AutoCloner

Multiple sequence alignment - TraesCS7B01G424200

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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	TraesCS7B01G424200	chr7B	100.000	2660	0	0	1	2660	693249502	693246843	0.000000e+00	4913.0
1	TraesCS7B01G424200	chr7B	92.879	1924	99	20	744	2660	696899038	696897146	0.000000e+00	2760.0
2	TraesCS7B01G424200	chr7B	89.040	1770	134	25	912	2660	693867536	693865806	0.000000e+00	2139.0
3	TraesCS7B01G424200	chr7B	85.620	1961	187	43	747	2660	697256598	697254686	0.000000e+00	1971.0
4	TraesCS7B01G424200	chr7B	92.273	660	31	14	1	655	696899979	696899335	0.000000e+00	918.0
5	TraesCS7B01G424200	chr7B	85.657	495	48	10	279	757	693904979	693904492	1.420000e-137	499.0
6	TraesCS7B01G424200	chr7B	91.643	347	22	3	411	757	697256976	697256637	8.620000e-130	473.0
7	TraesCS7B01G424200	chr7B	87.220	313	34	4	1	308	697257700	697257389	4.210000e-93	351.0
8	TraesCS7B01G424200	chr7B	89.655	145	11	4	744	887	693904454	693904313	5.850000e-42	182.0
9	TraesCS7B01G424200	chr7B	91.579	95	5	1	287	381	697257376	697257285	7.730000e-26	128.0
10	TraesCS7B01G424200	chrUn	91.361	1933	126	23	744	2658	77648212	77646303	0.000000e+00	2606.0
11	TraesCS7B01G424200	chrUn	93.165	1229	64	7	744	1959	83440883	83439662	0.000000e+00	1786.0
12	TraesCS7B01G424200	chrUn	88.003	1342	121	23	1142	2472	317940740	317942052	0.000000e+00	1550.0
13	TraesCS7B01G424200	chrUn	88.228	790	43	15	1	757	77649022	77648250	0.000000e+00	898.0
14	TraesCS7B01G424200	chrUn	91.181	669	39	12	1996	2660	83439665	83439013	0.000000e+00	891.0
15	TraesCS7B01G424200	chrUn	82.837	973	115	37	1683	2632	317942044	317942987	0.000000e+00	824.0
16	TraesCS7B01G424200	chrUn	92.358	458	25	2	300	757	373622204	373622651	0.000000e+00	643.0
17	TraesCS7B01G424200	chrUn	90.055	362	25	7	401	755	83441280	83440923	2.410000e-125	459.0
18	TraesCS7B01G424200	chrUn	90.132	152	12	3	744	894	373622689	373622838	7.510000e-46	195.0
19	TraesCS7B01G424200	chr7D	88.986	1943	148	31	744	2658	607614840	607612936	0.000000e+00	2342.0
20	TraesCS7B01G424200	chr7D	88.582	1953	149	31	744	2660	610214703	610216617	0.000000e+00	2303.0
21	TraesCS7B01G424200	chr7D	89.024	738	42	13	37	757	607615593	607614878	0.000000e+00	878.0
22	TraesCS7B01G424200	chr7D	88.347	738	46	12	37	757	610213951	610214665	0.000000e+00	850.0
23	TraesCS7B01G424200	chr7A	86.037	1017	87	19	744	1733	699842134	699841146	0.000000e+00	1040.0
24	TraesCS7B01G424200	chr7A	90.816	588	39	4	175	757	699842749	699842172	0.000000e+00	773.0
25	TraesCS7B01G424200	chr7A	90.989	455	34	3	1768	2221	699841150	699840702	8.140000e-170	606.0
26	TraesCS7B01G424200	chr7A	89.960	249	21	3	2282	2527	699840693	699840446	4.270000e-83	318.0
27	TraesCS7B01G424200	chr7A	96.774	155	2	3	2509	2660	699840329	699840175	3.400000e-64	255.0
28	TraesCS7B01G424200	chr7A	72.118	850	176	42	987	1818	700160213	700159407	1.610000e-47	200.0
29	TraesCS7B01G424200	chr3A	84.906	159	16	4	1612	1770	673597171	673597021	1.280000e-33	154.0
30	TraesCS7B01G424200	chr2A	75.879	199	35	7	1527	1723	193550745	193550558	3.650000e-14	89.8

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	TraesCS7B01G424200	chr7B	693246843	693249502	2659	True	4913.000000	4913	100.0000	1	2660	1	chr7B.!!$R1	2659
1	TraesCS7B01G424200	chr7B	693865806	693867536	1730	True	2139.000000	2139	89.0400	912	2660	1	chr7B.!!$R2	1748
2	TraesCS7B01G424200	chr7B	696897146	696899979	2833	True	1839.000000	2760	92.5760	1	2660	2	chr7B.!!$R4	2659
3	TraesCS7B01G424200	chr7B	697254686	697257700	3014	True	730.750000	1971	89.0155	1	2660	4	chr7B.!!$R5	2659
4	TraesCS7B01G424200	chr7B	693904313	693904979	666	True	340.500000	499	87.6560	279	887	2	chr7B.!!$R3	608
5	TraesCS7B01G424200	chrUn	77646303	77649022	2719	True	1752.000000	2606	89.7945	1	2658	2	chrUn.!!$R1	2657
6	TraesCS7B01G424200	chrUn	317940740	317942987	2247	False	1187.000000	1550	85.4200	1142	2632	2	chrUn.!!$F1	1490
7	TraesCS7B01G424200	chrUn	83439013	83441280	2267	True	1045.333333	1786	91.4670	401	2660	3	chrUn.!!$R2	2259
8	TraesCS7B01G424200	chrUn	373622204	373622838	634	False	419.000000	643	91.2450	300	894	2	chrUn.!!$F2	594
9	TraesCS7B01G424200	chr7D	607612936	607615593	2657	True	1610.000000	2342	89.0050	37	2658	2	chr7D.!!$R1	2621
10	TraesCS7B01G424200	chr7D	610213951	610216617	2666	False	1576.500000	2303	88.4645	37	2660	2	chr7D.!!$F1	2623
11	TraesCS7B01G424200	chr7A	699840175	699842749	2574	True	598.400000	1040	90.9152	175	2660	5	chr7A.!!$R2	2485

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
470	813	0.106619	TACCACCAACCACCAACCAC	60.107	55.0	0.0	0.0	0.0	4.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2280	3736	0.539438	AAAAACTGGATGCTCCGCCA	60.539	50.0	0.0	0.0	40.17	5.69	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
34	35	1.807142	GGGTCTCTGTGCTTTGCTTAC	59.193	52.381	0.00	0.00	0.00	2.34
142	147	4.208746	TGGTTACAAAAACAGGTACCCAG	58.791	43.478	8.74	4.12	29.91	4.45
292	336	4.172505	CAAAATCACTCTCTCCAGACTCG	58.827	47.826	0.00	0.00	0.00	4.18
464	807	1.428718	TTCCCCTACCACCAACCACC	61.429	60.000	0.00	0.00	0.00	4.61
465	808	2.157452	CCCCTACCACCAACCACCA	61.157	63.158	0.00	0.00	0.00	4.17
466	809	1.721093	CCCCTACCACCAACCACCAA	61.721	60.000	0.00	0.00	0.00	3.67
467	810	0.538746	CCCTACCACCAACCACCAAC	60.539	60.000	0.00	0.00	0.00	3.77
468	811	0.538746	CCTACCACCAACCACCAACC	60.539	60.000	0.00	0.00	0.00	3.77
469	812	0.183971	CTACCACCAACCACCAACCA	59.816	55.000	0.00	0.00	0.00	3.67
470	813	0.106619	TACCACCAACCACCAACCAC	60.107	55.000	0.00	0.00	0.00	4.16
474	817	1.075600	CCAACCACCAACCACCCTT	60.076	57.895	0.00	0.00	0.00	3.95
488	831	3.157949	CCTTCCTCCTCCGCCTCC	61.158	72.222	0.00	0.00	0.00	4.30
592	941	1.068753	CAGAAGATCTCGCCCGCAT	59.931	57.895	0.00	0.00	0.00	4.73
958	1538	2.664851	CAGGCGTCAACGAGGCAA	60.665	61.111	6.75	0.00	44.00	4.52
1101	1681	2.559705	GGGTTGGGATGATTTGTTCCCT	60.560	50.000	9.29	0.00	42.72	4.20
1410	2023	5.190528	TGAGAATTCTAGCCAGTGGAAGATT	59.809	40.000	15.20	8.30	0.00	2.40
1447	2060	9.298250	TCTCACTACCTTATGATTATCAGTACC	57.702	37.037	0.29	0.00	0.00	3.34
1626	2263	1.063469	GCGCGCATATACACCAACTTT	59.937	47.619	29.10	0.00	0.00	2.66
1639	2276	2.176798	ACCAACTTTCCACCATCCTTGA	59.823	45.455	0.00	0.00	0.00	3.02
1645	2282	4.202609	ACTTTCCACCATCCTTGATGTCTT	60.203	41.667	3.62	0.00	38.28	3.01
1684	2321	6.485171	AGTGGTAAACTTTCTATTGCATCCT	58.515	36.000	0.00	0.00	34.57	3.24
1685	2322	7.630082	AGTGGTAAACTTTCTATTGCATCCTA	58.370	34.615	0.00	0.00	34.57	2.94
1686	2323	7.770897	AGTGGTAAACTTTCTATTGCATCCTAG	59.229	37.037	0.00	0.00	34.57	3.02
1740	2417	7.172703	ACAGCTTGTCTAACGCTTAACTTAATT	59.827	33.333	0.00	0.00	0.00	1.40
1776	2453	8.692710	TGAGATTAGTCATTCTGGTTTATACGT	58.307	33.333	0.00	0.00	0.00	3.57
1784	2461	8.378421	GTCATTCTGGTTTATACGTTTCAGTAC	58.622	37.037	0.00	0.00	0.00	2.73
1786	2463	8.592998	CATTCTGGTTTATACGTTTCAGTACTC	58.407	37.037	0.00	0.00	0.00	2.59
1883	2564	6.406370	TCTAATCGCTTTCCAGAGAAAATCA	58.594	36.000	0.00	0.00	41.40	2.57
1885	2566	4.008074	TCGCTTTCCAGAGAAAATCAGT	57.992	40.909	0.00	0.00	41.40	3.41
1891	2572	7.148340	CGCTTTCCAGAGAAAATCAGTAAAGAT	60.148	37.037	0.00	0.00	41.40	2.40
1923	2604	5.673514	TCACATAGCTTATGCATTCACTGA	58.326	37.500	3.54	0.00	42.74	3.41
1932	2615	7.941238	AGCTTATGCATTCACTGATATTTAGGT	59.059	33.333	3.54	0.00	42.74	3.08
1954	2637	6.494491	AGGTCTCATGAAATCACAAAAATGGA	59.506	34.615	0.00	0.00	0.00	3.41
1959	2642	9.263538	CTCATGAAATCACAAAAATGGAAGAAA	57.736	29.630	0.00	0.00	0.00	2.52
2039	2722	9.169592	GATCCAATTTTCATTTGATTGTTCCAT	57.830	29.630	0.00	0.00	27.33	3.41
2049	2732	3.753815	TGATTGTTCCATTCAGCTCACA	58.246	40.909	0.00	0.00	0.00	3.58
2087	2772	1.615883	AGCACGACTCATCTTGTCTGT	59.384	47.619	0.00	0.00	32.70	3.41
2207	2900	5.541845	TGTGGTCACAAATAAGAGACTCAG	58.458	41.667	5.02	0.00	38.56	3.35
2259	3712	3.918591	GCACAAGCTGTTTGATCTGAATG	59.081	43.478	11.31	0.00	39.21	2.67
2266	3719	3.264947	TGTTTGATCTGAATGAGCCTCG	58.735	45.455	0.00	0.00	0.00	4.63
2286	3743	2.481276	CGTAAGATCACTCATTGGCGGA	60.481	50.000	0.00	0.00	43.02	5.54
2348	3812	6.539649	TTGAACTATTTCACACCTCTTTCG	57.460	37.500	0.00	0.00	41.64	3.46
2384	3851	2.357637	ACGGCAAATATAAGCACGCAAT	59.642	40.909	2.25	0.00	0.00	3.56

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
142	147	7.565789	GCGACATCTCAGTTCAAACAATTTTTC	60.566	37.037	0.00	0.00	0.00	2.29
183	188	2.124403	CAGGCCCAGCACCTCATC	60.124	66.667	0.00	0.00	34.42	2.92
464	807	1.685820	GGAGGAGGAAGGGTGGTTG	59.314	63.158	0.00	0.00	0.00	3.77
465	808	1.918800	CGGAGGAGGAAGGGTGGTT	60.919	63.158	0.00	0.00	0.00	3.67
466	809	2.284699	CGGAGGAGGAAGGGTGGT	60.285	66.667	0.00	0.00	0.00	4.16
467	810	3.787001	GCGGAGGAGGAAGGGTGG	61.787	72.222	0.00	0.00	0.00	4.61
468	811	3.787001	GGCGGAGGAGGAAGGGTG	61.787	72.222	0.00	0.00	0.00	4.61
469	812	3.986116	GAGGCGGAGGAGGAAGGGT	62.986	68.421	0.00	0.00	0.00	4.34
470	813	3.157949	GAGGCGGAGGAGGAAGGG	61.158	72.222	0.00	0.00	0.00	3.95
474	817	4.144727	GAGGGAGGCGGAGGAGGA	62.145	72.222	0.00	0.00	0.00	3.71
495	838	2.679996	GGCCATTTCCTTGCCGGT	60.680	61.111	1.90	0.00	35.08	5.28
592	941	3.310307	TGACGCAGGTGGCAGCTA	61.310	61.111	20.14	0.00	45.17	3.32
650	999	4.388499	GCGTGGAGGAGGCGGAAA	62.388	66.667	0.00	0.00	0.00	3.13
936	1516	3.573772	CTCGTTGACGCCTGCTCCA	62.574	63.158	0.00	0.00	39.60	3.86
958	1538	0.179936	GCCTCTTCTATGGCTGCAGT	59.820	55.000	16.64	0.00	45.26	4.40
969	1549	4.416738	GCCCTTGCCGCCTCTTCT	62.417	66.667	0.00	0.00	0.00	2.85
1101	1681	2.409064	TGGTTGACTCTCCCTGGTTA	57.591	50.000	0.00	0.00	0.00	2.85
1447	2060	4.815308	CCTCTCAGTTGAAGCTTGGATATG	59.185	45.833	2.10	0.00	0.00	1.78
1626	2263	2.912295	TGAAGACATCAAGGATGGTGGA	59.088	45.455	10.64	0.00	43.60	4.02
1645	2282	3.973206	ACCACTTCATATTGTCGGTGA	57.027	42.857	0.00	0.00	0.00	4.02
1684	2321	6.039415	ACTATGAAGGGGAGGACATAACTA	57.961	41.667	0.00	0.00	0.00	2.24
1685	2322	4.897051	ACTATGAAGGGGAGGACATAACT	58.103	43.478	0.00	0.00	0.00	2.24
1686	2323	5.632034	AACTATGAAGGGGAGGACATAAC	57.368	43.478	0.00	0.00	0.00	1.89
1727	2375	9.478019	CTCAGTAATGAACAATTAAGTTAAGCG	57.522	33.333	1.21	0.00	32.47	4.68
1740	2417	9.591792	CAGAATGACTAATCTCAGTAATGAACA	57.408	33.333	0.00	0.00	39.69	3.18
1776	2453	8.653338	GCACAAGATAAATAACGAGTACTGAAA	58.347	33.333	0.00	0.00	0.00	2.69
1784	2461	6.250819	CCACAAGCACAAGATAAATAACGAG	58.749	40.000	0.00	0.00	0.00	4.18
1786	2463	5.123186	TCCCACAAGCACAAGATAAATAACG	59.877	40.000	0.00	0.00	0.00	3.18
1897	2578	7.283807	TCAGTGAATGCATAAGCTATGTGAAAT	59.716	33.333	0.00	0.00	42.74	2.17
1932	2615	8.180706	TCTTCCATTTTTGTGATTTCATGAGA	57.819	30.769	0.00	0.00	0.00	3.27
2039	2722	5.771153	TGAATGAATTTGTGTGAGCTGAA	57.229	34.783	0.00	0.00	0.00	3.02
2049	2732	6.144402	GTCGTGCTTGAATTGAATGAATTTGT	59.856	34.615	0.00	0.00	34.18	2.83
2102	2787	8.380099	ACTTTTCCGCATCCTTATGGTTATATA	58.620	33.333	0.00	0.00	33.38	0.86
2103	2788	7.231467	ACTTTTCCGCATCCTTATGGTTATAT	58.769	34.615	0.00	0.00	33.38	0.86
2104	2789	6.597562	ACTTTTCCGCATCCTTATGGTTATA	58.402	36.000	0.00	0.00	33.38	0.98
2105	2790	5.445964	ACTTTTCCGCATCCTTATGGTTAT	58.554	37.500	0.00	0.00	33.38	1.89
2106	2791	4.850680	ACTTTTCCGCATCCTTATGGTTA	58.149	39.130	0.00	0.00	33.38	2.85
2178	2869	5.011635	TCTCTTATTTGTGACCACAGCAGTA	59.988	40.000	2.92	0.00	42.94	2.74
2207	2900	8.514136	CAAGCTATTCTTGCTATACAGAGTAC	57.486	38.462	0.00	0.00	44.85	2.73
2259	3712	4.047822	CAATGAGTGATCTTACGAGGCTC	58.952	47.826	3.87	3.87	0.00	4.70
2266	3719	3.126831	CTCCGCCAATGAGTGATCTTAC	58.873	50.000	0.00	0.00	0.00	2.34
2280	3736	0.539438	AAAAACTGGATGCTCCGCCA	60.539	50.000	0.00	0.00	40.17	5.69
2286	3743	6.316140	GGAAACAAAAAGAAAAACTGGATGCT	59.684	34.615	0.00	0.00	0.00	3.79
2348	3812	0.744771	GCCGTTCATTGGGAGACTCC	60.745	60.000	13.60	13.60	35.23	3.85
2384	3851	2.852449	TCTTGCCACAACCGACAAATA	58.148	42.857	0.00	0.00	0.00	1.40
2456	3929	6.189133	ACAAACTTTTAACCCAGGTCAGTTA	58.811	36.000	0.00	0.00	0.00	2.24
2507	3980	3.322828	AGATTTGTGTTGCAGCCTTGAAT	59.677	39.130	0.00	0.00	0.00	2.57
2543	4154	8.537858	AGTAAATGAGTCCGGTAAACTTAGATT	58.462	33.333	0.00	0.00	0.00	2.40
2587	4200	2.260822	AGCTGGAATACATAGCCCGAT	58.739	47.619	0.00	0.00	38.18	4.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.