AutoCloner

Multiple sequence alignment - TraesCS5B01G364600

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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	TraesCS5B01G364600	chr5B	100.000	2276	0	0	1	2276	543261378	543259103	0	4204
1	TraesCS5B01G364600	chr3A	93.415	1306	83	2	1	1305	440509553	440510856	0	1932
2	TraesCS5B01G364600	chr7B	93.328	1304	85	1	1	1304	26210384	26209083	0	1925
3	TraesCS5B01G364600	chr1B	92.704	1302	92	2	1	1302	487940107	487941405	0	1875
4	TraesCS5B01G364600	chr1B	79.479	960	189	6	1321	2275	516916353	516915397	0	675
5	TraesCS5B01G364600	chr1B	79.289	956	190	6	1325	2275	516890806	516889854	0	662
6	TraesCS5B01G364600	chr6B	92.485	1304	96	1	1	1304	583194313	583193012	0	1864
7	TraesCS5B01G364600	chr6B	92.337	1305	97	2	1	1304	16962025	16960723	0	1853
8	TraesCS5B01G364600	chr5D	86.409	1295	169	5	12	1304	300148864	300147575	0	1410
9	TraesCS5B01G364600	chr5D	85.792	1295	176	6	12	1304	300324794	300323506	0	1365
10	TraesCS5B01G364600	chr4D	85.604	1299	176	9	12	1305	59513412	59512120	0	1352
11	TraesCS5B01G364600	chr4D	80.967	1303	245	2	1	1303	56748888	56747589	0	1029
12	TraesCS5B01G364600	chr3B	89.529	955	96	3	1325	2276	766550921	766549968	0	1206
13	TraesCS5B01G364600	chr2B	88.924	957	97	7	1326	2276	222528548	222529501	0	1171
14	TraesCS5B01G364600	chr7A	88.260	954	106	4	1326	2276	94149551	94150501	0	1136
15	TraesCS5B01G364600	chr2A	86.583	954	122	4	1327	2276	753442158	753443109	0	1048
16	TraesCS5B01G364600	chr2A	80.292	959	177	11	1325	2276	68243254	68242301	0	713
17	TraesCS5B01G364600	chr7D	80.957	961	165	15	1325	2276	85200127	85199176	0	745
18	TraesCS5B01G364600	chr5A	82.493	754	123	8	1512	2262	27229974	27230721	0	652

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	TraesCS5B01G364600	chr5B	543259103	543261378	2275	True	4204	4204	100.000	1	2276	1	chr5B.!!$R1	2275
1	TraesCS5B01G364600	chr3A	440509553	440510856	1303	False	1932	1932	93.415	1	1305	1	chr3A.!!$F1	1304
2	TraesCS5B01G364600	chr7B	26209083	26210384	1301	True	1925	1925	93.328	1	1304	1	chr7B.!!$R1	1303
3	TraesCS5B01G364600	chr1B	487940107	487941405	1298	False	1875	1875	92.704	1	1302	1	chr1B.!!$F1	1301
4	TraesCS5B01G364600	chr1B	516915397	516916353	956	True	675	675	79.479	1321	2275	1	chr1B.!!$R2	954
5	TraesCS5B01G364600	chr1B	516889854	516890806	952	True	662	662	79.289	1325	2275	1	chr1B.!!$R1	950
6	TraesCS5B01G364600	chr6B	583193012	583194313	1301	True	1864	1864	92.485	1	1304	1	chr6B.!!$R2	1303
7	TraesCS5B01G364600	chr6B	16960723	16962025	1302	True	1853	1853	92.337	1	1304	1	chr6B.!!$R1	1303
8	TraesCS5B01G364600	chr5D	300147575	300148864	1289	True	1410	1410	86.409	12	1304	1	chr5D.!!$R1	1292
9	TraesCS5B01G364600	chr5D	300323506	300324794	1288	True	1365	1365	85.792	12	1304	1	chr5D.!!$R2	1292
10	TraesCS5B01G364600	chr4D	59512120	59513412	1292	True	1352	1352	85.604	12	1305	1	chr4D.!!$R2	1293
11	TraesCS5B01G364600	chr4D	56747589	56748888	1299	True	1029	1029	80.967	1	1303	1	chr4D.!!$R1	1302
12	TraesCS5B01G364600	chr3B	766549968	766550921	953	True	1206	1206	89.529	1325	2276	1	chr3B.!!$R1	951
13	TraesCS5B01G364600	chr2B	222528548	222529501	953	False	1171	1171	88.924	1326	2276	1	chr2B.!!$F1	950
14	TraesCS5B01G364600	chr7A	94149551	94150501	950	False	1136	1136	88.260	1326	2276	1	chr7A.!!$F1	950
15	TraesCS5B01G364600	chr2A	753442158	753443109	951	False	1048	1048	86.583	1327	2276	1	chr2A.!!$F1	949
16	TraesCS5B01G364600	chr2A	68242301	68243254	953	True	713	713	80.292	1325	2276	1	chr2A.!!$R1	951
17	TraesCS5B01G364600	chr7D	85199176	85200127	951	True	745	745	80.957	1325	2276	1	chr7D.!!$R1	951
18	TraesCS5B01G364600	chr5A	27229974	27230721	747	False	652	652	82.493	1512	2262	1	chr5A.!!$F1	750

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
62	63	0.249911	GACGCTGGAAACTGTGGACT	60.25	55.0	0.0	0.0	43.29	3.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1495	1503	0.041238	ATTCCTCTGTCCCTCCGTGA	59.959	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
27	28	8.494433	AGGTTTGCATACTTTATCTCCTATGAA	58.506	33.333	7.25	0.00	0.00	2.57
42	43	4.140447	TCCTATGAATGTACCAGGAGGGAT	60.140	45.833	0.00	0.00	41.15	3.85
62	63	0.249911	GACGCTGGAAACTGTGGACT	60.250	55.000	0.00	0.00	43.29	3.85
76	77	6.163135	ACTGTGGACTAGCTAATTGATACC	57.837	41.667	0.00	0.00	0.00	2.73
196	197	0.686789	ATTTTCTTGCTTGGGCCCAC	59.313	50.000	28.70	15.82	37.74	4.61
197	198	0.689080	TTTTCTTGCTTGGGCCCACA	60.689	50.000	28.70	18.81	37.74	4.17
379	380	4.289101	TGGTGGAGGGTCGTCCGA	62.289	66.667	5.40	0.00	39.81	4.55
392	393	1.107538	CGTCCGAGGCATCCTTCCTA	61.108	60.000	0.00	0.00	31.76	2.94
525	526	1.768684	TTCTGGGAGCAGGCTTTCGT	61.769	55.000	0.00	0.00	0.00	3.85
637	638	6.040278	GGTCTCAGATGATCTCAGTAATGTGA	59.960	42.308	0.00	0.00	0.00	3.58
649	650	5.439721	TCAGTAATGTGAGCTATTTGGCAT	58.560	37.500	0.00	0.00	34.17	4.40
713	714	8.940397	TCCTTTTTCATCTGTTAAGAGGATTT	57.060	30.769	0.00	0.00	42.49	2.17
718	719	5.994250	TCATCTGTTAAGAGGATTTGGGAG	58.006	41.667	0.00	0.00	38.28	4.30
719	720	4.844349	TCTGTTAAGAGGATTTGGGAGG	57.156	45.455	0.00	0.00	0.00	4.30
849	850	7.595819	TGTGAATTTGGACTTCAATAAGGTT	57.404	32.000	0.00	0.00	37.01	3.50
966	967	1.470098	GCTTTGCGTGATGGAGTCATT	59.530	47.619	0.00	0.00	39.48	2.57
1052	1053	4.279922	TCTCTGGAACACTCGTCATAACAA	59.720	41.667	0.00	0.00	0.00	2.83
1147	1150	6.209192	TCAACATGTAAACAGATCAGCCAATT	59.791	34.615	0.00	0.00	0.00	2.32
1151	1154	7.394359	ACATGTAAACAGATCAGCCAATTTACT	59.606	33.333	0.00	0.00	34.89	2.24
1178	1181	4.118410	CACCTTTGTGCTAAACATGCAAA	58.882	39.130	0.00	0.00	42.41	3.68
1179	1182	4.209703	CACCTTTGTGCTAAACATGCAAAG	59.790	41.667	10.84	10.84	42.41	2.77
1209	1212	0.834612	TCACCGAAAGTTGGACTGGT	59.165	50.000	0.00	0.00	0.00	4.00
1212	1215	0.865769	CCGAAAGTTGGACTGGTTCG	59.134	55.000	7.56	7.56	37.87	3.95
1319	1322	3.915437	AAAAAGGTCGCCATTGTACAG	57.085	42.857	0.00	0.00	0.00	2.74
1320	1323	2.561478	AAAGGTCGCCATTGTACAGT	57.439	45.000	0.00	0.00	0.00	3.55
1321	1324	2.094762	AAGGTCGCCATTGTACAGTC	57.905	50.000	0.00	0.00	0.00	3.51
1322	1325	0.973632	AGGTCGCCATTGTACAGTCA	59.026	50.000	0.00	0.00	0.00	3.41
1323	1326	1.076332	GGTCGCCATTGTACAGTCAC	58.924	55.000	0.00	0.00	0.00	3.67
1370	1373	3.047877	CTTTTCCTTCGGCGGCGT	61.048	61.111	31.06	0.00	0.00	5.68
1422	1428	1.611936	CCGATCGAGAGCTAGGGATCA	60.612	57.143	18.66	0.00	36.04	2.92
1462	1468	1.122019	AGTCAGCCTTGTTCTCCGGT	61.122	55.000	0.00	0.00	0.00	5.28
1467	1474	0.606604	GCCTTGTTCTCCGGTGACTA	59.393	55.000	5.53	0.00	0.00	2.59
1495	1503	2.101582	GGATCTGAACACTATGGACGCT	59.898	50.000	0.00	0.00	0.00	5.07
1505	1513	2.561467	TATGGACGCTCACGGAGGGA	62.561	60.000	19.70	3.63	43.87	4.20
1514	1522	0.041238	TCACGGAGGGACAGAGGAAT	59.959	55.000	0.00	0.00	0.00	3.01
1539	1547	1.054978	GTAGGGGAGGCTAGGGTTGG	61.055	65.000	0.00	0.00	0.00	3.77
1559	1567	0.553819	AGATCCAGTAGCGGGAGTCT	59.446	55.000	0.00	0.00	37.96	3.24
1564	1572	0.173708	CAGTAGCGGGAGTCTGGTTC	59.826	60.000	0.00	0.00	0.00	3.62
1603	1611	2.586258	CGATGAACGGAGAAGATGGT	57.414	50.000	0.00	0.00	38.46	3.55
1615	1623	0.779997	AAGATGGTGGGAAGGTTGCT	59.220	50.000	0.00	0.00	0.00	3.91
1620	1628	1.973812	GTGGGAAGGTTGCTGGAGC	60.974	63.158	0.00	0.00	42.50	4.70
1621	1629	2.156098	TGGGAAGGTTGCTGGAGCT	61.156	57.895	0.00	0.00	42.66	4.09
1654	1662	2.628178	TCAGAAGGAAGACGAAGAAGCA	59.372	45.455	0.00	0.00	0.00	3.91
1666	1674	2.158986	CGAAGAAGCAGACTGGGATCAT	60.159	50.000	4.26	0.00	0.00	2.45
1687	1695	5.184287	TCATTATGGTCCGTCGCATAATCTA	59.816	40.000	11.39	3.99	32.73	1.98
1756	1764	0.698238	TGGATTTGTCTGGGGAGGTG	59.302	55.000	0.00	0.00	0.00	4.00
1835	1843	1.106285	GTTTAGCCATGCCTCCTTGG	58.894	55.000	0.00	0.00	38.85	3.61
1896	1904	4.137543	GTGACCTTCAACATCAAAGGACT	58.862	43.478	8.08	0.00	44.02	3.85
1970	1978	3.755467	GGGGGCCATGGTAGTTCT	58.245	61.111	14.67	0.00	0.00	3.01
2100	2108	5.221322	GCTTGACAAGAAAGAAGGAATTGGT	60.221	40.000	19.51	0.00	0.00	3.67
2112	2120	1.354368	GGAATTGGTGGAGAAGGTGGA	59.646	52.381	0.00	0.00	0.00	4.02
2140	2148	3.854666	GGTAGGAGAACCTTCGTTTACC	58.145	50.000	0.00	0.00	45.36	2.85
2180	2188	5.066593	GGAAGATCAATCCATCCAACTACC	58.933	45.833	11.57	0.00	36.92	3.18
2190	2198	1.122632	TCCAACTACCTGCGGGTTCA	61.123	55.000	25.37	4.44	44.73	3.18
2254	2262	8.047310	GTCCATATAACTTTGAAGGAGAGGAAA	58.953	37.037	0.00	0.00	0.00	3.13
2255	2263	8.047310	TCCATATAACTTTGAAGGAGAGGAAAC	58.953	37.037	0.00	0.00	0.00	2.78
2267	2275	2.165030	GAGAGGAAACGGTATTCGGTGA	59.835	50.000	0.00	0.00	44.45	4.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
7	8	9.372369	GGTACATTCATAGGAGATAAAGTATGC	57.628	37.037	0.00	0.00	0.00	3.14
27	28	1.414158	CGTCATCCCTCCTGGTACAT	58.586	55.000	0.00	0.00	38.20	2.29
42	43	0.531974	GTCCACAGTTTCCAGCGTCA	60.532	55.000	0.00	0.00	0.00	4.35
62	63	5.128171	ACCAGTTGTCGGTATCAATTAGCTA	59.872	40.000	0.00	0.00	34.02	3.32
334	335	0.104120	GCACCTTCGGCAAAACCTTT	59.896	50.000	0.00	0.00	35.61	3.11
355	356	1.375326	GACCCTCCACCAGAACACC	59.625	63.158	0.00	0.00	0.00	4.16
490	491	2.227388	CCAGAACAACTTGGCATGAGAC	59.773	50.000	7.45	0.00	0.00	3.36
525	526	1.438651	CCTGCGGAGATCGAACAAAA	58.561	50.000	5.10	0.00	42.43	2.44
637	638	8.435982	ACTCTATTTCTAGAATGCCAAATAGCT	58.564	33.333	5.89	0.00	38.15	3.32
700	701	4.225267	GTCTCCTCCCAAATCCTCTTAACA	59.775	45.833	0.00	0.00	0.00	2.41
713	714	0.543410	TAACGCCAAGTCTCCTCCCA	60.543	55.000	0.00	0.00	0.00	4.37
718	719	0.524862	TCGAGTAACGCCAAGTCTCC	59.475	55.000	0.00	0.00	42.26	3.71
719	720	2.563471	ATCGAGTAACGCCAAGTCTC	57.437	50.000	0.00	0.00	42.26	3.36
849	850	1.229177	TGCTACACCTCCAGCTCCA	60.229	57.895	0.00	0.00	38.63	3.86
966	967	2.950673	CCGCGCAGGTTAGCAAAA	59.049	55.556	8.75	0.00	34.51	2.44
1052	1053	0.846693	AGGAGCCACAACAGAAAGGT	59.153	50.000	0.00	0.00	0.00	3.50
1147	1150	3.430473	CACAAAGGTGGGCCAGTAA	57.570	52.632	6.40	0.00	41.45	2.24
1178	1181	2.631160	TTCGGTGACCAACAATGTCT	57.369	45.000	1.11	0.00	33.83	3.41
1179	1182	2.616842	ACTTTCGGTGACCAACAATGTC	59.383	45.455	1.11	0.00	0.00	3.06
1209	1212	3.245158	TGAGTAGGAAGGAAGGTCTCGAA	60.245	47.826	0.00	0.00	0.00	3.71
1212	1215	2.761767	GGTGAGTAGGAAGGAAGGTCTC	59.238	54.545	0.00	0.00	0.00	3.36
1306	1309	2.831685	AAGTGACTGTACAATGGCGA	57.168	45.000	0.00	0.00	0.00	5.54
1307	1310	3.364964	GGAAAAGTGACTGTACAATGGCG	60.365	47.826	0.00	0.00	0.00	5.69
1308	1311	3.057526	GGGAAAAGTGACTGTACAATGGC	60.058	47.826	0.00	0.00	0.00	4.40
1309	1312	3.506067	GGGGAAAAGTGACTGTACAATGG	59.494	47.826	0.00	0.00	0.00	3.16
1310	1313	4.398319	AGGGGAAAAGTGACTGTACAATG	58.602	43.478	0.00	0.00	0.00	2.82
1311	1314	4.724279	AGGGGAAAAGTGACTGTACAAT	57.276	40.909	0.00	0.00	0.00	2.71
1312	1315	4.041198	CCTAGGGGAAAAGTGACTGTACAA	59.959	45.833	0.00	0.00	33.58	2.41
1313	1316	3.581332	CCTAGGGGAAAAGTGACTGTACA	59.419	47.826	0.00	0.00	33.58	2.90
1314	1317	4.203654	CCTAGGGGAAAAGTGACTGTAC	57.796	50.000	0.00	0.00	33.58	2.90
1370	1373	2.542550	TGGATTTTAGGTGGACTCCGA	58.457	47.619	0.00	0.00	0.00	4.55
1373	1376	6.650120	TCTTACATGGATTTTAGGTGGACTC	58.350	40.000	0.00	0.00	0.00	3.36
1374	1377	6.636454	TCTTACATGGATTTTAGGTGGACT	57.364	37.500	0.00	0.00	0.00	3.85
1376	1379	7.990886	GTGTATCTTACATGGATTTTAGGTGGA	59.009	37.037	0.00	0.00	41.34	4.02
1377	1380	7.228706	GGTGTATCTTACATGGATTTTAGGTGG	59.771	40.741	0.00	0.00	41.34	4.61
1378	1381	7.042051	CGGTGTATCTTACATGGATTTTAGGTG	60.042	40.741	0.00	0.00	41.34	4.00
1379	1382	6.990349	CGGTGTATCTTACATGGATTTTAGGT	59.010	38.462	0.00	0.00	41.34	3.08
1382	1387	7.597369	CGATCGGTGTATCTTACATGGATTTTA	59.403	37.037	7.38	0.00	41.34	1.52
1422	1428	2.490217	CCAAGACGATCTCCGCGT	59.510	61.111	4.92	0.00	45.79	6.01
1462	1468	4.160439	GTGTTCAGATCCTCCATGTAGTCA	59.840	45.833	0.00	0.00	0.00	3.41
1467	1474	4.102210	CCATAGTGTTCAGATCCTCCATGT	59.898	45.833	0.00	0.00	0.00	3.21
1495	1503	0.041238	ATTCCTCTGTCCCTCCGTGA	59.959	55.000	0.00	0.00	0.00	4.35
1505	1513	2.389715	CCCTACTTCCGATTCCTCTGT	58.610	52.381	0.00	0.00	0.00	3.41
1514	1522	0.185416	CTAGCCTCCCCTACTTCCGA	59.815	60.000	0.00	0.00	0.00	4.55
1539	1547	0.955905	GACTCCCGCTACTGGATCTC	59.044	60.000	0.00	0.00	0.00	2.75
1579	1587	1.538512	TCTTCTCCGTTCATCGTCGTT	59.461	47.619	0.00	0.00	37.94	3.85
1603	1611	2.156098	AGCTCCAGCAACCTTCCCA	61.156	57.895	0.48	0.00	45.16	4.37
1615	1623	1.062364	GATCATCCCCATCAGCTCCA	58.938	55.000	0.00	0.00	0.00	3.86
1620	1628	2.977580	TCCTTCTGATCATCCCCATCAG	59.022	50.000	0.00	3.67	46.04	2.90
1621	1629	3.064773	TCCTTCTGATCATCCCCATCA	57.935	47.619	0.00	0.00	0.00	3.07
1654	1662	2.634940	CGGACCATAATGATCCCAGTCT	59.365	50.000	0.00	0.00	0.00	3.24
1666	1674	4.763279	TCTAGATTATGCGACGGACCATAA	59.237	41.667	8.27	8.27	38.04	1.90
1675	1683	3.499157	ACTCGTCCTCTAGATTATGCGAC	59.501	47.826	0.00	0.00	0.00	5.19
1687	1695	2.940410	GAGATTCTCGAACTCGTCCTCT	59.060	50.000	0.00	0.00	40.80	3.69
1756	1764	4.253685	TGACGTCCTTGATCAATTCTTCC	58.746	43.478	14.12	0.00	0.00	3.46
1835	1843	0.992802	GCGTTCCTCATCGAGTTCAC	59.007	55.000	0.00	0.00	0.00	3.18
1896	1904	3.450457	ACATTGAGCCAAAAACAGGTTGA	59.550	39.130	0.00	0.00	0.00	3.18
1964	1972	2.108168	CACCGGATCCCTTCAGAACTA	58.892	52.381	9.46	0.00	0.00	2.24
1970	1978	1.488812	CAATACCACCGGATCCCTTCA	59.511	52.381	9.46	0.00	0.00	3.02
2100	2108	2.783510	ACCTTCTTTTCCACCTTCTCCA	59.216	45.455	0.00	0.00	0.00	3.86
2140	2148	6.825213	TGATCTTCCCTTCATTAACAGTCATG	59.175	38.462	0.00	0.00	0.00	3.07
2180	2188	1.101049	ACAAACACCTGAACCCGCAG	61.101	55.000	0.00	0.00	35.66	5.18
2190	2198	4.202010	GCACTGTGACATTAACAAACACCT	60.202	41.667	12.86	0.00	0.00	4.00

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.