AutoCloner

Multiple sequence alignment - TraesCS5A01G340300

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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	TraesCS5A01G340300	chr5A	100.000	4529	0	0	1	4529	546976203	546971675	0.000000e+00	8364
1	TraesCS5A01G340300	chr5A	94.147	4357	177	28	231	4529	546691508	546695844	0.000000e+00	6562
2	TraesCS5A01G340300	chr5A	83.394	831	90	24	3725	4509	546897786	546896958	0.000000e+00	726
3	TraesCS5A01G340300	chr5A	81.429	560	65	17	3723	4268	546699163	546699697	5.420000e-114	422
4	TraesCS5A01G340300	chr5A	91.250	160	13	1	3558	3717	546698955	546699113	2.740000e-52	217
5	TraesCS5A01G340300	chr5D	93.426	4442	199	35	169	4529	431602615	431607044	0.000000e+00	6499
6	TraesCS5A01G340300	chr5D	86.228	668	77	12	3725	4379	431613222	431613887	0.000000e+00	710
7	TraesCS5A01G340300	chr5B	94.786	3893	139	25	683	4529	521147530	521151404	0.000000e+00	6006
8	TraesCS5A01G340300	chr5B	91.566	664	42	4	1	656	521142642	521143299	0.000000e+00	904
9	TraesCS5A01G340300	chr5B	85.693	671	82	10	3723	4379	521156847	521157517	0.000000e+00	695
10	TraesCS5A01G340300	chr5B	88.444	225	25	1	3493	3717	521156574	521156797	2.080000e-68	270
11	TraesCS5A01G340300	chr3D	84.919	431	55	6	8	430	607875139	607875567	1.160000e-115	427
12	TraesCS5A01G340300	chr2A	83.259	448	67	4	1	440	415261683	415262130	5.460000e-109	405
13	TraesCS5A01G340300	chr2D	82.774	447	64	7	1	437	331613448	331613005	1.980000e-103	387
14	TraesCS5A01G340300	chr7B	82.877	438	62	7	1	430	153435975	153436407	9.190000e-102	381
15	TraesCS5A01G340300	chr1A	82.648	438	66	6	3	433	513116503	513116937	3.310000e-101	379
16	TraesCS5A01G340300	chr1D	83.095	420	62	5	20	431	197732539	197732957	1.540000e-99	374
17	TraesCS5A01G340300	chr7D	82.460	439	62	9	2	429	573060552	573060118	1.990000e-98	370
18	TraesCS5A01G340300	chr7A	82.192	438	64	8	2	429	662428046	662427613	9.260000e-97	364
19	TraesCS5A01G340300	chr3A	82.692	416	59	3	1	408	223525361	223525771	1.550000e-94	357
20	TraesCS5A01G340300	chr3A	83.923	311	43	3	8	311	638710316	638710006	1.590000e-74	291
21	TraesCS5A01G340300	chr3B	80.846	449	70	11	2	441	778428789	778429230	5.610000e-89	339
22	TraesCS5A01G340300	chr6B	80.000	425	65	12	23	430	570217892	570217471	3.430000e-76	296
23	TraesCS5A01G340300	chr4A	80.890	382	61	8	56	428	520961735	520962113	1.590000e-74	291
24	TraesCS5A01G340300	chr6A	85.279	197	22	2	1	190	430591455	430591259	3.570000e-46	196

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	TraesCS5A01G340300	chr5A	546971675	546976203	4528	True	8364.000000	8364	100.0000	1	4529	1	chr5A.!!$R2	4528
1	TraesCS5A01G340300	chr5A	546691508	546699697	8189	False	2400.333333	6562	88.9420	231	4529	3	chr5A.!!$F1	4298
2	TraesCS5A01G340300	chr5A	546896958	546897786	828	True	726.000000	726	83.3940	3725	4509	1	chr5A.!!$R1	784
3	TraesCS5A01G340300	chr5D	431602615	431607044	4429	False	6499.000000	6499	93.4260	169	4529	1	chr5D.!!$F1	4360
4	TraesCS5A01G340300	chr5D	431613222	431613887	665	False	710.000000	710	86.2280	3725	4379	1	chr5D.!!$F2	654
5	TraesCS5A01G340300	chr5B	521147530	521151404	3874	False	6006.000000	6006	94.7860	683	4529	1	chr5B.!!$F2	3846
6	TraesCS5A01G340300	chr5B	521142642	521143299	657	False	904.000000	904	91.5660	1	656	1	chr5B.!!$F1	655
7	TraesCS5A01G340300	chr5B	521156574	521157517	943	False	482.500000	695	87.0685	3493	4379	2	chr5B.!!$F3	886

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
993	1056	0.041090	AGTCCCCGGCCATTGATTTT	59.959	50.000	2.24	0.00	0.00	1.82	F
1029	1106	1.613437	CCGCTTTGTTCCCATTTCTGT	59.387	47.619	0.00	0.00	0.00	3.41	F
2949	3048	1.003442	AGGGTATCTGGCAGAGGCA	59.997	57.895	23.24	7.71	43.71	4.75	F

Position	MSA Position	Penalty	Sequence	TM	GC	End Stability	Orientation
2514	2613	1.908619	TCACAGGCCTCATCAAGCTTA	59.091	47.619	3.09	R
2985	3084	2.097466	GGATGCATAAAGGTTGGTGTCG	59.903	50.000	4.35	R
4021	4180	2.200081	AGTGGAGGTGCATATTCTGGT	58.800	47.619	4.00	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
52	53	1.700739	TGACCAAAATACCCACGGACT	59.299	47.619	0.00	0.00	0.00	3.85
60	61	4.563140	AATACCCACGGACTAACATGTT	57.437	40.909	16.68	16.68	0.00	2.71
63	64	2.277084	CCCACGGACTAACATGTTAGC	58.723	52.381	35.03	27.83	44.74	3.09
65	66	3.187700	CCACGGACTAACATGTTAGCTC	58.812	50.000	35.03	29.21	44.74	4.09
73	74	5.767670	ACTAACATGTTAGCTCTCCCTCTA	58.232	41.667	35.03	7.04	44.74	2.43
83	84	3.071479	GCTCTCCCTCTATCTCACTACG	58.929	54.545	0.00	0.00	0.00	3.51
104	105	2.922740	TAAAGTGTGTGTCCCACTCC	57.077	50.000	0.00	0.00	42.17	3.85
111	112	1.923395	GTGTCCCACTCCATCCCCA	60.923	63.158	0.00	0.00	0.00	4.96
123	124	4.105697	ACTCCATCCCCAACAAAGTTCTTA	59.894	41.667	0.00	0.00	0.00	2.10
148	157	3.717400	TCTCTATGCTTGCTTACTCCG	57.283	47.619	0.00	0.00	0.00	4.63
162	171	3.296709	CTCCGGACAAGTGGGGACG	62.297	68.421	0.00	0.00	0.00	4.79
163	172	4.388499	CCGGACAAGTGGGGACGG	62.388	72.222	0.00	0.00	35.01	4.79
189	198	6.007076	ACCTATCATTGCGAGATAGAGAGAA	58.993	40.000	16.81	0.00	44.91	2.87
298	307	3.199071	AGCAAACACCTAATGGGACGATA	59.801	43.478	0.00	0.00	38.76	2.92
299	308	4.134563	GCAAACACCTAATGGGACGATAT	58.865	43.478	0.00	0.00	38.76	1.63
321	330	4.618920	AATCTTTGAGGTGTCTAACGGT	57.381	40.909	0.00	0.00	0.00	4.83
348	357	5.963176	TTGAGCAAGCATCTCACAAAATA	57.037	34.783	2.64	0.00	39.99	1.40
429	441	3.697542	AGTGGCGTAAATGATAAAACCCC	59.302	43.478	0.00	0.00	0.00	4.95
507	521	6.156949	AGGTCTATGACAAGTGATGGTGTAAT	59.843	38.462	0.07	0.00	33.68	1.89
509	523	7.653713	GGTCTATGACAAGTGATGGTGTAATAG	59.346	40.741	2.84	2.84	33.68	1.73
511	525	9.416284	TCTATGACAAGTGATGGTGTAATAGTA	57.584	33.333	7.67	0.00	0.00	1.82
551	570	1.688197	CTTTCACAACCCATGGCACTT	59.312	47.619	6.09	0.00	0.00	3.16
650	703	2.169769	ACGAGACCACCTCTCACAAAAA	59.830	45.455	0.00	0.00	45.43	1.94
993	1056	0.041090	AGTCCCCGGCCATTGATTTT	59.959	50.000	2.24	0.00	0.00	1.82
1029	1106	1.613437	CCGCTTTGTTCCCATTTCTGT	59.387	47.619	0.00	0.00	0.00	3.41
1216	1296	2.571757	CTCCAGAGCAACGCGGTA	59.428	61.111	12.47	0.00	0.00	4.02
1297	1390	4.767255	CCGGACAGAGTGCTGCCC	62.767	72.222	0.00	0.00	46.26	5.36
1534	1627	3.738281	CGAGGTCAATGTGATCCACTACC	60.738	52.174	0.00	0.00	35.11	3.18
1731	1830	4.308458	TTGGTGCCCGACGAGGTG	62.308	66.667	0.00	0.00	38.74	4.00
1819	1918	7.720957	TCTTTCAAAGATGGTCTTCTGAATCAA	59.279	33.333	0.00	4.44	35.27	2.57
1831	1930	5.415701	TCTTCTGAATCAAATACAGGGTTGC	59.584	40.000	0.00	0.00	33.19	4.17
1839	1938	2.128771	ATACAGGGTTGCATGGACAC	57.871	50.000	0.00	0.00	0.00	3.67
2091	2190	6.975772	GGACTTACAATACACTGATCTCACTC	59.024	42.308	0.00	0.00	0.00	3.51
2322	2421	4.136796	TGTATGTAAATGCTGGGATGCTC	58.863	43.478	0.00	0.00	0.00	4.26
2414	2513	1.969923	TGCATTTGGGAAGAAAGGGTG	59.030	47.619	0.00	0.00	0.00	4.61
2514	2613	5.052693	TCAAAGCATATGGGTTAGCAGAT	57.947	39.130	4.56	0.00	35.85	2.90
2562	2661	1.305802	TGGCATGGAGAGGTACGGT	60.306	57.895	0.00	0.00	0.00	4.83
2725	2824	2.952310	GGCAGCTTTACTAAGAATGGGG	59.048	50.000	0.00	0.00	32.92	4.96
2949	3048	1.003442	AGGGTATCTGGCAGAGGCA	59.997	57.895	23.24	7.71	43.71	4.75
2985	3084	8.443953	ACAAGCTTCTGAAATCATTAGATACC	57.556	34.615	0.00	0.00	33.08	2.73
3330	3429	6.073222	ACGATGTAACTTTCAAGGCACTAAAG	60.073	38.462	0.00	0.00	38.49	1.85
3504	3603	5.279809	GGGTCACTCTTGTACAAGGATACAA	60.280	44.000	30.35	12.87	41.63	2.41
3765	3914	9.361315	CTTCAAAAGATGCATCATGAATTTACA	57.639	29.630	27.90	14.75	30.99	2.41
3858	4010	3.664107	TCAAATCGGAACTCAGTTGAGG	58.336	45.455	13.30	0.00	46.13	3.86
3905	4057	2.890945	AGTGTGTTCTTGGCCATAAACC	59.109	45.455	21.64	15.42	0.00	3.27
3923	4075	1.756538	ACCAAGTTGCCCTCACAAAAG	59.243	47.619	0.00	0.00	0.00	2.27
3924	4076	1.756538	CCAAGTTGCCCTCACAAAAGT	59.243	47.619	0.00	0.00	0.00	2.66
3936	4090	5.181245	CCCTCACAAAAGTATGTTGGTAGTG	59.819	44.000	0.00	0.00	37.74	2.74
3952	4106	5.237815	TGGTAGTGCTTGTTCACAGATAAG	58.762	41.667	0.00	0.00	39.35	1.73
4054	4213	2.915604	ACCTCCACTTCTGACATTGGAT	59.084	45.455	2.45	0.00	37.51	3.41
4095	4254	6.407202	ACCAATACAACTGGATTCTGTAGTC	58.593	40.000	0.00	0.00	37.40	2.59
4182	4353	7.537306	TGAAACTGCTCTAATTTTAATCGCAAC	59.463	33.333	0.00	0.00	0.00	4.17
4349	4531	2.164338	GGCCCGGTCTTGAATGTAAAA	58.836	47.619	0.00	0.00	0.00	1.52
4372	4555	3.314635	GGTGCCATCATGATCTTCAGAAC	59.685	47.826	4.86	0.00	0.00	3.01
4373	4556	3.943381	GTGCCATCATGATCTTCAGAACA	59.057	43.478	4.86	0.00	0.00	3.18
4522	4722	4.570369	TGCACATAAATACGTCAGACATGG	59.430	41.667	0.41	0.00	0.00	3.66

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
6	7	2.224670	ACATGGTAAACGGGCTTTGAGA	60.225	45.455	0.00	0.00	0.00	3.27
52	53	6.615617	AGATAGAGGGAGAGCTAACATGTTA	58.384	40.000	17.16	17.16	0.00	2.41
60	61	4.020928	CGTAGTGAGATAGAGGGAGAGCTA	60.021	50.000	0.00	0.00	0.00	3.32
63	64	4.610605	TCGTAGTGAGATAGAGGGAGAG	57.389	50.000	0.00	0.00	0.00	3.20
65	66	6.938030	ACTTTATCGTAGTGAGATAGAGGGAG	59.062	42.308	8.10	0.00	37.22	4.30
73	74	6.268825	ACACACACTTTATCGTAGTGAGAT	57.731	37.500	9.74	0.00	44.52	2.75
104	105	8.150296	AGAAAAATAAGAACTTTGTTGGGGATG	58.850	33.333	0.00	0.00	0.00	3.51
123	124	6.037610	CGGAGTAAGCAAGCATAGAGAAAAAT	59.962	38.462	0.00	0.00	0.00	1.82
148	157	3.948719	TGCCGTCCCCACTTGTCC	61.949	66.667	0.00	0.00	0.00	4.02
162	171	2.175878	ATCTCGCAATGATAGGTGCC	57.824	50.000	0.00	0.00	37.47	5.01
163	172	4.082517	TCTCTATCTCGCAATGATAGGTGC	60.083	45.833	13.91	0.00	42.00	5.01
189	198	3.470868	ACCCCTAGACCCACATGTAATT	58.529	45.455	0.00	0.00	0.00	1.40
298	307	6.295719	ACCGTTAGACACCTCAAAGATTAT	57.704	37.500	0.00	0.00	0.00	1.28
299	308	5.733620	ACCGTTAGACACCTCAAAGATTA	57.266	39.130	0.00	0.00	0.00	1.75
321	330	5.963176	TGTGAGATGCTTGCTCAAAAATA	57.037	34.783	0.00	0.00	43.39	1.40
372	381	8.754991	TCACTACTCACTTTTCCCATTTAAAA	57.245	30.769	0.00	0.00	0.00	1.52
376	385	5.998363	GTCTCACTACTCACTTTTCCCATTT	59.002	40.000	0.00	0.00	0.00	2.32
479	493	5.352569	CACCATCACTTGTCATAGACCTTTC	59.647	44.000	0.00	0.00	0.00	2.62
488	502	7.125811	AGGTACTATTACACCATCACTTGTCAT	59.874	37.037	0.00	0.00	36.02	3.06
507	521	3.200385	GGGAGAGTGAGTGAGAGGTACTA	59.800	52.174	0.00	0.00	41.55	1.82
509	523	2.371306	GGGAGAGTGAGTGAGAGGTAC	58.629	57.143	0.00	0.00	0.00	3.34
511	525	0.322997	CGGGAGAGTGAGTGAGAGGT	60.323	60.000	0.00	0.00	0.00	3.85
650	703	8.472683	TCAAATTTTTGAAAACTCGTCACAAT	57.527	26.923	3.31	0.00	43.62	2.71
1029	1106	0.107752	GTTCCGCCGGTATTTGGGTA	60.108	55.000	1.63	0.00	0.00	3.69
1276	1369	3.314331	AGCACTCTGTCCGGTGGG	61.314	66.667	0.00	0.00	34.41	4.61
1297	1390	2.552231	CTACCCTTCCCCCTTTGCGG	62.552	65.000	0.00	0.00	0.00	5.69
1416	1509	3.073735	CTCTCCCGGCTGCTCAGT	61.074	66.667	0.00	0.00	0.00	3.41
1646	1739	1.524008	GCCCCCTTTGCAGTACACAC	61.524	60.000	0.00	0.00	0.00	3.82
1722	1821	1.517257	GCTCATGGTCACCTCGTCG	60.517	63.158	0.00	0.00	0.00	5.12
1731	1830	1.002430	TGAAGGACAGTGCTCATGGTC	59.998	52.381	0.00	0.00	0.00	4.02
1819	1918	2.446435	GTGTCCATGCAACCCTGTATT	58.554	47.619	0.00	0.00	0.00	1.89
1831	1930	3.813443	AGCTATAGCAAAGGTGTCCATG	58.187	45.455	26.07	0.00	45.16	3.66
1839	1938	7.667557	TGTAGGTATACAAGCTATAGCAAAGG	58.332	38.462	26.07	14.04	40.20	3.11
2091	2190	8.242053	ACATCAATTTCATTGCTTTCTCTGTAG	58.758	33.333	0.00	0.00	40.05	2.74
2119	2218	5.126222	TCATCTTACAGAAGTAGTGCTCTGG	59.874	44.000	0.00	0.00	34.77	3.86
2322	2421	2.310233	CCAACACCACGACTGCTCG	61.310	63.158	0.00	0.00	46.06	5.03
2514	2613	1.908619	TCACAGGCCTCATCAAGCTTA	59.091	47.619	0.00	0.00	0.00	3.09
2562	2661	8.640063	TGTAAGTCAAGTAATCAGGTAGTACA	57.360	34.615	2.06	0.00	30.94	2.90
2725	2824	2.674357	GGCATTCAACCATGTGCAAATC	59.326	45.455	6.13	0.00	39.27	2.17
2985	3084	2.097466	GGATGCATAAAGGTTGGTGTCG	59.903	50.000	0.00	0.00	0.00	4.35
3300	3399	4.226761	CCTTGAAAGTTACATCGTTTGGC	58.773	43.478	0.00	0.00	0.00	4.52
3330	3429	5.735766	ACTCCTTCTTTCACTAGTATTGGC	58.264	41.667	0.00	0.00	0.00	4.52
3858	4010	4.019231	ACCTCTCCCTCAAACCAATTCTAC	60.019	45.833	0.00	0.00	0.00	2.59
3905	4057	4.037923	ACATACTTTTGTGAGGGCAACTTG	59.962	41.667	0.00	0.00	0.00	3.16
3923	4075	4.513692	TGTGAACAAGCACTACCAACATAC	59.486	41.667	0.00	0.00	39.49	2.39
3924	4076	4.709250	TGTGAACAAGCACTACCAACATA	58.291	39.130	0.00	0.00	39.49	2.29
3936	4090	7.659652	AGTTTCTACTTATCTGTGAACAAGC	57.340	36.000	0.00	0.00	0.00	4.01
4021	4180	2.200081	AGTGGAGGTGCATATTCTGGT	58.800	47.619	0.00	0.00	0.00	4.00
4054	4213	3.274281	TGGTCCAGATAGGGCATATGA	57.726	47.619	6.97	0.00	46.80	2.15
4095	4254	9.678941	TTTATCAGCATATTCTCTGTACTAACG	57.321	33.333	0.00	0.00	0.00	3.18
4152	4322	9.055248	CGATTAAAATTAGAGCAGTTTCAACAG	57.945	33.333	0.00	0.00	0.00	3.16
4182	4353	9.846248	AAGAATGCTTAGTAAATGCTTAACTTG	57.154	29.630	0.00	0.00	31.07	3.16
4286	4466	2.969443	AGTATTGCAGCAAACGTCAC	57.031	45.000	12.97	5.61	0.00	3.67
4349	4531	2.775960	TCTGAAGATCATGATGGCACCT	59.224	45.455	14.30	0.00	0.00	4.00
4372	4555	3.755378	AGGCTTGTAGTCTGCAAAGAATG	59.245	43.478	4.85	0.00	0.00	2.67
4373	4556	4.026356	AGGCTTGTAGTCTGCAAAGAAT	57.974	40.909	4.85	0.00	0.00	2.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.