AutoCloner

Multiple sequence alignment - TraesCS6A01G362300

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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	TraesCS6A01G362300	chr6A	100.000	2437	0	0	1	2437	592274074	592276510	0.000000e+00	4501.0
1	TraesCS6A01G362300	chr6A	96.899	129	4	0	526	654	592274477	592274605	1.470000e-52	217.0
2	TraesCS6A01G362300	chr6A	96.899	129	4	0	404	532	592274599	592274727	1.470000e-52	217.0
3	TraesCS6A01G362300	chr6A	91.358	81	6	1	952	1031	592285291	592285371	2.560000e-20	110.0
4	TraesCS6A01G362300	chr6B	93.333	1260	71	5	359	1607	672099241	672100498	0.000000e+00	1849.0
5	TraesCS6A01G362300	chr6B	96.124	129	5	0	404	532	672099408	672099536	6.830000e-51	211.0
6	TraesCS6A01G362300	chr6B	94.574	129	7	0	526	654	672099286	672099414	1.480000e-47	200.0
7	TraesCS6A01G362300	chr6B	94.215	121	7	0	122	242	672098765	672098885	4.140000e-43	185.0
8	TraesCS6A01G362300	chr6B	90.840	131	12	0	1	131	672098600	672098730	2.490000e-40	176.0
9	TraesCS6A01G362300	chr6B	98.182	55	1	0	710	764	84039355	84039301	1.990000e-16	97.1
10	TraesCS6A01G362300	chr6B	83.505	97	13	3	710	803	416246770	416246866	1.200000e-13	87.9
11	TraesCS6A01G362300	chr3B	99.281	834	5	1	1605	2437	486797456	486798289	0.000000e+00	1506.0
12	TraesCS6A01G362300	chr3B	97.112	831	21	3	1608	2437	774821486	774822314	0.000000e+00	1399.0
13	TraesCS6A01G362300	chr3B	91.388	836	58	11	1608	2431	720235505	720234672	0.000000e+00	1133.0
14	TraesCS6A01G362300	chr3B	96.429	56	2	0	710	765	805684842	805684897	2.580000e-15	93.5
15	TraesCS6A01G362300	chr6D	93.309	807	45	5	801	1607	445717696	445718493	0.000000e+00	1182.0
16	TraesCS6A01G362300	chr6D	91.261	801	49	11	122	908	445716909	445717702	0.000000e+00	1072.0
17	TraesCS6A01G362300	chr6D	96.124	129	5	0	526	654	445717194	445717322	6.830000e-51	211.0
18	TraesCS6A01G362300	chr6D	93.023	129	4	3	404	532	445717316	445717439	1.490000e-42	183.0
19	TraesCS6A01G362300	chr6D	93.827	81	4	1	952	1031	445721797	445721877	1.180000e-23	121.0
20	TraesCS6A01G362300	chr7B	91.236	833	61	8	1608	2437	43673194	43674017	0.000000e+00	1123.0
21	TraesCS6A01G362300	chr5B	91.159	837	61	9	1604	2437	639763900	639763074	0.000000e+00	1123.0
22	TraesCS6A01G362300	chr2B	91.200	750	59	7	1605	2350	16305886	16306632	0.000000e+00	1013.0
23	TraesCS6A01G362300	chr2B	91.026	624	51	5	1608	2229	406538376	406538996	0.000000e+00	837.0
24	TraesCS6A01G362300	chr7A	91.801	622	48	3	1609	2229	669871236	669871855	0.000000e+00	863.0
25	TraesCS6A01G362300	chr7A	92.093	215	16	1	2223	2437	669871925	669872138	3.940000e-78	302.0
26	TraesCS6A01G362300	chr1D	90.967	631	45	9	1605	2229	6406095	6406719	0.000000e+00	839.0
27	TraesCS6A01G362300	chr1D	88.542	96	8	2	710	802	170833779	170833684	1.980000e-21	113.0
28	TraesCS6A01G362300	chrUn	100.000	375	0	0	2063	2437	478298925	478298551	0.000000e+00	693.0
29	TraesCS6A01G362300	chr3D	91.705	217	15	3	2223	2437	36169625	36169840	5.090000e-77	298.0
30	TraesCS6A01G362300	chr4D	85.567	97	11	3	710	803	435790502	435790598	5.550000e-17	99.0
31	TraesCS6A01G362300	chr4D	81.818	99	13	2	710	803	259763013	259763111	7.220000e-11	78.7
32	TraesCS6A01G362300	chr1A	96.364	55	2	0	710	764	371082786	371082840	9.280000e-15	91.6

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	TraesCS6A01G362300	chr6A	592274074	592276510	2436	False	1645.0	4501	97.932667	1	2437	3	chr6A.!!$F2	2436
1	TraesCS6A01G362300	chr6B	672098600	672100498	1898	False	524.2	1849	93.817200	1	1607	5	chr6B.!!$F2	1606
2	TraesCS6A01G362300	chr3B	486797456	486798289	833	False	1506.0	1506	99.281000	1605	2437	1	chr3B.!!$F1	832
3	TraesCS6A01G362300	chr3B	774821486	774822314	828	False	1399.0	1399	97.112000	1608	2437	1	chr3B.!!$F2	829
4	TraesCS6A01G362300	chr3B	720234672	720235505	833	True	1133.0	1133	91.388000	1608	2431	1	chr3B.!!$R1	823
5	TraesCS6A01G362300	chr6D	445716909	445721877	4968	False	553.8	1182	93.508800	122	1607	5	chr6D.!!$F1	1485
6	TraesCS6A01G362300	chr7B	43673194	43674017	823	False	1123.0	1123	91.236000	1608	2437	1	chr7B.!!$F1	829
7	TraesCS6A01G362300	chr5B	639763074	639763900	826	True	1123.0	1123	91.159000	1604	2437	1	chr5B.!!$R1	833
8	TraesCS6A01G362300	chr2B	16305886	16306632	746	False	1013.0	1013	91.200000	1605	2350	1	chr2B.!!$F1	745
9	TraesCS6A01G362300	chr2B	406538376	406538996	620	False	837.0	837	91.026000	1608	2229	1	chr2B.!!$F2	621
10	TraesCS6A01G362300	chr7A	669871236	669872138	902	False	582.5	863	91.947000	1609	2437	2	chr7A.!!$F1	828
11	TraesCS6A01G362300	chr1D	6406095	6406719	624	False	839.0	839	90.967000	1605	2229	1	chr1D.!!$F1	624

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
29	30	1.068055	CACCAGCAGAACATGGCTTTC	60.068	52.381	0.0	0.0	40.45	2.62	F
30	31	1.250328	CCAGCAGAACATGGCTTTCA	58.750	50.000	0.0	0.0	38.56	2.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1398	1804	0.111061	TTGAGGCTTGCCATCACTGT	59.889	50.000	14.54	0.0	0.0	3.55	R
1683	2607	3.306780	CGGGATTAGAGAGTTTGGTGTGT	60.307	47.826	0.00	0.0	0.0	3.72	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
24	25	2.177950	GCTCACCAGCAGAACATGG	58.822	57.895	0.00	0.00	46.06	3.66
29	30	1.068055	CACCAGCAGAACATGGCTTTC	60.068	52.381	0.00	0.00	40.45	2.62
30	31	1.250328	CCAGCAGAACATGGCTTTCA	58.750	50.000	0.00	0.00	38.56	2.69
50	51	6.455360	TTCAGAGTTTGTGCTTTTTCATCT	57.545	33.333	0.00	0.00	0.00	2.90
182	227	8.924511	TTCCCAAATATCCTAGCTAAATCTTG	57.075	34.615	0.00	0.52	0.00	3.02
193	238	8.328758	TCCTAGCTAAATCTTGAAAATTCTCCA	58.671	33.333	0.00	0.00	0.00	3.86
208	253	7.581213	AAATTCTCCATTGTTTATGCCGATA	57.419	32.000	0.00	0.00	32.60	2.92
214	259	7.448161	TCTCCATTGTTTATGCCGATAATTCAT	59.552	33.333	0.00	0.00	32.60	2.57
301	349	7.406104	AGAAAGCCACTTAGGTCTCAAATAAT	58.594	34.615	0.00	0.00	40.61	1.28
307	355	7.970614	GCCACTTAGGTCTCAAATAATGAAAAG	59.029	37.037	0.00	0.00	37.37	2.27
308	356	8.462016	CCACTTAGGTCTCAAATAATGAAAAGG	58.538	37.037	0.00	0.00	37.67	3.11
342	390	5.203528	AGGGGGTTCAATGATAGAACAATG	58.796	41.667	8.15	0.00	45.45	2.82
462	749	5.582269	TCTTTCCAATCTCTGAAATGCTACG	59.418	40.000	0.00	0.00	30.67	3.51
551	838	9.552114	GCTCTTTAATGATATGCATTGATGTAC	57.448	33.333	3.54	0.00	46.38	2.90
561	848	5.384063	TGCATTGATGTACCGATTTGTTT	57.616	34.783	0.00	0.00	0.00	2.83
670	959	7.789273	TGTTCTTTGTTTAACGTCCAATCTA	57.211	32.000	0.00	0.00	0.00	1.98
685	974	9.901172	ACGTCCAATCTATTTAATTACTTCCTT	57.099	29.630	0.00	0.00	0.00	3.36
745	1034	9.088512	GTGAATCTACACTCGAAAATATGTCTT	57.911	33.333	0.00	0.00	37.73	3.01
806	1104	3.544698	AGGAACAGAGGGAGTACTTGA	57.455	47.619	0.00	0.00	0.00	3.02
920	1318	2.300967	CCTTGGAGGCTAGTGGGCA	61.301	63.158	2.14	0.00	43.56	5.36
921	1319	1.685224	CTTGGAGGCTAGTGGGCAA	59.315	57.895	2.14	0.00	43.56	4.52
937	1335	6.904626	AGTGGGCAACAGATCTCTATAAATT	58.095	36.000	0.00	0.00	39.74	1.82
961	1359	8.709386	TTGACATCTTTTCTTCTATCTAGCAC	57.291	34.615	0.00	0.00	0.00	4.40
999	1397	8.366671	AGTACAACACATCTCTCTAACAAAAC	57.633	34.615	0.00	0.00	0.00	2.43
1012	1410	6.931281	TCTCTAACAAAACATGAGGACTTCAG	59.069	38.462	0.00	0.00	39.68	3.02
1023	1421	5.441718	TGAGGACTTCAGCAATCCTATTT	57.558	39.130	0.00	0.00	43.12	1.40
1050	1448	2.447408	TTGCCCTCATGCTGATGATT	57.553	45.000	0.00	0.00	37.97	2.57
1076	1482	8.990163	TCTTCAGGTATCTACATACACATACA	57.010	34.615	0.00	0.00	37.24	2.29
1077	1483	9.588096	TCTTCAGGTATCTACATACACATACAT	57.412	33.333	0.00	0.00	37.24	2.29
1078	1484	9.631452	CTTCAGGTATCTACATACACATACATG	57.369	37.037	0.00	0.00	37.24	3.21
1079	1485	8.706322	TCAGGTATCTACATACACATACATGT	57.294	34.615	2.69	2.69	42.84	3.21
1080	1486	8.793592	TCAGGTATCTACATACACATACATGTC	58.206	37.037	0.00	0.00	39.39	3.06
1081	1487	8.576442	CAGGTATCTACATACACATACATGTCA	58.424	37.037	0.00	0.00	39.39	3.58
1082	1488	9.314133	AGGTATCTACATACACATACATGTCAT	57.686	33.333	0.00	0.00	39.39	3.06
1083	1489	9.929180	GGTATCTACATACACATACATGTCATT	57.071	33.333	0.00	0.00	39.39	2.57
1097	1503	6.140303	ACATGTCATTCCATATGTTTGCTC	57.860	37.500	1.24	0.00	30.05	4.26
1198	1604	1.637553	AGGGCCAGTGTGATGAAATCT	59.362	47.619	6.18	0.00	45.81	2.40
1376	1782	9.862585	GTTTATGTTTGTGGAATGAAATTTGAC	57.137	29.630	0.00	0.00	36.07	3.18
1398	1804	7.613585	TGACTTTATGGTTGGTCGAGTAATAA	58.386	34.615	0.00	0.00	0.00	1.40
1407	1813	5.006153	TGGTCGAGTAATAACAGTGATGG	57.994	43.478	0.00	0.00	0.00	3.51
1526	1932	9.974750	GAATTGTACTCTTTAATACTTCAGTGC	57.025	33.333	0.00	0.00	0.00	4.40
1589	1995	1.889105	ATCCGTGGATGCACATCGC	60.889	57.895	18.05	0.18	38.69	4.58
1595	2001	1.002468	GTGGATGCACATCGCCATAAC	60.002	52.381	13.07	0.00	41.33	1.89
1683	2607	4.937620	CGAACTCTCAATCCCTGAAATGAA	59.062	41.667	0.00	0.00	32.17	2.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
4	5	1.531423	CATGTTCTGCTGGTGAGCTT	58.469	50.000	0.00	0.00	46.39	3.74
11	12	1.201647	CTGAAAGCCATGTTCTGCTGG	59.798	52.381	0.00	0.00	38.00	4.85
14	15	2.157738	ACTCTGAAAGCCATGTTCTGC	58.842	47.619	0.00	0.00	0.00	4.26
24	25	4.864247	TGAAAAAGCACAAACTCTGAAAGC	59.136	37.500	0.00	0.00	0.00	3.51
29	30	5.009410	AGGAGATGAAAAAGCACAAACTCTG	59.991	40.000	0.00	0.00	0.00	3.35
30	31	5.136105	AGGAGATGAAAAAGCACAAACTCT	58.864	37.500	0.00	0.00	0.00	3.24
70	71	6.318648	TGAATAGGCTCAGACGCAAAATATTT	59.681	34.615	0.00	0.00	0.00	1.40
80	81	4.052159	AGTGATTGAATAGGCTCAGACG	57.948	45.455	0.00	0.00	0.00	4.18
83	84	7.222872	AGGATTTAGTGATTGAATAGGCTCAG	58.777	38.462	0.00	0.00	0.00	3.35
182	227	6.329496	TCGGCATAAACAATGGAGAATTTTC	58.671	36.000	0.00	0.00	35.99	2.29
193	238	7.715657	ACACATGAATTATCGGCATAAACAAT	58.284	30.769	0.00	0.00	0.00	2.71
301	349	3.709141	CCCCTTGTTCCTTTTCCTTTTCA	59.291	43.478	0.00	0.00	0.00	2.69
307	355	1.968493	GAACCCCCTTGTTCCTTTTCC	59.032	52.381	0.00	0.00	38.94	3.13
308	356	2.673258	TGAACCCCCTTGTTCCTTTTC	58.327	47.619	1.84	0.00	43.17	2.29
320	368	4.956075	ACATTGTTCTATCATTGAACCCCC	59.044	41.667	9.17	0.00	42.04	5.40
561	848	6.489700	TGTGTAGCATTTCAGAGATTGGAAAA	59.510	34.615	0.00	0.00	36.67	2.29
837	1135	6.183360	GCGTGCAGATAGAGAGATTGGATATA	60.183	42.308	0.00	0.00	0.00	0.86
906	1304	1.078143	CTGTTGCCCACTAGCCTCC	60.078	63.158	0.00	0.00	0.00	4.30
907	1305	0.543749	ATCTGTTGCCCACTAGCCTC	59.456	55.000	0.00	0.00	0.00	4.70
937	1335	6.975197	CGTGCTAGATAGAAGAAAAGATGTCA	59.025	38.462	0.00	0.00	0.00	3.58
961	1359	5.743467	TGTGTTGTACTATGAACTTTTGCG	58.257	37.500	0.00	0.00	0.00	4.85
999	1397	3.278668	AGGATTGCTGAAGTCCTCATG	57.721	47.619	0.00	0.00	37.88	3.07
1012	1410	5.105595	GGGCAATGGAGATAAATAGGATTGC	60.106	44.000	0.00	0.00	42.13	3.56
1023	1421	2.060275	AGCATGAGGGCAATGGAGATA	58.940	47.619	0.00	0.00	35.83	1.98
1050	1448	9.416284	TGTATGTGTATGTAGATACCTGAAGAA	57.584	33.333	7.51	0.00	34.54	2.52
1076	1482	5.889853	ACAGAGCAAACATATGGAATGACAT	59.110	36.000	7.80	0.00	34.90	3.06
1077	1483	5.124297	CACAGAGCAAACATATGGAATGACA	59.876	40.000	7.80	0.00	0.00	3.58
1078	1484	5.575957	CACAGAGCAAACATATGGAATGAC	58.424	41.667	7.80	2.03	0.00	3.06
1079	1485	4.096833	GCACAGAGCAAACATATGGAATGA	59.903	41.667	7.80	0.00	44.79	2.57
1080	1486	4.357142	GCACAGAGCAAACATATGGAATG	58.643	43.478	7.80	4.14	44.79	2.67
1081	1487	4.644103	GCACAGAGCAAACATATGGAAT	57.356	40.909	7.80	0.00	44.79	3.01
1097	1503	4.318332	TGTTAAGGAAGATCACTGCACAG	58.682	43.478	0.00	0.00	0.00	3.66
1158	1564	1.065926	TCGTAGACTCTAGGACCGCAA	60.066	52.381	4.64	0.00	0.00	4.85
1198	1604	0.176910	TTGCACCAGTCACGACAAGA	59.823	50.000	0.00	0.00	0.00	3.02
1321	1727	6.887626	AATAAAGTTTTACGTCCATGTGGT	57.112	33.333	0.00	0.00	36.34	4.16
1376	1782	7.548075	ACTGTTATTACTCGACCAACCATAAAG	59.452	37.037	0.00	0.00	0.00	1.85
1398	1804	0.111061	TTGAGGCTTGCCATCACTGT	59.889	50.000	14.54	0.00	0.00	3.55
1407	1813	8.608844	AGTATTATTGTATACTTGAGGCTTGC	57.391	34.615	4.17	0.00	37.95	4.01
1526	1932	7.646130	GTCCTTCTCTATCGAATTCTTGTGTAG	59.354	40.741	3.52	0.00	0.00	2.74
1589	1995	9.996554	ACTTTTTCCTTTTGAATAAGGTTATGG	57.003	29.630	0.00	0.00	42.75	2.74
1595	2001	8.956533	TTTGGACTTTTTCCTTTTGAATAAGG	57.043	30.769	9.03	0.00	46.10	2.69
1683	2607	3.306780	CGGGATTAGAGAGTTTGGTGTGT	60.307	47.826	0.00	0.00	0.00	3.72

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.