AutoCloner

Multiple sequence alignment - TraesCS4B01G290700

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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	TraesCS4B01G290700	chr4B	100.000	2771	0	0	1	2771	575725105	575727875	0.000000e+00	5118
1	TraesCS4B01G290700	chr5D	93.843	1413	53	8	1030	2434	27979285	27977899	0.000000e+00	2097
2	TraesCS4B01G290700	chr6A	86.388	1653	195	20	1124	2770	16597793	16599421	0.000000e+00	1779
3	TraesCS4B01G290700	chr6A	83.561	1247	179	19	987	2224	15925248	15924019	0.000000e+00	1144
4	TraesCS4B01G290700	chr6A	82.343	1229	180	19	952	2176	15906972	15905777	0.000000e+00	1033
5	TraesCS4B01G290700	chr6A	82.262	1229	181	19	952	2176	15700695	15701890	0.000000e+00	1027
6	TraesCS4B01G290700	chr6A	81.910	1194	197	13	1036	2219	15914119	15912935	0.000000e+00	990
7	TraesCS4B01G290700	chr6A	79.412	1190	212	25	996	2172	16628992	16630161	0.000000e+00	809
8	TraesCS4B01G290700	chr6A	81.202	915	140	18	1490	2387	15934200	15933301	0.000000e+00	708
9	TraesCS4B01G290700	chr6A	85.409	281	29	11	2369	2648	15702100	15702369	5.840000e-72	281
10	TraesCS4B01G290700	chr6A	92.857	70	3	2	2318	2387	15701994	15702061	1.760000e-17	100
11	TraesCS4B01G290700	chr3B	91.765	935	64	10	1	928	709291640	709292568	0.000000e+00	1288
12	TraesCS4B01G290700	chr3B	91.444	935	65	13	1	928	647921246	647922172	0.000000e+00	1269
13	TraesCS4B01G290700	chr3B	90.727	949	74	12	1	942	15835977	15835036	0.000000e+00	1253
14	TraesCS4B01G290700	chr1D	91.346	936	73	8	3	934	4440725	4439794	0.000000e+00	1273
15	TraesCS4B01G290700	chr2B	91.426	933	69	11	1	928	708824803	708825729	0.000000e+00	1269
16	TraesCS4B01G290700	chr2B	90.053	935	83	8	1	928	101496982	101497913	0.000000e+00	1203
17	TraesCS4B01G290700	chr5B	91.450	924	67	11	12	928	699408953	699409871	0.000000e+00	1258
18	TraesCS4B01G290700	chr6B	90.522	939	80	8	1	934	435580400	435581334	0.000000e+00	1232
19	TraesCS4B01G290700	chr6B	82.507	1412	202	25	981	2384	26512143	26513517	0.000000e+00	1197
20	TraesCS4B01G290700	chr6B	84.848	1023	140	14	1141	2156	28730858	28729844	0.000000e+00	1016
21	TraesCS4B01G290700	chr6B	79.795	1366	225	38	1049	2387	26841904	26840563	0.000000e+00	946
22	TraesCS4B01G290700	chr6B	78.928	1362	238	36	1049	2387	26856796	26855461	0.000000e+00	880
23	TraesCS4B01G290700	chr6B	86.000	300	39	3	2390	2688	26686794	26686497	4.450000e-83	318
24	TraesCS4B01G290700	chr6B	85.211	284	37	5	2369	2651	26513559	26513838	1.260000e-73	287
25	TraesCS4B01G290700	chrUn	90.486	925	80	7	1	920	84022938	84023859	0.000000e+00	1214
26	TraesCS4B01G290700	chr6D	83.199	1363	185	26	987	2339	14941169	14939841	0.000000e+00	1208
27	TraesCS4B01G290700	chr6D	81.914	1421	194	34	986	2387	14503346	14504722	0.000000e+00	1142
28	TraesCS4B01G290700	chr6D	81.590	1396	219	22	1007	2387	15344829	15343457	0.000000e+00	1120
29	TraesCS4B01G290700	chr6D	79.565	1424	251	22	982	2387	14422058	14423459	0.000000e+00	981
30	TraesCS4B01G290700	chr6D	82.088	910	135	16	1490	2387	15352522	15351629	0.000000e+00	752
31	TraesCS4B01G290700	chr6D	80.945	635	78	19	1765	2387	15349400	15348797	1.940000e-126	462
32	TraesCS4B01G290700	chr6D	87.625	299	33	4	2391	2688	14791157	14790862	7.350000e-91	344
33	TraesCS4B01G290700	chr6D	86.572	283	34	4	2369	2651	14436521	14436799	2.680000e-80	309
34	TraesCS4B01G290700	chr6D	87.786	262	27	5	2369	2629	14939743	14939486	4.490000e-78	302
35	TraesCS4B01G290700	chr6D	83.784	296	40	7	2369	2661	14725940	14725650	9.780000e-70	274
36	TraesCS4B01G290700	chr6D	83.392	283	40	6	2369	2648	14443360	14443638	3.540000e-64	255

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	TraesCS4B01G290700	chr4B	575725105	575727875	2770	False	5118.000000	5118	100.000000	1	2771	1	chr4B.!!$F1	2770
1	TraesCS4B01G290700	chr5D	27977899	27979285	1386	True	2097.000000	2097	93.843000	1030	2434	1	chr5D.!!$R1	1404
2	TraesCS4B01G290700	chr6A	16597793	16599421	1628	False	1779.000000	1779	86.388000	1124	2770	1	chr6A.!!$F1	1646
3	TraesCS4B01G290700	chr6A	15924019	15925248	1229	True	1144.000000	1144	83.561000	987	2224	1	chr6A.!!$R3	1237
4	TraesCS4B01G290700	chr6A	15905777	15906972	1195	True	1033.000000	1033	82.343000	952	2176	1	chr6A.!!$R1	1224
5	TraesCS4B01G290700	chr6A	15912935	15914119	1184	True	990.000000	990	81.910000	1036	2219	1	chr6A.!!$R2	1183
6	TraesCS4B01G290700	chr6A	16628992	16630161	1169	False	809.000000	809	79.412000	996	2172	1	chr6A.!!$F2	1176
7	TraesCS4B01G290700	chr6A	15933301	15934200	899	True	708.000000	708	81.202000	1490	2387	1	chr6A.!!$R4	897
8	TraesCS4B01G290700	chr6A	15700695	15702369	1674	False	469.333333	1027	86.842667	952	2648	3	chr6A.!!$F3	1696
9	TraesCS4B01G290700	chr3B	709291640	709292568	928	False	1288.000000	1288	91.765000	1	928	1	chr3B.!!$F2	927
10	TraesCS4B01G290700	chr3B	647921246	647922172	926	False	1269.000000	1269	91.444000	1	928	1	chr3B.!!$F1	927
11	TraesCS4B01G290700	chr3B	15835036	15835977	941	True	1253.000000	1253	90.727000	1	942	1	chr3B.!!$R1	941
12	TraesCS4B01G290700	chr1D	4439794	4440725	931	True	1273.000000	1273	91.346000	3	934	1	chr1D.!!$R1	931
13	TraesCS4B01G290700	chr2B	708824803	708825729	926	False	1269.000000	1269	91.426000	1	928	1	chr2B.!!$F2	927
14	TraesCS4B01G290700	chr2B	101496982	101497913	931	False	1203.000000	1203	90.053000	1	928	1	chr2B.!!$F1	927
15	TraesCS4B01G290700	chr5B	699408953	699409871	918	False	1258.000000	1258	91.450000	12	928	1	chr5B.!!$F1	916
16	TraesCS4B01G290700	chr6B	435580400	435581334	934	False	1232.000000	1232	90.522000	1	934	1	chr6B.!!$F1	933
17	TraesCS4B01G290700	chr6B	28729844	28730858	1014	True	1016.000000	1016	84.848000	1141	2156	1	chr6B.!!$R4	1015
18	TraesCS4B01G290700	chr6B	26840563	26841904	1341	True	946.000000	946	79.795000	1049	2387	1	chr6B.!!$R2	1338
19	TraesCS4B01G290700	chr6B	26855461	26856796	1335	True	880.000000	880	78.928000	1049	2387	1	chr6B.!!$R3	1338
20	TraesCS4B01G290700	chr6B	26512143	26513838	1695	False	742.000000	1197	83.859000	981	2651	2	chr6B.!!$F2	1670
21	TraesCS4B01G290700	chrUn	84022938	84023859	921	False	1214.000000	1214	90.486000	1	920	1	chrUn.!!$F1	919
22	TraesCS4B01G290700	chr6D	14503346	14504722	1376	False	1142.000000	1142	81.914000	986	2387	1	chr6D.!!$F4	1401
23	TraesCS4B01G290700	chr6D	14422058	14423459	1401	False	981.000000	981	79.565000	982	2387	1	chr6D.!!$F1	1405
24	TraesCS4B01G290700	chr6D	15343457	15352522	9065	True	778.000000	1120	81.541000	1007	2387	3	chr6D.!!$R4	1380
25	TraesCS4B01G290700	chr6D	14939486	14941169	1683	True	755.000000	1208	85.492500	987	2629	2	chr6D.!!$R3	1642

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
761	776	0.611896	TGAGAGAGATCGTGTGGGCA	60.612	55.0	0.0	0.0	0.0	5.36	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2637	9490	0.397941	CAGCAGGTGGAAGGTCTCAA	59.602	55.0	0.0	0.0	0.0	3.02	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
87	90	1.039856	GCCCACACACCAGTTTTCAT	58.960	50.000	0.00	0.0	0.00	2.57
139	142	2.664851	CTTTGCCCACACGCTCGA	60.665	61.111	0.00	0.0	0.00	4.04
140	143	2.031919	TTTGCCCACACGCTCGAT	59.968	55.556	0.00	0.0	0.00	3.59
142	145	1.169661	TTTGCCCACACGCTCGATTT	61.170	50.000	0.00	0.0	0.00	2.17
163	167	2.489275	CGCCCACACCAAAGCTGTT	61.489	57.895	0.00	0.0	0.00	3.16
248	254	4.684484	AACTCTCTTTTACCCGAGTTGT	57.316	40.909	0.00	0.0	43.03	3.32
262	268	3.489059	CCGAGTTGTCATGTGTTTTTGCT	60.489	43.478	0.00	0.0	0.00	3.91
370	380	3.005155	GCACATGGCAACTCTCTCTTTTT	59.995	43.478	0.00	0.0	43.97	1.94
750	765	2.024941	TGATGTAGGTGGCTGAGAGAGA	60.025	50.000	0.00	0.0	0.00	3.10
761	776	0.611896	TGAGAGAGATCGTGTGGGCA	60.612	55.000	0.00	0.0	0.00	5.36
984	1002	3.033764	GACGCCGTTGTTCTCGCA	61.034	61.111	0.00	0.0	0.00	5.10
1015	7703	4.161295	CCATGCTCCGCCTCCGAA	62.161	66.667	0.00	0.0	36.29	4.30
1024	7712	2.357034	GCCTCCGAAAGTGCGTCA	60.357	61.111	0.00	0.0	0.00	4.35
1117	7835	2.043046	CGCCCCACATTTCCCCAT	60.043	61.111	0.00	0.0	0.00	4.00
1132	7850	1.780309	CCCCATATCCCAGTGGCTTTA	59.220	52.381	2.61	0.0	34.08	1.85
1333	8072	0.314935	CTGCGCCAAAGTGGACAAAT	59.685	50.000	4.18	0.0	40.96	2.32
1375	8114	4.344865	TTGCCGGCCTTGGTCTCC	62.345	66.667	26.77	0.0	0.00	3.71
1384	8123	0.970937	CCTTGGTCTCCTGCGTCCTA	60.971	60.000	0.00	0.0	0.00	2.94
1470	8209	2.953620	GCACTACTACCTGCCCCTCTTA	60.954	54.545	0.00	0.0	0.00	2.10
1524	8263	1.032657	GCTCGTCCTGCCTACTCTCA	61.033	60.000	0.00	0.0	0.00	3.27
1558	8297	1.355381	AGGTGATCAAGCCCAATGTCA	59.645	47.619	0.00	0.0	0.00	3.58
1583	8325	4.770874	GCGGGAGTGCGGCCTAAA	62.771	66.667	0.00	0.0	0.00	1.85
1836	8578	1.340697	TGCTCTCTGTAAGGCTCCGTA	60.341	52.381	0.00	0.0	0.00	4.02
2086	8828	3.135348	TGGAGAAGTTCATATGCCCTCAG	59.865	47.826	5.50	0.0	0.00	3.35
2099	8841	1.222936	CCTCAGAAGGAAGCCGCAT	59.777	57.895	0.00	0.0	46.67	4.73
2144	8886	0.106268	TGCTTGCAAAGGGGAAGTGA	60.106	50.000	0.00	0.0	46.35	3.41
2293	9075	3.561143	TGTTTTCTGTGGTATGCCTGTT	58.439	40.909	0.16	0.0	35.27	3.16
2294	9076	4.720046	TGTTTTCTGTGGTATGCCTGTTA	58.280	39.130	0.16	0.0	35.27	2.41
2295	9077	4.517453	TGTTTTCTGTGGTATGCCTGTTAC	59.483	41.667	0.16	0.0	35.27	2.50
2296	9078	4.359434	TTTCTGTGGTATGCCTGTTACA	57.641	40.909	0.16	0.0	35.27	2.41
2297	9079	4.568072	TTCTGTGGTATGCCTGTTACAT	57.432	40.909	0.16	0.0	35.27	2.29
2298	9080	4.137116	TCTGTGGTATGCCTGTTACATC	57.863	45.455	0.16	0.0	35.27	3.06
2351	9140	8.150945	TGCTAACTCCCTATGAAACTGATAATC	58.849	37.037	0.00	0.0	0.00	1.75
2492	9344	5.668558	AAAGAGTAACGTGGTGTCATTTC	57.331	39.130	0.00	0.0	0.00	2.17
2582	9435	7.020827	TCATTTCATTGTCTCTTAGGTTCCT	57.979	36.000	0.00	0.0	0.00	3.36
2637	9490	4.705507	TGCTTAGGTTAGACTTCGAGACAT	59.294	41.667	0.00	0.0	0.00	3.06
2644	9497	3.859411	AGACTTCGAGACATTGAGACC	57.141	47.619	0.00	0.0	0.00	3.85
2654	9507	1.271597	ACATTGAGACCTTCCACCTGC	60.272	52.381	0.00	0.0	0.00	4.85
2660	9513	2.046892	CCTTCCACCTGCTGTCCG	60.047	66.667	0.00	0.0	0.00	4.79
2672	9525	1.369692	CTGTCCGCCCTGTTACACA	59.630	57.895	0.00	0.0	0.00	3.72
2691	9544	1.140852	CAACACTGAGACCTTCCACCA	59.859	52.381	0.00	0.0	0.00	4.17
2719	9572	6.313519	TCCATTCTAACATAAAGAGTGGCT	57.686	37.500	9.15	0.0	45.63	4.75
2733	9586	5.438761	AGAGTGGCTAATTGTTGTGTTTC	57.561	39.130	0.00	0.0	0.00	2.78
2737	9590	3.243234	TGGCTAATTGTTGTGTTTCGTGG	60.243	43.478	0.00	0.0	0.00	4.94
2739	9592	3.728718	GCTAATTGTTGTGTTTCGTGGTG	59.271	43.478	0.00	0.0	0.00	4.17
2742	9595	3.743567	TTGTTGTGTTTCGTGGTGTAC	57.256	42.857	0.00	0.0	0.00	2.90

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
23	24	1.715785	CCCCCATGTGGTGAAAAAGT	58.284	50.000	0.00	0.00	0.00	2.66
87	90	4.641645	CCAACCCCTCTGCGTGCA	62.642	66.667	0.00	0.00	0.00	4.57
139	142	1.247567	CTTTGGTGTGGGCGAGAAAT	58.752	50.000	0.00	0.00	0.00	2.17
140	143	1.452145	GCTTTGGTGTGGGCGAGAAA	61.452	55.000	0.00	0.00	0.00	2.52
142	145	2.281484	GCTTTGGTGTGGGCGAGA	60.281	61.111	0.00	0.00	0.00	4.04
163	167	5.185454	CCCTGCAGAAATACATGACAACTA	58.815	41.667	17.39	0.00	0.00	2.24
248	254	4.991153	TGTACCAAGCAAAAACACATGA	57.009	36.364	0.00	0.00	0.00	3.07
340	350	0.670162	GTTGCCATGTGCTCACAAGT	59.330	50.000	6.81	0.00	45.41	3.16
655	669	0.905357	CCGGACCCTCTTCAATGTCT	59.095	55.000	0.00	0.00	0.00	3.41
716	730	4.735132	CATCACGGTCCCGCACGT	62.735	66.667	5.47	0.00	45.25	4.49
732	747	2.660572	GATCTCTCTCAGCCACCTACA	58.339	52.381	0.00	0.00	0.00	2.74
750	765	2.957402	ATGGATAATGCCCACACGAT	57.043	45.000	0.00	0.00	36.36	3.73
761	776	3.096092	ACGTGTGGGCAAAATGGATAAT	58.904	40.909	0.00	0.00	0.00	1.28
944	962	0.892063	GGCGATACAGAGATCCCCTC	59.108	60.000	0.00	0.00	42.28	4.30
947	965	1.080434	GCGGCGATACAGAGATCCC	60.080	63.158	12.98	0.00	0.00	3.85
948	966	1.080434	GGCGGCGATACAGAGATCC	60.080	63.158	12.98	0.00	0.00	3.36
949	967	1.442857	CGGCGGCGATACAGAGATC	60.443	63.158	29.19	0.00	0.00	2.75
968	986	3.036084	CTGCGAGAACAACGGCGT	61.036	61.111	6.77	6.77	0.00	5.68
1015	7703	0.034896	AGACGGGAAATGACGCACTT	59.965	50.000	0.00	0.00	0.00	3.16
1024	7712	2.112190	GGAAGAGAGGAGACGGGAAAT	58.888	52.381	0.00	0.00	0.00	2.17
1099	7811	1.576368	TATGGGGAAATGTGGGGCGT	61.576	55.000	0.00	0.00	0.00	5.68
1368	8107	0.039180	TCTTAGGACGCAGGAGACCA	59.961	55.000	0.00	0.00	0.00	4.02
1384	8123	1.455959	AGACTAGGCGGGCGATCTT	60.456	57.895	0.00	0.00	0.00	2.40
1470	8209	0.321996	GGAAGTTGTCGAAGGAGCCT	59.678	55.000	0.00	0.00	0.00	4.58
1583	8325	3.873361	CACCTTGACAATATCGCAGTCAT	59.127	43.478	0.00	0.00	41.42	3.06
1770	8512	6.600822	CAGACCACCTGAATGTATTCTTCAAT	59.399	38.462	6.21	0.00	45.78	2.57
1812	8554	3.006323	CGGAGCCTTACAGAGAGCAATAT	59.994	47.826	0.00	0.00	0.00	1.28
1813	8555	2.362397	CGGAGCCTTACAGAGAGCAATA	59.638	50.000	0.00	0.00	0.00	1.90
1814	8556	1.137872	CGGAGCCTTACAGAGAGCAAT	59.862	52.381	0.00	0.00	0.00	3.56
1815	8557	0.532573	CGGAGCCTTACAGAGAGCAA	59.467	55.000	0.00	0.00	0.00	3.91
1836	8578	6.553100	AGATTCCTTCGACTTCTTCAGGATAT	59.447	38.462	0.75	0.00	0.00	1.63
2086	8828	1.648467	GGTGTGATGCGGCTTCCTTC	61.648	60.000	12.65	5.07	0.00	3.46
2099	8841	1.905637	TAGTCTTCAGCGAGGTGTGA	58.094	50.000	2.10	0.41	0.00	3.58
2167	8911	2.704190	TCCTTGGCCCATTTTTGGTA	57.296	45.000	0.00	0.00	0.00	3.25
2293	9075	6.538945	TGACTAACTGGCATGTAAGATGTA	57.461	37.500	0.00	0.00	0.00	2.29
2294	9076	5.420725	TGACTAACTGGCATGTAAGATGT	57.579	39.130	0.00	0.00	0.00	3.06
2295	9077	6.722301	CAATGACTAACTGGCATGTAAGATG	58.278	40.000	0.00	0.00	45.29	2.90
2296	9078	5.297776	GCAATGACTAACTGGCATGTAAGAT	59.702	40.000	0.00	0.00	45.29	2.40
2297	9079	4.635765	GCAATGACTAACTGGCATGTAAGA	59.364	41.667	0.00	0.00	45.29	2.10
2298	9080	4.637534	AGCAATGACTAACTGGCATGTAAG	59.362	41.667	0.00	0.00	45.29	2.34
2351	9140	5.014544	ACATATATGGGGGTTCAGGAATCAG	59.985	44.000	16.96	0.00	0.00	2.90
2492	9344	7.000472	AGATCATACTGATACATTTTGGTGGG	59.000	38.462	0.00	0.00	37.20	4.61
2637	9490	0.397941	CAGCAGGTGGAAGGTCTCAA	59.602	55.000	0.00	0.00	0.00	3.02
2654	9507	1.369692	TGTGTAACAGGGCGGACAG	59.630	57.895	0.00	0.00	45.67	3.51
2672	9525	1.417890	CTGGTGGAAGGTCTCAGTGTT	59.582	52.381	0.00	0.00	0.00	3.32
2691	9544	9.014297	CCACTCTTTATGTTAGAATGGAAAACT	57.986	33.333	0.00	0.00	40.56	2.66
2719	9572	4.966965	ACACCACGAAACACAACAATTA	57.033	36.364	0.00	0.00	0.00	1.40
2733	9586	3.250744	CAGGACACATAAGTACACCACG	58.749	50.000	0.00	0.00	0.00	4.94
2737	9590	4.451096	CACAACCAGGACACATAAGTACAC	59.549	45.833	0.00	0.00	0.00	2.90
2739	9592	4.451096	CACACAACCAGGACACATAAGTAC	59.549	45.833	0.00	0.00	0.00	2.73
2742	9595	3.738982	TCACACAACCAGGACACATAAG	58.261	45.455	0.00	0.00	0.00	1.73

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.