AutoCloner

Multiple sequence alignment - TraesCS7A01G081800

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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	TraesCS7A01G081800	chr7A	100.000	2894	0	0	1	2894	47015821	47018714	0.000000e+00	5345.0
1	TraesCS7A01G081800	chr7A	76.164	1611	286	54	769	2313	47283136	47284714	0.000000e+00	758.0
2	TraesCS7A01G081800	chr7A	76.032	1235	235	36	773	1966	43015277	43014063	4.160000e-163	584.0
3	TraesCS7A01G081800	chr7A	78.416	783	130	23	772	1524	47225297	47224524	9.390000e-130	473.0
4	TraesCS7A01G081800	chr7A	79.104	469	77	17	774	1228	47000543	47001004	1.300000e-78	303.0
5	TraesCS7A01G081800	chr7A	82.085	307	47	8	327	630	13622943	13622642	3.700000e-64	255.0
6	TraesCS7A01G081800	chr4A	92.561	2608	134	26	1	2556	656479219	656481818	0.000000e+00	3687.0
7	TraesCS7A01G081800	chr4A	94.840	969	49	1	1297	2265	656264700	656265667	0.000000e+00	1511.0
8	TraesCS7A01G081800	chr4A	92.136	941	53	7	1828	2749	656816801	656815863	0.000000e+00	1308.0
9	TraesCS7A01G081800	chr4A	78.101	1169	210	32	773	1913	650831078	650832228	0.000000e+00	699.0
10	TraesCS7A01G081800	chr4A	90.672	461	27	6	2292	2749	656265652	656266099	1.480000e-167	599.0
11	TraesCS7A01G081800	chr4A	78.556	942	166	23	976	1899	655659029	655659952	3.210000e-164	588.0
12	TraesCS7A01G081800	chr4A	75.914	1204	237	42	773	1947	656550843	656552022	4.190000e-158	568.0
13	TraesCS7A01G081800	chr4A	92.308	143	10	1	2751	2893	656483383	656483524	4.890000e-48	202.0
14	TraesCS7A01G081800	chr4A	82.128	235	35	7	336	568	612381315	612381544	8.180000e-46	195.0
15	TraesCS7A01G081800	chr4A	91.852	135	10	1	2754	2888	656815349	656815216	1.370000e-43	187.0
16	TraesCS7A01G081800	chr4A	94.792	96	4	1	2743	2838	656266270	656266364	6.460000e-32	148.0
17	TraesCS7A01G081800	chrUn	93.605	1939	99	18	344	2265	48867299	48865369	0.000000e+00	2870.0
18	TraesCS7A01G081800	chrUn	91.537	709	39	14	344	1035	48878939	48878235	0.000000e+00	957.0
19	TraesCS7A01G081800	chrUn	91.537	709	39	14	344	1035	359259263	359259967	0.000000e+00	957.0
20	TraesCS7A01G081800	chrUn	75.330	1666	290	60	769	2369	48990371	48991980	0.000000e+00	688.0
21	TraesCS7A01G081800	chrUn	90.733	464	24	9	2304	2749	48865372	48864910	4.130000e-168	601.0
22	TraesCS7A01G081800	chrUn	75.000	1192	234	38	773	1928	289666340	289667503	2.590000e-135	492.0
23	TraesCS7A01G081800	chrUn	89.744	351	17	8	2417	2749	48877872	48877523	5.730000e-117	431.0
24	TraesCS7A01G081800	chrUn	94.000	50	3	0	2751	2800	48864337	48864288	3.090000e-10	76.8
25	TraesCS7A01G081800	chrUn	94.000	50	3	0	2751	2800	48876950	48876901	3.090000e-10	76.8
26	TraesCS7A01G081800	chr7D	95.920	1005	28	8	1025	2022	44550936	44551934	0.000000e+00	1616.0
27	TraesCS7A01G081800	chr7D	78.268	1201	213	34	773	1944	43169394	43168213	0.000000e+00	728.0
28	TraesCS7A01G081800	chr7D	94.565	368	16	4	2385	2749	44552068	44552434	1.510000e-157	566.0
29	TraesCS7A01G081800	chr7D	94.737	323	12	2	710	1027	44550511	44550833	5.570000e-137	497.0
30	TraesCS7A01G081800	chr7D	80.384	469	71	18	774	1228	44530551	44531012	1.280000e-88	337.0
31	TraesCS7A01G081800	chr7D	89.247	93	6	2	1933	2022	44551941	44552032	2.360000e-21	113.0
32	TraesCS7A01G081800	chr7D	93.333	45	1	2	1933	1977	44552039	44552081	6.690000e-07	65.8
33	TraesCS7A01G081800	chr3D	74.257	1278	261	44	784	2010	9243816	9245076	2.610000e-130	475.0
34	TraesCS7A01G081800	chr5D	80.952	252	39	9	381	627	2562800	2562553	1.060000e-44	191.0
35	TraesCS7A01G081800	chr5D	85.965	114	15	1	381	494	3270959	3271071	1.410000e-23	121.0

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	TraesCS7A01G081800	chr7A	47015821	47018714	2893	False	5345.000000	5345	100.000000	1	2894	1	chr7A.!!$F2	2893
1	TraesCS7A01G081800	chr7A	47283136	47284714	1578	False	758.000000	758	76.164000	769	2313	1	chr7A.!!$F3	1544
2	TraesCS7A01G081800	chr7A	43014063	43015277	1214	True	584.000000	584	76.032000	773	1966	1	chr7A.!!$R2	1193
3	TraesCS7A01G081800	chr7A	47224524	47225297	773	True	473.000000	473	78.416000	772	1524	1	chr7A.!!$R3	752
4	TraesCS7A01G081800	chr4A	656479219	656483524	4305	False	1944.500000	3687	92.434500	1	2893	2	chr4A.!!$F6	2892
5	TraesCS7A01G081800	chr4A	656264700	656266364	1664	False	752.666667	1511	93.434667	1297	2838	3	chr4A.!!$F5	1541
6	TraesCS7A01G081800	chr4A	656815216	656816801	1585	True	747.500000	1308	91.994000	1828	2888	2	chr4A.!!$R1	1060
7	TraesCS7A01G081800	chr4A	650831078	650832228	1150	False	699.000000	699	78.101000	773	1913	1	chr4A.!!$F2	1140
8	TraesCS7A01G081800	chr4A	655659029	655659952	923	False	588.000000	588	78.556000	976	1899	1	chr4A.!!$F3	923
9	TraesCS7A01G081800	chr4A	656550843	656552022	1179	False	568.000000	568	75.914000	773	1947	1	chr4A.!!$F4	1174
10	TraesCS7A01G081800	chrUn	48864288	48867299	3011	True	1182.600000	2870	92.779333	344	2800	3	chrUn.!!$R1	2456
11	TraesCS7A01G081800	chrUn	359259263	359259967	704	False	957.000000	957	91.537000	344	1035	1	chrUn.!!$F3	691
12	TraesCS7A01G081800	chrUn	48990371	48991980	1609	False	688.000000	688	75.330000	769	2369	1	chrUn.!!$F1	1600
13	TraesCS7A01G081800	chrUn	289666340	289667503	1163	False	492.000000	492	75.000000	773	1928	1	chrUn.!!$F2	1155
14	TraesCS7A01G081800	chrUn	48876901	48878939	2038	True	488.266667	957	91.760333	344	2800	3	chrUn.!!$R2	2456
15	TraesCS7A01G081800	chr7D	43168213	43169394	1181	True	728.000000	728	78.268000	773	1944	1	chr7D.!!$R1	1171
16	TraesCS7A01G081800	chr7D	44550511	44552434	1923	False	571.560000	1616	93.560400	710	2749	5	chr7D.!!$F2	2039
17	TraesCS7A01G081800	chr3D	9243816	9245076	1260	False	475.000000	475	74.257000	784	2010	1	chr3D.!!$F1	1226

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
436	471	0.109919	CGGCGGGTTCAAACTTTAGC	60.110	55.0	0.0	0.0	0.0	3.09	F
610	646	1.234821	CGGCTCAAAACCTTGTAGCA	58.765	50.0	0.0	0.0	37.4	3.49	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1238	1422	0.545071	TGGGACACCAGAGCTGATCA	60.545	55.000	0.0	0.0	43.37	2.92	R
2032	2401	1.202710	ACCACGTGACCATAGCACAAA	60.203	47.619	19.3	0.0	36.06	2.83	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
65	88	1.078324	AGAGTAAACCCCCTCCTTCGA	59.922	52.381	0.00	0.00	0.00	3.71
69	92	1.146452	AAACCCCCTCCTTCGACTTT	58.854	50.000	0.00	0.00	0.00	2.66
76	99	3.496160	CCCCTCCTTCGACTTTTTCAGAA	60.496	47.826	0.00	0.00	0.00	3.02
87	110	7.193595	TCGACTTTTTCAGAATGTTCCTTTTC	58.806	34.615	0.00	0.00	37.40	2.29
156	179	8.960591	ACAATAACAGATGTTAATAGCAAAGCT	58.039	29.630	9.33	0.00	42.93	3.74
170	193	4.809673	AGCAAAGCTTACATTTTAGCCAC	58.190	39.130	0.00	0.00	33.89	5.01
182	205	6.557110	ACATTTTAGCCACGCGTAAATATTT	58.443	32.000	13.44	5.89	30.15	1.40
316	350	1.069935	GACGAATCCTAGGCCAGGC	59.930	63.158	5.01	1.26	45.10	4.85
342	376	1.220206	CTTGGCGGATCTGACTGCT	59.780	57.895	9.31	0.00	41.36	4.24
370	404	1.458777	AGTCGGGAAGGTGTGGTGA	60.459	57.895	0.00	0.00	0.00	4.02
384	418	3.896133	GTGATCGCCGCCGGTCTA	61.896	66.667	4.45	0.00	44.75	2.59
436	471	0.109919	CGGCGGGTTCAAACTTTAGC	60.110	55.000	0.00	0.00	0.00	3.09
447	482	6.202762	GGTTCAAACTTTAGCTTGAAATTGGG	59.797	38.462	9.24	0.00	40.45	4.12
457	492	1.974265	TGAAATTGGGTCGACTGCAA	58.026	45.000	16.46	0.00	0.00	4.08
477	512	2.928801	TGGCTGACTTTGTGCTTCTA	57.071	45.000	0.00	0.00	0.00	2.10
564	600	7.332213	TGCTATTTTCAAATACAGCATGCTA	57.668	32.000	22.19	6.19	42.53	3.49
565	601	7.944061	TGCTATTTTCAAATACAGCATGCTAT	58.056	30.769	22.19	12.95	42.53	2.97
566	602	9.065798	TGCTATTTTCAAATACAGCATGCTATA	57.934	29.630	22.19	15.24	42.53	1.31
567	603	9.897744	GCTATTTTCAAATACAGCATGCTATAA	57.102	29.630	22.19	9.15	42.53	0.98
569	605	8.786937	ATTTTCAAATACAGCATGCTATAACG	57.213	30.769	22.19	10.36	42.53	3.18
595	631	2.366167	ATCTGGAGAAGGGCGGCT	60.366	61.111	9.56	0.00	0.00	5.52
610	646	1.234821	CGGCTCAAAACCTTGTAGCA	58.765	50.000	0.00	0.00	37.40	3.49
612	648	1.953686	GGCTCAAAACCTTGTAGCACA	59.046	47.619	0.00	0.00	37.40	4.57
661	712	4.158579	CGGCTGATAGATATAGCTGTCCAA	59.841	45.833	11.62	0.00	38.65	3.53
704	755	8.066595	CAGAACATATCATCCGAGTGATTTTTC	58.933	37.037	7.62	8.06	39.45	2.29
705	756	6.530913	ACATATCATCCGAGTGATTTTTCG	57.469	37.500	7.62	0.00	39.45	3.46
756	807	6.736853	GTGTCGTACTAATGTTTGCATCTTTC	59.263	38.462	0.00	0.00	33.50	2.62
758	814	7.172532	TGTCGTACTAATGTTTGCATCTTTCTT	59.827	33.333	0.00	0.00	33.50	2.52
1187	1365	1.660560	GCCGTAGTCGCCTTCTACCA	61.661	60.000	0.00	0.00	35.66	3.25
1238	1422	2.043115	TCTGGGTGTCATACTCCAGACT	59.957	50.000	14.31	0.00	44.64	3.24
1269	1471	0.320697	GTGTCCCAGTACAGTCACCC	59.679	60.000	0.00	0.00	0.00	4.61
1602	1830	2.846206	TGAGACATGGGCCTTTCAGTAT	59.154	45.455	4.53	0.00	0.00	2.12
1824	2077	3.525537	TCGTTTCCAAGAGAGCATGATC	58.474	45.455	1.78	1.78	0.00	2.92
1833	2086	2.361757	AGAGAGCATGATCTCACTTCCG	59.638	50.000	35.31	0.00	46.81	4.30
2032	2401	9.319143	GAACACTTTATATGTCTGAAGTAGCAT	57.681	33.333	0.00	0.00	31.58	3.79
2087	2456	7.014711	TCCTACCTATCTTGAGCATCTTGTTAG	59.985	40.741	0.00	0.00	34.92	2.34
2145	2528	0.108472	CTACCGTTCTCCCCCGTTTC	60.108	60.000	0.00	0.00	0.00	2.78
2154	2537	5.308014	GTTCTCCCCCGTTTCTACTTTAAA	58.692	41.667	0.00	0.00	0.00	1.52
2162	2545	5.912955	CCCGTTTCTACTTTAAAGTTTGCAG	59.087	40.000	25.07	16.18	40.37	4.41
2306	2736	3.969117	TTCATGTTCAGTGCACACTTC	57.031	42.857	21.04	7.35	40.20	3.01
2394	2824	1.692749	ATCCGGGGGAAGCTGCTTA	60.693	57.895	15.95	0.00	34.34	3.09
2486	2921	6.591001	TGGCAACATAGATATTTCTGCAGTA	58.409	36.000	14.67	0.00	46.17	2.74
2556	3016	9.950680	TCTGTTTCATTGACTTTCACTATTTTC	57.049	29.630	0.00	0.00	0.00	2.29
2612	3778	6.346477	AGAAATAAGTTGGGAGAAAAAGGC	57.654	37.500	0.00	0.00	0.00	4.35
2732	4188	4.956075	AGTTAATGGGCCCAAGTCATTAAG	59.044	41.667	32.58	0.00	41.24	1.85
2858	5057	1.615392	GTCTTGGATTTGTTGCTGGCT	59.385	47.619	0.00	0.00	0.00	4.75
2864	5063	1.069049	GATTTGTTGCTGGCTGGTGTT	59.931	47.619	0.00	0.00	0.00	3.32
2865	5064	0.901124	TTTGTTGCTGGCTGGTGTTT	59.099	45.000	0.00	0.00	0.00	2.83

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
44	45	1.207329	CGAAGGAGGGGGTTTACTCTG	59.793	57.143	0.00	0.00	34.22	3.35
65	88	8.066612	TCTGAAAAGGAACATTCTGAAAAAGT	57.933	30.769	0.00	0.00	33.90	2.66
131	154	9.793252	AAGCTTTGCTATTAACATCTGTTATTG	57.207	29.630	3.76	0.14	38.25	1.90
134	157	9.443323	TGTAAGCTTTGCTATTAACATCTGTTA	57.557	29.630	3.20	0.00	38.25	2.41
137	160	9.793252	AAATGTAAGCTTTGCTATTAACATCTG	57.207	29.630	3.20	0.00	38.25	2.90
155	178	4.587211	TTACGCGTGGCTAAAATGTAAG	57.413	40.909	24.59	0.00	0.00	2.34
156	179	5.548706	ATTTACGCGTGGCTAAAATGTAA	57.451	34.783	24.59	0.00	0.00	2.41
182	205	8.043113	AGATTGTACTACTTGCATTTCTGATGA	58.957	33.333	0.00	0.00	0.00	2.92
342	376	0.250234	CTTCCCGACTCATCAAGCCA	59.750	55.000	0.00	0.00	0.00	4.75
370	404	3.900892	CTGTAGACCGGCGGCGAT	61.901	66.667	34.49	18.66	0.00	4.58
384	418	0.419459	ACTTCCTCTCCATCCCCTGT	59.581	55.000	0.00	0.00	0.00	4.00
436	471	1.879380	TGCAGTCGACCCAATTTCAAG	59.121	47.619	13.01	0.00	0.00	3.02
447	482	0.671781	AGTCAGCCATTGCAGTCGAC	60.672	55.000	7.70	7.70	41.13	4.20
457	492	2.283145	AGAAGCACAAAGTCAGCCAT	57.717	45.000	0.00	0.00	0.00	4.40
477	512	8.627208	AAATATGAGGCATAATCGATTTGAGT	57.373	30.769	17.19	5.50	29.74	3.41
545	581	7.696035	CACGTTATAGCATGCTGTATTTGAAAA	59.304	33.333	30.42	9.84	0.00	2.29
555	591	5.441700	GCTATACACGTTATAGCATGCTG	57.558	43.478	30.42	15.25	46.99	4.41
564	600	6.294787	CCTTCTCCAGATGCTATACACGTTAT	60.295	42.308	0.00	0.00	0.00	1.89
565	601	5.009710	CCTTCTCCAGATGCTATACACGTTA	59.990	44.000	0.00	0.00	0.00	3.18
566	602	4.202161	CCTTCTCCAGATGCTATACACGTT	60.202	45.833	0.00	0.00	0.00	3.99
567	603	3.319405	CCTTCTCCAGATGCTATACACGT	59.681	47.826	0.00	0.00	0.00	4.49
568	604	3.305676	CCCTTCTCCAGATGCTATACACG	60.306	52.174	0.00	0.00	0.00	4.49
569	605	3.556004	GCCCTTCTCCAGATGCTATACAC	60.556	52.174	0.00	0.00	0.00	2.90
595	631	6.952773	AAATAGTGTGCTACAAGGTTTTGA	57.047	33.333	0.00	0.00	37.73	2.69
623	661	0.515564	AGCCGATACGTGCAAACAAC	59.484	50.000	0.00	0.00	0.00	3.32
661	712	6.189677	TGTTCTGTTTCATCACTCGTTTTT	57.810	33.333	0.00	0.00	0.00	1.94
673	724	5.812127	CACTCGGATGATATGTTCTGTTTCA	59.188	40.000	0.00	0.00	0.00	2.69
678	729	7.488187	AAAATCACTCGGATGATATGTTCTG	57.512	36.000	3.20	0.00	38.40	3.02
704	755	5.405935	AAAAGGATGAAAAGGGATTTCCG	57.594	39.130	0.00	0.00	45.67	4.30
705	756	6.768483	TGAAAAAGGATGAAAAGGGATTTCC	58.232	36.000	0.00	0.00	45.67	3.13
756	807	6.939132	AGATGGTCATGCTGATAAGAAAAG	57.061	37.500	0.00	0.00	0.00	2.27
758	814	5.525012	CGAAGATGGTCATGCTGATAAGAAA	59.475	40.000	0.00	0.00	0.00	2.52
931	989	2.039746	TCGTTGTTCAATGATGGGGAGT	59.960	45.455	3.68	0.00	0.00	3.85
1060	1229	4.247380	CCCCAGGATGAGGAGCGC	62.247	72.222	0.00	0.00	39.69	5.92
1061	1230	4.247380	GCCCCAGGATGAGGAGCG	62.247	72.222	0.00	0.00	39.69	5.03
1062	1231	3.092511	TGCCCCAGGATGAGGAGC	61.093	66.667	0.00	0.00	39.69	4.70
1187	1365	2.813907	ACTCTCTAGATGTGTGGTGCT	58.186	47.619	0.00	0.00	0.00	4.40
1238	1422	0.545071	TGGGACACCAGAGCTGATCA	60.545	55.000	0.00	0.00	43.37	2.92
1602	1830	3.381045	CATCGCTAACAAGCTAATCCGA	58.619	45.455	0.00	0.00	0.00	4.55
1824	2077	6.869636	TTGTGTCTCAAACAACGGAAGTGAG	61.870	44.000	0.00	0.00	40.31	3.51
1833	2086	6.363577	TCATCTTCTTGTGTCTCAAACAAC	57.636	37.500	0.00	0.00	40.31	3.32
2032	2401	1.202710	ACCACGTGACCATAGCACAAA	60.203	47.619	19.30	0.00	36.06	2.83
2042	2411	2.537401	GATAACTAGCACCACGTGACC	58.463	52.381	19.30	4.47	35.23	4.02
2087	2456	8.233190	GCATAGATATTCCATTGTTTAGAGCAC	58.767	37.037	0.00	0.00	0.00	4.40
2154	2537	6.633500	TTGTGCTTCTTAATACTGCAAACT	57.367	33.333	0.00	0.00	35.34	2.66
2162	2545	7.602753	ACCATTCCTTTTGTGCTTCTTAATAC	58.397	34.615	0.00	0.00	0.00	1.89
2225	2608	8.927675	ACTAACCATTCCAACAACTAAATGTA	57.072	30.769	0.00	0.00	32.02	2.29
2306	2736	3.629858	GCCAAAAGCAATAGGAGCG	57.370	52.632	0.00	0.00	42.97	5.03
2394	2824	6.759272	ACACTGTAGTAACAATCAGACACAT	58.241	36.000	0.00	0.00	34.49	3.21
2428	2858	3.164268	TGGCTGTATTGAAGTGGCAATT	58.836	40.909	0.00	0.00	39.15	2.32
2493	2928	6.871492	TCATCGCTATCAGAAACAAAACACTA	59.129	34.615	0.00	0.00	0.00	2.74
2556	3016	1.884235	ACAGCCAACCTCTTTTCTCG	58.116	50.000	0.00	0.00	0.00	4.04
2612	3778	9.847224	AAGATTATATACCACCAAAGTACCAAG	57.153	33.333	0.00	0.00	0.00	3.61
2732	4188	7.062605	CAGAAGACATGGTTAATTTTGCACATC	59.937	37.037	0.00	0.00	0.00	3.06
2838	5037	1.615392	AGCCAGCAACAAATCCAAGAC	59.385	47.619	0.00	0.00	0.00	3.01

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.