AutoCloner

Multiple sequence alignment - TraesCS7A01G100400

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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	TraesCS7A01G100400	chr7A	100.000	2321	0	0	514	2834	61791977	61794297	0.000000e+00	4287.0
1	TraesCS7A01G100400	chr7A	86.504	452	46	10	1396	1840	63700555	63700998	1.530000e-132	483.0
2	TraesCS7A01G100400	chr7A	100.000	248	0	0	1	248	61791464	61791711	2.570000e-125	459.0
3	TraesCS7A01G100400	chr7A	87.248	149	18	1	960	1107	63700227	63700375	4.860000e-38	169.0
4	TraesCS7A01G100400	chr7A	91.398	93	8	0	1	93	55435766	55435674	8.240000e-26	128.0
5	TraesCS7A01G100400	chr7A	100.000	30	0	0	1365	1394	61792792	61792821	3.940000e-04	56.5
6	TraesCS7A01G100400	chr7A	100.000	30	0	0	1329	1358	61792828	61792857	3.940000e-04	56.5
7	TraesCS7A01G100400	chr7D	96.494	1369	45	3	1329	2696	56987145	56988511	0.000000e+00	2259.0
8	TraesCS7A01G100400	chr7D	89.842	886	29	20	515	1394	56986344	56987174	0.000000e+00	1081.0
9	TraesCS7A01G100400	chr7D	85.315	572	50	22	1365	1920	59100715	59100162	6.860000e-156	560.0
10	TraesCS7A01G100400	chr7D	95.631	206	8	1	44	248	56986010	56986215	2.100000e-86	329.0
11	TraesCS7A01G100400	chr7D	95.000	80	4	0	168	247	170999842	170999763	2.960000e-25	126.0
12	TraesCS7A01G100400	chr7D	100.000	30	0	0	1365	1394	56987109	56987138	3.940000e-04	56.5
13	TraesCS7A01G100400	chr4A	92.364	1375	78	16	1342	2696	674354855	674353488	0.000000e+00	1932.0
14	TraesCS7A01G100400	chr4A	84.531	1364	145	39	1365	2696	676550025	676548696	0.000000e+00	1290.0
15	TraesCS7A01G100400	chr4A	92.271	634	36	6	515	1143	673980299	673979674	0.000000e+00	887.0
16	TraesCS7A01G100400	chr4A	90.396	656	39	13	2057	2696	673978507	673977860	0.000000e+00	841.0
17	TraesCS7A01G100400	chr4A	89.328	506	27	9	1534	2027	673978990	673978500	6.710000e-171	610.0
18	TraesCS7A01G100400	chr4A	90.881	318	24	5	1220	1535	673979465	673979151	3.380000e-114	422.0
19	TraesCS7A01G100400	chr4A	83.333	300	31	8	868	1154	674355302	674355009	2.800000e-65	259.0
20	TraesCS7A01G100400	chr4A	91.617	167	13	1	1	166	673980577	673980411	2.200000e-56	230.0
21	TraesCS7A01G100400	chr4A	89.062	128	14	0	980	1107	676550377	676550250	2.920000e-35	159.0
22	TraesCS7A01G100400	chr3D	92.925	1258	69	10	1342	2585	545227732	545228983	0.000000e+00	1812.0
23	TraesCS7A01G100400	chr3D	80.320	437	42	28	729	1148	545227163	545227572	9.930000e-75	291.0
24	TraesCS7A01G100400	chr3D	97.248	109	3	0	2726	2834	545229369	545229477	4.820000e-43	185.0
25	TraesCS7A01G100400	chr3D	97.674	86	2	0	2611	2696	545228974	545229059	6.330000e-32	148.0
26	TraesCS7A01G100400	chr3D	95.402	87	4	0	162	248	348135364	348135278	3.810000e-29	139.0
27	TraesCS7A01G100400	chr3B	96.512	86	3	0	163	248	548846944	548846859	2.940000e-30	143.0
28	TraesCS7A01G100400	chr3B	93.548	93	6	0	156	248	674424184	674424276	3.810000e-29	139.0
29	TraesCS7A01G100400	chr6B	95.455	88	4	0	161	248	641674168	641674081	1.060000e-29	141.0
30	TraesCS7A01G100400	chr5D	95.506	89	2	2	162	248	328911552	328911640	1.060000e-29	141.0
31	TraesCS7A01G100400	chr2D	96.429	84	3	0	165	248	392691157	392691240	3.810000e-29	139.0
32	TraesCS7A01G100400	chr5B	92.632	95	4	3	156	248	166366142	166366049	1.770000e-27	134.0

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	TraesCS7A01G100400	chr7A	61791464	61794297	2833	False	1214.750	4287	100.00000	1	2834	4	chr7A.!!$F1	2833
1	TraesCS7A01G100400	chr7A	63700227	63700998	771	False	326.000	483	86.87600	960	1840	2	chr7A.!!$F2	880
2	TraesCS7A01G100400	chr7D	56986010	56988511	2501	False	931.375	2259	95.49175	44	2696	4	chr7D.!!$F1	2652
3	TraesCS7A01G100400	chr7D	59100162	59100715	553	True	560.000	560	85.31500	1365	1920	1	chr7D.!!$R1	555
4	TraesCS7A01G100400	chr4A	674353488	674355302	1814	True	1095.500	1932	87.84850	868	2696	2	chr4A.!!$R2	1828
5	TraesCS7A01G100400	chr4A	676548696	676550377	1681	True	724.500	1290	86.79650	980	2696	2	chr4A.!!$R3	1716
6	TraesCS7A01G100400	chr4A	673977860	673980577	2717	True	598.000	887	90.89860	1	2696	5	chr4A.!!$R1	2695
7	TraesCS7A01G100400	chr3D	545227163	545229477	2314	False	609.000	1812	92.04175	729	2834	4	chr3D.!!$F1	2105

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
40	41	1.080569	CGATTGCACCCAAACAGCC	60.081	57.895	0.0	0.0	34.05	4.85	F
1120	1140	0.323360	CCCCGCATCCCTCAAAAAGA	60.323	55.000	0.0	0.0	0.00	2.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1657	2085	0.036732	TTCTGCGCATTCACCTTCCT	59.963	50.0	12.24	0.0	0.00	3.36	R
2724	3207	0.833287	GCCTACTGCCATCTGGAGAA	59.167	55.0	0.00	0.0	37.39	2.87	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
26	27	9.148104	GGTTTACAATACAGTCTAAACTCGATT	57.852	33.333	0.00	0.00	31.71	3.34
30	31	6.090898	ACAATACAGTCTAAACTCGATTGCAC	59.909	38.462	0.00	0.00	37.76	4.57
36	37	2.793278	AAACTCGATTGCACCCAAAC	57.207	45.000	0.00	0.00	34.05	2.93
38	39	1.238439	ACTCGATTGCACCCAAACAG	58.762	50.000	0.00	0.00	34.05	3.16
40	41	1.080569	CGATTGCACCCAAACAGCC	60.081	57.895	0.00	0.00	34.05	4.85
59	60	3.372730	TGCGCGGGGTACTACGTT	61.373	61.111	8.83	0.00	0.00	3.99
176	178	3.827722	TGTTTCAAAATTCTCCCTCCGT	58.172	40.909	0.00	0.00	0.00	4.69
189	191	3.626930	TCCCTCCGTCCCAAAATAATTG	58.373	45.455	0.00	0.00	0.00	2.32
974	991	2.436824	GTCCTCTTTGGCGCCCTC	60.437	66.667	26.77	0.00	35.26	4.30
1116	1136	3.338250	AGCCCCGCATCCCTCAAA	61.338	61.111	0.00	0.00	0.00	2.69
1117	1137	2.362375	GCCCCGCATCCCTCAAAA	60.362	61.111	0.00	0.00	0.00	2.44
1118	1138	1.981853	GCCCCGCATCCCTCAAAAA	60.982	57.895	0.00	0.00	0.00	1.94
1119	1139	1.948721	GCCCCGCATCCCTCAAAAAG	61.949	60.000	0.00	0.00	0.00	2.27
1120	1140	0.323360	CCCCGCATCCCTCAAAAAGA	60.323	55.000	0.00	0.00	0.00	2.52
1121	1141	0.811281	CCCGCATCCCTCAAAAAGAC	59.189	55.000	0.00	0.00	0.00	3.01
1124	1144	0.811281	GCATCCCTCAAAAAGACCCG	59.189	55.000	0.00	0.00	0.00	5.28
1135	1159	0.830866	AAAGACCCGTCGGTTCCTCT	60.831	55.000	11.06	1.54	44.88	3.69
1148	1190	3.174779	GGTTCCTCTTCCTCCTGTTACT	58.825	50.000	0.00	0.00	0.00	2.24
1163	1226	5.103643	TCCTGTTACTCTCCTAGCCAAGATA	60.104	44.000	0.00	0.00	0.00	1.98
1213	1285	0.822164	GGTCGCACCTGGTATGTAGT	59.178	55.000	0.00	0.00	34.73	2.73
1453	1709	2.173519	CATGGGTGGACAAAATGAGCT	58.826	47.619	0.00	0.00	0.00	4.09
1455	1711	1.425066	TGGGTGGACAAAATGAGCTCT	59.575	47.619	16.19	0.00	0.00	4.09
1573	2001	4.462483	TGGTTTATGAGGCTGACCAATTTC	59.538	41.667	0.00	0.00	37.44	2.17
1657	2085	1.986757	GTGGAGAGGAGGCTGCTCA	60.987	63.158	33.24	14.62	37.29	4.26
1854	2282	1.199097	CAGTTTGTATGCACGGAACCC	59.801	52.381	0.00	0.00	0.00	4.11
1858	2286	1.855295	TGTATGCACGGAACCCTCTA	58.145	50.000	0.00	0.00	0.00	2.43
1873	2304	7.878127	CGGAACCCTCTAAATATTCATACATGT	59.122	37.037	2.69	2.69	0.00	3.21
2174	2639	4.903045	TGTTGCCTTATAGTATAGGGGC	57.097	45.455	17.56	19.15	39.93	5.80
2226	2691	5.982890	AATGTTTAAAGGTCCATCCAGTG	57.017	39.130	0.00	0.00	39.02	3.66
2280	2759	8.642908	AGTTTGTAAGGTGTTTCTTAAATTGC	57.357	30.769	0.00	0.00	31.85	3.56
2296	2777	3.508744	ATTGCTTTTCCGCTACCAATG	57.491	42.857	0.00	0.00	0.00	2.82
2505	2988	7.761249	AGGTTTCTGAATGTTTTGAGTTTTGAG	59.239	33.333	0.00	0.00	0.00	3.02
2592	3075	6.239204	GCCAACCCTGTAAGTATCAAAAGTTT	60.239	38.462	0.00	0.00	0.00	2.66
2696	3179	3.191162	TCTGCACTGTTCCATTAATGCAC	59.809	43.478	10.11	9.12	38.11	4.57
2697	3180	2.889678	TGCACTGTTCCATTAATGCACA	59.110	40.909	10.11	12.87	38.11	4.57
2698	3181	3.244976	GCACTGTTCCATTAATGCACAC	58.755	45.455	10.11	6.46	33.27	3.82
2699	3182	3.305267	GCACTGTTCCATTAATGCACACA	60.305	43.478	10.11	10.32	33.27	3.72
2700	3183	4.229096	CACTGTTCCATTAATGCACACAC	58.771	43.478	10.11	2.57	0.00	3.82
2701	3184	3.888323	ACTGTTCCATTAATGCACACACA	59.112	39.130	10.11	6.58	0.00	3.72
2702	3185	4.340666	ACTGTTCCATTAATGCACACACAA	59.659	37.500	10.11	0.00	0.00	3.33
2703	3186	5.163468	ACTGTTCCATTAATGCACACACAAA	60.163	36.000	10.11	0.00	0.00	2.83
2705	3188	5.752472	TGTTCCATTAATGCACACACAAAAG	59.248	36.000	10.11	0.00	0.00	2.27
2706	3189	5.781210	TCCATTAATGCACACACAAAAGA	57.219	34.783	10.11	0.00	0.00	2.52
2707	3190	5.771469	TCCATTAATGCACACACAAAAGAG	58.229	37.500	10.11	0.00	0.00	2.85
2708	3191	4.386652	CCATTAATGCACACACAAAAGAGC	59.613	41.667	10.11	0.00	0.00	4.09
2709	3192	4.916983	TTAATGCACACACAAAAGAGCT	57.083	36.364	0.00	0.00	0.00	4.09
2710	3193	2.787601	ATGCACACACAAAAGAGCTG	57.212	45.000	0.00	0.00	0.00	4.24
2711	3194	0.101040	TGCACACACAAAAGAGCTGC	59.899	50.000	0.00	0.00	0.00	5.25
2712	3195	0.101040	GCACACACAAAAGAGCTGCA	59.899	50.000	1.02	0.00	0.00	4.41
2713	3196	1.469595	GCACACACAAAAGAGCTGCAA	60.470	47.619	1.02	0.00	0.00	4.08
2714	3197	2.456989	CACACACAAAAGAGCTGCAAG	58.543	47.619	1.02	0.00	0.00	4.01
2715	3198	2.094675	ACACACAAAAGAGCTGCAAGT	58.905	42.857	1.02	0.00	35.30	3.16
2716	3199	2.493278	ACACACAAAAGAGCTGCAAGTT	59.507	40.909	1.02	0.00	35.30	2.66
2717	3200	2.855963	CACACAAAAGAGCTGCAAGTTG	59.144	45.455	1.02	0.00	35.30	3.16
2718	3201	2.754552	ACACAAAAGAGCTGCAAGTTGA	59.245	40.909	7.16	0.00	35.30	3.18
2719	3202	3.193267	ACACAAAAGAGCTGCAAGTTGAA	59.807	39.130	7.16	0.00	35.30	2.69
2720	3203	4.142093	ACACAAAAGAGCTGCAAGTTGAAT	60.142	37.500	7.16	0.00	35.30	2.57
2721	3204	4.208460	CACAAAAGAGCTGCAAGTTGAATG	59.792	41.667	7.16	0.00	35.30	2.67
2722	3205	4.098349	ACAAAAGAGCTGCAAGTTGAATGA	59.902	37.500	7.16	0.00	35.30	2.57
2723	3206	3.911661	AAGAGCTGCAAGTTGAATGAC	57.088	42.857	7.16	0.00	35.30	3.06
2724	3207	3.137446	AGAGCTGCAAGTTGAATGACT	57.863	42.857	7.16	0.00	35.30	3.41
2761	3524	3.604582	AGGCAGACAAACTAGATTCAGC	58.395	45.455	0.00	0.00	0.00	4.26

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
21	22	1.523154	GGCTGTTTGGGTGCAATCGA	61.523	55.000	0.00	0.00	0.00	3.59
26	27	3.215568	CACGGCTGTTTGGGTGCA	61.216	61.111	0.00	0.00	0.00	4.57
94	95	8.885494	TGATACATGTTCATATCATCGTTCAA	57.115	30.769	2.30	0.00	33.78	2.69
102	103	5.106987	GCACGCATGATACATGTTCATATCA	60.107	40.000	17.49	14.45	41.00	2.15
103	104	5.106987	TGCACGCATGATACATGTTCATATC	60.107	40.000	17.49	10.14	32.63	1.63
166	168	2.257391	TATTTTGGGACGGAGGGAGA	57.743	50.000	0.00	0.00	0.00	3.71
176	178	6.916360	AAGCTTGAGACAATTATTTTGGGA	57.084	33.333	0.00	0.00	0.00	4.37
189	191	9.857957	AGTATAAAGTTGTACTAAGCTTGAGAC	57.142	33.333	9.86	4.39	34.01	3.36
710	714	8.512138	GCTGCCCAATTTACTCGTTTATATATT	58.488	33.333	0.00	0.00	0.00	1.28
711	715	7.148474	CGCTGCCCAATTTACTCGTTTATATAT	60.148	37.037	0.00	0.00	0.00	0.86
712	716	6.146510	CGCTGCCCAATTTACTCGTTTATATA	59.853	38.462	0.00	0.00	0.00	0.86
829	835	0.035439	TGGGGCGAGGAAGTGATTTC	60.035	55.000	0.00	0.00	34.93	2.17
974	991	1.429825	CGAGCTAGACTGGACACGG	59.570	63.158	0.00	0.00	0.00	4.94
1121	1141	1.946475	GAGGAAGAGGAACCGACGGG	61.946	65.000	20.00	0.00	40.11	5.28
1124	1144	0.533032	CAGGAGGAAGAGGAACCGAC	59.467	60.000	0.00	0.00	0.00	4.79
1135	1159	3.627747	GGCTAGGAGAGTAACAGGAGGAA	60.628	52.174	0.00	0.00	0.00	3.36
1148	1190	4.470602	TCGAACATATCTTGGCTAGGAGA	58.529	43.478	0.00	0.00	0.00	3.71
1163	1226	2.941064	CACAGAGGATTGCATCGAACAT	59.059	45.455	0.00	0.00	0.00	2.71
1213	1285	6.145534	GCGCTGCAAGTTCTATGTACAATATA	59.854	38.462	0.00	0.00	35.30	0.86
1453	1709	2.130426	GCTCATCCGGCTCCAGAGA	61.130	63.158	0.00	0.00	0.00	3.10
1455	1711	2.042537	AGCTCATCCGGCTCCAGA	60.043	61.111	0.00	0.00	34.70	3.86
1544	1970	4.947388	GGTCAGCCTCATAAACCAATTACA	59.053	41.667	0.00	0.00	0.00	2.41
1633	2061	0.043940	AGCCTCCTCTCCACTGGATT	59.956	55.000	0.00	0.00	0.00	3.01
1657	2085	0.036732	TTCTGCGCATTCACCTTCCT	59.963	50.000	12.24	0.00	0.00	3.36
2174	2639	8.579682	CTTGAGAAACAAGGGTTTATTTCTTG	57.420	34.615	0.00	0.00	46.84	3.02
2217	2682	6.018751	CAGTCATAATAACGAACACTGGATGG	60.019	42.308	0.00	0.00	0.00	3.51
2226	2691	9.750882	GTTCCTTAAACAGTCATAATAACGAAC	57.249	33.333	0.00	0.00	37.82	3.95
2279	2758	1.810151	TGACATTGGTAGCGGAAAAGC	59.190	47.619	0.00	0.00	37.41	3.51
2280	2759	4.701956	AATGACATTGGTAGCGGAAAAG	57.298	40.909	0.00	0.00	0.00	2.27
2296	2777	3.767673	GGGTTCCCCTTTTAGGAAATGAC	59.232	47.826	0.00	0.00	44.84	3.06
2505	2988	6.283694	TGAAGCCTGACACTCATACATTATC	58.716	40.000	0.00	0.00	0.00	1.75
2696	3179	2.855963	CAACTTGCAGCTCTTTTGTGTG	59.144	45.455	0.00	0.00	0.00	3.82
2697	3180	2.754552	TCAACTTGCAGCTCTTTTGTGT	59.245	40.909	0.00	0.00	0.00	3.72
2698	3181	3.425577	TCAACTTGCAGCTCTTTTGTG	57.574	42.857	0.00	0.00	0.00	3.33
2699	3182	4.098349	TCATTCAACTTGCAGCTCTTTTGT	59.902	37.500	0.00	0.00	0.00	2.83
2700	3183	4.443394	GTCATTCAACTTGCAGCTCTTTTG	59.557	41.667	0.00	0.00	0.00	2.44
2701	3184	4.340381	AGTCATTCAACTTGCAGCTCTTTT	59.660	37.500	0.00	0.00	0.00	2.27
2702	3185	3.887716	AGTCATTCAACTTGCAGCTCTTT	59.112	39.130	0.00	0.00	0.00	2.52
2703	3186	3.484407	AGTCATTCAACTTGCAGCTCTT	58.516	40.909	0.00	0.00	0.00	2.85
2705	3188	3.501445	AGAAGTCATTCAACTTGCAGCTC	59.499	43.478	0.00	0.00	39.55	4.09
2706	3189	3.484407	AGAAGTCATTCAACTTGCAGCT	58.516	40.909	0.00	0.00	39.55	4.24
2707	3190	3.365767	GGAGAAGTCATTCAACTTGCAGC	60.366	47.826	0.00	0.00	39.55	5.25
2708	3191	3.817084	TGGAGAAGTCATTCAACTTGCAG	59.183	43.478	0.00	0.00	39.55	4.41
2709	3192	3.817084	CTGGAGAAGTCATTCAACTTGCA	59.183	43.478	0.00	0.00	39.55	4.08
2710	3193	4.067896	TCTGGAGAAGTCATTCAACTTGC	58.932	43.478	0.00	0.00	39.55	4.01
2711	3194	5.123502	CCATCTGGAGAAGTCATTCAACTTG	59.876	44.000	0.00	0.00	37.17	3.16
2712	3195	5.251764	CCATCTGGAGAAGTCATTCAACTT	58.748	41.667	0.00	0.00	38.71	2.66
2713	3196	4.841422	CCATCTGGAGAAGTCATTCAACT	58.159	43.478	0.00	0.00	37.94	3.16
2714	3197	3.376546	GCCATCTGGAGAAGTCATTCAAC	59.623	47.826	0.00	0.00	37.39	3.18
2715	3198	3.009363	TGCCATCTGGAGAAGTCATTCAA	59.991	43.478	0.00	0.00	37.39	2.69
2716	3199	2.573009	TGCCATCTGGAGAAGTCATTCA	59.427	45.455	0.00	0.00	37.39	2.57
2717	3200	3.204526	CTGCCATCTGGAGAAGTCATTC	58.795	50.000	0.00	0.00	37.39	2.67
2718	3201	2.575279	ACTGCCATCTGGAGAAGTCATT	59.425	45.455	0.00	0.00	37.39	2.57
2719	3202	2.194859	ACTGCCATCTGGAGAAGTCAT	58.805	47.619	0.00	0.00	37.39	3.06
2720	3203	1.649321	ACTGCCATCTGGAGAAGTCA	58.351	50.000	0.00	0.00	37.39	3.41
2721	3204	2.102252	CCTACTGCCATCTGGAGAAGTC	59.898	54.545	0.00	0.00	37.39	3.01
2722	3205	2.114616	CCTACTGCCATCTGGAGAAGT	58.885	52.381	0.00	3.03	37.39	3.01
2723	3206	1.202627	GCCTACTGCCATCTGGAGAAG	60.203	57.143	0.00	0.00	37.39	2.85
2724	3207	0.833287	GCCTACTGCCATCTGGAGAA	59.167	55.000	0.00	0.00	37.39	2.87
2761	3524	6.378710	TTCATATGGTCTTCTCACTACTCG	57.621	41.667	2.13	0.00	0.00	4.18
2798	3561	5.598417	TCTCTATGTAAGCATGCACCTTAGA	59.402	40.000	21.98	19.17	36.58	2.10
2801	3564	4.760530	TCTCTATGTAAGCATGCACCTT	57.239	40.909	21.98	8.25	36.58	3.50

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.