AutoCloner

Multiple sequence alignment - TraesCS7B01G426300

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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	TraesCS7B01G426300	chr7B	100.000	4729	0	0	1	4729	695576177	695571449	0.000000e+00	8733
1	TraesCS7B01G426300	chr3B	96.617	4730	157	3	1	4729	817686345	817691072	0.000000e+00	7845
2	TraesCS7B01G426300	chr3B	96.553	3974	136	1	756	4729	817710255	817714227	0.000000e+00	6578
3	TraesCS7B01G426300	chr3B	96.644	3308	107	3	761	4065	745188	748494	0.000000e+00	5491
4	TraesCS7B01G426300	chr6B	96.191	4726	179	1	1	4726	83866046	83870770	0.000000e+00	7729
5	TraesCS7B01G426300	chr6A	96.068	4731	181	4	1	4729	307922646	307917919	0.000000e+00	7701
6	TraesCS7B01G426300	chr7A	95.983	4730	188	2	1	4729	395513525	395518253	0.000000e+00	7681
7	TraesCS7B01G426300	chr7A	90.928	1422	100	20	3228	4632	298784568	298785977	0.000000e+00	1884
8	TraesCS7B01G426300	chr7A	83.279	305	45	6	4427	4729	29872060	29872360	4.660000e-70	276
9	TraesCS7B01G426300	chr1A	95.442	4739	178	13	1	4729	236391030	236395740	0.000000e+00	7520
10	TraesCS7B01G426300	chr5A	96.308	3954	146	0	776	4729	631069218	631065265	0.000000e+00	6493
11	TraesCS7B01G426300	chr5A	96.216	3409	127	2	1	3408	213046759	213050166	0.000000e+00	5579
12	TraesCS7B01G426300	chr2A	95.549	1393	58	4	1	1392	290318353	290319742	0.000000e+00	2226
13	TraesCS7B01G426300	chr2A	90.000	560	50	6	1	558	549728839	549728284	0.000000e+00	719
14	TraesCS7B01G426300	chr2A	89.336	572	58	3	1	570	680895184	680894614	0.000000e+00	715
15	TraesCS7B01G426300	chr2A	89.046	566	56	6	1	563	475497189	475496627	0.000000e+00	697
16	TraesCS7B01G426300	chr3A	91.016	679	49	3	4063	4729	499571826	499572504	0.000000e+00	905

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	TraesCS7B01G426300	chr7B	695571449	695576177	4728	True	8733	8733	100.000	1	4729	1	chr7B.!!$R1	4728
1	TraesCS7B01G426300	chr3B	817686345	817691072	4727	False	7845	7845	96.617	1	4729	1	chr3B.!!$F2	4728
2	TraesCS7B01G426300	chr3B	817710255	817714227	3972	False	6578	6578	96.553	756	4729	1	chr3B.!!$F3	3973
3	TraesCS7B01G426300	chr3B	745188	748494	3306	False	5491	5491	96.644	761	4065	1	chr3B.!!$F1	3304
4	TraesCS7B01G426300	chr6B	83866046	83870770	4724	False	7729	7729	96.191	1	4726	1	chr6B.!!$F1	4725
5	TraesCS7B01G426300	chr6A	307917919	307922646	4727	True	7701	7701	96.068	1	4729	1	chr6A.!!$R1	4728
6	TraesCS7B01G426300	chr7A	395513525	395518253	4728	False	7681	7681	95.983	1	4729	1	chr7A.!!$F3	4728
7	TraesCS7B01G426300	chr7A	298784568	298785977	1409	False	1884	1884	90.928	3228	4632	1	chr7A.!!$F2	1404
8	TraesCS7B01G426300	chr1A	236391030	236395740	4710	False	7520	7520	95.442	1	4729	1	chr1A.!!$F1	4728
9	TraesCS7B01G426300	chr5A	631065265	631069218	3953	True	6493	6493	96.308	776	4729	1	chr5A.!!$R1	3953
10	TraesCS7B01G426300	chr5A	213046759	213050166	3407	False	5579	5579	96.216	1	3408	1	chr5A.!!$F1	3407
11	TraesCS7B01G426300	chr2A	290318353	290319742	1389	False	2226	2226	95.549	1	1392	1	chr2A.!!$F1	1391
12	TraesCS7B01G426300	chr2A	549728284	549728839	555	True	719	719	90.000	1	558	1	chr2A.!!$R2	557
13	TraesCS7B01G426300	chr2A	680894614	680895184	570	True	715	715	89.336	1	570	1	chr2A.!!$R3	569
14	TraesCS7B01G426300	chr2A	475496627	475497189	562	True	697	697	89.046	1	563	1	chr2A.!!$R1	562
15	TraesCS7B01G426300	chr3A	499571826	499572504	678	False	905	905	91.016	4063	4729	1	chr3A.!!$F1	666

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	Hairpin	End Stability	Orientation
608	612	0.395862	CTCCTCCTCTCGCACCCTTA	60.396	60.000	0.00	0.00	2.69	F
995	1008	0.918983	ATGGTTGTGGATGGGACGAT	59.081	50.000	0.00	0.00	3.73	F
1201	1214	1.125093	ATGTGTCAACCACCCCTCGA	61.125	55.000	0.00	43.85	4.04	F
1981	1994	1.153706	CCATCGGTACCACCACGTC	60.154	63.158	13.54	38.47	4.34	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1960	1973	1.153706	GTGGTGGTACCGATGGTCG	60.154	63.158	7.57	0.00	42.58	4.79	R
2014	2027	1.306825	AGAGCAGAGGAGGCATGGT	60.307	57.895	0.00	0.00	0.00	3.55	R
3054	3069	0.610174	TGCTCACTAACCTGCAGGAG	59.390	55.000	39.19	27.61	38.94	3.69	R
3866	3881	0.108615	CAACTCAGGAGGCCACTACG	60.109	60.000	5.01	0.00	30.68	3.51	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
70	71	5.705905	GGTAGCTACAGTTCAAATTTGACCT	59.294	40.000	24.75	16.10	36.83	3.85
445	448	6.694447	AGCACCTTACTTTTAGTCGATTACA	58.306	36.000	0.00	0.00	0.00	2.41
530	534	1.996292	CGCGGATCGTGGATAATCAT	58.004	50.000	0.00	0.00	33.47	2.45
608	612	0.395862	CTCCTCCTCTCGCACCCTTA	60.396	60.000	0.00	0.00	0.00	2.69
794	798	1.455217	GCCCTCTAGTACTCGCCCA	60.455	63.158	0.00	0.00	0.00	5.36
850	854	2.579873	CCCTAACTTCGTCGGGATCTA	58.420	52.381	0.00	0.00	39.08	1.98
995	1008	0.918983	ATGGTTGTGGATGGGACGAT	59.081	50.000	0.00	0.00	0.00	3.73
1079	1092	3.036091	CTCCATCCAATTTGGCCATCTT	58.964	45.455	6.09	0.00	37.47	2.40
1192	1205	1.163420	TGTCCGTGCATGTGTCAACC	61.163	55.000	4.96	0.00	0.00	3.77
1199	1212	1.244019	GCATGTGTCAACCACCCCTC	61.244	60.000	0.00	0.00	43.85	4.30
1201	1214	1.125093	ATGTGTCAACCACCCCTCGA	61.125	55.000	0.00	0.00	43.85	4.04
1291	1304	2.351276	GATGGAACTGGTGCCCGT	59.649	61.111	0.00	0.00	0.00	5.28
1310	1323	3.310774	CCGTAAGCGAGTAGTACAGCTTA	59.689	47.826	25.94	25.94	46.59	3.09
1331	1344	2.079925	GCCTCTGCTTGTACTTCCTTG	58.920	52.381	0.00	0.00	33.53	3.61
1338	1351	5.827797	TCTGCTTGTACTTCCTTGTTTGATT	59.172	36.000	0.00	0.00	0.00	2.57
1533	1546	6.602803	TGCAATATGGTGTATGTTCAACTCAT	59.397	34.615	0.00	0.00	0.00	2.90
1653	1666	3.819564	TGTATGCTATGACAGACACCC	57.180	47.619	0.00	0.00	36.88	4.61
1787	1800	5.949952	TGTTCTCCTAGACATGCAGTTAGTA	59.050	40.000	0.00	0.00	0.00	1.82
1822	1835	3.821600	AGCGAAGACACAAGAGAAGACTA	59.178	43.478	0.00	0.00	0.00	2.59
1909	1922	1.384583	TCCTCGAGGAGCAGAAGGT	59.615	57.895	30.49	0.00	39.78	3.50
1960	1973	2.456577	ACTCTGCTCCTCTTCTTCCTC	58.543	52.381	0.00	0.00	0.00	3.71
1981	1994	1.153706	CCATCGGTACCACCACGTC	60.154	63.158	13.54	0.00	38.47	4.34
1987	2000	4.619320	TACCACCACGTCCCCGGT	62.619	66.667	0.00	0.00	38.78	5.28
2512	2527	3.758554	GCACCAACTCCAACAAGTGATAT	59.241	43.478	0.00	0.00	0.00	1.63
2638	2653	9.959749	CCTGTTTGCTTGAAAGTAATTTTAGTA	57.040	29.630	0.00	0.00	30.76	1.82
2662	2677	3.610040	TCTTTGATGGAGCGCTAAGAA	57.390	42.857	11.50	0.00	0.00	2.52
2713	2728	1.479323	ACTACCGCCGTGTGATTATGT	59.521	47.619	0.00	0.00	0.00	2.29
2779	2794	4.010349	CTCCCTGGAACATTAGTTTGTCC	58.990	47.826	0.00	0.00	38.30	4.02
2827	2842	9.264719	GGATATTATTTGCTGCTTATGCTTTTT	57.735	29.630	0.00	0.00	40.48	1.94
2910	2925	9.072375	TCCATGATTTTGTTATGTACTGTTTGA	57.928	29.630	0.00	0.00	0.00	2.69
3038	3053	3.328535	ACCCATGGTCTTGTTCCTTTT	57.671	42.857	11.73	0.00	0.00	2.27
3054	3069	3.895041	TCCTTTTCCCATGGTCTTGTTTC	59.105	43.478	11.73	0.00	0.00	2.78
3161	3176	2.041405	CCACCTCCCTCTCCCTCC	60.041	72.222	0.00	0.00	0.00	4.30
3174	3189	2.269241	CCTCCGCTCCCAAACCTC	59.731	66.667	0.00	0.00	0.00	3.85
3224	3239	5.109210	TGTCAACTTGTGTGTCAGTAAGAG	58.891	41.667	0.00	0.00	0.00	2.85
3386	3401	6.127647	GCATTTTGATGATCTCCTTGTACCAA	60.128	38.462	0.00	0.00	0.00	3.67
3621	3636	8.180844	AGCTTCTATTAGGGGATAATCTACTGT	58.819	37.037	0.00	0.00	35.63	3.55
3866	3881	6.128418	GCTCTCTCACTTGAGTTGGTTTAATC	60.128	42.308	6.15	0.00	42.60	1.75
3882	3897	1.115467	AATCGTAGTGGCCTCCTGAG	58.885	55.000	3.32	0.00	0.00	3.35
4147	4178	1.260561	GCGAAGACGTGAAGAAAAGCA	59.739	47.619	0.00	0.00	41.98	3.91
4197	4228	8.616076	CAAAGAGTTGTCTGTTCTATTTGACTT	58.384	33.333	5.86	0.00	40.51	3.01
4227	4267	7.534723	TTGTAATAGCTGGTATACCTAGGTG	57.465	40.000	25.33	7.52	36.82	4.00
4510	4554	5.583932	AGGACAAAGCCCAGAGATAAAAAT	58.416	37.500	0.00	0.00	0.00	1.82
4611	4656	3.117663	GGATAGGCCCATGTAGAAAACCA	60.118	47.826	0.00	0.00	0.00	3.67

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
474	477	5.291293	ACCAATCAAAACGCAGTATACAC	57.709	39.130	5.50	0.00	45.00	2.90
530	534	0.385751	GATCCAGAAGCATCCGACGA	59.614	55.000	0.00	0.00	0.00	4.20
542	546	3.781307	CGGGCCGTTGGATCCAGA	61.781	66.667	19.97	3.48	0.00	3.86
608	612	3.069980	GCGTCAGTGCGAGGGAGAT	62.070	63.158	10.49	0.00	0.00	2.75
736	740	1.592400	GATGGTGAGGGTCGTCGACA	61.592	60.000	25.64	4.85	33.68	4.35
794	798	4.265056	GCCACGGGTGAGGGTTGT	62.265	66.667	0.00	0.00	0.00	3.32
850	854	2.746277	GCCGTCGCTGGATTTGGT	60.746	61.111	0.00	0.00	0.00	3.67
896	900	2.764547	GGAGGGGAGCGGCTTACT	60.765	66.667	2.97	2.60	0.00	2.24
904	908	1.448119	GCGCAAATAAGGAGGGGAGC	61.448	60.000	0.30	0.00	0.00	4.70
995	1008	3.083349	CCCCTCCTGCCATCGTCA	61.083	66.667	0.00	0.00	0.00	4.35
1192	1205	0.103937	GAGCTCAAGATCGAGGGGTG	59.896	60.000	9.40	0.00	33.36	4.61
1199	1212	3.186001	GCAATACATGGAGCTCAAGATCG	59.814	47.826	17.19	0.00	0.00	3.69
1201	1214	4.135306	CAGCAATACATGGAGCTCAAGAT	58.865	43.478	17.19	0.89	34.61	2.40
1291	1304	3.314635	GGCTAAGCTGTACTACTCGCTTA	59.685	47.826	16.12	16.12	42.22	3.09
1319	1332	9.739276	ATCATCTAATCAAACAAGGAAGTACAA	57.261	29.630	0.00	0.00	0.00	2.41
1331	1344	7.041508	CCTGGTCTAAGCATCATCTAATCAAAC	60.042	40.741	0.00	0.00	0.00	2.93
1338	1351	5.458595	TCTTCCTGGTCTAAGCATCATCTA	58.541	41.667	0.00	0.00	0.00	1.98
1533	1546	7.522073	GCACCAAAATACTCAGACTGAAATCAA	60.522	37.037	6.61	0.00	0.00	2.57
1653	1666	3.142951	TCAATTGTTTACCTCACCACCG	58.857	45.455	5.13	0.00	0.00	4.94
1766	1779	6.129874	ACATACTAACTGCATGTCTAGGAGA	58.870	40.000	0.00	0.00	26.70	3.71
1772	1785	7.286546	AGACAGATACATACTAACTGCATGTCT	59.713	37.037	4.46	4.46	38.07	3.41
1822	1835	9.542462	AAATGTAGCACATACTATCGTTGTAAT	57.458	29.630	2.80	0.00	37.97	1.89
1849	1862	6.043938	ACAGATATGTTATACAACCCGGGATT	59.956	38.462	32.02	15.41	33.41	3.01
1940	1953	2.456577	GAGGAAGAAGAGGAGCAGAGT	58.543	52.381	0.00	0.00	0.00	3.24
1960	1973	1.153706	GTGGTGGTACCGATGGTCG	60.154	63.158	7.57	0.00	42.58	4.79
1981	1994	4.778143	CGCCTTGGAAGACCGGGG	62.778	72.222	6.32	0.00	39.42	5.73
2014	2027	1.306825	AGAGCAGAGGAGGCATGGT	60.307	57.895	0.00	0.00	0.00	3.55
2195	2209	1.746517	GACACCTGAACCCACGTCT	59.253	57.895	0.00	0.00	0.00	4.18
2420	2435	4.158949	CCATCTCTCCAATGCAATTTCACA	59.841	41.667	0.00	0.00	31.22	3.58
2553	2568	2.347731	GGTGTACCTAGTGCAAGAAGC	58.652	52.381	0.00	0.00	45.96	3.86
2638	2653	2.706339	AGCGCTCCATCAAAGAATCT	57.294	45.000	2.64	0.00	0.00	2.40
2713	2728	9.577222	AACTAATAAAAACAAACTAGGCACCTA	57.423	29.630	0.00	0.00	0.00	3.08
2779	2794	1.737793	GCGTATCAGTGGAAACAAGGG	59.262	52.381	0.00	0.00	46.06	3.95
2827	2842	6.127563	TGTTACTGCCTAATACTGTCGATCAA	60.128	38.462	0.00	0.00	0.00	2.57
2841	2856	9.687210	CGATACTAATTAATGTGTTACTGCCTA	57.313	33.333	0.00	0.00	0.00	3.93
2864	2879	7.339212	TCATGGATTTGATTTCAAGTAACCGAT	59.661	33.333	0.00	0.00	37.15	4.18
2937	2952	5.472137	GTGTTCTCAGGTTTGCCTTAACATA	59.528	40.000	8.33	0.00	44.18	2.29
3038	3053	2.040278	CAGGAGAAACAAGACCATGGGA	59.960	50.000	18.09	0.00	0.00	4.37
3054	3069	0.610174	TGCTCACTAACCTGCAGGAG	59.390	55.000	39.19	27.61	38.94	3.69
3161	3176	4.766375	TCTAATAAAGAGGTTTGGGAGCG	58.234	43.478	0.00	0.00	0.00	5.03
3200	3215	5.670485	TCTTACTGACACACAAGTTGACAT	58.330	37.500	10.54	0.00	0.00	3.06
3224	3239	8.957466	ACAGGACCTTAGATAATTAGTTTTTGC	58.043	33.333	0.00	0.00	0.00	3.68
3258	3273	6.878317	TCCAGTAGCAATGTCATATATAGGC	58.122	40.000	0.00	0.00	0.00	3.93
3386	3401	2.002586	CGCTTCATTGACGGACTCATT	58.997	47.619	0.00	0.00	0.00	2.57
3558	3573	0.454600	CAAGGCATAGCAAGCACAGG	59.545	55.000	0.00	0.00	0.00	4.00
3866	3881	0.108615	CAACTCAGGAGGCCACTACG	60.109	60.000	5.01	0.00	30.68	3.51
3882	3897	3.999001	GCACCTACCCAACTAAGTACAAC	59.001	47.826	0.00	0.00	0.00	3.32
4049	4080	6.223852	AGTTACGCACAGCTATATTTGCTAT	58.776	36.000	3.13	0.00	38.92	2.97
4269	4309	6.952935	AGAGAACATATGAAACTCGTCAAC	57.047	37.500	10.38	0.00	33.53	3.18
4329	4373	0.608130	TCAGGTTCCCATCTCACACG	59.392	55.000	0.00	0.00	0.00	4.49
4436	4480	7.111247	TGGAAAATATATTTTGGAGCTGGTG	57.889	36.000	24.60	0.00	39.86	4.17
4479	4523	1.960689	TGGGCTTTGTCCTTTTACAGC	59.039	47.619	0.00	0.00	0.00	4.40
4490	4534	4.774200	AGCATTTTTATCTCTGGGCTTTGT	59.226	37.500	0.00	0.00	0.00	2.83
4510	4554	1.481772	GCCAAGCCCAATATTTCAGCA	59.518	47.619	4.45	0.00	0.00	4.41
4571	4615	6.183360	GCCTATCCCAACAATTCGACATTTTA	60.183	38.462	0.00	0.00	0.00	1.52
4591	4636	4.601406	TTGGTTTTCTACATGGGCCTAT	57.399	40.909	4.53	0.00	0.00	2.57
4611	4656	1.005924	AGATTCAGCCCGGTCCAATTT	59.994	47.619	0.00	0.00	0.00	1.82

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.