AutoCloner

Multiple sequence alignment - TraesCS5D01G025100

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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	TraesCS5D01G025100	chr5D	100.000	4331	0	0	1	4331	22403088	22398758	0.000000e+00	7998.0
1	TraesCS5D01G025100	chr5D	88.830	1316	114	15	1734	3027	22435089	22433785	0.000000e+00	1585.0
2	TraesCS5D01G025100	chr5D	79.981	1039	97	47	670	1661	22436103	22435129	0.000000e+00	664.0
3	TraesCS5D01G025100	chr5D	89.884	346	29	2	3043	3383	22433712	22433368	1.430000e-119	440.0
4	TraesCS5D01G025100	chr5D	79.476	458	66	13	3442	3881	22433287	22432840	2.530000e-77	300.0
5	TraesCS5D01G025100	chr5D	84.774	243	23	8	59	293	22436360	22436124	9.370000e-57	231.0
6	TraesCS5D01G025100	chr5A	96.148	4310	105	23	53	4331	15868442	15864163	0.000000e+00	6983.0
7	TraesCS5D01G025100	chr5B	93.422	1961	94	17	1742	3691	15560091	15558155	0.000000e+00	2874.0
8	TraesCS5D01G025100	chr5B	89.026	1294	114	12	1734	3005	16003500	16002213	0.000000e+00	1578.0
9	TraesCS5D01G025100	chr5B	95.026	945	27	5	784	1711	15561202	15560261	0.000000e+00	1467.0
10	TraesCS5D01G025100	chr5B	90.547	804	52	11	1	788	15562118	15561323	0.000000e+00	1042.0
11	TraesCS5D01G025100	chr5B	82.160	852	82	35	821	1627	16004392	16003566	0.000000e+00	667.0
12	TraesCS5D01G025100	chr5B	85.597	611	54	20	3743	4331	15558150	15557552	1.030000e-170	610.0
13	TraesCS5D01G025100	chr5B	87.863	379	33	7	3043	3413	16002122	16001749	2.390000e-117	433.0
14	TraesCS5D01G025100	chr5B	83.846	260	23	14	58	303	16004755	16004501	3.370000e-56	230.0
15	TraesCS5D01G025100	chr5B	93.846	65	2	2	1673	1736	370194705	370194768	3.570000e-16	97.1
16	TraesCS5D01G025100	chr5B	93.846	65	2	2	1673	1736	370239565	370239628	3.570000e-16	97.1
17	TraesCS5D01G025100	chr2B	83.427	531	50	10	1168	1669	178773942	178773421	3.950000e-125	459.0
18	TraesCS5D01G025100	chr2B	88.532	218	23	2	1736	1953	178773382	178773167	3.320000e-66	263.0
19	TraesCS5D01G025100	chr2B	82.081	173	25	3	3945	4116	566624803	566624970	4.510000e-30	143.0
20	TraesCS5D01G025100	chr2B	94.737	57	2	1	1679	1735	321689847	321689902	2.150000e-13	87.9
21	TraesCS5D01G025100	chr7D	84.940	166	15	5	3954	4114	265692826	265692986	4.480000e-35	159.0
22	TraesCS5D01G025100	chr2D	83.735	166	21	3	3950	4114	410600665	410600825	7.500000e-33	152.0
23	TraesCS5D01G025100	chr1D	84.868	152	17	5	3964	4114	104291540	104291686	9.700000e-32	148.0
24	TraesCS5D01G025100	chr1D	94.737	57	2	1	1679	1735	351255328	351255383	2.150000e-13	87.9
25	TraesCS5D01G025100	chr6B	84.828	145	18	1	3970	4114	345218570	345218710	4.510000e-30	143.0
26	TraesCS5D01G025100	chr2A	80.925	173	27	3	3945	4116	625025647	625025814	9.770000e-27	132.0
27	TraesCS5D01G025100	chr7B	81.212	165	25	4	3951	4114	427397774	427397933	1.260000e-25	128.0
28	TraesCS5D01G025100	chr3A	94.030	67	3	1	1673	1739	67912179	67912114	2.760000e-17	100.0
29	TraesCS5D01G025100	chr4A	95.082	61	1	2	1679	1738	6936559	6936618	1.280000e-15	95.3
30	TraesCS5D01G025100	chr6A	94.737	57	2	1	1679	1735	573510818	573510873	2.150000e-13	87.9

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	TraesCS5D01G025100	chr5D	22398758	22403088	4330	True	7998.00	7998	100.00000	1	4331	1	chr5D.!!$R1	4330
1	TraesCS5D01G025100	chr5D	22432840	22436360	3520	True	644.00	1585	84.58900	59	3881	5	chr5D.!!$R2	3822
2	TraesCS5D01G025100	chr5A	15864163	15868442	4279	True	6983.00	6983	96.14800	53	4331	1	chr5A.!!$R1	4278
3	TraesCS5D01G025100	chr5B	15557552	15562118	4566	True	1498.25	2874	91.14800	1	4331	4	chr5B.!!$R1	4330
4	TraesCS5D01G025100	chr5B	16001749	16004755	3006	True	727.00	1578	85.72375	58	3413	4	chr5B.!!$R2	3355
5	TraesCS5D01G025100	chr2B	178773167	178773942	775	True	361.00	459	85.97950	1168	1953	2	chr2B.!!$R1	785

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
26	27	1.145738	ACAGAGTGGTGAAATTGCCCT	59.854	47.619	0.00	0.0	0.00	5.19	F
120	125	1.477295	TCACATATGTGGCCGTCGTTA	59.523	47.619	30.56	9.6	45.65	3.18	F
470	496	1.667830	CCGGTTGCTCGCTTCTTCA	60.668	57.895	0.00	0.0	0.00	3.02	F
661	695	2.418368	TGGCATGCCGTCTCTTAATT	57.582	45.000	30.87	0.0	39.42	1.40	F
2423	2812	1.238439	CGTGTTCAATGCCTCTGGTT	58.762	50.000	0.00	0.0	0.00	3.67	F
2986	3395	0.388520	TCCACGAGATGACAACTGCG	60.389	55.000	0.00	0.0	0.00	5.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1029	1228	1.339055	GCCATGACTAGAACCAGTGCA	60.339	52.381	0.00	0.00	0.00	4.57	R
1834	2222	3.243975	CCAGAAGCAAAGCAAATTCAGGT	60.244	43.478	0.00	0.00	0.00	4.00	R
2423	2812	2.359531	CCGGAAACCAGTACTTTTGCAA	59.640	45.455	0.00	0.00	0.00	4.08	R
2673	3062	4.214119	ACCATCTTCAACACAGTGAAATCG	59.786	41.667	7.81	0.00	37.08	3.34	R
3309	3791	2.690497	TCAGGCAGAGCATACTACACTC	59.310	50.000	0.00	0.00	0.00	3.51	R
3923	4482	3.819564	TGCCCACAGTACTATGCTTAG	57.180	47.619	0.00	5.13	0.00	2.18	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
24	25	2.229792	TCACAGAGTGGTGAAATTGCC	58.770	47.619	0.00	0.00	44.34	4.52
26	27	1.145738	ACAGAGTGGTGAAATTGCCCT	59.854	47.619	0.00	0.00	0.00	5.19
27	28	2.242043	CAGAGTGGTGAAATTGCCCTT	58.758	47.619	0.00	0.00	0.00	3.95
28	29	2.029649	CAGAGTGGTGAAATTGCCCTTG	60.030	50.000	0.00	0.00	0.00	3.61
29	30	1.963515	GAGTGGTGAAATTGCCCTTGT	59.036	47.619	0.00	0.00	0.00	3.16
32	33	4.159557	AGTGGTGAAATTGCCCTTGTATT	58.840	39.130	0.00	0.00	0.00	1.89
39	40	6.366061	GTGAAATTGCCCTTGTATTCAACTTC	59.634	38.462	0.00	0.00	0.00	3.01
41	42	5.649782	ATTGCCCTTGTATTCAACTTCAG	57.350	39.130	0.00	0.00	0.00	3.02
49	50	6.128007	CCTTGTATTCAACTTCAGCGGTAAAT	60.128	38.462	0.00	0.00	0.00	1.40
120	125	1.477295	TCACATATGTGGCCGTCGTTA	59.523	47.619	30.56	9.60	45.65	3.18
280	302	7.063308	CCAAATTTGACATGTTAGTATGTTGCC	59.937	37.037	19.86	0.00	41.15	4.52
281	303	4.937696	TTGACATGTTAGTATGTTGCCG	57.062	40.909	0.00	0.00	41.15	5.69
282	304	3.932822	TGACATGTTAGTATGTTGCCGT	58.067	40.909	0.00	0.00	41.15	5.68
283	305	3.930229	TGACATGTTAGTATGTTGCCGTC	59.070	43.478	0.00	0.00	41.15	4.79
300	322	4.881273	TGCCGTCTGCTACAATATTCATTT	59.119	37.500	0.00	0.00	42.00	2.32
399	425	4.520492	ACAAACAACAGCCTGAGGAATAAG	59.480	41.667	0.65	0.00	0.00	1.73
430	456	2.158827	GCCACCCAAGAAACAAACCAAT	60.159	45.455	0.00	0.00	0.00	3.16
470	496	1.667830	CCGGTTGCTCGCTTCTTCA	60.668	57.895	0.00	0.00	0.00	3.02
487	516	5.514274	TCTTCAAACTTGAAAAATCGCCT	57.486	34.783	6.36	0.00	45.61	5.52
661	695	2.418368	TGGCATGCCGTCTCTTAATT	57.582	45.000	30.87	0.00	39.42	1.40
663	697	3.466836	TGGCATGCCGTCTCTTAATTAG	58.533	45.455	30.87	0.00	39.42	1.73
671	705	5.106712	TGCCGTCTCTTAATTAGTTGCTTTG	60.107	40.000	0.00	0.00	0.00	2.77
728	765	4.769488	TGGCATGCCATTGTTTAGAAGTAA	59.231	37.500	35.59	6.75	41.89	2.24
947	1135	6.036577	AGCCAATAATTGATTGTTCGGTTT	57.963	33.333	0.00	0.00	43.09	3.27
977	1165	6.149640	GTGTTATCCTTTTCTGTTCCTCTTCC	59.850	42.308	0.00	0.00	0.00	3.46
981	1169	3.416156	CTTTTCTGTTCCTCTTCCCCTG	58.584	50.000	0.00	0.00	0.00	4.45
1137	1336	2.974794	CCCTCATCAGGTCACCATGATA	59.025	50.000	0.00	0.00	38.30	2.15
1339	1553	5.745227	TCTTCCAGTTGTTTGTCTCTTCTT	58.255	37.500	0.00	0.00	0.00	2.52
1340	1554	5.817816	TCTTCCAGTTGTTTGTCTCTTCTTC	59.182	40.000	0.00	0.00	0.00	2.87
2423	2812	1.238439	CGTGTTCAATGCCTCTGGTT	58.762	50.000	0.00	0.00	0.00	3.67
2673	3062	6.595772	AGTATCGTTGCTCTGAAATTGATC	57.404	37.500	0.00	0.00	0.00	2.92
2696	3085	4.214119	CGATTTCACTGTGTTGAAGATGGT	59.786	41.667	7.79	0.00	36.84	3.55
2986	3395	0.388520	TCCACGAGATGACAACTGCG	60.389	55.000	0.00	0.00	0.00	5.18
3054	3528	9.962759	GTAAAACCTATGAACTATGTTGTTACG	57.037	33.333	0.00	0.00	0.00	3.18
3309	3791	2.083774	TGCCTTTTGTAGCAAGGATCG	58.916	47.619	4.02	0.00	43.32	3.69
3408	3890	2.034812	GCACCAGGATAGGACTTCTACG	59.965	54.545	0.00	0.00	0.00	3.51
3519	4036	4.813697	GGCCTGATGATTTAGTCTCAAGAC	59.186	45.833	0.00	1.79	45.08	3.01
3719	4239	3.073062	AGACATTGTAGTTCTGCCTGGTT	59.927	43.478	0.00	0.00	0.00	3.67
3923	4482	5.202640	CGGTAGCAAGTCAGTTTGTAAAAC	58.797	41.667	0.00	0.00	0.00	2.43
3953	4512	1.786937	ACTGTGGGCATTGGTCAAAA	58.213	45.000	0.00	0.00	0.00	2.44
3960	4519	5.105146	TGTGGGCATTGGTCAAAATAATACC	60.105	40.000	0.00	0.00	0.00	2.73
4329	4893	5.825593	AAGTGAAATAGTCCTGTGAAGGA	57.174	39.130	0.00	0.00	35.23	3.36

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
5	6	1.270550	GGGCAATTTCACCACTCTGTG	59.729	52.381	0.00	0.00	37.59	3.66
20	21	3.255642	GCTGAAGTTGAATACAAGGGCAA	59.744	43.478	0.00	0.00	36.64	4.52
22	23	2.159517	CGCTGAAGTTGAATACAAGGGC	60.160	50.000	0.00	0.00	36.64	5.19
24	25	3.074412	ACCGCTGAAGTTGAATACAAGG	58.926	45.455	0.00	0.00	36.64	3.61
26	27	6.811253	ATTTACCGCTGAAGTTGAATACAA	57.189	33.333	0.00	0.00	0.00	2.41
27	28	6.811253	AATTTACCGCTGAAGTTGAATACA	57.189	33.333	0.00	0.00	0.00	2.29
28	29	9.783256	AAATAATTTACCGCTGAAGTTGAATAC	57.217	29.630	0.00	0.00	0.00	1.89
32	33	7.331440	TCGTAAATAATTTACCGCTGAAGTTGA	59.669	33.333	0.00	0.00	41.87	3.18
39	40	8.054236	CAGTAAGTCGTAAATAATTTACCGCTG	58.946	37.037	0.00	0.00	41.87	5.18
41	42	7.898946	ACAGTAAGTCGTAAATAATTTACCGC	58.101	34.615	0.00	0.00	41.87	5.68
106	107	0.248012	TGTGATAACGACGGCCACAT	59.752	50.000	2.24	0.00	33.42	3.21
120	125	5.121811	GTGATCAGTAGCCAAAGATGTGAT	58.878	41.667	0.00	0.00	0.00	3.06
252	266	7.169158	ACATACTAACATGTCAAATTTGGGG	57.831	36.000	17.90	7.81	33.89	4.96
253	267	7.063308	GCAACATACTAACATGTCAAATTTGGG	59.937	37.037	17.90	8.13	38.19	4.12
280	302	8.982685	AGACATAAATGAATATTGTAGCAGACG	58.017	33.333	0.00	0.00	0.00	4.18
291	313	6.256539	CGGCGCTCATAGACATAAATGAATAT	59.743	38.462	7.64	0.00	31.97	1.28
292	314	5.576774	CGGCGCTCATAGACATAAATGAATA	59.423	40.000	7.64	0.00	31.97	1.75
300	322	0.596577	GGTCGGCGCTCATAGACATA	59.403	55.000	7.64	0.00	35.49	2.29
339	365	4.530857	GGTCGGGACATGGGAGCG	62.531	72.222	0.00	0.00	0.00	5.03
399	425	3.125520	TTGGGTGGCCAAGACTTTC	57.874	52.632	7.24	0.00	0.00	2.62
430	456	2.128535	TGGGTGTTACTTCCAAGGTGA	58.871	47.619	0.00	0.00	0.00	4.02
470	496	2.547855	GGCCAGGCGATTTTTCAAGTTT	60.548	45.455	5.00	0.00	0.00	2.66
487	516	2.347490	GTTCTTGCTCGGAGGCCA	59.653	61.111	5.01	0.00	0.00	5.36
578	612	2.366640	TGATAGAGAGGACCCGGAAG	57.633	55.000	0.73	0.00	0.00	3.46
581	615	5.546621	TTTAAATGATAGAGAGGACCCGG	57.453	43.478	0.00	0.00	0.00	5.73
684	718	6.093404	GCCAAAGAAAGCAACTTATTACTCC	58.907	40.000	0.00	0.00	0.00	3.85
692	726	2.486918	GCATGCCAAAGAAAGCAACTT	58.513	42.857	6.36	0.00	43.36	2.66
947	1135	5.300792	GGAACAGAAAAGGATAACACCAACA	59.699	40.000	0.00	0.00	0.00	3.33
977	1165	6.227298	TCTGAAAGCTATAGAGAAACAGGG	57.773	41.667	3.21	0.00	0.00	4.45
981	1169	5.994668	CCCCATCTGAAAGCTATAGAGAAAC	59.005	44.000	3.21	0.00	0.00	2.78
1029	1228	1.339055	GCCATGACTAGAACCAGTGCA	60.339	52.381	0.00	0.00	0.00	4.57
1137	1336	4.774200	ACCCAAAGCTCAATTTTAGCAGAT	59.226	37.500	11.20	0.00	42.62	2.90
1834	2222	3.243975	CCAGAAGCAAAGCAAATTCAGGT	60.244	43.478	0.00	0.00	0.00	4.00
2051	2439	7.233757	AGAGAATTAATGCTCGTAAGGTAGGAT	59.766	37.037	16.39	0.00	36.29	3.24
2423	2812	2.359531	CCGGAAACCAGTACTTTTGCAA	59.640	45.455	0.00	0.00	0.00	4.08
2673	3062	4.214119	ACCATCTTCAACACAGTGAAATCG	59.786	41.667	7.81	0.00	37.08	3.34
2696	3085	1.475571	CCAGCATCCATTCCATCGTCA	60.476	52.381	0.00	0.00	0.00	4.35
3028	3437	9.962759	CGTAACAACATAGTTCATAGGTTTTAC	57.037	33.333	0.00	0.00	36.27	2.01
3029	3438	8.658609	GCGTAACAACATAGTTCATAGGTTTTA	58.341	33.333	0.00	0.00	36.27	1.52
3030	3439	7.173562	TGCGTAACAACATAGTTCATAGGTTTT	59.826	33.333	0.00	0.00	36.27	2.43
3031	3440	6.651643	TGCGTAACAACATAGTTCATAGGTTT	59.348	34.615	0.00	0.00	36.27	3.27
3032	3441	6.167685	TGCGTAACAACATAGTTCATAGGTT	58.832	36.000	0.00	0.00	38.89	3.50
3033	3442	5.726397	TGCGTAACAACATAGTTCATAGGT	58.274	37.500	0.00	0.00	33.07	3.08
3034	3443	6.656314	TTGCGTAACAACATAGTTCATAGG	57.344	37.500	0.00	0.00	31.73	2.57
3309	3791	2.690497	TCAGGCAGAGCATACTACACTC	59.310	50.000	0.00	0.00	0.00	3.51
3408	3890	3.813724	AGTTCCCGCAAAAACTAGAGAAC	59.186	43.478	0.00	0.00	34.05	3.01
3544	4061	3.712218	AGTATGTCTTTCTTCTAGCCCCC	59.288	47.826	0.00	0.00	0.00	5.40
3545	4062	5.360649	AAGTATGTCTTTCTTCTAGCCCC	57.639	43.478	0.00	0.00	31.57	5.80
3719	4239	8.892723	GTGTAATCCATCTATGTCAAACATTCA	58.107	33.333	0.00	0.00	39.88	2.57
3923	4482	3.819564	TGCCCACAGTACTATGCTTAG	57.180	47.619	0.00	5.13	0.00	2.18
3953	4512	4.799579	AGTTTGGAAAGGAGGGGGTATTAT	59.200	41.667	0.00	0.00	0.00	1.28
3960	4519	5.191921	ACTCTTATAGTTTGGAAAGGAGGGG	59.808	44.000	0.00	0.00	33.35	4.79
4082	4641	7.710907	CCTCCGTTCTGAAATATAAGATGTTCA	59.289	37.037	0.00	0.00	0.00	3.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.