AutoCloner

Multiple sequence alignment - TraesCS3B01G336900

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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	TraesCS3B01G336900	chr3B	100.000	2624	0	0	1	2624	542896603	542899226	0.000000e+00	4846.0
1	TraesCS3B01G336900	chr3B	90.719	2489	114	38	163	2624	542928830	542931228	0.000000e+00	3208.0
2	TraesCS3B01G336900	chr3B	81.754	707	78	28	723	1414	543173871	543174541	6.390000e-151	544.0
3	TraesCS3B01G336900	chr3B	89.786	421	39	2	1250	1670	543067779	543068195	1.070000e-148	536.0
4	TraesCS3B01G336900	chr3B	96.198	263	10	0	322	584	543173450	543173712	5.190000e-117	431.0
5	TraesCS3B01G336900	chr3B	98.089	157	3	0	9	165	542928491	542928647	9.250000e-70	274.0
6	TraesCS3B01G336900	chr3B	84.375	224	18	7	76	288	543035454	543035671	1.230000e-48	204.0
7	TraesCS3B01G336900	chr3D	91.002	1767	91	25	878	2624	416575501	416577219	0.000000e+00	2320.0
8	TraesCS3B01G336900	chr3D	84.639	651	72	16	1024	1670	416951671	416952297	7.980000e-175	623.0
9	TraesCS3B01G336900	chr3D	80.317	757	102	32	873	1605	416562149	416562882	1.790000e-146	529.0
10	TraesCS3B01G336900	chr3D	90.133	375	35	2	1259	1633	416915592	416915964	1.090000e-133	486.0
11	TraesCS3B01G336900	chr3D	84.211	532	37	15	365	867	416575006	416575519	8.500000e-130	473.0
12	TraesCS3B01G336900	chr3D	98.069	259	5	0	322	580	416948967	416949225	3.980000e-123	451.0
13	TraesCS3B01G336900	chr3D	91.379	290	13	4	86	375	416566774	416567051	1.140000e-103	387.0
14	TraesCS3B01G336900	chr3D	85.312	320	18	17	719	1030	416949374	416949672	1.180000e-78	303.0
15	TraesCS3B01G336900	chr3D	87.879	264	15	6	322	576	416914137	416914392	7.100000e-76	294.0
16	TraesCS3B01G336900	chr3D	81.452	372	33	19	875	1225	416915243	416915599	3.330000e-69	272.0
17	TraesCS3B01G336900	chr3D	100.000	45	0	0	11	55	416912266	416912310	1.670000e-12	84.2
18	TraesCS3B01G336900	chr3A	84.354	1911	146	80	76	1930	533996013	533994200	0.000000e+00	1731.0
19	TraesCS3B01G336900	chr3A	81.447	636	85	24	890	1517	534162105	534161495	8.440000e-135	490.0
20	TraesCS3B01G336900	chr3A	80.000	170	24	4	1623	1792	533979895	533979736	1.650000e-22	117.0
21	TraesCS3B01G336900	chr5B	80.952	1596	180	61	587	2112	511292021	511293562	0.000000e+00	1149.0
22	TraesCS3B01G336900	chr5D	79.739	1456	163	74	752	2125	423474091	423475496	0.000000e+00	933.0
23	TraesCS3B01G336900	chr5A	83.492	1048	107	31	607	1614	536970278	536971299	0.000000e+00	917.0

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	TraesCS3B01G336900	chr3B	542896603	542899226	2623	False	4846.00	4846	100.0000	1	2624	1	chr3B.!!$F1	2623
1	TraesCS3B01G336900	chr3B	542928491	542931228	2737	False	1741.00	3208	94.4040	9	2624	2	chr3B.!!$F4	2615
2	TraesCS3B01G336900	chr3B	543173450	543174541	1091	False	487.50	544	88.9760	322	1414	2	chr3B.!!$F5	1092
3	TraesCS3B01G336900	chr3D	416575006	416577219	2213	False	1396.50	2320	87.6065	365	2624	2	chr3D.!!$F2	2259
4	TraesCS3B01G336900	chr3D	416948967	416952297	3330	False	459.00	623	89.3400	322	1670	3	chr3D.!!$F4	1348
5	TraesCS3B01G336900	chr3D	416562149	416567051	4902	False	458.00	529	85.8480	86	1605	2	chr3D.!!$F1	1519
6	TraesCS3B01G336900	chr3D	416912266	416915964	3698	False	284.05	486	89.8660	11	1633	4	chr3D.!!$F3	1622
7	TraesCS3B01G336900	chr3A	533994200	533996013	1813	True	1731.00	1731	84.3540	76	1930	1	chr3A.!!$R2	1854
8	TraesCS3B01G336900	chr3A	534161495	534162105	610	True	490.00	490	81.4470	890	1517	1	chr3A.!!$R3	627
9	TraesCS3B01G336900	chr5B	511292021	511293562	1541	False	1149.00	1149	80.9520	587	2112	1	chr5B.!!$F1	1525
10	TraesCS3B01G336900	chr5D	423474091	423475496	1405	False	933.00	933	79.7390	752	2125	1	chr5D.!!$F1	1373
11	TraesCS3B01G336900	chr5A	536970278	536971299	1021	False	917.00	917	83.4920	607	1614	1	chr5A.!!$F1	1007

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
618	2457	0.040692	GTGTGTGTGTGCAGCTCATG	60.041	55.0	0.0	0.0	0.0	3.07	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2224	9712	0.532862	CGCTCCCACAAGTCAAGTGT	60.533	55.0	0.0	0.0	35.24	3.55	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
107	108	2.254152	AGTTGATGAGTGGGCTCCTA	57.746	50.000	0.00	0.00	40.95	2.94
152	159	4.998051	ACAATGTAACTCATCCAAGGGTT	58.002	39.130	0.00	0.00	35.48	4.11
379	2174	1.412343	AGAGCAGGCTAGCTAGCTTTC	59.588	52.381	37.42	28.02	46.75	2.62
514	2318	3.665745	ACTTCGCGGTAGTTTCCTTTA	57.334	42.857	6.13	0.00	0.00	1.85
544	2351	0.178767	TGCCATGAGATGAACCGGAG	59.821	55.000	9.46	0.00	0.00	4.63
576	2383	0.871722	GTGTGTGTGTGTGTGTGTGT	59.128	50.000	0.00	0.00	0.00	3.72
577	2384	0.871057	TGTGTGTGTGTGTGTGTGTG	59.129	50.000	0.00	0.00	0.00	3.82
578	2385	0.871722	GTGTGTGTGTGTGTGTGTGT	59.128	50.000	0.00	0.00	0.00	3.72
579	2386	0.871057	TGTGTGTGTGTGTGTGTGTG	59.129	50.000	0.00	0.00	0.00	3.82
580	2387	0.871722	GTGTGTGTGTGTGTGTGTGT	59.128	50.000	0.00	0.00	0.00	3.72
581	2388	0.871057	TGTGTGTGTGTGTGTGTGTG	59.129	50.000	0.00	0.00	0.00	3.82
582	2389	0.871722	GTGTGTGTGTGTGTGTGTGT	59.128	50.000	0.00	0.00	0.00	3.72
583	2390	0.871057	TGTGTGTGTGTGTGTGTGTG	59.129	50.000	0.00	0.00	0.00	3.82
584	2391	0.871722	GTGTGTGTGTGTGTGTGTGT	59.128	50.000	0.00	0.00	0.00	3.72
585	2392	0.871057	TGTGTGTGTGTGTGTGTGTG	59.129	50.000	0.00	0.00	0.00	3.82
615	2454	1.353103	GTGTGTGTGTGTGCAGCTC	59.647	57.895	0.00	0.00	0.00	4.09
616	2455	1.078567	TGTGTGTGTGTGCAGCTCA	60.079	52.632	0.00	0.00	0.00	4.26
617	2456	0.464193	TGTGTGTGTGTGCAGCTCAT	60.464	50.000	0.00	0.00	0.00	2.90
618	2457	0.040692	GTGTGTGTGTGCAGCTCATG	60.041	55.000	0.00	0.00	0.00	3.07
700	2581	0.613777	CCTCGGCCACTTAAACTCCT	59.386	55.000	2.24	0.00	0.00	3.69
716	2598	2.427245	CCTCCCTCCACCACTAGCG	61.427	68.421	0.00	0.00	0.00	4.26
717	2599	1.682684	CTCCCTCCACCACTAGCGT	60.683	63.158	0.00	0.00	0.00	5.07
735	2638	2.927014	GCGTGCTCTGTAGTTGTAGCTT	60.927	50.000	0.00	0.00	35.95	3.74
750	2653	0.773644	AGCTTGAGCCCCTTCAGAAA	59.226	50.000	0.00	0.00	43.38	2.52
869	3408	5.377478	TGTCCTTTTCCTCTTCTTCTTTCC	58.623	41.667	0.00	0.00	0.00	3.13
871	3410	4.082845	CCTTTTCCTCTTCTTCTTTCCCC	58.917	47.826	0.00	0.00	0.00	4.81
979	3545	3.744846	GCTGATCTCGTCCTACTCCTACA	60.745	52.174	0.00	0.00	0.00	2.74
980	3546	4.062293	CTGATCTCGTCCTACTCCTACAG	58.938	52.174	0.00	0.00	0.00	2.74
1229	5886	1.301244	GACCGATCCATCATGCGCT	60.301	57.895	9.73	0.00	0.00	5.92
1244	5903	1.450134	CGCTAAGCTGGCATGGTGA	60.450	57.895	11.60	0.00	0.00	4.02
1292	5957	2.791927	CATCGAGCTGACGGACGA	59.208	61.111	0.00	0.00	39.01	4.20
1339	6004	2.109126	GTCGGGATTCTGTGCTGCC	61.109	63.158	0.00	0.00	0.00	4.85
1483	6148	2.283529	GCCGTCTGGGTCTTCCTCA	61.284	63.158	0.00	0.00	38.44	3.86
1575	6240	3.721706	CTCAGCTTCCGGGCCCTT	61.722	66.667	22.43	0.00	0.00	3.95
1654	6473	3.891977	GTGGATCAGCTCATGAGGTACTA	59.108	47.826	26.06	15.19	42.53	1.82
1655	6474	3.891977	TGGATCAGCTCATGAGGTACTAC	59.108	47.826	26.06	17.00	42.53	2.73
1669	6489	4.382291	AGGTACTACTGATGAGAGCGTAG	58.618	47.826	0.00	0.00	36.02	3.51
1682	6502	1.003008	GAGCGTAGTTCTAGGGCGTAC	60.003	57.143	0.00	0.00	33.98	3.67
1683	6503	1.020437	GCGTAGTTCTAGGGCGTACT	58.980	55.000	0.00	0.00	0.00	2.73
1684	6504	1.003008	GCGTAGTTCTAGGGCGTACTC	60.003	57.143	0.00	0.00	0.00	2.59
1714	6534	2.475187	GCATTGATTCTGCTGTGACGAC	60.475	50.000	0.00	0.00	36.68	4.34
1717	6537	1.613437	TGATTCTGCTGTGACGACTGA	59.387	47.619	0.00	0.00	0.00	3.41
1718	6538	2.232208	TGATTCTGCTGTGACGACTGAT	59.768	45.455	0.00	0.00	0.00	2.90
1750	6600	6.288294	AGTGCCATATTTGCGAATCTAGTAA	58.712	36.000	1.35	0.00	0.00	2.24
1923	6788	7.363431	TGTGATCGTCAGACATGAGTTATATC	58.637	38.462	0.00	0.00	35.66	1.63
1924	6789	7.229506	TGTGATCGTCAGACATGAGTTATATCT	59.770	37.037	0.00	0.00	35.66	1.98
2224	9712	2.678580	TGGAGATCCACACGCCGA	60.679	61.111	0.00	0.00	42.01	5.54
2244	9732	1.598130	ACTTGACTTGTGGGAGCGC	60.598	57.895	0.00	0.00	0.00	5.92
2245	9733	2.664851	TTGACTTGTGGGAGCGCG	60.665	61.111	0.00	0.00	0.00	6.86
2265	9753	2.353030	GTTTCACCACAACGCCGC	60.353	61.111	0.00	0.00	0.00	6.53
2371	9859	2.882927	TCGTGGAGTCGATATTTGGG	57.117	50.000	0.00	0.00	34.85	4.12
2375	9863	3.195661	GTGGAGTCGATATTTGGGTCAC	58.804	50.000	0.00	0.00	0.00	3.67
2411	10339	7.555087	TCATCCAAAGAGTTGTGAAATTGTTT	58.445	30.769	0.00	0.00	32.40	2.83
2431	10359	1.695242	TCACAACTTACACATCCCGGT	59.305	47.619	0.00	0.00	0.00	5.28
2482	10410	6.610075	AGGCATAATTGAACTTTGTTGGAT	57.390	33.333	0.00	0.00	0.00	3.41
2483	10411	6.400568	AGGCATAATTGAACTTTGTTGGATG	58.599	36.000	0.00	0.00	0.00	3.51
2488	10416	5.612725	ATTGAACTTTGTTGGATGTGGTT	57.387	34.783	0.00	0.00	0.00	3.67
2489	10417	4.647424	TGAACTTTGTTGGATGTGGTTC	57.353	40.909	0.00	0.00	34.20	3.62
2490	10418	4.019858	TGAACTTTGTTGGATGTGGTTCA	58.980	39.130	0.00	0.00	39.04	3.18
2559	10487	7.476540	AATTTAGAACCCCAACTCCAAATAC	57.523	36.000	0.00	0.00	0.00	1.89
2610	10538	1.829222	GACGATTGGAGGGTGGTTCTA	59.171	52.381	0.00	0.00	0.00	2.10

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
1	2	1.028905	CCACCAAAGGTCTCGCAAAA	58.971	50.000	0.00	0.00	31.02	2.44
4	5	1.371183	CTCCACCAAAGGTCTCGCA	59.629	57.895	0.00	0.00	31.02	5.10
5	6	2.035442	GCTCCACCAAAGGTCTCGC	61.035	63.158	0.00	0.00	31.02	5.03
6	7	0.035458	AAGCTCCACCAAAGGTCTCG	59.965	55.000	0.00	0.00	31.02	4.04
7	8	1.072331	TGAAGCTCCACCAAAGGTCTC	59.928	52.381	0.00	0.00	31.02	3.36
379	2174	2.188829	CATGCATACGGGGCAGTGG	61.189	63.158	0.00	0.00	45.68	4.00
514	2318	1.064240	TCTCATGGCAATGGCAGTGAT	60.064	47.619	20.42	0.64	42.43	3.06
544	2351	0.034059	CACACACACAGGGAGGAGAC	59.966	60.000	0.00	0.00	0.00	3.36
576	2383	0.871057	CACACACACACACACACACA	59.129	50.000	0.00	0.00	0.00	3.72
577	2384	0.871722	ACACACACACACACACACAC	59.128	50.000	0.00	0.00	0.00	3.82
578	2385	0.871057	CACACACACACACACACACA	59.129	50.000	0.00	0.00	0.00	3.72
579	2386	0.871722	ACACACACACACACACACAC	59.128	50.000	0.00	0.00	0.00	3.82
580	2387	0.871057	CACACACACACACACACACA	59.129	50.000	0.00	0.00	0.00	3.72
581	2388	0.871722	ACACACACACACACACACAC	59.128	50.000	0.00	0.00	0.00	3.82
582	2389	0.871057	CACACACACACACACACACA	59.129	50.000	0.00	0.00	0.00	3.72
583	2390	0.871722	ACACACACACACACACACAC	59.128	50.000	0.00	0.00	0.00	3.82
584	2391	0.871057	CACACACACACACACACACA	59.129	50.000	0.00	0.00	0.00	3.72
585	2392	0.871722	ACACACACACACACACACAC	59.128	50.000	0.00	0.00	0.00	3.82
615	2454	2.114331	GAGCAGCCGTAGCATGCATG	62.114	60.000	22.70	22.70	42.22	4.06
616	2455	1.890979	GAGCAGCCGTAGCATGCAT	60.891	57.895	21.98	7.68	42.22	3.96
617	2456	2.512286	GAGCAGCCGTAGCATGCA	60.512	61.111	21.98	2.77	42.22	3.96
618	2457	3.634072	CGAGCAGCCGTAGCATGC	61.634	66.667	10.51	10.51	43.56	4.06
625	2464	3.324099	CTACGTGTCGAGCAGCCGT	62.324	63.158	0.00	0.00	34.77	5.68
700	2581	1.982395	CACGCTAGTGGTGGAGGGA	60.982	63.158	8.42	0.00	44.34	4.20
716	2598	3.914312	TCAAGCTACAACTACAGAGCAC	58.086	45.455	0.00	0.00	37.40	4.40
717	2599	3.615110	GCTCAAGCTACAACTACAGAGCA	60.615	47.826	0.00	0.00	44.77	4.26
735	2638	2.867109	CTTCTTTCTGAAGGGGCTCA	57.133	50.000	0.00	0.00	46.25	4.26
750	2653	2.638480	TGTTAGCTTGGTGTGCTTCT	57.362	45.000	0.00	0.00	41.46	2.85
869	3408	6.358974	AGAAGAAGAAGAAGAAGAAGAGGG	57.641	41.667	0.00	0.00	0.00	4.30
871	3410	9.196552	GAAGAAGAAGAAGAAGAAGAAGAAGAG	57.803	37.037	0.00	0.00	0.00	2.85
935	3482	6.016276	CAGCAACAACTTATGGTTAGGTTCTT	60.016	38.462	0.00	0.00	36.23	2.52
979	3545	2.175069	TCGATCCAAGCTAGGTAGGACT	59.825	50.000	0.00	0.00	32.04	3.85
980	3546	2.584236	TCGATCCAAGCTAGGTAGGAC	58.416	52.381	0.00	0.00	32.04	3.85
1050	5646	3.314083	GGCATCCCGGATCTTCTTC	57.686	57.895	0.73	0.00	0.00	2.87
1140	5745	0.901827	ACACATGGATGTACTCGGCA	59.098	50.000	0.00	0.00	39.39	5.69
1229	5886	1.141657	GAGGATCACCATGCCAGCTTA	59.858	52.381	0.00	0.00	38.94	3.09
1237	5896	1.474677	GGACTGCAGAGGATCACCATG	60.475	57.143	23.35	0.00	37.82	3.66
1244	5903	1.273495	TGAAGGAGGACTGCAGAGGAT	60.273	52.381	23.35	2.64	28.91	3.24
1430	6095	0.544357	ATGGAAGAGGACGGTGACCA	60.544	55.000	1.11	0.00	0.00	4.02
1483	6148	3.152400	GTATCCTGGGTCGGCGGT	61.152	66.667	7.21	0.00	0.00	5.68
1575	6240	1.616327	CCACCCATCACCTCCCAGA	60.616	63.158	0.00	0.00	0.00	3.86
1654	6473	3.880490	CCTAGAACTACGCTCTCATCAGT	59.120	47.826	0.00	0.00	0.00	3.41
1655	6474	3.252215	CCCTAGAACTACGCTCTCATCAG	59.748	52.174	0.00	0.00	0.00	2.90
1669	6489	3.807553	ACTCTAGAGTACGCCCTAGAAC	58.192	50.000	24.04	0.00	40.34	3.01
1678	6498	7.536964	CAGAATCAATGCATACTCTAGAGTACG	59.463	40.741	30.33	24.83	45.61	3.67
1679	6499	7.328249	GCAGAATCAATGCATACTCTAGAGTAC	59.672	40.741	30.33	20.42	43.31	2.73
1682	6502	6.366604	CAGCAGAATCAATGCATACTCTAGAG	59.633	42.308	18.49	18.49	46.31	2.43
1683	6503	6.183360	ACAGCAGAATCAATGCATACTCTAGA	60.183	38.462	0.00	0.00	46.31	2.43
1684	6504	5.990386	ACAGCAGAATCAATGCATACTCTAG	59.010	40.000	0.00	0.00	46.31	2.43
1698	6518	2.354109	TCAGTCGTCACAGCAGAATC	57.646	50.000	0.00	0.00	0.00	2.52
1718	6538	4.039852	TCGCAAATATGGCACTACTCCATA	59.960	41.667	4.43	4.43	46.92	2.74
1750	6600	8.370266	TGGATACTAATTAACACTACACCAGT	57.630	34.615	0.00	0.00	35.73	4.00
2224	9712	0.532862	CGCTCCCACAAGTCAAGTGT	60.533	55.000	0.00	0.00	35.24	3.55
2343	9831	2.644676	TCGACTCCACGATCAGAAGAT	58.355	47.619	0.00	0.00	37.37	2.40
2369	9857	4.058817	GGATGATTGATAACTCGTGACCC	58.941	47.826	0.00	0.00	0.00	4.46
2371	9859	6.535150	TCTTTGGATGATTGATAACTCGTGAC	59.465	38.462	0.00	0.00	0.00	3.67
2375	9863	7.065085	ACAACTCTTTGGATGATTGATAACTCG	59.935	37.037	0.00	0.00	37.00	4.18
2411	10339	1.695242	ACCGGGATGTGTAAGTTGTGA	59.305	47.619	6.32	0.00	0.00	3.58
2431	10359	1.910671	ACCCCATTAGTTTGAGGCGTA	59.089	47.619	0.00	0.00	0.00	4.42
2482	10410	7.732025	TGTATTTCTCTCTTAGTTGAACCACA	58.268	34.615	0.00	0.00	0.00	4.17
2483	10411	8.779354	ATGTATTTCTCTCTTAGTTGAACCAC	57.221	34.615	0.00	0.00	0.00	4.16
2541	10469	2.089201	CCGTATTTGGAGTTGGGGTTC	58.911	52.381	0.00	0.00	0.00	3.62
2575	10503	1.324383	TCGTCCTATGCGGCTAATCA	58.676	50.000	0.00	0.00	0.00	2.57
2576	10504	2.656560	ATCGTCCTATGCGGCTAATC	57.343	50.000	0.00	0.00	0.00	1.75

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.