AutoCloner

Multiple sequence alignment - TraesCS3A01G120700

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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	TraesCS3A01G120700	chr3A	100.000	3419	0	0	1	3419	94860142	94856724	0.000000e+00	6314.0
1	TraesCS3A01G120700	chr3A	93.450	1603	79	17	826	2402	94255483	94253881	0.000000e+00	2355.0
2	TraesCS3A01G120700	chr3A	91.823	1223	82	10	1216	2428	94384152	94382938	0.000000e+00	1688.0
3	TraesCS3A01G120700	chr3A	83.237	1563	204	32	856	2391	95359833	95358302	0.000000e+00	1382.0
4	TraesCS3A01G120700	chr3A	86.463	458	40	10	775	1229	94385136	94384698	1.850000e-132	483.0
5	TraesCS3A01G120700	chr3A	80.100	402	47	19	2423	2809	94202596	94202213	5.620000e-68	268.0
6	TraesCS3A01G120700	chr3D	94.198	2344	101	22	707	3023	80917790	80915455	0.000000e+00	3542.0
7	TraesCS3A01G120700	chr3D	89.073	2114	129	38	751	2809	80601596	80599530	0.000000e+00	2531.0
8	TraesCS3A01G120700	chr3D	91.060	1622	107	18	819	2428	80630634	80629039	0.000000e+00	2158.0
9	TraesCS3A01G120700	chr3D	83.387	1559	202	33	856	2391	81122335	81120811	0.000000e+00	1391.0
10	TraesCS3A01G120700	chr3D	93.128	713	39	4	1	711	80918872	80918168	0.000000e+00	1037.0
11	TraesCS3A01G120700	chr3D	85.859	198	18	5	3222	3419	80912013	80911826	5.790000e-48	202.0
12	TraesCS3A01G120700	chr3B	94.560	1728	83	5	784	2500	126401015	126399288	0.000000e+00	2660.0
13	TraesCS3A01G120700	chr3B	90.720	1681	141	10	756	2428	126459259	126457586	0.000000e+00	2226.0
14	TraesCS3A01G120700	chr3B	83.483	1562	201	30	856	2391	126733747	126732217	0.000000e+00	1402.0
15	TraesCS3A01G120700	chr3B	82.420	529	66	17	135	650	126401689	126401175	1.460000e-118	436.0
16	TraesCS3A01G120700	chr3B	80.935	535	79	11	867	1381	126715194	126714663	5.310000e-108	401.0
17	TraesCS3A01G120700	chr3B	83.696	276	37	4	268	535	126459726	126459451	1.570000e-63	254.0
18	TraesCS3A01G120700	chr4D	79.745	548	82	23	2879	3418	499580672	499580146	1.500000e-98	370.0
19	TraesCS3A01G120700	chr7A	79.683	379	58	15	2818	3190	42032403	42032768	4.380000e-64	255.0
20	TraesCS3A01G120700	chr6B	83.721	215	30	3	405	615	72383558	72383345	7.480000e-47	198.0
21	TraesCS3A01G120700	chr6A	74.648	426	64	29	2834	3252	48145294	48145682	7.640000e-32	148.0
22	TraesCS3A01G120700	chr1D	82.979	141	14	7	2807	2941	493059672	493059536	5.990000e-23	119.0
23	TraesCS3A01G120700	chr1A	86.869	99	11	2	2831	2928	534418364	534418267	3.610000e-20	110.0
24	TraesCS3A01G120700	chr2A	80.451	133	20	3	3270	3396	753969449	753969317	2.810000e-16	97.1
25	TraesCS3A01G120700	chr5B	80.435	138	15	9	2812	2941	536239561	536239694	1.010000e-15	95.3

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	TraesCS3A01G120700	chr3A	94856724	94860142	3418	True	6314.000000	6314	100.000000	1	3419	1	chr3A.!!$R3	3418
1	TraesCS3A01G120700	chr3A	94253881	94255483	1602	True	2355.000000	2355	93.450000	826	2402	1	chr3A.!!$R2	1576
2	TraesCS3A01G120700	chr3A	95358302	95359833	1531	True	1382.000000	1382	83.237000	856	2391	1	chr3A.!!$R4	1535
3	TraesCS3A01G120700	chr3A	94382938	94385136	2198	True	1085.500000	1688	89.143000	775	2428	2	chr3A.!!$R5	1653
4	TraesCS3A01G120700	chr3D	80599530	80601596	2066	True	2531.000000	2531	89.073000	751	2809	1	chr3D.!!$R1	2058
5	TraesCS3A01G120700	chr3D	80629039	80630634	1595	True	2158.000000	2158	91.060000	819	2428	1	chr3D.!!$R2	1609
6	TraesCS3A01G120700	chr3D	80911826	80918872	7046	True	1593.666667	3542	91.061667	1	3419	3	chr3D.!!$R4	3418
7	TraesCS3A01G120700	chr3D	81120811	81122335	1524	True	1391.000000	1391	83.387000	856	2391	1	chr3D.!!$R3	1535
8	TraesCS3A01G120700	chr3B	126399288	126401689	2401	True	1548.000000	2660	88.490000	135	2500	2	chr3B.!!$R3	2365
9	TraesCS3A01G120700	chr3B	126732217	126733747	1530	True	1402.000000	1402	83.483000	856	2391	1	chr3B.!!$R2	1535
10	TraesCS3A01G120700	chr3B	126457586	126459726	2140	True	1240.000000	2226	87.208000	268	2428	2	chr3B.!!$R4	2160
11	TraesCS3A01G120700	chr3B	126714663	126715194	531	True	401.000000	401	80.935000	867	1381	1	chr3B.!!$R1	514
12	TraesCS3A01G120700	chr4D	499580146	499580672	526	True	370.000000	370	79.745000	2879	3418	1	chr4D.!!$R1	539

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
886	1367	0.174845	CGACTTGCCCCATTCGTCTA	59.825	55.0	0.0	0.0	0.0	2.59	F
1140	1671	0.324091	ACTCCGTCAAGTCCCCGTAT	60.324	55.0	0.0	0.0	0.0	3.06	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1758	2874	2.516227	ACTGATTGACGAGGGAGAGA	57.484	50.0	0.00	0.00	0.00	3.10	R
3075	5338	0.108281	GGCCCAGTCTTAGACGTTCC	60.108	60.0	6.73	3.85	37.67	3.62	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
48	49	3.521126	ACCAATAACTGCTCCTGATGTCT	59.479	43.478	0.00	0.00	0.00	3.41
52	53	5.782893	ATAACTGCTCCTGATGTCTAGAC	57.217	43.478	16.32	16.32	0.00	2.59
54	55	3.435275	ACTGCTCCTGATGTCTAGACAA	58.565	45.455	28.43	13.00	45.41	3.18
72	73	3.141398	ACAAGACACGTGCAAGATGAAT	58.859	40.909	17.22	0.00	0.00	2.57
168	169	7.518188	AGAAAAGACACTAGAGAAATTTGGGA	58.482	34.615	0.00	0.00	0.00	4.37
242	248	7.172361	ACGAAAAATAATCCCATGTTTGGTTTG	59.828	33.333	0.00	0.00	41.91	2.93
256	262	3.586470	TGGTTTGAGGAGGTTTGCTAA	57.414	42.857	0.00	0.00	0.00	3.09
311	317	7.441157	TCACACTACTGTTTTACCTGAAGAATG	59.559	37.037	0.00	0.00	0.00	2.67
365	378	3.118811	TGTTGCAGAAGAAAAGTTTGGGG	60.119	43.478	0.00	0.00	0.00	4.96
377	390	6.839134	AGAAAAGTTTGGGGAGTCAAGTATTT	59.161	34.615	0.00	0.00	0.00	1.40
449	468	4.010349	ACAAACTTAGGCAGTATCAAGGC	58.990	43.478	0.00	0.00	32.94	4.35
467	486	1.567504	GCCAGCATCACAATCAATGC	58.432	50.000	0.00	0.00	46.84	3.56
483	502	2.886523	CAATGCAAGGTCTTCAAGGTGA	59.113	45.455	0.00	0.00	0.00	4.02
496	515	2.557056	TCAAGGTGAAGAGAGTGTACCG	59.443	50.000	0.00	0.00	36.55	4.02
497	516	2.557056	CAAGGTGAAGAGAGTGTACCGA	59.443	50.000	0.00	0.00	36.55	4.69
498	517	3.088789	AGGTGAAGAGAGTGTACCGAT	57.911	47.619	0.00	0.00	36.55	4.18
599	622	2.016961	CATCTGGATGAAACGGCGG	58.983	57.895	13.24	0.00	41.20	6.13
718	1196	8.444783	AGACCTGGTATACAAAATATATTGCCA	58.555	33.333	0.00	0.00	33.52	4.92
746	1224	1.193874	GCGTGAAAACTTAGTCCGGTG	59.806	52.381	0.00	0.00	0.00	4.94
754	1232	0.818296	CTTAGTCCGGTGTCCTCCTG	59.182	60.000	0.00	0.00	0.00	3.86
844	1323	1.605992	CAAGGAGCTGGCTGATGGA	59.394	57.895	0.00	0.00	0.00	3.41
886	1367	0.174845	CGACTTGCCCCATTCGTCTA	59.825	55.000	0.00	0.00	0.00	2.59
914	1395	8.143835	CCATTAATCAACCTACCATTTTCATCC	58.856	37.037	0.00	0.00	0.00	3.51
1140	1671	0.324091	ACTCCGTCAAGTCCCCGTAT	60.324	55.000	0.00	0.00	0.00	3.06
1153	1684	1.731433	CCCGTATCATGACCCGTCGT	61.731	60.000	13.07	0.00	0.00	4.34
1389	2481	2.095263	GCTTAATTGCAGCAACGGAGAA	60.095	45.455	10.85	0.00	37.22	2.87
1391	2483	1.609208	AATTGCAGCAACGGAGAAGT	58.391	45.000	10.85	0.00	0.00	3.01
1392	2484	0.877071	ATTGCAGCAACGGAGAAGTG	59.123	50.000	10.85	0.00	0.00	3.16
1513	2623	2.561037	TTCGGTCTCGTGAGCTGCA	61.561	57.895	14.02	0.00	38.45	4.41
1713	2829	1.434622	GCTGCTCCACGACCATGATG	61.435	60.000	0.00	0.00	0.00	3.07
1852	2968	3.019003	ATCAACGCCTCCTCCGTGG	62.019	63.158	0.00	0.00	39.13	4.94
1974	3090	1.993370	GTCAAGATCGGGAACAAGACG	59.007	52.381	0.00	0.00	0.00	4.18
2377	3499	4.980805	GCACCGTGACCTTCGCCA	62.981	66.667	1.65	0.00	0.00	5.69
2507	3653	6.867293	TCGAGAAATGAGATTCTATCATGCAG	59.133	38.462	0.00	0.00	39.70	4.41
2514	3660	5.176741	AGATTCTATCATGCAGGGGAATC	57.823	43.478	22.26	22.26	39.22	2.52
2551	3697	8.655970	CGTTACTATGAGATTTGTCATGTTTCA	58.344	33.333	0.76	0.00	37.72	2.69
2555	3701	8.025445	ACTATGAGATTTGTCATGTTTCAAAGC	58.975	33.333	15.29	15.29	37.72	3.51
2749	3906	5.858475	AGAAAATAGCGTGAATCTCAAACG	58.142	37.500	0.00	0.00	40.22	3.60
2850	4014	6.709018	AGTATAAAGCAAGGTGTGTTTGTT	57.291	33.333	0.00	0.00	30.02	2.83
2876	4040	3.889196	TTTTCTTCCGTTCATCGTTGG	57.111	42.857	0.00	0.00	37.94	3.77
2887	4051	5.342259	CCGTTCATCGTTGGAAAGATTTTTC	59.658	40.000	0.06	0.06	38.86	2.29
2903	4067	8.848474	AAGATTTTTCTTTCTATTCGAGGTGA	57.152	30.769	0.00	0.00	0.00	4.02
2928	4092	8.732746	ATACTAAATTTTTGTGCGTCTATCCT	57.267	30.769	0.00	0.00	0.00	3.24
2929	4093	9.826574	ATACTAAATTTTTGTGCGTCTATCCTA	57.173	29.630	0.00	0.00	0.00	2.94
2930	4094	8.197988	ACTAAATTTTTGTGCGTCTATCCTAG	57.802	34.615	0.00	0.00	0.00	3.02
2968	4132	5.646360	GGTTTCTCCAGAATTCCGTAATTGA	59.354	40.000	0.65	0.00	34.29	2.57
2974	4138	2.241176	AGAATTCCGTAATTGAGCCCCA	59.759	45.455	0.65	0.00	35.41	4.96
2977	4141	1.078708	CCGTAATTGAGCCCCACGT	60.079	57.895	0.00	0.00	0.00	4.49
3018	4182	2.177016	AGCCCACTTATTATTCCCCCAC	59.823	50.000	0.00	0.00	0.00	4.61
3024	5287	5.190677	CACTTATTATTCCCCCACGAAGTT	58.809	41.667	0.00	0.00	41.61	2.66
3038	5301	3.684788	CACGAAGTTGGGAAGACCTTATG	59.315	47.826	0.00	0.00	41.61	1.90
3040	5303	4.529377	ACGAAGTTGGGAAGACCTTATGTA	59.471	41.667	0.00	0.00	37.78	2.29
3075	5338	5.878116	TGATAAATAGTTGAACCTTCCCACG	59.122	40.000	0.00	0.00	0.00	4.94
3077	5340	1.719529	TAGTTGAACCTTCCCACGGA	58.280	50.000	0.00	0.00	0.00	4.69
3095	5358	0.606604	GAACGTCTAAGACTGGGCCA	59.393	55.000	5.85	5.85	0.00	5.36
3176	7570	9.898152	TCTTTCTCTTTCTCTTTCTCTTTTTCT	57.102	29.630	0.00	0.00	0.00	2.52
3299	7710	5.246307	TGGTTCCGGTTTTGAAAAATGTTT	58.754	33.333	0.00	0.00	0.00	2.83

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
21	22	6.543831	ACATCAGGAGCAGTTATTGGTATTTC	59.456	38.462	0.00	0.00	37.72	2.17
48	49	3.005367	TCATCTTGCACGTGTCTTGTCTA	59.995	43.478	18.38	0.00	0.00	2.59
52	53	3.818961	ATTCATCTTGCACGTGTCTTG	57.181	42.857	18.38	8.38	0.00	3.02
54	55	5.470098	ACTTTTATTCATCTTGCACGTGTCT	59.530	36.000	18.38	0.00	0.00	3.41
102	103	7.947890	AGACCCCTATATCAAAAGTTCAAAACA	59.052	33.333	0.00	0.00	0.00	2.83
118	119	5.162980	TGACAATCTCTAGCAGACCCCTATA	60.163	44.000	0.00	0.00	32.26	1.31
124	125	4.727507	TCTTGACAATCTCTAGCAGACC	57.272	45.455	0.00	0.00	32.26	3.85
212	218	7.063308	CCAAACATGGGATTATTTTTCGTTCAG	59.937	37.037	0.00	0.00	0.00	3.02
218	224	8.614469	TCAAACCAAACATGGGATTATTTTTC	57.386	30.769	0.00	0.00	0.00	2.29
242	248	4.907809	AGGTAAAGTTAGCAAACCTCCTC	58.092	43.478	3.33	0.00	35.67	3.71
256	262	6.511017	ACTTTTCAGGTAAGGAGGTAAAGT	57.489	37.500	0.00	0.00	31.74	2.66
287	293	7.280356	ACATTCTTCAGGTAAAACAGTAGTGT	58.720	34.615	0.00	0.00	39.19	3.55
288	294	7.730364	ACATTCTTCAGGTAAAACAGTAGTG	57.270	36.000	0.00	0.00	0.00	2.74
340	353	5.111293	CCAAACTTTTCTTCTGCAACATGT	58.889	37.500	0.00	0.00	0.00	3.21
377	390	9.356433	CATATGCTTGTTATTTGACACAATCAA	57.644	29.630	0.00	0.00	45.92	2.57
449	468	2.951457	TGCATTGATTGTGATGCTGG	57.049	45.000	9.39	0.00	46.68	4.85
483	502	4.597004	TGGTAGAATCGGTACACTCTCTT	58.403	43.478	0.00	0.00	0.00	2.85
496	515	5.741011	TGGTATTTCCACACTGGTAGAATC	58.259	41.667	0.00	0.00	41.93	2.52
497	516	5.772393	TGGTATTTCCACACTGGTAGAAT	57.228	39.130	0.00	0.00	41.93	2.40
577	600	1.406539	GCCGTTTCATCCAGATGCAAT	59.593	47.619	2.63	0.00	38.65	3.56
599	622	0.458260	AACACAAACCGGAACTTGGC	59.542	50.000	9.46	0.00	0.00	4.52
693	790	8.630054	TGGCAATATATTTTGTATACCAGGTC	57.370	34.615	0.00	0.00	0.00	3.85
718	1196	5.220796	GGACTAAGTTTTCACGCACTTCTTT	60.221	40.000	0.00	0.00	34.92	2.52
746	1224	1.326951	GGAGAGCTGGACAGGAGGAC	61.327	65.000	0.00	0.00	0.00	3.85
754	1232	1.646189	GTTCGATTGGAGAGCTGGAC	58.354	55.000	0.00	0.00	0.00	4.02
844	1323	3.988976	ATGGTATGAACTGTGACTGCT	57.011	42.857	0.00	0.00	0.00	4.24
848	1327	4.110482	GTCGGTATGGTATGAACTGTGAC	58.890	47.826	0.00	0.00	0.00	3.67
886	1367	6.957020	TGAAAATGGTAGGTTGATTAATGGGT	59.043	34.615	0.00	0.00	0.00	4.51
914	1395	6.708285	AGTATTAATAGGGGAATTGGCGTAG	58.292	40.000	0.00	0.00	0.00	3.51
1140	1671	1.290955	GGTGAACGACGGGTCATGA	59.709	57.895	0.00	0.00	0.00	3.07
1389	2481	3.325753	GCCAGACCAGGAGCCACT	61.326	66.667	0.00	0.00	0.00	4.00
1713	2829	3.467226	TCCCCGATGAACGAGCCC	61.467	66.667	0.00	0.00	45.77	5.19
1758	2874	2.516227	ACTGATTGACGAGGGAGAGA	57.484	50.000	0.00	0.00	0.00	3.10
2377	3499	2.667536	CTTGGCGCAGTCTGCTGT	60.668	61.111	22.13	0.00	44.32	4.40
2482	3628	6.752168	TGCATGATAGAATCTCATTTCTCGA	58.248	36.000	0.00	0.00	37.20	4.04
2507	3653	3.821421	ACGATGAACAGTAGATTCCCC	57.179	47.619	0.00	0.00	0.00	4.81
2514	3660	9.737427	AAATCTCATAGTAACGATGAACAGTAG	57.263	33.333	0.00	0.00	33.01	2.57
2551	3697	7.440523	AGAGAAAAATCTGATGTAACGCTTT	57.559	32.000	0.00	0.00	0.00	3.51
2555	3701	6.633668	ACGAGAGAAAAATCTGATGTAACG	57.366	37.500	0.00	0.00	0.00	3.18
2824	3981	6.430000	ACAAACACACCTTGCTTTATACTAGG	59.570	38.462	0.00	0.00	36.29	3.02
2828	3985	6.500041	TGAACAAACACACCTTGCTTTATAC	58.500	36.000	0.00	0.00	0.00	1.47
2829	3986	6.701145	TGAACAAACACACCTTGCTTTATA	57.299	33.333	0.00	0.00	0.00	0.98
2861	4025	8.204607	GAAAAATCTTTCCAACGATGAACGGAA	61.205	37.037	0.00	0.00	39.60	4.30
2903	4067	8.732746	AGGATAGACGCACAAAAATTTAGTAT	57.267	30.769	0.00	0.00	0.00	2.12
2928	4092	8.817092	TGGAGAAACCTTCTTTTTCTTTTCTA	57.183	30.769	0.00	0.00	42.21	2.10
2929	4093	7.615757	TCTGGAGAAACCTTCTTTTTCTTTTCT	59.384	33.333	0.00	0.00	42.21	2.52
2930	4094	7.772166	TCTGGAGAAACCTTCTTTTTCTTTTC	58.228	34.615	0.00	0.00	42.21	2.29
2949	4113	3.561725	GGCTCAATTACGGAATTCTGGAG	59.438	47.826	18.44	14.31	32.73	3.86
2990	4154	4.511826	GGAATAATAAGTGGGCTGACTTCG	59.488	45.833	5.84	0.00	37.38	3.79
3018	4182	3.939066	ACATAAGGTCTTCCCAACTTCG	58.061	45.455	0.00	0.00	34.66	3.79
3024	5287	4.523083	GTGCAATACATAAGGTCTTCCCA	58.477	43.478	0.00	0.00	34.66	4.37
3038	5301	8.556194	TCAACTATTTATCATTCCGTGCAATAC	58.444	33.333	0.00	0.00	0.00	1.89
3040	5303	7.566760	TCAACTATTTATCATTCCGTGCAAT	57.433	32.000	0.00	0.00	0.00	3.56
3075	5338	0.108281	GGCCCAGTCTTAGACGTTCC	60.108	60.000	6.73	3.85	37.67	3.62
3077	5340	0.608640	CTGGCCCAGTCTTAGACGTT	59.391	55.000	1.39	0.00	37.67	3.99
3081	5344	3.727387	GGCTGGCCCAGTCTTAGA	58.273	61.111	13.35	0.00	32.76	2.10
3095	5358	1.176619	CGAAAAAGGGGAAACGGGCT	61.177	55.000	0.00	0.00	0.00	5.19
3239	7633	9.748708	TTCTGACGAATTTCTGAAATTTTGAAT	57.251	25.926	24.57	11.84	40.97	2.57
3246	7657	7.452880	TGGAATTCTGACGAATTTCTGAAAT	57.547	32.000	9.76	9.76	46.87	2.17
3247	7658	6.875948	TGGAATTCTGACGAATTTCTGAAA	57.124	33.333	5.15	5.15	46.87	2.69
3277	7688	5.351740	TCAAACATTTTTCAAAACCGGAACC	59.648	36.000	9.46	0.00	0.00	3.62
3299	7710	9.216117	TGAAACGGGAAATTTTTAAAAGTTTCA	57.784	25.926	32.36	28.12	46.75	2.69
3331	7742	8.450578	TGAGAACAGTTTTTGAATGTGTAGAT	57.549	30.769	0.00	0.00	0.00	1.98

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.