AutoCloner

Multiple sequence alignment - TraesCS5B01G208600

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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	TraesCS5B01G208600	chr5B	100.000	4379	0	0	1	4379	378509565	378513943	0.000000e+00	8087.0
1	TraesCS5B01G208600	chr5B	84.826	2781	260	77	922	3637	378068231	378070914	0.000000e+00	2649.0
2	TraesCS5B01G208600	chr5B	82.638	1653	163	61	798	2416	377978009	377979571	0.000000e+00	1349.0
3	TraesCS5B01G208600	chr5B	91.027	691	59	2	2637	3324	377979619	377980309	0.000000e+00	929.0
4	TraesCS5B01G208600	chr5B	83.670	643	64	25	1001	1637	377698587	377699194	6.360000e-158	568.0
5	TraesCS5B01G208600	chr5B	88.479	217	24	1	1987	2202	377844490	377844706	1.210000e-65	261.0
6	TraesCS5B01G208600	chr5B	88.837	215	20	3	417	631	377976204	377976414	1.210000e-65	261.0
7	TraesCS5B01G208600	chr5B	84.416	77	6	3	799	870	378068140	378068215	2.180000e-08	71.3
8	TraesCS5B01G208600	chr5A	94.277	4403	179	31	1	4379	430509439	430505086	0.000000e+00	6667.0
9	TraesCS5B01G208600	chr5A	84.387	1883	202	46	1757	3624	430957990	430956185	0.000000e+00	1764.0
10	TraesCS5B01G208600	chr5A	89.447	995	91	11	2637	3625	431029495	431028509	0.000000e+00	1243.0
11	TraesCS5B01G208600	chr5A	86.852	829	74	20	807	1620	431045269	431044461	0.000000e+00	894.0
12	TraesCS5B01G208600	chr5A	88.356	730	58	9	929	1657	430958691	430957988	0.000000e+00	852.0
13	TraesCS5B01G208600	chr5A	84.038	639	46	24	1615	2249	431030128	431029542	8.220000e-157	564.0
14	TraesCS5B01G208600	chr5A	92.647	136	8	2	3663	3797	427318907	427318773	1.240000e-45	195.0
15	TraesCS5B01G208600	chr5D	95.349	3677	131	18	1	3647	326117107	326120773	0.000000e+00	5806.0
16	TraesCS5B01G208600	chr5D	87.255	1020	105	9	2621	3637	325664861	325665858	0.000000e+00	1140.0
17	TraesCS5B01G208600	chr5D	94.708	718	22	4	3671	4379	326121027	326121737	0.000000e+00	1101.0
18	TraesCS5B01G208600	chr5D	89.791	764	64	9	2531	3285	325648108	325648866	0.000000e+00	966.0
19	TraesCS5B01G208600	chr5D	89.148	728	58	16	933	1655	325646757	325647468	0.000000e+00	887.0
20	TraesCS5B01G208600	chr5D	89.116	735	51	11	941	1672	325663603	325664311	0.000000e+00	887.0
21	TraesCS5B01G208600	chr5D	83.515	643	71	21	1001	1637	325422710	325423323	6.360000e-158	568.0
22	TraesCS5B01G208600	chr5D	84.499	529	44	18	1728	2249	325664330	325664827	5.090000e-134	488.0
23	TraesCS5B01G208600	chr5D	85.393	445	54	7	1967	2405	325647610	325648049	6.680000e-123	451.0
24	TraesCS5B01G208600	chr5D	85.535	318	32	8	3323	3637	325652098	325652404	1.960000e-83	320.0
25	TraesCS5B01G208600	chr5D	86.066	244	25	8	417	654	325646227	325646467	2.020000e-63	254.0
26	TraesCS5B01G208600	chr5D	92.481	133	10	0	3663	3795	497493775	497493643	1.610000e-44	191.0
27	TraesCS5B01G208600	chr5D	83.117	77	7	3	799	870	325646666	325646741	1.020000e-06	65.8
28	TraesCS5B01G208600	chr7D	84.103	780	96	17	1730	2498	50650380	50651142	0.000000e+00	728.0
29	TraesCS5B01G208600	chr4A	82.420	785	111	14	1730	2504	482875610	482874843	0.000000e+00	660.0
30	TraesCS5B01G208600	chr6D	82.308	780	107	19	1730	2498	36220046	36220805	0.000000e+00	647.0
31	TraesCS5B01G208600	chr6D	92.086	139	10	1	3663	3800	427226661	427226799	1.240000e-45	195.0
32	TraesCS5B01G208600	chr7A	83.186	678	86	12	1822	2497	22039262	22039913	2.920000e-166	595.0
33	TraesCS5B01G208600	chr7A	82.275	677	92	13	1822	2497	21616749	21617398	1.060000e-155	560.0
34	TraesCS5B01G208600	chr7B	92.647	136	8	2	3663	3797	450794814	450794948	1.240000e-45	195.0
35	TraesCS5B01G208600	chr6B	92.647	136	8	2	3663	3797	623719534	623719400	1.240000e-45	195.0
36	TraesCS5B01G208600	chr2D	91.852	135	11	0	3663	3797	612337056	612336922	5.780000e-44	189.0
37	TraesCS5B01G208600	chr1A	87.879	165	15	4	3636	3797	554032995	554032833	5.780000e-44	189.0

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	TraesCS5B01G208600	chr5B	378509565	378513943	4378	False	8087.000000	8087	100.000000	1	4379	1	chr5B.!!$F3	4378
1	TraesCS5B01G208600	chr5B	378068140	378070914	2774	False	1360.150000	2649	84.621000	799	3637	2	chr5B.!!$F5	2838
2	TraesCS5B01G208600	chr5B	377976204	377980309	4105	False	846.333333	1349	87.500667	417	3324	3	chr5B.!!$F4	2907
3	TraesCS5B01G208600	chr5B	377698587	377699194	607	False	568.000000	568	83.670000	1001	1637	1	chr5B.!!$F1	636
4	TraesCS5B01G208600	chr5A	430505086	430509439	4353	True	6667.000000	6667	94.277000	1	4379	1	chr5A.!!$R2	4378
5	TraesCS5B01G208600	chr5A	430956185	430958691	2506	True	1308.000000	1764	86.371500	929	3624	2	chr5A.!!$R4	2695
6	TraesCS5B01G208600	chr5A	431028509	431030128	1619	True	903.500000	1243	86.742500	1615	3625	2	chr5A.!!$R5	2010
7	TraesCS5B01G208600	chr5A	431044461	431045269	808	True	894.000000	894	86.852000	807	1620	1	chr5A.!!$R3	813
8	TraesCS5B01G208600	chr5D	326117107	326121737	4630	False	3453.500000	5806	95.028500	1	4379	2	chr5D.!!$F4	4378
9	TraesCS5B01G208600	chr5D	325663603	325665858	2255	False	838.333333	1140	86.956667	941	3637	3	chr5D.!!$F3	2696
10	TraesCS5B01G208600	chr5D	325422710	325423323	613	False	568.000000	568	83.515000	1001	1637	1	chr5D.!!$F1	636
11	TraesCS5B01G208600	chr5D	325646227	325652404	6177	False	490.633333	966	86.508333	417	3637	6	chr5D.!!$F2	3220
12	TraesCS5B01G208600	chr7D	50650380	50651142	762	False	728.000000	728	84.103000	1730	2498	1	chr7D.!!$F1	768
13	TraesCS5B01G208600	chr4A	482874843	482875610	767	True	660.000000	660	82.420000	1730	2504	1	chr4A.!!$R1	774
14	TraesCS5B01G208600	chr6D	36220046	36220805	759	False	647.000000	647	82.308000	1730	2498	1	chr6D.!!$F1	768
15	TraesCS5B01G208600	chr7A	22039262	22039913	651	False	595.000000	595	83.186000	1822	2497	1	chr7A.!!$F2	675
16	TraesCS5B01G208600	chr7A	21616749	21617398	649	False	560.000000	560	82.275000	1822	2497	1	chr7A.!!$F1	675

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	2144	0.031178	AAAACCTACGTCGTGTCGCT	59.969	50.000	8.47	0.0	0.00	4.93	F
742	2211	1.152567	CCAACCACCACCACCACAT	60.153	57.895	0.00	0.0	0.00	3.21	F
775	2244	1.243342	TTGCCCTGTTTGCTCCATCG	61.243	55.000	0.00	0.0	0.00	3.84	F
1296	2871	1.294138	CTTCGGCCCGGTCTACAAA	59.706	57.895	1.90	0.0	0.00	2.83	F
1320	2895	2.559840	GTCGACGACAAGCTCCGA	59.440	61.111	22.66	0.0	32.09	4.55	F
1450	3062	2.681848	CCAGCAGATCAATTTCGAAGCT	59.318	45.455	0.00	0.0	0.00	3.74	F
2967	4657	0.898320	AGCGCTCTGACAGGTTGTAT	59.102	50.000	2.64	0.0	0.00	2.29	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2274	3948	3.131396	GAGGTGTGAAGTTGTGTTCGAT	58.869	45.455	0.0	0.0	0.00	3.59	R
2613	4297	4.041049	TGCGTTACAAGCTGAACAATTTG	58.959	39.130	0.0	0.0	35.28	2.32	R
2645	4330	4.811969	TGTTAGGGAAATAGCACGAAGA	57.188	40.909	0.0	0.0	0.00	2.87	R
2928	4618	1.789523	TGAGGTATGGTCTAGCCCAC	58.210	55.000	0.0	0.0	37.31	4.61	R
2967	4657	2.501723	GAGAGCTGGGTCCATGACTTTA	59.498	50.000	0.0	0.0	32.47	1.85	R
3337	8158	2.553602	TGTAGCTCGACGACCTTTGTTA	59.446	45.455	0.0	0.0	0.00	2.41	R
4093	9221	0.392998	CGGTCCAGCTTGCCAGTATT	60.393	55.000	0.0	0.0	0.00	1.89	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
178	180	1.674221	CCAGGCCGTTCTCTTCTTCTG	60.674	57.143	0.00	0.00	0.00	3.02
209	211	4.844085	TGATCTTGAAACTTCCAGTCCCTA	59.156	41.667	0.00	0.00	0.00	3.53
216	218	1.903183	ACTTCCAGTCCCTAGAGCAAC	59.097	52.381	0.00	0.00	0.00	4.17
260	262	2.545106	GGCTTGCACAAAGTCCAAATTG	59.455	45.455	0.00	0.00	38.25	2.32
317	323	3.914364	CCTGCGCTTTCTGTCAATTTTAC	59.086	43.478	9.73	0.00	0.00	2.01
619	641	3.074390	TCACTTTGATCCACCCATGTTCT	59.926	43.478	0.00	0.00	0.00	3.01
675	2144	0.031178	AAAACCTACGTCGTGTCGCT	59.969	50.000	8.47	0.00	0.00	4.93
687	2156	1.335597	CGTGTCGCTGGTAGAAACTCA	60.336	52.381	0.00	0.00	0.00	3.41
693	2162	1.404315	GCTGGTAGAAACTCAGGTCCG	60.404	57.143	0.00	0.00	0.00	4.79
694	2163	1.893801	CTGGTAGAAACTCAGGTCCGT	59.106	52.381	0.00	0.00	0.00	4.69
696	2165	2.036733	TGGTAGAAACTCAGGTCCGTTG	59.963	50.000	0.00	0.00	0.00	4.10
738	2207	2.520741	CCACCAACCACCACCACC	60.521	66.667	0.00	0.00	0.00	4.61
739	2208	2.277072	CACCAACCACCACCACCA	59.723	61.111	0.00	0.00	0.00	4.17
740	2209	2.124693	CACCAACCACCACCACCAC	61.125	63.158	0.00	0.00	0.00	4.16
741	2210	2.277072	CCAACCACCACCACCACA	59.723	61.111	0.00	0.00	0.00	4.17
742	2211	1.152567	CCAACCACCACCACCACAT	60.153	57.895	0.00	0.00	0.00	3.21
775	2244	1.243342	TTGCCCTGTTTGCTCCATCG	61.243	55.000	0.00	0.00	0.00	3.84
787	2273	1.379443	TCCATCGCAGTCCTACGGT	60.379	57.895	0.00	0.00	0.00	4.83
857	2401	2.370445	ATCCTCCACCCAAGCCGAG	61.370	63.158	0.00	0.00	0.00	4.63
858	2402	2.822643	ATCCTCCACCCAAGCCGAGA	62.823	60.000	0.00	0.00	0.00	4.04
880	2424	1.404851	CCGCCTTCTCTTTCTCTCCAC	60.405	57.143	0.00	0.00	0.00	4.02
904	2452	1.893786	CTCACCTGACCTTCTCCCG	59.106	63.158	0.00	0.00	0.00	5.14
1040	2600	4.122515	GTTCTCGTGCTGCGTCGC	62.123	66.667	11.10	11.10	42.13	5.19
1269	2844	2.510691	CGCGCCAATTACCTCGGT	60.511	61.111	0.00	0.00	0.00	4.69
1296	2871	1.294138	CTTCGGCCCGGTCTACAAA	59.706	57.895	1.90	0.00	0.00	2.83
1301	2876	2.975536	CCCGGTCTACAAAGGCGA	59.024	61.111	0.00	0.00	0.00	5.54
1320	2895	2.559840	GTCGACGACAAGCTCCGA	59.440	61.111	22.66	0.00	32.09	4.55
1450	3062	2.681848	CCAGCAGATCAATTTCGAAGCT	59.318	45.455	0.00	0.00	0.00	3.74
1473	3088	4.253685	TGGTCAATGAACAGCTAGCTTAC	58.746	43.478	16.46	9.91	0.00	2.34
1481	3097	3.460857	ACAGCTAGCTTACTATGTGGC	57.539	47.619	16.46	0.00	0.00	5.01
1812	3447	5.133941	GTCCCCTGAAGTTTCTTTTCTCTT	58.866	41.667	0.00	0.00	0.00	2.85
2261	3935	5.376756	TTTGGGAACTGTAGTAGTGGTTT	57.623	39.130	0.00	0.00	40.26	3.27
2331	4008	9.797556	AATTACTACAAAAGTGTCTGAAAAACC	57.202	29.630	0.00	0.00	39.39	3.27
2537	4221	6.882610	TTTAGCAATCAATGTCAGTTCACT	57.117	33.333	0.00	0.00	0.00	3.41
2582	4266	6.519353	TTCACGAACAGTAGTACAATTGTG	57.481	37.500	21.42	5.66	0.00	3.33
2645	4330	5.411361	TCAGCTTGTAACGCATTGTATTTCT	59.589	36.000	0.00	0.00	0.00	2.52
2967	4657	0.898320	AGCGCTCTGACAGGTTGTAT	59.102	50.000	2.64	0.00	0.00	2.29
3397	8283	2.468915	AGGACTAAGGTAGGGAAGTGC	58.531	52.381	0.00	0.00	0.00	4.40
3422	8308	7.577046	GCGTAGGACAGAATGGTATGTACATAT	60.577	40.741	18.27	2.65	43.62	1.78
3525	8411	2.502130	GGAAAGGTCTCAGGGGACTTAG	59.498	54.545	0.00	0.00	40.21	2.18
3561	8449	5.003160	TCTTGATAGTGACAATGGGTGTTG	58.997	41.667	0.00	0.00	41.96	3.33
3613	8502	5.972935	ACAAAAGTCCGGTTTTGATTTTCT	58.027	33.333	27.71	9.21	46.19	2.52
3768	8895	7.189079	TCAAAAACCTAAACAAATTGACCCT	57.811	32.000	0.00	0.00	0.00	4.34
3895	9022	9.727627	TTTCATTTGCATAAATTTTGGTTCAAC	57.272	25.926	0.00	0.00	34.34	3.18
3926	9053	8.095792	TCCATTGTTTGCAAATGAAATGAGTAT	58.904	29.630	28.58	7.15	38.21	2.12
4081	9209	6.096141	TGTGACAAGTTAATGTTGATGGTGTT	59.904	34.615	7.35	0.00	32.57	3.32
4164	9292	1.392589	GGGATGGGCAAGTACATGTG	58.607	55.000	9.11	0.00	0.00	3.21
4187	9315	5.221823	TGACCTGACATATTGAAGGTTGACA	60.222	40.000	7.66	1.49	37.82	3.58
4349	9478	3.129462	CGTCCAGCTGAGACAAGAGATAA	59.871	47.826	25.32	0.00	33.70	1.75

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
178	180	6.329496	TGGAAGTTTCAAGATCAACAAACAC	58.671	36.000	13.01	8.17	32.20	3.32
209	211	5.293560	GTGAAAAGTAGAGTGAGTTGCTCT	58.706	41.667	0.00	0.00	44.57	4.09
216	218	4.681942	CGTTCTGGTGAAAAGTAGAGTGAG	59.318	45.833	0.00	0.00	33.52	3.51
260	262	3.173151	ACCATTCACCTTGGGAAATTCC	58.827	45.455	2.79	2.79	38.64	3.01
317	323	0.599558	TGGTCGAACCGTACCTGAAG	59.400	55.000	0.00	0.00	42.58	3.02
340	346	3.003275	TCAATTTGCAGGAACGAGTGAAC	59.997	43.478	0.00	0.00	0.00	3.18
619	641	3.211045	CTCAAACCTTCTTCGTGGGAAA	58.789	45.455	0.00	0.00	0.00	3.13
675	2144	2.005370	ACGGACCTGAGTTTCTACCA	57.995	50.000	0.00	0.00	0.00	3.25
687	2156	2.284699	CTCCCTCCCAACGGACCT	60.285	66.667	0.00	0.00	33.32	3.85
738	2207	1.002857	AAGGGAGGGAAGGGAATGTG	58.997	55.000	0.00	0.00	0.00	3.21
739	2208	1.002857	CAAGGGAGGGAAGGGAATGT	58.997	55.000	0.00	0.00	0.00	2.71
740	2209	0.396278	GCAAGGGAGGGAAGGGAATG	60.396	60.000	0.00	0.00	0.00	2.67
741	2210	1.584717	GGCAAGGGAGGGAAGGGAAT	61.585	60.000	0.00	0.00	0.00	3.01
742	2211	2.238701	GGCAAGGGAGGGAAGGGAA	61.239	63.158	0.00	0.00	0.00	3.97
830	2369	2.592308	GTGGAGGATGGAGTGGCC	59.408	66.667	0.00	0.00	37.10	5.36
857	2401	0.899019	AGAGAAAGAGAAGGCGGGTC	59.101	55.000	0.00	0.00	0.00	4.46
858	2402	0.899019	GAGAGAAAGAGAAGGCGGGT	59.101	55.000	0.00	0.00	0.00	5.28
880	2424	0.248843	GAAGGTCAGGTGAGCAGGAG	59.751	60.000	11.53	0.00	44.42	3.69
995	2555	3.474230	GATTTCGCGGCCATGGCAG	62.474	63.158	36.56	33.25	44.11	4.85
1260	2835	4.745751	CCGCCGCAACCGAGGTAA	62.746	66.667	0.00	0.00	36.29	2.85
1296	2871	3.590443	CTTGTCGTCGACGTCGCCT	62.590	63.158	34.40	0.00	40.80	5.52
1301	2876	2.254651	GGAGCTTGTCGTCGACGT	59.745	61.111	34.40	16.81	40.80	4.34
1450	3062	3.423539	AGCTAGCTGTTCATTGACCAA	57.576	42.857	18.57	0.00	0.00	3.67
1812	3447	3.888323	CAGCTCAGCTATCCTCTTGACTA	59.112	47.826	0.00	0.00	36.40	2.59
2210	3876	6.976934	ATCCTTTTCAAAACTGCCTCTTTA	57.023	33.333	0.00	0.00	0.00	1.85
2274	3948	3.131396	GAGGTGTGAAGTTGTGTTCGAT	58.869	45.455	0.00	0.00	0.00	3.59
2537	4221	9.431887	GTGAATTACTAATCTGTAGGTGTTTCA	57.568	33.333	0.00	0.00	0.00	2.69
2613	4297	4.041049	TGCGTTACAAGCTGAACAATTTG	58.959	39.130	0.00	0.00	35.28	2.32
2645	4330	4.811969	TGTTAGGGAAATAGCACGAAGA	57.188	40.909	0.00	0.00	0.00	2.87
2928	4618	1.789523	TGAGGTATGGTCTAGCCCAC	58.210	55.000	0.00	0.00	37.31	4.61
2967	4657	2.501723	GAGAGCTGGGTCCATGACTTTA	59.498	50.000	0.00	0.00	32.47	1.85
3337	8158	2.553602	TGTAGCTCGACGACCTTTGTTA	59.446	45.455	0.00	0.00	0.00	2.41
3397	8283	5.509716	TGTACATACCATTCTGTCCTACG	57.490	43.478	0.00	0.00	0.00	3.51
3525	8411	2.222227	ATCAAGAAGAAAGGTGGGCC	57.778	50.000	0.00	0.00	0.00	5.80
3561	8449	8.299570	CACTGTTTTGCATCCCTATATTTATCC	58.700	37.037	0.00	0.00	0.00	2.59
3613	8502	6.713762	AACATCTTGAACAACAATCCTTGA	57.286	33.333	0.00	0.00	37.88	3.02
3642	8531	2.366972	CCCCCTCCCGGTGATTCT	60.367	66.667	0.00	0.00	0.00	2.40
3768	8895	2.156098	GCACGGTTTCCCTCATAAACA	58.844	47.619	0.00	0.00	38.34	2.83
3786	8913	0.465705	TGGCATTTTGGTTTTCGGCA	59.534	45.000	0.00	0.00	0.00	5.69
3891	9018	2.620585	TGCAAACAATGGACGATGTTGA	59.379	40.909	0.00	0.00	39.57	3.18
3895	9022	4.236147	TCATTTGCAAACAATGGACGATG	58.764	39.130	15.41	4.89	35.21	3.84
3940	9067	3.700538	AGAATCACAAAAGCCCTGCATA	58.299	40.909	0.00	0.00	0.00	3.14
4030	9157	7.548780	AGTGTAGTTTCATGTTGCATTGTTTTT	59.451	29.630	0.00	0.00	0.00	1.94
4081	9209	9.542462	CAGCTTGCCAGTATTAAGTATTAACTA	57.458	33.333	0.00	0.00	44.35	2.24
4093	9221	0.392998	CGGTCCAGCTTGCCAGTATT	60.393	55.000	0.00	0.00	0.00	1.89
4094	9222	1.221840	CGGTCCAGCTTGCCAGTAT	59.778	57.895	0.00	0.00	0.00	2.12
4164	9292	5.122396	GTGTCAACCTTCAATATGTCAGGTC	59.878	44.000	1.41	0.00	38.80	3.85
4187	9315	5.367945	TGACTTGACCTTAGTCCTTTTGT	57.632	39.130	0.00	0.00	42.81	2.83
4349	9478	2.456577	GTGGTTGCATTCCTATTGGGT	58.543	47.619	9.35	0.00	36.25	4.51

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.