AutoCloner

Multiple sequence alignment - TraesCS7B01G352900

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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	TraesCS7B01G352900	chr7B	100.000	2750	0	0	1	2750	610361452	610358703	0.000000e+00	5079
1	TraesCS7B01G352900	chr1B	95.692	1834	62	7	934	2750	444871812	444869979	0.000000e+00	2933
2	TraesCS7B01G352900	chr1B	93.227	251	11	3	686	930	444872094	444871844	5.600000e-97	364
3	TraesCS7B01G352900	chr2B	95.303	1831	53	13	934	2750	77853437	77855248	0.000000e+00	2874
4	TraesCS7B01G352900	chr2B	95.932	1770	56	7	996	2750	41878671	41880439	0.000000e+00	2856
5	TraesCS7B01G352900	chr2B	95.087	1832	57	7	934	2750	77809479	77811292	0.000000e+00	2854
6	TraesCS7B01G352900	chr2B	95.486	288	6	4	654	934	77853120	77853407	1.160000e-123	453
7	TraesCS7B01G352900	chr2B	95.139	288	7	4	654	934	77809162	77809449	5.400000e-122	448
8	TraesCS7B01G352900	chr2B	89.024	328	26	4	1	322	707615413	707615736	5.520000e-107	398
9	TraesCS7B01G352900	chr2B	94.531	128	6	1	684	810	41868313	41868440	2.160000e-46	196
10	TraesCS7B01G352900	chr2B	79.767	257	35	14	356	598	707615797	707616050	1.310000e-38	171
11	TraesCS7B01G352900	chrUn	95.928	1768	56	6	998	2750	245553268	245555034	0.000000e+00	2852
12	TraesCS7B01G352900	chrUn	95.158	1363	50	6	1403	2750	272843918	272845279	0.000000e+00	2137
13	TraesCS7B01G352900	chrUn	94.792	864	32	4	1900	2750	372881751	372882614	0.000000e+00	1334
14	TraesCS7B01G352900	chrUn	94.560	864	34	4	1900	2750	372864748	372863885	0.000000e+00	1323
15	TraesCS7B01G352900	chrUn	100.000	40	0	0	944	983	245553231	245553270	1.060000e-09	75
16	TraesCS7B01G352900	chr7D	93.205	1295	73	5	1471	2750	45285495	45286789	0.000000e+00	1890
17	TraesCS7B01G352900	chr7D	92.243	954	58	6	1471	2408	45284169	45285122	0.000000e+00	1338
18	TraesCS7B01G352900	chr7D	89.294	850	30	17	654	1472	45281257	45282076	0.000000e+00	1009
19	TraesCS7B01G352900	chr1D	88.057	628	30	13	1	602	404275120	404274512	0.000000e+00	702
20	TraesCS7B01G352900	chr3B	83.106	586	51	27	1	569	30086838	30087392	8.850000e-135	490
21	TraesCS7B01G352900	chr2A	89.329	328	25	4	1	322	528426918	528426595	1.190000e-108	403
22	TraesCS7B01G352900	chr2A	80.516	349	32	18	2	337	545739278	545739603	4.580000e-58	235
23	TraesCS7B01G352900	chr6B	78.965	599	80	31	2	579	463402303	463401730	1.560000e-97	366
24	TraesCS7B01G352900	chr6B	78.469	627	85	34	2	605	132948707	132949306	5.600000e-97	364
25	TraesCS7B01G352900	chr5A	78.425	635	85	36	2	613	680744796	680744191	1.560000e-97	366
26	TraesCS7B01G352900	chr1A	78.261	621	85	34	2	599	517179016	517178423	1.210000e-93	353
27	TraesCS7B01G352900	chr4B	77.829	654	84	34	2	613	245453574	245452940	5.640000e-92	348

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	TraesCS7B01G352900	chr7B	610358703	610361452	2749	True	5079.000000	5079	100.000000	1	2750	1	chr7B.!!$R1	2749
1	TraesCS7B01G352900	chr1B	444869979	444872094	2115	True	1648.500000	2933	94.459500	686	2750	2	chr1B.!!$R1	2064
2	TraesCS7B01G352900	chr2B	41878671	41880439	1768	False	2856.000000	2856	95.932000	996	2750	1	chr2B.!!$F2	1754
3	TraesCS7B01G352900	chr2B	77853120	77855248	2128	False	1663.500000	2874	95.394500	654	2750	2	chr2B.!!$F4	2096
4	TraesCS7B01G352900	chr2B	77809162	77811292	2130	False	1651.000000	2854	95.113000	654	2750	2	chr2B.!!$F3	2096
5	TraesCS7B01G352900	chr2B	707615413	707616050	637	False	284.500000	398	84.395500	1	598	2	chr2B.!!$F5	597
6	TraesCS7B01G352900	chrUn	272843918	272845279	1361	False	2137.000000	2137	95.158000	1403	2750	1	chrUn.!!$F1	1347
7	TraesCS7B01G352900	chrUn	245553231	245555034	1803	False	1463.500000	2852	97.964000	944	2750	2	chrUn.!!$F3	1806
8	TraesCS7B01G352900	chrUn	372881751	372882614	863	False	1334.000000	1334	94.792000	1900	2750	1	chrUn.!!$F2	850
9	TraesCS7B01G352900	chrUn	372863885	372864748	863	True	1323.000000	1323	94.560000	1900	2750	1	chrUn.!!$R1	850
10	TraesCS7B01G352900	chr7D	45281257	45286789	5532	False	1412.333333	1890	91.580667	654	2750	3	chr7D.!!$F1	2096
11	TraesCS7B01G352900	chr1D	404274512	404275120	608	True	702.000000	702	88.057000	1	602	1	chr1D.!!$R1	601
12	TraesCS7B01G352900	chr3B	30086838	30087392	554	False	490.000000	490	83.106000	1	569	1	chr3B.!!$F1	568
13	TraesCS7B01G352900	chr6B	463401730	463402303	573	True	366.000000	366	78.965000	2	579	1	chr6B.!!$R1	577
14	TraesCS7B01G352900	chr6B	132948707	132949306	599	False	364.000000	364	78.469000	2	605	1	chr6B.!!$F1	603
15	TraesCS7B01G352900	chr5A	680744191	680744796	605	True	366.000000	366	78.425000	2	613	1	chr5A.!!$R1	611
16	TraesCS7B01G352900	chr1A	517178423	517179016	593	True	353.000000	353	78.261000	2	599	1	chr1A.!!$R1	597
17	TraesCS7B01G352900	chr4B	245452940	245453574	634	True	348.000000	348	77.829000	2	613	1	chr4B.!!$R1	611

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
97	101	0.032217	CCCCTCTCTTCCTCTGCTCT	60.032	60.0	0.00	0.0	0.0	4.09	F
652	739	0.105593	CAGCTGGCTACATGTCGGAT	59.894	55.0	5.57	0.0	0.0	4.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1747	3966	0.183492	AGCTTGCCAAACTGGTCTCA	59.817	50.0	0.0	0.0	40.46	3.27	R
1956	4179	0.610174	TGAAGTCGCCTCTTGCTCAT	59.390	50.0	0.0	0.0	38.05	2.90	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
97	101	0.032217	CCCCTCTCTTCCTCTGCTCT	60.032	60.000	0.00	0.00	0.00	4.09
109	113	2.495270	CCTCTGCTCTGAAGTTGCTAGA	59.505	50.000	0.00	0.00	0.00	2.43
169	173	0.546598	AGATCGATGGGTTGGGTTCC	59.453	55.000	0.54	0.00	0.00	3.62
170	174	0.254747	GATCGATGGGTTGGGTTCCA	59.745	55.000	0.54	0.00	37.46	3.53
172	176	0.701731	TCGATGGGTTGGGTTCCATT	59.298	50.000	0.00	0.00	43.20	3.16
173	177	1.076350	TCGATGGGTTGGGTTCCATTT	59.924	47.619	0.00	0.00	43.20	2.32
222	232	1.982226	TCCTTCTCATTCCGTTTCCCA	59.018	47.619	0.00	0.00	0.00	4.37
579	666	1.062685	CGATGACGGACGACCAGAG	59.937	63.158	4.48	0.00	35.59	3.35
582	669	3.063084	GACGGACGACCAGAGGCT	61.063	66.667	4.48	0.00	35.59	4.58
586	673	1.655329	GGACGACCAGAGGCTATCG	59.345	63.158	0.00	8.00	40.39	2.92
605	692	2.895404	TCGCCGCTTTATTAGTAGGGAT	59.105	45.455	0.00	0.00	0.00	3.85
607	694	4.523943	TCGCCGCTTTATTAGTAGGGATAA	59.476	41.667	0.00	0.00	0.00	1.75
609	696	5.347907	CGCCGCTTTATTAGTAGGGATAAAG	59.652	44.000	10.10	10.10	43.63	1.85
611	698	7.104290	GCCGCTTTATTAGTAGGGATAAAGAT	58.896	38.462	16.01	0.00	43.54	2.40
612	699	8.255905	GCCGCTTTATTAGTAGGGATAAAGATA	58.744	37.037	16.01	0.00	43.54	1.98
633	720	7.983307	AGATAAAGATTGAAGATGAACACAGC	58.017	34.615	0.00	0.00	0.00	4.40
634	721	7.609146	AGATAAAGATTGAAGATGAACACAGCA	59.391	33.333	0.00	0.00	0.00	4.41
635	722	5.624344	AAGATTGAAGATGAACACAGCAG	57.376	39.130	0.00	0.00	0.00	4.24
636	723	3.439476	AGATTGAAGATGAACACAGCAGC	59.561	43.478	0.00	0.00	0.00	5.25
637	724	2.556144	TGAAGATGAACACAGCAGCT	57.444	45.000	0.00	0.00	32.63	4.24
638	725	2.148768	TGAAGATGAACACAGCAGCTG	58.851	47.619	21.54	21.54	37.52	4.24
639	726	1.467734	GAAGATGAACACAGCAGCTGG	59.532	52.381	26.38	16.87	35.51	4.85
640	727	0.959372	AGATGAACACAGCAGCTGGC	60.959	55.000	26.38	12.69	45.30	4.85
649	736	3.403277	GCAGCTGGCTACATGTCG	58.597	61.111	17.12	0.00	40.25	4.35
650	737	2.176273	GCAGCTGGCTACATGTCGG	61.176	63.158	17.12	0.00	40.25	4.79
651	738	1.517361	CAGCTGGCTACATGTCGGA	59.483	57.895	5.57	0.00	0.00	4.55
652	739	0.105593	CAGCTGGCTACATGTCGGAT	59.894	55.000	5.57	0.00	0.00	4.18
695	782	2.651361	CGAACCTGCTCTGACCGT	59.349	61.111	0.00	0.00	0.00	4.83
1075	1199	1.625818	GGAAGGAGCCTGTTGAGAAGA	59.374	52.381	0.00	0.00	0.00	2.87
1109	1233	1.601759	CCATGATGGGGCGCCTTAG	60.602	63.158	28.56	9.34	32.67	2.18
1335	1459	3.325870	TGATTTCGCGAACAAGTCTGAT	58.674	40.909	23.33	9.73	0.00	2.90
1535	3753	3.325293	ACTGATCGACAAGAACTGCAT	57.675	42.857	3.31	0.00	0.00	3.96
1641	3859	2.307686	GTGGGTGACAATAAGGAAGGGA	59.692	50.000	0.00	0.00	0.00	4.20
1747	3966	0.546267	ATGTCAGTCCCCAGCAGACT	60.546	55.000	0.00	0.00	45.45	3.24
1810	4029	2.545810	CCCCAGAGGAGAGAAGAAAGT	58.454	52.381	0.00	0.00	38.24	2.66
1882	4105	0.494095	AAGACAGAGGAGGGGGAAGT	59.506	55.000	0.00	0.00	0.00	3.01
1931	4154	3.733337	AGCAGAACTTCTCGTGAAACAT	58.267	40.909	1.12	0.00	35.74	2.71
1956	4179	2.634453	TGAATGAGACTGTGAAGCCTGA	59.366	45.455	0.00	0.00	0.00	3.86
2054	4277	4.891756	AGAAATTATTCTCTACGGACCCGA	59.108	41.667	16.07	0.00	42.26	5.14
2062	4285	1.672854	CTACGGACCCGAAGATGCCA	61.673	60.000	16.07	0.00	42.83	4.92
2071	4295	3.199946	ACCCGAAGATGCCAGAAAATCTA	59.800	43.478	0.00	0.00	32.79	1.98
2090	4314	5.401531	TCTATACGCAAGAGAAAACCAGT	57.598	39.130	0.00	0.00	43.62	4.00
2119	4343	0.494551	TGGGAGTAAAGGAGGTGGGA	59.505	55.000	0.00	0.00	0.00	4.37
2226	4460	0.105964	CACTGGTTTGGACGAGGACA	59.894	55.000	0.00	0.00	36.08	4.02
2266	4502	5.440610	ACAAGAATGACCAGTTCTGTTTCT	58.559	37.500	0.00	0.62	36.14	2.52
2338	4574	2.516225	GCGCGGGGCTTCCTATTT	60.516	61.111	8.83	0.00	39.11	1.40
2370	4606	0.530744	AGCAATGAAGGTCGTCGCTA	59.469	50.000	0.00	0.00	0.00	4.26
2478	6040	2.172505	TCAGAAACAAAGCTGGACAGGA	59.827	45.455	1.01	0.00	33.05	3.86
2504	6066	5.741011	AGGATGAAGCGAATTAAGGTGTTA	58.259	37.500	0.00	0.00	0.00	2.41
2651	6213	0.477597	TCACTGGGGAGGATGGGTTT	60.478	55.000	0.00	0.00	0.00	3.27
2672	6234	3.031736	TGTCTGGAGGCTTACTGGTATC	58.968	50.000	0.00	0.00	0.00	2.24

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
97	101	1.799181	GCTCGCGATCTAGCAACTTCA	60.799	52.381	10.36	0.00	38.63	3.02
133	137	3.442273	CGATCTCCCTAAGATAGAGTGGC	59.558	52.174	0.00	0.00	45.06	5.01
173	177	3.951680	AGTGGAAAAGGAGCGAAGAAAAA	59.048	39.130	0.00	0.00	0.00	1.94
190	200	4.934797	ATGAGAAGGAATTCCAAGTGGA	57.065	40.909	26.22	5.97	43.73	4.02
222	232	1.168714	GCAAGACGGAGCAAAGGAAT	58.831	50.000	0.00	0.00	0.00	3.01
483	569	3.387374	TCAAGTTAACCTGAACCGGTACA	59.613	43.478	8.00	0.00	35.89	2.90
582	669	4.081406	TCCCTACTAATAAAGCGGCGATA	58.919	43.478	12.98	0.00	0.00	2.92
586	673	6.461640	TCTTTATCCCTACTAATAAAGCGGC	58.538	40.000	9.08	0.00	41.79	6.53
607	694	8.457261	GCTGTGTTCATCTTCAATCTTTATCTT	58.543	33.333	0.00	0.00	0.00	2.40
609	696	7.755591	TGCTGTGTTCATCTTCAATCTTTATC	58.244	34.615	0.00	0.00	0.00	1.75
611	698	6.348786	GCTGCTGTGTTCATCTTCAATCTTTA	60.349	38.462	0.00	0.00	0.00	1.85
612	699	5.564259	GCTGCTGTGTTCATCTTCAATCTTT	60.564	40.000	0.00	0.00	0.00	2.52
613	700	4.082895	GCTGCTGTGTTCATCTTCAATCTT	60.083	41.667	0.00	0.00	0.00	2.40
614	701	3.439476	GCTGCTGTGTTCATCTTCAATCT	59.561	43.478	0.00	0.00	0.00	2.40
615	702	3.439476	AGCTGCTGTGTTCATCTTCAATC	59.561	43.478	0.00	0.00	0.00	2.67
616	703	3.190744	CAGCTGCTGTGTTCATCTTCAAT	59.809	43.478	21.21	0.00	0.00	2.57
617	704	2.551032	CAGCTGCTGTGTTCATCTTCAA	59.449	45.455	21.21	0.00	0.00	2.69
618	705	2.148768	CAGCTGCTGTGTTCATCTTCA	58.851	47.619	21.21	0.00	0.00	3.02
619	706	1.467734	CCAGCTGCTGTGTTCATCTTC	59.532	52.381	26.41	0.00	0.00	2.87
620	707	1.531423	CCAGCTGCTGTGTTCATCTT	58.469	50.000	26.41	0.00	0.00	2.40
621	708	0.959372	GCCAGCTGCTGTGTTCATCT	60.959	55.000	26.41	0.00	36.87	2.90
622	709	1.505353	GCCAGCTGCTGTGTTCATC	59.495	57.895	26.41	4.69	36.87	2.92
623	710	3.677527	GCCAGCTGCTGTGTTCAT	58.322	55.556	26.41	0.00	36.87	2.57
632	719	2.176273	CCGACATGTAGCCAGCTGC	61.176	63.158	8.66	3.91	41.71	5.25
633	720	0.105593	ATCCGACATGTAGCCAGCTG	59.894	55.000	6.78	6.78	0.00	4.24
634	721	1.341531	GTATCCGACATGTAGCCAGCT	59.658	52.381	0.00	0.00	0.00	4.24
635	722	1.605712	GGTATCCGACATGTAGCCAGC	60.606	57.143	0.00	0.00	0.00	4.85
636	723	1.964223	AGGTATCCGACATGTAGCCAG	59.036	52.381	0.00	0.00	0.00	4.85
637	724	1.961394	GAGGTATCCGACATGTAGCCA	59.039	52.381	0.00	0.00	0.00	4.75
638	725	2.229302	GAGAGGTATCCGACATGTAGCC	59.771	54.545	0.00	0.00	0.00	3.93
639	726	2.095668	CGAGAGGTATCCGACATGTAGC	60.096	54.545	0.00	0.00	0.00	3.58
640	727	2.095668	GCGAGAGGTATCCGACATGTAG	60.096	54.545	0.00	0.00	0.00	2.74
641	728	1.878088	GCGAGAGGTATCCGACATGTA	59.122	52.381	0.00	0.00	0.00	2.29
642	729	0.669077	GCGAGAGGTATCCGACATGT	59.331	55.000	0.00	0.00	0.00	3.21
643	730	0.386100	CGCGAGAGGTATCCGACATG	60.386	60.000	0.00	0.00	0.00	3.21
644	731	0.534427	TCGCGAGAGGTATCCGACAT	60.534	55.000	3.71	0.00	34.84	3.06
645	732	1.153309	TCGCGAGAGGTATCCGACA	60.153	57.895	3.71	0.00	34.84	4.35
646	733	1.159098	AGTCGCGAGAGGTATCCGAC	61.159	60.000	10.24	3.56	46.05	4.79
647	734	1.145598	AGTCGCGAGAGGTATCCGA	59.854	57.895	10.24	0.00	43.49	4.55
648	735	1.280142	CAGTCGCGAGAGGTATCCG	59.720	63.158	10.24	0.00	43.49	4.18
649	736	1.655329	CCAGTCGCGAGAGGTATCC	59.345	63.158	10.24	0.00	43.49	2.59
650	737	1.008309	GCCAGTCGCGAGAGGTATC	60.008	63.158	23.17	5.66	43.49	2.24
651	738	3.121019	GCCAGTCGCGAGAGGTAT	58.879	61.111	23.17	0.00	43.49	2.73
880	969	1.078988	CGGGGCAAATTGCTGCAAT	60.079	52.632	21.48	21.48	44.28	3.56
1075	1199	2.606826	GGAGTCCACCCCTTCCGT	60.607	66.667	3.60	0.00	0.00	4.69
1335	1459	1.342474	CCCTCTTGAGCCCTGTCTCTA	60.342	57.143	0.00	0.00	34.29	2.43
1535	3753	2.290287	CCCTCGTCCACATCCACCA	61.290	63.158	0.00	0.00	0.00	4.17
1632	3850	0.543749	CATCCTCGCTTCCCTTCCTT	59.456	55.000	0.00	0.00	0.00	3.36
1641	3859	4.130118	GGTCATATTTCACATCCTCGCTT	58.870	43.478	0.00	0.00	0.00	4.68
1747	3966	0.183492	AGCTTGCCAAACTGGTCTCA	59.817	50.000	0.00	0.00	40.46	3.27
1882	4105	4.671590	TCAGGGACGGAGCCACGA	62.672	66.667	4.54	0.00	37.61	4.35
1931	4154	2.550855	GCTTCACAGTCTCATTCACCCA	60.551	50.000	0.00	0.00	0.00	4.51
1956	4179	0.610174	TGAAGTCGCCTCTTGCTCAT	59.390	50.000	0.00	0.00	38.05	2.90
2054	4277	5.368145	TGCGTATAGATTTTCTGGCATCTT	58.632	37.500	0.00	0.00	31.89	2.40
2062	4285	7.606456	TGGTTTTCTCTTGCGTATAGATTTTCT	59.394	33.333	0.00	0.00	0.00	2.52
2071	4295	5.978814	AGATACTGGTTTTCTCTTGCGTAT	58.021	37.500	0.00	0.00	0.00	3.06
2090	4314	3.469771	TCCTTTACTCCCAGCCCTAGATA	59.530	47.826	0.00	0.00	0.00	1.98
2119	4343	1.988846	AGAAAGCTTCCCCTTAGCAGT	59.011	47.619	0.00	0.00	41.11	4.40
2266	4502	3.440127	CCTTTTGATTCCCCTGGCTTTA	58.560	45.455	0.00	0.00	0.00	1.85
2331	4567	3.181454	GCTTACTGCAGGGCTAAATAGGA	60.181	47.826	19.93	0.00	42.31	2.94
2478	6040	4.878397	CACCTTAATTCGCTTCATCCTCTT	59.122	41.667	0.00	0.00	0.00	2.85
2651	6213	2.615986	TACCAGTAAGCCTCCAGACA	57.384	50.000	0.00	0.00	0.00	3.41
2672	6234	1.148157	CGTGCTTCGGCTCACCATAG	61.148	60.000	0.00	0.00	42.37	2.23

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.