AutoCloner

Multiple sequence alignment - TraesCS3B01G472300

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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	TraesCS3B01G472300	chr3B	100.000	2447	0	0	1	2447	720975088	720972642	0.000000e+00	4519
1	TraesCS3B01G472300	chr3B	97.192	2137	58	2	312	2447	27415122	27417257	0.000000e+00	3613
2	TraesCS3B01G472300	chr3B	97.192	2137	57	2	312	2447	751971545	751969411	0.000000e+00	3611
3	TraesCS3B01G472300	chr3B	84.566	311	38	3	1	311	710181207	710181507	1.420000e-77	300
4	TraesCS3B01G472300	chr6B	97.286	2137	53	4	312	2447	46332884	46335016	0.000000e+00	3620
5	TraesCS3B01G472300	chr1B	97.240	2138	57	2	312	2447	679286303	679284166	0.000000e+00	3620
6	TraesCS3B01G472300	chr4A	97.056	2140	59	3	310	2447	700664557	700666694	0.000000e+00	3600
7	TraesCS3B01G472300	chr4B	97.100	2138	55	4	311	2447	653996644	653998775	0.000000e+00	3598
8	TraesCS3B01G472300	chr4B	97.055	2139	58	3	312	2447	88998638	88996502	0.000000e+00	3596
9	TraesCS3B01G472300	chr7B	97.052	2137	60	2	312	2447	609817089	609819223	0.000000e+00	3594
10	TraesCS3B01G472300	chr5B	97.052	2137	60	3	312	2447	611821847	611819713	0.000000e+00	3594
11	TraesCS3B01G472300	chr5B	82.692	312	30	11	1	312	577251569	577251282	3.120000e-64	255
12	TraesCS3B01G472300	chr2B	86.538	312	42	0	1	312	621066545	621066856	6.480000e-91	344
13	TraesCS3B01G472300	chr4D	84.899	298	23	6	15	312	397499627	397499902	5.150000e-72	281
14	TraesCS3B01G472300	chr5D	81.847	314	46	4	1	312	515799579	515799275	1.120000e-63	254
15	TraesCS3B01G472300	chr5A	80.449	312	43	9	1	312	624802523	624802230	3.170000e-54	222
16	TraesCS3B01G472300	chr7D	89.032	155	17	0	1	155	53539153	53538999	2.480000e-45	193
17	TraesCS3B01G472300	chr7D	91.791	134	9	2	44	176	477863735	477863603	4.160000e-43	185
18	TraesCS3B01G472300	chr7D	87.919	149	18	0	1	149	135339179	135339031	2.500000e-40	176
19	TraesCS3B01G472300	chr2D	94.017	117	7	0	196	312	104269740	104269624	6.950000e-41	178
20	TraesCS3B01G472300	chr6D	90.833	120	11	0	1	120	290313696	290313577	7.000000e-36	161
21	TraesCS3B01G472300	chr3D	83.673	147	23	1	164	309	116339089	116339235	1.180000e-28	137

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	TraesCS3B01G472300	chr3B	720972642	720975088	2446	True	4519	4519	100.000	1	2447	1	chr3B.!!$R1	2446
1	TraesCS3B01G472300	chr3B	27415122	27417257	2135	False	3613	3613	97.192	312	2447	1	chr3B.!!$F1	2135
2	TraesCS3B01G472300	chr3B	751969411	751971545	2134	True	3611	3611	97.192	312	2447	1	chr3B.!!$R2	2135
3	TraesCS3B01G472300	chr6B	46332884	46335016	2132	False	3620	3620	97.286	312	2447	1	chr6B.!!$F1	2135
4	TraesCS3B01G472300	chr1B	679284166	679286303	2137	True	3620	3620	97.240	312	2447	1	chr1B.!!$R1	2135
5	TraesCS3B01G472300	chr4A	700664557	700666694	2137	False	3600	3600	97.056	310	2447	1	chr4A.!!$F1	2137
6	TraesCS3B01G472300	chr4B	653996644	653998775	2131	False	3598	3598	97.100	311	2447	1	chr4B.!!$F1	2136
7	TraesCS3B01G472300	chr4B	88996502	88998638	2136	True	3596	3596	97.055	312	2447	1	chr4B.!!$R1	2135
8	TraesCS3B01G472300	chr7B	609817089	609819223	2134	False	3594	3594	97.052	312	2447	1	chr7B.!!$F1	2135
9	TraesCS3B01G472300	chr5B	611819713	611821847	2134	True	3594	3594	97.052	312	2447	1	chr5B.!!$R2	2135

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
55	56	0.462759	CTCATTCCTCCAGTTCGGCC	60.463	60.0	0.0	0.0	33.14	6.13	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1954	1964	0.099968	GTTGCAGCATCATCGTGCAT	59.9	50.0	0.0	0.0	46.18	3.96	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)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
36	37	8.634475	AAAACTGTCAAACTGAAATAAAGAGC	57.366	30.769	0.00	0.00	0.00	4.09
37	38	7.573968	AACTGTCAAACTGAAATAAAGAGCT	57.426	32.000	0.00	0.00	0.00	4.09
38	39	7.195839	ACTGTCAAACTGAAATAAAGAGCTC	57.804	36.000	5.27	5.27	0.00	4.09
39	40	6.767902	ACTGTCAAACTGAAATAAAGAGCTCA	59.232	34.615	17.77	0.00	0.00	4.26
40	41	7.446625	ACTGTCAAACTGAAATAAAGAGCTCAT	59.553	33.333	17.77	0.00	0.00	2.90
41	42	8.169977	TGTCAAACTGAAATAAAGAGCTCATT	57.830	30.769	17.77	13.37	0.00	2.57
42	43	8.292448	TGTCAAACTGAAATAAAGAGCTCATTC	58.708	33.333	17.77	11.91	0.00	2.67
43	44	7.752686	GTCAAACTGAAATAAAGAGCTCATTCC	59.247	37.037	17.77	0.00	0.00	3.01
44	45	7.667219	TCAAACTGAAATAAAGAGCTCATTCCT	59.333	33.333	17.77	0.00	0.00	3.36
45	46	7.622893	AACTGAAATAAAGAGCTCATTCCTC	57.377	36.000	17.77	8.32	0.00	3.71
46	47	6.118852	ACTGAAATAAAGAGCTCATTCCTCC	58.881	40.000	17.77	2.22	0.00	4.30
47	48	6.065976	TGAAATAAAGAGCTCATTCCTCCA	57.934	37.500	17.77	4.77	0.00	3.86
48	49	6.118170	TGAAATAAAGAGCTCATTCCTCCAG	58.882	40.000	17.77	0.00	0.00	3.86
49	50	5.707066	AATAAAGAGCTCATTCCTCCAGT	57.293	39.130	17.77	0.00	0.00	4.00
50	51	5.707066	ATAAAGAGCTCATTCCTCCAGTT	57.293	39.130	17.77	0.00	0.00	3.16
51	52	3.625649	AAGAGCTCATTCCTCCAGTTC	57.374	47.619	17.77	0.00	0.00	3.01
52	53	1.480137	AGAGCTCATTCCTCCAGTTCG	59.520	52.381	17.77	0.00	0.00	3.95
53	54	0.539051	AGCTCATTCCTCCAGTTCGG	59.461	55.000	0.00	0.00	0.00	4.30
54	55	1.092345	GCTCATTCCTCCAGTTCGGC	61.092	60.000	0.00	0.00	33.14	5.54
55	56	0.462759	CTCATTCCTCCAGTTCGGCC	60.463	60.000	0.00	0.00	33.14	6.13
56	57	1.815421	CATTCCTCCAGTTCGGCCG	60.815	63.158	22.12	22.12	33.14	6.13
57	58	3.682292	ATTCCTCCAGTTCGGCCGC	62.682	63.158	23.51	7.63	33.14	6.53
74	75	4.676951	CTGCCGCCCCTTTTCCCA	62.677	66.667	0.00	0.00	0.00	4.37
75	76	4.676951	TGCCGCCCCTTTTCCCAG	62.677	66.667	0.00	0.00	0.00	4.45
107	108	4.953868	CACGCCGGTCACGTCCAA	62.954	66.667	1.90	0.00	42.96	3.53
108	109	4.955774	ACGCCGGTCACGTCCAAC	62.956	66.667	1.90	0.00	40.28	3.77
111	112	4.692475	CCGGTCACGTCCAACCCC	62.692	72.222	0.00	0.00	38.78	4.95
113	114	3.932483	GGTCACGTCCAACCCCGT	61.932	66.667	0.00	0.00	37.90	5.28
114	115	2.356673	GTCACGTCCAACCCCGTC	60.357	66.667	0.00	0.00	34.59	4.79
115	116	3.980989	TCACGTCCAACCCCGTCG	61.981	66.667	0.00	0.00	34.59	5.12
136	137	3.818787	GCAACCCATCGCCTGCAG	61.819	66.667	6.78	6.78	34.87	4.41
137	138	3.136123	CAACCCATCGCCTGCAGG	61.136	66.667	29.34	29.34	38.53	4.85
239	240	4.873129	CCGTGCCCATCCTCGTCG	62.873	72.222	0.00	0.00	0.00	5.12
240	241	4.873129	CGTGCCCATCCTCGTCGG	62.873	72.222	0.00	0.00	0.00	4.79
244	245	4.530857	CCCATCCTCGTCGGCCAC	62.531	72.222	2.24	0.00	0.00	5.01
245	246	3.770040	CCATCCTCGTCGGCCACA	61.770	66.667	2.24	0.00	0.00	4.17
246	247	2.509336	CATCCTCGTCGGCCACAC	60.509	66.667	2.24	0.00	0.00	3.82
247	248	3.771160	ATCCTCGTCGGCCACACC	61.771	66.667	2.24	0.00	0.00	4.16
266	267	4.813526	CGTCGCCTCCGTCGTCTG	62.814	72.222	0.00	0.00	40.23	3.51
489	490	1.770749	TTCCGGTTGGTGGGACGAAT	61.771	55.000	0.00	0.00	36.30	3.34
1024	1030	4.781616	TGGTATCCGCCCCCGTCA	62.782	66.667	0.00	0.00	0.00	4.35
1179	1187	3.732048	ATTCCAACCGACCCTATTGTT	57.268	42.857	0.00	0.00	0.00	2.83
1274	1283	5.889853	AGATGATATTGGAGTTGCATGTTGT	59.110	36.000	0.00	0.00	0.00	3.32
1377	1386	3.557898	CCGAGGCTTGGTATCATTATGCT	60.558	47.826	13.06	0.00	0.00	3.79
1487	1496	9.836864	TTAATTAATTTAGATGCTCTGCAGAGA	57.163	29.630	41.20	27.44	43.65	3.10
1666	1676	0.105964	CGGTTCAAGACACACCTCCA	59.894	55.000	0.00	0.00	0.00	3.86
1717	1727	0.183492	AGTGGCTGAGGCAAACAAGA	59.817	50.000	11.29	0.00	40.46	3.02
1733	1743	7.870445	GGCAAACAAGAAGAATGGTTTTATGTA	59.130	33.333	0.00	0.00	31.57	2.29
1806	1816	1.004745	CTCCACACCCACCTGCTTTAT	59.995	52.381	0.00	0.00	0.00	1.40
1826	1836	1.331214	AAGGGTTTCATGCCACACTG	58.669	50.000	0.03	0.00	0.00	3.66
1861	1871	1.379527	GCACGGAGAAATAGGGGTTG	58.620	55.000	0.00	0.00	0.00	3.77
1899	1909	6.091441	GCAAAGAAGAAGAGTACGATGACAAT	59.909	38.462	0.00	0.00	0.00	2.71
1921	1931	0.618107	TGTGCCCCCTGAATACGGTA	60.618	55.000	0.00	0.00	0.00	4.02
1951	1961	3.390967	TGAACATCAAGAGGAACCAGACA	59.609	43.478	0.00	0.00	0.00	3.41
1954	1964	5.762179	ACATCAAGAGGAACCAGACAATA	57.238	39.130	0.00	0.00	0.00	1.90
2088	2098	5.220854	CGAAAGTCAAAAGGAGAAGCTGAAA	60.221	40.000	0.00	0.00	0.00	2.69
2298	2308	2.504367	ACATACGCAGCAAAGAAGGTT	58.496	42.857	0.00	0.00	0.00	3.50
2439	2449	1.142748	CAGACGAGATGACCCTGGC	59.857	63.158	0.00	0.00	0.00	4.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
10	11	9.087424	GCTCTTTATTTCAGTTTGACAGTTTTT	57.913	29.630	0.00	0.00	0.00	1.94
11	12	8.470002	AGCTCTTTATTTCAGTTTGACAGTTTT	58.530	29.630	0.00	0.00	0.00	2.43
12	13	8.000780	AGCTCTTTATTTCAGTTTGACAGTTT	57.999	30.769	0.00	0.00	0.00	2.66
13	14	7.283127	TGAGCTCTTTATTTCAGTTTGACAGTT	59.717	33.333	16.19	0.00	0.00	3.16
14	15	6.767902	TGAGCTCTTTATTTCAGTTTGACAGT	59.232	34.615	16.19	0.00	0.00	3.55
15	16	7.194607	TGAGCTCTTTATTTCAGTTTGACAG	57.805	36.000	16.19	0.00	0.00	3.51
16	17	7.750229	ATGAGCTCTTTATTTCAGTTTGACA	57.250	32.000	16.19	0.00	0.00	3.58
17	18	7.752686	GGAATGAGCTCTTTATTTCAGTTTGAC	59.247	37.037	16.19	0.00	0.00	3.18
18	19	7.667219	AGGAATGAGCTCTTTATTTCAGTTTGA	59.333	33.333	16.19	0.00	0.00	2.69
19	20	7.824672	AGGAATGAGCTCTTTATTTCAGTTTG	58.175	34.615	16.19	0.00	0.00	2.93
20	21	7.121907	GGAGGAATGAGCTCTTTATTTCAGTTT	59.878	37.037	16.19	0.00	0.00	2.66
21	22	6.601217	GGAGGAATGAGCTCTTTATTTCAGTT	59.399	38.462	16.19	0.00	0.00	3.16
22	23	6.118852	GGAGGAATGAGCTCTTTATTTCAGT	58.881	40.000	16.19	0.00	0.00	3.41
23	24	6.118170	TGGAGGAATGAGCTCTTTATTTCAG	58.882	40.000	16.19	0.00	0.00	3.02
24	25	6.065976	TGGAGGAATGAGCTCTTTATTTCA	57.934	37.500	16.19	8.56	0.00	2.69
25	26	6.118852	ACTGGAGGAATGAGCTCTTTATTTC	58.881	40.000	16.19	12.07	0.00	2.17
26	27	6.072199	ACTGGAGGAATGAGCTCTTTATTT	57.928	37.500	16.19	4.08	0.00	1.40
27	28	5.707066	ACTGGAGGAATGAGCTCTTTATT	57.293	39.130	16.19	6.37	0.00	1.40
28	29	5.679601	GAACTGGAGGAATGAGCTCTTTAT	58.320	41.667	16.19	7.22	0.00	1.40
29	30	4.382040	CGAACTGGAGGAATGAGCTCTTTA	60.382	45.833	16.19	0.00	0.00	1.85
30	31	3.618507	CGAACTGGAGGAATGAGCTCTTT	60.619	47.826	16.19	15.15	0.00	2.52
31	32	2.093764	CGAACTGGAGGAATGAGCTCTT	60.094	50.000	16.19	5.66	0.00	2.85
32	33	1.480137	CGAACTGGAGGAATGAGCTCT	59.520	52.381	16.19	0.00	0.00	4.09
33	34	1.472376	CCGAACTGGAGGAATGAGCTC	60.472	57.143	6.82	6.82	42.00	4.09
34	35	0.539051	CCGAACTGGAGGAATGAGCT	59.461	55.000	0.00	0.00	42.00	4.09
35	36	1.092345	GCCGAACTGGAGGAATGAGC	61.092	60.000	0.00	0.00	42.00	4.26
36	37	0.462759	GGCCGAACTGGAGGAATGAG	60.463	60.000	0.00	0.00	42.00	2.90
37	38	1.602237	GGCCGAACTGGAGGAATGA	59.398	57.895	0.00	0.00	42.00	2.57
38	39	1.815421	CGGCCGAACTGGAGGAATG	60.815	63.158	24.07	0.00	42.00	2.67
39	40	2.584608	CGGCCGAACTGGAGGAAT	59.415	61.111	24.07	0.00	42.00	3.01
40	41	4.388499	GCGGCCGAACTGGAGGAA	62.388	66.667	33.48	0.00	42.00	3.36
57	58	4.676951	TGGGAAAAGGGGCGGCAG	62.677	66.667	12.47	0.00	0.00	4.85
58	59	4.676951	CTGGGAAAAGGGGCGGCA	62.677	66.667	12.47	0.00	0.00	5.69
90	91	4.953868	TTGGACGTGACCGGCGTG	62.954	66.667	10.42	0.00	45.55	5.34
91	92	4.955774	GTTGGACGTGACCGGCGT	62.956	66.667	6.01	2.42	45.55	5.68
94	95	4.692475	GGGGTTGGACGTGACCGG	62.692	72.222	0.00	0.00	38.78	5.28
96	97	3.871248	GACGGGGTTGGACGTGACC	62.871	68.421	0.00	0.00	44.24	4.02
97	98	2.356673	GACGGGGTTGGACGTGAC	60.357	66.667	0.00	0.00	44.24	3.67
98	99	3.980989	CGACGGGGTTGGACGTGA	61.981	66.667	0.00	0.00	44.24	4.35
119	120	3.818787	CTGCAGGCGATGGGTTGC	61.819	66.667	5.57	0.00	37.09	4.17
120	121	3.136123	CCTGCAGGCGATGGGTTG	61.136	66.667	22.33	0.00	0.00	3.77
222	223	4.873129	CGACGAGGATGGGCACGG	62.873	72.222	0.00	0.00	0.00	4.94
223	224	4.873129	CCGACGAGGATGGGCACG	62.873	72.222	0.00	0.00	45.00	5.34
227	228	4.530857	GTGGCCGACGAGGATGGG	62.531	72.222	0.00	0.00	45.00	4.00
228	229	3.770040	TGTGGCCGACGAGGATGG	61.770	66.667	0.00	0.00	45.00	3.51
229	230	2.509336	GTGTGGCCGACGAGGATG	60.509	66.667	0.00	0.00	45.00	3.51
230	231	3.771160	GGTGTGGCCGACGAGGAT	61.771	66.667	0.00	0.00	45.00	3.24
249	250	4.813526	CAGACGACGGAGGCGACG	62.814	72.222	1.02	0.00	37.36	5.12
263	264	4.704833	GACAAGGCTGGGCGCAGA	62.705	66.667	32.72	0.00	41.67	4.26
301	302	4.183686	TACTAGTGCGCGGACGGC	62.184	66.667	25.16	1.15	40.57	5.68
302	303	1.985447	TTCTACTAGTGCGCGGACGG	61.985	60.000	25.16	22.36	40.57	4.79
303	304	0.179181	TTTCTACTAGTGCGCGGACG	60.179	55.000	25.16	14.41	44.07	4.79
304	305	1.918609	CTTTTCTACTAGTGCGCGGAC	59.081	52.381	24.26	24.26	0.00	4.79
305	306	1.135199	CCTTTTCTACTAGTGCGCGGA	60.135	52.381	8.83	0.00	0.00	5.54
306	307	1.278238	CCTTTTCTACTAGTGCGCGG	58.722	55.000	8.83	0.00	0.00	6.46
307	308	1.278238	CCCTTTTCTACTAGTGCGCG	58.722	55.000	5.39	0.00	0.00	6.86
308	309	1.653151	CCCCTTTTCTACTAGTGCGC	58.347	55.000	5.39	0.00	0.00	6.09
489	490	4.467084	GAGGCGCATTGGTCCCGA	62.467	66.667	10.83	0.00	0.00	5.14
1024	1030	0.259065	TCATAGACAGGACGAGGGCT	59.741	55.000	0.00	0.00	0.00	5.19
1274	1283	1.748493	TGTGATCATCGACGACATCCA	59.252	47.619	0.00	3.21	0.00	3.41
1377	1386	7.369607	CAATCAATGTAACAACTGATCCAACA	58.630	34.615	0.00	0.00	0.00	3.33
1666	1676	2.483014	TGCACGCCCTTAATGTACTT	57.517	45.000	0.00	0.00	0.00	2.24
1717	1727	7.981225	GCATGGACAATACATAAAACCATTCTT	59.019	33.333	0.00	0.00	34.96	2.52
1733	1743	3.245371	CCCACATATAGGGCATGGACAAT	60.245	47.826	0.00	0.00	39.96	2.71
1758	1768	2.414293	CCGGTCAGAGTAAGACTTCGTG	60.414	54.545	0.00	0.00	36.29	4.35
1806	1816	2.158534	ACAGTGTGGCATGAAACCCTTA	60.159	45.455	0.00	0.00	0.00	2.69
1826	1836	1.127951	CGTGCCTCGTCCAAACATTAC	59.872	52.381	0.00	0.00	34.52	1.89
1861	1871	1.808411	TCTTTGCCGTCTTCCATCAC	58.192	50.000	0.00	0.00	0.00	3.06
1899	1909	1.142060	CCGTATTCAGGGGGCACATAA	59.858	52.381	0.00	0.00	0.00	1.90
1921	1931	5.426689	TCCTCTTGATGTTCAGTAGCATT	57.573	39.130	0.00	0.00	0.00	3.56
1951	1961	2.619646	TTGCAGCATCATCGTGCATATT	59.380	40.909	0.00	0.00	46.18	1.28
1954	1964	0.099968	GTTGCAGCATCATCGTGCAT	59.900	50.000	0.00	0.00	46.18	3.96
2088	2098	3.553096	GGTCCTCTAACATGCGATCGAAT	60.553	47.826	21.57	12.08	0.00	3.34
2200	2210	4.038271	TCTCAAATCCTTTGTCAGGCAT	57.962	40.909	0.04	0.00	43.55	4.40
2298	2308	3.242867	CTCCAATCCTAGAGGGCATACA	58.757	50.000	0.00	0.00	35.41	2.29
2403	2413	6.322491	TCGTCTGATCTTATACCATAATGCG	58.678	40.000	0.00	0.00	0.00	4.73

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.