AutoCloner

Multiple sequence alignment - TraesCS7B01G023200

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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	TraesCS7B01G023200	chr7B	100.000	2550	0	0	1	2550	22313073	22315622	0.000000e+00	4710
1	TraesCS7B01G023200	chr7B	96.097	538	21	0	2	539	430083052	430082515	0.000000e+00	878
2	TraesCS7B01G023200	chr7B	95.911	538	22	0	2	539	236542222	236541685	0.000000e+00	872
3	TraesCS7B01G023200	chr7B	95.725	538	23	0	2	539	232943764	232943227	0.000000e+00	867
4	TraesCS7B01G023200	chr7B	94.789	403	21	0	540	942	52060418	52060820	1.670000e-176	628
5	TraesCS7B01G023200	chr5B	93.998	2016	84	17	538	2550	26059380	26057399	0.000000e+00	3018
6	TraesCS7B01G023200	chr5B	96.097	538	21	0	2	539	128008349	128007812	0.000000e+00	878
7	TraesCS7B01G023200	chr5B	95.911	538	22	0	2	539	119813081	119812544	0.000000e+00	872
8	TraesCS7B01G023200	chr5B	95.062	405	18	1	537	939	317969012	317969416	9.950000e-179	636
9	TraesCS7B01G023200	chr5B	94.595	407	22	0	536	942	682396000	682395594	4.630000e-177	630
10	TraesCS7B01G023200	chr2D	93.920	2023	84	24	534	2550	64508691	64510680	0.000000e+00	3018
11	TraesCS7B01G023200	chr2D	95.701	1605	62	7	937	2538	610930996	610932596	0.000000e+00	2575
12	TraesCS7B01G023200	chr3B	93.409	2018	92	12	537	2550	53523440	53525420	0.000000e+00	2952
13	TraesCS7B01G023200	chr3B	92.875	2021	107	9	535	2550	687040061	687042049	0.000000e+00	2900
14	TraesCS7B01G023200	chr3B	96.053	532	21	0	8	539	331183938	331183407	0.000000e+00	867
15	TraesCS7B01G023200	chrUn	92.868	2033	105	24	526	2550	60558697	60560697	0.000000e+00	2915
16	TraesCS7B01G023200	chr1B	95.021	1647	75	5	908	2550	542265279	542266922	0.000000e+00	2580
17	TraesCS7B01G023200	chr1B	95.365	1618	68	7	937	2550	672222140	672223754	0.000000e+00	2566
18	TraesCS7B01G023200	chr1B	96.449	535	19	0	2	536	355531115	355531649	0.000000e+00	883
19	TraesCS7B01G023200	chr1B	95.911	538	22	0	2	539	484799801	484799264	0.000000e+00	872
20	TraesCS7B01G023200	chr1B	94.363	408	21	1	537	942	663786492	663786899	2.150000e-175	625
21	TraesCS7B01G023200	chr1B	93.541	418	23	4	526	942	671392196	671392610	1.000000e-173	619
22	TraesCS7B01G023200	chr2B	94.769	1644	68	12	910	2550	546410629	546412257	0.000000e+00	2543
23	TraesCS7B01G023200	chr2B	95.725	538	23	0	2	539	764380480	764381017	0.000000e+00	867
24	TraesCS7B01G023200	chr2B	94.595	407	20	2	537	942	776161410	776161815	1.670000e-176	628
25	TraesCS7B01G023200	chr2B	93.525	417	24	2	529	942	36241838	36242254	3.600000e-173	617
26	TraesCS7B01G023200	chr6A	95.297	404	17	2	539	942	30121956	30121555	7.690000e-180	640

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	TraesCS7B01G023200	chr7B	22313073	22315622	2549	False	4710	4710	100.000	1	2550	1	chr7B.!!$F1	2549
1	TraesCS7B01G023200	chr7B	430082515	430083052	537	True	878	878	96.097	2	539	1	chr7B.!!$R3	537
2	TraesCS7B01G023200	chr7B	236541685	236542222	537	True	872	872	95.911	2	539	1	chr7B.!!$R2	537
3	TraesCS7B01G023200	chr7B	232943227	232943764	537	True	867	867	95.725	2	539	1	chr7B.!!$R1	537
4	TraesCS7B01G023200	chr5B	26057399	26059380	1981	True	3018	3018	93.998	538	2550	1	chr5B.!!$R1	2012
5	TraesCS7B01G023200	chr5B	128007812	128008349	537	True	878	878	96.097	2	539	1	chr5B.!!$R3	537
6	TraesCS7B01G023200	chr5B	119812544	119813081	537	True	872	872	95.911	2	539	1	chr5B.!!$R2	537
7	TraesCS7B01G023200	chr2D	64508691	64510680	1989	False	3018	3018	93.920	534	2550	1	chr2D.!!$F1	2016
8	TraesCS7B01G023200	chr2D	610930996	610932596	1600	False	2575	2575	95.701	937	2538	1	chr2D.!!$F2	1601
9	TraesCS7B01G023200	chr3B	53523440	53525420	1980	False	2952	2952	93.409	537	2550	1	chr3B.!!$F1	2013
10	TraesCS7B01G023200	chr3B	687040061	687042049	1988	False	2900	2900	92.875	535	2550	1	chr3B.!!$F2	2015
11	TraesCS7B01G023200	chr3B	331183407	331183938	531	True	867	867	96.053	8	539	1	chr3B.!!$R1	531
12	TraesCS7B01G023200	chrUn	60558697	60560697	2000	False	2915	2915	92.868	526	2550	1	chrUn.!!$F1	2024
13	TraesCS7B01G023200	chr1B	542265279	542266922	1643	False	2580	2580	95.021	908	2550	1	chr1B.!!$F2	1642
14	TraesCS7B01G023200	chr1B	672222140	672223754	1614	False	2566	2566	95.365	937	2550	1	chr1B.!!$F5	1613
15	TraesCS7B01G023200	chr1B	355531115	355531649	534	False	883	883	96.449	2	536	1	chr1B.!!$F1	534
16	TraesCS7B01G023200	chr1B	484799264	484799801	537	True	872	872	95.911	2	539	1	chr1B.!!$R1	537
17	TraesCS7B01G023200	chr2B	546410629	546412257	1628	False	2543	2543	94.769	910	2550	1	chr2B.!!$F2	1640
18	TraesCS7B01G023200	chr2B	764380480	764381017	537	False	867	867	95.725	2	539	1	chr2B.!!$F3	537

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
707	708	0.400213	CTTACAGGTGGGACCAAGCA	59.6	55.0	0.0	0.0	41.95	3.91	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2037	2052	0.53087	GCCATCTGTCCTAGCGGTTC	60.531	60.0	0.0	0.0	0.0	3.62	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
122	123	1.674980	GGACGTGGACGAGGACTCT	60.675	63.158	6.12	0.00	43.02	3.24
123	124	1.242665	GGACGTGGACGAGGACTCTT	61.243	60.000	6.12	0.00	43.02	2.85
138	139	3.261137	GGACTCTTAGTAAGGTGGCAGTT	59.739	47.826	10.02	0.00	0.00	3.16
150	151	2.483538	GGTGGCAGTTTTGTTGCTCATT	60.484	45.455	0.00	0.00	41.27	2.57
162	163	5.843673	TGTTGCTCATTGTGGTTCTAAAA	57.156	34.783	0.00	0.00	0.00	1.52
194	195	3.119101	AGTGTCTACCGGAATAGTTGCAG	60.119	47.826	9.46	0.00	0.00	4.41
249	250	1.823470	GTGTGTTGTGCTGAGCCCA	60.823	57.895	0.23	0.00	0.00	5.36
416	417	6.677781	TCATATAGCCAACAGTTTAGTTGC	57.322	37.500	0.00	0.00	45.73	4.17
569	570	1.777878	TCCTTTTGCCCTTAGTGGTGA	59.222	47.619	0.00	0.00	0.00	4.02
570	571	2.378547	TCCTTTTGCCCTTAGTGGTGAT	59.621	45.455	0.00	0.00	0.00	3.06
625	626	1.003696	GCTCAGTTTTGCCCCTAGTCT	59.996	52.381	0.00	0.00	0.00	3.24
633	634	2.903357	CCCCTAGTCTGTGCGCAT	59.097	61.111	15.91	0.00	0.00	4.73
707	708	0.400213	CTTACAGGTGGGACCAAGCA	59.600	55.000	0.00	0.00	41.95	3.91
729	730	2.813061	CAGAGGCGGCCAATTTTATTG	58.187	47.619	23.09	3.50	0.00	1.90
811	812	2.289444	CGGGTGTGCTATATAAGTGGGG	60.289	54.545	0.00	0.00	0.00	4.96
829	830	4.760047	GACAGCGGCGGTGACCAT	62.760	66.667	41.06	22.06	34.87	3.55
982	983	4.514577	CGGCGGCGTTGAGATCCT	62.515	66.667	24.74	0.00	0.00	3.24
1084	1087	3.834447	TTCGTCTGTCCACGGTGCG	62.834	63.158	1.68	0.00	40.35	5.34
1121	1124	1.002087	GAGGGTTTCTCACACACCGAT	59.998	52.381	0.00	0.00	42.02	4.18
1133	1136	2.150390	CACACCGATGAACCACAATCA	58.850	47.619	0.00	0.00	0.00	2.57
1162	1166	2.117156	ATGTGCAGCGAGAATGGGC	61.117	57.895	0.00	0.00	0.00	5.36
1263	1267	3.960102	TGACATGCTTCTTTCTTTGGGTT	59.040	39.130	0.00	0.00	0.00	4.11
1278	1282	1.598701	GGGTTGATGCTCTGGCCAAC	61.599	60.000	7.01	0.00	38.76	3.77
1371	1375	0.456995	CACGAGCTCCGGAAGAAGAC	60.457	60.000	5.23	0.00	43.93	3.01
1443	1447	6.887002	GGATGTTGAAGAAGAAGGTTAGGAAT	59.113	38.462	0.00	0.00	0.00	3.01
1484	1488	6.619329	ACCAATACCCATTTGCAAATACTT	57.381	33.333	23.69	12.87	0.00	2.24
1490	1494	5.934781	ACCCATTTGCAAATACTTTTTGGA	58.065	33.333	23.69	0.00	0.00	3.53
1728	1742	7.284919	TGATCAATGAAATGCAGCTAATGAT	57.715	32.000	0.00	0.00	0.00	2.45
1842	1856	8.987890	CCGTGATTTAAATCAAAGACCAAAATT	58.012	29.630	28.02	0.00	46.13	1.82
1861	1875	3.574284	TTTCATGGAAAATGTGCCTCG	57.426	42.857	0.00	0.00	0.00	4.63
1894	1908	4.904253	TGTTTACACCTAGTGCCAAAAC	57.096	40.909	11.17	11.17	36.98	2.43
1925	1940	8.546597	AACATTTTTAAGGGCATTACATTGAC	57.453	30.769	0.00	0.00	0.00	3.18
2037	2052	3.134127	GTTTAGGGCTGCGCTGGG	61.134	66.667	27.01	3.88	0.00	4.45
2176	2196	3.126171	GTGGTTTTCCTTTGTTTTGCACC	59.874	43.478	0.00	0.00	41.38	5.01
2201	2221	3.975479	TTTTGGAGGGTTGGAAGGTTA	57.025	42.857	0.00	0.00	0.00	2.85
2345	2368	5.538849	TTTTGAATAAAACGGAGGGCTTT	57.461	34.783	0.00	0.00	31.13	3.51
2414	2437	4.906618	TCATGACTTGGTTTAGGGAAGAC	58.093	43.478	0.00	0.00	0.00	3.01
2440	2464	1.112315	TGCTTGGGCACGGACATTTT	61.112	50.000	0.00	0.00	44.28	1.82

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
102	103	1.228490	AGTCCTCGTCCACGTCCTT	60.228	57.895	0.00	0.00	40.80	3.36
122	123	4.202070	GCAACAAAACTGCCACCTTACTAA	60.202	41.667	0.00	0.00	33.51	2.24
123	124	3.316868	GCAACAAAACTGCCACCTTACTA	59.683	43.478	0.00	0.00	33.51	1.82
138	139	5.843673	TTAGAACCACAATGAGCAACAAA	57.156	34.783	0.00	0.00	0.00	2.83
150	151	7.230510	ACACTGCATTAGAATTTTAGAACCACA	59.769	33.333	0.00	0.00	0.00	4.17
162	163	3.704566	TCCGGTAGACACTGCATTAGAAT	59.295	43.478	0.00	0.00	0.00	2.40
194	195	9.476202	AAATTAAGCACACCTGAAATTAAACTC	57.524	29.630	0.00	0.00	0.00	3.01
249	250	7.880195	AGAAGAAACATAACATAGTTCTGCTGT	59.120	33.333	0.00	0.00	0.00	4.40
416	417	4.524328	ACTAAGCACCCTGAAATTCTTTGG	59.476	41.667	0.00	0.00	0.00	3.28
569	570	2.097825	GGGCAAAACTGAGCAGATGAT	58.902	47.619	4.21	0.00	0.00	2.45
570	571	1.074405	AGGGCAAAACTGAGCAGATGA	59.926	47.619	4.21	0.00	0.00	2.92
625	626	2.049526	AACGAGTCGATGCGCACA	60.050	55.556	21.50	0.00	0.00	4.57
633	634	3.113322	CAAAGTTCACAGAACGAGTCGA	58.887	45.455	21.50	0.00	0.00	4.20
707	708	0.323360	TAAAATTGGCCGCCTCTGCT	60.323	50.000	11.61	0.00	34.43	4.24
829	830	2.983592	TCGTGCTCTCTGTCGCCA	60.984	61.111	0.00	0.00	0.00	5.69
1054	1057	3.257393	GACAGACGAAGACATGCATCTT	58.743	45.455	2.16	2.16	41.74	2.40
1084	1087	2.908940	CCGATCAATGCCTGCCCC	60.909	66.667	0.00	0.00	0.00	5.80
1090	1093	1.025041	GAAACCCTCCGATCAATGCC	58.975	55.000	0.00	0.00	0.00	4.40
1121	1124	3.417069	AGAACGGATGATTGTGGTTCA	57.583	42.857	5.20	0.00	39.45	3.18
1133	1136	1.656652	GCTGCACATGTAGAACGGAT	58.343	50.000	0.00	0.00	0.00	4.18
1162	1166	2.023673	TGCAATTGCCCCGATTCTTAG	58.976	47.619	26.94	0.00	41.18	2.18
1263	1267	0.321919	GAGTGTTGGCCAGAGCATCA	60.322	55.000	5.11	0.00	42.56	3.07
1278	1282	6.732531	TCTTGCAGTTCATTTATCAGAGTG	57.267	37.500	0.00	0.00	0.00	3.51
1371	1375	3.197790	CGTGCTTCGCCCTCCATG	61.198	66.667	0.00	0.00	0.00	3.66
1484	1488	8.887264	ATTACCATACCTACAAATGTCCAAAA	57.113	30.769	0.00	0.00	0.00	2.44
1490	1494	5.526111	GTGCGATTACCATACCTACAAATGT	59.474	40.000	0.00	0.00	0.00	2.71
1573	1577	8.617290	ACTAGGTGAATTTCTCGTACAATTTT	57.383	30.769	0.00	0.00	0.00	1.82
1582	1586	9.329913	CAACATTTAAACTAGGTGAATTTCTCG	57.670	33.333	0.00	0.00	0.00	4.04
1728	1742	7.234577	ACCTTAATTGTTTGGCTCTGGAATAAA	59.765	33.333	0.00	0.00	0.00	1.40
1801	1815	4.981806	ATCACGGTGTATTTGAATTGGG	57.018	40.909	8.17	0.00	0.00	4.12
1842	1856	1.818060	CCGAGGCACATTTTCCATGAA	59.182	47.619	0.00	0.00	0.00	2.57
1861	1875	3.197983	AGGTGTAAACATCTACCAGAGCC	59.802	47.826	0.00	0.00	35.13	4.70
1894	1908	8.997323	TGTAATGCCCTTAAAAATGTTCATTTG	58.003	29.630	10.84	0.42	0.00	2.32
2037	2052	0.530870	GCCATCTGTCCTAGCGGTTC	60.531	60.000	0.00	0.00	0.00	3.62
2120	2135	3.313249	TGCAAACATTCACAGTCTCACAG	59.687	43.478	0.00	0.00	0.00	3.66
2129	2149	0.590984	CGCGTGTGCAAACATTCACA	60.591	50.000	8.00	0.00	42.97	3.58
2176	2196	3.306019	CCTTCCAACCCTCCAAAATTTCG	60.306	47.826	0.00	0.00	0.00	3.46
2201	2221	3.120041	GGCAGTGCAAACATACGTTTTT	58.880	40.909	18.61	0.00	42.82	1.94
2345	2368	1.068948	TGAAAATCGGAGGGGGTGAA	58.931	50.000	0.00	0.00	0.00	3.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.