AutoCloner

Multiple sequence alignment - TraesCS7D01G392200

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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	TraesCS7D01G392200	chr7D	100.000	3509	0	0	1	3509	507229326	507232834	0.000000e+00	6481.0
1	TraesCS7D01G392200	chr7D	95.137	946	35	5	2571	3509	498414593	498413652	0.000000e+00	1482.0
2	TraesCS7D01G392200	chr7D	90.031	973	63	19	1520	2471	506901691	506902650	0.000000e+00	1229.0
3	TraesCS7D01G392200	chr7D	85.773	485	37	22	982	1440	506901165	506901643	5.270000e-133	484.0
4	TraesCS7D01G392200	chr7D	82.600	477	55	19	2027	2480	506819027	506819498	2.540000e-106	396.0
5	TraesCS7D01G392200	chr7D	86.859	312	23	10	2184	2482	506904341	506904647	2.020000e-87	333.0
6	TraesCS7D01G392200	chr7D	91.943	211	15	2	1520	1729	506818244	506818453	9.530000e-76	294.0
7	TraesCS7D01G392200	chr7D	89.474	209	19	3	1234	1441	506817979	506818185	9.660000e-66	261.0
8	TraesCS7D01G392200	chr7D	87.709	179	22	0	1262	1440	507302898	507303076	3.550000e-50	209.0
9	TraesCS7D01G392200	chr7D	84.507	213	24	3	1000	1211	506816564	506816768	5.940000e-48	202.0
10	TraesCS7D01G392200	chr5D	96.835	948	18	4	2570	3509	302011204	302010261	0.000000e+00	1574.0
11	TraesCS7D01G392200	chr5D	96.343	957	24	4	2560	3509	117886028	117886980	0.000000e+00	1563.0
12	TraesCS7D01G392200	chr5D	96.519	948	20	5	2570	3509	90695932	90694990	0.000000e+00	1555.0
13	TraesCS7D01G392200	chr7B	91.810	989	50	11	1510	2476	535637155	535638134	0.000000e+00	1349.0
14	TraesCS7D01G392200	chr7B	94.821	502	22	2	1019	1520	535636513	535637010	0.000000e+00	780.0
15	TraesCS7D01G392200	chr7B	84.253	743	79	23	1000	1729	535491330	535492047	0.000000e+00	689.0
16	TraesCS7D01G392200	chr7B	82.114	492	54	18	1804	2264	535494565	535495053	1.180000e-104	390.0
17	TraesCS7D01G392200	chr7B	78.591	369	56	14	1084	1439	535697477	535697835	4.560000e-54	222.0
18	TraesCS7D01G392200	chr7B	92.857	126	5	2	2570	2691	744173145	744173270	2.780000e-41	180.0
19	TraesCS7D01G392200	chr7B	91.566	83	6	1	463	544	109853327	109853245	2.860000e-21	113.0
20	TraesCS7D01G392200	chr5A	94.438	827	39	1	2690	3509	617222867	617223693	0.000000e+00	1266.0
21	TraesCS7D01G392200	chr5A	87.259	259	27	6	538	793	451403321	451403576	1.230000e-74	291.0
22	TraesCS7D01G392200	chr5A	90.441	136	8	3	2560	2691	196312341	196312207	1.290000e-39	174.0
23	TraesCS7D01G392200	chr5A	76.786	168	33	6	1272	1436	479397426	479397262	4.820000e-14	89.8
24	TraesCS7D01G392200	chr5B	94.337	830	36	5	2690	3509	692442643	692441815	0.000000e+00	1262.0
25	TraesCS7D01G392200	chr5B	89.872	859	56	17	2571	3409	686641033	686641880	0.000000e+00	1075.0
26	TraesCS7D01G392200	chr5B	89.419	860	58	17	2571	3409	686676549	686677396	0.000000e+00	1053.0
27	TraesCS7D01G392200	chr5B	93.045	532	30	1	2690	3214	125264272	125264803	0.000000e+00	771.0
28	TraesCS7D01G392200	chr5B	88.065	553	54	8	1	544	615027318	615027867	0.000000e+00	645.0
29	TraesCS7D01G392200	chr5B	86.400	250	29	5	549	797	222409014	222409259	5.770000e-68	268.0
30	TraesCS7D01G392200	chr3B	93.954	827	42	2	2690	3509	39603271	39602446	0.000000e+00	1243.0
31	TraesCS7D01G392200	chr2A	90.909	572	31	14	2937	3506	546776553	546777105	0.000000e+00	749.0
32	TraesCS7D01G392200	chr2A	84.429	289	34	6	561	846	162297378	162297098	1.240000e-69	274.0
33	TraesCS7D01G392200	chr7A	91.084	572	19	11	1494	2041	575100209	575100772	0.000000e+00	745.0
34	TraesCS7D01G392200	chr7A	87.801	623	50	13	882	1494	575099331	575099937	0.000000e+00	706.0
35	TraesCS7D01G392200	chr7A	88.222	450	38	10	2035	2470	575101455	575101903	1.120000e-144	523.0
36	TraesCS7D01G392200	chr7A	80.303	726	87	30	1804	2480	574685617	574686335	6.760000e-137	497.0
37	TraesCS7D01G392200	chr7A	85.321	436	22	22	2559	2954	99582527	99582960	2.520000e-111	412.0
38	TraesCS7D01G392200	chr7A	83.589	457	53	14	1000	1439	574684452	574684903	3.260000e-110	409.0
39	TraesCS7D01G392200	chr7A	90.783	217	18	2	1513	1729	574684947	574685161	4.430000e-74	289.0
40	TraesCS7D01G392200	chr7A	91.824	159	13	0	1282	1440	577206351	577206509	4.560000e-54	222.0
41	TraesCS7D01G392200	chr6B	88.478	460	38	8	11	465	604713822	604714271	3.080000e-150	542.0
42	TraesCS7D01G392200	chr6B	86.335	322	14	12	2690	3003	560628791	560629090	1.210000e-84	324.0
43	TraesCS7D01G392200	chr6B	84.320	338	30	5	210	543	105860682	105861000	3.400000e-80	309.0
44	TraesCS7D01G392200	chr6B	86.179	246	29	5	549	792	717167041	717167283	9.660000e-66	261.0
45	TraesCS7D01G392200	chr6B	92.035	113	5	4	52	162	105860569	105860679	4.690000e-34	156.0
46	TraesCS7D01G392200	chr3D	84.699	549	48	17	1	528	26280029	26280562	1.870000e-142	516.0
47	TraesCS7D01G392200	chr3D	85.231	325	19	8	1	325	593444891	593445186	1.220000e-79	307.0
48	TraesCS7D01G392200	chr3D	90.816	98	5	1	403	496	593445186	593445283	1.020000e-25	128.0
49	TraesCS7D01G392200	chr3D	91.250	80	7	0	464	543	523778237	523778316	3.700000e-20	110.0
50	TraesCS7D01G392200	chr2B	85.441	522	46	16	18	529	799257760	799257259	1.870000e-142	516.0
51	TraesCS7D01G392200	chr2B	83.747	443	60	10	111	544	581055534	581055973	3.260000e-110	409.0
52	TraesCS7D01G392200	chr2B	78.686	563	97	16	1	543	455681810	455681251	1.550000e-93	353.0
53	TraesCS7D01G392200	chr6A	88.217	314	30	5	1	307	26627004	26627317	5.530000e-98	368.0
54	TraesCS7D01G392200	chr6A	81.733	427	19	31	2570	2957	162191498	162191092	5.690000e-78	302.0
55	TraesCS7D01G392200	chr6A	73.298	573	106	39	2	544	584005462	584006017	2.170000e-37	167.0
56	TraesCS7D01G392200	chr6A	90.244	82	6	2	463	543	327491767	327491687	4.790000e-19	106.0
57	TraesCS7D01G392200	chr2D	90.295	237	19	4	549	783	613463892	613464126	1.220000e-79	307.0
58	TraesCS7D01G392200	chr2D	88.115	244	25	4	541	781	613461987	613462229	1.590000e-73	287.0
59	TraesCS7D01G392200	chr1D	87.755	245	26	4	541	782	55972778	55973021	2.060000e-72	283.0
60	TraesCS7D01G392200	chr1A	83.219	292	37	10	567	847	577585133	577584843	1.250000e-64	257.0
61	TraesCS7D01G392200	chr1A	82.019	317	42	12	549	851	577586601	577586286	4.490000e-64	255.0
62	TraesCS7D01G392200	chr4D	89.157	83	9	0	462	544	487454342	487454424	1.720000e-18	104.0
63	TraesCS7D01G392200	chr3A	76.812	207	26	16	2	192	714623559	714623759	2.880000e-16	97.1

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	TraesCS7D01G392200	chr7D	507229326	507232834	3508	False	6481.000000	6481	100.000000	1	3509	1	chr7D.!!$F1	3508
1	TraesCS7D01G392200	chr7D	498413652	498414593	941	True	1482.000000	1482	95.137000	2571	3509	1	chr7D.!!$R1	938
2	TraesCS7D01G392200	chr7D	506901165	506904647	3482	False	682.000000	1229	87.554333	982	2482	3	chr7D.!!$F4	1500
3	TraesCS7D01G392200	chr7D	506816564	506819498	2934	False	288.250000	396	87.131000	1000	2480	4	chr7D.!!$F3	1480
4	TraesCS7D01G392200	chr5D	302010261	302011204	943	True	1574.000000	1574	96.835000	2570	3509	1	chr5D.!!$R2	939
5	TraesCS7D01G392200	chr5D	117886028	117886980	952	False	1563.000000	1563	96.343000	2560	3509	1	chr5D.!!$F1	949
6	TraesCS7D01G392200	chr5D	90694990	90695932	942	True	1555.000000	1555	96.519000	2570	3509	1	chr5D.!!$R1	939
7	TraesCS7D01G392200	chr7B	535636513	535638134	1621	False	1064.500000	1349	93.315500	1019	2476	2	chr7B.!!$F4	1457
8	TraesCS7D01G392200	chr7B	535491330	535495053	3723	False	539.500000	689	83.183500	1000	2264	2	chr7B.!!$F3	1264
9	TraesCS7D01G392200	chr5A	617222867	617223693	826	False	1266.000000	1266	94.438000	2690	3509	1	chr5A.!!$F2	819
10	TraesCS7D01G392200	chr5B	692441815	692442643	828	True	1262.000000	1262	94.337000	2690	3509	1	chr5B.!!$R1	819
11	TraesCS7D01G392200	chr5B	686641033	686641880	847	False	1075.000000	1075	89.872000	2571	3409	1	chr5B.!!$F4	838
12	TraesCS7D01G392200	chr5B	686676549	686677396	847	False	1053.000000	1053	89.419000	2571	3409	1	chr5B.!!$F5	838
13	TraesCS7D01G392200	chr5B	125264272	125264803	531	False	771.000000	771	93.045000	2690	3214	1	chr5B.!!$F1	524
14	TraesCS7D01G392200	chr5B	615027318	615027867	549	False	645.000000	645	88.065000	1	544	1	chr5B.!!$F3	543
15	TraesCS7D01G392200	chr3B	39602446	39603271	825	True	1243.000000	1243	93.954000	2690	3509	1	chr3B.!!$R1	819
16	TraesCS7D01G392200	chr2A	546776553	546777105	552	False	749.000000	749	90.909000	2937	3506	1	chr2A.!!$F1	569
17	TraesCS7D01G392200	chr7A	575099331	575101903	2572	False	658.000000	745	89.035667	882	2470	3	chr7A.!!$F4	1588
18	TraesCS7D01G392200	chr7A	574684452	574686335	1883	False	398.333333	497	84.891667	1000	2480	3	chr7A.!!$F3	1480
19	TraesCS7D01G392200	chr3D	26280029	26280562	533	False	516.000000	516	84.699000	1	528	1	chr3D.!!$F1	527
20	TraesCS7D01G392200	chr2B	799257259	799257760	501	True	516.000000	516	85.441000	18	529	1	chr2B.!!$R2	511
21	TraesCS7D01G392200	chr2B	455681251	455681810	559	True	353.000000	353	78.686000	1	543	1	chr2B.!!$R1	542
22	TraesCS7D01G392200	chr2D	613461987	613464126	2139	False	297.000000	307	89.205000	541	783	2	chr2D.!!$F1	242
23	TraesCS7D01G392200	chr1A	577584843	577586601	1758	True	256.000000	257	82.619000	549	851	2	chr1A.!!$R1	302

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
954	2279	0.104855	GGCCGAGTGATATGTGCTGA	59.895	55.0	0.0	0.0	0.0	4.26	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2525	9660	0.109919	GACGAAAACGGTGGATTGCC	60.11	55.0	0.0	0.0	0.0	4.52	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
27	29	5.362987	TTGTGTTTTAACAAATGTTCGCG	57.637	34.783	0.00	0.00	41.21	5.87
279	302	4.377021	CACTACCAAGTAACAGCAAGTCA	58.623	43.478	0.00	0.00	33.48	3.41
280	303	4.211374	CACTACCAAGTAACAGCAAGTCAC	59.789	45.833	0.00	0.00	33.48	3.67
301	324	4.806247	CACATTTAGTAGAGTGGCTAGCAC	59.194	45.833	18.24	12.66	0.00	4.40
307	330	3.578716	AGTAGAGTGGCTAGCACTTTGAA	59.421	43.478	18.24	3.20	32.33	2.69
333	356	0.107410	AACGTGAGCACTTGGGTTCA	60.107	50.000	0.00	0.00	0.00	3.18
392	423	0.249120	TGTTGGTACAGGATCCGCTG	59.751	55.000	5.98	2.38	42.39	5.18
426	462	3.868757	TCCTGGTTCTGTCGTAGATTG	57.131	47.619	0.00	0.00	40.67	2.67
450	489	2.426522	TGGCAGAAACAAATCGGAGAG	58.573	47.619	0.00	0.00	43.63	3.20
452	491	1.806542	GCAGAAACAAATCGGAGAGCA	59.193	47.619	0.00	0.00	43.63	4.26
453	492	2.226437	GCAGAAACAAATCGGAGAGCAA	59.774	45.455	0.00	0.00	43.63	3.91
693	2001	8.812147	TTACTAAATAATCTACGTCAGCATGG	57.188	34.615	0.00	0.00	36.16	3.66
700	2008	3.585862	TCTACGTCAGCATGGAAAGTTC	58.414	45.455	0.00	0.00	36.16	3.01
737	2046	5.682943	TTTTTCCGTTGTGTTAGAGGATG	57.317	39.130	0.00	0.00	0.00	3.51
740	2049	2.094906	TCCGTTGTGTTAGAGGATGACG	60.095	50.000	0.00	0.00	0.00	4.35
742	2051	1.654105	GTTGTGTTAGAGGATGACGCG	59.346	52.381	3.53	3.53	30.79	6.01
751	2060	6.035650	TGTTAGAGGATGACGCGAAAATAAAG	59.964	38.462	15.93	0.00	0.00	1.85
753	2062	3.006940	AGGATGACGCGAAAATAAAGCA	58.993	40.909	15.93	0.00	0.00	3.91
759	2068	1.199097	CGCGAAAATAAAGCAGTGGGT	59.801	47.619	0.00	0.00	0.00	4.51
767	2076	2.236959	AAAGCAGTGGGTTGGTGGGT	62.237	55.000	0.00	0.00	34.38	4.51
770	2079	3.507713	AGTGGGTTGGTGGGTGGG	61.508	66.667	0.00	0.00	0.00	4.61
772	2081	4.865228	TGGGTTGGTGGGTGGGGA	62.865	66.667	0.00	0.00	0.00	4.81
773	2082	4.295199	GGGTTGGTGGGTGGGGAC	62.295	72.222	0.00	0.00	0.00	4.46
800	2118	4.950205	AAACTAGACGAAAAGAGGGACA	57.050	40.909	0.00	0.00	0.00	4.02
828	2147	7.971368	AAAACATAAATACCAGCCTACCAAT	57.029	32.000	0.00	0.00	0.00	3.16

Showing 1 to 25 of 145 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
16	18	2.519002	TCCGAATTCGCGAACATTTG	57.481	45.000	26.00	18.36	38.18	2.32
27	29	8.616076	ACTGTAATGAATGATTCTTCCGAATTC	58.384	33.333	6.73	0.00	39.89	2.17
208	229	4.806247	GCGTCATATACTGAGAGCAAAACT	59.194	41.667	0.00	0.00	38.14	2.66
279	302	5.012328	GTGCTAGCCACTCTACTAAATGT	57.988	43.478	13.29	0.00	41.35	2.71
301	324	2.286418	GCTCACGTTGGACACTTCAAAG	60.286	50.000	0.00	0.00	0.00	2.77
307	330	0.178068	AAGTGCTCACGTTGGACACT	59.822	50.000	11.42	8.20	43.14	3.55
426	462	3.712187	TCCGATTTGTTTCTGCCAAAAC	58.288	40.909	4.54	4.54	39.16	2.43
450	489	1.957186	TACGTCAACGCACCCTTGC	60.957	57.895	1.81	0.00	46.21	4.01
452	491	1.662446	CGTACGTCAACGCACCCTT	60.662	57.895	7.22	0.00	44.43	3.95
453	492	2.049802	CGTACGTCAACGCACCCT	60.050	61.111	7.22	0.00	44.43	4.34
569	611	7.693952	TCGCTCAATCACATTAATTAGGAAAC	58.306	34.615	0.00	0.00	0.00	2.78
665	1973	9.982651	ATGCTGACGTAGATTATTTAGTAATGT	57.017	29.630	0.00	0.00	33.16	2.71
679	1987	3.258372	AGAACTTTCCATGCTGACGTAGA	59.742	43.478	0.00	0.00	0.00	2.59
680	1988	3.369147	CAGAACTTTCCATGCTGACGTAG	59.631	47.826	0.00	0.00	0.00	3.51
682	1990	2.146342	CAGAACTTTCCATGCTGACGT	58.854	47.619	0.00	0.00	0.00	4.34
685	1993	3.614092	GGATCAGAACTTTCCATGCTGA	58.386	45.455	0.00	0.00	39.61	4.26
720	2028	2.259618	CGTCATCCTCTAACACAACGG	58.740	52.381	0.00	0.00	0.00	4.44
721	2029	1.654105	GCGTCATCCTCTAACACAACG	59.346	52.381	0.00	0.00	0.00	4.10
722	2030	1.654105	CGCGTCATCCTCTAACACAAC	59.346	52.381	0.00	0.00	0.00	3.32
729	2038	4.506654	GCTTTATTTTCGCGTCATCCTCTA	59.493	41.667	5.77	0.00	0.00	2.43
735	2044	3.426159	CCACTGCTTTATTTTCGCGTCAT	60.426	43.478	5.77	0.00	0.00	3.06
737	2046	2.505866	CCACTGCTTTATTTTCGCGTC	58.494	47.619	5.77	0.00	0.00	5.19
740	2049	2.986479	CAACCCACTGCTTTATTTTCGC	59.014	45.455	0.00	0.00	0.00	4.70
742	2051	4.306600	CACCAACCCACTGCTTTATTTTC	58.693	43.478	0.00	0.00	0.00	2.29
751	2060	2.912025	CACCCACCAACCCACTGC	60.912	66.667	0.00	0.00	0.00	4.40

Showing 1 to 25 of 140 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.