Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016282.1 Corchorus capsularis cultivar CVL-1 contig16303, 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: 9479
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30


Found at i:1148 original size:5 final size:5

Alignment explanation


    Indices: 1138--1169  Score: 57
    Period size: 5  Copynumber: 6.6  Consensus size: 5

       1128 TAAGGGGAAA

                                                   
       1138 AAAAG AAAAG AAAAG AAAAG AAAAG -AAAG AAA
          1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAA

       1170 TCGTCAAATT


Statistics
Matches: 26,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   4    4  0.15
   5   22  0.85

ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00


Consensus pattern (5 bp):   
AAAAG

Found at i:1158 original size:15 final size:14

Alignment explanation


    Indices: 1134--1169  Score: 56
    Period size: 14  Copynumber: 2.6  Consensus size: 14

       1124 GACATAAGGG

                          
       1134 GAAA-AAAAGAAAA
          1 GAAAGAAAAGAAAA

                           
       1147 GAAAAGAAAAGAAAA
          1 G-AAAGAAAAGAAAA

                    
       1162 GAAAGAAA
          1 GAAAGAAA

       1170 TCGTCAAATT


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  13    1  0.05
  14   10  0.48
  15   10  0.48

ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00


Consensus pattern (14 bp):   
GAAAGAAAAGAAAA

Found at i:3184 original size:29 final size:29

Alignment explanation


    Indices: 3104--3184  Score: 99
    Period size: 29  Copynumber: 2.7  Consensus size: 29

       3094 GCTTAATACC

                  *              **        
       3104 CAAATTAGCCCCTTAACTATCCATTTTGGGA
          1 CAAATTGGCCCCTTAACT-T-TTTTTTGGGA

                            *            
       3135 CAAATTGGCCCCTTAATTTTTTTTTGGGA
          1 CAAATTGGCCCCTTAACTTTTTTTTGGGA

                          *      
       3164 CAAATTGGCCCCTTGACTTTT
          1 CAAATTGGCCCCTTAACTTTT

       3185 AAAAACGAGA


Statistics
Matches: 44,  Mismatches: 6, Indels: 2
        0.85            0.12        0.04

Matches are distributed among these distances:
  29   27  0.61
  30    1  0.02
  31   16  0.36

ACGTcount: A:0.23, C:0.23, G:0.15, T:0.38


Consensus pattern (29 bp):   
CAAATTGGCCCCTTAACTTTTTTTTGGGA

Found at i:3912 original size:29 final size:29

Alignment explanation


    Indices: 3875--3932  Score: 98
    Period size: 29  Copynumber: 2.0  Consensus size: 29

       3865 TCTCGTTTTT

                *                        
       3875 AAAAGTTAAGGGGTCAATTTGTCCCAAAA
          1 AAAAATTAAGGGGTCAATTTGTCCCAAAA

                                   *     
       3904 AAAAATTAAGGGGTCAATTTGTCTCAAAA
          1 AAAAATTAAGGGGTCAATTTGTCCCAAAA

       3933 TGGATAGTTA


Statistics
Matches: 27,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  29   27  1.00

ACGTcount: A:0.43, C:0.12, G:0.19, T:0.26


Consensus pattern (29 bp):   
AAAAATTAAGGGGTCAATTTGTCCCAAAA

Found at i:4049 original size:46 final size:46

Alignment explanation


    Indices: 3983--4074  Score: 184
    Period size: 46  Copynumber: 2.0  Consensus size: 46

       3973 AATAGGTGGA

                                                          
       3983 GGAGCCCAACAGGAGCGACATGAGATCACATGTGGTCGGTACTACT
          1 GGAGCCCAACAGGAGCGACATGAGATCACATGTGGTCGGTACTACT

                                                          
       4029 GGAGCCCAACAGGAGCGACATGAGATCACATGTGGTCGGTACTACT
          1 GGAGCCCAACAGGAGCGACATGAGATCACATGTGGTCGGTACTACT

       4075 TTCTTACTGT


Statistics
Matches: 46,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  46   46  1.00

ACGTcount: A:0.28, C:0.24, G:0.30, T:0.17


Consensus pattern (46 bp):   
GGAGCCCAACAGGAGCGACATGAGATCACATGTGGTCGGTACTACT

Found at i:4259 original size:59 final size:59

Alignment explanation


    Indices: 4195--4314  Score: 240
    Period size: 59  Copynumber: 2.0  Consensus size: 59

       4185 AGAACCCTTT

                                                                       
       4195 CCTGGTCTATATTGGTGAGTTGACTCTTCTTTTTAGTATACTAAGGAGCCCGAGTCATG
          1 CCTGGTCTATATTGGTGAGTTGACTCTTCTTTTTAGTATACTAAGGAGCCCGAGTCATG

                                                                       
       4254 CCTGGTCTATATTGGTGAGTTGACTCTTCTTTTTAGTATACTAAGGAGCCCGAGTCATG
          1 CCTGGTCTATATTGGTGAGTTGACTCTTCTTTTTAGTATACTAAGGAGCCCGAGTCATG

              
       4313 CC
          1 CC

       4315 GCGGGATTTC


Statistics
Matches: 61,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  59   61  1.00

ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37


Consensus pattern (59 bp):   
CCTGGTCTATATTGGTGAGTTGACTCTTCTTTTTAGTATACTAAGGAGCCCGAGTCATG

Found at i:4418 original size:23 final size:23

Alignment explanation


    Indices: 4388--4439  Score: 104
    Period size: 23  Copynumber: 2.3  Consensus size: 23

       4378 GATCATAATC

                                   
       4388 AGAAATTCAATTCTTAGTTGAAA
          1 AGAAATTCAATTCTTAGTTGAAA

                                   
       4411 AGAAATTCAATTCTTAGTTGAAA
          1 AGAAATTCAATTCTTAGTTGAAA

                  
       4434 AGAAAT
          1 AGAAAT

       4440 AAAAGTGCAA


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  23   29  1.00

ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33


Consensus pattern (23 bp):   
AGAAATTCAATTCTTAGTTGAAA
Done.