AutoCloner

Multiple sequence alignment - TraesCS7A01G455500

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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	TraesCS7A01G455500	chr7A	100.000	2213	0	0	1	2213	651976879	651974667	0.000000e+00	4087.0
1	TraesCS7A01G455500	chr7A	96.757	185	6	0	1508	1692	651975189	651975005	2.130000e-80	309.0
2	TraesCS7A01G455500	chr7A	96.757	185	6	0	1691	1875	651975372	651975188	2.130000e-80	309.0
3	TraesCS7A01G455500	chr7A	79.755	163	22	4	490	650	651952689	651952536	8.360000e-20	108.0
4	TraesCS7A01G455500	chr7A	100.000	29	0	0	391	419	179907473	179907501	1.000000e-03	54.7
5	TraesCS7A01G455500	chr7A	100.000	29	0	0	391	419	180166991	180167019	1.000000e-03	54.7
6	TraesCS7A01G455500	chr7A	100.000	29	0	0	391	419	180373549	180373577	1.000000e-03	54.7
7	TraesCS7A01G455500	chr1A	97.087	1579	31	5	648	2213	292527640	292526064	0.000000e+00	2647.0
8	TraesCS7A01G455500	chr1A	97.838	185	4	0	1508	1692	292526596	292526412	9.860000e-84	320.0
9	TraesCS7A01G455500	chr1A	97.297	185	5	0	1691	1875	292526779	292526595	4.590000e-82	315.0
10	TraesCS7A01G455500	chr2D	93.942	1073	29	16	653	1692	537004507	537005576	0.000000e+00	1589.0
11	TraesCS7A01G455500	chr2D	94.393	535	16	3	1691	2213	537005392	537005924	0.000000e+00	809.0
12	TraesCS7A01G455500	chr2B	84.380	621	67	18	644	1246	764898033	764897425	1.140000e-162	582.0
13	TraesCS7A01G455500	chr5B	83.280	622	73	23	641	1246	548128751	548129357	5.370000e-151	544.0
14	TraesCS7A01G455500	chr5B	85.047	214	27	4	1015	1224	170633052	170633264	1.720000e-51	213.0
15	TraesCS7A01G455500	chr6B	82.665	623	73	19	644	1246	705391688	705392295	9.060000e-144	520.0
16	TraesCS7A01G455500	chr5D	81.260	635	67	30	640	1246	458681558	458682168	1.200000e-127	466.0
17	TraesCS7A01G455500	chr7B	87.606	355	38	3	3	351	616746239	616745885	7.360000e-110	407.0
18	TraesCS7A01G455500	chr7B	87.812	320	25	5	345	650	616745837	616745518	1.620000e-96	363.0
19	TraesCS7A01G455500	chr7B	85.903	227	27	2	130	351	616552816	616552590	1.020000e-58	237.0
20	TraesCS7A01G455500	chr7B	84.834	211	27	2	130	335	616754592	616754382	8.010000e-50	207.0
21	TraesCS7A01G455500	chr7B	84.138	145	18	3	414	554	616737718	616737575	3.830000e-28	135.0
22	TraesCS7A01G455500	chr7B	98.246	57	1	0	3	59	616754727	616754671	1.400000e-17	100.0
23	TraesCS7A01G455500	chr7B	95.918	49	1	1	40	87	616738113	616738065	6.550000e-11	78.7
24	TraesCS7A01G455500	chr7B	86.301	73	7	3	17	87	616281532	616281461	2.360000e-10	76.8
25	TraesCS7A01G455500	chr7B	100.000	31	0	0	390	420	692318844	692318814	8.530000e-05	58.4
26	TraesCS7A01G455500	chr5A	79.588	583	91	18	653	1222	105461189	105460622	2.060000e-105	392.0
27	TraesCS7A01G455500	chrUn	92.949	156	7	4	867	1022	340647350	340647199	7.950000e-55	224.0
28	TraesCS7A01G455500	chr3A	92.949	156	7	4	867	1022	738617507	738617356	7.950000e-55	224.0
29	TraesCS7A01G455500	chr3A	100.000	28	0	0	390	417	100017961	100017988	4.000000e-03	52.8
30	TraesCS7A01G455500	chr3A	100.000	28	0	0	390	417	100348331	100348358	4.000000e-03	52.8
31	TraesCS7A01G455500	chr3B	83.230	161	15	7	1782	1942	829255230	829255378	1.070000e-28	137.0
32	TraesCS7A01G455500	chr3B	90.110	91	7	2	1599	1689	829255230	829255318	1.390000e-22	117.0
33	TraesCS7A01G455500	chr7D	90.588	85	7	1	4	87	565488772	565488688	6.460000e-21	111.0
34	TraesCS7A01G455500	chr4B	100.000	28	0	0	390	417	108417753	108417780	4.000000e-03	52.8
35	TraesCS7A01G455500	chr3D	100.000	28	0	0	391	418	533884277	533884304	4.000000e-03	52.8
36	TraesCS7A01G455500	chr2A	100.000	28	0	0	1909	1936	10514149	10514176	4.000000e-03	52.8

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	TraesCS7A01G455500	chr7A	651974667	651976879	2212	True	1568.333333	4087	97.838000	1	2213	3	chr7A.!!$R2	2212
1	TraesCS7A01G455500	chr1A	292526064	292527640	1576	True	1094.000000	2647	97.407333	648	2213	3	chr1A.!!$R1	1565
2	TraesCS7A01G455500	chr2D	537004507	537005924	1417	False	1199.000000	1589	94.167500	653	2213	2	chr2D.!!$F1	1560
3	TraesCS7A01G455500	chr2B	764897425	764898033	608	True	582.000000	582	84.380000	644	1246	1	chr2B.!!$R1	602
4	TraesCS7A01G455500	chr5B	548128751	548129357	606	False	544.000000	544	83.280000	641	1246	1	chr5B.!!$F2	605
5	TraesCS7A01G455500	chr6B	705391688	705392295	607	False	520.000000	520	82.665000	644	1246	1	chr6B.!!$F1	602
6	TraesCS7A01G455500	chr5D	458681558	458682168	610	False	466.000000	466	81.260000	640	1246	1	chr5D.!!$F1	606
7	TraesCS7A01G455500	chr7B	616745518	616746239	721	True	385.000000	407	87.709000	3	650	2	chr7B.!!$R5	647
8	TraesCS7A01G455500	chr5A	105460622	105461189	567	True	392.000000	392	79.588000	653	1222	1	chr5A.!!$R1	569

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
334	341	0.036388	TCGCTTCCATCCACTTCCAC	60.036	55.0	0.0	0.0	0.0	4.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2028	2178	3.930336	TGTGAGATGCAGGTACTTTCAG	58.07	45.455	0.0	0.0	34.6	3.02	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
39	40	6.979817	GGTGATAAAATTAAGATGTGCATGCA	59.020	34.615	18.46	18.46	0.00	3.96
65	66	4.453819	AGATAGCACAAGTGAGTTTGCTTC	59.546	41.667	12.48	10.43	42.74	3.86
66	67	2.368439	AGCACAAGTGAGTTTGCTTCA	58.632	42.857	4.04	0.00	42.74	3.02
74	75	1.532437	TGAGTTTGCTTCAGTGCATCG	59.468	47.619	0.00	0.00	42.96	3.84
80	81	1.281899	GCTTCAGTGCATCGTACCTC	58.718	55.000	0.00	0.00	0.00	3.85
83	84	0.613572	TCAGTGCATCGTACCTCCCA	60.614	55.000	0.00	0.00	0.00	4.37
85	86	0.981183	AGTGCATCGTACCTCCCAAA	59.019	50.000	0.00	0.00	0.00	3.28
86	87	1.559682	AGTGCATCGTACCTCCCAAAT	59.440	47.619	0.00	0.00	0.00	2.32
87	88	1.940613	GTGCATCGTACCTCCCAAATC	59.059	52.381	0.00	0.00	0.00	2.17
88	89	1.837439	TGCATCGTACCTCCCAAATCT	59.163	47.619	0.00	0.00	0.00	2.40
107	109	7.332182	CCAAATCTGAAAGTAACCACTACTCTC	59.668	40.741	0.00	0.00	40.14	3.20
151	153	8.967918	ACTACTTTCCAAATAATTTAGAAGGGC	58.032	33.333	0.00	0.00	0.00	5.19
159	161	9.230122	CCAAATAATTTAGAAGGGCATTTTTGT	57.770	29.630	0.00	0.00	0.00	2.83
166	168	5.391312	AGAAGGGCATTTTTGTATGTCAC	57.609	39.130	0.00	0.00	31.75	3.67
170	172	3.056607	GGGCATTTTTGTATGTCACTGCT	60.057	43.478	0.00	0.00	31.75	4.24
185	187	6.941857	TGTCACTGCTAATGTAGATTAACCA	58.058	36.000	0.00	0.00	0.00	3.67
207	209	1.651987	TGATTTGTACTGCTAGCGCC	58.348	50.000	10.77	0.00	34.43	6.53
209	211	1.327764	GATTTGTACTGCTAGCGCCAC	59.672	52.381	10.77	7.78	34.43	5.01
212	214	3.833645	TACTGCTAGCGCCACGGG	61.834	66.667	10.77	0.00	34.43	5.28
239	241	0.263172	TCCTCCTCCACCTCATCCTC	59.737	60.000	0.00	0.00	0.00	3.71
245	247	3.107601	CCTCCACCTCATCCTCTGTTAA	58.892	50.000	0.00	0.00	0.00	2.01
261	263	3.305720	TGTTAACACAGGTCCTGAGTCT	58.694	45.455	26.18	15.34	34.48	3.24
268	270	1.821753	CAGGTCCTGAGTCTTGACGAT	59.178	52.381	14.26	0.00	32.44	3.73
274	276	0.817654	TGAGTCTTGACGATGCGGAT	59.182	50.000	0.00	0.00	0.00	4.18
288	290	2.151202	TGCGGATGTCAAGTTCTTTCC	58.849	47.619	0.00	0.00	0.00	3.13
290	292	2.683968	CGGATGTCAAGTTCTTTCCGA	58.316	47.619	14.44	0.00	41.44	4.55
302	304	1.284982	CTTTCCGACGGACTGCACAG	61.285	60.000	18.12	2.20	0.00	3.66
303	305	2.709125	TTTCCGACGGACTGCACAGG	62.709	60.000	18.12	0.00	0.00	4.00
319	326	1.210478	ACAGGCATAAGACCAATCGCT	59.790	47.619	0.00	0.00	0.00	4.93
323	330	2.288666	GCATAAGACCAATCGCTTCCA	58.711	47.619	0.00	0.00	0.00	3.53
334	341	0.036388	TCGCTTCCATCCACTTCCAC	60.036	55.000	0.00	0.00	0.00	4.02
335	342	1.361668	CGCTTCCATCCACTTCCACG	61.362	60.000	0.00	0.00	0.00	4.94
361	422	0.460311	CACACGTACTCCCTCCATCC	59.540	60.000	0.00	0.00	0.00	3.51
365	426	0.969894	CGTACTCCCTCCATCCCATC	59.030	60.000	0.00	0.00	0.00	3.51
389	450	6.830324	TCATATAAGGCATTTTTGCAGAGACT	59.170	34.615	0.00	0.00	36.33	3.24
424	485	5.363868	TGAGATGGAGGGAGTATGTAACAAG	59.636	44.000	0.00	0.00	0.00	3.16
435	496	7.389607	GGGAGTATGTAACAAGCTAACTTTGAA	59.610	37.037	0.00	0.00	32.29	2.69
437	498	7.793902	AGTATGTAACAAGCTAACTTTGAACG	58.206	34.615	0.00	0.00	32.29	3.95
448	509	6.147164	AGCTAACTTTGAACGATTTGATTCGA	59.853	34.615	0.31	0.00	41.62	3.71
450	511	4.698276	ACTTTGAACGATTTGATTCGACG	58.302	39.130	0.31	0.00	41.62	5.12
451	512	2.780361	TGAACGATTTGATTCGACGC	57.220	45.000	0.31	0.00	41.62	5.19
453	514	2.476997	TGAACGATTTGATTCGACGCAA	59.523	40.909	0.31	0.00	41.62	4.85
454	515	3.124466	TGAACGATTTGATTCGACGCAAT	59.876	39.130	0.31	0.00	41.62	3.56
455	516	4.327627	TGAACGATTTGATTCGACGCAATA	59.672	37.500	0.31	0.00	41.62	1.90
456	517	4.178156	ACGATTTGATTCGACGCAATAC	57.822	40.909	0.31	0.00	41.62	1.89
460	525	3.989705	TTGATTCGACGCAATACACAG	57.010	42.857	0.00	0.00	0.00	3.66
463	528	2.717580	TTCGACGCAATACACAGACT	57.282	45.000	0.00	0.00	0.00	3.24
468	533	1.421410	CGCAATACACAGACTCGCCC	61.421	60.000	0.00	0.00	0.00	6.13
487	552	0.316204	CAGTTGGCCAAAAGGCTCTG	59.684	55.000	22.47	17.86	42.93	3.35
537	602	6.968131	TTTTTCTGGTCGATCTGATGTTAG	57.032	37.500	6.06	0.00	0.00	2.34
548	615	4.119442	TCTGATGTTAGAAACGTAGGGC	57.881	45.455	0.00	0.00	0.00	5.19
613	688	3.119101	CCTATTAAGTGACTGCACCGAGT	60.119	47.826	0.00	0.00	46.32	4.18
618	693	1.016130	GTGACTGCACCGAGTCCATG	61.016	60.000	1.77	0.00	41.59	3.66
651	726	7.123098	TGGTCTCTTACATCGTGGTTATTTCTA	59.877	37.037	0.00	0.00	0.00	2.10
664	739	7.210873	GTGGTTATTTCTAGGGACTGTCTATG	58.789	42.308	7.85	0.00	41.52	2.23
826	906	0.542333	TCGACAACAACCCACTCCAA	59.458	50.000	0.00	0.00	0.00	3.53
1636	1775	7.989741	ACCATGTTTTCACATTGTAAATCCAAA	59.010	29.630	0.00	0.00	41.16	3.28
1646	1785	9.862585	CACATTGTAAATCCAAAAGTAAAAAGC	57.137	29.630	0.00	0.00	0.00	3.51
2095	2246	4.260375	GGTTGCTCATGATTACGCTAACAG	60.260	45.833	0.00	0.00	0.00	3.16
2208	2359	9.836864	AGAACTGATACTCAATGTAATATGCAA	57.163	29.630	0.00	0.00	34.45	4.08

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	2.200373	ATCACCCTCCGGAGTTTTTG	57.800	50.000	29.25	18.99	0.00	2.44
1	2	4.376225	TTTATCACCCTCCGGAGTTTTT	57.624	40.909	29.25	12.68	0.00	1.94
9	10	6.513393	GCACATCTTAATTTTATCACCCTCCG	60.513	42.308	0.00	0.00	0.00	4.63
39	40	4.453819	GCAAACTCACTTGTGCTATCTCTT	59.546	41.667	0.00	0.00	34.13	2.85
65	66	0.249120	TTGGGAGGTACGATGCACTG	59.751	55.000	0.00	0.00	0.00	3.66
66	67	0.981183	TTTGGGAGGTACGATGCACT	59.019	50.000	0.00	0.00	0.00	4.40
74	75	5.646793	GGTTACTTTCAGATTTGGGAGGTAC	59.353	44.000	0.00	0.00	0.00	3.34
80	81	6.238648	AGTAGTGGTTACTTTCAGATTTGGG	58.761	40.000	0.00	0.00	39.64	4.12
83	84	7.387643	GGAGAGTAGTGGTTACTTTCAGATTT	58.612	38.462	7.05	0.00	42.46	2.17
85	86	5.125739	CGGAGAGTAGTGGTTACTTTCAGAT	59.874	44.000	7.05	0.00	42.46	2.90
86	87	4.458295	CGGAGAGTAGTGGTTACTTTCAGA	59.542	45.833	7.05	0.00	42.46	3.27
87	88	4.458295	TCGGAGAGTAGTGGTTACTTTCAG	59.542	45.833	7.05	3.90	42.46	3.02
88	89	4.401022	TCGGAGAGTAGTGGTTACTTTCA	58.599	43.478	7.05	0.00	42.46	2.69
107	109	1.202268	AGTCGCTACTTTCCGATTCGG	60.202	52.381	19.16	19.16	39.94	4.30
122	124	9.704098	CTTCTAAATTATTTGGAAAGTAGTCGC	57.296	33.333	15.35	0.00	39.22	5.19
132	134	9.447157	CAAAAATGCCCTTCTAAATTATTTGGA	57.553	29.630	0.00	0.00	0.00	3.53
151	153	9.494479	CTACATTAGCAGTGACATACAAAAATG	57.506	33.333	0.00	0.00	0.00	2.32
159	161	8.700973	TGGTTAATCTACATTAGCAGTGACATA	58.299	33.333	0.00	0.00	29.42	2.29
160	162	7.564793	TGGTTAATCTACATTAGCAGTGACAT	58.435	34.615	0.00	0.00	29.42	3.06
212	214	2.123251	TGGAGGAGGAGGGCGATC	60.123	66.667	0.00	0.00	0.00	3.69
245	247	1.689273	GTCAAGACTCAGGACCTGTGT	59.311	52.381	25.50	25.50	40.25	3.72
255	257	0.817654	ATCCGCATCGTCAAGACTCA	59.182	50.000	0.00	0.00	0.00	3.41
261	263	1.337728	ACTTGACATCCGCATCGTCAA	60.338	47.619	0.00	0.00	44.95	3.18
268	270	2.151202	GGAAAGAACTTGACATCCGCA	58.849	47.619	0.00	0.00	0.00	5.69
274	276	1.409790	TCCGTCGGAAAGAACTTGACA	59.590	47.619	12.68	0.00	0.00	3.58
288	290	4.662961	TGCCTGTGCAGTCCGTCG	62.663	66.667	0.00	0.00	44.23	5.12
302	304	1.604278	GGAAGCGATTGGTCTTATGCC	59.396	52.381	0.00	0.00	0.00	4.40
303	305	2.288666	TGGAAGCGATTGGTCTTATGC	58.711	47.619	0.00	0.00	0.00	3.14
306	308	2.503765	TGGATGGAAGCGATTGGTCTTA	59.496	45.455	0.00	0.00	0.00	2.10
311	313	1.672881	GAAGTGGATGGAAGCGATTGG	59.327	52.381	0.00	0.00	0.00	3.16
319	326	0.613260	CTCCGTGGAAGTGGATGGAA	59.387	55.000	0.00	0.00	32.83	3.53
323	330	0.179000	GCATCTCCGTGGAAGTGGAT	59.821	55.000	0.00	0.00	32.83	3.41
334	341	0.525668	GGAGTACGTGTGCATCTCCG	60.526	60.000	0.00	0.00	35.94	4.63
335	342	0.179108	GGGAGTACGTGTGCATCTCC	60.179	60.000	0.00	5.83	42.53	3.71
361	422	6.751157	TCTGCAAAAATGCCTTATATGATGG	58.249	36.000	0.00	0.00	0.00	3.51
365	426	7.035840	AGTCTCTGCAAAAATGCCTTATATG	57.964	36.000	0.00	0.00	0.00	1.78
405	466	3.450904	AGCTTGTTACATACTCCCTCCA	58.549	45.455	0.00	0.00	0.00	3.86
406	467	5.128991	AGTTAGCTTGTTACATACTCCCTCC	59.871	44.000	0.00	0.00	0.00	4.30
420	481	6.371809	TCAAATCGTTCAAAGTTAGCTTGT	57.628	33.333	0.00	0.00	34.71	3.16
424	485	6.246540	GTCGAATCAAATCGTTCAAAGTTAGC	59.753	38.462	0.00	0.00	43.19	3.09
435	496	3.615056	TGTATTGCGTCGAATCAAATCGT	59.385	39.130	0.00	0.00	43.19	3.73
437	498	4.892655	TGTGTATTGCGTCGAATCAAATC	58.107	39.130	0.00	3.06	0.00	2.17
448	509	0.736325	GGCGAGTCTGTGTATTGCGT	60.736	55.000	0.00	0.00	0.00	5.24
450	511	0.391130	TGGGCGAGTCTGTGTATTGC	60.391	55.000	0.00	0.00	0.00	3.56
451	512	1.066858	ACTGGGCGAGTCTGTGTATTG	60.067	52.381	0.00	0.00	0.00	1.90
453	514	1.066858	CAACTGGGCGAGTCTGTGTAT	60.067	52.381	1.62	0.00	31.73	2.29
454	515	0.317160	CAACTGGGCGAGTCTGTGTA	59.683	55.000	1.62	0.00	31.73	2.90
455	516	1.069765	CAACTGGGCGAGTCTGTGT	59.930	57.895	1.62	0.00	31.73	3.72
456	517	1.669115	CCAACTGGGCGAGTCTGTG	60.669	63.158	1.62	0.00	31.73	3.66
487	552	3.692791	AAAGTTTCAAAGGCTCGACAC	57.307	42.857	0.00	0.00	0.00	3.67
618	693	2.484889	GATGTAAGAGACCAATCCGGC	58.515	52.381	0.00	0.00	39.03	6.13
624	699	5.670792	ATAACCACGATGTAAGAGACCAA	57.329	39.130	0.00	0.00	0.00	3.67
625	700	5.670792	AATAACCACGATGTAAGAGACCA	57.329	39.130	0.00	0.00	0.00	4.02
626	701	6.338937	AGAAATAACCACGATGTAAGAGACC	58.661	40.000	0.00	0.00	0.00	3.85
664	739	6.756074	TGAAATGGAAAACACTCAAATGTCAC	59.244	34.615	0.00	0.00	30.55	3.67
765	845	2.281208	CCGACCCGTTTTGGCTGA	60.281	61.111	0.00	0.00	35.87	4.26
1223	1339	9.793259	TTCAATGTTAATTTCTAGGAGAACTGT	57.207	29.630	0.00	0.00	33.26	3.55
1383	1522	7.470192	AGAATTTACCAGGGATTTTTCTCTGA	58.530	34.615	4.44	0.00	0.00	3.27
1831	1970	9.983804	GTAATTACATTGGAAACTACTTACAGC	57.016	33.333	10.81	0.00	0.00	4.40
2028	2178	3.930336	TGTGAGATGCAGGTACTTTCAG	58.070	45.455	0.00	0.00	34.60	3.02
2095	2246	9.758651	ACCCATTTTTAAAAAGTAGAATGTCAC	57.241	29.630	17.72	0.00	0.00	3.67

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.