AutoCloner

Multiple sequence alignment - TraesCS5B01G570900

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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	TraesCS5B01G570900	chr5B	100.000	2618	0	0	1	2618	712417404	712420021	0.000000e+00	4835.0
1	TraesCS5B01G570900	chr5B	90.566	53	4	1	2536	2587	547438197	547438249	4.680000e-08	69.4
2	TraesCS5B01G570900	chr5D	94.579	2638	95	16	1	2618	562038319	562040928	0.000000e+00	4036.0
3	TraesCS5B01G570900	chr5D	85.995	1171	143	9	450	1609	562052172	562053332	0.000000e+00	1234.0
4	TraesCS5B01G570900	chr5D	84.279	229	28	3	446	673	562051944	562052165	1.580000e-52	217.0
5	TraesCS5B01G570900	chr5D	83.505	97	4	3	2534	2618	218579852	218579948	2.160000e-11	80.5
6	TraesCS5B01G570900	chr5D	97.059	34	1	0	2585	2618	13342286	13342253	1.010000e-04	58.4
7	TraesCS5B01G570900	chr7B	95.717	1891	63	7	1	1884	737785	735906	0.000000e+00	3027.0
8	TraesCS5B01G570900	chr7B	89.122	763	38	11	1893	2618	734845	734091	0.000000e+00	907.0
9	TraesCS5B01G570900	chr7B	86.939	245	28	1	446	690	737731	737491	3.320000e-69	272.0
10	TraesCS5B01G570900	chr7B	93.750	48	3	0	2534	2581	620682587	620682634	3.610000e-09	73.1
11	TraesCS5B01G570900	chr4A	75.532	658	133	19	829	1476	725856935	725857574	5.480000e-77	298.0
12	TraesCS5B01G570900	chr4A	92.157	153	11	1	294	446	511131681	511131530	5.670000e-52	215.0
13	TraesCS5B01G570900	chr4A	91.558	154	12	1	296	449	535039238	535039390	7.340000e-51	211.0
14	TraesCS5B01G570900	chr4B	92.157	153	11	1	294	446	217725124	217725275	5.670000e-52	215.0
15	TraesCS5B01G570900	chr4B	93.750	48	3	0	2534	2581	648744567	648744614	3.610000e-09	73.1
16	TraesCS5B01G570900	chr4B	91.667	48	4	0	2534	2581	654200293	654200340	1.680000e-07	67.6
17	TraesCS5B01G570900	chr6A	91.558	154	12	1	293	446	133810163	133810315	7.340000e-51	211.0
18	TraesCS5B01G570900	chr6A	92.568	148	10	1	299	446	339577010	339576864	7.340000e-51	211.0
19	TraesCS5B01G570900	chr2A	91.503	153	12	1	294	446	651820097	651819946	2.640000e-50	209.0
20	TraesCS5B01G570900	chr2B	92.414	145	10	1	299	443	437240418	437240275	3.420000e-49	206.0
21	TraesCS5B01G570900	chr2D	92.157	102	7	1	2431	2532	76876159	76876259	2.720000e-30	143.0
22	TraesCS5B01G570900	chr2D	96.970	33	1	0	2586	2618	456850437	456850469	3.640000e-04	56.5
23	TraesCS5B01G570900	chr3D	91.667	96	8	0	2432	2527	574525157	574525062	1.630000e-27	134.0
24	TraesCS5B01G570900	chr7A	73.008	389	80	14	829	1209	11761895	11761524	2.130000e-21	113.0
25	TraesCS5B01G570900	chr7A	97.059	34	0	1	2534	2567	44729330	44729362	3.640000e-04	56.5
26	TraesCS5B01G570900	chr7D	72.751	389	76	17	832	1209	12312719	12312350	1.280000e-18	104.0
27	TraesCS5B01G570900	chr7D	83.505	97	4	3	2534	2618	90745217	90745313	2.160000e-11	80.5
28	TraesCS5B01G570900	chr4D	85.417	96	3	2	2534	2618	69009645	69009740	3.590000e-14	89.8
29	TraesCS5B01G570900	chr3B	92.857	42	3	0	2491	2532	783022753	783022794	7.820000e-06	62.1
30	TraesCS5B01G570900	chr1B	79.592	98	7	6	2534	2618	543855405	543855502	1.010000e-04	58.4

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	TraesCS5B01G570900	chr5B	712417404	712420021	2617	False	4835.0	4835	100.000000	1	2618	1	chr5B.!!$F2	2617
1	TraesCS5B01G570900	chr5D	562038319	562040928	2609	False	4036.0	4036	94.579000	1	2618	1	chr5D.!!$F2	2617
2	TraesCS5B01G570900	chr5D	562051944	562053332	1388	False	725.5	1234	85.137000	446	1609	2	chr5D.!!$F3	1163
3	TraesCS5B01G570900	chr7B	734091	737785	3694	True	1402.0	3027	90.592667	1	2618	3	chr7B.!!$R1	2617
4	TraesCS5B01G570900	chr4A	725856935	725857574	639	False	298.0	298	75.532000	829	1476	1	chr4A.!!$F2	647

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
805	812	0.179076	TGTGCACAGACTGGACACTG	60.179	55.0	17.42	8.22	45.6	3.66	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2591	3701	0.402887	AAACCGGGACTAAAGGGGTG	59.597	55.0	6.32	0.0	0.0	4.61	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)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
54	55	9.764363	GATCCATGTTAGATGTTAGATGTTGTA	57.236	33.333	0.00	0.00	0.00	2.41
122	123	6.157904	TGATCAAGTTGTGTTGCATTAATGG	58.842	36.000	17.02	0.00	0.00	3.16
214	215	8.093307	ACATTGAGCATTAATACGATGAGATCT	58.907	33.333	16.62	0.00	0.00	2.75
249	250	9.264719	CACTGATATATTCTTGTGCATTCTACA	57.735	33.333	0.00	0.00	0.00	2.74
253	254	6.834959	ATATTCTTGTGCATTCTACAGACG	57.165	37.500	0.00	0.00	0.00	4.18
259	260	2.932614	GTGCATTCTACAGACGCTCATT	59.067	45.455	0.00	0.00	0.00	2.57
263	264	4.387256	GCATTCTACAGACGCTCATTATCC	59.613	45.833	0.00	0.00	0.00	2.59
339	340	3.159070	CAGACGATGTGTGCACGG	58.841	61.111	13.13	1.29	0.00	4.94
344	345	0.672091	ACGATGTGTGCACGGCAATA	60.672	50.000	13.13	0.00	41.47	1.90
453	454	4.854399	TGCAAAGTAGTTCCGTTTCATTG	58.146	39.130	0.00	0.00	0.00	2.82
805	812	0.179076	TGTGCACAGACTGGACACTG	60.179	55.000	17.42	8.22	45.60	3.66
815	822	7.044181	CACAGACTGGACACTGATTAATATGT	58.956	38.462	7.51	0.00	37.54	2.29
871	878	2.561733	TCTCACTGCACGCACTATAC	57.438	50.000	0.00	0.00	0.00	1.47
879	886	4.932799	ACTGCACGCACTATACATAAAACA	59.067	37.500	0.00	0.00	0.00	2.83
962	972	2.373335	TCACTCTATCTCCCTCTGCC	57.627	55.000	0.00	0.00	0.00	4.85
1061	1078	2.005451	CGTCTTCATGCTCCTTTCCAG	58.995	52.381	0.00	0.00	0.00	3.86
1082	1099	1.828595	TGCCATTACTACTCAAGCCGA	59.171	47.619	0.00	0.00	0.00	5.54
1130	1147	3.214328	CAACAAGCCTTGTAGTGGAAGT	58.786	45.455	11.10	0.00	44.59	3.01
1164	1181	3.003763	GGCGAGACCCAAGACCCT	61.004	66.667	0.00	0.00	0.00	4.34
1791	1812	4.393371	GGACAGAAATGAGTAAGCCAGAAC	59.607	45.833	0.00	0.00	0.00	3.01
1799	1820	5.051891	TGAGTAAGCCAGAACGTTAGTAC	57.948	43.478	0.00	0.00	0.00	2.73
1800	1821	4.763793	TGAGTAAGCCAGAACGTTAGTACT	59.236	41.667	0.00	0.00	0.00	2.73
1801	1822	5.939883	TGAGTAAGCCAGAACGTTAGTACTA	59.060	40.000	0.00	0.00	0.00	1.82
1849	1870	5.528870	TCTGGCACGTCTACACAATATATG	58.471	41.667	0.00	0.00	0.00	1.78
1925	2998	0.103026	CATGTCTCGATCGCCTCCAA	59.897	55.000	11.09	0.00	0.00	3.53
1938	3011	1.172180	CCTCCAAAAAGCTGGCACGA	61.172	55.000	0.00	0.00	36.32	4.35
1967	3040	2.654863	GTGGCCATGCTAACCTTATGT	58.345	47.619	9.72	0.00	0.00	2.29
1968	3041	2.618709	GTGGCCATGCTAACCTTATGTC	59.381	50.000	9.72	0.00	0.00	3.06
1969	3042	2.509548	TGGCCATGCTAACCTTATGTCT	59.490	45.455	0.00	0.00	0.00	3.41
1970	3043	3.053693	TGGCCATGCTAACCTTATGTCTT	60.054	43.478	0.00	0.00	0.00	3.01
1976	3049	5.880054	TGCTAACCTTATGTCTTCTTTGC	57.120	39.130	0.00	0.00	0.00	3.68
1982	3055	3.502211	CCTTATGTCTTCTTTGCGTTGGT	59.498	43.478	0.00	0.00	0.00	3.67
2025	3098	0.950836	AATGCGTTAGCTTGCACACA	59.049	45.000	9.74	0.00	45.07	3.72
2031	3104	2.096417	CGTTAGCTTGCACACAGTAACC	60.096	50.000	0.00	0.00	0.00	2.85
2035	3108	2.170260	CTTGCACACAGTAACCGGCG	62.170	60.000	0.00	0.00	0.00	6.46
2083	3156	2.384828	TCCAAATACGCAGCTCTCCTA	58.615	47.619	0.00	0.00	0.00	2.94
2304	3387	5.654603	TCGTCCTAATGAAGCTGAGTAAA	57.345	39.130	0.00	0.00	0.00	2.01
2329	3412	1.699634	ACTGCCTCTTTGGTGCTTCTA	59.300	47.619	0.00	0.00	38.35	2.10
2333	3416	2.884639	GCCTCTTTGGTGCTTCTACAAA	59.115	45.455	0.00	0.00	38.35	2.83
2354	3437	5.467035	AATGGGAATTGTGTTACTTGTGG	57.533	39.130	0.00	0.00	0.00	4.17
2379	3489	1.771255	AGTGGCTTTGGAGAACAGAGT	59.229	47.619	0.00	0.00	33.98	3.24
2451	3561	9.909644	TGTATTCACTAGTAGAAAACAGACTTC	57.090	33.333	3.59	0.00	0.00	3.01
2454	3564	7.342769	TCACTAGTAGAAAACAGACTTCACA	57.657	36.000	3.59	0.00	0.00	3.58
2571	3681	1.227556	CCGGGACTAAATGGGCTCG	60.228	63.158	0.00	0.00	0.00	5.03
2589	3699	4.590553	TGGGGCCCCAGTCTGTCA	62.591	66.667	41.29	15.37	41.89	3.58
2590	3700	4.035102	GGGGCCCCAGTCTGTCAC	62.035	72.222	37.61	3.27	35.81	3.67
2591	3701	4.035102	GGGCCCCAGTCTGTCACC	62.035	72.222	12.23	0.00	0.00	4.02
2592	3702	3.249189	GGCCCCAGTCTGTCACCA	61.249	66.667	0.00	0.00	0.00	4.17

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
191	192	9.981114	TTTAGATCTCATCGTATTAATGCTCAA	57.019	29.630	0.00	0.00	0.00	3.02
234	235	2.029020	AGCGTCTGTAGAATGCACAAGA	60.029	45.455	0.00	0.00	32.18	3.02
249	250	3.381908	GGATATCCGGATAATGAGCGTCT	59.618	47.826	27.35	8.17	0.00	4.18
253	254	7.445121	TGATAATGGATATCCGGATAATGAGC	58.555	38.462	27.35	13.24	39.83	4.26
259	260	8.727100	ATAGCTTGATAATGGATATCCGGATA	57.273	34.615	25.97	25.97	39.83	2.59
339	340	1.599542	GGACGGAGCTGATTGTATTGC	59.400	52.381	0.00	0.00	0.00	3.56
344	345	1.742761	CAATGGACGGAGCTGATTGT	58.257	50.000	0.00	0.00	0.00	2.71
522	523	9.147732	TCTCATAGTAACACATCTAACATCCAT	57.852	33.333	0.00	0.00	0.00	3.41
523	524	8.533569	TCTCATAGTAACACATCTAACATCCA	57.466	34.615	0.00	0.00	0.00	3.41
871	878	4.967575	GTGTTCGTGAGGTTGTGTTTTATG	59.032	41.667	0.00	0.00	0.00	1.90
879	886	0.106149	GGAGGTGTTCGTGAGGTTGT	59.894	55.000	0.00	0.00	0.00	3.32
962	972	3.744660	ACAAGCCTTGAACTGTCCTTAG	58.255	45.455	12.25	0.00	0.00	2.18
1061	1078	1.933853	CGGCTTGAGTAGTAATGGCAC	59.066	52.381	0.00	0.00	0.00	5.01
1094	1111	2.008242	TGTTGCCTTAGGTTTGCCAT	57.992	45.000	0.00	0.00	37.19	4.40
1119	1136	3.202906	GTTCTTGCACACTTCCACTACA	58.797	45.455	0.00	0.00	0.00	2.74
1130	1147	2.664851	CCGAGGCGTTCTTGCACA	60.665	61.111	0.00	0.00	36.28	4.57
1164	1181	6.096705	ACAAACAGAATTCCTTTGTGACATCA	59.903	34.615	22.24	0.00	36.87	3.07
1479	1500	1.300620	CTCGTTGGAAGTGTCGCCA	60.301	57.895	0.00	0.00	0.00	5.69
1639	1660	9.604626	CAAATTTATTATCCTTTCTCGCAGATC	57.395	33.333	0.00	0.00	33.89	2.75
1672	1693	6.260870	TGCCACAACAAACGTTATGATTAT	57.739	33.333	0.00	0.00	0.00	1.28
1849	1870	9.486497	TCTTCATCATATTCAAAGATAGCAGAC	57.514	33.333	0.00	0.00	0.00	3.51
1925	2998	1.373590	AACGTGTCGTGCCAGCTTTT	61.374	50.000	0.00	0.00	39.99	2.27
1938	3011	2.855514	GCATGGCCACCAAACGTGT	61.856	57.895	8.16	0.00	41.26	4.49
1967	3040	3.859411	ACAAAACCAACGCAAAGAAGA	57.141	38.095	0.00	0.00	0.00	2.87
1968	3041	4.919677	AAACAAAACCAACGCAAAGAAG	57.080	36.364	0.00	0.00	0.00	2.85
1969	3042	5.674933	AAAAACAAAACCAACGCAAAGAA	57.325	30.435	0.00	0.00	0.00	2.52
2025	3098	2.124860	GAATGCCCGCCGGTTACT	60.125	61.111	1.90	0.00	0.00	2.24
2083	3156	4.285517	AGGATCCATGCACTCGAGATTTAT	59.714	41.667	21.68	4.97	0.00	1.40
2304	3387	1.813513	CACCAAAGAGGCAGTCGATT	58.186	50.000	0.00	0.00	43.14	3.34
2329	3412	6.279882	CACAAGTAACACAATTCCCATTTGT	58.720	36.000	0.00	0.00	37.79	2.83
2333	3416	3.258123	GCCACAAGTAACACAATTCCCAT	59.742	43.478	0.00	0.00	0.00	4.00
2354	3437	1.268079	GTTCTCCAAAGCCACTCAAGC	59.732	52.381	0.00	0.00	0.00	4.01
2379	3489	9.120538	GATTATATTCCAGGAAGTGCAAGTAAA	57.879	33.333	8.20	0.00	0.00	2.01
2451	3561	3.059884	CGGGACTAATGATCCGAATGTG	58.940	50.000	0.00	0.00	44.69	3.21
2454	3564	2.326428	ACCGGGACTAATGATCCGAAT	58.674	47.619	6.32	0.00	44.69	3.34
2571	3681	4.035102	GACAGACTGGGGCCCCAC	62.035	72.222	41.29	30.63	41.89	4.61
2583	3693	1.975680	GACTAAAGGGGTGGTGACAGA	59.024	52.381	0.00	0.00	44.46	3.41
2587	3697	1.196104	CGGGACTAAAGGGGTGGTGA	61.196	60.000	0.00	0.00	0.00	4.02
2589	3699	1.921857	CCGGGACTAAAGGGGTGGT	60.922	63.158	0.00	0.00	0.00	4.16
2590	3700	1.494716	AACCGGGACTAAAGGGGTGG	61.495	60.000	6.32	0.00	0.00	4.61
2591	3701	0.402887	AAACCGGGACTAAAGGGGTG	59.597	55.000	6.32	0.00	0.00	4.61
2592	3702	0.402887	CAAACCGGGACTAAAGGGGT	59.597	55.000	6.32	0.00	0.00	4.95

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.