AutoCloner

Multiple sequence alignment - TraesCS2B01G627900

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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	TraesCS2B01G627900	chr2B	100.000	3521	0	0	1	3521	799578238	799574718	0.000000e+00	6503.0
1	TraesCS2B01G627900	chr2B	87.273	330	41	1	2559	2887	799595660	799595331	3.320000e-100	375.0
2	TraesCS2B01G627900	chr2B	82.890	263	35	4	1337	1589	17464224	17463962	9.830000e-56	228.0
3	TraesCS2B01G627900	chr2B	88.800	125	13	1	2559	2682	799597536	799597412	6.090000e-33	152.0
4	TraesCS2B01G627900	chr2B	79.909	219	31	11	3303	3515	93004794	93004583	7.870000e-32	148.0
5	TraesCS2B01G627900	chr2B	84.177	158	19	6	2413	2568	799599386	799599233	7.870000e-32	148.0
6	TraesCS2B01G627900	chr2B	81.461	178	27	6	3330	3505	100349174	100349001	1.320000e-29	141.0
7	TraesCS2B01G627900	chr2B	96.250	80	3	0	666	745	799584308	799584229	7.930000e-27	132.0
8	TraesCS2B01G627900	chr2B	92.157	51	3	1	1627	1676	789132727	789132777	1.750000e-08	71.3
9	TraesCS2B01G627900	chr2B	97.368	38	1	0	1050	1087	799584070	799584033	8.160000e-07	65.8
10	TraesCS2B01G627900	chr2D	87.739	2455	176	55	466	2872	642099699	642102076	0.000000e+00	2750.0
11	TraesCS2B01G627900	chr2D	88.728	1863	143	30	1044	2872	598328706	598330535	0.000000e+00	2215.0
12	TraesCS2B01G627900	chr2D	93.782	579	17	4	466	1044	598328108	598328667	0.000000e+00	852.0
13	TraesCS2B01G627900	chr2D	86.848	479	59	3	2413	2890	642212778	642213253	1.860000e-147	532.0
14	TraesCS2B01G627900	chr2D	94.819	193	8	2	188	380	598327916	598328106	2.050000e-77	300.0
15	TraesCS2B01G627900	chr2D	93.782	193	10	2	188	380	642099507	642099697	4.450000e-74	289.0
16	TraesCS2B01G627900	chr2D	75.000	288	53	12	3234	3507	381866036	381866318	7.990000e-22	115.0
17	TraesCS2B01G627900	chr2A	89.716	1478	108	20	1044	2485	767017985	767019454	0.000000e+00	1847.0
18	TraesCS2B01G627900	chr2A	83.836	829	79	16	1678	2472	766981478	766982285	0.000000e+00	737.0
19	TraesCS2B01G627900	chr2A	89.840	561	30	7	488	1044	767017409	767017946	0.000000e+00	695.0
20	TraesCS2B01G627900	chr2A	90.965	487	37	6	3026	3508	767020239	767020722	0.000000e+00	649.0
21	TraesCS2B01G627900	chr2A	83.101	574	55	15	2472	3034	767019668	767020210	5.280000e-133	484.0
22	TraesCS2B01G627900	chr2A	82.178	606	55	24	2278	2872	767147005	767146442	4.110000e-129	472.0
23	TraesCS2B01G627900	chr2A	84.466	515	33	20	809	1296	766980989	766981483	6.880000e-127	464.0
24	TraesCS2B01G627900	chr2A	86.072	359	25	11	3170	3507	766983225	766983579	2.580000e-96	363.0
25	TraesCS2B01G627900	chr2A	91.429	245	20	1	2543	2786	766982321	766982565	5.630000e-88	335.0
26	TraesCS2B01G627900	chr2A	89.844	128	5	5	1182	1301	767147315	767147188	1.310000e-34	158.0
27	TraesCS2B01G627900	chr2A	78.750	160	12	5	1678	1815	767147200	767147041	1.740000e-13	87.9
28	TraesCS2B01G627900	chr3B	86.486	296	37	3	1385	1677	829275139	829274844	4.380000e-84	322.0
29	TraesCS2B01G627900	chr3B	84.000	100	7	9	3235	3331	818866246	818866153	1.740000e-13	87.9
30	TraesCS2B01G627900	chr7A	81.408	355	45	12	1337	1677	29834924	29834577	1.610000e-68	270.0
31	TraesCS2B01G627900	chr7A	91.579	95	6	2	379	472	108210425	108210518	2.850000e-26	130.0
32	TraesCS2B01G627900	chr7A	90.909	99	4	5	380	475	612025788	612025884	1.030000e-25	128.0
33	TraesCS2B01G627900	chr6A	82.462	325	31	13	1377	1677	447628614	447628292	9.690000e-66	261.0
34	TraesCS2B01G627900	chr6A	76.863	255	43	12	3281	3521	550717241	550716989	2.850000e-26	130.0
35	TraesCS2B01G627900	chr6A	90.000	100	6	3	366	465	607960042	607959947	3.690000e-25	126.0
36	TraesCS2B01G627900	chr1A	79.455	404	50	14	1297	1677	254185246	254184853	4.510000e-64	255.0
37	TraesCS2B01G627900	chr1A	78.505	214	31	11	3302	3505	496125487	496125279	3.690000e-25	126.0
38	TraesCS2B01G627900	chr1A	86.747	83	8	3	3251	3332	517642761	517642681	4.840000e-14	89.8
39	TraesCS2B01G627900	chr4A	81.115	323	38	10	1377	1677	108368932	108368611	1.630000e-58	237.0
40	TraesCS2B01G627900	chr4A	100.000	28	0	0	1650	1677	581149020	581149047	6.000000e-03	52.8
41	TraesCS2B01G627900	chr5B	79.235	366	51	14	1337	1681	615706404	615706043	7.600000e-57	231.0
42	TraesCS2B01G627900	chr5B	91.579	95	7	1	379	473	375770589	375770496	2.850000e-26	130.0
43	TraesCS2B01G627900	chr7D	85.648	216	27	4	1377	1589	550839789	550840003	1.270000e-54	224.0
44	TraesCS2B01G627900	chr7D	91.753	97	6	2	389	485	626199960	626199866	2.210000e-27	134.0
45	TraesCS2B01G627900	chr7D	90.909	99	5	4	376	471	506141364	506141461	2.850000e-26	130.0
46	TraesCS2B01G627900	chr7B	82.500	160	25	3	3358	3515	71134530	71134688	1.700000e-28	137.0
47	TraesCS2B01G627900	chr3A	80.899	178	31	3	3329	3506	696709648	696709822	1.700000e-28	137.0
48	TraesCS2B01G627900	chr3A	89.796	49	5	0	577	625	102107801	102107753	2.930000e-06	63.9
49	TraesCS2B01G627900	chr5D	92.473	93	5	2	379	470	504793016	504792925	7.930000e-27	132.0
50	TraesCS2B01G627900	chr5D	80.447	179	24	10	3336	3510	539864426	539864255	3.690000e-25	126.0
51	TraesCS2B01G627900	chr5D	77.778	207	25	14	3245	3441	445800675	445800870	1.340000e-19	108.0
52	TraesCS2B01G627900	chr6B	91.579	95	6	2	379	472	225523450	225523357	2.850000e-26	130.0
53	TraesCS2B01G627900	chr4D	87.736	106	11	2	373	478	10971621	10971518	4.770000e-24	122.0
54	TraesCS2B01G627900	chr6D	75.912	274	39	22	3250	3507	308936961	308936699	7.990000e-22	115.0
55	TraesCS2B01G627900	chr3D	74.653	288	53	12	3241	3511	547616814	547617098	3.720000e-20	110.0
56	TraesCS2B01G627900	chr3D	77.222	180	37	4	3331	3510	560872717	560872892	6.220000e-18	102.0
57	TraesCS2B01G627900	chr1D	74.627	268	57	10	3251	3515	46461114	46460855	1.340000e-19	108.0

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	TraesCS2B01G627900	chr2B	799574718	799578238	3520	True	6503.000000	6503	100.000000	1	3521	1	chr2B.!!$R4	3520
1	TraesCS2B01G627900	chr2B	799595331	799599386	4055	True	225.000000	375	86.750000	2413	2887	3	chr2B.!!$R6	474
2	TraesCS2B01G627900	chr2D	642099507	642102076	2569	False	1519.500000	2750	90.760500	188	2872	2	chr2D.!!$F4	2684
3	TraesCS2B01G627900	chr2D	598327916	598330535	2619	False	1122.333333	2215	92.443000	188	2872	3	chr2D.!!$F3	2684
4	TraesCS2B01G627900	chr2A	767017409	767020722	3313	False	918.750000	1847	88.405500	488	3508	4	chr2A.!!$F2	3020
5	TraesCS2B01G627900	chr2A	766980989	766983579	2590	False	474.750000	737	86.450750	809	3507	4	chr2A.!!$F1	2698
6	TraesCS2B01G627900	chr2A	767146442	767147315	873	True	239.300000	472	83.590667	1182	2872	3	chr2A.!!$R1	1690

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
111	112	0.299895	CGATGCTCGCATTGTCTGAC	59.700	55.0	5.79	0.00	36.70	3.51	F
1747	1842	0.385751	TTGATCGCCTCGAGATGGAC	59.614	55.0	15.71	3.06	39.91	4.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1795	1908	0.391228	TCTTGTTCTGCTGTGCCGTA	59.609	50.0	0.0	0.0	0.0	4.02	R
2820	7179	0.034059	CGCCCTCATCTCATGTACCC	59.966	60.0	0.0	0.0	0.0	3.69	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
21	22	3.951775	AGCTCAACTACTGTGAAGAGG	57.048	47.619	0.00	0.00	0.00	3.69
22	23	3.235200	AGCTCAACTACTGTGAAGAGGT	58.765	45.455	0.00	0.00	0.00	3.85
23	24	3.643792	AGCTCAACTACTGTGAAGAGGTT	59.356	43.478	0.00	0.00	31.71	3.50
24	25	4.101741	AGCTCAACTACTGTGAAGAGGTTT	59.898	41.667	0.00	0.00	31.71	3.27
25	26	5.304614	AGCTCAACTACTGTGAAGAGGTTTA	59.695	40.000	0.00	0.00	31.71	2.01
26	27	5.989777	GCTCAACTACTGTGAAGAGGTTTAA	59.010	40.000	0.00	0.00	0.00	1.52
27	28	6.146347	GCTCAACTACTGTGAAGAGGTTTAAG	59.854	42.308	0.00	0.00	0.00	1.85
28	29	7.356089	TCAACTACTGTGAAGAGGTTTAAGA	57.644	36.000	0.00	0.00	0.00	2.10
29	30	7.963532	TCAACTACTGTGAAGAGGTTTAAGAT	58.036	34.615	0.00	0.00	0.00	2.40
30	31	8.429641	TCAACTACTGTGAAGAGGTTTAAGATT	58.570	33.333	0.00	0.00	0.00	2.40
31	32	9.057089	CAACTACTGTGAAGAGGTTTAAGATTT	57.943	33.333	0.00	0.00	0.00	2.17
32	33	8.608844	ACTACTGTGAAGAGGTTTAAGATTTG	57.391	34.615	0.00	0.00	0.00	2.32
33	34	8.429641	ACTACTGTGAAGAGGTTTAAGATTTGA	58.570	33.333	0.00	0.00	0.00	2.69
34	35	7.497925	ACTGTGAAGAGGTTTAAGATTTGAC	57.502	36.000	0.00	0.00	0.00	3.18
35	36	7.054124	ACTGTGAAGAGGTTTAAGATTTGACA	58.946	34.615	0.00	0.00	0.00	3.58
36	37	7.556275	ACTGTGAAGAGGTTTAAGATTTGACAA	59.444	33.333	0.00	0.00	0.00	3.18
37	38	8.463930	TGTGAAGAGGTTTAAGATTTGACAAT	57.536	30.769	0.00	0.00	0.00	2.71
38	39	8.567948	TGTGAAGAGGTTTAAGATTTGACAATC	58.432	33.333	0.00	0.00	39.45	2.67
39	40	7.746475	GTGAAGAGGTTTAAGATTTGACAATCG	59.254	37.037	0.00	0.00	43.38	3.34
40	41	7.659799	TGAAGAGGTTTAAGATTTGACAATCGA	59.340	33.333	0.00	0.00	43.38	3.59
41	42	8.567285	AAGAGGTTTAAGATTTGACAATCGAT	57.433	30.769	0.00	0.00	43.38	3.59
42	43	7.978982	AGAGGTTTAAGATTTGACAATCGATG	58.021	34.615	0.00	0.00	43.38	3.84
44	45	8.110860	AGGTTTAAGATTTGACAATCGATGTT	57.889	30.769	0.00	0.00	44.12	2.71
45	46	8.237267	AGGTTTAAGATTTGACAATCGATGTTC	58.763	33.333	0.00	0.00	44.12	3.18
46	47	8.237267	GGTTTAAGATTTGACAATCGATGTTCT	58.763	33.333	0.00	0.00	44.12	3.01

Showing 1 to 25 of 232 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	3.643792	ACCTCTTCACAGTAGTTGAGCTT	59.356	43.478	0.00	0.00	0.00	3.74
1	2	3.235200	ACCTCTTCACAGTAGTTGAGCT	58.765	45.455	0.00	0.00	0.00	4.09
2	3	3.669251	ACCTCTTCACAGTAGTTGAGC	57.331	47.619	0.00	0.00	0.00	4.26
3	4	7.434492	TCTTAAACCTCTTCACAGTAGTTGAG	58.566	38.462	0.00	0.00	0.00	3.02
4	5	7.356089	TCTTAAACCTCTTCACAGTAGTTGA	57.644	36.000	0.00	0.00	0.00	3.18
5	6	8.608844	AATCTTAAACCTCTTCACAGTAGTTG	57.391	34.615	0.00	0.00	0.00	3.16
6	7	9.057089	CAAATCTTAAACCTCTTCACAGTAGTT	57.943	33.333	0.00	0.00	0.00	2.24
7	8	8.429641	TCAAATCTTAAACCTCTTCACAGTAGT	58.570	33.333	0.00	0.00	0.00	2.73
8	9	8.713271	GTCAAATCTTAAACCTCTTCACAGTAG	58.287	37.037	0.00	0.00	0.00	2.57
9	10	8.208224	TGTCAAATCTTAAACCTCTTCACAGTA	58.792	33.333	0.00	0.00	0.00	2.74
10	11	7.054124	TGTCAAATCTTAAACCTCTTCACAGT	58.946	34.615	0.00	0.00	0.00	3.55
11	12	7.496529	TGTCAAATCTTAAACCTCTTCACAG	57.503	36.000	0.00	0.00	0.00	3.66
12	13	7.873719	TTGTCAAATCTTAAACCTCTTCACA	57.126	32.000	0.00	0.00	0.00	3.58
13	14	7.746475	CGATTGTCAAATCTTAAACCTCTTCAC	59.254	37.037	0.00	0.00	40.15	3.18
14	15	7.659799	TCGATTGTCAAATCTTAAACCTCTTCA	59.340	33.333	0.00	0.00	40.15	3.02
15	16	8.029642	TCGATTGTCAAATCTTAAACCTCTTC	57.970	34.615	0.00	0.00	40.15	2.87
16	17	7.979444	TCGATTGTCAAATCTTAAACCTCTT	57.021	32.000	0.00	0.00	40.15	2.85
17	18	7.607991	ACATCGATTGTCAAATCTTAAACCTCT	59.392	33.333	0.00	0.00	40.15	3.69
18	19	7.752695	ACATCGATTGTCAAATCTTAAACCTC	58.247	34.615	0.00	0.00	40.15	3.85
19	20	7.687941	ACATCGATTGTCAAATCTTAAACCT	57.312	32.000	0.00	0.00	40.15	3.50
20	21	8.237267	AGAACATCGATTGTCAAATCTTAAACC	58.763	33.333	0.00	0.00	40.15	3.27
21	22	9.612620	AAGAACATCGATTGTCAAATCTTAAAC	57.387	29.630	0.00	0.00	40.15	2.01
22	23	9.611284	CAAGAACATCGATTGTCAAATCTTAAA	57.389	29.630	0.00	0.00	40.15	1.52
23	24	8.783093	ACAAGAACATCGATTGTCAAATCTTAA	58.217	29.630	0.00	0.00	40.15	1.85
24	25	8.322906	ACAAGAACATCGATTGTCAAATCTTA	57.677	30.769	0.00	0.00	40.15	2.10

Showing 1 to 25 of 214 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.