AutoCloner

Multiple sequence alignment - TraesCS1B01G203300

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Download Multiple Sequence Alignment: (Fasta) (Clustal)

BLAST Results

Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

	qseqid	sseqid	percentage.identical	alignment.length	no.mismatch	no.gap.openings	qstart	qend	sstart	send	evalue	bitscore
0	TraesCS1B01G203300	chr1B	100.000	5263	0	0	1	5263	365018305	365023567	0.000000e+00	9720
1	TraesCS1B01G203300	chr1B	99.800	500	1	0	1	500	366290786	366290287	0.000000e+00	918
2	TraesCS1B01G203300	chr1B	98.649	74	0	1	427	500	365013977	365013905	4.280000e-26	130
3	TraesCS1B01G203300	chr1D	95.227	4819	130	32	497	5261	231467735	231462963	0.000000e+00	7533
4	TraesCS1B01G203300	chr1A	95.134	4829	125	35	497	5261	317810678	317815460	0.000000e+00	7515
5	TraesCS1B01G203300	chr7B	99.799	497	0	1	1	496	711537862	711538358	0.000000e+00	911
6	TraesCS1B01G203300	chr7B	99.398	498	1	1	1	496	685273142	685272645	0.000000e+00	902
7	TraesCS1B01G203300	chr7B	100.000	71	0	0	427	497	685277470	685277540	1.190000e-26	132
8	TraesCS1B01G203300	chr7B	100.000	71	0	0	427	497	711533534	711533464	1.190000e-26	132
9	TraesCS1B01G203300	chr2B	99.197	498	2	1	1	496	68607145	68607642	0.000000e+00	896
10	TraesCS1B01G203300	chr2B	87.455	279	35	0	3176	3454	578137511	578137233	6.570000e-84	322
11	TraesCS1B01G203300	chr2B	85.897	156	22	0	2086	2241	578138610	578138455	3.260000e-37	167
12	TraesCS1B01G203300	chr4D	97.791	498	9	1	1	496	182087100	182087597	0.000000e+00	857
13	TraesCS1B01G203300	chr5A	95.960	495	18	1	4	496	221348413	221348907	0.000000e+00	802
14	TraesCS1B01G203300	chr5A	86.885	305	33	6	3177	3479	708807355	708807056	8.450000e-88	335
15	TraesCS1B01G203300	chr2A	88.172	279	33	0	3176	3454	637678932	637678654	3.040000e-87	333
16	TraesCS1B01G203300	chr2A	85.897	156	22	0	2086	2241	637680040	637679885	3.260000e-37	167
17	TraesCS1B01G203300	chr4B	86.799	303	32	7	3177	3475	671632078	671631780	1.090000e-86	331
18	TraesCS1B01G203300	chrUn	87.633	283	31	4	3177	3457	28396958	28397238	5.080000e-85	326
19	TraesCS1B01G203300	chr2D	87.455	279	35	0	3176	3454	492509715	492509437	6.570000e-84	322
20	TraesCS1B01G203300	chr2D	84.713	157	22	2	2086	2241	492510808	492510653	7.060000e-34	156
21	TraesCS1B01G203300	chr6D	86.667	285	33	4	3172	3454	313281969	313281688	1.420000e-80	311
22	TraesCS1B01G203300	chr6D	83.660	153	23	2	2085	2236	313282694	313282543	5.490000e-30	143
23	TraesCS1B01G203300	chr3B	89.510	143	15	0	6	148	620611667	620611809	1.160000e-41	182
24	TraesCS1B01G203300	chr6B	82.051	156	26	2	2082	2236	512872807	512872961	1.190000e-26	132
25	TraesCS1B01G203300	chr6A	82.237	152	27	0	2085	2236	450465984	450465833	1.190000e-26	132

These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

	query	scaffold	start	end	length	rev.comp	avg.bitscore	max.bitscore	avg.percent.identical	query.start	query.end	num_hsp	groupid	homo_length
0	TraesCS1B01G203300	chr1B	365018305	365023567	5262	False	9720.0	9720	100.0000	1	5263	1	chr1B.!!$F1	5262
1	TraesCS1B01G203300	chr1D	231462963	231467735	4772	True	7533.0	7533	95.2270	497	5261	1	chr1D.!!$R1	4764
2	TraesCS1B01G203300	chr1A	317810678	317815460	4782	False	7515.0	7515	95.1340	497	5261	1	chr1A.!!$F1	4764
3	TraesCS1B01G203300	chr2B	578137233	578138610	1377	True	244.5	322	86.6760	2086	3454	2	chr2B.!!$R1	1368
4	TraesCS1B01G203300	chr2A	637678654	637680040	1386	True	250.0	333	87.0345	2086	3454	2	chr2A.!!$R1	1368
5	TraesCS1B01G203300	chr2D	492509437	492510808	1371	True	239.0	322	86.0840	2086	3454	2	chr2D.!!$R1	1368
6	TraesCS1B01G203300	chr6D	313281688	313282694	1006	True	227.0	311	85.1635	2085	3454	2	chr6D.!!$R1	1369

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
327	328	0.034616	GCAGATAGCTTGGCCGATCT	59.965	55.0	1.11	1.11	41.15	2.75	F
1483	1518	0.035056	CTGGAGGCCGGAAATTGTCT	60.035	55.0	5.05	0.00	29.82	3.41	F
1724	1770	0.466124	AGTAAGCTTCAGATCCGGCC	59.534	55.0	0.00	0.00	0.00	6.13	F
1725	1771	0.876342	GTAAGCTTCAGATCCGGCCG	60.876	60.0	21.04	21.04	0.00	6.13	F
2223	2272	0.957395	AGACGTACCGCTTCTTCCGA	60.957	55.0	0.00	0.00	0.00	4.55	F
4036	4376	1.694955	GACGAGGACGAGGACGACTC	61.695	65.0	0.00	0.00	42.66	3.36	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1726	1772	0.552848	TTCTCTGGGATTGATGCCCC	59.447	55.000	0.00	45.4	5.80	R
2394	2569	0.538287	AGAAGCTCAAGTTGCCCACC	60.538	55.000	0.00	0.0	4.61	R
3258	3598	2.245438	CTTCCCAGAGCGGTCCCTTC	62.245	65.000	11.73	0.0	3.46	R
3633	3973	3.569690	CCGCCGCCATTACCGTTC	61.570	66.667	0.00	0.0	3.95	R
4100	4440	0.111061	TCTGATGTTGTTGCTGCCCT	59.889	50.000	0.00	0.0	5.19	R
4937	5304	2.239654	CACCTTTCTTCCTCATGGCCTA	59.760	50.000	3.32	0.0	3.93	R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
20	21	1.751552	GTACGACTAGCATGTACGCC	58.248	55.000	0.00	0.00	30.35	5.68
21	22	0.305617	TACGACTAGCATGTACGCCG	59.694	55.000	0.00	0.00	0.00	6.46
22	23	2.293627	CGACTAGCATGTACGCCGC	61.294	63.158	0.00	0.00	0.00	6.53
23	24	1.949631	GACTAGCATGTACGCCGCC	60.950	63.158	0.00	0.00	0.00	6.13
24	25	2.661866	CTAGCATGTACGCCGCCC	60.662	66.667	0.00	0.00	0.00	6.13
25	26	3.439513	CTAGCATGTACGCCGCCCA	62.440	63.158	0.00	0.00	0.00	5.36
26	27	3.439513	TAGCATGTACGCCGCCCAG	62.440	63.158	0.00	0.00	0.00	4.45
78	79	1.082235	GTCTATACGACGAGGCCGC	60.082	63.158	0.00	0.00	39.95	6.53
79	80	2.254651	CTATACGACGAGGCCGCC	59.745	66.667	0.00	0.00	39.95	6.13
80	81	2.203252	TATACGACGAGGCCGCCT	60.203	61.111	13.16	13.16	39.95	5.52
81	82	2.185103	CTATACGACGAGGCCGCCTC	62.185	65.000	27.17	27.17	46.44	4.70
92	93	3.452786	CCGCCTCGCCTCTCTGAA	61.453	66.667	0.00	0.00	0.00	3.02
93	94	2.103934	CGCCTCGCCTCTCTGAAG	59.896	66.667	0.00	0.00	0.00	3.02
94	95	2.498726	GCCTCGCCTCTCTGAAGG	59.501	66.667	2.66	2.66	39.62	3.46
95	96	2.055042	GCCTCGCCTCTCTGAAGGA	61.055	63.158	9.23	0.00	38.87	3.36
96	97	2.015227	GCCTCGCCTCTCTGAAGGAG	62.015	65.000	9.23	6.66	43.12	3.69
97	98	1.437160	CTCGCCTCTCTGAAGGAGC	59.563	63.158	9.23	0.00	41.60	4.70
98	99	2.015227	CTCGCCTCTCTGAAGGAGCC	62.015	65.000	9.23	0.00	41.60	4.70
99	100	2.498726	GCCTCTCTGAAGGAGCCG	59.501	66.667	9.23	0.00	41.60	5.52
100	101	3.087666	GCCTCTCTGAAGGAGCCGG	62.088	68.421	0.00	0.00	41.60	6.13
101	102	2.498726	CTCTCTGAAGGAGCCGGC	59.501	66.667	21.89	21.89	41.60	6.13
102	103	3.077556	TCTCTGAAGGAGCCGGCC	61.078	66.667	26.15	15.07	41.60	6.13
103	104	4.521062	CTCTGAAGGAGCCGGCCG	62.521	72.222	26.15	21.04	35.08	6.13
105	106	4.821589	CTGAAGGAGCCGGCCGTC	62.822	72.222	26.15	15.79	37.02	4.79
128	129	4.593864	GCCGACGAGCAGGGGATC	62.594	72.222	0.00	0.00	0.00	3.36

Showing 1 to 25 of 279 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
1	2	1.751552	GGCGTACATGCTAGTCGTAC	58.248	55.000	0.00	7.86	33.67	3.67
2	3	0.305617	CGGCGTACATGCTAGTCGTA	59.694	55.000	0.00	0.00	34.52	3.43
3	4	1.063649	CGGCGTACATGCTAGTCGT	59.936	57.895	0.00	0.00	34.52	4.34
4	5	2.293627	GCGGCGTACATGCTAGTCG	61.294	63.158	9.37	4.82	34.52	4.18
5	6	1.949631	GGCGGCGTACATGCTAGTC	60.950	63.158	9.37	0.00	34.52	2.59
6	7	2.106332	GGCGGCGTACATGCTAGT	59.894	61.111	9.37	0.00	34.52	2.57
7	8	2.661866	GGGCGGCGTACATGCTAG	60.662	66.667	9.37	0.00	34.52	3.42
8	9	3.439513	CTGGGCGGCGTACATGCTA	62.440	63.158	9.37	0.00	34.52	3.49
9	10	4.838152	CTGGGCGGCGTACATGCT	62.838	66.667	9.37	0.00	34.52	3.79
60	61	1.082235	GCGGCCTCGTCGTATAGAC	60.082	63.158	0.00	0.00	46.16	2.59
61	62	2.256591	GGCGGCCTCGTCGTATAGA	61.257	63.158	12.87	0.00	38.89	1.98
62	63	2.185103	GAGGCGGCCTCGTCGTATAG	62.185	65.000	31.44	0.00	46.91	1.31
63	64	2.203252	AGGCGGCCTCGTCGTATA	60.203	61.111	17.69	0.00	46.91	1.47
64	65	3.593794	GAGGCGGCCTCGTCGTAT	61.594	66.667	31.44	2.62	46.91	3.06
75	76	3.423162	CTTCAGAGAGGCGAGGCGG	62.423	68.421	0.00	0.00	0.00	6.13
76	77	2.103934	CTTCAGAGAGGCGAGGCG	59.896	66.667	0.00	0.00	0.00	5.52
77	78	2.015227	CTCCTTCAGAGAGGCGAGGC	62.015	65.000	0.00	0.00	46.50	4.70
78	79	2.015227	GCTCCTTCAGAGAGGCGAGG	62.015	65.000	0.00	0.00	46.50	4.63
79	80	1.437160	GCTCCTTCAGAGAGGCGAG	59.563	63.158	0.00	0.00	46.50	5.03
80	81	2.055042	GGCTCCTTCAGAGAGGCGA	61.055	63.158	0.00	0.00	46.50	5.54
81	82	2.498726	GGCTCCTTCAGAGAGGCG	59.501	66.667	0.00	0.00	46.50	5.52
83	84	3.087666	GCCGGCTCCTTCAGAGAGG	62.088	68.421	22.15	0.00	46.50	3.69
84	85	2.498726	GCCGGCTCCTTCAGAGAG	59.501	66.667	22.15	0.00	46.50	3.20
85	86	3.077556	GGCCGGCTCCTTCAGAGA	61.078	66.667	28.56	0.00	46.50	3.10
86	87	4.521062	CGGCCGGCTCCTTCAGAG	62.521	72.222	28.56	2.86	46.29	3.35

Showing 1 to 25 of 307 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.