AutoCloner

Multiple sequence alignment - TraesCS4B01G333300

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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	TraesCS4B01G333300	chr4B	100.000	3823	0	0	1	3823	623784824	623788646	0.000000e+00	7060
1	TraesCS4B01G333300	chr4B	94.714	3443	159	16	388	3823	623644428	623647854	0.000000e+00	5328
2	TraesCS4B01G333300	chr4B	78.650	1096	192	29	2103	3178	623954525	623953452	0.000000e+00	689
3	TraesCS4B01G333300	chr4B	94.828	348	15	3	2	346	623644085	623644432	1.210000e-149	540
4	TraesCS4B01G333300	chr4B	75.753	697	115	38	1042	1695	623955624	623954939	6.210000e-78	302
5	TraesCS4B01G333300	chr4B	77.979	386	83	2	2442	2826	624529129	624529513	1.370000e-59	241
6	TraesCS4B01G333300	chr4B	77.681	345	59	15	1094	1430	623654666	623655000	1.080000e-45	195
7	TraesCS4B01G333300	chr4D	92.148	3859	199	41	1	3823	487873551	487877341	0.000000e+00	5352
8	TraesCS4B01G333300	chr4D	77.952	1279	222	38	1923	3179	488172652	488173892	0.000000e+00	745
9	TraesCS4B01G333300	chr4D	79.299	942	163	24	1896	2824	488034321	488035243	6.970000e-177	630
10	TraesCS4B01G333300	chr4D	78.448	464	71	22	1036	1479	488171716	488172170	3.760000e-70	276
11	TraesCS4B01G333300	chr7A	88.120	2845	224	47	1031	3823	621311375	621314157	0.000000e+00	3277
12	TraesCS4B01G333300	chr7A	87.765	1038	110	15	1	1029	621307556	621308585	0.000000e+00	1197
13	TraesCS4B01G333300	chr7B	88.908	2281	181	37	1605	3823	582937524	582939794	0.000000e+00	2745
14	TraesCS4B01G333300	chr7B	85.560	1018	127	16	1	1009	582933250	582934256	0.000000e+00	1048
15	TraesCS4B01G333300	chr7B	89.628	511	46	4	1031	1539	582937018	582937523	0.000000e+00	643
16	TraesCS4B01G333300	chr7D	88.351	2292	178	32	1605	3823	539949797	539952072	0.000000e+00	2671
17	TraesCS4B01G333300	chr7D	86.457	1019	122	13	1	1009	539945307	539946319	0.000000e+00	1103
18	TraesCS4B01G333300	chr7D	88.889	513	47	7	1031	1539	539949290	539949796	1.170000e-174	623
19	TraesCS4B01G333300	chr5A	78.830	855	143	24	2193	3039	669740996	669741820	3.360000e-150	542
20	TraesCS4B01G333300	chr5A	77.778	387	82	4	2442	2826	669987142	669987526	6.380000e-58	235
21	TraesCS4B01G333300	chr5A	82.090	201	33	3	1037	1235	670081701	670081900	6.570000e-38	169

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	TraesCS4B01G333300	chr4B	623784824	623788646	3822	False	7060.000000	7060	100.0000	1	3823	1	chr4B.!!$F2	3822
1	TraesCS4B01G333300	chr4B	623644085	623647854	3769	False	2934.000000	5328	94.7710	2	3823	2	chr4B.!!$F4	3821
2	TraesCS4B01G333300	chr4B	623953452	623955624	2172	True	495.500000	689	77.2015	1042	3178	2	chr4B.!!$R1	2136
3	TraesCS4B01G333300	chr4D	487873551	487877341	3790	False	5352.000000	5352	92.1480	1	3823	1	chr4D.!!$F1	3822
4	TraesCS4B01G333300	chr4D	488034321	488035243	922	False	630.000000	630	79.2990	1896	2824	1	chr4D.!!$F2	928
5	TraesCS4B01G333300	chr4D	488171716	488173892	2176	False	510.500000	745	78.2000	1036	3179	2	chr4D.!!$F3	2143
6	TraesCS4B01G333300	chr7A	621307556	621314157	6601	False	2237.000000	3277	87.9425	1	3823	2	chr7A.!!$F1	3822
7	TraesCS4B01G333300	chr7B	582933250	582939794	6544	False	1478.666667	2745	88.0320	1	3823	3	chr7B.!!$F1	3822
8	TraesCS4B01G333300	chr7D	539945307	539952072	6765	False	1465.666667	2671	87.8990	1	3823	3	chr7D.!!$F1	3822
9	TraesCS4B01G333300	chr5A	669740996	669741820	824	False	542.000000	542	78.8300	2193	3039	1	chr5A.!!$F1	846

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
381	386	3.632145	CACCCACCAAGCCAAATAGATAC	59.368	47.826	0.00	0.00	0.00	2.24	F
1062	4057	1.401761	TCTTGCAGTTTGTGGCACAT	58.598	45.000	22.73	3.32	44.52	3.21	F
1528	4561	3.495331	TGGACATGTGCAAAGTTACCAT	58.505	40.909	18.56	0.00	0.00	3.55	F
2629	5754	0.251742	CCAACTCCTCCAATGGGCAA	60.252	55.000	0.00	0.00	0.00	4.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1825	4903	0.885196	GGCAAGCCACGGTTTATGAA	59.115	50.000	6.14	0.00	35.81	2.57	R
2146	5265	0.987294	AGTCCATGTTGTAGCAGCCT	59.013	50.000	0.00	0.00	0.00	4.58	R
2659	5784	1.006832	GTCTGTGAATAATGCGGCGT	58.993	50.000	9.37	0.00	0.00	5.68	R
3643	6786	1.126846	CACGAAGATGGCGTCTGAAAC	59.873	52.381	10.56	2.15	40.44	2.78	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
210	214	6.921914	TGACATGTTCACAAATATGAATGCA	58.078	32.000	0.00	0.00	40.60	3.96
218	222	8.752254	GTTCACAAATATGAATGCAAGATGATG	58.248	33.333	0.00	0.00	40.60	3.07
381	386	3.632145	CACCCACCAAGCCAAATAGATAC	59.368	47.826	0.00	0.00	0.00	2.24
383	388	4.724798	ACCCACCAAGCCAAATAGATACTA	59.275	41.667	0.00	0.00	0.00	1.82
469	474	7.490657	TTTTAGTCTGAGGTAGCCTTCATAA	57.509	36.000	0.00	0.00	31.76	1.90
673	679	6.380560	TGAACATTAGCATGGATGGATTTTGA	59.619	34.615	0.00	0.00	34.27	2.69
843	850	4.929819	ACCCCAACAATTGTTAGTTGAC	57.070	40.909	22.87	0.00	46.01	3.18
850	857	4.839796	ACAATTGTTAGTTGACCGTTTCG	58.160	39.130	4.92	0.00	0.00	3.46
1002	1013	4.361451	CCACTGCTTTTGGCTAGTTATG	57.639	45.455	0.00	0.00	42.39	1.90
1033	4028	6.017770	TGGAAATTGTTAGTTACGTCACTTGG	60.018	38.462	7.85	0.00	0.00	3.61
1062	4057	1.401761	TCTTGCAGTTTGTGGCACAT	58.598	45.000	22.73	3.32	44.52	3.21
1203	4198	6.422333	TGCAGGACATGGTAATAAATCAAGA	58.578	36.000	0.00	0.00	0.00	3.02
1242	4238	4.468713	TGGCTGGCATGTAAGCATTATTA	58.531	39.130	19.26	1.23	41.36	0.98
1434	4448	5.957842	TCATATTTATTTGCGGGCTAAGG	57.042	39.130	0.00	0.00	0.00	2.69
1479	4499	4.574599	ACTTGTGCCATTTTTCTCTGAC	57.425	40.909	0.00	0.00	0.00	3.51
1528	4561	3.495331	TGGACATGTGCAAAGTTACCAT	58.505	40.909	18.56	0.00	0.00	3.55
1530	4563	4.699735	TGGACATGTGCAAAGTTACCATAG	59.300	41.667	18.56	0.00	0.00	2.23
1651	4692	5.473039	AGATGTTAACTTGCTGCCAAATTC	58.527	37.500	7.22	0.00	0.00	2.17
1681	4722	9.368674	CAACAAAGCATTTCATCCATATGTTTA	57.631	29.630	1.24	0.00	35.03	2.01
1884	4968	7.359431	CGAACCAATTCATTTGTTCTCCATTTG	60.359	37.037	12.30	0.00	34.14	2.32
2115	5234	5.897050	TCTAACCCACACACAAAAACAATC	58.103	37.500	0.00	0.00	0.00	2.67
2146	5265	8.833493	CAACAGAGAGATAATTATGATGCAACA	58.167	33.333	1.78	0.00	0.00	3.33
2309	5428	8.558700	GTGTTTCATCCTTTTTGTATGCATTTT	58.441	29.630	3.54	0.00	0.00	1.82
2327	5446	6.097981	TGCATTTTCATAGCCATGTTATTCCA	59.902	34.615	0.00	0.00	33.57	3.53
2395	5520	7.795482	TTACAACCTAATAATTGGTGGATCG	57.205	36.000	0.00	0.00	36.57	3.69
2486	5611	2.915869	AGAAGTGGAGATTGGTGGGTA	58.084	47.619	0.00	0.00	0.00	3.69
2598	5723	7.017055	GCAATTTGGTGCATTTGTTAAATCTC	58.983	34.615	0.00	0.00	44.29	2.75
2629	5754	0.251742	CCAACTCCTCCAATGGGCAA	60.252	55.000	0.00	0.00	0.00	4.52
2659	5784	2.595750	CCAAATGGTGGTAAGGGTCA	57.404	50.000	0.00	0.00	43.20	4.02
2668	5793	1.743995	GTAAGGGTCACGCCGCATT	60.744	57.895	0.00	0.00	38.44	3.56
2776	5901	3.716353	TGCCACTCTATCACCCATATTGT	59.284	43.478	0.00	0.00	0.00	2.71
2826	5951	6.495181	TCCTGGAGGTTGTATGAGATAAGATC	59.505	42.308	0.00	0.00	36.34	2.75
2943	6070	9.444600	CCTAAAGCTACACTATGAAAACCTTTA	57.555	33.333	0.00	0.00	0.00	1.85
2990	6117	7.043565	TCGTACTTAAATTGACCTAACCATCC	58.956	38.462	0.00	0.00	0.00	3.51
3003	6130	7.016268	TGACCTAACCATCCAAGGAGTTATATC	59.984	40.741	0.00	1.48	34.34	1.63
3030	6157	9.817809	GAATAGTTGTATGTTTAGATGTGAGGA	57.182	33.333	0.00	0.00	0.00	3.71
3199	6333	4.218200	CCTGAAATGAATTGGCAGTACACA	59.782	41.667	0.00	0.00	0.00	3.72
3318	6452	1.372501	AGGAGGGCCTACAACACATT	58.627	50.000	20.33	0.00	44.74	2.71
3336	6470	8.725148	CAACACATTAAGTTTTCTATCTCTGCT	58.275	33.333	0.00	0.00	0.00	4.24
3394	6528	1.133025	CACAAATGCTCGTTGGATCCC	59.867	52.381	9.90	0.00	0.00	3.85
3504	6642	1.555075	AGCAATACATGGTCGTGGTCT	59.445	47.619	0.00	0.00	33.56	3.85
3540	6678	9.772605	TCCCGGAGTTTCTATACCATATTAATA	57.227	33.333	0.73	0.00	0.00	0.98
3582	6721	6.020971	TGCGAATTCAACACTAACTCTCTA	57.979	37.500	6.22	0.00	0.00	2.43
3639	6782	0.744057	CACACGCCATCCATGCACTA	60.744	55.000	0.00	0.00	0.00	2.74
3643	6786	1.745087	ACGCCATCCATGCACTAAAAG	59.255	47.619	0.00	0.00	0.00	2.27
3660	6803	4.489679	AAAAGTTTCAGACGCCATCTTC	57.510	40.909	0.00	0.00	34.41	2.87
3712	6865	6.050432	TGTTTGTTTTCTACGGAGTACATGT	58.950	36.000	2.69	2.69	45.11	3.21
3734	6887	9.599866	CATGTCAGTTCAGTTATTACTCCATTA	57.400	33.333	0.00	0.00	30.26	1.90
3738	6891	9.817809	TCAGTTCAGTTATTACTCCATTATCAC	57.182	33.333	0.00	0.00	30.26	3.06

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
68	72	5.981088	ACTGAAAATGACATGCCATGTTA	57.019	34.783	12.36	8.41	45.03	2.41
210	214	8.677148	AGTGTTGTAGTTGTTTACATCATCTT	57.323	30.769	1.65	0.00	36.31	2.40
218	222	8.339714	TCAGCAATTAGTGTTGTAGTTGTTTAC	58.660	33.333	0.00	0.00	39.36	2.01
340	345	7.229106	GGTGGGTGTGTCTGTTTACTTTTATTA	59.771	37.037	0.00	0.00	0.00	0.98
343	348	4.883006	GGTGGGTGTGTCTGTTTACTTTTA	59.117	41.667	0.00	0.00	0.00	1.52
349	354	2.925724	CTTGGTGGGTGTGTCTGTTTA	58.074	47.619	0.00	0.00	0.00	2.01
560	565	0.235926	GAAGCTCAAACACGTGCTCC	59.764	55.000	17.22	0.00	34.78	4.70
637	643	8.533657	TCCATGCTAATGTTCAAATCATTCTTT	58.466	29.630	0.00	0.00	36.92	2.52
638	644	8.070034	TCCATGCTAATGTTCAAATCATTCTT	57.930	30.769	0.00	0.00	36.92	2.52
647	653	6.795144	AAATCCATCCATGCTAATGTTCAA	57.205	33.333	0.00	0.00	31.27	2.69
843	850	2.940147	TCAATTTTGATGGCGAAACGG	58.060	42.857	0.00	0.00	30.44	4.44
850	857	8.938906	ACATAAAGAACAATCAATTTTGATGGC	58.061	29.630	6.56	0.00	46.60	4.40
1002	1013	5.413523	ACGTAACTAACAATTTCCATGGGAC	59.586	40.000	13.02	0.00	0.00	4.46
1033	4028	3.054878	CAAACTGCAAGATGGAAGCAAC	58.945	45.455	0.00	0.00	37.89	4.17
1062	4057	8.059461	TCATTAGGACCTCTAGAATGTGTTAGA	58.941	37.037	12.44	0.00	0.00	2.10
1203	4198	4.456911	CCAGCCAACTTGATCGCATTATAT	59.543	41.667	0.00	0.00	0.00	0.86
1242	4238	2.176364	AGGCTATGTGCATGGGAAGAAT	59.824	45.455	0.00	0.00	45.15	2.40
1434	4448	2.952310	CCTAGTTTTCAAGGGGCATAGC	59.048	50.000	0.00	0.00	0.00	2.97
1548	4583	4.978099	AGAAGGAAATGAGCTCACTTGAA	58.022	39.130	20.97	0.00	0.00	2.69
1640	4681	2.747396	TGTTGATGGAATTTGGCAGC	57.253	45.000	0.00	0.00	0.00	5.25
1651	4692	4.823157	TGGATGAAATGCTTTGTTGATGG	58.177	39.130	0.00	0.00	34.76	3.51
1681	4722	2.698855	ATGAGCTACACGCAAAGGAT	57.301	45.000	0.00	0.00	42.61	3.24
1706	4755	9.255304	TCTGTAAAATTTTGTCCATAAACTTGC	57.745	29.630	13.76	0.00	0.00	4.01
1825	4903	0.885196	GGCAAGCCACGGTTTATGAA	59.115	50.000	6.14	0.00	35.81	2.57
1884	4968	2.885266	GTCAAGAAGGGGAGTTTCCAAC	59.115	50.000	0.00	0.00	38.64	3.77
1968	5069	1.683917	GAGGATGTGAGTCGCCATAGT	59.316	52.381	0.23	0.00	0.00	2.12
2080	5199	5.472137	TGTGTGGGTTAGAAACTTTCTATGC	59.528	40.000	11.30	8.06	41.58	3.14
2146	5265	0.987294	AGTCCATGTTGTAGCAGCCT	59.013	50.000	0.00	0.00	0.00	4.58
2309	5428	7.744733	TCATAAGTGGAATAACATGGCTATGA	58.255	34.615	17.90	0.00	37.73	2.15
2327	5446	7.487189	CGACCACGTAGTTAGATTTTCATAAGT	59.513	37.037	0.00	0.00	41.61	2.24
2486	5611	6.938030	TCGGGATTTTATTGAAGCCGTAATAT	59.062	34.615	0.00	0.00	35.95	1.28
2598	5723	3.243535	GGAGGAGTTGGAAGTGCTTTTTG	60.244	47.826	0.00	0.00	29.52	2.44
2659	5784	1.006832	GTCTGTGAATAATGCGGCGT	58.993	50.000	9.37	0.00	0.00	5.68
2668	5793	9.330063	GGTCAATGAATCTAATGTCTGTGAATA	57.670	33.333	0.00	0.00	0.00	1.75
3003	6130	8.755941	CCTCACATCTAAACATACAACTATTCG	58.244	37.037	0.00	0.00	0.00	3.34
3056	6183	3.056107	TCGTTACCATCCCACAAGAGAAG	60.056	47.826	0.00	0.00	0.00	2.85
3218	6352	3.520290	TCGTGGCACCTAAGAGTAATG	57.480	47.619	12.86	0.00	0.00	1.90
3229	6363	2.331451	GTGTTGCTTCGTGGCACC	59.669	61.111	12.86	0.00	42.27	5.01
3258	6392	5.508994	CCAAGTTTCTTCATTTTACCGCCTT	60.509	40.000	0.00	0.00	0.00	4.35
3318	6452	7.133891	GCAAACAGCAGAGATAGAAAACTTA	57.866	36.000	0.00	0.00	44.79	2.24
3466	6604	5.372343	TTGCTGGAATTAGGATCAAGCTA	57.628	39.130	4.69	0.00	43.09	3.32
3591	6734	5.895636	TGACAAAGAGAGTTTTTCTTGCA	57.104	34.783	0.00	0.00	35.87	4.08
3596	6739	6.919662	TGCATCAATGACAAAGAGAGTTTTTC	59.080	34.615	0.00	0.00	0.00	2.29
3639	6782	3.058914	CGAAGATGGCGTCTGAAACTTTT	60.059	43.478	10.56	0.00	37.23	2.27
3643	6786	1.126846	CACGAAGATGGCGTCTGAAAC	59.873	52.381	10.56	2.15	40.44	2.78
3674	6827	2.305928	ACAAACATGTGCCAACAGCTA	58.694	42.857	0.00	0.00	44.23	3.32
3712	6865	9.817809	GTGATAATGGAGTAATAACTGAACTGA	57.182	33.333	0.00	0.00	35.56	3.41
3734	6887	6.040166	GCTATTTGGACTCATTTGATGGTGAT	59.960	38.462	0.00	0.00	0.00	3.06
3738	6891	7.309012	CCATAGCTATTTGGACTCATTTGATGG	60.309	40.741	7.51	0.00	34.81	3.51

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.