AutoCloner

Multiple sequence alignment - TraesCS1B01G109700

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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	TraesCS1B01G109700	chr1B	100.000	4482	0	0	1	4482	121764665	121760184	0.000000e+00	8277.0
1	TraesCS1B01G109700	chr1B	89.837	1102	50	23	3013	4111	428096420	428097462	0.000000e+00	1358.0
2	TraesCS1B01G109700	chr1B	93.624	894	38	12	1395	2275	428095005	428095892	0.000000e+00	1317.0
3	TraesCS1B01G109700	chr1B	96.226	424	14	1	2498	2921	428095995	428096416	0.000000e+00	693.0
4	TraesCS1B01G109700	chr6B	95.045	2563	81	15	1	2532	457287868	457285321	0.000000e+00	3988.0
5	TraesCS1B01G109700	chr6B	96.303	1596	52	4	2591	4186	457285320	457283732	0.000000e+00	2614.0
6	TraesCS1B01G109700	chr6B	93.697	1523	62	16	777	2275	550346983	550348495	0.000000e+00	2250.0
7	TraesCS1B01G109700	chr6B	88.849	1112	57	25	3003	4111	550349010	550350057	0.000000e+00	1304.0
8	TraesCS1B01G109700	chr6B	95.251	737	32	3	1	735	550346253	550346988	0.000000e+00	1164.0
9	TraesCS1B01G109700	chr6B	94.090	423	22	2	2498	2920	550348597	550349016	1.360000e-179	640.0
10	TraesCS1B01G109700	chr6B	88.889	72	7	1	716	787	252553889	252553819	2.220000e-13	87.9
11	TraesCS1B01G109700	chr2B	95.271	2453	67	18	1	2434	516288569	516290991	0.000000e+00	3842.0
12	TraesCS1B01G109700	chr2B	97.065	1465	38	4	2716	4179	516300883	516302343	0.000000e+00	2462.0
13	TraesCS1B01G109700	chr2B	97.987	298	6	0	2424	2721	516291804	516292101	6.650000e-143	518.0
14	TraesCS1B01G109700	chr4B	92.217	2531	146	28	4	2509	409736479	409733975	0.000000e+00	3535.0
15	TraesCS1B01G109700	chr4B	91.696	1999	108	31	2521	4482	409733452	409731475	0.000000e+00	2719.0
16	TraesCS1B01G109700	chr4B	91.546	1999	116	28	2521	4482	409712103	409710121	0.000000e+00	2706.0
17	TraesCS1B01G109700	chr4B	90.671	611	53	3	1899	2509	409713233	409712627	0.000000e+00	809.0
18	TraesCS1B01G109700	chr7B	94.275	1799	73	15	2313	4111	227756932	227758700	0.000000e+00	2724.0
19	TraesCS1B01G109700	chr7B	94.083	1521	61	13	777	2275	227755415	227756928	0.000000e+00	2283.0
20	TraesCS1B01G109700	chr7B	95.920	1054	39	2	2313	3366	227777994	227779043	0.000000e+00	1705.0
21	TraesCS1B01G109700	chr7B	96.472	737	24	2	1	735	227754684	227755420	0.000000e+00	1216.0
22	TraesCS1B01G109700	chr7B	93.421	684	26	7	1604	2275	227777314	227777990	0.000000e+00	996.0
23	TraesCS1B01G109700	chr7B	89.577	614	35	13	3498	4111	227799972	227800556	0.000000e+00	752.0
24	TraesCS1B01G109700	chr7B	78.475	446	73	18	3233	3662	198611156	198610718	2.050000e-68	270.0
25	TraesCS1B01G109700	chr7B	100.000	34	0	0	4153	4186	227758698	227758731	3.740000e-06	63.9
26	TraesCS1B01G109700	chr7B	100.000	34	0	0	4153	4186	227800554	227800587	3.740000e-06	63.9
27	TraesCS1B01G109700	chr6D	84.050	1047	125	33	781	1803	227527111	227528139	0.000000e+00	970.0
28	TraesCS1B01G109700	chr6D	83.949	704	100	9	5	702	424953132	424952436	0.000000e+00	662.0
29	TraesCS1B01G109700	chr6D	89.671	426	40	3	2085	2509	226776456	226776878	1.420000e-149	540.0
30	TraesCS1B01G109700	chr6D	80.691	492	86	5	4	491	218378375	218377889	1.520000e-99	374.0
31	TraesCS1B01G109700	chr2D	83.792	1018	129	26	805	1803	354687981	354688981	0.000000e+00	933.0
32	TraesCS1B01G109700	chr3B	82.468	1021	132	28	805	1803	233302984	233301989	0.000000e+00	850.0
33	TraesCS1B01G109700	chr3B	80.717	223	37	6	4209	4429	233248883	233248665	7.710000e-38	169.0
34	TraesCS1B01G109700	chr3D	84.247	876	102	24	728	1578	133259668	133258804	0.000000e+00	821.0
35	TraesCS1B01G109700	chr4D	82.434	945	125	26	729	1646	344294848	344293918	0.000000e+00	787.0
36	TraesCS1B01G109700	chr4D	83.734	707	97	13	5	702	344295648	344294951	0.000000e+00	652.0
37	TraesCS1B01G109700	chr4D	87.793	426	47	4	2085	2509	63266185	63266606	1.120000e-135	494.0
38	TraesCS1B01G109700	chr4D	77.636	550	82	20	3233	3763	344251961	344251434	3.390000e-76	296.0
39	TraesCS1B01G109700	chr5D	84.339	779	94	18	781	1539	43335072	43335842	0.000000e+00	737.0
40	TraesCS1B01G109700	chr5D	85.830	247	27	6	2767	3007	43335888	43336132	5.750000e-64	255.0
41	TraesCS1B01G109700	chr5A	83.144	706	108	7	3	702	432464941	432464241	6.320000e-178	634.0
42	TraesCS1B01G109700	chr2A	87.588	427	48	4	2085	2509	114308531	114308954	1.450000e-134	490.0
43	TraesCS1B01G109700	chr4A	89.453	256	24	2	2255	2509	598703059	598702806	2.010000e-83	320.0
44	TraesCS1B01G109700	chr4A	90.960	177	14	2	1920	2096	401156076	401156250	2.080000e-58	237.0

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	TraesCS1B01G109700	chr1B	121760184	121764665	4481	True	8277.000000	8277	100.00000	1	4482	1	chr1B.!!$R1	4481
1	TraesCS1B01G109700	chr1B	428095005	428097462	2457	False	1122.666667	1358	93.22900	1395	4111	3	chr1B.!!$F1	2716
2	TraesCS1B01G109700	chr6B	457283732	457287868	4136	True	3301.000000	3988	95.67400	1	4186	2	chr6B.!!$R2	4185
3	TraesCS1B01G109700	chr6B	550346253	550350057	3804	False	1339.500000	2250	92.97175	1	4111	4	chr6B.!!$F1	4110
4	TraesCS1B01G109700	chr2B	516300883	516302343	1460	False	2462.000000	2462	97.06500	2716	4179	1	chr2B.!!$F1	1463
5	TraesCS1B01G109700	chr2B	516288569	516292101	3532	False	2180.000000	3842	96.62900	1	2721	2	chr2B.!!$F2	2720
6	TraesCS1B01G109700	chr4B	409731475	409736479	5004	True	3127.000000	3535	91.95650	4	4482	2	chr4B.!!$R2	4478
7	TraesCS1B01G109700	chr4B	409710121	409713233	3112	True	1757.500000	2706	91.10850	1899	4482	2	chr4B.!!$R1	2583
8	TraesCS1B01G109700	chr7B	227754684	227758731	4047	False	1571.725000	2724	96.20750	1	4186	4	chr7B.!!$F1	4185
9	TraesCS1B01G109700	chr7B	227777314	227779043	1729	False	1350.500000	1705	94.67050	1604	3366	2	chr7B.!!$F2	1762
10	TraesCS1B01G109700	chr7B	227799972	227800587	615	False	407.950000	752	94.78850	3498	4186	2	chr7B.!!$F3	688
11	TraesCS1B01G109700	chr6D	227527111	227528139	1028	False	970.000000	970	84.05000	781	1803	1	chr6D.!!$F2	1022
12	TraesCS1B01G109700	chr6D	424952436	424953132	696	True	662.000000	662	83.94900	5	702	1	chr6D.!!$R2	697
13	TraesCS1B01G109700	chr2D	354687981	354688981	1000	False	933.000000	933	83.79200	805	1803	1	chr2D.!!$F1	998
14	TraesCS1B01G109700	chr3B	233301989	233302984	995	True	850.000000	850	82.46800	805	1803	1	chr3B.!!$R2	998
15	TraesCS1B01G109700	chr3D	133258804	133259668	864	True	821.000000	821	84.24700	728	1578	1	chr3D.!!$R1	850
16	TraesCS1B01G109700	chr4D	344293918	344295648	1730	True	719.500000	787	83.08400	5	1646	2	chr4D.!!$R2	1641
17	TraesCS1B01G109700	chr4D	344251434	344251961	527	True	296.000000	296	77.63600	3233	3763	1	chr4D.!!$R1	530
18	TraesCS1B01G109700	chr5D	43335072	43336132	1060	False	496.000000	737	85.08450	781	3007	2	chr5D.!!$F1	2226
19	TraesCS1B01G109700	chr5A	432464241	432464941	700	True	634.000000	634	83.14400	3	702	1	chr5A.!!$R1	699

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	Hairpin	End Stability	Orientation
252	254	2.428890	ACAAAGAGATACCAGCCTCTCG	59.571	50.0	0.00	42.21	4.04	F
1712	1854	2.670019	AGGACCTTACCCAACAAACC	57.330	50.0	0.00	0.00	3.27	F
1825	1980	2.158667	CCCTCCACCACTGTACTGTTTT	60.159	50.0	2.16	0.00	2.43	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1826	1981	4.623932	AGTAGGCAGAAACATGAACTGA	57.376	40.909	17.34	0.89	34.07	3.41	R
3466	5020	5.565834	GCGGAAAAGTCAATTTGGTATTGGA	60.566	40.000	0.00	0.00	0.00	3.53	R
3781	5337	3.887110	AGTATGCATGTGATCCCAACATG	59.113	43.478	16.51	16.51	42.79	3.21	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
68	70	9.627123	TTCTTTCTCATCAGGAAGAAGTTTTTA	57.373	29.630	0.00	0.00	45.83	1.52
83	85	8.340618	AGAAGTTTTTATATCAGCTGAAGCAA	57.659	30.769	22.50	11.55	45.16	3.91
252	254	2.428890	ACAAAGAGATACCAGCCTCTCG	59.571	50.000	0.00	0.00	42.21	4.04
323	325	9.184523	TCCAACTAGGTTATAATTCCAACAATG	57.815	33.333	0.00	0.00	39.02	2.82
457	468	2.938451	TGAATAATGCAGAAGCTGGACG	59.062	45.455	0.00	0.00	42.74	4.79
528	539	6.051717	GCAGCTAAACTTCAATCTCCTGATA	58.948	40.000	0.00	0.00	31.70	2.15
712	725	8.319143	ACCTCGGAAAATAATATGAAATACCG	57.681	34.615	0.00	0.00	38.31	4.02
906	1000	8.658840	AGTAGTTCTCCTTCTTTATTCTCTGT	57.341	34.615	0.00	0.00	0.00	3.41
1007	1101	8.488668	TGAGATTGGAGATGAAGTGATGAATTA	58.511	33.333	0.00	0.00	0.00	1.40
1082	1176	8.394121	GCCTTATCTCAAGAAATACTGTTTCAG	58.606	37.037	1.60	0.00	37.52	3.02
1107	1201	8.241367	AGTTTGTACTTTACTGTGAGTTTTTGG	58.759	33.333	4.38	0.00	0.00	3.28
1246	1363	9.056005	GTCATTTGATCCTATTAGTTGCATACA	57.944	33.333	0.00	0.00	0.00	2.29
1426	1560	5.179533	GGTTCTACTTTCCATCAACTCTCC	58.820	45.833	0.00	0.00	0.00	3.71
1550	1684	6.888105	ACCCTTTGATTTCAACAGAAACAAT	58.112	32.000	0.00	0.00	34.36	2.71
1712	1854	2.670019	AGGACCTTACCCAACAAACC	57.330	50.000	0.00	0.00	0.00	3.27
1752	1894	9.376075	TCATTTTTCTTCTTTGTGTTTGCATAA	57.624	25.926	0.00	0.00	0.00	1.90
1825	1980	2.158667	CCCTCCACCACTGTACTGTTTT	60.159	50.000	2.16	0.00	0.00	2.43
1826	1981	3.551846	CCTCCACCACTGTACTGTTTTT	58.448	45.455	2.16	0.00	0.00	1.94
2002	2157	9.060347	CATATTGTATGTTCACCTCAAGCTAAT	57.940	33.333	0.00	0.00	0.00	1.73
2036	2191	5.106038	ACATTGGACATCAAAGCATACTGTG	60.106	40.000	0.00	0.00	39.05	3.66
2101	2262	7.757611	TCCATCCCTAACCTTTAGTTAACAAA	58.242	34.615	8.61	5.82	40.43	2.83
2214	2376	4.080526	AGTCAACAACAACTACTCCCAACT	60.081	41.667	0.00	0.00	0.00	3.16
2338	2504	4.560136	TGCTGCGTCATGTTTCTTTAAA	57.440	36.364	0.00	0.00	0.00	1.52
2434	3436	2.679349	GCTGAATCTGACCTCCAACTCC	60.679	54.545	0.00	0.00	0.00	3.85
2597	4111	2.353858	CCAAGGCTGGATTGCACAA	58.646	52.632	0.00	0.00	46.92	3.33
2940	4461	2.355197	TGTATGTGCAAACCTGGATCG	58.645	47.619	0.00	0.00	0.00	3.69
3024	4545	7.176690	CCTGTTTTTAGCTTTTCTAGGAATGGA	59.823	37.037	0.00	0.00	0.00	3.41
3156	4679	3.213206	TGTCTATGCACATTCCATCCC	57.787	47.619	0.00	0.00	0.00	3.85
3466	5020	5.240013	ACAAGCTGAAAGAAGGAGATCTT	57.760	39.130	0.00	0.00	41.34	2.40
3634	5188	1.705256	TTTTGCTACCACGAGCTACG	58.295	50.000	0.00	0.00	43.27	3.51
3789	5345	4.997395	GCACTACATACTATCCATGTTGGG	59.003	45.833	0.00	0.00	38.32	4.12
4027	5585	2.159585	CCTTACGCATGCGATGAAAACA	60.160	45.455	43.72	17.24	42.83	2.83
4098	5676	8.035394	GTGATTAGAATTCCAAGTGAGTACTCA	58.965	37.037	21.74	21.74	35.69	3.41
4133	5711	9.499585	CTTTCTTCATGCATCTGTGTTATTTAG	57.500	33.333	0.00	0.00	0.00	1.85
4144	5722	9.817365	CATCTGTGTTATTTAGAAACTTGTCAG	57.183	33.333	0.00	0.00	0.00	3.51
4187	5766	9.878667	TGGTTCGTGTTTTCTTCATCTATAATA	57.121	29.630	0.00	0.00	0.00	0.98
4273	5852	5.929992	ACAGATCACCAAATGCAATTTCAAG	59.070	36.000	0.00	0.00	44.81	3.02
4373	5952	7.492994	AGCGAATTAGTTCAAATCTAGTTCTCC	59.507	37.037	0.00	0.00	34.34	3.71
4420	5999	8.428063	ACAAAAATTCAACTCCATACCATCAAA	58.572	29.630	0.00	0.00	0.00	2.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
68	70	8.631480	TTGATATCATTTGCTTCAGCTGATAT	57.369	30.769	19.04	16.33	43.23	1.63
252	254	5.163713	GGAATTCCTTCACTTGTATCACAGC	60.164	44.000	17.73	0.00	32.70	4.40
294	296	8.164733	TGTTGGAATTATAACCTAGTTGGACAA	58.835	33.333	0.00	0.00	39.71	3.18
360	370	4.976224	TGGAATGTTGCTCAGAATCATG	57.024	40.909	0.00	0.00	0.00	3.07
405	416	2.757868	AGCCTGCAAAACACACAAAGTA	59.242	40.909	0.00	0.00	0.00	2.24
528	539	8.463930	TGAGATATTTTCAGTTTCTTTGGTGT	57.536	30.769	0.00	0.00	0.00	4.16
691	703	6.904498	TGCCGGTATTTCATATTATTTTCCG	58.096	36.000	1.90	0.00	35.02	4.30
712	725	3.467374	TGGTTGAACCAGAAAAATGCC	57.533	42.857	14.05	0.00	44.79	4.40
903	997	8.506437	TCAATATCAACAAAAAGAGTGCTACAG	58.494	33.333	0.00	0.00	0.00	2.74
906	1000	7.121168	CCCTCAATATCAACAAAAAGAGTGCTA	59.879	37.037	0.00	0.00	0.00	3.49
1082	1176	8.024865	ACCAAAAACTCACAGTAAAGTACAAAC	58.975	33.333	0.00	0.00	0.00	2.93
1712	1854	8.552034	AGAAGAAAAATGAACTTACAAGAGACG	58.448	33.333	0.00	0.00	0.00	4.18
1825	1980	4.973168	AGTAGGCAGAAACATGAACTGAA	58.027	39.130	17.34	4.68	34.07	3.02
1826	1981	4.623932	AGTAGGCAGAAACATGAACTGA	57.376	40.909	17.34	0.89	34.07	3.41
2002	2157	7.094805	GCTTTGATGTCCAATGTTCAACTACTA	60.095	37.037	0.00	0.00	34.23	1.82
2338	2504	2.309755	TCTTCTGTTCCATGGCCATTCT	59.690	45.455	17.92	0.00	0.00	2.40
2503	3505	4.715297	GGGATAACTGACAGAGGGAGTTTA	59.285	45.833	10.08	0.00	32.27	2.01
2940	4461	9.899226	AATGAGCTACTTCACTAATTTGTTTTC	57.101	29.630	0.00	0.00	0.00	2.29
3175	4712	9.823647	AGGATAGATATAAACAAAGTCACACTG	57.176	33.333	0.00	0.00	0.00	3.66
3223	4760	5.999205	AATCAAATGGGCATAACAGAACA	57.001	34.783	0.00	0.00	0.00	3.18
3227	4764	6.319658	ACTGACTAATCAAATGGGCATAACAG	59.680	38.462	0.00	0.00	33.30	3.16
3466	5020	5.565834	GCGGAAAAGTCAATTTGGTATTGGA	60.566	40.000	0.00	0.00	0.00	3.53
3595	5149	9.127277	AGCAAAAAGTTTAAACATCTAGTACCA	57.873	29.630	20.06	0.00	0.00	3.25
3634	5188	6.043411	AGAAGATTTCCAACATAGACGCTAC	58.957	40.000	0.00	0.00	0.00	3.58
3781	5337	3.887110	AGTATGCATGTGATCCCAACATG	59.113	43.478	16.51	16.51	42.79	3.21
3789	5345	6.933521	AGGATTCACTTAGTATGCATGTGATC	59.066	38.462	15.21	13.75	37.47	2.92
4027	5585	3.052036	GCGTTTTCAGCAATCATGTTGT	58.948	40.909	8.97	0.00	38.73	3.32
4098	5676	9.570468	ACAGATGCATGAAGAAAGTATAATGAT	57.430	29.630	2.46	0.00	0.00	2.45
4344	5923	9.267096	GAACTAGATTTGAACTAATTCGCTTTG	57.733	33.333	0.00	0.00	37.69	2.77

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.