AutoCloner

Multiple sequence alignment - TraesCS1D01G021200

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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	TraesCS1D01G021200	chr1D	100.000	4556	0	0	1	4556	9090068	9085513	0.000000e+00	8414
1	TraesCS1D01G021200	chr1D	93.756	1121	48	7	192	1305	9327641	9326536	0.000000e+00	1663
2	TraesCS1D01G021200	chr1D	93.958	662	37	3	1302	1963	9312493	9311835	0.000000e+00	998
3	TraesCS1D01G021200	chr1D	77.840	1620	321	30	1743	3346	9590993	9592590	0.000000e+00	968
4	TraesCS1D01G021200	chr1D	82.278	1027	175	5	1673	2697	8839789	8838768	0.000000e+00	881
5	TraesCS1D01G021200	chr1D	87.978	732	88	0	1959	2690	9310004	9309273	0.000000e+00	865
6	TraesCS1D01G021200	chr1D	81.800	511	85	6	2894	3403	9029701	9029198	5.450000e-114	422
7	TraesCS1D01G021200	chr1B	88.322	3528	323	39	1	3503	13040899	13044362	0.000000e+00	4150
8	TraesCS1D01G021200	chr1B	78.476	3308	530	115	223	3435	12430313	12427093	0.000000e+00	1997
9	TraesCS1D01G021200	chr1B	84.885	913	128	4	1639	2549	12637750	12638654	0.000000e+00	913
10	TraesCS1D01G021200	chr1B	80.726	1240	155	32	260	1449	12636408	12637613	0.000000e+00	889
11	TraesCS1D01G021200	chr1B	81.327	980	176	6	1743	2720	12813525	12812551	0.000000e+00	789
12	TraesCS1D01G021200	chr1B	80.840	976	179	6	1743	2717	13238363	13239331	0.000000e+00	760
13	TraesCS1D01G021200	chr1B	78.638	969	189	13	2537	3499	12640101	12641057	1.080000e-175	627
14	TraesCS1D01G021200	chr1B	80.581	757	104	22	449	1198	13300010	13299290	1.110000e-150	544
15	TraesCS1D01G021200	chr1B	81.077	724	99	20	483	1198	13340618	13339925	1.110000e-150	544
16	TraesCS1D01G021200	chr1B	81.455	550	86	12	2894	3435	12812389	12811848	1.950000e-118	436
17	TraesCS1D01G021200	chr1B	85.106	141	21	0	3011	3151	13277940	13277800	1.320000e-30	145
18	TraesCS1D01G021200	chr1A	83.557	1788	257	29	1741	3502	10484957	10483181	0.000000e+00	1639
19	TraesCS1D01G021200	chr1A	92.776	969	64	6	3592	4556	482800556	482801522	0.000000e+00	1397
20	TraesCS1D01G021200	chr1A	84.166	1061	161	5	1669	2724	10471467	10470409	0.000000e+00	1022
21	TraesCS1D01G021200	chr1A	82.280	1044	134	23	273	1289	10472812	10471793	0.000000e+00	856
22	TraesCS1D01G021200	chr1A	82.515	509	79	7	2894	3400	10470251	10469751	5.410000e-119	438
23	TraesCS1D01G021200	chr7D	94.575	977	47	6	3585	4556	533623988	533623013	0.000000e+00	1506
24	TraesCS1D01G021200	chr3D	97.691	866	18	2	3691	4556	15905199	15906062	0.000000e+00	1487
25	TraesCS1D01G021200	chr2D	94.410	966	44	7	3596	4556	5433458	5432498	0.000000e+00	1476
26	TraesCS1D01G021200	chr5B	93.750	960	50	9	3603	4556	334057191	334058146	0.000000e+00	1432
27	TraesCS1D01G021200	chr5B	92.665	968	62	8	3595	4556	640284047	640285011	0.000000e+00	1386
28	TraesCS1D01G021200	chr6B	92.690	985	63	9	3577	4556	607120540	607121520	0.000000e+00	1411
29	TraesCS1D01G021200	chr4A	92.577	970	66	6	3591	4556	735689444	735688477	0.000000e+00	1387
30	TraesCS1D01G021200	chr4A	76.355	203	40	8	3150	3345	674939252	674939453	8.060000e-18	102
31	TraesCS1D01G021200	chr7A	92.497	973	65	8	3589	4556	34525209	34526178	0.000000e+00	1386
32	TraesCS1D01G021200	chr7B	72.177	496	106	21	3020	3493	750607476	750606991	6.190000e-24	122

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	TraesCS1D01G021200	chr1D	9085513	9090068	4555	True	8414.000000	8414	100.000000	1	4556	1	chr1D.!!$R3	4555
1	TraesCS1D01G021200	chr1D	9326536	9327641	1105	True	1663.000000	1663	93.756000	192	1305	1	chr1D.!!$R4	1113
2	TraesCS1D01G021200	chr1D	9590993	9592590	1597	False	968.000000	968	77.840000	1743	3346	1	chr1D.!!$F1	1603
3	TraesCS1D01G021200	chr1D	9309273	9312493	3220	True	931.500000	998	90.968000	1302	2690	2	chr1D.!!$R5	1388
4	TraesCS1D01G021200	chr1D	8838768	8839789	1021	True	881.000000	881	82.278000	1673	2697	1	chr1D.!!$R1	1024
5	TraesCS1D01G021200	chr1D	9029198	9029701	503	True	422.000000	422	81.800000	2894	3403	1	chr1D.!!$R2	509
6	TraesCS1D01G021200	chr1B	13040899	13044362	3463	False	4150.000000	4150	88.322000	1	3503	1	chr1B.!!$F1	3502
7	TraesCS1D01G021200	chr1B	12427093	12430313	3220	True	1997.000000	1997	78.476000	223	3435	1	chr1B.!!$R1	3212
8	TraesCS1D01G021200	chr1B	12636408	12641057	4649	False	809.666667	913	81.416333	260	3499	3	chr1B.!!$F3	3239
9	TraesCS1D01G021200	chr1B	13238363	13239331	968	False	760.000000	760	80.840000	1743	2717	1	chr1B.!!$F2	974
10	TraesCS1D01G021200	chr1B	12811848	12813525	1677	True	612.500000	789	81.391000	1743	3435	2	chr1B.!!$R5	1692
11	TraesCS1D01G021200	chr1B	13299290	13300010	720	True	544.000000	544	80.581000	449	1198	1	chr1B.!!$R3	749
12	TraesCS1D01G021200	chr1B	13339925	13340618	693	True	544.000000	544	81.077000	483	1198	1	chr1B.!!$R4	715
13	TraesCS1D01G021200	chr1A	10483181	10484957	1776	True	1639.000000	1639	83.557000	1741	3502	1	chr1A.!!$R1	1761
14	TraesCS1D01G021200	chr1A	482800556	482801522	966	False	1397.000000	1397	92.776000	3592	4556	1	chr1A.!!$F1	964
15	TraesCS1D01G021200	chr1A	10469751	10472812	3061	True	772.000000	1022	82.987000	273	3400	3	chr1A.!!$R2	3127
16	TraesCS1D01G021200	chr7D	533623013	533623988	975	True	1506.000000	1506	94.575000	3585	4556	1	chr7D.!!$R1	971
17	TraesCS1D01G021200	chr3D	15905199	15906062	863	False	1487.000000	1487	97.691000	3691	4556	1	chr3D.!!$F1	865
18	TraesCS1D01G021200	chr2D	5432498	5433458	960	True	1476.000000	1476	94.410000	3596	4556	1	chr2D.!!$R1	960
19	TraesCS1D01G021200	chr5B	334057191	334058146	955	False	1432.000000	1432	93.750000	3603	4556	1	chr5B.!!$F1	953
20	TraesCS1D01G021200	chr5B	640284047	640285011	964	False	1386.000000	1386	92.665000	3595	4556	1	chr5B.!!$F2	961
21	TraesCS1D01G021200	chr6B	607120540	607121520	980	False	1411.000000	1411	92.690000	3577	4556	1	chr6B.!!$F1	979
22	TraesCS1D01G021200	chr4A	735688477	735689444	967	True	1387.000000	1387	92.577000	3591	4556	1	chr4A.!!$R1	965
23	TraesCS1D01G021200	chr7A	34525209	34526178	969	False	1386.000000	1386	92.497000	3589	4556	1	chr7A.!!$F1	967

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	Hairpin	End Stability	Orientation
486	528	0.105760	TGGTGCCCACTGGTGAAATT	60.106	50.000	1.93	0.0	1.82	F
1970	3940	1.553248	TGGGACCATAAGAACTGTCCG	59.447	52.381	0.00	46.6	4.79	F
3285	6724	0.179059	TGGTGAAGTTGAAGCTGCGA	60.179	50.000	0.00	0.0	5.10	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
2120	4090	0.249363	GTCGTCCGCTATTTCCTCCC	60.249	60.0	0.00	0.00	4.30	R
3541	6995	0.106708	ACTTTTCACTCGCTCCAGCA	59.893	50.0	0.00	42.21	4.41	R
4525	7992	0.396811	GGGGATATCCGACACCCTTG	59.603	60.0	15.69	41.79	3.61	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
49	50	4.877251	TGTAATTACCCTGCCGTTATTGAC	59.123	41.667	13.01	0.00	0.00	3.18
90	91	2.096013	TGTGTGCGACGTTGAAAATTGA	59.904	40.909	7.08	0.00	0.00	2.57
101	102	7.216920	ACGTTGAAAATTGAAAGTAAACAGC	57.783	32.000	0.00	0.00	0.00	4.40
181	182	6.415702	CATTTTTCAAACAGAATGCACACTG	58.584	36.000	16.96	16.96	42.53	3.66
234	237	8.883731	GCTTGTATCTTAGATTGTGCTTTCTTA	58.116	33.333	0.00	0.00	0.00	2.10
247	250	2.831526	GCTTTCTTAAGGAAATGGGGCA	59.168	45.455	1.85	0.00	42.25	5.36
382	400	6.015180	ACATGGATTAACATTGCTCACTTGTT	60.015	34.615	0.00	0.00	37.37	2.83
486	528	0.105760	TGGTGCCCACTGGTGAAATT	60.106	50.000	1.93	0.00	0.00	1.82
517	559	2.043652	CCAAGGGTGCAGATGGGG	60.044	66.667	0.00	0.00	0.00	4.96
561	604	2.889988	CGCATTCGGACGATGGCA	60.890	61.111	15.11	0.00	0.00	4.92
652	697	5.250543	TCAGATCAACCTACCCAAGAATTCA	59.749	40.000	8.44	0.00	0.00	2.57
683	728	4.815108	GTGGGGAATGGGCGGTCC	62.815	72.222	0.00	0.00	0.00	4.46
913	961	5.534207	TGCAAAATTGATGAAGGAGTTGT	57.466	34.783	0.00	0.00	0.00	3.32
914	962	5.916318	TGCAAAATTGATGAAGGAGTTGTT	58.084	33.333	0.00	0.00	0.00	2.83
987	1035	5.121105	TCTAATGCAGAGTGGAACATGATG	58.879	41.667	0.00	0.00	44.52	3.07
988	1036	3.639672	ATGCAGAGTGGAACATGATGA	57.360	42.857	0.00	0.00	44.52	2.92
989	1037	2.703416	TGCAGAGTGGAACATGATGAC	58.297	47.619	0.00	0.00	44.52	3.06
990	1038	2.303890	TGCAGAGTGGAACATGATGACT	59.696	45.455	0.00	0.00	44.52	3.41
991	1039	2.935201	GCAGAGTGGAACATGATGACTC	59.065	50.000	0.00	1.46	44.52	3.36
992	1040	3.369261	GCAGAGTGGAACATGATGACTCT	60.369	47.826	8.27	8.27	44.52	3.24
993	1041	4.468765	AGAGTGGAACATGATGACTCTG	57.531	45.455	12.13	0.00	44.52	3.35
994	1042	2.935201	GAGTGGAACATGATGACTCTGC	59.065	50.000	0.00	0.00	44.52	4.26
995	1043	2.303890	AGTGGAACATGATGACTCTGCA	59.696	45.455	0.00	0.00	44.52	4.41
996	1044	3.054582	AGTGGAACATGATGACTCTGCAT	60.055	43.478	0.00	0.00	44.52	3.96
997	1045	3.693085	GTGGAACATGATGACTCTGCATT	59.307	43.478	0.00	0.00	44.52	3.56

Showing 1 to 25 of 165 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
5	6	4.220602	ACAGGGACCAAACAATATTGCTTC	59.779	41.667	15.48	4.88	0.00	3.86
49	50	2.281070	ACGGGTGCTGCTTCACTG	60.281	61.111	0.00	0.00	37.16	3.66
146	147	8.458573	TCTGTTTGAAAAATGCTAACCTAGAA	57.541	30.769	0.00	0.00	0.00	2.10
163	164	2.780065	GCAGTGTGCATTCTGTTTGA	57.220	45.000	17.84	0.00	44.26	2.69
181	182	4.113354	GCACACAGGTTACTACTCATAGC	58.887	47.826	0.00	0.00	30.75	2.97
348	356	6.678900	GCAATGTTAATCCATGTTGAGAGACC	60.679	42.308	0.00	0.00	0.00	3.85
382	400	3.175438	TCCATCTTGAGAGACCTGTGA	57.825	47.619	0.00	0.00	33.99	3.58
416	434	2.412847	CGGTTTGAGCTTGATTCCGTTC	60.413	50.000	9.13	0.00	33.20	3.95
486	528	1.699634	CCCTTGGACTGGTCTTCTGAA	59.300	52.381	0.67	0.00	0.00	3.02
561	604	3.416156	GTGAGATTCCTCCAAAGCAGTT	58.584	45.455	0.00	0.00	38.66	3.16
652	697	0.401738	CCCCACACAGTGATCACCTT	59.598	55.000	22.21	6.61	35.23	3.50
683	728	3.396260	TGACTAGAGTGGTTTTTCCCG	57.604	47.619	0.00	0.00	34.77	5.14
720	765	5.129634	TCAAACATGGCACTAAGTTCTTGA	58.870	37.500	0.00	0.00	0.00	3.02
895	943	6.494835	AGCCTTAACAACTCCTTCATCAATTT	59.505	34.615	0.00	0.00	0.00	1.82
913	961	7.162082	CACCTCTTTCTTTCTCTAAGCCTTAA	58.838	38.462	0.00	0.00	33.66	1.85
914	962	6.702329	CACCTCTTTCTTTCTCTAAGCCTTA	58.298	40.000	0.00	0.00	33.66	2.69
987	1035	7.976135	AATTGGTATCATCTAATGCAGAGTC	57.024	36.000	0.00	0.00	36.48	3.36
988	1036	8.757982	AAAATTGGTATCATCTAATGCAGAGT	57.242	30.769	0.00	0.00	36.48	3.24
989	1037	8.295288	GGAAAATTGGTATCATCTAATGCAGAG	58.705	37.037	0.00	0.00	36.48	3.35
990	1038	7.779326	TGGAAAATTGGTATCATCTAATGCAGA	59.221	33.333	0.00	0.00	37.79	4.26
991	1039	7.944061	TGGAAAATTGGTATCATCTAATGCAG	58.056	34.615	0.00	0.00	0.00	4.41
992	1040	7.894753	TGGAAAATTGGTATCATCTAATGCA	57.105	32.000	0.00	0.00	0.00	3.96
993	1041	7.816031	CCATGGAAAATTGGTATCATCTAATGC	59.184	37.037	5.56	0.00	0.00	3.56
994	1042	9.081204	TCCATGGAAAATTGGTATCATCTAATG	57.919	33.333	13.46	0.00	34.48	1.90
995	1043	9.659135	TTCCATGGAAAATTGGTATCATCTAAT	57.341	29.630	25.13	0.00	34.48	1.73

Showing 1 to 25 of 170 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.