AutoCloner

Multiple sequence alignment - TraesCS1A01G362000

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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	TraesCS1A01G362000	chr1A	100.000	4031	0	0	1	4031	542440997	542436967	0.000000e+00	7444.0
1	TraesCS1A01G362000	chr1A	88.076	2734	266	35	747	3441	499623889	499621177	0.000000e+00	3188.0
2	TraesCS1A01G362000	chr1A	94.340	106	6	0	594	699	498400937	498400832	3.220000e-36	163.0
3	TraesCS1A01G362000	chr1D	97.512	3376	58	10	677	4031	446708324	446704954	0.000000e+00	5746.0
4	TraesCS1A01G362000	chr1D	88.037	2725	273	28	747	3441	403948356	403945655	0.000000e+00	3177.0
5	TraesCS1A01G362000	chr1D	97.585	207	5	0	406	612	446708747	446708541	4.960000e-94	355.0
6	TraesCS1A01G362000	chr1B	96.858	3374	68	11	674	4031	611523197	611526548	0.000000e+00	5609.0
7	TraesCS1A01G362000	chr1B	88.281	2722	267	35	747	3441	543469009	543466313	0.000000e+00	3212.0
8	TraesCS1A01G362000	chr1B	94.551	624	19	3	1	609	611522354	611522977	0.000000e+00	950.0
9	TraesCS1A01G362000	chr1B	75.920	299	43	15	3500	3786	543466315	543466034	4.230000e-25	126.0
10	TraesCS1A01G362000	chr3D	78.012	1469	297	20	1502	2957	442040140	442041595	0.000000e+00	900.0
11	TraesCS1A01G362000	chr3D	96.842	95	3	0	596	690	135534095	135534001	4.170000e-35	159.0
12	TraesCS1A01G362000	chr3B	77.301	1467	311	17	1502	2957	579284921	579286376	0.000000e+00	845.0
13	TraesCS1A01G362000	chr3B	77.301	1467	311	17	1502	2957	579301578	579303033	0.000000e+00	845.0
14	TraesCS1A01G362000	chr3B	94.898	98	5	0	592	689	556644797	556644700	1.940000e-33	154.0
15	TraesCS1A01G362000	chr5A	97.849	93	2	0	593	685	612226844	612226752	1.160000e-35	161.0
16	TraesCS1A01G362000	chr7A	96.842	95	2	1	599	692	173487650	173487556	1.500000e-34	158.0
17	TraesCS1A01G362000	chr2D	96.809	94	3	0	593	686	192312610	192312703	1.500000e-34	158.0
18	TraesCS1A01G362000	chr5B	94.949	99	4	1	595	692	26770409	26770507	1.940000e-33	154.0
19	TraesCS1A01G362000	chr5B	94.444	54	1	2	1250	1301	429846290	429846237	9.290000e-12	82.4
20	TraesCS1A01G362000	chr3A	94.949	99	4	1	587	685	269549829	269549732	1.940000e-33	154.0
21	TraesCS1A01G362000	chr6A	92.453	106	6	2	599	702	478526474	478526369	2.510000e-32	150.0
22	TraesCS1A01G362000	chr2B	94.444	54	1	2	1250	1301	36363415	36363362	9.290000e-12	82.4

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	TraesCS1A01G362000	chr1A	542436967	542440997	4030	True	7444.0	7444	100.0000	1	4031	1	chr1A.!!$R3	4030
1	TraesCS1A01G362000	chr1A	499621177	499623889	2712	True	3188.0	3188	88.0760	747	3441	1	chr1A.!!$R2	2694
2	TraesCS1A01G362000	chr1D	403945655	403948356	2701	True	3177.0	3177	88.0370	747	3441	1	chr1D.!!$R1	2694
3	TraesCS1A01G362000	chr1D	446704954	446708747	3793	True	3050.5	5746	97.5485	406	4031	2	chr1D.!!$R2	3625
4	TraesCS1A01G362000	chr1B	611522354	611526548	4194	False	3279.5	5609	95.7045	1	4031	2	chr1B.!!$F1	4030
5	TraesCS1A01G362000	chr1B	543466034	543469009	2975	True	1669.0	3212	82.1005	747	3786	2	chr1B.!!$R1	3039
6	TraesCS1A01G362000	chr3D	442040140	442041595	1455	False	900.0	900	78.0120	1502	2957	1	chr3D.!!$F1	1455
7	TraesCS1A01G362000	chr3B	579284921	579286376	1455	False	845.0	845	77.3010	1502	2957	1	chr3B.!!$F1	1455
8	TraesCS1A01G362000	chr3B	579301578	579303033	1455	False	845.0	845	77.3010	1502	2957	1	chr3B.!!$F2	1455

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	Hairpin	End Stability	Orientation
204	220	1.740296	CTACCGCCAACGAACCTGG	60.740	63.158	43.93	4.45	F
888	1063	2.639839	ACATGCAGTACTTTCTCCAGGT	59.360	45.455	0.00	4.00	F
1217	1393	3.560025	GGATCATTCACCACCTTCAGTGT	60.560	47.826	45.74	3.55	F
2848	3027	0.890683	CAGTTGCTCCCCAAATGTCC	59.109	55.000	42.78	4.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1217	1393	2.598000	CGAAAAACCATTCGCGGTAA	57.402	45.000	6.13	0.00	44.69	2.85	R
2213	2392	2.567169	AGACACACTGGGATCGATTCAA	59.433	45.455	5.94	0.00	0.00	2.69	R
2987	3166	1.078143	GATCCACACAGGCAGGTCC	60.078	63.158	0.00	0.00	37.29	4.46	R
3782	4016	0.250684	TCTGAACAAATGGCGAGGCA	60.251	50.000	0.88	0.88	0.00	4.75	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	3.386768	TTAGAAGCAGCCCGATATCAC	57.613	47.619	3.12	0.00	0.00	3.06
77	78	4.537015	CATTTGTCGTCTTTCTTTCCCAC	58.463	43.478	0.00	0.00	0.00	4.61
87	102	2.426431	TCTTTCCCACCCACCTCTTA	57.574	50.000	0.00	0.00	0.00	2.10
202	218	2.212110	ACCTACCGCCAACGAACCT	61.212	57.895	0.00	0.00	43.93	3.50
204	220	1.740296	CTACCGCCAACGAACCTGG	60.740	63.158	0.00	0.00	43.93	4.45
212	228	3.530910	AACGAACCTGGCCCTGTCG	62.531	63.158	0.00	7.00	0.00	4.35
217	233	2.742372	CCTGGCCCTGTCGTTTCG	60.742	66.667	0.00	0.00	0.00	3.46
308	324	8.041323	AGGATTATTGTGTAGTGGAACAGTTAG	58.959	37.037	0.00	0.00	40.27	2.34
368	384	5.735285	TGTTATGCAACCCAAATCATGAA	57.265	34.783	0.00	0.00	33.41	2.57
502	518	4.081420	AGTTAGTGTTATCCAGCTGTCCTG	60.081	45.833	13.81	0.00	41.41	3.86
604	620	6.313164	GGTCCAATGCTACTTGTTTAGTACTC	59.687	42.308	0.00	0.00	38.33	2.59
609	625	5.331069	TGCTACTTGTTTAGTACTCCCTCT	58.669	41.667	0.00	0.00	38.33	3.69
612	628	6.376581	GCTACTTGTTTAGTACTCCCTCTGTA	59.623	42.308	0.00	0.00	38.33	2.74
613	629	7.094032	GCTACTTGTTTAGTACTCCCTCTGTAA	60.094	40.741	0.00	0.00	38.33	2.41
614	630	7.607615	ACTTGTTTAGTACTCCCTCTGTAAA	57.392	36.000	0.00	0.00	34.56	2.01
616	632	7.289549	ACTTGTTTAGTACTCCCTCTGTAAACT	59.710	37.037	0.00	0.00	34.56	2.66
617	633	8.710749	TTGTTTAGTACTCCCTCTGTAAACTA	57.289	34.615	0.00	0.00	33.48	2.24
618	634	8.710749	TGTTTAGTACTCCCTCTGTAAACTAA	57.289	34.615	0.00	0.00	33.48	2.24
628	644	7.883217	TCCCTCTGTAAACTAATATAAGAGCG	58.117	38.462	0.00	0.00	0.00	5.03
629	645	7.504911	TCCCTCTGTAAACTAATATAAGAGCGT	59.495	37.037	0.00	0.00	0.00	5.07
646	662	9.953697	ATAAGAGCGTTTAGATCACTACTTTAG	57.046	33.333	0.00	0.00	37.82	1.85
648	664	8.503458	AGAGCGTTTAGATCACTACTTTAGTA	57.497	34.615	0.00	0.00	37.82	1.82
649	665	8.954350	AGAGCGTTTAGATCACTACTTTAGTAA	58.046	33.333	0.00	0.00	37.82	2.24
651	667	9.733219	AGCGTTTAGATCACTACTTTAGTAATC	57.267	33.333	0.00	0.00	37.23	1.75
652	668	9.733219	GCGTTTAGATCACTACTTTAGTAATCT	57.267	33.333	4.72	4.72	37.23	2.40
888	1063	2.639839	ACATGCAGTACTTTCTCCAGGT	59.360	45.455	0.00	0.00	0.00	4.00
1217	1393	3.560025	GGATCATTCACCACCTTCAGTGT	60.560	47.826	0.00	0.00	45.74	3.55
2213	2392	2.964209	ACGTGACCTATCATCTGGGAT	58.036	47.619	0.00	0.00	37.14	3.85
2848	3027	0.890683	CAGTTGCTCCCCAAATGTCC	59.109	55.000	0.00	0.00	42.78	4.02
2987	3166	2.665165	AGAGACCAGTCATAGAGCCAG	58.335	52.381	0.00	0.00	0.00	4.85
3039	3235	7.040340	TGTCGTGGGTTATTTTGATGTACATTT	60.040	33.333	10.30	0.00	0.00	2.32
3047	3243	8.921670	GTTATTTTGATGTACATTTTGGTGGAC	58.078	33.333	10.30	0.58	33.38	4.02
3091	3287	6.319911	GCTAGGTAAGATTCTTTGCCTGATTT	59.680	38.462	22.24	7.53	42.23	2.17
3322	3530	8.486210	ACCGCATATGTATAATTGATGATAGGT	58.514	33.333	4.29	0.00	0.00	3.08
3350	3564	5.468072	CACAACTCTAGTCTTGAAATGCTGT	59.532	40.000	8.55	0.00	0.00	4.40
3355	3569	7.390027	ACTCTAGTCTTGAAATGCTGTGTAAT	58.610	34.615	0.00	0.00	0.00	1.89
3364	3578	9.277565	CTTGAAATGCTGTGTAATACATGTTAC	57.722	33.333	2.30	1.74	38.92	2.50
3365	3579	8.560355	TGAAATGCTGTGTAATACATGTTACT	57.440	30.769	2.30	0.00	38.92	2.24
3366	3580	9.008965	TGAAATGCTGTGTAATACATGTTACTT	57.991	29.630	2.30	0.00	38.92	2.24
3367	3581	9.840427	GAAATGCTGTGTAATACATGTTACTTT	57.160	29.630	2.30	0.00	38.92	2.66
3419	3633	7.093902	TGTGTTTATACTAGCTACAGCAGAAGT	60.094	37.037	3.70	6.57	45.16	3.01
3421	3635	8.404000	TGTTTATACTAGCTACAGCAGAAGTAC	58.596	37.037	3.70	0.00	45.16	2.73
3486	3700	5.066593	GGGATTAGAACATCCACCATCTTC	58.933	45.833	2.23	0.00	44.36	2.87
3557	3771	3.862267	CGCATTTTTGGATTAATTGCGGA	59.138	39.130	16.74	0.00	44.77	5.54
3772	4006	1.404391	GCTGAGACAGAATGCCCATTG	59.596	52.381	2.81	0.00	42.53	2.82
3774	4008	0.743097	GAGACAGAATGCCCATTGCC	59.257	55.000	0.00	0.00	42.53	4.52
3775	4009	1.033746	AGACAGAATGCCCATTGCCG	61.034	55.000	0.00	0.00	42.53	5.69
3776	4010	1.304381	ACAGAATGCCCATTGCCGT	60.304	52.632	0.00	0.00	42.53	5.68
3777	4011	1.140161	CAGAATGCCCATTGCCGTG	59.860	57.895	0.00	0.00	40.16	4.94
3778	4012	1.304381	AGAATGCCCATTGCCGTGT	60.304	52.632	0.00	0.00	40.16	4.49
3779	4013	0.899717	AGAATGCCCATTGCCGTGTT	60.900	50.000	0.00	0.00	40.16	3.32
3782	4016	1.484038	ATGCCCATTGCCGTGTTATT	58.516	45.000	0.00	0.00	40.16	1.40
3859	4097	3.251729	TGCTGCAAATCTGTCTTGTCTTC	59.748	43.478	0.00	0.00	0.00	2.87

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
15	16	5.246203	AGTGATATCGGGCTGCTTCTAATAA	59.754	40.000	0.00	0.00	0.00	1.40
25	26	0.035458	GGGGAAGTGATATCGGGCTG	59.965	60.000	0.00	0.00	0.00	4.85
77	78	4.141937	TGTCGATTGAAGATAAGAGGTGGG	60.142	45.833	0.00	0.00	0.00	4.61
87	102	4.080919	TGTTGGAGGATGTCGATTGAAGAT	60.081	41.667	0.00	0.00	0.00	2.40
135	150	4.829492	AGGAGACATTGGAAAAACTGAAGG	59.171	41.667	0.00	0.00	0.00	3.46
192	208	2.672996	CAGGGCCAGGTTCGTTGG	60.673	66.667	6.18	0.00	38.78	3.77
202	218	0.748729	AAAACGAAACGACAGGGCCA	60.749	50.000	6.18	0.00	0.00	5.36
204	220	3.930400	AAAAACGAAACGACAGGGC	57.070	47.368	0.00	0.00	0.00	5.19
308	324	5.278808	GGTTTCACCACAATTTTAGTCCTCC	60.279	44.000	0.00	0.00	38.42	4.30
492	508	2.237143	TGGAAGAATACCAGGACAGCTG	59.763	50.000	13.48	13.48	33.22	4.24
502	518	7.445945	ACTAGCACTGATAATGGAAGAATACC	58.554	38.462	0.00	0.00	0.00	2.73
604	620	7.659186	ACGCTCTTATATTAGTTTACAGAGGG	58.341	38.462	8.36	8.36	42.53	4.30
622	638	7.828712	ACTAAAGTAGTGATCTAAACGCTCTT	58.171	34.615	0.00	0.00	37.69	2.85
623	639	7.393841	ACTAAAGTAGTGATCTAAACGCTCT	57.606	36.000	0.00	0.00	37.69	4.09
625	641	9.733219	GATTACTAAAGTAGTGATCTAAACGCT	57.267	33.333	11.11	0.00	44.10	5.07
655	671	9.710818	TCCCTCTGTAAACTAATATAAGAGTGT	57.289	33.333	0.00	0.00	0.00	3.55
657	673	9.939424	ACTCCCTCTGTAAACTAATATAAGAGT	57.061	33.333	0.00	0.00	0.00	3.24
663	679	8.871125	CCATGTACTCCCTCTGTAAACTAATAT	58.129	37.037	0.00	0.00	0.00	1.28
664	680	8.063153	TCCATGTACTCCCTCTGTAAACTAATA	58.937	37.037	0.00	0.00	0.00	0.98
666	682	6.258354	TCCATGTACTCCCTCTGTAAACTAA	58.742	40.000	0.00	0.00	0.00	2.24
669	685	5.416271	TTCCATGTACTCCCTCTGTAAAC	57.584	43.478	0.00	0.00	0.00	2.01
670	686	4.469945	CCTTCCATGTACTCCCTCTGTAAA	59.530	45.833	0.00	0.00	0.00	2.01
671	687	4.030913	CCTTCCATGTACTCCCTCTGTAA	58.969	47.826	0.00	0.00	0.00	2.41
672	688	3.271225	TCCTTCCATGTACTCCCTCTGTA	59.729	47.826	0.00	0.00	0.00	2.74
680	851	5.904362	AAAGCATTTCCTTCCATGTACTC	57.096	39.130	0.00	0.00	27.08	2.59
720	891	6.667414	ACCATAATTGCCCTTTGAGAATTACA	59.333	34.615	0.00	0.00	0.00	2.41
888	1063	4.462483	GTGAATCCTTAAGCATGGTTCCAA	59.538	41.667	14.50	2.96	0.00	3.53
1191	1367	4.478203	TGAAGGTGGTGAATGATCCAAAA	58.522	39.130	0.00	0.00	35.38	2.44
1217	1393	2.598000	CGAAAAACCATTCGCGGTAA	57.402	45.000	6.13	0.00	44.69	2.85
2213	2392	2.567169	AGACACACTGGGATCGATTCAA	59.433	45.455	5.94	0.00	0.00	2.69
2987	3166	1.078143	GATCCACACAGGCAGGTCC	60.078	63.158	0.00	0.00	37.29	4.46
3047	3243	2.093869	AGCTTATTGGCTTGCATGTTGG	60.094	45.455	1.14	0.00	39.86	3.77
3091	3287	5.657826	ATACATTGGCAATACAGCAAACA	57.342	34.783	13.23	0.00	35.83	2.83
3265	3472	8.629158	TGTTCTTACAGCACTTTGTGATAAAAT	58.371	29.630	1.52	0.00	35.23	1.82
3322	3530	6.147821	GCATTTCAAGACTAGAGTTGTGCTTA	59.852	38.462	0.00	0.00	0.00	3.09
3355	3569	9.603921	GCTATGGGTAAAGTAAAGTAACATGTA	57.396	33.333	0.00	0.00	0.00	2.29
3364	3578	5.066505	CAGCTTGGCTATGGGTAAAGTAAAG	59.933	44.000	0.00	0.00	36.40	1.85
3365	3579	4.947388	CAGCTTGGCTATGGGTAAAGTAAA	59.053	41.667	0.00	0.00	36.40	2.01
3366	3580	4.523083	CAGCTTGGCTATGGGTAAAGTAA	58.477	43.478	0.00	0.00	36.40	2.24
3367	3581	3.684413	GCAGCTTGGCTATGGGTAAAGTA	60.684	47.826	0.00	0.00	36.40	2.24
3368	3582	2.945890	GCAGCTTGGCTATGGGTAAAGT	60.946	50.000	0.00	0.00	36.40	2.66
3369	3583	1.678101	GCAGCTTGGCTATGGGTAAAG	59.322	52.381	0.00	0.00	36.40	1.85
3419	3633	0.322456	ATGCAGAAAGCCAAGCCGTA	60.322	50.000	0.00	0.00	44.83	4.02
3421	3635	1.138247	GATGCAGAAAGCCAAGCCG	59.862	57.895	0.00	0.00	44.83	5.52
3473	3687	5.221342	GGTAGTACTCAGAAGATGGTGGATG	60.221	48.000	0.00	0.00	0.00	3.51
3486	3700	7.633193	ACTACTTTGAGATGGTAGTACTCAG	57.367	40.000	0.00	0.00	42.61	3.35
3772	4006	2.403586	GCGAGGCAATAACACGGC	59.596	61.111	0.00	0.00	0.00	5.68
3774	4008	0.732571	AATGGCGAGGCAATAACACG	59.267	50.000	2.86	0.00	0.00	4.49
3775	4009	2.094752	ACAAATGGCGAGGCAATAACAC	60.095	45.455	2.86	0.00	0.00	3.32
3776	4010	2.166829	ACAAATGGCGAGGCAATAACA	58.833	42.857	2.86	0.00	0.00	2.41
3777	4011	2.939460	ACAAATGGCGAGGCAATAAC	57.061	45.000	2.86	0.00	0.00	1.89
3778	4012	2.822561	TGAACAAATGGCGAGGCAATAA	59.177	40.909	2.86	0.00	0.00	1.40
3779	4013	2.423185	CTGAACAAATGGCGAGGCAATA	59.577	45.455	2.86	0.00	0.00	1.90
3782	4016	0.250684	TCTGAACAAATGGCGAGGCA	60.251	50.000	0.88	0.88	0.00	4.75
3812	4050	5.328886	ACATACATCAATACACGCAATCG	57.671	39.130	0.00	0.00	42.43	3.34

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.