AutoCloner

Multiple sequence alignment - TraesCS3A01G003400

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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	TraesCS3A01G003400	chr3A	100.000	2599	0	0	1	2599	1796362	1798960	0.000000e+00	4800.0
1	TraesCS3A01G003400	chr3A	86.121	807	79	14	1038	1812	1789558	1790363	0.000000e+00	839.0
2	TraesCS3A01G003400	chr3A	87.676	284	23	5	734	1015	1789155	1789428	1.160000e-83	320.0
3	TraesCS3A01G003400	chr3A	76.672	583	113	17	1013	1583	1851920	1852491	4.200000e-78	302.0
4	TraesCS3A01G003400	chr3A	90.783	217	19	1	1502	1717	1859549	1859765	3.270000e-74	289.0
5	TraesCS3A01G003400	chr3A	85.338	266	35	4	2316	2578	208836432	208836168	3.300000e-69	272.0
6	TraesCS3A01G003400	chr3A	91.304	69	6	0	1746	1814	1770278	1770346	7.660000e-16	95.3
7	TraesCS3A01G003400	chr3A	92.453	53	4	0	1762	1814	1792170	1792222	2.770000e-10	76.8
8	TraesCS3A01G003400	chr3A	100.000	32	0	0	1012	1043	1789458	1789489	2.790000e-05	60.2
9	TraesCS3A01G003400	chr3D	96.197	1525	54	2	292	1814	2240287	2238765	0.000000e+00	2492.0
10	TraesCS3A01G003400	chr3D	85.507	1104	99	34	758	1812	2243677	2242586	0.000000e+00	1096.0
11	TraesCS3A01G003400	chr3D	79.459	813	130	22	1013	1806	2256696	2255902	2.280000e-150	542.0
12	TraesCS3A01G003400	chr3D	76.558	738	121	33	840	1552	2202030	2201320	8.840000e-95	357.0
13	TraesCS3A01G003400	chr3D	92.035	226	17	1	1502	1726	2200938	2200713	1.500000e-82	316.0
14	TraesCS3A01G003400	chr3D	86.722	241	30	1	1074	1314	2201195	2200957	1.530000e-67	267.0
15	TraesCS3A01G003400	chr3D	91.935	62	5	0	1753	1814	2271791	2271730	1.280000e-13	87.9
16	TraesCS3A01G003400	chr3B	96.678	1144	37	1	672	1814	4422023	4420880	0.000000e+00	1901.0
17	TraesCS3A01G003400	chr3B	85.765	1131	94	38	734	1812	4434455	4433340	0.000000e+00	1134.0
18	TraesCS3A01G003400	chr3B	93.824	680	27	5	2	678	4423100	4422433	0.000000e+00	1009.0
19	TraesCS3A01G003400	chr3B	89.266	531	50	5	2070	2599	671000132	670999608	0.000000e+00	658.0
20	TraesCS3A01G003400	chr3B	77.593	540	101	17	1143	1671	4418625	4418095	2.510000e-80	309.0
21	TraesCS3A01G003400	chr3B	76.139	461	90	12	1036	1491	4490770	4490325	9.360000e-55	224.0
22	TraesCS3A01G003400	chr3B	91.339	127	11	0	1813	1939	671003431	671003305	9.560000e-40	174.0
23	TraesCS3A01G003400	chr3B	75.465	269	39	15	1560	1814	4490240	4489985	3.540000e-19	106.0
24	TraesCS3A01G003400	chr4B	95.045	666	31	1	1936	2599	31816020	31815355	0.000000e+00	1046.0
25	TraesCS3A01G003400	chr4B	81.037	617	76	25	1988	2578	580803888	580803287	1.100000e-123	453.0
26	TraesCS3A01G003400	chr4B	93.077	130	8	1	1811	1939	31829496	31829367	3.410000e-44	189.0
27	TraesCS3A01G003400	chr4B	97.222	36	1	0	708	743	667693217	667693252	7.770000e-06	62.1
28	TraesCS3A01G003400	chr4A	95.030	664	33	0	1936	2599	587252489	587253152	0.000000e+00	1044.0
29	TraesCS3A01G003400	chr4A	94.346	283	15	1	1936	2218	587251860	587252141	1.430000e-117	433.0
30	TraesCS3A01G003400	chr4A	84.228	298	39	6	2	293	608476889	608477184	1.520000e-72	283.0
31	TraesCS3A01G003400	chr4A	90.698	129	12	0	1809	1937	587251496	587251624	3.440000e-39	172.0
32	TraesCS3A01G003400	chr4A	95.283	106	5	0	1832	1937	587252148	587252253	4.450000e-38	169.0
33	TraesCS3A01G003400	chr1B	88.814	590	57	4	2010	2599	532069081	532068501	0.000000e+00	715.0
34	TraesCS3A01G003400	chr1B	84.564	298	33	9	2	293	7073883	7073593	1.520000e-72	283.0
35	TraesCS3A01G003400	chr1B	84.774	243	30	7	430	667	3705492	3705252	1.200000e-58	237.0
36	TraesCS3A01G003400	chr1B	90.551	127	12	0	1813	1939	532069758	532069632	4.450000e-38	169.0
37	TraesCS3A01G003400	chr2B	81.395	602	73	20	2001	2578	50350960	50350374	3.050000e-124	455.0
38	TraesCS3A01G003400	chr2B	80.097	618	75	29	1988	2578	83945076	83944480	1.440000e-112	416.0
39	TraesCS3A01G003400	chr2B	85.135	296	38	4	2	293	92098605	92098898	5.440000e-77	298.0
40	TraesCS3A01G003400	chr5A	87.129	303	29	8	2	297	18052688	18052987	4.140000e-88	335.0
41	TraesCS3A01G003400	chr5A	100.000	37	0	0	702	738	675348754	675348718	4.640000e-08	69.4
42	TraesCS3A01G003400	chr5A	100.000	35	0	0	702	736	675321424	675321390	6.000000e-07	65.8
43	TraesCS3A01G003400	chr5A	100.000	35	0	0	702	736	675346753	675346719	6.000000e-07	65.8
44	TraesCS3A01G003400	chr5A	97.222	36	1	0	708	743	706419533	706419498	7.770000e-06	62.1
45	TraesCS3A01G003400	chr1D	85.859	297	35	4	2	293	232082230	232082524	2.510000e-80	309.0
46	TraesCS3A01G003400	chr1D	84.539	304	37	8	2	300	199628431	199628133	2.530000e-75	292.0
47	TraesCS3A01G003400	chr5D	85.000	300	35	7	2	293	331121554	331121851	1.960000e-76	296.0
48	TraesCS3A01G003400	chr7A	84.211	304	39	6	2	300	619160532	619160831	1.180000e-73	287.0
49	TraesCS3A01G003400	chr4D	85.870	276	30	6	430	699	441294472	441294200	4.230000e-73	285.0
50	TraesCS3A01G003400	chr7D	83.630	281	34	6	425	699	419764523	419764797	1.190000e-63	254.0
51	TraesCS3A01G003400	chr7D	81.786	280	39	7	426	698	603800394	603800120	9.360000e-55	224.0
52	TraesCS3A01G003400	chr6A	83.895	267	37	5	438	699	2072315	2072050	1.540000e-62	250.0
53	TraesCS3A01G003400	chr5B	83.333	276	38	7	430	699	711135350	711135077	5.550000e-62	248.0
54	TraesCS3A01G003400	chr6B	81.545	233	35	6	471	698	38074547	38074776	4.420000e-43	185.0

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	TraesCS3A01G003400	chr3A	1796362	1798960	2598	False	4800.000000	4800	100.00000	1	2599	1	chr3A.!!$F2	2598
1	TraesCS3A01G003400	chr3A	1789155	1792222	3067	False	324.000000	839	91.56250	734	1814	4	chr3A.!!$F5	1080
2	TraesCS3A01G003400	chr3A	1851920	1852491	571	False	302.000000	302	76.67200	1013	1583	1	chr3A.!!$F3	570
3	TraesCS3A01G003400	chr3D	2238765	2243677	4912	True	1794.000000	2492	90.85200	292	1814	2	chr3D.!!$R4	1522
4	TraesCS3A01G003400	chr3D	2255902	2256696	794	True	542.000000	542	79.45900	1013	1806	1	chr3D.!!$R1	793
5	TraesCS3A01G003400	chr3D	2200713	2202030	1317	True	313.333333	357	85.10500	840	1726	3	chr3D.!!$R3	886
6	TraesCS3A01G003400	chr3B	4433340	4434455	1115	True	1134.000000	1134	85.76500	734	1812	1	chr3B.!!$R1	1078
7	TraesCS3A01G003400	chr3B	4418095	4423100	5005	True	1073.000000	1901	89.36500	2	1814	3	chr3B.!!$R2	1812
8	TraesCS3A01G003400	chr3B	670999608	671003431	3823	True	416.000000	658	90.30250	1813	2599	2	chr3B.!!$R4	786
9	TraesCS3A01G003400	chr4B	31815355	31816020	665	True	1046.000000	1046	95.04500	1936	2599	1	chr4B.!!$R1	663
10	TraesCS3A01G003400	chr4B	580803287	580803888	601	True	453.000000	453	81.03700	1988	2578	1	chr4B.!!$R3	590
11	TraesCS3A01G003400	chr4A	587251496	587253152	1656	False	454.500000	1044	93.83925	1809	2599	4	chr4A.!!$F2	790
12	TraesCS3A01G003400	chr1B	532068501	532069758	1257	True	442.000000	715	89.68250	1813	2599	2	chr1B.!!$R3	786
13	TraesCS3A01G003400	chr2B	50350374	50350960	586	True	455.000000	455	81.39500	2001	2578	1	chr2B.!!$R1	577
14	TraesCS3A01G003400	chr2B	83944480	83945076	596	True	416.000000	416	80.09700	1988	2578	1	chr2B.!!$R2	590

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
455	457	1.564348	ATCACCTGTGGTGGTTATCCC	59.436	52.381	15.65	0.0	45.95	3.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1854	6851	0.181114	CGATGGGGAGCTCCAAATCA	59.819	55.0	33.29	23.53	40.62	2.57	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
35	36	4.237349	AGGCCACAAAACTCAAATTACG	57.763	40.909	5.01	0.00	0.00	3.18
41	42	6.319399	CCACAAAACTCAAATTACGGATACC	58.681	40.000	0.00	0.00	0.00	2.73
48	49	9.675464	AAACTCAAATTACGGATACCAAGATAA	57.325	29.630	0.00	0.00	0.00	1.75
85	86	9.968870	ATGCTTTGCAATTCAACATTTATTTTT	57.031	22.222	0.00	0.00	43.62	1.94
127	128	3.909430	CATGCATGCAAGAAAACTGAGT	58.091	40.909	26.68	0.00	0.00	3.41
128	129	3.358707	TGCATGCAAGAAAACTGAGTG	57.641	42.857	20.30	0.00	0.00	3.51
129	130	2.950975	TGCATGCAAGAAAACTGAGTGA	59.049	40.909	20.30	0.00	0.00	3.41
175	177	7.104043	ACGACTACATACAAGCAGGTATTAA	57.896	36.000	0.00	0.00	31.75	1.40
194	196	3.314541	AAACAGGTTGCTAGTACGAGG	57.685	47.619	5.08	0.00	0.00	4.63
218	220	8.912988	AGGAAATATCATTAATTTTTGCCTCGA	58.087	29.630	0.00	0.00	30.46	4.04
233	235	2.213499	CCTCGATTAGTGTTGATGGCC	58.787	52.381	0.00	0.00	0.00	5.36
247	249	4.011966	TGATGGCCTTGTATAGATGCAG	57.988	45.455	3.32	0.00	0.00	4.41
248	250	3.647590	TGATGGCCTTGTATAGATGCAGA	59.352	43.478	3.32	0.00	0.00	4.26
251	253	4.392047	TGGCCTTGTATAGATGCAGAATG	58.608	43.478	3.32	0.00	40.87	2.67
297	299	9.968870	GTATAAGTAAATGAAGGGAGTAGTCAG	57.031	37.037	0.00	0.00	0.00	3.51
311	313	6.238981	GGGAGTAGTCAGTTTGGCTATACTAC	60.239	46.154	0.00	0.00	36.89	2.73
409	411	5.820947	GTGGTTGTTCTCTGGAGTAAAGAAA	59.179	40.000	0.00	0.00	31.26	2.52
410	412	6.317893	GTGGTTGTTCTCTGGAGTAAAGAAAA	59.682	38.462	0.00	0.00	31.26	2.29
411	413	6.887545	TGGTTGTTCTCTGGAGTAAAGAAAAA	59.112	34.615	0.00	0.00	31.26	1.94
412	414	7.559897	TGGTTGTTCTCTGGAGTAAAGAAAAAT	59.440	33.333	0.00	0.00	30.96	1.82
413	415	7.862873	GGTTGTTCTCTGGAGTAAAGAAAAATG	59.137	37.037	0.00	0.00	30.96	2.32
414	416	8.406297	GTTGTTCTCTGGAGTAAAGAAAAATGT	58.594	33.333	0.00	0.00	30.96	2.71
415	417	9.621629	TTGTTCTCTGGAGTAAAGAAAAATGTA	57.378	29.630	0.00	0.00	31.26	2.29
416	418	9.793259	TGTTCTCTGGAGTAAAGAAAAATGTAT	57.207	29.630	0.00	0.00	31.26	2.29
455	457	1.564348	ATCACCTGTGGTGGTTATCCC	59.436	52.381	15.65	0.00	45.95	3.85
466	468	3.650942	GGTGGTTATCCCCATGTCTCATA	59.349	47.826	0.00	0.00	36.74	2.15
474	476	8.812972	GTTATCCCCATGTCTCATATACTAACA	58.187	37.037	0.00	0.00	0.00	2.41
736	1156	1.816224	CCGGGTGGTAGGAAACATTTG	59.184	52.381	0.00	0.00	0.00	2.32
748	1168	4.018688	AGGAAACATTTGTACTACCCCCTC	60.019	45.833	0.00	0.00	0.00	4.30
958	1379	5.847111	TTACTACGTATCTTCCACTGCAT	57.153	39.130	0.00	0.00	0.00	3.96
992	1413	2.440539	AAATAGTATCAGGAGGCGCG	57.559	50.000	0.00	0.00	0.00	6.86
1097	1633	2.289694	GGTGGTGCTTCTCTTCTTGCTA	60.290	50.000	0.00	0.00	0.00	3.49
1447	1993	3.438087	CCTGTAGGAATGACTGCAACAAG	59.562	47.826	0.00	0.00	37.39	3.16
1744	2748	2.291365	TCCATAGAGCTTGCGTACGTA	58.709	47.619	17.90	10.06	0.00	3.57
1848	6845	2.423446	GAGCCACCTATGAGCCCG	59.577	66.667	0.00	0.00	0.00	6.13
1854	6851	1.990060	ACCTATGAGCCCGCACAGT	60.990	57.895	0.00	0.00	0.00	3.55
1884	6881	1.068083	CCCCATCGTCCGATCACTG	59.932	63.158	0.00	0.00	31.62	3.66
1898	6895	3.231736	ACTGCCACGAACGTCCCT	61.232	61.111	0.00	0.00	0.00	4.20
1962	8222	2.572095	TTATGTGTGCCTCGGAGCCG	62.572	60.000	1.74	1.74	41.35	5.52
2111	10866	5.587289	TCCTTGTGCTGTTTGTTCATTTAC	58.413	37.500	0.00	0.00	0.00	2.01
2207	11341	1.417890	AGCCCCAAGATTATGAGACGG	59.582	52.381	0.00	0.00	0.00	4.79
2300	12696	3.792956	CAGTTCCGATGCATGTTTTATGC	59.207	43.478	2.46	5.00	44.76	3.14
2437	12837	3.319137	TGCATCAGTCGAGCTAAAACT	57.681	42.857	0.00	0.00	0.00	2.66
2440	12916	3.929610	GCATCAGTCGAGCTAAAACTTCT	59.070	43.478	0.00	0.00	0.00	2.85
2469	12945	5.174761	GCAAAAACAGTCGTGCAAATATTCA	59.825	36.000	0.00	0.00	36.97	2.57
2505	13419	4.125703	CAGATGATGTAGCTTTGGAGGAC	58.874	47.826	0.00	0.00	0.00	3.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
85	86	5.538849	TGCGGTGTATTAATGATCCTACA	57.461	39.130	0.00	0.00	0.00	2.74
122	123	6.276847	ACACTCAACTACTTTCTTCACTCAG	58.723	40.000	0.00	0.00	0.00	3.35
123	124	6.127451	TGACACTCAACTACTTTCTTCACTCA	60.127	38.462	0.00	0.00	0.00	3.41
124	125	6.273825	TGACACTCAACTACTTTCTTCACTC	58.726	40.000	0.00	0.00	0.00	3.51
125	126	6.222038	TGACACTCAACTACTTTCTTCACT	57.778	37.500	0.00	0.00	0.00	3.41
126	127	7.484035	AATGACACTCAACTACTTTCTTCAC	57.516	36.000	0.00	0.00	0.00	3.18
127	128	7.381408	CGTAATGACACTCAACTACTTTCTTCA	59.619	37.037	0.00	0.00	0.00	3.02
128	129	7.594015	TCGTAATGACACTCAACTACTTTCTTC	59.406	37.037	0.00	0.00	0.00	2.87
129	130	7.431249	TCGTAATGACACTCAACTACTTTCTT	58.569	34.615	0.00	0.00	0.00	2.52
175	177	2.522185	TCCTCGTACTAGCAACCTGTT	58.478	47.619	0.00	0.00	0.00	3.16
212	214	1.599542	GCCATCAACACTAATCGAGGC	59.400	52.381	0.00	0.00	0.00	4.70
218	220	7.136822	TCTATACAAGGCCATCAACACTAAT	57.863	36.000	5.01	0.00	0.00	1.73
284	286	2.339769	AGCCAAACTGACTACTCCCTT	58.660	47.619	0.00	0.00	0.00	3.95
311	313	9.677567	CCCGGATTACTTATCAATACAAAATTG	57.322	33.333	0.73	0.00	34.77	2.32
409	411	6.435277	AGGATGCACTTCTGTTGAATACATTT	59.565	34.615	0.00	0.00	35.85	2.32
410	412	5.948162	AGGATGCACTTCTGTTGAATACATT	59.052	36.000	0.00	0.00	35.85	2.71
411	413	5.503927	AGGATGCACTTCTGTTGAATACAT	58.496	37.500	0.00	0.00	35.85	2.29
412	414	4.910195	AGGATGCACTTCTGTTGAATACA	58.090	39.130	0.00	0.00	34.95	2.29
413	415	6.763135	TGATAGGATGCACTTCTGTTGAATAC	59.237	38.462	0.00	0.00	0.00	1.89
414	416	6.763135	GTGATAGGATGCACTTCTGTTGAATA	59.237	38.462	0.00	0.00	32.44	1.75
415	417	5.587844	GTGATAGGATGCACTTCTGTTGAAT	59.412	40.000	0.00	0.00	32.44	2.57
416	418	4.937620	GTGATAGGATGCACTTCTGTTGAA	59.062	41.667	0.00	0.00	32.44	2.69
417	419	4.507710	GTGATAGGATGCACTTCTGTTGA	58.492	43.478	0.00	0.00	32.44	3.18
418	420	3.624861	GGTGATAGGATGCACTTCTGTTG	59.375	47.826	0.00	0.00	35.43	3.33
447	449	6.875972	AGTATATGAGACATGGGGATAACC	57.124	41.667	0.00	0.00	39.11	2.85
624	628	4.633126	ACGTCTCGTACTTTGAGTATGCTA	59.367	41.667	3.08	0.00	38.73	3.49
722	1142	5.188434	GGGGTAGTACAAATGTTTCCTACC	58.812	45.833	18.73	18.73	39.41	3.18
731	1151	4.501571	CGATCAGAGGGGGTAGTACAAATG	60.502	50.000	2.06	0.00	0.00	2.32
736	1156	1.133544	ACCGATCAGAGGGGGTAGTAC	60.134	57.143	0.00	0.00	0.00	2.73
992	1413	5.738909	AGGTGAGTTGCTATATGATATGGC	58.261	41.667	13.13	13.13	0.00	4.40
1097	1633	2.290641	GCATGGAGAAAACAACGACAGT	59.709	45.455	0.00	0.00	0.00	3.55
1331	1877	1.202698	ACTCCTTTCAGCCACAGTGTC	60.203	52.381	0.00	0.00	0.00	3.67
1447	1993	2.287849	GCACCCTTTCTTCTTGCAGTTC	60.288	50.000	0.00	0.00	33.24	3.01
1744	2748	6.206243	GCTGATGTATAGAAGCCAATCAACAT	59.794	38.462	0.00	0.00	0.00	2.71
1848	6845	0.807496	GGAGCTCCAAATCACTGTGC	59.193	55.000	28.43	0.00	35.64	4.57
1854	6851	0.181114	CGATGGGGAGCTCCAAATCA	59.819	55.000	33.29	23.53	40.62	2.57
1884	6881	0.953960	AAATCAGGGACGTTCGTGGC	60.954	55.000	16.18	0.00	0.00	5.01
1898	6895	3.002791	GTTGATGACCGAGCTGAAATCA	58.997	45.455	0.00	0.00	0.00	2.57
1962	8222	1.065345	GGAGGAACTTTAGAGGCCACC	60.065	57.143	5.01	0.00	41.55	4.61
2111	10866	5.546526	AGCTACTTTCTTGAGAGGAAACTG	58.453	41.667	0.00	0.00	44.43	3.16
2207	11341	7.174946	CCAGAATCTAGTAGAGAAGATGGAGAC	59.825	44.444	5.98	0.00	37.85	3.36
2401	12801	3.763360	TGATGCAACCTTGAAATAGTGGG	59.237	43.478	0.00	0.00	0.00	4.61
2437	12837	4.788201	GCACGACTGTTTTTGCATACAGAA	60.788	41.667	23.10	0.00	43.45	3.02
2440	12916	2.356069	TGCACGACTGTTTTTGCATACA	59.644	40.909	7.55	0.00	40.01	2.29
2469	12945	2.937519	TCATCTGGACGCAGAGTAGAT	58.062	47.619	0.00	0.00	34.35	1.98
2505	13419	5.578776	AGCTTAAGGACAAAAAGAAACACG	58.421	37.500	4.29	0.00	0.00	4.49

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.