AutoCloner

Multiple sequence alignment - TraesCS3B01G328200

Loading Multiple Alignment...

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	TraesCS3B01G328200	chr3B	100.000	2943	0	0	1	2943	529795958	529798900	0.000000e+00	5435
1	TraesCS3B01G328200	chr3B	97.190	605	17	0	2339	2943	605503616	605503012	0.000000e+00	1024
2	TraesCS3B01G328200	chr3B	80.742	431	40	20	240	656	529725852	529726253	2.220000e-76	296
3	TraesCS3B01G328200	chr3B	80.723	332	56	8	2336	2662	529799824	529799496	4.870000e-63	252
4	TraesCS3B01G328200	chr3A	92.054	2064	92	30	37	2053	525296550	525298588	0.000000e+00	2837
5	TraesCS3B01G328200	chr3A	93.493	1675	77	10	687	2335	525628057	525629725	0.000000e+00	2460
6	TraesCS3B01G328200	chr3A	87.750	400	31	11	240	638	525627666	525628048	4.470000e-123	451
7	TraesCS3B01G328200	chr3A	84.362	243	35	3	2423	2664	733497671	733497431	4.900000e-58	235
8	TraesCS3B01G328200	chr3A	78.979	333	63	7	2338	2664	733496789	733497120	1.370000e-53	220
9	TraesCS3B01G328200	chr3A	88.148	135	10	3	441	575	525291719	525291847	3.930000e-34	156
10	TraesCS3B01G328200	chr3A	88.506	87	9	1	570	656	525291971	525292056	1.440000e-18	104
11	TraesCS3B01G328200	chr3D	91.043	2110	104	33	240	2305	403692665	403694733	0.000000e+00	2771
12	TraesCS3B01G328200	chr3D	93.989	1414	59	12	657	2054	403352126	403353529	0.000000e+00	2117
13	TraesCS3B01G328200	chr3D	88.316	659	42	13	37	664	403351296	403351950	0.000000e+00	758
14	TraesCS3B01G328200	chr3D	88.889	198	17	2	2057	2254	403674175	403674367	3.790000e-59	239
15	TraesCS3B01G328200	chr3D	83.206	262	27	10	234	480	403330636	403330895	1.060000e-54	224
16	TraesCS3B01G328200	chr3D	89.595	173	13	1	489	656	403341321	403341493	6.390000e-52	215
17	TraesCS3B01G328200	chr7B	96.469	623	21	1	2321	2943	337125086	337124465	0.000000e+00	1027
18	TraesCS3B01G328200	chr7B	88.060	134	14	2	2318	2451	577799479	577799610	1.090000e-34	158
19	TraesCS3B01G328200	chr7A	91.615	322	27	0	2336	2657	706066386	706066065	2.080000e-121	446
20	TraesCS3B01G328200	chr1A	91.429	280	23	1	2664	2943	584871792	584871514	1.650000e-102	383
21	TraesCS3B01G328200	chr6D	84.393	346	42	8	2330	2664	86933162	86932818	2.190000e-86	329
22	TraesCS3B01G328200	chr6D	88.889	108	10	2	2662	2768	86932781	86932675	6.620000e-27	132
23	TraesCS3B01G328200	chr4A	84.071	339	42	6	2336	2664	493700050	493700386	1.700000e-82	316
24	TraesCS3B01G328200	chr5D	84.146	246	34	3	2420	2664	1683702	1683943	1.760000e-57	233

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	TraesCS3B01G328200	chr3B	529795958	529798900	2942	False	5435.0	5435	100.0000	1	2943	1	chr3B.!!$F2	2942
1	TraesCS3B01G328200	chr3B	605503012	605503616	604	True	1024.0	1024	97.1900	2339	2943	1	chr3B.!!$R2	604
2	TraesCS3B01G328200	chr3A	525296550	525298588	2038	False	2837.0	2837	92.0540	37	2053	1	chr3A.!!$F1	2016
3	TraesCS3B01G328200	chr3A	525627666	525629725	2059	False	1455.5	2460	90.6215	240	2335	2	chr3A.!!$F4	2095
4	TraesCS3B01G328200	chr3D	403692665	403694733	2068	False	2771.0	2771	91.0430	240	2305	1	chr3D.!!$F4	2065
5	TraesCS3B01G328200	chr3D	403351296	403353529	2233	False	1437.5	2117	91.1525	37	2054	2	chr3D.!!$F5	2017
6	TraesCS3B01G328200	chr7B	337124465	337125086	621	True	1027.0	1027	96.4690	2321	2943	1	chr7B.!!$R1	622

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
25	26	0.109919	CGGTTTAGCCCAAACGAAGC	60.11	55.0	0.0	0.0	46.35	3.86	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1981	2262	1.210931	CCAAGCACATCCACAAGCG	59.789	57.895	0.0	0.0	0.0	4.68	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
19	20	2.283316	GGCCCGGTTTAGCCCAAA	60.283	61.111	8.17	0.00	43.76	3.28
20	21	2.642254	GGCCCGGTTTAGCCCAAAC	61.642	63.158	8.17	3.48	43.76	2.93
21	22	2.985117	GCCCGGTTTAGCCCAAACG	61.985	63.158	0.00	1.31	46.35	3.60
22	23	1.302671	CCCGGTTTAGCCCAAACGA	60.303	57.895	0.00	0.00	46.35	3.85
23	24	0.890090	CCCGGTTTAGCCCAAACGAA	60.890	55.000	0.00	0.00	46.35	3.85
24	25	0.519961	CCGGTTTAGCCCAAACGAAG	59.480	55.000	4.52	0.50	46.35	3.79
25	26	0.109919	CGGTTTAGCCCAAACGAAGC	60.110	55.000	0.00	0.00	46.35	3.86
26	27	1.244816	GGTTTAGCCCAAACGAAGCT	58.755	50.000	0.00	0.00	46.35	3.74
27	28	1.199327	GGTTTAGCCCAAACGAAGCTC	59.801	52.381	0.00	0.00	46.35	4.09
28	29	1.199327	GTTTAGCCCAAACGAAGCTCC	59.801	52.381	0.00	0.00	37.38	4.70
29	30	0.672401	TTAGCCCAAACGAAGCTCCG	60.672	55.000	0.00	0.00	38.06	4.63
30	31	2.515996	TAGCCCAAACGAAGCTCCGG	62.516	60.000	0.00	0.00	38.06	5.14
31	32	3.431725	CCCAAACGAAGCTCCGGC	61.432	66.667	0.00	0.00	39.06	6.13
32	33	3.431725	CCAAACGAAGCTCCGGCC	61.432	66.667	0.00	0.00	39.73	6.13
33	34	3.431725	CAAACGAAGCTCCGGCCC	61.432	66.667	0.00	0.00	39.73	5.80
34	35	3.637273	AAACGAAGCTCCGGCCCT	61.637	61.111	0.00	0.00	39.73	5.19
35	36	3.901797	AAACGAAGCTCCGGCCCTG	62.902	63.158	0.00	0.00	39.73	4.45
90	91	3.694566	AGTTCAAAGACACCTGGTTTCAC	59.305	43.478	14.93	4.36	0.00	3.18
99	100	5.765182	AGACACCTGGTTTCACTTAAATGAG	59.235	40.000	14.93	0.00	0.00	2.90
101	102	5.531287	ACACCTGGTTTCACTTAAATGAGAC	59.469	40.000	0.00	0.00	33.90	3.36
113	114	5.189934	ACTTAAATGAGACCGGAGAGGAAAT	59.810	40.000	9.46	0.00	45.00	2.17
179	187	5.581126	TTTGATGCTTGTTTGACTCTTGT	57.419	34.783	0.00	0.00	0.00	3.16
180	188	5.581126	TTGATGCTTGTTTGACTCTTGTT	57.419	34.783	0.00	0.00	0.00	2.83
181	189	6.691754	TTGATGCTTGTTTGACTCTTGTTA	57.308	33.333	0.00	0.00	0.00	2.41
184	192	8.032952	TGATGCTTGTTTGACTCTTGTTATAG	57.967	34.615	0.00	0.00	0.00	1.31
185	193	7.661437	TGATGCTTGTTTGACTCTTGTTATAGT	59.339	33.333	0.00	0.00	0.00	2.12
187	195	7.217200	TGCTTGTTTGACTCTTGTTATAGTCT	58.783	34.615	0.00	0.00	42.17	3.24
188	196	8.364894	TGCTTGTTTGACTCTTGTTATAGTCTA	58.635	33.333	0.00	0.00	42.17	2.59
189	197	8.865001	GCTTGTTTGACTCTTGTTATAGTCTAG	58.135	37.037	0.00	0.00	42.17	2.43
190	198	9.360093	CTTGTTTGACTCTTGTTATAGTCTAGG	57.640	37.037	0.00	0.00	42.17	3.02
191	199	7.837863	TGTTTGACTCTTGTTATAGTCTAGGG	58.162	38.462	0.00	0.00	42.17	3.53
194	202	5.594725	TGACTCTTGTTATAGTCTAGGGCAG	59.405	44.000	0.00	0.00	42.17	4.85
370	404	3.659092	CGCCAGCCGCAGAAACAA	61.659	61.111	0.00	0.00	37.30	2.83
526	560	1.951130	CATCGCCGATCAACCGAGG	60.951	63.158	0.00	0.00	34.21	4.63
563	599	2.502947	CTCTGTCCATCCTCCATTGACA	59.497	50.000	0.00	0.00	35.31	3.58
638	687	5.626955	GGACTATACTAATCACGCCGTTAAC	59.373	44.000	0.00	0.00	0.00	2.01
639	688	5.207768	ACTATACTAATCACGCCGTTAACG	58.792	41.667	20.99	20.99	39.44	3.18
893	1127	4.418328	AATTGGCCCCGCGCACTA	62.418	61.111	8.75	0.00	40.31	2.74
1025	1278	2.167693	CCATCGCAAGGGACAGTACTAA	59.832	50.000	0.00	0.00	38.47	2.24
1246	1514	2.733593	GCGTTCGTCTCCGTGCTT	60.734	61.111	0.00	0.00	35.01	3.91
1531	1799	2.826702	GTGTTCCACGTCCCCTGT	59.173	61.111	0.00	0.00	0.00	4.00
1941	2222	6.884832	TCAGAGGTGTGAAATACGGAAATAT	58.115	36.000	0.00	0.00	0.00	1.28
1944	2225	7.709182	CAGAGGTGTGAAATACGGAAATATACA	59.291	37.037	0.00	0.00	0.00	2.29
1947	2228	6.017687	GGTGTGAAATACGGAAATATACACCC	60.018	42.308	10.69	0.00	45.93	4.61
1948	2229	6.017687	GTGTGAAATACGGAAATATACACCCC	60.018	42.308	0.00	0.00	32.13	4.95
1949	2230	6.126710	TGTGAAATACGGAAATATACACCCCT	60.127	38.462	0.00	0.00	0.00	4.79
1950	2231	6.204108	GTGAAATACGGAAATATACACCCCTG	59.796	42.308	0.00	0.00	0.00	4.45
2079	2360	2.680339	GCTCTGTTTTCTCTGGCCATAC	59.320	50.000	5.51	0.00	0.00	2.39
2094	2375	2.106683	ATACCGCTTGTTCCGCTGC	61.107	57.895	0.00	0.00	0.00	5.25
2101	2382	1.336240	GCTTGTTCCGCTGCTGATTTT	60.336	47.619	0.00	0.00	0.00	1.82
2269	2560	4.588805	CCGTTTCGGTACCATTTTCTAC	57.411	45.455	13.54	0.00	42.73	2.59
2276	2567	4.155099	TCGGTACCATTTTCTACGTACGAA	59.845	41.667	24.41	5.43	33.43	3.85
2278	2569	5.160641	GGTACCATTTTCTACGTACGAACA	58.839	41.667	24.41	5.54	33.43	3.18
2305	2596	6.712547	GTCTTGTGCTTGCTTAGGGATAATAT	59.287	38.462	0.00	0.00	0.00	1.28
2306	2597	7.878127	GTCTTGTGCTTGCTTAGGGATAATATA	59.122	37.037	0.00	0.00	0.00	0.86
2331	2622	5.471116	GGCAATGGCATTCTTTTCTTTCTTT	59.529	36.000	10.36	0.00	43.71	2.52
2418	2709	5.385198	TCAAAACCAGCAAATCTTAGTCCT	58.615	37.500	0.00	0.00	0.00	3.85
2435	2726	3.134081	AGTCCTTCAACTTCTCAAACCGA	59.866	43.478	0.00	0.00	0.00	4.69
2553	2844	3.486875	CCCGTTTTAATTTAGCTGAGCGG	60.487	47.826	0.00	0.00	35.79	5.52
2594	2885	1.882623	GGTTGAGCAACAAGAGAAGGG	59.117	52.381	14.55	0.00	42.85	3.95
2657	2948	4.269523	TGCAGGCGGCCAAAGAGT	62.270	61.111	23.09	0.00	43.89	3.24
2856	3147	3.385577	GAACAGGACAGAGACAACAGAC	58.614	50.000	0.00	0.00	0.00	3.51
2925	3216	1.738099	GCTCTGTCGACGTTGCCAT	60.738	57.895	11.62	0.00	0.00	4.40
2932	3223	2.314647	CGACGTTGCCATGGTCGTT	61.315	57.895	23.98	13.35	46.07	3.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
3	4	2.967397	GTTTGGGCTAAACCGGGC	59.033	61.111	14.81	0.00	42.25	6.13
4	5	0.890090	TTCGTTTGGGCTAAACCGGG	60.890	55.000	19.04	7.12	44.62	5.73
5	6	0.519961	CTTCGTTTGGGCTAAACCGG	59.480	55.000	19.04	0.00	44.62	5.28
6	7	0.109919	GCTTCGTTTGGGCTAAACCG	60.110	55.000	19.04	14.25	44.62	4.44
7	8	1.199327	GAGCTTCGTTTGGGCTAAACC	59.801	52.381	19.04	6.62	44.62	3.27
8	9	1.199327	GGAGCTTCGTTTGGGCTAAAC	59.801	52.381	15.63	15.63	44.13	2.01
9	10	1.530323	GGAGCTTCGTTTGGGCTAAA	58.470	50.000	0.00	0.00	36.37	1.85
10	11	0.672401	CGGAGCTTCGTTTGGGCTAA	60.672	55.000	6.14	0.00	36.37	3.09
11	12	1.079405	CGGAGCTTCGTTTGGGCTA	60.079	57.895	6.14	0.00	36.37	3.93
12	13	2.358737	CGGAGCTTCGTTTGGGCT	60.359	61.111	6.14	0.00	39.16	5.19
13	14	3.431725	CCGGAGCTTCGTTTGGGC	61.432	66.667	14.59	0.00	0.00	5.36
14	15	3.431725	GCCGGAGCTTCGTTTGGG	61.432	66.667	14.59	0.00	35.50	4.12
15	16	3.431725	GGCCGGAGCTTCGTTTGG	61.432	66.667	14.59	0.00	39.73	3.28
16	17	3.431725	GGGCCGGAGCTTCGTTTG	61.432	66.667	14.59	0.00	39.73	2.93
17	18	3.637273	AGGGCCGGAGCTTCGTTT	61.637	61.111	14.59	0.00	39.73	3.60
18	19	4.394712	CAGGGCCGGAGCTTCGTT	62.395	66.667	14.59	0.00	39.73	3.85
21	22	4.416738	AAGCAGGGCCGGAGCTTC	62.417	66.667	22.38	0.00	44.67	3.86
41	42	1.339291	GCAGCAAGAAAGTGAAAGGCT	59.661	47.619	0.00	0.00	0.00	4.58
90	91	4.737855	TTCCTCTCCGGTCTCATTTAAG	57.262	45.455	0.00	0.00	0.00	1.85
99	100	3.897141	AAGAGAATTTCCTCTCCGGTC	57.103	47.619	0.00	0.00	42.31	4.79
101	102	4.081420	TGAGAAAGAGAATTTCCTCTCCGG	60.081	45.833	0.00	0.00	42.31	5.14
167	175	6.757478	GCCCTAGACTATAACAAGAGTCAAAC	59.243	42.308	4.96	0.00	43.81	2.93
173	181	4.262249	GCCTGCCCTAGACTATAACAAGAG	60.262	50.000	0.00	0.00	0.00	2.85
174	182	3.641906	GCCTGCCCTAGACTATAACAAGA	59.358	47.826	0.00	0.00	0.00	3.02
175	183	3.244249	GGCCTGCCCTAGACTATAACAAG	60.244	52.174	0.00	0.00	0.00	3.16
176	184	2.704065	GGCCTGCCCTAGACTATAACAA	59.296	50.000	0.00	0.00	0.00	2.83
179	187	2.787339	TGGCCTGCCCTAGACTATAA	57.213	50.000	3.32	0.00	34.56	0.98
180	188	2.540383	CATGGCCTGCCCTAGACTATA	58.460	52.381	3.32	0.00	34.56	1.31
181	189	1.356124	CATGGCCTGCCCTAGACTAT	58.644	55.000	3.32	0.00	34.56	2.12
184	192	2.203266	GCATGGCCTGCCCTAGAC	60.203	66.667	14.21	0.00	45.66	2.59
217	248	2.482721	AGTGCATACTTGGTGTTAACGC	59.517	45.455	10.77	10.77	31.66	4.84
370	404	0.737219	GCAATGGCAGCGAAAGATCT	59.263	50.000	0.00	0.00	40.72	2.75
704	936	7.455641	TTTTTAACTCTCGAGATCTCTCTGT	57.544	36.000	17.03	5.45	40.75	3.41
944	1186	2.027625	GTTTCAGTCGTGGGCGGAG	61.028	63.158	0.00	0.00	38.89	4.63
945	1187	2.029964	GTTTCAGTCGTGGGCGGA	59.970	61.111	0.00	0.00	38.89	5.54
955	1206	4.106663	TGGTGGGGTTTTATAGGTTTCAGT	59.893	41.667	0.00	0.00	0.00	3.41
1025	1278	2.729194	CTCCAGTAGTGGCTAGAGTGT	58.271	52.381	12.14	0.00	44.60	3.55
1246	1514	4.016790	AGGAGCAGGGAGAGGCCA	62.017	66.667	5.01	0.00	38.95	5.36
1531	1799	4.994201	GCGAGCCACGTGTCGACA	62.994	66.667	26.77	15.76	44.60	4.35
1806	2074	2.393271	ATCTACAGAGTGTTGCTGCC	57.607	50.000	0.00	0.00	36.86	4.85
1860	2132	1.472480	CGAATGGCGAGAACCCAAAAT	59.528	47.619	0.00	0.00	44.57	1.82
1941	2222	3.104512	CATAGGACACTTCAGGGGTGTA	58.895	50.000	0.00	0.00	46.23	2.90
1944	2225	2.344093	ACATAGGACACTTCAGGGGT	57.656	50.000	0.00	0.00	0.00	4.95
1947	2228	8.893727	CCTAATTAAAACATAGGACACTTCAGG	58.106	37.037	0.00	0.00	38.81	3.86
1948	2229	8.398665	GCCTAATTAAAACATAGGACACTTCAG	58.601	37.037	2.34	0.00	38.81	3.02
1949	2230	7.885922	TGCCTAATTAAAACATAGGACACTTCA	59.114	33.333	2.34	0.00	38.81	3.02
1950	2231	8.182227	GTGCCTAATTAAAACATAGGACACTTC	58.818	37.037	13.49	0.00	38.81	3.01
1981	2262	1.210931	CCAAGCACATCCACAAGCG	59.789	57.895	0.00	0.00	0.00	4.68
2055	2336	1.447945	GCCAGAGAAAACAGAGCTCC	58.552	55.000	10.93	0.00	0.00	4.70
2079	2360	4.093952	CAGCAGCGGAACAAGCGG	62.094	66.667	0.00	0.00	40.04	5.52
2094	2375	4.418392	GCAGCCAGTCATAACAAAATCAG	58.582	43.478	0.00	0.00	0.00	2.90
2223	2511	6.411630	TCTCACAAAATAAACCGGTAATCG	57.588	37.500	8.00	0.21	38.88	3.34
2269	2560	2.058798	AGCACAAGACATGTTCGTACG	58.941	47.619	9.53	9.53	41.46	3.67
2276	2567	2.816087	CCTAAGCAAGCACAAGACATGT	59.184	45.455	0.00	0.00	45.34	3.21
2278	2569	2.040278	TCCCTAAGCAAGCACAAGACAT	59.960	45.455	0.00	0.00	0.00	3.06
2305	2596	5.481473	AGAAAGAAAAGAATGCCATTGCCTA	59.519	36.000	0.00	0.00	36.33	3.93
2306	2597	4.285260	AGAAAGAAAAGAATGCCATTGCCT	59.715	37.500	0.00	0.00	36.33	4.75
2331	2622	8.862085	AGGACGAAAAATATACTTTTCCCAAAA	58.138	29.630	12.45	0.00	40.64	2.44
2418	2709	7.562454	AAGTAATTCGGTTTGAGAAGTTGAA	57.438	32.000	0.00	0.00	0.00	2.69
2553	2844	1.014044	TCGCCAACTGCTCGATGAAC	61.014	55.000	0.00	0.00	38.05	3.18
2594	2885	0.252197	AACAAGGTCGATGGCTACCC	59.748	55.000	0.00	0.00	36.34	3.69
2657	2948	1.067416	CTAGCCGTGATAGCCGCAA	59.933	57.895	0.00	0.00	0.00	4.85
2833	3124	1.068588	TGTTGTCTCTGTCCTGTTCCG	59.931	52.381	0.00	0.00	0.00	4.30
2925	3216	3.056458	ATGCGAGGACAACGACCA	58.944	55.556	0.00	0.00	0.00	4.02

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.