AutoCloner

Multiple sequence alignment - TraesCS3D01G411700

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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	TraesCS3D01G411700	chr3D	100.000	3292	0	0	1	3292	524300452	524297161	0.000000e+00	6080.0
1	TraesCS3D01G411700	chr3A	91.871	2645	129	24	673	3292	658892293	658889710	0.000000e+00	3615.0
2	TraesCS3D01G411700	chr3A	89.532	363	31	4	2	363	658894426	658894070	1.390000e-123	453.0
3	TraesCS3D01G411700	chr3A	91.946	149	11	1	527	674	658893913	658893765	1.200000e-49	207.0
4	TraesCS3D01G411700	chr3A	89.062	64	6	1	368	431	658893985	658893923	9.790000e-11	78.7
5	TraesCS3D01G411700	chr3A	100.000	36	0	0	1268	1303	695909755	695909720	2.120000e-07	67.6
6	TraesCS3D01G411700	chr3B	93.142	1327	64	12	1303	2608	691709654	691708334	0.000000e+00	1921.0
7	TraesCS3D01G411700	chr3B	93.489	983	43	9	2315	3291	691714639	691713672	0.000000e+00	1441.0
8	TraesCS3D01G411700	chr3B	97.238	688	19	0	2605	3292	691708073	691707386	0.000000e+00	1166.0
9	TraesCS3D01G411700	chr3B	95.122	369	14	2	381	749	691737134	691736770	2.200000e-161	579.0
10	TraesCS3D01G411700	chr3B	89.827	462	22	5	772	1233	691715073	691714637	1.330000e-158	569.0
11	TraesCS3D01G411700	chr3B	89.209	278	17	5	1004	1269	691711284	691711008	5.260000e-88	335.0
12	TraesCS3D01G411700	chr3B	86.942	291	32	6	2	289	691737957	691737670	4.100000e-84	322.0
13	TraesCS3D01G411700	chr3B	91.556	225	19	0	139	363	691735184	691734960	8.870000e-81	311.0
14	TraesCS3D01G411700	chr3B	84.281	299	28	15	502	786	691715389	691715096	1.160000e-69	274.0
15	TraesCS3D01G411700	chr3B	95.312	128	6	0	798	925	691711449	691711322	1.550000e-48	204.0
16	TraesCS3D01G411700	chr3B	90.400	125	10	2	218	341	691737677	691737554	2.630000e-36	163.0
17	TraesCS3D01G411700	chr7A	88.476	269	31	0	1332	1600	10358625	10358357	3.170000e-85	326.0
18	TraesCS3D01G411700	chr7A	95.455	44	0	2	1263	1304	697006932	697006889	5.890000e-08	69.4
19	TraesCS3D01G411700	chr7D	79.412	272	55	1	1332	1603	110220648	110220918	1.210000e-44	191.0
20	TraesCS3D01G411700	chr1A	95.833	48	1	1	1257	1303	29287068	29287021	3.520000e-10	76.8
21	TraesCS3D01G411700	chr4D	93.878	49	1	2	1253	1300	469582262	469582309	4.560000e-09	73.1
22	TraesCS3D01G411700	chr5A	86.364	66	7	2	1254	1318	619169094	619169030	1.640000e-08	71.3
23	TraesCS3D01G411700	chr2A	92.000	50	2	2	1255	1303	680593644	680593596	5.890000e-08	69.4
24	TraesCS3D01G411700	chr2A	95.349	43	0	2	1260	1300	66004766	66004808	2.120000e-07	67.6
25	TraesCS3D01G411700	chr6D	89.091	55	3	3	1250	1303	27848404	27848352	7.620000e-07	65.8

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	TraesCS3D01G411700	chr3D	524297161	524300452	3291	True	6080.000000	6080	100.000000	1	3292	1	chr3D.!!$R1	3291
1	TraesCS3D01G411700	chr3A	658889710	658894426	4716	True	1088.425000	3615	90.602750	2	3292	4	chr3A.!!$R2	3290
2	TraesCS3D01G411700	chr3B	691707386	691715389	8003	True	844.285714	1921	91.785429	502	3292	7	chr3B.!!$R1	2790
3	TraesCS3D01G411700	chr3B	691734960	691737957	2997	True	343.750000	579	91.005000	2	749	4	chr3B.!!$R2	747

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
164	166	0.106149	AGTGCCTCGGAAGTTTTCGT	59.894	50.0	0.0	0.0	0.0	3.85	F
377	466	0.321564	TTGCAGTGTTCCATCCTCCG	60.322	55.0	0.0	0.0	0.0	4.63	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1423	9835	0.541063	TGAGTAGAAGGGTGCCACGA	60.541	55.0	0.0	0.0	0.0	4.35	R
2326	10760	0.035056	CTGGGGTTTCCTTCGCTGAT	60.035	55.0	0.0	0.0	36.2	2.90	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
42	43	3.826729	GGTTGGTGCCAAAGTATTCTTCT	59.173	43.478	5.09	0.00	37.70	2.85
78	80	2.526120	GCGCGTCTTGACCATAGCC	61.526	63.158	8.43	0.00	0.00	3.93
90	92	2.930562	ATAGCCCGATGCCCCCTC	60.931	66.667	0.00	0.00	42.71	4.30
146	148	3.690460	ACCCAGGAATTTGTAGAAGCAG	58.310	45.455	0.00	0.00	0.00	4.24
149	151	3.119708	CCAGGAATTTGTAGAAGCAGTGC	60.120	47.826	7.13	7.13	0.00	4.40
151	153	3.084786	GGAATTTGTAGAAGCAGTGCCT	58.915	45.455	12.58	5.22	0.00	4.75
152	154	3.127721	GGAATTTGTAGAAGCAGTGCCTC	59.872	47.826	12.58	8.85	0.00	4.70
159	161	0.603975	GAAGCAGTGCCTCGGAAGTT	60.604	55.000	12.58	0.00	0.00	2.66
164	166	0.106149	AGTGCCTCGGAAGTTTTCGT	59.894	50.000	0.00	0.00	0.00	3.85
179	181	0.976641	TTCGTTGCAGACCAGGAGAT	59.023	50.000	0.00	0.00	0.00	2.75
233	236	4.155644	CCTCTTGGAGAAGAAAATGCTGAC	59.844	45.833	0.00	0.00	37.77	3.51
253	256	4.897076	TGACAAGGGACTGTACAAACTCTA	59.103	41.667	0.00	0.00	40.86	2.43
266	269	6.817641	TGTACAAACTCTAAAGACCACGAAAA	59.182	34.615	0.00	0.00	0.00	2.29
267	270	6.937436	ACAAACTCTAAAGACCACGAAAAT	57.063	33.333	0.00	0.00	0.00	1.82
280	347	1.066716	ACGAAAATCGGTCGAATCCCA	60.067	47.619	4.66	0.00	45.59	4.37
298	365	7.471260	CGAATCCCAGAGAAGAAGACATAGAAT	60.471	40.741	0.00	0.00	0.00	2.40
299	366	7.688918	ATCCCAGAGAAGAAGACATAGAATT	57.311	36.000	0.00	0.00	0.00	2.17
343	410	8.130307	ACAAATTGTTTGCTCATGTTTAGAAC	57.870	30.769	0.00	0.00	44.39	3.01
370	459	4.081752	ACAGTTTCATTTTGCAGTGTTCCA	60.082	37.500	0.00	0.00	0.00	3.53
377	466	0.321564	TTGCAGTGTTCCATCCTCCG	60.322	55.000	0.00	0.00	0.00	4.63
378	467	2.109126	GCAGTGTTCCATCCTCCGC	61.109	63.158	0.00	0.00	0.00	5.54
386	833	1.598962	CCATCCTCCGCGATGCAAT	60.599	57.895	8.23	0.00	38.68	3.56
448	895	3.256631	GGAGGTAACCAGACGAGTACAAA	59.743	47.826	0.00	0.00	37.17	2.83
467	914	8.755028	AGTACAAACTTAAGAATTGGTTTGGTT	58.245	29.630	21.33	7.13	46.71	3.67
533	980	1.794701	CACAACATGTGTCTCTCGTGG	59.205	52.381	0.00	0.00	43.08	4.94
574	1047	5.754406	TCTTTCCACTGTGCAATGAAAAATG	59.246	36.000	1.29	0.00	0.00	2.32
616	1089	1.687494	GAGAACATGTCGAGTGGCGC	61.687	60.000	0.00	0.00	40.61	6.53
631	1104	1.569479	GGCGCTGTTGAGTTGACCTC	61.569	60.000	7.64	0.00	40.89	3.85
720	2666	4.917415	AGACATTTGTTCGCATTGTTAAGC	59.083	37.500	0.00	0.00	0.00	3.09
721	2667	4.870363	ACATTTGTTCGCATTGTTAAGCT	58.130	34.783	0.00	0.00	0.00	3.74
722	2668	6.007936	ACATTTGTTCGCATTGTTAAGCTA	57.992	33.333	0.00	0.00	0.00	3.32
843	4337	2.603560	GGAGCTTCGAACTTTACATCCG	59.396	50.000	0.00	0.00	0.00	4.18
846	4340	1.323534	CTTCGAACTTTACATCCGCCG	59.676	52.381	0.00	0.00	0.00	6.46
933	4427	2.124403	GCCAGGCAGCAGCAGTAT	60.124	61.111	6.55	0.00	44.61	2.12
972	4466	1.526455	ACGAGCTAGCCCTACTCCG	60.526	63.158	12.13	6.50	0.00	4.63
1120	8204	4.980805	GCCGTGCCGTCCTTGACA	62.981	66.667	0.00	0.00	32.09	3.58
1122	8206	3.041940	CGTGCCGTCCTTGACACC	61.042	66.667	0.00	0.00	32.09	4.16
1167	8251	4.766891	CAGGTCAGACCAATTTAACCACAT	59.233	41.667	22.31	0.00	41.95	3.21
1170	8254	5.335661	GGTCAGACCAATTTAACCACATCAC	60.336	44.000	15.43	0.00	38.42	3.06
1171	8255	5.240623	GTCAGACCAATTTAACCACATCACA	59.759	40.000	0.00	0.00	0.00	3.58
1210	8295	8.798402	TCTTGATTAATTTGTCACCGGTATTTT	58.202	29.630	6.87	0.00	0.00	1.82
1247	8416	1.263356	AGGCGTCTAGTGGTAGCAAA	58.737	50.000	0.00	0.00	0.00	3.68
1248	8417	1.204941	AGGCGTCTAGTGGTAGCAAAG	59.795	52.381	0.00	0.00	0.00	2.77
1532	9944	3.386237	GACTGCCTCCGCCTCACT	61.386	66.667	0.00	0.00	0.00	3.41
1546	9969	3.365265	CACTTGCACCTTCCCCGC	61.365	66.667	0.00	0.00	0.00	6.13
1581	10004	4.636435	ACTGGCCCGACAAACCCG	62.636	66.667	0.00	0.00	0.00	5.28
1623	10052	7.517614	AAAGCTCTCTCATATCATAACTCGA	57.482	36.000	0.00	0.00	0.00	4.04
1659	10091	8.574251	TTTTGTCTATGTGGCACATAATAACT	57.426	30.769	33.04	15.79	44.52	2.24
1672	10104	9.331282	GGCACATAATAACTAATGAAGAGAGTT	57.669	33.333	0.00	0.00	37.24	3.01
1694	10126	8.674263	AGTTGATGAAACCATCTCTTATCATC	57.326	34.615	6.62	6.62	42.06	2.92
1708	10142	7.614494	TCTCTTATCATCATTCCATGCGATAA	58.386	34.615	0.00	0.00	35.26	1.75
1733	10167	5.623169	TCCATCATATGCATACATGTGTGT	58.377	37.500	21.76	7.57	43.68	3.72
1736	10170	6.238814	CCATCATATGCATACATGTGTGTTGT	60.239	38.462	21.76	11.65	43.68	3.32
1738	10172	8.508875	CATCATATGCATACATGTGTGTTGTAT	58.491	33.333	21.76	14.52	43.68	2.29
1846	10280	1.153667	GTCTCCTGCGGCTTCTCTG	60.154	63.158	0.00	0.00	0.00	3.35
2014	10448	2.363925	GCTCCTCCTACCCGGTGT	60.364	66.667	0.00	0.00	0.00	4.16
2015	10449	2.424733	GCTCCTCCTACCCGGTGTC	61.425	68.421	0.00	0.00	0.00	3.67
2093	10527	2.228138	ACGCCTTTGTCGTCAACTTA	57.772	45.000	0.00	0.00	34.84	2.24
2143	10577	2.866156	TCTCAACAGAGCAAGTTGTTCG	59.134	45.455	13.26	10.85	44.97	3.95
2156	10590	2.735134	AGTTGTTCGTTCAAGTATCGGC	59.265	45.455	2.09	0.00	30.41	5.54
2226	10660	1.568504	ACGGGGTTCTCAAGAGCATA	58.431	50.000	0.00	0.00	0.00	3.14
2264	10698	2.124736	CCCGGTGATGCCACGAAT	60.125	61.111	0.00	0.00	44.09	3.34
2304	10738	2.345244	CCTGACGCAGACTGCCTT	59.655	61.111	21.55	8.90	41.12	4.35
2326	10760	3.706373	GCCCAGCGGAGGAGTTCA	61.706	66.667	0.00	0.00	0.00	3.18
2451	10885	3.320626	TCTCAGCATCTCTCAACAAACG	58.679	45.455	0.00	0.00	0.00	3.60
2577	11011	4.652421	AGCTACCTACCCGATGTTGATTTA	59.348	41.667	0.00	0.00	0.00	1.40
2648	11346	4.754618	TGTGCATCTTGATGTCGTAAAAGT	59.245	37.500	11.61	0.00	0.00	2.66
2949	11647	4.019591	AGCCGGACCAGATAAAAAGTTAGT	60.020	41.667	5.05	0.00	0.00	2.24
2978	11676	6.369890	ACTTTCACACATGTACAGATGATGAC	59.630	38.462	14.39	0.00	0.00	3.06
3009	11707	4.150098	GTGTGTGTAAGACGAAAGGATGTC	59.850	45.833	0.00	0.00	29.10	3.06
3100	11798	6.984740	TTGATCAAACGATTGTTTAGCAAC	57.015	33.333	10.79	3.01	46.33	4.17
3114	11813	5.127194	TGTTTAGCAACCAACAATAACACCA	59.873	36.000	0.00	0.00	29.81	4.17

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
5	6	7.227156	TGGCACCAACCAAAATTTTAATGTAT	58.773	30.769	2.44	0.00	36.55	2.29
42	43	4.473643	CAACGGTGGAAGCAGGAA	57.526	55.556	0.00	0.00	0.00	3.36
107	109	5.407407	TGGGTTTAAACAAGTTTGCTTCA	57.593	34.783	19.57	0.45	34.23	3.02
146	148	0.942252	AACGAAAACTTCCGAGGCAC	59.058	50.000	0.00	0.00	0.00	5.01
149	151	0.941542	TGCAACGAAAACTTCCGAGG	59.058	50.000	0.00	0.00	0.00	4.63
151	153	1.595794	GTCTGCAACGAAAACTTCCGA	59.404	47.619	0.00	0.00	0.00	4.55
152	154	1.333791	GGTCTGCAACGAAAACTTCCG	60.334	52.381	0.00	0.00	0.00	4.30
159	161	0.756294	TCTCCTGGTCTGCAACGAAA	59.244	50.000	0.00	0.00	0.00	3.46
164	166	1.300963	GGCATCTCCTGGTCTGCAA	59.699	57.895	15.77	0.00	36.34	4.08
214	216	4.279169	CCTTGTCAGCATTTTCTTCTCCAA	59.721	41.667	0.00	0.00	0.00	3.53
215	217	3.822735	CCTTGTCAGCATTTTCTTCTCCA	59.177	43.478	0.00	0.00	0.00	3.86
233	236	6.424207	GTCTTTAGAGTTTGTACAGTCCCTTG	59.576	42.308	0.00	0.00	0.00	3.61
266	269	1.683917	CTTCTCTGGGATTCGACCGAT	59.316	52.381	0.00	0.00	0.00	4.18
267	270	1.103803	CTTCTCTGGGATTCGACCGA	58.896	55.000	0.00	0.00	0.00	4.69
280	347	9.767228	CATGATCAATTCTATGTCTTCTTCTCT	57.233	33.333	0.00	0.00	0.00	3.10
298	365	8.731275	ATTTGTATTTCGGTAGTCATGATCAA	57.269	30.769	0.00	0.00	0.00	2.57
299	366	8.611757	CAATTTGTATTTCGGTAGTCATGATCA	58.388	33.333	0.00	0.00	0.00	2.92
343	410	7.306749	GGAACACTGCAAAATGAAACTGTTATG	60.307	37.037	0.00	0.00	0.00	1.90
347	414	4.081752	TGGAACACTGCAAAATGAAACTGT	60.082	37.500	0.00	0.00	0.00	3.55
370	459	1.665916	CGATTGCATCGCGGAGGAT	60.666	57.895	6.13	0.00	46.55	3.24
386	833	2.893215	TCCTTCTCTAGTGAACCCGA	57.107	50.000	3.12	0.00	0.00	5.14
525	972	1.004277	GTGAGTTGCGACCACGAGAG	61.004	60.000	0.00	0.00	42.66	3.20
533	980	4.745620	GGAAAGATATAGGTGAGTTGCGAC	59.254	45.833	0.00	0.00	0.00	5.19
574	1047	2.084546	GTTGCATCACCCCAGTCTTAC	58.915	52.381	0.00	0.00	0.00	2.34
616	1089	0.249868	TGGCGAGGTCAACTCAACAG	60.250	55.000	0.00	0.00	46.98	3.16
631	1104	2.349886	GCTCAACTAATCAGAAGTGGCG	59.650	50.000	0.00	0.00	0.00	5.69
846	4340	2.877396	GCAATTTGCTCCGCATAGC	58.123	52.632	14.11	0.36	40.96	2.97
933	4427	3.189080	GTGTTATCTGATTGCACTGCACA	59.811	43.478	2.26	0.00	38.71	4.57
972	4466	1.864029	GCAAGGCAACAAGAACGAACC	60.864	52.381	0.00	0.00	41.41	3.62
1122	8206	2.358737	AAACCGAGCTCCTTGCCG	60.359	61.111	8.47	0.00	44.23	5.69
1167	8251	2.880268	CAAGACAAGATGCTTGGTGTGA	59.120	45.455	11.40	0.00	38.22	3.58
1170	8254	4.778534	AATCAAGACAAGATGCTTGGTG	57.221	40.909	11.40	6.74	41.31	4.17
1171	8255	7.472334	AATTAATCAAGACAAGATGCTTGGT	57.528	32.000	11.40	0.00	41.31	3.67
1300	8515	7.065803	GCATGCTTACAAGTACTTCCTTCATAA	59.934	37.037	11.37	0.00	0.00	1.90
1423	9835	0.541063	TGAGTAGAAGGGTGCCACGA	60.541	55.000	0.00	0.00	0.00	4.35
1478	9890	1.295423	GCCGGTCTCAAAGGTGCTA	59.705	57.895	1.90	0.00	0.00	3.49
1532	9944	4.659172	CCTGCGGGGAAGGTGCAA	62.659	66.667	2.57	0.00	38.30	4.08
1546	9969	3.001414	CAGTGATTCTTGCTGTCTCCTG	58.999	50.000	0.00	0.00	0.00	3.86
1581	10004	6.015265	AGAGCTTTATACTACCGGAATCCTTC	60.015	42.308	9.46	0.00	0.00	3.46
1587	10010	5.443283	TGAGAGAGCTTTATACTACCGGAA	58.557	41.667	9.46	0.00	0.00	4.30
1623	10052	6.149474	GCCACATAGACAAAAACTAGATGTGT	59.851	38.462	11.97	5.56	33.07	3.72
1659	10091	8.498054	GATGGTTTCATCAACTCTCTTCATTA	57.502	34.615	1.92	0.00	46.74	1.90
1708	10142	6.717997	ACACACATGTATGCATATGATGGATT	59.282	34.615	22.83	10.75	41.74	3.01
1867	10301	1.221021	GGCCCCTCGAAGTAGTTGG	59.779	63.158	0.00	0.00	0.00	3.77
1979	10413	1.516386	CGTGATGAGGTTCCGGTCG	60.516	63.158	0.00	0.00	0.00	4.79
2093	10527	2.656947	TTAACTCAAGTTGCAGGCCT	57.343	45.000	0.00	0.00	38.90	5.19
2143	10577	1.129326	CGATCCGCCGATACTTGAAC	58.871	55.000	0.00	0.00	0.00	3.18
2156	10590	8.962111	CAACATATATAGTGATGATTCGATCCG	58.038	37.037	0.00	0.00	0.00	4.18
2214	10648	1.406898	CGGTGCTCTATGCTCTTGAGA	59.593	52.381	1.30	0.00	43.37	3.27
2217	10651	0.531532	CCCGGTGCTCTATGCTCTTG	60.532	60.000	0.00	0.00	43.37	3.02
2226	10660	2.660064	GGTCATCACCCGGTGCTCT	61.660	63.158	13.19	0.00	36.54	4.09
2264	10698	0.250989	GATGAAAACCCCCACCGACA	60.251	55.000	0.00	0.00	0.00	4.35
2326	10760	0.035056	CTGGGGTTTCCTTCGCTGAT	60.035	55.000	0.00	0.00	36.20	2.90
2451	10885	9.503427	GTGGTGTTTCATATATTTTTGTCTAGC	57.497	33.333	0.00	0.00	0.00	3.42
2495	10929	5.935945	ACGATGACAATCATAAACCCCATA	58.064	37.500	0.00	0.00	37.20	2.74
2577	11011	7.395190	TCACCAAACGTACATGTATACTAGT	57.605	36.000	9.18	0.00	0.00	2.57
2648	11346	6.697455	TGCACAATAAATTTCTTACGCAAACA	59.303	30.769	0.00	0.00	0.00	2.83
2701	11399	6.003950	TCCAAGAAAGGTTCTCGATGATTTT	58.996	36.000	0.00	0.00	39.61	1.82
2949	11647	2.877786	CTGTACATGTGTGAAAGTGCCA	59.122	45.455	9.11	0.00	0.00	4.92
2978	11676	0.594602	TCTTACACACACCGGTCTCG	59.405	55.000	2.59	0.00	0.00	4.04
3009	11707	5.711036	AGACCCTAGCCTATAATGTCGTTAG	59.289	44.000	0.00	0.00	0.00	2.34
3100	11798	8.879342	TTAATGAAAAGTGGTGTTATTGTTGG	57.121	30.769	0.00	0.00	0.00	3.77
3147	11846	5.334879	CCCAAAATAGAAACACCTTCTGTCG	60.335	44.000	0.00	0.00	44.47	4.35

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.