AutoCloner

Multiple sequence alignment - TraesCS5D01G497100

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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	TraesCS5D01G497100	chr5D	100.000	2264	0	0	1	2264	527485984	527488247	0.000000e+00	4181.0
1	TraesCS5D01G497100	chr5D	90.705	312	29	0	1953	2264	403618428	403618739	1.250000e-112	416.0
2	TraesCS5D01G497100	chr4A	92.096	1379	83	14	568	1945	598516201	598517554	0.000000e+00	1919.0
3	TraesCS5D01G497100	chr4A	92.949	312	22	0	1953	2264	598517943	598518254	2.650000e-124	455.0
4	TraesCS5D01G497100	chr4A	88.994	318	34	1	172	489	598515534	598515850	2.110000e-105	392.0
5	TraesCS5D01G497100	chr5A	95.293	1126	52	1	643	1768	588455242	588454118	0.000000e+00	1784.0
6	TraesCS5D01G497100	chr5A	92.366	393	28	2	102	493	588455880	588455489	1.960000e-155	558.0
7	TraesCS5D01G497100	chr5A	85.630	341	31	8	28	361	484667843	484667514	2.150000e-90	342.0
8	TraesCS5D01G497100	chr5A	92.405	79	4	2	415	492	484630019	484629942	6.610000e-21	111.0
9	TraesCS5D01G497100	chr1A	93.867	1125	53	10	568	1691	259893545	259892436	0.000000e+00	1681.0
10	TraesCS5D01G497100	chr1A	81.382	521	41	20	1	500	259894062	259893577	7.640000e-100	374.0
11	TraesCS5D01G497100	chr1A	79.822	337	45	18	566	886	587714376	587714047	8.140000e-55	224.0
12	TraesCS5D01G497100	chr3D	94.288	1103	52	7	589	1691	230694418	230695509	0.000000e+00	1677.0
13	TraesCS5D01G497100	chr3D	93.269	312	21	0	1953	2264	230594260	230594571	5.700000e-126	460.0
14	TraesCS5D01G497100	chr3D	92.949	312	22	0	1953	2264	230711558	230711869	2.650000e-124	455.0
15	TraesCS5D01G497100	chr3D	91.961	311	25	0	1954	2264	230696233	230696543	9.600000e-119	436.0
16	TraesCS5D01G497100	chr3D	87.696	382	29	10	45	417	230647958	230648330	1.610000e-116	429.0
17	TraesCS5D01G497100	chr3D	86.768	393	38	7	29	417	230706762	230707144	2.080000e-115	425.0
18	TraesCS5D01G497100	chr3D	91.054	313	26	2	1953	2264	486671037	486670726	2.690000e-114	422.0
19	TraesCS5D01G497100	chr3D	89.744	273	28	0	1680	1952	230710896	230711168	1.290000e-92	350.0
20	TraesCS5D01G497100	chr3D	89.416	274	29	0	1680	1953	230695571	230695844	1.660000e-91	346.0
21	TraesCS5D01G497100	chr3D	88.278	273	28	1	1680	1952	230593603	230593871	7.800000e-85	324.0
22	TraesCS5D01G497100	chr3D	82.143	168	15	5	385	551	486682736	486682889	1.820000e-26	130.0
23	TraesCS5D01G497100	chr3D	80.319	188	12	6	420	596	486682908	486682735	3.950000e-23	119.0
24	TraesCS5D01G497100	chr4B	88.992	1299	87	21	436	1691	612515449	612514164	0.000000e+00	1555.0
25	TraesCS5D01G497100	chr4B	87.105	380	27	13	1	378	612516004	612515645	5.820000e-111	411.0
26	TraesCS5D01G497100	chr4B	81.771	192	23	7	383	564	609394269	609394080	1.400000e-32	150.0
27	TraesCS5D01G497100	chr7B	88.811	1278	124	15	631	1891	65835632	65836907	0.000000e+00	1550.0
28	TraesCS5D01G497100	chr7B	86.895	496	44	11	1	492	685906482	685906960	9.200000e-149	536.0
29	TraesCS5D01G497100	chr2B	89.965	1136	78	23	568	1691	40122445	40123556	0.000000e+00	1434.0
30	TraesCS5D01G497100	chr2B	90.530	982	76	10	568	1538	609251222	609252197	0.000000e+00	1282.0
31	TraesCS5D01G497100	chr2B	87.869	305	35	2	584	886	25568278	25568582	7.690000e-95	357.0
32	TraesCS5D01G497100	chr2B	87.097	310	34	5	107	414	609250375	609250680	1.660000e-91	346.0
33	TraesCS5D01G497100	chr2B	88.417	259	24	2	1680	1938	730044407	730044659	7.860000e-80	307.0
34	TraesCS5D01G497100	chr2B	85.348	273	38	2	106	378	40121721	40121991	4.760000e-72	281.0
35	TraesCS5D01G497100	chr2B	83.333	156	15	6	416	561	171771766	171771920	1.410000e-27	134.0
36	TraesCS5D01G497100	chr2B	94.737	38	2	0	568	605	171766540	171766503	2.430000e-05	60.2
37	TraesCS5D01G497100	chr6D	95.021	723	36	0	969	1691	43206470	43205748	0.000000e+00	1136.0
38	TraesCS5D01G497100	chr6D	88.803	259	29	0	1680	1938	43205686	43205428	3.630000e-83	318.0
39	TraesCS5D01G497100	chr6D	81.967	366	44	8	62	419	380049255	380048904	7.910000e-75	291.0
40	TraesCS5D01G497100	chr6D	100.000	30	0	0	567	596	358099135	358099164	3.140000e-04	56.5
41	TraesCS5D01G497100	chr6D	100.000	30	0	0	567	596	358100033	358100062	3.140000e-04	56.5
42	TraesCS5D01G497100	chr1D	95.513	312	14	0	1953	2264	465922126	465922437	1.210000e-137	499.0
43	TraesCS5D01G497100	chr1D	88.971	272	30	0	1680	1951	465921430	465921701	1.000000e-88	337.0
44	TraesCS5D01G497100	chr5B	85.504	476	44	16	14	480	415419796	415419337	7.320000e-130	473.0
45	TraesCS5D01G497100	chr5B	94.737	38	2	0	568	605	453756230	453756193	2.430000e-05	60.2
46	TraesCS5D01G497100	chr5B	94.737	38	2	0	568	605	453758251	453758214	2.430000e-05	60.2
47	TraesCS5D01G497100	chr1B	92.628	312	23	0	1953	2264	642720282	642720593	1.230000e-122	449.0
48	TraesCS5D01G497100	chr1B	87.546	273	34	0	1680	1952	642719639	642719911	1.310000e-82	316.0
49	TraesCS5D01G497100	chr1B	96.875	32	1	0	565	596	507403421	507403452	1.000000e-03	54.7
50	TraesCS5D01G497100	chr7D	91.026	312	28	0	1953	2264	579953181	579952870	2.690000e-114	422.0
51	TraesCS5D01G497100	chr7D	83.562	146	13	7	419	554	564826860	564827004	2.360000e-25	126.0
52	TraesCS5D01G497100	chr3B	82.171	516	58	18	42	550	677722510	677722998	1.620000e-111	412.0
53	TraesCS5D01G497100	chr7A	90.625	256	24	0	1680	1935	188643644	188643899	7.740000e-90	340.0
54	TraesCS5D01G497100	chr3A	81.707	328	38	16	568	880	717928156	717928476	1.040000e-63	254.0
55	TraesCS5D01G497100	chr3A	80.909	330	42	15	566	880	42802088	42802411	8.080000e-60	241.0
56	TraesCS5D01G497100	chr2A	80.422	332	39	18	568	880	131898369	131898693	1.750000e-56	230.0
57	TraesCS5D01G497100	chrUn	81.771	192	23	7	383	564	401170386	401170197	1.400000e-32	150.0

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	TraesCS5D01G497100	chr5D	527485984	527488247	2263	False	4181.000000	4181	100.000000	1	2264	1	chr5D.!!$F2	2263
1	TraesCS5D01G497100	chr4A	598515534	598518254	2720	False	922.000000	1919	91.346333	172	2264	3	chr4A.!!$F1	2092
2	TraesCS5D01G497100	chr5A	588454118	588455880	1762	True	1171.000000	1784	93.829500	102	1768	2	chr5A.!!$R3	1666
3	TraesCS5D01G497100	chr1A	259892436	259894062	1626	True	1027.500000	1681	87.624500	1	1691	2	chr1A.!!$R2	1690
4	TraesCS5D01G497100	chr3D	230694418	230696543	2125	False	819.666667	1677	91.888333	589	2264	3	chr3D.!!$F4	1675
5	TraesCS5D01G497100	chr3D	230706762	230711869	5107	False	410.000000	455	89.820333	29	2264	3	chr3D.!!$F5	2235
6	TraesCS5D01G497100	chr3D	230593603	230594571	968	False	392.000000	460	90.773500	1680	2264	2	chr3D.!!$F3	584
7	TraesCS5D01G497100	chr4B	612514164	612516004	1840	True	983.000000	1555	88.048500	1	1691	2	chr4B.!!$R2	1690
8	TraesCS5D01G497100	chr7B	65835632	65836907	1275	False	1550.000000	1550	88.811000	631	1891	1	chr7B.!!$F1	1260
9	TraesCS5D01G497100	chr2B	40121721	40123556	1835	False	857.500000	1434	87.656500	106	1691	2	chr2B.!!$F4	1585
10	TraesCS5D01G497100	chr2B	609250375	609252197	1822	False	814.000000	1282	88.813500	107	1538	2	chr2B.!!$F5	1431
11	TraesCS5D01G497100	chr6D	43205428	43206470	1042	True	727.000000	1136	91.912000	969	1938	2	chr6D.!!$R2	969
12	TraesCS5D01G497100	chr1D	465921430	465922437	1007	False	418.000000	499	92.242000	1680	2264	2	chr1D.!!$F1	584
13	TraesCS5D01G497100	chr1B	642719639	642720593	954	False	382.500000	449	90.087000	1680	2264	2	chr1B.!!$F2	584

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
675	1363	0.099791	CCCCACACACAAACACGAAC	59.9	55.0	0.0	0.0	0.0	3.95	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1692	5048	0.464036	ACCTCACAAGCTCACGACAA	59.536	50.0	0.0	0.0	0.0	3.18	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	2.933287	TGAGATGCCGGGGTGGTT	60.933	61.111	2.18	0.00	41.21	3.67
21	22	4.740822	AGATGCCGGGGTGGTTGC	62.741	66.667	2.18	0.00	41.21	4.17
43	44	4.381932	GCAGGAGGAAGAAGAAGAAGAGAG	60.382	50.000	0.00	0.00	0.00	3.20
82	85	3.225940	AGAAGGAAAAAGGACCTTGCTG	58.774	45.455	7.72	0.00	45.08	4.41
158	172	6.367422	GCTATGAGTCCTAAATGACTATGTGC	59.633	42.308	0.00	0.00	45.41	4.57
159	173	5.939764	TGAGTCCTAAATGACTATGTGCT	57.060	39.130	0.00	0.00	45.41	4.40
160	174	7.603180	ATGAGTCCTAAATGACTATGTGCTA	57.397	36.000	0.00	0.00	45.41	3.49
161	175	7.603180	TGAGTCCTAAATGACTATGTGCTAT	57.397	36.000	0.00	0.00	45.41	2.97
162	176	7.436933	TGAGTCCTAAATGACTATGTGCTATG	58.563	38.462	0.00	0.00	45.41	2.23
163	177	7.069950	TGAGTCCTAAATGACTATGTGCTATGT	59.930	37.037	0.00	0.00	45.41	2.29
164	178	7.212976	AGTCCTAAATGACTATGTGCTATGTG	58.787	38.462	0.00	0.00	43.65	3.21
188	202	6.149308	TGTTTTGGACAACTCTATGTGCTATG	59.851	38.462	0.86	0.00	41.65	2.23
189	203	5.420725	TTGGACAACTCTATGTGCTATGT	57.579	39.130	0.86	0.00	41.65	2.29
309	323	4.293662	TGTGACATAGTATGCCAACCAA	57.706	40.909	10.16	0.00	0.00	3.67
335	350	8.601845	AAAACCTAAAAAGCATTTGGTATGTC	57.398	30.769	0.00	0.00	39.02	3.06
347	362	6.682113	GCATTTGGTATGTCAAATCAGCAGAT	60.682	38.462	5.47	0.00	43.16	2.90
381	396	2.941333	CTGAGGCGTTGCACTGTG	59.059	61.111	2.76	2.76	0.00	3.66
396	411	2.742372	GTGTAGTGCAGCACCCGG	60.742	66.667	22.41	0.00	34.49	5.73
415	450	1.807165	CGCATAGACGCTGCACACT	60.807	57.895	0.00	0.00	39.64	3.55
480	828	1.026182	CCAGATGTGCAGCGCCTAAA	61.026	55.000	2.29	0.00	0.00	1.85
518	1064	3.133946	CCTCTCCCTTAGGCGCTC	58.866	66.667	7.64	0.00	0.00	5.03
524	1070	1.524621	CCCTTAGGCGCTCCACATG	60.525	63.158	7.64	0.00	33.74	3.21
675	1363	0.099791	CCCCACACACAAACACGAAC	59.900	55.000	0.00	0.00	0.00	3.95
699	1387	4.814041	GCCTCCCCTCTGCCCTCT	62.814	72.222	0.00	0.00	0.00	3.69
748	1860	1.003118	TCCAGAGATTTTGTCCGTGGG	59.997	52.381	0.00	0.00	0.00	4.61
758	1870	2.027625	GTCCGTGGGTCTCAAAGCG	61.028	63.158	0.00	0.00	0.00	4.68
1132	3891	1.549203	GCCATGTTGGTGTGGAGATT	58.451	50.000	0.00	0.00	40.46	2.40
1185	3944	0.041238	AGTCATGGACGGAAGGGAGA	59.959	55.000	0.00	0.00	37.67	3.71
1400	4596	5.640147	TGTCCAAAAGGACCAATATCAAGT	58.360	37.500	11.79	0.00	38.04	3.16
1411	4607	6.884836	GGACCAATATCAAGTTTGTCTTAGGT	59.115	38.462	0.00	0.00	34.66	3.08
1692	5048	6.219417	TCCATGCCGTATTTTTCATGAATT	57.781	33.333	9.40	0.27	38.77	2.17
1833	5189	7.518731	TTACTTGTGTTTGTTCAAATTGCTC	57.481	32.000	1.33	0.00	0.00	4.26
1862	5218	7.193595	AGTTCAAGTTATTGTAAGTGTTGTGC	58.806	34.615	0.00	0.00	37.68	4.57
1864	5220	8.339714	GTTCAAGTTATTGTAAGTGTTGTGCTA	58.660	33.333	0.00	0.00	37.68	3.49
1869	5225	8.721478	AGTTATTGTAAGTGTTGTGCTATTCAG	58.279	33.333	0.00	0.00	0.00	3.02
1870	5226	8.504005	GTTATTGTAAGTGTTGTGCTATTCAGT	58.496	33.333	0.00	0.00	0.00	3.41
1908	5264	4.883585	TGTCAAAAGAGCTCATGTTTCTGT	59.116	37.500	17.77	0.00	0.00	3.41
1916	5272	6.058183	AGAGCTCATGTTTCTGTAGTTTTGT	58.942	36.000	17.77	0.00	0.00	2.83
1938	5294	3.535629	TAACAGCAGTGCAGCGCCT	62.536	57.895	19.20	0.00	40.15	5.52
1947	5303	2.282783	TGCAGCGCCTAGGACTCAA	61.283	57.895	14.75	0.00	0.00	3.02
1992	5775	7.147776	ACACAAGTACCACACTACTAAGAGTTT	60.148	37.037	0.00	0.00	36.04	2.66
1993	5776	7.381678	CACAAGTACCACACTACTAAGAGTTTC	59.618	40.741	0.00	0.00	36.04	2.78
2226	6009	4.293610	CCACCTTTGGGTTGCCTT	57.706	55.556	0.00	0.00	44.73	4.35

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
19	20	3.242867	TCTTCTTCTTCTTCCTCCTGCA	58.757	45.455	0.00	0.00	0.00	4.41
21	22	4.160252	CCTCTCTTCTTCTTCTTCCTCCTG	59.840	50.000	0.00	0.00	0.00	3.86
43	44	6.764379	TCCTTCTTCTTCTTCTTCTTCTTCC	58.236	40.000	0.00	0.00	0.00	3.46
82	85	2.551459	GTCATGGTGCTCTATTGCATCC	59.449	50.000	0.00	0.00	45.23	3.51
99	102	4.405358	ACACATTTTGGTTCACAAGGTCAT	59.595	37.500	0.00	0.00	40.82	3.06
158	172	7.521529	CACATAGAGTTGTCCAAAACACATAG	58.478	38.462	0.00	0.00	37.70	2.23
159	173	6.072728	GCACATAGAGTTGTCCAAAACACATA	60.073	38.462	0.00	0.00	37.70	2.29
160	174	5.278463	GCACATAGAGTTGTCCAAAACACAT	60.278	40.000	0.00	0.00	37.70	3.21
161	175	4.036262	GCACATAGAGTTGTCCAAAACACA	59.964	41.667	0.00	0.00	37.70	3.72
162	176	4.275936	AGCACATAGAGTTGTCCAAAACAC	59.724	41.667	0.00	0.00	37.70	3.32
163	177	4.460263	AGCACATAGAGTTGTCCAAAACA	58.540	39.130	0.00	0.00	35.59	2.83
164	178	6.149474	ACATAGCACATAGAGTTGTCCAAAAC	59.851	38.462	0.00	0.00	0.00	2.43
188	202	8.198109	ACATAGTCATACACACATAAAGGAGAC	58.802	37.037	0.00	0.00	0.00	3.36
189	203	8.197439	CACATAGTCATACACACATAAAGGAGA	58.803	37.037	0.00	0.00	0.00	3.71
309	323	8.972458	ACATACCAAATGCTTTTTAGGTTTTT	57.028	26.923	10.99	0.00	0.00	1.94
364	379	0.599991	TACACAGTGCAACGCCTCAG	60.600	55.000	0.00	0.00	45.86	3.35
366	381	0.600255	ACTACACAGTGCAACGCCTC	60.600	55.000	0.00	0.00	45.86	4.70
404	419	1.724582	GGTTTTCCAGTGTGCAGCGT	61.725	55.000	0.00	0.00	40.31	5.07
415	450	3.806949	AGCATTCCAGTAGGTTTTCCA	57.193	42.857	0.00	0.00	43.73	3.53
545	1091	2.991250	AGCTCGAATGGCTTATGTTGT	58.009	42.857	0.00	0.00	36.56	3.32
641	1329	3.216292	GGGTGTGTGTGTGTGGGC	61.216	66.667	0.00	0.00	0.00	5.36
675	1363	2.040278	AGAGGGGAGGCACTGAGG	59.960	66.667	0.00	0.00	41.55	3.86
699	1387	2.046447	AGGATTTGAGAGGGGGAGAGAA	59.954	50.000	0.00	0.00	0.00	2.87
748	1860	0.673956	GGAGGGGTTCGCTTTGAGAC	60.674	60.000	0.00	0.00	0.00	3.36
758	1870	4.045736	AGATTACCTTAAGGGAGGGGTTC	58.954	47.826	25.31	11.43	41.31	3.62
1132	3891	1.754226	GGACACCTTCACCTTGCAAAA	59.246	47.619	0.00	0.00	0.00	2.44
1185	3944	7.308589	GCATAGTTCGGGCATACAAAATATCTT	60.309	37.037	0.00	0.00	0.00	2.40
1400	4596	0.605319	CCGCTGGCACCTAAGACAAA	60.605	55.000	0.00	0.00	0.00	2.83
1692	5048	0.464036	ACCTCACAAGCTCACGACAA	59.536	50.000	0.00	0.00	0.00	3.18
1701	5057	6.458751	CCAACATATCACATAACCTCACAAGC	60.459	42.308	0.00	0.00	0.00	4.01
1833	5189	9.438291	CAACACTTACAATAACTTGAACTTCAG	57.562	33.333	0.00	0.00	36.20	3.02
1862	5218	8.752766	ACAGCAATTTCAATTCAACTGAATAG	57.247	30.769	5.40	0.00	43.41	1.73
1864	5220	7.211573	TGACAGCAATTTCAATTCAACTGAAT	58.788	30.769	0.00	0.00	45.91	2.57
1869	5225	7.908230	TCTTTTGACAGCAATTTCAATTCAAC	58.092	30.769	0.00	0.00	33.25	3.18
1870	5226	7.254522	GCTCTTTTGACAGCAATTTCAATTCAA	60.255	33.333	0.00	0.00	33.25	2.69
1908	5264	5.818336	TGCACTGCTGTTAACTACAAAACTA	59.182	36.000	7.22	0.00	36.02	2.24
1916	5272	1.428448	CGCTGCACTGCTGTTAACTA	58.572	50.000	7.22	0.00	0.00	2.24
1938	5294	1.476891	CTTGTAGGCGCTTGAGTCCTA	59.523	52.381	7.64	0.00	0.00	2.94
1992	5775	5.190726	TGTGAGGTTATGTGATATGTTGGGA	59.809	40.000	0.00	0.00	0.00	4.37
1993	5776	5.436175	TGTGAGGTTATGTGATATGTTGGG	58.564	41.667	0.00	0.00	0.00	4.12
2082	5865	3.342627	CAGGAACACGCGCGGAAA	61.343	61.111	35.22	0.00	0.00	3.13
2226	6009	1.606668	GCCCATCGACTTTGACAACAA	59.393	47.619	0.00	0.00	0.00	2.83
2241	6024	1.252904	ATACGCCGGTATACGCCCAT	61.253	55.000	1.90	0.00	42.52	4.00

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.