AutoCloner

Multiple sequence alignment - TraesCS2A01G473700

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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	TraesCS2A01G473700	chr2A	100.000	2633	0	0	1	2633	715289211	715291843	0.000000e+00	4863
1	TraesCS2A01G473700	chr2A	98.531	1021	13	1	1	1019	715281364	715282384	0.000000e+00	1801
2	TraesCS2A01G473700	chr2A	96.624	1007	33	1	1	1006	18095502	18096508	0.000000e+00	1670
3	TraesCS2A01G473700	chr4A	96.271	1019	38	0	1	1019	457292279	457293297	0.000000e+00	1672
4	TraesCS2A01G473700	chr3A	96.105	1027	34	5	1	1021	398513939	398514965	0.000000e+00	1670
5	TraesCS2A01G473700	chr3A	95.805	1025	37	4	1	1019	398504577	398505601	0.000000e+00	1650
6	TraesCS2A01G473700	chr6A	96.101	1026	30	8	4	1020	189637207	189636183	0.000000e+00	1664
7	TraesCS2A01G473700	chr1A	96.101	1026	30	7	4	1019	159091630	159090605	0.000000e+00	1664
8	TraesCS2A01G473700	chr7A	95.631	1030	38	6	4	1026	465943393	465942364	0.000000e+00	1646
9	TraesCS2A01G473700	chr3B	95.793	1022	40	3	1	1019	507395049	507396070	0.000000e+00	1646
10	TraesCS2A01G473700	chr2B	89.070	613	61	2	1020	1626	693325092	693325704	0.000000e+00	756
11	TraesCS2A01G473700	chr2B	86.949	613	71	9	1020	1626	693727376	693727985	0.000000e+00	680
12	TraesCS2A01G473700	chr2B	86.524	653	44	19	2019	2633	693347993	693348639	0.000000e+00	678
13	TraesCS2A01G473700	chr2B	85.577	624	56	9	1020	1630	693741054	693741656	8.000000e-175	623
14	TraesCS2A01G473700	chr2B	83.654	624	73	20	1020	1622	693368568	693369183	6.360000e-156	560
15	TraesCS2A01G473700	chr2B	81.260	651	40	37	2019	2627	693729629	693730239	4.000000e-123	451
16	TraesCS2A01G473700	chr2B	86.957	414	33	13	1620	2020	693849462	693849867	1.860000e-121	446
17	TraesCS2A01G473700	chr2B	81.624	468	50	12	1189	1626	693345990	693346451	3.220000e-94	355
18	TraesCS2A01G473700	chr2B	81.905	420	55	15	1620	2020	693326107	693326524	4.200000e-88	335
19	TraesCS2A01G473700	chr2B	82.469	405	47	12	2019	2404	693370767	693371166	1.510000e-87	333
20	TraesCS2A01G473700	chr2B	82.474	388	20	18	2277	2627	693777540	693777916	1.980000e-76	296
21	TraesCS2A01G473700	chr2B	87.805	246	24	5	2070	2312	693850696	693850938	1.540000e-72	283
22	TraesCS2A01G473700	chr2D	87.580	628	59	9	1020	1630	577112091	577112716	0.000000e+00	710

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	TraesCS2A01G473700	chr2A	715289211	715291843	2632	False	4863.0	4863	100.0000	1	2633	1	chr2A.!!$F3	2632
1	TraesCS2A01G473700	chr2A	715281364	715282384	1020	False	1801.0	1801	98.5310	1	1019	1	chr2A.!!$F2	1018
2	TraesCS2A01G473700	chr2A	18095502	18096508	1006	False	1670.0	1670	96.6240	1	1006	1	chr2A.!!$F1	1005
3	TraesCS2A01G473700	chr4A	457292279	457293297	1018	False	1672.0	1672	96.2710	1	1019	1	chr4A.!!$F1	1018
4	TraesCS2A01G473700	chr3A	398513939	398514965	1026	False	1670.0	1670	96.1050	1	1021	1	chr3A.!!$F2	1020
5	TraesCS2A01G473700	chr3A	398504577	398505601	1024	False	1650.0	1650	95.8050	1	1019	1	chr3A.!!$F1	1018
6	TraesCS2A01G473700	chr6A	189636183	189637207	1024	True	1664.0	1664	96.1010	4	1020	1	chr6A.!!$R1	1016
7	TraesCS2A01G473700	chr1A	159090605	159091630	1025	True	1664.0	1664	96.1010	4	1019	1	chr1A.!!$R1	1015
8	TraesCS2A01G473700	chr7A	465942364	465943393	1029	True	1646.0	1646	95.6310	4	1026	1	chr7A.!!$R1	1022
9	TraesCS2A01G473700	chr3B	507395049	507396070	1021	False	1646.0	1646	95.7930	1	1019	1	chr3B.!!$F1	1018
10	TraesCS2A01G473700	chr2B	693741054	693741656	602	False	623.0	623	85.5770	1020	1630	1	chr2B.!!$F1	610
11	TraesCS2A01G473700	chr2B	693727376	693730239	2863	False	565.5	680	84.1045	1020	2627	2	chr2B.!!$F6	1607
12	TraesCS2A01G473700	chr2B	693325092	693326524	1432	False	545.5	756	85.4875	1020	2020	2	chr2B.!!$F3	1000
13	TraesCS2A01G473700	chr2B	693345990	693348639	2649	False	516.5	678	84.0740	1189	2633	2	chr2B.!!$F4	1444
14	TraesCS2A01G473700	chr2B	693368568	693371166	2598	False	446.5	560	83.0615	1020	2404	2	chr2B.!!$F5	1384
15	TraesCS2A01G473700	chr2B	693849462	693850938	1476	False	364.5	446	87.3810	1620	2312	2	chr2B.!!$F7	692
16	TraesCS2A01G473700	chr2D	577112091	577112716	625	False	710.0	710	87.5800	1020	1630	1	chr2D.!!$F1	610

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
642	660	0.392998	CCTGGGTTGCTTGCGAGTAT	60.393	55.0	2.14	0.0	0.0	2.12	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1808	2319	0.719465	GCACGTACGGTTGATGGAAG	59.281	55.0	21.06	0.0	0.0	3.46	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
30	31	0.742505	CGCATTACTAGTGACGGGGA	59.257	55.000	5.39	0.00	0.00	4.81
642	660	0.392998	CCTGGGTTGCTTGCGAGTAT	60.393	55.000	2.14	0.00	0.00	2.12
660	678	8.194769	TGCGAGTATATTCAAAGTACTCATTGA	58.805	33.333	5.99	5.99	42.69	2.57
1052	1070	7.708322	GGAGGAAATTAAAATTTGGAGATCTGC	59.292	37.037	7.39	7.39	38.64	4.26
1169	1187	0.396060	GGGGTGGATTTGCAGCAAAA	59.604	50.000	24.15	5.63	36.90	2.44
1193	1214	4.592942	ACAGCACCAGTATCATTGTCAAT	58.407	39.130	0.00	0.00	0.00	2.57
1233	1254	7.281774	ACAATGGATGATACACTAGCAAAAGAG	59.718	37.037	0.00	0.00	0.00	2.85
1235	1256	5.059833	GGATGATACACTAGCAAAAGAGGG	58.940	45.833	0.00	0.00	0.00	4.30
1239	1260	1.144913	ACACTAGCAAAAGAGGGGCAA	59.855	47.619	0.00	0.00	0.00	4.52
1280	1301	3.056328	GGAGGAGGCAAACACGGC	61.056	66.667	0.00	0.00	0.00	5.68
1281	1302	2.281484	GAGGAGGCAAACACGGCA	60.281	61.111	0.00	0.00	0.00	5.69
1330	1351	2.495270	GCACATCTCTCCAACTCTCTGA	59.505	50.000	0.00	0.00	0.00	3.27
1331	1352	3.675775	GCACATCTCTCCAACTCTCTGAC	60.676	52.174	0.00	0.00	0.00	3.51
1336	1357	2.811317	CCAACTCTCTGACGGCGC	60.811	66.667	6.90	0.00	0.00	6.53
1347	1371	3.649277	GACGGCGCTGGTCATCAGT	62.649	63.158	22.44	0.00	45.08	3.41
1394	1418	0.936691	AATGCCCTCCAAGCCCTAAT	59.063	50.000	0.00	0.00	0.00	1.73
1458	1500	0.692419	CCTCCCTGCTACACCTGGAT	60.692	60.000	0.00	0.00	0.00	3.41
1547	1608	3.490933	CGTTGCGGAGAGGATTTGAGATA	60.491	47.826	0.00	0.00	0.00	1.98
1656	2151	3.011595	TGGAACCATCCCAGAAATCACAT	59.988	43.478	0.00	0.00	45.95	3.21
1665	2160	7.389884	CCATCCCAGAAATCACATTATAGACTG	59.610	40.741	0.00	0.00	0.00	3.51
1704	2205	3.008049	ACTTCCTTGCTCGTACCAATTCT	59.992	43.478	0.00	0.00	0.00	2.40
1750	2259	3.678056	TTTTCTGATACCACAGACGCT	57.322	42.857	0.00	0.00	44.94	5.07
1769	2279	3.846335	CGCTAACTCATTTTTCTTTCGGC	59.154	43.478	0.00	0.00	0.00	5.54
1808	2319	5.865552	ACTGCATATTCTGAACATTGTTTGC	59.134	36.000	3.08	8.13	0.00	3.68
1819	2330	3.993920	ACATTGTTTGCTTCCATCAACC	58.006	40.909	0.00	0.00	0.00	3.77
1820	2331	2.791383	TTGTTTGCTTCCATCAACCG	57.209	45.000	0.00	0.00	0.00	4.44
1821	2332	1.686355	TGTTTGCTTCCATCAACCGT	58.314	45.000	0.00	0.00	0.00	4.83
1822	2333	2.852449	TGTTTGCTTCCATCAACCGTA	58.148	42.857	0.00	0.00	0.00	4.02
1860	2386	2.030805	GCATCACTTTCACCTTGTGGAC	60.031	50.000	0.00	0.00	37.04	4.02
1878	2404	6.279405	TGTGGACTTATCCCCATATATGGAT	58.721	40.000	29.98	19.31	46.02	3.41
1910	2437	4.447138	TGAGGTCCTGTGTGGTATTTTT	57.553	40.909	0.00	0.00	37.07	1.94
1911	2438	4.141287	TGAGGTCCTGTGTGGTATTTTTG	58.859	43.478	0.00	0.00	37.07	2.44
1926	2454	7.437862	GTGGTATTTTTGTCATGTCAACACATT	59.562	33.333	4.81	0.00	40.66	2.71
1981	2696	6.398234	TCTGCCTAAGTTATCTGTCTGATC	57.602	41.667	0.00	0.00	36.65	2.92
2066	3765	9.997482	GTCACAACTGAAAAATCTTAAACACTA	57.003	29.630	0.00	0.00	0.00	2.74
2106	3806	2.596851	GGTTCTCTGCCTGGGAGCA	61.597	63.158	10.78	0.00	41.46	4.26
2131	3832	8.564574	CAGTACAGTTTTTAGCCTTGTTAATCA	58.435	33.333	0.00	0.00	0.00	2.57
2140	3841	3.464833	AGCCTTGTTAATCATCCCCATCT	59.535	43.478	0.00	0.00	0.00	2.90
2167	3868	1.620819	AGTCTGCACACGAGGATCTTT	59.379	47.619	0.00	0.00	0.00	2.52
2168	3869	2.037772	AGTCTGCACACGAGGATCTTTT	59.962	45.455	0.00	0.00	0.00	2.27
2181	3882	6.710744	ACGAGGATCTTTTGTGTTGTATCTTT	59.289	34.615	0.00	0.00	0.00	2.52
2220	3921	7.591006	ACATAAATCTGGTAAGTACGTGTTG	57.409	36.000	0.00	0.00	0.00	3.33
2423	4160	2.810439	TTGCAGTTACATTTGGTGCC	57.190	45.000	0.00	0.00	32.99	5.01
2429	4166	0.955178	TTACATTTGGTGCCGGTGTG	59.045	50.000	1.90	0.00	0.00	3.82
2468	4205	6.322931	AGGATCATAAAATGGGGGAATAACC	58.677	40.000	0.00	0.00	38.08	2.85
2485	4222	8.573035	GGGAATAACCGATATTTTGCAGATTTA	58.427	33.333	0.00	0.00	40.11	1.40
2532	4269	4.340894	TTTCAGTTCGATGCTACATTGC	57.659	40.909	0.00	0.00	0.00	3.56
2534	4271	2.931969	TCAGTTCGATGCTACATTGCAG	59.068	45.455	0.00	0.00	46.71	4.41
2535	4272	2.931969	CAGTTCGATGCTACATTGCAGA	59.068	45.455	0.00	0.00	46.71	4.26
2536	4273	3.558829	CAGTTCGATGCTACATTGCAGAT	59.441	43.478	0.00	0.00	46.71	2.90
2541	4296	4.622740	TCGATGCTACATTGCAGATATTCG	59.377	41.667	0.00	0.00	46.71	3.34
2628	4386	0.671472	CCATCTCAGTGCTTGCGTCA	60.671	55.000	0.00	0.00	0.00	4.35

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
2	3	1.557832	ACTAGTAATGCGGGCTCCAAA	59.442	47.619	0.00	0.00	0.00	3.28
642	660	6.939730	TGGCAAGTCAATGAGTACTTTGAATA	59.060	34.615	10.81	0.00	40.22	1.75
660	678	6.036577	CCAATTAAATAACCAGTGGCAAGT	57.963	37.500	9.78	0.00	0.00	3.16
1026	1044	7.708322	GCAGATCTCCAAATTTTAATTTCCTCC	59.292	37.037	0.00	0.00	36.52	4.30
1052	1070	5.997746	TGTGTCAATTCCTTTCCAGTAGAAG	59.002	40.000	0.00	0.00	35.40	2.85
1058	1076	4.823989	AGAACTGTGTCAATTCCTTTCCAG	59.176	41.667	0.00	0.00	0.00	3.86
1114	1132	9.689075	CTGTGTTATGTTTTCACAACGATATAG	57.311	33.333	0.00	0.00	39.76	1.31
1169	1187	4.397420	TGACAATGATACTGGTGCTGTTT	58.603	39.130	0.00	0.00	0.00	2.83
1187	1208	7.335171	CCATTGTAACATCTGAAGAGATTGACA	59.665	37.037	0.00	0.00	36.75	3.58
1193	1214	7.186570	TCATCCATTGTAACATCTGAAGAGA	57.813	36.000	0.00	0.00	0.00	3.10
1233	1254	2.424956	CTCTGCTATTTCTTGTTGCCCC	59.575	50.000	0.00	0.00	0.00	5.80
1235	1256	3.084786	ACCTCTGCTATTTCTTGTTGCC	58.915	45.455	0.00	0.00	0.00	4.52
1239	1260	3.840666	TCTCCACCTCTGCTATTTCTTGT	59.159	43.478	0.00	0.00	0.00	3.16
1280	1301	1.337071	GCAACAGCCCATCATCATCTG	59.663	52.381	0.00	0.00	0.00	2.90
1281	1302	1.214673	AGCAACAGCCCATCATCATCT	59.785	47.619	0.00	0.00	0.00	2.90
1330	1351	1.884075	TAACTGATGACCAGCGCCGT	61.884	55.000	2.29	0.00	46.81	5.68
1331	1352	0.530650	ATAACTGATGACCAGCGCCG	60.531	55.000	2.29	0.00	46.81	6.46
1347	1371	1.624312	TGAACTACCGCACCACCATAA	59.376	47.619	0.00	0.00	0.00	1.90
1394	1418	3.258123	GCAATCTTCTAACCAAAGGGCAA	59.742	43.478	0.00	0.00	37.90	4.52
1458	1500	1.005394	GCCCTTCACGGACGAAAGA	60.005	57.895	0.00	0.00	33.16	2.52
1489	1550	1.002544	GGTGAGAGAGGTGAGGTTTGG	59.997	57.143	0.00	0.00	0.00	3.28
1665	2160	7.762382	CAAGGAAGTATTTGTTACCTTGGATC	58.238	38.462	0.00	0.00	45.76	3.36
1704	2205	3.616219	CAAGGGTAATGGTGGAAATCGA	58.384	45.455	0.00	0.00	0.00	3.59
1733	2241	3.353557	AGTTAGCGTCTGTGGTATCAGA	58.646	45.455	0.00	0.00	41.40	3.27
1748	2256	5.048153	AGCCGAAAGAAAAATGAGTTAGC	57.952	39.130	0.00	0.00	0.00	3.09
1750	2259	5.300792	ACCAAGCCGAAAGAAAAATGAGTTA	59.699	36.000	0.00	0.00	0.00	2.24
1769	2279	2.977405	GCAGTAGCAAGTGAACCAAG	57.023	50.000	0.00	0.00	41.58	3.61
1808	2319	0.719465	GCACGTACGGTTGATGGAAG	59.281	55.000	21.06	0.00	0.00	3.46
1819	2330	2.809601	GGACCAGCTGCACGTACG	60.810	66.667	15.01	15.01	0.00	3.67
1820	2331	2.809601	CGGACCAGCTGCACGTAC	60.810	66.667	8.66	0.34	0.00	3.67
1821	2332	3.299977	ACGGACCAGCTGCACGTA	61.300	61.111	21.50	0.00	35.85	3.57
1822	2333	4.969196	CACGGACCAGCTGCACGT	62.969	66.667	18.58	18.58	38.43	4.49
1878	2404	1.220749	GGACCTCATGCGCCAACTA	59.779	57.895	4.18	0.00	0.00	2.24
1910	2437	5.592282	ACTTACCAAATGTGTTGACATGACA	59.408	36.000	0.00	0.00	42.30	3.58
1911	2438	6.072112	ACTTACCAAATGTGTTGACATGAC	57.928	37.500	0.00	0.00	42.30	3.06
1926	2454	6.488344	TCAGACAATTTGCATGTACTTACCAA	59.512	34.615	0.00	0.00	0.00	3.67
1981	2696	7.396540	ACTAATAGAACTGGGAGCAATTTTG	57.603	36.000	0.00	0.00	0.00	2.44
2027	3726	6.852858	TCAGTTGTGACGTAAATCAAATCA	57.147	33.333	0.00	0.00	0.00	2.57
2040	3739	8.911247	AGTGTTTAAGATTTTTCAGTTGTGAC	57.089	30.769	0.00	0.00	30.10	3.67
2066	3765	5.536161	ACCTGCAAAGTAGATGAAAACACAT	59.464	36.000	0.00	0.00	0.00	3.21
2106	3806	8.685838	TGATTAACAAGGCTAAAAACTGTACT	57.314	30.769	0.00	0.00	0.00	2.73
2131	3832	4.096190	CAGACTTTGCATAGATGGGGAT	57.904	45.455	11.39	0.00	0.00	3.85
2157	3858	6.727824	AAGATACAACACAAAAGATCCTCG	57.272	37.500	0.00	0.00	0.00	4.63
2220	3921	9.262358	GTATCAGTAATATGGTTGGAGAAGTTC	57.738	37.037	0.00	0.00	0.00	3.01
2440	4177	3.149196	CCCCCATTTTATGATCCTCACG	58.851	50.000	0.00	0.00	0.00	4.35
2452	4189	7.505258	CAAAATATCGGTTATTCCCCCATTTT	58.495	34.615	0.00	0.00	31.85	1.82
2453	4190	6.463755	GCAAAATATCGGTTATTCCCCCATTT	60.464	38.462	0.00	0.00	29.96	2.32
2511	4248	3.750652	TGCAATGTAGCATCGAACTGAAA	59.249	39.130	0.00	0.00	40.11	2.69
2532	4269	6.630443	GCAACAAAGCTTATGACGAATATCTG	59.370	38.462	0.00	0.00	0.00	2.90
2533	4270	6.540189	AGCAACAAAGCTTATGACGAATATCT	59.460	34.615	0.00	0.00	43.70	1.98
2534	4271	6.719365	AGCAACAAAGCTTATGACGAATATC	58.281	36.000	0.00	0.00	43.70	1.63
2535	4272	6.683974	AGCAACAAAGCTTATGACGAATAT	57.316	33.333	0.00	0.00	43.70	1.28
2536	4273	7.603963	TTAGCAACAAAGCTTATGACGAATA	57.396	32.000	0.00	0.00	43.70	1.75
2541	4296	8.519492	TTTCATTTAGCAACAAAGCTTATGAC	57.481	30.769	0.00	0.00	43.70	3.06
2584	4342	9.622004	GGTTAGAAAGGTATTCTTGTAAAAAGC	57.378	33.333	0.00	0.00	35.55	3.51

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.