AutoCloner

Multiple sequence alignment - TraesCS7B01G080000

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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	TraesCS7B01G080000	chr7B	100.000	2339	0	0	1	2339	89907500	89909838	0.000000e+00	4320.0
1	TraesCS7B01G080000	chr7B	98.370	368	6	0	1362	1729	89883564	89883931	0.000000e+00	647.0
2	TraesCS7B01G080000	chr7B	96.667	360	11	1	1371	1729	89917710	89918069	4.300000e-167	597.0
3	TraesCS7B01G080000	chr7B	93.247	385	18	2	1	377	89883197	89883581	5.640000e-156	560.0
4	TraesCS7B01G080000	chr7B	82.292	288	27	11	79	342	89786521	89786808	6.500000e-56	228.0
5	TraesCS7B01G080000	chr4B	97.441	977	24	1	390	1365	182287362	182286386	0.000000e+00	1664.0
6	TraesCS7B01G080000	chr3B	96.920	974	29	1	390	1362	670760569	670759596	0.000000e+00	1631.0
7	TraesCS7B01G080000	chr3B	76.020	196	36	9	1733	1920	676119728	676119536	8.900000e-15	91.6
8	TraesCS7B01G080000	chr2A	95.298	957	45	0	404	1360	433377683	433376727	0.000000e+00	1519.0
9	TraesCS7B01G080000	chr5A	94.330	970	54	1	393	1362	563443779	563442811	0.000000e+00	1485.0
10	TraesCS7B01G080000	chr5A	93.854	960	59	0	404	1363	563563616	563562657	0.000000e+00	1447.0
11	TraesCS7B01G080000	chr6D	94.179	962	55	1	404	1364	413277230	413278191	0.000000e+00	1465.0
12	TraesCS7B01G080000	chr1B	93.848	959	59	0	404	1362	611789990	611790948	0.000000e+00	1445.0
13	TraesCS7B01G080000	chr6A	93.750	960	59	1	404	1363	371337886	371338844	0.000000e+00	1439.0
14	TraesCS7B01G080000	chr6A	84.043	282	40	4	2059	2338	573178404	573178682	1.380000e-67	267.0
15	TraesCS7B01G080000	chr6A	82.353	102	15	3	1843	1942	573178244	573178344	4.140000e-13	86.1
16	TraesCS7B01G080000	chr4D	93.245	977	62	4	390	1364	127148504	127149478	0.000000e+00	1435.0
17	TraesCS7B01G080000	chr4D	87.591	137	14	3	1368	1503	482348048	482347914	3.110000e-34	156.0
18	TraesCS7B01G080000	chr3D	91.290	620	45	4	1727	2339	358884434	358883817	0.000000e+00	837.0
19	TraesCS7B01G080000	chr3D	88.976	127	11	3	1368	1493	385391646	385391522	1.120000e-33	154.0
20	TraesCS7B01G080000	chr7D	95.455	242	10	1	1488	1729	128478388	128478628	3.650000e-103	385.0
21	TraesCS7B01G080000	chr7D	87.912	273	31	1	2068	2338	178478596	178478324	1.040000e-83	320.0
22	TraesCS7B01G080000	chr7D	90.640	203	15	4	1493	1693	128746193	128746393	1.380000e-67	267.0
23	TraesCS7B01G080000	chr7D	90.991	111	7	3	53	162	128743890	128743998	1.870000e-31	147.0
24	TraesCS7B01G080000	chr2B	87.857	280	32	1	2061	2338	731537498	731537777	6.230000e-86	327.0
25	TraesCS7B01G080000	chr2B	82.589	224	32	5	1729	1946	731537221	731537443	8.530000e-45	191.0
26	TraesCS7B01G080000	chr7A	90.698	129	8	4	1367	1493	467590250	467590124	4.000000e-38	169.0
27	TraesCS7B01G080000	chr7A	89.844	128	9	4	1367	1492	467585559	467585434	6.690000e-36	161.0
28	TraesCS7B01G080000	chr5D	88.976	127	11	3	1368	1493	487527272	487527148	1.120000e-33	154.0
29	TraesCS7B01G080000	chr6B	79.310	174	28	6	1724	1891	42765938	42766109	5.280000e-22	115.0
30	TraesCS7B01G080000	chr6B	77.295	207	32	12	1724	1920	8147161	8146960	8.840000e-20	108.0
31	TraesCS7B01G080000	chrUn	93.243	74	5	0	1418	1491	330519556	330519483	2.460000e-20	110.0
32	TraesCS7B01G080000	chr1A	79.630	162	21	9	1725	1877	545885828	545885670	3.180000e-19	106.0
33	TraesCS7B01G080000	chr4A	97.143	35	1	0	1418	1452	593681739	593681705	2.510000e-05	60.2

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	TraesCS7B01G080000	chr7B	89907500	89909838	2338	False	4320.0	4320	100.0000	1	2339	1	chr7B.!!$F2	2338
1	TraesCS7B01G080000	chr7B	89883197	89883931	734	False	603.5	647	95.8085	1	1729	2	chr7B.!!$F4	1728
2	TraesCS7B01G080000	chr4B	182286386	182287362	976	True	1664.0	1664	97.4410	390	1365	1	chr4B.!!$R1	975
3	TraesCS7B01G080000	chr3B	670759596	670760569	973	True	1631.0	1631	96.9200	390	1362	1	chr3B.!!$R1	972
4	TraesCS7B01G080000	chr2A	433376727	433377683	956	True	1519.0	1519	95.2980	404	1360	1	chr2A.!!$R1	956
5	TraesCS7B01G080000	chr5A	563442811	563443779	968	True	1485.0	1485	94.3300	393	1362	1	chr5A.!!$R1	969
6	TraesCS7B01G080000	chr5A	563562657	563563616	959	True	1447.0	1447	93.8540	404	1363	1	chr5A.!!$R2	959
7	TraesCS7B01G080000	chr6D	413277230	413278191	961	False	1465.0	1465	94.1790	404	1364	1	chr6D.!!$F1	960
8	TraesCS7B01G080000	chr1B	611789990	611790948	958	False	1445.0	1445	93.8480	404	1362	1	chr1B.!!$F1	958
9	TraesCS7B01G080000	chr6A	371337886	371338844	958	False	1439.0	1439	93.7500	404	1363	1	chr6A.!!$F1	959
10	TraesCS7B01G080000	chr4D	127148504	127149478	974	False	1435.0	1435	93.2450	390	1364	1	chr4D.!!$F1	974
11	TraesCS7B01G080000	chr3D	358883817	358884434	617	True	837.0	837	91.2900	1727	2339	1	chr3D.!!$R1	612
12	TraesCS7B01G080000	chr7D	128743890	128746393	2503	False	207.0	267	90.8155	53	1693	2	chr7D.!!$F2	1640
13	TraesCS7B01G080000	chr2B	731537221	731537777	556	False	259.0	327	85.2230	1729	2338	2	chr2B.!!$F1	609

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
777	1298	0.465705	TGACTCGGATCTCAATGGGC	59.534	55.0	0.0	0.0	0.0	5.36	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1937	3663	0.249073	CGCTGGAACCTGGACGATAG	60.249	60.0	0.0	0.0	46.19	2.08	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
48	51	2.257207	TCAAAGGGGTGTAGAGAGTGG	58.743	52.381	0.00	0.00	0.00	4.00
55	58	4.041321	AGGGGTGTAGAGAGTGGTTTTTAC	59.959	45.833	0.00	0.00	0.00	2.01
110	113	4.766373	TGCTTGAACTCCATGATGCTAAAA	59.234	37.500	0.00	0.00	0.00	1.52
136	139	5.163794	ACACACCTTTTGTACAAGAAACGAG	60.164	40.000	8.56	1.79	35.67	4.18
156	159	6.530120	ACGAGGACAATAATGCATATAACCA	58.470	36.000	0.00	0.00	0.00	3.67
189	192	6.791887	ATGAAATATGTTGTAGCTGATCGG	57.208	37.500	0.00	0.00	0.00	4.18
263	272	4.126390	CGCTGCGTGCAACTCTCG	62.126	66.667	14.93	0.00	43.06	4.04
278	287	7.642586	GTGCAACTCTCGTTTATTTAACAACTT	59.357	33.333	0.00	0.00	36.50	2.66
313	322	5.391312	AAATGATCCTAAGTTTGTGCCAC	57.609	39.130	0.00	0.00	0.00	5.01
316	325	1.873698	TCCTAAGTTTGTGCCACGAC	58.126	50.000	0.00	0.00	0.00	4.34
328	337	1.429148	GCCACGACCAAGCTATTCGG	61.429	60.000	14.05	3.69	37.07	4.30
367	376	2.095768	CCTTACCACACACAAAGCATCG	60.096	50.000	0.00	0.00	0.00	3.84
369	378	0.662619	ACCACACACAAAGCATCGTG	59.337	50.000	0.00	0.00	39.10	4.35
370	379	0.661187	CCACACACAAAGCATCGTGC	60.661	55.000	2.28	2.28	45.46	5.34
387	396	8.164058	GCATCGTGCTAACTAATAGAAGATAC	57.836	38.462	0.00	0.00	40.96	2.24
388	397	7.007546	GCATCGTGCTAACTAATAGAAGATACG	59.992	40.741	0.00	6.36	40.96	3.06
764	1285	7.017645	CAGGAATTAACTCAAAATGTGACTCG	58.982	38.462	0.00	0.00	31.13	4.18
777	1298	0.465705	TGACTCGGATCTCAATGGGC	59.534	55.000	0.00	0.00	0.00	5.36
887	1409	3.961477	TGTGAAACTCAATGTTGACGG	57.039	42.857	0.00	0.00	39.13	4.79
893	1415	2.417719	ACTCAATGTTGACGGCTCTTC	58.582	47.619	0.00	0.00	32.90	2.87
926	1448	2.284493	GGAGGGTACGATGGGGGA	59.716	66.667	0.00	0.00	0.00	4.81
936	1458	1.768870	ACGATGGGGGAAGTATTGAGG	59.231	52.381	0.00	0.00	0.00	3.86
988	1510	4.517285	GAATGGAAAGATAGACCACTGCA	58.483	43.478	0.00	0.00	36.49	4.41
1110	1632	2.422519	GGTGATTGAGACCATGCAGGAT	60.423	50.000	0.00	0.00	41.22	3.24
1312	1955	3.955771	TTGTAACGCTTCTCACAAACC	57.044	42.857	0.00	0.00	0.00	3.27
1722	3440	5.149273	GGCTTGATTGTATTGCATATGTCG	58.851	41.667	4.29	0.00	0.00	4.35
1787	3505	0.994995	CGATTTGAGTGTCTCAGCCG	59.005	55.000	0.00	2.55	41.75	5.52
1798	3516	2.833582	TCAGCCGTCGGATCCTCC	60.834	66.667	17.49	0.00	0.00	4.30
1822	3542	2.000447	GTACGGTGCAGATCAAAGTCC	59.000	52.381	0.00	0.00	0.00	3.85
1897	3622	1.511768	GAGCTCGCGTTTACCTCCT	59.488	57.895	5.77	0.00	0.00	3.69
1937	3663	2.128035	CCAGTATTCTCATTCGGACGC	58.872	52.381	0.00	0.00	0.00	5.19
1941	3667	4.854291	CAGTATTCTCATTCGGACGCTATC	59.146	45.833	0.00	0.00	0.00	2.08
1955	3681	0.530870	GCTATCGTCCAGGTTCCAGC	60.531	60.000	0.00	0.00	0.00	4.85
1957	3683	0.968901	TATCGTCCAGGTTCCAGCGT	60.969	55.000	0.00	0.00	0.00	5.07
1971	3697	0.673644	CAGCGTTGTTCCTTCCGGAT	60.674	55.000	4.15	0.00	39.58	4.18
1990	3716	4.082245	CGGATGAACTGCCCTAAAAACAAT	60.082	41.667	0.00	0.00	0.00	2.71
1992	3718	4.864704	TGAACTGCCCTAAAAACAATCC	57.135	40.909	0.00	0.00	0.00	3.01
2001	3727	4.076394	CCTAAAAACAATCCCCTCGAACA	58.924	43.478	0.00	0.00	0.00	3.18
2025	3751	2.263540	GCCGCCACCGTTTCTCTA	59.736	61.111	0.00	0.00	0.00	2.43
2034	3760	3.187700	CACCGTTTCTCTATTCCTTCCG	58.812	50.000	0.00	0.00	0.00	4.30
2035	3761	2.830321	ACCGTTTCTCTATTCCTTCCGT	59.170	45.455	0.00	0.00	0.00	4.69
2065	3796	1.150135	AGGACTCTGTTCCTTCCTCCA	59.850	52.381	0.00	0.00	44.22	3.86
2066	3797	2.192263	GGACTCTGTTCCTTCCTCCAT	58.808	52.381	0.00	0.00	32.24	3.41
2072	3803	1.918262	TGTTCCTTCCTCCATGATGCT	59.082	47.619	0.00	0.00	0.00	3.79
2096	3827	1.372997	GCCGTCGTTGAGCTTCTGA	60.373	57.895	0.00	0.00	0.00	3.27
2148	3879	1.115467	CCGCCATGTACTCTTCCTCT	58.885	55.000	0.00	0.00	0.00	3.69
2191	3922	1.373435	CCACCGTGCCTTAACCAGA	59.627	57.895	0.00	0.00	0.00	3.86
2257	3988	1.207329	AGTTCACCAGGGCGACTATTC	59.793	52.381	0.00	0.00	0.00	1.75
2273	4004	5.334957	CGACTATTCCATGTACTAGCGATGT	60.335	44.000	0.00	0.00	0.00	3.06

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
16	17	1.443802	CCCTTTGAAGAGCGTCCTTC	58.556	55.000	10.62	10.62	42.09	3.46
48	51	7.235080	GGCTCGTCATTTTCTCTAGTAAAAAC	58.765	38.462	8.95	4.77	30.20	2.43
55	58	3.810310	AGGGCTCGTCATTTTCTCTAG	57.190	47.619	0.00	0.00	0.00	2.43
110	113	6.539464	TCGTTTCTTGTACAAAAGGTGTGTAT	59.461	34.615	10.03	0.00	41.89	2.29
136	139	8.462016	GGATTCTGGTTATATGCATTATTGTCC	58.538	37.037	3.54	1.56	0.00	4.02
189	192	1.067565	TCATCGTGTGAGCTTCTCCAC	60.068	52.381	0.00	0.00	32.43	4.02
290	299	5.123186	CGTGGCACAAACTTAGGATCATTTA	59.877	40.000	19.09	0.00	44.16	1.40
313	322	1.480219	GCGTCCGAATAGCTTGGTCG	61.480	60.000	0.00	0.00	37.37	4.79
316	325	2.871427	GCGCGTCCGAATAGCTTGG	61.871	63.158	8.43	0.00	36.29	3.61
367	376	9.733219	ACTTTCGTATCTTCTATTAGTTAGCAC	57.267	33.333	0.00	0.00	0.00	4.40
369	378	9.947669	TGACTTTCGTATCTTCTATTAGTTAGC	57.052	33.333	0.00	0.00	0.00	3.09
700	1221	6.184789	GTCTTTCCCACCATAGATACCAAAA	58.815	40.000	0.00	0.00	0.00	2.44
764	1285	3.015327	GCTATGATGCCCATTGAGATCC	58.985	50.000	0.00	0.00	36.71	3.36
887	1409	3.310227	CAGCAAGTCATGATCAGAAGAGC	59.690	47.826	0.00	1.20	0.00	4.09
893	1415	2.562635	CCTCCAGCAAGTCATGATCAG	58.437	52.381	0.00	0.00	0.00	2.90
926	1448	3.326880	ACCTTTGTCGTCCCTCAATACTT	59.673	43.478	0.00	0.00	0.00	2.24
936	1458	4.142752	GCAATAAACCTACCTTTGTCGTCC	60.143	45.833	0.00	0.00	0.00	4.79
988	1510	1.153369	CCGCCATGAGAACATCCGT	60.153	57.895	0.00	0.00	34.15	4.69
1110	1632	2.997315	CCCGCTGACTGTCCTCCA	60.997	66.667	5.17	0.00	0.00	3.86
1365	2020	3.992260	AGCTAGGTAGTTAGCACGATG	57.008	47.619	7.66	0.00	46.69	3.84
1366	2021	4.515944	CAGTAGCTAGGTAGTTAGCACGAT	59.484	45.833	6.56	0.00	46.69	3.73
1367	2022	3.875727	CAGTAGCTAGGTAGTTAGCACGA	59.124	47.826	6.56	0.00	46.69	4.35
1368	2023	3.548415	GCAGTAGCTAGGTAGTTAGCACG	60.548	52.174	6.56	0.00	46.69	5.34
1369	2024	3.967401	GCAGTAGCTAGGTAGTTAGCAC	58.033	50.000	6.56	0.00	46.69	4.40
1704	3422	3.501828	TGGCCGACATATGCAATACAATC	59.498	43.478	1.58	0.00	0.00	2.67
1711	3429	4.991153	TTTTAATGGCCGACATATGCAA	57.009	36.364	1.58	0.00	39.40	4.08
1798	3516	3.498397	ACTTTGATCTGCACCGTACTTTG	59.502	43.478	0.00	0.00	0.00	2.77
1892	3617	1.078426	CACAGCCCGGTAAAGGAGG	60.078	63.158	0.00	0.00	0.00	4.30
1897	3622	1.377229	CCTTCCACAGCCCGGTAAA	59.623	57.895	0.00	0.00	0.00	2.01
1937	3663	0.249073	CGCTGGAACCTGGACGATAG	60.249	60.000	0.00	0.00	46.19	2.08
1941	3667	2.030562	AACGCTGGAACCTGGACG	59.969	61.111	0.00	0.00	0.00	4.79
1945	3671	0.535102	AGGAACAACGCTGGAACCTG	60.535	55.000	0.00	0.00	0.00	4.00
1971	3697	3.576550	GGGATTGTTTTTAGGGCAGTTCA	59.423	43.478	0.00	0.00	0.00	3.18
2014	3740	2.830321	ACGGAAGGAATAGAGAAACGGT	59.170	45.455	0.00	0.00	0.00	4.83
2024	3750	1.483004	TCCATCGCAACGGAAGGAATA	59.517	47.619	0.00	0.00	0.00	1.75
2025	3751	0.251916	TCCATCGCAACGGAAGGAAT	59.748	50.000	0.00	0.00	0.00	3.01
2034	3760	1.338200	ACAGAGTCCTTCCATCGCAAC	60.338	52.381	0.00	0.00	0.00	4.17
2035	3761	0.976641	ACAGAGTCCTTCCATCGCAA	59.023	50.000	0.00	0.00	0.00	4.85
2085	3816	1.001293	AGACGCACATCAGAAGCTCAA	59.999	47.619	0.00	0.00	0.00	3.02
2086	3817	0.605083	AGACGCACATCAGAAGCTCA	59.395	50.000	0.00	0.00	0.00	4.26
2096	3827	2.046892	GTGGAGGCAGACGCACAT	60.047	61.111	0.00	0.00	41.24	3.21
2148	3879	1.685224	CAGGTAAGAAGGGGCTGCA	59.315	57.895	0.50	0.00	0.00	4.41
2191	3922	3.541713	GAGCCGATTCTCCCGCCT	61.542	66.667	0.00	0.00	0.00	5.52
2195	3926	2.066999	AGGGTGAGCCGATTCTCCC	61.067	63.158	14.70	14.70	46.58	4.30
2257	3988	4.202060	ACTCAAGACATCGCTAGTACATGG	60.202	45.833	0.00	0.00	0.00	3.66
2273	4004	7.147620	TGGGTTTCTACTTTCTACAACTCAAGA	60.148	37.037	0.00	0.00	0.00	3.02

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.