AutoCloner

Multiple sequence alignment - TraesCS2B01G594600

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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	TraesCS2B01G594600	chr2B	100.000	1528	0	0	1	1528	779150759	779149232	0.000000e+00	2822.0
1	TraesCS2B01G594600	chr2B	93.121	1541	74	10	1	1528	779254421	779255942	0.000000e+00	2230.0
2	TraesCS2B01G594600	chr2B	84.036	1541	208	14	3	1527	779182478	779183996	0.000000e+00	1448.0
3	TraesCS2B01G594600	chr2B	100.000	566	0	0	1822	2387	779148938	779148373	0.000000e+00	1046.0
4	TraesCS2B01G594600	chr2B	77.217	1387	239	42	1	1352	779261210	779262554	0.000000e+00	739.0
5	TraesCS2B01G594600	chr2B	87.850	321	22	4	1873	2193	779256231	779256534	6.270000e-96	361.0
6	TraesCS2B01G594600	chr2B	87.586	145	14	3	2242	2383	779256515	779256658	5.280000e-37	165.0
7	TraesCS2B01G594600	chr2B	94.175	103	6	0	2283	2385	335806308	335806410	8.830000e-35	158.0
8	TraesCS2B01G594600	chr2D	94.156	1540	58	10	1	1527	635164846	635166366	0.000000e+00	2316.0
9	TraesCS2B01G594600	chr2D	77.850	1386	240	42	1	1352	635206221	635207573	0.000000e+00	797.0
10	TraesCS2B01G594600	chr2D	95.200	375	18	0	1873	2247	635166875	635167249	5.680000e-166	593.0
11	TraesCS2B01G594600	chr2D	86.926	283	24	8	2114	2385	635167194	635167474	2.980000e-79	305.0
12	TraesCS2B01G594600	chr2D	92.500	80	6	0	2114	2193	635167272	635167351	5.390000e-22	115.0
13	TraesCS2B01G594600	chr2D	97.778	45	0	1	1823	1867	635166460	635166503	2.540000e-10	76.8
14	TraesCS2B01G594600	chr2A	93.247	1540	73	9	1	1528	777624340	777622820	0.000000e+00	2239.0
15	TraesCS2B01G594600	chr2A	83.401	1482	216	15	3	1475	777809099	777807639	0.000000e+00	1347.0
16	TraesCS2B01G594600	chr2A	79.532	1368	229	33	5	1352	777836413	777835077	0.000000e+00	928.0
17	TraesCS2B01G594600	chr2A	84.574	188	20	6	933	1120	777902269	777902447	6.780000e-41	178.0
18	TraesCS2B01G594600	chr2A	98.246	57	1	0	1873	1929	777622316	777622260	1.510000e-17	100.0
19	TraesCS2B01G594600	chr2A	97.778	45	0	1	1823	1867	777622727	777622684	2.540000e-10	76.8
20	TraesCS2B01G594600	chr1D	96.078	102	4	0	2284	2385	101104159	101104260	1.470000e-37	167.0
21	TraesCS2B01G594600	chr1D	95.000	100	4	1	2287	2385	90634455	90634554	3.180000e-34	156.0
22	TraesCS2B01G594600	chr1B	96.000	100	3	1	2287	2385	150543397	150543298	6.830000e-36	161.0
23	TraesCS2B01G594600	chr1B	95.000	100	5	0	2286	2385	559075111	559075012	8.830000e-35	158.0
24	TraesCS2B01G594600	chr3A	91.964	112	8	1	2274	2385	56398010	56398120	3.180000e-34	156.0
25	TraesCS2B01G594600	chr6D	93.204	103	7	0	2283	2385	378032338	378032440	4.110000e-33	152.0

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	TraesCS2B01G594600	chr2B	779148373	779150759	2386	True	1934.000000	2822	100.000000	1	2387	2	chr2B.!!$R1	2386
1	TraesCS2B01G594600	chr2B	779182478	779183996	1518	False	1448.000000	1448	84.036000	3	1527	1	chr2B.!!$F2	1524
2	TraesCS2B01G594600	chr2B	779254421	779256658	2237	False	918.666667	2230	89.519000	1	2383	3	chr2B.!!$F4	2382
3	TraesCS2B01G594600	chr2B	779261210	779262554	1344	False	739.000000	739	77.217000	1	1352	1	chr2B.!!$F3	1351
4	TraesCS2B01G594600	chr2D	635206221	635207573	1352	False	797.000000	797	77.850000	1	1352	1	chr2D.!!$F1	1351
5	TraesCS2B01G594600	chr2D	635164846	635167474	2628	False	681.160000	2316	93.312000	1	2385	5	chr2D.!!$F2	2384
6	TraesCS2B01G594600	chr2A	777807639	777809099	1460	True	1347.000000	1347	83.401000	3	1475	1	chr2A.!!$R1	1472
7	TraesCS2B01G594600	chr2A	777835077	777836413	1336	True	928.000000	928	79.532000	5	1352	1	chr2A.!!$R2	1347
8	TraesCS2B01G594600	chr2A	777622260	777624340	2080	True	805.266667	2239	96.423667	1	1929	3	chr2A.!!$R3	1928

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
904	934	0.387929	TCTCACCGACCACACAAGAC	59.612	55.0	0.0	0.0	0.0	3.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2092	2505	0.386113	GATGGACGGGCTCTACACTC	59.614	60.0	0.0	0.0	0.0	3.51	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
43	44	3.833271	TTGTACACATCGCGCGCG	61.833	61.111	44.84	44.84	41.35	6.86
367	368	4.672251	GCATGGGCCAATGAGTCT	57.328	55.556	25.26	0.00	0.00	3.24
557	579	1.541588	CAGTGGCCGATCGATGAGATA	59.458	52.381	18.66	0.00	40.26	1.98
558	580	1.815613	AGTGGCCGATCGATGAGATAG	59.184	52.381	18.66	0.00	40.26	2.08
559	581	1.813178	GTGGCCGATCGATGAGATAGA	59.187	52.381	18.66	0.00	40.26	1.98
560	582	2.087646	TGGCCGATCGATGAGATAGAG	58.912	52.381	18.66	0.00	40.26	2.43
561	583	2.290323	TGGCCGATCGATGAGATAGAGA	60.290	50.000	18.66	0.00	40.26	3.10
562	584	2.096819	GGCCGATCGATGAGATAGAGAC	59.903	54.545	18.66	0.00	40.26	3.36
563	585	2.744741	GCCGATCGATGAGATAGAGACA	59.255	50.000	18.66	0.00	40.26	3.41
564	586	3.376859	GCCGATCGATGAGATAGAGACAT	59.623	47.826	18.66	0.00	40.26	3.06
565	587	4.142491	GCCGATCGATGAGATAGAGACATT	60.142	45.833	18.66	0.00	40.26	2.71
566	588	5.331098	CCGATCGATGAGATAGAGACATTG	58.669	45.833	18.66	0.00	40.26	2.82
567	589	5.123027	CCGATCGATGAGATAGAGACATTGA	59.877	44.000	18.66	0.00	40.26	2.57
568	590	6.348868	CCGATCGATGAGATAGAGACATTGAA	60.349	42.308	18.66	0.00	40.26	2.69
569	591	6.742264	CGATCGATGAGATAGAGACATTGAAG	59.258	42.308	10.26	0.00	40.26	3.02
570	592	7.360776	CGATCGATGAGATAGAGACATTGAAGA	60.361	40.741	10.26	0.00	40.26	2.87
571	593	7.200778	TCGATGAGATAGAGACATTGAAGAG	57.799	40.000	0.00	0.00	33.32	2.85
572	594	5.858049	CGATGAGATAGAGACATTGAAGAGC	59.142	44.000	0.00	0.00	0.00	4.09
573	595	6.514705	CGATGAGATAGAGACATTGAAGAGCA	60.515	42.308	0.00	0.00	0.00	4.26
574	596	6.535963	TGAGATAGAGACATTGAAGAGCAA	57.464	37.500	0.00	0.00	41.53	3.91
575	597	6.939622	TGAGATAGAGACATTGAAGAGCAAA	58.060	36.000	0.00	0.00	40.48	3.68
628	650	0.462759	GCTAGGAGCGCAGGTGAATT	60.463	55.000	11.47	0.00	39.88	2.17
640	662	2.359354	TGAATTCCGGTGGCGTGG	60.359	61.111	0.00	0.00	0.00	4.94
657	679	2.218603	GTGGACAAGATCGTTGGTGTT	58.781	47.619	8.95	0.00	0.00	3.32
684	706	2.045926	GCTGACGTGGAGGCCATT	60.046	61.111	5.01	0.00	35.28	3.16
863	887	3.492756	GCTGTCTTCTTCAGAGTGTTCAC	59.507	47.826	0.00	0.00	35.20	3.18
896	926	4.345859	AATACAAAGTTCTCACCGACCA	57.654	40.909	0.00	0.00	0.00	4.02
903	933	1.116308	TTCTCACCGACCACACAAGA	58.884	50.000	0.00	0.00	0.00	3.02
904	934	0.387929	TCTCACCGACCACACAAGAC	59.612	55.000	0.00	0.00	0.00	3.01
907	937	0.461163	CACCGACCACACAAGACACA	60.461	55.000	0.00	0.00	0.00	3.72
1162	1207	9.407380	AGTTACATGCATCAAATGAATACCTTA	57.593	29.630	0.00	0.00	0.00	2.69
1185	1230	4.561735	AATTTCGTTCGCTTCTTCCAAA	57.438	36.364	0.00	0.00	0.00	3.28
1369	1414	3.411446	CTGGTGATGGCTTCAGTAAACA	58.589	45.455	2.94	0.00	34.17	2.83
1935	2348	2.268298	GATTGCTTTGCTTGCCAGATG	58.732	47.619	0.00	0.00	0.00	2.90
1985	2398	2.457598	TGCTCGATTAGGTGAGAAGGT	58.542	47.619	0.00	0.00	34.04	3.50
1999	2412	3.108376	GAGAAGGTGACCTTGGGAGTAT	58.892	50.000	23.60	0.00	44.82	2.12
2027	2440	7.121611	TCACATCCTTTACACGTGATTAGACTA	59.878	37.037	25.01	0.00	31.92	2.59
2080	2493	1.455408	GCCTTGAAATTTTTGTCGGCG	59.545	47.619	0.00	0.00	0.00	6.46
2112	2525	0.324368	AGTGTAGAGCCCGTCCATCA	60.324	55.000	0.00	0.00	0.00	3.07
2134	2547	7.864108	TCACACATGGTTAAAATCTCCTATG	57.136	36.000	0.00	0.00	0.00	2.23
2137	2550	5.593909	CACATGGTTAAAATCTCCTATGGCA	59.406	40.000	0.00	0.00	0.00	4.92
2148	2561	2.416547	CTCCTATGGCAAACACAGTTCG	59.583	50.000	0.00	0.00	0.00	3.95
2164	2577	4.062293	CAGTTCGGAATTGTCACCTTACA	58.938	43.478	5.18	0.00	0.00	2.41
2189	2602	3.360340	GCGATAGGGGCTGCATGC	61.360	66.667	11.82	11.82	41.94	4.06
2231	2644	6.998074	TCCTATCACAAACACAGTTCTGAATT	59.002	34.615	6.83	0.00	0.00	2.17
2253	2755	2.911143	CCTTACGATGGGGCTGCT	59.089	61.111	0.00	0.00	0.00	4.24

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
43	44	3.499737	CATTCGACCACGCCTGCC	61.500	66.667	0.00	0.00	39.58	4.85
50	51	2.798148	AAGTCCGGGCATTCGACCAC	62.798	60.000	9.71	0.00	42.68	4.16
367	368	0.537653	TGTCGTTGTCCTGGTTGTCA	59.462	50.000	0.00	0.00	0.00	3.58
551	573	6.535963	TTGCTCTTCAATGTCTCTATCTCA	57.464	37.500	0.00	0.00	0.00	3.27
557	579	3.993081	CTCGTTTGCTCTTCAATGTCTCT	59.007	43.478	0.00	0.00	34.12	3.10
558	580	3.990469	TCTCGTTTGCTCTTCAATGTCTC	59.010	43.478	0.00	0.00	34.12	3.36
559	581	3.743396	GTCTCGTTTGCTCTTCAATGTCT	59.257	43.478	0.00	0.00	34.12	3.41
560	582	3.494626	TGTCTCGTTTGCTCTTCAATGTC	59.505	43.478	0.00	0.00	34.12	3.06
561	583	3.466836	TGTCTCGTTTGCTCTTCAATGT	58.533	40.909	0.00	0.00	34.12	2.71
562	584	4.675190	ATGTCTCGTTTGCTCTTCAATG	57.325	40.909	0.00	0.00	34.12	2.82
563	585	4.756642	TCAATGTCTCGTTTGCTCTTCAAT	59.243	37.500	0.00	0.00	34.12	2.57
564	586	4.126437	TCAATGTCTCGTTTGCTCTTCAA	58.874	39.130	0.00	0.00	0.00	2.69
565	587	3.727726	TCAATGTCTCGTTTGCTCTTCA	58.272	40.909	0.00	0.00	0.00	3.02
566	588	3.124297	CCTCAATGTCTCGTTTGCTCTTC	59.876	47.826	0.00	0.00	0.00	2.87
567	589	3.070018	CCTCAATGTCTCGTTTGCTCTT	58.930	45.455	0.00	0.00	0.00	2.85
568	590	2.300152	TCCTCAATGTCTCGTTTGCTCT	59.700	45.455	0.00	0.00	0.00	4.09
569	591	2.670414	CTCCTCAATGTCTCGTTTGCTC	59.330	50.000	0.00	0.00	0.00	4.26
570	592	2.693069	CTCCTCAATGTCTCGTTTGCT	58.307	47.619	0.00	0.00	0.00	3.91
571	593	1.129437	GCTCCTCAATGTCTCGTTTGC	59.871	52.381	0.00	0.00	0.00	3.68
572	594	2.416747	TGCTCCTCAATGTCTCGTTTG	58.583	47.619	0.00	0.00	0.00	2.93
573	595	2.839486	TGCTCCTCAATGTCTCGTTT	57.161	45.000	0.00	0.00	0.00	3.60
574	596	2.808543	GTTTGCTCCTCAATGTCTCGTT	59.191	45.455	0.00	0.00	34.12	3.85
575	597	2.417719	GTTTGCTCCTCAATGTCTCGT	58.582	47.619	0.00	0.00	34.12	4.18
628	650	4.308458	CTTGTCCACGCCACCGGA	62.308	66.667	9.46	0.00	39.22	5.14
640	662	1.069227	GCCAACACCAACGATCTTGTC	60.069	52.381	0.00	0.00	0.00	3.18
684	706	1.213678	TCTAGGGACGGGATCTCGAAA	59.786	52.381	24.50	0.64	30.35	3.46
795	817	2.169789	CATGACGAGCAGCCCGAAG	61.170	63.158	2.12	0.00	0.00	3.79
863	887	8.826710	TGAGAACTTTGTATTTCTAGTTGTGTG	58.173	33.333	0.00	0.00	32.04	3.82
871	895	6.161381	GGTCGGTGAGAACTTTGTATTTCTA	58.839	40.000	0.00	0.00	32.04	2.10
876	900	3.070446	TGTGGTCGGTGAGAACTTTGTAT	59.930	43.478	0.00	0.00	37.49	2.29
896	926	4.072131	AGTTGTGTTCTTGTGTCTTGTGT	58.928	39.130	0.00	0.00	0.00	3.72
903	933	3.366052	AAGGGAGTTGTGTTCTTGTGT	57.634	42.857	0.00	0.00	0.00	3.72
904	934	6.039270	TGAATTAAGGGAGTTGTGTTCTTGTG	59.961	38.462	0.00	0.00	0.00	3.33
907	937	6.601332	TCTGAATTAAGGGAGTTGTGTTCTT	58.399	36.000	0.00	0.00	0.00	2.52
1162	1207	5.873179	TTGGAAGAAGCGAACGAAATTAT	57.127	34.783	0.00	0.00	0.00	1.28
1352	1397	3.684305	CACGATGTTTACTGAAGCCATCA	59.316	43.478	0.00	0.00	36.38	3.07
1369	1414	4.094646	TCACCCGCCATGCACGAT	62.095	61.111	7.82	0.00	0.00	3.73
1498	1546	1.357137	TGACATGGGTCTTACTGGCA	58.643	50.000	0.00	0.00	44.61	4.92
1821	1869	9.097946	ACAGAGGTAGTAGGTGTTTTATAAGTT	57.902	33.333	0.00	0.00	0.00	2.66
1865	1913	8.939929	CATGTTGAACTACTCAATAAGTGACAT	58.060	33.333	0.00	0.00	45.74	3.06
1869	1917	7.672983	ACCATGTTGAACTACTCAATAAGTG	57.327	36.000	0.00	0.00	45.74	3.16
1870	1918	7.544566	CGTACCATGTTGAACTACTCAATAAGT	59.455	37.037	0.00	0.00	45.74	2.24
1871	1919	7.544566	ACGTACCATGTTGAACTACTCAATAAG	59.455	37.037	0.00	0.00	45.74	1.73
1935	2348	0.519077	GCAAGCAAGCACACTACTCC	59.481	55.000	0.00	0.00	0.00	3.85
1985	2398	3.184382	TGTGAGATACTCCCAAGGTCA	57.816	47.619	0.00	0.00	0.00	4.02
1991	2404	5.128827	GTGTAAAGGATGTGAGATACTCCCA	59.871	44.000	0.00	0.00	31.08	4.37
1999	2412	4.801330	ATCACGTGTAAAGGATGTGAGA	57.199	40.909	16.51	0.00	41.48	3.27
2010	2423	8.102800	TGAAAGTCTAGTCTAATCACGTGTAA	57.897	34.615	16.51	0.00	0.00	2.41
2011	2424	7.677454	TGAAAGTCTAGTCTAATCACGTGTA	57.323	36.000	16.51	2.58	0.00	2.90
2080	2493	3.512680	CTCTACACTCGTGAACATTCCC	58.487	50.000	3.74	0.00	0.00	3.97
2092	2505	0.386113	GATGGACGGGCTCTACACTC	59.614	60.000	0.00	0.00	0.00	3.51
2112	2525	5.594317	GCCATAGGAGATTTTAACCATGTGT	59.406	40.000	0.00	0.00	0.00	3.72
2134	2547	2.223711	ACAATTCCGAACTGTGTTTGCC	60.224	45.455	0.00	0.00	0.00	4.52
2137	2550	3.066203	GGTGACAATTCCGAACTGTGTTT	59.934	43.478	0.00	0.00	0.00	2.83
2164	2577	1.152963	GCCCCTATCGCACACCATT	60.153	57.895	0.00	0.00	0.00	3.16
2189	2602	5.527214	TGATAGGAGATTTTAACCATGTGCG	59.473	40.000	0.00	0.00	0.00	5.34
2272	2774	7.610305	ACCAATTATCCTCTTAACACACGAAAT	59.390	33.333	0.00	0.00	0.00	2.17
2276	2778	6.737254	AACCAATTATCCTCTTAACACACG	57.263	37.500	0.00	0.00	0.00	4.49
2280	2782	7.147915	GGCATCAAACCAATTATCCTCTTAACA	60.148	37.037	0.00	0.00	0.00	2.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.