AutoCloner

Multiple sequence alignment - TraesCS3A01G341500

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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	TraesCS3A01G341500	chr3A	100.000	3579	0	0	1	3579	588832085	588835663	0.000000e+00	6610.0
1	TraesCS3A01G341500	chr3A	93.239	636	35	5	1	631	674987790	674987158	0.000000e+00	929.0
2	TraesCS3A01G341500	chr3A	92.552	631	39	5	1	625	674986101	674985473	0.000000e+00	898.0
3	TraesCS3A01G341500	chr3D	96.127	2866	95	7	715	3579	447128935	447131785	0.000000e+00	4663.0
4	TraesCS3A01G341500	chr3D	96.471	85	3	0	624	708	447128515	447128599	1.340000e-29	141.0
5	TraesCS3A01G341500	chr3B	98.028	1521	30	0	2059	3579	586516704	586518224	0.000000e+00	2643.0
6	TraesCS3A01G341500	chr3B	95.772	1301	43	6	770	2068	586515243	586516533	0.000000e+00	2087.0
7	TraesCS3A01G341500	chr3B	96.078	51	1	1	713	763	586515166	586515215	8.240000e-12	82.4
8	TraesCS3A01G341500	chr7B	92.936	637	36	6	1	631	311714203	311713570	0.000000e+00	918.0
9	TraesCS3A01G341500	chr7B	92.857	630	37	5	1	624	311712513	311711886	0.000000e+00	907.0
10	TraesCS3A01G341500	chr5A	92.465	637	39	6	1	631	693421728	693421095	0.000000e+00	902.0
11	TraesCS3A01G341500	chr5A	92.540	630	40	4	1	625	693420037	693419410	0.000000e+00	896.0
12	TraesCS3A01G341500	chr2A	92.468	624	39	7	1	618	734695529	734696150	0.000000e+00	885.0
13	TraesCS3A01G341500	chr2A	91.223	638	45	10	1	631	734693839	734694472	0.000000e+00	857.0
14	TraesCS3A01G341500	chr4D	91.366	637	45	8	1	631	216709228	216708596	0.000000e+00	863.0
15	TraesCS3A01G341500	chr6B	91.636	538	36	2	3050	3579	707362546	707362010	0.000000e+00	736.0

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	TraesCS3A01G341500	chr3A	588832085	588835663	3578	False	6610.000000	6610	100.0000	1	3579	1	chr3A.!!$F1	3578
1	TraesCS3A01G341500	chr3A	674985473	674987790	2317	True	913.500000	929	92.8955	1	631	2	chr3A.!!$R1	630
2	TraesCS3A01G341500	chr3D	447128515	447131785	3270	False	2402.000000	4663	96.2990	624	3579	2	chr3D.!!$F1	2955
3	TraesCS3A01G341500	chr3B	586515166	586518224	3058	False	1604.133333	2643	96.6260	713	3579	3	chr3B.!!$F1	2866
4	TraesCS3A01G341500	chr7B	311711886	311714203	2317	True	912.500000	918	92.8965	1	631	2	chr7B.!!$R1	630
5	TraesCS3A01G341500	chr5A	693419410	693421728	2318	True	899.000000	902	92.5025	1	631	2	chr5A.!!$R1	630
6	TraesCS3A01G341500	chr2A	734693839	734696150	2311	False	871.000000	885	91.8455	1	631	2	chr2A.!!$F1	630
7	TraesCS3A01G341500	chr4D	216708596	216709228	632	True	863.000000	863	91.3660	1	631	1	chr4D.!!$R1	630
8	TraesCS3A01G341500	chr6B	707362010	707362546	536	True	736.000000	736	91.6360	3050	3579	1	chr6B.!!$R1	529

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
454	461	0.248458	AAACTGTTTTGCGCGTGAGG	60.248	50.0	8.43	0.00	0.00	3.86	F
1356	1843	0.251354	TCATTGAGGAGACTGGCAGC	59.749	55.0	15.89	7.65	44.43	5.25	F
2223	3441	2.159128	ACAGAGAAGATGCTGATCACCG	60.159	50.0	0.00	0.00	36.07	4.94	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
1569	2105	0.038251	TTCTAGTGTGCTGTGCGGAG	60.038	55.0	0.00	4.63	R
2512	3730	0.179029	CACCACCGAAACTTGGACCT	60.179	55.0	36.28	3.85	R
3044	4287	1.609626	AGGTAGTAGAGGAGGCAGGA	58.390	55.0	0.00	3.86	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
40	41	1.207089	CACGCCCACCTGAAGAGATAA	59.793	52.381	0.00	0.00	0.00	1.75
125	126	1.202817	ACCACAAACGGACCAACAAAC	59.797	47.619	0.00	0.00	0.00	2.93
375	380	8.707796	ATAGAGATGTATTTTCGAGGGTAGAA	57.292	34.615	0.00	0.00	0.00	2.10
378	383	7.124448	AGAGATGTATTTTCGAGGGTAGAAACT	59.876	37.037	0.00	0.00	37.33	2.66
392	397	7.222161	AGGGTAGAAACTCGTATCAAGTTTTT	58.778	34.615	3.07	0.83	44.72	1.94
397	402	6.766467	AGAAACTCGTATCAAGTTTTTGAGGT	59.234	34.615	3.07	0.00	45.89	3.85
399	404	8.441312	AAACTCGTATCAAGTTTTTGAGGTAA	57.559	30.769	0.00	0.00	45.89	2.85
429	434	3.904136	ACCTCTTTGTTGCGATTTCTG	57.096	42.857	0.00	0.00	0.00	3.02
430	435	2.030805	ACCTCTTTGTTGCGATTTCTGC	60.031	45.455	0.00	0.00	0.00	4.26
431	436	2.030893	CCTCTTTGTTGCGATTTCTGCA	60.031	45.455	0.00	0.00	41.38	4.41
438	445	2.704725	TGCGATTTCTGCAAGGAAAC	57.295	45.000	3.47	0.00	33.17	2.78
454	461	0.248458	AAACTGTTTTGCGCGTGAGG	60.248	50.000	8.43	0.00	0.00	3.86
455	462	1.373590	AACTGTTTTGCGCGTGAGGT	61.374	50.000	8.43	0.00	0.00	3.85
456	463	1.369209	CTGTTTTGCGCGTGAGGTG	60.369	57.895	8.43	0.00	0.00	4.00
464	471	4.409218	GCGTGAGGTGCCGTCGTA	62.409	66.667	0.00	0.00	0.00	3.43
465	472	2.503375	CGTGAGGTGCCGTCGTAC	60.503	66.667	0.00	0.00	0.00	3.67
472	479	0.389426	GGTGCCGTCGTACAGATTGT	60.389	55.000	0.00	0.00	0.00	2.71
475	482	2.063266	TGCCGTCGTACAGATTGTTTC	58.937	47.619	0.00	0.00	0.00	2.78
486	493	3.243873	ACAGATTGTTTCTCTCGTGCTGA	60.244	43.478	0.00	0.00	29.93	4.26
545	552	2.202756	GCGGGCGAGAGGTTACTG	60.203	66.667	0.00	0.00	0.00	2.74
548	555	1.381928	CGGGCGAGAGGTTACTGCTA	61.382	60.000	0.00	0.00	0.00	3.49
591	598	4.025401	CGGGCCGCAACAACAGAC	62.025	66.667	15.42	0.00	0.00	3.51
618	625	2.428622	CCAACGGGGTTCGGTCTT	59.571	61.111	0.00	0.00	44.45	3.01
679	731	2.258726	GGCCACACGGGTCTTTCAC	61.259	63.158	0.00	0.00	38.65	3.18
711	763	8.618677	GCCCCTTATTCAACTTATTGTTAGTAC	58.381	37.037	0.00	0.00	37.07	2.73
861	1263	2.554032	CCACAGGGAAGCAACAAAGTAG	59.446	50.000	0.00	0.00	35.59	2.57
931	1334	1.070604	AGGGTGCCTATGGGATGATG	58.929	55.000	0.00	0.00	33.58	3.07
932	1335	1.067295	GGGTGCCTATGGGATGATGA	58.933	55.000	0.00	0.00	33.58	2.92
933	1336	1.637553	GGGTGCCTATGGGATGATGAT	59.362	52.381	0.00	0.00	33.58	2.45
1137	1540	1.416049	CACCAAGATTGACGCGTCG	59.584	57.895	31.88	18.94	0.00	5.12
1188	1591	0.748367	TCTCGGTCTCGGTGGATGAG	60.748	60.000	0.00	0.00	36.95	2.90
1193	1596	0.531532	GTCTCGGTGGATGAGCATGG	60.532	60.000	0.00	0.00	33.41	3.66
1284	1687	1.970114	CCAGGGAGCTGCAGTTGTG	60.970	63.158	16.64	6.40	0.00	3.33
1308	1795	5.934625	GCAGTTGAAGGAGTATCTTGAGAAA	59.065	40.000	0.00	0.00	33.73	2.52
1311	1798	8.663911	CAGTTGAAGGAGTATCTTGAGAAATTC	58.336	37.037	0.00	0.00	33.73	2.17
1314	1801	4.698575	AGGAGTATCTTGAGAAATTCGCC	58.301	43.478	0.00	0.00	33.73	5.54
1356	1843	0.251354	TCATTGAGGAGACTGGCAGC	59.749	55.000	15.89	7.65	44.43	5.25
1532	2067	6.208007	TGAGATGCTGATCAAAACACTTTCAT	59.792	34.615	0.00	0.00	0.00	2.57
1569	2105	7.378181	AGTCAACACATACATTTTCCAAATCC	58.622	34.615	0.00	0.00	0.00	3.01
1614	2153	8.856153	TGGCAGTCAGAACTAAAATAACAATA	57.144	30.769	0.00	0.00	33.25	1.90
1615	2154	9.290988	TGGCAGTCAGAACTAAAATAACAATAA	57.709	29.630	0.00	0.00	33.25	1.40
1950	2984	2.397597	TGGTAGAGTATGCTGCCATGA	58.602	47.619	0.00	0.00	44.25	3.07
1951	2985	2.974794	TGGTAGAGTATGCTGCCATGAT	59.025	45.455	0.00	0.00	44.25	2.45
2223	3441	2.159128	ACAGAGAAGATGCTGATCACCG	60.159	50.000	0.00	0.00	36.07	4.94
2512	3730	0.766131	TTGGCGAAACCCTCTTACCA	59.234	50.000	0.00	0.00	37.83	3.25
2769	3987	0.663269	GCCACTAACAAAAGCGTGCC	60.663	55.000	0.00	0.00	0.00	5.01
3044	4287	1.140452	CATGCACCAGCTCCTACATCT	59.860	52.381	0.00	0.00	42.74	2.90
3117	4360	1.431496	CATGTCAGTCACACATGCGA	58.569	50.000	0.00	0.00	43.48	5.10
3419	4670	2.620251	TGGCATACATGTCTACCAGC	57.380	50.000	0.00	0.00	32.56	4.85
3468	4719	4.193334	CGCGAGCCAGTCCGATCA	62.193	66.667	0.00	0.00	0.00	2.92
3509	4760	1.059584	TCCTCCCAACCTTCAGTGCA	61.060	55.000	0.00	0.00	0.00	4.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
40	41	3.389002	ACAAGCCTCCTGCAAATTCTTTT	59.611	39.130	0.00	0.00	44.83	2.27
190	191	5.957168	AGGTACCTTCTAAAACTAGGACTCC	59.043	44.000	9.21	0.00	33.21	3.85
366	371	5.579564	ACTTGATACGAGTTTCTACCCTC	57.420	43.478	0.00	0.00	0.00	4.30
375	380	7.713942	AGTTACCTCAAAAACTTGATACGAGTT	59.286	33.333	0.00	0.00	38.92	3.01
378	383	8.441312	AAAGTTACCTCAAAAACTTGATACGA	57.559	30.769	1.56	0.00	43.35	3.43
397	402	7.066043	TCGCAACAAAGAGGTTTTCTAAAGTTA	59.934	33.333	0.00	0.00	34.14	2.24
399	404	5.355910	TCGCAACAAAGAGGTTTTCTAAAGT	59.644	36.000	0.00	0.00	34.14	2.66
415	420	1.952990	TCCTTGCAGAAATCGCAACAA	59.047	42.857	8.03	0.00	44.13	2.83
429	434	0.576798	GCGCAAAACAGTTTCCTTGC	59.423	50.000	0.30	10.12	40.58	4.01
430	435	0.845768	CGCGCAAAACAGTTTCCTTG	59.154	50.000	8.75	0.00	0.00	3.61
431	436	0.454196	ACGCGCAAAACAGTTTCCTT	59.546	45.000	5.73	0.00	0.00	3.36
432	437	0.248458	CACGCGCAAAACAGTTTCCT	60.248	50.000	5.73	0.00	0.00	3.36
438	445	1.369209	CACCTCACGCGCAAAACAG	60.369	57.895	5.73	0.00	0.00	3.16
454	461	1.425412	AACAATCTGTACGACGGCAC	58.575	50.000	0.00	0.00	0.00	5.01
455	462	2.063266	GAAACAATCTGTACGACGGCA	58.937	47.619	0.00	0.00	0.00	5.69
456	463	2.334838	AGAAACAATCTGTACGACGGC	58.665	47.619	0.00	0.00	36.88	5.68
458	465	3.538782	CGAGAGAAACAATCTGTACGACG	59.461	47.826	0.00	0.00	38.96	5.12
459	466	4.321217	CACGAGAGAAACAATCTGTACGAC	59.679	45.833	0.00	0.00	38.96	4.34
460	467	4.473199	CACGAGAGAAACAATCTGTACGA	58.527	43.478	0.00	0.00	38.96	3.43
461	468	3.059570	GCACGAGAGAAACAATCTGTACG	59.940	47.826	0.00	0.00	38.96	3.67
462	469	4.090642	CAGCACGAGAGAAACAATCTGTAC	59.909	45.833	0.00	0.00	38.96	2.90
463	470	4.022329	TCAGCACGAGAGAAACAATCTGTA	60.022	41.667	0.00	0.00	38.96	2.74
464	471	3.062763	CAGCACGAGAGAAACAATCTGT	58.937	45.455	0.00	0.00	38.96	3.41
465	472	3.320626	TCAGCACGAGAGAAACAATCTG	58.679	45.455	0.00	0.00	38.96	2.90
472	479	1.080501	CGGCTCAGCACGAGAGAAA	60.081	57.895	0.00	0.00	45.45	2.52
475	482	4.426112	TGCGGCTCAGCACGAGAG	62.426	66.667	11.22	0.00	45.45	3.20
486	493	3.443588	GGTTTGAACCTTGCGGCT	58.556	55.556	5.66	0.00	45.75	5.52
527	534	2.678934	AGTAACCTCTCGCCCGCA	60.679	61.111	0.00	0.00	0.00	5.69
545	552	1.402984	CGACACTCCACCTTCAGTAGC	60.403	57.143	0.00	0.00	0.00	3.58
548	555	0.389391	CACGACACTCCACCTTCAGT	59.611	55.000	0.00	0.00	0.00	3.41
591	598	2.186903	CCCGTTGGTGAGATCCGG	59.813	66.667	0.00	0.00	38.39	5.14
611	618	3.370103	GGAACCACCATGATAAAGACCGA	60.370	47.826	0.00	0.00	38.79	4.69
618	625	7.505585	GGAATAATGAAGGAACCACCATGATAA	59.494	37.037	0.00	0.00	42.04	1.75
679	731	2.450476	AGTTGAATAAGGGGCAGCAAG	58.550	47.619	0.00	0.00	0.00	4.01
861	1263	7.681903	ACGATAATAAGGATTTGTTTCGTGTC	58.318	34.615	0.00	0.00	34.03	3.67
931	1334	4.113354	GGGATACGATGCGGAGATTTATC	58.887	47.826	0.00	0.00	37.60	1.75
932	1335	3.118738	GGGGATACGATGCGGAGATTTAT	60.119	47.826	0.00	0.00	37.60	1.40
933	1336	2.232941	GGGGATACGATGCGGAGATTTA	59.767	50.000	0.00	0.00	37.60	1.40
988	1391	5.077134	AGCTTTTTCATTTGTATGAGGGC	57.923	39.130	0.00	0.00	41.60	5.19
1137	1540	2.611224	CCAGCTTGCATTTGAGTTTCCC	60.611	50.000	0.00	0.00	0.00	3.97
1188	1591	4.746309	TGCTGGGCCAGACCATGC	62.746	66.667	37.07	21.39	40.36	4.06
1193	1596	3.341202	ATCTGCTGCTGGGCCAGAC	62.341	63.158	37.07	26.15	34.77	3.51
1284	1687	5.078411	TCTCAAGATACTCCTTCAACTGC	57.922	43.478	0.00	0.00	0.00	4.40
1288	1775	6.313905	GCGAATTTCTCAAGATACTCCTTCAA	59.686	38.462	0.00	0.00	0.00	2.69
1308	1795	0.678048	GCTCCTCACTTTGGGCGAAT	60.678	55.000	0.00	0.00	0.00	3.34
1311	1798	0.962356	AATGCTCCTCACTTTGGGCG	60.962	55.000	0.00	0.00	0.00	6.13
1314	1801	3.063510	TCTGAATGCTCCTCACTTTGG	57.936	47.619	0.00	0.00	0.00	3.28
1532	2067	1.542915	GTGTTGACTACGCTCCTACCA	59.457	52.381	0.00	0.00	34.37	3.25
1569	2105	0.038251	TTCTAGTGTGCTGTGCGGAG	60.038	55.000	0.00	0.00	0.00	4.63
1614	2153	7.447853	ACAAAACAATACCAATTTCCATGCATT	59.552	29.630	0.00	0.00	0.00	3.56
1615	2154	6.941436	ACAAAACAATACCAATTTCCATGCAT	59.059	30.769	0.00	0.00	0.00	3.96
1616	2155	6.294473	ACAAAACAATACCAATTTCCATGCA	58.706	32.000	0.00	0.00	0.00	3.96
1620	2159	6.574350	ACGAACAAAACAATACCAATTTCCA	58.426	32.000	0.00	0.00	0.00	3.53
1625	2164	5.676532	TCGACGAACAAAACAATACCAAT	57.323	34.783	0.00	0.00	0.00	3.16
1690	2229	5.663456	TGTTAGGTCACGTACTGAACTTTT	58.337	37.500	15.16	0.00	45.54	2.27
1746	2285	8.154203	TGGATAGATTTGCCGATAAAGATACAA	58.846	33.333	0.00	0.00	0.00	2.41
1818	2357	5.132502	CCTACCAATGGATCAAGCATGTTA	58.867	41.667	6.16	0.00	0.00	2.41
1837	2376	7.439655	CCATTCTCTGTACATTCTAAAGCCTAC	59.560	40.741	0.00	0.00	0.00	3.18
1907	2469	3.004106	AGCATGCTGACTTTCACTTGTTC	59.996	43.478	21.98	0.00	0.00	3.18
2017	3053	7.926674	TTGAAGCTCATCTTAATTCATGTGA	57.073	32.000	0.00	0.00	34.56	3.58
2223	3441	1.483415	TCACCGGCCTGGAATTACTAC	59.517	52.381	18.74	0.00	42.00	2.73
2512	3730	0.179029	CACCACCGAAACTTGGACCT	60.179	55.000	0.00	0.00	36.28	3.85
2601	3819	4.829064	TTTTGTTACAAGCTAGCACTGG	57.171	40.909	18.83	5.46	0.00	4.00
2769	3987	3.862124	CGAGAGCGGAACAGTTGG	58.138	61.111	0.00	0.00	0.00	3.77
3044	4287	1.609626	AGGTAGTAGAGGAGGCAGGA	58.390	55.000	0.00	0.00	0.00	3.86
3419	4670	1.858707	CGTGCGTGCTTGTAATGCG	60.859	57.895	0.00	0.00	40.34	4.73
3468	4719	3.181445	ACGGTGCATGGGTACATTATCAT	60.181	43.478	0.00	0.00	34.35	2.45
3509	4760	3.429141	GCATGTGCGCAGACTGCT	61.429	61.111	24.36	2.95	42.25	4.24

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.