AutoCloner

Multiple sequence alignment - TraesCS2D01G437300

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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	TraesCS2D01G437300	chr2D	100.000	2546	0	0	1	2546	547488261	547490806	0.000000e+00	4702.0
1	TraesCS2D01G437300	chr2D	89.346	1483	118	20	512	1965	547450301	547451772	0.000000e+00	1827.0
2	TraesCS2D01G437300	chr2D	80.756	1720	205	50	612	2254	547286127	547287797	0.000000e+00	1227.0
3	TraesCS2D01G437300	chr2D	81.291	1224	141	39	788	1965	547426969	547428150	0.000000e+00	911.0
4	TraesCS2D01G437300	chr2D	90.227	706	43	12	107	797	547426239	547426933	0.000000e+00	898.0
5	TraesCS2D01G437300	chr2D	82.795	959	110	16	788	1712	547278128	547279065	0.000000e+00	806.0
6	TraesCS2D01G437300	chr2D	86.574	432	25	11	407	810	547547695	547548121	1.800000e-121	446.0
7	TraesCS2D01G437300	chr2D	83.471	484	45	10	1798	2254	547279112	547279587	3.920000e-113	418.0
8	TraesCS2D01G437300	chr2D	89.919	248	23	1	2299	2546	547428189	547428434	4.090000e-83	318.0
9	TraesCS2D01G437300	chr2D	95.935	123	5	0	2424	2546	547451891	547452013	1.540000e-47	200.0
10	TraesCS2D01G437300	chr2D	86.957	138	12	2	512	643	382172111	382171974	1.580000e-32	150.0
11	TraesCS2D01G437300	chr2D	100.000	37	0	0	469	505	382172365	382172329	4.550000e-08	69.4
12	TraesCS2D01G437300	chr2D	100.000	35	0	0	2428	2462	547451861	547451895	5.880000e-07	65.8
13	TraesCS2D01G437300	chr2A	93.028	1090	60	7	910	1992	690805346	690806426	0.000000e+00	1578.0
14	TraesCS2D01G437300	chr2A	82.379	1135	148	27	797	1894	690747279	690748398	0.000000e+00	941.0
15	TraesCS2D01G437300	chr2A	85.379	896	102	19	803	1688	691392185	691391309	0.000000e+00	902.0
16	TraesCS2D01G437300	chr2A	92.982	570	22	3	1977	2546	690807212	690807763	0.000000e+00	815.0
17	TraesCS2D01G437300	chr2A	93.064	346	23	1	1	345	691392532	691392187	2.920000e-139	505.0
18	TraesCS2D01G437300	chr2A	84.513	452	38	18	512	946	690804779	690805215	3.920000e-113	418.0
19	TraesCS2D01G437300	chr2A	89.420	293	28	2	2255	2546	690748510	690748800	1.440000e-97	366.0
20	TraesCS2D01G437300	chr2A	82.222	360	36	14	512	859	690794849	690795192	4.150000e-73	285.0
21	TraesCS2D01G437300	chr2A	78.417	278	48	8	222	488	690796706	690796982	1.210000e-38	171.0
22	TraesCS2D01G437300	chr2B	95.039	907	34	4	786	1690	653796071	653796968	0.000000e+00	1415.0
23	TraesCS2D01G437300	chr2B	82.969	1462	162	37	853	2254	653788261	653789695	0.000000e+00	1240.0
24	TraesCS2D01G437300	chr2B	86.667	795	86	9	907	1688	653808259	653809046	0.000000e+00	863.0
25	TraesCS2D01G437300	chr2B	81.173	1142	119	28	1447	2546	653772859	653773946	0.000000e+00	830.0
26	TraesCS2D01G437300	chr2B	87.050	139	10	2	512	642	780869907	780870045	1.580000e-32	150.0
27	TraesCS2D01G437300	chr2B	86.719	128	9	2	512	632	653795863	653795989	4.420000e-28	135.0
28	TraesCS2D01G437300	chr5D	83.571	140	14	3	512	642	538668945	538669084	3.440000e-24	122.0
29	TraesCS2D01G437300	chr5D	83.212	137	18	3	512	647	539035881	539036013	1.240000e-23	121.0
30	TraesCS2D01G437300	chr5D	100.000	30	0	0	469	498	519335811	519335782	3.540000e-04	56.5
31	TraesCS2D01G437300	chr5A	82.143	140	22	2	512	648	470079758	470079897	1.600000e-22	117.0
32	TraesCS2D01G437300	chr6A	93.478	46	1	2	472	516	764239	764195	1.630000e-07	67.6
33	TraesCS2D01G437300	chr7D	88.679	53	5	1	467	518	165862265	165862317	2.110000e-06	63.9
34	TraesCS2D01G437300	chr7B	88.679	53	5	1	467	518	129928976	129929028	2.110000e-06	63.9
35	TraesCS2D01G437300	chr5B	91.304	46	4	0	471	516	445553328	445553283	2.110000e-06	63.9
36	TraesCS2D01G437300	chr5B	100.000	29	0	0	474	502	680321161	680321133	1.000000e-03	54.7

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	TraesCS2D01G437300	chr2D	547488261	547490806	2545	False	4702.0	4702	100.000000	1	2546	1	chr2D.!!$F2	2545
1	TraesCS2D01G437300	chr2D	547286127	547287797	1670	False	1227.0	1227	80.756000	612	2254	1	chr2D.!!$F1	1642
2	TraesCS2D01G437300	chr2D	547426239	547428434	2195	False	709.0	911	87.145667	107	2546	3	chr2D.!!$F5	2439
3	TraesCS2D01G437300	chr2D	547450301	547452013	1712	False	697.6	1827	95.093667	512	2546	3	chr2D.!!$F6	2034
4	TraesCS2D01G437300	chr2D	547278128	547279587	1459	False	612.0	806	83.133000	788	2254	2	chr2D.!!$F4	1466
5	TraesCS2D01G437300	chr2A	690804779	690807763	2984	False	937.0	1578	90.174333	512	2546	3	chr2A.!!$F3	2034
6	TraesCS2D01G437300	chr2A	691391309	691392532	1223	True	703.5	902	89.221500	1	1688	2	chr2A.!!$R1	1687
7	TraesCS2D01G437300	chr2A	690747279	690748800	1521	False	653.5	941	85.899500	797	2546	2	chr2A.!!$F1	1749
8	TraesCS2D01G437300	chr2A	690794849	690796982	2133	False	228.0	285	80.319500	222	859	2	chr2A.!!$F2	637
9	TraesCS2D01G437300	chr2B	653788261	653789695	1434	False	1240.0	1240	82.969000	853	2254	1	chr2B.!!$F2	1401
10	TraesCS2D01G437300	chr2B	653808259	653809046	787	False	863.0	863	86.667000	907	1688	1	chr2B.!!$F3	781
11	TraesCS2D01G437300	chr2B	653772859	653773946	1087	False	830.0	830	81.173000	1447	2546	1	chr2B.!!$F1	1099
12	TraesCS2D01G437300	chr2B	653795863	653796968	1105	False	775.0	1415	90.879000	512	1690	2	chr2B.!!$F5	1178

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
241	242	1.006832	GCAGTAGCACCCGTTGTATG	58.993	55.0	0.0	0.0	41.58	2.39	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2185	4426	0.44231	TGCGTCTTTATTGCGAGTGC	59.558	50.0	0.0	0.0	43.2	4.4	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
176	177	1.065854	GGTGATTGAGTGGGTCTCTGG	60.066	57.143	0.00	0.00	43.13	3.86
225	226	3.921119	TTATTTCCAGTTGTGCAGCAG	57.079	42.857	0.00	0.00	0.00	4.24
241	242	1.006832	GCAGTAGCACCCGTTGTATG	58.993	55.000	0.00	0.00	41.58	2.39
328	329	2.109799	CGTAGCAGGCCCCATGAG	59.890	66.667	0.00	0.00	0.00	2.90
397	399	5.502153	TTTAGGCGTGTTTGTGTTAATGT	57.498	34.783	0.00	0.00	0.00	2.71
402	404	3.489398	GCGTGTTTGTGTTAATGTCCCAA	60.489	43.478	0.00	0.00	0.00	4.12
444	446	8.905103	ACGGCATTTGAACTTATTGTATAAAC	57.095	30.769	0.00	0.00	0.00	2.01
446	448	7.305190	CGGCATTTGAACTTATTGTATAAACGC	60.305	37.037	0.00	0.00	0.00	4.84
503	518	2.107953	GCCGAGCTCCATGGAGAC	59.892	66.667	40.29	30.08	44.53	3.36
508	523	1.339610	CGAGCTCCATGGAGACCTTAG	59.660	57.143	40.29	22.55	44.53	2.18
633	659	1.067821	TGAAGCGCGGTTTCCAAAATT	59.932	42.857	25.80	0.00	0.00	1.82
656	682	3.003689	CCCTACTCGGCAAAAGCATATTG	59.996	47.826	0.00	0.00	0.00	1.90
766	835	5.782845	AGAAGGTCTGATAAGAAGTGTCCTT	59.217	40.000	0.00	0.00	35.81	3.36
993	2132	3.005050	CACCAAATCAACTGAGCACACAT	59.995	43.478	0.00	0.00	0.00	3.21
1556	2910	1.594034	GCCATACTGAGTACGTCGACG	60.594	57.143	34.58	34.58	46.33	5.12
1663	3041	6.544564	TCAAGTAATGGGAAATTCGGATTACC	59.455	38.462	15.95	3.65	32.29	2.85
1705	3086	6.982852	TGTTACTTTGGTTTTGTTCAGTTCA	58.017	32.000	0.00	0.00	0.00	3.18
1713	3094	3.547054	TTTGTTCAGTTCACCCGTACT	57.453	42.857	0.00	0.00	0.00	2.73
1723	3104	1.344114	TCACCCGTACTGTAAACCACC	59.656	52.381	0.00	0.00	0.00	4.61
1731	3112	4.081531	CGTACTGTAAACCACCTTATCCCA	60.082	45.833	0.00	0.00	0.00	4.37
2179	4420	3.712091	ATGCGGTGTAGTAGAGTTAGC	57.288	47.619	0.00	0.00	0.00	3.09
2180	4421	2.439409	TGCGGTGTAGTAGAGTTAGCA	58.561	47.619	0.00	0.00	0.00	3.49
2181	4422	2.163010	TGCGGTGTAGTAGAGTTAGCAC	59.837	50.000	0.00	0.00	0.00	4.40
2182	4423	2.422832	GCGGTGTAGTAGAGTTAGCACT	59.577	50.000	0.00	0.00	35.17	4.40
2183	4424	3.119566	GCGGTGTAGTAGAGTTAGCACTT	60.120	47.826	0.00	0.00	31.22	3.16
2184	4425	4.095483	GCGGTGTAGTAGAGTTAGCACTTA	59.905	45.833	0.00	0.00	31.22	2.24
2185	4426	5.730010	GCGGTGTAGTAGAGTTAGCACTTAG	60.730	48.000	0.00	0.00	31.22	2.18
2205	4446	1.786928	GCACTCGCAATAAAGACGCAC	60.787	52.381	0.00	0.00	38.36	5.34
2237	4478	4.332543	TCGAAATGAAATGATCCCGTTCTG	59.667	41.667	0.00	0.00	0.00	3.02
2238	4479	4.094887	CGAAATGAAATGATCCCGTTCTGT	59.905	41.667	0.00	0.00	0.00	3.41
2255	4496	4.831674	TCTGTCATGGACATCAGAACAT	57.168	40.909	0.00	0.00	41.94	2.71
2273	4514	0.177141	ATCCCGTTGTACCATGGACG	59.823	55.000	21.47	17.58	35.44	4.79
2313	4554	8.737175	CCTTCTCTTTCTCATGAAAATCATCAA	58.263	33.333	0.00	0.00	41.09	2.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
19	20	3.324713	CCTCCAGTTAGGCCCCAG	58.675	66.667	0.00	0.00	37.29	4.45
28	29	1.536662	AGTTCGAGGGCCTCCAGTT	60.537	57.895	27.36	8.62	34.83	3.16
30	31	2.581354	CAGTTCGAGGGCCTCCAG	59.419	66.667	27.36	14.74	34.83	3.86
52	53	4.497473	TGGCATGACTTTTAAAGGAACG	57.503	40.909	9.64	0.00	0.00	3.95
94	95	4.378459	CGCAAACACCAATTAGAAGAGGTC	60.378	45.833	0.00	0.00	30.44	3.85
105	106	0.239879	CTAACGCCGCAAACACCAAT	59.760	50.000	0.00	0.00	0.00	3.16
225	226	1.066716	TGTCCATACAACGGGTGCTAC	60.067	52.381	0.00	0.00	30.91	3.58
241	242	0.302890	CAATCGCAATCTCGCTGTCC	59.697	55.000	0.00	0.00	0.00	4.02
253	254	0.461870	ATAACGCTCAGGCAATCGCA	60.462	50.000	0.00	0.00	41.24	5.10
310	311	3.466791	CTCATGGGGCCTGCTACGG	62.467	68.421	0.84	0.00	0.00	4.02
313	314	0.621571	AAGTCTCATGGGGCCTGCTA	60.622	55.000	0.84	0.00	0.00	3.49
376	378	4.023878	GGACATTAACACAAACACGCCTAA	60.024	41.667	0.00	0.00	0.00	2.69
393	395	7.494922	AAATAAAATAGCCTGTTGGGACATT	57.505	32.000	0.00	0.00	39.30	2.71
397	399	6.095720	CCGTAAAATAAAATAGCCTGTTGGGA	59.904	38.462	0.00	0.00	37.23	4.37
402	404	6.709018	ATGCCGTAAAATAAAATAGCCTGT	57.291	33.333	0.00	0.00	0.00	4.00
441	443	4.377021	TCGCCTCATTTATAGATGCGTTT	58.623	39.130	11.38	0.00	45.85	3.60
444	446	4.667668	GCTTTCGCCTCATTTATAGATGCG	60.668	45.833	6.53	6.53	46.65	4.73
503	518	5.518487	ACGTGTGCAAAATTTCAAACTAAGG	59.482	36.000	0.00	0.00	0.00	2.69
508	523	5.061064	TGTGTACGTGTGCAAAATTTCAAAC	59.939	36.000	0.00	0.00	0.00	2.93
633	659	0.618458	ATGCTTTTGCCGAGTAGGGA	59.382	50.000	0.00	0.00	46.87	4.20
724	778	5.648960	ACCTTCTTCCTTTCGTACACAAAAA	59.351	36.000	0.00	0.00	0.00	1.94
725	779	5.187687	ACCTTCTTCCTTTCGTACACAAAA	58.812	37.500	0.00	0.00	0.00	2.44
781	850	3.889520	ACATACGACTTCCTTCTTCCC	57.110	47.619	0.00	0.00	0.00	3.97
784	853	5.109903	GCATGTACATACGACTTCCTTCTT	58.890	41.667	8.32	0.00	0.00	2.52
993	2132	2.749682	ACCTGCTGCATCGGTGAA	59.250	55.556	12.25	0.00	0.00	3.18
1556	2910	1.402968	TGACGTAGCTTCCGTATGGAC	59.597	52.381	2.15	0.00	46.45	4.02
1559	2913	1.674441	TCCTGACGTAGCTTCCGTATG	59.326	52.381	10.62	7.08	38.92	2.39
1663	3041	1.069823	ACAGACAGCTTCAGTCACAGG	59.930	52.381	5.57	0.00	38.46	4.00
1705	3086	1.720781	AGGTGGTTTACAGTACGGGT	58.279	50.000	0.00	0.00	0.00	5.28
1713	3094	6.904654	AGTATAGTGGGATAAGGTGGTTTACA	59.095	38.462	0.00	0.00	0.00	2.41
1723	3104	9.507329	AATAACATTGCAGTATAGTGGGATAAG	57.493	33.333	9.60	0.00	0.00	1.73
1731	3112	7.442364	CAGCTACCAATAACATTGCAGTATAGT	59.558	37.037	0.00	0.00	0.00	2.12
1884	3286	4.101741	ACACAAATCAGGATAGAGTAGGGC	59.898	45.833	0.00	0.00	0.00	5.19
1969	3404	9.385902	CCTTGATGCAATTACTATTTGAATACG	57.614	33.333	0.00	0.00	0.00	3.06
1982	4218	8.107095	ACCTTTTAGTACTCCTTGATGCAATTA	58.893	33.333	0.00	0.00	0.00	1.40
1986	4222	5.012664	TCACCTTTTAGTACTCCTTGATGCA	59.987	40.000	0.00	0.00	0.00	3.96
2058	4295	6.095160	TCTCTCGAGGTTGTTAGTTTCTATCC	59.905	42.308	13.56	0.00	0.00	2.59
2092	4329	5.867330	TGTTAGATTTGGTTTTCCCTCGTA	58.133	37.500	0.00	0.00	39.73	3.43
2179	4420	4.490959	CGTCTTTATTGCGAGTGCTAAGTG	60.491	45.833	0.00	0.00	43.34	3.16
2180	4421	3.612860	CGTCTTTATTGCGAGTGCTAAGT	59.387	43.478	0.00	0.00	43.34	2.24
2181	4422	3.542291	GCGTCTTTATTGCGAGTGCTAAG	60.542	47.826	0.00	0.00	43.34	2.18
2182	4423	2.347452	GCGTCTTTATTGCGAGTGCTAA	59.653	45.455	0.00	0.00	43.34	3.09
2183	4424	1.924524	GCGTCTTTATTGCGAGTGCTA	59.075	47.619	0.00	0.00	43.34	3.49
2184	4425	0.721718	GCGTCTTTATTGCGAGTGCT	59.278	50.000	0.00	0.00	43.34	4.40
2185	4426	0.442310	TGCGTCTTTATTGCGAGTGC	59.558	50.000	0.00	0.00	43.20	4.40
2237	4478	3.209410	GGGATGTTCTGATGTCCATGAC	58.791	50.000	0.00	0.00	32.31	3.06
2238	4479	2.158914	CGGGATGTTCTGATGTCCATGA	60.159	50.000	0.00	0.00	32.31	3.07
2273	4514	4.828072	AGAGAAGGGTCATGGTTCTAAC	57.172	45.455	0.00	0.00	30.55	2.34
2353	4595	9.559958	CTACTGCTTATTGTCTTTTGTTATTGG	57.440	33.333	0.00	0.00	0.00	3.16

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.