AutoCloner

Multiple sequence alignment - TraesCS5B01G313400

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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	TraesCS5B01G313400	chr5B	100.000	2702	0	0	424	3125	495480717	495478016	0.000000e+00	4990.0
1	TraesCS5B01G313400	chr5B	83.000	100	11	3	483	579	467066311	467066215	5.550000e-13	86.1
2	TraesCS5B01G313400	chr5B	100.000	36	0	0	1	36	495481140	495481105	2.010000e-07	67.6
3	TraesCS5B01G313400	chr6A	92.204	2732	171	27	424	3125	22906164	22903445	0.000000e+00	3827.0
4	TraesCS5B01G313400	chr3D	93.164	2560	153	14	573	3125	379812504	379809960	0.000000e+00	3738.0
5	TraesCS5B01G313400	chr3D	100.000	29	0	0	489	517	20573405	20573377	2.000000e-03	54.7
6	TraesCS5B01G313400	chr6D	93.122	2559	159	12	573	3125	436529477	436526930	0.000000e+00	3735.0
7	TraesCS5B01G313400	chr6D	93.058	2564	161	14	568	3125	460496180	460498732	0.000000e+00	3733.0
8	TraesCS5B01G313400	chr3A	92.229	2638	199	6	490	3124	734661848	734659214	0.000000e+00	3731.0
9	TraesCS5B01G313400	chr5D	92.874	2568	163	14	568	3125	352831970	352834527	0.000000e+00	3711.0
10	TraesCS5B01G313400	chr2D	92.952	2554	165	12	575	3125	83951318	83948777	0.000000e+00	3705.0
11	TraesCS5B01G313400	chr2D	92.829	2566	162	15	568	3123	431506164	431508717	0.000000e+00	3699.0
12	TraesCS5B01G313400	chr1D	92.893	2561	162	14	568	3123	467392256	467394801	0.000000e+00	3703.0
13	TraesCS5B01G313400	chr1D	87.209	86	2	3	501	578	339309348	339309432	4.290000e-14	89.8
14	TraesCS5B01G313400	chr1D	86.047	86	3	3	501	578	462971643	462971727	2.000000e-12	84.2
15	TraesCS5B01G313400	chr4A	83.168	101	6	5	484	576	651987860	651987957	7.180000e-12	82.4
16	TraesCS5B01G313400	chr1A	90.741	54	2	1	483	536	386417085	386417035	5.590000e-08	69.4
17	TraesCS5B01G313400	chr2B	82.759	87	4	5	502	578	741990801	741990886	2.010000e-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	TraesCS5B01G313400	chr5B	495478016	495481140	3124	True	2528.8	4990	100.000	1	3125	2	chr5B.!!$R2	3124
1	TraesCS5B01G313400	chr6A	22903445	22906164	2719	True	3827.0	3827	92.204	424	3125	1	chr6A.!!$R1	2701
2	TraesCS5B01G313400	chr3D	379809960	379812504	2544	True	3738.0	3738	93.164	573	3125	1	chr3D.!!$R2	2552
3	TraesCS5B01G313400	chr6D	436526930	436529477	2547	True	3735.0	3735	93.122	573	3125	1	chr6D.!!$R1	2552
4	TraesCS5B01G313400	chr6D	460496180	460498732	2552	False	3733.0	3733	93.058	568	3125	1	chr6D.!!$F1	2557
5	TraesCS5B01G313400	chr3A	734659214	734661848	2634	True	3731.0	3731	92.229	490	3124	1	chr3A.!!$R1	2634
6	TraesCS5B01G313400	chr5D	352831970	352834527	2557	False	3711.0	3711	92.874	568	3125	1	chr5D.!!$F1	2557
7	TraesCS5B01G313400	chr2D	83948777	83951318	2541	True	3705.0	3705	92.952	575	3125	1	chr2D.!!$R1	2550
8	TraesCS5B01G313400	chr2D	431506164	431508717	2553	False	3699.0	3699	92.829	568	3123	1	chr2D.!!$F1	2555
9	TraesCS5B01G313400	chr1D	467392256	467394801	2545	False	3703.0	3703	92.893	568	3123	1	chr1D.!!$F3	2555

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
739	763	1.068816	GCTGAAAACGCGTATTTGGGT	60.069	47.619	14.46	0.0	36.47	4.51	F
1683	1707	0.251341	GCAAGAAGAAGGGCCCTCAA	60.251	55.000	28.84	0.0	0.00	3.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1844	1879	0.473694	TGCTCCCTCCTGAACCAAGA	60.474	55.0	0.00	0.00	0.00	3.02	R
2762	2801	0.405198	TGAGGGTAGTGTACACGGGA	59.595	55.0	19.93	7.24	37.12	5.14	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
541	553	1.197812	GGAAACCCTAGCGAACCCTA	58.802	55.000	0.00	0.00	0.00	3.53
650	673	5.523438	TTTGTTTTAGCCCCTGTAGTTTG	57.477	39.130	0.00	0.00	0.00	2.93
653	676	5.390387	TGTTTTAGCCCCTGTAGTTTGATT	58.610	37.500	0.00	0.00	0.00	2.57
707	730	1.527370	GCGTAGAAGCCCCTGGAAT	59.473	57.895	0.00	0.00	0.00	3.01
718	741	2.368548	GCCCCTGGAATTGTCTGTTTTT	59.631	45.455	0.00	0.00	0.00	1.94
739	763	1.068816	GCTGAAAACGCGTATTTGGGT	60.069	47.619	14.46	0.00	36.47	4.51
749	773	5.530712	ACGCGTATTTGGGTTTTAAAATGT	58.469	33.333	11.67	0.00	0.00	2.71
785	809	7.926555	TCAATTTTTGGGCTATTTTTCACGTAA	59.073	29.630	0.00	0.00	0.00	3.18
788	812	6.636562	TTTGGGCTATTTTTCACGTAAGAA	57.363	33.333	0.00	0.00	43.62	2.52
812	836	9.393249	GAAATGCGCTTAACATGCTATATTTTA	57.607	29.630	9.73	0.00	0.00	1.52
879	903	5.180492	TGTTTCGCACTCTTAACCATTAAGG	59.820	40.000	8.15	3.07	42.23	2.69
882	906	5.553123	TCGCACTCTTAACCATTAAGGAAA	58.447	37.500	8.15	0.00	42.23	3.13
986	1010	6.446781	ACCTGCTGTAATCTCATGATTTTG	57.553	37.500	0.00	0.00	42.37	2.44
1036	1060	3.004752	ACAAGGAGTTTGCTGAGTTGT	57.995	42.857	0.00	0.00	40.59	3.32
1070	1094	2.258109	GAACTACCTGTCCTGGTCCTT	58.742	52.381	0.00	0.00	41.22	3.36
1085	1109	2.365617	GGTCCTTGGATTGCGAGATCTA	59.634	50.000	0.00	0.00	0.00	1.98
1122	1146	0.685131	TCCTGAGGGCGATCGGTAAA	60.685	55.000	18.30	0.00	0.00	2.01
1127	1151	2.437396	GGGCGATCGGTAAAGGGGA	61.437	63.158	18.30	0.00	0.00	4.81
1234	1258	6.779539	TCTGAAAGATGAGTATATGGCTGAGA	59.220	38.462	0.00	0.00	38.67	3.27
1236	1260	6.552725	TGAAAGATGAGTATATGGCTGAGAGT	59.447	38.462	0.00	0.00	0.00	3.24
1292	1316	1.871039	GTTTGAGCGGCTGAAGTACAA	59.129	47.619	7.50	0.66	0.00	2.41
1351	1375	1.214367	GTTTGCGGACTTCAAGACGA	58.786	50.000	9.82	0.00	0.00	4.20
1368	1392	3.517901	AGACGATTGGGGAGTACAATTCA	59.482	43.478	0.00	0.00	38.57	2.57
1516	1540	3.196254	GGGGAACTACACGAGGTATTCAA	59.804	47.826	0.00	0.00	0.00	2.69
1521	1545	7.092716	GGAACTACACGAGGTATTCAAAGTTA	58.907	38.462	0.00	0.00	0.00	2.24
1541	1565	0.544357	ATTGACGTCCTCCAGGTGGA	60.544	55.000	14.12	6.11	43.08	4.02
1683	1707	0.251341	GCAAGAAGAAGGGCCCTCAA	60.251	55.000	28.84	0.00	0.00	3.02
1737	1772	1.616628	GGGAGGGAAGAGGCCTCAA	60.617	63.158	33.90	0.00	32.77	3.02
1816	1851	3.326747	GAGGTCGTTGAAGCATACAAGT	58.673	45.455	0.00	0.00	0.00	3.16
1835	1870	0.965866	TCTCGGAAGGCACGTGAGAT	60.966	55.000	22.23	3.01	31.14	2.75
1844	1879	0.742281	GCACGTGAGATGCACCTCAT	60.742	55.000	22.23	0.00	44.09	2.90
1967	2002	0.673644	GCAGCTTTGGCGGTCTCTAA	60.674	55.000	0.00	0.00	44.37	2.10
1969	2004	2.359900	CAGCTTTGGCGGTCTCTAATT	58.640	47.619	0.00	0.00	44.37	1.40
2036	2074	2.368548	TGCCGCCACTAGATATTGATGT	59.631	45.455	0.00	0.00	0.00	3.06
2039	2077	4.380531	CCGCCACTAGATATTGATGTTGT	58.619	43.478	0.00	0.00	0.00	3.32
2067	2105	7.127801	TCCAAGATGATTTCTAAGGAGGATCAA	59.872	37.037	0.00	0.00	35.16	2.57
2089	2127	4.207955	ACTCACTAGTATGGAGATTGCGA	58.792	43.478	13.97	0.00	32.84	5.10
2109	2147	3.499918	CGACTGAAGTGAATGGCTTCTTT	59.500	43.478	6.61	0.00	41.94	2.52
2127	2165	4.894784	TCTTTACCAAGTCCACTTAGCAG	58.105	43.478	0.00	0.00	34.28	4.24
2128	2166	3.695830	TTACCAAGTCCACTTAGCAGG	57.304	47.619	0.00	0.00	34.28	4.85
2254	2293	7.439056	GGCGATTGGATGACATTTATTTCATTT	59.561	33.333	0.00	0.00	32.43	2.32
2420	2459	1.341531	GATAGCGCCACCACTCATACT	59.658	52.381	2.29	0.00	0.00	2.12
2434	2473	8.808529	CACCACTCATACTATTTTACGAGAAAG	58.191	37.037	0.00	0.00	0.00	2.62
2484	2523	7.582667	TCTCCGAGAAGTATTATGACAATCA	57.417	36.000	0.00	0.00	0.00	2.57
2534	2573	3.255149	CCGGACGAGCCACTATTATACTT	59.745	47.826	0.00	0.00	35.94	2.24
2544	2583	6.670027	AGCCACTATTATACTTCCTATGGGAG	59.330	42.308	0.00	0.00	43.29	4.30
2578	2617	5.645929	TCATTAATGATGCGTTGTTGTACCT	59.354	36.000	14.23	0.00	35.64	3.08
2634	2673	1.139256	TCCGCGCTAATGGTTTCCATA	59.861	47.619	5.56	0.00	44.40	2.74
2665	2704	2.582052	TGATGAAAACGGCAAGGAGTT	58.418	42.857	0.00	0.00	0.00	3.01
2706	2745	3.119495	GGATGCAGGTGGTAAACATGTTC	60.119	47.826	12.39	0.00	42.63	3.18
2719	2758	3.126001	ACATGTTCTCGAAAGGCTTCA	57.874	42.857	0.00	0.00	0.00	3.02
2750	2789	5.953548	TGACACAGGGCTATACTACACTAAA	59.046	40.000	0.00	0.00	0.00	1.85
2753	2792	7.858498	ACACAGGGCTATACTACACTAAAATT	58.142	34.615	0.00	0.00	0.00	1.82
2812	2851	7.595502	CGTTTTTAGAAGCTCTGAACTCTTCTA	59.404	37.037	14.45	14.45	43.17	2.10
2895	2934	6.832520	ACTTGCATGGTCATAATGTTAACA	57.167	33.333	11.41	11.41	0.00	2.41
2908	2947	9.739276	TCATAATGTTAACATGAAGAACTTCCT	57.261	29.630	21.46	4.26	38.77	3.36
2971	3010	2.434336	AGTTAGTCATTAGGCCATCGCA	59.566	45.455	5.01	0.00	36.38	5.10
3048	3093	1.452108	GGTCCAATTCAGCCCCTCG	60.452	63.158	0.00	0.00	0.00	4.63

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
554	566	2.656069	GGTCCACAGAAGCCCGCTA	61.656	63.158	0.00	0.00	0.00	4.26
629	652	4.794334	TCAAACTACAGGGGCTAAAACAA	58.206	39.130	0.00	0.00	0.00	2.83
650	673	7.844653	CAGGAATAAACTACGCGTAAAAGAATC	59.155	37.037	20.97	13.86	0.00	2.52
653	676	5.062558	GCAGGAATAAACTACGCGTAAAAGA	59.937	40.000	20.97	6.74	0.00	2.52
718	741	1.068885	CCCAAATACGCGTTTTCAGCA	60.069	47.619	20.78	0.00	34.19	4.41
739	763	9.771534	AAATTGAATTCCCGAGACATTTTAAAA	57.228	25.926	2.51	2.51	0.00	1.52
749	773	3.056179	GCCCAAAAATTGAATTCCCGAGA	60.056	43.478	2.27	0.00	0.00	4.04
785	809	6.808008	ATATAGCATGTTAAGCGCATTTCT	57.192	33.333	11.47	0.00	37.01	2.52
786	810	7.858052	AAATATAGCATGTTAAGCGCATTTC	57.142	32.000	11.47	0.00	37.01	2.17
860	884	5.873179	TTTCCTTAATGGTTAAGAGTGCG	57.127	39.130	10.24	0.00	44.19	5.34
907	931	9.840427	ACTTATTCAATAAAAATGACGTTCCAG	57.160	29.630	0.00	0.00	0.00	3.86
986	1010	0.242017	GGCCATCTGCGATTTATGCC	59.758	55.000	0.00	0.00	42.61	4.40
1138	1162	0.613260	TCGAACTTGGGATCAGTGGG	59.387	55.000	0.00	0.00	0.00	4.61
1182	1206	3.256879	GTGACAGGTGATGACAGAGAGAA	59.743	47.826	0.00	0.00	34.20	2.87
1184	1208	2.094286	GGTGACAGGTGATGACAGAGAG	60.094	54.545	0.00	0.00	34.20	3.20
1189	1213	2.826128	GAGTAGGTGACAGGTGATGACA	59.174	50.000	0.00	0.00	0.00	3.58
1234	1258	1.271597	CCAAAGGCCAGAAGCACTACT	60.272	52.381	5.01	0.00	46.50	2.57
1236	1260	1.064003	TCCAAAGGCCAGAAGCACTA	58.936	50.000	5.01	0.00	46.50	2.74
1292	1316	0.952497	CTCTGCACGTGGCTTCACAT	60.952	55.000	18.88	0.00	45.15	3.21
1351	1375	5.256474	CAGAACTGAATTGTACTCCCCAAT	58.744	41.667	0.00	0.00	34.07	3.16
1368	1392	3.067106	CGTACAAATCTGGTGCAGAACT	58.933	45.455	0.00	0.00	44.04	3.01
1516	1540	3.326880	ACCTGGAGGACGTCAATTAACTT	59.673	43.478	18.91	0.00	38.94	2.66
1521	1545	0.324943	CCACCTGGAGGACGTCAATT	59.675	55.000	18.91	1.61	38.94	2.32
1603	1627	1.203441	AGAGCATTCACCTCCTGGCA	61.203	55.000	0.00	0.00	36.63	4.92
1726	1761	1.003003	GAAGCAGTCTTGAGGCCTCTT	59.997	52.381	32.28	16.25	31.48	2.85
1737	1772	1.598130	GCCACAACGGAAGCAGTCT	60.598	57.895	0.00	0.00	36.56	3.24
1816	1851	0.965866	ATCTCACGTGCCTTCCGAGA	60.966	55.000	11.67	7.02	37.16	4.04
1835	1870	1.271543	CCTGAACCAAGATGAGGTGCA	60.272	52.381	0.00	0.00	42.49	4.57
1844	1879	0.473694	TGCTCCCTCCTGAACCAAGA	60.474	55.000	0.00	0.00	0.00	3.02
2067	2105	4.036971	GTCGCAATCTCCATACTAGTGAGT	59.963	45.833	5.39	0.00	39.92	3.41
2089	2127	4.762251	GGTAAAGAAGCCATTCACTTCAGT	59.238	41.667	6.31	0.00	44.87	3.41
2109	2147	1.278127	GCCTGCTAAGTGGACTTGGTA	59.722	52.381	2.14	0.00	36.88	3.25
2127	2165	4.279420	GGAATCATGATAACCAAAGAGGCC	59.721	45.833	20.22	0.00	43.14	5.19
2128	2166	4.023707	CGGAATCATGATAACCAAAGAGGC	60.024	45.833	22.92	3.54	43.14	4.70
2282	2321	6.405538	TGCACACATCTCAGAACATAACATA	58.594	36.000	0.00	0.00	0.00	2.29
2466	2505	5.057149	GCCGGTGATTGTCATAATACTTCT	58.943	41.667	1.90	0.00	0.00	2.85
2534	2573	3.523157	TGATCAAAGTTGCTCCCATAGGA	59.477	43.478	0.00	0.00	41.08	2.94
2544	2583	5.745294	ACGCATCATTAATGATCAAAGTTGC	59.255	36.000	24.94	22.39	45.23	4.17
2606	2645	1.135046	CATTAGCGCGGATGTCTCTG	58.865	55.000	8.83	0.00	0.00	3.35
2634	2673	3.623060	CCGTTTTCATCATCGGTCTCAAT	59.377	43.478	0.00	0.00	38.45	2.57
2665	2704	1.207089	CCCGCTTTGTGATGAGTAGGA	59.793	52.381	0.00	0.00	0.00	2.94
2706	2745	3.186409	TCAAACGAATGAAGCCTTTCGAG	59.814	43.478	16.54	8.61	46.47	4.04
2719	2758	2.851263	TAGCCCTGTGTCAAACGAAT	57.149	45.000	0.00	0.00	0.00	3.34
2750	2789	3.551259	CACGGGAGGTGCTACAATT	57.449	52.632	0.00	0.00	40.33	2.32
2762	2801	0.405198	TGAGGGTAGTGTACACGGGA	59.595	55.000	19.93	7.24	37.12	5.14
2812	2851	2.032620	CTAACCTATCGTGCCAGAGGT	58.967	52.381	0.00	0.00	44.35	3.85
2875	2914	7.338957	TCTTCATGTTAACATTATGACCATGCA	59.661	33.333	18.50	0.00	33.61	3.96
2895	2934	3.519510	TCGGGATTCAGGAAGTTCTTCAT	59.480	43.478	13.44	4.58	0.00	2.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.