AutoCloner

Multiple sequence alignment - TraesCS4B01G081000

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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	TraesCS4B01G081000	chr4B	100.000	3914	0	0	1	3914	78621264	78625177	0.000000e+00	7228
1	TraesCS4B01G081000	chr4B	91.971	411	29	4	30	438	115058124	115057716	1.220000e-159	573
2	TraesCS4B01G081000	chr4B	91.133	406	30	6	37	438	12268432	12268029	2.660000e-151	545
3	TraesCS4B01G081000	chr1B	93.953	3903	208	21	30	3914	197457713	197453821	0.000000e+00	5875
4	TraesCS4B01G081000	chr1B	93.609	3192	186	10	34	3211	401790323	401793510	0.000000e+00	4748
5	TraesCS4B01G081000	chr1B	91.084	415	33	4	27	438	73796577	73796990	3.420000e-155	558
6	TraesCS4B01G081000	chr2D	92.113	3626	222	38	322	3914	543503626	543500032	0.000000e+00	5053
7	TraesCS4B01G081000	chr5D	91.934	3620	232	34	322	3914	438205893	438202307	0.000000e+00	5012
8	TraesCS4B01G081000	chr5D	90.395	3394	279	33	555	3912	383616031	383612649	0.000000e+00	4418
9	TraesCS4B01G081000	chr6D	90.237	3636	289	45	322	3912	426968101	426964487	0.000000e+00	4687
10	TraesCS4B01G081000	chr2B	88.962	3642	334	51	322	3910	366597161	366593535	0.000000e+00	4436
11	TraesCS4B01G081000	chr2B	89.583	2448	191	40	27	2424	760365067	760367500	0.000000e+00	3049
12	TraesCS4B01G081000	chr2B	86.288	2166	215	44	322	2425	485407208	485409353	0.000000e+00	2279
13	TraesCS4B01G081000	chr6A	89.149	3594	321	47	356	3914	245447238	245450797	0.000000e+00	4412
14	TraesCS4B01G081000	chr1A	88.506	3654	311	56	322	3914	124221335	124217730	0.000000e+00	4320
15	TraesCS4B01G081000	chr4D	87.698	3666	353	70	324	3912	170233666	170237310	0.000000e+00	4181
16	TraesCS4B01G081000	chr5B	87.423	2449	217	47	30	2427	615692523	615690115	0.000000e+00	2732
17	TraesCS4B01G081000	chr5B	89.614	414	37	6	30	438	78454990	78454578	4.480000e-144	521
18	TraesCS4B01G081000	chr7B	92.048	415	29	4	27	438	134447093	134447506	7.290000e-162	580

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	TraesCS4B01G081000	chr4B	78621264	78625177	3913	False	7228	7228	100.000	1	3914	1	chr4B.!!$F1	3913
1	TraesCS4B01G081000	chr1B	197453821	197457713	3892	True	5875	5875	93.953	30	3914	1	chr1B.!!$R1	3884
2	TraesCS4B01G081000	chr1B	401790323	401793510	3187	False	4748	4748	93.609	34	3211	1	chr1B.!!$F2	3177
3	TraesCS4B01G081000	chr2D	543500032	543503626	3594	True	5053	5053	92.113	322	3914	1	chr2D.!!$R1	3592
4	TraesCS4B01G081000	chr5D	438202307	438205893	3586	True	5012	5012	91.934	322	3914	1	chr5D.!!$R2	3592
5	TraesCS4B01G081000	chr5D	383612649	383616031	3382	True	4418	4418	90.395	555	3912	1	chr5D.!!$R1	3357
6	TraesCS4B01G081000	chr6D	426964487	426968101	3614	True	4687	4687	90.237	322	3912	1	chr6D.!!$R1	3590
7	TraesCS4B01G081000	chr2B	366593535	366597161	3626	True	4436	4436	88.962	322	3910	1	chr2B.!!$R1	3588
8	TraesCS4B01G081000	chr2B	760365067	760367500	2433	False	3049	3049	89.583	27	2424	1	chr2B.!!$F2	2397
9	TraesCS4B01G081000	chr2B	485407208	485409353	2145	False	2279	2279	86.288	322	2425	1	chr2B.!!$F1	2103
10	TraesCS4B01G081000	chr6A	245447238	245450797	3559	False	4412	4412	89.149	356	3914	1	chr6A.!!$F1	3558
11	TraesCS4B01G081000	chr1A	124217730	124221335	3605	True	4320	4320	88.506	322	3914	1	chr1A.!!$R1	3592
12	TraesCS4B01G081000	chr4D	170233666	170237310	3644	False	4181	4181	87.698	324	3912	1	chr4D.!!$F1	3588
13	TraesCS4B01G081000	chr5B	615690115	615692523	2408	True	2732	2732	87.423	30	2427	1	chr5B.!!$R2	2397

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
402	409	0.596577	GGAAGTTGTCCGCCCTTTTC	59.403	55.0	0.00	0.00	36.40	2.29	F
1429	1821	0.180406	ACGTGGAAGACTGCCTTTGT	59.820	50.0	0.00	0.00	34.68	2.83	F
2531	3018	0.244178	TGCGTGGACGTACAATGCTA	59.756	50.0	22.52	9.94	42.22	3.49	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
1518	1910	0.596082	CAGGAAACAAACGGGCGAAT	59.404	50.0	0.00	3.34	R
2748	3236	0.037326	TGACACAGATGGCGGAGTTC	60.037	55.0	36.14	3.01	R
3354	3864	1.135046	CTCCATGTCGTCATCATCGC	58.865	55.0	31.15	4.58	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
17	18	4.226803	ATTGCGCAGTTTTGTCGC	57.773	50.000	11.31	0.00	44.42	5.19
18	19	1.371635	ATTGCGCAGTTTTGTCGCC	60.372	52.632	11.31	0.00	43.94	5.54
19	20	3.798639	TTGCGCAGTTTTGTCGCCG	62.799	57.895	11.31	0.00	43.94	6.46
20	21	4.307908	GCGCAGTTTTGTCGCCGT	62.308	61.111	0.30	0.00	41.04	5.68
21	22	2.127758	CGCAGTTTTGTCGCCGTC	60.128	61.111	0.00	0.00	0.00	4.79
22	23	2.127758	GCAGTTTTGTCGCCGTCG	60.128	61.111	0.00	0.00	0.00	5.12
23	24	2.127758	CAGTTTTGTCGCCGTCGC	60.128	61.111	0.00	0.00	35.26	5.19
54	55	5.120399	CAAATATGCTTTCCATGTGGCAAT	58.880	37.500	0.00	0.00	38.21	3.56
56	57	3.706600	ATGCTTTCCATGTGGCAATTT	57.293	38.095	0.00	0.00	38.21	1.82
208	210	4.832266	TGGCAACTCATTTTTATGTGAGGT	59.168	37.500	7.23	0.00	44.72	3.85
212	214	6.294176	GCAACTCATTTTTATGTGAGGTCAGT	60.294	38.462	7.23	0.00	44.72	3.41
301	305	6.096987	TGTTTAACATGGCAACTTGAACCTAA	59.903	34.615	0.00	0.00	44.16	2.69
310	314	5.576774	GGCAACTTGAACCTAATACATTTGC	59.423	40.000	0.00	0.00	34.80	3.68
402	409	0.596577	GGAAGTTGTCCGCCCTTTTC	59.403	55.000	0.00	0.00	36.40	2.29
412	563	1.172180	CGCCCTTTTCTTGGAGTGCA	61.172	55.000	0.00	0.00	0.00	4.57
415	566	2.825532	GCCCTTTTCTTGGAGTGCATTA	59.174	45.455	0.00	0.00	0.00	1.90
514	676	6.991938	AGTTGCCACATTATATGTTTTGTGT	58.008	32.000	0.00	0.00	42.70	3.72
662	1003	1.157641	ACAGTCCTAGGGGGTGGGTA	61.158	60.000	9.46	0.00	36.25	3.69
696	1044	2.802247	GCCTCATTTGCCACTTTCAAAC	59.198	45.455	0.00	0.00	36.40	2.93
739	1087	5.740290	TTCTACTAGCTGGCAACTACTTT	57.260	39.130	0.00	0.00	37.61	2.66
866	1233	8.951243	ACTATCCTCTTCAAATGCTTAAACTTC	58.049	33.333	0.00	0.00	0.00	3.01
951	1323	5.221362	TGCATTTCTTTCTATATCCGTCGGA	60.221	40.000	18.01	18.01	35.55	4.55
955	1327	7.514784	TTTCTTTCTATATCCGTCGGATGTA	57.485	36.000	32.49	28.03	43.06	2.29
1010	1384	1.079474	TTAGCACAATGGCTCGCGA	60.079	52.632	9.26	9.26	44.54	5.87
1046	1423	8.492782	AGATGATGAGGACTTCATTGATTTACT	58.507	33.333	1.10	0.00	46.51	2.24
1060	1437	6.417191	TTGATTTACTACAACAGAATCGCC	57.583	37.500	0.00	0.00	31.15	5.54
1064	1441	1.480954	ACTACAACAGAATCGCCCGAT	59.519	47.619	0.00	0.00	36.23	4.18
1082	1459	3.000041	CGATTGGTCGGACAAAAGATGA	59.000	45.455	10.76	0.00	44.00	2.92
1123	1505	5.068987	CCACCCCCATATGTTTTAATGTCAG	59.931	44.000	1.24	0.00	0.00	3.51
1177	1560	3.878086	TTTCACGACACTGAAAGATGC	57.122	42.857	0.00	0.00	35.63	3.91
1263	1650	2.034305	ACGCCTGACTATATTGACCGAC	59.966	50.000	0.00	0.00	0.00	4.79
1269	1656	5.117355	TGACTATATTGACCGACGGATTC	57.883	43.478	23.38	9.42	0.00	2.52
1429	1821	0.180406	ACGTGGAAGACTGCCTTTGT	59.820	50.000	0.00	0.00	34.68	2.83
1518	1910	8.088981	GTGAATAATAAGATCGAGGAAGCCTTA	58.911	37.037	0.00	0.00	31.76	2.69
1567	1959	2.626266	TCCATGCCGAATACGACTATGT	59.374	45.455	0.00	0.00	42.66	2.29
1633	2025	6.544928	TTAAGATGAAGCTCCTCATGTACA	57.455	37.500	5.62	0.00	36.15	2.90
1657	2049	3.781079	TCTCAACTGTTTTTGTGCCTG	57.219	42.857	0.00	0.00	0.00	4.85
1770	2168	3.834813	TGTCATCTGGAAGCTAGTCACTT	59.165	43.478	0.00	0.00	0.00	3.16
2060	2500	1.466856	ACAAGATCGTGCATGGCAAT	58.533	45.000	8.68	0.00	41.47	3.56
2204	2680	8.830201	ATTCATTTCATACATCTACTCTCTGC	57.170	34.615	0.00	0.00	0.00	4.26
2221	2698	3.419943	TCTGCTGTACAATTTGCATGGA	58.580	40.909	7.84	1.31	34.79	3.41
2334	2814	6.070824	GCAAATCTTTTTCCTTCATCCCCTTA	60.071	38.462	0.00	0.00	0.00	2.69
2345	2825	6.068853	TCCTTCATCCCCTTAAACTTGATGAT	60.069	38.462	0.00	0.00	40.86	2.45
2525	3012	1.167781	TGTCTCTGCGTGGACGTACA	61.168	55.000	0.00	0.00	42.22	2.90
2531	3018	0.244178	TGCGTGGACGTACAATGCTA	59.756	50.000	22.52	9.94	42.22	3.49
2767	3255	0.037326	GAACTCCGCCATCTGTGTCA	60.037	55.000	0.00	0.00	0.00	3.58
2834	3328	9.274206	GTTAGTCACTGTTCCTTATTTTCTCTT	57.726	33.333	0.00	0.00	0.00	2.85
2911	3406	1.042559	CAGTGTGTTTGGTGGGCCTT	61.043	55.000	4.53	0.00	35.27	4.35
2962	3457	3.173151	TCAGCTCCATCTTGTCCTGTTA	58.827	45.455	0.00	0.00	0.00	2.41
3135	3645	1.009829	GTTGAGCATCTAGTTGGGCG	58.990	55.000	3.05	0.00	34.92	6.13
3276	3786	1.907807	GGCCAACTGGTTGCCATGA	60.908	57.895	2.41	0.00	39.16	3.07
3339	3849	5.508657	CGCAAGATGAACTAGATGGAGATGA	60.509	44.000	0.00	0.00	43.02	2.92
3354	3864	1.759445	AGATGATGGTCTCGACAAGGG	59.241	52.381	0.00	0.00	0.00	3.95
3544	4058	0.991920	GGGTTCCAGAGGATGTTGGA	59.008	55.000	0.00	0.00	41.59	3.53
3706	4228	2.490991	GTGTCTCACACTTTGTACCCC	58.509	52.381	0.00	0.00	45.27	4.95

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
4	5	2.127758	GACGGCGACAAAACTGCG	60.128	61.111	16.62	0.00	0.00	5.18
5	6	2.127758	CGACGGCGACAAAACTGC	60.128	61.111	16.62	0.00	40.82	4.40
6	7	2.127758	GCGACGGCGACAAAACTG	60.128	61.111	18.90	0.00	40.82	3.16
18	19	0.996462	ATATTTGTGACACCGCGACG	59.004	50.000	8.23	0.00	0.00	5.12
19	20	1.529010	GCATATTTGTGACACCGCGAC	60.529	52.381	8.23	0.00	0.00	5.19
20	21	0.724549	GCATATTTGTGACACCGCGA	59.275	50.000	8.23	0.00	0.00	5.87
21	22	0.726827	AGCATATTTGTGACACCGCG	59.273	50.000	0.00	0.00	0.00	6.46
22	23	2.919666	AAGCATATTTGTGACACCGC	57.080	45.000	2.45	0.00	0.00	5.68
23	24	3.190327	TGGAAAGCATATTTGTGACACCG	59.810	43.478	2.45	0.00	0.00	4.94
24	25	4.782019	TGGAAAGCATATTTGTGACACC	57.218	40.909	2.45	0.00	0.00	4.16
25	26	5.574055	CACATGGAAAGCATATTTGTGACAC	59.426	40.000	0.00	0.00	36.06	3.67
26	27	5.336610	CCACATGGAAAGCATATTTGTGACA	60.337	40.000	0.00	0.00	36.06	3.58
27	28	5.104374	CCACATGGAAAGCATATTTGTGAC	58.896	41.667	0.00	0.00	36.06	3.67
28	29	4.381825	GCCACATGGAAAGCATATTTGTGA	60.382	41.667	0.87	0.00	36.06	3.58
54	55	7.144661	CAGCCATAGTGTGTTCACAAAATAAA	58.855	34.615	7.22	0.00	46.01	1.40
56	57	5.767665	ACAGCCATAGTGTGTTCACAAAATA	59.232	36.000	7.22	2.50	46.01	1.40
208	210	0.251634	TGTGGCAACTCACACACTGA	59.748	50.000	0.00	0.00	42.20	3.41
301	305	6.513806	TGTATTCACAAGCAGCAAATGTAT	57.486	33.333	0.00	0.00	0.00	2.29
310	314	3.853831	TTGCCATGTATTCACAAGCAG	57.146	42.857	0.00	0.00	44.22	4.24
373	379	1.956477	GGACAACTTCCACTGCACAAT	59.044	47.619	0.00	0.00	45.10	2.71
393	399	1.172180	TGCACTCCAAGAAAAGGGCG	61.172	55.000	0.00	0.00	45.09	6.13
402	409	6.753279	CCATGTTAAACATAATGCACTCCAAG	59.247	38.462	0.00	0.00	36.53	3.61
412	563	7.602265	GGTTCAAGTTGCCATGTTAAACATAAT	59.398	33.333	0.00	0.00	36.53	1.28
415	566	5.070313	AGGTTCAAGTTGCCATGTTAAACAT	59.930	36.000	0.00	0.00	39.91	2.71
514	676	3.806949	AAGGGCAAACATCTTCCACTA	57.193	42.857	0.00	0.00	0.00	2.74
607	922	3.891977	TGGCAACTAAACACATTGGCTTA	59.108	39.130	10.53	0.00	46.12	3.09
662	1003	4.765856	GCAAATGAGGCAGATCATAGGAAT	59.234	41.667	0.00	0.00	39.00	3.01
721	1069	4.040461	TGAAGAAAGTAGTTGCCAGCTAGT	59.960	41.667	0.00	0.00	0.00	2.57
739	1087	3.575630	GACGTGTATGTGCTTCTGAAGA	58.424	45.455	21.06	0.55	0.00	2.87
809	1168	5.259832	TGTGATGAACATGCACAAAAAGA	57.740	34.783	13.30	0.00	39.36	2.52
843	1204	6.127897	CCGAAGTTTAAGCATTTGAAGAGGAT	60.128	38.462	0.00	0.00	0.00	3.24
866	1233	0.678950	AAACTCAAATGGTTGGCCCG	59.321	50.000	0.00	0.00	35.29	6.13
951	1323	7.175990	ACACGTTAGGGTGAAATGAAAATACAT	59.824	33.333	0.00	0.00	40.38	2.29
1029	1403	8.547967	TCTGTTGTAGTAAATCAATGAAGTCC	57.452	34.615	0.00	0.00	0.00	3.85
1038	1415	4.873827	GGGCGATTCTGTTGTAGTAAATCA	59.126	41.667	0.00	0.00	0.00	2.57
1046	1423	2.276201	CAATCGGGCGATTCTGTTGTA	58.724	47.619	0.00	0.00	42.30	2.41
1064	1441	2.139917	CGTCATCTTTTGTCCGACCAA	58.860	47.619	0.00	0.00	0.00	3.67
1082	1459	2.550208	GGTGGAAAAGTGACCTCATCGT	60.550	50.000	0.00	0.00	0.00	3.73
1177	1560	8.928733	CATAACAGAAAAAGGATCATTTGTTGG	58.071	33.333	14.84	5.96	0.00	3.77
1216	1603	2.755650	CGAAGCCCTATTGCGATAACT	58.244	47.619	0.00	0.00	36.02	2.24
1263	1650	3.181503	CCTTTTGCTCATCAGTGAATCCG	60.182	47.826	0.00	0.00	33.05	4.18
1269	1656	1.471684	GCTCCCTTTTGCTCATCAGTG	59.528	52.381	0.00	0.00	0.00	3.66
1429	1821	2.499693	TGCAGAACACGGATTCCTCATA	59.500	45.455	0.30	0.00	0.00	2.15
1518	1910	0.596082	CAGGAAACAAACGGGCGAAT	59.404	50.000	0.00	0.00	0.00	3.34
1567	1959	1.600636	CCTCCAGCGAAGTTGCCAA	60.601	57.895	0.00	0.00	37.43	4.52
1633	2025	4.586001	AGGCACAAAAACAGTTGAGATCAT	59.414	37.500	0.00	0.00	32.59	2.45
1657	2049	1.372087	CTTGGGCGAAGAGATGTGGC	61.372	60.000	2.75	0.00	32.82	5.01
1805	2208	8.490355	CACAAATTTCAGGATAAAAAGTTGCTC	58.510	33.333	7.64	0.00	41.58	4.26
1817	2226	4.501915	CCTGCACAACACAAATTTCAGGAT	60.502	41.667	11.11	0.00	41.62	3.24
2060	2500	9.829507	ATTCACATAAACAATGAAAACAAAGGA	57.170	25.926	0.00	0.00	39.07	3.36
2195	2670	4.893608	TGCAAATTGTACAGCAGAGAGTA	58.106	39.130	3.57	0.00	32.48	2.59
2204	2680	4.880759	TGGTTTCCATGCAAATTGTACAG	58.119	39.130	0.00	0.00	0.00	2.74
2221	2698	3.006110	CCACAAGCTCAACATCATGGTTT	59.994	43.478	0.00	0.00	0.00	3.27
2334	2814	8.868522	TGTAGATTCCTTCAATCATCAAGTTT	57.131	30.769	0.00	0.00	43.27	2.66
2525	3012	3.367703	GCAAGCACAACCTTGATAGCATT	60.368	43.478	6.12	0.00	43.79	3.56
2531	3018	1.959085	CGGCAAGCACAACCTTGAT	59.041	52.632	6.12	0.00	43.79	2.57
2748	3236	0.037326	TGACACAGATGGCGGAGTTC	60.037	55.000	0.00	0.00	36.14	3.01
2767	3255	7.496346	AAAAGAGGGGAAAAGAAGAAGTTTT	57.504	32.000	0.00	0.00	0.00	2.43
2834	3328	7.561021	TCAGCAAAAACAACTAAGATGTGTA	57.439	32.000	0.00	0.00	0.00	2.90
2911	3406	4.219115	TCCATCCACTTGCCAAAGTTTTA	58.781	39.130	0.00	0.00	44.47	1.52
3115	3625	1.406069	CGCCCAACTAGATGCTCAACT	60.406	52.381	0.00	0.00	0.00	3.16
3211	3721	4.626081	AACTGCCTCGCAACCGCT	62.626	61.111	0.00	0.00	38.41	5.52
3250	3760	0.467290	AACCAGTTGGCCGATGTGTT	60.467	50.000	0.00	0.00	39.32	3.32
3276	3786	0.242017	GCTGTTGTAGTCGTACCGGT	59.758	55.000	13.98	13.98	0.00	5.28
3339	3849	1.330655	ATCGCCCTTGTCGAGACCAT	61.331	55.000	0.34	0.00	39.47	3.55
3354	3864	1.135046	CTCCATGTCGTCATCATCGC	58.865	55.000	0.00	0.00	31.15	4.58
3394	3907	4.084589	CGAACTTCAACATGTTCATCGTCA	60.085	41.667	8.48	0.00	41.67	4.35
3585	4099	1.183549	GTCGAACCTCCTCCTAGCAA	58.816	55.000	0.00	0.00	0.00	3.91
3699	4221	4.779993	AAAAATGGCAAAAAGGGGTACA	57.220	36.364	0.00	0.00	0.00	2.90
3722	4245	2.202623	GTCGCCTCGCTGTAGTGG	60.203	66.667	0.00	0.00	0.00	4.00
3725	4248	2.580867	GCTGTCGCCTCGCTGTAG	60.581	66.667	0.00	0.00	0.00	2.74
3726	4249	3.062466	AGCTGTCGCCTCGCTGTA	61.062	61.111	0.00	0.00	36.60	2.74
3727	4250	4.731612	CAGCTGTCGCCTCGCTGT	62.732	66.667	5.25	0.00	44.50	4.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.