AutoCloner

Multiple sequence alignment - TraesCS5A01G093100

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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	TraesCS5A01G093100	chr5A	100.000	4407	0	0	1	4407	129595848	129600254	0.000000e+00	8139
1	TraesCS5A01G093100	chr5A	98.670	827	11	0	1	827	44092616	44093442	0.000000e+00	1467
2	TraesCS5A01G093100	chr5A	93.125	160	9	1	1	158	33168698	33168857	2.650000e-57	233
3	TraesCS5A01G093100	chr5D	95.879	2475	63	18	1969	4407	119482884	119485355	0.000000e+00	3969
4	TraesCS5A01G093100	chr5D	95.478	1150	47	5	824	1971	119481648	119482794	0.000000e+00	1831
5	TraesCS5A01G093100	chr5B	95.264	1858	64	12	1969	3824	132284253	132286088	0.000000e+00	2922
6	TraesCS5A01G093100	chr5B	93.777	1141	60	8	824	1959	132282256	132283390	0.000000e+00	1703
7	TraesCS5A01G093100	chr5B	98.585	636	7	2	3772	4407	132286091	132286724	0.000000e+00	1123
8	TraesCS5A01G093100	chr5B	94.653	692	33	4	824	1513	132280852	132281541	0.000000e+00	1070
9	TraesCS5A01G093100	chr5B	94.509	692	34	4	824	1513	132279463	132280152	0.000000e+00	1064
10	TraesCS5A01G093100	chr5B	94.574	129	7	0	164	292	513613933	513613805	2.690000e-47	200
11	TraesCS5A01G093100	chr4B	99.033	827	8	0	1	827	251997530	251998356	0.000000e+00	1483
12	TraesCS5A01G093100	chr4B	98.088	837	16	0	1	837	395244064	395244900	0.000000e+00	1458
13	TraesCS5A01G093100	chr4B	94.030	134	8	0	164	297	564154017	564154150	2.080000e-48	204
14	TraesCS5A01G093100	chr2A	98.620	797	11	0	31	827	442717682	442716886	0.000000e+00	1411
15	TraesCS5A01G093100	chr2A	98.925	558	6	0	270	827	442716885	442716328	0.000000e+00	998
16	TraesCS5A01G093100	chr2A	99.507	203	1	0	1	203	442717885	442717683	1.940000e-98	370
17	TraesCS5A01G093100	chr7A	96.372	827	30	0	1	827	16637414	16636588	0.000000e+00	1362
18	TraesCS5A01G093100	chr7A	96.627	593	19	1	236	827	16636587	16635995	0.000000e+00	983
19	TraesCS5A01G093100	chr3A	94.786	537	28	0	291	827	27583464	27584000	0.000000e+00	837
20	TraesCS5A01G093100	chr3A	84.074	270	34	5	2760	3023	25031877	25032143	7.320000e-63	252
21	TraesCS5A01G093100	chr7B	94.118	544	32	0	291	834	226424398	226424941	0.000000e+00	828
22	TraesCS5A01G093100	chr7B	93.125	160	9	1	1	158	226421507	226421666	2.650000e-57	233
23	TraesCS5A01G093100	chr4D	89.455	275	26	2	2749	3023	27569008	27569279	1.170000e-90	344
24	TraesCS5A01G093100	chr4A	89.091	275	27	3	2749	3023	575700939	575700668	5.460000e-89	339
25	TraesCS5A01G093100	chr4A	94.574	129	7	0	164	292	11702213	11702341	2.690000e-47	200
26	TraesCS5A01G093100	chr2D	86.296	270	33	3	2754	3023	500812024	500811759	1.550000e-74	291
27	TraesCS5A01G093100	chr3B	93.168	161	9	1	1	159	12308309	12308469	7.370000e-58	235
28	TraesCS5A01G093100	chr3B	95.349	129	6	0	164	292	669726872	669726744	5.780000e-49	206

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	TraesCS5A01G093100	chr5A	129595848	129600254	4406	False	8139.000000	8139	100.000000	1	4407	1	chr5A.!!$F3	4406
1	TraesCS5A01G093100	chr5A	44092616	44093442	826	False	1467.000000	1467	98.670000	1	827	1	chr5A.!!$F2	826
2	TraesCS5A01G093100	chr5D	119481648	119485355	3707	False	2900.000000	3969	95.678500	824	4407	2	chr5D.!!$F1	3583
3	TraesCS5A01G093100	chr5B	132279463	132286724	7261	False	1576.400000	2922	95.357600	824	4407	5	chr5B.!!$F1	3583
4	TraesCS5A01G093100	chr4B	251997530	251998356	826	False	1483.000000	1483	99.033000	1	827	1	chr4B.!!$F1	826
5	TraesCS5A01G093100	chr4B	395244064	395244900	836	False	1458.000000	1458	98.088000	1	837	1	chr4B.!!$F2	836
6	TraesCS5A01G093100	chr2A	442716328	442717885	1557	True	926.333333	1411	99.017333	1	827	3	chr2A.!!$R1	826
7	TraesCS5A01G093100	chr7A	16635995	16637414	1419	True	1172.500000	1362	96.499500	1	827	2	chr7A.!!$R1	826
8	TraesCS5A01G093100	chr3A	27583464	27584000	536	False	837.000000	837	94.786000	291	827	1	chr3A.!!$F2	536
9	TraesCS5A01G093100	chr7B	226421507	226424941	3434	False	530.500000	828	93.621500	1	834	2	chr7B.!!$F1	833

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	Hairpin	End Stability	Orientation
852	4778	0.822121	GTGCCAGGTTTTCCGTTCCT	60.822	55.000	46.35	3.36	F
874	6189	1.202510	CCCTCCGAGAATCTGCTCTTG	60.203	57.143	32.71	3.02	F
1755	8479	1.468520	CGTTGGCATCTTTCATCGGTT	59.531	47.619	0.00	4.44	F
2019	9596	1.868713	ATGGATTGCCTGCCAATGAA	58.131	45.000	44.02	2.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
2652	10235	1.113788	GGCGTACCACTGTACCCATA	58.886	55.000	43.69	2.74	R
2737	10320	5.595257	AGAACTACTATTCCCGTCTTTCC	57.405	43.478	0.00	3.13	R
3035	10647	1.001706	GCTTCTTTCGGTTGTGTTCCC	60.002	52.381	0.00	3.97	R
4006	11673	0.247736	AATGAGACAGTGACCTCCGC	59.752	55.000	0.00	5.54	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
281	644	9.196139	TGCAAATAAGGCCTTAAATAGTATGTT	57.804	29.630	28.50	12.29	0.00	2.71
847	4773	2.028385	ACTACTAGTGCCAGGTTTTCCG	60.028	50.000	5.39	0.00	46.35	4.30
852	4778	0.822121	GTGCCAGGTTTTCCGTTCCT	60.822	55.000	0.00	0.00	46.35	3.36
874	6189	1.202510	CCCTCCGAGAATCTGCTCTTG	60.203	57.143	0.00	0.00	32.71	3.02
1112	7831	3.991051	ACACTCTGGTCGGTGCCG	61.991	66.667	3.94	3.94	36.99	5.69
1252	7972	3.133721	TGGTTGGCTACAAATTGTTTGCT	59.866	39.130	18.00	0.00	44.39	3.91
1343	8064	4.436200	CGATCTCTTTCTCTCGTGAATTCG	59.564	45.833	0.04	0.00	0.00	3.34
1344	8065	4.098055	TCTCTTTCTCTCGTGAATTCGG	57.902	45.455	0.04	0.00	0.00	4.30
1384	8105	5.957220	CGTATGTCACACAATTTAATGTCCG	59.043	40.000	0.00	0.00	0.00	4.79
1398	8119	9.689501	AATTTAATGTCCGGTTCCTAAATCTTA	57.310	29.630	0.00	0.00	0.00	2.10
1416	8137	6.884280	ATCTTAATGCTATTTAGGTGCCAC	57.116	37.500	0.00	0.00	0.00	5.01
1433	8154	4.932799	GTGCCACCAAGTTAGTTTTGTTTT	59.067	37.500	0.00	0.00	0.00	2.43
1481	8202	4.682860	AGCGAATTCACTTTGCAATTCTTG	59.317	37.500	0.00	0.00	45.39	3.02
1550	8271	3.020984	TGATTTGGTTAGGCGATTTCCC	58.979	45.455	0.00	0.00	0.00	3.97
1563	8284	4.805719	GGCGATTTCCCTTCAATTTCATTC	59.194	41.667	0.00	0.00	0.00	2.67
1714	8438	2.017138	TCCACAAATATTGCGCTCGA	57.983	45.000	9.73	0.00	0.00	4.04
1755	8479	1.468520	CGTTGGCATCTTTCATCGGTT	59.531	47.619	0.00	0.00	0.00	4.44
1845	8569	2.555199	CGGATCAGTGTCCTCATTTCC	58.445	52.381	9.24	0.00	36.07	3.13
1847	8571	1.936547	GATCAGTGTCCTCATTTCCGC	59.063	52.381	0.00	0.00	0.00	5.54
1854	8578	3.689649	GTGTCCTCATTTCCGCAACTTAT	59.310	43.478	0.00	0.00	0.00	1.73
1865	8589	4.257731	TCCGCAACTTATTGTGCTTATGA	58.742	39.130	0.00	0.00	43.70	2.15
1899	8623	6.691754	TGTCAGTTCATTCTGCAAGTAAAA	57.308	33.333	0.00	0.00	35.63	1.52
1932	8656	8.221965	TCATGTAGTAGTGAATCAGAACGTAT	57.778	34.615	0.00	0.00	0.00	3.06
1936	8660	9.170734	TGTAGTAGTGAATCAGAACGTATAAGT	57.829	33.333	0.00	0.00	0.00	2.24
1963	8687	3.372730	GCGTTTGGGATGCCTGCA	61.373	61.111	4.35	0.00	34.03	4.41
2019	9596	1.868713	ATGGATTGCCTGCCAATGAA	58.131	45.000	0.00	0.00	44.02	2.57
2114	9691	8.486210	AGTGTGGATAATTAGCAAATAGACTGA	58.514	33.333	2.72	0.00	0.00	3.41
2115	9692	9.109393	GTGTGGATAATTAGCAAATAGACTGAA	57.891	33.333	2.72	0.00	0.00	3.02
2124	9701	9.638176	ATTAGCAAATAGACTGAAAATCATCCT	57.362	29.630	0.00	0.00	0.00	3.24
2167	9746	1.937899	GTCCGTGCCGTGCTTAATATT	59.062	47.619	0.00	0.00	0.00	1.28
2503	10086	6.295349	GCAGCCTTCCTTCTATACTAATAGCA	60.295	42.308	0.00	0.00	35.90	3.49
2661	10244	9.634021	TTATGTGATTAGCAAATTATGGGTACA	57.366	29.630	0.00	0.00	0.00	2.90
2816	10399	9.592196	AGGAGAAATGGCAATACAATTATATGT	57.408	29.630	0.00	0.00	37.32	2.29
2847	10458	6.659745	ATATGCACAGATGTAATTGCCATT	57.340	33.333	0.00	0.00	33.86	3.16
2967	10579	4.223032	AGGAAGTATGTGGTGGTACTCTTG	59.777	45.833	0.00	0.00	31.10	3.02
3035	10647	2.838736	CATATCTTGGTCCACGGAAGG	58.161	52.381	0.00	0.00	0.00	3.46
3066	10678	2.159653	CCGAAAGAAGCACACAGTATGC	60.160	50.000	0.00	0.00	42.53	3.14
3145	10757	3.949754	TCAGCATCCTCTTTATTTGCCTG	59.050	43.478	0.00	0.00	33.85	4.85
3156	10768	7.723172	CCTCTTTATTTGCCTGAGGATATTCTT	59.277	37.037	0.65	0.00	45.07	2.52
3217	10829	1.152756	GGCCCAATACTTCCGGCAT	60.153	57.895	0.00	0.00	43.50	4.40
3247	10859	1.546029	GGAGTCCTTGCCAAATTGACC	59.454	52.381	0.41	0.00	0.00	4.02
3382	10994	1.004745	TCTCTTGGTGGGCAATCTTCC	59.995	52.381	0.00	0.00	0.00	3.46
3427	11039	4.755629	TGATGGTTTGGATTTTAACGTCGA	59.244	37.500	0.00	0.00	0.00	4.20
3711	11323	7.228706	AGTGAAAGACATTTCGACCTATGTTTT	59.771	33.333	8.03	6.49	46.55	2.43
3747	11359	7.039363	CCACCAGGGATAAAAAGTGTAAAATCA	60.039	37.037	0.00	0.00	40.01	2.57
3791	11458	6.635030	AACTCTGAAGTAAAACATGGAACC	57.365	37.500	0.00	0.00	33.48	3.62
3795	11462	6.361433	TCTGAAGTAAAACATGGAACCAGAA	58.639	36.000	0.00	0.00	0.00	3.02
3984	11651	2.795681	CGATGAATCAAAATGTGCCCGG	60.796	50.000	0.00	0.00	0.00	5.73
4006	11673	3.409570	CTCCTGATGCCATGGATTGTAG	58.590	50.000	18.40	6.21	0.00	2.74

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
281	644	1.879380	CAACCATCGGCAAACTTGAGA	59.121	47.619	0.00	0.00	0.00	3.27
554	4479	5.363562	ACTAAATCAGAGTGCATCCATCA	57.636	39.130	0.00	0.00	0.00	3.07
839	4765	1.228459	AGGGCAGGAACGGAAAACC	60.228	57.895	0.00	0.00	0.00	3.27
847	4773	0.179070	GATTCTCGGAGGGCAGGAAC	60.179	60.000	4.96	0.00	0.00	3.62
852	4778	1.680522	GAGCAGATTCTCGGAGGGCA	61.681	60.000	4.96	0.00	0.00	5.36
874	6189	0.179012	TTTGGAGGGTGTTTCCGGAC	60.179	55.000	1.83	0.00	37.54	4.79
919	7638	0.108585	TGGAGGTCAGCTTTGTCACC	59.891	55.000	0.00	0.00	0.00	4.02
1112	7831	3.855853	GCCTCTCCTCCGGCCTTC	61.856	72.222	0.00	0.00	40.43	3.46
1204	7923	1.342819	GCTCGGAGCTATGGTTGAGAT	59.657	52.381	22.32	0.00	38.45	2.75
1226	7946	4.173036	ACAATTTGTAGCCAACCAATCG	57.827	40.909	0.00	0.00	0.00	3.34
1270	7990	5.904941	GGATTCATCCACACAATAAATGCA	58.095	37.500	0.51	0.00	46.38	3.96
1318	8038	5.766150	ATTCACGAGAGAAAGAGATCGAT	57.234	39.130	0.00	0.00	38.50	3.59
1353	8074	5.702622	AATTGTGTGACATACGAATCGAG	57.297	39.130	10.55	1.08	0.00	4.04
1398	8119	3.380471	TGGTGGCACCTAAATAGCATT	57.620	42.857	34.69	0.00	39.58	3.56
1481	8202	4.278919	TGATAAACGTCAACTTTTTCCCCC	59.721	41.667	0.00	0.00	0.00	5.40
1550	8271	1.742831	TCGCCCCGAATGAAATTGAAG	59.257	47.619	0.00	0.00	36.07	3.02
1563	8284	0.097499	GAACGGTTTATTTCGCCCCG	59.903	55.000	0.00	0.00	44.06	5.73
1755	8479	4.877378	ATTGGCATCTTGAAAAGCTTGA	57.123	36.364	0.00	0.00	45.70	3.02
1845	8569	4.788100	GTGTCATAAGCACAATAAGTTGCG	59.212	41.667	0.00	0.00	38.96	4.85
1847	8571	6.072508	ACTGGTGTCATAAGCACAATAAGTTG	60.073	38.462	0.00	0.00	41.20	3.16
1854	8578	4.085357	AGAACTGGTGTCATAAGCACAA	57.915	40.909	0.00	0.00	38.51	3.33
1865	8589	3.627395	TGAACTGACAAGAACTGGTGT	57.373	42.857	0.00	0.00	0.00	4.16
1932	8656	3.754323	CCCAAACGCTCAATGGTAACTTA	59.246	43.478	0.00	0.00	32.13	2.24
1936	8660	2.570415	TCCCAAACGCTCAATGGTAA	57.430	45.000	0.00	0.00	32.13	2.85
1963	8687	8.712228	AACCTCTTAGAAAAGTGAATCCAAAT	57.288	30.769	0.00	0.00	34.13	2.32
2019	9596	2.922740	ACCATCATATTACCGCCGTT	57.077	45.000	0.00	0.00	0.00	4.44
2058	9635	7.684187	GCAAATTGACTAGAGAGCAGAGACTAT	60.684	40.741	0.00	0.00	0.00	2.12
2114	9691	8.105829	ACTCACACTTCATAAGAGGATGATTTT	58.894	33.333	0.00	0.00	35.77	1.82
2115	9692	7.628234	ACTCACACTTCATAAGAGGATGATTT	58.372	34.615	0.00	0.00	35.77	2.17
2118	9695	5.127845	GGACTCACACTTCATAAGAGGATGA	59.872	44.000	0.00	0.00	33.96	2.92
2119	9696	5.128499	AGGACTCACACTTCATAAGAGGATG	59.872	44.000	0.00	0.00	0.00	3.51
2120	9697	5.276440	AGGACTCACACTTCATAAGAGGAT	58.724	41.667	0.00	0.00	0.00	3.24
2121	9698	4.678256	AGGACTCACACTTCATAAGAGGA	58.322	43.478	0.00	0.00	0.00	3.71
2122	9699	5.413309	AAGGACTCACACTTCATAAGAGG	57.587	43.478	0.00	0.00	0.00	3.69
2123	9700	5.641209	CCAAAGGACTCACACTTCATAAGAG	59.359	44.000	0.00	0.00	0.00	2.85
2124	9701	5.071788	ACCAAAGGACTCACACTTCATAAGA	59.928	40.000	0.00	0.00	0.00	2.10
2167	9746	5.186021	TGCAAAGTTTTTCAAGGTGAGGTTA	59.814	36.000	0.00	0.00	0.00	2.85
2503	10086	4.202182	GGCCAAAATGCATATGACTCATGT	60.202	41.667	6.97	0.00	0.00	3.21
2652	10235	1.113788	GGCGTACCACTGTACCCATA	58.886	55.000	0.00	0.00	43.69	2.74
2737	10320	5.595257	AGAACTACTATTCCCGTCTTTCC	57.405	43.478	0.00	0.00	0.00	3.13
2896	10508	1.321743	CGAAGTGTGACGAGCTAATGC	59.678	52.381	0.00	0.00	40.05	3.56
2905	10517	7.730067	TTAGTAACATTATCGAAGTGTGACG	57.270	36.000	8.97	0.00	33.37	4.35
2957	10569	6.474140	TGTTAAGACAGAACAAGAGTACCA	57.526	37.500	0.00	0.00	33.93	3.25
3035	10647	1.001706	GCTTCTTTCGGTTGTGTTCCC	60.002	52.381	0.00	0.00	0.00	3.97
3066	10678	1.532868	CTGAACCACTCCAAAGCTTCG	59.467	52.381	0.00	0.00	0.00	3.79
3078	10690	1.728971	CTGATTCGCTGACTGAACCAC	59.271	52.381	0.00	0.00	0.00	4.16
3145	10757	6.653989	TGGGAAGAAGAACAAGAATATCCTC	58.346	40.000	0.00	0.00	0.00	3.71
3156	10768	4.574828	CGAAGAACTTTGGGAAGAAGAACA	59.425	41.667	0.00	0.00	36.69	3.18
3247	10859	1.792301	CACACATTCGAGCAGCTGG	59.208	57.895	17.12	0.00	0.00	4.85
3382	10994	1.524621	CAATGTAGCAGCTCGGGGG	60.525	63.158	0.00	0.00	0.00	5.40
3396	11008	8.667463	GTTAAAATCCAAACCATCAATCCAATG	58.333	33.333	0.00	0.00	0.00	2.82
3518	11130	7.439655	GCTCAACAGTATCCCTAAGATTTACAG	59.560	40.741	0.00	0.00	36.33	2.74
3711	11323	8.570038	TTTTTATCCCTGGTGGTACTATATGA	57.430	34.615	0.00	0.00	34.77	2.15
3747	11359	6.820335	AGTTTTTGCTTTAGCCAGAAGAATT	58.180	32.000	0.00	0.00	41.18	2.17
3791	11458	7.644986	TTACGGCAAATTAAATTGGTTTCTG	57.355	32.000	5.45	0.00	0.00	3.02
3795	11462	6.941857	AGGATTACGGCAAATTAAATTGGTT	58.058	32.000	5.45	0.00	0.00	3.67
3984	11651	0.959553	CAATCCATGGCATCAGGAGC	59.040	55.000	6.96	0.00	34.40	4.70
4006	11673	0.247736	AATGAGACAGTGACCTCCGC	59.752	55.000	0.00	0.00	0.00	5.54

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.