AutoCloner

Multiple sequence alignment - TraesCS4B01G349700

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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	TraesCS4B01G349700	chr4B	100.000	4272	0	0	1	4272	642736125	642740396	0.000000e+00	7890.0
1	TraesCS4B01G349700	chr7D	96.426	3553	67	12	774	4272	499627551	499624005	0.000000e+00	5803.0
2	TraesCS4B01G349700	chr7D	96.023	352	12	2	211	560	623872338	623871987	4.790000e-159	571.0
3	TraesCS4B01G349700	chr7D	92.899	169	10	2	578	745	553505280	553505113	1.190000e-60	244.0
4	TraesCS4B01G349700	chr7A	96.335	1610	44	9	1031	2629	109230796	109229191	0.000000e+00	2632.0
5	TraesCS4B01G349700	chr7A	95.926	1620	49	13	1031	2639	61493737	61492124	0.000000e+00	2610.0
6	TraesCS4B01G349700	chr7A	96.203	79	3	0	1	79	588285277	588285199	3.470000e-26	130.0
7	TraesCS4B01G349700	chr2B	93.329	1484	41	12	774	2248	30335664	30334230	0.000000e+00	2139.0
8	TraesCS4B01G349700	chr2B	96.719	823	23	3	3453	4272	30331547	30330726	0.000000e+00	1367.0
9	TraesCS4B01G349700	chr2B	90.963	1007	32	23	2494	3461	30332723	30331737	0.000000e+00	1301.0
10	TraesCS4B01G349700	chr2B	96.852	540	13	2	1	536	267913086	267912547	0.000000e+00	900.0
11	TraesCS4B01G349700	chr2B	96.317	543	13	2	1	536	334879154	334878612	0.000000e+00	885.0
12	TraesCS4B01G349700	chr2B	95.370	540	20	3	1	536	334880241	334879703	0.000000e+00	854.0
13	TraesCS4B01G349700	chr2B	97.338	263	6	1	2231	2493	30334048	30333787	3.030000e-121	446.0
14	TraesCS4B01G349700	chr2B	77.857	280	27	19	3279	3551	211158741	211158992	1.600000e-29	141.0
15	TraesCS4B01G349700	chr3B	89.557	1647	97	29	914	2493	812459598	812461236	0.000000e+00	2019.0
16	TraesCS4B01G349700	chr3B	77.955	313	35	17	3247	3551	62383708	62383994	9.500000e-37	165.0
17	TraesCS4B01G349700	chr3B	93.182	44	2	1	3151	3193	62383630	62383673	3.570000e-06	63.9
18	TraesCS4B01G349700	chr5B	97.199	821	21	2	3453	4272	649444967	649444148	0.000000e+00	1387.0
19	TraesCS4B01G349700	chr5B	96.070	687	21	3	2494	3176	649446029	649445345	0.000000e+00	1114.0
20	TraesCS4B01G349700	chr5B	92.537	335	11	5	3141	3461	649445351	649445017	6.470000e-128	468.0
21	TraesCS4B01G349700	chr5B	93.750	80	4	1	1	79	272837943	272838022	7.500000e-23	119.0
22	TraesCS4B01G349700	chr5B	96.970	33	1	0	3425	3457	185222848	185222880	5.970000e-04	56.5
23	TraesCS4B01G349700	chrUn	94.861	720	28	4	73	784	49427901	49428619	0.000000e+00	1116.0
24	TraesCS4B01G349700	chrUn	85.043	575	38	15	3291	3857	64134493	64135027	3.760000e-150	542.0
25	TraesCS4B01G349700	chrUn	89.303	402	30	7	3457	3857	368435668	368436057	3.840000e-135	492.0
26	TraesCS4B01G349700	chrUn	88.806	402	32	4	3457	3857	31637323	31636934	8.310000e-132	481.0
27	TraesCS4B01G349700	chr3D	89.898	881	43	23	914	1749	604685813	604686692	0.000000e+00	1092.0
28	TraesCS4B01G349700	chr3D	89.460	759	60	12	1749	2493	604686728	604687480	0.000000e+00	941.0
29	TraesCS4B01G349700	chr3D	94.940	415	18	1	3858	4272	419468685	419469096	0.000000e+00	647.0
30	TraesCS4B01G349700	chr3D	95.455	352	11	3	211	560	12732408	12732060	1.340000e-154	556.0
31	TraesCS4B01G349700	chr3D	95.455	352	11	3	211	560	574894337	574893989	1.340000e-154	556.0
32	TraesCS4B01G349700	chr3D	89.303	402	30	7	3457	3857	519173558	519173169	3.840000e-135	492.0
33	TraesCS4B01G349700	chr3A	89.091	880	48	22	917	1749	734885639	734886517	0.000000e+00	1050.0
34	TraesCS4B01G349700	chr3A	88.864	880	48	24	917	1749	734840257	734841133	0.000000e+00	1037.0
35	TraesCS4B01G349700	chr3A	93.198	691	36	6	1749	2430	734841169	734841857	0.000000e+00	1005.0
36	TraesCS4B01G349700	chr3A	92.909	691	38	6	1749	2430	734886553	734887241	0.000000e+00	994.0
37	TraesCS4B01G349700	chr3A	95.192	416	19	1	3858	4272	706834367	706834782	0.000000e+00	656.0
38	TraesCS4B01G349700	chr3A	93.525	417	26	1	3857	4272	10964758	10965174	1.690000e-173	619.0
39	TraesCS4B01G349700	chr3A	78.413	315	34	10	3247	3553	33951870	33951582	1.580000e-39	174.0
40	TraesCS4B01G349700	chr3A	97.826	46	1	0	2446	2491	734842093	734842138	3.540000e-11	80.5
41	TraesCS4B01G349700	chr3A	97.826	46	1	0	2446	2491	734887477	734887522	3.540000e-11	80.5
42	TraesCS4B01G349700	chr5A	81.202	1314	139	54	1156	2372	623024435	623023133	0.000000e+00	959.0
43	TraesCS4B01G349700	chr5A	87.209	86	7	3	2494	2577	158249036	158249119	1.260000e-15	95.3
44	TraesCS4B01G349700	chr7B	96.111	540	17	2	1	536	115810675	115811214	0.000000e+00	878.0
45	TraesCS4B01G349700	chr7B	91.667	108	7	1	76	183	61809552	61809447	9.570000e-32	148.0
46	TraesCS4B01G349700	chr5D	81.702	858	80	27	2575	3359	179360122	179360975	1.000000e-180	643.0
47	TraesCS4B01G349700	chr5D	89.070	430	37	7	1818	2246	498731447	498731027	3.780000e-145	525.0
48	TraesCS4B01G349700	chr5D	96.364	220	6	2	558	776	112946775	112946557	1.130000e-95	361.0
49	TraesCS4B01G349700	chr6A	94.245	417	23	1	3857	4272	11417748	11417332	1.680000e-178	636.0
50	TraesCS4B01G349700	chr6A	93.750	416	25	1	3858	4272	11432803	11432388	1.300000e-174	623.0
51	TraesCS4B01G349700	chr4A	93.647	425	24	3	3849	4270	727746347	727746771	2.170000e-177	632.0
52	TraesCS4B01G349700	chr2D	95.376	346	11	3	217	560	86088968	86089310	2.900000e-151	545.0
53	TraesCS4B01G349700	chr2D	78.769	325	46	17	921	1231	547166308	547165993	3.370000e-46	196.0
54	TraesCS4B01G349700	chr2D	91.406	128	9	2	2494	2619	476921951	476921824	1.580000e-39	174.0
55	TraesCS4B01G349700	chr1A	89.303	402	30	7	3457	3857	514937359	514936970	3.840000e-135	492.0
56	TraesCS4B01G349700	chr1A	89.303	402	30	7	3457	3857	515194058	515193669	3.840000e-135	492.0
57	TraesCS4B01G349700	chr1A	80.479	292	37	6	3150	3425	48876482	48876195	5.600000e-49	206.0
58	TraesCS4B01G349700	chr4D	89.055	402	31	7	3457	3857	31538681	31539070	1.790000e-133	486.0
59	TraesCS4B01G349700	chr4D	100.000	28	0	0	3430	3457	425163402	425163375	8.000000e-03	52.8
60	TraesCS4B01G349700	chr6D	88.261	230	23	1	914	1143	7262162	7262387	5.440000e-69	272.0
61	TraesCS4B01G349700	chr6D	91.406	128	9	2	2494	2619	130277666	130277539	1.580000e-39	174.0
62	TraesCS4B01G349700	chr6D	91.406	128	9	2	2494	2619	367003398	367003271	1.580000e-39	174.0
63	TraesCS4B01G349700	chr6D	90.179	112	7	3	73	183	7260669	7260777	4.450000e-30	143.0
64	TraesCS4B01G349700	chr6D	94.937	79	4	0	1	79	22671839	22671761	1.610000e-24	124.0
65	TraesCS4B01G349700	chr6D	93.671	79	5	0	1	79	22356111	22356033	7.500000e-23	119.0
66	TraesCS4B01G349700	chr6D	92.405	79	6	0	1	79	22832403	22832325	3.490000e-21	113.0
67	TraesCS4B01G349700	chr2A	88.261	230	23	1	920	1149	17648024	17647799	5.440000e-69	272.0
68	TraesCS4B01G349700	chr2A	77.370	327	41	16	3247	3566	429128121	429127821	3.420000e-36	163.0
69	TraesCS4B01G349700	chr2A	92.593	108	6	1	76	183	17649466	17649361	2.060000e-33	154.0
70	TraesCS4B01G349700	chr1D	92.899	169	10	2	578	745	464634951	464635118	1.190000e-60	244.0
71	TraesCS4B01G349700	chr1D	96.970	33	1	0	3425	3457	111818625	111818657	5.970000e-04	56.5
72	TraesCS4B01G349700	chr1B	83.626	171	20	2	3247	3410	348055708	348055877	2.060000e-33	154.0
73	TraesCS4B01G349700	chr6B	91.753	97	6	1	87	183	626526620	626526714	2.680000e-27	134.0

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	TraesCS4B01G349700	chr4B	642736125	642740396	4271	False	7890.000000	7890	100.000000	1	4272	1	chr4B.!!$F1	4271
1	TraesCS4B01G349700	chr7D	499624005	499627551	3546	True	5803.000000	5803	96.426000	774	4272	1	chr7D.!!$R1	3498
2	TraesCS4B01G349700	chr7A	109229191	109230796	1605	True	2632.000000	2632	96.335000	1031	2629	1	chr7A.!!$R2	1598
3	TraesCS4B01G349700	chr7A	61492124	61493737	1613	True	2610.000000	2610	95.926000	1031	2639	1	chr7A.!!$R1	1608
4	TraesCS4B01G349700	chr2B	30330726	30335664	4938	True	1313.250000	2139	94.587250	774	4272	4	chr2B.!!$R2	3498
5	TraesCS4B01G349700	chr2B	267912547	267913086	539	True	900.000000	900	96.852000	1	536	1	chr2B.!!$R1	535
6	TraesCS4B01G349700	chr2B	334878612	334880241	1629	True	869.500000	885	95.843500	1	536	2	chr2B.!!$R3	535
7	TraesCS4B01G349700	chr3B	812459598	812461236	1638	False	2019.000000	2019	89.557000	914	2493	1	chr3B.!!$F1	1579
8	TraesCS4B01G349700	chr5B	649444148	649446029	1881	True	989.666667	1387	95.268667	2494	4272	3	chr5B.!!$R1	1778
9	TraesCS4B01G349700	chrUn	49427901	49428619	718	False	1116.000000	1116	94.861000	73	784	1	chrUn.!!$F1	711
10	TraesCS4B01G349700	chrUn	64134493	64135027	534	False	542.000000	542	85.043000	3291	3857	1	chrUn.!!$F2	566
11	TraesCS4B01G349700	chr3D	604685813	604687480	1667	False	1016.500000	1092	89.679000	914	2493	2	chr3D.!!$F2	1579
12	TraesCS4B01G349700	chr3A	734885639	734887522	1883	False	708.166667	1050	93.275333	917	2491	3	chr3A.!!$F4	1574
13	TraesCS4B01G349700	chr3A	734840257	734842138	1881	False	707.500000	1037	93.296000	917	2491	3	chr3A.!!$F3	1574
14	TraesCS4B01G349700	chr5A	623023133	623024435	1302	True	959.000000	959	81.202000	1156	2372	1	chr5A.!!$R1	1216
15	TraesCS4B01G349700	chr7B	115810675	115811214	539	False	878.000000	878	96.111000	1	536	1	chr7B.!!$F1	535
16	TraesCS4B01G349700	chr5D	179360122	179360975	853	False	643.000000	643	81.702000	2575	3359	1	chr5D.!!$F1	784
17	TraesCS4B01G349700	chr6D	7260669	7262387	1718	False	207.500000	272	89.220000	73	1143	2	chr6D.!!$F1	1070
18	TraesCS4B01G349700	chr2A	17647799	17649466	1667	True	213.000000	272	90.427000	76	1149	2	chr2A.!!$R2	1073

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
582	2107	0.108662	GAAAATCAAGGCCAAGGCGG	60.109	55.0	5.01	0.0	43.06	6.13	F
598	2123	0.589729	GCGGCTCATTTGCGTGTATG	60.590	55.0	0.00	0.0	0.00	2.39	F
624	2149	0.878416	GCTGGCACACAATCCGTTAA	59.122	50.0	0.00	0.0	0.00	2.01	F
2248	4370	0.597377	TGCGTCGGTGCTGCATATAG	60.597	55.0	5.27	0.0	32.86	1.31	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2142	4264	0.388649	CCGAGTGGTTCCACTTCTCG	60.389	60.000	22.93	20.48	45.99	4.04	R
2248	4370	7.578189	GCTTAACCAACCTTATTTTAGAACCCC	60.578	40.741	0.00	0.00	0.00	4.95	R
2823	6462	3.123621	CGCACTACATTGTCTCCTTGAAC	59.876	47.826	0.00	0.00	0.00	3.18	R
3868	7848	0.459411	GAAGAAGAGGAGCTGGCGAC	60.459	60.000	0.00	0.00	0.00	5.19	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
66	1154	4.400961	GGAGAAGCCAGCCAGCGT	62.401	66.667	0.00	0.00	38.01	5.07
183	1271	3.842923	CGCCGCAGATCACCCTCT	61.843	66.667	0.00	0.00	0.00	3.69
184	1272	2.202987	GCCGCAGATCACCCTCTG	60.203	66.667	0.00	0.00	44.51	3.35
188	1276	1.524482	GCAGATCACCCTCTGGTCC	59.476	63.158	0.00	0.00	45.57	4.46
189	1277	1.267574	GCAGATCACCCTCTGGTCCA	61.268	60.000	0.00	0.00	45.57	4.02
190	1278	1.504912	CAGATCACCCTCTGGTCCAT	58.495	55.000	0.00	0.00	45.57	3.41
191	1279	1.140452	CAGATCACCCTCTGGTCCATG	59.860	57.143	0.00	0.00	45.57	3.66
193	1281	1.639635	ATCACCCTCTGGTCCATGGC	61.640	60.000	6.96	1.78	45.57	4.40
197	1285	2.503061	CTCTGGTCCATGGCCTCG	59.497	66.667	21.23	14.19	0.00	4.63
198	1286	2.038813	TCTGGTCCATGGCCTCGA	59.961	61.111	21.23	15.74	0.00	4.04
199	1287	2.187946	CTGGTCCATGGCCTCGAC	59.812	66.667	21.23	6.59	0.00	4.20
200	1288	3.723235	CTGGTCCATGGCCTCGACG	62.723	68.421	21.23	0.00	0.00	5.12
201	1289	4.530857	GGTCCATGGCCTCGACGG	62.531	72.222	6.96	0.00	0.00	4.79
233	1321	3.546397	GCGCTCGCGTTCTTCCTC	61.546	66.667	13.18	0.00	42.09	3.71
234	1322	2.881352	CGCTCGCGTTCTTCCTCC	60.881	66.667	5.77	0.00	34.35	4.30
235	1323	2.509561	GCTCGCGTTCTTCCTCCC	60.510	66.667	5.77	0.00	0.00	4.30
236	1324	2.184579	CTCGCGTTCTTCCTCCCC	59.815	66.667	5.77	0.00	0.00	4.81
237	1325	3.372554	CTCGCGTTCTTCCTCCCCC	62.373	68.421	5.77	0.00	0.00	5.40
238	1326	3.702048	CGCGTTCTTCCTCCCCCA	61.702	66.667	0.00	0.00	0.00	4.96
242	1330	0.466124	CGTTCTTCCTCCCCCATCTC	59.534	60.000	0.00	0.00	0.00	2.75
253	1341	0.825840	CCCCATCTCGTCTCCTCTCC	60.826	65.000	0.00	0.00	0.00	3.71
254	1342	1.169661	CCCATCTCGTCTCCTCTCCG	61.170	65.000	0.00	0.00	0.00	4.63
255	1343	1.169661	CCATCTCGTCTCCTCTCCGG	61.170	65.000	0.00	0.00	0.00	5.14
256	1344	0.464735	CATCTCGTCTCCTCTCCGGT	60.465	60.000	0.00	0.00	0.00	5.28
257	1345	0.179040	ATCTCGTCTCCTCTCCGGTC	60.179	60.000	0.00	0.00	0.00	4.79

Showing 1 to 25 of 250 entries

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Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
66	1154	0.404426	TGAGGAGGAGGTCAGAACGA	59.596	55.000	0.00	0.00	0.00	3.85
183	1271	3.770040	CGTCGAGGCCATGGACCA	61.770	66.667	16.13	0.00	33.34	4.02
184	1272	4.530857	CCGTCGAGGCCATGGACC	62.531	72.222	16.13	15.57	33.34	4.46
216	1304	3.546397	GAGGAAGAACGCGAGCGC	61.546	66.667	15.93	8.99	44.19	5.92
217	1305	2.881352	GGAGGAAGAACGCGAGCG	60.881	66.667	15.93	16.38	46.03	5.03
218	1306	2.509561	GGGAGGAAGAACGCGAGC	60.510	66.667	15.93	3.51	0.00	5.03
219	1307	2.184579	GGGGAGGAAGAACGCGAG	59.815	66.667	15.93	0.00	0.00	5.03
220	1308	3.387947	GGGGGAGGAAGAACGCGA	61.388	66.667	15.93	0.00	0.00	5.87
221	1309	2.925162	GATGGGGGAGGAAGAACGCG	62.925	65.000	3.53	3.53	0.00	6.01
222	1310	1.153147	GATGGGGGAGGAAGAACGC	60.153	63.158	0.00	0.00	0.00	4.84
223	1311	0.466124	GAGATGGGGGAGGAAGAACG	59.534	60.000	0.00	0.00	0.00	3.95
224	1312	0.466124	CGAGATGGGGGAGGAAGAAC	59.534	60.000	0.00	0.00	0.00	3.01
225	1313	0.042731	ACGAGATGGGGGAGGAAGAA	59.957	55.000	0.00	0.00	0.00	2.52
226	1314	0.397254	GACGAGATGGGGGAGGAAGA	60.397	60.000	0.00	0.00	0.00	2.87
227	1315	0.397816	AGACGAGATGGGGGAGGAAG	60.398	60.000	0.00	0.00	0.00	3.46
228	1316	0.397254	GAGACGAGATGGGGGAGGAA	60.397	60.000	0.00	0.00	0.00	3.36
229	1317	1.230497	GAGACGAGATGGGGGAGGA	59.770	63.158	0.00	0.00	0.00	3.71
230	1318	1.834822	GGAGACGAGATGGGGGAGG	60.835	68.421	0.00	0.00	0.00	4.30
231	1319	0.825840	GAGGAGACGAGATGGGGGAG	60.826	65.000	0.00	0.00	0.00	4.30
232	1320	1.230497	GAGGAGACGAGATGGGGGA	59.770	63.158	0.00	0.00	0.00	4.81
233	1321	0.825840	GAGAGGAGACGAGATGGGGG	60.826	65.000	0.00	0.00	0.00	5.40
234	1322	0.825840	GGAGAGGAGACGAGATGGGG	60.826	65.000	0.00	0.00	0.00	4.96
235	1323	1.169661	CGGAGAGGAGACGAGATGGG	61.170	65.000	0.00	0.00	0.00	4.00
236	1324	1.169661	CCGGAGAGGAGACGAGATGG	61.170	65.000	0.00	0.00	45.00	3.51
237	1325	0.464735	ACCGGAGAGGAGACGAGATG	60.465	60.000	9.46	0.00	45.00	2.90

Showing 1 to 25 of 273 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.