AutoCloner

Multiple sequence alignment - TraesCS7D01G427400

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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	TraesCS7D01G427400	chr7D	100.000	2216	0	0	1	2216	548554189	548551974	0.000000e+00	4093
1	TraesCS7D01G427400	chr7D	90.876	833	72	4	1	831	344252406	344251576	0.000000e+00	1114
2	TraesCS7D01G427400	chr7D	90.745	832	75	2	1	831	334251288	334252118	0.000000e+00	1109
3	TraesCS7D01G427400	chr7B	87.852	1383	163	4	836	2216	357731674	357733053	0.000000e+00	1618
4	TraesCS7D01G427400	chr7B	87.563	1383	168	3	836	2216	357658810	357660190	0.000000e+00	1598
5	TraesCS7D01G427400	chr7B	85.676	740	106	0	1475	2214	174682624	174683363	0.000000e+00	780
6	TraesCS7D01G427400	chr5D	96.992	831	25	0	1	831	155058256	155059086	0.000000e+00	1397
7	TraesCS7D01G427400	chr5D	90.505	832	76	3	1	831	495332208	495333037	0.000000e+00	1096
8	TraesCS7D01G427400	chr5D	72.667	1211	299	27	982	2177	209721725	209720532	7.470000e-100	374
9	TraesCS7D01G427400	chr5D	71.016	1280	314	50	921	2172	503918231	503919481	2.820000e-64	255
10	TraesCS7D01G427400	chr1B	83.948	1383	222	0	834	2216	615737382	615736000	0.000000e+00	1325
11	TraesCS7D01G427400	chr1B	72.655	1258	321	22	932	2178	266878324	266879569	1.590000e-106	396
12	TraesCS7D01G427400	chr2A	88.312	1001	115	2	1217	2216	606690893	606689894	0.000000e+00	1199
13	TraesCS7D01G427400	chr2A	89.439	303	31	1	842	1144	606704603	606704302	4.470000e-102	381
14	TraesCS7D01G427400	chrUn	90.614	831	78	0	1	831	212277064	212276234	0.000000e+00	1103
15	TraesCS7D01G427400	chrUn	89.378	386	41	0	980	1365	480098244	480098629	9.200000e-134	486
16	TraesCS7D01G427400	chr3D	90.625	832	74	3	1	831	243232348	243231520	0.000000e+00	1101
17	TraesCS7D01G427400	chr4B	90.625	832	73	3	1	831	329595035	329595862	0.000000e+00	1099
18	TraesCS7D01G427400	chr2D	90.493	831	79	0	1	831	273086516	273087346	0.000000e+00	1098
19	TraesCS7D01G427400	chr6D	90.299	835	76	3	1	831	214118251	214117418	0.000000e+00	1088
20	TraesCS7D01G427400	chr4A	80.757	925	163	7	1071	1993	321258456	321257545	0.000000e+00	708
21	TraesCS7D01G427400	chr1D	83.840	526	82	3	1690	2214	117826636	117826113	4.250000e-137	497

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	TraesCS7D01G427400	chr7D	548551974	548554189	2215	True	4093	4093	100.000	1	2216	1	chr7D.!!$R2	2215
1	TraesCS7D01G427400	chr7D	344251576	344252406	830	True	1114	1114	90.876	1	831	1	chr7D.!!$R1	830
2	TraesCS7D01G427400	chr7D	334251288	334252118	830	False	1109	1109	90.745	1	831	1	chr7D.!!$F1	830
3	TraesCS7D01G427400	chr7B	357731674	357733053	1379	False	1618	1618	87.852	836	2216	1	chr7B.!!$F3	1380
4	TraesCS7D01G427400	chr7B	357658810	357660190	1380	False	1598	1598	87.563	836	2216	1	chr7B.!!$F2	1380
5	TraesCS7D01G427400	chr7B	174682624	174683363	739	False	780	780	85.676	1475	2214	1	chr7B.!!$F1	739
6	TraesCS7D01G427400	chr5D	155058256	155059086	830	False	1397	1397	96.992	1	831	1	chr5D.!!$F1	830
7	TraesCS7D01G427400	chr5D	495332208	495333037	829	False	1096	1096	90.505	1	831	1	chr5D.!!$F2	830
8	TraesCS7D01G427400	chr5D	209720532	209721725	1193	True	374	374	72.667	982	2177	1	chr5D.!!$R1	1195
9	TraesCS7D01G427400	chr5D	503918231	503919481	1250	False	255	255	71.016	921	2172	1	chr5D.!!$F3	1251
10	TraesCS7D01G427400	chr1B	615736000	615737382	1382	True	1325	1325	83.948	834	2216	1	chr1B.!!$R1	1382
11	TraesCS7D01G427400	chr1B	266878324	266879569	1245	False	396	396	72.655	932	2178	1	chr1B.!!$F1	1246
12	TraesCS7D01G427400	chr2A	606689894	606690893	999	True	1199	1199	88.312	1217	2216	1	chr2A.!!$R1	999
13	TraesCS7D01G427400	chrUn	212276234	212277064	830	True	1103	1103	90.614	1	831	1	chrUn.!!$R1	830
14	TraesCS7D01G427400	chr3D	243231520	243232348	828	True	1101	1101	90.625	1	831	1	chr3D.!!$R1	830
15	TraesCS7D01G427400	chr4B	329595035	329595862	827	False	1099	1099	90.625	1	831	1	chr4B.!!$F1	830
16	TraesCS7D01G427400	chr2D	273086516	273087346	830	False	1098	1098	90.493	1	831	1	chr2D.!!$F1	830
17	TraesCS7D01G427400	chr6D	214117418	214118251	833	True	1088	1088	90.299	1	831	1	chr6D.!!$R1	830
18	TraesCS7D01G427400	chr4A	321257545	321258456	911	True	708	708	80.757	1071	1993	1	chr4A.!!$R1	922
19	TraesCS7D01G427400	chr1D	117826113	117826636	523	True	497	497	83.840	1690	2214	1	chr1D.!!$R1	524

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
844	851	1.067213	TGCAAATCATCTGGACGTCGA	60.067	47.619	9.92	4.47	0.0	4.2	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1734	1741	0.400213	TGCAGTTGAACTTCCCGGAT	59.6	50.0	0.73	0.0	0.0	4.18	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
53	54	2.692041	GAGGATGGCTCAAAAGGAATGG	59.308	50.000	0.00	0.00	0.00	3.16
91	92	5.888161	AGTTTCTCAAAGATGTTGGAGTTGT	59.112	36.000	6.87	0.00	35.43	3.32
228	229	3.699538	TGTAGCACCTATCATTCGAGTGT	59.300	43.478	7.87	0.00	0.00	3.55
282	286	8.896744	TGCTTATCATAAGAAAGAACAAGATGG	58.103	33.333	8.74	0.00	0.00	3.51
373	377	7.119846	GCTTCACAAGTAATATGTCCAAGTCTT	59.880	37.037	0.00	0.00	0.00	3.01
377	381	7.387673	CACAAGTAATATGTCCAAGTCTTCACA	59.612	37.037	0.00	0.00	0.00	3.58
424	428	6.933521	GCACTCAATACAAGGTGATATGAGAT	59.066	38.462	6.86	0.00	32.12	2.75
610	617	5.358725	TGCAACGTACTAGAGGTAATCATGA	59.641	40.000	0.00	0.00	31.56	3.07
733	740	6.037281	GCAAGAAGTCCTAGGTAAATAGCAAC	59.963	42.308	9.08	0.00	0.00	4.17
822	829	3.073062	AGCAACAAGTATCTCCACCAAGT	59.927	43.478	0.00	0.00	0.00	3.16
831	838	6.058183	AGTATCTCCACCAAGTATGCAAATC	58.942	40.000	0.00	0.00	0.00	2.17
832	839	4.299586	TCTCCACCAAGTATGCAAATCA	57.700	40.909	0.00	0.00	0.00	2.57
840	847	4.260907	CCAAGTATGCAAATCATCTGGACG	60.261	45.833	0.00	0.00	36.63	4.79
844	851	1.067213	TGCAAATCATCTGGACGTCGA	60.067	47.619	9.92	4.47	0.00	4.20
862	869	4.150627	CGTCGATCACAGAAACAACATTCT	59.849	41.667	0.00	0.00	40.23	2.40
864	871	6.453003	CGTCGATCACAGAAACAACATTCTAG	60.453	42.308	0.00	0.00	37.56	2.43
963	970	3.637273	AGTGACAAGGGGGTCGGC	61.637	66.667	0.00	0.00	40.72	5.54
1045	1052	5.872617	CGATATCAAGGGTTGTCAACTTACA	59.127	40.000	15.17	0.00	0.00	2.41
1173	1180	1.862827	GAACAACGTTTGACTACGCCT	59.137	47.619	0.00	0.00	45.06	5.52
1194	1201	1.601759	GCAGCAGAAGGCCTTCACA	60.602	57.895	39.84	0.00	46.50	3.58
1215	1222	4.514066	ACAAAACTCTTGGGCTTACGTTAG	59.486	41.667	0.00	0.00	0.00	2.34
1314	1321	1.517242	CTGTCACTTCTTGTCAGCCC	58.483	55.000	0.00	0.00	35.08	5.19
1366	1373	3.529533	CATTCGAATCCTCAAGCTCAGT	58.470	45.455	7.92	0.00	0.00	3.41
1367	1374	2.949451	TCGAATCCTCAAGCTCAGTC	57.051	50.000	0.00	0.00	0.00	3.51
1469	1476	1.363530	ATTTGGCTCGGGGGATCCAT	61.364	55.000	15.23	0.00	34.36	3.41
1575	1582	3.376078	CGCCTGTTTGCATGGCCT	61.376	61.111	3.32	0.00	43.42	5.19
1646	1653	1.101049	CAAGCCAAACCAGACCGTGT	61.101	55.000	0.00	0.00	0.00	4.49
1652	1659	1.066908	CAAACCAGACCGTGTTGCATT	59.933	47.619	0.00	0.00	0.00	3.56
1662	1669	1.608590	CGTGTTGCATTTCCAGGTCTT	59.391	47.619	0.00	0.00	0.00	3.01
1689	1696	2.162681	CCACTCCCAATTCCTCAACAC	58.837	52.381	0.00	0.00	0.00	3.32
1701	1708	2.052047	CTCAACACCCGTGGGACCTT	62.052	60.000	13.01	0.00	38.96	3.50
1786	1793	5.127491	TGGTGGATAAGAGAACACGTTTTT	58.873	37.500	0.00	0.00	34.78	1.94
1945	1952	2.487934	GTGAGCTGTTCCGATATGCAT	58.512	47.619	3.79	3.79	0.00	3.96
2057	2064	0.473755	TTCACTCAAGCTTGCCCTCA	59.526	50.000	21.99	2.95	0.00	3.86
2181	2188	1.683365	GCATTGGGGCATCACCACT	60.683	57.895	0.00	0.00	45.20	4.00

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
46	47	1.923148	CCTAAAGGTGACCCCATTCCT	59.077	52.381	0.00	0.00	34.66	3.36
53	54	3.326880	TGAGAAACTCCTAAAGGTGACCC	59.673	47.826	0.00	0.00	36.34	4.46
91	92	3.070476	TGTGAAGGCATACAAGATGCA	57.930	42.857	11.35	0.00	46.21	3.96
228	229	5.163248	TGAGAACACTTGTTGGGTATCTCAA	60.163	40.000	0.00	0.00	40.14	3.02
282	286	4.081406	TCATATGCTTTCATACCATGCCC	58.919	43.478	0.00	0.00	37.94	5.36
373	377	4.273235	CCTTGCTATGCGTATTGATTGTGA	59.727	41.667	0.00	0.00	0.00	3.58
377	381	3.565482	CCACCTTGCTATGCGTATTGATT	59.435	43.478	0.00	0.00	0.00	2.57
424	428	6.070824	TGTCTCTTGTCTCCATTAGTTGCATA	60.071	38.462	0.00	0.00	0.00	3.14
610	617	5.407502	CATTTGCTCACATGACATGATTGT	58.592	37.500	22.19	0.00	39.32	2.71
668	675	6.479884	ACTTTCCTCATATCTTGCTTTCACT	58.520	36.000	0.00	0.00	0.00	3.41
733	740	1.482182	TGGGAGAGTCATGATGTTCCG	59.518	52.381	0.00	0.00	0.00	4.30
822	829	3.123050	CGACGTCCAGATGATTTGCATA	58.877	45.455	10.58	0.00	37.34	3.14
831	838	1.401905	TCTGTGATCGACGTCCAGATG	59.598	52.381	14.90	0.00	0.00	2.90
832	839	1.751437	TCTGTGATCGACGTCCAGAT	58.249	50.000	14.90	10.70	0.00	2.90
840	847	5.597813	AGAATGTTGTTTCTGTGATCGAC	57.402	39.130	0.00	0.00	34.68	4.20
844	851	5.940470	GGGTCTAGAATGTTGTTTCTGTGAT	59.060	40.000	0.00	0.00	36.63	3.06
862	869	1.347707	CAGGTGTTGCTTCAGGGTCTA	59.652	52.381	0.00	0.00	0.00	2.59
864	871	0.108585	TCAGGTGTTGCTTCAGGGTC	59.891	55.000	0.00	0.00	0.00	4.46
963	970	1.672356	CCCTTGTTGGAGGACTGCG	60.672	63.158	0.00	0.00	39.25	5.18
1057	1064	6.769341	TGATCAACAGCAACAATGATAGCTAT	59.231	34.615	5.76	5.76	35.19	2.97
1194	1201	4.514066	CACTAACGTAAGCCCAAGAGTTTT	59.486	41.667	0.00	0.00	45.62	2.43
1270	1277	3.490348	CCAACATCTCCTTTGGTTCTGT	58.510	45.455	0.00	0.00	37.98	3.41
1410	1417	0.687354	TCCCTTGCTGGAGTGAGAAC	59.313	55.000	0.00	0.00	38.35	3.01
1469	1476	4.629634	CCATGATTCGTTGTTGTAGTGCTA	59.370	41.667	0.00	0.00	0.00	3.49
1575	1582	6.003950	GTGCTTTATATGGGCCTTCATCTTA	58.996	40.000	4.53	0.00	0.00	2.10
1646	1653	4.751767	AACAAAAGACCTGGAAATGCAA	57.248	36.364	0.00	0.00	0.00	4.08
1689	1696	1.268992	TGGTGATAAGGTCCCACGGG	61.269	60.000	0.00	0.00	0.00	5.28
1701	1708	5.793817	CCATCGATAAAGTCCATGGTGATA	58.206	41.667	12.58	1.84	39.83	2.15
1734	1741	0.400213	TGCAGTTGAACTTCCCGGAT	59.600	50.000	0.73	0.00	0.00	4.18
1786	1793	2.093658	GGGCGATAGGAACAAAGTGAGA	60.094	50.000	0.00	0.00	0.00	3.27
1878	1885	2.105128	CTGTCCGAGACGATGGCC	59.895	66.667	0.00	0.00	34.95	5.36
1945	1952	2.435410	CATCCGCAGCTCTGTGCA	60.435	61.111	4.39	0.00	44.21	4.57
2057	2064	1.000993	ATCCAGAGACTCCAGCGGT	59.999	57.895	0.00	0.00	0.00	5.68
2181	2188	0.960364	GTACCGACGTACTGGGTGGA	60.960	60.000	9.56	0.00	41.50	4.02

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.