AutoCloner

Multiple sequence alignment - TraesCS7A01G094500

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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	TraesCS7A01G094500	chr7A	100.000	2384	0	0	1	2384	57804353	57801970	0.000000e+00	4403.0
1	TraesCS7A01G094500	chr7A	93.057	1253	73	6	257	1497	57865510	57864260	0.000000e+00	1820.0
2	TraesCS7A01G094500	chr7A	88.855	655	37	11	1634	2272	57864136	57863502	0.000000e+00	773.0
3	TraesCS7A01G094500	chr7A	97.143	35	1	0	2272	2306	57863486	57863452	2.560000e-05	60.2
4	TraesCS7A01G094500	chr7D	87.705	2253	167	36	61	2272	54320973	54318790	0.000000e+00	2525.0
5	TraesCS7A01G094500	chr7D	86.497	2007	157	31	57	2023	54355047	54353115	0.000000e+00	2100.0
6	TraesCS7A01G094500	chr7D	88.709	1727	131	21	572	2272	54337396	54335708	0.000000e+00	2050.0
7	TraesCS7A01G094500	chr7D	91.166	1132	64	10	352	1451	54311948	54310821	0.000000e+00	1504.0
8	TraesCS7A01G094500	chr7D	84.833	389	35	14	1654	2030	54310811	54310435	1.040000e-98	370.0
9	TraesCS7A01G094500	chr7D	80.645	248	18	19	2043	2275	54310383	54310151	5.270000e-37	165.0
10	TraesCS7A01G094500	chr7D	83.065	124	10	7	2271	2384	54309978	54309856	4.190000e-18	102.0
11	TraesCS7A01G094500	chrUn	92.168	881	62	3	572	1451	49140767	49139893	0.000000e+00	1238.0
12	TraesCS7A01G094500	chrUn	91.714	881	66	3	572	1451	49113928	49113054	0.000000e+00	1216.0
13	TraesCS7A01G094500	chrUn	91.629	884	67	3	569	1451	384623891	384624768	0.000000e+00	1216.0
14	TraesCS7A01G094500	chrUn	87.938	771	42	22	1654	2384	49113026	49112267	0.000000e+00	861.0
15	TraesCS7A01G094500	chrUn	87.938	771	42	22	1654	2384	49139865	49139106	0.000000e+00	861.0
16	TraesCS7A01G094500	chrUn	92.290	441	21	6	1654	2090	384624796	384625227	4.360000e-172	614.0
17	TraesCS7A01G094500	chrUn	83.468	496	35	19	1925	2384	329826066	329825582	3.670000e-113	418.0
18	TraesCS7A01G094500	chrUn	83.468	496	35	19	1925	2384	329829073	329829557	3.670000e-113	418.0
19	TraesCS7A01G094500	chr4A	92.164	855	64	1	597	1451	669899039	669898188	0.000000e+00	1205.0
20	TraesCS7A01G094500	chr4A	87.938	771	42	22	1654	2384	669892280	669891521	0.000000e+00	861.0
21	TraesCS7A01G094500	chr4A	84.888	536	65	7	3	534	669899604	669899081	5.840000e-146	527.0
22	TraesCS7A01G094500	chr4B	86.127	173	23	1	1460	1631	544132799	544132971	4.050000e-43	185.0
23	TraesCS7A01G094500	chr2A	87.195	164	20	1	1469	1631	249493204	249493041	4.050000e-43	185.0
24	TraesCS7A01G094500	chr2A	87.195	164	20	1	1469	1631	336819161	336818998	4.050000e-43	185.0
25	TraesCS7A01G094500	chr2A	85.965	171	22	2	1462	1631	252896190	252896021	5.230000e-42	182.0
26	TraesCS7A01G094500	chr6A	85.714	175	24	1	1460	1633	598186678	598186852	1.460000e-42	183.0
27	TraesCS7A01G094500	chr6A	86.585	164	21	1	1469	1631	316928048	316927885	1.880000e-41	180.0
28	TraesCS7A01G094500	chr5B	86.047	172	23	1	1460	1630	497781860	497782031	1.460000e-42	183.0

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	TraesCS7A01G094500	chr7A	57801970	57804353	2383	True	4403.00	4403	100.000000	1	2384	1	chr7A.!!$R1	2383
1	TraesCS7A01G094500	chr7A	57863452	57865510	2058	True	884.40	1820	93.018333	257	2306	3	chr7A.!!$R2	2049
2	TraesCS7A01G094500	chr7D	54318790	54320973	2183	True	2525.00	2525	87.705000	61	2272	1	chr7D.!!$R1	2211
3	TraesCS7A01G094500	chr7D	54353115	54355047	1932	True	2100.00	2100	86.497000	57	2023	1	chr7D.!!$R3	1966
4	TraesCS7A01G094500	chr7D	54335708	54337396	1688	True	2050.00	2050	88.709000	572	2272	1	chr7D.!!$R2	1700
5	TraesCS7A01G094500	chr7D	54309856	54311948	2092	True	535.25	1504	84.927250	352	2384	4	chr7D.!!$R4	2032
6	TraesCS7A01G094500	chrUn	49139106	49140767	1661	True	1049.50	1238	90.053000	572	2384	2	chrUn.!!$R3	1812
7	TraesCS7A01G094500	chrUn	49112267	49113928	1661	True	1038.50	1216	89.826000	572	2384	2	chrUn.!!$R2	1812
8	TraesCS7A01G094500	chrUn	384623891	384625227	1336	False	915.00	1216	91.959500	569	2090	2	chrUn.!!$F2	1521
9	TraesCS7A01G094500	chr4A	669898188	669899604	1416	True	866.00	1205	88.526000	3	1451	2	chr4A.!!$R2	1448
10	TraesCS7A01G094500	chr4A	669891521	669892280	759	True	861.00	861	87.938000	1654	2384	1	chr4A.!!$R1	730

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
105	106	0.667993	CCACGTGGCATGAACTTTGT	59.332	50.0	24.02	0.0	0.00	2.83	F
743	783	0.819582	GGGATGTTGGCATTGTCCAG	59.180	55.0	12.64	0.0	37.44	3.86	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1112	1152	0.605589	CTTCTCCAACGCCTCTGAGT	59.394	55.0	3.66	0.0	0.0	3.41	R
2350	2753	0.309302	CGGGAAAACATGCGTCAACA	59.691	50.0	0.00	0.0	0.0	3.33	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
26	27	5.697633	ACGAAAGCTATTTCAAGTTCCGTAA	59.302	36.000	0.00	0.00	44.27	3.18
52	53	3.006967	GGGAGCTCAACAAACTCAGTCTA	59.993	47.826	17.19	0.00	31.88	2.59
63	64	2.299521	ACTCAGTCTACCATAGCGGAC	58.700	52.381	0.00	0.00	38.63	4.79
77	78	3.955650	AGCGGACTACACAACAACTAT	57.044	42.857	0.00	0.00	0.00	2.12
78	79	4.267349	AGCGGACTACACAACAACTATT	57.733	40.909	0.00	0.00	0.00	1.73
105	106	0.667993	CCACGTGGCATGAACTTTGT	59.332	50.000	24.02	0.00	0.00	2.83
106	107	1.876799	CCACGTGGCATGAACTTTGTA	59.123	47.619	24.02	0.00	0.00	2.41
122	123	1.320344	TGTAGAGTACGGCCTGCCAG	61.320	60.000	9.17	3.86	35.37	4.85
188	189	1.422402	TGCCGAGTTCCCTTTACCTTT	59.578	47.619	0.00	0.00	0.00	3.11
206	207	2.254546	TTCTCTCAACAACGGCATGT	57.745	45.000	0.00	0.00	34.24	3.21
208	209	2.959516	TCTCTCAACAACGGCATGTAG	58.040	47.619	0.00	0.00	32.02	2.74
219	220	1.153568	GCATGTAGCTGCCGAGTCA	60.154	57.895	0.00	0.00	41.15	3.41
252	254	2.593257	AGAAACGTACTCGCTTACTGC	58.407	47.619	0.00	0.00	41.18	4.40
267	269	4.789802	GCTTACTGCTTTTTGTCGAGCTTT	60.790	41.667	0.00	0.00	39.60	3.51
289	291	2.143122	GTGATTTGACTCTCGGCAACA	58.857	47.619	0.00	0.00	0.00	3.33
291	293	2.548057	TGATTTGACTCTCGGCAACAAC	59.452	45.455	0.00	0.00	0.00	3.32
343	345	6.115446	GGTTGAGATGTCATGTTGGAAGATA	58.885	40.000	0.00	0.00	30.85	1.98
377	379	7.658179	TGTTCAAAACATGTTACAGCAAAAA	57.342	28.000	12.39	0.00	36.25	1.94
412	414	8.765488	ATTTTCCCAAATCAAAGAAAATTGGT	57.235	26.923	4.23	0.00	43.07	3.67
480	482	9.541143	GAGAATTGAACCAAGGAATAACAAAAA	57.459	29.630	0.00	0.00	0.00	1.94
512	517	5.046910	ACAACGATGGATGCTAAAACAAG	57.953	39.130	0.00	0.00	0.00	3.16
588	627	2.098871	CCATGCATGCACGTCGTG	59.901	61.111	25.37	21.02	36.51	4.35
720	760	1.679898	GAACCTGTCCTCCCACCAG	59.320	63.158	0.00	0.00	0.00	4.00
743	783	0.819582	GGGATGTTGGCATTGTCCAG	59.180	55.000	12.64	0.00	37.44	3.86
1032	1072	1.144093	CCGGAGAGGATGACTAGGTCT	59.856	57.143	0.00	0.00	45.00	3.85
1071	1111	1.286260	GACGAAGCTGTCCACGAGT	59.714	57.895	0.00	0.00	32.61	4.18
1112	1152	0.890683	GGGACGAGGAACTTAACCGA	59.109	55.000	0.00	0.00	41.55	4.69
1224	1264	1.926561	CCGAGAAAGCGATGATGTCA	58.073	50.000	0.00	0.00	0.00	3.58
1332	1372	4.443266	GCGCTGAGCTTCTCCGGT	62.443	66.667	1.78	0.00	44.04	5.28
1391	1434	2.038863	TCACAACCCTAGGTGACCAT	57.961	50.000	8.29	0.00	39.00	3.55
1395	1438	1.762957	CAACCCTAGGTGACCATCGAT	59.237	52.381	8.29	0.00	35.34	3.59
1461	1511	8.592809	TGTTTGCATTGTAATTAAGGAGGAAAT	58.407	29.630	0.00	0.00	0.00	2.17
1464	1514	8.359875	TGCATTGTAATTAAGGAGGAAATTGA	57.640	30.769	0.00	0.00	0.00	2.57
1473	1523	3.818180	AGGAGGAAATTGATAGCTGCTG	58.182	45.455	13.43	0.00	0.00	4.41
1490	1540	2.046604	GGGTTGGCCGGTGAGTAC	60.047	66.667	1.90	0.00	34.97	2.73
1491	1541	2.745037	GGTTGGCCGGTGAGTACA	59.255	61.111	1.90	0.00	0.00	2.90
1506	1560	5.474189	GGTGAGTACAGGATTAGTAGGCTAG	59.526	48.000	0.00	0.00	0.00	3.42
1534	1588	8.579682	GGCAAGTTAATCAGCCATTTAATTAG	57.420	34.615	9.35	0.00	46.26	1.73
1544	1598	8.958119	TCAGCCATTTAATTAGTTAATCGTCT	57.042	30.769	0.00	0.00	30.34	4.18
1600	1684	5.353394	ACGAGTAGGGATTAATCAGCAAA	57.647	39.130	17.07	0.00	0.00	3.68
1602	1686	6.357367	ACGAGTAGGGATTAATCAGCAAATT	58.643	36.000	17.07	0.00	0.00	1.82
1639	1736	6.436843	ACGAATTCTTGAACAAGTTCTTGT	57.563	33.333	11.75	11.75	40.14	3.16
1641	1738	8.154649	ACGAATTCTTGAACAAGTTCTTGTAT	57.845	30.769	16.84	8.71	40.14	2.29
1652	1749	9.472361	GAACAAGTTCTTGTATTGAGTAGTACA	57.528	33.333	16.84	0.00	36.69	2.90
1889	1989	0.319813	GCCGCCATTGTTTCAAGCTT	60.320	50.000	0.00	0.00	0.00	3.74
2016	2150	2.612972	GGCTGCTTATATAGGCGAGCAA	60.613	50.000	26.63	8.02	43.75	3.91
2030	2164	1.137872	CGAGCAATCCAAGACCTAGCT	59.862	52.381	0.00	0.00	0.00	3.32
2033	2167	3.379452	AGCAATCCAAGACCTAGCTAGT	58.621	45.455	19.31	7.69	0.00	2.57
2072	2245	2.330231	TTGCGGATCTTTTTGCTTCG	57.670	45.000	0.00	0.00	0.00	3.79
2073	2246	0.109781	TGCGGATCTTTTTGCTTCGC	60.110	50.000	0.00	0.00	41.68	4.70
2074	2247	1.128147	GCGGATCTTTTTGCTTCGCG	61.128	55.000	0.00	0.00	32.72	5.87
2161	2334	4.579384	ACAACCCAGTGGCACCGG	62.579	66.667	15.27	14.13	33.59	5.28
2180	2371	0.318784	GAGGGCGTCGGTGATGATAC	60.319	60.000	0.00	0.00	0.00	2.24
2181	2372	1.040893	AGGGCGTCGGTGATGATACA	61.041	55.000	0.00	0.00	0.00	2.29
2182	2373	0.179094	GGGCGTCGGTGATGATACAA	60.179	55.000	0.00	0.00	0.00	2.41
2262	2470	0.464554	GGCTCACTAACCCTGATGGC	60.465	60.000	0.00	0.00	37.83	4.40
2270	2498	0.464373	AACCCTGATGGCTACATGCG	60.464	55.000	0.00	0.00	44.05	4.73
2309	2712	3.531538	ACCGGTCATGTGTAAGCTATTG	58.468	45.455	0.00	0.00	0.00	1.90
2317	2720	7.435488	GGTCATGTGTAAGCTATTGTGTAGTAG	59.565	40.741	0.00	0.00	0.00	2.57
2318	2721	7.974501	GTCATGTGTAAGCTATTGTGTAGTAGT	59.025	37.037	0.00	0.00	0.00	2.73
2319	2722	9.181061	TCATGTGTAAGCTATTGTGTAGTAGTA	57.819	33.333	0.00	0.00	0.00	1.82
2320	2723	9.797556	CATGTGTAAGCTATTGTGTAGTAGTAA	57.202	33.333	0.00	0.00	0.00	2.24
2342	2745	9.747898	AGTAATATAGTAGCTAGATCAAGCAGT	57.252	33.333	0.00	0.00	45.30	4.40
2363	2766	2.819019	TGGATTGATGTTGACGCATGTT	59.181	40.909	0.00	0.00	0.00	2.71

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	5.697633	ACGGAACTTGAAATAGCTTTCGTTA	59.302	36.000	0.00	0.00	43.10	3.18
1	2	4.514066	ACGGAACTTGAAATAGCTTTCGTT	59.486	37.500	0.00	0.00	43.10	3.85
8	9	4.271687	CGCATTACGGAACTTGAAATAGC	58.728	43.478	0.00	0.00	38.44	2.97
26	27	0.250901	AGTTTGTTGAGCTCCCGCAT	60.251	50.000	12.15	0.00	39.10	4.73
38	39	4.495422	CGCTATGGTAGACTGAGTTTGTT	58.505	43.478	0.00	0.00	0.00	2.83
39	40	3.119101	CCGCTATGGTAGACTGAGTTTGT	60.119	47.826	0.00	0.00	0.00	2.83
52	53	1.897133	TGTTGTGTAGTCCGCTATGGT	59.103	47.619	0.00	0.00	39.52	3.55
97	98	3.251571	CAGGCCGTACTCTACAAAGTTC	58.748	50.000	0.00	0.00	0.00	3.01
105	106	1.000019	ACTGGCAGGCCGTACTCTA	60.000	57.895	20.34	0.00	39.42	2.43
106	107	2.283966	ACTGGCAGGCCGTACTCT	60.284	61.111	20.34	0.00	39.42	3.24
138	139	6.830873	ATAAACTCGGCTTATACGGACTAT	57.169	37.500	0.00	0.00	0.00	2.12
188	189	2.930887	GCTACATGCCGTTGTTGAGAGA	60.931	50.000	0.00	0.00	35.15	3.10
252	254	6.253298	TCAAATCACAAAAGCTCGACAAAAAG	59.747	34.615	0.00	0.00	0.00	2.27
267	269	2.542020	TGCCGAGAGTCAAATCACAA	57.458	45.000	0.00	0.00	0.00	3.33
289	291	0.379316	GAAAGTTGGTCGTTGGCGTT	59.621	50.000	0.00	0.00	39.49	4.84
291	293	1.281656	GGAAAGTTGGTCGTTGGCG	59.718	57.895	0.00	0.00	39.92	5.69
399	401	4.094590	TGTGCTGCAAACCAATTTTCTTTG	59.905	37.500	2.77	0.00	0.00	2.77
406	408	4.511082	GTGTAAATGTGCTGCAAACCAATT	59.489	37.500	2.77	0.40	0.00	2.32
412	414	4.319139	ACATGTGTAAATGTGCTGCAAA	57.681	36.364	2.77	0.00	39.32	3.68
481	483	4.037923	AGCATCCATCGTTGTTGTCTTTTT	59.962	37.500	0.00	0.00	0.00	1.94
494	496	3.763097	TGCTTGTTTTAGCATCCATCG	57.237	42.857	0.00	0.00	45.72	3.84
512	517	4.151867	CCGAGTTACCTCTGTAAAGTTTGC	59.848	45.833	0.00	0.00	38.62	3.68
525	552	3.751698	GCTTGTTTTCATCCGAGTTACCT	59.248	43.478	0.00	0.00	0.00	3.08
542	578	2.306805	TCACTCCATCTCCATTGCTTGT	59.693	45.455	0.00	0.00	0.00	3.16
546	582	2.106166	AGGATCACTCCATCTCCATTGC	59.894	50.000	0.00	0.00	44.79	3.56
743	783	4.148825	AGACGGCGAGGATGGTGC	62.149	66.667	16.62	0.00	0.00	5.01
1071	1111	1.300620	CACGTCCAACCTCAGCGAA	60.301	57.895	0.00	0.00	0.00	4.70
1112	1152	0.605589	CTTCTCCAACGCCTCTGAGT	59.394	55.000	3.66	0.00	0.00	3.41
1451	1494	4.205587	CAGCAGCTATCAATTTCCTCCTT	58.794	43.478	0.00	0.00	0.00	3.36
1453	1496	2.883386	CCAGCAGCTATCAATTTCCTCC	59.117	50.000	0.00	0.00	0.00	4.30
1461	1511	0.680921	GCCAACCCAGCAGCTATCAA	60.681	55.000	0.00	0.00	0.00	2.57
1464	1514	2.276740	GGCCAACCCAGCAGCTAT	59.723	61.111	0.00	0.00	0.00	2.97
1473	1523	2.046604	GTACTCACCGGCCAACCC	60.047	66.667	0.00	0.00	0.00	4.11
1490	1540	2.229302	GCCGACTAGCCTACTAATCCTG	59.771	54.545	0.00	0.00	0.00	3.86
1491	1541	2.158505	TGCCGACTAGCCTACTAATCCT	60.159	50.000	0.00	0.00	0.00	3.24
1552	1606	5.531287	GGGTCACCGAATAGCTGATAAAATT	59.469	40.000	0.00	0.00	0.00	1.82
1554	1608	4.163458	AGGGTCACCGAATAGCTGATAAAA	59.837	41.667	0.00	0.00	43.47	1.52
1566	1620	1.679944	CCTACTCGTAGGGTCACCGAA	60.680	57.143	14.08	0.00	46.96	4.30
1600	1684	8.765219	CAAGAATTCGTCCGATTAATCAGTAAT	58.235	33.333	15.57	4.89	34.97	1.89
1602	1686	7.485810	TCAAGAATTCGTCCGATTAATCAGTA	58.514	34.615	15.57	0.00	0.00	2.74
1607	1691	6.978343	TGTTCAAGAATTCGTCCGATTAAT	57.022	33.333	0.00	0.00	0.00	1.40
1639	1736	6.515832	TCGTCGAGGTATGTACTACTCAATA	58.484	40.000	4.85	0.00	0.00	1.90
1641	1738	4.758688	TCGTCGAGGTATGTACTACTCAA	58.241	43.478	4.85	0.00	0.00	3.02
1818	1915	1.844771	CGTGTGCTTTGCTGCTGCTA	61.845	55.000	17.00	6.36	40.48	3.49
1995	2118	1.066858	TGCTCGCCTATATAAGCAGCC	60.067	52.381	17.59	2.90	39.69	4.85
2143	2316	3.286751	CGGTGCCACTGGGTTGTG	61.287	66.667	0.00	0.00	37.66	3.33
2161	2334	0.318784	GTATCATCACCGACGCCCTC	60.319	60.000	0.00	0.00	0.00	4.30
2262	2470	4.244862	TGCATATGTACATCCGCATGTAG	58.755	43.478	21.88	0.00	44.61	2.74
2270	2498	3.436704	CCGGTTCATGCATATGTACATCC	59.563	47.826	12.68	3.00	36.60	3.51
2317	2720	9.781834	CACTGCTTGATCTAGCTACTATATTAC	57.218	37.037	25.85	0.00	41.76	1.89
2318	2721	8.961634	CCACTGCTTGATCTAGCTACTATATTA	58.038	37.037	25.85	5.49	41.76	0.98
2319	2722	7.671819	TCCACTGCTTGATCTAGCTACTATATT	59.328	37.037	25.85	0.72	41.76	1.28
2320	2723	7.178573	TCCACTGCTTGATCTAGCTACTATAT	58.821	38.462	25.85	5.05	41.76	0.86
2321	2724	6.543735	TCCACTGCTTGATCTAGCTACTATA	58.456	40.000	25.85	7.43	41.76	1.31
2342	2745	2.435422	ACATGCGTCAACATCAATCCA	58.565	42.857	0.00	0.00	0.00	3.41
2350	2753	0.309302	CGGGAAAACATGCGTCAACA	59.691	50.000	0.00	0.00	0.00	3.33
2352	2755	1.953017	CCGGGAAAACATGCGTCAA	59.047	52.632	0.00	0.00	0.00	3.18
2353	2756	2.622011	GCCGGGAAAACATGCGTCA	61.622	57.895	2.18	0.00	0.00	4.35
2363	2766	1.302192	CTTCTCAACGGCCGGGAAA	60.302	57.895	31.76	19.22	0.00	3.13

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.