AutoCloner

Multiple sequence alignment - TraesCS4B01G288700

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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	TraesCS4B01G288700	chr4B	100.000	2366	0	0	1	2366	573504102	573501737	0.000000e+00	4370.0
1	TraesCS4B01G288700	chr4B	97.658	854	19	1	1	854	671054197	671053345	0.000000e+00	1465.0
2	TraesCS4B01G288700	chr7A	98.118	850	16	0	1	850	571354318	571353469	0.000000e+00	1482.0
3	TraesCS4B01G288700	chr7A	98.333	60	1	0	795	854	238253597	238253538	3.220000e-19	106.0
4	TraesCS4B01G288700	chr6B	97.547	856	19	1	1	854	353090996	353090141	0.000000e+00	1463.0
5	TraesCS4B01G288700	chr6B	94.576	719	38	1	1648	2366	217121006	217121723	0.000000e+00	1110.0
6	TraesCS4B01G288700	chr1A	97.524	848	21	0	1	848	510355363	510354516	0.000000e+00	1450.0
7	TraesCS4B01G288700	chr4A	96.966	857	16	5	1	852	433889018	433889869	0.000000e+00	1430.0
8	TraesCS4B01G288700	chr4A	97.536	771	16	2	1	771	591567645	591566878	0.000000e+00	1315.0
9	TraesCS4B01G288700	chr4A	95.105	715	32	3	1654	2366	744191656	744190943	0.000000e+00	1123.0
10	TraesCS4B01G288700	chr4A	91.718	809	49	13	850	1655	9550066	9550859	0.000000e+00	1107.0
11	TraesCS4B01G288700	chr7B	97.330	824	17	4	1	820	54785297	54784475	0.000000e+00	1395.0
12	TraesCS4B01G288700	chr7B	94.803	712	37	0	1655	2366	674574069	674573358	0.000000e+00	1110.0
13	TraesCS4B01G288700	chr7B	96.429	56	2	0	795	850	742588727	742588782	2.500000e-15	93.5
14	TraesCS4B01G288700	chr3B	97.778	810	17	1	54	863	146317533	146318341	0.000000e+00	1395.0
15	TraesCS4B01G288700	chr3B	94.366	710	39	1	1656	2365	715143547	715144255	0.000000e+00	1088.0
16	TraesCS4B01G288700	chrUn	97.536	771	16	2	1	771	416770810	416771577	0.000000e+00	1315.0
17	TraesCS4B01G288700	chr5A	95.652	713	28	3	1656	2366	679653237	679652526	0.000000e+00	1142.0
18	TraesCS4B01G288700	chr5B	95.225	712	34	0	1653	2364	622062099	622062810	0.000000e+00	1127.0
19	TraesCS4B01G288700	chr2B	94.803	712	36	1	1656	2366	672795893	672795182	0.000000e+00	1109.0
20	TraesCS4B01G288700	chr2B	94.522	712	35	3	1655	2366	714146576	714147283	0.000000e+00	1096.0
21	TraesCS4B01G288700	chr2B	100.000	57	0	0	795	851	392862500	392862444	3.220000e-19	106.0
22	TraesCS4B01G288700	chr1B	94.233	711	38	2	1656	2366	575829454	575830161	0.000000e+00	1083.0
23	TraesCS4B01G288700	chr4D	85.104	819	70	29	850	1655	459268620	459267841	0.000000e+00	789.0

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	TraesCS4B01G288700	chr4B	573501737	573504102	2365	True	4370	4370	100.000	1	2366	1	chr4B.!!$R1	2365
1	TraesCS4B01G288700	chr4B	671053345	671054197	852	True	1465	1465	97.658	1	854	1	chr4B.!!$R2	853
2	TraesCS4B01G288700	chr7A	571353469	571354318	849	True	1482	1482	98.118	1	850	1	chr7A.!!$R2	849
3	TraesCS4B01G288700	chr6B	353090141	353090996	855	True	1463	1463	97.547	1	854	1	chr6B.!!$R1	853
4	TraesCS4B01G288700	chr6B	217121006	217121723	717	False	1110	1110	94.576	1648	2366	1	chr6B.!!$F1	718
5	TraesCS4B01G288700	chr1A	510354516	510355363	847	True	1450	1450	97.524	1	848	1	chr1A.!!$R1	847
6	TraesCS4B01G288700	chr4A	433889018	433889869	851	False	1430	1430	96.966	1	852	1	chr4A.!!$F2	851
7	TraesCS4B01G288700	chr4A	591566878	591567645	767	True	1315	1315	97.536	1	771	1	chr4A.!!$R1	770
8	TraesCS4B01G288700	chr4A	744190943	744191656	713	True	1123	1123	95.105	1654	2366	1	chr4A.!!$R2	712
9	TraesCS4B01G288700	chr4A	9550066	9550859	793	False	1107	1107	91.718	850	1655	1	chr4A.!!$F1	805
10	TraesCS4B01G288700	chr7B	54784475	54785297	822	True	1395	1395	97.330	1	820	1	chr7B.!!$R1	819
11	TraesCS4B01G288700	chr7B	674573358	674574069	711	True	1110	1110	94.803	1655	2366	1	chr7B.!!$R2	711
12	TraesCS4B01G288700	chr3B	146317533	146318341	808	False	1395	1395	97.778	54	863	1	chr3B.!!$F1	809
13	TraesCS4B01G288700	chr3B	715143547	715144255	708	False	1088	1088	94.366	1656	2365	1	chr3B.!!$F2	709
14	TraesCS4B01G288700	chrUn	416770810	416771577	767	False	1315	1315	97.536	1	771	1	chrUn.!!$F1	770
15	TraesCS4B01G288700	chr5A	679652526	679653237	711	True	1142	1142	95.652	1656	2366	1	chr5A.!!$R1	710
16	TraesCS4B01G288700	chr5B	622062099	622062810	711	False	1127	1127	95.225	1653	2364	1	chr5B.!!$F1	711
17	TraesCS4B01G288700	chr2B	672795182	672795893	711	True	1109	1109	94.803	1656	2366	1	chr2B.!!$R2	710
18	TraesCS4B01G288700	chr2B	714146576	714147283	707	False	1096	1096	94.522	1655	2366	1	chr2B.!!$F1	711
19	TraesCS4B01G288700	chr1B	575829454	575830161	707	False	1083	1083	94.233	1656	2366	1	chr1B.!!$F1	710
20	TraesCS4B01G288700	chr4D	459267841	459268620	779	True	789	789	85.104	850	1655	1	chr4D.!!$R1	805

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
907	923	0.387565	TTGCTTTCGCCTTTTCCCAC	59.612	50.0	0.0	0.0	34.43	4.61	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1952	1986	0.885879	ACCGTAGTTCAGCGACATGA	59.114	50.0	0.0	0.0	0.0	3.07	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
89	91	6.603997	ACCTCCTCTTGTAATGTAGTCTAGTG	59.396	42.308	0.00	0.00	0.00	2.74
183	186	6.697395	TGTAATGTAGTCTAGTTGCACACAT	58.303	36.000	0.00	0.00	0.00	3.21
314	319	3.076621	CACACACATATGCTCAGTTGGT	58.923	45.455	1.58	0.00	0.00	3.67
396	404	2.086094	CACACATATGCTCAGTTGGCA	58.914	47.619	1.58	0.00	44.05	4.92
551	565	1.024046	CGTCGAAACATCCCCATGCA	61.024	55.000	0.00	0.00	32.57	3.96
600	614	1.153353	GATTCCAGCGGTGAAAACGA	58.847	50.000	17.83	0.70	0.00	3.85
761	777	5.195001	AGCGGACAAAAATTACACACATT	57.805	34.783	0.00	0.00	0.00	2.71
905	921	1.713597	CATTGCTTTCGCCTTTTCCC	58.286	50.000	0.00	0.00	34.43	3.97
906	922	1.000731	CATTGCTTTCGCCTTTTCCCA	59.999	47.619	0.00	0.00	34.43	4.37
907	923	0.387565	TTGCTTTCGCCTTTTCCCAC	59.612	50.000	0.00	0.00	34.43	4.61
908	924	1.081442	GCTTTCGCCTTTTCCCACG	60.081	57.895	0.00	0.00	0.00	4.94
959	975	2.108514	CCATTGCTCGCATCGGTGT	61.109	57.895	0.00	0.00	0.00	4.16
983	999	0.693622	TCCTCAGTCCTCACTCGTCT	59.306	55.000	0.00	0.00	0.00	4.18
1011	1027	4.499865	GCAACATAGAAGATGAGGTCGCTA	60.500	45.833	0.00	0.00	0.00	4.26
1026	1042	3.193614	CTACCGCTGCTGCTGCTG	61.194	66.667	25.43	21.90	40.48	4.41
1094	1110	1.301401	CGTCGGCCAAGTTGAAGGA	60.301	57.895	2.24	0.00	0.00	3.36
1097	1113	2.335712	CGGCCAAGTTGAAGGAGGC	61.336	63.158	2.24	0.00	44.48	4.70
1098	1114	1.228552	GGCCAAGTTGAAGGAGGCA	60.229	57.895	3.87	0.00	46.96	4.75
1105	1121	1.901464	TTGAAGGAGGCAAACCCGC	60.901	57.895	0.00	0.00	39.21	6.13
1106	1122	3.431725	GAAGGAGGCAAACCCGCG	61.432	66.667	0.00	0.00	39.21	6.46
1191	1207	2.576832	CCTGACGTACGTGGGGGTT	61.577	63.158	28.16	0.00	0.00	4.11
1193	1209	2.091102	CTGACGTACGTGGGGGTTGT	62.091	60.000	28.16	0.00	0.00	3.32
1361	1377	3.452627	AGGTTCAGGAAGATCGCAATAGT	59.547	43.478	0.00	0.00	0.00	2.12
1388	1404	0.676782	ACAGGGCAAGTATCAACCGC	60.677	55.000	0.00	0.00	0.00	5.68
1389	1405	0.392998	CAGGGCAAGTATCAACCGCT	60.393	55.000	0.00	0.00	0.00	5.52
1390	1406	1.134521	CAGGGCAAGTATCAACCGCTA	60.135	52.381	0.00	0.00	0.00	4.26
1393	1409	2.101917	GGGCAAGTATCAACCGCTAGTA	59.898	50.000	0.00	0.00	0.00	1.82
1396	1412	3.550678	GCAAGTATCAACCGCTAGTACAC	59.449	47.826	0.00	0.00	0.00	2.90
1397	1413	4.677250	GCAAGTATCAACCGCTAGTACACT	60.677	45.833	0.00	0.00	0.00	3.55
1398	1414	4.634184	AGTATCAACCGCTAGTACACTG	57.366	45.455	0.00	0.00	0.00	3.66
1399	1415	4.267536	AGTATCAACCGCTAGTACACTGA	58.732	43.478	0.00	0.00	0.00	3.41
1400	1416	3.505464	ATCAACCGCTAGTACACTGAC	57.495	47.619	0.00	0.00	0.00	3.51
1412	1438	1.014352	ACACTGACGTCTTTGTTGGC	58.986	50.000	17.92	0.00	0.00	4.52
1424	1450	0.319986	TTGTTGGCTCACGCGTATGA	60.320	50.000	13.44	5.11	36.88	2.15
1451	1477	4.342772	CAAGTTTGTTTCTGTCGTCCTTG	58.657	43.478	0.00	0.00	0.00	3.61
1475	1501	4.742438	TTCGAGTGCCAGTGTATTTTTC	57.258	40.909	0.00	0.00	0.00	2.29
1479	1505	5.992829	TCGAGTGCCAGTGTATTTTTCTTAA	59.007	36.000	0.00	0.00	0.00	1.85
1514	1540	2.081462	GTAAGTGGCCGTGCAATAAGT	58.919	47.619	0.00	0.00	0.00	2.24
1549	1577	6.455913	GCACAATGTGATTGCCATATGTTTTC	60.456	38.462	18.66	0.00	43.98	2.29
1556	1584	7.027161	GTGATTGCCATATGTTTTCTAACGTT	58.973	34.615	5.88	5.88	37.06	3.99
1557	1585	8.178964	GTGATTGCCATATGTTTTCTAACGTTA	58.821	33.333	7.94	7.94	37.06	3.18
1558	1586	8.898761	TGATTGCCATATGTTTTCTAACGTTAT	58.101	29.630	8.76	0.00	37.06	1.89
1608	1636	5.511088	TCACGCGAGTTTATCTCTTTTTC	57.489	39.130	15.93	0.00	46.40	2.29
1611	1639	6.864685	TCACGCGAGTTTATCTCTTTTTCTTA	59.135	34.615	15.93	0.00	46.40	2.10
1613	1641	6.643770	ACGCGAGTTTATCTCTTTTTCTTACA	59.356	34.615	15.93	0.00	46.40	2.41
1621	1650	9.503399	TTTATCTCTTTTTCTTACAGGGAGTTC	57.497	33.333	0.00	0.00	0.00	3.01
1639	1668	6.766467	GGGAGTTCACCTATTATTTACACTGG	59.234	42.308	0.00	0.00	0.00	4.00
1643	1672	7.336931	AGTTCACCTATTATTTACACTGGCTTG	59.663	37.037	0.00	0.00	0.00	4.01
1693	1722	2.030958	CGTGTGGGCGTTAAGGGAC	61.031	63.158	0.00	0.00	0.00	4.46
1766	1796	1.066454	GTGGGCAAAACAACTAACGCT	59.934	47.619	0.00	0.00	0.00	5.07
1860	1894	1.400737	GGTACGTCAGGCCTCATACT	58.599	55.000	0.00	0.00	0.00	2.12
1897	1931	0.876777	CCACGTGACACTTTACCGCA	60.877	55.000	19.30	0.00	0.00	5.69
1952	1986	4.893424	ATGTTCGTTTAAGTGCAGTTGT	57.107	36.364	17.21	0.00	0.00	3.32
2028	2062	0.689055	ACTGCAGTTGCCATCTCAGA	59.311	50.000	15.25	0.00	41.18	3.27
2144	2179	3.179902	TGCCACCTACTAACACTAGGT	57.820	47.619	0.00	0.00	44.20	3.08
2176	2211	4.103153	TCTCAGGTCAAAGTTCCAGATTGT	59.897	41.667	0.00	0.00	0.00	2.71
2275	2310	3.179902	TGCCACCTACTAACACTAGGT	57.820	47.619	0.00	0.00	44.20	3.08
2293	2328	3.104512	AGGTAGTTGCCATGTAGCACTA	58.895	45.455	0.00	0.62	43.97	2.74

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
89	91	6.035843	CCAACTAAATATCAATGTGTGTGCC	58.964	40.000	0.00	0.00	0.00	5.01
183	186	6.374333	GTCTTCCTGCCAACTAAACATCAATA	59.626	38.462	0.00	0.00	0.00	1.90
314	319	4.215399	GTGCAACTAGACTAAATTGCCACA	59.785	41.667	20.53	6.94	45.45	4.17
551	565	5.978814	ACGTGCTCTTCAAAACTATATCCT	58.021	37.500	0.00	0.00	0.00	3.24
600	614	0.575390	CGCGCGTCGGAATTAAGATT	59.425	50.000	24.19	0.00	33.78	2.40
649	664	6.145209	CACATATGCATTTGTTTCGGTTTTCA	59.855	34.615	18.66	0.00	0.00	2.69
761	777	3.744214	CGGCTGGCCTAAAATAGACATGA	60.744	47.826	3.32	0.00	0.00	3.07
905	921	1.588674	TTGGCCCGATTTATAGCGTG	58.411	50.000	0.00	0.00	0.00	5.34
906	922	2.218603	CTTTGGCCCGATTTATAGCGT	58.781	47.619	0.00	0.00	0.00	5.07
907	923	2.218603	ACTTTGGCCCGATTTATAGCG	58.781	47.619	0.00	0.00	0.00	4.26
908	924	3.477530	AGACTTTGGCCCGATTTATAGC	58.522	45.455	0.00	0.00	0.00	2.97
959	975	1.003646	AGTGAGGACTGAGGAGGCTA	58.996	55.000	0.00	0.00	0.00	3.93
983	999	6.515696	CGACCTCATCTTCTATGTTGCTATCA	60.516	42.308	0.00	0.00	0.00	2.15
1027	1043	3.123620	GACCGCTCCAAGCAGCAG	61.124	66.667	0.00	0.00	42.58	4.24
1028	1044	4.704833	GGACCGCTCCAAGCAGCA	62.705	66.667	0.00	0.00	42.58	4.41
1035	1051	4.361971	ACGAGGAGGACCGCTCCA	62.362	66.667	9.82	0.00	43.19	3.86
1078	1094	1.374947	CCTCCTTCAACTTGGCCGA	59.625	57.895	0.00	0.00	0.00	5.54
1088	1104	2.282180	GCGGGTTTGCCTCCTTCA	60.282	61.111	0.00	0.00	34.45	3.02
1105	1121	4.838152	CTGGATCACCACGCCCCG	62.838	72.222	0.00	0.00	41.77	5.73
1107	1123	4.408821	TGCTGGATCACCACGCCC	62.409	66.667	0.00	0.00	41.77	6.13
1110	1126	1.742880	CACCTGCTGGATCACCACG	60.743	63.158	17.64	0.00	41.77	4.94
1229	1245	1.612442	ACCACCAGGCGGTAGATGT	60.612	57.895	0.00	0.00	46.94	3.06
1274	1290	4.436998	GGCACTCGTACTGCGCCT	62.437	66.667	4.18	0.00	39.73	5.52
1388	1404	4.680110	CCAACAAAGACGTCAGTGTACTAG	59.320	45.833	19.50	10.99	0.00	2.57
1389	1405	4.613944	CCAACAAAGACGTCAGTGTACTA	58.386	43.478	19.50	0.00	0.00	1.82
1390	1406	3.454375	CCAACAAAGACGTCAGTGTACT	58.546	45.455	19.50	4.31	0.00	2.73
1393	1409	1.014352	GCCAACAAAGACGTCAGTGT	58.986	50.000	19.50	17.45	0.00	3.55
1396	1412	1.261619	GTGAGCCAACAAAGACGTCAG	59.738	52.381	19.50	9.67	0.00	3.51
1397	1413	1.295792	GTGAGCCAACAAAGACGTCA	58.704	50.000	19.50	0.00	0.00	4.35
1398	1414	0.232303	CGTGAGCCAACAAAGACGTC	59.768	55.000	7.70	7.70	0.00	4.34
1399	1415	2.307363	CGTGAGCCAACAAAGACGT	58.693	52.632	0.00	0.00	0.00	4.34
1412	1438	2.094258	ACTTGCAAATCATACGCGTGAG	59.906	45.455	24.59	14.42	0.00	3.51
1424	1450	4.743493	ACGACAGAAACAAACTTGCAAAT	58.257	34.783	0.00	0.00	0.00	2.32
1451	1477	1.726853	ATACACTGGCACTCGAAAGC	58.273	50.000	0.34	0.34	0.00	3.51
1475	1501	1.625818	ACACTGGCACTCCCTCTTAAG	59.374	52.381	0.00	0.00	0.00	1.85
1479	1505	1.270907	CTTACACTGGCACTCCCTCT	58.729	55.000	0.00	0.00	0.00	3.69
1514	1540	2.942804	TCACATTGTGCTGGGAGAAAA	58.057	42.857	12.04	0.00	32.98	2.29
1549	1577	9.946165	TCGATTCAGGCATATATATAACGTTAG	57.054	33.333	14.25	0.00	0.00	2.34
1608	1636	9.543783	GTAAATAATAGGTGAACTCCCTGTAAG	57.456	37.037	0.00	0.00	33.35	2.34
1611	1639	7.182206	AGTGTAAATAATAGGTGAACTCCCTGT	59.818	37.037	0.00	0.00	33.35	4.00
1613	1641	7.365652	CCAGTGTAAATAATAGGTGAACTCCCT	60.366	40.741	0.00	0.00	36.04	4.20
1621	1650	7.391148	AACAAGCCAGTGTAAATAATAGGTG	57.609	36.000	0.00	0.00	0.00	4.00
1639	1668	4.628074	GGGACCCTTCTTTAAAAACAAGC	58.372	43.478	2.09	0.00	0.00	4.01
1643	1672	6.432162	AGTTATCGGGACCCTTCTTTAAAAAC	59.568	38.462	9.41	0.65	0.00	2.43
1693	1722	4.828409	ACAGAACATGTGGGCAGG	57.172	55.556	0.00	0.00	41.91	4.85
1897	1931	4.029186	CATGGCAACTGCGTGCGT	62.029	61.111	0.00	0.00	45.91	5.24
1952	1986	0.885879	ACCGTAGTTCAGCGACATGA	59.114	50.000	0.00	0.00	0.00	3.07
2028	2062	5.750352	AAATGGCAATCTGGAACTTTGAT	57.250	34.783	0.00	0.00	0.00	2.57
2063	2098	2.567169	AGACCACACATAGCAACAGCTA	59.433	45.455	0.00	0.00	44.34	3.32
2073	2108	2.496070	GCAGTAGACCAGACCACACATA	59.504	50.000	0.00	0.00	0.00	2.29
2144	2179	3.327757	ACTTTGACCTGAGATGGCAACTA	59.672	43.478	0.00	0.00	37.61	2.24

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.