AutoCloner

Multiple sequence alignment - TraesCS3A01G027100

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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	TraesCS3A01G027100	chr3A	100.000	2963	0	0	1	2963	14276944	14279906	0.000000e+00	5472
1	TraesCS3A01G027100	chr3A	84.670	848	98	17	1313	2147	35090978	35090150	0.000000e+00	817
2	TraesCS3A01G027100	chr3A	84.670	848	98	17	1313	2147	35148815	35147987	0.000000e+00	817
3	TraesCS3A01G027100	chr1A	99.313	2184	15	0	780	2963	540201262	540203445	0.000000e+00	3951
4	TraesCS3A01G027100	chr1A	94.444	180	7	3	576	754	540201089	540201266	1.050000e-69	274
5	TraesCS3A01G027100	chr4A	96.637	1368	40	4	1588	2953	651356917	651358280	0.000000e+00	2266
6	TraesCS3A01G027100	chr4A	94.700	1000	38	12	599	1587	651355880	651356875	0.000000e+00	1539
7	TraesCS3A01G027100	chr4A	86.573	782	82	14	2180	2948	8981437	8980666	0.000000e+00	841
8	TraesCS3A01G027100	chr4A	82.636	789	91	27	794	1562	9052765	9052003	0.000000e+00	656
9	TraesCS3A01G027100	chr4A	82.077	809	97	17	790	1585	9048482	9047709	0.000000e+00	647
10	TraesCS3A01G027100	chr4A	86.265	597	74	7	1588	2182	9047666	9047076	2.490000e-180	641
11	TraesCS3A01G027100	chr4A	92.325	456	23	6	139	584	85898063	85897610	3.220000e-179	638
12	TraesCS3A01G027100	chr4A	87.619	525	59	5	1588	2111	9051100	9050581	3.270000e-169	604
13	TraesCS3A01G027100	chr4A	87.111	450	42	11	2100	2538	9049249	9048805	2.050000e-136	496
14	TraesCS3A01G027100	chr4A	94.326	141	6	1	1	139	85898234	85898094	6.430000e-52	215
15	TraesCS3A01G027100	chr1B	95.669	1316	44	8	1588	2900	268102924	268104229	0.000000e+00	2102
16	TraesCS3A01G027100	chr1B	94.274	1013	37	10	589	1587	268101877	268102882	0.000000e+00	1530
17	TraesCS3A01G027100	chr2B	84.937	1029	119	18	1154	2171	38258478	38257475	0.000000e+00	1009
18	TraesCS3A01G027100	chr2B	82.967	364	51	6	974	1331	457109075	457109433	4.770000e-83	318
19	TraesCS3A01G027100	chr2B	92.199	141	9	1	1	139	219624771	219624911	6.480000e-47	198
20	TraesCS3A01G027100	chr7A	87.567	748	79	11	1412	2147	576090059	576090804	0.000000e+00	854
21	TraesCS3A01G027100	chr7A	93.836	438	17	4	154	584	236375945	236376379	0.000000e+00	651
22	TraesCS3A01G027100	chr7A	95.683	139	6	0	1	139	236375755	236375893	1.070000e-54	224
23	TraesCS3A01G027100	chr4B	85.142	848	93	19	1313	2147	475798985	475798158	0.000000e+00	837
24	TraesCS3A01G027100	chr5A	86.782	749	84	12	1412	2147	637184905	637184159	0.000000e+00	821
25	TraesCS3A01G027100	chr5A	95.338	429	14	3	154	577	60772123	60772550	0.000000e+00	676
26	TraesCS3A01G027100	chr5A	93.571	140	8	1	1	139	60771932	60772071	1.080000e-49	207
27	TraesCS3A01G027100	chrUn	84.670	848	98	17	1313	2147	309100559	309101387	0.000000e+00	817
28	TraesCS3A01G027100	chrUn	84.670	848	98	17	1313	2147	309112638	309111810	0.000000e+00	817
29	TraesCS3A01G027100	chrUn	95.833	144	6	0	434	577	82561170	82561027	1.780000e-57	233
30	TraesCS3A01G027100	chr5D	86.815	584	68	5	1591	2169	537912147	537911568	0.000000e+00	643
31	TraesCS3A01G027100	chr5D	83.871	341	32	10	1252	1586	537912518	537912195	1.330000e-78	303
32	TraesCS3A01G027100	chr3B	91.904	457	25	7	139	584	734175893	734175438	1.940000e-176	628
33	TraesCS3A01G027100	chr3B	93.511	262	14	2	139	397	683591780	683592041	1.290000e-103	387
34	TraesCS3A01G027100	chr3B	92.908	141	8	1	1	139	683591609	683591749	1.390000e-48	204
35	TraesCS3A01G027100	chr7B	89.978	449	32	7	139	584	255198170	255198608	4.290000e-158	568
36	TraesCS3A01G027100	chr2A	93.548	310	17	2	154	461	390323008	390322700	2.690000e-125	459
37	TraesCS3A01G027100	chr2A	94.245	139	8	0	1	139	390323198	390323060	2.310000e-51	213
38	TraesCS3A01G027100	chr2A	93.600	125	8	0	460	584	390322617	390322493	1.400000e-43	187
39	TraesCS3A01G027100	chr2A	85.981	107	11	3	1227	1331	522072743	522072847	8.680000e-21	111
40	TraesCS3A01G027100	chr4D	97.638	254	5	1	139	392	105236841	105237093	4.540000e-118	435
41	TraesCS3A01G027100	chr4D	96.403	139	5	0	1	139	29424096	29423958	2.300000e-56	230
42	TraesCS3A01G027100	chr4D	97.561	123	3	0	17	139	105236688	105236810	8.320000e-51	211
43	TraesCS3A01G027100	chr4D	96.923	65	2	0	520	584	29423789	29423725	3.120000e-20	110
44	TraesCS3A01G027100	chr6B	89.655	348	19	6	139	481	542697737	542698072	7.590000e-116	427
45	TraesCS3A01G027100	chr1D	97.122	139	4	0	1	139	319525462	319525324	4.940000e-58	235
46	TraesCS3A01G027100	chr1D	90.625	128	9	2	460	584	319525160	319525033	1.830000e-37	167
47	TraesCS3A01G027100	chr7D	95.327	107	4	1	355	461	89873527	89873632	5.080000e-38	169
48	TraesCS3A01G027100	chr2D	87.619	105	11	2	1228	1331	386248880	386248983	1.440000e-23	121

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	TraesCS3A01G027100	chr3A	14276944	14279906	2962	False	5472.000000	5472	100.000000	1	2963	1	chr3A.!!$F1	2962
1	TraesCS3A01G027100	chr3A	35090150	35090978	828	True	817.000000	817	84.670000	1313	2147	1	chr3A.!!$R1	834
2	TraesCS3A01G027100	chr3A	35147987	35148815	828	True	817.000000	817	84.670000	1313	2147	1	chr3A.!!$R2	834
3	TraesCS3A01G027100	chr1A	540201089	540203445	2356	False	2112.500000	3951	96.878500	576	2963	2	chr1A.!!$F1	2387
4	TraesCS3A01G027100	chr4A	651355880	651358280	2400	False	1902.500000	2266	95.668500	599	2953	2	chr4A.!!$F1	2354
5	TraesCS3A01G027100	chr4A	8980666	8981437	771	True	841.000000	841	86.573000	2180	2948	1	chr4A.!!$R1	768
6	TraesCS3A01G027100	chr4A	9047076	9052765	5689	True	608.800000	656	85.141600	790	2538	5	chr4A.!!$R2	1748
7	TraesCS3A01G027100	chr4A	85897610	85898234	624	True	426.500000	638	93.325500	1	584	2	chr4A.!!$R3	583
8	TraesCS3A01G027100	chr1B	268101877	268104229	2352	False	1816.000000	2102	94.971500	589	2900	2	chr1B.!!$F1	2311
9	TraesCS3A01G027100	chr2B	38257475	38258478	1003	True	1009.000000	1009	84.937000	1154	2171	1	chr2B.!!$R1	1017
10	TraesCS3A01G027100	chr7A	576090059	576090804	745	False	854.000000	854	87.567000	1412	2147	1	chr7A.!!$F1	735
11	TraesCS3A01G027100	chr7A	236375755	236376379	624	False	437.500000	651	94.759500	1	584	2	chr7A.!!$F2	583
12	TraesCS3A01G027100	chr4B	475798158	475798985	827	True	837.000000	837	85.142000	1313	2147	1	chr4B.!!$R1	834
13	TraesCS3A01G027100	chr5A	637184159	637184905	746	True	821.000000	821	86.782000	1412	2147	1	chr5A.!!$R1	735
14	TraesCS3A01G027100	chr5A	60771932	60772550	618	False	441.500000	676	94.454500	1	577	2	chr5A.!!$F1	576
15	TraesCS3A01G027100	chrUn	309100559	309101387	828	False	817.000000	817	84.670000	1313	2147	1	chrUn.!!$F1	834
16	TraesCS3A01G027100	chrUn	309111810	309112638	828	True	817.000000	817	84.670000	1313	2147	1	chrUn.!!$R2	834
17	TraesCS3A01G027100	chr5D	537911568	537912518	950	True	473.000000	643	85.343000	1252	2169	2	chr5D.!!$R1	917
18	TraesCS3A01G027100	chr2A	390322493	390323198	705	True	286.333333	459	93.797667	1	584	3	chr2A.!!$R1	583

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
770	832	0.03582	ACGGTTCGCTCTCTCTCTCT	60.036	55.0	0.0	0.0	0.0	3.1	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2560	7007	3.971245	AATAGCATTTCGGCCCAAAAA	57.029	38.095	0.0	0.0	0.0	1.94	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
84	87	6.659242	TGTTCTTTTCTGAATCAATAGTCCCC	59.341	38.462	0.00	0.00	0.00	4.81
107	111	5.886474	CCCCTCGCTATAGTATATCAGAACA	59.114	44.000	0.84	0.00	0.00	3.18
157	192	2.268730	AGACGGTCGAAACGGATAAC	57.731	50.000	14.20	2.36	35.23	1.89
183	224	1.468054	GGAAAATGAGGTGCATGACGC	60.468	52.381	0.00	0.00	37.28	5.19
263	304	7.911130	TTGAGGATTATTTATGGGATGCAAA	57.089	32.000	0.00	0.00	0.00	3.68
310	353	8.843308	ATGGAAGGAATTGGATGATTAAAAGA	57.157	30.769	0.00	0.00	0.00	2.52
331	374	5.851720	AGAAATGAGATGCATGACGTCTAT	58.148	37.500	17.92	5.91	45.00	1.98
467	519	6.470235	GCATGTTGCAAGACACTTATATGAAC	59.530	38.462	0.00	0.00	44.26	3.18
469	521	7.686438	TGTTGCAAGACACTTATATGAACAT	57.314	32.000	0.00	0.00	0.00	2.71
474	526	7.769970	TGCAAGACACTTATATGAACATGATGA	59.230	33.333	0.00	0.00	0.00	2.92
475	527	8.281194	GCAAGACACTTATATGAACATGATGAG	58.719	37.037	0.00	0.00	0.00	2.90
488	540	5.183530	ACATGATGAGTTCCAGGATTTCA	57.816	39.130	0.00	6.00	0.00	2.69
515	569	6.095377	GCTGCAAACAGTAGAGCATTTAAAT	58.905	36.000	0.00	0.00	46.30	1.40
639	699	4.070552	GTTCGCTCGCCTCCCACT	62.071	66.667	0.00	0.00	0.00	4.00
752	814	4.864334	CAGCCCCCATCTCCGCAC	62.864	72.222	0.00	0.00	0.00	5.34
756	818	4.096003	CCCCATCTCCGCACGGTT	62.096	66.667	9.23	0.00	36.47	4.44
757	819	2.511600	CCCATCTCCGCACGGTTC	60.512	66.667	9.23	0.00	36.47	3.62
758	820	2.885644	CCATCTCCGCACGGTTCG	60.886	66.667	9.23	0.00	36.47	3.95
759	821	3.554692	CATCTCCGCACGGTTCGC	61.555	66.667	9.23	0.00	36.47	4.70
760	822	3.760035	ATCTCCGCACGGTTCGCT	61.760	61.111	9.23	0.00	36.47	4.93
761	823	3.701604	ATCTCCGCACGGTTCGCTC	62.702	63.158	9.23	0.00	36.47	5.03
762	824	4.421479	CTCCGCACGGTTCGCTCT	62.421	66.667	9.23	0.00	36.47	4.09
763	825	4.415332	TCCGCACGGTTCGCTCTC	62.415	66.667	9.23	0.00	36.47	3.20
764	826	4.421479	CCGCACGGTTCGCTCTCT	62.421	66.667	0.00	0.00	0.00	3.10
765	827	2.876645	CGCACGGTTCGCTCTCTC	60.877	66.667	0.00	0.00	0.00	3.20
766	828	2.569134	GCACGGTTCGCTCTCTCT	59.431	61.111	0.00	0.00	0.00	3.10
767	829	1.515304	GCACGGTTCGCTCTCTCTC	60.515	63.158	0.00	0.00	0.00	3.20
768	830	1.928706	GCACGGTTCGCTCTCTCTCT	61.929	60.000	0.00	0.00	0.00	3.10
769	831	0.098025	CACGGTTCGCTCTCTCTCTC	59.902	60.000	0.00	0.00	0.00	3.20
770	832	0.035820	ACGGTTCGCTCTCTCTCTCT	60.036	55.000	0.00	0.00	0.00	3.10
771	833	0.655733	CGGTTCGCTCTCTCTCTCTC	59.344	60.000	0.00	0.00	0.00	3.20
772	834	1.742411	CGGTTCGCTCTCTCTCTCTCT	60.742	57.143	0.00	0.00	0.00	3.10
773	835	1.940613	GGTTCGCTCTCTCTCTCTCTC	59.059	57.143	0.00	0.00	0.00	3.20
774	836	2.420129	GGTTCGCTCTCTCTCTCTCTCT	60.420	54.545	0.00	0.00	0.00	3.10
775	837	2.866762	GTTCGCTCTCTCTCTCTCTCTC	59.133	54.545	0.00	0.00	0.00	3.20
776	838	2.388735	TCGCTCTCTCTCTCTCTCTCT	58.611	52.381	0.00	0.00	0.00	3.10
777	839	2.766263	TCGCTCTCTCTCTCTCTCTCTT	59.234	50.000	0.00	0.00	0.00	2.85
778	840	2.868583	CGCTCTCTCTCTCTCTCTCTTG	59.131	54.545	0.00	0.00	0.00	3.02
779	841	3.209410	GCTCTCTCTCTCTCTCTCTTGG	58.791	54.545	0.00	0.00	0.00	3.61
780	842	3.209410	CTCTCTCTCTCTCTCTCTTGGC	58.791	54.545	0.00	0.00	0.00	4.52
1032	1142	1.194781	AGGTGCTCAAGGACATCGGT	61.195	55.000	4.02	0.00	38.19	4.69
1217	1329	4.350245	TCCCCTGCTGCGTATATAGTAAT	58.650	43.478	0.00	0.00	0.00	1.89
1969	6408	8.208224	TCAACATGTCTGGTCTCTAAAAGTTAA	58.792	33.333	0.00	0.00	0.00	2.01
1994	6433	1.869767	GACCATCATTCGTGCATCCTC	59.130	52.381	0.00	0.00	0.00	3.71
2560	7007	0.896940	CACCCTGGAAGCATGCAACT	60.897	55.000	21.98	3.18	0.00	3.16

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
84	87	6.374613	TGTGTTCTGATATACTATAGCGAGGG	59.625	42.308	0.00	0.00	0.00	4.30
107	111	7.436118	ACATACCGACGTATATAAATTGGTGT	58.564	34.615	13.46	6.89	33.23	4.16
157	192	6.095377	GTCATGCACCTCATTTTCCTTTTAG	58.905	40.000	0.00	0.00	31.79	1.85
203	244	5.576447	TTCATAGCCCGAAATTCCTTTTC	57.424	39.130	0.00	0.00	40.34	2.29
263	304	6.662234	CCATCCTTTCATGTATGGCAATATCT	59.338	38.462	0.00	0.00	33.02	1.98
310	353	6.091849	GCATATAGACGTCATGCATCTCATTT	59.908	38.462	25.89	2.97	43.59	2.32
331	374	7.102346	CCCACAATTCCTTTTTACAATGCATA	58.898	34.615	0.00	0.00	0.00	3.14
467	519	4.579340	CCTGAAATCCTGGAACTCATCATG	59.421	45.833	0.00	0.00	36.07	3.07
469	521	3.054139	CCCTGAAATCCTGGAACTCATCA	60.054	47.826	0.00	0.61	36.07	3.07
474	526	1.005215	CAGCCCTGAAATCCTGGAACT	59.995	52.381	0.00	0.00	36.07	3.01
475	527	1.467920	CAGCCCTGAAATCCTGGAAC	58.532	55.000	0.00	0.00	36.07	3.62
488	540	0.322008	GCTCTACTGTTTGCAGCCCT	60.322	55.000	0.00	0.00	46.30	5.19
578	634	7.782644	ACTGCTCCTTTATGAGTAGAGATTACT	59.217	37.037	12.14	0.00	44.87	2.24
613	669	2.641783	GCGAGCGAACGAACGAACA	61.642	57.895	14.32	0.00	35.09	3.18
639	699	1.271127	TGGTGGCTTCGATGGATGGA	61.271	55.000	0.00	0.00	0.00	3.41
751	813	0.035820	AGAGAGAGAGAGCGAACCGT	60.036	55.000	0.00	0.00	0.00	4.83
752	814	0.655733	GAGAGAGAGAGAGCGAACCG	59.344	60.000	0.00	0.00	0.00	4.44
753	815	1.940613	GAGAGAGAGAGAGAGCGAACC	59.059	57.143	0.00	0.00	0.00	3.62
754	816	2.866762	GAGAGAGAGAGAGAGAGCGAAC	59.133	54.545	0.00	0.00	0.00	3.95
755	817	2.766263	AGAGAGAGAGAGAGAGAGCGAA	59.234	50.000	0.00	0.00	0.00	4.70
756	818	2.388735	AGAGAGAGAGAGAGAGAGCGA	58.611	52.381	0.00	0.00	0.00	4.93
757	819	2.868583	CAAGAGAGAGAGAGAGAGAGCG	59.131	54.545	0.00	0.00	0.00	5.03
758	820	3.209410	CCAAGAGAGAGAGAGAGAGAGC	58.791	54.545	0.00	0.00	0.00	4.09
759	821	3.209410	GCCAAGAGAGAGAGAGAGAGAG	58.791	54.545	0.00	0.00	0.00	3.20
760	822	2.575735	TGCCAAGAGAGAGAGAGAGAGA	59.424	50.000	0.00	0.00	0.00	3.10
761	823	2.684881	GTGCCAAGAGAGAGAGAGAGAG	59.315	54.545	0.00	0.00	0.00	3.20
762	824	2.722094	GTGCCAAGAGAGAGAGAGAGA	58.278	52.381	0.00	0.00	0.00	3.10
763	825	1.401552	CGTGCCAAGAGAGAGAGAGAG	59.598	57.143	0.00	0.00	0.00	3.20
764	826	1.458398	CGTGCCAAGAGAGAGAGAGA	58.542	55.000	0.00	0.00	0.00	3.10
765	827	0.179140	GCGTGCCAAGAGAGAGAGAG	60.179	60.000	0.00	0.00	0.00	3.20
766	828	0.895559	TGCGTGCCAAGAGAGAGAGA	60.896	55.000	0.00	0.00	0.00	3.10
767	829	0.735632	GTGCGTGCCAAGAGAGAGAG	60.736	60.000	0.00	0.00	0.00	3.20
768	830	1.290324	GTGCGTGCCAAGAGAGAGA	59.710	57.895	0.00	0.00	0.00	3.10
769	831	0.601046	TTGTGCGTGCCAAGAGAGAG	60.601	55.000	0.00	0.00	0.00	3.20
770	832	0.880278	GTTGTGCGTGCCAAGAGAGA	60.880	55.000	0.00	0.00	0.00	3.10
771	833	1.571460	GTTGTGCGTGCCAAGAGAG	59.429	57.895	0.00	0.00	0.00	3.20
772	834	1.891919	GGTTGTGCGTGCCAAGAGA	60.892	57.895	0.00	0.00	0.00	3.10
773	835	1.893808	AGGTTGTGCGTGCCAAGAG	60.894	57.895	0.00	0.00	0.00	2.85
774	836	2.186160	CAGGTTGTGCGTGCCAAGA	61.186	57.895	0.00	0.00	0.00	3.02
775	837	1.518056	ATCAGGTTGTGCGTGCCAAG	61.518	55.000	0.00	0.00	33.35	3.61
776	838	1.514678	GATCAGGTTGTGCGTGCCAA	61.515	55.000	0.00	0.00	33.35	4.52
777	839	1.965930	GATCAGGTTGTGCGTGCCA	60.966	57.895	0.00	0.00	33.35	4.92
778	840	2.690778	GGATCAGGTTGTGCGTGCC	61.691	63.158	0.00	0.00	33.35	5.01
779	841	2.690778	GGGATCAGGTTGTGCGTGC	61.691	63.158	0.00	0.00	33.35	5.34
780	842	1.003355	AGGGATCAGGTTGTGCGTG	60.003	57.895	0.00	0.00	0.00	5.34
1032	1142	2.230892	GACGTTGACATTGCCGTCA	58.769	52.632	6.20	0.46	46.53	4.35
1217	1329	0.618968	ACACCCAAAAGTTTGCCCCA	60.619	50.000	0.00	0.00	36.86	4.96
1969	6408	4.456911	GGATGCACGAATGATGGTCAATAT	59.543	41.667	0.00	0.00	0.00	1.28
2560	7007	3.971245	AATAGCATTTCGGCCCAAAAA	57.029	38.095	0.00	0.00	0.00	1.94

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.