AutoCloner

Multiple sequence alignment - TraesCS1D01G333700

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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	TraesCS1D01G333700	chr1D	100.000	2849	0	0	1	2849	423738783	423735935	0.000000e+00	5262.0
1	TraesCS1D01G333700	chr1D	91.232	2281	152	14	575	2838	423655559	423657808	0.000000e+00	3061.0
2	TraesCS1D01G333700	chr1D	95.320	406	17	1	181	586	423655123	423655526	0.000000e+00	643.0
3	TraesCS1D01G333700	chr1D	92.553	94	7	0	30	123	423653922	423654015	4.950000e-28	135.0
4	TraesCS1D01G333700	chr1A	92.163	1812	99	21	575	2372	519849295	519851077	0.000000e+00	2519.0
5	TraesCS1D01G333700	chr1A	93.846	975	49	5	1164	2137	520007308	520006344	0.000000e+00	1458.0
6	TraesCS1D01G333700	chr1A	93.793	580	36	0	578	1157	520009722	520009143	0.000000e+00	872.0
7	TraesCS1D01G333700	chr1A	94.774	421	17	4	166	586	519848847	519849262	0.000000e+00	651.0
8	TraesCS1D01G333700	chr1A	77.026	1197	214	39	660	1830	519852954	519854115	5.180000e-177	630.0
9	TraesCS1D01G333700	chr1A	77.464	1096	195	38	674	1754	519843936	519844994	2.430000e-170	608.0
10	TraesCS1D01G333700	chr1A	91.019	412	21	2	175	586	520010153	520009758	2.500000e-150	542.0
11	TraesCS1D01G333700	chr1A	94.574	258	10	1	2538	2791	519851074	519851331	2.060000e-106	396.0
12	TraesCS1D01G333700	chr1A	96.644	149	3	2	26	173	520010338	520010191	2.190000e-61	246.0
13	TraesCS1D01G333700	chr1A	92.647	136	3	1	43	171	519848671	519848806	3.750000e-44	189.0
14	TraesCS1D01G333700	chr1A	97.297	37	1	0	2148	2184	94732301	94732337	2.370000e-06	63.9
15	TraesCS1D01G333700	chr1B	93.955	1555	63	5	575	2129	573042175	573043698	0.000000e+00	2322.0
16	TraesCS1D01G333700	chr1B	78.530	1374	235	41	658	2004	573046050	573047390	0.000000e+00	848.0
17	TraesCS1D01G333700	chr1B	87.941	680	60	11	2191	2849	573043705	573044383	0.000000e+00	782.0
18	TraesCS1D01G333700	chr1B	89.144	479	31	8	2371	2842	573051812	573052276	6.840000e-161	577.0
19	TraesCS1D01G333700	chr1B	91.990	412	21	6	175	586	573041743	573042142	4.120000e-158	568.0
20	TraesCS1D01G333700	chr1B	76.044	551	86	26	1686	2231	573043990	573044499	7.880000e-61	244.0
21	TraesCS1D01G333700	chr1B	88.312	154	8	3	30	173	573041545	573041698	2.920000e-40	176.0
22	TraesCS1D01G333700	chr1B	95.000	40	2	0	2148	2187	311125732	311125693	2.370000e-06	63.9
23	TraesCS1D01G333700	chr1B	95.000	40	2	0	2148	2187	461426888	461426849	2.370000e-06	63.9
24	TraesCS1D01G333700	chr5A	90.141	142	14	0	366	507	77791589	77791448	4.850000e-43	185.0
25	TraesCS1D01G333700	chr7B	84.021	194	26	4	319	508	699372046	699372238	6.270000e-42	182.0
26	TraesCS1D01G333700	chr7A	84.021	194	26	4	319	508	700679536	700679344	6.270000e-42	182.0
27	TraesCS1D01G333700	chr7D	87.919	149	18	0	360	508	610782549	610782401	2.920000e-40	176.0
28	TraesCS1D01G333700	chr5B	88.732	142	16	0	366	507	90183843	90183702	1.050000e-39	174.0
29	TraesCS1D01G333700	chr5B	97.297	37	1	0	2148	2184	169050407	169050443	2.370000e-06	63.9
30	TraesCS1D01G333700	chr4A	71.299	331	77	12	672	990	734219216	734218892	5.090000e-08	69.4
31	TraesCS1D01G333700	chr3D	95.455	44	1	1	948	990	62808393	62808350	5.090000e-08	69.4
32	TraesCS1D01G333700	chr3D	97.297	37	1	0	2148	2184	198611068	198611104	2.370000e-06	63.9
33	TraesCS1D01G333700	chr2B	97.500	40	1	0	951	990	383888738	383888699	5.090000e-08	69.4
34	TraesCS1D01G333700	chr5D	97.368	38	1	0	2147	2184	517677943	517677980	6.590000e-07	65.8
35	TraesCS1D01G333700	chr4D	97.297	37	1	0	2148	2184	241291865	241291901	2.370000e-06	63.9

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	TraesCS1D01G333700	chr1D	423735935	423738783	2848	True	5262.000000	5262	100.000000	1	2849	1	chr1D.!!$R1	2848
1	TraesCS1D01G333700	chr1D	423653922	423657808	3886	False	1279.666667	3061	93.035000	30	2838	3	chr1D.!!$F1	2808
2	TraesCS1D01G333700	chr1A	519843936	519854115	10179	False	832.166667	2519	88.108000	43	2791	6	chr1A.!!$F2	2748
3	TraesCS1D01G333700	chr1A	520006344	520010338	3994	True	779.500000	1458	93.825500	26	2137	4	chr1A.!!$R1	2111
4	TraesCS1D01G333700	chr1B	573041545	573047390	5845	False	823.333333	2322	86.128667	30	2849	6	chr1B.!!$F2	2819

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
904	6723	0.031314	CATCCGTGGTCTCAGGATCG	59.969	60.0	0.0	0.0	42.4	3.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2812	10536	0.179234	TTTGAGCGGTGTTCCAGTGA	59.821	50.0	0.0	0.0	0.0	3.41	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
173	5884	2.876645	CGGAGACTTCGCAGCGAC	60.877	66.667	19.37	6.37	34.89	5.19
174	5885	2.507324	GGAGACTTCGCAGCGACC	60.507	66.667	19.37	11.61	34.89	4.79
499	6273	1.254284	CCTCTCAACCTCGACTGCCT	61.254	60.000	0.00	0.00	0.00	4.75
676	6495	2.123769	AGCTGCTGCAACCACCAA	60.124	55.556	18.42	0.00	42.74	3.67
701	6520	2.611518	GTCCATCTTCAGGTTCTCGTG	58.388	52.381	0.00	0.00	0.00	4.35
835	6654	1.549815	CTCGCTGCAGAGCATCATCG	61.550	60.000	20.43	8.92	46.62	3.84
904	6723	0.031314	CATCCGTGGTCTCAGGATCG	59.969	60.000	0.00	0.00	42.40	3.69
909	6728	1.464734	GTGGTCTCAGGATCGACTCA	58.535	55.000	0.00	0.00	0.00	3.41
961	6780	8.777865	TTCTAGGTTTGTAGAACTCATCATTG	57.222	34.615	0.00	0.00	34.69	2.82
990	6809	2.695147	CCCTTCACTTGAAAGGTTGCTT	59.305	45.455	0.00	0.00	32.33	3.91
992	6811	4.340950	CCCTTCACTTGAAAGGTTGCTTTA	59.659	41.667	0.00	0.00	32.33	1.85
1017	6836	4.572909	TGAGAATGGATATGAGAATGCGG	58.427	43.478	0.00	0.00	0.00	5.69
1131	6950	1.417517	CAGGTAGCTATGCCATGTCCA	59.582	52.381	0.00	0.00	32.66	4.02
1150	6969	5.528690	TGTCCATTATGCTTCTTGCTACATC	59.471	40.000	0.00	0.00	43.37	3.06
1207	8854	4.811024	GCCGAAATCTTACATGTCATCTGA	59.189	41.667	0.00	0.00	0.00	3.27
1208	8855	5.277058	GCCGAAATCTTACATGTCATCTGAC	60.277	44.000	0.00	3.34	44.97	3.51
1209	8856	6.045318	CCGAAATCTTACATGTCATCTGACT	58.955	40.000	0.00	0.00	44.99	3.41
1221	8872	8.412456	ACATGTCATCTGACTTACTTATCTCTG	58.588	37.037	11.35	0.00	44.99	3.35
1244	8896	7.720515	TCTGAATATTGTGTTCCATGCATGATA	59.279	33.333	28.31	15.18	0.00	2.15
1305	8957	6.015856	GCCTACTATCAAGATCTTAGCTGTGA	60.016	42.308	7.86	0.91	0.00	3.58
1367	9019	5.726980	AATGCTTTGTATGCTTGGAGAAA	57.273	34.783	0.00	0.00	0.00	2.52
1392	9044	6.612247	TGTATATGAAGGTAATGGTTTGCG	57.388	37.500	0.00	0.00	0.00	4.85
1394	9046	3.848272	ATGAAGGTAATGGTTTGCGTG	57.152	42.857	0.00	0.00	0.00	5.34
1509	9162	0.617413	AGACAGATTCACCAGCAGGG	59.383	55.000	0.00	0.00	44.81	4.45
1660	9313	3.244526	TGCAAAACTGCTAGAGTCCATCA	60.245	43.478	0.00	0.00	31.73	3.07
1662	9315	3.902881	AAACTGCTAGAGTCCATCAGG	57.097	47.619	0.00	0.00	31.73	3.86
1692	9345	5.835280	GGTTGATTCCAGGGATTACAATGAT	59.165	40.000	0.00	0.00	0.00	2.45
1694	9347	6.264771	TGATTCCAGGGATTACAATGATGA	57.735	37.500	0.00	0.00	0.00	2.92
1768	9422	2.483876	GTGCTCAGCTCTGTGTTACAA	58.516	47.619	0.00	0.00	0.00	2.41
1852	9506	4.564372	CGTTCACATGTAGATGTTGAGAGG	59.436	45.833	2.09	0.00	41.12	3.69
1853	9507	4.743057	TCACATGTAGATGTTGAGAGGG	57.257	45.455	2.09	0.00	41.12	4.30
1957	9623	9.490379	CTGTAGTCTTTCTAACCTTGTGTTATT	57.510	33.333	0.00	0.00	38.71	1.40
1958	9624	9.841295	TGTAGTCTTTCTAACCTTGTGTTATTT	57.159	29.630	0.00	0.00	38.71	1.40
2029	9695	3.758755	TGGCCAGAGTCAGCTATATTG	57.241	47.619	0.00	0.00	0.00	1.90
2054	9720	0.979665	ATATCATCTGGGGGTGCTCG	59.020	55.000	0.00	0.00	0.00	5.03
2125	9791	6.701841	TGAAGATTGTACAGTGTCTTCTCAAC	59.298	38.462	28.54	15.61	44.22	3.18
2138	9804	3.190744	TCTTCTCAACGTCTATTGCGAGT	59.809	43.478	0.00	0.00	0.00	4.18
2143	9809	2.921121	CAACGTCTATTGCGAGTTAGCA	59.079	45.455	0.00	0.00	46.54	3.49
2186	9852	5.986135	TGCAAGAAGAAGACTCTGAAAGTAC	59.014	40.000	0.00	0.00	38.74	2.73
2235	9901	4.487714	TCTGTTGTTCTTTCCACTGTCT	57.512	40.909	0.00	0.00	0.00	3.41
2247	9914	1.273606	CCACTGTCTGACTAGGGTGTG	59.726	57.143	9.51	8.06	0.00	3.82
2255	9922	1.069513	TGACTAGGGTGTGTTGAACCG	59.930	52.381	0.00	0.00	38.70	4.44
2263	9930	2.511879	GTGTGTTGAACCGTGTTGTTC	58.488	47.619	0.00	0.00	43.90	3.18
2281	9948	7.112984	GTGTTGTTCGATTGACAAGGTAAATTC	59.887	37.037	1.45	0.00	37.65	2.17
2321	9988	5.941555	TGTTGAAAAACTGGGTTTGGTAT	57.058	34.783	0.00	0.00	35.80	2.73
2434	10101	3.209410	GGATACTTGTGAAGCCATCAGG	58.791	50.000	0.00	0.00	39.19	3.86
2479	10151	3.616956	TCACAGGCTACTCAATGAAGG	57.383	47.619	0.00	0.00	0.00	3.46
2525	10208	5.423610	CAGATGGAGAAGAGGGTTTCTAGAA	59.576	44.000	0.00	0.00	37.53	2.10
2532	10215	2.835156	AGAGGGTTTCTAGAAGTGCTCC	59.165	50.000	5.12	4.74	33.23	4.70
2533	10216	1.909986	AGGGTTTCTAGAAGTGCTCCC	59.090	52.381	5.12	12.69	0.00	4.30
2544	10227	1.986882	AGTGCTCCCCTTTGTTTCAG	58.013	50.000	0.00	0.00	0.00	3.02
2644	10331	0.250770	GAAAGTCGGTCTGGCCCTTT	60.251	55.000	0.00	0.00	33.37	3.11
2645	10332	0.185175	AAAGTCGGTCTGGCCCTTTT	59.815	50.000	0.00	0.00	28.47	2.27
2710	10397	7.964624	ACTTAGCTAGTCTTTCTAACCTTGTT	58.035	34.615	0.00	0.00	28.23	2.83
2795	10519	4.348168	GGAGTCAGCTATATTTTCTGGGGA	59.652	45.833	0.00	0.00	0.00	4.81
2796	10520	5.297569	AGTCAGCTATATTTTCTGGGGAC	57.702	43.478	0.00	0.00	0.00	4.46
2812	10536	2.231235	GGGGACGCTCATTTTGATTGTT	59.769	45.455	0.00	0.00	0.00	2.83
2842	10567	5.659440	ACACCGCTCAAATTATTCCATTT	57.341	34.783	0.00	0.00	0.00	2.32

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
6	7	8.301002	GCCCTTAGTGTTTATGTGTTTTTATCA	58.699	33.333	0.00	0.00	0.00	2.15
7	8	8.301002	TGCCCTTAGTGTTTATGTGTTTTTATC	58.699	33.333	0.00	0.00	0.00	1.75
10	11	6.472686	TGCCCTTAGTGTTTATGTGTTTTT	57.527	33.333	0.00	0.00	0.00	1.94
11	12	6.462347	CCTTGCCCTTAGTGTTTATGTGTTTT	60.462	38.462	0.00	0.00	0.00	2.43
13	14	4.522789	CCTTGCCCTTAGTGTTTATGTGTT	59.477	41.667	0.00	0.00	0.00	3.32
14	15	4.079253	CCTTGCCCTTAGTGTTTATGTGT	58.921	43.478	0.00	0.00	0.00	3.72
15	16	4.331968	TCCTTGCCCTTAGTGTTTATGTG	58.668	43.478	0.00	0.00	0.00	3.21
16	17	4.650972	TCCTTGCCCTTAGTGTTTATGT	57.349	40.909	0.00	0.00	0.00	2.29
18	19	4.341487	GGTTCCTTGCCCTTAGTGTTTAT	58.659	43.478	0.00	0.00	0.00	1.40
19	20	3.758425	GGTTCCTTGCCCTTAGTGTTTA	58.242	45.455	0.00	0.00	0.00	2.01
20	21	2.594131	GGTTCCTTGCCCTTAGTGTTT	58.406	47.619	0.00	0.00	0.00	2.83
21	22	1.544759	CGGTTCCTTGCCCTTAGTGTT	60.545	52.381	0.00	0.00	0.00	3.32
22	23	0.036306	CGGTTCCTTGCCCTTAGTGT	59.964	55.000	0.00	0.00	0.00	3.55
24	25	1.065418	CATCGGTTCCTTGCCCTTAGT	60.065	52.381	0.00	0.00	0.00	2.24
26	27	0.254747	CCATCGGTTCCTTGCCCTTA	59.745	55.000	0.00	0.00	0.00	2.69
27	28	1.000896	CCATCGGTTCCTTGCCCTT	60.001	57.895	0.00	0.00	0.00	3.95
28	29	1.923395	TCCATCGGTTCCTTGCCCT	60.923	57.895	0.00	0.00	0.00	5.19
394	6168	3.500654	GGGGAGGAGGAAGATTATCTCGA	60.501	52.174	0.00	0.00	0.00	4.04
676	6495	1.827399	AACCTGAAGATGGACGCCGT	61.827	55.000	0.00	0.00	0.00	5.68
721	6540	1.451028	GGAGATGGCACTGGCTGAC	60.451	63.158	3.97	0.00	40.87	3.51
792	6611	1.278127	TCCGAGATTTTGACCTCCACC	59.722	52.381	0.00	0.00	0.00	4.61
846	6665	0.185901	ACAAGCTTTCCAGGGCAGAA	59.814	50.000	0.00	0.00	0.00	3.02
847	6666	0.185901	AACAAGCTTTCCAGGGCAGA	59.814	50.000	0.00	0.00	0.00	4.26
990	6809	7.763071	CGCATTCTCATATCCATTCTCAGATAA	59.237	37.037	0.00	0.00	0.00	1.75
992	6811	6.107343	CGCATTCTCATATCCATTCTCAGAT	58.893	40.000	0.00	0.00	0.00	2.90
1017	6836	1.641577	GTGCGGAGATTACTGACACC	58.358	55.000	0.00	0.00	0.00	4.16
1175	8822	7.771183	ACATGTAAGATTTCGGCACAAAATAT	58.229	30.769	0.00	0.00	0.00	1.28
1177	8824	6.024552	ACATGTAAGATTTCGGCACAAAAT	57.975	33.333	0.00	0.00	0.00	1.82
1180	8827	4.068599	TGACATGTAAGATTTCGGCACAA	58.931	39.130	0.00	0.00	0.00	3.33
1244	8896	2.412847	GCTAACAACGCGCAATCTCTTT	60.413	45.455	5.73	0.00	0.00	2.52
1367	9019	7.284489	ACGCAAACCATTACCTTCATATACAAT	59.716	33.333	0.00	0.00	0.00	2.71
1392	9044	8.235359	ACACTACCACTTTATAGAGTATCCAC	57.765	38.462	0.00	0.00	33.66	4.02
1394	9046	9.530633	CAAACACTACCACTTTATAGAGTATCC	57.469	37.037	0.00	0.00	33.66	2.59
1509	9162	5.342259	GTGTTTATGACGCCAGAAATTTGTC	59.658	40.000	0.00	0.00	36.12	3.18
1660	9313	1.005215	CCTGGAATCAACCTCAAGCCT	59.995	52.381	0.00	0.00	0.00	4.58
1662	9315	1.004745	TCCCTGGAATCAACCTCAAGC	59.995	52.381	0.00	0.00	0.00	4.01
1692	9345	6.016693	TCCTACATTGTTCTGCGAAAAATTCA	60.017	34.615	0.00	0.00	0.00	2.57
1694	9347	6.325919	TCCTACATTGTTCTGCGAAAAATT	57.674	33.333	0.00	1.67	0.00	1.82
1768	9422	4.214119	CGAAACATCATTGTGAGAACCTGT	59.786	41.667	0.00	0.00	35.83	4.00
2029	9695	3.808618	GCACCCCCAGATGATATCTTCAC	60.809	52.174	18.04	2.23	37.58	3.18
2054	9720	4.261447	GGTGTACCAGTGGACAATCAAAAC	60.261	45.833	18.40	2.52	35.64	2.43
2083	9749	1.234821	TCACTGCAAATGGAACCGTC	58.765	50.000	0.00	0.00	0.00	4.79
2125	9791	2.402049	CGATGCTAACTCGCAATAGACG	59.598	50.000	0.00	0.00	44.06	4.18
2138	9804	8.021955	CATATAAGAATGCAACTCGATGCTAA	57.978	34.615	11.96	0.00	46.54	3.09
2186	9852	7.630242	TTTCCTTTATGCAAACTCAGATAGG	57.370	36.000	0.00	0.00	30.80	2.57
2235	9901	1.069513	CGGTTCAACACACCCTAGTCA	59.930	52.381	0.00	0.00	0.00	3.41
2247	9914	3.033185	CAATCGAACAACACGGTTCAAC	58.967	45.455	6.82	0.00	45.82	3.18
2255	9922	3.963383	ACCTTGTCAATCGAACAACAC	57.037	42.857	0.00	0.00	33.30	3.32
2281	9948	9.853555	TTTTCAACATTGTACATGCCTTTATAG	57.146	29.630	0.00	0.00	0.00	1.31
2308	9975	3.397955	ACTCCAGAAATACCAAACCCAGT	59.602	43.478	0.00	0.00	0.00	4.00
2321	9988	7.086685	AGGTAAGAATAACCAACTCCAGAAA	57.913	36.000	0.00	0.00	39.64	2.52
2452	10119	7.603180	TCATTGAGTAGCCTGTGAATATAGT	57.397	36.000	0.00	0.00	0.00	2.12
2492	10164	4.309099	CTCTTCTCCATCTGAAGCTATGC	58.691	47.826	0.00	0.00	40.31	3.14
2495	10167	3.303938	CCCTCTTCTCCATCTGAAGCTA	58.696	50.000	0.00	0.00	40.31	3.32
2496	10168	2.117865	CCCTCTTCTCCATCTGAAGCT	58.882	52.381	0.00	0.00	40.31	3.74
2525	10208	1.494721	TCTGAAACAAAGGGGAGCACT	59.505	47.619	0.00	0.00	0.00	4.40
2532	10215	3.571401	ACAATCTGCTCTGAAACAAAGGG	59.429	43.478	0.00	0.00	0.00	3.95
2533	10216	4.276678	TGACAATCTGCTCTGAAACAAAGG	59.723	41.667	0.00	0.00	0.00	3.11
2644	10331	8.049117	AGTGAGATATGCAAGAATAACTCCAAA	58.951	33.333	0.00	0.00	33.31	3.28
2645	10332	7.568349	AGTGAGATATGCAAGAATAACTCCAA	58.432	34.615	0.00	0.00	33.31	3.53
2710	10397	6.783708	AATAACACAAAGTTCAGGGACAAA	57.216	33.333	0.00	0.00	41.64	2.83
2747	10434	4.021544	GCCATTGTTGTTTGGTCCTGATTA	60.022	41.667	0.00	0.00	35.34	1.75
2795	10519	4.539870	CAGTGAACAATCAAAATGAGCGT	58.460	39.130	0.00	0.00	37.30	5.07
2796	10520	3.916172	CCAGTGAACAATCAAAATGAGCG	59.084	43.478	0.00	0.00	37.30	5.03
2812	10536	0.179234	TTTGAGCGGTGTTCCAGTGA	59.821	50.000	0.00	0.00	0.00	3.41
2824	10548	5.005012	CACTGCAAATGGAATAATTTGAGCG	59.995	40.000	12.55	3.80	46.13	5.03

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.