AutoCloner

Multiple sequence alignment - TraesCS7D01G016000

Loading Multiple Alignment...

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	TraesCS7D01G016000	chr7D	100.000	2282	0	0	1	2282	7071379	7073660	0.000000e+00	4215
1	TraesCS7D01G016000	chr7D	86.779	1301	110	29	314	1577	6965967	6967242	0.000000e+00	1393
2	TraesCS7D01G016000	chr7D	79.772	1315	148	58	315	1579	7194739	7193493	0.000000e+00	846
3	TraesCS7D01G016000	chr7D	96.117	206	7	1	1	206	7191278	7191074	3.630000e-88	335
4	TraesCS7D01G016000	chr7D	96.098	205	7	1	1	205	7195319	7195116	1.310000e-87	333
5	TraesCS7D01G016000	chr7D	95.610	205	9	0	1	205	6965277	6965481	1.690000e-86	329
6	TraesCS7D01G016000	chr7D	94.712	208	10	1	1	207	7188297	7188090	2.830000e-84	322
7	TraesCS7D01G016000	chr7A	93.993	1981	95	14	314	2282	7912131	7914099	0.000000e+00	2977
8	TraesCS7D01G016000	chr7A	87.958	1420	122	27	169	1577	7907613	7908994	0.000000e+00	1629
9	TraesCS7D01G016000	chr7A	81.714	875	100	30	316	1160	8121375	8120531	0.000000e+00	675
10	TraesCS7D01G016000	chr7A	78.533	736	120	24	341	1051	7791895	7792617	1.240000e-122	449
11	TraesCS7D01G016000	chr7A	96.569	204	7	0	1	204	8077183	8076980	2.810000e-89	339
12	TraesCS7D01G016000	chr7A	85.017	287	34	7	1366	1644	8078066	8077781	1.330000e-72	283
13	TraesCS7D01G016000	chr7A	85.017	287	34	7	1366	1644	8198332	8198047	1.330000e-72	283
14	TraesCS7D01G016000	chrUn	92.608	1921	98	17	390	2282	51206638	51204734	0.000000e+00	2721
15	TraesCS7D01G016000	chrUn	84.662	991	118	15	601	1576	51220879	51219908	0.000000e+00	957
16	TraesCS7D01G016000	chrUn	81.266	379	52	11	1354	1725	51229852	51230218	2.870000e-74	289
17	TraesCS7D01G016000	chrUn	81.266	379	52	11	1354	1725	289098955	289098589	2.870000e-74	289
18	TraesCS7D01G016000	chrUn	87.179	156	10	9	314	463	477544479	477544328	3.900000e-38	169
19	TraesCS7D01G016000	chrUn	83.784	148	21	2	313	457	34119049	34119196	1.100000e-28	137
20	TraesCS7D01G016000	chr4A	92.423	937	45	8	470	1398	732976638	732977556	0.000000e+00	1314
21	TraesCS7D01G016000	chr4A	84.789	1019	97	24	474	1476	733059513	733058537	0.000000e+00	970
22	TraesCS7D01G016000	chr4A	84.843	1016	96	22	477	1476	733241520	733240547	0.000000e+00	970
23	TraesCS7D01G016000	chr4A	84.691	1019	98	24	474	1476	733119326	733118350	0.000000e+00	965
24	TraesCS7D01G016000	chr4A	94.611	334	18	0	1418	1751	732978251	732978584	3.360000e-143	518
25	TraesCS7D01G016000	chr4A	92.834	307	19	1	1	304	732973059	732973365	2.080000e-120	442
26	TraesCS7D01G016000	chr4A	95.146	206	10	0	1	206	732971047	732971252	2.190000e-85	326
27	TraesCS7D01G016000	chr4A	95.122	205	10	0	1	205	733060384	733060180	7.860000e-85	324
28	TraesCS7D01G016000	chr4A	95.122	205	10	0	1	205	733120198	733119994	7.860000e-85	324
29	TraesCS7D01G016000	chr4A	87.179	156	10	9	314	463	733059704	733059553	3.900000e-38	169
30	TraesCS7D01G016000	chr4A	87.179	156	10	9	314	463	733119517	733119366	3.900000e-38	169
31	TraesCS7D01G016000	chr4A	85.256	156	13	9	314	463	733241714	733241563	3.930000e-33	152
32	TraesCS7D01G016000	chr5B	83.117	154	23	2	313	463	526876017	526875864	1.100000e-28	137
33	TraesCS7D01G016000	chr4B	83.784	148	21	2	313	457	555285031	555285178	1.100000e-28	137

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	TraesCS7D01G016000	chr7D	7071379	7073660	2281	False	4215.000000	4215	100.000000	1	2282	1	chr7D.!!$F1	2281
1	TraesCS7D01G016000	chr7D	6965277	6967242	1965	False	861.000000	1393	91.194500	1	1577	2	chr7D.!!$F2	1576
2	TraesCS7D01G016000	chr7D	7188090	7195319	7229	True	459.000000	846	91.674750	1	1579	4	chr7D.!!$R1	1578
3	TraesCS7D01G016000	chr7A	7907613	7914099	6486	False	2303.000000	2977	90.975500	169	2282	2	chr7A.!!$F2	2113
4	TraesCS7D01G016000	chr7A	8120531	8121375	844	True	675.000000	675	81.714000	316	1160	1	chr7A.!!$R1	844
5	TraesCS7D01G016000	chr7A	7791895	7792617	722	False	449.000000	449	78.533000	341	1051	1	chr7A.!!$F1	710
6	TraesCS7D01G016000	chr7A	8076980	8078066	1086	True	311.000000	339	90.793000	1	1644	2	chr7A.!!$R3	1643
7	TraesCS7D01G016000	chrUn	51204734	51206638	1904	True	2721.000000	2721	92.608000	390	2282	1	chrUn.!!$R1	1892
8	TraesCS7D01G016000	chrUn	51219908	51220879	971	True	957.000000	957	84.662000	601	1576	1	chrUn.!!$R2	975
9	TraesCS7D01G016000	chr4A	732971047	732978584	7537	False	650.000000	1314	93.753500	1	1751	4	chr4A.!!$F1	1750
10	TraesCS7D01G016000	chr4A	733240547	733241714	1167	True	561.000000	970	85.049500	314	1476	2	chr4A.!!$R3	1162
11	TraesCS7D01G016000	chr4A	733058537	733060384	1847	True	487.666667	970	89.030000	1	1476	3	chr4A.!!$R1	1475
12	TraesCS7D01G016000	chr4A	733118350	733120198	1848	True	486.000000	965	88.997333	1	1476	3	chr4A.!!$R2	1475

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
786	7442	0.958382	GCCTGACGGGTGCATACAAA	60.958	55.0	1.33	0.0	37.43	2.83	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2033	14654	1.210478	ACAGCAAGAATCGTATGGCCT	59.79	47.619	3.32	0.0	0.0	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)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
29	913	1.751349	AAGTTGCGTAGTGGACCGGT	61.751	55.000	6.92	6.92	0.00	5.28
59	943	2.347490	GAAAGCTGGGCCTCACGA	59.653	61.111	4.53	0.00	0.00	4.35
255	4935	2.758423	GGTGGTTGTGAGGTTGAGTTTT	59.242	45.455	0.00	0.00	0.00	2.43
285	4968	4.983671	AGTGTTTCCTGTTTCACCTTTC	57.016	40.909	0.00	0.00	0.00	2.62
293	4976	3.243201	CCTGTTTCACCTTTCTGTGCTTC	60.243	47.826	0.00	0.00	36.17	3.86
294	4977	3.620488	TGTTTCACCTTTCTGTGCTTCT	58.380	40.909	0.00	0.00	36.17	2.85
304	4990	5.122082	CCTTTCTGTGCTTCTGATCTTCTTC	59.878	44.000	0.00	0.00	0.00	2.87
307	4993	5.236282	TCTGTGCTTCTGATCTTCTTCTTG	58.764	41.667	0.00	0.00	0.00	3.02
308	4994	4.965814	TGTGCTTCTGATCTTCTTCTTGT	58.034	39.130	0.00	0.00	0.00	3.16
309	4995	5.371526	TGTGCTTCTGATCTTCTTCTTGTT	58.628	37.500	0.00	0.00	0.00	2.83
310	4996	6.524734	TGTGCTTCTGATCTTCTTCTTGTTA	58.475	36.000	0.00	0.00	0.00	2.41
311	4997	6.425114	TGTGCTTCTGATCTTCTTCTTGTTAC	59.575	38.462	0.00	0.00	0.00	2.50
312	4998	6.425114	GTGCTTCTGATCTTCTTCTTGTTACA	59.575	38.462	0.00	0.00	0.00	2.41
351	5535	2.072298	GTTCATCACTCACACTCAGCC	58.928	52.381	0.00	0.00	0.00	4.85
450	7059	2.423185	CGGAAGACAGCCATGCATTAAA	59.577	45.455	0.00	0.00	0.00	1.52
463	7072	7.014038	AGCCATGCATTAAATTTTCACCAAAAA	59.986	29.630	0.00	0.00	40.98	1.94
515	7154	1.903404	GTCAAGGCCAACCACCAGG	60.903	63.158	5.01	0.00	39.06	4.45
524	7163	1.381056	AACCACCAGGCAACAGCAA	60.381	52.632	0.00	0.00	39.06	3.91
527	7166	2.906897	ACCAGGCAACAGCAACCG	60.907	61.111	0.00	0.00	41.41	4.44
641	7284	6.381481	TCAACAATCATAATCACAGATGCC	57.619	37.500	0.00	0.00	0.00	4.40
707	7350	1.339438	TGGCAACCATTCTCTGCTCTC	60.339	52.381	0.00	0.00	36.32	3.20
713	7356	2.093075	ACCATTCTCTGCTCTCCACATG	60.093	50.000	0.00	0.00	0.00	3.21
774	7430	1.632422	GCAAATCATTTGGCCTGACG	58.368	50.000	12.14	0.00	40.94	4.35
785	7441	1.376683	GCCTGACGGGTGCATACAA	60.377	57.895	1.33	0.00	37.43	2.41
786	7442	0.958382	GCCTGACGGGTGCATACAAA	60.958	55.000	1.33	0.00	37.43	2.83
881	7548	3.559171	GCTTCCCATACCAACAGACAGAA	60.559	47.826	0.00	0.00	0.00	3.02
1189	9101	0.108329	ACGTCGTGGGCAGATAAAGG	60.108	55.000	0.00	0.00	0.00	3.11
1237	13178	3.760035	TCGCTTCGGCACTCCTCC	61.760	66.667	0.00	0.00	41.88	4.30
1238	13179	3.764466	CGCTTCGGCACTCCTCCT	61.764	66.667	0.00	0.00	41.88	3.69
1239	13180	2.185608	GCTTCGGCACTCCTCCTC	59.814	66.667	0.00	0.00	41.33	3.71
1249	13190	2.374184	CACTCCTCCTCAGGACTACTG	58.626	57.143	0.00	0.00	44.75	2.74
1273	13214	0.514691	GCAGCTTCCAGTTCTTGACG	59.485	55.000	0.00	0.00	0.00	4.35
1666	14284	1.136891	CCGCATCTGATGGTGTACTCA	59.863	52.381	18.60	0.00	0.00	3.41
1862	14483	3.543680	TGCTATTGTTCCTAGGTCTGC	57.456	47.619	9.08	5.80	0.00	4.26
1906	14527	2.232452	CTGAACCAGAGTGACGGAGAAT	59.768	50.000	0.00	0.00	32.44	2.40
1941	14562	4.992381	AGAAATTCTTCTTTCCGACACG	57.008	40.909	0.00	0.00	38.89	4.49
1962	14583	9.798885	GACACGTAGCATGAATATTTATTCTTC	57.201	33.333	10.72	0.00	41.93	2.87
1964	14585	7.475565	CACGTAGCATGAATATTTATTCTTCGC	59.524	37.037	14.77	5.49	41.93	4.70
1970	14591	8.712363	GCATGAATATTTATTCTTCGCTCAGTA	58.288	33.333	10.72	0.00	41.93	2.74
2017	14638	6.560253	ACGGCCATATTCAGTGATTTATTC	57.440	37.500	2.24	0.00	0.00	1.75
2036	14657	8.825667	TTTATTCAAAGGTTGATTAACAAGGC	57.174	30.769	2.50	0.00	39.84	4.35
2054	14675	2.017049	GGCCATACGATTCTTGCTGTT	58.983	47.619	0.00	0.00	0.00	3.16
2145	14766	7.698130	GGCAAACATGACAAATTCTAGTGATAC	59.302	37.037	0.00	0.00	0.00	2.24

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
29	913	1.752694	GCTTTCGCATAGGCCCCAA	60.753	57.895	0.00	0.00	36.38	4.12
167	1051	3.019003	TTGGAGTAGGCTGCGAGGC	62.019	63.158	0.00	2.19	41.73	4.70
168	1052	1.153549	GTTGGAGTAGGCTGCGAGG	60.154	63.158	0.00	0.00	35.69	4.63
170	1054	1.529152	TTCGTTGGAGTAGGCTGCGA	61.529	55.000	0.00	0.00	35.69	5.10
171	1055	1.080093	TTCGTTGGAGTAGGCTGCG	60.080	57.895	0.00	0.00	35.69	5.18
172	1056	1.019805	GGTTCGTTGGAGTAGGCTGC	61.020	60.000	0.00	0.00	0.00	5.25
255	4935	4.699925	AACAGGAAACACTAACTAGGCA	57.300	40.909	0.00	0.00	0.00	4.75
285	4968	4.996122	ACAAGAAGAAGATCAGAAGCACAG	59.004	41.667	0.00	0.00	0.00	3.66
293	4976	7.736447	AAAGGTGTAACAAGAAGAAGATCAG	57.264	36.000	0.00	0.00	39.98	2.90
294	4977	9.436957	GATAAAGGTGTAACAAGAAGAAGATCA	57.563	33.333	0.00	0.00	39.98	2.92
309	4995	9.952030	TGAACAAGACATTATGATAAAGGTGTA	57.048	29.630	0.00	0.00	0.00	2.90
310	4996	8.862325	TGAACAAGACATTATGATAAAGGTGT	57.138	30.769	0.00	0.00	0.00	4.16
311	4997	9.941664	GATGAACAAGACATTATGATAAAGGTG	57.058	33.333	0.00	0.00	0.00	4.00
312	4998	9.685276	TGATGAACAAGACATTATGATAAAGGT	57.315	29.630	0.00	0.00	0.00	3.50
351	5535	1.565759	TCCATCCCATGAACCAGGAAG	59.434	52.381	0.00	0.00	32.26	3.46
430	7032	4.660789	ATTTAATGCATGGCTGTCTTCC	57.339	40.909	0.00	0.00	0.00	3.46
463	7072	4.887071	TGAACACCTGTGCTCTACAAATTT	59.113	37.500	0.00	0.00	39.20	1.82
464	7073	4.460263	TGAACACCTGTGCTCTACAAATT	58.540	39.130	0.00	0.00	39.20	1.82
467	7076	2.806745	GCTGAACACCTGTGCTCTACAA	60.807	50.000	0.00	0.00	39.20	2.41
472	7111	0.819259	TTGGCTGAACACCTGTGCTC	60.819	55.000	0.00	0.00	0.00	4.26
515	7154	0.799534	GATGATGCGGTTGCTGTTGC	60.800	55.000	0.00	0.00	43.34	4.17
517	7156	0.806868	CTGATGATGCGGTTGCTGTT	59.193	50.000	0.00	0.00	43.34	3.16
518	7157	0.036105	TCTGATGATGCGGTTGCTGT	60.036	50.000	0.00	0.00	43.34	4.40
524	7163	0.176680	GTCCTGTCTGATGATGCGGT	59.823	55.000	0.00	0.00	0.00	5.68
527	7166	2.033049	GCATTGTCCTGTCTGATGATGC	59.967	50.000	0.00	0.00	32.29	3.91
641	7284	7.871973	CCAGAGTATTAATCTGTCCATGAAGAG	59.128	40.741	17.25	0.00	42.18	2.85
774	7430	4.846779	TCTTTGACTTTTGTATGCACCC	57.153	40.909	0.00	0.00	0.00	4.61
785	7441	7.715657	TGTGTTATCTGCAAATCTTTGACTTT	58.284	30.769	6.84	0.00	40.55	2.66
786	7442	7.275888	TGTGTTATCTGCAAATCTTTGACTT	57.724	32.000	6.84	0.00	40.55	3.01
881	7548	5.127356	GCAACCCTGTATGTAGACTCTAGTT	59.873	44.000	0.00	0.00	0.00	2.24
1189	9101	0.458543	ACGATGTGTGCGATCCTCAC	60.459	55.000	5.96	5.96	38.19	3.51
1249	13190	3.016474	GAACTGGAAGCTGCGACGC	62.016	63.158	14.19	14.19	37.60	5.19
1273	13214	7.948278	ACAGAGTTAGTTACATTCACTTGTC	57.052	36.000	0.00	0.00	0.00	3.18
1290	13231	8.157476	AGAACAAATCCTAACATGTACAGAGTT	58.843	33.333	17.35	17.35	0.00	3.01
1666	14284	4.079253	ACATATTTGACTGGTTCGCCTTT	58.921	39.130	0.00	0.00	38.36	3.11
1941	14562	8.712363	TGAGCGAAGAATAAATATTCATGCTAC	58.288	33.333	18.38	14.46	43.43	3.58
1962	14583	2.370281	ACACTGTGGAATACTGAGCG	57.630	50.000	13.09	0.00	33.00	5.03
1964	14585	4.692625	CCAGAAACACTGTGGAATACTGAG	59.307	45.833	13.09	5.29	44.40	3.35
1970	14591	6.783708	TTTAAACCAGAAACACTGTGGAAT	57.216	33.333	13.09	0.00	44.40	3.01
1987	14608	5.945155	TCACTGAATATGGCCGTTTTAAAC	58.055	37.500	0.77	0.00	0.00	2.01
1995	14616	6.558771	TGAATAAATCACTGAATATGGCCG	57.441	37.500	0.00	0.00	31.50	6.13
2017	14638	4.599047	TGGCCTTGTTAATCAACCTTTG	57.401	40.909	3.32	0.00	33.41	2.77
2033	14654	1.210478	ACAGCAAGAATCGTATGGCCT	59.790	47.619	3.32	0.00	0.00	5.19
2036	14657	6.250819	CAACTTAACAGCAAGAATCGTATGG	58.749	40.000	0.00	0.00	0.00	2.74
2054	14675	2.196595	ACCTCATAGCTGGGCAACTTA	58.803	47.619	0.00	0.00	0.00	2.24
2145	14766	6.699642	GTCTAGGATTTTCTAGCTACTTGCAG	59.300	42.308	0.00	0.00	45.94	4.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.