Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006348.1 Hibiscus syriacus cultivar Beakdansim tig00015184_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: 90833
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:3306 original size:59 final size:58
Alignment explanation
Indices: 3205--3371 Score: 160
Period size: 59 Copynumber: 2.8 Consensus size: 58
3195 AAATCGATAG
* * * * *
3205 TTTGGGAAAG-AATTGAAATGTTCAAAAGTATGGGGACCAATTTAGAATAG-GTTCATAC
1 TTTGGGAATGAAATTG-AATATTCAAAAGTTTGAGGACCAATTTAGAATAGAG-TCATAA
* * *
3263 TTTGGGAATGAAATTATAATATTCAAAAGTTTGAGGACTAATTTAGAATGAGAGTCCTAA
1 TTTGGGAATGAAATT-GAATATTCAAAAGTTTGAGGACCAATTTAGAAT-AGAGTCATAA
* * * *
3323 TTTGGGGATGAAATTGAATGTTTAAAAGTTTAGAGG-CCAATTTAAAATA
1 TTTGGGAATGAAATTGAATATTCAAAAGTTT-GAGGACCAATTTAGAATA
3372 AAAGTTATAG
Statistics
Matches: 90, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
58 10 0.11
59 55 0.61
60 24 0.27
61 1 0.01
ACGTcount: A:0.39, C:0.07, G:0.22, T:0.32
Consensus pattern (58 bp):
TTTGGGAATGAAATTGAATATTCAAAAGTTTGAGGACCAATTTAGAATAGAGTCATAA
Found at i:3644 original size:17 final size:18
Alignment explanation
Indices: 3622--3655 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
3612 GTTAATCCCC
3622 TTTTTCTTTTT-TTCTCA
1 TTTTTCTTTTTCTTCTCA
3639 TTTTTCTTTTTCTTCTC
1 TTTTTCTTTTTCTTCTC
3656 TCCTCACATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTTCTTTTTCTTCTCA
Found at i:3649 original size:18 final size:17
Alignment explanation
Indices: 3622--3655 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
3612 GTTAATCCCC
*
3622 TTTTTCTTTTTTTCTCA
1 TTTTTCTTTTCTTCTCA
3639 TTTTTCTTTTTCTTCTC
1 TTTTTC-TTTTCTTCTC
3656 TCCTCACATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTCTTTTCTTCTCA
Found at i:5538 original size:18 final size:19
Alignment explanation
Indices: 5500--5540 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
5490 ATGTGATTCA
5500 AATTTGATAATAAAAAAAG
1 AATTTGATAATAAAAAAAG
* *
5519 AATTTGA-AATGAAAACAG
1 AATTTGATAATAAAAAAAG
5537 AATT
1 AATT
5541 AATGAGGTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.59, C:0.02, G:0.12, T:0.27
Consensus pattern (19 bp):
AATTTGATAATAAAAAAAG
Found at i:10834 original size:16 final size:16
Alignment explanation
Indices: 10815--10852 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
10805 AATAAAAATA
*
10815 ATTTTAAATTTTTTAT
1 ATTTTAAATATTTTAT
10831 ATTTT--ATATTTTAT
1 ATTTTAAATATTTTAT
10845 ATTTTAAA
1 ATTTTAAA
10853 ATTAAGTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
14 13 0.68
16 6 0.32
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
ATTTTAAATATTTTAT
Found at i:10907 original size:22 final size:22
Alignment explanation
Indices: 10860--10907 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
10850 AAAATTAAGT
*
10860 TTAAAATATGATTTAAAAAATA
1 TTAAAATATGAATTAAAAAATA
10882 -TAAAA-ATGAATTATAAAAATA
1 TTAAAATATGAATTA-AAAAATA
10903 TTAAA
1 TTAAA
10908 TTATAAAAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 7 0.30
21 12 0.52
22 4 0.17
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (22 bp):
TTAAAATATGAATTAAAAAATA
Found at i:10946 original size:21 final size:21
Alignment explanation
Indices: 10922--10982 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
10912 AAAAGTTTAA
10922 TTTAATATTTACTTTTATATT
1 TTTAATATTTACTTTTATATT
* ** *
10943 TTTAAGATTTACAAATTGTATT
1 TTTAATATTTAC-TTTTATATT
10965 TTT-ATATTTACTTTTATA
1 TTTAATATTTACTTTTATA
10983 ATTCAATATT
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
20 4 0.13
21 18 0.58
22 9 0.29
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.61
Consensus pattern (21 bp):
TTTAATATTTACTTTTATATT
Found at i:11010 original size:14 final size:16
Alignment explanation
Indices: 10976--11012 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
10966 TTATATTTAC
10976 TTTTATAATTCAATAT
1 TTTTATAATTCAATAT
10992 TTTTATAATTC-AT-T
1 TTTTATAATTCAATAT
11006 TTTTATA
1 TTTTATA
11013 TTTAAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 8 0.38
15 2 0.10
16 11 0.52
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTATAATTCAATAT
Found at i:11034 original size:19 final size:19
Alignment explanation
Indices: 11006--11068 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
10996 ATAATTCATT
*
11006 TTTTATATTTAAAATTATA
1 TTTTAAATTTAAAATTATA
* *
11025 TTTTAAATTTAATATTAAA
1 TTTTAAATTTAAAATTATA
* *
11044 TATAAAATTTTTAAAATTAT-
1 TTTTAAA--TTTAAAATTATA
11064 TTTTA
1 TTTTA
11069 TTGGAAATAT
Statistics
Matches: 33, Mismatches: 9, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
19 21 0.64
20 3 0.09
21 9 0.27
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTTAAATTTAAAATTATA
Found at i:11418 original size:33 final size:32
Alignment explanation
Indices: 11377--11443 Score: 98
Period size: 33 Copynumber: 2.1 Consensus size: 32
11367 TAATTGGTGT
11377 AAATATTTAATTAAATTTAATTAAAAGAATTA
1 AAATATTTAATTAAATTTAATTAAAAGAATTA
* **
11409 AAATAATTTAATTAAATTTATTTAATTGAATTA
1 AAAT-ATTTAATTAAATTTAATTAAAAGAATTA
11442 AA
1 AA
11444 CTAGTGACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
32 4 0.13
33 27 0.87
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (32 bp):
AAATATTTAATTAAATTTAATTAAAAGAATTA
Found at i:15539 original size:34 final size:34
Alignment explanation
Indices: 15472--15539 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
15462 GGAATTCAAG
* **
15472 CAGTGGAATTCAAGAGATGAAGTAAGACTTAAGA
1 CAGTGGAATTCAAGAGAAGAAGTAAGAAGTAAGA
*
15506 CAGTGGAATTCAAGCAGAAGAAG-ATGAAGTAAGA
1 CAGTGGAATTCAAG-AGAAGAAGTAAGAAGTAAGA
15540 GAAAGTTAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
34 22 0.76
35 7 0.24
ACGTcount: A:0.46, C:0.09, G:0.28, T:0.18
Consensus pattern (34 bp):
CAGTGGAATTCAAGAGAAGAAGTAAGAAGTAAGA
Found at i:15817 original size:14 final size:15
Alignment explanation
Indices: 15788--15820 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
15778 AGATTTAAGA
15788 TTTAAATGTTTAGGG
1 TTTAAATGTTTAGGG
*
15803 TTTAAA-GTTTGGGG
1 TTTAAATGTTTAGGG
15817 TTTA
1 TTTA
15821 GGTTTATGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.48
Consensus pattern (15 bp):
TTTAAATGTTTAGGG
Found at i:15958 original size:2 final size:2
Alignment explanation
Indices: 15953--16071 Score: 58
Period size: 2 Copynumber: 68.5 Consensus size: 2
15943 TTAATATAAA
* *
15953 AT AT AT A- AA AT AT -T AT AT AT AT A- AT -T A- AT AT A- AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
15989 AT AT A- AA AT AT -T AT AT AT GT AT A- AT -T A- AT AT A- AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
16025 AT AT A- AA AT AT -T AT AT AT AT AT A- AT -T A- AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16061 AT AT AT AT AT A
1 AT AT AT AT AT A
16072 ATTGGGTCGG
Statistics
Matches: 92, Mismatches: 7, Indels: 36
0.68 0.05 0.27
Matches are distributed among these distances:
1 18 0.20
2 74 0.80
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (2 bp):
AT
Found at i:16006 original size:36 final size:36
Alignment explanation
Indices: 15936--16065 Score: 228
Period size: 36 Copynumber: 3.7 Consensus size: 36
15926 GGGTTTGTAT
15936 TATATAATTAATATAAAATATATAAAATA-T-TATA
1 TATATAATTAATATAAAATATATAAAATATTATATA
15970 TATATAATTAATATAAAATATATAAAATATTATATA
1 TATATAATTAATATAAAATATATAAAATATTATATA
*
16006 TGTATAATTAATATAAAATATATAAAATATTATATA
1 TATATAATTAATATAAAATATATAAAATATTATATA
*
16042 TATATAATTAATATAATATATATA
1 TATATAATTAATATAAAATATATA
16066 TATATAATTG
Statistics
Matches: 91, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
34 29 0.32
35 1 0.01
36 61 0.67
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (36 bp):
TATATAATTAATATAAAATATATAAAATATTATATA
Found at i:17803 original size:17 final size:18
Alignment explanation
Indices: 17770--17806 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
17760 TTGAAAAACC
17770 GGATGTAGAGAACAACGA
1 GGATGTAGAGAACAACGA
17788 GGATG-AGAGGAA-AACGA
1 GGATGTAGA-GAACAACGA
17805 GG
1 GG
17807 CTTGGTTCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.43, C:0.08, G:0.41, T:0.08
Consensus pattern (18 bp):
GGATGTAGAGAACAACGA
Found at i:28161 original size:12 final size:12
Alignment explanation
Indices: 28144--28168 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28134 GTGGACAATC
28144 TGTAAAGTCCTA
1 TGTAAAGTCCTA
28156 TGTAAAGTCCTA
1 TGTAAAGTCCTA
28168 T
1 T
28169 AGATGTAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (12 bp):
TGTAAAGTCCTA
Found at i:28854 original size:5 final size:5
Alignment explanation
Indices: 28834--28869 Score: 54
Period size: 5 Copynumber: 6.8 Consensus size: 5
28824 ATTTCTAAAC
28834 AAATGA AAACTA AAATA AAATA AAATA AAATA AAAT
1 AAAT-A AAA-TA AAATA AAATA AAATA AAATA AAAT
28870 GGTGGGTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 21 0.72
6 7 0.24
7 1 0.03
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:28862 original size:15 final size:17
Alignment explanation
Indices: 28834--28870 Score: 60
Period size: 15 Copynumber: 2.3 Consensus size: 17
28824 ATTTCTAAAC
28834 AAATGAAAACTAAAATA
1 AAATGAAAACTAAAATA
28851 AAAT-AAAA-TAAAATA
1 AAATGAAAACTAAAATA
28866 AAATG
1 AAATG
28871 GTGGGTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 11 0.58
16 4 0.21
17 4 0.21
ACGTcount: A:0.73, C:0.03, G:0.05, T:0.19
Consensus pattern (17 bp):
AAATGAAAACTAAAATA
Found at i:34869 original size:22 final size:21
Alignment explanation
Indices: 34808--34861 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
34798 AGAGAAACAT
* *
34808 ATTATAAATA-TATCTTTTAA
1 ATTATAAATATTTTATTTTAA
34828 A-TA-AAATATTATTATTTTAA
1 ATTATAAATATT-TTATTTTAA
34848 ATTATAAATATTTT
1 ATTATAAATATTTT
34862 TTTATTAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
18 5 0.18
19 3 0.11
20 9 0.32
21 4 0.14
22 7 0.25
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
ATTATAAATATTTTATTTTAA
Found at i:35311 original size:2 final size:2
Alignment explanation
Indices: 35304--35333 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
35294 CCATACAATA
35304 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35334 CAATATTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49245 original size:18 final size:19
Alignment explanation
Indices: 49210--49246 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
49200 CACGGAATGT
49210 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
49230 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
49247 GGATTACTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:60275 original size:4 final size:4
Alignment explanation
Indices: 60268--60338 Score: 74
Period size: 4 Copynumber: 18.2 Consensus size: 4
60258 TCCATGCATG
* * * *
60268 TGTA TGTA --TA TGTG TGTA TCTA TGTA TGTG TGTG TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
* *
60314 TGCA TGCA TGTA TGTA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA T
60339 CAACATTTTA
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
2 2 0.04
4 55 0.96
ACGTcount: A:0.21, C:0.04, G:0.27, T:0.48
Consensus pattern (4 bp):
TGTA
Found at i:66186 original size:2 final size:2
Alignment explanation
Indices: 66179--66208 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
66169 TTCAATTTGA
66179 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
66209 CATTCTGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:75186 original size:26 final size:26
Alignment explanation
Indices: 75132--75188 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
75122 ATATCTGAAA
**
75132 TTTTT-CATTAAAATAAACTCATATT
1 TTTTTACATTAAAATAAACTCATAAC
*
75157 TTTTTACATTAAAAT-AATTCAATAAC
1 TTTTTACATTAAAATAAACTC-ATAAC
75183 TTTTTA
1 TTTTTA
75189 AAATTATACT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 9 0.33
26 18 0.67
ACGTcount: A:0.40, C:0.11, G:0.00, T:0.49
Consensus pattern (26 bp):
TTTTTACATTAAAATAAACTCATAAC
Found at i:76685 original size:6 final size:6
Alignment explanation
Indices: 76674--76699 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
76664 CGATCGCTTG
76674 CAATCA CAATCA CAATCA CAATCA CA
1 CAATCA CAATCA CAATCA CAATCA CA
76700 CTTGACGCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.35, G:0.00, T:0.15
Consensus pattern (6 bp):
CAATCA
Found at i:77136 original size:23 final size:24
Alignment explanation
Indices: 77085--77148 Score: 57
Period size: 23 Copynumber: 2.9 Consensus size: 24
77075 TTAGATTATG
* *
77085 ACATCAAT-TATTTTTTA-AAATG
1 ACATCAATATTTTTTTTATAAATA
*
77107 ACGTCAATATTTTTTTTATAAA-A
1 ACATCAATATTTTTTTTATAAATA
*
77130 ACATCAA-A-TTTATTTATAA
1 ACATCAATATTTTTTTTATAA
77149 TAATATTATA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
21 10 0.29
22 8 0.23
23 14 0.40
24 3 0.09
ACGTcount: A:0.42, C:0.09, G:0.03, T:0.45
Consensus pattern (24 bp):
ACATCAATATTTTTTTTATAAATA
Found at i:84946 original size:16 final size:16
Alignment explanation
Indices: 84925--84957 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
84915 AAATTAAAAG
84925 AGTTTTACACTATGTA
1 AGTTTTACACTATGTA
84941 AGTTTTACACTATGTA
1 AGTTTTACACTATGTA
84957 A
1 A
84958 ATGGATCATA
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:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (16 bp):
AGTTTTACACTATGTA
Found at i:85444 original size:2 final size:2
Alignment explanation
Indices: 85437--85466 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
85427 TTATCCCAAA
85437 AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
85467 CTATTATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:89714 original size:17 final size:17
Alignment explanation
Indices: 89692--89727 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
89682 CCTTAATTTT
89692 TACAACCAAGTATTTAA
1 TACAACCAAGTATTTAA
89709 TACAACCAAGTATTTAA
1 TACAACCAAGTATTTAA
89726 TA
1 TA
89728 TCAAGGGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.47, C:0.17, G:0.06, T:0.31
Consensus pattern (17 bp):
TACAACCAAGTATTTAA
Done.