AutoCloner

Multiple sequence alignment - TraesCS1D01G358700

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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	TraesCS1D01G358700	chr1D	100.000	2318	0	0	1	2318	442379573	442377256	0.000000e+00	4281.0
1	TraesCS1D01G358700	chr1D	79.211	837	106	30	1478	2258	442409172	442408348	9.490000e-144	520.0
2	TraesCS1D01G358700	chr1D	78.457	376	46	20	1351	1709	441957220	441957577	1.800000e-51	213.0
3	TraesCS1D01G358700	chr7D	95.160	1343	59	2	1	1343	205159895	205158559	0.000000e+00	2115.0
4	TraesCS1D01G358700	chr7D	94.161	1353	73	3	1	1350	76799522	76800871	0.000000e+00	2056.0
5	TraesCS1D01G358700	chr6B	91.660	1343	112	0	1	1343	708391319	708389977	0.000000e+00	1860.0
6	TraesCS1D01G358700	chr6B	86.960	1342	173	1	2	1343	623439798	623441137	0.000000e+00	1507.0
7	TraesCS1D01G358700	chr2B	88.227	1342	158	0	2	1343	115905325	115903984	0.000000e+00	1604.0
8	TraesCS1D01G358700	chr7B	87.118	1343	173	0	1	1343	621911852	621910510	0.000000e+00	1522.0
9	TraesCS1D01G358700	chr1B	85.981	1341	182	4	2	1341	539123097	539124432	0.000000e+00	1430.0
10	TraesCS1D01G358700	chr1B	94.613	594	30	2	1697	2288	600977234	600976641	0.000000e+00	918.0
11	TraesCS1D01G358700	chr1B	79.644	899	116	29	1414	2258	600985452	600984567	3.320000e-163	584.0
12	TraesCS1D01G358700	chr1B	85.714	252	27	6	1447	1691	600977459	600977210	8.220000e-65	257.0
13	TraesCS1D01G358700	chr1B	94.340	53	2	1	1342	1394	600979674	600979623	1.910000e-11	80.5
14	TraesCS1D01G358700	chr4B	84.925	1340	198	4	5	1342	514183773	514182436	0.000000e+00	1352.0
15	TraesCS1D01G358700	chr1A	89.990	959	49	26	1343	2284	536341700	536342628	0.000000e+00	1195.0
16	TraesCS1D01G358700	chr1A	82.470	502	71	8	1765	2258	536297756	536298248	7.660000e-115	424.0
17	TraesCS1D01G358700	chrUn	82.156	1345	234	5	2	1343	307306740	307308081	0.000000e+00	1149.0

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	TraesCS1D01G358700	chr1D	442377256	442379573	2317	True	4281.0	4281	100.000000	1	2318	1	chr1D.!!$R1	2317
1	TraesCS1D01G358700	chr1D	442408348	442409172	824	True	520.0	520	79.211000	1478	2258	1	chr1D.!!$R2	780
2	TraesCS1D01G358700	chr7D	205158559	205159895	1336	True	2115.0	2115	95.160000	1	1343	1	chr7D.!!$R1	1342
3	TraesCS1D01G358700	chr7D	76799522	76800871	1349	False	2056.0	2056	94.161000	1	1350	1	chr7D.!!$F1	1349
4	TraesCS1D01G358700	chr6B	708389977	708391319	1342	True	1860.0	1860	91.660000	1	1343	1	chr6B.!!$R1	1342
5	TraesCS1D01G358700	chr6B	623439798	623441137	1339	False	1507.0	1507	86.960000	2	1343	1	chr6B.!!$F1	1341
6	TraesCS1D01G358700	chr2B	115903984	115905325	1341	True	1604.0	1604	88.227000	2	1343	1	chr2B.!!$R1	1341
7	TraesCS1D01G358700	chr7B	621910510	621911852	1342	True	1522.0	1522	87.118000	1	1343	1	chr7B.!!$R1	1342
8	TraesCS1D01G358700	chr1B	539123097	539124432	1335	False	1430.0	1430	85.981000	2	1341	1	chr1B.!!$F1	1339
9	TraesCS1D01G358700	chr1B	600984567	600985452	885	True	584.0	584	79.644000	1414	2258	1	chr1B.!!$R1	844
10	TraesCS1D01G358700	chr1B	600976641	600979674	3033	True	418.5	918	91.555667	1342	2288	3	chr1B.!!$R2	946
11	TraesCS1D01G358700	chr4B	514182436	514183773	1337	True	1352.0	1352	84.925000	5	1342	1	chr4B.!!$R1	1337
12	TraesCS1D01G358700	chr1A	536341700	536342628	928	False	1195.0	1195	89.990000	1343	2284	1	chr1A.!!$F2	941
13	TraesCS1D01G358700	chrUn	307306740	307308081	1341	False	1149.0	1149	82.156000	2	1343	1	chrUn.!!$F1	1341

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
274	275	1.133598	CCAATGGTGCGTCGAGTACTA	59.866	52.381	0.0	0.0	35.67	1.82	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2098	4321	1.372499	CGCGGTTGAAGACGAGGAA	60.372	57.895	0.0	0.0	0.0	3.36	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
274	275	1.133598	CCAATGGTGCGTCGAGTACTA	59.866	52.381	0.00	0.00	35.67	1.82
352	355	7.085116	TCAAAAATTGAAAATCAATGCATGGC	58.915	30.769	0.00	0.00	45.57	4.40
579	585	1.176527	GGCTAACTTCATTGCTGGCA	58.823	50.000	0.00	0.00	0.00	4.92
609	615	2.159327	TCGACGTCCGAGATATGCTA	57.841	50.000	10.58	0.00	43.23	3.49
653	659	2.682856	GGCAGCTCCGTAATGATTTGAA	59.317	45.455	0.00	0.00	0.00	2.69
778	784	7.797121	ATTAAAGGGAAAATGTCAACCTCAT	57.203	32.000	0.00	0.00	0.00	2.90
1069	1075	3.463944	GTTCAAACGGACTCCTCTGAAA	58.536	45.455	5.40	0.00	0.00	2.69
1259	1268	1.729881	CTATTTGGCTTGGCTCGGC	59.270	57.895	0.00	0.00	0.00	5.54
1391	1400	2.517450	CGAAGACGAGGCAATCCGC	61.517	63.158	0.00	0.00	42.66	5.54
1399	1410	3.869272	GGCAATCCGCACGAGCTG	61.869	66.667	2.73	0.00	45.17	4.24
1405	1416	1.021390	ATCCGCACGAGCTGGAAAAG	61.021	55.000	18.29	0.00	43.20	2.27
1417	1428	5.456822	CGAGCTGGAAAAGAAAACAAAAGAG	59.543	40.000	0.00	0.00	0.00	2.85
1527	3690	1.658717	CTCCGATCGCATGGACGTC	60.659	63.158	10.32	7.13	0.00	4.34
1528	3691	3.024609	CCGATCGCATGGACGTCG	61.025	66.667	10.32	0.00	36.80	5.12
1529	3692	3.024609	CGATCGCATGGACGTCGG	61.025	66.667	9.92	2.71	34.93	4.79
1530	3693	2.104331	GATCGCATGGACGTCGGT	59.896	61.111	9.92	0.00	0.00	4.69
1531	3694	1.944676	GATCGCATGGACGTCGGTC	60.945	63.158	9.92	0.00	42.66	4.79
1532	3695	3.751401	ATCGCATGGACGTCGGTCG	62.751	63.158	9.92	10.25	44.39	4.79
1535	3698	4.771356	CATGGACGTCGGTCGCGT	62.771	66.667	9.92	11.15	44.39	6.01
2031	4251	2.697425	CGCTTCGACTTCCGCATG	59.303	61.111	0.00	0.00	38.37	4.06
2284	4512	1.254954	GTGGAACGGACTCTACACCT	58.745	55.000	0.00	0.00	0.00	4.00
2285	4513	1.201880	GTGGAACGGACTCTACACCTC	59.798	57.143	0.00	0.00	0.00	3.85
2286	4514	0.450983	GGAACGGACTCTACACCTCG	59.549	60.000	0.00	0.00	0.00	4.63
2287	4515	1.446907	GAACGGACTCTACACCTCGA	58.553	55.000	0.00	0.00	0.00	4.04
2288	4516	2.015587	GAACGGACTCTACACCTCGAT	58.984	52.381	0.00	0.00	0.00	3.59
2289	4517	2.125773	ACGGACTCTACACCTCGATT	57.874	50.000	0.00	0.00	0.00	3.34
2290	4518	2.015587	ACGGACTCTACACCTCGATTC	58.984	52.381	0.00	0.00	0.00	2.52
2291	4519	1.334243	CGGACTCTACACCTCGATTCC	59.666	57.143	0.00	0.00	0.00	3.01
2292	4520	2.376109	GGACTCTACACCTCGATTCCA	58.624	52.381	0.00	0.00	31.44	3.53
2293	4521	2.099427	GGACTCTACACCTCGATTCCAC	59.901	54.545	0.00	0.00	31.44	4.02
2294	4522	2.099427	GACTCTACACCTCGATTCCACC	59.901	54.545	0.00	0.00	0.00	4.61
2295	4523	2.100197	CTCTACACCTCGATTCCACCA	58.900	52.381	0.00	0.00	0.00	4.17
2296	4524	1.822990	TCTACACCTCGATTCCACCAC	59.177	52.381	0.00	0.00	0.00	4.16
2297	4525	0.899720	TACACCTCGATTCCACCACC	59.100	55.000	0.00	0.00	0.00	4.61
2298	4526	1.125093	ACACCTCGATTCCACCACCA	61.125	55.000	0.00	0.00	0.00	4.17
2299	4527	0.036164	CACCTCGATTCCACCACCAA	59.964	55.000	0.00	0.00	0.00	3.67
2300	4528	0.324943	ACCTCGATTCCACCACCAAG	59.675	55.000	0.00	0.00	0.00	3.61
2301	4529	1.026718	CCTCGATTCCACCACCAAGC	61.027	60.000	0.00	0.00	0.00	4.01
2302	4530	1.361668	CTCGATTCCACCACCAAGCG	61.362	60.000	0.00	0.00	32.75	4.68
2303	4531	1.375396	CGATTCCACCACCAAGCGA	60.375	57.895	0.00	0.00	33.26	4.93
2304	4532	1.635663	CGATTCCACCACCAAGCGAC	61.636	60.000	0.00	0.00	33.26	5.19
2305	4533	1.303317	ATTCCACCACCAAGCGACC	60.303	57.895	0.00	0.00	0.00	4.79
2306	4534	3.818121	TTCCACCACCAAGCGACCG	62.818	63.158	0.00	0.00	0.00	4.79
2307	4535	4.619227	CCACCACCAAGCGACCGT	62.619	66.667	0.00	0.00	0.00	4.83
2308	4536	3.041940	CACCACCAAGCGACCGTC	61.042	66.667	0.00	0.00	0.00	4.79
2309	4537	3.542676	ACCACCAAGCGACCGTCA	61.543	61.111	0.00	0.00	0.00	4.35
2310	4538	2.047274	CCACCAAGCGACCGTCAT	60.047	61.111	0.00	0.00	0.00	3.06
2311	4539	2.390599	CCACCAAGCGACCGTCATG	61.391	63.158	0.00	0.00	0.00	3.07
2312	4540	1.374125	CACCAAGCGACCGTCATGA	60.374	57.895	0.00	0.00	0.00	3.07
2313	4541	1.079819	ACCAAGCGACCGTCATGAG	60.080	57.895	0.00	0.00	0.00	2.90
2314	4542	2.456119	CCAAGCGACCGTCATGAGC	61.456	63.158	0.00	0.00	0.00	4.26
2315	4543	1.737735	CAAGCGACCGTCATGAGCA	60.738	57.895	0.00	0.00	0.00	4.26
2316	4544	1.738099	AAGCGACCGTCATGAGCAC	60.738	57.895	0.00	0.00	0.00	4.40
2317	4545	2.432456	GCGACCGTCATGAGCACA	60.432	61.111	0.00	0.00	0.00	4.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
13	14	0.247736	CAGTTCCCCTTCGGAGTGAG	59.752	60.000	0.00	0.00	43.39	3.51
147	148	4.927049	AGAAATCATCTCTTTGGCAAGGA	58.073	39.130	11.79	11.79	30.46	3.36
151	152	3.194116	GCCAAGAAATCATCTCTTTGGCA	59.806	43.478	18.20	0.00	41.59	4.92
185	186	1.066454	CCGTGAACCCACCACTTTTTC	59.934	52.381	0.00	0.00	40.12	2.29
291	292	1.818674	CAAATGTAGTTCCACCCAGCC	59.181	52.381	0.00	0.00	0.00	4.85
334	337	3.589495	TCGCCATGCATTGATTTTCAA	57.411	38.095	1.13	0.00	41.09	2.69
352	355	0.173481	ATCGTCCCTGTCACACATCG	59.827	55.000	0.00	0.00	0.00	3.84
579	585	1.694639	GGACGTCGATCGAACACTTT	58.305	50.000	21.31	0.02	42.86	2.66
609	615	5.816777	CCAAATCCGCCAAATGAACATAATT	59.183	36.000	0.00	0.00	0.00	1.40
653	659	2.430367	GCACTTCCTTCCCGTGGT	59.570	61.111	0.00	0.00	0.00	4.16
778	784	1.074775	GGGTTGGCACCATCACAGA	59.925	57.895	8.11	0.00	46.43	3.41
848	854	2.743752	CCATCAACTGACAGCGCCG	61.744	63.158	2.29	0.00	0.00	6.46
1243	1252	2.036256	AGCCGAGCCAAGCCAAAT	59.964	55.556	0.00	0.00	0.00	2.32
1259	1268	4.060900	CAAATCCTCGATACATGGTGGAG	58.939	47.826	0.00	1.62	32.95	3.86
1391	1400	3.691049	TGTTTTCTTTTCCAGCTCGTG	57.309	42.857	0.00	0.00	0.00	4.35
1399	1410	8.467598	ACCTAGTTCTCTTTTGTTTTCTTTTCC	58.532	33.333	0.00	0.00	0.00	3.13
1405	1416	8.890124	AGTCTACCTAGTTCTCTTTTGTTTTC	57.110	34.615	0.00	0.00	0.00	2.29
1417	1428	8.250143	ACTACTAGTAGGAGTCTACCTAGTTC	57.750	42.308	29.05	0.00	45.24	3.01
1534	3697	4.899239	CATGCTCCCTCGGGCGAC	62.899	72.222	0.00	0.00	34.68	5.19
1576	3760	2.576832	GGACCACGTCTTCCGGGAA	61.577	63.158	9.52	9.52	45.03	3.97
2098	4321	1.372499	CGCGGTTGAAGACGAGGAA	60.372	57.895	0.00	0.00	0.00	3.36
2172	4397	2.682893	GCTGAAGCACACTATCGGG	58.317	57.895	0.00	0.00	41.59	5.14
2284	4512	1.375396	CGCTTGGTGGTGGAATCGA	60.375	57.895	0.00	0.00	0.00	3.59
2285	4513	1.375396	TCGCTTGGTGGTGGAATCG	60.375	57.895	0.00	0.00	0.00	3.34
2286	4514	1.305930	GGTCGCTTGGTGGTGGAATC	61.306	60.000	0.00	0.00	0.00	2.52
2287	4515	1.303317	GGTCGCTTGGTGGTGGAAT	60.303	57.895	0.00	0.00	0.00	3.01
2288	4516	2.112297	GGTCGCTTGGTGGTGGAA	59.888	61.111	0.00	0.00	0.00	3.53
2289	4517	4.308458	CGGTCGCTTGGTGGTGGA	62.308	66.667	0.00	0.00	0.00	4.02
2290	4518	4.619227	ACGGTCGCTTGGTGGTGG	62.619	66.667	0.00	0.00	0.00	4.61
2291	4519	3.041940	GACGGTCGCTTGGTGGTG	61.042	66.667	0.00	0.00	0.00	4.17
2292	4520	2.879233	ATGACGGTCGCTTGGTGGT	61.879	57.895	3.34	0.00	0.00	4.16
2293	4521	2.047274	ATGACGGTCGCTTGGTGG	60.047	61.111	3.34	0.00	0.00	4.61
2294	4522	1.354337	CTCATGACGGTCGCTTGGTG	61.354	60.000	3.34	0.00	0.00	4.17
2295	4523	1.079819	CTCATGACGGTCGCTTGGT	60.080	57.895	3.34	0.00	0.00	3.67
2296	4524	2.456119	GCTCATGACGGTCGCTTGG	61.456	63.158	3.34	0.00	0.00	3.61
2297	4525	1.737735	TGCTCATGACGGTCGCTTG	60.738	57.895	3.34	1.78	0.00	4.01
2298	4526	1.738099	GTGCTCATGACGGTCGCTT	60.738	57.895	3.34	0.00	0.00	4.68
2299	4527	2.125912	GTGCTCATGACGGTCGCT	60.126	61.111	3.34	0.00	0.00	4.93
2300	4528	2.432456	TGTGCTCATGACGGTCGC	60.432	61.111	3.34	1.29	0.00	5.19

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.