AutoCloner

Multiple sequence alignment - TraesCS2A01G103100

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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	TraesCS2A01G103100	chr2A	100.000	2261	0	0	1	2261	56916794	56919054	0.000000e+00	4176.0
1	TraesCS2A01G103100	chr2A	77.758	571	115	11	4	571	619238409	619238970	7.730000e-90	340.0
2	TraesCS2A01G103100	chr2A	72.000	500	121	16	765	1260	115786852	115786368	1.820000e-26	130.0
3	TraesCS2A01G103100	chr2D	94.329	1393	69	8	1	1391	39831939	39830555	0.000000e+00	2126.0
4	TraesCS2A01G103100	chr2D	93.619	1332	63	10	1	1324	55315512	55316829	0.000000e+00	1969.0
5	TraesCS2A01G103100	chr2D	85.870	1104	110	26	184	1260	55357766	55356682	0.000000e+00	1133.0
6	TraesCS2A01G103100	chr2D	91.779	815	22	8	1477	2261	39830551	39829752	0.000000e+00	1092.0
7	TraesCS2A01G103100	chr2D	84.941	591	37	21	1692	2261	55369405	55369964	3.280000e-153	551.0
8	TraesCS2A01G103100	chr2D	78.809	571	108	11	4	571	476913036	476913596	2.740000e-99	372.0
9	TraesCS2A01G103100	chr2D	87.218	133	15	2	1	133	55360162	55360032	1.400000e-32	150.0
10	TraesCS2A01G103100	chr2B	88.088	1679	112	40	622	2261	87842041	87843670	0.000000e+00	1912.0
11	TraesCS2A01G103100	chr2B	94.481	616	28	3	1	616	87841393	87842002	0.000000e+00	944.0
12	TraesCS2A01G103100	chr7D	90.954	608	49	4	1653	2260	559667907	559668508	0.000000e+00	813.0
13	TraesCS2A01G103100	chr7D	80.822	219	16	9	1458	1651	559667660	559667877	5.030000e-32	148.0
14	TraesCS2A01G103100	chr4A	83.647	850	84	21	1458	2260	520190187	520189346	0.000000e+00	749.0
15	TraesCS2A01G103100	chr4A	88.673	565	60	4	13	575	529634918	529634356	0.000000e+00	686.0
16	TraesCS2A01G103100	chr4A	84.830	501	66	9	756	1253	529634142	529633649	1.560000e-136	496.0
17	TraesCS2A01G103100	chr4A	75.742	573	108	19	13	571	531105114	531104559	2.230000e-65	259.0
18	TraesCS2A01G103100	chr4B	90.121	577	53	4	1	575	96630624	96631198	0.000000e+00	747.0
19	TraesCS2A01G103100	chr4B	83.431	513	71	12	746	1253	96631429	96631932	4.400000e-127	464.0
20	TraesCS2A01G103100	chr7B	83.120	859	71	35	1458	2261	620580444	620579605	0.000000e+00	715.0
21	TraesCS2A01G103100	chr4D	88.735	577	61	4	1	575	65860614	65861188	0.000000e+00	702.0
22	TraesCS2A01G103100	chr4D	87.398	611	49	15	1653	2261	191270919	191270335	0.000000e+00	676.0
23	TraesCS2A01G103100	chr4D	83.594	512	74	9	746	1254	65861380	65861884	2.630000e-129	472.0
24	TraesCS2A01G103100	chr4D	83.929	224	9	3	1458	1656	191271165	191270944	2.960000e-44	189.0
25	TraesCS2A01G103100	chr3B	74.839	155	35	4	771	923	111673895	111673743	1.450000e-07	67.6

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	TraesCS2A01G103100	chr2A	56916794	56919054	2260	False	4176.0	4176	100.0000	1	2261	1	chr2A.!!$F1	2260
1	TraesCS2A01G103100	chr2A	619238409	619238970	561	False	340.0	340	77.7580	4	571	1	chr2A.!!$F2	567
2	TraesCS2A01G103100	chr2D	55315512	55316829	1317	False	1969.0	1969	93.6190	1	1324	1	chr2D.!!$F1	1323
3	TraesCS2A01G103100	chr2D	39829752	39831939	2187	True	1609.0	2126	93.0540	1	2261	2	chr2D.!!$R1	2260
4	TraesCS2A01G103100	chr2D	55356682	55360162	3480	True	641.5	1133	86.5440	1	1260	2	chr2D.!!$R2	1259
5	TraesCS2A01G103100	chr2D	55369405	55369964	559	False	551.0	551	84.9410	1692	2261	1	chr2D.!!$F2	569
6	TraesCS2A01G103100	chr2D	476913036	476913596	560	False	372.0	372	78.8090	4	571	1	chr2D.!!$F3	567
7	TraesCS2A01G103100	chr2B	87841393	87843670	2277	False	1428.0	1912	91.2845	1	2261	2	chr2B.!!$F1	2260
8	TraesCS2A01G103100	chr7D	559667660	559668508	848	False	480.5	813	85.8880	1458	2260	2	chr7D.!!$F1	802
9	TraesCS2A01G103100	chr4A	520189346	520190187	841	True	749.0	749	83.6470	1458	2260	1	chr4A.!!$R1	802
10	TraesCS2A01G103100	chr4A	529633649	529634918	1269	True	591.0	686	86.7515	13	1253	2	chr4A.!!$R3	1240
11	TraesCS2A01G103100	chr4A	531104559	531105114	555	True	259.0	259	75.7420	13	571	1	chr4A.!!$R2	558
12	TraesCS2A01G103100	chr4B	96630624	96631932	1308	False	605.5	747	86.7760	1	1253	2	chr4B.!!$F1	1252
13	TraesCS2A01G103100	chr7B	620579605	620580444	839	True	715.0	715	83.1200	1458	2261	1	chr7B.!!$R1	803
14	TraesCS2A01G103100	chr4D	65860614	65861884	1270	False	587.0	702	86.1645	1	1254	2	chr4D.!!$F1	1253
15	TraesCS2A01G103100	chr4D	191270335	191271165	830	True	432.5	676	85.6635	1458	2261	2	chr4D.!!$R1	803

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
740	3089	0.178981	CCGGCTCCCATTCCAATGAT	60.179	55.0	0.56	0.0	38.7	2.45	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2078	4527	0.551131	ATCCACTGGCCTCCTCCTTT	60.551	55.0	3.32	0.0	0.0	3.11	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
737	3086	2.123726	GCCGGCTCCCATTCCAAT	60.124	61.111	22.15	0.00	0.00	3.16
740	3089	0.178981	CCGGCTCCCATTCCAATGAT	60.179	55.000	0.56	0.00	38.70	2.45
873	3222	1.446792	CACGAGCACCTGCCTACTG	60.447	63.158	0.00	0.00	43.38	2.74
1059	3408	2.027625	CGAGGTCGTCCACAAAGCC	61.028	63.158	0.51	0.00	35.89	4.35
1122	3480	3.008923	TCACCATGTGTCTTATGCAGGAA	59.991	43.478	0.00	0.00	34.79	3.36
1191	3549	1.878102	GCCGATCATCCGTTTGCCTAT	60.878	52.381	0.00	0.00	0.00	2.57
1287	3653	2.092592	ACGTAGGATGTTGGAATTCCCC	60.093	50.000	21.90	14.56	34.29	4.81
1302	3669	6.940298	TGGAATTCCCCTATTTCGAATACATC	59.060	38.462	21.90	0.00	34.29	3.06
1312	3680	4.530094	TTCGAATACATCCATGCGTTTC	57.470	40.909	0.00	0.00	0.00	2.78
1314	3682	3.555547	TCGAATACATCCATGCGTTTCAG	59.444	43.478	0.00	0.00	0.00	3.02
1317	3685	5.428496	AATACATCCATGCGTTTCAGATG	57.572	39.130	4.83	4.83	40.12	2.90
1318	3686	2.989909	ACATCCATGCGTTTCAGATGA	58.010	42.857	11.35	0.00	38.15	2.92
1319	3687	2.941064	ACATCCATGCGTTTCAGATGAG	59.059	45.455	11.35	0.00	38.15	2.90
1320	3688	3.200483	CATCCATGCGTTTCAGATGAGA	58.800	45.455	1.00	0.00	37.16	3.27
1321	3689	3.548745	TCCATGCGTTTCAGATGAGAT	57.451	42.857	0.00	0.00	0.00	2.75
1331	3699	5.352293	CGTTTCAGATGAGATGATGACCAAA	59.648	40.000	0.00	0.00	0.00	3.28
1378	3747	8.132995	AGGTTTACAAGTTAATTTGTTCCTTCG	58.867	33.333	19.79	0.00	41.31	3.79
1385	3754	5.949952	AGTTAATTTGTTCCTTCGGGCTTAT	59.050	36.000	0.00	0.00	34.44	1.73
1391	3760	4.340617	TGTTCCTTCGGGCTTATTTGATT	58.659	39.130	0.00	0.00	34.44	2.57
1392	3761	4.157656	TGTTCCTTCGGGCTTATTTGATTG	59.842	41.667	0.00	0.00	34.44	2.67
1393	3762	2.687935	TCCTTCGGGCTTATTTGATTGC	59.312	45.455	0.00	0.00	34.44	3.56
1394	3763	2.689983	CCTTCGGGCTTATTTGATTGCT	59.310	45.455	0.00	0.00	0.00	3.91
1395	3764	3.131046	CCTTCGGGCTTATTTGATTGCTT	59.869	43.478	0.00	0.00	0.00	3.91
1396	3765	4.354587	CTTCGGGCTTATTTGATTGCTTC	58.645	43.478	0.00	0.00	0.00	3.86
1397	3766	3.620488	TCGGGCTTATTTGATTGCTTCT	58.380	40.909	0.00	0.00	0.00	2.85
1398	3767	4.016444	TCGGGCTTATTTGATTGCTTCTT	58.984	39.130	0.00	0.00	0.00	2.52
1399	3768	4.096382	TCGGGCTTATTTGATTGCTTCTTC	59.904	41.667	0.00	0.00	0.00	2.87
1400	3769	4.142403	CGGGCTTATTTGATTGCTTCTTCA	60.142	41.667	0.00	0.00	0.00	3.02
1401	3770	5.622007	CGGGCTTATTTGATTGCTTCTTCAA	60.622	40.000	0.00	0.00	0.00	2.69
1402	3771	6.343703	GGGCTTATTTGATTGCTTCTTCAAT	58.656	36.000	0.00	0.00	39.20	2.57
1411	3780	3.861276	TGCTTCTTCAATCAGCCATTG	57.139	42.857	0.33	0.33	43.15	2.82
1412	3781	2.494471	TGCTTCTTCAATCAGCCATTGG	59.506	45.455	0.00	0.00	42.18	3.16
1413	3782	2.494870	GCTTCTTCAATCAGCCATTGGT	59.505	45.455	4.26	0.00	42.18	3.67
1414	3783	3.428589	GCTTCTTCAATCAGCCATTGGTC	60.429	47.826	4.26	0.00	42.18	4.02
1415	3784	2.358957	TCTTCAATCAGCCATTGGTCG	58.641	47.619	4.26	0.00	42.18	4.79
1416	3785	2.086869	CTTCAATCAGCCATTGGTCGT	58.913	47.619	4.26	0.00	42.18	4.34
1436	3805	3.241900	CGTTTGATCTGCTCGAGTGATTG	60.242	47.826	15.13	0.43	0.00	2.67
1452	3821	3.807631	TTGCTCGCTGGCTCGTTGT	62.808	57.895	0.00	0.00	0.00	3.32
1469	3843	4.026062	TCGTTGTTGTCAGTTTCAGATTCG	60.026	41.667	0.00	0.00	0.00	3.34
1475	3849	3.489416	TGTCAGTTTCAGATTCGTCGTTG	59.511	43.478	0.00	0.00	0.00	4.10
1507	3881	1.547372	GTTCCACGCCTAGGTACTCAA	59.453	52.381	11.31	0.00	41.75	3.02
1552	3926	3.205784	AGAGGTGCTAATCATGCCTTC	57.794	47.619	0.00	0.00	0.00	3.46
1599	3998	1.195448	GACACACCAATTCAGACGCAG	59.805	52.381	0.00	0.00	0.00	5.18
1920	4367	4.459390	TCAATCTGTTCAATGCAATGGG	57.541	40.909	1.05	0.00	0.00	4.00
2062	4511	0.826715	GAGCTACAGGCATCCAGTCA	59.173	55.000	0.00	0.00	44.79	3.41
2071	4520	1.552337	GGCATCCAGTCAGACAGAGAA	59.448	52.381	2.66	0.00	0.00	2.87
2101	4550	0.980231	GAGGAGGCCAGTGGATGTCT	60.980	60.000	15.20	4.20	0.00	3.41
2117	4566	5.168569	GGATGTCTCAAACTGTTGTCGATA	58.831	41.667	0.00	0.00	36.07	2.92

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
873	3222	2.126031	GCCGACGTCCACCTTCTC	60.126	66.667	10.58	0.00	0.00	2.87
945	3294	1.376466	GAGGCCCAGCTTGTTGAGA	59.624	57.895	0.00	0.00	0.00	3.27
1059	3408	0.523546	CCTCGTTCACCTCGATGACG	60.524	60.000	0.00	0.44	36.73	4.35
1191	3549	1.060729	TCCCCTCGTCCACAATGAAA	58.939	50.000	0.00	0.00	0.00	2.69
1261	3620	3.795623	TTCCAACATCCTACGTAGCTC	57.204	47.619	17.41	0.00	0.00	4.09
1287	3653	5.845985	ACGCATGGATGTATTCGAAATAG	57.154	39.130	0.00	0.00	0.00	1.73
1302	3669	3.200483	TCATCTCATCTGAAACGCATGG	58.800	45.455	0.00	0.00	0.00	3.66
1350	3719	9.594478	AAGGAACAAATTAACTTGTAAACCTTG	57.406	29.630	22.56	0.00	41.01	3.61
1378	3747	5.329035	TGAAGAAGCAATCAAATAAGCCC	57.671	39.130	0.00	0.00	0.00	5.19
1391	3760	2.494471	CCAATGGCTGATTGAAGAAGCA	59.506	45.455	9.71	0.00	43.87	3.91
1392	3761	2.494870	ACCAATGGCTGATTGAAGAAGC	59.505	45.455	0.00	0.00	43.87	3.86
1393	3762	3.181503	CGACCAATGGCTGATTGAAGAAG	60.182	47.826	0.00	0.00	43.87	2.85
1394	3763	2.749076	CGACCAATGGCTGATTGAAGAA	59.251	45.455	0.00	0.00	43.87	2.52
1395	3764	2.290260	ACGACCAATGGCTGATTGAAGA	60.290	45.455	0.00	0.00	43.87	2.87
1396	3765	2.086869	ACGACCAATGGCTGATTGAAG	58.913	47.619	0.00	4.60	43.87	3.02
1397	3766	2.198827	ACGACCAATGGCTGATTGAA	57.801	45.000	0.00	0.00	43.87	2.69
1398	3767	2.198827	AACGACCAATGGCTGATTGA	57.801	45.000	0.00	0.00	43.87	2.57
1399	3768	2.228582	TCAAACGACCAATGGCTGATTG	59.771	45.455	0.00	3.63	41.20	2.67
1400	3769	2.513753	TCAAACGACCAATGGCTGATT	58.486	42.857	0.00	0.00	0.00	2.57
1401	3770	2.198827	TCAAACGACCAATGGCTGAT	57.801	45.000	0.00	0.00	0.00	2.90
1402	3771	2.083774	GATCAAACGACCAATGGCTGA	58.916	47.619	0.00	0.00	0.00	4.26
1403	3772	2.086869	AGATCAAACGACCAATGGCTG	58.913	47.619	0.00	0.00	0.00	4.85
1404	3773	2.086869	CAGATCAAACGACCAATGGCT	58.913	47.619	0.00	0.00	0.00	4.75
1405	3774	1.468054	GCAGATCAAACGACCAATGGC	60.468	52.381	0.00	0.00	0.00	4.40
1406	3775	2.086869	AGCAGATCAAACGACCAATGG	58.913	47.619	0.00	0.00	0.00	3.16
1407	3776	2.222886	CGAGCAGATCAAACGACCAATG	60.223	50.000	0.00	0.00	0.00	2.82
1408	3777	2.002586	CGAGCAGATCAAACGACCAAT	58.997	47.619	0.00	0.00	0.00	3.16
1409	3778	1.000394	TCGAGCAGATCAAACGACCAA	60.000	47.619	0.00	0.00	0.00	3.67
1410	3779	0.601057	TCGAGCAGATCAAACGACCA	59.399	50.000	0.00	0.00	0.00	4.02
1411	3780	1.272781	CTCGAGCAGATCAAACGACC	58.727	55.000	0.00	0.00	0.00	4.79
1412	3781	1.651138	CACTCGAGCAGATCAAACGAC	59.349	52.381	13.61	0.00	0.00	4.34
1413	3782	1.539827	TCACTCGAGCAGATCAAACGA	59.460	47.619	13.61	0.00	0.00	3.85
1414	3783	1.982612	TCACTCGAGCAGATCAAACG	58.017	50.000	13.61	0.00	0.00	3.60
1415	3784	3.484886	GCAATCACTCGAGCAGATCAAAC	60.485	47.826	13.61	3.81	0.00	2.93
1416	3785	2.674852	GCAATCACTCGAGCAGATCAAA	59.325	45.455	13.61	0.00	0.00	2.69
1436	3805	3.044305	AACAACGAGCCAGCGAGC	61.044	61.111	0.00	0.00	34.83	5.03
1452	3821	3.713288	ACGACGAATCTGAAACTGACAA	58.287	40.909	0.00	0.00	0.00	3.18
1469	3843	1.021968	ACTGAAACTTGGGCAACGAC	58.978	50.000	0.00	0.00	37.60	4.34
1475	3849	0.310854	CGTGGAACTGAAACTTGGGC	59.689	55.000	0.00	0.00	31.75	5.36
1552	3926	1.741528	TGGCATGTATCAGTGCACTG	58.258	50.000	36.07	36.07	43.00	3.66
1599	3998	1.457346	CAGTGTCCATGGCTCCTTTC	58.543	55.000	6.96	0.00	0.00	2.62
1884	4330	3.067180	CAGATTGATTGATGGTTTCGGGG	59.933	47.826	0.00	0.00	0.00	5.73
2062	4511	4.224818	CCTCCTTTGAATCCTTCTCTGTCT	59.775	45.833	0.00	0.00	0.00	3.41
2071	4520	0.922626	GGCCTCCTCCTTTGAATCCT	59.077	55.000	0.00	0.00	0.00	3.24
2078	4527	0.551131	ATCCACTGGCCTCCTCCTTT	60.551	55.000	3.32	0.00	0.00	3.11
2101	4550	5.838529	TCAGAACTATCGACAACAGTTTGA	58.161	37.500	0.00	0.68	36.48	2.69
2117	4566	3.579709	CGTAGCACACTTGATCAGAACT	58.420	45.455	0.00	0.00	0.00	3.01

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.