AutoCloner

Multiple sequence alignment - TraesCS1A01G329800

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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	TraesCS1A01G329800	chr1A	100.000	4791	0	0	1	4791	518797602	518792812	0.000000e+00	8848
1	TraesCS1A01G329800	chr1A	96.896	4220	91	4	1	4206	18497309	18493116	0.000000e+00	7031
2	TraesCS1A01G329800	chr1A	94.247	591	30	3	4205	4791	495751580	495752170	0.000000e+00	900
3	TraesCS1A01G329800	chr1A	94.247	591	30	3	4205	4791	498422764	498422174	0.000000e+00	900
4	TraesCS1A01G329800	chr3A	97.062	4221	106	7	1	4207	416039912	416044128	0.000000e+00	7092
5	TraesCS1A01G329800	chr3A	94.247	591	30	3	4205	4791	575992495	575993085	0.000000e+00	900
6	TraesCS1A01G329800	chr3A	79.607	917	139	37	2086	2981	104460061	104460950	8.810000e-172	614
7	TraesCS1A01G329800	chr6B	93.127	4001	218	16	259	4203	100715189	100719188	0.000000e+00	5812
8	TraesCS1A01G329800	chr6B	93.129	2707	151	12	259	2930	100749840	100752546	0.000000e+00	3936
9	TraesCS1A01G329800	chr6B	94.232	1283	70	3	2924	4203	100760932	100762213	0.000000e+00	1956
10	TraesCS1A01G329800	chr3D	94.648	2074	75	15	1368	3410	432089652	432091720	0.000000e+00	3182
11	TraesCS1A01G329800	chr3D	92.800	1375	64	17	2	1373	432075767	432077109	0.000000e+00	1958
12	TraesCS1A01G329800	chr3D	82.846	787	89	31	2086	2857	87942951	87943706	0.000000e+00	664
13	TraesCS1A01G329800	chr6A	97.071	1707	45	2	1	1702	607377609	607379315	0.000000e+00	2870
14	TraesCS1A01G329800	chr6A	97.907	1577	24	1	2640	4207	607382812	607384388	0.000000e+00	2721
15	TraesCS1A01G329800	chr6A	97.674	731	17	0	1905	2635	607379313	607380043	0.000000e+00	1256
16	TraesCS1A01G329800	chr6A	94.000	50	1	2	257	304	607377816	607377865	1.850000e-09	75
17	TraesCS1A01G329800	chr6D	92.732	1995	107	7	87	2072	156258435	156256470	0.000000e+00	2846
18	TraesCS1A01G329800	chr6D	93.734	1899	104	6	2322	4206	156259401	156261298	0.000000e+00	2833
19	TraesCS1A01G329800	chr6D	92.328	1929	79	10	2322	4208	156256446	156254545	0.000000e+00	2678
20	TraesCS1A01G329800	chr5B	87.407	1739	183	25	698	2421	565832206	565833923	0.000000e+00	1965
21	TraesCS1A01G329800	chr5B	87.407	1739	183	25	698	2421	565904810	565906527	0.000000e+00	1965
22	TraesCS1A01G329800	chr5B	94.576	590	28	3	4205	4791	629917477	629916889	0.000000e+00	909
23	TraesCS1A01G329800	chr2D	87.407	1739	183	25	698	2421	642015177	642016894	0.000000e+00	1965
24	TraesCS1A01G329800	chr2D	86.763	1594	164	18	2617	4194	579218877	579217315	0.000000e+00	1731
25	TraesCS1A01G329800	chr4D	96.444	1153	39	2	3056	4207	304695349	304696500	0.000000e+00	1901
26	TraesCS1A01G329800	chr4D	95.170	352	14	3	2748	3098	304695012	304695361	1.950000e-153	553
27	TraesCS1A01G329800	chr4D	84.161	423	36	15	1	420	304694625	304695019	9.730000e-102	381
28	TraesCS1A01G329800	chr1D	94.966	596	26	3	4198	4790	467052762	467053356	0.000000e+00	931
29	TraesCS1A01G329800	chr1D	94.237	590	31	2	4205	4791	370122352	370122941	0.000000e+00	898
30	TraesCS1A01G329800	chr5A	94.737	589	28	2	4205	4791	635891938	635892525	0.000000e+00	913
31	TraesCS1A01G329800	chr7A	94.416	591	29	3	4205	4791	670923763	670923173	0.000000e+00	905
32	TraesCS1A01G329800	chr7D	94.407	590	30	2	4205	4791	52098813	52099402	0.000000e+00	904
33	TraesCS1A01G329800	chr3B	79.844	769	90	34	2125	2857	137597854	137598593	7.160000e-138	501
34	TraesCS1A01G329800	chr7B	84.977	213	28	4	3995	4206	682741203	682741412	3.760000e-51	213

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	TraesCS1A01G329800	chr1A	518792812	518797602	4790	True	8848.0	8848	100.000	1	4791	1	chr1A.!!$R3	4790
1	TraesCS1A01G329800	chr1A	18493116	18497309	4193	True	7031.0	7031	96.896	1	4206	1	chr1A.!!$R1	4205
2	TraesCS1A01G329800	chr1A	495751580	495752170	590	False	900.0	900	94.247	4205	4791	1	chr1A.!!$F1	586
3	TraesCS1A01G329800	chr1A	498422174	498422764	590	True	900.0	900	94.247	4205	4791	1	chr1A.!!$R2	586
4	TraesCS1A01G329800	chr3A	416039912	416044128	4216	False	7092.0	7092	97.062	1	4207	1	chr3A.!!$F2	4206
5	TraesCS1A01G329800	chr3A	575992495	575993085	590	False	900.0	900	94.247	4205	4791	1	chr3A.!!$F3	586
6	TraesCS1A01G329800	chr3A	104460061	104460950	889	False	614.0	614	79.607	2086	2981	1	chr3A.!!$F1	895
7	TraesCS1A01G329800	chr6B	100715189	100719188	3999	False	5812.0	5812	93.127	259	4203	1	chr6B.!!$F1	3944
8	TraesCS1A01G329800	chr6B	100749840	100752546	2706	False	3936.0	3936	93.129	259	2930	1	chr6B.!!$F2	2671
9	TraesCS1A01G329800	chr6B	100760932	100762213	1281	False	1956.0	1956	94.232	2924	4203	1	chr6B.!!$F3	1279
10	TraesCS1A01G329800	chr3D	432089652	432091720	2068	False	3182.0	3182	94.648	1368	3410	1	chr3D.!!$F3	2042
11	TraesCS1A01G329800	chr3D	432075767	432077109	1342	False	1958.0	1958	92.800	2	1373	1	chr3D.!!$F2	1371
12	TraesCS1A01G329800	chr3D	87942951	87943706	755	False	664.0	664	82.846	2086	2857	1	chr3D.!!$F1	771
13	TraesCS1A01G329800	chr6A	607377609	607384388	6779	False	1730.5	2870	96.663	1	4207	4	chr6A.!!$F1	4206
14	TraesCS1A01G329800	chr6D	156259401	156261298	1897	False	2833.0	2833	93.734	2322	4206	1	chr6D.!!$F1	1884
15	TraesCS1A01G329800	chr6D	156254545	156258435	3890	True	2762.0	2846	92.530	87	4208	2	chr6D.!!$R1	4121
16	TraesCS1A01G329800	chr5B	565832206	565833923	1717	False	1965.0	1965	87.407	698	2421	1	chr5B.!!$F1	1723
17	TraesCS1A01G329800	chr5B	565904810	565906527	1717	False	1965.0	1965	87.407	698	2421	1	chr5B.!!$F2	1723
18	TraesCS1A01G329800	chr5B	629916889	629917477	588	True	909.0	909	94.576	4205	4791	1	chr5B.!!$R1	586
19	TraesCS1A01G329800	chr2D	642015177	642016894	1717	False	1965.0	1965	87.407	698	2421	1	chr2D.!!$F1	1723
20	TraesCS1A01G329800	chr2D	579217315	579218877	1562	True	1731.0	1731	86.763	2617	4194	1	chr2D.!!$R1	1577
21	TraesCS1A01G329800	chr4D	304694625	304696500	1875	False	945.0	1901	91.925	1	4207	3	chr4D.!!$F1	4206
22	TraesCS1A01G329800	chr1D	467052762	467053356	594	False	931.0	931	94.966	4198	4790	1	chr1D.!!$F2	592
23	TraesCS1A01G329800	chr1D	370122352	370122941	589	False	898.0	898	94.237	4205	4791	1	chr1D.!!$F1	586
24	TraesCS1A01G329800	chr5A	635891938	635892525	587	False	913.0	913	94.737	4205	4791	1	chr5A.!!$F1	586
25	TraesCS1A01G329800	chr7A	670923173	670923763	590	True	905.0	905	94.416	4205	4791	1	chr7A.!!$R1	586
26	TraesCS1A01G329800	chr7D	52098813	52099402	589	False	904.0	904	94.407	4205	4791	1	chr7D.!!$F1	586
27	TraesCS1A01G329800	chr3B	137597854	137598593	739	False	501.0	501	79.844	2125	2857	1	chr3B.!!$F1	732

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	Hairpin	End Stability	Orientation
464	468	0.107703	GGCTGTACATGGTGCTGCTA	60.108	55.000	13.79	41.14	3.49	F
1257	1270	1.338973	TGACACCGAGTGACAACTACC	59.661	52.381	10.46	35.61	3.18	F
2636	5467	1.028130	TGAACATTTTCAGCGCACCA	58.972	45.000	11.47	36.79	4.17	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1506	1521	2.736144	TTCACGTCCTAAAGCATCGT	57.264	45.000	0.00	35.12	3.73	R
2966	5861	5.987019	TGGGCTATAAAAGTACCCATTCT	57.013	39.130	0.00	45.65	2.40	R
4220	7152	1.889829	ACTCCGGAAGTTGAGAGAGTG	59.110	52.381	5.23	33.03	3.51	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
268	272	1.365633	GGAGATCTGTAGCTGGGCG	59.634	63.158	0.00	0.00	0.00	6.13
354	358	2.555547	GGAAGCTGGCAAACTGCGT	61.556	57.895	0.00	0.00	46.21	5.24
379	383	0.320683	TGCTTGCGTACATGAGCTGT	60.321	50.000	0.00	0.00	42.13	4.40
464	468	0.107703	GGCTGTACATGGTGCTGCTA	60.108	55.000	13.79	0.00	41.14	3.49
479	483	4.748102	GTGCTGCTAGTGTAAACTTGTGTA	59.252	41.667	0.00	0.00	0.00	2.90
535	545	4.228210	TCATACAGGAGCTGAAAGGGAAAT	59.772	41.667	0.00	0.00	35.18	2.17
541	551	2.299867	GAGCTGAAAGGGAAATGGCAAA	59.700	45.455	0.00	0.00	0.00	3.68
646	658	4.021807	TGTTCCTCGTATGTACTGCTTGAA	60.022	41.667	0.00	0.00	0.00	2.69
684	696	8.455598	TGCTGAGTTGTTTTTGTTAAAGTAAC	57.544	30.769	0.00	0.00	39.11	2.50
808	821	9.851686	TTATCAATATGATAGCTTTGGTTGTCT	57.148	29.630	0.00	0.00	40.13	3.41
1257	1270	1.338973	TGACACCGAGTGACAACTACC	59.661	52.381	10.46	0.00	35.61	3.18
2054	2069	6.725364	ACTTACTGATCAAATGTGGGAAGAT	58.275	36.000	8.85	0.00	0.00	2.40
2284	2349	7.797038	ATTTGCTGAATTGCTTCTTTCTTTT	57.203	28.000	0.00	0.00	32.29	2.27
2287	2352	6.518493	TGCTGAATTGCTTCTTTCTTTTCAT	58.482	32.000	0.00	0.00	32.29	2.57
2636	5467	1.028130	TGAACATTTTCAGCGCACCA	58.972	45.000	11.47	0.00	36.79	4.17
2638	5469	2.035704	TGAACATTTTCAGCGCACCAAT	59.964	40.909	11.47	0.00	36.79	3.16
2942	5808	2.224499	TGCACTATCACTTGCTGGAACA	60.224	45.455	0.00	0.00	39.62	3.18
2966	5861	7.232534	ACATTTTTACACTCCATTTCCTTGCTA	59.767	33.333	0.00	0.00	0.00	3.49
2972	5867	4.337555	CACTCCATTTCCTTGCTAGAATGG	59.662	45.833	17.18	17.18	46.26	3.16
3674	6602	3.518303	GGTTTGGGTCTCTAGGTATGTGT	59.482	47.826	0.00	0.00	0.00	3.72
3789	6719	9.959749	GTTGTATGGACTTGTTCTTTTGATTAA	57.040	29.630	0.00	0.00	0.00	1.40
4068	6999	4.623863	ACAGAAAAATGGCTATCCCCAAT	58.376	39.130	0.00	0.00	38.61	3.16
4220	7152	4.781934	ACACATCCTTATAAAGAGGTGCC	58.218	43.478	22.50	0.00	35.71	5.01
4238	7172	1.257743	CCACTCTCTCAACTTCCGGA	58.742	55.000	0.00	0.00	0.00	5.14
4250	7184	2.547990	ACTTCCGGAGTGGGACTAAAT	58.452	47.619	3.34	0.00	37.17	1.40
4267	7201	8.529476	GGGACTAAATTTTAGTCTCACTCACTA	58.471	37.037	32.66	0.00	42.92	2.74
4305	7240	3.511146	TGAATGGGCCAAGAGAATTTCAC	59.489	43.478	11.89	0.00	0.00	3.18
4433	7369	0.531200	CCGGTGGTTAGTGGAGACTC	59.469	60.000	0.00	0.00	33.21	3.36
4444	7380	6.459923	GTTAGTGGAGACTCTGAAGTTGAAT	58.540	40.000	1.74	0.00	35.28	2.57
4447	7383	6.360618	AGTGGAGACTCTGAAGTTGAATTTT	58.639	36.000	1.74	0.00	35.28	1.82
4499	7435	6.923508	TCATAACTTGAATAGTGGACTATGCG	59.076	38.462	0.00	0.00	37.31	4.73
4560	7496	0.824109	CTTGACCGATACTGGGCTGA	59.176	55.000	0.00	0.00	38.15	4.26
4611	7547	1.065418	CGTCATACTCCAGGGCCTTTT	60.065	52.381	1.32	0.00	0.00	2.27
4770	7706	3.806625	AAATATCAACCTGCCATGCAC	57.193	42.857	0.00	0.00	33.79	4.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
268	272	3.537874	ATCTACCTCCCGCGCCAC	61.538	66.667	0.00	0.00	0.00	5.01
320	324	0.981183	TTCCTACATCTGTTGCCCGT	59.019	50.000	0.00	0.00	0.00	5.28
327	331	1.279496	TGCCAGCTTCCTACATCTGT	58.721	50.000	0.00	0.00	0.00	3.41
354	358	3.892740	ATGTACGCAAGCACGCCCA	62.893	57.895	0.00	0.00	45.62	5.36
379	383	0.449786	CACGTTCACACCACAAGCAA	59.550	50.000	0.00	0.00	0.00	3.91
384	388	0.320858	ACACACACGTTCACACCACA	60.321	50.000	0.00	0.00	0.00	4.17
464	468	5.295787	CACACACCATACACAAGTTTACACT	59.704	40.000	0.00	0.00	33.11	3.55
479	483	1.241165	CATCAGCACACACACACCAT	58.759	50.000	0.00	0.00	0.00	3.55
535	545	0.538057	CCCTGACTTCAGCTTTGCCA	60.538	55.000	0.26	0.00	42.47	4.92
541	551	0.545309	TGTAGCCCCTGACTTCAGCT	60.545	55.000	0.26	0.00	42.47	4.24
646	658	2.932261	ACTCAGCATGCACATCATCAT	58.068	42.857	21.98	0.00	34.76	2.45
684	696	9.859427	ACATTACTTCATCAATTACAAATGGTG	57.141	29.630	0.00	0.00	0.00	4.17
1033	1046	3.243873	TGACCAACAGTGTGCAAAAACAA	60.244	39.130	0.00	0.00	0.00	2.83
1129	1142	2.357009	GCTCACCAATTGCATGGAGTAG	59.643	50.000	13.35	7.86	43.54	2.57
1257	1270	6.364165	CAGATTTGTGCCTACATTGACAAAAG	59.636	38.462	0.00	0.00	40.61	2.27
1266	1279	6.543831	GGATCTAAACAGATTTGTGCCTACAT	59.456	38.462	0.00	0.00	37.67	2.29
1331	1346	5.620738	ACATGTGTACCATCAATAGCTCT	57.379	39.130	0.00	0.00	0.00	4.09
1506	1521	2.736144	TTCACGTCCTAAAGCATCGT	57.264	45.000	0.00	0.00	35.12	3.73
2034	2049	4.080919	TCGATCTTCCCACATTTGATCAGT	60.081	41.667	0.00	0.00	34.80	3.41
2054	2069	4.215185	TGATGCTGCAAATAGTTTTGTCGA	59.785	37.500	6.36	0.00	43.43	4.20
2284	2349	6.662755	AGATTAAATTCCAGCAGGTACATGA	58.337	36.000	12.53	0.00	35.89	3.07
2287	2352	8.902806	CATAAAGATTAAATTCCAGCAGGTACA	58.097	33.333	0.00	0.00	35.89	2.90
2636	5467	6.653526	TGTGATGTGAGTTCCAATCAAATT	57.346	33.333	0.00	0.00	0.00	1.82
2638	5469	6.462552	TTTGTGATGTGAGTTCCAATCAAA	57.537	33.333	0.00	0.00	0.00	2.69
2942	5808	6.670695	AGCAAGGAAATGGAGTGTAAAAAT	57.329	33.333	0.00	0.00	0.00	1.82
2966	5861	5.987019	TGGGCTATAAAAGTACCCATTCT	57.013	39.130	0.00	0.00	45.65	2.40
3674	6602	4.673968	TCAGCTTCAGGAAAGGTACTCTA	58.326	43.478	0.00	0.00	43.77	2.43
3789	6719	6.427547	CCATGCATAGTTCAATGTTTTGGTTT	59.572	34.615	0.00	0.00	33.44	3.27
4001	6932	4.805192	CCCGTTTTTCAATATGAGGCAATG	59.195	41.667	0.00	0.00	0.00	2.82
4021	6952	4.162690	GTGGGTGAGGCTAGCCCG	62.163	72.222	30.42	0.00	45.19	6.13
4068	6999	7.174413	TGTTTGGTTAGAAGGATGAATCATGA	58.826	34.615	0.00	0.00	0.00	3.07
4220	7152	1.889829	ACTCCGGAAGTTGAGAGAGTG	59.110	52.381	5.23	0.00	33.03	3.51
4250	7184	7.812690	TGTAGTGTAGTGAGTGAGACTAAAA	57.187	36.000	0.00	0.00	0.00	1.52
4305	7240	3.073678	GCCCAAAGCCCAACTAAAATTG	58.926	45.455	0.00	0.00	34.35	2.32
4499	7435	5.473796	TCACGGAAAACTTGTAGTTCAAC	57.526	39.130	0.00	0.00	37.47	3.18
4632	7568	2.677199	GTCGCAGTCTGTGAGAATTGA	58.323	47.619	16.39	0.00	37.59	2.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.