AutoCloner

Multiple sequence alignment - TraesCS1D01G048500

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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	TraesCS1D01G048500	chr1D	100.000	2887	0	0	1	2887	28288731	28291617	0.000000e+00	5332.0
1	TraesCS1D01G048500	chr1D	90.871	712	44	5	1	702	54651288	54651988	0.000000e+00	935.0
2	TraesCS1D01G048500	chr1D	90.182	713	42	6	1	702	247237972	247238667	0.000000e+00	904.0
3	TraesCS1D01G048500	chr1D	87.761	719	60	16	1	702	6080854	6081561	0.000000e+00	815.0
4	TraesCS1D01G048500	chr1D	85.507	621	52	12	867	1478	29483683	29483092	5.290000e-172	614.0
5	TraesCS1D01G048500	chr1D	92.417	211	14	2	1525	1734	29483090	29482881	1.680000e-77	300.0
6	TraesCS1D01G048500	chr1D	87.912	182	17	5	703	882	288787603	288787425	2.920000e-50	209.0
7	TraesCS1D01G048500	chr1D	100.000	28	0	0	1806	1833	29482755	29482728	5.000000e-03	52.8
8	TraesCS1D01G048500	chr2D	91.457	714	41	4	1	704	346650303	346651006	0.000000e+00	963.0
9	TraesCS1D01G048500	chr2D	91.102	708	43	4	5	702	360594893	360595590	0.000000e+00	941.0
10	TraesCS1D01G048500	chr2D	86.271	539	55	11	174	702	426637708	426637179	4.170000e-158	568.0
11	TraesCS1D01G048500	chr2D	89.773	176	13	5	703	877	207640009	207640180	1.350000e-53	220.0
12	TraesCS1D01G048500	chr2D	89.655	174	15	3	703	875	618294607	618294778	4.840000e-53	219.0
13	TraesCS1D01G048500	chr2D	89.595	173	13	5	703	874	534726783	534726615	6.270000e-52	215.0
14	TraesCS1D01G048500	chr2D	83.913	230	30	6	1861	2086	577477395	577477169	2.250000e-51	213.0
15	TraesCS1D01G048500	chr1B	87.385	872	63	22	867	1731	46883516	46884347	0.000000e+00	957.0
16	TraesCS1D01G048500	chr7D	90.897	725	44	10	1	715	367516113	367515401	0.000000e+00	953.0
17	TraesCS1D01G048500	chr7D	90.743	713	44	6	1	702	256550245	256550946	0.000000e+00	931.0
18	TraesCS1D01G048500	chr7D	81.704	716	96	19	3	702	621188569	621189265	5.400000e-157	564.0
19	TraesCS1D01G048500	chr7D	87.318	481	37	12	232	700	118227761	118228229	1.970000e-146	529.0
20	TraesCS1D01G048500	chr7D	100.000	28	0	0	2393	2420	471866900	471866927	5.000000e-03	52.8
21	TraesCS1D01G048500	chr6D	90.909	715	45	4	1	705	289522765	289522061	0.000000e+00	942.0
22	TraesCS1D01G048500	chr3D	91.024	713	42	7	1	702	311512899	311512198	0.000000e+00	942.0
23	TraesCS1D01G048500	chr3D	89.045	712	56	11	1	702	498892801	498892102	0.000000e+00	863.0
24	TraesCS1D01G048500	chr3D	85.890	489	38	19	232	702	323976700	323977175	2.580000e-135	492.0
25	TraesCS1D01G048500	chr3D	88.701	177	14	6	703	876	232921508	232921681	8.100000e-51	211.0
26	TraesCS1D01G048500	chr4D	88.780	713	57	7	1	702	202966854	202967554	0.000000e+00	852.0
27	TraesCS1D01G048500	chr4D	92.308	572	34	1	1	562	454537021	454537592	0.000000e+00	804.0
28	TraesCS1D01G048500	chr4D	90.204	490	31	7	223	702	45509741	45509259	8.780000e-175	623.0
29	TraesCS1D01G048500	chr4D	82.459	724	89	24	18	721	366080424	366081129	1.480000e-167	599.0
30	TraesCS1D01G048500	chr4D	86.912	489	34	16	232	702	133584790	133584314	3.300000e-144	521.0
31	TraesCS1D01G048500	chr4D	88.636	176	15	5	703	876	35636283	35636455	2.920000e-50	209.0
32	TraesCS1D01G048500	chr4D	86.792	53	2	1	2393	2445	383781325	383781278	1.000000e-03	54.7
33	TraesCS1D01G048500	chr4D	88.889	45	2	3	2393	2437	471963064	471963023	5.000000e-03	52.8
34	TraesCS1D01G048500	chr1A	86.137	642	60	14	867	1503	29279860	29280477	0.000000e+00	665.0
35	TraesCS1D01G048500	chr1A	90.127	314	12	12	2549	2851	29281078	29281383	9.700000e-105	390.0
36	TraesCS1D01G048500	chr1A	93.367	196	13	0	1536	1731	29280472	29280667	1.010000e-74	291.0
37	TraesCS1D01G048500	chr1A	82.927	287	35	9	2274	2558	29280852	29281126	2.220000e-61	246.0
38	TraesCS1D01G048500	chr1A	88.889	54	4	2	2035	2086	177971874	177971821	6.680000e-07	65.8
39	TraesCS1D01G048500	chr1A	87.037	54	5	2	2035	2086	177976399	177976346	3.110000e-05	60.2
40	TraesCS1D01G048500	chr5D	88.993	536	37	10	178	702	166157686	166157162	0.000000e+00	643.0
41	TraesCS1D01G048500	chr5D	88.619	536	39	10	178	702	166229420	166228896	1.460000e-177	632.0
42	TraesCS1D01G048500	chr4B	82.277	694	88	20	28	703	472614440	472615116	4.170000e-158	568.0
43	TraesCS1D01G048500	chr4B	96.875	32	0	1	2044	2075	546079312	546079282	5.000000e-03	52.8
44	TraesCS1D01G048500	chr4B	96.875	32	0	1	2044	2075	546082865	546082835	5.000000e-03	52.8
45	TraesCS1D01G048500	chr3B	81.301	738	101	21	5	725	164422742	164422025	5.400000e-157	564.0
46	TraesCS1D01G048500	chr3B	80.505	713	91	31	41	724	519610587	519609894	1.190000e-138	503.0
47	TraesCS1D01G048500	chr3B	85.714	70	8	2	2017	2084	827051292	827051223	3.990000e-09	73.1
48	TraesCS1D01G048500	chr3B	85.714	70	8	2	2017	2084	827597442	827597373	3.990000e-09	73.1
49	TraesCS1D01G048500	chr3B	94.286	35	1	1	2393	2427	59991990	59992023	5.000000e-03	52.8
50	TraesCS1D01G048500	chr5B	81.385	650	83	25	94	723	363607253	363606622	2.000000e-136	496.0
51	TraesCS1D01G048500	chr5B	87.234	188	19	5	703	888	510816421	510816237	2.920000e-50	209.0
52	TraesCS1D01G048500	chr5B	86.614	127	6	8	1998	2118	420967747	420967868	2.330000e-26	130.0
53	TraesCS1D01G048500	chr5B	86.992	123	3	9	2014	2128	546433505	546433388	3.020000e-25	126.0
54	TraesCS1D01G048500	chr5B	85.039	127	8	9	1998	2118	420972433	420972554	5.050000e-23	119.0
55	TraesCS1D01G048500	chr5B	90.588	85	2	4	2014	2096	546439333	546439253	1.090000e-19	108.0
56	TraesCS1D01G048500	chr5B	82.927	123	9	7	2164	2274	293456578	293456700	1.830000e-17	100.0
57	TraesCS1D01G048500	chr5B	97.917	48	1	0	2176	2223	293451684	293451731	1.840000e-12	84.2
58	TraesCS1D01G048500	chr5B	89.796	49	4	1	2026	2073	510393633	510393585	8.640000e-06	62.1
59	TraesCS1D01G048500	chr2B	77.740	584	80	32	174	727	214880766	214880203	2.160000e-81	313.0
60	TraesCS1D01G048500	chr2B	88.073	109	3	8	2028	2128	32963077	32963183	1.410000e-23	121.0
61	TraesCS1D01G048500	chr2B	92.593	81	3	3	2028	2107	32954931	32955009	2.350000e-21	113.0
62	TraesCS1D01G048500	chr4A	84.170	259	27	11	1971	2223	108079080	108078830	3.720000e-59	239.0
63	TraesCS1D01G048500	chr6B	89.714	175	12	5	703	874	163220988	163220817	4.840000e-53	219.0
64	TraesCS1D01G048500	chr6B	92.079	101	7	1	2174	2273	2193421	2193321	1.080000e-29	141.0
65	TraesCS1D01G048500	chr6B	100.000	34	0	0	2240	2273	705581750	705581717	2.400000e-06	63.9
66	TraesCS1D01G048500	chr6B	94.286	35	1	1	2393	2427	706325460	706325493	5.000000e-03	52.8
67	TraesCS1D01G048500	chr7B	89.595	173	14	4	703	874	568089849	568090018	1.740000e-52	217.0
68	TraesCS1D01G048500	chr7B	92.500	40	2	1	2388	2427	284307291	284307253	4.020000e-04	56.5
69	TraesCS1D01G048500	chrUn	94.545	110	6	0	2164	2273	141691831	141691940	1.380000e-38	171.0
70	TraesCS1D01G048500	chr7A	85.484	62	7	2	2212	2273	713904015	713903956	2.400000e-06	63.9
71	TraesCS1D01G048500	chr5A	94.286	35	1	1	2393	2427	18097150	18097117	5.000000e-03	52.8
72	TraesCS1D01G048500	chr3A	94.286	35	1	1	2393	2427	743485816	743485783	5.000000e-03	52.8
73	TraesCS1D01G048500	chr3A	100.000	28	0	0	2393	2420	747431701	747431728	5.000000e-03	52.8

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	TraesCS1D01G048500	chr1D	28288731	28291617	2886	False	5332.000000	5332	100.000000	1	2887	1	chr1D.!!$F2	2886
1	TraesCS1D01G048500	chr1D	54651288	54651988	700	False	935.000000	935	90.871000	1	702	1	chr1D.!!$F3	701
2	TraesCS1D01G048500	chr1D	247237972	247238667	695	False	904.000000	904	90.182000	1	702	1	chr1D.!!$F4	701
3	TraesCS1D01G048500	chr1D	6080854	6081561	707	False	815.000000	815	87.761000	1	702	1	chr1D.!!$F1	701
4	TraesCS1D01G048500	chr1D	29482728	29483683	955	True	322.266667	614	92.641333	867	1833	3	chr1D.!!$R2	966
5	TraesCS1D01G048500	chr2D	346650303	346651006	703	False	963.000000	963	91.457000	1	704	1	chr2D.!!$F2	703
6	TraesCS1D01G048500	chr2D	360594893	360595590	697	False	941.000000	941	91.102000	5	702	1	chr2D.!!$F3	697
7	TraesCS1D01G048500	chr2D	426637179	426637708	529	True	568.000000	568	86.271000	174	702	1	chr2D.!!$R1	528
8	TraesCS1D01G048500	chr1B	46883516	46884347	831	False	957.000000	957	87.385000	867	1731	1	chr1B.!!$F1	864
9	TraesCS1D01G048500	chr7D	367515401	367516113	712	True	953.000000	953	90.897000	1	715	1	chr7D.!!$R1	714
10	TraesCS1D01G048500	chr7D	256550245	256550946	701	False	931.000000	931	90.743000	1	702	1	chr7D.!!$F2	701
11	TraesCS1D01G048500	chr7D	621188569	621189265	696	False	564.000000	564	81.704000	3	702	1	chr7D.!!$F4	699
12	TraesCS1D01G048500	chr6D	289522061	289522765	704	True	942.000000	942	90.909000	1	705	1	chr6D.!!$R1	704
13	TraesCS1D01G048500	chr3D	311512198	311512899	701	True	942.000000	942	91.024000	1	702	1	chr3D.!!$R1	701
14	TraesCS1D01G048500	chr3D	498892102	498892801	699	True	863.000000	863	89.045000	1	702	1	chr3D.!!$R2	701
15	TraesCS1D01G048500	chr4D	202966854	202967554	700	False	852.000000	852	88.780000	1	702	1	chr4D.!!$F2	701
16	TraesCS1D01G048500	chr4D	454537021	454537592	571	False	804.000000	804	92.308000	1	562	1	chr4D.!!$F4	561
17	TraesCS1D01G048500	chr4D	366080424	366081129	705	False	599.000000	599	82.459000	18	721	1	chr4D.!!$F3	703
18	TraesCS1D01G048500	chr1A	29279860	29281383	1523	False	398.000000	665	88.139500	867	2851	4	chr1A.!!$F1	1984
19	TraesCS1D01G048500	chr5D	166157162	166157686	524	True	643.000000	643	88.993000	178	702	1	chr5D.!!$R1	524
20	TraesCS1D01G048500	chr5D	166228896	166229420	524	True	632.000000	632	88.619000	178	702	1	chr5D.!!$R2	524
21	TraesCS1D01G048500	chr4B	472614440	472615116	676	False	568.000000	568	82.277000	28	703	1	chr4B.!!$F1	675
22	TraesCS1D01G048500	chr3B	164422025	164422742	717	True	564.000000	564	81.301000	5	725	1	chr3B.!!$R1	720
23	TraesCS1D01G048500	chr3B	519609894	519610587	693	True	503.000000	503	80.505000	41	724	1	chr3B.!!$R2	683
24	TraesCS1D01G048500	chr5B	363606622	363607253	631	True	496.000000	496	81.385000	94	723	1	chr5B.!!$R1	629
25	TraesCS1D01G048500	chr2B	214880203	214880766	563	True	313.000000	313	77.740000	174	727	1	chr2B.!!$R1	553

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
790	835	0.032515	TTCGGAGGTGCTCATAGGGA	60.033	55.0	0.00	31.08	4.20	F
863	908	0.038983	TGCTTTGCGCTCGTACTGTA	60.039	50.0	9.73	40.11	2.74	F
1774	1833	0.029700	ACGTTTAGTTTTGGCCGTGC	59.970	50.0	0.00	0.00	5.34	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1755	1814	0.029700	GCACGGCCAAAACTAAACGT	59.970	50.0	2.24	0.00	34.61	3.99	R
1883	1998	0.035881	TCCGACTAGGACACACGACT	59.964	55.0	0.00	0.00	45.98	4.18	R
2720	2856	0.179189	CAGATTGGAAAGAACGCGGC	60.179	55.0	12.47	1.16	0.00	6.53	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
322	329	5.062683	CAGAAGATAGGTGACACGATGTTTG	59.937	44.000	0.00	0.20	0.00	2.93
465	494	3.827008	AGCCTGTATGATTGTGATCGT	57.173	42.857	0.00	0.00	34.91	3.73
484	513	3.535561	CGTCTCTACGGACTAAACCCTA	58.464	50.000	0.00	0.00	45.50	3.53
562	603	1.908066	ATCCGAACGCCAAGTTTCGC	61.908	55.000	0.00	0.00	44.35	4.70
563	604	2.127383	CGAACGCCAAGTTTCGCC	60.127	61.111	0.00	0.00	44.35	5.54
564	605	2.887889	CGAACGCCAAGTTTCGCCA	61.888	57.895	0.00	0.00	44.35	5.69
565	606	1.357334	GAACGCCAAGTTTCGCCAA	59.643	52.632	0.00	0.00	44.35	4.52
566	607	0.660300	GAACGCCAAGTTTCGCCAAG	60.660	55.000	0.00	0.00	44.35	3.61
567	608	1.381165	AACGCCAAGTTTCGCCAAGT	61.381	50.000	0.00	0.00	40.88	3.16
662	707	0.035820	GTCCGGCCCAAGTCACATAA	60.036	55.000	0.00	0.00	0.00	1.90
705	750	0.252284	ATCCAGGACTCCCTCAACGT	60.252	55.000	0.00	0.00	42.02	3.99
706	751	0.471211	TCCAGGACTCCCTCAACGTT	60.471	55.000	0.00	0.00	42.02	3.99
722	767	2.823628	GTTCCCGTCAACGAAGAGG	58.176	57.895	3.71	0.00	43.02	3.69
723	768	0.669625	GTTCCCGTCAACGAAGAGGG	60.670	60.000	3.71	11.72	43.02	4.30
724	769	1.117142	TTCCCGTCAACGAAGAGGGT	61.117	55.000	15.54	0.00	40.95	4.34
726	771	1.080025	CCGTCAACGAAGAGGGTCC	60.080	63.158	3.71	0.00	43.02	4.46
727	772	1.533469	CCGTCAACGAAGAGGGTCCT	61.533	60.000	3.71	0.00	43.02	3.85
728	773	1.171308	CGTCAACGAAGAGGGTCCTA	58.829	55.000	0.00	0.00	43.02	2.94
729	774	1.135460	CGTCAACGAAGAGGGTCCTAC	60.135	57.143	0.00	0.00	43.02	3.18
730	775	1.135460	GTCAACGAAGAGGGTCCTACG	60.135	57.143	0.00	8.38	0.00	3.51
731	776	0.172803	CAACGAAGAGGGTCCTACGG	59.827	60.000	12.47	0.00	0.00	4.02
732	777	0.251519	AACGAAGAGGGTCCTACGGT	60.252	55.000	12.47	5.87	0.00	4.83
733	778	0.964358	ACGAAGAGGGTCCTACGGTG	60.964	60.000	12.47	0.00	0.00	4.94
734	779	0.679002	CGAAGAGGGTCCTACGGTGA	60.679	60.000	0.00	0.00	0.00	4.02
735	780	0.816373	GAAGAGGGTCCTACGGTGAC	59.184	60.000	0.00	0.00	0.00	3.67

Showing 1 to 25 of 567 entries

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Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
150	152	3.000041	GTCATCTACAACAATGTCGCCA	59.000	45.455	0.00	0.00	41.05	5.69
301	307	3.684788	GCAAACATCGTGTCACCTATCTT	59.315	43.478	0.00	0.00	0.00	2.40
309	315	0.888736	CCTGGGCAAACATCGTGTCA	60.889	55.000	0.00	0.00	0.00	3.58
411	419	6.068823	GGTTTAGCCATTACGATCTCGTGC	62.069	50.000	15.08	9.64	44.51	5.34
465	494	3.197766	TCGTAGGGTTTAGTCCGTAGAGA	59.802	47.826	0.00	0.00	0.00	3.10
484	513	3.892104	TAGGCCCCTTCGGTGTCGT	62.892	63.158	0.00	0.00	37.69	4.34
562	603	1.080569	GCGTGGATGGCAAACTTGG	60.081	57.895	0.00	0.00	0.00	3.61
563	604	0.031857	TTGCGTGGATGGCAAACTTG	59.968	50.000	0.00	0.00	46.49	3.16
564	605	2.424474	TTGCGTGGATGGCAAACTT	58.576	47.368	0.00	0.00	46.49	2.66
565	606	4.172625	TTGCGTGGATGGCAAACT	57.827	50.000	0.00	0.00	46.49	2.66
612	657	5.591877	GCCATGGAGATACAAGACAAAAGAT	59.408	40.000	18.40	0.00	0.00	2.40
705	750	1.117142	ACCCTCTTCGTTGACGGGAA	61.117	55.000	3.48	0.00	38.30	3.97
706	751	1.530013	GACCCTCTTCGTTGACGGGA	61.530	60.000	3.48	2.47	38.30	5.14
726	771	6.364165	TCTTGAAATTTACGAAGTCACCGTAG	59.636	38.462	0.00	0.00	43.93	3.51
727	772	6.215121	TCTTGAAATTTACGAAGTCACCGTA	58.785	36.000	0.00	0.00	43.93	4.02
728	773	5.051816	TCTTGAAATTTACGAAGTCACCGT	58.948	37.500	0.00	0.00	43.93	4.83
729	774	5.585500	TCTTGAAATTTACGAAGTCACCG	57.415	39.130	0.00	0.00	43.93	4.94
730	775	7.129109	TCATCTTGAAATTTACGAAGTCACC	57.871	36.000	0.00	0.00	43.93	4.02
733	778	9.374960	GCATATCATCTTGAAATTTACGAAGTC	57.625	33.333	0.00	0.00	43.93	3.01
735	780	7.531871	CGGCATATCATCTTGAAATTTACGAAG	59.468	37.037	0.00	0.00	0.00	3.79
736	781	7.351981	CGGCATATCATCTTGAAATTTACGAA	58.648	34.615	0.00	0.00	0.00	3.85
737	782	6.073276	CCGGCATATCATCTTGAAATTTACGA	60.073	38.462	0.00	0.00	0.00	3.43
738	783	6.079763	CCGGCATATCATCTTGAAATTTACG	58.920	40.000	0.00	0.00	0.00	3.18
739	784	5.858581	GCCGGCATATCATCTTGAAATTTAC	59.141	40.000	24.80	0.00	0.00	2.01
740	785	5.048083	GGCCGGCATATCATCTTGAAATTTA	60.048	40.000	30.85	0.00	0.00	1.40

Showing 1 to 25 of 598 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.