AutoCloner

Multiple sequence alignment - TraesCS1D01G029600

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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	TraesCS1D01G029600	chr1D	100.000	5714	0	0	1	5714	11629501	11635214	0.000000e+00	10552.0
1	TraesCS1D01G029600	chr1D	94.000	700	41	1	3526	4224	11632337	11633036	0.000000e+00	1059.0
2	TraesCS1D01G029600	chr1D	94.000	700	41	1	2837	3536	11633026	11633724	0.000000e+00	1059.0
3	TraesCS1D01G029600	chr1B	92.835	2638	176	8	2645	5278	17388681	17391309	0.000000e+00	3812.0
4	TraesCS1D01G029600	chr1B	90.435	1631	148	7	3526	5151	17516725	17518352	0.000000e+00	2141.0
5	TraesCS1D01G029600	chr1B	85.967	1582	186	15	857	2427	17463835	17465391	0.000000e+00	1659.0
6	TraesCS1D01G029600	chr1B	86.804	1508	167	13	865	2362	17386996	17388481	0.000000e+00	1653.0
7	TraesCS1D01G029600	chr1B	93.861	1010	59	1	2577	3586	17465387	17466393	0.000000e+00	1519.0
8	TraesCS1D01G029600	chr1B	87.601	992	110	9	2551	3536	17516438	17517422	0.000000e+00	1138.0
9	TraesCS1D01G029600	chr1B	93.143	700	47	1	2837	3536	17389563	17390261	0.000000e+00	1026.0
10	TraesCS1D01G029600	chr1B	92.714	700	50	1	3526	4224	17388874	17389573	0.000000e+00	1009.0
11	TraesCS1D01G029600	chr1B	92.330	704	53	1	3526	4228	17465644	17466347	0.000000e+00	1000.0
12	TraesCS1D01G029600	chr1B	84.489	548	37	21	5182	5714	17518332	17518846	1.110000e-136	497.0
13	TraesCS1D01G029600	chr1B	80.846	449	77	6	796	1237	17490193	17490639	1.520000e-90	344.0
14	TraesCS1D01G029600	chr1B	80.752	452	73	10	796	1237	17443864	17444311	1.970000e-89	340.0
15	TraesCS1D01G029600	chr1B	80.645	434	73	6	795	1220	17475668	17476098	5.520000e-85	326.0
16	TraesCS1D01G029600	chr1B	81.667	420	51	15	795	1209	17512575	17512973	5.520000e-85	326.0
17	TraesCS1D01G029600	chr1B	80.096	417	76	4	795	1204	17473067	17473483	2.590000e-78	303.0
18	TraesCS1D01G029600	chr1B	82.370	346	54	4	795	1134	17510302	17510646	1.560000e-75	294.0
19	TraesCS1D01G029600	chr1B	89.848	197	9	4	2399	2584	17388486	17388682	5.720000e-60	243.0
20	TraesCS1D01G029600	chr1A	92.701	2055	135	9	513	2558	13771960	13774008	0.000000e+00	2950.0
21	TraesCS1D01G029600	chr1A	93.612	1315	82	2	3529	4841	13774367	13775681	0.000000e+00	1962.0
22	TraesCS1D01G029600	chr1A	90.808	990	83	4	2551	3536	13774078	13775063	0.000000e+00	1317.0
23	TraesCS1D01G029600	chr1A	94.798	519	26	1	1	518	13769704	13770222	0.000000e+00	808.0
24	TraesCS1D01G029600	chr1A	91.613	310	17	4	5405	5714	13781585	13781885	2.460000e-113	420.0
25	TraesCS1D01G029600	chr6B	72.091	971	228	31	219	1162	585627455	585628409	9.500000e-63	252.0
26	TraesCS1D01G029600	chr3A	94.444	36	2	0	4727	4762	98184330	98184365	8.000000e-04	56.5
27	TraesCS1D01G029600	chr3A	94.286	35	2	0	4728	4762	695716547	695716513	3.000000e-03	54.7
28	TraesCS1D01G029600	chr2B	100.000	30	0	0	4725	4754	496313433	496313462	8.000000e-04	56.5
29	TraesCS1D01G029600	chr7D	94.286	35	2	0	4728	4762	434821054	434821088	3.000000e-03	54.7
30	TraesCS1D01G029600	chr5A	94.286	35	2	0	4728	4762	89786740	89786774	3.000000e-03	54.7
31	TraesCS1D01G029600	chr4A	87.755	49	2	2	4710	4754	291812155	291812107	3.000000e-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	TraesCS1D01G029600	chr1D	11629501	11635214	5713	False	4223.333333	10552	96.000000	1	5714	3	chr1D.!!$F1	5713
1	TraesCS1D01G029600	chr1B	17386996	17391309	4313	False	1548.600000	3812	91.068800	865	5278	5	chr1B.!!$F3	4413
2	TraesCS1D01G029600	chr1B	17463835	17466393	2558	False	1392.666667	1659	90.719333	857	4228	3	chr1B.!!$F4	3371
3	TraesCS1D01G029600	chr1B	17510302	17518846	8544	False	879.200000	2141	85.312400	795	5714	5	chr1B.!!$F6	4919
4	TraesCS1D01G029600	chr1B	17473067	17476098	3031	False	314.500000	326	80.370500	795	1220	2	chr1B.!!$F5	425
5	TraesCS1D01G029600	chr1A	13769704	13775681	5977	False	1759.250000	2950	92.979750	1	4841	4	chr1A.!!$F2	4840
6	TraesCS1D01G029600	chr6B	585627455	585628409	954	False	252.000000	252	72.091000	219	1162	1	chr6B.!!$F1	943

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
797	2554	0.177141	TGATCGGGATTTGACGGGAC	59.823	55.000	0.00	0.00	0.00	4.46	F
1369	10546	1.081641	GACGAGGACGAAAGCGACA	60.082	57.895	0.00	0.00	42.66	4.35	F
3196	12690	0.104304	ATAACTACCTGAAGGCGGCG	59.896	55.000	0.51	0.51	39.32	6.46	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1692	10873	0.032540	GCTTGGTTGGTGAAGCTTGG	59.967	55.0	2.10	0.0	41.21	3.61	R
3334	12828	0.033090	AGAAGGTTTCGGTGTCGGAC	59.967	55.0	0.00	0.0	36.95	4.79	R
5189	15378	0.029567	CACTCGAGGGCTAAGCTACG	59.970	60.0	18.41	0.0	0.00	3.51	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
32	33	8.496707	AATTTTCTTGCAAAACAGAGTGAAAT	57.503	26.923	0.00	0.00	0.00	2.17
92	93	7.676683	AACCATCTTAGCTAGGTTTAGATCA	57.323	36.000	8.87	0.00	41.33	2.92
174	176	3.259902	GCGGGAATTAGATCCGTAATCC	58.740	50.000	0.00	0.00	44.97	3.01
199	201	4.099633	TGAATCTGAGTGAGGTTCCTCAT	58.900	43.478	22.05	12.46	40.70	2.90
314	317	6.206048	CCCGGATCTTTTAGTACAAGTTTGTT	59.794	38.462	0.73	0.00	42.35	2.83
315	318	7.255346	CCCGGATCTTTTAGTACAAGTTTGTTT	60.255	37.037	0.73	0.00	42.35	2.83
330	333	7.929245	ACAAGTTTGTTTGGAAAAGTTTAGTGT	59.071	29.630	0.00	0.00	38.47	3.55
350	353	6.692486	AGTGTCACTCAAAATCTTCTATCGT	58.308	36.000	0.00	0.00	0.00	3.73
371	374	2.060050	AGAGGGTGACTAGTGATCCG	57.940	55.000	5.94	0.00	0.00	4.18
378	381	1.476891	TGACTAGTGATCCGGTCAAGC	59.523	52.381	0.00	0.00	38.90	4.01
389	392	2.037641	TCCGGTCAAGCATCTATCATGG	59.962	50.000	0.00	0.00	0.00	3.66
395	398	5.311265	GTCAAGCATCTATCATGGAATCCA	58.689	41.667	3.67	3.67	38.19	3.41
528	2276	4.585581	GGAACCTAGTAAAAGGCCAAAACA	59.414	41.667	5.01	0.00	40.62	2.83
541	2297	2.478539	GCCAAAACAGAGCCATCGAATC	60.479	50.000	0.00	0.00	0.00	2.52
629	2385	4.266714	TGTATGGTGTGAGTGATCTCGTA	58.733	43.478	0.00	0.00	43.09	3.43
630	2386	4.335594	TGTATGGTGTGAGTGATCTCGTAG	59.664	45.833	0.00	0.00	43.09	3.51
672	2428	5.352293	TGCGATCAATATGTCATAAGATGCC	59.648	40.000	13.10	6.88	0.00	4.40
674	2430	5.295292	CGATCAATATGTCATAAGATGCCCC	59.705	44.000	13.10	2.51	0.00	5.80
679	2435	1.280710	TGTCATAAGATGCCCCGTGTT	59.719	47.619	0.00	0.00	0.00	3.32
685	2441	0.981183	AGATGCCCCGTGTTAGAACA	59.019	50.000	0.00	0.00	36.38	3.18
720	2476	5.716703	CCCTTTGGATTACCTTTTCTGATGT	59.283	40.000	0.00	0.00	37.04	3.06
771	2528	6.482973	TCTTTGCATTTCCCAAAAGAATTCAC	59.517	34.615	8.44	0.00	32.37	3.18
779	2536	3.558505	CCAAAAGAATTCACGCAGTCTG	58.441	45.455	8.44	0.00	41.61	3.51
797	2554	0.177141	TGATCGGGATTTGACGGGAC	59.823	55.000	0.00	0.00	0.00	4.46
841	4872	1.439353	CCCATCCTCAAATCGTGCGG	61.439	60.000	0.00	0.00	32.92	5.69

Showing 1 to 25 of 658 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
12	13	8.994429	TTTTTATTTCACTCTGTTTTGCAAGA	57.006	26.923	0.00	0.00	0.00	3.02
43	44	5.126222	AGAGATGCTCTCACATTAGAAACGA	59.874	40.000	13.42	0.00	45.73	3.85
45	46	7.223777	GGTTAGAGATGCTCTCACATTAGAAAC	59.776	40.741	13.42	3.00	45.73	2.78
92	93	4.791069	ACCGGGTAGGGCCACGAT	62.791	66.667	6.32	0.00	46.96	3.73
174	176	2.996621	GGAACCTCACTCAGATTCAACG	59.003	50.000	0.00	0.00	0.00	4.10
199	201	0.982852	ACTCGGGATGCCATTCCTCA	60.983	55.000	3.39	0.00	35.97	3.86
209	211	1.755179	ATCAAAAGGCACTCGGGATG	58.245	50.000	0.00	0.00	38.49	3.51
314	317	7.455641	TTTGAGTGACACTAAACTTTTCCAA	57.544	32.000	8.41	2.39	0.00	3.53
315	318	7.455641	TTTTGAGTGACACTAAACTTTTCCA	57.544	32.000	8.41	0.00	0.00	3.53
330	333	8.191446	CCTCTTACGATAGAAGATTTTGAGTGA	58.809	37.037	0.00	0.00	41.38	3.41
350	353	3.552875	CGGATCACTAGTCACCCTCTTA	58.447	50.000	0.00	0.00	0.00	2.10
371	374	4.699257	GGATTCCATGATAGATGCTTGACC	59.301	45.833	0.00	0.00	0.00	4.02
378	381	6.293698	TGTCACTTGGATTCCATGATAGATG	58.706	40.000	21.83	11.21	33.58	2.90
528	2276	0.692419	AGGGTGGATTCGATGGCTCT	60.692	55.000	0.00	0.00	0.00	4.09
541	2297	3.643792	TGGGAACATTTGTTAAAGGGTGG	59.356	43.478	0.00	0.00	38.56	4.61
600	2356	6.596888	AGATCACTCACACCATACAAAATCAG	59.403	38.462	0.00	0.00	0.00	2.90
609	2365	4.524053	ACTACGAGATCACTCACACCATA	58.476	43.478	0.00	0.00	42.72	2.74
654	2410	4.154737	CACGGGGCATCTTATGACATATTG	59.845	45.833	0.00	0.00	41.20	1.90
672	2428	6.258068	GGATAGAAATCTTGTTCTAACACGGG	59.742	42.308	0.00	0.00	42.04	5.28
674	2430	7.042335	AGGGATAGAAATCTTGTTCTAACACG	58.958	38.462	0.00	0.00	42.04	4.49
679	2435	8.158025	TCCAAAGGGATAGAAATCTTGTTCTA	57.842	34.615	0.00	0.00	42.73	2.10
763	2520	2.534298	CGATCAGACTGCGTGAATTCT	58.466	47.619	7.05	0.00	0.00	2.40
771	2528	0.933097	CAAATCCCGATCAGACTGCG	59.067	55.000	0.00	0.00	0.00	5.18
779	2536	0.874607	CGTCCCGTCAAATCCCGATC	60.875	60.000	0.00	0.00	0.00	3.69
797	2554	9.495754	GGAATCAAAAAGTCTTCTTCATAATCG	57.504	33.333	0.00	0.00	32.90	3.34

Showing 1 to 25 of 706 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.