AutoCloner

Multiple sequence alignment - TraesCS2D01G194100

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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	TraesCS2D01G194100	chr2D	100.000	4571	0	0	1	4571	139056851	139061421	0.000000e+00	8442.0
1	TraesCS2D01G194100	chr2A	96.233	3212	91	16	1070	4256	161858395	161855189	0.000000e+00	5234.0
2	TraesCS2D01G194100	chr2A	90.691	333	23	6	676	1007	161858813	161858488	1.950000e-118	436.0
3	TraesCS2D01G194100	chr2B	96.039	2903	69	8	1384	4256	197717836	197720722	0.000000e+00	4682.0
4	TraesCS2D01G194100	chr2B	84.937	478	49	14	670	1142	197716996	197717455	3.220000e-126	462.0
5	TraesCS2D01G194100	chr2B	82.018	456	48	16	1	433	197716552	197716996	1.560000e-94	357.0
6	TraesCS2D01G194100	chr2B	84.906	212	30	2	433	644	659525582	659525791	3.580000e-51	213.0
7	TraesCS2D01G194100	chr2B	84.906	212	30	2	433	644	659526354	659526563	3.580000e-51	213.0
8	TraesCS2D01G194100	chr5B	89.172	314	33	1	4255	4568	245961361	245961673	1.540000e-104	390.0
9	TraesCS2D01G194100	chr5B	82.883	222	33	3	433	654	87069408	87069192	1.300000e-45	195.0
10	TraesCS2D01G194100	chr5B	73.810	168	36	3	1	166	571181787	571181948	4.940000e-05	60.2
11	TraesCS2D01G194100	chr1B	88.194	288	31	3	4281	4568	616563047	616563331	1.570000e-89	340.0
12	TraesCS2D01G194100	chr7A	85.374	294	38	5	4276	4569	4305793	4306081	2.670000e-77	300.0
13	TraesCS2D01G194100	chr4D	89.385	179	15	4	4334	4510	326970866	326971042	5.950000e-54	222.0
14	TraesCS2D01G194100	chr1A	83.556	225	34	3	433	656	14073069	14072847	1.670000e-49	207.0
15	TraesCS2D01G194100	chr1A	93.750	48	1	2	4276	4323	61249903	61249948	2.280000e-08	71.3
16	TraesCS2D01G194100	chr3D	83.721	215	33	2	442	656	455868116	455867904	7.750000e-48	202.0
17	TraesCS2D01G194100	chr3D	89.583	48	5	0	1	48	550454704	550454751	1.370000e-05	62.1
18	TraesCS2D01G194100	chr6A	85.789	190	21	5	4347	4534	326543670	326543485	3.610000e-46	196.0
19	TraesCS2D01G194100	chr6A	85.246	61	7	2	4285	4345	184349011	184348953	1.370000e-05	62.1
20	TraesCS2D01G194100	chr7D	86.047	86	5	5	4295	4377	540534967	540535048	8.150000e-13	86.1
21	TraesCS2D01G194100	chr7D	88.889	63	4	3	4263	4325	523119575	523119634	1.760000e-09	75.0
22	TraesCS2D01G194100	chr4A	86.765	68	9	0	302	369	12646761	12646828	4.900000e-10	76.8
23	TraesCS2D01G194100	chr1D	83.333	78	11	2	4295	4371	420640504	420640580	2.280000e-08	71.3
24	TraesCS2D01G194100	chrUn	90.566	53	3	1	97	149	9912579	9912629	8.210000e-08	69.4
25	TraesCS2D01G194100	chr5D	80.682	88	13	3	4288	4373	474551973	474552058	1.060000e-06	65.8
26	TraesCS2D01G194100	chr3A	100.000	28	0	0	1	28	716033281	716033254	8.000000e-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	TraesCS2D01G194100	chr2D	139056851	139061421	4570	False	8442.000000	8442	100.000000	1	4571	1	chr2D.!!$F1	4570
1	TraesCS2D01G194100	chr2A	161855189	161858813	3624	True	2835.000000	5234	93.462000	676	4256	2	chr2A.!!$R1	3580
2	TraesCS2D01G194100	chr2B	197716552	197720722	4170	False	1833.666667	4682	87.664667	1	4256	3	chr2B.!!$F1	4255
3	TraesCS2D01G194100	chr2B	659525582	659526563	981	False	213.000000	213	84.906000	433	644	2	chr2B.!!$F2	211

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	Hairpin	End Stability	Orientation
122	123	0.179009	CCATCGGCAATGACCAGGAT	60.179	55.0	0.00	37.59	3.24	F
488	512	0.179034	GACTGGCCATCCATCCTGAC	60.179	60.0	5.51	42.51	3.51	F
1067	1130	0.036294	AGTTCAGAACGCCTAAGCCC	60.036	55.0	7.68	36.23	5.19	F
1377	1450	0.335361	TCCACCTCTACACCCTCTCC	59.665	60.0	0.00	0.00	3.71	F
2070	2279	0.450583	TTACTAGCGTCCTGAGTGCG	59.549	55.0	0.00	0.00	5.34	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1048	1111	0.036294	GGGCTTAGGCGTTCTGAACT	60.036	55.000	17.60	2.8	39.81	3.01	R
1602	1811	0.908198	GAAGGGAGTCAGAGGCATGT	59.092	55.000	0.00	0.0	0.00	3.21	R
2070	2279	1.372872	GAACCCGGCATTTGCACAC	60.373	57.895	4.74	0.0	44.36	3.82	R
2373	2582	2.779430	TGCAAGACCTCCATGGACATAT	59.221	45.455	11.44	0.0	39.71	1.78	R
3578	4053	0.751452	TGCCATGACAGCAAGCAAAA	59.249	45.000	0.00	0.0	37.28	2.44	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
24	25	4.278419	CCTTATTCCATTTTTAGGGAGCCG	59.722	45.833	0.00	0.00	34.02	5.52
37	38	1.675641	GAGCCGCCATCACCTTGTT	60.676	57.895	0.00	0.00	0.00	2.83
51	52	4.828939	TCACCTTGTTTTTCTGAGCATGAT	59.171	37.500	0.00	0.00	0.00	2.45
55	56	6.072286	ACCTTGTTTTTCTGAGCATGATACAG	60.072	38.462	0.00	0.13	0.00	2.74
67	68	3.750130	GCATGATACAGACCATAAGCAGG	59.250	47.826	0.00	0.00	0.00	4.85
68	69	4.744867	GCATGATACAGACCATAAGCAGGT	60.745	45.833	0.00	0.00	43.46	4.00
70	71	5.023533	TGATACAGACCATAAGCAGGTTC	57.976	43.478	0.00	0.00	40.09	3.62
71	72	4.716784	TGATACAGACCATAAGCAGGTTCT	59.283	41.667	0.00	0.00	40.09	3.01
72	73	5.897250	TGATACAGACCATAAGCAGGTTCTA	59.103	40.000	0.00	0.00	40.09	2.10
73	74	4.744795	ACAGACCATAAGCAGGTTCTAG	57.255	45.455	0.00	0.00	40.09	2.43
74	75	4.353777	ACAGACCATAAGCAGGTTCTAGA	58.646	43.478	0.00	0.00	40.09	2.43
75	76	4.777896	ACAGACCATAAGCAGGTTCTAGAA	59.222	41.667	0.00	0.00	40.09	2.10
76	77	5.248477	ACAGACCATAAGCAGGTTCTAGAAA	59.752	40.000	6.78	0.00	40.09	2.52
77	78	5.582665	CAGACCATAAGCAGGTTCTAGAAAC	59.417	44.000	12.89	12.89	40.09	2.78
78	79	5.248477	AGACCATAAGCAGGTTCTAGAAACA	59.752	40.000	22.29	1.49	40.09	2.83
79	80	5.246307	ACCATAAGCAGGTTCTAGAAACAC	58.754	41.667	22.29	13.54	35.33	3.32
87	88	6.262496	AGCAGGTTCTAGAAACACCTAAAAAC	59.738	38.462	22.29	6.69	39.01	2.43
88	89	6.038936	GCAGGTTCTAGAAACACCTAAAAACA	59.961	38.462	22.29	0.00	39.01	2.83
113	114	1.153086	GAGCACTCCCATCGGCAAT	60.153	57.895	0.00	0.00	0.00	3.56
122	123	0.179009	CCATCGGCAATGACCAGGAT	60.179	55.000	0.00	0.00	37.59	3.24
130	131	2.593468	AATGACCAGGATCCACCGCG	62.593	60.000	15.82	0.00	44.74	6.46
134	135	2.892425	CAGGATCCACCGCGCTTC	60.892	66.667	15.82	0.00	44.74	3.86
149	150	0.182299	GCTTCCATGGCTCTAAGGCT	59.818	55.000	6.96	0.00	41.96	4.58
167	169	2.035832	GGCTACAAGAGAGAGGCAGATC	59.964	54.545	0.00	0.00	35.89	2.75
168	170	2.692557	GCTACAAGAGAGAGGCAGATCA	59.307	50.000	0.00	0.00	0.00	2.92

Showing 1 to 25 of 421 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
11	12	0.329931	TGATGGCGGCTCCCTAAAAA	59.670	50.000	11.43	0.00	0.00	1.94
12	13	0.393808	GTGATGGCGGCTCCCTAAAA	60.394	55.000	11.43	0.00	0.00	1.52
24	25	3.858503	GCTCAGAAAAACAAGGTGATGGC	60.859	47.826	0.00	0.00	0.00	4.40
37	38	5.164620	TGGTCTGTATCATGCTCAGAAAA	57.835	39.130	13.07	5.31	39.42	2.29
51	52	5.516044	TCTAGAACCTGCTTATGGTCTGTA	58.484	41.667	0.00	0.00	36.69	2.74
55	56	5.351740	GTGTTTCTAGAACCTGCTTATGGTC	59.648	44.000	4.18	0.00	36.69	4.02
67	68	7.918562	TGCATTGTTTTTAGGTGTTTCTAGAAC	59.081	33.333	4.18	1.55	0.00	3.01
68	69	8.001881	TGCATTGTTTTTAGGTGTTTCTAGAA	57.998	30.769	0.00	0.00	0.00	2.10
70	71	6.863126	CCTGCATTGTTTTTAGGTGTTTCTAG	59.137	38.462	0.00	0.00	0.00	2.43
71	72	6.547880	TCCTGCATTGTTTTTAGGTGTTTCTA	59.452	34.615	0.00	0.00	0.00	2.10
72	73	5.362430	TCCTGCATTGTTTTTAGGTGTTTCT	59.638	36.000	0.00	0.00	0.00	2.52
73	74	5.596845	TCCTGCATTGTTTTTAGGTGTTTC	58.403	37.500	0.00	0.00	0.00	2.78
74	75	5.600696	CTCCTGCATTGTTTTTAGGTGTTT	58.399	37.500	0.00	0.00	0.00	2.83
75	76	4.501400	GCTCCTGCATTGTTTTTAGGTGTT	60.501	41.667	0.00	0.00	39.41	3.32
76	77	3.005791	GCTCCTGCATTGTTTTTAGGTGT	59.994	43.478	0.00	0.00	39.41	4.16
77	78	3.005684	TGCTCCTGCATTGTTTTTAGGTG	59.994	43.478	0.00	0.00	45.31	4.00
78	79	3.230134	TGCTCCTGCATTGTTTTTAGGT	58.770	40.909	0.00	0.00	45.31	3.08
79	80	3.940209	TGCTCCTGCATTGTTTTTAGG	57.060	42.857	0.00	0.00	45.31	2.69
103	104	0.179009	ATCCTGGTCATTGCCGATGG	60.179	55.000	0.00	0.00	36.37	3.51
107	108	1.097547	GTGGATCCTGGTCATTGCCG	61.098	60.000	14.23	0.00	0.00	5.69
113	114	3.770040	CGCGGTGGATCCTGGTCA	61.770	66.667	14.23	0.00	0.00	4.02
122	123	4.776322	CCATGGAAGCGCGGTGGA	62.776	66.667	13.41	0.00	31.59	4.02
130	131	0.182299	AGCCTTAGAGCCATGGAAGC	59.818	55.000	18.40	6.43	0.00	3.86
134	135	2.435805	TCTTGTAGCCTTAGAGCCATGG	59.564	50.000	7.63	7.63	0.00	3.66
149	150	2.692557	GCTGATCTGCCTCTCTCTTGTA	59.307	50.000	13.26	0.00	0.00	2.41

Showing 1 to 25 of 401 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.