):   
TTTTTCCGTTTTTCCTT

Found at i:5781 original size:13 final size:14

Alignment explanation


    Indices: 5758--5786  Score: 51
    Period size: 13  Copynumber: 2.1  Consensus size: 14

       5748 ACTTCTACTC

                          
       5758 AATGCATGAATGCA
          1 AATGCATGAATGCA

                          
       5772 AATG-ATGAATGCA
          1 AATGCATGAATGCA

              
       5785 AA
          1 AA

       5787 GTCCAATTAT


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  13   11  0.73
  14    4  0.27

ACGTcount: A:0.48, C:0.10, G:0.21, T:0.21


Consensus pattern (14 bp):   
AATGCATGAATGCA

Found at i:9582 original size:35 final size:35

Alignment explanation


    Indices: 9542--9610  Score: 138
    Period size: 35  Copynumber: 2.0  Consensus size: 35

       9532 TTTACTTCTT

                                               
       9542 TTCTTACCCCCTTTCTGTTCTAATTGTTTTGAGCC
          1 TTCTTACCCCCTTTCTGTTCTAATTGTTTTGAGCC

                                              
       9577 TTCTTACCCCCTTTCTGTTCTAATTGTTTTGAGC
          1 TTCTTACCCCCTTTCTGTTCTAATTGTTTTGAGC

       9611 GTAACATGGG


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  35   34  1.00

ACGTcount: A:0.12, C:0.28, G:0.12, T:0.49


Consensus pattern (35 bp):   
TTCTTACCCCCTTTCTGTTCTAATTGTTTTGAGCC

Found at i:10773 original size:57 final size:57

Alignment explanation


    Indices: 10685--10798  Score: 212
    Period size: 57  Copynumber: 2.0  Consensus size: 57

      10675 CCAACCGTTT

                                                                      
      10685 TATAATTTGCTCCTATATATAACATCACATCAAGATATATCACATA-TCTATATATCA
          1 TATAATTTGCTCCTATATATAACATCACATCAAGATATATCACATACT-TATATATCA

                                                                     
      10742 TATAATTTGCTCCTATATATAACATCACATCAAGATATATCACATACTTATATATCA
          1 TATAATTTGCTCCTATATATAACATCACATCAAGATATATCACATACTTATATATCA

      10799 CATATCAAAT


Statistics
Matches: 56,  Mismatches: 0, Indels: 2
        0.97            0.00        0.03

Matches are distributed among these distances:
  57   55  0.98
  58    1  0.02

ACGTcount: A:0.40, C:0.19, G:0.04, T:0.37


Consensus pattern (57 bp):   
TATAATTTGCTCCTATATATAACATCACATCAAGATATATCACATACTTATATATCA

Found at i:11325 original size:48 final size:48

Alignment explanation


    Indices: 11269--11368  Score: 191
    Period size: 48  Copynumber: 2.1  Consensus size: 48

      11259 ATCAGGAGTG

                                                            
      11269 TAACAAACTCTGGAGTCCTTTTCCAACAAGGAATTAACAACATCAAAA
          1 TAACAAACTCTGGAGTCCTTTTCCAACAAGGAATTAACAACATCAAAA

                                            *               
      11317 TAACAAACTCTGGAGTCCTTTTCCAACAAGGACTTAACAACATCAAAA
          1 TAACAAACTCTGGAGTCCTTTTCCAACAAGGAATTAACAACATCAAAA

                
      11365 TAAC
          1 TAAC

      11369 TGAAATGTGC


Statistics
Matches: 51,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  48   51  1.00

ACGTcount: A:0.43, C:0.24, G:0.10, T:0.23


Consensus pattern (48 bp):   
TAACAAACTCTGGAGTCCTTTTCCAACAAGGAATTAACAACATCAAAA

Found at i:12428 original size:57 final size:57

Alignment explanation


    Indices: 12340--12453  Score: 203
    Period size: 57  Copynumber: 2.0  Consensus size: 57

      12330 CCAACCGTTT

                                                                      
      12340 TATAATTTACTCCTATATATAACATCACATCAAGATATATCACATA-TCTATATATCA
          1 TATAATTTACTCCTATATATAACATCACATCAAGATATATCACATACT-TATATATCA

                    *                                                
      12397 TATAATTTGCTCCTATATATAACATCACATCAAGATATATCACATACTTATATATCA
          1 TATAATTTACTCCTATATATAACATCACATCAAGATATATCACATACTTATATATCA

      12454 CATATCAAAT


Statistics
Matches: 55,  Mismatches: 1, Indels: 2
        0.95            0.02        0.03

Matches are distributed among these distances:
  57   54  0.98
  58    1  0.02

ACGTcount: A:0.41, C:0.19, G:0.03, T:0.37


Consensus pattern (57 bp):   
TATAATTTACTCCTATATATAACATCACATCAAGATATATCACATACTTATATATCA
Done.