AutoCloner

Multiple sequence alignment - TraesCS1B01G162800

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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	TraesCS1B01G162800	chr1B	100.000	2276	0	0	1	2276	282309557	282311832	0.000000e+00	4204.0
1	TraesCS1B01G162800	chr1B	94.235	1301	75	0	1	1301	613239724	613238424	0.000000e+00	1988.0
2	TraesCS1B01G162800	chr1B	78.776	1291	259	14	17	1301	18863230	18861949	0.000000e+00	852.0
3	TraesCS1B01G162800	chr1B	92.090	531	40	2	1746	2276	206860286	206860814	0.000000e+00	747.0
4	TraesCS1B01G162800	chr1B	86.964	606	60	4	1315	1919	206919712	206920299	0.000000e+00	664.0
5	TraesCS1B01G162800	chr1B	89.779	362	37	0	1915	2276	206922746	206923107	4.430000e-127	464.0
6	TraesCS1B01G162800	chr5D	94.939	1304	65	1	1	1303	565330907	565329604	0.000000e+00	2041.0
7	TraesCS1B01G162800	chr5D	81.383	1128	194	15	173	1292	532832822	532831703	0.000000e+00	905.0
8	TraesCS1B01G162800	chr2B	94.854	1302	66	1	1	1301	698957492	698956191	0.000000e+00	2032.0
9	TraesCS1B01G162800	chr2B	87.571	177	22	0	1332	1508	278274249	278274073	2.960000e-49	206.0
10	TraesCS1B01G162800	chr3B	94.526	1096	60	0	206	1301	675149952	675148857	0.000000e+00	1692.0
11	TraesCS1B01G162800	chr3B	94.203	207	12	0	1	207	675150234	675150028	1.310000e-82	316.0
12	TraesCS1B01G162800	chr6D	85.933	1308	173	10	1	1301	48448874	48450177	0.000000e+00	1386.0
13	TraesCS1B01G162800	chr6D	85.510	490	65	6	1567	2053	128030555	128030069	7.250000e-140	507.0
14	TraesCS1B01G162800	chr7A	84.433	1304	195	7	1	1301	43470445	43469147	0.000000e+00	1277.0
15	TraesCS1B01G162800	chr6B	89.588	922	94	2	1318	2239	295155446	295154527	0.000000e+00	1170.0
16	TraesCS1B01G162800	chr6B	85.243	515	65	10	1547	2054	323435638	323435128	9.320000e-144	520.0
17	TraesCS1B01G162800	chr6B	85.132	491	66	7	1567	2054	323442915	323442429	1.570000e-136	496.0
18	TraesCS1B01G162800	chr6B	97.826	46	1	0	2231	2276	295153920	295153875	1.870000e-11	80.5
19	TraesCS1B01G162800	chr4D	92.702	781	57	0	1	781	44915165	44914385	0.000000e+00	1127.0
20	TraesCS1B01G162800	chr4D	87.931	174	21	0	1332	1505	317640574	317640747	2.960000e-49	206.0
21	TraesCS1B01G162800	chr4D	78.652	267	52	5	2001	2265	142538065	142537802	3.010000e-39	172.0
22	TraesCS1B01G162800	chr5A	80.283	1273	242	9	32	1301	367708603	367709869	0.000000e+00	952.0
23	TraesCS1B01G162800	chr4A	85.816	564	77	3	1567	2128	428705895	428706457	1.510000e-166	595.0
24	TraesCS1B01G162800	chr4A	88.636	176	18	2	1334	1508	471326935	471327109	1.770000e-51	213.0
25	TraesCS1B01G162800	chr1D	85.918	490	61	8	1567	2053	143261275	143261759	1.210000e-142	516.0
26	TraesCS1B01G162800	chr1D	84.898	490	67	7	1567	2053	122182086	122181601	2.630000e-134	488.0
27	TraesCS1B01G162800	chr1D	86.559	186	25	0	1320	1505	242960051	242960236	2.960000e-49	206.0
28	TraesCS1B01G162800	chr6A	85.336	491	65	7	1567	2053	307540529	307540042	3.380000e-138	501.0
29	TraesCS1B01G162800	chr5B	83.074	514	76	10	1547	2053	250908925	250909434	7.410000e-125	457.0
30	TraesCS1B01G162800	chr3A	80.469	512	84	14	1762	2265	372025335	372025838	5.930000e-101	377.0
31	TraesCS1B01G162800	chr2A	79.134	508	91	13	1765	2265	273022240	273021741	1.010000e-88	337.0
32	TraesCS1B01G162800	chr2A	88.701	177	20	0	1332	1508	191198925	191198749	1.370000e-52	217.0
33	TraesCS1B01G162800	chr4B	89.908	218	19	2	2062	2276	213599488	213599271	6.190000e-71	278.0
34	TraesCS1B01G162800	chr4B	86.239	218	27	2	2062	2276	213580992	213580775	1.360000e-57	233.0
35	TraesCS1B01G162800	chrUn	86.239	218	27	2	2062	2276	327996835	327996618	1.360000e-57	233.0
36	TraesCS1B01G162800	chr2D	87.429	175	22	0	1334	1508	231071315	231071141	3.830000e-48	202.0
37	TraesCS1B01G162800	chr7B	87.006	177	23	0	1332	1508	338073064	338072888	1.380000e-47	200.0

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	TraesCS1B01G162800	chr1B	282309557	282311832	2275	False	4204.00	4204	100.0000	1	2276	1	chr1B.!!$F2	2275
1	TraesCS1B01G162800	chr1B	613238424	613239724	1300	True	1988.00	1988	94.2350	1	1301	1	chr1B.!!$R2	1300
2	TraesCS1B01G162800	chr1B	18861949	18863230	1281	True	852.00	852	78.7760	17	1301	1	chr1B.!!$R1	1284
3	TraesCS1B01G162800	chr1B	206860286	206860814	528	False	747.00	747	92.0900	1746	2276	1	chr1B.!!$F1	530
4	TraesCS1B01G162800	chr1B	206919712	206923107	3395	False	564.00	664	88.3715	1315	2276	2	chr1B.!!$F3	961
5	TraesCS1B01G162800	chr5D	565329604	565330907	1303	True	2041.00	2041	94.9390	1	1303	1	chr5D.!!$R2	1302
6	TraesCS1B01G162800	chr5D	532831703	532832822	1119	True	905.00	905	81.3830	173	1292	1	chr5D.!!$R1	1119
7	TraesCS1B01G162800	chr2B	698956191	698957492	1301	True	2032.00	2032	94.8540	1	1301	1	chr2B.!!$R2	1300
8	TraesCS1B01G162800	chr3B	675148857	675150234	1377	True	1004.00	1692	94.3645	1	1301	2	chr3B.!!$R1	1300
9	TraesCS1B01G162800	chr6D	48448874	48450177	1303	False	1386.00	1386	85.9330	1	1301	1	chr6D.!!$F1	1300
10	TraesCS1B01G162800	chr7A	43469147	43470445	1298	True	1277.00	1277	84.4330	1	1301	1	chr7A.!!$R1	1300
11	TraesCS1B01G162800	chr6B	295153875	295155446	1571	True	625.25	1170	93.7070	1318	2276	2	chr6B.!!$R3	958
12	TraesCS1B01G162800	chr6B	323435128	323435638	510	True	520.00	520	85.2430	1547	2054	1	chr6B.!!$R1	507
13	TraesCS1B01G162800	chr4D	44914385	44915165	780	True	1127.00	1127	92.7020	1	781	1	chr4D.!!$R1	780
14	TraesCS1B01G162800	chr5A	367708603	367709869	1266	False	952.00	952	80.2830	32	1301	1	chr5A.!!$F1	1269
15	TraesCS1B01G162800	chr4A	428705895	428706457	562	False	595.00	595	85.8160	1567	2128	1	chr4A.!!$F1	561
16	TraesCS1B01G162800	chr5B	250908925	250909434	509	False	457.00	457	83.0740	1547	2053	1	chr5B.!!$F1	506
17	TraesCS1B01G162800	chr3A	372025335	372025838	503	False	377.00	377	80.4690	1762	2265	1	chr3A.!!$F1	503

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
911	992	1.16527	GCATGGTGTAAGCCGTCTTT	58.835	50.0	0.0	0.0	33.85	2.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1799	1909	0.740868	CGATTCCCTCTTTCAGCGCA	60.741	55.0	11.47	0.0	0.0	6.09	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
24	25	3.539604	CTCCATTGTCTCAATGACTCCC	58.460	50.000	19.74	0.00	45.54	4.30
165	166	6.404184	CCATTCTTAACATACCATTGCGACAA	60.404	38.462	0.00	0.00	0.00	3.18
170	171	2.236146	ACATACCATTGCGACAAGGAGA	59.764	45.455	5.94	0.00	0.00	3.71
261	340	2.157668	TCTCGTGAATCAAAAAGAGCGC	59.842	45.455	0.00	0.00	0.00	5.92
357	436	6.365520	ACTCAAAGTAGTCCCAAAAGTCATT	58.634	36.000	0.00	0.00	0.00	2.57
385	464	4.280019	GGCGGGTGTTGAGGGGTT	62.280	66.667	0.00	0.00	0.00	4.11
449	528	5.005740	AGAAACAAGCACATGCAAGATCTA	58.994	37.500	6.64	0.00	45.16	1.98
505	585	3.930400	CATTGTATGCATGTGCGCT	57.070	47.368	10.16	0.00	45.83	5.92
665	745	3.942130	ATGGATGTCTCGCAATCGATA	57.058	42.857	0.00	0.00	44.56	2.92
911	992	1.165270	GCATGGTGTAAGCCGTCTTT	58.835	50.000	0.00	0.00	33.85	2.52
923	1004	1.369625	CCGTCTTTAGGTGTCATGGC	58.630	55.000	0.00	0.00	0.00	4.40
1253	1336	0.475906	AACCTTCTGGCTGACTGCTT	59.524	50.000	4.20	0.00	42.39	3.91
1303	1390	6.173339	TCTCTGAAGTTCCTCGCAAAAATAT	58.827	36.000	0.00	0.00	0.00	1.28
1304	1391	7.327975	TCTCTGAAGTTCCTCGCAAAAATATA	58.672	34.615	0.00	0.00	0.00	0.86
1305	1392	7.277981	TCTCTGAAGTTCCTCGCAAAAATATAC	59.722	37.037	0.00	0.00	0.00	1.47
1306	1393	6.876789	TCTGAAGTTCCTCGCAAAAATATACA	59.123	34.615	0.00	0.00	0.00	2.29
1307	1394	7.064609	TCTGAAGTTCCTCGCAAAAATATACAG	59.935	37.037	0.00	0.00	0.00	2.74
1308	1395	5.485662	AGTTCCTCGCAAAAATATACAGC	57.514	39.130	0.00	0.00	0.00	4.40
1309	1396	5.186198	AGTTCCTCGCAAAAATATACAGCT	58.814	37.500	0.00	0.00	0.00	4.24
1310	1397	5.065218	AGTTCCTCGCAAAAATATACAGCTG	59.935	40.000	13.48	13.48	0.00	4.24
1311	1398	3.312421	TCCTCGCAAAAATATACAGCTGC	59.688	43.478	15.27	0.00	0.00	5.25
1313	1400	2.375110	CGCAAAAATATACAGCTGCGG	58.625	47.619	15.27	0.00	46.50	5.69
1331	1418	2.287103	GCGGCTACAGCTATAAAACCAC	59.713	50.000	0.54	0.00	41.70	4.16
1353	1440	3.077556	AGCGTGCGGAAGAGGGAT	61.078	61.111	0.00	0.00	0.00	3.85
1357	1444	0.174845	CGTGCGGAAGAGGGATGTTA	59.825	55.000	0.00	0.00	0.00	2.41
1367	1454	1.136305	GAGGGATGTTAGTACGCTGCA	59.864	52.381	0.00	0.00	0.00	4.41
1374	1461	2.094700	TGTTAGTACGCTGCAAGGAGAG	60.095	50.000	0.00	0.00	0.00	3.20
1375	1462	2.124277	TAGTACGCTGCAAGGAGAGA	57.876	50.000	0.00	0.00	0.00	3.10
1464	1551	1.941999	GCAAGATGAAGCAGGGCCAC	61.942	60.000	6.18	0.00	0.00	5.01
1505	1592	3.714963	TGCGTGTGTGCAGATGCG	61.715	61.111	8.62	5.82	45.83	4.73
1506	1593	3.716006	GCGTGTGTGCAGATGCGT	61.716	61.111	10.59	0.00	45.83	5.24
1507	1594	2.171701	CGTGTGTGCAGATGCGTG	59.828	61.111	0.00	0.00	45.83	5.34
1508	1595	2.127118	GTGTGTGCAGATGCGTGC	60.127	61.111	0.00	0.00	45.83	5.34
1515	1602	3.184206	CAGATGCGTGCATGTGCT	58.816	55.556	17.43	4.12	40.06	4.40
1516	1603	1.226295	CAGATGCGTGCATGTGCTG	60.226	57.895	17.43	12.08	40.06	4.41
1517	1604	1.376295	AGATGCGTGCATGTGCTGA	60.376	52.632	12.81	0.00	42.66	4.26
1518	1605	1.062047	GATGCGTGCATGTGCTGAG	59.938	57.895	12.81	0.00	42.66	3.35
1592	1699	0.183492	AGCAAAACAGAGGAGGTGCA	59.817	50.000	0.00	0.00	34.44	4.57
1690	1798	3.733337	AGACTCACAACAAGAAATCGCT	58.267	40.909	0.00	0.00	0.00	4.93
1691	1799	4.130118	AGACTCACAACAAGAAATCGCTT	58.870	39.130	0.00	0.00	0.00	4.68
1718	1826	3.284323	GTGTCTCGCACAACTCTAGAA	57.716	47.619	0.00	0.00	46.91	2.10
1755	1863	1.270839	CGGTGATGAGGAAACAGTGGT	60.271	52.381	0.00	0.00	0.00	4.16
1779	1887	2.747686	GTGGAGCTTGGACCCGAA	59.252	61.111	0.00	0.00	0.00	4.30
1793	1901	1.279271	ACCCGAAGAATCAAGGACCAG	59.721	52.381	0.00	0.00	0.00	4.00
1882	1993	3.808728	CAAGGAGAGGTCAAAACACTCA	58.191	45.455	0.00	0.00	34.33	3.41
1936	4498	0.520404	TCGAAGGAGACGGACGAAAG	59.480	55.000	0.00	0.00	33.17	2.62
2049	4612	3.614143	GACGAATTAGCCGGCGAG	58.386	61.111	23.20	12.23	0.00	5.03
2085	4648	2.284995	AAGAAGGAGAGGCCGGCT	60.285	61.111	28.56	12.77	43.43	5.52
2096	4659	0.105964	AGGCCGGCTATGAGAAGAGA	60.106	55.000	28.56	0.00	0.00	3.10
2183	4746	4.116328	CGCCGTCGAGGAAGCAGA	62.116	66.667	6.70	0.00	45.00	4.26
2186	4749	1.880340	CCGTCGAGGAAGCAGATGC	60.880	63.158	6.70	0.00	45.00	3.91

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
137	138	5.659463	GCAATGGTATGTTAAGAATGGCAA	58.341	37.500	0.00	0.00	0.00	4.52
165	166	4.442192	GCAAGAATATCTTCACCGTCTCCT	60.442	45.833	0.00	0.00	33.78	3.69
170	171	3.941483	CCAAGCAAGAATATCTTCACCGT	59.059	43.478	0.00	0.00	33.78	4.83
261	340	0.396060	GCCCCTCATCTAGAGCCAAG	59.604	60.000	0.00	0.00	43.31	3.61
357	436	2.043852	ACCCGCCACCAAAACACA	60.044	55.556	0.00	0.00	0.00	3.72
385	464	2.618816	GGGTGCACTCATCAGGAATGAA	60.619	50.000	17.98	0.00	43.78	2.57
449	528	0.105453	ATCCTCGTCCATAGCCAGGT	60.105	55.000	0.00	0.00	0.00	4.00
500	580	4.020617	CCTCCCAGAACCAGCGCA	62.021	66.667	11.47	0.00	0.00	6.09
505	585	2.610859	GGCCTCCTCCCAGAACCA	60.611	66.667	0.00	0.00	0.00	3.67
665	745	0.387202	CCCTTCTCGATCATGCGTCT	59.613	55.000	0.00	0.00	0.00	4.18
1129	1211	6.238320	GCAGGACTGTTTGCTGATCTTATTAG	60.238	42.308	9.96	0.00	46.53	1.73
1308	1395	2.544267	GGTTTTATAGCTGTAGCCGCAG	59.456	50.000	0.00	1.17	43.38	5.18
1309	1396	2.093394	TGGTTTTATAGCTGTAGCCGCA	60.093	45.455	0.00	0.00	43.38	5.69
1310	1397	2.287103	GTGGTTTTATAGCTGTAGCCGC	59.713	50.000	0.00	1.23	43.38	6.53
1311	1398	2.538449	CGTGGTTTTATAGCTGTAGCCG	59.462	50.000	0.00	0.00	43.38	5.52
1312	1399	2.870411	CCGTGGTTTTATAGCTGTAGCC	59.130	50.000	0.00	0.00	43.38	3.93
1313	1400	2.287103	GCCGTGGTTTTATAGCTGTAGC	59.713	50.000	0.00	0.00	42.49	3.58
1316	1403	1.066716	TCGCCGTGGTTTTATAGCTGT	60.067	47.619	0.00	0.00	0.00	4.40
1353	1440	1.890489	TCTCCTTGCAGCGTACTAACA	59.110	47.619	0.00	0.00	0.00	2.41
1357	1444	1.407258	GATCTCTCCTTGCAGCGTACT	59.593	52.381	0.00	0.00	0.00	2.73
1367	1454	1.480137	CCTCTTGCACGATCTCTCCTT	59.520	52.381	0.00	0.00	0.00	3.36
1374	1461	1.372087	CCCAAGCCTCTTGCACGATC	61.372	60.000	0.00	0.00	44.83	3.69
1375	1462	1.377725	CCCAAGCCTCTTGCACGAT	60.378	57.895	0.00	0.00	44.83	3.73
1487	1574	2.127118	GCATCTGCACACACGCAC	60.127	61.111	0.00	0.00	41.59	5.34
1492	1579	2.591144	TGCACGCATCTGCACACA	60.591	55.556	2.72	0.00	42.36	3.72
1503	1590	4.471726	GCCTCAGCACATGCACGC	62.472	66.667	6.64	0.00	45.16	5.34
1504	1591	4.156622	CGCCTCAGCACATGCACG	62.157	66.667	6.64	0.00	45.16	5.34
1505	1592	3.807538	CCGCCTCAGCACATGCAC	61.808	66.667	6.64	0.00	45.16	4.57
1506	1593	4.334118	ACCGCCTCAGCACATGCA	62.334	61.111	6.64	0.00	45.16	3.96
1507	1594	3.807538	CACCGCCTCAGCACATGC	61.808	66.667	0.00	0.00	39.83	4.06
1508	1595	3.807538	GCACCGCCTCAGCACATG	61.808	66.667	0.00	0.00	39.83	3.21
1509	1596	3.965539	GAGCACCGCCTCAGCACAT	62.966	63.158	0.00	0.00	39.83	3.21
1510	1597	4.687215	GAGCACCGCCTCAGCACA	62.687	66.667	0.00	0.00	39.83	4.57
1592	1699	2.341543	CCGCTCTCTGTGCACAGT	59.658	61.111	38.41	0.00	44.12	3.55
1655	1762	0.391661	GAGTCTTTCATGCGCCTCCA	60.392	55.000	4.18	0.00	0.00	3.86
1664	1771	6.662616	CGATTTCTTGTTGTGAGTCTTTCAT	58.337	36.000	0.00	0.00	38.29	2.57
1710	1818	2.763448	GTGCCCTGTCATCTTCTAGAGT	59.237	50.000	0.00	0.00	0.00	3.24
1714	1822	1.951209	TGGTGCCCTGTCATCTTCTA	58.049	50.000	0.00	0.00	0.00	2.10
1718	1826	1.524002	CGATGGTGCCCTGTCATCT	59.476	57.895	0.00	0.00	36.18	2.90
1755	1863	2.115910	CCAAGCTCCACCTTGCCA	59.884	61.111	0.00	0.00	40.62	4.92
1779	1887	2.770164	CCGTTCTGGTCCTTGATTCT	57.230	50.000	0.00	0.00	0.00	2.40
1793	1901	1.493311	CTCTTTCAGCGCACCGTTC	59.507	57.895	11.47	0.00	0.00	3.95
1799	1909	0.740868	CGATTCCCTCTTTCAGCGCA	60.741	55.000	11.47	0.00	0.00	6.09
1882	1993	1.378250	ATCGAACCTCGTCTCCGGT	60.378	57.895	0.00	0.00	41.35	5.28
1936	4498	2.613506	CCCCTTCGTTTGCACCGTC	61.614	63.158	5.02	0.00	0.00	4.79
2049	4612	0.903454	TCTTCCTCGGGTCAACCTCC	60.903	60.000	0.00	0.00	36.97	4.30
2085	4648	1.988293	CCGGAGGCTCTCTTCTCATA	58.012	55.000	15.23	0.00	46.14	2.15
2183	4746	2.978298	TAGGAGCTACCGCCGAGCAT	62.978	60.000	0.00	0.00	42.69	3.79
2186	4749	2.894565	CGTAGGAGCTACCGCCGAG	61.895	68.421	0.00	0.00	44.74	4.63
2221	4784	2.509336	GCCATGACCGAGACGTGG	60.509	66.667	0.00	0.00	44.47	4.94

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.