AutoCloner

Multiple sequence alignment - TraesCS5B01G088600

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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	TraesCS5B01G088600	chr5B	100.000	2687	0	0	1	2687	113824463	113821777	0.000000e+00	4963.0
1	TraesCS5B01G088600	chr5B	91.702	952	58	13	894	1837	113805884	113804946	0.000000e+00	1301.0
2	TraesCS5B01G088600	chr5D	95.654	2715	62	19	1	2687	104448074	104445388	0.000000e+00	4309.0
3	TraesCS5B01G088600	chr5D	92.537	871	51	9	894	1758	104398467	104397605	0.000000e+00	1236.0
4	TraesCS5B01G088600	chr5D	82.031	256	36	8	357	603	14026050	14026304	2.710000e-50	209.0
5	TraesCS5B01G088600	chr5A	90.859	1827	90	30	1	1795	106856818	106855037	0.000000e+00	2377.0
6	TraesCS5B01G088600	chr5A	92.720	728	45	6	894	1616	93188350	93189074	0.000000e+00	1044.0
7	TraesCS5B01G088600	chr5A	86.382	492	41	7	1937	2408	93066210	93066695	5.130000e-142	514.0
8	TraesCS5B01G088600	chr5A	90.253	277	27	0	2410	2686	93066655	93066931	1.970000e-96	363.0
9	TraesCS5B01G088600	chr5A	90.066	151	9	4	1791	1941	106854900	106854756	9.820000e-45	191.0
10	TraesCS5B01G088600	chr7A	82.857	245	32	7	368	603	96146874	96147117	7.540000e-51	211.0
11	TraesCS5B01G088600	chr1D	83.550	231	32	5	357	582	437843473	437843702	7.540000e-51	211.0
12	TraesCS5B01G088600	chr2B	82.329	249	32	9	366	603	63848257	63848010	3.510000e-49	206.0
13	TraesCS5B01G088600	chr1A	82.377	244	36	7	365	603	463926634	463926393	3.510000e-49	206.0
14	TraesCS5B01G088600	chr3D	82.186	247	34	7	366	603	251397635	251397390	1.260000e-48	204.0
15	TraesCS5B01G088600	chr3D	85.981	107	12	3	42	145	425145855	425145749	7.860000e-21	111.0
16	TraesCS5B01G088600	chr1B	81.712	257	35	9	357	603	409675809	409676063	1.260000e-48	204.0
17	TraesCS5B01G088600	chr1B	82.400	125	16	4	42	161	513973251	513973128	1.320000e-18	104.0
18	TraesCS5B01G088600	chr3A	83.200	125	16	4	42	161	563400498	563400622	2.830000e-20	110.0
19	TraesCS5B01G088600	chr6A	92.982	57	2	1	2149	2205	99971813	99971867	6.170000e-12	82.4
20	TraesCS5B01G088600	chr2A	91.071	56	3	2	2149	2203	1549055	1549001	1.030000e-09	75.0
21	TraesCS5B01G088600	chr3B	81.429	70	10	2	2116	2184	819649767	819649700	1.000000e-03	54.7

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	TraesCS5B01G088600	chr5B	113821777	113824463	2686	True	4963.0	4963	100.0000	1	2687	1	chr5B.!!$R2	2686
1	TraesCS5B01G088600	chr5B	113804946	113805884	938	True	1301.0	1301	91.7020	894	1837	1	chr5B.!!$R1	943
2	TraesCS5B01G088600	chr5D	104445388	104448074	2686	True	4309.0	4309	95.6540	1	2687	1	chr5D.!!$R2	2686
3	TraesCS5B01G088600	chr5D	104397605	104398467	862	True	1236.0	1236	92.5370	894	1758	1	chr5D.!!$R1	864
4	TraesCS5B01G088600	chr5A	106854756	106856818	2062	True	1284.0	2377	90.4625	1	1941	2	chr5A.!!$R1	1940
5	TraesCS5B01G088600	chr5A	93188350	93189074	724	False	1044.0	1044	92.7200	894	1616	1	chr5A.!!$F1	722
6	TraesCS5B01G088600	chr5A	93066210	93066931	721	False	438.5	514	88.3175	1937	2686	2	chr5A.!!$F2	749

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
744	755	0.884704	AACATCTGGTGCACCGACAC	60.885	55.0	30.07	7.26	39.43	3.67	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2558	2787	0.108472	CTGCAGCGATGGAGTTGAGA	60.108	55.0	14.58	0.0	0.0	3.27	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
38	39	7.201617	GCCAATAGACATGAGTTTACAACCTAC	60.202	40.741	0.00	0.00	0.00	3.18
236	238	1.630878	AGGTCTTGTCCTGGGAACATC	59.369	52.381	0.00	0.00	41.51	3.06
245	247	4.283212	TGTCCTGGGAACATCCAATTTTTC	59.717	41.667	0.00	0.00	41.51	2.29
250	252	5.062528	TGGGAACATCCAATTTTTCTTTGC	58.937	37.500	0.00	0.00	38.64	3.68
310	312	4.767578	AGCATGTGAGAGTTGGTATCAT	57.232	40.909	0.00	0.00	0.00	2.45
352	354	3.508012	CCACGAGGGAGAATATCTAGTGG	59.492	52.174	7.28	7.28	43.81	4.00
574	583	5.795972	TCACATTGATGCCAAATTTGTCAT	58.204	33.333	14.19	14.19	35.67	3.06
582	591	8.030744	TGATGCCAAATTTGTCATTTTGTATG	57.969	30.769	15.30	0.00	32.23	2.39
744	755	0.884704	AACATCTGGTGCACCGACAC	60.885	55.000	30.07	7.26	39.43	3.67
960	1015	1.391157	CCGCTCCTCTCTCTTCCCTG	61.391	65.000	0.00	0.00	0.00	4.45
1143	1198	2.288643	GGCCTCCCCTCCATCTCT	59.711	66.667	0.00	0.00	0.00	3.10
1707	1765	2.049063	ACAGAGCTTCCGTGTCGC	60.049	61.111	0.00	0.00	0.00	5.19
1741	1799	0.108992	TTGCCGTACTTCTACGCCAG	60.109	55.000	0.00	0.00	43.82	4.85
1772	1833	4.318332	CCGTCGTACTACGTTTCAGTTAAC	59.682	45.833	17.39	0.00	43.14	2.01
1776	1837	6.085588	GTCGTACTACGTTTCAGTTAACAGTC	59.914	42.308	8.61	0.00	43.14	3.51
1794	1996	3.306166	CAGTCCGTGAGCGTTAATTAAGG	59.694	47.826	12.51	12.51	36.15	2.69
2012	2214	7.508687	TCTTCTTCTTTATGTGCTATGCCATA	58.491	34.615	0.00	0.00	0.00	2.74
2018	2220	6.707608	TCTTTATGTGCTATGCCATAAGTCAG	59.292	38.462	10.72	8.00	35.19	3.51
2019	2221	4.694760	ATGTGCTATGCCATAAGTCAGA	57.305	40.909	0.00	0.00	0.00	3.27
2020	2222	3.797039	TGTGCTATGCCATAAGTCAGAC	58.203	45.455	0.00	0.00	0.00	3.51
2021	2223	3.452264	TGTGCTATGCCATAAGTCAGACT	59.548	43.478	0.00	0.00	0.00	3.24
2022	2224	4.080919	TGTGCTATGCCATAAGTCAGACTT	60.081	41.667	19.81	19.81	41.97	3.01
2190	2397	6.557568	TCAGTTAATGGAAAAGGGGTTATGT	58.442	36.000	0.00	0.00	0.00	2.29
2279	2507	3.101437	TGGTCCTAAATAAGCCGAGACA	58.899	45.455	0.00	0.00	0.00	3.41
2356	2585	3.954258	AGATTTTTCATTTAGGCCCTCCG	59.046	43.478	0.00	0.00	37.47	4.63
2392	2621	4.109050	GCATTTTGTAGTCCTCTCTCTCG	58.891	47.826	0.00	0.00	0.00	4.04
2404	2633	2.363680	CTCTCTCTCGCTCTCTCTCTCT	59.636	54.545	0.00	0.00	0.00	3.10
2407	2636	2.362397	TCTCTCGCTCTCTCTCTCTCTC	59.638	54.545	0.00	0.00	0.00	3.20
2408	2637	2.363680	CTCTCGCTCTCTCTCTCTCTCT	59.636	54.545	0.00	0.00	0.00	3.10
2409	2638	2.766263	TCTCGCTCTCTCTCTCTCTCTT	59.234	50.000	0.00	0.00	0.00	2.85
2410	2639	3.197766	TCTCGCTCTCTCTCTCTCTCTTT	59.802	47.826	0.00	0.00	0.00	2.52
2411	2640	4.404394	TCTCGCTCTCTCTCTCTCTCTTTA	59.596	45.833	0.00	0.00	0.00	1.85
2412	2641	4.693283	TCGCTCTCTCTCTCTCTCTTTAG	58.307	47.826	0.00	0.00	0.00	1.85
2413	2642	3.248602	CGCTCTCTCTCTCTCTCTTTAGC	59.751	52.174	0.00	0.00	0.00	3.09
2414	2643	4.199310	GCTCTCTCTCTCTCTCTTTAGCA	58.801	47.826	0.00	0.00	0.00	3.49
2415	2644	4.823989	GCTCTCTCTCTCTCTCTTTAGCAT	59.176	45.833	0.00	0.00	0.00	3.79
2416	2645	5.300286	GCTCTCTCTCTCTCTCTTTAGCATT	59.700	44.000	0.00	0.00	0.00	3.56
2417	2646	6.183360	GCTCTCTCTCTCTCTCTTTAGCATTT	60.183	42.308	0.00	0.00	0.00	2.32
2418	2647	7.631377	GCTCTCTCTCTCTCTCTTTAGCATTTT	60.631	40.741	0.00	0.00	0.00	1.82
2419	2648	7.546358	TCTCTCTCTCTCTCTTTAGCATTTTG	58.454	38.462	0.00	0.00	0.00	2.44
2420	2649	7.178274	TCTCTCTCTCTCTCTTTAGCATTTTGT	59.822	37.037	0.00	0.00	0.00	2.83
2421	2650	8.354711	TCTCTCTCTCTCTTTAGCATTTTGTA	57.645	34.615	0.00	0.00	0.00	2.41
2422	2651	8.465999	TCTCTCTCTCTCTTTAGCATTTTGTAG	58.534	37.037	0.00	0.00	0.00	2.74
2423	2652	8.128322	TCTCTCTCTCTTTAGCATTTTGTAGT	57.872	34.615	0.00	0.00	0.00	2.73
2424	2653	8.247562	TCTCTCTCTCTTTAGCATTTTGTAGTC	58.752	37.037	0.00	0.00	0.00	2.59
2461	2690	2.155279	CTCTCTCTCAGTTCGACCACA	58.845	52.381	0.00	0.00	0.00	4.17
2491	2720	0.397941	CAGGAGAACTGGAGGCAACA	59.602	55.000	0.00	0.00	43.70	3.33
2520	2749	3.280920	GCTACTGGCGAGGAAGATG	57.719	57.895	0.00	0.00	0.00	2.90

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
310	312	3.325425	TGGGAAGGTGTGAAAGTATCGAA	59.675	43.478	0.00	0.0	0.00	3.71
352	354	3.660111	GCACCACAAGCACCGGTC	61.660	66.667	2.59	0.0	0.00	4.79
574	583	6.796426	TCAAAACATTGACCGACATACAAAA	58.204	32.000	0.00	0.0	0.00	2.44
582	591	4.684242	GGGAAATTCAAAACATTGACCGAC	59.316	41.667	0.00	0.0	0.00	4.79
684	695	9.676195	AAATGTTTGAAAAACAGGAAACAAAAG	57.324	25.926	10.90	0.0	32.78	2.27
744	755	0.038067	TGGTGTTATCGGTGACCACG	60.038	55.000	1.11	0.0	33.44	4.94
960	1015	4.303282	GCTATAGCTTGTGTCTTAGAGGC	58.697	47.826	17.75	0.0	38.21	4.70
1707	1765	0.449388	GGCAAAGCGAGAAGGACATG	59.551	55.000	0.00	0.0	0.00	3.21
1772	1833	3.306166	CCTTAATTAACGCTCACGGACTG	59.694	47.826	0.00	0.0	46.04	3.51
1776	1837	1.937899	CCCCTTAATTAACGCTCACGG	59.062	52.381	0.00	0.0	46.04	4.94
1794	1996	4.494484	GACATTTGTATGAAAACTGGCCC	58.506	43.478	0.00	0.0	35.65	5.80
2020	2222	2.593257	GTCGACGGAGACTTAACCAAG	58.407	52.381	0.00	0.0	38.09	3.61
2021	2223	2.712057	GTCGACGGAGACTTAACCAA	57.288	50.000	0.00	0.0	38.09	3.67
2084	2291	5.007234	TGAGTTTTCGTGTCAAGTACAATGG	59.993	40.000	0.00	0.0	40.63	3.16
2180	2387	1.364269	TTGAACCGGACATAACCCCT	58.636	50.000	9.46	0.0	0.00	4.79
2244	2462	0.527817	GGACCAATCGCCGAGTACAG	60.528	60.000	0.00	0.0	0.00	2.74
2356	2585	9.543018	GACTACAAAATGCTAATATAAATCGCC	57.457	33.333	0.00	0.0	0.00	5.54
2389	2618	2.898729	AGAGAGAGAGAGAGAGCGAG	57.101	55.000	0.00	0.0	0.00	5.03
2392	2621	4.199310	TGCTAAAGAGAGAGAGAGAGAGC	58.801	47.826	0.00	0.0	0.00	4.09
2404	2633	7.179338	AGAGAGGACTACAAAATGCTAAAGAGA	59.821	37.037	0.00	0.0	0.00	3.10
2407	2636	7.327214	AGAGAGAGGACTACAAAATGCTAAAG	58.673	38.462	0.00	0.0	0.00	1.85
2408	2637	7.179338	AGAGAGAGAGGACTACAAAATGCTAAA	59.821	37.037	0.00	0.0	0.00	1.85
2409	2638	6.665680	AGAGAGAGAGGACTACAAAATGCTAA	59.334	38.462	0.00	0.0	0.00	3.09
2410	2639	6.191315	AGAGAGAGAGGACTACAAAATGCTA	58.809	40.000	0.00	0.0	0.00	3.49
2411	2640	5.022787	AGAGAGAGAGGACTACAAAATGCT	58.977	41.667	0.00	0.0	0.00	3.79
2412	2641	5.127031	AGAGAGAGAGAGGACTACAAAATGC	59.873	44.000	0.00	0.0	0.00	3.56
2413	2642	6.603201	AGAGAGAGAGAGAGGACTACAAAATG	59.397	42.308	0.00	0.0	0.00	2.32
2414	2643	6.731467	AGAGAGAGAGAGAGGACTACAAAAT	58.269	40.000	0.00	0.0	0.00	1.82
2415	2644	6.012858	AGAGAGAGAGAGAGAGGACTACAAAA	60.013	42.308	0.00	0.0	0.00	2.44
2416	2645	5.487488	AGAGAGAGAGAGAGAGGACTACAAA	59.513	44.000	0.00	0.0	0.00	2.83
2417	2646	5.030147	AGAGAGAGAGAGAGAGGACTACAA	58.970	45.833	0.00	0.0	0.00	2.41
2418	2647	4.620723	AGAGAGAGAGAGAGAGGACTACA	58.379	47.826	0.00	0.0	0.00	2.74
2419	2648	4.896482	AGAGAGAGAGAGAGAGAGGACTAC	59.104	50.000	0.00	0.0	0.00	2.73
2420	2649	5.103473	AGAGAGAGAGAGAGAGAGAGGACTA	60.103	48.000	0.00	0.0	0.00	2.59
2421	2650	3.964031	GAGAGAGAGAGAGAGAGAGGACT	59.036	52.174	0.00	0.0	0.00	3.85
2422	2651	3.964031	AGAGAGAGAGAGAGAGAGAGGAC	59.036	52.174	0.00	0.0	0.00	3.85
2423	2652	4.078922	AGAGAGAGAGAGAGAGAGAGAGGA	60.079	50.000	0.00	0.0	0.00	3.71
2424	2653	4.222336	AGAGAGAGAGAGAGAGAGAGAGG	58.778	52.174	0.00	0.0	0.00	3.69
2461	2690	1.846124	TTCTCCTGCCCCCTTTCGT	60.846	57.895	0.00	0.0	0.00	3.85
2484	2713	1.446792	CTGCTCGTCGATGTTGCCT	60.447	57.895	17.63	0.0	0.00	4.75
2491	2720	1.730487	CCAGTAGCTGCTCGTCGAT	59.270	57.895	4.91	0.0	0.00	3.59
2520	2749	1.062148	GCTCGTCATTCCCTTTAACGC	59.938	52.381	0.00	0.0	33.58	4.84
2558	2787	0.108472	CTGCAGCGATGGAGTTGAGA	60.108	55.000	14.58	0.0	0.00	3.27

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.