AutoCloner

Multiple sequence alignment - TraesCS7A01G079800

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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	TraesCS7A01G079800	chr7A	100.000	2904	0	0	1	2904	45716882	45713979	0.000000e+00	5363.0
1	TraesCS7A01G079800	chr7A	86.916	321	36	5	1	319	346992253	346991937	3.560000e-94	355.0
2	TraesCS7A01G079800	chr7A	86.943	314	37	3	1	310	441995225	441995538	1.660000e-92	350.0
3	TraesCS7A01G079800	chr7A	88.636	176	20	0	521	696	255699949	255699774	6.300000e-52	215.0
4	TraesCS7A01G079800	chr5A	98.030	2386	39	4	521	2904	437069227	437066848	0.000000e+00	4139.0
5	TraesCS7A01G079800	chr5A	100.000	28	0	0	2559	2586	437067109	437067082	5.000000e-03	52.8
6	TraesCS7A01G079800	chr1A	97.611	2386	47	5	521	2904	564762661	564765038	0.000000e+00	4082.0
7	TraesCS7A01G079800	chr1A	100.000	28	0	0	2559	2586	564764777	564764804	5.000000e-03	52.8
8	TraesCS7A01G079800	chr6D	90.724	2016	146	16	522	2507	232749438	232751442	0.000000e+00	2649.0
9	TraesCS7A01G079800	chr6D	86.984	315	39	2	1	314	65937740	65938053	1.280000e-93	353.0
10	TraesCS7A01G079800	chr3D	91.705	1748	103	20	789	2505	232455242	232453506	0.000000e+00	2386.0
11	TraesCS7A01G079800	chr3D	89.873	316	30	2	1	314	125981608	125981293	3.480000e-109	405.0
12	TraesCS7A01G079800	chr3D	79.429	175	24	8	2584	2756	595025137	595024973	2.370000e-21	113.0
13	TraesCS7A01G079800	chr6A	92.321	1133	55	9	522	1629	171808790	171809915	0.000000e+00	1581.0
14	TraesCS7A01G079800	chr6A	95.604	728	26	4	1704	2426	171809914	171810640	0.000000e+00	1162.0
15	TraesCS7A01G079800	chr6A	87.961	407	28	5	2501	2904	171810632	171811020	7.330000e-126	460.0
16	TraesCS7A01G079800	chr6A	87.500	80	10	0	2675	2754	59898768	59898847	3.080000e-15	93.5
17	TraesCS7A01G079800	chr3A	92.776	526	34	2	1	522	265923238	265923763	0.000000e+00	758.0
18	TraesCS7A01G079800	chr1D	87.460	311	38	1	1	310	354550607	354550297	9.900000e-95	357.0
19	TraesCS7A01G079800	chr2D	86.984	315	39	2	1	314	356454664	356454351	1.280000e-93	353.0
20	TraesCS7A01G079800	chr2D	88.940	217	20	2	306	519	350121878	350122093	6.170000e-67	265.0
21	TraesCS7A01G079800	chr2D	88.393	224	19	5	306	522	385139173	385139396	2.220000e-66	263.0
22	TraesCS7A01G079800	chr7D	86.817	311	40	1	1	310	148482113	148481803	2.140000e-91	346.0
23	TraesCS7A01G079800	chr7D	77.143	175	29	8	2584	2755	498534178	498534344	1.110000e-14	91.6
24	TraesCS7A01G079800	chr2A	86.817	311	40	1	1	310	54399069	54399379	2.140000e-91	346.0
25	TraesCS7A01G079800	chr4D	89.908	218	19	3	306	522	48010425	48010210	7.930000e-71	278.0
26	TraesCS7A01G079800	chr4D	89.041	219	21	3	306	522	211466495	211466278	4.770000e-68	268.0
27	TraesCS7A01G079800	chr4D	89.041	219	21	3	306	522	219754499	219754716	4.770000e-68	268.0
28	TraesCS7A01G079800	chr4D	88.182	220	23	3	306	522	75347506	75347287	2.870000e-65	259.0
29	TraesCS7A01G079800	chr1B	88.940	217	21	3	307	522	154419248	154419034	6.170000e-67	265.0
30	TraesCS7A01G079800	chr1B	86.905	84	9	2	2675	2757	628651262	628651344	3.080000e-15	93.5
31	TraesCS7A01G079800	chr5B	88.584	219	20	4	307	522	354184091	354183875	7.980000e-66	261.0
32	TraesCS7A01G079800	chr2B	82.677	127	19	2	1505	1628	646205743	646205869	3.060000e-20	110.0
33	TraesCS7A01G079800	chr2B	81.890	127	20	2	1505	1628	135701968	135702094	1.420000e-18	104.0
34	TraesCS7A01G079800	chrUn	78.261	161	26	5	2593	2752	82485460	82485308	8.570000e-16	95.3
35	TraesCS7A01G079800	chr5D	88.608	79	7	2	2675	2752	106810016	106809939	8.570000e-16	95.3

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	TraesCS7A01G079800	chr7A	45713979	45716882	2903	True	5363.000000	5363	100.0000	1	2904	1	chr7A.!!$R1	2903
1	TraesCS7A01G079800	chr5A	437066848	437069227	2379	True	2095.900000	4139	99.0150	521	2904	2	chr5A.!!$R1	2383
2	TraesCS7A01G079800	chr1A	564762661	564765038	2377	False	2067.400000	4082	98.8055	521	2904	2	chr1A.!!$F1	2383
3	TraesCS7A01G079800	chr6D	232749438	232751442	2004	False	2649.000000	2649	90.7240	522	2507	1	chr6D.!!$F2	1985
4	TraesCS7A01G079800	chr3D	232453506	232455242	1736	True	2386.000000	2386	91.7050	789	2505	1	chr3D.!!$R2	1716
5	TraesCS7A01G079800	chr6A	171808790	171811020	2230	False	1067.666667	1581	91.9620	522	2904	3	chr6A.!!$F2	2382
6	TraesCS7A01G079800	chr3A	265923238	265923763	525	False	758.000000	758	92.7760	1	522	1	chr3A.!!$F1	521

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
776	782	0.106149	AATCTCGCCCGTGTATTCCC	59.894	55.0	0.0	0.0	0.0	3.97	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2507	2562	1.568606	CACGATGAGCTGATCACCTG	58.431	55.0	13.8	1.5	41.91	4.0	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
32	33	1.561542	AGGAAGGGAGCCATACAAGTG	59.438	52.381	0.00	0.00	0.00	3.16
41	42	5.701290	GGGAGCCATACAAGTGTAATCATAC	59.299	44.000	0.00	0.00	33.76	2.39
56	57	0.749649	CATACGCAAGAGGAGAGGCT	59.250	55.000	0.00	0.00	43.62	4.58
135	136	9.586435	CAAAGTTTTGACTAGGAAGTTTTTCAT	57.414	29.630	0.00	0.00	40.55	2.57
152	153	8.450180	AGTTTTTCATAAACAACTTTTTGCCAG	58.550	29.630	0.00	0.00	36.00	4.85
171	172	6.991938	TGCCAGAAAAGTATAATGCTTGTTT	58.008	32.000	0.00	0.00	0.00	2.83
236	238	6.446781	ACGACTTAGCTAGTTAATGTGCTA	57.553	37.500	0.00	0.00	37.17	3.49
248	250	3.939740	AATGTGCTAGGTGGTGATGAT	57.060	42.857	0.00	0.00	0.00	2.45
250	252	1.303309	GTGCTAGGTGGTGATGATGC	58.697	55.000	0.00	0.00	0.00	3.91
252	254	1.134310	TGCTAGGTGGTGATGATGCAG	60.134	52.381	0.00	0.00	0.00	4.41
253	255	1.813092	GCTAGGTGGTGATGATGCAGG	60.813	57.143	0.00	0.00	0.00	4.85
256	258	2.124612	TGGTGATGATGCAGGCCG	60.125	61.111	0.00	0.00	0.00	6.13
262	264	0.873054	GATGATGCAGGCCGAGATTG	59.127	55.000	0.00	0.00	0.00	2.67
309	311	2.835431	AGTCCCGAGATGGCCGAG	60.835	66.667	0.00	0.00	35.87	4.63
380	382	1.697432	TGAAGTGATGACGAAACCCCT	59.303	47.619	0.00	0.00	0.00	4.79
389	391	1.971695	CGAAACCCCTGGTTCAGCC	60.972	63.158	0.00	0.00	46.20	4.85
425	427	2.029369	GGTACGCCGGTGTGACAA	59.971	61.111	30.54	7.68	0.00	3.18
427	429	2.354891	TACGCCGGTGTGACAACG	60.355	61.111	30.54	17.28	44.86	4.10
648	653	2.769663	TGGCCTAAATACATCTGACCGT	59.230	45.455	3.32	0.00	0.00	4.83
689	694	9.636348	TGTAGCAATTACTGTTGGCTGACCATA	62.636	40.741	0.00	0.00	38.29	2.74
724	729	2.226330	CGAAATTTCCCATGCCCGATA	58.774	47.619	12.54	0.00	0.00	2.92
776	782	0.106149	AATCTCGCCCGTGTATTCCC	59.894	55.000	0.00	0.00	0.00	3.97
797	803	4.532521	CCCTAATCTCTCCCATATCCGTTT	59.467	45.833	0.00	0.00	0.00	3.60
878	886	1.225704	CTTCCACCCATCTGGCCTC	59.774	63.158	3.32	0.00	37.83	4.70
886	894	3.483869	ATCTGGCCTCCCCGCTTC	61.484	66.667	3.32	0.00	35.87	3.86
899	907	3.443925	GCTTCCCGCTTGCCCTTC	61.444	66.667	0.00	0.00	35.14	3.46
900	908	2.352805	CTTCCCGCTTGCCCTTCT	59.647	61.111	0.00	0.00	0.00	2.85
1054	1062	2.107705	CGAGGTACACGCTCTGGAT	58.892	57.895	0.00	0.00	34.76	3.41
1059	1067	2.348104	TACACGCTCTGGATGCCGT	61.348	57.895	0.00	0.00	0.00	5.68
1061	1069	3.695606	ACGCTCTGGATGCCGTGT	61.696	61.111	0.00	0.00	0.00	4.49
1280	1304	1.609501	AGGTCAGCAACGCCTCCTA	60.610	57.895	0.00	0.00	0.00	2.94
1443	1476	1.211212	TGCCTGCAATCTAGCTCACAT	59.789	47.619	0.00	0.00	34.99	3.21
1530	1564	5.707298	TGACAGAAATTTCAGGATTGTCTCC	59.293	40.000	25.52	10.93	45.33	3.71
1835	1878	9.896645	AATGAACTGTGTGATTAATGATAGTCT	57.103	29.630	0.00	0.00	0.00	3.24
1988	2033	8.644374	TTTGTTCTATAGCTATTTTTGGGTGT	57.356	30.769	12.39	0.00	0.00	4.16
2021	2068	9.672086	TTGTTTTGCTTTATGTTGTATAGTCAC	57.328	29.630	0.00	0.00	0.00	3.67
2304	2355	5.567138	AGTTTATGCTTGTCTGGTTATGC	57.433	39.130	0.00	0.00	0.00	3.14
2507	2562	6.765989	TCACACCATACAAGAATTATACAGCC	59.234	38.462	0.00	0.00	0.00	4.85
2526	2581	1.568606	CAGGTGATCAGCTCATCGTG	58.431	55.000	24.19	9.62	40.17	4.35
2646	2701	1.471119	ACGGACACATACGGATGTCT	58.529	50.000	11.26	0.00	44.82	3.41
2708	2763	8.839947	TCATTTTGCTTCGTATGTAATTCATG	57.160	30.769	0.00	0.00	37.91	3.07
2710	2765	9.715123	CATTTTGCTTCGTATGTAATTCATGTA	57.285	29.630	0.00	0.00	37.91	2.29
2716	2771	9.586150	GCTTCGTATGTAATTCATGTAGAAATG	57.414	33.333	0.00	0.00	40.22	2.32

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
17	18	4.150897	TGATTACACTTGTATGGCTCCC	57.849	45.455	0.00	0.00	0.00	4.30
19	20	5.107453	GCGTATGATTACACTTGTATGGCTC	60.107	44.000	0.00	0.00	0.00	4.70
32	33	4.551388	CCTCTCCTCTTGCGTATGATTAC	58.449	47.826	0.00	0.00	0.00	1.89
41	42	0.177604	ATGAAGCCTCTCCTCTTGCG	59.822	55.000	0.00	0.00	0.00	4.85
56	57	7.390823	GTTTATTTGGGGGCTTCTTTTATGAA	58.609	34.615	0.00	0.00	0.00	2.57
99	100	7.556275	TCCTAGTCAAAACTTTGTTTCTGACAT	59.444	33.333	23.26	16.68	39.18	3.06
109	110	8.980143	TGAAAAACTTCCTAGTCAAAACTTTG	57.020	30.769	0.00	0.00	36.92	2.77
152	153	6.526674	CGGTCCAAACAAGCATTATACTTTTC	59.473	38.462	0.00	0.00	0.00	2.29
171	172	4.942483	TCAGTTTAACTTTTGTTCGGTCCA	59.058	37.500	0.00	0.00	42.45	4.02
213	215	5.326200	AGCACATTAACTAGCTAAGTCGT	57.674	39.130	0.00	0.00	37.50	4.34
236	238	1.077212	GCCTGCATCATCACCACCT	60.077	57.895	0.00	0.00	0.00	4.00
256	258	1.519455	CTCGTCCCACCGCAATCTC	60.519	63.158	0.00	0.00	0.00	2.75
288	290	4.899239	GCCATCTCGGGACTGGCG	62.899	72.222	18.77	0.00	45.35	5.69
320	322	2.584608	GTGTCATACTGCCGGCCT	59.415	61.111	26.77	11.92	0.00	5.19
325	327	1.641577	GACTTCGGTGTCATACTGCC	58.358	55.000	4.31	0.00	36.97	4.85
351	353	5.097742	TCGTCATCACTTCATTAACCCAT	57.902	39.130	0.00	0.00	0.00	4.00
380	382	2.741092	GTCACCTCGGCTGAACCA	59.259	61.111	0.00	0.00	39.03	3.67
429	431	0.105964	TAAATGATCTGGGTCGGGCG	59.894	55.000	0.00	0.00	0.00	6.13
648	653	2.011548	GCTACATGCAATCGTGACCCA	61.012	52.381	0.00	0.00	42.31	4.51
724	729	1.929860	CTGTGTGGGGCCTGATCCAT	61.930	60.000	0.84	0.00	35.28	3.41
776	782	4.932200	GCAAACGGATATGGGAGAGATTAG	59.068	45.833	0.00	0.00	0.00	1.73
797	803	2.627699	GACAACATTTTCTTGGAGGGCA	59.372	45.455	0.00	0.00	0.00	5.36
895	903	4.148825	CGTGGGGAGCGGAGAAGG	62.149	72.222	0.00	0.00	0.00	3.46
896	904	4.821589	GCGTGGGGAGCGGAGAAG	62.822	72.222	0.00	0.00	0.00	2.85
1059	1067	1.925415	GCAATGAGCGCATCCACACA	61.925	55.000	11.47	0.00	32.35	3.72
1061	1069	3.189921	GCAATGAGCGCATCCACA	58.810	55.556	11.47	1.65	32.35	4.17
1280	1304	2.526873	AGGAACAGTGCGAGGGGT	60.527	61.111	0.00	0.00	0.00	4.95
1443	1476	5.470098	AGAAGCGAAGTCAGAAATTTGCTAA	59.530	36.000	10.50	0.00	43.75	3.09
1530	1564	1.682854	ACCCATGCGGCAATTCTAATG	59.317	47.619	6.82	0.00	33.26	1.90
1988	2033	8.770438	ACAACATAAAGCAAAACAAAGAAAGA	57.230	26.923	0.00	0.00	0.00	2.52
2021	2068	3.955471	TGATGGGGCTTGAGTTTTCTAG	58.045	45.455	0.00	0.00	0.00	2.43
2304	2355	4.631377	TGTGACGCTCTGGAAGAAAATATG	59.369	41.667	0.00	0.00	46.34	1.78
2507	2562	1.568606	CACGATGAGCTGATCACCTG	58.431	55.000	13.80	1.50	41.91	4.00
2689	2744	8.710835	TTTCTACATGAATTACATACGAAGCA	57.289	30.769	0.00	0.00	37.46	3.91

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.