AutoCloner

Multiple sequence alignment - TraesCS2D01G357100

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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	TraesCS2D01G357100	chr2D	100.000	2621	0	0	1	2621	459316493	459313873	0.000000e+00	4841
1	TraesCS2D01G357100	chr2D	94.370	746	27	8	2	737	394556367	394555627	0.000000e+00	1131
2	TraesCS2D01G357100	chr2D	81.193	218	28	7	15	220	450569816	450569600	2.090000e-36	163
3	TraesCS2D01G357100	chr2B	94.343	1909	76	13	737	2621	540709578	540707678	0.000000e+00	2898
4	TraesCS2D01G357100	chr2A	91.196	1931	107	37	739	2621	602483351	602481436	0.000000e+00	2566
5	TraesCS2D01G357100	chr6D	94.758	744	30	6	2	737	58050493	58049751	0.000000e+00	1149
6	TraesCS2D01G357100	chr6D	77.833	406	51	19	352	725	58051038	58051436	5.680000e-52	215
7	TraesCS2D01G357100	chr3B	86.752	702	71	15	54	737	673137156	673137853	0.000000e+00	761
8	TraesCS2D01G357100	chr5B	84.967	459	34	9	3	453	263943234	263942803	1.440000e-117	433
9	TraesCS2D01G357100	chr5B	78.632	234	36	8	511	737	363557089	363556863	2.720000e-30	143
10	TraesCS2D01G357100	chr1A	88.013	317	31	3	156	466	160524647	160524332	4.120000e-98	368
11	TraesCS2D01G357100	chr3D	82.128	235	32	7	509	737	32283282	32283052	2.660000e-45	193
12	TraesCS2D01G357100	chr3D	82.128	235	32	5	509	737	32283701	32283471	2.660000e-45	193
13	TraesCS2D01G357100	chr4D	82.353	221	31	5	520	735	340093476	340093259	4.450000e-43	185
14	TraesCS2D01G357100	chr7D	80.822	219	27	9	15	220	633184520	633184304	9.710000e-35	158
15	TraesCS2D01G357100	chr7D	83.234	167	23	1	576	737	616232190	616232024	5.840000e-32	148
16	TraesCS2D01G357100	chr1D	79.817	218	31	6	15	220	403043117	403042901	2.100000e-31	147
17	TraesCS2D01G357100	chr5A	78.788	198	30	11	4	197	638643824	638643635	3.540000e-24	122

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	TraesCS2D01G357100	chr2D	459313873	459316493	2620	True	4841	4841	100.000	1	2621	1	chr2D.!!$R3	2620
1	TraesCS2D01G357100	chr2D	394555627	394556367	740	True	1131	1131	94.370	2	737	1	chr2D.!!$R1	735
2	TraesCS2D01G357100	chr2B	540707678	540709578	1900	True	2898	2898	94.343	737	2621	1	chr2B.!!$R1	1884
3	TraesCS2D01G357100	chr2A	602481436	602483351	1915	True	2566	2566	91.196	739	2621	1	chr2A.!!$R1	1882
4	TraesCS2D01G357100	chr6D	58049751	58050493	742	True	1149	1149	94.758	2	737	1	chr6D.!!$R1	735
5	TraesCS2D01G357100	chr3B	673137156	673137853	697	False	761	761	86.752	54	737	1	chr3B.!!$F1	683

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
654	675	0.588252	ATGTGCACGCTTGAGTCAAC	59.412	50.0	13.13	0.0	0.0	3.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1903	1951	0.322322	TTAGTTGCGATTCCCACGGT	59.678	50.0	0.0	0.0	0.0	4.83	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
458	472	2.727278	CCGGTTTTTGTGTTAATTCGCC	59.273	45.455	0.00	0.00	0.00	5.54
594	613	4.394712	CTCACAGACGGGTGGGGC	62.395	72.222	4.64	0.00	39.27	5.80
654	675	0.588252	ATGTGCACGCTTGAGTCAAC	59.412	50.000	13.13	0.00	0.00	3.18
659	680	2.939756	TGCACGCTTGAGTCAACTTAAA	59.060	40.909	0.08	0.00	0.00	1.52
812	839	1.809567	CTTTGGTGCAGGCAGTTCCC	61.810	60.000	0.00	0.00	34.51	3.97
858	885	2.104331	CGAGATCCCAACGGTCGG	59.896	66.667	0.00	0.00	0.00	4.79
946	973	2.105128	CTCCGATCACCACGCTCC	59.895	66.667	0.00	0.00	0.00	4.70
949	976	4.530857	CGATCACCACGCTCCCCC	62.531	72.222	0.00	0.00	0.00	5.40
982	1009	4.074970	TCCTTCTCAATTCCAAGCACTTC	58.925	43.478	0.00	0.00	0.00	3.01
1200	1227	1.449601	CCCGGTCAACAAGATCCCG	60.450	63.158	0.00	0.00	36.08	5.14
1427	1457	3.645268	CTGCCCCCACCAAGGTAGC	62.645	68.421	0.00	0.00	34.66	3.58
1448	1478	1.379916	CCTGCACATGAACCCCTCA	59.620	57.895	0.00	0.00	38.81	3.86
1455	1485	2.029649	CACATGAACCCCTCAAAGCTTG	60.030	50.000	0.00	0.00	37.67	4.01
1480	1510	0.108585	GCTCCCCGAATCTGCCATTA	59.891	55.000	0.00	0.00	0.00	1.90
1482	1512	0.108585	TCCCCGAATCTGCCATTAGC	59.891	55.000	0.00	0.00	44.14	3.09
1625	1667	1.745141	GCTTCCAATGCTCTGATCCGT	60.745	52.381	0.00	0.00	0.00	4.69
1681	1723	9.300681	TCCTTGTTCTTCTGTTTGATTATTGAT	57.699	29.630	0.00	0.00	0.00	2.57
1682	1724	9.565213	CCTTGTTCTTCTGTTTGATTATTGATC	57.435	33.333	0.00	0.00	35.21	2.92
1683	1725	9.270576	CTTGTTCTTCTGTTTGATTATTGATCG	57.729	33.333	0.00	0.00	37.60	3.69
1684	1726	8.546597	TGTTCTTCTGTTTGATTATTGATCGA	57.453	30.769	0.00	0.00	37.60	3.59
1742	1784	5.408604	GTCAGATCGATGGTTTGTAAGTTGT	59.591	40.000	0.54	0.00	0.00	3.32
1796	1843	3.125316	CCATTCAGTTTGCGTCCTACTTC	59.875	47.826	0.00	0.00	0.00	3.01
1888	1936	1.963515	ACTCAAAATCCACCCTGCAAC	59.036	47.619	0.00	0.00	0.00	4.17
1903	1951	4.638421	CCCTGCAACTCCGTTATAAATTCA	59.362	41.667	0.00	0.00	0.00	2.57
1933	1981	1.062294	TCGCAACTAAAACAAACGCGT	59.938	42.857	5.58	5.58	41.77	6.01
1936	1984	2.696255	CAACTAAAACAAACGCGTCGT	58.304	42.857	14.44	10.80	43.97	4.34
1977	2025	2.032071	ACCTTCCAAGTTCGGCCG	59.968	61.111	22.12	22.12	0.00	6.13
2235	2283	4.731503	CGCAGCAGCAGTTCACGC	62.732	66.667	0.82	0.00	42.27	5.34
2311	2359	2.047274	CGGTGTGCCAAGATCGGT	60.047	61.111	0.00	0.00	34.09	4.69
2373	2421	3.243535	CCTGAACCAGGCTGTTCTTTTTC	60.244	47.826	21.79	12.26	45.13	2.29
2374	2422	3.360867	TGAACCAGGCTGTTCTTTTTCA	58.639	40.909	21.79	14.00	43.96	2.69
2375	2423	3.960102	TGAACCAGGCTGTTCTTTTTCAT	59.040	39.130	21.79	0.00	43.96	2.57
2376	2424	5.136828	TGAACCAGGCTGTTCTTTTTCATA	58.863	37.500	21.79	5.38	43.96	2.15
2377	2425	5.241506	TGAACCAGGCTGTTCTTTTTCATAG	59.758	40.000	21.79	4.75	43.96	2.23
2378	2426	3.507622	ACCAGGCTGTTCTTTTTCATAGC	59.492	43.478	14.43	0.00	0.00	2.97
2379	2427	3.760684	CCAGGCTGTTCTTTTTCATAGCT	59.239	43.478	14.43	0.00	0.00	3.32
2405	2455	6.388278	AGTTCAGAAACTACCGATGTAACTC	58.612	40.000	0.00	0.00	43.98	3.01
2406	2456	5.320549	TCAGAAACTACCGATGTAACTCC	57.679	43.478	0.00	0.00	0.00	3.85
2407	2457	4.103357	CAGAAACTACCGATGTAACTCCG	58.897	47.826	0.00	0.00	0.00	4.63
2412	2462	4.488879	ACTACCGATGTAACTCCGTTTTC	58.511	43.478	0.00	0.00	0.00	2.29
2470	2526	5.246145	ACTAGCACTGTAATCTTACGACC	57.754	43.478	0.00	0.00	36.45	4.79
2526	2608	5.877012	TGCTGAGATACACAGGAAAAATCTC	59.123	40.000	0.00	0.00	41.82	2.75

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
359	370	4.082787	CCACCAAACATTCACATGTCTACC	60.083	45.833	0.00	0.00	43.34	3.18
614	633	1.370414	GGTCACAACATGCACGTGC	60.370	57.895	33.11	33.11	42.50	5.34
618	637	1.804151	ACATACGGTCACAACATGCAC	59.196	47.619	0.00	0.00	0.00	4.57
743	769	4.477780	TGTTTTTCTTTTGCGACGAGTTT	58.522	34.783	0.00	0.00	0.00	2.66
812	839	4.919653	CACTGATGAGTGGGGTCG	57.080	61.111	4.13	0.00	45.26	4.79
946	973	1.617839	AAGGAGCAGAGGGAAGGGG	60.618	63.158	0.00	0.00	0.00	4.79
949	976	1.566211	TGAGAAGGAGCAGAGGGAAG	58.434	55.000	0.00	0.00	0.00	3.46
982	1009	1.667724	CATCTTGGCTTAAGGCTCGTG	59.332	52.381	27.19	16.91	41.69	4.35
1427	1457	1.379044	GGGGTTCATGTGCAGGGAG	60.379	63.158	0.00	0.00	0.00	4.30
1455	1485	2.028337	GATTCGGGGAGCGAGCTC	59.972	66.667	16.14	16.14	42.04	4.09
1460	1490	2.947938	AATGGCAGATTCGGGGAGCG	62.948	60.000	0.00	0.00	0.00	5.03
1480	1510	2.132762	CAACAGAAACCTCGTAACGCT	58.867	47.619	0.00	0.00	0.00	5.07
1482	1512	1.193874	GCCAACAGAAACCTCGTAACG	59.806	52.381	0.00	0.00	0.00	3.18
1683	1725	4.348656	TGTACAATACGCTCGAACTCATC	58.651	43.478	0.00	0.00	0.00	2.92
1684	1726	4.365899	TGTACAATACGCTCGAACTCAT	57.634	40.909	0.00	0.00	0.00	2.90
1742	1784	6.605471	AACTGGTGATAGTTACATGACAGA	57.395	37.500	0.00	0.00	39.03	3.41
1796	1843	1.578583	ACCGAAACAAACTGACGGAG	58.421	50.000	0.00	0.00	45.31	4.63
1872	1920	1.632589	GGAGTTGCAGGGTGGATTTT	58.367	50.000	0.00	0.00	0.00	1.82
1888	1936	3.558418	CCCACGGTGAATTTATAACGGAG	59.442	47.826	10.28	0.00	0.00	4.63
1903	1951	0.322322	TTAGTTGCGATTCCCACGGT	59.678	50.000	0.00	0.00	0.00	4.83
1933	1981	1.000052	TGTCGGCTGTTGTTGATACGA	60.000	47.619	0.00	0.00	0.00	3.43
1936	1984	3.610040	ATCTGTCGGCTGTTGTTGATA	57.390	42.857	0.00	0.00	0.00	2.15
1977	2025	2.490685	GGGTCTCTCTCGCGTTCC	59.509	66.667	5.77	0.00	0.00	3.62
1991	2039	1.333636	CCATCTTCAGAGCTCCGGGT	61.334	60.000	10.93	0.00	0.00	5.28
2132	2180	3.343788	CTGGCACGAGACCGACCTC	62.344	68.421	0.00	0.00	39.50	3.85
2257	2305	4.933064	GCTGGGACGCCGATCTCG	62.933	72.222	0.00	3.19	39.44	4.04
2373	2421	6.561614	TCGGTAGTTTCTGAACTAAGCTATG	58.438	40.000	0.96	0.00	46.80	2.23
2374	2422	6.770746	TCGGTAGTTTCTGAACTAAGCTAT	57.229	37.500	0.96	0.00	46.80	2.97
2375	2423	6.152323	ACATCGGTAGTTTCTGAACTAAGCTA	59.848	38.462	0.96	0.00	46.80	3.32
2376	2424	5.047235	ACATCGGTAGTTTCTGAACTAAGCT	60.047	40.000	0.96	0.00	46.80	3.74
2377	2425	5.169295	ACATCGGTAGTTTCTGAACTAAGC	58.831	41.667	0.96	0.00	46.80	3.09
2378	2426	8.027771	AGTTACATCGGTAGTTTCTGAACTAAG	58.972	37.037	0.96	0.28	46.80	2.18
2379	2427	7.889469	AGTTACATCGGTAGTTTCTGAACTAA	58.111	34.615	0.96	0.00	46.80	2.24
2435	2485	6.607004	ACAGTGCTAGTTACAACTATCCTT	57.393	37.500	2.43	0.00	40.46	3.36
2437	2487	8.414778	AGATTACAGTGCTAGTTACAACTATCC	58.585	37.037	2.43	0.00	40.46	2.59
2526	2608	4.974103	CTGTTGTTCAGGTTCTTCTACG	57.026	45.455	0.00	0.00	40.23	3.51

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.