AutoCloner

Multiple sequence alignment - TraesCS1A01G053300

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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	TraesCS1A01G053300	chr1A	100.000	1940	0	0	988	2927	35485992	35487931	0.000000e+00	3583
1	TraesCS1A01G053300	chr1A	89.649	1797	175	7	1134	2927	35525792	35527580	0.000000e+00	2278
2	TraesCS1A01G053300	chr1A	89.965	1734	158	10	989	2709	35578654	35576924	0.000000e+00	2224
3	TraesCS1A01G053300	chr1A	87.010	1709	160	31	1011	2692	35536206	35537879	0.000000e+00	1869
4	TraesCS1A01G053300	chr1A	100.000	604	0	0	1	604	35485005	35485608	0.000000e+00	1116
5	TraesCS1A01G053300	chr1A	86.535	557	47	13	1	541	35535436	35535980	3.250000e-164	588
6	TraesCS1A01G053300	chr1A	87.526	473	40	11	1	464	35514530	35514992	2.000000e-146	529
7	TraesCS1A01G053300	chr1A	84.043	564	54	22	48	603	35579245	35578710	7.240000e-141	510
8	TraesCS1A01G053300	chr1A	90.233	215	21	0	2713	2927	35576297	35576083	6.180000e-72	281
9	TraesCS1A01G053300	chr1A	88.785	214	18	3	2718	2927	35538510	35538721	1.040000e-64	257
10	TraesCS1A01G053300	chr1D	91.538	1950	144	10	994	2927	36315606	36317550	0.000000e+00	2667
11	TraesCS1A01G053300	chr1D	92.990	913	58	6	1801	2709	36362374	36361464	0.000000e+00	1327
12	TraesCS1A01G053300	chr1D	89.179	804	75	6	989	1781	36363158	36362356	0.000000e+00	992
13	TraesCS1A01G053300	chr1D	77.714	1050	176	33	1594	2630	24145469	24146473	9.030000e-165	590
14	TraesCS1A01G053300	chr1D	84.397	564	51	22	48	604	36363750	36363217	1.200000e-143	520
15	TraesCS1A01G053300	chr1D	89.116	294	18	7	136	420	36314955	36315243	1.290000e-93	353
16	TraesCS1A01G053300	chr1B	85.384	1642	191	28	991	2600	56016955	56018579	0.000000e+00	1657
17	TraesCS1A01G053300	chr1B	91.286	1205	91	7	1004	2196	56140945	56139743	0.000000e+00	1631
18	TraesCS1A01G053300	chr1B	87.961	1221	130	7	989	2196	55998301	55999517	0.000000e+00	1424
19	TraesCS1A01G053300	chr1B	87.469	1229	129	11	989	2196	55977034	55978258	0.000000e+00	1393
20	TraesCS1A01G053300	chr1B	94.193	706	39	2	2224	2927	55978255	55978960	0.000000e+00	1075
21	TraesCS1A01G053300	chr1B	94.193	706	39	2	2224	2927	55999514	56000219	0.000000e+00	1075
22	TraesCS1A01G053300	chr1B	91.598	488	39	2	2224	2709	56139746	56139259	0.000000e+00	673
23	TraesCS1A01G053300	chr1B	89.598	423	26	10	48	464	56016184	56016594	3.340000e-144	521
24	TraesCS1A01G053300	chr1B	83.942	548	50	22	48	580	55976428	55976952	9.430000e-135	490
25	TraesCS1A01G053300	chr1B	86.557	424	44	8	48	464	56141739	56141322	3.440000e-124	455
26	TraesCS1A01G053300	chr1B	84.928	345	33	11	127	464	55997571	55997903	6.050000e-87	331
27	TraesCS1A01G053300	chr1B	92.093	215	17	0	2713	2927	56138633	56138419	1.320000e-78	303
28	TraesCS1A01G053300	chr1B	90.233	215	14	3	1	215	55944634	55944841	1.030000e-69	274
29	TraesCS1A01G053300	chr1B	90.233	215	14	3	1	215	55955887	55956094	1.030000e-69	274
30	TraesCS1A01G053300	chr1B	88.479	217	19	5	2713	2927	56019015	56019227	1.040000e-64	257

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	TraesCS1A01G053300	chr1A	35485005	35487931	2926	False	2349.500000	3583	100.000000	1	2927	2	chr1A.!!$F3	2926
1	TraesCS1A01G053300	chr1A	35525792	35527580	1788	False	2278.000000	2278	89.649000	1134	2927	1	chr1A.!!$F2	1793
2	TraesCS1A01G053300	chr1A	35576083	35579245	3162	True	1005.000000	2224	88.080333	48	2927	3	chr1A.!!$R1	2879
3	TraesCS1A01G053300	chr1A	35535436	35538721	3285	False	904.666667	1869	87.443333	1	2927	3	chr1A.!!$F4	2926
4	TraesCS1A01G053300	chr1D	36314955	36317550	2595	False	1510.000000	2667	90.327000	136	2927	2	chr1D.!!$F2	2791
5	TraesCS1A01G053300	chr1D	36361464	36363750	2286	True	946.333333	1327	88.855333	48	2709	3	chr1D.!!$R1	2661
6	TraesCS1A01G053300	chr1D	24145469	24146473	1004	False	590.000000	590	77.714000	1594	2630	1	chr1D.!!$F1	1036
7	TraesCS1A01G053300	chr1B	55976428	55978960	2532	False	986.000000	1393	88.534667	48	2927	3	chr1B.!!$F3	2879
8	TraesCS1A01G053300	chr1B	55997571	56000219	2648	False	943.333333	1424	89.027333	127	2927	3	chr1B.!!$F4	2800
9	TraesCS1A01G053300	chr1B	56016184	56019227	3043	False	811.666667	1657	87.820333	48	2927	3	chr1B.!!$F5	2879
10	TraesCS1A01G053300	chr1B	56138419	56141739	3320	True	765.500000	1631	90.383500	48	2927	4	chr1B.!!$R1	2879

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
390	406	1.131126	CGCAGGAAGGTACATTGCAAG	59.869	52.381	14.25	7.14	34.56	4.01	F
1346	1413	0.037419	GTCAACCGCCATGGCAAAAT	60.037	50.000	34.93	15.86	43.94	1.82	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1389	1456	0.243907	GCTGTAGCCTCTCGTTGACA	59.756	55.0	0.0	0.0	34.31	3.58	R
2899	3830	0.734889	GGTCGAGTTGCATGGGAATG	59.265	55.0	0.0	0.0	0.00	2.67	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
95	97	4.040936	TGGAGTTTTTGGGCAGCTATTA	57.959	40.909	0.00	0.00	0.00	0.98
151	154	1.218704	AGGGTTGGCATATTGCTGGAT	59.781	47.619	0.00	0.00	44.28	3.41
227	231	7.558444	TGGTTTTAGGTTGTCAATTTGACTACT	59.442	33.333	29.74	23.82	46.92	2.57
297	305	7.535599	GCTGTAGAATGAAGCTTTAAAGTGTTC	59.464	37.037	16.38	17.60	34.05	3.18
387	403	1.933853	CTACGCAGGAAGGTACATTGC	59.066	52.381	3.33	3.33	0.00	3.56
390	406	1.131126	CGCAGGAAGGTACATTGCAAG	59.869	52.381	14.25	7.14	34.56	4.01
475	495	3.746492	GTGTACACACATGACTTTCTCCC	59.254	47.826	21.14	0.00	45.75	4.30
481	508	3.146066	CACATGACTTTCTCCCGGAAAA	58.854	45.455	0.73	0.00	42.52	2.29
482	509	3.568007	CACATGACTTTCTCCCGGAAAAA	59.432	43.478	0.73	0.00	42.52	1.94
515	544	7.622893	AAACATAAAATGGCAAAAACACACT	57.377	28.000	0.00	0.00	33.60	3.55
519	548	5.544136	AAAATGGCAAAAACACACTGTTC	57.456	34.783	0.00	0.00	40.14	3.18
1032	1088	2.675423	CCACCCTCGTCCTCGTCA	60.675	66.667	0.00	0.00	38.33	4.35
1038	1094	2.231529	CCCTCGTCCTCGTCATATCTT	58.768	52.381	0.00	0.00	38.33	2.40
1090	1156	1.670590	GCCGCAGCCAGATCTAGAT	59.329	57.895	4.47	4.47	0.00	1.98
1114	1180	3.022401	GCAAAAGCGGCGATCGTGA	62.022	57.895	17.81	0.00	41.72	4.35
1117	1183	3.932580	AAAGCGGCGATCGTGAGCA	62.933	57.895	24.82	0.00	41.72	4.26
1181	1247	1.956170	CGGCTTTCCCATCGGATCG	60.956	63.158	0.00	0.00	38.24	3.69
1205	1271	3.097162	GGAAGGTGGGGCTAGGGG	61.097	72.222	0.00	0.00	0.00	4.79
1272	1338	2.997315	CGAGGGAGGCTGGTGTCA	60.997	66.667	0.00	0.00	0.00	3.58
1293	1359	0.612453	TGCCATCAATGCTCAAGCCA	60.612	50.000	0.00	0.00	41.18	4.75
1302	1369	2.988839	GCTCAAGCCATGGGGGAGT	61.989	63.158	15.13	0.00	40.01	3.85
1346	1413	0.037419	GTCAACCGCCATGGCAAAAT	60.037	50.000	34.93	15.86	43.94	1.82
1347	1414	0.683973	TCAACCGCCATGGCAAAATT	59.316	45.000	34.93	19.75	43.94	1.82
1350	1417	3.055530	TCAACCGCCATGGCAAAATTATT	60.056	39.130	34.93	14.96	43.94	1.40
1365	1432	1.546589	TTATTGCCTCGGACACGGGT	61.547	55.000	0.00	0.00	39.51	5.28
1374	1441	1.911766	GGACACGGGTTCCTCCTCA	60.912	63.158	0.00	0.00	36.25	3.86
1389	1456	6.196918	TCCTCCTCAAATCAGCAATATGAT	57.803	37.500	0.00	0.00	41.72	2.45
1394	1461	6.829811	TCCTCAAATCAGCAATATGATGTCAA	59.170	34.615	0.00	0.00	39.84	3.18
1518	1585	3.884774	TTGAAGGCACGCCCTGGT	61.885	61.111	3.95	0.00	45.62	4.00
1549	1616	1.153107	CTTGCGATGCCATCCCTCA	60.153	57.895	0.00	0.00	0.00	3.86
1563	1630	4.457496	CTCATGGCCACGACCGCT	62.457	66.667	8.16	0.00	0.00	5.52
1876	1956	1.815421	CTGCTATTTCCTGGCGCGT	60.815	57.895	8.43	0.00	33.18	6.01
2018	2101	6.209192	TCACATTCAATTCAGTGCTACCATTT	59.791	34.615	0.00	0.00	32.25	2.32
2068	2151	7.009179	TGTTCAGATAGAATCAGAGTTGGTT	57.991	36.000	0.00	0.00	38.76	3.67
2217	2301	3.438216	TCATCAGCAATTGGAAGGACA	57.562	42.857	7.72	0.00	0.00	4.02
2244	2328	7.938140	ATGTGGTGTACTAGTAATTGCATTT	57.062	32.000	3.61	0.00	0.00	2.32
2271	2355	5.576447	TGATGCTCGAGTTAGTATGTTCA	57.424	39.130	15.13	0.00	0.00	3.18
2278	2390	6.697455	GCTCGAGTTAGTATGTTCATTGATGA	59.303	38.462	15.13	0.00	34.44	2.92
2335	2463	9.060347	CAATATCAATGCTAGTACCAACTTCAT	57.940	33.333	0.00	0.00	37.15	2.57
2336	2464	6.932356	ATCAATGCTAGTACCAACTTCATG	57.068	37.500	0.00	0.00	37.15	3.07
2337	2465	4.635765	TCAATGCTAGTACCAACTTCATGC	59.364	41.667	0.00	0.00	37.15	4.06
2338	2466	3.694043	TGCTAGTACCAACTTCATGCA	57.306	42.857	0.00	0.00	37.15	3.96
2339	2467	4.220693	TGCTAGTACCAACTTCATGCAT	57.779	40.909	0.00	0.00	37.15	3.96
2340	2468	5.351948	TGCTAGTACCAACTTCATGCATA	57.648	39.130	0.00	0.00	37.15	3.14
2455	2589	3.834056	TGGGGCCGGGACCAAAAA	61.834	61.111	23.29	0.00	32.89	1.94
2683	2825	2.042831	GTGTGAGTGGGGCTGATGC	61.043	63.158	0.00	0.00	38.76	3.91
2711	2853	0.859788	AGTTCGTGCACGCGTTTTTG	60.860	50.000	33.63	6.04	39.60	2.44
2747	3675	6.828788	GGGGGTTATTTCTTTGTTTTACCAA	58.171	36.000	0.00	0.00	0.00	3.67
2766	3694	3.865745	CCAAAGCGACTATTCCTACAGTG	59.134	47.826	0.00	0.00	0.00	3.66

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
8	9	2.159627	GCACAACCGGCTACATATATGC	59.840	50.000	12.79	0.00	0.00	3.14
17	19	2.346284	AAACAGGGCACAACCGGCTA	62.346	55.000	0.00	0.00	40.62	3.93
19	21	2.304901	AAAAACAGGGCACAACCGGC	62.305	55.000	0.00	0.00	40.62	6.13
196	200	5.743636	ATTGACAACCTAAAACCATGCAT	57.256	34.783	0.00	0.00	0.00	3.96
197	201	5.543507	AATTGACAACCTAAAACCATGCA	57.456	34.783	0.00	0.00	0.00	3.96
315	331	8.267620	TGATCTACACATTTACCTTCATGTTG	57.732	34.615	0.00	0.00	30.90	3.33
387	403	9.124807	GGATCACCGTTTTTAAAACTAATCTTG	57.875	33.333	16.96	6.38	0.00	3.02
501	528	1.895798	TGGAACAGTGTGTTTTTGCCA	59.104	42.857	0.00	0.00	41.28	4.92
987	1043	0.175531	GCGGCATTTAAAGCATGGGT	59.824	50.000	0.00	0.00	0.00	4.51
1032	1088	5.708230	GTGGTGAGGACGAGATCTAAGATAT	59.292	44.000	0.00	0.00	0.00	1.63
1038	1094	2.366533	GTGTGGTGAGGACGAGATCTA	58.633	52.381	0.00	0.00	0.00	1.98
1218	1284	2.913060	GGATCTACCTCCGCGGCT	60.913	66.667	23.51	7.74	35.61	5.52
1267	1333	1.131883	GAGCATTGATGGCAGTGACAC	59.868	52.381	0.00	0.00	33.97	3.67
1272	1338	0.815734	GCTTGAGCATTGATGGCAGT	59.184	50.000	0.00	0.00	41.59	4.40
1293	1359	4.096003	CGCCGTTGACTCCCCCAT	62.096	66.667	0.00	0.00	0.00	4.00
1342	1409	2.422127	CCGTGTCCGAGGCAATAATTTT	59.578	45.455	0.00	0.00	35.63	1.82
1346	1413	1.219664	CCCGTGTCCGAGGCAATAA	59.780	57.895	0.00	0.00	35.63	1.40
1347	1414	1.546589	AACCCGTGTCCGAGGCAATA	61.547	55.000	0.00	0.00	35.63	1.90
1350	1417	3.998672	GAACCCGTGTCCGAGGCA	61.999	66.667	0.00	0.00	35.63	4.75
1354	1421	2.993264	GGAGGAACCCGTGTCCGA	60.993	66.667	0.00	0.00	35.63	4.55
1365	1432	6.005066	TCATATTGCTGATTTGAGGAGGAA	57.995	37.500	0.00	0.00	0.00	3.36
1374	1441	6.539826	TCTCGTTGACATCATATTGCTGATTT	59.460	34.615	0.00	0.00	33.59	2.17
1389	1456	0.243907	GCTGTAGCCTCTCGTTGACA	59.756	55.000	0.00	0.00	34.31	3.58
1394	1461	1.893786	CCAAGCTGTAGCCTCTCGT	59.106	57.895	0.00	0.00	43.38	4.18
1432	1499	3.443045	GTTGCCGGTGCCTGATGG	61.443	66.667	1.90	0.00	36.33	3.51
1530	1597	1.153086	GAGGGATGGCATCGCAAGT	60.153	57.895	36.15	21.93	43.92	3.16
1574	1641	2.203195	ACTCAAACGCCTGCTGCA	60.203	55.556	0.88	0.88	41.33	4.41
1657	1724	5.530915	CGTAGATGTCTTCCTCAATCTCTCT	59.469	44.000	0.00	0.00	0.00	3.10
1658	1725	5.278266	CCGTAGATGTCTTCCTCAATCTCTC	60.278	48.000	0.00	0.00	0.00	3.20
1659	1726	4.582656	CCGTAGATGTCTTCCTCAATCTCT	59.417	45.833	0.00	0.00	0.00	3.10
1822	1898	6.941857	AGCGTTTATGGAATTAAAATGGGTT	58.058	32.000	0.00	0.00	0.00	4.11
1876	1956	5.045651	ACTCCATGTTGATCTGTGATAACCA	60.046	40.000	0.00	0.00	0.00	3.67
1956	2036	4.552166	TTCACTTTGCTTGCTTACTGTC	57.448	40.909	0.00	0.00	0.00	3.51
2056	2139	5.440610	GGATCCATACAAACCAACTCTGAT	58.559	41.667	6.95	0.00	0.00	2.90
2068	2151	2.278657	TCCTGGTGGGATCCATACAA	57.721	50.000	15.23	4.67	39.58	2.41
2147	2230	7.931407	AGTGCTATTACGGAAATGAATATCACA	59.069	33.333	9.30	0.00	35.84	3.58
2217	2301	9.627123	AATGCAATTACTAGTACACCACATTAT	57.373	29.630	0.91	0.00	32.46	1.28
2244	2328	5.590663	ACATACTAACTCGAGCATCAAGAGA	59.409	40.000	13.61	0.00	36.03	3.10
2302	2426	8.156820	TGGTACTAGCATTGATATTGCAATAGT	58.843	33.333	22.76	15.81	42.62	2.12
2313	2437	5.297776	GCATGAAGTTGGTACTAGCATTGAT	59.702	40.000	0.00	0.00	33.17	2.57
2455	2589	1.029681	GTGCCAGGGTTTTCGAAACT	58.970	50.000	10.79	1.55	0.00	2.66
2741	3669	5.186409	ACTGTAGGAATAGTCGCTTTGGTAA	59.814	40.000	0.00	0.00	0.00	2.85
2747	3675	4.219944	TGAACACTGTAGGAATAGTCGCTT	59.780	41.667	0.00	0.00	0.00	4.68
2766	3694	5.284079	AGCATTGTCACAAAAGACATGAAC	58.716	37.500	0.00	0.00	46.90	3.18
2840	3771	7.798596	ATGACTTGAGATGAATCAATGGTAC	57.201	36.000	0.00	0.00	38.47	3.34
2899	3830	0.734889	GGTCGAGTTGCATGGGAATG	59.265	55.000	0.00	0.00	0.00	2.67
2903	3834	0.893270	TTTGGGTCGAGTTGCATGGG	60.893	55.000	0.00	0.00	0.00	4.00

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.