AutoCloner

Multiple sequence alignment - TraesCS7B01G417200

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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	TraesCS7B01G417200	chr7B	100.000	2264	0	0	1	2264	685201726	685203989	0.000000e+00	4181
1	TraesCS7B01G417200	chr7B	95.767	1323	39	3	1	1308	34282319	34280999	0.000000e+00	2117
2	TraesCS7B01G417200	chr7B	82.914	954	86	43	1349	2264	577214653	577215567	0.000000e+00	787
3	TraesCS7B01G417200	chr6B	95.444	1339	38	6	1	1319	425587398	425588733	0.000000e+00	2113
4	TraesCS7B01G417200	chr6B	95.943	838	22	7	1	832	578524209	578525040	0.000000e+00	1349
5	TraesCS7B01G417200	chr6B	92.849	895	34	10	1386	2264	578550943	578551823	0.000000e+00	1271
6	TraesCS7B01G417200	chr5D	95.184	1329	39	5	1	1308	387840694	387839370	0.000000e+00	2076
7	TraesCS7B01G417200	chr5D	89.238	446	33	4	1834	2264	387827808	387827363	5.500000e-151	544
8	TraesCS7B01G417200	chr4A	94.520	1332	47	7	1	1308	737660718	737662047	0.000000e+00	2032
9	TraesCS7B01G417200	chr4A	94.459	758	32	7	557	1308	664929963	664929210	0.000000e+00	1158
10	TraesCS7B01G417200	chr4A	88.837	860	48	8	1426	2264	664927216	664926384	0.000000e+00	1013
11	TraesCS7B01G417200	chr4A	90.196	714	46	4	1384	2094	737664066	737664758	0.000000e+00	909
12	TraesCS7B01G417200	chr4A	87.958	191	8	4	2089	2264	737694531	737694721	6.340000e-51	211
13	TraesCS7B01G417200	chr2A	94.482	1323	55	3	1	1308	372742751	372744070	0.000000e+00	2023
14	TraesCS7B01G417200	chr3A	94.234	1318	60	4	1	1303	44774237	44772921	0.000000e+00	1999
15	TraesCS7B01G417200	chr3A	94.868	760	28	6	556	1308	145558437	145557682	0.000000e+00	1177
16	TraesCS7B01G417200	chr1D	97.111	796	20	1	1	793	490888707	490889502	0.000000e+00	1339
17	TraesCS7B01G417200	chr1D	95.526	760	26	4	556	1308	297551587	297550829	0.000000e+00	1208
18	TraesCS7B01G417200	chr5B	94.687	847	24	3	1	832	16010531	16011371	0.000000e+00	1295
19	TraesCS7B01G417200	chr5B	94.296	824	32	2	1456	2264	526184429	526185252	0.000000e+00	1247
20	TraesCS7B01G417200	chr5B	87.589	419	34	9	1349	1763	246980100	246980504	9.470000e-129	470
21	TraesCS7B01G417200	chr4B	94.471	850	26	3	1	835	598448988	598448145	0.000000e+00	1290
22	TraesCS7B01G417200	chr2B	94.276	856	22	8	1	835	579908061	579908910	0.000000e+00	1284
23	TraesCS7B01G417200	chr2B	94.168	823	41	3	1	822	138731705	138732521	0.000000e+00	1247
24	TraesCS7B01G417200	chr2B	85.668	928	77	26	1380	2264	689380598	689379684	0.000000e+00	926
25	TraesCS7B01G417200	chr2B	82.476	953	91	41	1349	2264	154582100	154581187	0.000000e+00	765
26	TraesCS7B01G417200	chr2B	80.469	384	47	15	1349	1729	798604350	798604708	3.710000e-68	268
27	TraesCS7B01G417200	chr2D	95.590	771	19	1	1	756	524910382	524909612	0.000000e+00	1221
28	TraesCS7B01G417200	chr7A	89.076	833	63	18	1	822	595033104	595032289	0.000000e+00	1009
29	TraesCS7B01G417200	chr7A	82.396	960	79	40	1349	2264	497716132	497715219	0.000000e+00	754
30	TraesCS7B01G417200	chr3B	87.023	917	56	23	1384	2264	16195846	16194957	0.000000e+00	976
31	TraesCS7B01G417200	chr3B	90.683	483	30	5	1349	1825	173093119	173093592	1.480000e-176	628
32	TraesCS7B01G417200	chr3B	91.156	441	24	3	1838	2263	173093569	173094009	3.240000e-163	584
33	TraesCS7B01G417200	chr7D	83.147	896	88	30	1383	2264	133435855	133436701	0.000000e+00	760
34	TraesCS7B01G417200	chr7D	89.391	443	36	5	1383	1825	133522786	133523217	4.250000e-152	547
35	TraesCS7B01G417200	chr1B	82.396	960	79	40	1349	2264	649297940	649297027	0.000000e+00	754
36	TraesCS7B01G417200	chr6D	89.686	446	31	4	1834	2264	969488	969933	2.540000e-154	555
37	TraesCS7B01G417200	chrUn	88.789	446	34	5	1834	2264	134521189	134520745	1.190000e-147	532
38	TraesCS7B01G417200	chrUn	88.462	442	36	4	1838	2264	196642432	196641991	9.270000e-144	520
39	TraesCS7B01G417200	chr3D	83.149	451	65	7	1821	2264	597206967	597207413	3.500000e-108	401

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	TraesCS7B01G417200	chr7B	685201726	685203989	2263	False	4181.0	4181	100.0000	1	2264	1	chr7B.!!$F2	2263
1	TraesCS7B01G417200	chr7B	34280999	34282319	1320	True	2117.0	2117	95.7670	1	1308	1	chr7B.!!$R1	1307
2	TraesCS7B01G417200	chr7B	577214653	577215567	914	False	787.0	787	82.9140	1349	2264	1	chr7B.!!$F1	915
3	TraesCS7B01G417200	chr6B	425587398	425588733	1335	False	2113.0	2113	95.4440	1	1319	1	chr6B.!!$F1	1318
4	TraesCS7B01G417200	chr6B	578524209	578525040	831	False	1349.0	1349	95.9430	1	832	1	chr6B.!!$F2	831
5	TraesCS7B01G417200	chr6B	578550943	578551823	880	False	1271.0	1271	92.8490	1386	2264	1	chr6B.!!$F3	878
6	TraesCS7B01G417200	chr5D	387839370	387840694	1324	True	2076.0	2076	95.1840	1	1308	1	chr5D.!!$R2	1307
7	TraesCS7B01G417200	chr4A	737660718	737664758	4040	False	1470.5	2032	92.3580	1	2094	2	chr4A.!!$F2	2093
8	TraesCS7B01G417200	chr4A	664926384	664929963	3579	True	1085.5	1158	91.6480	557	2264	2	chr4A.!!$R1	1707
9	TraesCS7B01G417200	chr2A	372742751	372744070	1319	False	2023.0	2023	94.4820	1	1308	1	chr2A.!!$F1	1307
10	TraesCS7B01G417200	chr3A	44772921	44774237	1316	True	1999.0	1999	94.2340	1	1303	1	chr3A.!!$R1	1302
11	TraesCS7B01G417200	chr3A	145557682	145558437	755	True	1177.0	1177	94.8680	556	1308	1	chr3A.!!$R2	752
12	TraesCS7B01G417200	chr1D	490888707	490889502	795	False	1339.0	1339	97.1110	1	793	1	chr1D.!!$F1	792
13	TraesCS7B01G417200	chr1D	297550829	297551587	758	True	1208.0	1208	95.5260	556	1308	1	chr1D.!!$R1	752
14	TraesCS7B01G417200	chr5B	16010531	16011371	840	False	1295.0	1295	94.6870	1	832	1	chr5B.!!$F1	831
15	TraesCS7B01G417200	chr5B	526184429	526185252	823	False	1247.0	1247	94.2960	1456	2264	1	chr5B.!!$F3	808
16	TraesCS7B01G417200	chr4B	598448145	598448988	843	True	1290.0	1290	94.4710	1	835	1	chr4B.!!$R1	834
17	TraesCS7B01G417200	chr2B	579908061	579908910	849	False	1284.0	1284	94.2760	1	835	1	chr2B.!!$F2	834
18	TraesCS7B01G417200	chr2B	138731705	138732521	816	False	1247.0	1247	94.1680	1	822	1	chr2B.!!$F1	821
19	TraesCS7B01G417200	chr2B	689379684	689380598	914	True	926.0	926	85.6680	1380	2264	1	chr2B.!!$R2	884
20	TraesCS7B01G417200	chr2B	154581187	154582100	913	True	765.0	765	82.4760	1349	2264	1	chr2B.!!$R1	915
21	TraesCS7B01G417200	chr2D	524909612	524910382	770	True	1221.0	1221	95.5900	1	756	1	chr2D.!!$R1	755
22	TraesCS7B01G417200	chr7A	595032289	595033104	815	True	1009.0	1009	89.0760	1	822	1	chr7A.!!$R2	821
23	TraesCS7B01G417200	chr7A	497715219	497716132	913	True	754.0	754	82.3960	1349	2264	1	chr7A.!!$R1	915
24	TraesCS7B01G417200	chr3B	16194957	16195846	889	True	976.0	976	87.0230	1384	2264	1	chr3B.!!$R1	880
25	TraesCS7B01G417200	chr3B	173093119	173094009	890	False	606.0	628	90.9195	1349	2263	2	chr3B.!!$F1	914
26	TraesCS7B01G417200	chr7D	133435855	133436701	846	False	760.0	760	83.1470	1383	2264	1	chr7D.!!$F1	881
27	TraesCS7B01G417200	chr1B	649297027	649297940	913	True	754.0	754	82.3960	1349	2264	1	chr1B.!!$R1	915

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
490	491	0.107017	AGCGGTCATTTCATGGAGGG	60.107	55.0	0.0	0.0	0.0	4.3	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1343	1571	0.107214	CGCCATGGTCCTTGGTATGT	60.107	55.0	21.75	0.0	36.57	2.29	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
37	38	1.205064	CAAGCAAGTCTTCACGGCG	59.795	57.895	4.80	4.80	34.12	6.46
236	237	1.324736	GCGAAGGCGAGAAACATACAG	59.675	52.381	0.00	0.00	40.82	2.74
333	334	1.423921	ACCCTTTCTTGGACCAATCGT	59.576	47.619	7.54	0.00	0.00	3.73
490	491	0.107017	AGCGGTCATTTCATGGAGGG	60.107	55.000	0.00	0.00	0.00	4.30
675	723	1.272769	GTCGTAGAGGGAGCACAAGTT	59.727	52.381	0.00	0.00	36.95	2.66
679	727	3.427773	CGTAGAGGGAGCACAAGTTCTAC	60.428	52.174	0.00	0.00	35.73	2.59
684	768	2.565834	GGGAGCACAAGTTCTACAGGTA	59.434	50.000	0.00	0.00	0.00	3.08
685	805	3.007614	GGGAGCACAAGTTCTACAGGTAA	59.992	47.826	0.00	0.00	0.00	2.85
929	1157	8.121305	TGTTTGTTCATACAATTCCTAGCATT	57.879	30.769	0.00	0.00	43.43	3.56
1075	1303	2.907897	GAAGACGTGGATGGAGGCCG	62.908	65.000	0.00	0.00	0.00	6.13
1114	1342	0.323725	GAAGGATGTGCCCACACCAT	60.324	55.000	16.64	8.97	46.86	3.55
1182	1410	2.746362	CAAGAAGTCATGGACAGAAGGC	59.254	50.000	0.00	0.00	34.60	4.35
1328	1556	7.304497	ACTATCTATGAACATACCAAGGACC	57.696	40.000	0.00	0.00	0.00	4.46
1329	1557	4.665833	TCTATGAACATACCAAGGACCG	57.334	45.455	0.00	0.00	0.00	4.79
1332	1560	2.538222	TGAACATACCAAGGACCGGTA	58.462	47.619	7.34	1.19	43.06	4.02
1338	1566	4.950205	ATACCAAGGACCGGTATGTTAG	57.050	45.455	7.34	0.00	45.91	2.34
1339	1567	1.835531	ACCAAGGACCGGTATGTTAGG	59.164	52.381	7.34	7.96	34.02	2.69
1340	1568	1.835531	CCAAGGACCGGTATGTTAGGT	59.164	52.381	7.34	0.00	41.63	3.08
1341	1569	2.419574	CCAAGGACCGGTATGTTAGGTG	60.420	54.545	7.34	0.00	38.57	4.00
1342	1570	2.235402	CAAGGACCGGTATGTTAGGTGT	59.765	50.000	7.34	0.00	38.57	4.16
1343	1571	3.386932	AGGACCGGTATGTTAGGTGTA	57.613	47.619	7.34	0.00	38.57	2.90
1344	1572	3.026694	AGGACCGGTATGTTAGGTGTAC	58.973	50.000	7.34	0.00	38.57	2.90
1345	1573	2.760092	GGACCGGTATGTTAGGTGTACA	59.240	50.000	7.34	0.00	38.57	2.90
1347	1575	4.584325	GGACCGGTATGTTAGGTGTACATA	59.416	45.833	7.34	0.00	38.57	2.29
1357	2556	2.910544	AGGTGTACATACCAAGGACCA	58.089	47.619	0.00	0.00	43.37	4.02
1410	3718	4.640690	AGGACCCTGGCGTCTGGT	62.641	66.667	12.29	6.86	33.07	4.00
1411	3719	4.083862	GGACCCTGGCGTCTGGTC	62.084	72.222	17.61	17.61	46.31	4.02
1412	3720	2.997897	GACCCTGGCGTCTGGTCT	60.998	66.667	18.31	1.59	44.17	3.85
1415	3723	2.681778	CCTGGCGTCTGGTCTCCT	60.682	66.667	4.52	0.00	0.00	3.69
1416	3724	2.575993	CTGGCGTCTGGTCTCCTG	59.424	66.667	0.00	0.00	0.00	3.86
1417	3725	1.979155	CTGGCGTCTGGTCTCCTGA	60.979	63.158	0.00	0.00	0.00	3.86
1470	3848	5.045578	GTCTGGTCCCCTGTGCATATATATT	60.046	44.000	0.00	0.00	0.00	1.28
1558	3969	8.489559	CACAGGAAACAACATTTCACATAAATG	58.510	33.333	8.52	8.52	41.91	2.32
1848	4314	0.753479	TCGCTAGCCTCCTCCTCTTG	60.753	60.000	9.66	0.00	0.00	3.02
1849	4315	1.743321	CGCTAGCCTCCTCCTCTTGG	61.743	65.000	9.66	0.00	0.00	3.61
1854	4320	0.397816	GCCTCCTCCTCTTGGCTAGA	60.398	60.000	0.00	0.00	41.92	2.43
2140	4621	0.677731	TTGCCTCCTCTTCATTGCCG	60.678	55.000	0.00	0.00	0.00	5.69
2225	4724	2.934932	TGGGCTGAGCACCATGGA	60.935	61.111	21.47	0.00	0.00	3.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
37	38	9.855361	CAATTCTGTCGAATATGATAACTTGTC	57.145	33.333	0.00	0.00	38.89	3.18
236	237	2.031157	CACGGTTTCTCCATCACAAACC	60.031	50.000	3.17	3.17	43.87	3.27
333	334	1.496060	CCATGGTACTCAGGCCACTA	58.504	55.000	5.01	0.00	37.62	2.74
490	491	3.589988	CCACAGTTGATAGTGTCAGGAC	58.410	50.000	0.00	0.00	38.29	3.85
675	723	7.724506	CCCTCTATGAACACTATTACCTGTAGA	59.275	40.741	0.00	0.00	0.00	2.59
679	727	6.551601	ACTCCCTCTATGAACACTATTACCTG	59.448	42.308	0.00	0.00	0.00	4.00
684	768	7.620094	ACTTGTACTCCCTCTATGAACACTATT	59.380	37.037	0.00	0.00	0.00	1.73
685	805	7.068839	CACTTGTACTCCCTCTATGAACACTAT	59.931	40.741	0.00	0.00	0.00	2.12
1075	1303	2.372172	TCTCCTTCTCCTTGTCCAAACC	59.628	50.000	0.00	0.00	0.00	3.27
1114	1342	2.655090	ACATCACCACACCAACATGA	57.345	45.000	0.00	0.00	0.00	3.07
1182	1410	2.032924	GGGACACACGAAAAACCTTCTG	59.967	50.000	0.00	0.00	0.00	3.02
1308	1536	3.386726	CCGGTCCTTGGTATGTTCATAGA	59.613	47.826	0.00	0.00	0.00	1.98
1310	1538	3.109151	ACCGGTCCTTGGTATGTTCATA	58.891	45.455	0.00	0.00	38.15	2.15
1320	1548	1.835531	ACCTAACATACCGGTCCTTGG	59.164	52.381	12.40	10.07	0.00	3.61
1321	1549	2.235402	ACACCTAACATACCGGTCCTTG	59.765	50.000	12.40	10.70	0.00	3.61
1322	1550	2.543635	ACACCTAACATACCGGTCCTT	58.456	47.619	12.40	3.11	0.00	3.36
1323	1551	2.242882	ACACCTAACATACCGGTCCT	57.757	50.000	12.40	0.00	0.00	3.85
1324	1552	2.760092	TGTACACCTAACATACCGGTCC	59.240	50.000	12.40	0.00	0.00	4.46
1325	1553	4.660789	ATGTACACCTAACATACCGGTC	57.339	45.455	12.40	0.00	35.82	4.79
1332	1560	5.104652	GGTCCTTGGTATGTACACCTAACAT	60.105	44.000	0.00	0.00	39.50	2.71
1333	1561	4.223477	GGTCCTTGGTATGTACACCTAACA	59.777	45.833	0.00	0.00	39.50	2.41
1334	1562	4.223477	TGGTCCTTGGTATGTACACCTAAC	59.777	45.833	0.00	0.00	39.50	2.34
1335	1563	4.427637	TGGTCCTTGGTATGTACACCTAA	58.572	43.478	0.00	0.00	39.50	2.69
1337	1565	2.910544	TGGTCCTTGGTATGTACACCT	58.089	47.619	0.00	0.00	39.50	4.00
1338	1566	3.541632	CATGGTCCTTGGTATGTACACC	58.458	50.000	0.00	0.00	39.20	4.16
1339	1567	3.541632	CCATGGTCCTTGGTATGTACAC	58.458	50.000	14.53	0.00	0.00	2.90
1340	1568	2.092646	GCCATGGTCCTTGGTATGTACA	60.093	50.000	21.75	0.00	36.57	2.90
1341	1569	2.572290	GCCATGGTCCTTGGTATGTAC	58.428	52.381	21.75	3.90	36.57	2.90
1342	1570	1.140052	CGCCATGGTCCTTGGTATGTA	59.860	52.381	21.75	0.00	36.57	2.29
1343	1571	0.107214	CGCCATGGTCCTTGGTATGT	60.107	55.000	21.75	0.00	36.57	2.29
1344	1572	0.107214	ACGCCATGGTCCTTGGTATG	60.107	55.000	21.75	15.19	36.57	2.39
1345	1573	0.180406	GACGCCATGGTCCTTGGTAT	59.820	55.000	21.75	12.21	36.57	2.73
1347	1575	2.224159	AGACGCCATGGTCCTTGGT	61.224	57.895	21.75	6.20	37.66	3.67
1370	2569	2.364324	GGCGTCTGGTTATATGTCAGGA	59.636	50.000	0.00	0.00	0.00	3.86
1380	2579	1.675219	GGTCCTTGGCGTCTGGTTA	59.325	57.895	0.00	0.00	0.00	2.85
1410	3718	3.318275	GCGTCTGGTTATATGTCAGGAGA	59.682	47.826	0.00	0.00	0.00	3.71
1411	3719	3.553096	GGCGTCTGGTTATATGTCAGGAG	60.553	52.174	0.00	0.00	0.00	3.69
1412	3720	2.364324	GGCGTCTGGTTATATGTCAGGA	59.636	50.000	0.00	0.00	0.00	3.86
1415	3723	3.431626	CCTTGGCGTCTGGTTATATGTCA	60.432	47.826	0.00	0.00	0.00	3.58
1416	3724	3.131396	CCTTGGCGTCTGGTTATATGTC	58.869	50.000	0.00	0.00	0.00	3.06
1417	3725	2.769663	TCCTTGGCGTCTGGTTATATGT	59.230	45.455	0.00	0.00	0.00	2.29
1419	3727	2.104281	GGTCCTTGGCGTCTGGTTATAT	59.896	50.000	0.00	0.00	0.00	0.86
1421	3729	0.252197	GGTCCTTGGCGTCTGGTTAT	59.748	55.000	0.00	0.00	0.00	1.89
1422	3730	1.675219	GGTCCTTGGCGTCTGGTTA	59.325	57.895	0.00	0.00	0.00	2.85
1423	3731	2.430367	GGTCCTTGGCGTCTGGTT	59.570	61.111	0.00	0.00	0.00	3.67
1424	3732	3.637273	GGGTCCTTGGCGTCTGGT	61.637	66.667	0.00	0.00	0.00	4.00
1655	4067	5.968528	ACTTGTTGCCGTTTATTTCCATA	57.031	34.783	0.00	0.00	0.00	2.74
1848	4314	2.123640	AGGCGGAGGAGTCTAGCC	60.124	66.667	9.55	9.55	42.82	3.93
1849	4315	2.197605	GGAGGCGGAGGAGTCTAGC	61.198	68.421	0.00	0.00	0.00	3.42
2183	4682	0.466555	GTGTTTGCACCTGGTACCCA	60.467	55.000	10.07	0.00	39.61	4.51

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.