AutoCloner

Multiple sequence alignment - TraesCS2D01G164800

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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	TraesCS2D01G164800	chr2D	100.000	2594	0	0	1	2594	109129667	109127074	0.000000e+00	4791.0
1	TraesCS2D01G164800	chr2D	88.089	764	78	9	742	1498	109030462	109031219	0.000000e+00	894.0
2	TraesCS2D01G164800	chr2D	90.563	551	49	3	951	1498	109554189	109554739	0.000000e+00	726.0
3	TraesCS2D01G164800	chr2D	81.757	296	22	16	657	942	109553859	109554132	4.350000e-53	219.0
4	TraesCS2D01G164800	chr2B	88.998	1118	87	13	1500	2594	158863207	158862103	0.000000e+00	1351.0
5	TraesCS2D01G164800	chr2B	93.864	880	22	9	644	1498	158863208	158864080	0.000000e+00	1297.0
6	TraesCS2D01G164800	chr2B	90.550	836	46	13	675	1504	159098100	159098908	0.000000e+00	1075.0
7	TraesCS2D01G164800	chr7D	92.638	652	39	7	1	643	529431816	529432467	0.000000e+00	929.0
8	TraesCS2D01G164800	chr7D	83.978	724	84	10	1692	2387	625726791	625726072	0.000000e+00	665.0
9	TraesCS2D01G164800	chr5B	91.398	651	44	7	1	644	166585537	166586182	0.000000e+00	881.0
10	TraesCS2D01G164800	chr5B	89.862	651	42	10	1	644	166590304	166590937	0.000000e+00	815.0
11	TraesCS2D01G164800	chr5B	85.170	735	92	15	1683	2404	66051524	66050794	0.000000e+00	737.0
12	TraesCS2D01G164800	chr5B	83.075	709	82	15	1692	2368	10101190	10100488	6.140000e-171	610.0
13	TraesCS2D01G164800	chr5B	82.953	657	92	14	1764	2404	591561440	591560788	2.240000e-160	575.0
14	TraesCS2D01G164800	chr5D	85.830	741	70	12	1693	2404	64139528	64140262	0.000000e+00	754.0
15	TraesCS2D01G164800	chr5D	80.150	665	95	23	1773	2404	217647974	217647314	1.820000e-126	462.0
16	TraesCS2D01G164800	chr3D	85.675	726	88	10	1693	2404	3153819	3154542	0.000000e+00	750.0
17	TraesCS2D01G164800	chr3D	81.329	557	99	4	954	1506	22272536	22273091	5.090000e-122	448.0
18	TraesCS2D01G164800	chr2A	86.637	666	82	7	838	1498	105407225	105407888	0.000000e+00	730.0
19	TraesCS2D01G164800	chr7A	83.425	724	89	13	1692	2387	721372365	721371645	0.000000e+00	643.0
20	TraesCS2D01G164800	chr3B	83.780	709	70	20	1733	2404	52701233	52700533	4.710000e-177	630.0
21	TraesCS2D01G164800	chr3B	81.358	751	108	16	1683	2404	736320160	736319413	1.340000e-162	582.0
22	TraesCS2D01G164800	chr1B	84.639	651	81	10	1768	2403	681147030	681146384	4.710000e-177	630.0
23	TraesCS2D01G164800	chr1B	84.504	484	41	9	1951	2403	673451446	673451926	5.090000e-122	448.0
24	TraesCS2D01G164800	chr1B	82.301	452	45	17	1985	2404	163585577	163586025	2.450000e-95	359.0
25	TraesCS2D01G164800	chr1D	83.428	706	77	17	1733	2404	259684313	259685012	1.020000e-173	619.0
26	TraesCS2D01G164800	chr3A	82.143	756	102	20	1683	2408	560132904	560132152	3.670000e-173	617.0
27	TraesCS2D01G164800	chr3A	82.081	519	85	5	995	1506	31962935	31962418	1.100000e-118	436.0
28	TraesCS2D01G164800	chr7B	83.582	670	73	14	1768	2404	688135936	688135271	6.180000e-166	593.0
29	TraesCS2D01G164800	chr6D	80.602	665	92	23	1773	2404	436247444	436246784	1.810000e-131	479.0
30	TraesCS2D01G164800	chr4A	94.444	36	2	0	2402	2437	607643049	607643084	3.610000e-04	56.5
31	TraesCS2D01G164800	chr6A	96.875	32	1	0	2402	2433	18652517	18652486	1.000000e-03	54.7

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	TraesCS2D01G164800	chr2D	109127074	109129667	2593	True	4791.0	4791	100.000	1	2594	1	chr2D.!!$R1	2593
1	TraesCS2D01G164800	chr2D	109030462	109031219	757	False	894.0	894	88.089	742	1498	1	chr2D.!!$F1	756
2	TraesCS2D01G164800	chr2D	109553859	109554739	880	False	472.5	726	86.160	657	1498	2	chr2D.!!$F2	841
3	TraesCS2D01G164800	chr2B	158862103	158863207	1104	True	1351.0	1351	88.998	1500	2594	1	chr2B.!!$R1	1094
4	TraesCS2D01G164800	chr2B	158863208	158864080	872	False	1297.0	1297	93.864	644	1498	1	chr2B.!!$F1	854
5	TraesCS2D01G164800	chr2B	159098100	159098908	808	False	1075.0	1075	90.550	675	1504	1	chr2B.!!$F2	829
6	TraesCS2D01G164800	chr7D	529431816	529432467	651	False	929.0	929	92.638	1	643	1	chr7D.!!$F1	642
7	TraesCS2D01G164800	chr7D	625726072	625726791	719	True	665.0	665	83.978	1692	2387	1	chr7D.!!$R1	695
8	TraesCS2D01G164800	chr5B	166585537	166586182	645	False	881.0	881	91.398	1	644	1	chr5B.!!$F1	643
9	TraesCS2D01G164800	chr5B	166590304	166590937	633	False	815.0	815	89.862	1	644	1	chr5B.!!$F2	643
10	TraesCS2D01G164800	chr5B	66050794	66051524	730	True	737.0	737	85.170	1683	2404	1	chr5B.!!$R2	721
11	TraesCS2D01G164800	chr5B	10100488	10101190	702	True	610.0	610	83.075	1692	2368	1	chr5B.!!$R1	676
12	TraesCS2D01G164800	chr5B	591560788	591561440	652	True	575.0	575	82.953	1764	2404	1	chr5B.!!$R3	640
13	TraesCS2D01G164800	chr5D	64139528	64140262	734	False	754.0	754	85.830	1693	2404	1	chr5D.!!$F1	711
14	TraesCS2D01G164800	chr5D	217647314	217647974	660	True	462.0	462	80.150	1773	2404	1	chr5D.!!$R1	631
15	TraesCS2D01G164800	chr3D	3153819	3154542	723	False	750.0	750	85.675	1693	2404	1	chr3D.!!$F1	711
16	TraesCS2D01G164800	chr3D	22272536	22273091	555	False	448.0	448	81.329	954	1506	1	chr3D.!!$F2	552
17	TraesCS2D01G164800	chr2A	105407225	105407888	663	False	730.0	730	86.637	838	1498	1	chr2A.!!$F1	660
18	TraesCS2D01G164800	chr7A	721371645	721372365	720	True	643.0	643	83.425	1692	2387	1	chr7A.!!$R1	695
19	TraesCS2D01G164800	chr3B	52700533	52701233	700	True	630.0	630	83.780	1733	2404	1	chr3B.!!$R1	671
20	TraesCS2D01G164800	chr3B	736319413	736320160	747	True	582.0	582	81.358	1683	2404	1	chr3B.!!$R2	721
21	TraesCS2D01G164800	chr1B	681146384	681147030	646	True	630.0	630	84.639	1768	2403	1	chr1B.!!$R1	635
22	TraesCS2D01G164800	chr1D	259684313	259685012	699	False	619.0	619	83.428	1733	2404	1	chr1D.!!$F1	671
23	TraesCS2D01G164800	chr3A	560132152	560132904	752	True	617.0	617	82.143	1683	2408	1	chr3A.!!$R2	725
24	TraesCS2D01G164800	chr3A	31962418	31962935	517	True	436.0	436	82.081	995	1506	1	chr3A.!!$R1	511
25	TraesCS2D01G164800	chr7B	688135271	688135936	665	True	593.0	593	83.582	1768	2404	1	chr7B.!!$R1	636
26	TraesCS2D01G164800	chr6D	436246784	436247444	660	True	479.0	479	80.602	1773	2404	1	chr6D.!!$R1	631

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
758	779	0.671781	CTGCTGAGAAGGTTCGGTGG	60.672	60.0	0.0	0.0	0.0	4.61	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2247	2396	0.461163	CAAGACCACACACACCGTCA	60.461	55.0	0.0	0.0	0.0	4.35	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
26	27	3.055385	TGGCATAGACTGGAGTACCAAAC	60.055	47.826	0.00	0.00	46.32	2.93
32	33	3.056035	AGACTGGAGTACCAAACGAATCC	60.056	47.826	0.00	0.00	46.32	3.01
36	37	0.738412	AGTACCAAACGAATCCGGCG	60.738	55.000	0.00	0.00	40.78	6.46
69	70	5.570034	CGAGGGGTAACTTAGTCATTTTCCA	60.570	44.000	0.00	0.00	0.00	3.53
90	91	2.076207	AGGTTACGTTGGGCCTTTTT	57.924	45.000	4.53	0.00	0.00	1.94
143	145	2.501610	GGATCTCACGGCCCTGAC	59.498	66.667	0.00	0.00	0.00	3.51
163	165	6.210287	TGACCGTTTAGTTTCCAAACAAAT	57.790	33.333	5.03	0.00	41.30	2.32
164	166	7.330900	TGACCGTTTAGTTTCCAAACAAATA	57.669	32.000	5.03	0.00	41.30	1.40
256	258	4.785914	TCACTCCATGGGAATTTGTACCTA	59.214	41.667	13.02	0.00	0.00	3.08
275	277	4.837860	ACCTACTCTGAAGATGATGGATCC	59.162	45.833	4.20	4.20	0.00	3.36
309	311	2.732658	GGTGTCGTTCGTGGAGGT	59.267	61.111	0.00	0.00	0.00	3.85
341	343	2.303022	AGAAATGGAGAAAGACGGAGCA	59.697	45.455	0.00	0.00	0.00	4.26
395	397	2.284625	TGGAGGGACGAGCATGGT	60.285	61.111	0.00	0.00	0.00	3.55
434	442	0.739813	GACGTAAACGAGGGCTGCAT	60.740	55.000	9.86	0.00	43.02	3.96
440	448	0.745845	AACGAGGGCTGCATGTCATC	60.746	55.000	0.50	0.00	0.00	2.92
445	453	1.160329	GGGCTGCATGTCATCCGTAC	61.160	60.000	0.50	0.00	31.77	3.67
513	522	4.992688	TGCGATTACTATTTTGCCCTTTG	58.007	39.130	0.00	0.00	0.00	2.77
514	523	4.702612	TGCGATTACTATTTTGCCCTTTGA	59.297	37.500	0.00	0.00	0.00	2.69
515	524	5.034797	GCGATTACTATTTTGCCCTTTGAC	58.965	41.667	0.00	0.00	0.00	3.18
614	624	7.301054	GGATTGACAAAAATAGACTGTCTGTG	58.699	38.462	20.19	11.75	40.14	3.66
630	640	5.531634	TGTCTGTGTTAGTTTAAGGGTACG	58.468	41.667	0.00	0.00	0.00	3.67
719	729	7.414319	GCACTACTACGAATAAAGTGAGAGTCT	60.414	40.741	5.03	0.00	39.93	3.24
758	779	0.671781	CTGCTGAGAAGGTTCGGTGG	60.672	60.000	0.00	0.00	0.00	4.61
925	960	1.173043	CTCTTCCTCGCTGTCTCACT	58.827	55.000	0.00	0.00	0.00	3.41
942	993	2.009051	CACTCACACACACACACACAT	58.991	47.619	0.00	0.00	0.00	3.21
1161	1253	1.372683	CCTCATCGATTCCCCGCAT	59.627	57.895	0.00	0.00	0.00	4.73
1252	1344	1.680651	CCACAGGTCGAGCTCCTCT	60.681	63.158	15.54	0.00	32.37	3.69
1313	1405	2.099652	CTCTCCAACACGCACCTCCA	62.100	60.000	0.00	0.00	0.00	3.86
1498	1590	2.294078	ACCAGGAGCTTCGGGGAAG	61.294	63.158	16.33	1.06	42.03	3.46
1580	1672	5.352293	TCGATGACAAATGGAATCAGACTTG	59.648	40.000	0.00	0.00	0.00	3.16
1637	1729	0.106318	GGGGCTCTGCAAGAATGGAT	60.106	55.000	0.00	0.00	46.34	3.41
1650	1742	7.879070	TGCAAGAATGGATATAAGCAAATCTC	58.121	34.615	0.00	0.00	0.00	2.75
1667	1759	6.660722	CAAATCTCTGATGATCTGCTAAAGC	58.339	40.000	0.00	0.00	42.50	3.51
1671	1763	7.117285	TCTCTGATGATCTGCTAAAGCTTAA	57.883	36.000	0.00	0.00	42.66	1.85
1675	1767	6.882656	TGATGATCTGCTAAAGCTTAACTCT	58.117	36.000	0.00	0.00	42.66	3.24
1729	1821	2.203056	CCGCATCGCTTCCATCCA	60.203	61.111	0.00	0.00	0.00	3.41
1731	1824	0.320683	CCGCATCGCTTCCATCCATA	60.321	55.000	0.00	0.00	0.00	2.74
1778	1874	2.747855	CACGCTTTCCCTGGGCTC	60.748	66.667	8.22	0.00	0.00	4.70
1859	1955	3.403057	CTTGTGTGGCGACGACGG	61.403	66.667	9.67	0.00	40.15	4.79
1936	2032	1.080569	CAATGGGTGCGCCTTTGTC	60.081	57.895	17.49	0.00	34.45	3.18
2237	2351	4.047822	GAGAGGTGATGACGATGACATTC	58.952	47.826	0.00	0.00	0.00	2.67
2238	2352	3.448660	AGAGGTGATGACGATGACATTCA	59.551	43.478	0.00	0.00	0.00	2.57
2239	2353	3.790091	AGGTGATGACGATGACATTCAG	58.210	45.455	0.00	0.00	0.00	3.02
2241	2355	2.286294	GTGATGACGATGACATTCAGGC	59.714	50.000	0.00	0.00	0.00	4.85
2242	2356	2.093553	TGATGACGATGACATTCAGGCA	60.094	45.455	0.00	0.00	41.62	4.75
2247	2396	2.086869	CGATGACATTCAGGCAACCTT	58.913	47.619	0.00	0.00	39.98	3.50
2314	2484	4.398044	CCTATTCTTTGGGCGTGTTGTAAT	59.602	41.667	0.00	0.00	0.00	1.89
2337	2507	0.936600	TTTCGTCCGGGTTTTCGTTC	59.063	50.000	0.00	0.00	0.00	3.95
2343	2513	3.125658	CGTCCGGGTTTTCGTTCATTAAT	59.874	43.478	0.00	0.00	0.00	1.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
5	6	3.532542	GTTTGGTACTCCAGTCTATGCC	58.467	50.000	0.00	0.00	45.22	4.40
26	27	2.967076	CATGGACCGCCGGATTCG	60.967	66.667	11.71	0.00	36.79	3.34
32	33	4.873129	CCTCGTCATGGACCGCCG	62.873	72.222	0.00	0.00	36.79	6.46
36	37	0.177373	GTTACCCCTCGTCATGGACC	59.823	60.000	0.00	0.00	0.00	4.46
69	70	2.076207	AAAGGCCCAACGTAACCTTT	57.924	45.000	14.72	14.72	45.44	3.11
106	107	5.560722	TCCGAAATTATTGGCCTCTATCA	57.439	39.130	3.32	0.00	0.00	2.15
143	145	7.480542	CGAGATATTTGTTTGGAAACTAAACGG	59.519	37.037	4.02	0.00	40.10	4.44
163	165	2.300152	GTTGGGATGCAGGATCGAGATA	59.700	50.000	0.00	0.00	30.87	1.98
164	166	1.071385	GTTGGGATGCAGGATCGAGAT	59.929	52.381	0.00	0.00	30.87	2.75
256	258	3.570540	TCGGATCCATCATCTTCAGAGT	58.429	45.455	13.41	0.00	0.00	3.24
275	277	2.417516	CCCTAGCACCCACGATCG	59.582	66.667	14.88	14.88	0.00	3.69
309	311	4.753516	TCTCCATTTCTTTATGCCTCGA	57.246	40.909	0.00	0.00	0.00	4.04
363	365	0.458543	CTCCACAATCAGGTCCGTCG	60.459	60.000	0.00	0.00	0.00	5.12
434	442	1.471287	CTCTGGTTCGTACGGATGACA	59.529	52.381	16.52	6.89	0.00	3.58
440	448	4.741342	AGTATTTTCTCTGGTTCGTACGG	58.259	43.478	16.52	0.00	0.00	4.02
445	453	8.610035	GGGTATTTTAGTATTTTCTCTGGTTCG	58.390	37.037	0.00	0.00	0.00	3.95
513	522	3.949842	AAGTAACGGAGTACCTTGGTC	57.050	47.619	0.00	0.00	45.00	4.02
514	523	4.101430	TGAAAAGTAACGGAGTACCTTGGT	59.899	41.667	0.00	0.00	45.00	3.67
515	524	4.450080	GTGAAAAGTAACGGAGTACCTTGG	59.550	45.833	0.00	0.00	45.00	3.61
580	590	5.720371	ATTTTTGTCAATCCGATGGTCAA	57.280	34.783	0.00	0.00	0.00	3.18
614	624	7.148573	GCTCTTTTACCGTACCCTTAAACTAAC	60.149	40.741	0.00	0.00	0.00	2.34
630	640	2.352960	CGCAATGGAGAGCTCTTTTACC	59.647	50.000	19.36	14.80	0.00	2.85
719	729	4.693283	CAGACAAACACAGAGTGAACCTA	58.307	43.478	3.88	0.00	36.96	3.08
731	741	2.565841	ACCTTCTCAGCAGACAAACAC	58.434	47.619	0.00	0.00	0.00	3.32
758	779	3.325293	TGAGACTGAACTCCAATCTGC	57.675	47.619	0.00	0.00	30.49	4.26
925	960	3.812609	GGAATATGTGTGTGTGTGTGTGA	59.187	43.478	0.00	0.00	0.00	3.58
942	993	4.827835	TGTGGATTTTGGACGTTTGGAATA	59.172	37.500	0.00	0.00	0.00	1.75
1313	1405	2.509336	CGCCGGCGAGAAAGTCAT	60.509	61.111	44.86	0.00	42.83	3.06
1498	1590	2.278013	GTCGTGACGATCGCCCTC	60.278	66.667	16.60	6.11	38.42	4.30
1580	1672	0.666577	ACAACGTTAGCTGAGGCGAC	60.667	55.000	0.00	0.00	44.37	5.19
1637	1729	7.902387	GCAGATCATCAGAGATTTGCTTATA	57.098	36.000	10.93	0.00	46.66	0.98
1650	1742	6.985645	AGAGTTAAGCTTTAGCAGATCATCAG	59.014	38.462	3.20	0.00	45.16	2.90
1729	1821	1.134560	GTCTTCAAGACGACGCCCTAT	59.865	52.381	0.65	0.00	35.28	2.57
1731	1824	1.289380	GTCTTCAAGACGACGCCCT	59.711	57.895	0.65	0.00	35.28	5.19
1894	1990	2.021068	ATCAGACCGCCGACATGAGG	62.021	60.000	0.00	3.38	0.00	3.86
1897	1993	1.153568	ACATCAGACCGCCGACATG	60.154	57.895	0.00	0.00	0.00	3.21
1936	2032	2.057316	CTCTGTCACAGCGAGAAACAG	58.943	52.381	0.00	0.00	38.91	3.16
2073	2182	2.229543	TCTGATTTTGCTGATGCGCTTT	59.770	40.909	9.73	0.00	43.34	3.51
2084	2193	1.200948	GGACTGGCAGTCTGATTTTGC	59.799	52.381	38.04	20.56	44.46	3.68
2147	2260	3.411351	CGAACGAGCAACACCCGG	61.411	66.667	0.00	0.00	0.00	5.73
2247	2396	0.461163	CAAGACCACACACACCGTCA	60.461	55.000	0.00	0.00	0.00	4.35
2282	2450	1.338020	CCAAAGAATAGGGCATTCCGC	59.662	52.381	0.00	0.00	43.63	5.54
2314	2484	1.023502	GAAAACCCGGACGAAAACCA	58.976	50.000	0.73	0.00	0.00	3.67
2337	2507	6.261826	AGAAGAAGAGAATTGCCCGATTAATG	59.738	38.462	0.00	0.00	0.00	1.90
2343	2513	3.703001	AAGAAGAAGAGAATTGCCCGA	57.297	42.857	0.00	0.00	0.00	5.14
2404	2574	9.831737	CTCCATCCATAAAGAAATATAAAAGCG	57.168	33.333	0.00	0.00	0.00	4.68
2478	2648	0.818040	GCTGGTTCCCTCAACAACGT	60.818	55.000	0.00	0.00	36.61	3.99

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.