Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002450.1 Hibiscus syriacus cultivar Beakdansim tig00005020_pilon, 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: 54656
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:2718 original size:17 final size:17
Alignment explanation
Indices: 2684--2726 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
2674 TATGCACACG
*
2684 TGATATGAGAAGAAGAA
1 TGATATGAGAACAAGAA
* *
2701 TGATATGAGCACATGAA
1 TGATATGAGAACAAGAA
2718 T-ATATGAGA
1 TGATATGAGA
2727 GCTTCCAAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.47, C:0.05, G:0.26, T:0.23
Consensus pattern (17 bp):
TGATATGAGAACAAGAA
Found at i:5253 original size:24 final size:20
Alignment explanation
Indices: 5221--5278 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
5211 GCGTGGATAG
5221 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
*
5245 TGCATCGATACACTGTAGAA
1 TGCATCGATGCACTGTAGAA
*
5265 TGTATCGATGCACT
1 TGCATCGATGCACT
5279 TCAAGGGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 16 0.52
22 1 0.03
23 2 0.06
24 12 0.39
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:10638 original size:16 final size:17
Alignment explanation
Indices: 10613--10646 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
10603 ATTTATATAA
10613 TATTTCAATAT-TATGT
1 TATTTCAATATCTATGT
*
10629 TATTTTAATATCTATGT
1 TATTTCAATATCTATGT
10646 T
1 T
10647 GAATATAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.59
Consensus pattern (17 bp):
TATTTCAATATCTATGT
Found at i:16065 original size:3 final size:3
Alignment explanation
Indices: 16048--16103 Score: 75
Period size: 3 Copynumber: 20.0 Consensus size: 3
16038 CTATAAAAGC
16048 ATT A-T ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
16093 -TT ATT AAT ATT
1 ATT ATT ATT ATT
16104 TTTACAGGCT
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
2 8 0.17
3 39 0.83
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:17425 original size:3 final size:3
Alignment explanation
Indices: 17412--17454 Score: 63
Period size: 3 Copynumber: 14.7 Consensus size: 3
17402 TTGTATATGT
17412 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TT
17455 TTCTTTCTGA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 4 0.11
3 30 0.81
4 3 0.08
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (3 bp):
TTA
Found at i:21466 original size:203 final size:202
Alignment explanation
Indices: 21106--21573 Score: 498
Period size: 203 Copynumber: 2.3 Consensus size: 202
21096 GAATTGTTCG
* * * * **
21106 CAACATAGCTCAAGGCGAGAAGGGCTATCTGTTAACG-AGAACTTTCGAGTTCAATTTCATTCGG
1 CAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAACGAAAAACTTTCGAGTTCGATTCCATTCAA
* * * * * * *
21170 CTTGAAGGCTTATCAACCGTACAGTAGCAGCGATATACTACTTTTAAGTTGAAGTTTAAACTGAG
66 CTCGAA-GATTATCAACCGTACAGTAGCAACAAGATACTACTTTTAAGTTGAAGCTCAAACTGAG
* * * * * *
21235 GTTTTTAAGTCAATAAGAAAACCTGGGATTGGCTACAATTTAGTAAC-ACGAAACTATCTCTCAG
130 GTCTTTAAGTCAAGAAGAAAACCTGGGATGGGCTACAATTTAGCAACAACG-AACTATATCCCAG
*
21299 TCGAATTTA
194 TCAAATTTA
*
21308 CAACATAGCTCAAGGCGAGAAGGGCTATTTGTCAACGAAAAACTTTCGAGTTCGATTCCATTCAA
1 CAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAACGAAAAACTTTCGAGTTCGATTCCATTCAA
* ** **
21373 CTCGATA-ATATATCAACTGTATGGTAGCAACAAGGA-ACTACTTTTTGGTTGAAGCTCAAACTG
66 CTCGA-AGAT-TATCAACCGTACAGTAGCAACAA-GATACTACTTTTAAGTTGAAGCTCAAACTG
** * *
21436 AGGTCTTTAAGTCAAGAAGAAGAA-CTGGGATGGGCTGTAATTTAGCCACAATGAACTATATCCC
128 AGGTCTTTAAGTCAAGAAGAA-AACCTGGGATGGGCTACAATTTAGCAACAACGAACTATATCCC
21500 AGTCAAATTTA
192 AGTCAAATTTA
** * * ** * *
21511 CAGTATAGCTCAAGGAGAGAATGATTATCTGTCAAC-AAAAACCTTCGAGTTCGATTCTATTCA
1 CAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAACGAAAAACTTTCGAGTTCGATTCCATTCA
21574 GCTCAAGGGA
Statistics
Matches: 221, Mismatches: 39, Indels: 12
0.81 0.14 0.04
Matches are distributed among these distances:
202 61 0.28
203 154 0.70
204 6 0.03
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (202 bp):
CAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAACGAAAAACTTTCGAGTTCGATTCCATTCAA
CTCGAAGATTATCAACCGTACAGTAGCAACAAGATACTACTTTTAAGTTGAAGCTCAAACTGAGG
TCTTTAAGTCAAGAAGAAAACCTGGGATGGGCTACAATTTAGCAACAACGAACTATATCCCAGTC
AAATTTA
Found at i:22154 original size:2 final size:2
Alignment explanation
Indices: 22149--22187 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
22139 ACCCAGACAA
*
22149 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
22188 CAATAAAGCT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:23213 original size:21 final size:21
Alignment explanation
Indices: 23189--23228 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
23179 CGTGTTGAAG
23189 AATTCAAGA-TCAAGAATCAGA
1 AATTC-AGATTCAAGAATCAGA
*
23210 AATTCAGATTCCAGAATCA
1 AATTCAGATTCAAGAATCA
23229 AGAGTCATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.47, C:0.17, G:0.12, T:0.23
Consensus pattern (21 bp):
AATTCAGATTCAAGAATCAGA
Found at i:24501 original size:3 final size:3
Alignment explanation
Indices: 24484--24546 Score: 96
Period size: 3 Copynumber: 22.0 Consensus size: 3
24474 CTACTAAAAC
24484 ATT A-T ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
24530 ATT ATT -TT ATT AAT ATT
1 ATT ATT ATT ATT ATT ATT
24547 TTTTCATGCC
Statistics
Matches: 55, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
2 6 0.11
3 49 0.89
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:25145 original size:20 final size:20
Alignment explanation
Indices: 25116--25154 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
25106 AGAGCTCATA
*
25116 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
25136 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
25155 GTGGTGAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:26590 original size:19 final size:20
Alignment explanation
Indices: 26553--26593 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
26543 CATCAGATAA
26553 TTTCCACAACATTCATTCATT
1 TTTCCACAACATT-ATTCATT
*
26574 TTTCCATAACATT-TTCATT
1 TTTCCACAACATTATTCATT
26593 T
1 T
26594 GCAAATGACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
21 12 0.63
ACGTcount: A:0.27, C:0.24, G:0.00, T:0.49
Consensus pattern (20 bp):
TTTCCACAACATTATTCATT
Found at i:28892 original size:13 final size:13
Alignment explanation
Indices: 28870--28905 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
28860 AGCAACAACG
*
28870 AAGACAATGCTGC
1 AAGACCATGCTGC
28883 AAGACCATGCTGC
1 AAGACCATGCTGC
28896 AAGACCATGC
1 AAGACCATGC
28906 AACCTCTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.36, C:0.28, G:0.22, T:0.14
Consensus pattern (13 bp):
AAGACCATGCTGC
Found at i:30719 original size:12 final size:12
Alignment explanation
Indices: 30702--30729 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
30692 ACCGTTCATC
30702 GATCAAATGCTG
1 GATCAAATGCTG
30714 GATCAAATGCTG
1 GATCAAATGCTG
30726 GATC
1 GATC
30730 GACTTGCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (12 bp):
GATCAAATGCTG
Found at i:34098 original size:16 final size:16
Alignment explanation
Indices: 34077--34109 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
34067 GTTAAGCATG
34077 GACTTGATACAAACAC
1 GACTTGATACAAACAC
34093 GACTTGATACAAACAC
1 GACTTGATACAAACAC
34109 G
1 G
34110 CACACACCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.24, G:0.15, T:0.18
Consensus pattern (16 bp):
GACTTGATACAAACAC
Found at i:36824 original size:4 final size:4
Alignment explanation
Indices: 36802--36838 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
36792 TTTGTATATG
*
36802 TTTA TTTA ATTA -TTA -TTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
36839 TCTTTCTGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
3 6 0.19
4 25 0.81
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:42504 original size:4 final size:4
Alignment explanation
Indices: 42495--42529 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
42485 ACTGCTAATT
* *
42495 TTTA TTTA TTTC TTTA CTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
42530 TATGTTCGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:44304 original size:16 final size:16
Alignment explanation
Indices: 44285--44315 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
44275 TTTTTAACTA
*
44285 ATTGCTTTTTGATTTT
1 ATTGCTTTTAGATTTT
44301 ATTGCTTTTAGATTT
1 ATTGCTTTTAGATTT
44316 GAACATATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.06, G:0.13, T:0.65
Consensus pattern (16 bp):
ATTGCTTTTAGATTTT
Done.