Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014045.1 Corchorus capsularis cultivar CVL-1 contig14066, 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: 14447
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33


Found at i:358 original size:6 final size:6

Alignment explanation


    Indices: 349--392  Score: 65
    Period size: 6  Copynumber: 7.7  Consensus size: 6

        339 CGTTTCTGTT

                                                   *             
        349 TTTTTG TTTTTG TTTTTG -TTTTG TTTTTG -TTTCG TTTTTG TTTT
          1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTT

        393 GTTGTCAAAA


Statistics
Matches: 34,  Mismatches: 2, Indels: 4
        0.85            0.05        0.10

Matches are distributed among these distances:
   5    9  0.26
   6   25  0.74

ACGTcount: A:0.00, C:0.02, G:0.16, T:0.82


Consensus pattern (6 bp):   
TTTTTG

Found at i:370 original size:11 final size:11

Alignment explanation


    Indices: 349--395  Score: 76
    Period size: 11  Copynumber: 4.2  Consensus size: 11

        339 CGTTTCTGTT

                        
        349 TTTTTGTTTTTG
          1 TTTTTG-TTTTG

                       
        361 TTTTTGTTTTG
          1 TTTTTGTTTTG

                     * 
        372 TTTTTGTTTCG
          1 TTTTTGTTTTG

                       
        383 TTTTTGTTTTG
          1 TTTTTGTTTTG

              
        394 TT
          1 TT

        396 GTCAAAATTT


Statistics
Matches: 33,  Mismatches: 2, Indels: 1
        0.92            0.06        0.03

Matches are distributed among these distances:
  11   27  0.82
  12    6  0.18

ACGTcount: A:0.00, C:0.02, G:0.17, T:0.81


Consensus pattern (11 bp):   
TTTTTGTTTTG

Found at i:372 original size:17 final size:16

Alignment explanation


    Indices: 349--392  Score: 61
    Period size: 17  Copynumber: 2.6  Consensus size: 16

        339 CGTTTCTGTT

                           *
        349 TTTTTGTTTTTGTTTT
          1 TTTTTGTTTTTGTTTC

                             
        365 TGTTTTGTTTTTGTTTC
          1 T-TTTTGTTTTTGTTTC

                       
        382 GTTTTTGTTTT
          1 -TTTTTGTTTT

        393 GTTGTCAAAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 3
        0.86            0.03        0.10

Matches are distributed among these distances:
  16    1  0.04
  17   23  0.92
  18    1  0.04

ACGTcount: A:0.00, C:0.02, G:0.16, T:0.82


Consensus pattern (16 bp):   
TTTTTGTTTTTGTTTC

Found at i:385 original size:22 final size:22

Alignment explanation


    Indices: 338--395  Score: 77
    Period size: 22  Copynumber: 2.7  Consensus size: 22

        328 CCGTTTGGTA

                  *               
        338 TCGTTTCTGTTTT-TTTGTTTT
          1 TCGTTTTTGTTTTGTTTGTTTT

                                   
        359 T-GTTTTTGTTTTGTTT-TTGTT
          1 TCGTTTTTGTTTTGTTTGTT-TT

                            
        380 TCGTTTTTGTTTTGTT
          1 TCGTTTTTGTTTTGTT

        396 GTCAAAATTT


Statistics
Matches: 33,  Mismatches: 1, Indels: 5
        0.85            0.03        0.13

Matches are distributed among these distances:
  20   12  0.36
  21    7  0.21
  22   14  0.42

ACGTcount: A:0.00, C:0.05, G:0.17, T:0.78


Consensus pattern (22 bp):   
TCGTTTTTGTTTTGTTTGTTTT

Found at i:8022 original size:24 final size:24

Alignment explanation


    Indices: 7994--8043  Score: 100
    Period size: 24  Copynumber: 2.1  Consensus size: 24

       7984 AATGCACTTA

                                    
       7994 TCTACCCCATATTCTAAAGCTATC
          1 TCTACCCCATATTCTAAAGCTATC

                                    
       8018 TCTACCCCATATTCTAAAGCTATC
          1 TCTACCCCATATTCTAAAGCTATC

              
       8042 TC
          1 TC

       8044 AAAACCAAAC


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  24   26  1.00

ACGTcount: A:0.28, C:0.34, G:0.04, T:0.34


Consensus pattern (24 bp):   
TCTACCCCATATTCTAAAGCTATC

Found at i:9600 original size:68 final size:68

Alignment explanation


    Indices: 9490--9625  Score: 238
    Period size: 68  Copynumber: 2.0  Consensus size: 68

       9480 CATTTGTTCC

                                                                             
       9490 ATTAGGAGAATGTTCCTCAATGTACTGCATATCAAGGAAACAGTAAAATTCAGTCAATAATTACA
          1 ATTAGGAGAATGTTCCTCAATGTACTGCATATCAAGGAAACAGTAAAATTCAGTCAATAATTACA

               
       9555 AAT
         66 AAT

                             *                    *                          
       9558 ATTAGGAGAATGTTCCTTAATGTACTGCA-ATTCAAGGTAACAGTAAAATTCAGTCAATAATTAC
          1 ATTAGGAGAATGTTCCTCAATGTACTGCATA-TCAAGGAAACAGTAAAATTCAGTCAATAATTAC

                
       9622 AAAT
         65 AAAT

       9626 TATTCAATAA


Statistics
Matches: 65,  Mismatches: 2, Indels: 2
        0.94            0.03        0.03

Matches are distributed among these distances:
  67    1  0.02
  68   64  0.98

ACGTcount: A:0.42, C:0.14, G:0.15, T:0.29


Consensus pattern (68 bp):   
ATTAGGAGAATGTTCCTCAATGTACTGCATATCAAGGAAACAGTAAAATTCAGTCAATAATTACA
AAT

Found at i:14417 original size:2 final size:2

Alignment explanation


    Indices: 14410--14447  Score: 76
    Period size: 2  Copynumber: 19.0  Consensus size: 2

      14400 TGATTTTAAT

                                                                    
      14410 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   36  1.00

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


Consensus pattern (2 bp):   
TA

Done.