AutoCloner

Multiple sequence alignment - TraesCS5A01G115800

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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	TraesCS5A01G115800	chr5A	100.000	4423	0	0	1	4423	235246972	235242550	0.000000e+00	8168.0
1	TraesCS5A01G115800	chrUn	96.727	3636	95	10	1	3625	115653046	115656668	0.000000e+00	6034.0
2	TraesCS5A01G115800	chr5B	96.115	3063	72	17	588	3613	214264058	214261006	0.000000e+00	4953.0
3	TraesCS5A01G115800	chr5B	94.162	531	28	2	1	528	214279961	214279431	0.000000e+00	806.0
4	TraesCS5A01G115800	chr2A	90.785	803	57	10	3630	4423	711936809	711936015	0.000000e+00	1057.0
5	TraesCS5A01G115800	chr2A	85.246	61	7	2	399	457	294435172	294435112	1.330000e-05	62.1
6	TraesCS5A01G115800	chr1B	90.311	805	62	11	3626	4422	333811062	333811858	0.000000e+00	1040.0
7	TraesCS5A01G115800	chr4D	90.299	804	60	11	3625	4423	491563493	491564283	0.000000e+00	1037.0
8	TraesCS5A01G115800	chr4D	89.578	806	64	11	3627	4423	25888642	25887848	0.000000e+00	1005.0
9	TraesCS5A01G115800	chr4D	90.288	659	52	11	3770	4423	15530799	15531450	0.000000e+00	852.0
10	TraesCS5A01G115800	chr4B	88.960	779	71	9	3626	4394	38235579	38234806	0.000000e+00	948.0
11	TraesCS5A01G115800	chr7A	88.075	805	69	13	3624	4423	653345522	653344740	0.000000e+00	929.0
12	TraesCS5A01G115800	chr7A	89.104	670	63	5	3757	4423	68141611	68140949	0.000000e+00	824.0
13	TraesCS5A01G115800	chr7B	87.484	799	84	10	3629	4423	81605348	81604562	0.000000e+00	907.0
14	TraesCS5A01G115800	chr3B	85.357	560	71	9	1	556	166518418	166518970	1.790000e-158	569.0
15	TraesCS5A01G115800	chr3D	85.179	560	72	9	1	556	114320828	114320276	8.300000e-157	564.0
16	TraesCS5A01G115800	chr3D	76.773	564	100	28	1	546	484593627	484593077	2.010000e-73	287.0
17	TraesCS5A01G115800	chr4A	82.609	529	78	13	1	523	678296823	678296303	5.220000e-124	455.0
18	TraesCS5A01G115800	chr4A	80.680	559	81	19	6	555	395023265	395023805	4.120000e-110	409.0
19	TraesCS5A01G115800	chr2B	80.297	538	92	12	6	536	499003661	499003131	1.150000e-105	394.0
20	TraesCS5A01G115800	chr2B	84.800	125	17	2	2845	2968	722325511	722325388	1.670000e-24	124.0
21	TraesCS5A01G115800	chr2D	84.000	125	18	2	2845	2968	594577231	594577108	7.770000e-23	119.0
22	TraesCS5A01G115800	chr2D	83.333	96	13	3	1	95	282693232	282693325	7.880000e-13	86.1
23	TraesCS5A01G115800	chr6B	84.507	71	9	1	2265	2333	353557569	353557499	7.940000e-08	69.4
24	TraesCS5A01G115800	chr3A	76.129	155	23	11	147	296	353790699	353790844	7.940000e-08	69.4
25	TraesCS5A01G115800	chr6D	97.368	38	1	0	2265	2302	242219704	242219667	1.030000e-06	65.8
26	TraesCS5A01G115800	chr1D	100.000	31	0	0	2269	2299	260568937	260568967	1.720000e-04	58.4
27	TraesCS5A01G115800	chr1A	79.070	86	14	4	2271	2352	67028992	67029077	6.180000e-04	56.5

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	TraesCS5A01G115800	chr5A	235242550	235246972	4422	True	8168	8168	100.000	1	4423	1	chr5A.!!$R1	4422
1	TraesCS5A01G115800	chrUn	115653046	115656668	3622	False	6034	6034	96.727	1	3625	1	chrUn.!!$F1	3624
2	TraesCS5A01G115800	chr5B	214261006	214264058	3052	True	4953	4953	96.115	588	3613	1	chr5B.!!$R1	3025
3	TraesCS5A01G115800	chr5B	214279431	214279961	530	True	806	806	94.162	1	528	1	chr5B.!!$R2	527
4	TraesCS5A01G115800	chr2A	711936015	711936809	794	True	1057	1057	90.785	3630	4423	1	chr2A.!!$R2	793
5	TraesCS5A01G115800	chr1B	333811062	333811858	796	False	1040	1040	90.311	3626	4422	1	chr1B.!!$F1	796
6	TraesCS5A01G115800	chr4D	491563493	491564283	790	False	1037	1037	90.299	3625	4423	1	chr4D.!!$F2	798
7	TraesCS5A01G115800	chr4D	25887848	25888642	794	True	1005	1005	89.578	3627	4423	1	chr4D.!!$R1	796
8	TraesCS5A01G115800	chr4D	15530799	15531450	651	False	852	852	90.288	3770	4423	1	chr4D.!!$F1	653
9	TraesCS5A01G115800	chr4B	38234806	38235579	773	True	948	948	88.960	3626	4394	1	chr4B.!!$R1	768
10	TraesCS5A01G115800	chr7A	653344740	653345522	782	True	929	929	88.075	3624	4423	1	chr7A.!!$R2	799
11	TraesCS5A01G115800	chr7A	68140949	68141611	662	True	824	824	89.104	3757	4423	1	chr7A.!!$R1	666
12	TraesCS5A01G115800	chr7B	81604562	81605348	786	True	907	907	87.484	3629	4423	1	chr7B.!!$R1	794
13	TraesCS5A01G115800	chr3B	166518418	166518970	552	False	569	569	85.357	1	556	1	chr3B.!!$F1	555
14	TraesCS5A01G115800	chr3D	114320276	114320828	552	True	564	564	85.179	1	556	1	chr3D.!!$R1	555
15	TraesCS5A01G115800	chr3D	484593077	484593627	550	True	287	287	76.773	1	546	1	chr3D.!!$R2	545
16	TraesCS5A01G115800	chr4A	678296303	678296823	520	True	455	455	82.609	1	523	1	chr4A.!!$R1	522
17	TraesCS5A01G115800	chr4A	395023265	395023805	540	False	409	409	80.680	6	555	1	chr4A.!!$F1	549
18	TraesCS5A01G115800	chr2B	499003131	499003661	530	True	394	394	80.297	6	536	1	chr2B.!!$R1	530

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
791	812	0.894835	TCGAGACTGGCTGCACAATA	59.105	50.000	0.50	0.0	1.90	F
977	998	1.127343	AAGGAGTGGAGGAGCATAGC	58.873	55.000	0.00	0.0	2.97	F
1528	1567	2.478890	CCGGGAGTACATCGACGCT	61.479	63.158	0.00	0.0	5.07	F
2146	2201	0.105408	GTGCGTAACCGTATGGGGAT	59.895	55.000	5.82	41.6	3.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1659	1698	1.663388	CAGGTTCACGTACTGCGCA	60.663	57.895	10.98	10.98	46.11	6.09	R
2026	2070	2.941333	CGGCGGCATATGCTCAAG	59.059	61.111	26.12	15.90	41.70	3.02	R
3197	3263	0.318614	CCAGCACGGCGTTGAAAAAT	60.319	50.000	11.19	0.00	0.00	1.82	R
4010	4100	0.179108	GGCGCTACTACCTTGTGGAG	60.179	60.000	7.64	0.00	37.04	3.86	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
369	374	2.441164	TTGCCGGCAAGGTTGTGT	60.441	55.556	37.30	0.00	43.70	3.72
375	380	1.270625	CCGGCAAGGTTGTGTTCTCTA	60.271	52.381	0.00	0.00	34.51	2.43
382	387	5.178809	GCAAGGTTGTGTTCTCTATAAACGT	59.821	40.000	0.00	0.00	0.00	3.99
383	388	6.590357	CAAGGTTGTGTTCTCTATAAACGTG	58.410	40.000	0.00	0.00	0.00	4.49
411	419	8.297470	ACTCAAATACTCATAAATGCACCAAT	57.703	30.769	0.00	0.00	0.00	3.16
556	577	1.772063	GATTGCCGTATGCCGACACC	61.772	60.000	0.00	0.00	40.16	4.16
557	578	3.961838	TTGCCGTATGCCGACACCC	62.962	63.158	0.00	0.00	40.16	4.61
558	579	4.460683	GCCGTATGCCGACACCCA	62.461	66.667	0.00	0.00	39.56	4.51
563	584	1.299541	GTATGCCGACACCCATCAAG	58.700	55.000	0.00	0.00	0.00	3.02
575	596	3.691118	CACCCATCAAGAATGTTCGTCAT	59.309	43.478	0.00	0.00	38.57	3.06
700	721	6.969828	AATCTTTAGCTAGTAGTTGTGCAC	57.030	37.500	10.75	10.75	0.00	4.57
711	732	3.529341	TTGTGCACGCACTCGGGAT	62.529	57.895	21.76	0.00	46.30	3.85
749	770	7.746916	CGTTCTCTATAATTGGAGTCGATGTAG	59.253	40.741	0.00	0.00	34.18	2.74
762	783	6.412362	AGTCGATGTAGATTGATAAAGCCT	57.588	37.500	0.00	0.00	0.00	4.58
791	812	0.894835	TCGAGACTGGCTGCACAATA	59.105	50.000	0.50	0.00	0.00	1.90
885	906	1.402259	AGTGACGATGAAGTAGGAGCG	59.598	52.381	0.00	0.00	0.00	5.03
895	916	3.075005	TAGGAGCGTCTGGTGGGC	61.075	66.667	0.00	0.00	0.00	5.36
957	978	6.889177	TCAGTGAGTCATAGAGAAAGAGTGAT	59.111	38.462	0.00	0.00	0.00	3.06
974	995	2.703007	GTGATAAGGAGTGGAGGAGCAT	59.297	50.000	0.00	0.00	0.00	3.79
975	996	3.898123	GTGATAAGGAGTGGAGGAGCATA	59.102	47.826	0.00	0.00	0.00	3.14
976	997	4.021544	GTGATAAGGAGTGGAGGAGCATAG	60.022	50.000	0.00	0.00	0.00	2.23
977	998	1.127343	AAGGAGTGGAGGAGCATAGC	58.873	55.000	0.00	0.00	0.00	2.97
1212	1251	4.404122	CTGTCATGACATGGCATGTGCC	62.404	54.545	34.93	24.82	44.93	5.01
1285	1324	8.781196	GTGATAATATGTGCATCAGTCTGAATT	58.219	33.333	6.64	3.02	29.64	2.17
1528	1567	2.478890	CCGGGAGTACATCGACGCT	61.479	63.158	0.00	0.00	0.00	5.07
1543	1582	2.663196	GCTGTCCGGTGCTACCTT	59.337	61.111	0.00	0.00	35.66	3.50
1804	1843	5.893255	TGATTAGTTAGCCCAGCAAATTGAT	59.107	36.000	0.00	0.00	0.00	2.57
2026	2070	6.036626	GCACTGGTAGCTCTATCTTTCTTTTC	59.963	42.308	0.00	0.00	0.00	2.29
2070	2120	1.407299	CCGGATGTCATCTTTGAGCCA	60.407	52.381	12.54	0.00	30.85	4.75
2146	2201	0.105408	GTGCGTAACCGTATGGGGAT	59.895	55.000	5.82	0.00	41.60	3.85
2147	2202	0.831966	TGCGTAACCGTATGGGGATT	59.168	50.000	5.82	0.00	41.60	3.01
2148	2203	1.209990	TGCGTAACCGTATGGGGATTT	59.790	47.619	5.82	0.00	41.60	2.17
2149	2204	2.291365	GCGTAACCGTATGGGGATTTT	58.709	47.619	5.82	0.00	41.60	1.82
2150	2205	2.032426	GCGTAACCGTATGGGGATTTTG	59.968	50.000	5.82	0.00	41.60	2.44
2151	2206	2.032426	CGTAACCGTATGGGGATTTTGC	59.968	50.000	5.82	0.00	41.60	3.68
3044	3110	0.814410	CGAGGCTGGAGAGCTACGTA	60.814	60.000	0.00	0.00	45.44	3.57
3083	3149	0.374758	CCAAGATCATCAACGCCACG	59.625	55.000	0.00	0.00	0.00	4.94
3091	3157	1.257936	CATCAACGCCACGTACTATGC	59.742	52.381	0.00	0.00	39.99	3.14
3426	3492	1.420430	CGCCACCCCCTTCTAGAATA	58.580	55.000	5.44	0.00	0.00	1.75
3558	3625	4.115401	TGATTGATCGATCGATCCATCC	57.885	45.455	40.68	30.92	45.50	3.51
3566	3633	3.057245	TCGATCGATCCATCCATCAAGTC	60.057	47.826	19.51	0.00	0.00	3.01
3672	3739	4.217836	GCCTAGGGCTAAAACTAACTGT	57.782	45.455	11.72	0.00	46.69	3.55
3699	3766	9.313323	CTAAATATAATGTCAAAATACCACGCG	57.687	33.333	3.53	3.53	0.00	6.01
3865	3943	6.151817	GGAGACTTGCTTAATTCAAGGTCATT	59.848	38.462	16.91	1.95	43.77	2.57
4016	4106	3.478857	ACCATTAACACGAACTCCACA	57.521	42.857	0.00	0.00	0.00	4.17
4027	4117	2.731341	CGAACTCCACAAGGTAGTAGCG	60.731	54.545	0.00	0.00	35.89	4.26
4113	4206	4.007581	TGGGTCCTCTTCATCTTGGATA	57.992	45.455	0.00	0.00	0.00	2.59
4166	4262	9.798994	AAACTGACTAGATATAGTTTAACACCG	57.201	33.333	0.74	0.00	40.45	4.94
4255	4361	5.862323	AGATTAGTTATTACCTATGCGTGCG	59.138	40.000	0.00	0.00	0.00	5.34
4288	4397	6.214191	AGCAATAGTTCGAGAAGATCAGAA	57.786	37.500	0.00	0.00	0.00	3.02
4289	4398	6.272318	AGCAATAGTTCGAGAAGATCAGAAG	58.728	40.000	0.00	0.00	0.00	2.85
4290	4399	5.461737	GCAATAGTTCGAGAAGATCAGAAGG	59.538	44.000	0.00	0.00	0.00	3.46
4301	4410	3.832527	AGATCAGAAGGAGGAGACTAGC	58.167	50.000	0.00	0.00	44.43	3.42
4314	4423	0.972983	GACTAGCAGAGGCAGGTGGA	60.973	60.000	0.00	0.00	44.61	4.02
4321	4433	2.122413	AGGCAGGTGGACAGGACA	60.122	61.111	0.00	0.00	0.00	4.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
369	374	5.988310	TTGAGTCCCACGTTTATAGAGAA	57.012	39.130	0.00	0.00	0.00	2.87
375	380	6.045072	TGAGTATTTGAGTCCCACGTTTAT	57.955	37.500	0.00	0.00	0.00	1.40
382	387	6.318648	GTGCATTTATGAGTATTTGAGTCCCA	59.681	38.462	0.00	0.00	0.00	4.37
383	388	6.238759	GGTGCATTTATGAGTATTTGAGTCCC	60.239	42.308	0.00	0.00	0.00	4.46
411	419	1.338389	GCGTAAAACCCTACTCCTGCA	60.338	52.381	0.00	0.00	0.00	4.41
556	577	4.813161	AGCTATGACGAACATTCTTGATGG	59.187	41.667	0.00	0.00	40.21	3.51
557	578	5.980698	AGCTATGACGAACATTCTTGATG	57.019	39.130	0.00	0.00	40.07	3.07
558	579	6.344500	AGAAGCTATGACGAACATTCTTGAT	58.656	36.000	0.00	0.00	40.07	2.57
563	584	6.144724	GTGGATAGAAGCTATGACGAACATTC	59.855	42.308	0.00	0.00	40.07	2.67
575	596	5.326069	GAGGGTAGATGTGGATAGAAGCTA	58.674	45.833	0.00	0.00	0.00	3.32
700	721	2.121538	TCCTCTCATCCCGAGTGCG	61.122	63.158	0.00	0.00	42.88	5.34
749	770	7.489435	TCGATCGATCAATAGGCTTTATCAATC	59.511	37.037	24.40	0.00	0.00	2.67
762	783	3.057946	CAGCCAGTCTCGATCGATCAATA	60.058	47.826	24.40	8.81	0.00	1.90
885	906	5.163301	CCACATATATATAGGCCCACCAGAC	60.163	48.000	0.00	0.00	39.06	3.51
895	916	5.453903	GCAGGAGCCACCACATATATATAGG	60.454	48.000	2.88	2.88	42.04	2.57
957	978	2.091055	AGCTATGCTCCTCCACTCCTTA	60.091	50.000	0.00	0.00	30.62	2.69
974	995	1.562942	TCGTGTCTTCCCCTCTAGCTA	59.437	52.381	0.00	0.00	0.00	3.32
975	996	0.331954	TCGTGTCTTCCCCTCTAGCT	59.668	55.000	0.00	0.00	0.00	3.32
976	997	0.741915	CTCGTGTCTTCCCCTCTAGC	59.258	60.000	0.00	0.00	0.00	3.42
977	998	2.092861	TCTCTCGTGTCTTCCCCTCTAG	60.093	54.545	0.00	0.00	0.00	2.43
1212	1251	3.570550	CCTCCCTATTGTTCGTCCTCTAG	59.429	52.174	0.00	0.00	0.00	2.43
1285	1324	0.609151	CCAGGATGCCAATGTTGCAA	59.391	50.000	0.00	0.00	42.92	4.08
1528	1567	0.542467	TACCAAGGTAGCACCGGACA	60.542	55.000	9.46	0.00	44.90	4.02
1659	1698	1.663388	CAGGTTCACGTACTGCGCA	60.663	57.895	10.98	10.98	46.11	6.09
2026	2070	2.941333	CGGCGGCATATGCTCAAG	59.059	61.111	26.12	15.90	41.70	3.02
2146	2201	8.579682	TTTAAAAAGCAAAAGCAAAAGCAAAA	57.420	23.077	0.00	0.00	0.00	2.44
2147	2202	8.754230	ATTTAAAAAGCAAAAGCAAAAGCAAA	57.246	23.077	0.00	0.00	0.00	3.68
2148	2203	8.242739	AGATTTAAAAAGCAAAAGCAAAAGCAA	58.757	25.926	0.00	0.00	0.00	3.91
2149	2204	7.697291	CAGATTTAAAAAGCAAAAGCAAAAGCA	59.303	29.630	0.00	0.00	0.00	3.91
2150	2205	7.909641	TCAGATTTAAAAAGCAAAAGCAAAAGC	59.090	29.630	0.00	0.00	0.00	3.51
2151	2206	9.940166	ATCAGATTTAAAAAGCAAAAGCAAAAG	57.060	25.926	0.00	0.00	0.00	2.27
3083	3149	3.984765	GGCACGCGCGCATAGTAC	61.985	66.667	32.58	15.36	39.92	2.73
3197	3263	0.318614	CCAGCACGGCGTTGAAAAAT	60.319	50.000	11.19	0.00	0.00	1.82
3426	3492	7.228108	TGGAGTACTCGTTAATAATCAGTCGAT	59.772	37.037	16.56	0.00	0.00	3.59
3554	3621	5.864418	AAAATGGATGGACTTGATGGATG	57.136	39.130	0.00	0.00	0.00	3.51
3558	3625	6.927416	TCAAGAAAAATGGATGGACTTGATG	58.073	36.000	0.00	0.00	37.77	3.07
3566	3633	7.279313	GGAATCAACATCAAGAAAAATGGATGG	59.721	37.037	0.00	0.00	41.03	3.51
3687	3754	2.163412	ACATTGATGCGCGTGGTATTTT	59.837	40.909	6.97	0.00	0.00	1.82
3699	3766	5.509272	GCATACATATAACGCACATTGATGC	59.491	40.000	0.00	0.00	42.48	3.91
3764	3841	8.575649	TTGTTTAATGGAATTTCCTCTCCTAC	57.424	34.615	16.25	8.15	37.87	3.18
3765	3842	9.768215	ATTTGTTTAATGGAATTTCCTCTCCTA	57.232	29.630	16.25	0.00	37.87	2.94
3823	3900	6.488683	CAAGTCTCCACTAATTTGGTACCAAA	59.511	38.462	35.78	35.78	40.05	3.28
3841	3919	6.749923	ATGACCTTGAATTAAGCAAGTCTC	57.250	37.500	15.59	11.42	40.79	3.36
3865	3943	5.129634	TCTGCTATTGTTGGTGAAGAAACA	58.870	37.500	0.00	0.00	34.57	2.83
4010	4100	0.179108	GGCGCTACTACCTTGTGGAG	60.179	60.000	7.64	0.00	37.04	3.86
4087	4179	5.782331	TCCAAGATGAAGAGGACCCATATAG	59.218	44.000	0.00	0.00	0.00	1.31
4150	4243	7.012044	AGTGAATTGGCGGTGTTAAACTATATC	59.988	37.037	0.00	0.00	0.00	1.63
4156	4252	3.003897	TCAGTGAATTGGCGGTGTTAAAC	59.996	43.478	0.00	0.00	0.00	2.01
4166	4262	1.615392	AGGCAAACTCAGTGAATTGGC	59.385	47.619	25.42	25.42	45.51	4.52
4237	4343	2.096909	CAGCGCACGCATAGGTAATAAC	60.097	50.000	18.24	0.00	44.88	1.89
4247	4353	0.999406	CTAAACTACAGCGCACGCAT	59.001	50.000	18.24	7.41	44.88	4.73
4255	4361	6.034591	TCTCGAACTATTGCTAAACTACAGC	58.965	40.000	0.00	0.00	39.56	4.40
4288	4397	0.106217	GCCTCTGCTAGTCTCCTCCT	60.106	60.000	0.00	0.00	33.53	3.69
4289	4398	0.396417	TGCCTCTGCTAGTCTCCTCC	60.396	60.000	0.00	0.00	38.71	4.30
4290	4399	1.032014	CTGCCTCTGCTAGTCTCCTC	58.968	60.000	0.00	0.00	38.71	3.71
4301	4410	1.915266	TCCTGTCCACCTGCCTCTG	60.915	63.158	0.00	0.00	0.00	3.35
4397	4510	0.037232	CTCTCAAACGGAGGACCCAC	60.037	60.000	0.00	0.00	44.19	4.61
4403	4516	1.153745	CGCCTCTCTCAAACGGAGG	60.154	63.158	0.00	0.00	46.65	4.30

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.