AutoCloner

Multiple sequence alignment - TraesCS5B01G079500

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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	TraesCS5B01G079500	chr5B	100.000	3464	0	0	1	3464	96849637	96853100	0.000000e+00	6397.0
1	TraesCS5B01G079500	chr5D	93.875	1747	50	19	694	2397	91552335	91554067	0.000000e+00	2580.0
2	TraesCS5B01G079500	chr5D	97.326	1047	17	4	2411	3454	91554113	91555151	0.000000e+00	1768.0
3	TraesCS5B01G079500	chr5D	95.578	701	25	6	12	710	91551684	91552380	0.000000e+00	1118.0
4	TraesCS5B01G079500	chr5D	83.333	138	18	5	545	681	91411712	91411845	4.690000e-24	122.0
5	TraesCS5B01G079500	chr5A	93.580	1729	67	17	694	2386	85254875	85256595	0.000000e+00	2538.0
6	TraesCS5B01G079500	chr5A	93.982	565	24	8	1	564	85178319	85178874	0.000000e+00	846.0
7	TraesCS5B01G079500	chr5A	90.566	212	15	1	3258	3464	85257241	85257452	3.410000e-70	276.0
8	TraesCS5B01G079500	chr5A	94.702	151	5	3	560	710	85254772	85254919	7.480000e-57	231.0
9	TraesCS5B01G079500	chr5A	89.011	182	13	2	2616	2790	85256880	85257061	5.820000e-53	219.0
10	TraesCS5B01G079500	chr5A	81.857	237	31	8	17	248	28435831	28436060	4.560000e-44	189.0
11	TraesCS5B01G079500	chr5A	90.756	119	7	1	2411	2529	85256646	85256760	4.630000e-34	156.0
12	TraesCS5B01G079500	chr5A	85.315	143	16	4	540	681	85172088	85172226	3.600000e-30	143.0
13	TraesCS5B01G079500	chr5A	93.878	49	2	1	2549	2596	85256844	85256892	4.800000e-09	73.1
14	TraesCS5B01G079500	chr7B	83.036	224	22	16	36	248	325601484	325601266	4.560000e-44	189.0
15	TraesCS5B01G079500	chr7B	86.076	158	18	2	2798	2952	229095703	229095547	2.140000e-37	167.0
16	TraesCS5B01G079500	chr7D	87.919	149	17	1	2791	2939	34757011	34756864	1.280000e-39	174.0
17	TraesCS5B01G079500	chr7D	87.013	154	17	3	2791	2944	436459770	436459620	1.650000e-38	171.0
18	TraesCS5B01G079500	chr7D	86.250	160	18	4	2781	2937	535326655	535326813	1.650000e-38	171.0
19	TraesCS5B01G079500	chr2B	85.799	169	18	4	63	229	443416164	443416328	1.280000e-39	174.0
20	TraesCS5B01G079500	chr2B	85.057	174	20	4	58	229	121858264	121858433	4.600000e-39	172.0
21	TraesCS5B01G079500	chr2B	89.394	66	4	2	570	634	44900916	44900853	2.870000e-11	80.5
22	TraesCS5B01G079500	chr2B	100.000	29	0	0	2032	2060	632989201	632989229	2.000000e-03	54.7
23	TraesCS5B01G079500	chr4D	87.417	151	17	2	2791	2940	74079358	74079507	4.600000e-39	172.0
24	TraesCS5B01G079500	chr3A	87.417	151	18	1	2791	2941	582283222	582283371	4.600000e-39	172.0
25	TraesCS5B01G079500	chr3D	86.335	161	17	4	2780	2936	315480419	315480578	1.650000e-38	171.0
26	TraesCS5B01G079500	chr1D	85.380	171	17	5	61	229	345534997	345535161	1.650000e-38	171.0
27	TraesCS5B01G079500	chr1B	87.013	154	17	3	2785	2937	632021078	632020927	1.650000e-38	171.0
28	TraesCS5B01G079500	chr4B	83.511	188	23	5	61	245	321280884	321281066	5.950000e-38	169.0
29	TraesCS5B01G079500	chr4B	80.519	77	12	3	21	94	646673998	646673922	4.830000e-04	56.5
30	TraesCS5B01G079500	chr6A	83.246	191	21	6	61	245	224398671	224398856	7.690000e-37	165.0
31	TraesCS5B01G079500	chrUn	91.818	110	5	2	3120	3227	42246236	42246343	2.150000e-32	150.0
32	TraesCS5B01G079500	chr2A	87.879	66	7	1	570	635	30278553	30278617	3.710000e-10	76.8
33	TraesCS5B01G079500	chr2A	92.500	40	3	0	2021	2060	677547133	677547172	1.340000e-04	58.4
34	TraesCS5B01G079500	chr2D	100.000	29	0	0	2032	2060	533166294	533166322	2.000000e-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	TraesCS5B01G079500	chr5B	96849637	96853100	3463	False	6397.000000	6397	100.000000	1	3464	1	chr5B.!!$F1	3463
1	TraesCS5B01G079500	chr5D	91551684	91555151	3467	False	1822.000000	2580	95.593000	12	3454	3	chr5D.!!$F2	3442
2	TraesCS5B01G079500	chr5A	85178319	85178874	555	False	846.000000	846	93.982000	1	564	1	chr5A.!!$F3	563
3	TraesCS5B01G079500	chr5A	85254772	85257452	2680	False	582.183333	2538	92.082167	560	3464	6	chr5A.!!$F4	2904

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
827	835	0.392193	ATGCTCGAGTTTCCAGGCTG	60.392	55.0	15.13	7.75	0.00	4.85	F
1139	1175	0.896940	TCCGTCTACCGCTCCAAGTT	60.897	55.0	0.00	0.00	34.38	2.66	F
1311	1347	0.899720	TCGACCATAACCTCGCCTTT	59.100	50.0	0.00	0.00	0.00	3.11	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
1638	1674	0.787084	ACAACTCCTCCTCCTCCTCA	59.213	55.000	0.00	3.86	R
2403	2473	5.087323	ACTACCTGACAAGAATGAGAAGGA	58.913	41.667	32.18	3.36	R
3227	3403	2.184322	GATTCTCCGCTCCACGCA	59.816	61.111	41.76	5.24	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
96	97	1.553704	GACGTATCAACCTCCCCAAGT	59.446	52.381	0.00	0.00	0.00	3.16
186	188	9.357161	AGAGAGAGGTGTCGATAAACTAAATAT	57.643	33.333	0.00	0.00	0.00	1.28
430	432	6.788684	TGCCATCATGAAAGAAACATTTTG	57.211	33.333	0.00	0.00	0.00	2.44
691	694	1.133325	TGTGGGCTGCTTCCCTAAAAA	60.133	47.619	13.72	0.00	46.67	1.94
712	715	5.582689	AAAAACTATATGTGGGCTGCTTC	57.417	39.130	0.00	0.00	0.00	3.86
713	716	2.938956	ACTATATGTGGGCTGCTTCC	57.061	50.000	0.00	0.00	0.00	3.46
714	717	1.421646	ACTATATGTGGGCTGCTTCCC	59.578	52.381	0.00	6.87	46.73	3.97
715	718	1.701847	CTATATGTGGGCTGCTTCCCT	59.298	52.381	13.72	0.00	46.67	4.20
716	719	1.819753	ATATGTGGGCTGCTTCCCTA	58.180	50.000	13.72	5.06	46.67	3.53
717	720	1.590591	TATGTGGGCTGCTTCCCTAA	58.409	50.000	13.72	4.12	46.67	2.69
741	744	3.652057	AAACTATATGTGGGCTGCAGT	57.348	42.857	16.64	0.00	0.00	4.40
814	817	0.588233	GCTGCGTGAATGAATGCTCG	60.588	55.000	0.00	0.00	33.04	5.03
815	818	1.001624	CTGCGTGAATGAATGCTCGA	58.998	50.000	0.00	0.00	33.04	4.04
827	835	0.392193	ATGCTCGAGTTTCCAGGCTG	60.392	55.000	15.13	7.75	0.00	4.85
931	962	4.899239	CGACCATCTCCTGCGGCC	62.899	72.222	0.00	0.00	0.00	6.13
946	977	3.787001	GCCGGTAAGCTGCCTCCT	61.787	66.667	1.90	0.00	0.00	3.69
965	997	1.103987	TCTCCTCTCCTCGCATTCCG	61.104	60.000	0.00	0.00	38.61	4.30
1139	1175	0.896940	TCCGTCTACCGCTCCAAGTT	60.897	55.000	0.00	0.00	34.38	2.66
1197	1233	1.228124	CCACCGCAAGAAACTCCCA	60.228	57.895	0.00	0.00	43.02	4.37
1311	1347	0.899720	TCGACCATAACCTCGCCTTT	59.100	50.000	0.00	0.00	0.00	3.11
1332	1368	1.071385	CTGAAGGAATCTCCCGGGATG	59.929	57.143	27.07	18.30	37.19	3.51
1638	1674	6.721318	TGGTCATGATGATGATGATGATGAT	58.279	36.000	0.00	0.00	40.78	2.45
1658	1727	1.150135	TGAGGAGGAGGAGGAGTTGTT	59.850	52.381	0.00	0.00	0.00	2.83
1866	1935	2.089980	GGTCAGATTGCTGCTGTTGAT	58.910	47.619	0.00	0.00	42.01	2.57
1867	1936	2.159421	GGTCAGATTGCTGCTGTTGATG	60.159	50.000	0.00	0.00	42.01	3.07
2111	2180	2.221055	CAGGCGACACAAAAGACTACAC	59.779	50.000	0.00	0.00	0.00	2.90
2354	2424	7.785506	AGGTAGCAACTTGGTTAGATCTAGTAT	59.214	37.037	2.02	0.00	0.00	2.12
2397	2467	3.633525	CCATGGTTGGACTTGGATGTATG	59.366	47.826	2.57	0.00	46.92	2.39
2398	2468	4.525996	CATGGTTGGACTTGGATGTATGA	58.474	43.478	0.00	0.00	0.00	2.15
2400	2470	4.525996	TGGTTGGACTTGGATGTATGATG	58.474	43.478	0.00	0.00	0.00	3.07
2401	2471	4.018506	TGGTTGGACTTGGATGTATGATGT	60.019	41.667	0.00	0.00	0.00	3.06
2402	2472	5.190726	TGGTTGGACTTGGATGTATGATGTA	59.809	40.000	0.00	0.00	0.00	2.29
2403	2473	6.126507	TGGTTGGACTTGGATGTATGATGTAT	60.127	38.462	0.00	0.00	0.00	2.29
2404	2474	6.428159	GGTTGGACTTGGATGTATGATGTATC	59.572	42.308	0.00	0.00	0.00	2.24
2405	2475	6.114187	TGGACTTGGATGTATGATGTATCC	57.886	41.667	0.00	0.00	40.59	2.59
2407	2477	6.329986	TGGACTTGGATGTATGATGTATCCTT	59.670	38.462	9.98	0.00	40.77	3.36
2408	2478	6.876257	GGACTTGGATGTATGATGTATCCTTC	59.124	42.308	9.98	5.39	40.77	3.46
3176	3352	4.737855	TCTAAGAATGTGGAGTACCTGC	57.262	45.455	0.00	0.00	37.04	4.85
3181	3357	0.462581	ATGTGGAGTACCTGCATGCG	60.463	55.000	14.09	7.87	33.78	4.73
3185	3361	4.457496	AGTACCTGCATGCGCGCT	62.457	61.111	33.29	15.19	42.97	5.92
3186	3362	3.929948	GTACCTGCATGCGCGCTC	61.930	66.667	33.29	20.71	42.97	5.03
3187	3363	4.147449	TACCTGCATGCGCGCTCT	62.147	61.111	33.29	17.06	42.97	4.09

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
8	9	9.206870	AGTTATATTTCACTTTTTGGCACATTG	57.793	29.630	0.00	0.00	39.30	2.82
10	11	9.777297	AAAGTTATATTTCACTTTTTGGCACAT	57.223	25.926	0.00	0.00	39.69	3.21
96	97	1.695242	TGAGGGCAAACGAGGTCTAAA	59.305	47.619	0.00	0.00	0.00	1.85
123	125	4.038763	TGGTCATATTTATCGAGTTCGGCT	59.961	41.667	1.26	0.00	40.29	5.52
186	188	9.734984	ATAATGATTATGATGCTCTCATGTTCA	57.265	29.630	11.25	12.56	44.48	3.18
430	432	9.705290	ATTTTTGTATTAGACACATGGGAAAAC	57.295	29.630	0.00	0.00	37.96	2.43
435	437	8.137437	GGATCATTTTTGTATTAGACACATGGG	58.863	37.037	0.00	0.00	37.96	4.00
538	541	6.514947	GCATGGCAAGTTTTTATATCATGGA	58.485	36.000	0.00	0.00	33.50	3.41
549	552	0.317770	CGTGTCGCATGGCAAGTTTT	60.318	50.000	0.00	0.00	0.00	2.43
639	642	6.630444	ATTGTCATGGCAGATTCATAACTC	57.370	37.500	0.00	0.00	0.00	3.01
640	643	8.408601	GTTAATTGTCATGGCAGATTCATAACT	58.591	33.333	0.00	0.00	0.00	2.24
691	694	3.954258	GGAAGCAGCCCACATATAGTTTT	59.046	43.478	0.00	0.00	0.00	2.43
692	695	3.555966	GGAAGCAGCCCACATATAGTTT	58.444	45.455	0.00	0.00	0.00	2.66
693	696	3.214696	GGAAGCAGCCCACATATAGTT	57.785	47.619	0.00	0.00	0.00	2.24
694	697	2.938956	GGAAGCAGCCCACATATAGT	57.061	50.000	0.00	0.00	0.00	2.12
741	744	3.708236	AAAGCCCAGGACTAGGAGATA	57.292	47.619	0.00	0.00	0.00	1.98
799	802	3.484229	GGAAACTCGAGCATTCATTCACG	60.484	47.826	24.56	0.00	0.00	4.35
802	805	3.064545	CCTGGAAACTCGAGCATTCATTC	59.935	47.826	24.56	14.62	0.00	2.67
803	806	3.012518	CCTGGAAACTCGAGCATTCATT	58.987	45.455	24.56	6.00	0.00	2.57
814	817	0.034670	AGGATGCAGCCTGGAAACTC	60.035	55.000	25.67	0.00	36.76	3.01
815	818	0.034670	GAGGATGCAGCCTGGAAACT	60.035	55.000	31.80	1.06	38.73	2.66
827	835	0.469917	TCGAGGGAAATGGAGGATGC	59.530	55.000	0.00	0.00	0.00	3.91
860	872	2.675423	TCCGTGTCTCGTGGAGGG	60.675	66.667	0.00	0.00	37.94	4.30
931	962	1.439644	GAGAGGAGGCAGCTTACCG	59.560	63.158	0.00	0.00	0.00	4.02
943	974	0.260230	AATGCGAGGAGAGGAGAGGA	59.740	55.000	0.00	0.00	0.00	3.71
946	977	1.103987	CGGAATGCGAGGAGAGGAGA	61.104	60.000	0.00	0.00	0.00	3.71
1311	1347	0.338467	TCCCGGGAGATTCCTTCAGA	59.662	55.000	22.63	0.00	36.57	3.27
1332	1368	1.378124	CGGAGAAGTCGAGAGTCCCC	61.378	65.000	0.00	0.00	0.00	4.81
1638	1674	0.787084	ACAACTCCTCCTCCTCCTCA	59.213	55.000	0.00	0.00	0.00	3.86
1658	1727	4.337060	CGTGCACTGACGTCCGGA	62.337	66.667	16.19	0.00	34.56	5.14
1739	1808	1.545582	CCAAATCATGCTTGTTCCGGT	59.454	47.619	0.00	0.00	0.00	5.28
1866	1935	2.203139	CGTGTCACCCCTTGCACA	60.203	61.111	0.00	0.00	34.01	4.57
1867	1936	1.098712	TTTCGTGTCACCCCTTGCAC	61.099	55.000	0.00	0.00	0.00	4.57
2359	2429	7.345691	CCAACCATGGGCATAATATATCACTA	58.654	38.462	18.09	0.00	43.51	2.74
2397	2467	6.705381	CCTGACAAGAATGAGAAGGATACATC	59.295	42.308	0.00	0.00	41.41	3.06
2398	2468	6.157645	ACCTGACAAGAATGAGAAGGATACAT	59.842	38.462	0.00	0.00	41.41	2.29
2400	2470	5.983540	ACCTGACAAGAATGAGAAGGATAC	58.016	41.667	0.00	0.00	32.18	2.24
2401	2471	6.897966	ACTACCTGACAAGAATGAGAAGGATA	59.102	38.462	0.00	0.00	32.18	2.59
2402	2472	5.723887	ACTACCTGACAAGAATGAGAAGGAT	59.276	40.000	0.00	0.00	32.18	3.24
2403	2473	5.087323	ACTACCTGACAAGAATGAGAAGGA	58.913	41.667	0.00	0.00	32.18	3.36
2404	2474	5.413309	ACTACCTGACAAGAATGAGAAGG	57.587	43.478	0.00	0.00	33.24	3.46
2405	2475	6.931281	TGAAACTACCTGACAAGAATGAGAAG	59.069	38.462	0.00	0.00	0.00	2.85
2407	2477	6.419484	TGAAACTACCTGACAAGAATGAGA	57.581	37.500	0.00	0.00	0.00	3.27
2408	2478	6.652481	ACATGAAACTACCTGACAAGAATGAG	59.348	38.462	0.00	0.00	0.00	2.90
3110	3284	5.280011	CCCGAACAGCTCCTTAATACCATAT	60.280	44.000	0.00	0.00	0.00	1.78
3185	3361	3.211045	AGTTTCAGCTAAAAACCGCAGA	58.789	40.909	16.31	0.00	37.33	4.26
3186	3362	3.555518	GAGTTTCAGCTAAAAACCGCAG	58.444	45.455	16.31	0.00	37.33	5.18
3187	3363	2.292292	GGAGTTTCAGCTAAAAACCGCA	59.708	45.455	16.31	0.00	37.33	5.69
3188	3364	2.664698	CGGAGTTTCAGCTAAAAACCGC	60.665	50.000	13.72	9.61	39.42	5.68
3189	3365	2.664698	GCGGAGTTTCAGCTAAAAACCG	60.665	50.000	18.94	18.94	44.08	4.44
3190	3366	2.351447	GGCGGAGTTTCAGCTAAAAACC	60.351	50.000	16.31	8.06	37.71	3.27
3191	3367	2.351447	GGGCGGAGTTTCAGCTAAAAAC	60.351	50.000	13.43	13.43	37.71	2.43
3227	3403	2.184322	GATTCTCCGCTCCACGCA	59.816	61.111	0.00	0.00	41.76	5.24
3252	3428	2.308866	AGCATTGTTACAGTTAGGGCCT	59.691	45.455	12.58	12.58	0.00	5.19
3376	3557	0.250901	TGGGCAGGTTCTGAAGCTTC	60.251	55.000	19.89	19.89	37.06	3.86
3405	3586	3.584733	AAGGTAGGATCATGAAAGGCC	57.415	47.619	0.00	0.00	0.00	5.19

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.