AutoCloner

Multiple sequence alignment - TraesCS5D01G044600

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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	TraesCS5D01G044600	chr5D	100.000	3266	0	0	1	3266	43404783	43408048	0.000000e+00	6032.0
1	TraesCS5D01G044600	chr5D	81.994	2327	356	34	999	3266	43316285	43318607	0.000000e+00	1917.0
2	TraesCS5D01G044600	chr5D	81.523	2154	332	48	1161	3258	43748021	43750164	0.000000e+00	1712.0
3	TraesCS5D01G044600	chr5D	77.739	2309	410	58	1013	3266	537630740	537632999	0.000000e+00	1321.0
4	TraesCS5D01G044600	chr5D	93.119	683	28	7	1	664	438396823	438397505	0.000000e+00	983.0
5	TraesCS5D01G044600	chr5D	91.753	679	31	7	1	664	298027569	298026901	0.000000e+00	920.0
6	TraesCS5D01G044600	chr5D	85.380	171	23	2	999	1168	43735575	43735744	3.350000e-40	176.0
7	TraesCS5D01G044600	chr5D	95.238	42	2	0	726	767	43405477	43405518	2.100000e-07	67.6
8	TraesCS5D01G044600	chr5D	95.238	42	2	0	695	736	43405508	43405549	2.100000e-07	67.6
9	TraesCS5D01G044600	chr5A	95.296	2636	87	14	665	3266	33179606	33182238	0.000000e+00	4146.0
10	TraesCS5D01G044600	chr5A	95.238	42	2	0	726	767	33179636	33179677	2.100000e-07	67.6
11	TraesCS5D01G044600	chr5B	92.277	1515	95	7	1771	3266	41272204	41273715	0.000000e+00	2130.0
12	TraesCS5D01G044600	chr5B	81.417	2244	354	38	1079	3266	41084431	41086667	0.000000e+00	1775.0
13	TraesCS5D01G044600	chr5B	92.670	1105	39	11	665	1742	41270856	41271945	0.000000e+00	1554.0
14	TraesCS5D01G044600	chr5B	95.238	42	2	0	695	736	41270917	41270958	2.100000e-07	67.6
15	TraesCS5D01G044600	chr7D	94.698	679	24	9	1	668	503843088	503843765	0.000000e+00	1044.0
16	TraesCS5D01G044600	chr7D	93.917	674	28	5	1	664	32565104	32565774	0.000000e+00	1005.0
17	TraesCS5D01G044600	chr7D	92.263	685	35	6	1	669	457187601	457186919	0.000000e+00	955.0
18	TraesCS5D01G044600	chrUn	94.362	674	27	4	1	664	103459316	103459988	0.000000e+00	1024.0
19	TraesCS5D01G044600	chr3D	91.483	681	26	13	1	664	12307382	12308047	0.000000e+00	907.0
20	TraesCS5D01G044600	chr3D	89.927	685	42	22	1	664	209070569	209069891	0.000000e+00	857.0
21	TraesCS5D01G044600	chr6D	91.069	683	31	19	1	664	466263176	466263847	0.000000e+00	896.0
22	TraesCS5D01G044600	chr4A	78.971	661	119	13	2618	3264	631676839	631677493	1.800000e-117	433.0

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	TraesCS5D01G044600	chr5D	43404783	43408048	3265	False	2055.733333	6032	96.825333	1	3266	3	chr5D.!!$F6	3265
1	TraesCS5D01G044600	chr5D	43316285	43318607	2322	False	1917.000000	1917	81.994000	999	3266	1	chr5D.!!$F1	2267
2	TraesCS5D01G044600	chr5D	43748021	43750164	2143	False	1712.000000	1712	81.523000	1161	3258	1	chr5D.!!$F3	2097
3	TraesCS5D01G044600	chr5D	537630740	537632999	2259	False	1321.000000	1321	77.739000	1013	3266	1	chr5D.!!$F5	2253
4	TraesCS5D01G044600	chr5D	438396823	438397505	682	False	983.000000	983	93.119000	1	664	1	chr5D.!!$F4	663
5	TraesCS5D01G044600	chr5D	298026901	298027569	668	True	920.000000	920	91.753000	1	664	1	chr5D.!!$R1	663
6	TraesCS5D01G044600	chr5A	33179606	33182238	2632	False	2106.800000	4146	95.267000	665	3266	2	chr5A.!!$F1	2601
7	TraesCS5D01G044600	chr5B	41084431	41086667	2236	False	1775.000000	1775	81.417000	1079	3266	1	chr5B.!!$F1	2187
8	TraesCS5D01G044600	chr5B	41270856	41273715	2859	False	1250.533333	2130	93.395000	665	3266	3	chr5B.!!$F2	2601
9	TraesCS5D01G044600	chr7D	503843088	503843765	677	False	1044.000000	1044	94.698000	1	668	1	chr7D.!!$F2	667
10	TraesCS5D01G044600	chr7D	32565104	32565774	670	False	1005.000000	1005	93.917000	1	664	1	chr7D.!!$F1	663
11	TraesCS5D01G044600	chr7D	457186919	457187601	682	True	955.000000	955	92.263000	1	669	1	chr7D.!!$R1	668
12	TraesCS5D01G044600	chrUn	103459316	103459988	672	False	1024.000000	1024	94.362000	1	664	1	chrUn.!!$F1	663
13	TraesCS5D01G044600	chr3D	12307382	12308047	665	False	907.000000	907	91.483000	1	664	1	chr3D.!!$F1	663
14	TraesCS5D01G044600	chr3D	209069891	209070569	678	True	857.000000	857	89.927000	1	664	1	chr3D.!!$R1	663
15	TraesCS5D01G044600	chr6D	466263176	466263847	671	False	896.000000	896	91.069000	1	664	1	chr6D.!!$F1	663
16	TraesCS5D01G044600	chr4A	631676839	631677493	654	False	433.000000	433	78.971000	2618	3264	1	chr4A.!!$F1	646

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
869	934	0.396435	AGCAACGACTTGACCCATGA	59.604	50.0	0.0	0.0	0.0	3.07	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2400	2749	0.387929	TAGTCCTGCGGAAATAGGCG	59.612	55.0	0.0	0.0	31.38	5.52	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
131	132	1.080434	GTTCTCGCGGAAGAGCAGT	60.080	57.895	6.13	0.00	38.12	4.40
260	261	1.198759	GGTTGGAGTAGGTGGAGGCA	61.199	60.000	0.00	0.00	0.00	4.75
273	274	1.634973	TGGAGGCATTGGAAGACATGA	59.365	47.619	0.00	0.00	0.00	3.07
278	279	3.134623	AGGCATTGGAAGACATGACGATA	59.865	43.478	0.00	0.00	0.00	2.92
397	434	3.075005	GGAGAGGTAGTGGCGGCA	61.075	66.667	7.97	7.97	0.00	5.69
600	663	4.482952	TGTCTCCTCGTACATACAGAGA	57.517	45.455	10.50	6.12	32.51	3.10
869	934	0.396435	AGCAACGACTTGACCCATGA	59.604	50.000	0.00	0.00	0.00	3.07
877	942	3.131223	CGACTTGACCCATGACTATGACT	59.869	47.826	0.00	0.00	36.36	3.41
879	944	4.096681	ACTTGACCCATGACTATGACTGA	58.903	43.478	0.00	0.00	36.36	3.41
884	949	4.774124	ACCCATGACTATGACTGATTGTG	58.226	43.478	0.00	0.00	36.36	3.33
894	959	0.604578	ACTGATTGTGTGGCCATTGC	59.395	50.000	9.72	2.53	0.00	3.56
927	992	1.407989	GCCATTTCTCCCTCTCCACAG	60.408	57.143	0.00	0.00	0.00	3.66
928	993	1.407989	CCATTTCTCCCTCTCCACAGC	60.408	57.143	0.00	0.00	0.00	4.40
929	994	1.558756	CATTTCTCCCTCTCCACAGCT	59.441	52.381	0.00	0.00	0.00	4.24
930	995	1.734655	TTTCTCCCTCTCCACAGCTT	58.265	50.000	0.00	0.00	0.00	3.74
1332	1410	3.451402	AAGGTTAGTGAATGGGGTTCC	57.549	47.619	0.00	0.00	35.91	3.62
1381	1465	1.915489	TCAGATCTTTTGGCCCTGCTA	59.085	47.619	0.00	0.00	0.00	3.49
1552	1651	1.134310	AGCTCATGGACAATGATCGCA	60.134	47.619	6.78	0.00	44.40	5.10
1605	1704	3.463944	TGTTGGACGAGAAAAGGAGAAC	58.536	45.455	0.00	0.00	0.00	3.01
1635	1734	0.323360	TTGGATGGCTAGCCAACACC	60.323	55.000	38.81	35.00	46.78	4.16
1650	1749	3.424703	CAACACCTCAGATGAATTGGGT	58.575	45.455	0.00	0.00	0.00	4.51
1658	1763	6.125029	CCTCAGATGAATTGGGTGAAACTAT	58.875	40.000	0.00	0.00	36.74	2.12
1664	1769	5.579047	TGAATTGGGTGAAACTATGGTCAT	58.421	37.500	0.00	0.00	36.74	3.06
1667	1772	7.671819	TGAATTGGGTGAAACTATGGTCATAAA	59.328	33.333	0.00	0.00	36.74	1.40
1723	1831	1.379044	GGTGGCATGGGGAAGACTG	60.379	63.158	0.00	0.00	0.00	3.51
1745	1853	2.219458	CTTGGCTCAGAGCATATGTGG	58.781	52.381	24.09	3.01	44.75	4.17
1759	1945	4.321718	CATATGTGGGCAAGATGAGGTAG	58.678	47.826	0.00	0.00	0.00	3.18
1833	2171	6.237490	CGACATCGGTGACAAGTAAAATACTC	60.237	42.308	0.65	0.00	35.13	2.59
1888	2226	3.142951	CATTTGGAACCACTACAACGGA	58.857	45.455	0.00	0.00	0.00	4.69
2137	2476	8.140677	AGATGATAAAAATCTTGAGCTCTTCG	57.859	34.615	16.19	3.23	29.94	3.79
2138	2477	6.668541	TGATAAAAATCTTGAGCTCTTCGG	57.331	37.500	16.19	2.58	0.00	4.30
2173	2515	3.609853	TCCGGTTTGAATCCAAGAGATG	58.390	45.455	0.00	0.00	34.56	2.90
2186	2528	8.651589	AATCCAAGAGATGATGCATATTTGAT	57.348	30.769	0.00	0.00	34.56	2.57
2220	2562	6.044682	AGAACAAATTGCAAAGAAACTGAGG	58.955	36.000	1.71	0.00	0.00	3.86
2250	2592	0.600782	TGGTAACGAAGGTTGTCGCC	60.601	55.000	0.00	0.00	45.00	5.54
2400	2749	3.746492	ACAGATTTGCTTTCGGTACTGTC	59.254	43.478	0.64	0.00	33.06	3.51
2871	3241	1.948834	TCCATGCACAATTATGGAGCG	59.051	47.619	3.90	0.00	45.87	5.03
3221	3606	2.027745	TCTGCAGGGTCTTGAGAATGTC	60.028	50.000	15.13	0.00	0.00	3.06

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
194	195	0.928229	GCGACATCAACGTCCATACC	59.072	55.000	0.00	0.00	31.91	2.73
278	279	1.383248	CCTCCCTCCCCACGATCTT	60.383	63.158	0.00	0.00	0.00	2.40
384	421	3.322466	AAGCTGCCGCCACTACCT	61.322	61.111	0.00	0.00	36.60	3.08
600	663	5.127491	GCAGTACCTGTAGTATCTGTCTCT	58.873	45.833	0.00	0.00	34.87	3.10
632	695	3.691118	GTGTACATGTACGTAGGTCTGGA	59.309	47.826	26.59	6.41	38.85	3.86
802	867	3.693526	ATTTCCATGGTCACCATCCAT	57.306	42.857	6.26	0.00	43.15	3.41
804	869	4.026052	AGAAATTTCCATGGTCACCATCC	58.974	43.478	6.26	0.00	43.15	3.51
805	870	5.665916	AAGAAATTTCCATGGTCACCATC	57.334	39.130	6.26	4.99	43.15	3.51
869	934	2.305635	TGGCCACACAATCAGTCATAGT	59.694	45.455	0.00	0.00	0.00	2.12
877	942	0.317799	GTGCAATGGCCACACAATCA	59.682	50.000	8.16	0.00	40.13	2.57
879	944	0.319083	CTGTGCAATGGCCACACAAT	59.681	50.000	23.41	0.00	43.25	2.71
884	949	4.659480	CAACTGTGCAATGGCCAC	57.341	55.556	8.16	0.00	40.13	5.01
894	959	2.295349	AGAAATGGCTGAAGCAACTGTG	59.705	45.455	4.43	0.00	44.36	3.66
909	974	1.558756	AGCTGTGGAGAGGGAGAAATG	59.441	52.381	0.00	0.00	0.00	2.32
927	992	4.192000	TTCTGCTAGCGCTGAAGC	57.808	55.556	22.90	22.66	45.38	3.86
930	995	3.070159	AGGATAATTTCTGCTAGCGCTGA	59.930	43.478	22.90	5.45	41.55	4.26
1332	1410	3.274288	GTGCTTCATCTTACCAAGAGGG	58.726	50.000	1.23	0.00	41.61	4.30
1552	1651	7.255139	GGTTGCACTTAATGTTGAACTAGTCTT	60.255	37.037	0.00	0.00	0.00	3.01
1605	1704	4.153117	GCTAGCCATCCAATAATCTGTTCG	59.847	45.833	2.29	0.00	0.00	3.95
1635	1734	6.039047	CCATAGTTTCACCCAATTCATCTGAG	59.961	42.308	0.00	0.00	0.00	3.35
1723	1831	1.236628	CATATGCTCTGAGCCAAGGC	58.763	55.000	25.61	2.02	41.51	4.35
1745	1853	3.873910	TGCTTTACTACCTCATCTTGCC	58.126	45.455	0.00	0.00	0.00	4.52
1759	1945	7.251281	GTCCAGATGACCTTAAAATGCTTTAC	58.749	38.462	0.00	0.00	38.09	2.01
1888	2226	3.194005	TGCGAGTTTCTCTTTGAGGTT	57.806	42.857	0.00	0.00	0.00	3.50
2137	2476	0.740737	CCGGAAAAGGCATGATGACC	59.259	55.000	0.00	0.00	0.00	4.02
2138	2477	1.463674	ACCGGAAAAGGCATGATGAC	58.536	50.000	9.46	0.00	33.69	3.06
2173	2515	9.970395	TTCTCCAATTAACATCAAATATGCATC	57.030	29.630	0.19	0.00	0.00	3.91
2186	2528	7.984050	TCTTTGCAATTTGTTCTCCAATTAACA	59.016	29.630	0.00	0.00	33.92	2.41
2230	2572	0.788391	GCGACAACCTTCGTTACCAG	59.212	55.000	0.00	0.00	41.26	4.00
2400	2749	0.387929	TAGTCCTGCGGAAATAGGCG	59.612	55.000	0.00	0.00	31.38	5.52
2445	2797	5.543405	TCAATCCTGAACCAATCCACATTTT	59.457	36.000	0.00	0.00	0.00	1.82
2871	3241	0.313672	TTGACAGCAAAACGGGATGC	59.686	50.000	0.92	0.92	42.87	3.91
3221	3606	6.824305	TTCTTAGCTTCTTCCCAATTCTTG	57.176	37.500	0.00	0.00	0.00	3.02

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.