AutoCloner

Multiple sequence alignment - TraesCS3A01G032600

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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	TraesCS3A01G032600	chr3A	100.000	3317	0	0	1	3317	18832012	18828696	0.000000e+00	6126.0
1	TraesCS3A01G032600	chr3A	84.327	1946	237	29	422	2342	18837868	18835966	0.000000e+00	1842.0
2	TraesCS3A01G032600	chr3A	97.118	937	15	4	2381	3317	31635663	31636587	0.000000e+00	1570.0
3	TraesCS3A01G032600	chr3A	91.429	105	7	2	2851	2954	18829263	18829160	3.450000e-30	143.0
4	TraesCS3A01G032600	chrUn	92.442	2408	118	25	1	2388	37706242	37703879	0.000000e+00	3380.0
5	TraesCS3A01G032600	chrUn	84.898	1854	205	46	547	2380	37503981	37505779	0.000000e+00	1803.0
6	TraesCS3A01G032600	chrUn	83.282	1304	200	15	1059	2356	37181801	37180510	0.000000e+00	1184.0
7	TraesCS3A01G032600	chrUn	84.914	643	66	11	435	1061	37795659	37796286	3.630000e-174	621.0
8	TraesCS3A01G032600	chrUn	86.694	496	63	2	969	1461	37869673	37870168	6.260000e-152	547.0
9	TraesCS3A01G032600	chrUn	86.694	496	63	2	969	1461	333562661	333563156	6.260000e-152	547.0
10	TraesCS3A01G032600	chrUn	85.714	364	41	7	50	413	37550009	37550361	1.120000e-99	374.0
11	TraesCS3A01G032600	chrUn	85.714	364	41	7	50	413	366049262	366048910	1.120000e-99	374.0
12	TraesCS3A01G032600	chrUn	84.469	367	47	7	590	955	37869203	37869560	1.460000e-93	353.0
13	TraesCS3A01G032600	chrUn	84.469	367	47	7	590	955	333562191	333562548	1.460000e-93	353.0
14	TraesCS3A01G032600	chrUn	90.654	107	10	0	422	528	37503583	37503689	3.450000e-30	143.0
15	TraesCS3A01G032600	chr3D	92.234	2408	154	18	1	2388	17748933	17746539	0.000000e+00	3380.0
16	TraesCS3A01G032600	chr3D	84.461	1937	244	29	419	2340	17779081	17777187	0.000000e+00	1857.0
17	TraesCS3A01G032600	chr3D	78.395	324	65	5	2007	2327	507534523	507534202	4.340000e-49	206.0
18	TraesCS3A01G032600	chr3D	89.394	66	4	3	2385	2448	29625102	29625166	2.740000e-11	80.5
19	TraesCS3A01G032600	chr6A	96.888	932	13	3	2387	3317	555587451	555586535	0.000000e+00	1546.0
20	TraesCS3A01G032600	chr7B	91.468	879	60	8	2446	3317	117987724	117986854	0.000000e+00	1194.0
21	TraesCS3A01G032600	chr7B	87.631	477	41	12	2850	3317	436974985	436975452	3.770000e-149	538.0
22	TraesCS3A01G032600	chr6B	87.420	469	47	9	2851	3312	664051698	664051235	2.270000e-146	529.0
23	TraesCS3A01G032600	chr6B	82.310	277	33	12	2583	2853	390656432	390656166	3.330000e-55	226.0
24	TraesCS3A01G032600	chr4D	78.318	844	166	14	959	1801	461562175	461561348	2.270000e-146	529.0
25	TraesCS3A01G032600	chr2B	86.574	432	45	9	2870	3294	115856557	115856982	6.480000e-127	464.0
26	TraesCS3A01G032600	chr2B	85.792	366	42	9	2960	3317	140886302	140886665	2.420000e-101	379.0
27	TraesCS3A01G032600	chr2B	90.909	55	5	0	2384	2438	391039275	391039329	1.280000e-09	75.0
28	TraesCS3A01G032600	chr4A	83.795	469	40	18	2847	3306	33241166	33241607	2.380000e-111	412.0
29	TraesCS3A01G032600	chr4A	82.942	469	41	19	2847	3306	33221405	33221843	1.440000e-103	387.0
30	TraesCS3A01G032600	chr4A	88.525	61	5	2	2380	2439	716142033	716141974	4.590000e-09	73.1
31	TraesCS3A01G032600	chr4A	89.474	57	5	1	2384	2439	716366224	716366280	1.650000e-08	71.3
32	TraesCS3A01G032600	chr6D	82.189	466	57	20	2859	3315	22361093	22360645	8.690000e-101	377.0
33	TraesCS3A01G032600	chr7D	83.051	413	52	15	2446	2853	517259351	517259750	3.150000e-95	359.0
34	TraesCS3A01G032600	chr2D	86.076	316	35	7	2980	3288	552577809	552578122	6.860000e-87	331.0
35	TraesCS3A01G032600	chr2D	81.875	320	52	5	2007	2321	639461282	639461600	7.060000e-67	265.0
36	TraesCS3A01G032600	chr1B	94.444	54	1	2	2376	2429	421528999	421529050	7.630000e-12	82.4
37	TraesCS3A01G032600	chr3B	95.556	45	2	0	2385	2429	456967580	456967536	4.590000e-09	73.1
38	TraesCS3A01G032600	chr2A	92.157	51	3	1	2382	2431	775099252	775099202	1.650000e-08	71.3

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	TraesCS3A01G032600	chr3A	18828696	18832012	3316	True	3134.5	6126	95.7145	1	3317	2	chr3A.!!$R2	3316
1	TraesCS3A01G032600	chr3A	18835966	18837868	1902	True	1842.0	1842	84.3270	422	2342	1	chr3A.!!$R1	1920
2	TraesCS3A01G032600	chr3A	31635663	31636587	924	False	1570.0	1570	97.1180	2381	3317	1	chr3A.!!$F1	936
3	TraesCS3A01G032600	chrUn	37703879	37706242	2363	True	3380.0	3380	92.4420	1	2388	1	chrUn.!!$R2	2387
4	TraesCS3A01G032600	chrUn	37180510	37181801	1291	True	1184.0	1184	83.2820	1059	2356	1	chrUn.!!$R1	1297
5	TraesCS3A01G032600	chrUn	37503583	37505779	2196	False	973.0	1803	87.7760	422	2380	2	chrUn.!!$F3	1958
6	TraesCS3A01G032600	chrUn	37795659	37796286	627	False	621.0	621	84.9140	435	1061	1	chrUn.!!$F2	626
7	TraesCS3A01G032600	chrUn	37869203	37870168	965	False	450.0	547	85.5815	590	1461	2	chrUn.!!$F4	871
8	TraesCS3A01G032600	chrUn	333562191	333563156	965	False	450.0	547	85.5815	590	1461	2	chrUn.!!$F5	871
9	TraesCS3A01G032600	chr3D	17746539	17748933	2394	True	3380.0	3380	92.2340	1	2388	1	chr3D.!!$R1	2387
10	TraesCS3A01G032600	chr3D	17777187	17779081	1894	True	1857.0	1857	84.4610	419	2340	1	chr3D.!!$R2	1921
11	TraesCS3A01G032600	chr6A	555586535	555587451	916	True	1546.0	1546	96.8880	2387	3317	1	chr6A.!!$R1	930
12	TraesCS3A01G032600	chr7B	117986854	117987724	870	True	1194.0	1194	91.4680	2446	3317	1	chr7B.!!$R1	871
13	TraesCS3A01G032600	chr4D	461561348	461562175	827	True	529.0	529	78.3180	959	1801	1	chr4D.!!$R1	842

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
141	146	0.252197	GTTAGGGTCCGCTGGTCATT	59.748	55.0	0.0	0.0	0.0	2.57	F
1108	1541	0.036388	CTACCTCACACCAATGGCGT	60.036	55.0	0.0	0.0	0.0	5.68	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1646	2081	0.539986	GGCCTTAACGATGGACCTGA	59.460	55.000	0.0	0.0	0.0	3.86	R
2612	3059	1.139058	ACCACAACTATGATCGAGCCC	59.861	52.381	0.0	0.0	0.0	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)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
41	42	2.829003	TAGCTAGCTCGCGCACCT	60.829	61.111	23.26	2.02	39.10	4.00
48	49	4.827087	CTCGCGCACCTGAGCCAT	62.827	66.667	8.75	0.00	37.57	4.40
133	138	2.820037	GCAGCAGTTAGGGTCCGC	60.820	66.667	0.00	0.00	0.00	5.54
141	146	0.252197	GTTAGGGTCCGCTGGTCATT	59.748	55.000	0.00	0.00	0.00	2.57
161	166	2.023223	GCGTTGAGGCGTTTCGGTA	61.023	57.895	0.00	0.00	0.00	4.02
211	220	1.202940	GCTGAAAGTTTCCTCCCACCT	60.203	52.381	13.01	0.00	35.30	4.00
214	223	2.374170	TGAAAGTTTCCTCCCACCTACC	59.626	50.000	13.01	0.00	0.00	3.18
270	279	5.591067	GTCCCCAATCTCGTAGATATAGAGG	59.409	48.000	0.00	0.00	32.89	3.69
279	288	3.757493	CGTAGATATAGAGGAAACGGCCT	59.243	47.826	0.00	0.00	42.17	5.19
282	291	1.420430	TATAGAGGAAACGGCCTGGG	58.580	55.000	0.00	0.00	38.73	4.45
328	337	2.044123	AGAGGATGGACGATTTTGCC	57.956	50.000	0.00	0.00	0.00	4.52
330	339	1.064134	GGATGGACGATTTTGCCGC	59.936	57.895	0.00	0.00	0.00	6.53
337	346	2.096218	GGACGATTTTGCCGCATCTATC	60.096	50.000	0.00	0.00	0.00	2.08
343	352	3.626924	GCCGCATCTATCCGGGGT	61.627	66.667	0.00	0.00	44.49	4.95
369	378	1.389609	AACGTCCGCATCCCGTAGAT	61.390	55.000	0.00	0.00	33.88	1.98
415	424	4.372656	CTTTTTACGGGATCTGCTAGAGG	58.627	47.826	0.00	0.00	0.00	3.69
425	434	4.406003	GGATCTGCTAGAGGTGGTTTAAGA	59.594	45.833	0.00	0.00	0.00	2.10
433	442	8.161425	TGCTAGAGGTGGTTTAAGAAGTTTATT	58.839	33.333	0.00	0.00	0.00	1.40
515	524	3.569701	ACTTTCTACCACATGCAAACCTG	59.430	43.478	0.00	0.00	0.00	4.00
694	1020	4.780815	TGGCAGTATAGTGGAAAGGAATG	58.219	43.478	9.60	0.00	0.00	2.67
697	1023	5.297029	GGCAGTATAGTGGAAAGGAATGTTC	59.703	44.000	9.60	0.00	0.00	3.18
861	1189	3.114616	CGACGAGCACAGCCCAAG	61.115	66.667	0.00	0.00	0.00	3.61
890	1218	7.906160	AGTTCCACGAGTGAATAATTAAATCG	58.094	34.615	4.59	4.46	35.00	3.34
908	1236	8.556213	TTAAATCGGTGTTAATTTCTGTAGCT	57.444	30.769	0.00	0.00	0.00	3.32
938	1267	5.545658	AAATGGATGCTATATAAACCGCG	57.454	39.130	0.00	0.00	0.00	6.46
1108	1541	0.036388	CTACCTCACACCAATGGCGT	60.036	55.000	0.00	0.00	0.00	5.68
1234	1668	4.821589	CGTTCCTCAGCCGCCTCC	62.822	72.222	0.00	0.00	0.00	4.30
1290	1724	0.259065	ACGAGGCTGGGATCTACAGA	59.741	55.000	18.12	0.00	38.20	3.41
1352	1786	1.335182	CGACGGTGATGCTAGTCAGAT	59.665	52.381	0.00	0.00	33.56	2.90
1646	2081	0.034896	GGTGGTGATGGAACGACAGT	59.965	55.000	0.00	0.00	31.04	3.55
1915	2354	8.803397	ACATTCTTTTGAGGTACCCTTTATAC	57.197	34.615	8.74	0.00	31.76	1.47
2005	2447	5.070001	ACACACTGCTTAACCACATACATT	58.930	37.500	0.00	0.00	0.00	2.71
2310	2752	0.745468	GGGGTGTCATCGAGGTCTAC	59.255	60.000	0.00	0.00	0.00	2.59
2343	2785	2.496470	TGCTGCAAATGATGTAATGGCA	59.504	40.909	0.00	0.00	0.00	4.92
2412	2858	3.124270	ATTGATGGCGCGCGTTGA	61.124	55.556	32.35	15.81	0.00	3.18
2612	3059	3.062763	GGTATGATTGATGAGAGTGCCG	58.937	50.000	0.00	0.00	0.00	5.69
2632	3079	1.139058	GGGCTCGATCATAGTTGTGGT	59.861	52.381	0.00	0.00	0.00	4.16
2633	3080	2.420129	GGGCTCGATCATAGTTGTGGTT	60.420	50.000	0.00	0.00	0.00	3.67
2634	3081	2.609459	GGCTCGATCATAGTTGTGGTTG	59.391	50.000	0.00	0.00	0.00	3.77
2635	3082	2.030946	GCTCGATCATAGTTGTGGTTGC	59.969	50.000	0.00	0.00	0.00	4.17
2636	3083	3.261580	CTCGATCATAGTTGTGGTTGCA	58.738	45.455	0.00	0.00	0.00	4.08
2637	3084	3.669536	TCGATCATAGTTGTGGTTGCAA	58.330	40.909	0.00	0.00	0.00	4.08
2638	3085	4.068599	TCGATCATAGTTGTGGTTGCAAA	58.931	39.130	0.00	0.00	0.00	3.68
2639	3086	4.699735	TCGATCATAGTTGTGGTTGCAAAT	59.300	37.500	0.00	0.00	0.00	2.32
2672	3119	8.475331	AATAATCGTAGGCAAGTATAAATCCG	57.525	34.615	0.00	0.00	0.00	4.18
3155	3610	1.928868	CCCTCTGATGCAAGGGTTTT	58.071	50.000	12.45	0.00	46.21	2.43

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
115	120	2.125106	CGGACCCTAACTGCTGCC	60.125	66.667	0.00	0.00	0.00	4.85
116	121	2.820037	GCGGACCCTAACTGCTGC	60.820	66.667	0.00	0.00	36.79	5.25
117	122	2.982130	AGCGGACCCTAACTGCTG	59.018	61.111	0.00	0.00	46.37	4.41
122	127	0.252197	AATGACCAGCGGACCCTAAC	59.748	55.000	1.50	0.00	0.00	2.34
133	138	1.926511	GCCTCAACGCCAATGACCAG	61.927	60.000	0.00	0.00	0.00	4.00
141	146	3.342627	CGAAACGCCTCAACGCCA	61.343	61.111	0.00	0.00	36.19	5.69
161	166	0.883370	GTCTTTCCCAACGCGACCTT	60.883	55.000	15.93	0.00	0.00	3.50
201	210	0.115745	AGAAACGGTAGGTGGGAGGA	59.884	55.000	0.00	0.00	0.00	3.71
211	220	6.297582	TGGACCTGAAAATAAAGAAACGGTA	58.702	36.000	0.00	0.00	0.00	4.02
214	223	6.677913	ACATGGACCTGAAAATAAAGAAACG	58.322	36.000	0.00	0.00	0.00	3.60
247	256	5.491439	TCCTCTATATCTACGAGATTGGGGA	59.509	44.000	0.00	0.00	36.20	4.81
270	279	0.465460	TGCATATCCCAGGCCGTTTC	60.465	55.000	0.00	0.00	31.20	2.78
279	288	1.148273	GCGGAACCTGCATATCCCA	59.852	57.895	6.91	0.00	0.00	4.37
282	291	3.502191	TTTTTGCGGAACCTGCATATC	57.498	42.857	0.93	0.00	42.84	1.63
304	313	6.627287	CGGCAAAATCGTCCATCCTCTATATA	60.627	42.308	0.00	0.00	0.00	0.86
307	316	3.744660	GGCAAAATCGTCCATCCTCTAT	58.255	45.455	0.00	0.00	0.00	1.98
315	324	0.676466	AGATGCGGCAAAATCGTCCA	60.676	50.000	6.82	0.00	0.00	4.02
328	337	1.754380	TTCCACCCCGGATAGATGCG	61.754	60.000	0.73	0.00	45.80	4.73
330	339	3.290948	TTTTTCCACCCCGGATAGATG	57.709	47.619	0.73	0.00	45.80	2.90
369	378	0.037512	TCCGACAAAATAACCGCCGA	60.038	50.000	0.00	0.00	0.00	5.54
425	434	6.930164	TGCATGTGCTGAAAATGAATAAACTT	59.070	30.769	6.55	0.00	42.66	2.66
433	442	3.391965	GGTTTGCATGTGCTGAAAATGA	58.608	40.909	6.55	0.00	42.66	2.57
515	524	2.861935	GGCTTGCATGTATTTGATGTGC	59.138	45.455	1.14	0.00	36.39	4.57
638	956	6.942532	TTCATGGACAGCTCATTAATTACC	57.057	37.500	0.00	0.00	0.00	2.85
694	1020	3.486108	CGGACACAAGATATAGCACGAAC	59.514	47.826	0.00	0.00	0.00	3.95
697	1023	3.043586	GACGGACACAAGATATAGCACG	58.956	50.000	0.00	0.00	0.00	5.34
890	1218	5.642063	TGCTACAGCTACAGAAATTAACACC	59.358	40.000	2.44	0.00	42.66	4.16
938	1267	6.518736	GTGTTGATTTTACTTACGTAGCTTGC	59.481	38.462	0.00	0.00	0.00	4.01
946	1275	6.962116	TGTTGTGTGTGTTGATTTTACTTACG	59.038	34.615	0.00	0.00	0.00	3.18
953	1282	3.506810	CGGTGTTGTGTGTGTTGATTTT	58.493	40.909	0.00	0.00	0.00	1.82
954	1283	2.159310	CCGGTGTTGTGTGTGTTGATTT	60.159	45.455	0.00	0.00	0.00	2.17
1108	1541	2.334946	GCTGGATGGCGCAACTGAA	61.335	57.895	10.83	0.00	0.00	3.02
1234	1668	4.093952	CGTGGAAAGCAGCCGCAG	62.094	66.667	0.00	0.00	42.27	5.18
1290	1724	0.611340	GGTAGGACAGTGGGACGAGT	60.611	60.000	0.00	0.00	0.00	4.18
1383	1817	2.831770	ATGGCCGCCTCCATGTAG	59.168	61.111	11.61	0.00	44.72	2.74
1646	2081	0.539986	GGCCTTAACGATGGACCTGA	59.460	55.000	0.00	0.00	0.00	3.86
2005	2447	3.132646	AGAACAAGCTGACATGGCAAAAA	59.867	39.130	1.11	0.00	0.00	1.94
2310	2752	1.255882	TTGCAGCACAACCTTATGGG	58.744	50.000	0.00	0.00	41.89	4.00
2343	2785	7.802949	CCACTACTTTATGGATACCAAAGGGTT	60.803	40.741	0.00	0.00	40.87	4.11
2412	2858	1.595794	CGTAAAAATAGACGGGCGCAT	59.404	47.619	10.83	0.00	35.43	4.73
2470	2916	6.542735	CCTTCCCTACTATTTGCTACTTTTCC	59.457	42.308	0.00	0.00	0.00	3.13
2580	3027	4.694760	TCAATCATACCTAGCATGCACT	57.305	40.909	21.98	1.90	0.00	4.40
2612	3059	1.139058	ACCACAACTATGATCGAGCCC	59.861	52.381	0.00	0.00	0.00	5.19
2635	3082	8.572828	TGCCTACGATTATTATTGCAAATTTG	57.427	30.769	14.03	14.03	0.00	2.32
2636	3083	9.248291	CTTGCCTACGATTATTATTGCAAATTT	57.752	29.630	1.71	0.00	37.07	1.82
2637	3084	8.413229	ACTTGCCTACGATTATTATTGCAAATT	58.587	29.630	1.71	0.00	37.07	1.82
2638	3085	7.940850	ACTTGCCTACGATTATTATTGCAAAT	58.059	30.769	1.71	0.00	37.07	2.32
2639	3086	7.328277	ACTTGCCTACGATTATTATTGCAAA	57.672	32.000	1.71	0.00	37.07	3.68
2672	3119	1.153289	ATCTCCTGGATGTGCGTGC	60.153	57.895	0.00	0.00	32.69	5.34

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.