AutoCloner

Multiple sequence alignment - TraesCS4D01G016400

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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	TraesCS4D01G016400	chr4D	100.000	3286	0	0	409	3694	7418167	7414882	0.000000e+00	6069.0
1	TraesCS4D01G016400	chr4D	100.000	169	0	0	1	169	7418575	7418407	2.770000e-81	313.0
2	TraesCS4D01G016400	chr4D	100.000	33	0	0	88	120	187957684	187957716	1.110000e-05	62.1
3	TraesCS4D01G016400	chr4D	100.000	33	0	0	88	120	247755104	247755072	1.110000e-05	62.1
4	TraesCS4D01G016400	chr4B	89.718	1702	98	34	589	2246	13285519	13283851	0.000000e+00	2102.0
5	TraesCS4D01G016400	chr4B	93.049	1338	62	14	2245	3555	13283822	13282489	0.000000e+00	1927.0
6	TraesCS4D01G016400	chr4B	89.015	1229	86	19	2245	3429	385038271	385037048	0.000000e+00	1476.0
7	TraesCS4D01G016400	chr4B	89.474	399	29	6	1814	2205	385040451	385040059	3.310000e-135	492.0
8	TraesCS4D01G016400	chr4B	88.608	79	7	2	43	121	636802231	636802155	1.090000e-15	95.3
9	TraesCS4D01G016400	chr4A	94.193	1326	47	15	939	2246	596223778	596222465	0.000000e+00	1995.0
10	TraesCS4D01G016400	chr4A	94.987	1117	30	8	2245	3344	596222436	596221329	0.000000e+00	1729.0
11	TraesCS4D01G016400	chr4A	90.368	353	16	5	3324	3658	596221171	596220819	7.280000e-122	448.0
12	TraesCS4D01G016400	chr4A	90.541	296	7	3	983	1275	161397983	161397706	4.510000e-99	372.0
13	TraesCS4D01G016400	chr7B	89.260	1229	83	19	2242	3426	552982633	552983856	0.000000e+00	1493.0
14	TraesCS4D01G016400	chr7B	89.097	1229	85	21	2242	3426	263413346	263414569	0.000000e+00	1482.0
15	TraesCS4D01G016400	chr7B	89.223	399	30	6	1814	2205	263411668	263412060	1.540000e-133	486.0
16	TraesCS4D01G016400	chr2B	89.233	1226	83	19	2245	3426	391901039	391899819	0.000000e+00	1487.0
17	TraesCS4D01G016400	chr2B	89.716	1128	91	17	2245	3353	47005755	47004634	0.000000e+00	1417.0
18	TraesCS4D01G016400	chr2B	89.455	1157	73	19	2245	3358	689559597	689558447	0.000000e+00	1415.0
19	TraesCS4D01G016400	chr2B	90.455	440	29	6	1814	2246	269027049	269027482	5.350000e-158	568.0
20	TraesCS4D01G016400	chr2B	89.724	399	28	7	1814	2205	689561777	689561385	7.120000e-137	497.0
21	TraesCS4D01G016400	chr2B	85.306	245	16	8	3429	3654	108226765	108227008	6.170000e-58	235.0
22	TraesCS4D01G016400	chr2B	83.740	246	19	7	3432	3657	495925452	495925208	2.890000e-51	213.0
23	TraesCS4D01G016400	chr2A	89.233	1226	83	19	2245	3426	435372854	435371634	0.000000e+00	1487.0
24	TraesCS4D01G016400	chr2A	89.724	399	28	6	1814	2205	435375032	435374640	7.120000e-137	497.0
25	TraesCS4D01G016400	chr2A	97.436	39	0	1	88	125	739816996	739816958	8.560000e-07	65.8
26	TraesCS4D01G016400	chr5B	89.079	1227	83	21	2245	3426	651561910	651560690	0.000000e+00	1476.0
27	TraesCS4D01G016400	chr5B	87.243	243	24	6	3421	3657	642365621	642365380	1.690000e-68	270.0
28	TraesCS4D01G016400	chr5B	97.500	40	1	0	87	126	656158129	656158090	6.620000e-08	69.4
29	TraesCS4D01G016400	chr3B	89.113	1139	89	15	2242	3353	796734184	796735314	0.000000e+00	1384.0
30	TraesCS4D01G016400	chr3B	89.724	399	28	6	1814	2205	703530099	703529707	7.120000e-137	497.0
31	TraesCS4D01G016400	chr1B	89.376	433	33	6	1819	2244	78173682	78173256	1.950000e-147	532.0
32	TraesCS4D01G016400	chr1B	100.000	53	0	0	117	169	680778060	680778008	8.440000e-17	99.0
33	TraesCS4D01G016400	chr2D	96.284	296	8	2	983	1275	480771278	480770983	1.990000e-132	483.0
34	TraesCS4D01G016400	chr2D	95.946	296	9	2	983	1275	73844673	73844378	9.280000e-131	477.0
35	TraesCS4D01G016400	chr3D	92.923	325	15	7	957	1275	601615084	601615406	2.010000e-127	466.0
36	TraesCS4D01G016400	chr3D	100.000	34	0	0	88	121	21934525	21934558	3.080000e-06	63.9
37	TraesCS4D01G016400	chr3D	100.000	33	0	0	88	120	576285576	576285608	1.110000e-05	62.1
38	TraesCS4D01G016400	chr1D	94.983	299	12	2	980	1275	254635014	254635312	2.010000e-127	466.0
39	TraesCS4D01G016400	chr7A	85.714	238	19	9	3434	3657	91621568	91621332	1.710000e-58	237.0
40	TraesCS4D01G016400	chr5D	95.000	40	0	2	88	125	562986959	562986920	1.110000e-05	62.1
41	TraesCS4D01G016400	chr6B	94.737	38	2	0	88	125	393592886	393592849	3.980000e-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	TraesCS4D01G016400	chr4D	7414882	7418575	3693	True	3191.000000	6069	100.000000	1	3694	2	chr4D.!!$R2	3693
1	TraesCS4D01G016400	chr4B	13282489	13285519	3030	True	2014.500000	2102	91.383500	589	3555	2	chr4B.!!$R2	2966
2	TraesCS4D01G016400	chr4B	385037048	385040451	3403	True	984.000000	1476	89.244500	1814	3429	2	chr4B.!!$R3	1615
3	TraesCS4D01G016400	chr4A	596220819	596223778	2959	True	1390.666667	1995	93.182667	939	3658	3	chr4A.!!$R2	2719
4	TraesCS4D01G016400	chr7B	552982633	552983856	1223	False	1493.000000	1493	89.260000	2242	3426	1	chr7B.!!$F1	1184
5	TraesCS4D01G016400	chr7B	263411668	263414569	2901	False	984.000000	1482	89.160000	1814	3426	2	chr7B.!!$F2	1612
6	TraesCS4D01G016400	chr2B	391899819	391901039	1220	True	1487.000000	1487	89.233000	2245	3426	1	chr2B.!!$R2	1181
7	TraesCS4D01G016400	chr2B	47004634	47005755	1121	True	1417.000000	1417	89.716000	2245	3353	1	chr2B.!!$R1	1108
8	TraesCS4D01G016400	chr2B	689558447	689561777	3330	True	956.000000	1415	89.589500	1814	3358	2	chr2B.!!$R4	1544
9	TraesCS4D01G016400	chr2A	435371634	435375032	3398	True	992.000000	1487	89.478500	1814	3426	2	chr2A.!!$R2	1612
10	TraesCS4D01G016400	chr5B	651560690	651561910	1220	True	1476.000000	1476	89.079000	2245	3426	1	chr5B.!!$R2	1181
11	TraesCS4D01G016400	chr3B	796734184	796735314	1130	False	1384.000000	1384	89.113000	2242	3353	1	chr3B.!!$F1	1111

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
457	458	0.032615	TTTTGGCCACTCCCAACACT	60.033	50.0	3.88	0.00	44.17	3.55	F
541	542	0.033208	GGAATGGAGCCATGTGGGAA	60.033	55.0	2.18	0.00	40.01	3.97	F
895	911	0.034767	GGGCCTTTAGTTAACGGGCT	60.035	55.0	23.30	3.41	45.57	5.19	F
926	942	0.179048	ATGGATCCGCATTCGCTTCA	60.179	50.0	7.39	0.00	35.30	3.02	F
1973	2017	0.179097	TTCAACAAAGGTTTGCCGCC	60.179	50.0	2.27	0.00	41.79	6.13	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1971	2015	0.394899	AGGCAAGCACTAGAATGGGC	60.395	55.000	0.00	36.44	5.36	R
2126	2175	2.093341	GCAATGTTGAGGGGCAATTCAT	60.093	45.455	0.00	39.03	2.57	R
2228	4096	2.159198	GGTTAGCCAATGTCAATGCCAG	60.159	50.000	0.00	34.09	4.85	R
2243	4142	3.189287	CAGCCGGATATGATTTGGTTAGC	59.811	47.826	5.05	0.00	3.09	R
2926	4863	0.619543	TTACCTGCAGGACTACCCCC	60.620	60.000	39.19	38.94	5.40	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
25	26	8.677148	TTTAGTTATCCTAAACTGATCATGCC	57.323	34.615	0.00	0.00	40.02	4.40
26	27	6.252599	AGTTATCCTAAACTGATCATGCCA	57.747	37.500	0.00	0.00	38.28	4.92
27	28	6.058183	AGTTATCCTAAACTGATCATGCCAC	58.942	40.000	0.00	0.00	38.28	5.01
28	29	3.998913	TCCTAAACTGATCATGCCACA	57.001	42.857	0.00	0.00	0.00	4.17
29	30	4.299586	TCCTAAACTGATCATGCCACAA	57.700	40.909	0.00	0.00	0.00	3.33
30	31	4.009675	TCCTAAACTGATCATGCCACAAC	58.990	43.478	0.00	0.00	0.00	3.32
31	32	4.012374	CCTAAACTGATCATGCCACAACT	58.988	43.478	0.00	0.00	0.00	3.16
32	33	4.460382	CCTAAACTGATCATGCCACAACTT	59.540	41.667	0.00	0.00	0.00	2.66
33	34	3.928727	AACTGATCATGCCACAACTTG	57.071	42.857	0.00	0.00	0.00	3.16
34	35	1.542915	ACTGATCATGCCACAACTTGC	59.457	47.619	0.00	0.00	0.00	4.01
35	36	1.816835	CTGATCATGCCACAACTTGCT	59.183	47.619	0.00	0.00	0.00	3.91
36	37	2.230508	CTGATCATGCCACAACTTGCTT	59.769	45.455	0.00	0.00	0.00	3.91
37	38	2.629137	TGATCATGCCACAACTTGCTTT	59.371	40.909	0.00	0.00	0.00	3.51
38	39	3.825585	TGATCATGCCACAACTTGCTTTA	59.174	39.130	0.00	0.00	0.00	1.85
39	40	4.280425	TGATCATGCCACAACTTGCTTTAA	59.720	37.500	0.00	0.00	0.00	1.52
40	41	4.662468	TCATGCCACAACTTGCTTTAAA	57.338	36.364	0.00	0.00	0.00	1.52
41	42	4.619973	TCATGCCACAACTTGCTTTAAAG	58.380	39.130	11.02	11.02	0.00	1.85
42	43	4.340666	TCATGCCACAACTTGCTTTAAAGA	59.659	37.500	19.48	1.53	0.00	2.52
43	44	4.040445	TGCCACAACTTGCTTTAAAGAC	57.960	40.909	19.48	10.51	0.00	3.01
44	45	3.699038	TGCCACAACTTGCTTTAAAGACT	59.301	39.130	19.48	0.00	0.00	3.24
45	46	4.884744	TGCCACAACTTGCTTTAAAGACTA	59.115	37.500	19.48	6.52	0.00	2.59
46	47	5.534654	TGCCACAACTTGCTTTAAAGACTAT	59.465	36.000	19.48	0.00	0.00	2.12
47	48	6.086871	GCCACAACTTGCTTTAAAGACTATC	58.913	40.000	19.48	1.24	0.00	2.08
48	49	6.293955	GCCACAACTTGCTTTAAAGACTATCA	60.294	38.462	19.48	3.98	0.00	2.15
49	50	7.078228	CCACAACTTGCTTTAAAGACTATCAC	58.922	38.462	19.48	0.00	0.00	3.06

Showing 1 to 25 of 343 entries

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Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability
0	1	8.271458	TGGCATGATCAGTTTAGGATAACTAAA	58.729	33.333	0.09	46.58	1.85
1	2	7.715249	GTGGCATGATCAGTTTAGGATAACTAA	59.285	37.037	0.09	39.84	2.24
2	3	7.147567	TGTGGCATGATCAGTTTAGGATAACTA	60.148	37.037	0.09	36.24	2.24
3	4	6.058183	GTGGCATGATCAGTTTAGGATAACT	58.942	40.000	0.09	38.87	2.24
4	5	5.822519	TGTGGCATGATCAGTTTAGGATAAC	59.177	40.000	0.09	0.00	1.89
5	6	6.000246	TGTGGCATGATCAGTTTAGGATAA	58.000	37.500	0.09	0.00	1.75
6	7	5.628797	TGTGGCATGATCAGTTTAGGATA	57.371	39.130	0.09	0.00	2.59
7	8	4.508551	TGTGGCATGATCAGTTTAGGAT	57.491	40.909	0.09	0.00	3.24
8	9	3.998913	TGTGGCATGATCAGTTTAGGA	57.001	42.857	0.09	0.00	2.94
9	10	4.012374	AGTTGTGGCATGATCAGTTTAGG	58.988	43.478	0.09	0.00	2.69
10	11	5.396484	CAAGTTGTGGCATGATCAGTTTAG	58.604	41.667	0.09	0.00	1.85
11	12	4.321156	GCAAGTTGTGGCATGATCAGTTTA	60.321	41.667	0.09	0.00	2.01
12	13	3.553508	GCAAGTTGTGGCATGATCAGTTT	60.554	43.478	0.09	0.00	2.66
13	14	2.029649	GCAAGTTGTGGCATGATCAGTT	60.030	45.455	0.09	0.00	3.16
14	15	1.542915	GCAAGTTGTGGCATGATCAGT	59.457	47.619	0.09	0.00	3.41
15	16	1.816835	AGCAAGTTGTGGCATGATCAG	59.183	47.619	0.09	0.00	2.90
16	17	1.913778	AGCAAGTTGTGGCATGATCA	58.086	45.000	4.48	0.00	2.92
17	18	3.308438	AAAGCAAGTTGTGGCATGATC	57.692	42.857	4.48	0.00	2.92
18	19	4.870123	TTAAAGCAAGTTGTGGCATGAT	57.130	36.364	4.48	0.00	2.45
19	20	4.340666	TCTTTAAAGCAAGTTGTGGCATGA	59.659	37.500	10.51	0.00	3.07
20	21	4.445385	GTCTTTAAAGCAAGTTGTGGCATG	59.555	41.667	10.51	0.00	4.06
21	22	4.342092	AGTCTTTAAAGCAAGTTGTGGCAT	59.658	37.500	10.51	0.00	4.40
22	23	3.699038	AGTCTTTAAAGCAAGTTGTGGCA	59.301	39.130	10.51	0.00	4.92
23	24	4.307443	AGTCTTTAAAGCAAGTTGTGGC	57.693	40.909	10.51	0.00	5.01
24	25	7.078228	GTGATAGTCTTTAAAGCAAGTTGTGG	58.922	38.462	10.51	0.00	4.17

Showing 1 to 25 of 314 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.