AutoCloner

Multiple sequence alignment - TraesCS5B01G075400

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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	TraesCS5B01G075400	chr5B	100.000	2264	0	0	1	2264	89726818	89729081	0.000000e+00	4181.0
1	TraesCS5B01G075400	chr5B	87.534	2214	230	26	1	2190	584816929	584814738	0.000000e+00	2518.0
2	TraesCS5B01G075400	chr5B	90.742	1793	147	6	1	1788	64293431	64295209	0.000000e+00	2374.0
3	TraesCS5B01G075400	chr5B	92.563	1237	79	4	707	1941	387878839	387880064	0.000000e+00	1762.0
4	TraesCS5B01G075400	chr5B	82.796	279	42	5	1979	2253	387880062	387880338	6.250000e-61	244.0
5	TraesCS5B01G075400	chr5B	83.628	226	32	3	2031	2253	387880376	387880153	8.200000e-50	207.0
6	TraesCS5B01G075400	chr6B	90.162	2216	182	15	4	2214	281223409	281221225	0.000000e+00	2852.0
7	TraesCS5B01G075400	chr6B	86.907	1581	148	26	708	2253	605817498	605819054	0.000000e+00	1718.0
8	TraesCS5B01G075400	chr2D	90.248	2174	172	26	1	2157	632766140	632768290	0.000000e+00	2804.0
9	TraesCS5B01G075400	chr2D	93.277	1547	96	3	1	1543	476789251	476790793	0.000000e+00	2274.0
10	TraesCS5B01G075400	chr3B	88.573	2284	199	26	1	2253	809559737	809557485	0.000000e+00	2715.0
11	TraesCS5B01G075400	chr3B	79.845	129	22	4	2129	2255	21881590	21881716	8.610000e-15	91.6
12	TraesCS5B01G075400	chr3B	77.852	149	24	6	1913	2059	809557705	809557564	1.440000e-12	84.2
13	TraesCS5B01G075400	chr1D	88.417	2262	225	21	4	2253	14674863	14672627	0.000000e+00	2691.0
14	TraesCS5B01G075400	chr1D	88.754	1396	130	14	707	2096	446420011	446421385	0.000000e+00	1683.0
15	TraesCS5B01G075400	chr1D	84.028	144	23	0	2031	2174	446421501	446421358	3.030000e-29	139.0
16	TraesCS5B01G075400	chr4A	88.534	2163	210	21	55	2204	564697244	564699381	0.000000e+00	2586.0
17	TraesCS5B01G075400	chr2A	89.687	1978	162	17	3	1962	48624234	48622281	0.000000e+00	2484.0
18	TraesCS5B01G075400	chr2A	81.628	860	126	15	1410	2255	770003764	770002923	0.000000e+00	684.0
19	TraesCS5B01G075400	chr2A	87.636	275	33	1	1338	1611	150452194	150452468	3.630000e-83	318.0
20	TraesCS5B01G075400	chr2A	77.679	224	40	9	1977	2193	48611023	48610803	6.560000e-26	128.0
21	TraesCS5B01G075400	chr2B	93.080	1474	90	4	1	1467	546619166	546620634	0.000000e+00	2146.0
22	TraesCS5B01G075400	chr2B	90.450	1466	106	16	707	2157	215847876	215849322	0.000000e+00	1901.0
23	TraesCS5B01G075400	chr2B	87.764	474	36	8	1498	1960	546620617	546621079	3.310000e-148	534.0
24	TraesCS5B01G075400	chr1B	88.220	1511	126	20	714	2193	549918216	549916727	0.000000e+00	1757.0
25	TraesCS5B01G075400	chr1B	88.563	341	39	0	1274	1614	551877687	551877347	4.500000e-112	414.0
26	TraesCS5B01G075400	chrUn	88.295	1478	130	25	707	2162	10399877	10401333	0.000000e+00	1731.0
27	TraesCS5B01G075400	chrUn	88.459	1447	124	25	738	2162	349150181	349151606	0.000000e+00	1707.0
28	TraesCS5B01G075400	chr4B	85.110	544	50	13	1567	2098	9634866	9635390	5.540000e-146	527.0
29	TraesCS5B01G075400	chr4B	82.439	205	34	1	2032	2234	467347754	467347958	6.430000e-41	178.0
30	TraesCS5B01G075400	chr6D	80.349	229	38	7	2031	2255	377214449	377214224	1.390000e-37	167.0
31	TraesCS5B01G075400	chr3A	80.319	188	30	5	1913	2098	349070782	349070964	3.920000e-28	135.0
32	TraesCS5B01G075400	chr5D	88.393	112	12	1	2031	2141	520880583	520880694	1.410000e-27	134.0
33	TraesCS5B01G075400	chr7D	100.000	29	0	0	2227	2255	572999071	572999099	1.000000e-03	54.7

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	TraesCS5B01G075400	chr5B	89726818	89729081	2263	False	4181.0	4181	100.0000	1	2264	1	chr5B.!!$F2	2263
1	TraesCS5B01G075400	chr5B	584814738	584816929	2191	True	2518.0	2518	87.5340	1	2190	1	chr5B.!!$R2	2189
2	TraesCS5B01G075400	chr5B	64293431	64295209	1778	False	2374.0	2374	90.7420	1	1788	1	chr5B.!!$F1	1787
3	TraesCS5B01G075400	chr5B	387878839	387880338	1499	False	1003.0	1762	87.6795	707	2253	2	chr5B.!!$F3	1546
4	TraesCS5B01G075400	chr6B	281221225	281223409	2184	True	2852.0	2852	90.1620	4	2214	1	chr6B.!!$R1	2210
5	TraesCS5B01G075400	chr6B	605817498	605819054	1556	False	1718.0	1718	86.9070	708	2253	1	chr6B.!!$F1	1545
6	TraesCS5B01G075400	chr2D	632766140	632768290	2150	False	2804.0	2804	90.2480	1	2157	1	chr2D.!!$F2	2156
7	TraesCS5B01G075400	chr2D	476789251	476790793	1542	False	2274.0	2274	93.2770	1	1543	1	chr2D.!!$F1	1542
8	TraesCS5B01G075400	chr3B	809557485	809559737	2252	True	1399.6	2715	83.2125	1	2253	2	chr3B.!!$R1	2252
9	TraesCS5B01G075400	chr1D	14672627	14674863	2236	True	2691.0	2691	88.4170	4	2253	1	chr1D.!!$R1	2249
10	TraesCS5B01G075400	chr1D	446420011	446421385	1374	False	1683.0	1683	88.7540	707	2096	1	chr1D.!!$F1	1389
11	TraesCS5B01G075400	chr4A	564697244	564699381	2137	False	2586.0	2586	88.5340	55	2204	1	chr4A.!!$F1	2149
12	TraesCS5B01G075400	chr2A	48622281	48624234	1953	True	2484.0	2484	89.6870	3	1962	1	chr2A.!!$R2	1959
13	TraesCS5B01G075400	chr2A	770002923	770003764	841	True	684.0	684	81.6280	1410	2255	1	chr2A.!!$R3	845
14	TraesCS5B01G075400	chr2B	215847876	215849322	1446	False	1901.0	1901	90.4500	707	2157	1	chr2B.!!$F1	1450
15	TraesCS5B01G075400	chr2B	546619166	546621079	1913	False	1340.0	2146	90.4220	1	1960	2	chr2B.!!$F2	1959
16	TraesCS5B01G075400	chr1B	549916727	549918216	1489	True	1757.0	1757	88.2200	714	2193	1	chr1B.!!$R1	1479
17	TraesCS5B01G075400	chrUn	10399877	10401333	1456	False	1731.0	1731	88.2950	707	2162	1	chrUn.!!$F1	1455
18	TraesCS5B01G075400	chrUn	349150181	349151606	1425	False	1707.0	1707	88.4590	738	2162	1	chrUn.!!$F2	1424
19	TraesCS5B01G075400	chr4B	9634866	9635390	524	False	527.0	527	85.1100	1567	2098	1	chr4B.!!$F1	531

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
735	736	0.032017	GGACTAGCCTTGGAGAGGGA	60.032	60.0	0.0	0.0	46.4	4.2	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2242	2576	1.092348	GATTCAAACCCTACCGCCAC	58.908	55.0	0.0	0.0	0.0	5.01	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
48	49	5.177511	CACTTTCATCAAGCTCAACGAGTAA	59.822	40.000	0.00	0.00	35.65	2.24
218	219	2.478335	GATGAGCCGGGTGGGACAAA	62.478	60.000	12.94	0.00	44.16	2.83
255	256	4.161565	TCTTATGGTGGAGTTGCTTACGAT	59.838	41.667	0.00	0.00	0.00	3.73
258	259	2.563620	TGGTGGAGTTGCTTACGATGTA	59.436	45.455	0.00	0.00	0.00	2.29
310	311	2.041620	AGGCCACACAAGTATCATTGGT	59.958	45.455	5.01	0.00	34.36	3.67
354	355	1.067212	ACACGAGCGAGAAACTTGACT	59.933	47.619	0.00	0.00	0.00	3.41
426	427	2.115052	TTGACATGGGCGCCTTGT	59.885	55.556	27.92	27.92	43.19	3.16
466	467	1.137872	CCTCACAGTGGCCTGAGTATC	59.862	57.143	16.23	0.00	41.50	2.24
534	535	4.288366	AGGGGAAGAAGAAGAAAGAAGAGG	59.712	45.833	0.00	0.00	0.00	3.69
617	618	2.436646	CATGGAGGCACCGGACAC	60.437	66.667	9.46	0.00	42.61	3.67
642	643	3.317711	ACAATTGTGGAGAATGCAACGAA	59.682	39.130	11.07	0.00	39.09	3.85
662	663	4.152402	CGAAACAGGACACAATGTTAGGAG	59.848	45.833	0.00	0.00	38.66	3.69
667	668	3.264193	AGGACACAATGTTAGGAGATGCA	59.736	43.478	0.00	0.00	0.00	3.96
668	669	3.375299	GGACACAATGTTAGGAGATGCAC	59.625	47.826	0.00	0.00	0.00	4.57
669	670	3.002791	ACACAATGTTAGGAGATGCACG	58.997	45.455	0.00	0.00	0.00	5.34
680	681	3.452627	AGGAGATGCACGAAGAAACCTAT	59.547	43.478	0.00	0.00	0.00	2.57
710	711	1.578583	GGCACTAGTCAAACACGTGT	58.421	50.000	17.22	17.22	0.00	4.49
712	713	3.323243	GGCACTAGTCAAACACGTGTAT	58.677	45.455	23.69	9.58	0.00	2.29
735	736	0.032017	GGACTAGCCTTGGAGAGGGA	60.032	60.000	0.00	0.00	46.40	4.20
736	737	1.413808	GGACTAGCCTTGGAGAGGGAT	60.414	57.143	0.00	0.00	46.40	3.85
741	742	1.566298	GCCTTGGAGAGGGATGTGGT	61.566	60.000	0.00	0.00	46.40	4.16
742	743	1.879575	CCTTGGAGAGGGATGTGGTA	58.120	55.000	0.00	0.00	42.26	3.25
1214	1256	2.653726	TGTATGCCCCAACTATGCTTG	58.346	47.619	0.00	0.00	0.00	4.01
1397	1440	7.946776	AGAAGATATCCAAAAGGACCAATATGG	59.053	37.037	0.00	0.00	45.02	2.74
1403	1446	6.502138	TCCAAAAGGACCAATATGGAGATTT	58.498	36.000	2.85	0.00	40.96	2.17
1467	1510	1.489481	TGGAGGAAGAGCGTCATCAT	58.511	50.000	1.10	0.00	33.11	2.45
1474	1517	2.810439	AGAGCGTCATCATAAGGAGC	57.190	50.000	0.00	0.00	0.00	4.70
1611	1655	2.105821	ACGTGACAAGAAGGGGAAATGA	59.894	45.455	0.00	0.00	0.00	2.57
1624	1668	4.993705	GGGAAATGACCCCATATGACTA	57.006	45.455	3.65	0.00	43.81	2.59
1677	1721	1.136305	ACTCGTCATGTAACCGGATGG	59.864	52.381	9.46	0.00	42.84	3.51
1845	1905	5.332808	GCAATTTCTGTGATTTGTCTGCAAC	60.333	40.000	0.00	0.00	33.82	4.17
1879	1960	3.394836	GCTGAGAAGAGGGGCGGT	61.395	66.667	0.00	0.00	0.00	5.68
1949	2069	0.766674	TGGTGGTAGGGTGCTTGACT	60.767	55.000	0.00	0.00	0.00	3.41
1966	2086	0.889306	ACTCTACCGCCAGAGACAAC	59.111	55.000	15.92	0.00	44.11	3.32
1974	2094	1.146358	GCCAGAGACAACGGCGATAC	61.146	60.000	16.62	0.00	35.79	2.24
1975	2095	0.172578	CCAGAGACAACGGCGATACA	59.827	55.000	16.62	0.00	0.00	2.29
2099	2417	3.093835	CCATGGCGGTAGGGGGAA	61.094	66.667	0.00	0.00	0.00	3.97
2100	2418	2.460853	CCATGGCGGTAGGGGGAAT	61.461	63.158	0.00	0.00	0.00	3.01
2102	2425	0.768622	CATGGCGGTAGGGGGAATAA	59.231	55.000	0.00	0.00	0.00	1.40
2121	2444	6.310711	GGAATAAGGTACTGTGACGAGAAAAG	59.689	42.308	0.00	0.00	40.86	2.27
2190	2522	2.590092	GCTTGACCCTACCGCCAT	59.410	61.111	0.00	0.00	0.00	4.40
2214	2546	4.878397	GGTGCTAGCTTTTATCATCACAGT	59.122	41.667	17.23	0.00	0.00	3.55
2217	2550	6.018669	GTGCTAGCTTTTATCATCACAGTACC	60.019	42.308	17.23	0.00	0.00	3.34
2221	2554	9.988815	CTAGCTTTTATCATCACAGTACCTTAT	57.011	33.333	0.00	0.00	0.00	1.73
2255	2589	4.029809	GGCTGTGGCGGTAGGGTT	62.030	66.667	0.00	0.00	39.81	4.11
2256	2590	2.033602	GCTGTGGCGGTAGGGTTT	59.966	61.111	0.00	0.00	0.00	3.27
2257	2591	2.332654	GCTGTGGCGGTAGGGTTTG	61.333	63.158	0.00	0.00	0.00	2.93
2258	2592	1.373435	CTGTGGCGGTAGGGTTTGA	59.627	57.895	0.00	0.00	0.00	2.69
2259	2593	0.250553	CTGTGGCGGTAGGGTTTGAA	60.251	55.000	0.00	0.00	0.00	2.69
2260	2594	0.402504	TGTGGCGGTAGGGTTTGAAT	59.597	50.000	0.00	0.00	0.00	2.57
2261	2595	1.092348	GTGGCGGTAGGGTTTGAATC	58.908	55.000	0.00	0.00	0.00	2.52
2262	2596	0.034863	TGGCGGTAGGGTTTGAATCC	60.035	55.000	0.00	0.00	0.00	3.01
2263	2597	0.750546	GGCGGTAGGGTTTGAATCCC	60.751	60.000	3.02	3.02	44.90	3.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
48	49	5.392380	CGTGCTTTCAGAATGCTTTAGGAAT	60.392	40.000	18.99	0.00	34.76	3.01
141	142	4.157840	ACCAGTTGTTGTTTGGAAGACTTC	59.842	41.667	6.66	6.66	35.89	3.01
218	219	2.770232	CCATAAGACCTACCGTCCCTTT	59.230	50.000	0.00	0.00	43.08	3.11
255	256	3.695060	ACCAACGGTTTTTGATGTGTACA	59.305	39.130	0.00	0.00	27.29	2.90
258	259	2.737039	GCACCAACGGTTTTTGATGTGT	60.737	45.455	0.00	0.00	31.02	3.72
310	311	1.739466	GGTCATCAAATGCGAGCAAGA	59.261	47.619	0.57	1.37	0.00	3.02
339	340	3.673594	CGGATACAGTCAAGTTTCTCGCT	60.674	47.826	0.00	0.00	0.00	4.93
354	355	1.211703	ACCATTGTGCCATCGGATACA	59.788	47.619	0.00	0.00	0.00	2.29
426	427	6.015918	TGAGGCATCAAGGAAAGGATTAAAA	58.984	36.000	0.00	0.00	30.61	1.52
466	467	3.266964	CACAATGTCTGGGCCGTG	58.733	61.111	0.00	0.00	0.00	4.94
471	472	1.386533	GATCTGGCACAATGTCTGGG	58.613	55.000	0.00	0.00	38.70	4.45
534	535	5.923204	AGATCATCCATGTCACTCCTAAAC	58.077	41.667	0.00	0.00	0.00	2.01
569	570	4.079253	ACTACCAAATTGCTTCATTCCGT	58.921	39.130	0.00	0.00	0.00	4.69
617	618	3.663995	TGCATTCTCCACAATTGTTGG	57.336	42.857	8.77	13.71	34.12	3.77
642	643	4.974645	TCTCCTAACATTGTGTCCTGTT	57.025	40.909	0.00	0.00	38.95	3.16
662	663	4.873827	TGGTTATAGGTTTCTTCGTGCATC	59.126	41.667	0.00	0.00	0.00	3.91
667	668	4.687483	CGTGTTGGTTATAGGTTTCTTCGT	59.313	41.667	0.00	0.00	0.00	3.85
668	669	4.092383	CCGTGTTGGTTATAGGTTTCTTCG	59.908	45.833	0.00	0.00	0.00	3.79
669	670	4.393990	CCCGTGTTGGTTATAGGTTTCTTC	59.606	45.833	0.00	0.00	35.15	2.87
680	681	1.001181	GACTAGTGCCCGTGTTGGTTA	59.999	52.381	0.00	0.00	35.15	2.85
731	732	0.716591	TCCTCCACTACCACATCCCT	59.283	55.000	0.00	0.00	0.00	4.20
735	736	2.188817	GTCCTTCCTCCACTACCACAT	58.811	52.381	0.00	0.00	0.00	3.21
736	737	1.149288	AGTCCTTCCTCCACTACCACA	59.851	52.381	0.00	0.00	0.00	4.17
741	742	1.930914	AGGCTAGTCCTTCCTCCACTA	59.069	52.381	0.00	0.00	44.75	2.74
742	743	0.713579	AGGCTAGTCCTTCCTCCACT	59.286	55.000	0.00	0.00	44.75	4.00
769	770	3.551496	TTCCTCCACAGCCTTGGCG	62.551	63.158	5.95	4.19	36.48	5.69
774	775	0.413832	TAGTCCTTCCTCCACAGCCT	59.586	55.000	0.00	0.00	0.00	4.58
778	779	0.413832	AGGCTAGTCCTTCCTCCACA	59.586	55.000	0.00	0.00	44.75	4.17
991	1028	2.590821	GGATGAAGCCATGCCTACAAT	58.409	47.619	0.00	0.00	35.39	2.71
1214	1256	1.132640	GTTGGAAGCGCACGATCAC	59.867	57.895	11.47	0.00	0.00	3.06
1397	1440	1.332065	GCTGGCGCCTAAGAAAATCTC	59.668	52.381	29.70	0.00	0.00	2.75
1467	1510	2.498941	CCGCTCCATCCGCTCCTTA	61.499	63.158	0.00	0.00	0.00	2.69
1474	1517	2.125147	TTGCTTCCGCTCCATCCG	60.125	61.111	0.00	0.00	36.97	4.18
1611	1655	4.975794	AGGCTTTACTTAGTCATATGGGGT	59.024	41.667	2.13	0.00	0.00	4.95
1641	1685	3.119096	GTCCACCGAAGCGAAGGC	61.119	66.667	0.00	0.00	40.37	4.35
1642	1686	1.446272	GAGTCCACCGAAGCGAAGG	60.446	63.158	0.00	0.00	0.00	3.46
1643	1687	1.801913	CGAGTCCACCGAAGCGAAG	60.802	63.158	0.00	0.00	0.00	3.79
1644	1688	2.257371	CGAGTCCACCGAAGCGAA	59.743	61.111	0.00	0.00	0.00	4.70
1645	1689	2.974489	GACGAGTCCACCGAAGCGA	61.974	63.158	0.00	0.00	0.00	4.93
1646	1690	2.504244	GACGAGTCCACCGAAGCG	60.504	66.667	0.00	0.00	0.00	4.68
1677	1721	5.204409	TCATGATAAATTTGGCATGGCTC	57.796	39.130	21.08	8.09	38.82	4.70
1845	1905	5.233225	TCTCAGCACAATAGTTCACAGAAG	58.767	41.667	0.00	0.00	0.00	2.85
1949	2069	1.592400	CCGTTGTCTCTGGCGGTAGA	61.592	60.000	0.00	0.00	39.41	2.59
1983	2106	6.501781	TGGTTTATCGTTAGAGTAGCTTAGC	58.498	40.000	0.00	0.00	0.00	3.09
1984	2107	8.404000	TCTTGGTTTATCGTTAGAGTAGCTTAG	58.596	37.037	0.00	0.00	0.00	2.18
1994	2117	4.332819	CCAAGGCTCTTGGTTTATCGTTAG	59.667	45.833	20.06	0.00	34.92	2.34
1996	2119	3.081804	CCAAGGCTCTTGGTTTATCGTT	58.918	45.455	20.06	0.00	34.92	3.85
2059	2296	1.762522	CTGGCGGTAGGATCCTGCAT	61.763	60.000	28.38	4.27	0.00	3.96
2098	2416	6.645415	CACTTTTCTCGTCACAGTACCTTATT	59.355	38.462	0.00	0.00	0.00	1.40
2099	2417	6.015688	TCACTTTTCTCGTCACAGTACCTTAT	60.016	38.462	0.00	0.00	0.00	1.73
2100	2418	5.300034	TCACTTTTCTCGTCACAGTACCTTA	59.700	40.000	0.00	0.00	0.00	2.69
2102	2425	3.635373	TCACTTTTCTCGTCACAGTACCT	59.365	43.478	0.00	0.00	0.00	3.08
2190	2522	4.842574	TGTGATGATAAAAGCTAGCACCA	58.157	39.130	18.83	5.42	0.00	4.17
2197	2529	7.934120	GGATAAGGTACTGTGATGATAAAAGCT	59.066	37.037	0.00	0.00	40.86	3.74
2199	2531	7.661847	GGGGATAAGGTACTGTGATGATAAAAG	59.338	40.741	0.00	0.00	40.86	2.27
2242	2576	1.092348	GATTCAAACCCTACCGCCAC	58.908	55.000	0.00	0.00	0.00	5.01

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.