AutoCloner

Multiple sequence alignment - TraesCS2D01G133000

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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	TraesCS2D01G133000	chr2D	100.000	2481	0	0	1	2481	78407342	78404862	0.000000e+00	4582.0
1	TraesCS2D01G133000	chr2D	86.899	832	85	14	720	1538	78509201	78508381	0.000000e+00	911.0
2	TraesCS2D01G133000	chr2D	86.486	814	76	20	736	1539	78502565	78501776	0.000000e+00	863.0
3	TraesCS2D01G133000	chr2D	83.799	537	58	15	965	1483	145683392	145682867	1.330000e-132	483.0
4	TraesCS2D01G133000	chr2D	95.652	115	5	0	2367	2481	545780922	545780808	4.210000e-43	185.0
5	TraesCS2D01G133000	chr2D	86.458	96	9	4	1614	1709	78434216	78434125	4.370000e-18	102.0
6	TraesCS2D01G133000	chr2B	93.097	1695	73	11	701	2362	121377546	121375863	0.000000e+00	2442.0
7	TraesCS2D01G133000	chr2B	88.794	821	70	16	720	1530	121478935	121478127	0.000000e+00	987.0
8	TraesCS2D01G133000	chr2B	87.887	776	67	12	720	1483	121483466	121482706	0.000000e+00	887.0
9	TraesCS2D01G133000	chr2B	82.130	1080	105	41	702	1729	121433310	121432267	0.000000e+00	845.0
10	TraesCS2D01G133000	chr2B	83.003	959	102	32	805	1729	121383359	121382428	0.000000e+00	811.0
11	TraesCS2D01G133000	chr2B	88.907	622	49	13	857	1474	121475104	121474499	0.000000e+00	749.0
12	TraesCS2D01G133000	chr4D	98.999	699	7	0	1	699	308483804	308484502	0.000000e+00	1253.0
13	TraesCS2D01G133000	chr4D	98.712	699	9	0	1	699	145627565	145626867	0.000000e+00	1242.0
14	TraesCS2D01G133000	chr4D	98.712	699	9	0	1	699	439831780	439832478	0.000000e+00	1242.0
15	TraesCS2D01G133000	chr4D	98.291	702	12	0	1	702	361842957	361842256	0.000000e+00	1230.0
16	TraesCS2D01G133000	chr5D	98.857	700	7	1	1	700	101756808	101757506	0.000000e+00	1247.0
17	TraesCS2D01G133000	chr5D	98.856	699	8	0	1	699	565206610	565205912	0.000000e+00	1247.0
18	TraesCS2D01G133000	chr5D	98.426	699	11	0	1	699	501391413	501392111	0.000000e+00	1230.0
19	TraesCS2D01G133000	chr5D	95.690	116	4	1	2366	2481	494792687	494792801	4.210000e-43	185.0
20	TraesCS2D01G133000	chr3D	98.569	699	10	0	1	699	29299150	29299848	0.000000e+00	1236.0
21	TraesCS2D01G133000	chr6D	98.438	704	6	1	1	699	56795435	56796138	0.000000e+00	1234.0
22	TraesCS2D01G133000	chr2A	87.829	797	61	16	705	1482	78323109	78323888	0.000000e+00	902.0
23	TraesCS2D01G133000	chr2A	81.382	1042	98	49	715	1724	78742273	78741296	0.000000e+00	761.0
24	TraesCS2D01G133000	chr2A	84.173	834	71	24	720	1539	78756631	78755845	0.000000e+00	752.0
25	TraesCS2D01G133000	chr2A	84.052	765	64	30	720	1474	78773353	78772637	0.000000e+00	684.0
26	TraesCS2D01G133000	chr2A	84.170	657	59	28	981	1619	78263033	78263662	1.640000e-166	595.0
27	TraesCS2D01G133000	chr2A	84.073	496	52	13	1001	1483	156514600	156515081	1.050000e-123	453.0
28	TraesCS2D01G133000	chr2A	85.873	361	30	9	1126	1483	78255296	78255638	5.040000e-97	364.0
29	TraesCS2D01G133000	chr2A	86.250	240	30	3	2131	2368	78325628	78325866	8.800000e-65	257.0
30	TraesCS2D01G133000	chr2A	83.913	230	18	4	709	926	78262809	78263031	4.180000e-48	202.0
31	TraesCS2D01G133000	chr2A	82.759	145	17	7	1863	2004	78324358	78324497	3.350000e-24	122.0
32	TraesCS2D01G133000	chr2A	96.226	53	2	0	1538	1590	78323967	78324019	1.220000e-13	87.9
33	TraesCS2D01G133000	chrUn	95.726	117	3	1	2365	2481	101803186	101803072	1.170000e-43	187.0
34	TraesCS2D01G133000	chr1D	95.726	117	3	1	2365	2481	80993822	80993936	1.170000e-43	187.0
35	TraesCS2D01G133000	chr1D	95.690	116	3	1	2366	2481	435284674	435284787	4.210000e-43	185.0
36	TraesCS2D01G133000	chr1D	95.652	115	3	1	2367	2481	296920829	296920717	1.520000e-42	183.0
37	TraesCS2D01G133000	chr7D	95.690	116	3	2	2366	2481	10517154	10517267	4.210000e-43	185.0
38	TraesCS2D01G133000	chr7D	95.690	116	3	1	2366	2481	178478820	178478933	4.210000e-43	185.0
39	TraesCS2D01G133000	chr7D	93.023	129	2	5	2355	2481	515845289	515845166	5.450000e-42	182.0

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	TraesCS2D01G133000	chr2D	78404862	78407342	2480	True	4582.000000	4582	100.000000	1	2481	1	chr2D.!!$R1	2480
1	TraesCS2D01G133000	chr2D	78508381	78509201	820	True	911.000000	911	86.899000	720	1538	1	chr2D.!!$R4	818
2	TraesCS2D01G133000	chr2D	78501776	78502565	789	True	863.000000	863	86.486000	736	1539	1	chr2D.!!$R3	803
3	TraesCS2D01G133000	chr2D	145682867	145683392	525	True	483.000000	483	83.799000	965	1483	1	chr2D.!!$R5	518
4	TraesCS2D01G133000	chr2B	121375863	121377546	1683	True	2442.000000	2442	93.097000	701	2362	1	chr2B.!!$R1	1661
5	TraesCS2D01G133000	chr2B	121474499	121483466	8967	True	874.333333	987	88.529333	720	1530	3	chr2B.!!$R4	810
6	TraesCS2D01G133000	chr2B	121432267	121433310	1043	True	845.000000	845	82.130000	702	1729	1	chr2B.!!$R3	1027
7	TraesCS2D01G133000	chr2B	121382428	121383359	931	True	811.000000	811	83.003000	805	1729	1	chr2B.!!$R2	924
8	TraesCS2D01G133000	chr4D	308483804	308484502	698	False	1253.000000	1253	98.999000	1	699	1	chr4D.!!$F1	698
9	TraesCS2D01G133000	chr4D	145626867	145627565	698	True	1242.000000	1242	98.712000	1	699	1	chr4D.!!$R1	698
10	TraesCS2D01G133000	chr4D	439831780	439832478	698	False	1242.000000	1242	98.712000	1	699	1	chr4D.!!$F2	698
11	TraesCS2D01G133000	chr4D	361842256	361842957	701	True	1230.000000	1230	98.291000	1	702	1	chr4D.!!$R2	701
12	TraesCS2D01G133000	chr5D	101756808	101757506	698	False	1247.000000	1247	98.857000	1	700	1	chr5D.!!$F1	699
13	TraesCS2D01G133000	chr5D	565205912	565206610	698	True	1247.000000	1247	98.856000	1	699	1	chr5D.!!$R1	698
14	TraesCS2D01G133000	chr5D	501391413	501392111	698	False	1230.000000	1230	98.426000	1	699	1	chr5D.!!$F3	698
15	TraesCS2D01G133000	chr3D	29299150	29299848	698	False	1236.000000	1236	98.569000	1	699	1	chr3D.!!$F1	698
16	TraesCS2D01G133000	chr6D	56795435	56796138	703	False	1234.000000	1234	98.438000	1	699	1	chr6D.!!$F1	698
17	TraesCS2D01G133000	chr2A	78741296	78742273	977	True	761.000000	761	81.382000	715	1724	1	chr2A.!!$R1	1009
18	TraesCS2D01G133000	chr2A	78755845	78756631	786	True	752.000000	752	84.173000	720	1539	1	chr2A.!!$R2	819
19	TraesCS2D01G133000	chr2A	78772637	78773353	716	True	684.000000	684	84.052000	720	1474	1	chr2A.!!$R3	754
20	TraesCS2D01G133000	chr2A	78262809	78263662	853	False	398.500000	595	84.041500	709	1619	2	chr2A.!!$F3	910
21	TraesCS2D01G133000	chr2A	78323109	78325866	2757	False	342.225000	902	88.266000	705	2368	4	chr2A.!!$F4	1663

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
784	795	0.235926	GAAAAGGTCACTGCGTCTGC	59.764	55.0	0.0	0.0	43.2	4.26	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2439	10387	0.831966	TGGGCCGACGGTGTATTATT	59.168	50.0	16.73	0.0	0.0	1.4	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
309	310	0.999406	CAAGGCCACGATTGTCTACG	59.001	55.000	5.01	0.00	0.00	3.51
398	399	8.504812	TTGAGATTGATATCCATTTTGTTCGA	57.495	30.769	0.00	0.00	0.00	3.71
414	415	3.057456	TGTTCGAGAACAGGTAGCTCTTC	60.057	47.826	13.96	2.06	45.42	2.87
780	791	2.251642	GCCGAAAAGGTCACTGCGT	61.252	57.895	0.00	0.00	43.70	5.24
781	792	1.860078	CCGAAAAGGTCACTGCGTC	59.140	57.895	0.00	0.00	34.51	5.19
782	793	0.600255	CCGAAAAGGTCACTGCGTCT	60.600	55.000	0.00	0.00	34.51	4.18
783	794	0.508641	CGAAAAGGTCACTGCGTCTG	59.491	55.000	0.00	0.00	0.00	3.51
784	795	0.235926	GAAAAGGTCACTGCGTCTGC	59.764	55.000	0.00	0.00	43.20	4.26
1286	5911	4.767255	CCAGCGAAGAAGGCGGCT	62.767	66.667	5.25	5.25	35.84	5.52
1333	5958	3.161450	GGTCGGGCTGCTGGGATA	61.161	66.667	0.00	0.00	0.00	2.59
1487	6119	3.859961	GCTCGACAAGATTTGAAGATCGA	59.140	43.478	0.00	0.00	34.63	3.59
1502	6134	0.250513	ATCGAACAGCAGAACCCTCC	59.749	55.000	0.00	0.00	0.00	4.30
1531	6176	7.041107	TGTACAGTTTTAGTTTACTCGTTGGT	58.959	34.615	0.00	0.00	0.00	3.67
1663	7185	8.049117	AGTCATCCATGTATGTGTCTTGTTATT	58.951	33.333	0.00	0.00	0.00	1.40
1702	7514	8.037723	TGAATCCATGAGAATTCAATCCTCTA	57.962	34.615	8.44	0.00	36.78	2.43
1762	7613	5.650266	AGTTCTGACATAGACCTAGTCACTG	59.350	44.000	0.00	0.00	37.36	3.66
1768	7619	8.768501	TGACATAGACCTAGTCACTGATAATT	57.231	34.615	0.00	0.00	37.36	1.40
1900	8833	5.294552	GGTTTACTAGAGACATCATTGCACC	59.705	44.000	0.00	0.00	0.00	5.01
1952	8885	2.150397	AGTTGTACTGAAGACGGTGC	57.850	50.000	0.00	0.00	38.25	5.01
2025	9219	9.218525	AGGTAATCAAAATAGAGAGAAGATGGA	57.781	33.333	0.00	0.00	0.00	3.41
2029	9223	9.571816	AATCAAAATAGAGAGAAGATGGATTCC	57.428	33.333	0.00	0.00	0.00	3.01
2083	9278	8.501070	AGATGAAGTCCAAGATCCTCATTATTT	58.499	33.333	0.00	0.00	0.00	1.40
2090	9285	6.380846	TCCAAGATCCTCATTATTTTTGGTGG	59.619	38.462	0.00	0.00	36.21	4.61
2141	10083	2.576648	ACACAAGGGATCCTACCTTTCC	59.423	50.000	12.58	0.00	45.81	3.13
2268	10215	1.483415	AGCCCATGCCATTTGATGTTC	59.517	47.619	0.00	0.00	38.69	3.18
2305	10252	4.070009	GTTTCCCACCGAAGAAGTACAAT	58.930	43.478	0.00	0.00	0.00	2.71
2372	10320	5.509498	AGGGAACATGCAATCTAGCTAAAA	58.491	37.500	0.00	0.00	34.99	1.52
2373	10321	5.951747	AGGGAACATGCAATCTAGCTAAAAA	59.048	36.000	0.00	0.00	34.99	1.94
2374	10322	6.608808	AGGGAACATGCAATCTAGCTAAAAAT	59.391	34.615	0.00	0.00	34.99	1.82
2375	10323	7.124750	AGGGAACATGCAATCTAGCTAAAAATT	59.875	33.333	0.00	0.00	34.99	1.82
2377	10325	9.154847	GGAACATGCAATCTAGCTAAAAATTTT	57.845	29.630	0.00	0.00	34.99	1.82
2451	10399	7.391148	AGAATTTGCAAGAATAATACACCGT	57.609	32.000	0.00	0.00	0.00	4.83
2452	10400	7.472543	AGAATTTGCAAGAATAATACACCGTC	58.527	34.615	0.00	0.00	0.00	4.79
2453	10401	4.850859	TTGCAAGAATAATACACCGTCG	57.149	40.909	0.00	0.00	0.00	5.12
2457	10405	1.069668	AGAATAATACACCGTCGGCCC	59.930	52.381	12.28	0.00	0.00	5.80
2459	10407	0.105408	ATAATACACCGTCGGCCCAC	59.895	55.000	12.28	0.00	0.00	4.61
2460	10408	0.971959	TAATACACCGTCGGCCCACT	60.972	55.000	12.28	0.00	0.00	4.00
2461	10409	2.515996	AATACACCGTCGGCCCACTG	62.516	60.000	12.28	4.04	0.00	3.66

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
309	310	0.951558	ACCGCAGAAACATTGTCACC	59.048	50.000	0.00	0.00	0.00	4.02
398	399	2.515854	TGACGAAGAGCTACCTGTTCT	58.484	47.619	0.00	0.00	38.76	3.01
752	763	3.143728	GACCTTTTCGGCTTCCTTAACA	58.856	45.455	0.00	0.00	35.61	2.41
780	791	1.270785	TGATCTTTGAAGCCACGCAGA	60.271	47.619	0.00	0.00	0.00	4.26
781	792	1.159285	TGATCTTTGAAGCCACGCAG	58.841	50.000	0.00	0.00	0.00	5.18
782	793	1.266718	GTTGATCTTTGAAGCCACGCA	59.733	47.619	0.00	0.00	0.00	5.24
783	794	1.401539	GGTTGATCTTTGAAGCCACGC	60.402	52.381	0.00	0.00	0.00	5.34
784	795	1.135972	CGGTTGATCTTTGAAGCCACG	60.136	52.381	0.00	0.00	0.00	4.94
785	796	1.200020	CCGGTTGATCTTTGAAGCCAC	59.800	52.381	0.00	0.00	0.00	5.01
1286	5911	2.283101	GCCATGCACCTGGTTGGA	60.283	61.111	18.14	6.58	38.63	3.53
1487	6119	1.201429	ATCGGGAGGGTTCTGCTGTT	61.201	55.000	0.00	0.00	38.63	3.16
1502	6134	6.583806	ACGAGTAAACTAAAACTGTACATCGG	59.416	38.462	0.00	0.00	0.00	4.18
1531	6176	8.084590	GCTAGTGCTTGAAAGTTCTAGTAAAA	57.915	34.615	16.79	0.00	35.74	1.52
1604	6271	3.275617	TGATGGGTACACAGCAATACC	57.724	47.619	14.88	0.00	40.25	2.73
1702	7514	7.335422	TGCAAAATTGGCAATACGGAAAATAAT	59.665	29.630	14.05	0.00	38.54	1.28
1779	7630	3.322254	AGTGACTGGAGACCTTGTACAAG	59.678	47.826	25.79	25.79	38.14	3.16
1900	8833	7.776107	AGGAGGAAGAAAGAAGAAAAACAAAG	58.224	34.615	0.00	0.00	0.00	2.77
2025	9219	6.207614	GCTCCTAAGTGAAAACAAAGAGGAAT	59.792	38.462	0.00	0.00	31.64	3.01
2029	9223	4.083802	CGGCTCCTAAGTGAAAACAAAGAG	60.084	45.833	0.00	0.00	0.00	2.85
2090	9285	8.647226	GTGATAAAATTGAATAAGTTGTGGCAC	58.353	33.333	11.55	11.55	0.00	5.01
2141	10083	3.379688	TGGTCTCATTCTCTCATCAGTCG	59.620	47.826	0.00	0.00	0.00	4.18
2268	10215	2.549329	GGGAAACAATGCAAAAGCCAAG	59.451	45.455	0.00	0.00	0.00	3.61
2288	10235	7.837202	TGTAATTATTGTACTTCTTCGGTGG	57.163	36.000	0.00	0.00	0.00	4.61
2328	10275	3.832615	AGAAACCCGACGGCTTTATAT	57.167	42.857	8.86	0.00	0.00	0.86
2424	10372	9.139174	CGGTGTATTATTCTTGCAAATTCTTTT	57.861	29.630	0.00	0.00	0.00	2.27
2425	10373	8.303876	ACGGTGTATTATTCTTGCAAATTCTTT	58.696	29.630	0.00	0.00	0.00	2.52
2426	10374	7.826690	ACGGTGTATTATTCTTGCAAATTCTT	58.173	30.769	0.00	0.00	0.00	2.52
2427	10375	7.391148	ACGGTGTATTATTCTTGCAAATTCT	57.609	32.000	0.00	0.00	0.00	2.40
2428	10376	6.410914	CGACGGTGTATTATTCTTGCAAATTC	59.589	38.462	0.00	0.00	0.00	2.17
2429	10377	6.255215	CGACGGTGTATTATTCTTGCAAATT	58.745	36.000	0.00	0.00	0.00	1.82
2430	10378	5.220777	CCGACGGTGTATTATTCTTGCAAAT	60.221	40.000	5.48	0.00	0.00	2.32
2431	10379	4.093703	CCGACGGTGTATTATTCTTGCAAA	59.906	41.667	5.48	0.00	0.00	3.68
2432	10380	3.619483	CCGACGGTGTATTATTCTTGCAA	59.381	43.478	5.48	0.00	0.00	4.08
2433	10381	3.191669	CCGACGGTGTATTATTCTTGCA	58.808	45.455	5.48	0.00	0.00	4.08
2434	10382	2.033151	GCCGACGGTGTATTATTCTTGC	60.033	50.000	16.73	0.00	0.00	4.01
2435	10383	2.542595	GGCCGACGGTGTATTATTCTTG	59.457	50.000	16.73	0.00	0.00	3.02
2436	10384	2.484241	GGGCCGACGGTGTATTATTCTT	60.484	50.000	16.73	0.00	0.00	2.52
2437	10385	1.069668	GGGCCGACGGTGTATTATTCT	59.930	52.381	16.73	0.00	0.00	2.40
2439	10387	0.831966	TGGGCCGACGGTGTATTATT	59.168	50.000	16.73	0.00	0.00	1.40
2443	10391	2.682494	AGTGGGCCGACGGTGTAT	60.682	61.111	16.73	0.00	0.00	2.29
2444	10392	3.687102	CAGTGGGCCGACGGTGTA	61.687	66.667	16.73	0.00	0.00	2.90
2457	10405	2.433838	CTCAGTCGGCCTGCAGTG	60.434	66.667	13.81	5.37	41.25	3.66

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.