AutoCloner

Multiple sequence alignment - TraesCS1B01G194300

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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	TraesCS1B01G194300	chr1B	100.000	2708	0	0	1	2708	349548313	349545606	0.000000e+00	5001.0
1	TraesCS1B01G194300	chr1B	94.313	422	18	3	176	592	298781211	298780791	2.270000e-180	641.0
2	TraesCS1B01G194300	chr1B	84.062	320	43	5	1012	1327	349564102	349563787	4.380000e-78	302.0
3	TraesCS1B01G194300	chr1D	92.908	1114	50	6	901	1991	262287723	262288830	0.000000e+00	1592.0
4	TraesCS1B01G194300	chr1D	83.434	332	55	0	996	1327	262252724	262253055	2.620000e-80	309.0
5	TraesCS1B01G194300	chr1D	78.462	390	39	20	1638	1991	262296667	262297047	2.110000e-51	213.0
6	TraesCS1B01G194300	chr1A	91.971	1121	60	10	901	1996	337658637	337657522	0.000000e+00	1544.0
7	TraesCS1B01G194300	chr5B	93.647	913	34	7	1	901	587130415	587129515	0.000000e+00	1343.0
8	TraesCS1B01G194300	chr5B	92.192	730	28	11	1999	2704	251348015	251348739	0.000000e+00	1005.0
9	TraesCS1B01G194300	chr5B	90.736	367	29	2	2008	2369	429104129	429103763	4.050000e-133	484.0
10	TraesCS1B01G194300	chr5B	95.681	301	10	1	295	592	82166332	82166032	5.240000e-132	481.0
11	TraesCS1B01G194300	chr4B	92.013	914	45	9	1	898	573082320	573081419	0.000000e+00	1258.0
12	TraesCS1B01G194300	chr4B	82.857	455	32	21	42	472	420424956	420424524	1.530000e-97	366.0
13	TraesCS1B01G194300	chr4B	82.842	373	43	10	2244	2611	41866330	41866686	5.630000e-82	315.0
14	TraesCS1B01G194300	chr2A	88.738	737	49	16	1998	2708	156862836	156863564	0.000000e+00	870.0
15	TraesCS1B01G194300	chr2A	90.349	373	26	8	2003	2369	703050838	703051206	5.240000e-132	481.0
16	TraesCS1B01G194300	chr2A	84.127	315	47	1	1016	1327	733217332	733217018	4.380000e-78	302.0
17	TraesCS1B01G194300	chr6B	94.787	422	17	2	176	592	642552073	642552494	0.000000e+00	652.0
18	TraesCS1B01G194300	chr7D	83.573	694	96	8	1012	1697	80772354	80771671	3.800000e-178	634.0
19	TraesCS1B01G194300	chr7D	81.298	647	119	2	1013	1658	29057370	29056725	8.590000e-145	523.0
20	TraesCS1B01G194300	chr7D	91.053	380	22	9	1998	2369	5391568	5391943	1.120000e-138	503.0
21	TraesCS1B01G194300	chr7D	92.179	358	21	4	2003	2354	628210117	628209761	1.450000e-137	499.0
22	TraesCS1B01G194300	chr7D	84.062	320	45	4	1012	1325	22624663	22624344	1.220000e-78	303.0
23	TraesCS1B01G194300	chr7B	83.163	683	95	9	1012	1678	27974531	27973853	8.290000e-170	606.0
24	TraesCS1B01G194300	chr7B	89.757	371	30	6	2003	2369	103457091	103456725	4.080000e-128	468.0
25	TraesCS1B01G194300	chr7B	91.489	47	3	1	868	914	638163210	638163165	2.250000e-06	63.9
26	TraesCS1B01G194300	chr4A	82.827	658	105	4	1013	1663	701282934	701283590	1.400000e-162	582.0
27	TraesCS1B01G194300	chr4A	78.267	658	128	14	1012	1660	5115253	5114602	2.510000e-110	409.0
28	TraesCS1B01G194300	chr4A	83.646	373	38	10	2253	2618	573500201	573499845	2.010000e-86	329.0
29	TraesCS1B01G194300	chr4A	92.727	55	3	1	848	902	627809092	627809145	8.040000e-11	78.7
30	TraesCS1B01G194300	chr7A	82.675	658	106	5	1013	1663	29165568	29164912	6.500000e-161	577.0
31	TraesCS1B01G194300	chr7A	90.296	371	32	2	2002	2369	201255540	201255909	1.460000e-132	483.0
32	TraesCS1B01G194300	chrUn	90.155	386	29	7	1990	2369	1191057	1190675	6.740000e-136	494.0
33	TraesCS1B01G194300	chr4D	78.737	649	123	13	1012	1654	465357898	465358537	1.160000e-113	420.0
34	TraesCS1B01G194300	chr3D	83.864	471	43	13	2244	2708	541071688	541072131	4.170000e-113	418.0
35	TraesCS1B01G194300	chr3D	84.766	256	27	5	646	901	573074473	573074230	2.080000e-61	246.0
36	TraesCS1B01G194300	chr3D	86.634	202	27	0	714	915	28347215	28347416	9.760000e-55	224.0
37	TraesCS1B01G194300	chr2B	95.299	234	11	0	668	901	11823068	11823301	3.290000e-99	372.0
38	TraesCS1B01G194300	chr2B	92.553	188	11	1	457	644	11822593	11822777	1.600000e-67	267.0
39	TraesCS1B01G194300	chr2B	74.882	633	128	26	1013	1626	248137080	248137700	2.670000e-65	259.0
40	TraesCS1B01G194300	chr2B	100.000	34	0	0	637	670	11822761	11822794	2.250000e-06	63.9
41	TraesCS1B01G194300	chr5D	84.375	320	42	6	1013	1325	24974725	24974407	9.420000e-80	307.0
42	TraesCS1B01G194300	chr6D	86.275	204	15	2	270	473	84555458	84555648	2.730000e-50	209.0
43	TraesCS1B01G194300	chr6D	86.286	175	14	3	67	240	84555228	84555393	5.960000e-42	182.0
44	TraesCS1B01G194300	chr2D	94.444	54	3	0	848	901	417377261	417377208	1.730000e-12	84.2

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	TraesCS1B01G194300	chr1B	349545606	349548313	2707	True	5001.0	5001	100.000000	1	2708	1	chr1B.!!$R2	2707
1	TraesCS1B01G194300	chr1D	262287723	262288830	1107	False	1592.0	1592	92.908000	901	1991	1	chr1D.!!$F2	1090
2	TraesCS1B01G194300	chr1A	337657522	337658637	1115	True	1544.0	1544	91.971000	901	1996	1	chr1A.!!$R1	1095
3	TraesCS1B01G194300	chr5B	587129515	587130415	900	True	1343.0	1343	93.647000	1	901	1	chr5B.!!$R3	900
4	TraesCS1B01G194300	chr5B	251348015	251348739	724	False	1005.0	1005	92.192000	1999	2704	1	chr5B.!!$F1	705
5	TraesCS1B01G194300	chr4B	573081419	573082320	901	True	1258.0	1258	92.013000	1	898	1	chr4B.!!$R2	897
6	TraesCS1B01G194300	chr2A	156862836	156863564	728	False	870.0	870	88.738000	1998	2708	1	chr2A.!!$F1	710
7	TraesCS1B01G194300	chr7D	80771671	80772354	683	True	634.0	634	83.573000	1012	1697	1	chr7D.!!$R3	685
8	TraesCS1B01G194300	chr7D	29056725	29057370	645	True	523.0	523	81.298000	1013	1658	1	chr7D.!!$R2	645
9	TraesCS1B01G194300	chr7B	27973853	27974531	678	True	606.0	606	83.163000	1012	1678	1	chr7B.!!$R1	666
10	TraesCS1B01G194300	chr4A	701282934	701283590	656	False	582.0	582	82.827000	1013	1663	1	chr4A.!!$F2	650
11	TraesCS1B01G194300	chr4A	5114602	5115253	651	True	409.0	409	78.267000	1012	1660	1	chr4A.!!$R1	648
12	TraesCS1B01G194300	chr7A	29164912	29165568	656	True	577.0	577	82.675000	1013	1663	1	chr7A.!!$R1	650
13	TraesCS1B01G194300	chr4D	465357898	465358537	639	False	420.0	420	78.737000	1012	1654	1	chr4D.!!$F1	642
14	TraesCS1B01G194300	chr2B	248137080	248137700	620	False	259.0	259	74.882000	1013	1626	1	chr2B.!!$F1	613
15	TraesCS1B01G194300	chr2B	11822593	11823301	708	False	234.3	372	95.950667	457	901	3	chr2B.!!$F2	444

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
279	284	0.11319	CCTGCTGTTTCCCCCTCTTT	59.887	55.0	0.00	0.00	0.00	2.52	F
628	648	0.17907	GAGCACTACTAGGCCAAGGC	60.179	60.0	5.01	1.52	41.06	4.35	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1541	1876	0.643820	GGCGTCGATTAACTTGTCGG	59.356	55.000	0.0	0.0	38.34	4.79	R
1869	2229	1.228583	AGGAGGAGCTGTCACGACA	60.229	57.895	0.0	0.0	39.32	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
19	20	1.645034	CACGAGCGTCATCTTCCATT	58.355	50.000	0.00	0.00	0.00	3.16
134	137	5.338708	CCACCACCACATAATTCTCTTCTCT	60.339	44.000	0.00	0.00	0.00	3.10
137	140	6.047870	CCACCACATAATTCTCTTCTCTCAG	58.952	44.000	0.00	0.00	0.00	3.35
187	190	2.022240	CTGCGAGAAGAGGCCTACCC	62.022	65.000	4.42	0.00	36.11	3.69
221	224	8.633561	CAACCAAGAATCTAGAAGGAAAAGTTT	58.366	33.333	0.00	0.00	0.00	2.66
260	265	6.072286	TGCAATTGACAAGAGAAGGAAGATTC	60.072	38.462	10.34	0.00	0.00	2.52
279	284	0.113190	CCTGCTGTTTCCCCCTCTTT	59.887	55.000	0.00	0.00	0.00	2.52
412	428	7.828712	AGACTAAGAATAGTGGTTGTACTGTC	58.171	38.462	0.00	0.00	42.47	3.51
516	533	6.249951	AGGTGGGCATTGTACTGTTTAAATA	58.750	36.000	0.00	0.00	0.00	1.40
543	560	4.261405	CCTCTCTATTCGTCTTGCTACTGG	60.261	50.000	0.00	0.00	0.00	4.00
560	577	6.015688	TGCTACTGGAGAGTTAATTATACGGG	60.016	42.308	0.00	0.00	33.21	5.28
615	635	1.067776	GTACAACGGCACTAGAGCACT	60.068	52.381	14.31	0.00	35.83	4.40
616	636	1.254026	ACAACGGCACTAGAGCACTA	58.746	50.000	14.31	0.00	35.83	2.74
617	637	1.067776	ACAACGGCACTAGAGCACTAC	60.068	52.381	14.31	0.00	35.83	2.73
627	647	1.490574	AGAGCACTACTAGGCCAAGG	58.509	55.000	5.01	0.00	0.00	3.61
628	648	0.179070	GAGCACTACTAGGCCAAGGC	60.179	60.000	5.01	1.52	41.06	4.35
629	649	0.909610	AGCACTACTAGGCCAAGGCA	60.910	55.000	13.87	0.00	44.11	4.75
630	650	0.181350	GCACTACTAGGCCAAGGCAT	59.819	55.000	13.87	8.66	44.11	4.40
631	651	1.959042	CACTACTAGGCCAAGGCATG	58.041	55.000	13.87	4.68	44.11	4.06
632	652	1.210478	CACTACTAGGCCAAGGCATGT	59.790	52.381	13.87	10.22	44.11	3.21
633	653	1.486726	ACTACTAGGCCAAGGCATGTC	59.513	52.381	13.87	0.00	44.11	3.06
634	654	0.464036	TACTAGGCCAAGGCATGTCG	59.536	55.000	13.87	2.01	44.11	4.35
635	655	1.221840	CTAGGCCAAGGCATGTCGT	59.778	57.895	13.87	0.00	44.11	4.34
686	982	3.181511	GCATTATGCACACGAGCTGTTAA	60.182	43.478	12.80	0.00	44.26	2.01
733	1029	2.550855	GCTCACCACCTCAAGATGACAA	60.551	50.000	0.00	0.00	0.00	3.18
753	1049	3.740044	ATGCGAACGTATTTCAACAGG	57.260	42.857	0.00	0.00	33.24	4.00
775	1071	6.539826	CAGGTACATCTGCATCAATTAAGTGA	59.460	38.462	8.22	8.22	0.00	3.41
776	1072	7.066163	CAGGTACATCTGCATCAATTAAGTGAA	59.934	37.037	9.98	0.00	0.00	3.18
799	1097	8.723365	TGAATATTCCACTAAACCCACATATCT	58.277	33.333	12.90	0.00	0.00	1.98
981	1286	2.030562	ACGGAACCTTGAGGCACG	59.969	61.111	0.00	2.33	39.32	5.34
1473	1808	3.916392	CTTCTTCGGCGGCGACTGT	62.916	63.158	34.85	0.00	0.00	3.55
1500	1835	3.735029	GTCGACGTCCTGCTCGGT	61.735	66.667	10.58	0.00	0.00	4.69
1720	2058	1.299316	CAATAAAGCGGCATGGCGG	60.299	57.895	37.92	22.23	38.18	6.13
1818	2160	9.677567	TTTCTGTTTCTTTTTCTCGAATAATGG	57.322	29.630	0.00	0.00	0.00	3.16
1819	2161	7.305474	TCTGTTTCTTTTTCTCGAATAATGGC	58.695	34.615	0.00	0.00	0.00	4.40
1869	2229	6.104146	ACCAGTTTAAAAACTTGTGTGGTT	57.896	33.333	10.52	0.00	46.52	3.67
1933	2293	0.588252	CTGTCCTTGGCTTTGTCACG	59.412	55.000	0.00	0.00	0.00	4.35
2050	2410	7.172757	GCAACGGCAGAAATAACAAAATTATG	58.827	34.615	0.00	0.00	40.72	1.90
2079	2439	8.592155	CAATTTTTGTGATGATTGTATCTGCAG	58.408	33.333	7.63	7.63	0.00	4.41
2088	2448	4.754618	TGATTGTATCTGCAGAACACGTTT	59.245	37.500	22.50	4.57	0.00	3.60
2133	2493	6.458751	CTTAACCAAGATCCATGGAAACATCG	60.459	42.308	20.67	7.50	41.00	3.84
2211	2571	5.645067	TCTTGTCAAGCATCTCATCGAAATT	59.355	36.000	7.78	0.00	0.00	1.82
2497	2878	2.301346	CCGGCATGAAAGATAAAGCCT	58.699	47.619	0.00	0.00	39.91	4.58
2577	2960	2.079158	CACATGTCAGCACTTACCCTG	58.921	52.381	0.00	0.00	0.00	4.45

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
10	11	1.696063	CCAATGCGGGAATGGAAGAT	58.304	50.000	0.00	0.00	36.27	2.40
40	41	2.124403	ACGGAGATAGACGGCGGT	60.124	61.111	13.24	0.00	0.00	5.68
77	80	3.849951	CGGAGGTACATGGCGGCT	61.850	66.667	11.43	0.00	0.00	5.52
187	190	2.731572	AGATTCTTGGTTGATGCCTGG	58.268	47.619	0.00	0.00	0.00	4.45
196	199	8.768501	AAACTTTTCCTTCTAGATTCTTGGTT	57.231	30.769	0.00	0.00	0.00	3.67
221	224	5.999600	TGTCAATTGCAGATTCTCTTCTTGA	59.000	36.000	0.00	0.00	0.00	3.02
260	265	0.113190	AAAGAGGGGGAAACAGCAGG	59.887	55.000	0.00	0.00	0.00	4.85
279	284	3.197766	ACCTCGAGCTTTGTATGGATTGA	59.802	43.478	6.99	0.00	0.00	2.57
398	414	0.396811	GCAGGGACAGTACAACCACT	59.603	55.000	0.00	0.00	0.00	4.00
412	428	1.675415	GCAGAGAAACAGAGAGCAGGG	60.675	57.143	0.00	0.00	0.00	4.45
479	496	1.413077	GCCCACCTAGTCCATACAGAC	59.587	57.143	0.00	0.00	37.01	3.51
516	533	3.133721	AGCAAGACGAATAGAGAGGCAAT	59.866	43.478	0.00	0.00	0.00	3.56
543	560	8.828688	ATTAACTGCCCGTATAATTAACTCTC	57.171	34.615	0.00	0.00	0.00	3.20
560	577	8.911662	CCAACAAACAACACTATAATTAACTGC	58.088	33.333	0.00	0.00	0.00	4.40
574	591	0.605083	TGCAGCACCAACAAACAACA	59.395	45.000	0.00	0.00	0.00	3.33
615	635	0.464036	CGACATGCCTTGGCCTAGTA	59.536	55.000	13.38	2.30	0.00	1.82
616	636	1.221840	CGACATGCCTTGGCCTAGT	59.778	57.895	13.38	4.92	0.00	2.57
617	637	1.091771	CACGACATGCCTTGGCCTAG	61.092	60.000	7.29	7.29	0.00	3.02
686	982	0.111253	CACTGGTTCCTTGGGAGCTT	59.889	55.000	0.00	0.00	33.37	3.74
733	1029	3.071479	ACCTGTTGAAATACGTTCGCAT	58.929	40.909	0.00	0.00	39.30	4.73
775	1071	8.723365	TGAGATATGTGGGTTTAGTGGAATATT	58.277	33.333	0.00	0.00	0.00	1.28
776	1072	8.157476	GTGAGATATGTGGGTTTAGTGGAATAT	58.843	37.037	0.00	0.00	0.00	1.28
799	1097	7.066887	CGCCAAAGCCCATATATTATTATGTGA	59.933	37.037	3.68	0.00	30.55	3.58
987	1292	1.304052	TGCCATTTTCTCCCGTGGG	60.304	57.895	0.00	0.00	32.35	4.61
988	1293	0.322456	TCTGCCATTTTCTCCCGTGG	60.322	55.000	0.00	0.00	34.84	4.94
989	1294	0.804989	GTCTGCCATTTTCTCCCGTG	59.195	55.000	0.00	0.00	0.00	4.94
990	1295	0.400213	TGTCTGCCATTTTCTCCCGT	59.600	50.000	0.00	0.00	0.00	5.28
991	1296	0.804989	GTGTCTGCCATTTTCTCCCG	59.195	55.000	0.00	0.00	0.00	5.14
1415	1738	0.693767	CCTCAGGCCTTCCTCCAGAT	60.694	60.000	0.00	0.00	41.93	2.90
1500	1835	3.326578	ACCCACGGCACCATGCTA	61.327	61.111	0.13	0.00	44.28	3.49
1541	1876	0.643820	GGCGTCGATTAACTTGTCGG	59.356	55.000	0.00	0.00	38.34	4.79
1701	2039	1.723608	CCGCCATGCCGCTTTATTGA	61.724	55.000	0.00	0.00	0.00	2.57
1720	2058	2.113433	CATCAGCTGCTCACCAGGC	61.113	63.158	9.47	0.00	42.03	4.85
1730	2068	4.497674	GCTATTTTCTCCTTGCATCAGCTG	60.498	45.833	7.63	7.63	42.74	4.24
1731	2069	3.631227	GCTATTTTCTCCTTGCATCAGCT	59.369	43.478	0.00	0.00	42.74	4.24
1764	2106	6.096282	TGGCCATTTTAGTAATTCCAGCTAAC	59.904	38.462	0.00	0.00	0.00	2.34
1817	2159	5.408299	TCACATACTTGCATATTATGTCGCC	59.592	40.000	10.79	0.00	34.82	5.54
1818	2160	6.466308	TCACATACTTGCATATTATGTCGC	57.534	37.500	10.79	0.00	34.82	5.19
1827	2187	9.845740	AAACTGGTAATATCACATACTTGCATA	57.154	29.630	0.00	0.00	0.00	3.14
1869	2229	1.228583	AGGAGGAGCTGTCACGACA	60.229	57.895	0.00	0.00	39.32	4.35
1933	2293	3.702548	ACCAAAAGACAAACCCCACTAAC	59.297	43.478	0.00	0.00	0.00	2.34
1996	2356	6.159293	CACGGACATATGTGCTAGTCATATT	58.841	40.000	22.88	9.83	36.66	1.28
2056	2416	7.451501	TCTGCAGATACAATCATCACAAAAA	57.548	32.000	13.74	0.00	0.00	1.94
2079	2439	5.270853	AGTTTGCATGAACTAAACGTGTTC	58.729	37.500	9.63	9.63	42.77	3.18
2088	2448	8.296713	GGTTAAGATCAAAGTTTGCATGAACTA	58.703	33.333	10.90	0.00	38.86	2.24
2168	2528	9.219603	TGACAAGACAGGAACAATTAATTAGAG	57.780	33.333	0.00	0.00	0.00	2.43
2625	3010	9.599866	AAAGAGCAAAGCAAAATAGTAGTTTTT	57.400	25.926	0.00	0.00	0.00	1.94
2630	3015	7.061557	GCTCAAAAGAGCAAAGCAAAATAGTAG	59.938	37.037	12.23	0.00	46.73	2.57
2631	3016	6.863126	GCTCAAAAGAGCAAAGCAAAATAGTA	59.137	34.615	12.23	0.00	46.73	1.82
2676	3062	7.171678	GCTGTCAGTGAATTAATATGTAGGTCC	59.828	40.741	0.93	0.00	0.00	4.46

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.