AutoCloner

Multiple sequence alignment - TraesCS1B01G046600

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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	TraesCS1B01G046600	chr1B	100.000	3125	0	0	1	3125	26590191	26593315	0.000000e+00	5771
1	TraesCS1B01G046600	chr1B	96.074	1401	55	0	844	2244	26857327	26855927	0.000000e+00	2283
2	TraesCS1B01G046600	chr1B	98.406	251	4	0	1	251	240971679	240971929	2.860000e-120	442
3	TraesCS1B01G046600	chr1B	89.474	190	5	1	2055	2244	26617629	26617803	3.140000e-55	226
4	TraesCS1B01G046600	chr3B	97.860	888	13	3	2243	3125	10342907	10342021	0.000000e+00	1530
5	TraesCS1B01G046600	chr3B	83.181	1314	191	15	916	2223	556367849	556369138	0.000000e+00	1175
6	TraesCS1B01G046600	chr3B	92.268	582	28	2	252	832	692132737	692133302	0.000000e+00	809
7	TraesCS1B01G046600	chr3B	91.778	523	27	9	320	832	369998550	369999066	0.000000e+00	713
8	TraesCS1B01G046600	chr3B	98.024	253	5	0	1	253	342037285	342037537	1.030000e-119	440
9	TraesCS1B01G046600	chr2D	97.961	883	17	1	2243	3125	382432806	382433687	0.000000e+00	1530
10	TraesCS1B01G046600	chr2D	98.068	880	16	1	2246	3125	450382929	450382051	0.000000e+00	1530
11	TraesCS1B01G046600	chr3D	97.539	894	10	7	2243	3125	515550509	515549617	0.000000e+00	1519
12	TraesCS1B01G046600	chr3D	97.294	887	19	4	2243	3125	559090119	559091004	0.000000e+00	1500
13	TraesCS1B01G046600	chr3D	83.917	1256	173	17	972	2223	426000195	425998965	0.000000e+00	1173
14	TraesCS1B01G046600	chr3D	88.889	594	47	11	252	832	418003471	418004058	0.000000e+00	713
15	TraesCS1B01G046600	chr1D	97.627	885	18	2	2243	3125	427924229	427923346	0.000000e+00	1515
16	TraesCS1B01G046600	chr1D	87.956	274	30	2	1959	2229	18210214	18210487	1.400000e-83	320
17	TraesCS1B01G046600	chr5D	97.735	883	12	4	2243	3125	45660619	45661493	0.000000e+00	1513
18	TraesCS1B01G046600	chr5D	97.410	888	17	3	2243	3125	73405936	73406822	0.000000e+00	1507
19	TraesCS1B01G046600	chr7D	97.291	886	20	4	2243	3125	443320534	443319650	0.000000e+00	1500
20	TraesCS1B01G046600	chr4B	92.123	584	33	9	252	834	648505329	648505900	0.000000e+00	811
21	TraesCS1B01G046600	chr4B	98.413	252	4	0	1	252	556164516	556164767	7.950000e-121	444
22	TraesCS1B01G046600	chr4B	98.024	253	5	0	1	253	320161660	320161912	1.030000e-119	440
23	TraesCS1B01G046600	chr4B	82.308	260	26	14	588	834	630131314	630131566	1.140000e-49	207
24	TraesCS1B01G046600	chr4B	80.784	255	31	12	589	832	37925765	37926012	1.910000e-42	183
25	TraesCS1B01G046600	chr5B	91.695	590	35	8	253	832	281673189	281673774	0.000000e+00	806
26	TraesCS1B01G046600	chr5B	89.638	608	37	12	252	835	228168928	228169533	0.000000e+00	750
27	TraesCS1B01G046600	chr5B	90.550	582	34	6	252	832	551695785	551696346	0.000000e+00	750
28	TraesCS1B01G046600	chr5B	89.535	602	41	12	252	834	57989690	57990288	0.000000e+00	743
29	TraesCS1B01G046600	chr5B	98.406	251	4	0	1	251	269167096	269167346	2.860000e-120	442
30	TraesCS1B01G046600	chr5B	83.264	239	40	0	1119	1357	141585307	141585069	1.460000e-53	220
31	TraesCS1B01G046600	chr6B	90.986	588	44	6	252	834	705435314	705435897	0.000000e+00	784
32	TraesCS1B01G046600	chr7B	98.406	251	4	0	1	251	308710063	308709813	2.860000e-120	442
33	TraesCS1B01G046600	chr7B	98.406	251	4	0	1	251	308713807	308713557	2.860000e-120	442
34	TraesCS1B01G046600	chr2A	98.406	251	4	0	1	251	325316237	325315987	2.860000e-120	442
35	TraesCS1B01G046600	chr2A	79.082	196	37	4	2001	2194	156482242	156482435	7.030000e-27	132
36	TraesCS1B01G046600	chrUn	97.287	258	6	1	1	258	128031638	128031894	1.330000e-118	436
37	TraesCS1B01G046600	chrUn	81.923	260	27	14	588	834	340717141	340716889	5.280000e-48	202
38	TraesCS1B01G046600	chrUn	81.923	260	27	14	588	834	360426361	360426613	5.280000e-48	202

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	TraesCS1B01G046600	chr1B	26590191	26593315	3124	False	5771	5771	100.000	1	3125	1	chr1B.!!$F1	3124
1	TraesCS1B01G046600	chr1B	26855927	26857327	1400	True	2283	2283	96.074	844	2244	1	chr1B.!!$R1	1400
2	TraesCS1B01G046600	chr3B	10342021	10342907	886	True	1530	1530	97.860	2243	3125	1	chr3B.!!$R1	882
3	TraesCS1B01G046600	chr3B	556367849	556369138	1289	False	1175	1175	83.181	916	2223	1	chr3B.!!$F3	1307
4	TraesCS1B01G046600	chr3B	692132737	692133302	565	False	809	809	92.268	252	832	1	chr3B.!!$F4	580
5	TraesCS1B01G046600	chr3B	369998550	369999066	516	False	713	713	91.778	320	832	1	chr3B.!!$F2	512
6	TraesCS1B01G046600	chr2D	382432806	382433687	881	False	1530	1530	97.961	2243	3125	1	chr2D.!!$F1	882
7	TraesCS1B01G046600	chr2D	450382051	450382929	878	True	1530	1530	98.068	2246	3125	1	chr2D.!!$R1	879
8	TraesCS1B01G046600	chr3D	515549617	515550509	892	True	1519	1519	97.539	2243	3125	1	chr3D.!!$R2	882
9	TraesCS1B01G046600	chr3D	559090119	559091004	885	False	1500	1500	97.294	2243	3125	1	chr3D.!!$F2	882
10	TraesCS1B01G046600	chr3D	425998965	426000195	1230	True	1173	1173	83.917	972	2223	1	chr3D.!!$R1	1251
11	TraesCS1B01G046600	chr3D	418003471	418004058	587	False	713	713	88.889	252	832	1	chr3D.!!$F1	580
12	TraesCS1B01G046600	chr1D	427923346	427924229	883	True	1515	1515	97.627	2243	3125	1	chr1D.!!$R1	882
13	TraesCS1B01G046600	chr5D	45660619	45661493	874	False	1513	1513	97.735	2243	3125	1	chr5D.!!$F1	882
14	TraesCS1B01G046600	chr5D	73405936	73406822	886	False	1507	1507	97.410	2243	3125	1	chr5D.!!$F2	882
15	TraesCS1B01G046600	chr7D	443319650	443320534	884	True	1500	1500	97.291	2243	3125	1	chr7D.!!$R1	882
16	TraesCS1B01G046600	chr4B	648505329	648505900	571	False	811	811	92.123	252	834	1	chr4B.!!$F5	582
17	TraesCS1B01G046600	chr5B	281673189	281673774	585	False	806	806	91.695	253	832	1	chr5B.!!$F4	579
18	TraesCS1B01G046600	chr5B	228168928	228169533	605	False	750	750	89.638	252	835	1	chr5B.!!$F2	583
19	TraesCS1B01G046600	chr5B	551695785	551696346	561	False	750	750	90.550	252	832	1	chr5B.!!$F5	580
20	TraesCS1B01G046600	chr5B	57989690	57990288	598	False	743	743	89.535	252	834	1	chr5B.!!$F1	582
21	TraesCS1B01G046600	chr6B	705435314	705435897	583	False	784	784	90.986	252	834	1	chr6B.!!$F1	582
22	TraesCS1B01G046600	chr7B	308709813	308713807	3994	True	442	442	98.406	1	251	2	chr7B.!!$R1	250

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
23	24	0.681564	TTGGCCCAAAAGTGACGTGT	60.682	50.0	0.0	0.0	0.0	4.49	F
1488	1875	0.039764	ATCTGGAGGTGGTCGTCAGA	59.960	55.0	0.0	0.0	0.0	3.27	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1575	1962	0.035056	GGACCATGCAGTTGCCTAGT	60.035	55.000	1.06	0.0	41.18	2.57	R
2554	4995	1.408702	GTTTTTGGGAAGAGCTGTGCA	59.591	47.619	0.00	0.0	0.00	4.57	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
23	24	0.681564	TTGGCCCAAAAGTGACGTGT	60.682	50.000	0.00	0.00	0.00	4.49
233	234	6.375736	TGCAATATTTTTGGTCGTATCCAAGA	59.624	34.615	8.73	3.77	46.27	3.02
341	673	7.131907	AGACTACTCTCACTATGAGCTCTTA	57.868	40.000	16.19	12.12	43.95	2.10
398	730	2.494530	GGCCCGTTTTGTTGCCTCA	61.495	57.895	0.00	0.00	40.77	3.86
443	776	2.880890	AGCGCAAATGAACTCAAGAAGT	59.119	40.909	11.47	0.00	41.10	3.01
459	792	7.836685	ACTCAAGAAGTATCTCATTGAGGAGTA	59.163	37.037	13.59	2.71	40.24	2.59
835	1217	2.349886	GCCTGTTGAAGATGCTCTTACG	59.650	50.000	0.00	0.00	36.73	3.18
836	1218	3.589988	CCTGTTGAAGATGCTCTTACGT	58.410	45.455	0.00	0.00	36.73	3.57
837	1219	3.369147	CCTGTTGAAGATGCTCTTACGTG	59.631	47.826	0.00	0.00	36.73	4.49
838	1220	3.325870	TGTTGAAGATGCTCTTACGTGG	58.674	45.455	0.00	0.00	36.73	4.94
839	1221	3.244078	TGTTGAAGATGCTCTTACGTGGT	60.244	43.478	0.00	0.00	36.73	4.16
840	1222	4.021807	TGTTGAAGATGCTCTTACGTGGTA	60.022	41.667	0.00	0.00	36.73	3.25
841	1223	5.109903	GTTGAAGATGCTCTTACGTGGTAT	58.890	41.667	0.00	0.00	36.73	2.73
842	1224	4.933330	TGAAGATGCTCTTACGTGGTATC	58.067	43.478	0.00	0.74	36.73	2.24
858	1240	7.509546	ACGTGGTATCTATGGAATCTCAAAAT	58.490	34.615	0.00	0.00	0.00	1.82
872	1254	7.436376	GGAATCTCAAAATGAAAATTCCGATCC	59.564	37.037	13.84	0.00	34.59	3.36
1069	1456	3.921767	CTCAGCGCGCTTCCTGACA	62.922	63.158	34.58	8.22	34.60	3.58
1303	1690	3.073735	CCAGCTGCGAGGTCTCCT	61.074	66.667	8.66	0.00	36.03	3.69
1385	1772	3.986006	GTGCGTCGACACCCTCCA	61.986	66.667	17.16	0.00	34.35	3.86
1410	1797	2.352814	CGAGTTCTTCCAGACCAACGAT	60.353	50.000	0.00	0.00	0.00	3.73
1488	1875	0.039764	ATCTGGAGGTGGTCGTCAGA	59.960	55.000	0.00	0.00	0.00	3.27
1578	1965	2.351244	CCTCCGCAGCCTGACACTA	61.351	63.158	0.00	0.00	0.00	2.74
1696	2083	2.280797	GGGTGTTGAGCGAGTGCA	60.281	61.111	0.00	0.00	46.23	4.57
1697	2084	1.891919	GGGTGTTGAGCGAGTGCAA	60.892	57.895	0.00	0.00	46.23	4.08
1840	2227	3.063704	CAATGCTTGCCCGCCTGA	61.064	61.111	0.00	0.00	0.00	3.86
1857	2244	1.072331	CTGACCTGCCTAACCAACACT	59.928	52.381	0.00	0.00	0.00	3.55
1977	2364	3.411446	TCACGATGAGCTCAACCATTTT	58.589	40.909	22.50	1.08	0.00	1.82
1980	2367	3.686726	ACGATGAGCTCAACCATTTTCTC	59.313	43.478	22.50	9.27	0.00	2.87
2123	2511	2.225382	TCCAACTGGGACGTCTCATA	57.775	50.000	20.49	0.00	42.15	2.15
2208	2596	1.619332	GAGGAGGTTCCAGAGTCGTTT	59.381	52.381	0.00	0.00	39.61	3.60
3022	5734	5.073428	GTGGTTTTCCCTTTCTCTTCTCAT	58.927	41.667	0.00	0.00	39.73	2.90

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
23	24	5.643379	AAGTGCTGTTCAAAAAGTTCTCA	57.357	34.783	0.00	0.00	0.00	3.27
341	673	2.041976	CACTCGCACGGGATATCCT	58.958	57.895	21.18	0.00	35.95	3.24
398	730	2.688507	GGACGTCGAATGGCATGATAT	58.311	47.619	9.92	0.00	0.00	1.63
443	776	3.898123	GCCCACTACTCCTCAATGAGATA	59.102	47.826	12.53	0.00	36.22	1.98
459	792	2.037847	GGCCATTCCAAGCCCACT	59.962	61.111	0.00	0.00	43.76	4.00
633	972	7.704472	GTCTCACAACACATCCACAAAATAAAA	59.296	33.333	0.00	0.00	0.00	1.52
637	976	4.644234	TGTCTCACAACACATCCACAAAAT	59.356	37.500	0.00	0.00	0.00	1.82
700	1078	4.081030	CAGCACGCGCAACTCCAG	62.081	66.667	5.73	0.00	42.27	3.86
703	1081	3.599792	AATGCAGCACGCGCAACTC	62.600	57.895	5.73	0.00	46.97	3.01
704	1082	2.682256	AAAATGCAGCACGCGCAACT	62.682	50.000	5.73	0.00	46.97	3.16
705	1083	1.001240	TAAAATGCAGCACGCGCAAC	61.001	50.000	5.73	0.00	46.97	4.17
706	1084	0.728803	CTAAAATGCAGCACGCGCAA	60.729	50.000	5.73	0.00	46.97	4.85
707	1085	1.154244	CTAAAATGCAGCACGCGCA	60.154	52.632	5.73	10.12	46.97	6.09
708	1086	2.499603	GCTAAAATGCAGCACGCGC	61.500	57.895	5.73	0.00	46.97	6.86
709	1087	2.210375	CGCTAAAATGCAGCACGCG	61.210	57.895	3.53	3.53	46.97	6.01
710	1088	2.499603	GCGCTAAAATGCAGCACGC	61.500	57.895	9.70	9.70	39.04	5.34
711	1089	2.210375	CGCGCTAAAATGCAGCACG	61.210	57.895	5.56	0.00	39.04	5.34
712	1090	1.869132	CCGCGCTAAAATGCAGCAC	60.869	57.895	5.56	0.00	39.04	4.40
713	1091	2.484662	CCGCGCTAAAATGCAGCA	59.515	55.556	5.56	0.00	39.04	4.41
806	1188	0.753479	TCTTCAACAGGCGCCCAAAA	60.753	50.000	26.15	9.96	0.00	2.44
807	1189	0.539438	ATCTTCAACAGGCGCCCAAA	60.539	50.000	26.15	9.57	0.00	3.28
835	1217	8.908786	TCATTTTGAGATTCCATAGATACCAC	57.091	34.615	0.00	0.00	0.00	4.16
836	1218	9.919416	TTTCATTTTGAGATTCCATAGATACCA	57.081	29.630	0.00	0.00	0.00	3.25
842	1224	9.241317	CGGAATTTTCATTTTGAGATTCCATAG	57.759	33.333	21.63	10.94	43.51	2.23
858	1240	3.449746	AGGTTGGGATCGGAATTTTCA	57.550	42.857	0.00	0.00	0.00	2.69
864	1246	3.372241	GGGAATTAAGGTTGGGATCGGAA	60.372	47.826	0.00	0.00	0.00	4.30
872	1254	1.065998	TCGGACGGGAATTAAGGTTGG	60.066	52.381	0.00	0.00	0.00	3.77
961	1345	2.898705	AGCTGTCGATTGAATCTGGAC	58.101	47.619	3.43	5.12	0.00	4.02
1174	1561	1.734477	CGTCGCTGACCCTGAAGTG	60.734	63.158	3.65	0.00	0.00	3.16
1311	1698	4.373116	ATGCCGTCCACGAACGCT	62.373	61.111	0.00	0.00	43.02	5.07
1410	1797	1.113517	GGTCTACTATGCCTCCGCCA	61.114	60.000	0.00	0.00	0.00	5.69
1451	1838	3.691342	CTTCCACTCCCCACGCGA	61.691	66.667	15.93	0.00	0.00	5.87
1575	1962	0.035056	GGACCATGCAGTTGCCTAGT	60.035	55.000	1.06	0.00	41.18	2.57
1578	1965	2.036256	GGGACCATGCAGTTGCCT	59.964	61.111	1.06	0.00	41.18	4.75
1745	2132	1.681666	CCTGAGCACACCACCAGAT	59.318	57.895	0.00	0.00	0.00	2.90
1840	2227	0.843984	ACAGTGTTGGTTAGGCAGGT	59.156	50.000	0.00	0.00	0.00	4.00
1857	2244	2.338620	CCGAACACGAGCTCCACA	59.661	61.111	8.47	0.00	0.00	4.17
1925	2312	2.674084	GGCGGCAGAACCAACGTAC	61.674	63.158	3.07	0.00	39.03	3.67
1956	2343	2.768253	AATGGTTGAGCTCATCGTGA	57.232	45.000	19.04	0.00	0.00	4.35
1977	2364	2.562912	GTTGGCGACGTACCGAGA	59.437	61.111	0.23	0.00	0.00	4.04
1980	2367	2.125832	ATGGTTGGCGACGTACCG	60.126	61.111	7.76	0.00	39.72	4.02
2123	2511	2.743718	CCAGGAAGGTGTGCGTCT	59.256	61.111	0.00	0.00	0.00	4.18
2208	2596	1.274167	GCCGTCGACCATATTATCCCA	59.726	52.381	10.58	0.00	0.00	4.37
2554	4995	1.408702	GTTTTTGGGAAGAGCTGTGCA	59.591	47.619	0.00	0.00	0.00	4.57
2562	5003	4.763279	GGACGAATTAGGTTTTTGGGAAGA	59.237	41.667	0.00	0.00	0.00	2.87
2657	5098	4.543689	TCGTAGTCTACTCCATCCCAAAT	58.456	43.478	8.37	0.00	0.00	2.32
2873	5569	3.860754	GCAGCTTCCTTTTGCCGTTTTAT	60.861	43.478	0.00	0.00	31.79	1.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.