AutoCloner

Multiple sequence alignment - TraesCS1D01G009900

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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	TraesCS1D01G009900	chr1D	100.000	3068	0	0	1	3068	5355684	5358751	0.000000e+00	5666.0
1	TraesCS1D01G009900	chr1D	88.053	3097	248	64	3	3068	3711581	3708576	0.000000e+00	3557.0
2	TraesCS1D01G009900	chr1D	85.714	1904	187	45	1208	3068	5139396	5141257	0.000000e+00	1930.0
3	TraesCS1D01G009900	chr1D	86.159	1734	159	35	1013	2732	3826365	3824699	0.000000e+00	1797.0
4	TraesCS1D01G009900	chr1D	87.130	1352	108	24	480	1767	84072	85421	0.000000e+00	1472.0
5	TraesCS1D01G009900	chr1D	90.049	1025	76	20	3	1020	3842327	3841322	0.000000e+00	1304.0
6	TraesCS1D01G009900	chr1D	83.889	1409	157	39	1216	2575	7156339	7154952	0.000000e+00	1280.0
7	TraesCS1D01G009900	chr1D	83.031	1432	174	35	1193	2575	4342032	4343443	0.000000e+00	1234.0
8	TraesCS1D01G009900	chr1D	86.404	1015	102	24	430	1414	98698	99706	0.000000e+00	1077.0
9	TraesCS1D01G009900	chr1D	82.789	796	89	24	1786	2573	100219	100974	0.000000e+00	667.0
10	TraesCS1D01G009900	chr1D	83.475	587	59	20	1215	1767	99654	100236	2.110000e-141	512.0
11	TraesCS1D01G009900	chr1D	79.333	300	35	10	2795	3068	4347183	4347481	5.220000e-43	185.0
12	TraesCS1D01G009900	chr1D	100.000	31	0	0	2759	2789	4347036	4347066	1.190000e-04	58.4
13	TraesCS1D01G009900	chr1A	92.707	3099	172	20	5	3068	6516342	6519421	0.000000e+00	4421.0
14	TraesCS1D01G009900	chr1A	93.478	1748	76	14	486	2224	6561199	6562917	0.000000e+00	2562.0
15	TraesCS1D01G009900	chr1A	89.118	726	64	11	430	1142	4204250	4203527	0.000000e+00	889.0
16	TraesCS1D01G009900	chr1A	88.703	717	69	6	435	1142	4097477	4096764	0.000000e+00	865.0
17	TraesCS1D01G009900	chr1A	94.661	487	23	2	5	488	6560632	6561118	0.000000e+00	752.0
18	TraesCS1D01G009900	chr1A	87.409	548	61	5	1777	2322	4095936	4095395	9.340000e-175	623.0
19	TraesCS1D01G009900	chr1B	84.577	1407	151	37	1215	2575	6437233	6435847	0.000000e+00	1336.0
20	TraesCS1D01G009900	chr1B	83.065	1429	162	35	1179	2575	22185993	22187373	0.000000e+00	1225.0
21	TraesCS1D01G009900	chr1B	85.918	980	114	16	430	1390	5688349	5687375	0.000000e+00	1024.0
22	TraesCS1D01G009900	chr1B	88.092	697	63	12	671	1348	5585887	5585192	0.000000e+00	809.0
23	TraesCS1D01G009900	chr1B	84.173	695	82	17	735	1414	22185385	22186066	0.000000e+00	649.0
24	TraesCS1D01G009900	chr1B	82.218	568	80	15	1215	1767	5584908	5584347	1.290000e-128	470.0
25	TraesCS1D01G009900	chr1B	96.154	208	6	2	240	446	8159462	8159668	3.790000e-89	339.0
26	TraesCS1D01G009900	chr1B	94.444	180	7	1	72	248	8156579	8156758	1.080000e-69	274.0
27	TraesCS1D01G009900	chr1B	83.959	293	27	13	2795	3068	7314097	7313806	2.350000e-66	263.0
28	TraesCS1D01G009900	chr1B	80.537	298	34	12	2795	3068	22191156	22191453	1.110000e-49	207.0
29	TraesCS1D01G009900	chr1B	100.000	31	0	0	2759	2789	22191009	22191039	1.190000e-04	58.4
30	TraesCS1D01G009900	chr1B	96.875	32	1	0	2661	2692	8159944	8159975	2.000000e-03	54.7
31	TraesCS1D01G009900	chrUn	93.985	399	21	1	5	400	374223862	374224260	4.380000e-168	601.0
32	TraesCS1D01G009900	chrUn	93.734	399	22	1	5	400	349408926	349409324	2.040000e-166	595.0

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	TraesCS1D01G009900	chr1D	5355684	5358751	3067	False	5666.000000	5666	100.000000	1	3068	1	chr1D.!!$F3	3067
1	TraesCS1D01G009900	chr1D	3708576	3711581	3005	True	3557.000000	3557	88.053000	3	3068	1	chr1D.!!$R1	3065
2	TraesCS1D01G009900	chr1D	5139396	5141257	1861	False	1930.000000	1930	85.714000	1208	3068	1	chr1D.!!$F2	1860
3	TraesCS1D01G009900	chr1D	3824699	3826365	1666	True	1797.000000	1797	86.159000	1013	2732	1	chr1D.!!$R2	1719
4	TraesCS1D01G009900	chr1D	84072	85421	1349	False	1472.000000	1472	87.130000	480	1767	1	chr1D.!!$F1	1287
5	TraesCS1D01G009900	chr1D	3841322	3842327	1005	True	1304.000000	1304	90.049000	3	1020	1	chr1D.!!$R3	1017
6	TraesCS1D01G009900	chr1D	7154952	7156339	1387	True	1280.000000	1280	83.889000	1216	2575	1	chr1D.!!$R4	1359
7	TraesCS1D01G009900	chr1D	98698	100974	2276	False	752.000000	1077	84.222667	430	2573	3	chr1D.!!$F4	2143
8	TraesCS1D01G009900	chr1D	4342032	4347481	5449	False	492.466667	1234	87.454667	1193	3068	3	chr1D.!!$F5	1875
9	TraesCS1D01G009900	chr1A	6516342	6519421	3079	False	4421.000000	4421	92.707000	5	3068	1	chr1A.!!$F1	3063
10	TraesCS1D01G009900	chr1A	6560632	6562917	2285	False	1657.000000	2562	94.069500	5	2224	2	chr1A.!!$F2	2219
11	TraesCS1D01G009900	chr1A	4203527	4204250	723	True	889.000000	889	89.118000	430	1142	1	chr1A.!!$R1	712
12	TraesCS1D01G009900	chr1A	4095395	4097477	2082	True	744.000000	865	88.056000	435	2322	2	chr1A.!!$R2	1887
13	TraesCS1D01G009900	chr1B	6435847	6437233	1386	True	1336.000000	1336	84.577000	1215	2575	1	chr1B.!!$R2	1360
14	TraesCS1D01G009900	chr1B	5687375	5688349	974	True	1024.000000	1024	85.918000	430	1390	1	chr1B.!!$R1	960
15	TraesCS1D01G009900	chr1B	5584347	5585887	1540	True	639.500000	809	85.155000	671	1767	2	chr1B.!!$R4	1096
16	TraesCS1D01G009900	chr1B	22185385	22191453	6068	False	534.850000	1225	86.943750	735	3068	4	chr1B.!!$F2	2333
17	TraesCS1D01G009900	chr1B	8156579	8159975	3396	False	222.566667	339	95.824333	72	2692	3	chr1B.!!$F1	2620

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
22	24	3.556423	GGTCTAGAACTTCTTTTGCGGGA	60.556	47.826	0.0	0.0	0.0	5.14	F
1107	3936	0.321671	CTTCCTCGTCTTTGCCCTCA	59.678	55.000	0.0	0.0	0.0	3.86	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1514	5301	0.311790	CAAGACGTTGTGGCATTGCT	59.688	50.000	8.82	0.0	0.0	3.91	R
2913	10571	1.276138	TGGATGTCTATATGGCTGCCG	59.724	52.381	14.98	0.0	0.0	5.69	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
22	24	3.556423	GGTCTAGAACTTCTTTTGCGGGA	60.556	47.826	0.00	0.00	0.00	5.14
25	27	5.008316	GTCTAGAACTTCTTTTGCGGGAAAA	59.992	40.000	7.21	7.21	32.44	2.29
170	172	5.845614	TCCTTTTGGGTAGACAAAGTACCTA	59.154	40.000	0.00	0.00	40.97	3.08
217	219	3.873361	CACCTGAACATGCACCATAGTAG	59.127	47.826	0.00	0.00	0.00	2.57
341	3058	7.532571	CCCAAAAGATTTAGTAAAAGGTACCG	58.467	38.462	6.18	0.00	0.00	4.02
400	3118	7.839680	AACTTAGTCCACCAAAAGAATGATT	57.160	32.000	0.00	0.00	0.00	2.57
537	3347	6.328410	AGGGAATTCTATGAGTCATGTCATGA	59.672	38.462	16.15	11.62	37.72	3.07
547	3359	7.459795	TGAGTCATGTCATGATCTATACCTC	57.540	40.000	18.32	16.59	42.04	3.85
693	3509	4.327357	CGATTGCAACTTAGTCCTACACAG	59.673	45.833	0.00	0.00	0.00	3.66
832	3648	5.772393	ACCACACATCAGGGTTTCTATAA	57.228	39.130	0.00	0.00	0.00	0.98
950	3777	8.801882	AAAAATCATTTCTGATGCATCCAAAT	57.198	26.923	23.67	21.72	41.34	2.32
1060	3889	4.333372	ACAAGCATCAAAACCAAGCAAAAG	59.667	37.500	0.00	0.00	0.00	2.27
1107	3936	0.321671	CTTCCTCGTCTTTGCCCTCA	59.678	55.000	0.00	0.00	0.00	3.86
1206	4080	2.955660	CAACCATTACCACCACAACAGT	59.044	45.455	0.00	0.00	0.00	3.55
1212	4134	5.221422	CCATTACCACCACAACAGTCATTTT	60.221	40.000	0.00	0.00	0.00	1.82
1314	4599	3.081061	TCGCAGCAACAACCAATTCTAT	58.919	40.909	0.00	0.00	0.00	1.98
1425	5209	5.430462	CACAACAACAACAACAACAACTTG	58.570	37.500	0.00	0.00	0.00	3.16
1484	5271	1.273048	CAGCAGCTAAACCCATGCAAA	59.727	47.619	0.00	0.00	41.14	3.68
1514	5301	2.348620	CAGCAGTGCAGCCCTGTA	59.651	61.111	19.20	0.00	34.23	2.74
1600	5387	1.202663	ACAATGTTGCCAGCAATTGCA	60.203	42.857	30.89	9.98	45.16	4.08
1628	5415	1.474320	CCCGAACAATCCCGCTATGAA	60.474	52.381	0.00	0.00	0.00	2.57
1679	5496	0.459489	TGCAAGAACAACAACAGGGC	59.541	50.000	0.00	0.00	0.00	5.19
1810	5642	0.179020	CAACTGGGTCAACAGCCTCA	60.179	55.000	0.00	0.00	42.21	3.86
1811	5643	0.550914	AACTGGGTCAACAGCCTCAA	59.449	50.000	0.00	0.00	42.21	3.02
1812	5644	0.179018	ACTGGGTCAACAGCCTCAAC	60.179	55.000	0.00	0.00	42.21	3.18
1813	5645	0.179020	CTGGGTCAACAGCCTCAACA	60.179	55.000	0.00	0.00	41.28	3.33
1814	5646	0.257328	TGGGTCAACAGCCTCAACAA	59.743	50.000	0.00	0.00	41.28	2.83
1815	5647	0.668535	GGGTCAACAGCCTCAACAAC	59.331	55.000	0.00	0.00	37.19	3.32
1876	5712	1.202627	CCAGATAGCTCACCTTGAGGC	60.203	57.143	5.37	0.00	44.43	4.70
1878	5714	0.249657	GATAGCTCACCTTGAGGCGG	60.250	60.000	5.37	0.00	44.43	6.13
1941	5777	0.452618	CAATGTGCCGTTGTACAGCG	60.453	55.000	23.31	23.31	40.54	5.18
1949	5785	2.281208	TTGTACAGCGCCACCACC	60.281	61.111	2.29	0.00	0.00	4.61
2043	5882	0.304098	CCACCGTCGTCTAGTCGATC	59.696	60.000	14.92	8.23	41.78	3.69
2224	6071	4.002906	AGTTCATAAGTTCGTCTTGCCA	57.997	40.909	6.03	0.00	37.56	4.92
2440	6290	4.390264	TGACAATCACAACCGGTTTCATA	58.610	39.130	19.55	3.82	0.00	2.15
2499	6351	9.793252	AAATACTTCATTGATACTTTGCACATC	57.207	29.630	0.00	0.00	0.00	3.06
2500	6352	6.199937	ACTTCATTGATACTTTGCACATCC	57.800	37.500	0.00	0.00	0.00	3.51
2541	6395	9.992910	GAAAAACAGCTTTTTCTTGAATTTCAT	57.007	25.926	13.91	0.00	46.46	2.57
2604	6463	1.195115	CCCTAGACCAGCTAGCACAA	58.805	55.000	18.83	0.00	44.35	3.33
2653	6596	2.030451	TGTTGCATGCGTATTCTTTGCA	60.030	40.909	14.09	0.00	43.67	4.08
2720	6866	9.862585	CACATTTTTACTTAATGGAAAGCAAAC	57.137	29.630	0.00	0.00	37.32	2.93
2789	10336	5.032846	TCAACTTCACATCCTCCTCCTTAT	58.967	41.667	0.00	0.00	0.00	1.73
2791	10338	4.889780	ACTTCACATCCTCCTCCTTATCT	58.110	43.478	0.00	0.00	0.00	1.98
2792	10339	4.898861	ACTTCACATCCTCCTCCTTATCTC	59.101	45.833	0.00	0.00	0.00	2.75
2793	10340	4.542906	TCACATCCTCCTCCTTATCTCA	57.457	45.455	0.00	0.00	0.00	3.27
2843	10501	1.970640	TCAGACAGCCATACACAGTGT	59.029	47.619	11.87	11.87	0.00	3.55
2844	10502	2.368548	TCAGACAGCCATACACAGTGTT	59.631	45.455	12.53	0.00	0.00	3.32
2848	10506	4.997395	AGACAGCCATACACAGTGTTAAAG	59.003	41.667	12.53	0.00	0.00	1.85
2857	10515	8.832521	CCATACACAGTGTTAAAGTAAACAAGA	58.167	33.333	12.53	0.00	40.85	3.02
2875	10533	4.883585	ACAAGATGATGGCATTAACGATGT	59.116	37.500	0.00	4.96	38.07	3.06
2913	10571	1.378762	TGGCTAAACTGAGGCACCC	59.621	57.895	0.00	0.00	46.22	4.61
2960	10642	6.742109	AGCATGTAATCCAGAATATTGCAAC	58.258	36.000	0.00	0.00	33.56	4.17
3001	10685	6.839124	ATTTATGACAGAAATCCAGTGCAA	57.161	33.333	2.17	0.00	0.00	4.08
3046	10738	4.823442	TGGCTATGACCTTAGCAAATGATG	59.177	41.667	14.26	0.00	45.21	3.07
3047	10739	4.823989	GGCTATGACCTTAGCAAATGATGT	59.176	41.667	14.26	0.00	45.21	3.06

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	2.742589	CCCGCAAAAGAAGTTCTAGACC	59.257	50.000	5.65	0.00	0.00	3.85
1	2	3.660865	TCCCGCAAAAGAAGTTCTAGAC	58.339	45.455	5.65	0.00	0.00	2.59
25	27	7.944554	TGTTGGATTTTGAGAAGGTCTAGATTT	59.055	33.333	0.00	0.00	0.00	2.17
134	136	4.802307	ACCCAAAAGGAAAATTGCCAAAT	58.198	34.783	0.00	0.00	39.89	2.32
188	190	3.065371	GGTGCATGTTCAGGTGTATAAGC	59.935	47.826	0.00	0.00	0.00	3.09
310	3027	8.093927	CCTTTTACTAAATCTTTTGGGCATGAA	58.906	33.333	0.00	0.00	0.00	2.57
400	3118	6.777091	TGTGAAGAAGGATTTTTCTGGATCAA	59.223	34.615	0.00	0.00	37.48	2.57
662	3476	1.674359	AAGTTGCAATCGTGTGTGGA	58.326	45.000	0.59	0.00	0.00	4.02
693	3509	5.364778	ACCATAAACAAGAAAGGCAAAACC	58.635	37.500	0.00	0.00	39.61	3.27
832	3648	5.900865	TGTGCATATGATCACACACAAAT	57.099	34.783	15.56	0.00	38.07	2.32
960	3787	6.207417	CCTCTTTCCTTCTTTGCATCAACTTA	59.793	38.462	0.00	0.00	0.00	2.24
1060	3889	5.368145	TCATGATGGATTGGTGCTAACTAC	58.632	41.667	0.00	0.00	0.00	2.73
1206	4080	5.350504	AATGGTGGTTGTTGTGAAAATGA	57.649	34.783	0.00	0.00	0.00	2.57
1212	4134	3.511540	TGTGAAAATGGTGGTTGTTGTGA	59.488	39.130	0.00	0.00	0.00	3.58
1314	4599	0.313672	GAAAATGGTGGTTGCTGCGA	59.686	50.000	0.00	0.00	0.00	5.10
1433	5220	2.760092	TGGCTGAACAATAGGGATTTGC	59.240	45.455	0.00	0.00	0.00	3.68
1484	5271	1.209019	CACTGCTGCTGGAGGAATACT	59.791	52.381	16.21	0.00	35.84	2.12
1514	5301	0.311790	CAAGACGTTGTGGCATTGCT	59.688	50.000	8.82	0.00	0.00	3.91
1600	5387	1.474330	GGATTGTTCGGGGATTTGCT	58.526	50.000	0.00	0.00	0.00	3.91
1679	5496	0.595095	GCTGCTGAGGTTGGACAAAG	59.405	55.000	0.00	0.00	0.00	2.77
1810	5642	5.706369	TGTAGTACCTGTTGTTGTTGTTGTT	59.294	36.000	0.00	0.00	0.00	2.83
1811	5643	5.247084	TGTAGTACCTGTTGTTGTTGTTGT	58.753	37.500	0.00	0.00	0.00	3.32
1812	5644	5.220777	CCTGTAGTACCTGTTGTTGTTGTTG	60.221	44.000	0.00	0.00	0.00	3.33
1813	5645	4.879545	CCTGTAGTACCTGTTGTTGTTGTT	59.120	41.667	0.00	0.00	0.00	2.83
1814	5646	4.448210	CCTGTAGTACCTGTTGTTGTTGT	58.552	43.478	0.00	0.00	0.00	3.32
1815	5647	3.813166	CCCTGTAGTACCTGTTGTTGTTG	59.187	47.826	0.00	0.00	0.00	3.33
1876	5712	0.798776	GAGTGCAATGGAAGTCACCG	59.201	55.000	0.00	0.00	0.00	4.94
1878	5714	0.798776	CGGAGTGCAATGGAAGTCAC	59.201	55.000	0.00	0.00	0.00	3.67
2137	5984	7.897575	ATGAACATTGTCTAGAGAACACTTC	57.102	36.000	4.15	6.63	0.00	3.01
2488	6340	6.815089	TGAAAAATAAGTGGATGTGCAAAGT	58.185	32.000	0.00	0.00	0.00	2.66
2576	6435	1.340017	GCTGGTCTAGGGCATGAACAA	60.340	52.381	0.00	0.00	28.78	2.83
2707	6853	4.298332	CGTTGCTTAGTTTGCTTTCCATT	58.702	39.130	0.00	0.00	0.00	3.16
2720	6866	2.415512	GGTTTCTACCTGCGTTGCTTAG	59.584	50.000	0.00	0.00	41.53	2.18
2743	6890	2.158900	ACACACCCAGTCTCAAGTTCTG	60.159	50.000	0.00	0.00	0.00	3.02
2789	10336	6.040842	GGGCTATTGCTTTCCAATTAATGAGA	59.959	38.462	0.00	0.00	41.29	3.27
2791	10338	5.898972	AGGGCTATTGCTTTCCAATTAATGA	59.101	36.000	0.00	0.00	41.29	2.57
2792	10339	6.165700	AGGGCTATTGCTTTCCAATTAATG	57.834	37.500	0.00	0.00	41.29	1.90
2793	10340	5.898972	TGAGGGCTATTGCTTTCCAATTAAT	59.101	36.000	0.00	0.00	41.29	1.40
2848	10506	6.781138	TCGTTAATGCCATCATCTTGTTTAC	58.219	36.000	0.00	0.00	31.27	2.01
2857	10515	4.973168	ACCTACATCGTTAATGCCATCAT	58.027	39.130	0.00	0.00	39.12	2.45
2913	10571	1.276138	TGGATGTCTATATGGCTGCCG	59.724	52.381	14.98	0.00	0.00	5.69
2985	10668	5.916318	TGAAAAATTGCACTGGATTTCTGT	58.084	33.333	0.00	0.00	0.00	3.41
2990	10674	7.518689	CGTCATTTTGAAAAATTGCACTGGATT	60.519	33.333	0.00	0.00	36.52	3.01
3001	10685	6.293353	GCCAATGGAACGTCATTTTGAAAAAT	60.293	34.615	2.05	0.00	39.07	1.82

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.