AutoCloner

Multiple sequence alignment - TraesCS3B01G442600

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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	TraesCS3B01G442600	chr3B	100.000	3884	0	0	1	3884	682123573	682119690	0.000000e+00	7173.0
1	TraesCS3B01G442600	chr3B	87.126	1103	129	6	1677	2768	511631105	511632205	0.000000e+00	1238.0
2	TraesCS3B01G442600	chr3B	87.476	1038	123	5	1736	2768	706528420	706527385	0.000000e+00	1190.0
3	TraesCS3B01G442600	chr3B	87.118	1048	132	1	1713	2757	707572320	707573367	0.000000e+00	1184.0
4	TraesCS3B01G442600	chr3B	86.223	1067	133	9	1713	2768	707449686	707450749	0.000000e+00	1144.0
5	TraesCS3B01G442600	chr3B	84.490	980	83	28	736	1669	706529397	706528441	0.000000e+00	904.0
6	TraesCS3B01G442600	chr3B	80.882	680	70	33	766	1410	511630226	511630880	7.550000e-132	481.0
7	TraesCS3B01G442600	chr3B	93.151	146	9	1	3549	3693	682119881	682119736	3.040000e-51	213.0
8	TraesCS3B01G442600	chr3B	93.151	146	9	1	3693	3838	682120025	682119881	3.040000e-51	213.0
9	TraesCS3B01G442600	chr3B	82.828	198	22	8	1268	1459	511630819	511631010	2.400000e-37	167.0
10	TraesCS3B01G442600	chr3B	76.420	352	48	18	11	355	79940045	79940368	1.440000e-34	158.0
11	TraesCS3B01G442600	chr3B	86.667	75	8	2	2766	2839	511632167	511632240	8.940000e-12	82.4
12	TraesCS3B01G442600	chr3B	94.000	50	3	0	1144	1193	706528654	706528605	4.160000e-10	76.8
13	TraesCS3B01G442600	chr3B	89.831	59	3	2	1268	1326	511630903	511630958	5.380000e-09	73.1
14	TraesCS3B01G442600	chr3B	90.566	53	2	2	1450	1502	682122430	682122381	2.500000e-07	67.6
15	TraesCS3B01G442600	chrUn	86.881	1433	161	15	1349	2768	119081687	119080269	0.000000e+00	1580.0
16	TraesCS3B01G442600	chrUn	84.576	590	55	21	749	1326	119082317	119081752	1.580000e-153	553.0
17	TraesCS3B01G442600	chr3A	88.150	1038	116	5	1736	2768	669969860	669970895	0.000000e+00	1229.0
18	TraesCS3B01G442600	chr3A	87.700	1000	116	5	1774	2768	669986371	669985374	0.000000e+00	1158.0
19	TraesCS3B01G442600	chr3A	85.808	1064	141	9	1713	2768	671273509	671274570	0.000000e+00	1120.0
20	TraesCS3B01G442600	chr3A	88.806	402	28	9	1279	1669	669986810	669986415	9.760000e-131	477.0
21	TraesCS3B01G442600	chr3A	88.308	402	30	9	1279	1669	669969444	669969839	2.110000e-127	466.0
22	TraesCS3B01G442600	chr3A	81.967	610	55	27	745	1326	669987399	669986817	2.110000e-127	466.0
23	TraesCS3B01G442600	chr3A	81.422	619	60	25	736	1326	669968846	669969437	4.570000e-124	455.0
24	TraesCS3B01G442600	chr3A	95.652	115	5	0	3391	3505	308675918	308676032	6.630000e-43	185.0
25	TraesCS3B01G442600	chr3A	92.000	50	4	0	1144	1193	669969616	669969665	1.940000e-08	71.3
26	TraesCS3B01G442600	chr3D	87.958	1038	118	5	1736	2768	534669813	534668778	0.000000e+00	1218.0
27	TraesCS3B01G442600	chr3D	89.201	713	51	15	967	1669	534670530	534669834	0.000000e+00	867.0
28	TraesCS3B01G442600	chr3D	94.118	119	6	1	3381	3499	336616926	336616809	3.080000e-41	180.0
29	TraesCS3B01G442600	chr3D	89.000	100	11	0	745	844	534674506	534674407	1.470000e-24	124.0
30	TraesCS3B01G442600	chr3D	94.000	50	3	0	1144	1193	534670047	534669998	4.160000e-10	76.8
31	TraesCS3B01G442600	chr7B	80.172	348	54	8	3359	3693	684797490	684797835	3.000000e-61	246.0
32	TraesCS3B01G442600	chr7B	94.872	117	6	0	3385	3501	693255217	693255333	2.380000e-42	183.0
33	TraesCS3B01G442600	chr5B	96.522	115	4	0	3392	3506	294240033	294240147	1.420000e-44	191.0
34	TraesCS3B01G442600	chr4B	94.872	117	6	0	3383	3499	191365331	191365447	2.380000e-42	183.0
35	TraesCS3B01G442600	chr6B	94.828	116	6	0	3384	3499	195807048	195807163	8.570000e-42	182.0
36	TraesCS3B01G442600	chr6B	82.993	147	20	1	488	629	625804961	625804815	1.130000e-25	128.0
37	TraesCS3B01G442600	chr5D	94.118	119	6	1	3381	3499	293988689	293988806	3.080000e-41	180.0
38	TraesCS3B01G442600	chr4D	94.118	119	6	1	3381	3499	60634342	60634459	3.080000e-41	180.0
39	TraesCS3B01G442600	chr1D	88.028	142	17	0	488	629	180865881	180866022	6.670000e-38	169.0
40	TraesCS3B01G442600	chr7D	81.188	101	17	2	630	728	571797554	571797654	3.220000e-11	80.5

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	TraesCS3B01G442600	chr3B	682119690	682123573	3883	True	1916.650000	7173	94.217000	1	3884	4	chr3B.!!$R1	3883
1	TraesCS3B01G442600	chr3B	707572320	707573367	1047	False	1184.000000	1184	87.118000	1713	2757	1	chr3B.!!$F3	1044
2	TraesCS3B01G442600	chr3B	707449686	707450749	1063	False	1144.000000	1144	86.223000	1713	2768	1	chr3B.!!$F2	1055
3	TraesCS3B01G442600	chr3B	706527385	706529397	2012	True	723.600000	1190	88.655333	736	2768	3	chr3B.!!$R2	2032
4	TraesCS3B01G442600	chr3B	511630226	511632240	2014	False	408.300000	1238	85.466800	766	2839	5	chr3B.!!$F4	2073
5	TraesCS3B01G442600	chrUn	119080269	119082317	2048	True	1066.500000	1580	85.728500	749	2768	2	chrUn.!!$R1	2019
6	TraesCS3B01G442600	chr3A	671273509	671274570	1061	False	1120.000000	1120	85.808000	1713	2768	1	chr3A.!!$F2	1055
7	TraesCS3B01G442600	chr3A	669985374	669987399	2025	True	700.333333	1158	86.157667	745	2768	3	chr3A.!!$R1	2023
8	TraesCS3B01G442600	chr3A	669968846	669970895	2049	False	555.325000	1229	87.470000	736	2768	4	chr3A.!!$F3	2032
9	TraesCS3B01G442600	chr3D	534668778	534670530	1752	True	720.600000	1218	90.386333	967	2768	3	chr3D.!!$R3	1801

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
504	505	0.034059	CCGAGTCAGGACTGCTGTTT	59.966	55.0	6.68	0.00	42.66	2.83	F
964	992	0.035439	GGCGGAAACCCTCATCTTCA	60.035	55.0	0.00	0.00	0.00	3.02	F
2026	2221	0.035725	CCTTGACCATGAGCTGCTCA	60.036	55.0	32.07	32.07	44.99	4.26	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2361	2559	0.108992	GCAGCACCATGACACCATTG	60.109	55.0	0.00	0.00	0.00	2.82	R
2778	2991	0.315251	CGGCGAGATGATAGGCTTCA	59.685	55.0	0.00	0.00	0.00	3.02	R
3261	3474	0.033504	TGTTCAGTCGAGTGAAGCCC	59.966	55.0	31.03	21.22	37.12	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
57	58	7.716768	TTTTTGGAACTCGTCAAAAAGTTTT	57.283	28.000	9.10	0.00	43.51	2.43
58	59	7.716768	TTTTGGAACTCGTCAAAAAGTTTTT	57.283	28.000	7.79	7.79	39.13	1.94
87	88	6.973229	GCATAGGCAAACATTTCTTGAAAT	57.027	33.333	0.00	3.04	40.72	2.17
88	89	7.368480	GCATAGGCAAACATTTCTTGAAATT	57.632	32.000	5.92	0.00	40.72	1.82
89	90	7.458677	GCATAGGCAAACATTTCTTGAAATTC	58.541	34.615	5.92	0.00	40.72	2.17
90	91	7.669098	CATAGGCAAACATTTCTTGAAATTCG	58.331	34.615	5.92	0.12	0.00	3.34
91	92	5.841810	AGGCAAACATTTCTTGAAATTCGA	58.158	33.333	5.92	0.00	0.00	3.71
92	93	5.922544	AGGCAAACATTTCTTGAAATTCGAG	59.077	36.000	3.84	3.84	0.00	4.04
93	94	5.920273	GGCAAACATTTCTTGAAATTCGAGA	59.080	36.000	8.79	8.79	35.19	4.04
94	95	6.420604	GGCAAACATTTCTTGAAATTCGAGAA	59.579	34.615	18.92	18.92	43.26	2.87
95	96	7.276495	GCAAACATTTCTTGAAATTCGAGAAC	58.724	34.615	21.70	8.06	44.29	3.01
96	97	7.043458	GCAAACATTTCTTGAAATTCGAGAACA	60.043	33.333	21.70	14.53	44.29	3.18
97	98	8.806634	CAAACATTTCTTGAAATTCGAGAACAA	58.193	29.630	21.70	11.36	44.29	2.83
98	99	7.914537	ACATTTCTTGAAATTCGAGAACAAC	57.085	32.000	21.70	0.00	44.29	3.32
99	100	6.918022	ACATTTCTTGAAATTCGAGAACAACC	59.082	34.615	21.70	0.00	44.29	3.77
100	101	6.693315	TTTCTTGAAATTCGAGAACAACCT	57.307	33.333	21.70	0.00	44.29	3.50
101	102	7.795482	TTTCTTGAAATTCGAGAACAACCTA	57.205	32.000	21.70	6.87	44.29	3.08
102	103	7.979444	TTCTTGAAATTCGAGAACAACCTAT	57.021	32.000	18.92	0.00	40.87	2.57
103	104	7.364522	TCTTGAAATTCGAGAACAACCTATG	57.635	36.000	10.35	0.00	34.11	2.23
104	105	7.158697	TCTTGAAATTCGAGAACAACCTATGA	58.841	34.615	10.35	0.00	34.11	2.15
105	106	7.659799	TCTTGAAATTCGAGAACAACCTATGAA	59.340	33.333	10.35	0.00	34.11	2.57
106	107	7.737972	TGAAATTCGAGAACAACCTATGAAA	57.262	32.000	0.00	0.00	0.00	2.69
107	108	8.335532	TGAAATTCGAGAACAACCTATGAAAT	57.664	30.769	0.00	0.00	0.00	2.17
108	109	8.792633	TGAAATTCGAGAACAACCTATGAAATT	58.207	29.630	0.00	0.00	0.00	1.82
109	110	9.278734	GAAATTCGAGAACAACCTATGAAATTC	57.721	33.333	0.00	0.00	0.00	2.17

Showing 1 to 25 of 1,162 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
33	34	7.716768	AAAACTTTTTGACGAGTTCCAAAAA	57.283	28.000	0.00	0.00	44.81	1.94
34	35	7.716768	AAAAACTTTTTGACGAGTTCCAAAA	57.283	28.000	0.00	0.00	39.58	2.44
62	63	6.935771	ATTTCAAGAAATGTTTGCCTATGCAA	59.064	30.769	7.21	0.82	45.61	4.08
63	64	6.465948	ATTTCAAGAAATGTTTGCCTATGCA	58.534	32.000	7.21	0.00	41.59	3.96
64	65	6.973229	ATTTCAAGAAATGTTTGCCTATGC	57.027	33.333	7.21	0.00	39.36	3.14
65	66	7.541783	TCGAATTTCAAGAAATGTTTGCCTATG	59.458	33.333	8.66	0.00	40.57	2.23
66	67	7.601856	TCGAATTTCAAGAAATGTTTGCCTAT	58.398	30.769	8.66	0.00	40.57	2.57
67	68	6.976088	TCGAATTTCAAGAAATGTTTGCCTA	58.024	32.000	8.66	0.00	40.57	3.93
68	69	5.841810	TCGAATTTCAAGAAATGTTTGCCT	58.158	33.333	8.66	0.00	40.57	4.75
69	70	5.920273	TCTCGAATTTCAAGAAATGTTTGCC	59.080	36.000	8.66	0.00	40.57	4.52
70	71	6.991485	TCTCGAATTTCAAGAAATGTTTGC	57.009	33.333	8.66	0.00	40.57	3.68
71	72	8.338985	TGTTCTCGAATTTCAAGAAATGTTTG	57.661	30.769	8.66	0.45	40.57	2.93
72	73	8.807581	GTTGTTCTCGAATTTCAAGAAATGTTT	58.192	29.630	8.66	0.00	40.57	2.83
73	74	7.435192	GGTTGTTCTCGAATTTCAAGAAATGTT	59.565	33.333	8.66	0.00	40.57	2.71
74	75	6.918022	GGTTGTTCTCGAATTTCAAGAAATGT	59.082	34.615	8.66	0.59	40.57	2.71
75	76	7.141363	AGGTTGTTCTCGAATTTCAAGAAATG	58.859	34.615	8.66	0.00	40.57	2.32
76	77	7.277174	AGGTTGTTCTCGAATTTCAAGAAAT	57.723	32.000	1.42	2.31	42.35	2.17
77	78	6.693315	AGGTTGTTCTCGAATTTCAAGAAA	57.307	33.333	1.42	0.00	31.26	2.52
78	79	7.659799	TCATAGGTTGTTCTCGAATTTCAAGAA	59.340	33.333	0.00	0.00	0.00	2.52
79	80	7.158697	TCATAGGTTGTTCTCGAATTTCAAGA	58.841	34.615	0.00	0.00	0.00	3.02
80	81	7.364522	TCATAGGTTGTTCTCGAATTTCAAG	57.635	36.000	0.00	0.00	0.00	3.02
81	82	7.737972	TTCATAGGTTGTTCTCGAATTTCAA	57.262	32.000	0.00	0.00	0.00	2.69
82	83	7.737972	TTTCATAGGTTGTTCTCGAATTTCA	57.262	32.000	0.00	0.00	0.00	2.69
83	84	9.278734	GAATTTCATAGGTTGTTCTCGAATTTC	57.721	33.333	0.00	0.00	0.00	2.17
84	85	8.792633	TGAATTTCATAGGTTGTTCTCGAATTT	58.207	29.630	0.00	0.00	0.00	1.82

Showing 1 to 25 of 1,131 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.