AutoCloner

Multiple sequence alignment - TraesCS7A01G121100

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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	TraesCS7A01G121100	chr7A	100.000	3424	0	0	1	3424	77998026	78001449	0.000000e+00	6324
1	TraesCS7A01G121100	chr7A	94.147	1777	84	12	1664	3424	78141779	78140007	0.000000e+00	2687
2	TraesCS7A01G121100	chr7A	93.106	1668	98	9	1	1666	78143458	78141806	0.000000e+00	2427
3	TraesCS7A01G121100	chr7A	92.202	1680	109	14	1	1671	77876403	77878069	0.000000e+00	2357
4	TraesCS7A01G121100	chr7A	90.457	1729	118	14	1664	3377	77878090	77879786	0.000000e+00	2235
5	TraesCS7A01G121100	chr7A	83.424	923	132	16	751	1664	68916776	68915866	0.000000e+00	837
6	TraesCS7A01G121100	chr7D	92.010	3467	200	36	1	3424	73545256	73548688	0.000000e+00	4796
7	TraesCS7A01G121100	chr7D	91.858	3304	204	33	120	3377	73362459	73365743	0.000000e+00	4551
8	TraesCS7A01G121100	chr7D	94.287	1768	82	10	1673	3424	73620171	73618407	0.000000e+00	2687
9	TraesCS7A01G121100	chr7D	93.746	1663	95	5	5	1666	73621860	73620206	0.000000e+00	2486
10	TraesCS7A01G121100	chr7D	82.951	1003	127	34	1673	2650	64829859	64828876	0.000000e+00	865
11	TraesCS7A01G121100	chr7D	84.335	849	101	18	1826	2651	64808780	64807941	0.000000e+00	802
12	TraesCS7A01G121100	chr7D	86.082	388	37	7	3047	3424	73365789	73366169	5.320000e-108	401
13	TraesCS7A01G121100	chr7B	92.513	3366	172	26	112	3424	16706684	16710022	0.000000e+00	4747
14	TraesCS7A01G121100	chr7B	91.621	3473	224	33	1	3424	16514032	16517486	0.000000e+00	4739
15	TraesCS7A01G121100	chr7B	82.953	921	141	10	750	1664	6402944	6402034	0.000000e+00	817
16	TraesCS7A01G121100	chr7B	91.597	119	8	1	1	119	16682637	16682753	2.730000e-36	163

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	TraesCS7A01G121100	chr7A	77998026	78001449	3423	False	6324.0	6324	100.0000	1	3424	1	chr7A.!!$F1	3423
1	TraesCS7A01G121100	chr7A	78140007	78143458	3451	True	2557.0	2687	93.6265	1	3424	2	chr7A.!!$R2	3423
2	TraesCS7A01G121100	chr7A	77876403	77879786	3383	False	2296.0	2357	91.3295	1	3377	2	chr7A.!!$F2	3376
3	TraesCS7A01G121100	chr7A	68915866	68916776	910	True	837.0	837	83.4240	751	1664	1	chr7A.!!$R1	913
4	TraesCS7A01G121100	chr7D	73545256	73548688	3432	False	4796.0	4796	92.0100	1	3424	1	chr7D.!!$F1	3423
5	TraesCS7A01G121100	chr7D	73618407	73621860	3453	True	2586.5	2687	94.0165	5	3424	2	chr7D.!!$R3	3419
6	TraesCS7A01G121100	chr7D	73362459	73366169	3710	False	2476.0	4551	88.9700	120	3424	2	chr7D.!!$F2	3304
7	TraesCS7A01G121100	chr7D	64828876	64829859	983	True	865.0	865	82.9510	1673	2650	1	chr7D.!!$R2	977
8	TraesCS7A01G121100	chr7D	64807941	64808780	839	True	802.0	802	84.3350	1826	2651	1	chr7D.!!$R1	825
9	TraesCS7A01G121100	chr7B	16706684	16710022	3338	False	4747.0	4747	92.5130	112	3424	1	chr7B.!!$F3	3312
10	TraesCS7A01G121100	chr7B	16514032	16517486	3454	False	4739.0	4739	91.6210	1	3424	1	chr7B.!!$F1	3423
11	TraesCS7A01G121100	chr7B	6402034	6402944	910	True	817.0	817	82.9530	750	1664	1	chr7B.!!$R1	914

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
349	353	1.677052	GACTAGTCTCGTCCCATGACC	59.323	57.143	15.91	0.00	38.32	4.02	F
1364	1388	0.391597	TTTGGTCGTCCACTGGAGAC	59.608	55.000	0.00	14.64	44.22	3.36	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2319	2405	0.179179	GATTGCAAGGCGAGTGCTTC	60.179	55.0	4.94	5.82	42.69	3.86	R
3174	3650	0.771755	TCTCGCTGGCTCTAGGGATA	59.228	55.0	0.00	0.00	38.70	2.59	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
22	23	3.053619	GTGGGTCTATCATGGGGAAGTTT	60.054	47.826	0.00	0.00	0.00	2.66
56	57	5.175856	GTGAAAGTCATAGTACCGATCATGC	59.824	44.000	0.00	0.00	0.00	4.06
139	142	8.556194	CGTAGTATGGTGCAACATAATAATTGT	58.444	33.333	28.09	10.27	39.98	2.71
140	143	9.663904	GTAGTATGGTGCAACATAATAATTGTG	57.336	33.333	28.09	0.00	39.98	3.33
181	184	8.267620	TGAAACAAGTCATCATGGTTACATAG	57.732	34.615	0.00	0.00	34.99	2.23
339	343	6.472486	TGAATTTAATGCGAAGACTAGTCTCG	59.528	38.462	25.34	26.16	39.39	4.04
340	344	4.959596	TTAATGCGAAGACTAGTCTCGT	57.040	40.909	28.88	17.60	39.39	4.18
349	353	1.677052	GACTAGTCTCGTCCCATGACC	59.323	57.143	15.91	0.00	38.32	4.02
377	381	4.233632	TCTTGAATCATACACCCATGCA	57.766	40.909	0.00	0.00	0.00	3.96
434	439	4.737279	TCGTAATGTTTGTGTTGTGCATTG	59.263	37.500	0.00	0.00	32.79	2.82
448	453	3.662247	TGCATTGAATTGATGTGCACA	57.338	38.095	24.08	24.08	40.51	4.57
545	557	6.147864	AGATAGACAAGATCAAGACTCTGC	57.852	41.667	0.00	0.00	0.00	4.26
594	608	5.069318	TCACATGGCAAGTCAAAATAGTGA	58.931	37.500	0.00	0.00	0.00	3.41
736	753	6.715464	CATTCATTGTCCACCGAAACTATAC	58.285	40.000	0.00	0.00	0.00	1.47
900	921	7.653713	GTGATGCTATAAATATCATACCCTCCG	59.346	40.741	0.00	0.00	33.82	4.63
944	965	5.067936	ACACTCTTTCGGTATCATACCTCTG	59.932	44.000	12.26	0.00	46.81	3.35
1112	1135	1.355381	TGGCACCAACCATGAGAAGAT	59.645	47.619	0.00	0.00	33.75	2.40
1265	1289	2.128771	ACCAATAGTGACCATGGTGC	57.871	50.000	25.52	15.03	44.25	5.01
1357	1381	3.304861	GGGTATTTTGTTTGGTCGTCCAC	60.305	47.826	0.00	0.00	44.22	4.02
1364	1388	0.391597	TTTGGTCGTCCACTGGAGAC	59.608	55.000	0.00	14.64	44.22	3.36
1398	1422	3.776969	TGGAGATACAAGAAGAGGTGCAT	59.223	43.478	0.00	0.00	0.00	3.96
1413	1437	2.092429	GGTGCATATGGTGGAGGAGAAA	60.092	50.000	4.56	0.00	0.00	2.52
1420	1444	1.248486	GGTGGAGGAGAAAAAGGTGC	58.752	55.000	0.00	0.00	0.00	5.01
1437	1461	5.184892	AGGTGCTGTTGGAGAATAAGATT	57.815	39.130	0.00	0.00	0.00	2.40
1478	1502	2.850130	ACCACGTGCCAAGGGGTA	60.850	61.111	10.91	0.00	36.17	3.69
1509	1533	4.878397	CCAGAGGAACACAGGTTATTCATC	59.122	45.833	0.00	0.00	37.36	2.92
1535	1559	4.895297	TCATCCTTCCTAATTTTCCATGGC	59.105	41.667	6.96	0.00	0.00	4.40
1591	1617	5.623956	TGGAGATGTCGGGTGTATTTTAT	57.376	39.130	0.00	0.00	0.00	1.40
1592	1618	5.996644	TGGAGATGTCGGGTGTATTTTATT	58.003	37.500	0.00	0.00	0.00	1.40
1593	1619	6.419791	TGGAGATGTCGGGTGTATTTTATTT	58.580	36.000	0.00	0.00	0.00	1.40
1594	1620	6.887545	TGGAGATGTCGGGTGTATTTTATTTT	59.112	34.615	0.00	0.00	0.00	1.82
1595	1621	8.047911	TGGAGATGTCGGGTGTATTTTATTTTA	58.952	33.333	0.00	0.00	0.00	1.52
1653	1684	9.656040	TTTTCATTATCATGAATTGGAGGTTTG	57.344	29.630	0.00	0.00	46.68	2.93
1657	1688	9.439500	CATTATCATGAATTGGAGGTTTGTTTT	57.561	29.630	0.00	0.00	31.07	2.43
1734	1791	8.573035	ACAACCGACTTTATTTCATTATTGTGT	58.427	29.630	0.00	0.00	0.00	3.72
1994	2065	7.329962	GCACAAGGGTTAATATTTGGTTACAAC	59.670	37.037	0.00	0.00	36.06	3.32
2121	2207	3.812167	GCTCTTTCTCCATGGGTTGAGTT	60.812	47.826	13.02	0.00	0.00	3.01
2297	2383	3.025978	TGATGCTGACCCATGGAAAATC	58.974	45.455	15.22	5.83	0.00	2.17
2440	2526	6.787085	ATTCTAGTTTGGAGTTGTCTTTCG	57.213	37.500	0.00	0.00	0.00	3.46
2492	2583	7.607223	TGTTGTGAGAATGATATGATGTTGTCA	59.393	33.333	0.00	0.00	42.06	3.58
2569	2661	6.759497	ACTTCCTTCAAAGTATTGTATGGC	57.241	37.500	0.00	0.00	37.71	4.40
2629	2721	4.900635	AATGTGTGTTTGGAGAGTCAAC	57.099	40.909	0.00	0.00	0.00	3.18
2769	2861	2.268298	CGTGACAACGCTAATAGGCTT	58.732	47.619	0.00	0.00	43.98	4.35
2882	2974	8.679100	TGTGTGCATTAACTAGTTTTGTAGTTT	58.321	29.630	14.49	0.00	39.73	2.66
2920	3012	9.965824	CAAAGTGGTAAGTTGAGTATTGAAAAT	57.034	29.630	0.00	0.00	0.00	1.82
3026	3119	0.329261	TCCAACTCCATGGAGGCTTG	59.671	55.000	38.54	32.21	44.52	4.01
3083	3559	0.097150	GAGACGAAGCGGGCATTTTC	59.903	55.000	0.00	0.00	0.00	2.29
3085	3561	1.582610	GACGAAGCGGGCATTTTCCA	61.583	55.000	0.00	0.00	0.00	3.53
3158	3634	4.336433	CACAATAGAATCTTGGAATGCGGT	59.664	41.667	0.00	0.00	0.00	5.68
3359	3852	6.268617	TGGATCTTCAGATAGAATGTAGGGTG	59.731	42.308	0.00	0.00	35.25	4.61
3362	3855	6.679542	TCTTCAGATAGAATGTAGGGTGGTA	58.320	40.000	0.00	0.00	35.25	3.25

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
22	23	5.316167	ACTATGACTTTCACCATTGCTCAA	58.684	37.500	0.00	0.00	0.00	3.02
181	184	3.561725	CCTCGATATGAACAAGGCTTTCC	59.438	47.826	0.00	0.00	0.00	3.13
326	330	3.065648	GTCATGGGACGAGACTAGTCTTC	59.934	52.174	25.86	19.33	35.60	2.87
339	343	4.906618	TCAAGAAAGTTAGGTCATGGGAC	58.093	43.478	0.00	0.00	43.55	4.46
340	344	5.576563	TTCAAGAAAGTTAGGTCATGGGA	57.423	39.130	0.00	0.00	0.00	4.37
349	353	7.921786	TGGGTGTATGATTCAAGAAAGTTAG	57.078	36.000	0.00	0.00	0.00	2.34
377	381	0.322098	TGGTTGACCGGCGAATGATT	60.322	50.000	9.30	0.00	39.43	2.57
662	676	8.545472	GCCTCACCCAAAATATATATACCTACA	58.455	37.037	0.00	0.00	0.00	2.74
900	921	2.945668	GTTTGTATGGAGAGGGTGATGC	59.054	50.000	0.00	0.00	0.00	3.91
1112	1135	3.133691	GCCACGATATCATGCTTCTTGA	58.866	45.455	3.12	0.00	0.00	3.02
1265	1289	1.750778	GGCCATCCACAGTGTAAATGG	59.249	52.381	22.95	22.95	35.33	3.16
1357	1381	2.947652	CCATGGTTTGCATAGTCTCCAG	59.052	50.000	2.57	0.00	0.00	3.86
1364	1388	6.057533	TCTTGTATCTCCATGGTTTGCATAG	58.942	40.000	12.58	0.00	0.00	2.23
1398	1422	3.561313	GCACCTTTTTCTCCTCCACCATA	60.561	47.826	0.00	0.00	0.00	2.74
1413	1437	4.985538	TCTTATTCTCCAACAGCACCTTT	58.014	39.130	0.00	0.00	0.00	3.11
1420	1444	6.460676	GGGATGCAAATCTTATTCTCCAACAG	60.461	42.308	0.00	0.00	0.00	3.16
1437	1461	0.895100	GCACTGGTTGAGGGATGCAA	60.895	55.000	0.00	0.00	33.27	4.08
1478	1502	0.698818	GTGTTCCTCTGGGGTCCAAT	59.301	55.000	0.00	0.00	36.25	3.16
1509	1533	7.495055	CCATGGAAAATTAGGAAGGATGAAAG	58.505	38.462	5.56	0.00	0.00	2.62
1667	1698	9.745880	ATACATCTTGGTACTATTGTTTCTACG	57.254	33.333	0.00	0.00	0.00	3.51
1734	1791	9.411189	GTGGGTGGTATTAATTTATACTGGAAA	57.589	33.333	12.86	0.00	32.70	3.13
1740	1797	7.012610	ACAAGCGTGGGTGGTATTAATTTATAC	59.987	37.037	4.26	6.13	0.00	1.47
1746	1804	3.275999	GACAAGCGTGGGTGGTATTAAT	58.724	45.455	4.26	0.00	0.00	1.40
2121	2207	2.158559	CCATTTTCCACGACCACATGA	58.841	47.619	0.00	0.00	0.00	3.07
2232	2318	3.423154	GCGTTGGCTTCCTGACCG	61.423	66.667	0.00	0.00	35.83	4.79
2297	2383	8.659491	GCTTCCCAGAAATTAAAGCTATTTTTG	58.341	33.333	4.67	4.67	39.33	2.44
2319	2405	0.179179	GATTGCAAGGCGAGTGCTTC	60.179	55.000	4.94	5.82	42.69	3.86
2492	2583	3.117587	AGTTCACTAGCCCCTACTACGAT	60.118	47.826	0.00	0.00	0.00	3.73
2607	2699	4.704540	TGTTGACTCTCCAAACACACATTT	59.295	37.500	0.00	0.00	0.00	2.32
2608	2700	4.269183	TGTTGACTCTCCAAACACACATT	58.731	39.130	0.00	0.00	0.00	2.71
2611	2703	4.695217	TTTGTTGACTCTCCAAACACAC	57.305	40.909	0.00	0.00	0.00	3.82
2769	2861	2.687935	GCTGGTTTTCACCTTCTTGACA	59.312	45.455	0.00	0.00	44.61	3.58
2882	2974	3.678056	ACCACTTTGCTCTCAACGATA	57.322	42.857	0.00	0.00	30.75	2.92
2885	2977	3.131396	ACTTACCACTTTGCTCTCAACG	58.869	45.455	0.00	0.00	30.75	4.10
2930	3022	8.110860	AGTTCAGATAAACGTTTCCAATTGAT	57.889	30.769	18.42	3.12	34.27	2.57
3114	3590	4.387862	GTGTTTACACTCTACGGTCCAATG	59.612	45.833	5.78	0.00	43.25	2.82
3158	3634	2.504175	GGGATACAGTTGGCCTCTGTAA	59.496	50.000	30.01	19.92	46.65	2.41
3174	3650	0.771755	TCTCGCTGGCTCTAGGGATA	59.228	55.000	0.00	0.00	38.70	2.59
3229	3709	7.331791	AGAACTTAAGAAGTGATCGGCTATTT	58.668	34.615	10.09	0.00	41.91	1.40
3232	3723	5.916661	AGAACTTAAGAAGTGATCGGCTA	57.083	39.130	10.09	0.00	41.91	3.93
3359	3852	5.874895	AAAGTAGTGAAAATTCGGCTACC	57.125	39.130	16.83	6.58	38.19	3.18
3362	3855	8.038944	TGTATCTAAAGTAGTGAAAATTCGGCT	58.961	33.333	0.00	0.00	0.00	5.52

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.