AutoCloner

Multiple sequence alignment - TraesCS2D01G363400

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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	TraesCS2D01G363400	chr2D	100.000	2813	0	0	1	2813	469167268	469170080	0.000000e+00	5195.0
1	TraesCS2D01G363400	chr2D	83.158	95	12	3	428	520	10869038	10869130	1.800000e-12	84.2
2	TraesCS2D01G363400	chr2A	93.936	1781	67	12	672	2427	608937936	608939700	0.000000e+00	2652.0
3	TraesCS2D01G363400	chr2A	96.136	440	13	2	249	688	608930071	608930506	0.000000e+00	715.0
4	TraesCS2D01G363400	chr2A	93.023	387	23	3	2429	2813	608939765	608940149	1.890000e-156	562.0
5	TraesCS2D01G363400	chr2A	95.582	249	8	2	1	248	608929517	608929763	2.030000e-106	396.0
6	TraesCS2D01G363400	chr2A	92.473	186	13	1	2245	2429	705811152	705811337	5.970000e-67	265.0
7	TraesCS2D01G363400	chr2B	92.891	1674	79	18	510	2179	547836181	547837818	0.000000e+00	2396.0
8	TraesCS2D01G363400	chr2B	90.415	386	34	3	2429	2813	734839675	734840058	3.230000e-139	505.0
9	TraesCS2D01G363400	chr2B	87.336	458	30	13	9	449	547835737	547836183	1.500000e-137	499.0
10	TraesCS2D01G363400	chr2B	94.366	71	4	0	442	512	384186108	384186178	2.960000e-20	110.0
11	TraesCS2D01G363400	chr2B	95.652	69	1	2	445	512	384186181	384186114	2.960000e-20	110.0
12	TraesCS2D01G363400	chr3D	91.667	384	31	1	2431	2813	608806211	608806594	5.340000e-147	531.0
13	TraesCS2D01G363400	chr3D	94.054	185	9	2	2245	2429	562355628	562355446	2.130000e-71	279.0
14	TraesCS2D01G363400	chr7D	91.451	386	32	1	2429	2813	488690827	488690442	1.920000e-146	529.0
15	TraesCS2D01G363400	chr7D	90.674	386	34	2	2429	2813	631022610	631022994	1.930000e-141	512.0
16	TraesCS2D01G363400	chr7D	92.473	186	10	3	2245	2429	488691072	488690890	2.150000e-66	263.0
17	TraesCS2D01G363400	chr6D	91.214	387	29	4	2429	2812	397352428	397352044	3.210000e-144	521.0
18	TraesCS2D01G363400	chr6D	89.333	75	3	4	442	512	103006198	103006125	3.860000e-14	89.8
19	TraesCS2D01G363400	chr1B	90.722	388	29	5	2429	2813	667108208	667107825	6.950000e-141	510.0
20	TraesCS2D01G363400	chr1B	90.674	386	30	5	2431	2813	141285262	141284880	2.500000e-140	508.0
21	TraesCS2D01G363400	chr5D	89.899	396	31	7	2423	2813	95299872	95300263	4.180000e-138	501.0
22	TraesCS2D01G363400	chr5D	90.000	70	5	2	445	512	41139966	41140035	3.860000e-14	89.8
23	TraesCS2D01G363400	chr3A	94.086	186	9	2	2245	2429	341281998	341282182	5.930000e-72	281.0
24	TraesCS2D01G363400	chr3A	92.473	186	10	3	2245	2429	691587804	691587622	2.150000e-66	263.0
25	TraesCS2D01G363400	chr6A	92.973	185	11	2	2245	2429	146889535	146889353	4.620000e-68	268.0
26	TraesCS2D01G363400	chr1D	92.432	185	12	2	2245	2429	203875906	203875724	2.150000e-66	263.0
27	TraesCS2D01G363400	chr1D	91.979	187	12	2	2245	2429	395851560	395851745	2.780000e-65	259.0
28	TraesCS2D01G363400	chrUn	91.429	70	4	2	444	512	30123122	30123190	8.300000e-16	95.3
29	TraesCS2D01G363400	chr1A	89.041	73	6	2	446	516	29006201	29006273	3.860000e-14	89.8
30	TraesCS2D01G363400	chr5A	90.000	70	4	2	446	512	624782119	624782050	1.390000e-13	87.9

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	TraesCS2D01G363400	chr2D	469167268	469170080	2812	False	5195.0	5195	100.0000	1	2813	1	chr2D.!!$F2	2812
1	TraesCS2D01G363400	chr2A	608937936	608940149	2213	False	1607.0	2652	93.4795	672	2813	2	chr2A.!!$F3	2141
2	TraesCS2D01G363400	chr2A	608929517	608930506	989	False	555.5	715	95.8590	1	688	2	chr2A.!!$F2	687
3	TraesCS2D01G363400	chr2B	547835737	547837818	2081	False	1447.5	2396	90.1135	9	2179	2	chr2B.!!$F3	2170
4	TraesCS2D01G363400	chr7D	488690442	488691072	630	True	396.0	529	91.9620	2245	2813	2	chr7D.!!$R1	568

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
133	134	0.035598	TCACGGGTGGGTGTGTATTG	59.964	55.000	0.0	0.0	39.0	1.90	F
1145	1485	1.067354	GGAAGCTGGCATTGTTCAAGG	60.067	52.381	0.0	0.0	0.0	3.61	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1577	1920	0.038159	CGCTGAACCGAGAAAGGAGT	60.038	55.0	0.00	0.00	34.73	3.85	R
2206	2570	0.591236	CGGGTGAAATATTTGGCGCG	60.591	55.0	5.17	13.14	0.00	6.86	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
43	44	6.183360	GCTGTAGATGGTGAGAGATTTACAGA	60.183	42.308	11.74	0.00	38.59	3.41
115	116	6.873076	CATTCAGAGCCTTCTGGATATTAGTC	59.127	42.308	3.36	0.00	46.02	2.59
118	119	4.279671	AGAGCCTTCTGGATATTAGTCACG	59.720	45.833	0.00	0.00	34.57	4.35
133	134	0.035598	TCACGGGTGGGTGTGTATTG	59.964	55.000	0.00	0.00	39.00	1.90
235	238	5.336849	GCCCTCTACAGTCCATGTATATGTC	60.337	48.000	0.00	0.00	43.44	3.06
286	596	5.178061	TGTGTCTGTCATTGTCATATCCAC	58.822	41.667	0.00	0.00	0.00	4.02
306	616	4.559251	CCACGAACTTTTCTGAGAGATACG	59.441	45.833	0.00	0.00	0.00	3.06
357	691	8.030692	CCATATTGATGAACTTGAATGTGTGTT	58.969	33.333	0.00	0.00	34.73	3.32
456	790	8.747538	ACATAAATGTAAAATGTACTCCCTCC	57.252	34.615	0.00	0.00	39.68	4.30
522	856	5.745988	ACAGAGGGAGTAATAGGTAAGGA	57.254	43.478	0.00	0.00	0.00	3.36
741	1076	6.389830	TTGTCTGTTTTATGTGCAATCTGT	57.610	33.333	0.00	0.00	0.00	3.41
744	1079	5.048782	GTCTGTTTTATGTGCAATCTGTGGA	60.049	40.000	0.00	0.00	0.00	4.02
757	1093	3.328535	TCTGTGGAGGCACCTATATGA	57.671	47.619	1.84	0.00	39.86	2.15
784	1120	7.012515	GTGTGTCTGTCTACTAGCACTATACAT	59.987	40.741	0.00	0.00	0.00	2.29
787	1123	7.773690	TGTCTGTCTACTAGCACTATACATGAA	59.226	37.037	0.00	0.00	0.00	2.57
808	1147	7.296628	TGAATTATGGTTTGCCTGTTAAAGT	57.703	32.000	0.00	0.00	35.27	2.66
816	1155	5.529800	GGTTTGCCTGTTAAAGTTGACTAGA	59.470	40.000	0.00	0.00	0.00	2.43
856	1195	7.896383	TTATGGCTTGCCTGTTAAATTAGAT	57.104	32.000	13.18	0.00	0.00	1.98
861	1200	4.871871	TGCCTGTTAAATTAGATGGGGA	57.128	40.909	0.00	0.00	0.00	4.81
892	1231	4.154918	CCCAGTTAGTTCTCAGCACATTTC	59.845	45.833	0.00	0.00	0.00	2.17
954	1293	2.701423	TGTTCTGTGTGGTTGTAGCCTA	59.299	45.455	0.00	0.00	0.00	3.93
962	1301	1.633432	TGGTTGTAGCCTACCTGCATT	59.367	47.619	0.00	0.00	36.02	3.56
970	1310	2.755103	AGCCTACCTGCATTTAACTTGC	59.245	45.455	3.18	3.18	40.55	4.01
982	1322	5.663456	CATTTAACTTGCCATGGCTAACAT	58.337	37.500	35.53	20.24	42.51	2.71
1095	1435	6.607019	AGGATCACAGGTTAACCAAAAGTTA	58.393	36.000	26.26	10.79	40.05	2.24
1118	1458	1.990799	CAAATGTGCCTAGACGACGA	58.009	50.000	0.00	0.00	0.00	4.20
1121	1461	1.103803	ATGTGCCTAGACGACGATGT	58.896	50.000	0.00	0.00	0.00	3.06
1145	1485	1.067354	GGAAGCTGGCATTGTTCAAGG	60.067	52.381	0.00	0.00	0.00	3.61
1228	1568	1.162698	CACTGCTGTGGGAACTGATG	58.837	55.000	15.43	0.00	40.33	3.07
1342	1685	1.813513	TGTTAAGCCAGAAGAGCAGC	58.186	50.000	0.00	0.00	0.00	5.25
1343	1686	1.072173	TGTTAAGCCAGAAGAGCAGCA	59.928	47.619	0.00	0.00	0.00	4.41
1344	1687	1.736681	GTTAAGCCAGAAGAGCAGCAG	59.263	52.381	0.00	0.00	0.00	4.24
1558	1901	4.009370	GGTGAGTTCCTCAACTTTAGCT	57.991	45.455	2.06	0.00	44.06	3.32
1559	1902	3.997681	GGTGAGTTCCTCAACTTTAGCTC	59.002	47.826	2.06	0.00	44.06	4.09
1560	1903	3.997681	GTGAGTTCCTCAACTTTAGCTCC	59.002	47.826	0.00	0.00	43.37	4.70
1561	1904	3.254892	GAGTTCCTCAACTTTAGCTCCG	58.745	50.000	0.00	0.00	43.37	4.63
1566	1909	2.095718	CCTCAACTTTAGCTCCGTTTGC	60.096	50.000	0.00	0.00	0.00	3.68
1577	1920	3.630312	AGCTCCGTTTGCTTGTTTCTTAA	59.370	39.130	0.00	0.00	37.52	1.85
1602	1946	3.435671	CCTTTCTCGGTTCAGCGTATTTT	59.564	43.478	0.00	0.00	0.00	1.82
1603	1947	4.394795	CTTTCTCGGTTCAGCGTATTTTG	58.605	43.478	0.00	0.00	0.00	2.44
1604	1948	3.034721	TCTCGGTTCAGCGTATTTTGT	57.965	42.857	0.00	0.00	0.00	2.83
1605	1949	3.395639	TCTCGGTTCAGCGTATTTTGTT	58.604	40.909	0.00	0.00	0.00	2.83
1606	1950	3.810941	TCTCGGTTCAGCGTATTTTGTTT	59.189	39.130	0.00	0.00	0.00	2.83
1607	1951	3.879427	TCGGTTCAGCGTATTTTGTTTG	58.121	40.909	0.00	0.00	0.00	2.93
1608	1952	3.312973	TCGGTTCAGCGTATTTTGTTTGT	59.687	39.130	0.00	0.00	0.00	2.83
1609	1953	4.039032	CGGTTCAGCGTATTTTGTTTGTT	58.961	39.130	0.00	0.00	0.00	2.83
1610	1954	4.501198	CGGTTCAGCGTATTTTGTTTGTTT	59.499	37.500	0.00	0.00	0.00	2.83
1640	1984	4.680440	GCAAAAACCTGATGTGTTGGTCTT	60.680	41.667	0.00	0.00	32.98	3.01
1906	2250	7.636579	TGTGTAGGAACTAGGAACTGATACTA	58.363	38.462	0.00	0.00	44.14	1.82
2016	2360	3.434641	CAGTACGTACTTCCTTCGTCTCA	59.565	47.826	25.35	0.00	38.69	3.27
2206	2570	3.782893	CACGTATAGTTTTCTCGGTCGAC	59.217	47.826	7.13	7.13	0.00	4.20
2290	2655	2.630580	TGTATTCCAAAGCAAACCACCC	59.369	45.455	0.00	0.00	0.00	4.61
2295	2660	1.473080	CCAAAGCAAACCACCCTTGTG	60.473	52.381	0.00	0.00	42.39	3.33
2333	2698	2.749044	AGCAGCACATCAAGCCCG	60.749	61.111	0.00	0.00	0.00	6.13
2576	3005	0.749454	CCGGCAAGGATTTCTCCCAG	60.749	60.000	0.00	0.00	43.21	4.45
2581	3010	2.350522	CAAGGATTTCTCCCAGACACG	58.649	52.381	0.00	0.00	43.21	4.49
2593	3022	3.351416	GACACGAAACCCCACCGC	61.351	66.667	0.00	0.00	0.00	5.68
2623	3052	2.203294	GACCAGCCAAACCACCGT	60.203	61.111	0.00	0.00	0.00	4.83
2645	3074	2.819154	CACCATGCGCCATCACGA	60.819	61.111	4.18	0.00	34.06	4.35
2707	3138	1.219393	GGCCAAGAAGACCGGAGAG	59.781	63.158	9.46	0.00	0.00	3.20
2708	3139	1.258445	GGCCAAGAAGACCGGAGAGA	61.258	60.000	9.46	0.00	0.00	3.10
2719	3150	3.609703	GGAGAGAAGAGCCGAGCA	58.390	61.111	0.00	0.00	0.00	4.26

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
76	77	2.373169	TCTGAATGGGCAACAACTCTCT	59.627	45.455	0.00	0.00	39.74	3.10
115	116	0.958382	CCAATACACACCCACCCGTG	60.958	60.000	0.00	0.00	39.75	4.94
118	119	1.000145	CCCCAATACACACCCACCC	60.000	63.158	0.00	0.00	0.00	4.61
133	134	3.780804	AAAGCCAAAACAAATACCCCC	57.219	42.857	0.00	0.00	0.00	5.40
235	238	8.041829	ACATAGTATATTGACTAGTAGTGGCG	57.958	38.462	7.76	0.00	35.42	5.69
286	596	5.154932	ACACGTATCTCTCAGAAAAGTTCG	58.845	41.667	0.00	0.00	34.02	3.95
306	616	7.221259	GGTTGTGGTGTTTGAATAAAGTTACAC	59.779	37.037	0.00	0.00	0.00	2.90
357	691	5.299279	CACTCTTTCAGCCAACTCCTTTTTA	59.701	40.000	0.00	0.00	0.00	1.52
358	692	4.098501	CACTCTTTCAGCCAACTCCTTTTT	59.901	41.667	0.00	0.00	0.00	1.94
441	775	5.750352	TCTTTACGGAGGGAGTACATTTT	57.250	39.130	0.00	0.00	0.00	1.82
442	776	5.750352	TTCTTTACGGAGGGAGTACATTT	57.250	39.130	0.00	0.00	0.00	2.32
443	777	5.750352	TTTCTTTACGGAGGGAGTACATT	57.250	39.130	0.00	0.00	0.00	2.71
653	987	6.819649	TGCCTAATGTACATTAAGGTGTGTAC	59.180	38.462	27.12	17.83	46.74	2.90
741	1076	2.700371	CACACTCATATAGGTGCCTCCA	59.300	50.000	0.00	0.00	39.02	3.86
744	1079	3.386078	CAGACACACTCATATAGGTGCCT	59.614	47.826	7.02	0.00	36.99	4.75
757	1093	3.757270	AGTGCTAGTAGACAGACACACT	58.243	45.455	0.00	0.06	32.54	3.55
784	1120	7.296628	ACTTTAACAGGCAAACCATAATTCA	57.703	32.000	0.00	0.00	39.06	2.57
787	1123	7.015195	AGTCAACTTTAACAGGCAAACCATAAT	59.985	33.333	0.00	0.00	39.06	1.28
808	1147	6.392625	AAAGTCGCATATAGCTCTAGTCAA	57.607	37.500	0.00	0.00	42.61	3.18
816	1155	5.308825	AGCCATAAAAAGTCGCATATAGCT	58.691	37.500	0.00	0.00	42.61	3.32
833	1172	6.265196	CCATCTAATTTAACAGGCAAGCCATA	59.735	38.462	14.40	0.64	38.92	2.74
892	1231	5.984926	TGCTGTTGAAAATTAAAGCCTTCAG	59.015	36.000	0.00	0.00	0.00	3.02
954	1293	2.234414	CCATGGCAAGTTAAATGCAGGT	59.766	45.455	14.40	0.00	45.60	4.00
962	1301	6.379703	ACATAATGTTAGCCATGGCAAGTTAA	59.620	34.615	37.18	23.40	44.88	2.01
982	1322	8.965819	TGCTTCCATCTGCTTTAAATTACATAA	58.034	29.630	0.00	0.00	0.00	1.90
1099	1439	1.990799	TCGTCGTCTAGGCACATTTG	58.009	50.000	0.00	0.00	0.00	2.32
1118	1458	1.274167	CAATGCCAGCTTCCACAACAT	59.726	47.619	0.00	0.00	0.00	2.71
1121	1461	1.340889	GAACAATGCCAGCTTCCACAA	59.659	47.619	0.00	0.00	0.00	3.33
1145	1485	2.617774	GCCTCTGGATCATCTTGCTTTC	59.382	50.000	0.00	0.00	0.00	2.62
1228	1568	7.370383	TGATCAGATTGCTTTTCTTGGTTAAC	58.630	34.615	0.00	0.00	0.00	2.01
1342	1685	0.818445	CCTGGATTAGCAGCAGCCTG	60.818	60.000	0.00	0.00	43.56	4.85
1343	1686	1.277580	ACCTGGATTAGCAGCAGCCT	61.278	55.000	0.00	0.00	43.56	4.58
1344	1687	1.099879	CACCTGGATTAGCAGCAGCC	61.100	60.000	0.00	0.00	43.56	4.85
1552	1895	3.630312	AGAAACAAGCAAACGGAGCTAAA	59.370	39.130	0.00	0.00	42.53	1.85
1556	1899	2.492019	AAGAAACAAGCAAACGGAGC	57.508	45.000	0.00	0.00	0.00	4.70
1558	1901	4.035909	GGAGTTAAGAAACAAGCAAACGGA	59.964	41.667	0.00	0.00	38.12	4.69
1559	1902	4.036380	AGGAGTTAAGAAACAAGCAAACGG	59.964	41.667	0.00	0.00	38.12	4.44
1560	1903	5.169836	AGGAGTTAAGAAACAAGCAAACG	57.830	39.130	0.00	0.00	38.12	3.60
1561	1904	7.258441	AGAAAGGAGTTAAGAAACAAGCAAAC	58.742	34.615	0.00	0.00	38.12	2.93
1566	1909	5.758784	ACCGAGAAAGGAGTTAAGAAACAAG	59.241	40.000	0.00	0.00	34.80	3.16
1577	1920	0.038159	CGCTGAACCGAGAAAGGAGT	60.038	55.000	0.00	0.00	34.73	3.85
1609	1953	5.879223	ACACATCAGGTTTTTGCATCAAAAA	59.121	32.000	11.93	11.93	46.57	1.94
1610	1954	5.426504	ACACATCAGGTTTTTGCATCAAAA	58.573	33.333	1.05	1.05	40.85	2.44
1651	1995	0.690762	TACCCCTCTTCCACTGCAAC	59.309	55.000	0.00	0.00	0.00	4.17
1882	2226	8.694581	ATAGTATCAGTTCCTAGTTCCTACAC	57.305	38.462	0.00	0.00	0.00	2.90
2206	2570	0.591236	CGGGTGAAATATTTGGCGCG	60.591	55.000	5.17	13.14	0.00	6.86
2236	2600	2.946990	ACCCTTTTTCGGTACACTTGTG	59.053	45.455	0.00	0.00	0.00	3.33
2295	2660	2.103538	CCCAGCATTGCGATGTGC	59.896	61.111	15.45	3.51	46.70	4.57
2333	2698	7.841277	GCATTTGTTTCTTCTTCGTTTTCTTTC	59.159	33.333	0.00	0.00	0.00	2.62
2552	2981	1.136774	GAAATCCTTGCCGGTTCGC	59.863	57.895	1.90	0.00	0.00	4.70
2576	3005	3.351416	GCGGTGGGGTTTCGTGTC	61.351	66.667	0.00	0.00	0.00	3.67
2581	3010	3.299977	GTTGGGCGGTGGGGTTTC	61.300	66.667	0.00	0.00	0.00	2.78
2593	3022	3.894547	CTGGTCGGTTCCGGTTGGG	62.895	68.421	11.37	0.00	35.24	4.12
2603	3032	2.203294	GTGGTTTGGCTGGTCGGT	60.203	61.111	0.00	0.00	0.00	4.69
2623	3052	2.035469	ATGGCGCATGGTGTTGGA	59.965	55.556	10.83	0.00	0.00	3.53
2667	3096	0.730265	GTGTTGGTGTTCGCAGTGAA	59.270	50.000	0.00	0.00	0.00	3.18
2719	3150	3.772853	TTGTGCTGCTGCTCCCGTT	62.773	57.895	17.00	0.00	40.48	4.44

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.