AutoCloner

Multiple sequence alignment - TraesCS2D01G407300

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	TraesCS2D01G407300	chr2D	100.000	3401	0	0	1	3401	522688366	522691766	0.000000e+00	6281.0
1	TraesCS2D01G407300	chr2D	91.923	1461	114	2	990	2448	522749232	522750690	0.000000e+00	2041.0
2	TraesCS2D01G407300	chr2D	90.066	1520	141	8	906	2420	577609484	577607970	0.000000e+00	1962.0
3	TraesCS2D01G407300	chr2D	78.673	1402	266	22	1023	2403	522629719	522631108	0.000000e+00	902.0
4	TraesCS2D01G407300	chr2D	80.556	612	102	11	25	630	115150722	115150122	4.000000e-124	455.0
5	TraesCS2D01G407300	chr2D	87.560	209	10	4	2450	2656	522726235	522726429	9.490000e-56	228.0
6	TraesCS2D01G407300	chr2B	95.199	1708	72	4	742	2449	615735773	615737470	0.000000e+00	2691.0
7	TraesCS2D01G407300	chr2B	92.181	1458	114	0	991	2448	615788433	615789890	0.000000e+00	2061.0
8	TraesCS2D01G407300	chr2B	90.664	1521	133	7	906	2420	694943983	694945500	0.000000e+00	2013.0
9	TraesCS2D01G407300	chr2B	81.641	1389	235	14	1024	2402	615797455	615798833	0.000000e+00	1134.0
10	TraesCS2D01G407300	chr2B	82.166	757	103	23	2656	3401	585941907	585941172	3.730000e-174	621.0
11	TraesCS2D01G407300	chr2B	81.046	612	100	11	25	630	165779544	165778943	1.100000e-129	473.0
12	TraesCS2D01G407300	chr2B	80.229	612	103	12	25	630	165929224	165928625	8.660000e-121	444.0
13	TraesCS2D01G407300	chr2B	85.714	343	40	7	31	371	615734943	615735278	1.500000e-93	353.0
14	TraesCS2D01G407300	chr2B	83.624	287	44	2	339	624	99495278	99495562	2.010000e-67	267.0
15	TraesCS2D01G407300	chr2B	88.325	197	12	2	2453	2649	743320707	743320522	3.410000e-55	226.0
16	TraesCS2D01G407300	chr2B	87.019	208	15	2	2450	2657	615783954	615784149	1.230000e-54	224.0
17	TraesCS2D01G407300	chr2A	93.533	1732	96	5	930	2656	667959380	667961100	0.000000e+00	2564.0
18	TraesCS2D01G407300	chr2A	90.714	1443	133	1	979	2420	715806770	715808212	0.000000e+00	1921.0
19	TraesCS2D01G407300	chr2A	81.052	1388	237	20	1028	2402	667964302	667965676	0.000000e+00	1083.0
20	TraesCS2D01G407300	chr2A	78.914	1399	270	19	1022	2403	667942226	667943616	0.000000e+00	926.0
21	TraesCS2D01G407300	chr2A	86.424	604	47	15	22	625	667950344	667950912	2.230000e-176	628.0
22	TraesCS2D01G407300	chr2A	79.772	613	104	13	25	628	116832356	116831755	8.720000e-116	427.0
23	TraesCS2D01G407300	chr2A	78.583	593	107	11	25	608	116699488	116698907	1.150000e-99	374.0
24	TraesCS2D01G407300	chr3D	91.779	742	54	6	2656	3395	17881779	17882515	0.000000e+00	1026.0
25	TraesCS2D01G407300	chr3D	90.476	63	5	1	2656	2718	580334795	580334856	7.820000e-12	82.4
26	TraesCS2D01G407300	chr3D	90.741	54	4	1	2656	2709	600164675	600164623	1.690000e-08	71.3
27	TraesCS2D01G407300	chr7A	88.874	746	68	9	2656	3397	442278639	442277905	0.000000e+00	904.0
28	TraesCS2D01G407300	chr7A	89.348	460	49	0	2942	3401	634911865	634912324	2.280000e-161	579.0
29	TraesCS2D01G407300	chr7A	79.479	614	109	10	25	634	30157977	30157377	1.460000e-113	420.0
30	TraesCS2D01G407300	chr7A	77.905	611	112	17	25	628	421486691	421487285	3.230000e-95	359.0
31	TraesCS2D01G407300	chr7A	93.846	65	2	1	23	87	363982479	363982541	2.790000e-16	97.1
32	TraesCS2D01G407300	chr3A	87.567	748	81	6	2655	3397	639330525	639331265	0.000000e+00	856.0
33	TraesCS2D01G407300	chr3A	78.105	612	104	24	22	625	736102150	736102739	8.970000e-96	361.0
34	TraesCS2D01G407300	chr3A	77.381	420	74	14	25	442	492185558	492185158	2.640000e-56	230.0
35	TraesCS2D01G407300	chr7D	86.667	750	80	14	2656	3395	576064848	576064109	0.000000e+00	813.0
36	TraesCS2D01G407300	chr7D	92.593	54	2	2	2656	2709	176172894	176172945	3.640000e-10	76.8
37	TraesCS2D01G407300	chr6A	85.901	766	90	13	2641	3401	34679718	34680470	0.000000e+00	800.0
38	TraesCS2D01G407300	chr6A	78.818	609	114	10	24	628	73294518	73295115	2.460000e-106	396.0
39	TraesCS2D01G407300	chr1D	84.176	752	106	12	2656	3401	276728820	276729564	0.000000e+00	717.0
40	TraesCS2D01G407300	chr4D	81.389	763	120	16	2656	3401	339322867	339323624	1.350000e-168	603.0
41	TraesCS2D01G407300	chr4D	81.538	325	47	10	311	629	50807587	50807270	4.360000e-64	255.0
42	TraesCS2D01G407300	chr6D	78.748	607	109	17	24	624	57993412	57994004	4.120000e-104	388.0
43	TraesCS2D01G407300	chr6B	77.629	599	110	14	42	630	458572362	458571778	3.250000e-90	342.0
44	TraesCS2D01G407300	chr4A	79.392	296	51	8	22	315	188613554	188613267	2.070000e-47	200.0
45	TraesCS2D01G407300	chr3B	74.092	606	96	35	22	624	10723299	10723846	3.460000e-45	193.0
46	TraesCS2D01G407300	chr5A	88.148	135	12	4	2517	2649	550719872	550720004	1.260000e-34	158.0
47	TraesCS2D01G407300	chr5B	87.313	134	14	3	2517	2649	530263131	530263262	2.110000e-32	150.0
48	TraesCS2D01G407300	chr1B	89.706	68	5	2	2654	2721	554510453	554510518	6.050000e-13	86.1

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	TraesCS2D01G407300	chr2D	522688366	522691766	3400	False	6281.0	6281	100.0000	1	3401	1	chr2D.!!$F2	3400
1	TraesCS2D01G407300	chr2D	522749232	522750690	1458	False	2041.0	2041	91.9230	990	2448	1	chr2D.!!$F4	1458
2	TraesCS2D01G407300	chr2D	577607970	577609484	1514	True	1962.0	1962	90.0660	906	2420	1	chr2D.!!$R2	1514
3	TraesCS2D01G407300	chr2D	522629719	522631108	1389	False	902.0	902	78.6730	1023	2403	1	chr2D.!!$F1	1380
4	TraesCS2D01G407300	chr2D	115150122	115150722	600	True	455.0	455	80.5560	25	630	1	chr2D.!!$R1	605
5	TraesCS2D01G407300	chr2B	615788433	615789890	1457	False	2061.0	2061	92.1810	991	2448	1	chr2B.!!$F3	1457
6	TraesCS2D01G407300	chr2B	694943983	694945500	1517	False	2013.0	2013	90.6640	906	2420	1	chr2B.!!$F5	1514
7	TraesCS2D01G407300	chr2B	615734943	615737470	2527	False	1522.0	2691	90.4565	31	2449	2	chr2B.!!$F6	2418
8	TraesCS2D01G407300	chr2B	615797455	615798833	1378	False	1134.0	1134	81.6410	1024	2402	1	chr2B.!!$F4	1378
9	TraesCS2D01G407300	chr2B	585941172	585941907	735	True	621.0	621	82.1660	2656	3401	1	chr2B.!!$R3	745
10	TraesCS2D01G407300	chr2B	165778943	165779544	601	True	473.0	473	81.0460	25	630	1	chr2B.!!$R1	605
11	TraesCS2D01G407300	chr2B	165928625	165929224	599	True	444.0	444	80.2290	25	630	1	chr2B.!!$R2	605
12	TraesCS2D01G407300	chr2A	715806770	715808212	1442	False	1921.0	1921	90.7140	979	2420	1	chr2A.!!$F3	1441
13	TraesCS2D01G407300	chr2A	667959380	667965676	6296	False	1823.5	2564	87.2925	930	2656	2	chr2A.!!$F4	1726
14	TraesCS2D01G407300	chr2A	667942226	667943616	1390	False	926.0	926	78.9140	1022	2403	1	chr2A.!!$F1	1381
15	TraesCS2D01G407300	chr2A	667950344	667950912	568	False	628.0	628	86.4240	22	625	1	chr2A.!!$F2	603
16	TraesCS2D01G407300	chr2A	116831755	116832356	601	True	427.0	427	79.7720	25	628	1	chr2A.!!$R2	603
17	TraesCS2D01G407300	chr2A	116698907	116699488	581	True	374.0	374	78.5830	25	608	1	chr2A.!!$R1	583
18	TraesCS2D01G407300	chr3D	17881779	17882515	736	False	1026.0	1026	91.7790	2656	3395	1	chr3D.!!$F1	739
19	TraesCS2D01G407300	chr7A	442277905	442278639	734	True	904.0	904	88.8740	2656	3397	1	chr7A.!!$R2	741
20	TraesCS2D01G407300	chr7A	30157377	30157977	600	True	420.0	420	79.4790	25	634	1	chr7A.!!$R1	609
21	TraesCS2D01G407300	chr7A	421486691	421487285	594	False	359.0	359	77.9050	25	628	1	chr7A.!!$F2	603
22	TraesCS2D01G407300	chr3A	639330525	639331265	740	False	856.0	856	87.5670	2655	3397	1	chr3A.!!$F1	742
23	TraesCS2D01G407300	chr3A	736102150	736102739	589	False	361.0	361	78.1050	22	625	1	chr3A.!!$F2	603
24	TraesCS2D01G407300	chr7D	576064109	576064848	739	True	813.0	813	86.6670	2656	3395	1	chr7D.!!$R1	739
25	TraesCS2D01G407300	chr6A	34679718	34680470	752	False	800.0	800	85.9010	2641	3401	1	chr6A.!!$F1	760
26	TraesCS2D01G407300	chr6A	73294518	73295115	597	False	396.0	396	78.8180	24	628	1	chr6A.!!$F2	604
27	TraesCS2D01G407300	chr1D	276728820	276729564	744	False	717.0	717	84.1760	2656	3401	1	chr1D.!!$F1	745
28	TraesCS2D01G407300	chr4D	339322867	339323624	757	False	603.0	603	81.3890	2656	3401	1	chr4D.!!$F1	745
29	TraesCS2D01G407300	chr6D	57993412	57994004	592	False	388.0	388	78.7480	24	624	1	chr6D.!!$F1	600
30	TraesCS2D01G407300	chr6B	458571778	458572362	584	True	342.0	342	77.6290	42	630	1	chr6B.!!$R1	588

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
915	1105	0.037303	CTCCTTTGCTGGCTTCTGGA	59.963	55.0	0.0	0.0	0.0	3.86	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2536	2749	0.109412	GCTTCACATCAGCAACTGCC	60.109	55.0	0.0	0.0	43.38	4.85	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
17	18	3.880846	GCTTGGCTGGATTCCGCG	61.881	66.667	0.00	0.00	0.00	6.46
18	19	2.436646	CTTGGCTGGATTCCGCGT	60.437	61.111	4.92	0.00	0.00	6.01
19	20	2.435938	TTGGCTGGATTCCGCGTC	60.436	61.111	4.92	0.00	0.00	5.19
20	21	3.247056	TTGGCTGGATTCCGCGTCA	62.247	57.895	4.92	4.66	0.00	4.35
146	148	2.514803	GAATGCCTGTAAGTGGTGGTT	58.485	47.619	0.00	0.00	0.00	3.67
147	149	1.909700	ATGCCTGTAAGTGGTGGTTG	58.090	50.000	0.00	0.00	0.00	3.77
148	150	0.179004	TGCCTGTAAGTGGTGGTTGG	60.179	55.000	0.00	0.00	0.00	3.77
149	151	0.179001	GCCTGTAAGTGGTGGTTGGT	60.179	55.000	0.00	0.00	0.00	3.67
150	152	1.604604	CCTGTAAGTGGTGGTTGGTG	58.395	55.000	0.00	0.00	0.00	4.17
151	153	1.604604	CTGTAAGTGGTGGTTGGTGG	58.395	55.000	0.00	0.00	0.00	4.61
152	154	0.920438	TGTAAGTGGTGGTTGGTGGT	59.080	50.000	0.00	0.00	0.00	4.16
183	185	0.249489	CCTTCCGTCACGATGATCCC	60.249	60.000	0.00	0.00	0.00	3.85
593	735	4.335594	CGAAACATGATCTCCCCCTTTAAC	59.664	45.833	0.00	0.00	0.00	2.01
609	752	7.088272	CCCCTTTAACGAGATTTGGTTTTTAG	58.912	38.462	0.00	0.00	0.00	1.85
616	759	5.773176	ACGAGATTTGGTTTTTAGTGGGAAT	59.227	36.000	0.00	0.00	0.00	3.01
631	774	9.581289	TTTAGTGGGAATGAGAAAAATCAGTAA	57.419	29.630	0.00	0.00	31.44	2.24
632	775	7.693969	AGTGGGAATGAGAAAAATCAGTAAG	57.306	36.000	0.00	0.00	31.44	2.34
635	778	7.607991	GTGGGAATGAGAAAAATCAGTAAGAGA	59.392	37.037	0.00	0.00	31.44	3.10
636	779	8.331740	TGGGAATGAGAAAAATCAGTAAGAGAT	58.668	33.333	0.00	0.00	31.44	2.75
637	780	8.835439	GGGAATGAGAAAAATCAGTAAGAGATC	58.165	37.037	0.00	0.00	31.44	2.75
643	833	9.308318	GAGAAAAATCAGTAAGAGATCTGGTAC	57.692	37.037	0.00	1.90	33.13	3.34
644	834	8.261522	AGAAAAATCAGTAAGAGATCTGGTACC	58.738	37.037	4.43	4.43	33.13	3.34
648	838	3.068873	CAGTAAGAGATCTGGTACCAGGC	59.931	52.174	35.94	27.94	43.75	4.85
661	851	1.446016	ACCAGGCTACCAACTTTCCT	58.554	50.000	0.00	0.00	0.00	3.36
666	856	4.263331	CCAGGCTACCAACTTTCCTTTCTA	60.263	45.833	0.00	0.00	0.00	2.10

Showing 1 to 25 of 103 entries

Previous1 2 3 4 5Next

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	3.880846	CGCGGAATCCAGCCAAGC	61.881	66.667	0.00	0.00	0.00	4.01
1	2	2.436646	ACGCGGAATCCAGCCAAG	60.437	61.111	12.47	0.00	0.00	3.61
2	3	2.435938	GACGCGGAATCCAGCCAA	60.436	61.111	12.47	0.00	0.00	4.52
3	4	2.923426	GATGACGCGGAATCCAGCCA	62.923	60.000	12.47	0.00	0.00	4.75
4	5	2.203070	ATGACGCGGAATCCAGCC	60.203	61.111	12.47	0.00	0.00	4.85
5	6	2.247437	GGATGACGCGGAATCCAGC	61.247	63.158	27.79	13.59	41.78	4.85
6	7	0.179073	AAGGATGACGCGGAATCCAG	60.179	55.000	31.59	0.00	44.17	3.86
8	9	1.865340	GTTAAGGATGACGCGGAATCC	59.135	52.381	26.32	26.32	42.39	3.01
9	10	1.521423	CGTTAAGGATGACGCGGAATC	59.479	52.381	12.47	12.92	31.57	2.52
10	11	1.135527	TCGTTAAGGATGACGCGGAAT	59.864	47.619	12.47	2.60	38.33	3.01
11	12	0.527113	TCGTTAAGGATGACGCGGAA	59.473	50.000	12.47	0.00	38.33	4.30
13	14	1.352114	TTTCGTTAAGGATGACGCGG	58.648	50.000	12.47	0.00	38.33	6.46
14	15	3.306166	AGAATTTCGTTAAGGATGACGCG	59.694	43.478	3.53	3.53	38.33	6.01
15	16	4.859629	AGAATTTCGTTAAGGATGACGC	57.140	40.909	0.00	0.00	38.33	5.19
16	17	6.128661	TGTCAAGAATTTCGTTAAGGATGACG	60.129	38.462	16.45	0.71	39.67	4.35
17	18	7.129109	TGTCAAGAATTTCGTTAAGGATGAC	57.871	36.000	15.43	15.43	35.30	3.06
18	19	7.921786	ATGTCAAGAATTTCGTTAAGGATGA	57.078	32.000	0.00	0.00	0.00	2.92
19	20	8.970691	AAATGTCAAGAATTTCGTTAAGGATG	57.029	30.769	0.00	0.00	0.00	3.51
151	153	2.126031	GAAGGCTGGTCGTCGGAC	60.126	66.667	0.00	0.00	42.66	4.79
152	154	3.379445	GGAAGGCTGGTCGTCGGA	61.379	66.667	0.00	0.00	0.00	4.55
288	292	7.500720	TTTCTTATGGACATATGCATCTGTG	57.499	36.000	21.12	12.72	38.04	3.66
564	701	2.352960	GGGAGATCATGTTTCGTGCTTC	59.647	50.000	0.00	0.00	0.00	3.86
571	709	4.335594	CGTTAAAGGGGGAGATCATGTTTC	59.664	45.833	0.00	0.00	0.00	2.78
577	715	3.110293	TCTCGTTAAAGGGGGAGATCA	57.890	47.619	0.00	0.00	31.00	2.92
593	735	5.699097	TTCCCACTAAAAACCAAATCTCG	57.301	39.130	0.00	0.00	0.00	4.04

Showing 1 to 25 of 101 entries

Previous1 2 3 4 5Next

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.