AutoCloner

Multiple sequence alignment - TraesCS6B01G273700

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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	TraesCS6B01G273700	chr6B	100.000	2956	0	0	1	2956	494091077	494088122	0.000000e+00	5459.0
1	TraesCS6B01G273700	chr6B	98.918	832	9	0	1	832	383568972	383569803	0.000000e+00	1487.0
2	TraesCS6B01G273700	chr6D	91.539	2092	119	17	894	2947	327362772	327364843	0.000000e+00	2830.0
3	TraesCS6B01G273700	chr6A	85.751	1544	131	39	844	2379	466090722	466092184	0.000000e+00	1550.0
4	TraesCS6B01G273700	chr6A	92.821	585	33	7	2375	2954	466097832	466098412	0.000000e+00	839.0
5	TraesCS6B01G273700	chr5B	99.279	832	6	0	1	832	613641128	613640297	0.000000e+00	1504.0
6	TraesCS6B01G273700	chr4A	99.279	832	6	0	1	832	127488712	127487881	0.000000e+00	1504.0
7	TraesCS6B01G273700	chr4A	96.875	64	1	1	2509	2572	16469381	16469319	4.030000e-19	106.0
8	TraesCS6B01G273700	chr2B	99.159	832	7	0	1	832	753936636	753935805	0.000000e+00	1498.0
9	TraesCS6B01G273700	chr2B	98.438	832	12	1	1	832	790108220	790107390	0.000000e+00	1463.0
10	TraesCS6B01G273700	chr2B	95.455	66	2	1	2509	2574	674302585	674302649	1.450000e-18	104.0
11	TraesCS6B01G273700	chr7A	99.038	832	8	0	1	832	157171227	157170396	0.000000e+00	1493.0
12	TraesCS6B01G273700	chr7A	97.847	836	13	3	1	832	115323649	115322815	0.000000e+00	1439.0
13	TraesCS6B01G273700	chr1B	99.038	832	8	0	1	832	546703489	546702658	0.000000e+00	1493.0
14	TraesCS6B01G273700	chr1B	95.455	66	2	1	2509	2574	493871938	493871874	1.450000e-18	104.0
15	TraesCS6B01G273700	chr1B	91.667	72	5	1	2509	2580	493871907	493871977	6.740000e-17	99.0
16	TraesCS6B01G273700	chr3A	98.798	832	9	1	1	832	25928432	25927602	0.000000e+00	1480.0
17	TraesCS6B01G273700	chr3A	88.608	79	8	1	2494	2572	679696572	679696649	8.720000e-16	95.3
18	TraesCS6B01G273700	chr7D	97.059	68	2	0	2501	2568	566230980	566231047	6.700000e-22	115.0
19	TraesCS6B01G273700	chr4B	95.588	68	3	0	2501	2568	40557348	40557415	3.110000e-20	110.0

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	TraesCS6B01G273700	chr6B	494088122	494091077	2955	True	5459	5459	100.000	1	2956	1	chr6B.!!$R1	2955
1	TraesCS6B01G273700	chr6B	383568972	383569803	831	False	1487	1487	98.918	1	832	1	chr6B.!!$F1	831
2	TraesCS6B01G273700	chr6D	327362772	327364843	2071	False	2830	2830	91.539	894	2947	1	chr6D.!!$F1	2053
3	TraesCS6B01G273700	chr6A	466090722	466092184	1462	False	1550	1550	85.751	844	2379	1	chr6A.!!$F1	1535
4	TraesCS6B01G273700	chr6A	466097832	466098412	580	False	839	839	92.821	2375	2954	1	chr6A.!!$F2	579
5	TraesCS6B01G273700	chr5B	613640297	613641128	831	True	1504	1504	99.279	1	832	1	chr5B.!!$R1	831
6	TraesCS6B01G273700	chr4A	127487881	127488712	831	True	1504	1504	99.279	1	832	1	chr4A.!!$R2	831
7	TraesCS6B01G273700	chr2B	753935805	753936636	831	True	1498	1498	99.159	1	832	1	chr2B.!!$R1	831
8	TraesCS6B01G273700	chr2B	790107390	790108220	830	True	1463	1463	98.438	1	832	1	chr2B.!!$R2	831
9	TraesCS6B01G273700	chr7A	157170396	157171227	831	True	1493	1493	99.038	1	832	1	chr7A.!!$R2	831
10	TraesCS6B01G273700	chr7A	115322815	115323649	834	True	1439	1439	97.847	1	832	1	chr7A.!!$R1	831
11	TraesCS6B01G273700	chr1B	546702658	546703489	831	True	1493	1493	99.038	1	832	1	chr1B.!!$R2	831
12	TraesCS6B01G273700	chr3A	25927602	25928432	830	True	1480	1480	98.798	1	832	1	chr3A.!!$R1	831

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
894	899	0.752054	CCAACTCCCAAAGCAAGCAA	59.248	50.0	0.0	0.0	0.0	3.91	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2325	2341	0.099968	GCGTACGTGCACTCCTATCA	59.9	55.0	17.9	0.0	34.15	2.15	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
385	386	1.188219	CCGATCTGGATCCCGACCAT	61.188	60.000	9.90	0.00	42.00	3.55
531	534	3.842923	CCAGATCGGGCGCTGACT	61.843	66.667	7.64	3.70	34.06	3.41
834	839	3.787001	GGAGAGGGGGTGGCGAAG	61.787	72.222	0.00	0.00	0.00	3.79
883	888	2.663196	CGGTGACTCCCAACTCCC	59.337	66.667	0.00	0.00	0.00	4.30
891	896	1.251251	CTCCCAACTCCCAAAGCAAG	58.749	55.000	0.00	0.00	0.00	4.01
894	899	0.752054	CCAACTCCCAAAGCAAGCAA	59.248	50.000	0.00	0.00	0.00	3.91
895	900	1.138661	CCAACTCCCAAAGCAAGCAAA	59.861	47.619	0.00	0.00	0.00	3.68
1111	1116	2.659063	CCGGTCCAGAGCATCACCA	61.659	63.158	0.00	0.00	37.82	4.17
1116	1121	2.672908	CAGAGCATCACCAGGGCA	59.327	61.111	0.00	0.00	37.82	5.36
1127	1132	2.060383	CCAGGGCAGAGATCGACCA	61.060	63.158	0.00	0.00	0.00	4.02
1188	1193	0.679960	TCGATGACGAGAAGGAGGCA	60.680	55.000	0.00	0.00	43.81	4.75
1201	1206	1.101331	GGAGGCAGCAAGGATCAAAG	58.899	55.000	0.00	0.00	0.00	2.77
1202	1207	0.455005	GAGGCAGCAAGGATCAAAGC	59.545	55.000	0.00	0.00	0.00	3.51
1208	1213	2.163815	CAGCAAGGATCAAAGCCAAGAG	59.836	50.000	0.00	0.00	0.00	2.85
1303	1312	9.595823	TTTCATTCACTACCTAGTTTATACAGC	57.404	33.333	0.00	0.00	33.46	4.40
1304	1313	8.534954	TCATTCACTACCTAGTTTATACAGCT	57.465	34.615	0.00	0.00	33.46	4.24
1305	1314	9.636789	TCATTCACTACCTAGTTTATACAGCTA	57.363	33.333	0.00	0.00	33.46	3.32
1415	1425	6.655078	ACATGGAAAGAATATTGTATGGCC	57.345	37.500	0.00	0.00	0.00	5.36
1417	1427	5.042463	TGGAAAGAATATTGTATGGCCGA	57.958	39.130	0.00	0.00	0.00	5.54
1438	1448	4.662145	GAGTCATTTTGATACCTTTGCCG	58.338	43.478	0.00	0.00	0.00	5.69
1648	1659	2.031069	TCTCCTGATGTTACGCGCTATC	60.031	50.000	5.73	5.76	0.00	2.08
1650	1661	2.031069	TCCTGATGTTACGCGCTATCTC	60.031	50.000	5.73	0.00	0.00	2.75
1660	1671	2.423892	ACGCGCTATCTCTCTTTCTTCA	59.576	45.455	5.73	0.00	0.00	3.02
1707	1718	2.095768	CGCACACCTTAACAATGTCTGG	60.096	50.000	0.00	0.00	0.00	3.86
1807	1820	2.814097	GCAGGTGGAGGAAAAGCAGTTA	60.814	50.000	0.00	0.00	0.00	2.24
1943	1956	2.158449	CCAGATGAACGTGACTGCTTTC	59.842	50.000	0.00	0.00	0.00	2.62
2018	2033	7.482654	TTTTCCTTATGCGTCTCAATATGAG	57.517	36.000	0.88	0.88	45.59	2.90
2064	2079	5.623956	TGAAAAGGGTACTTCTTGAGTCA	57.376	39.130	0.00	0.00	39.86	3.41
2094	2109	6.704493	TGGAACAGCCTTATCATTTACGATAC	59.296	38.462	0.00	0.00	37.63	2.24
2095	2110	6.704493	GGAACAGCCTTATCATTTACGATACA	59.296	38.462	0.00	0.00	0.00	2.29
2101	2116	8.639761	AGCCTTATCATTTACGATACAAGTAGT	58.360	33.333	0.00	0.00	0.00	2.73
2252	2268	9.391006	GACACTCAAAATATCCATTACCAGTAA	57.609	33.333	0.00	0.00	0.00	2.24
2325	2341	5.164620	TCGATGACACCCATTATATGCAT	57.835	39.130	3.79	3.79	35.17	3.96
2332	2348	6.215227	TGACACCCATTATATGCATGATAGGA	59.785	38.462	10.16	0.00	0.00	2.94
2342	2358	2.128035	GCATGATAGGAGTGCACGTAC	58.872	52.381	12.01	5.76	38.68	3.67
2358	2374	0.179282	GTACGCGTGCTTGAAGTTCG	60.179	55.000	24.59	0.60	0.00	3.95
2363	2379	1.221466	CGTGCTTGAAGTTCGGAGCA	61.221	55.000	22.56	22.56	42.36	4.26
2439	2455	8.616076	GCTAGTATGTGAAATCAAGCAAATAGT	58.384	33.333	0.00	0.00	0.00	2.12
2469	2485	8.785329	AACAAAAACAAAATGACAATACACCT	57.215	26.923	0.00	0.00	0.00	4.00
2487	2503	8.761575	ATACACCTTTTGCAATCTAAAACATG	57.238	30.769	0.00	0.00	0.00	3.21
2488	2504	6.581712	ACACCTTTTGCAATCTAAAACATGT	58.418	32.000	0.00	0.00	0.00	3.21
2492	2508	6.930722	CCTTTTGCAATCTAAAACATGTTCCT	59.069	34.615	12.39	4.97	0.00	3.36
2496	2512	5.538053	TGCAATCTAAAACATGTTCCTTCCA	59.462	36.000	12.39	0.00	0.00	3.53
2597	2629	4.263905	TGAGTTCTTGGCCATACAGGAATT	60.264	41.667	6.09	3.59	38.47	2.17
2600	2632	5.652452	AGTTCTTGGCCATACAGGAATTTAC	59.348	40.000	6.09	0.00	38.47	2.01
2628	2660	6.451393	AGAACAGTAGAACACAGAAGCTAAG	58.549	40.000	0.00	0.00	0.00	2.18
2637	2669	4.904241	ACACAGAAGCTAAGCAGAAAGAT	58.096	39.130	0.00	0.00	0.00	2.40
2657	2689	8.837788	AAAGATTGCCAAAAGAAATTAGAAGG	57.162	30.769	0.00	0.00	0.00	3.46
2696	2728	5.948162	AGCATCATGAACTTGTTACCAATCT	59.052	36.000	0.00	0.00	0.00	2.40
2741	2774	7.559897	TGATAACCCCAAGGAAATATTTGACTC	59.440	37.037	5.17	0.00	36.73	3.36
2742	2775	5.536497	ACCCCAAGGAAATATTTGACTCT	57.464	39.130	5.17	0.00	36.73	3.24
2873	2919	2.928757	GCAGAACACACAGATAGAGCAG	59.071	50.000	0.00	0.00	0.00	4.24
2954	3006	7.994911	AGATCCAAAGTATATGAACATTCAGCA	59.005	33.333	0.23	0.00	41.08	4.41
2955	3007	7.320443	TCCAAAGTATATGAACATTCAGCAC	57.680	36.000	0.23	0.00	41.08	4.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
385	386	2.689471	CCTCCCAATGATGCGATTTTGA	59.311	45.455	0.00	0.00	0.00	2.69
527	530	2.741878	GCTTAGGCGCCAGATTTAGTCA	60.742	50.000	31.54	0.00	0.00	3.41
531	534	1.663695	GTGCTTAGGCGCCAGATTTA	58.336	50.000	31.54	9.03	42.54	1.40
832	837	0.767375	TTCAGGAAGGCACTCTGCTT	59.233	50.000	0.00	0.00	44.28	3.91
833	838	0.036022	GTTCAGGAAGGCACTCTGCT	59.964	55.000	0.00	0.00	44.28	4.24
834	839	0.250467	TGTTCAGGAAGGCACTCTGC	60.250	55.000	0.00	0.00	38.49	4.26
835	840	1.345741	TCTGTTCAGGAAGGCACTCTG	59.654	52.381	0.00	0.00	38.49	3.35
836	841	1.722034	TCTGTTCAGGAAGGCACTCT	58.278	50.000	0.00	0.00	38.49	3.24
837	842	2.421619	CTTCTGTTCAGGAAGGCACTC	58.578	52.381	0.00	0.00	38.49	3.51
839	844	0.877743	GCTTCTGTTCAGGAAGGCAC	59.122	55.000	0.00	0.00	40.13	5.01
840	845	0.767375	AGCTTCTGTTCAGGAAGGCA	59.233	50.000	0.00	0.00	40.13	4.75
841	846	1.003003	AGAGCTTCTGTTCAGGAAGGC	59.997	52.381	0.00	0.00	40.13	4.35
842	847	2.354604	GGAGAGCTTCTGTTCAGGAAGG	60.355	54.545	0.00	0.00	40.13	3.46
894	899	4.019501	ACCATCAGTCTCTTGAGCATCTTT	60.020	41.667	0.00	0.00	34.92	2.52
895	900	3.518705	ACCATCAGTCTCTTGAGCATCTT	59.481	43.478	0.00	0.00	34.92	2.40
911	916	4.406972	CCTATCCACTCTTCTCAACCATCA	59.593	45.833	0.00	0.00	0.00	3.07
975	980	3.118038	TCTCCCTCTCTCTAGAGTTGAGC	60.118	52.174	25.80	0.00	46.80	4.26
986	991	5.221501	CCTTTGATCATCTTCTCCCTCTCTC	60.222	48.000	0.00	0.00	0.00	3.20
1111	1116	1.139853	GAAATGGTCGATCTCTGCCCT	59.860	52.381	0.00	0.00	0.00	5.19
1116	1121	1.202463	CGCCAGAAATGGTCGATCTCT	60.202	52.381	0.00	0.00	32.86	3.10
1135	1140	0.036952	TCCTCCAGCTTCTTTCTGCG	60.037	55.000	0.00	0.00	0.00	5.18
1188	1193	2.224967	ACTCTTGGCTTTGATCCTTGCT	60.225	45.455	0.00	0.00	0.00	3.91
1201	1206	1.163554	CTTGCCTTGAGACTCTTGGC	58.836	55.000	23.38	23.38	43.49	4.52
1202	1207	2.557920	ACTTGCCTTGAGACTCTTGG	57.442	50.000	3.68	6.95	0.00	3.61
1208	1213	7.104290	AGGTAAAAGTATACTTGCCTTGAGAC	58.896	38.462	18.70	5.41	36.12	3.36
1301	1310	4.576330	AAAGAGGGTATGCAGTTTAGCT	57.424	40.909	0.00	0.00	34.99	3.32
1302	1311	6.753107	TTAAAAGAGGGTATGCAGTTTAGC	57.247	37.500	0.00	0.00	0.00	3.09
1303	1312	7.630924	CGATTAAAAGAGGGTATGCAGTTTAG	58.369	38.462	0.00	0.00	0.00	1.85
1304	1313	6.037830	GCGATTAAAAGAGGGTATGCAGTTTA	59.962	38.462	0.00	0.00	0.00	2.01
1305	1314	5.163652	GCGATTAAAAGAGGGTATGCAGTTT	60.164	40.000	0.00	0.00	0.00	2.66
1315	1324	9.805966	GTTTTTATTTTTGCGATTAAAAGAGGG	57.194	29.630	0.00	0.00	31.80	4.30
1413	1423	4.662145	CAAAGGTATCAAAATGACTCGGC	58.338	43.478	0.00	0.00	0.00	5.54
1415	1425	4.662145	GGCAAAGGTATCAAAATGACTCG	58.338	43.478	0.00	0.00	0.00	4.18
1417	1427	4.079253	ACGGCAAAGGTATCAAAATGACT	58.921	39.130	0.00	0.00	0.00	3.41
1463	1473	3.059800	GCTCTTAACACAGTTTGACCGAC	60.060	47.826	0.00	0.00	0.00	4.79
1648	1659	5.475220	TCACCAGTAGAGTGAAGAAAGAGAG	59.525	44.000	0.00	0.00	41.17	3.20
1650	1661	5.713792	TCACCAGTAGAGTGAAGAAAGAG	57.286	43.478	0.00	0.00	41.17	2.85
1660	1671	6.041409	CACCATATCAAGATCACCAGTAGAGT	59.959	42.308	0.00	0.00	0.00	3.24
1707	1718	0.391661	TTCGAACCATGCAGGAGAGC	60.392	55.000	0.00	0.00	41.22	4.09
1778	1791	1.067295	TCCTCCACCTGCACTTTCAT	58.933	50.000	0.00	0.00	0.00	2.57
1807	1820	6.066690	ACTGCTGGTTGATTTAGATATGCAT	58.933	36.000	3.79	3.79	0.00	3.96
1821	1834	2.048444	ATGGATGCTACTGCTGGTTG	57.952	50.000	0.00	0.00	40.48	3.77
1917	1930	3.120649	GCAGTCACGTTCATCTGGTAAAC	60.121	47.826	0.00	0.00	0.00	2.01
1943	1956	4.932200	GGTATCAGCATTTAGAAGATCCCG	59.068	45.833	0.00	0.00	0.00	5.14
2064	2079	3.370840	TGATAAGGCTGTTCCATGCTT	57.629	42.857	0.00	0.00	37.29	3.91
2089	2104	5.909477	TCCCCAAACATACTACTTGTATCG	58.091	41.667	0.00	0.00	39.66	2.92
2094	2109	4.269183	TGCATCCCCAAACATACTACTTG	58.731	43.478	0.00	0.00	0.00	3.16
2095	2110	4.018415	ACTGCATCCCCAAACATACTACTT	60.018	41.667	0.00	0.00	0.00	2.24
2101	2116	3.448093	TTCACTGCATCCCCAAACATA	57.552	42.857	0.00	0.00	0.00	2.29
2221	2237	6.446781	AATGGATATTTTGAGTGTCTGCTG	57.553	37.500	0.00	0.00	0.00	4.41
2224	2240	7.554118	ACTGGTAATGGATATTTTGAGTGTCTG	59.446	37.037	0.00	0.00	0.00	3.51
2225	2241	7.633789	ACTGGTAATGGATATTTTGAGTGTCT	58.366	34.615	0.00	0.00	0.00	3.41
2325	2341	0.099968	GCGTACGTGCACTCCTATCA	59.900	55.000	17.90	0.00	34.15	2.15
2342	2358	2.170985	CCGAACTTCAAGCACGCG	59.829	61.111	3.53	3.53	0.00	6.01
2358	2374	6.471146	AGAGTATATCATGATTTGGTGCTCC	58.529	40.000	14.65	0.00	0.00	4.70
2363	2379	7.805163	TGTTGGAGAGTATATCATGATTTGGT	58.195	34.615	14.65	0.96	0.00	3.67
2469	2485	7.440856	GGAAGGAACATGTTTTAGATTGCAAAA	59.559	33.333	13.36	0.00	0.00	2.44
2487	2503	7.892609	ACCACTTATTTTGTTATGGAAGGAAC	58.107	34.615	0.00	0.00	0.00	3.62
2488	2504	8.485578	AACCACTTATTTTGTTATGGAAGGAA	57.514	30.769	0.00	0.00	0.00	3.36
2597	2629	5.761726	TCTGTGTTCTACTGTTCTCTCGTAA	59.238	40.000	0.00	0.00	0.00	3.18
2600	2632	4.750952	TCTGTGTTCTACTGTTCTCTCG	57.249	45.455	0.00	0.00	0.00	4.04
2628	2660	6.549912	AATTTCTTTTGGCAATCTTTCTGC	57.450	33.333	0.00	0.00	39.16	4.26
2637	2669	7.537596	TCATCCTTCTAATTTCTTTTGGCAA	57.462	32.000	0.00	0.00	0.00	4.52
2657	2689	2.686405	TGATGCTCTTGTGCCATTCATC	59.314	45.455	0.00	0.00	0.00	2.92
2712	2745	7.123547	TCAAATATTTCCTTGGGGTTATCACAC	59.876	37.037	0.00	0.00	0.00	3.82
2715	2748	7.418378	AGTCAAATATTTCCTTGGGGTTATCA	58.582	34.615	0.00	0.00	0.00	2.15
2755	2790	2.910688	ACTTCGTTCAGCTTGAAGGA	57.089	45.000	15.33	14.46	45.82	3.36
2845	2891	0.532862	CTGTGTGTTCTGCCCTTCGT	60.533	55.000	0.00	0.00	0.00	3.85
2846	2892	0.249868	TCTGTGTGTTCTGCCCTTCG	60.250	55.000	0.00	0.00	0.00	3.79

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.