AutoCloner

Multiple sequence alignment - TraesCS1B01G180100

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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	TraesCS1B01G180100	chr1B	100.000	4400	0	0	1	4400	326911448	326915847	0.000000e+00	8126.0
1	TraesCS1B01G180100	chr1B	88.788	1106	93	14	1413	2495	327228260	327229357	0.000000e+00	1327.0
2	TraesCS1B01G180100	chr1B	88.225	1138	95	21	2494	3604	327229390	327230515	0.000000e+00	1323.0
3	TraesCS1B01G180100	chr1B	88.988	1008	77	9	395	1396	327227295	327228274	0.000000e+00	1216.0
4	TraesCS1B01G180100	chr1B	84.536	873	90	27	2709	3561	322475506	322476353	0.000000e+00	822.0
5	TraesCS1B01G180100	chr1B	88.855	655	49	5	1841	2495	327343065	327343695	0.000000e+00	784.0
6	TraesCS1B01G180100	chr1B	88.845	511	49	2	1961	2471	350442785	350442283	4.830000e-174	621.0
7	TraesCS1B01G180100	chr1B	84.945	631	45	22	527	1111	327339079	327339705	1.050000e-165	593.0
8	TraesCS1B01G180100	chr1B	83.721	645	83	17	759	1396	322473546	322474175	1.360000e-164	590.0
9	TraesCS1B01G180100	chr1B	88.462	442	44	6	1413	1853	327341193	327341628	1.080000e-145	527.0
10	TraesCS1B01G180100	chr1B	86.151	491	44	17	1	475	327226855	327227337	3.930000e-140	508.0
11	TraesCS1B01G180100	chr1B	84.783	368	51	4	1418	1785	322474166	322474528	8.990000e-97	364.0
12	TraesCS1B01G180100	chr1B	79.859	427	55	14	1	423	350444478	350444079	2.590000e-72	283.0
13	TraesCS1B01G180100	chr1B	84.815	270	25	5	1128	1396	327340953	327341207	1.570000e-64	257.0
14	TraesCS1B01G180100	chr1B	76.895	277	53	10	3608	3879	343994507	343994237	3.550000e-31	147.0
15	TraesCS1B01G180100	chr1D	94.266	2546	89	15	1413	3916	226943748	226946278	0.000000e+00	3840.0
16	TraesCS1B01G180100	chr1D	96.228	1405	42	7	1	1396	226942360	226943762	0.000000e+00	2290.0
17	TraesCS1B01G180100	chr1D	87.687	1941	136	50	1743	3604	227374625	227376541	0.000000e+00	2165.0
18	TraesCS1B01G180100	chr1D	91.135	1004	76	9	395	1390	227373210	227374208	0.000000e+00	1349.0
19	TraesCS1B01G180100	chr1D	86.545	1100	98	16	1419	2495	208416170	208415098	0.000000e+00	1166.0
20	TraesCS1B01G180100	chr1D	85.382	1033	103	27	2600	3604	208413329	208412317	0.000000e+00	1027.0
21	TraesCS1B01G180100	chr1D	88.509	818	70	10	2810	3604	226827568	226828384	0.000000e+00	968.0
22	TraesCS1B01G180100	chr1D	86.674	893	82	24	2700	3573	223164293	223165167	0.000000e+00	955.0
23	TraesCS1B01G180100	chr1D	90.432	648	47	8	1850	2495	226826343	226826977	0.000000e+00	839.0
24	TraesCS1B01G180100	chr1D	88.735	648	42	12	759	1396	226825346	226825972	0.000000e+00	763.0
25	TraesCS1B01G180100	chr1D	90.625	512	40	2	1961	2472	261723862	261724365	0.000000e+00	673.0
26	TraesCS1B01G180100	chr1D	92.391	460	32	2	3916	4372	226946323	226946782	0.000000e+00	652.0
27	TraesCS1B01G180100	chr1D	89.143	525	51	4	1955	2478	227648719	227649238	0.000000e+00	649.0
28	TraesCS1B01G180100	chr1D	86.519	586	55	14	2895	3457	226469232	226469816	1.340000e-174	623.0
29	TraesCS1B01G180100	chr1D	90.411	438	35	5	678	1111	208417413	208416979	1.780000e-158	569.0
30	TraesCS1B01G180100	chr1D	87.551	490	46	10	1	475	227372765	227373254	1.790000e-153	553.0
31	TraesCS1B01G180100	chr1D	88.987	454	38	8	667	1111	227646984	227647434	6.430000e-153	551.0
32	TraesCS1B01G180100	chr1D	85.516	504	60	5	656	1147	261722735	261723237	8.440000e-142	514.0
33	TraesCS1B01G180100	chr1D	87.918	389	42	3	1413	1800	226825958	226826342	1.870000e-123	453.0
34	TraesCS1B01G180100	chr1D	86.701	391	49	1	1413	1800	227648242	227648632	8.740000e-117	431.0
35	TraesCS1B01G180100	chr1D	86.286	350	42	5	1413	1758	227374200	227374547	4.150000e-100	375.0
36	TraesCS1B01G180100	chr1D	86.054	294	36	4	91	382	226824469	226824759	1.190000e-80	311.0
37	TraesCS1B01G180100	chr1D	87.361	269	22	2	1128	1395	227647998	227648255	9.250000e-77	298.0
38	TraesCS1B01G180100	chr1D	80.191	419	57	16	1	408	261722142	261722545	1.550000e-74	291.0
39	TraesCS1B01G180100	chr1D	86.296	270	25	2	1128	1396	208416420	208416162	2.590000e-72	283.0
40	TraesCS1B01G180100	chr1D	90.756	119	9	1	1278	1394	477867556	477867438	1.640000e-34	158.0
41	TraesCS1B01G180100	chr1D	86.093	151	12	6	527	668	208417602	208417452	2.120000e-33	154.0
42	TraesCS1B01G180100	chr1D	87.037	108	7	1	279	379	227646583	227646690	1.000000e-21	115.0
43	TraesCS1B01G180100	chr1D	80.368	163	13	11	59	206	208418390	208418232	6.020000e-19	106.0
44	TraesCS1B01G180100	chr1A	87.196	1109	106	17	1413	2495	294040053	294041151	0.000000e+00	1229.0
45	TraesCS1B01G180100	chr1A	86.288	1145	82	35	2494	3604	294041184	294042287	0.000000e+00	1175.0
46	TraesCS1B01G180100	chr1A	87.968	1014	69	21	395	1396	294039095	294040067	0.000000e+00	1147.0
47	TraesCS1B01G180100	chr1A	84.045	890	93	28	2709	3579	290126432	290127291	0.000000e+00	811.0
48	TraesCS1B01G180100	chr1A	89.194	509	45	4	1971	2478	338594656	338594157	1.040000e-175	627.0
49	TraesCS1B01G180100	chr1A	84.945	631	75	15	758	1384	290124481	290125095	4.830000e-174	621.0
50	TraesCS1B01G180100	chr1A	85.685	496	43	17	1	474	294038649	294039138	8.500000e-137	497.0
51	TraesCS1B01G180100	chr1A	84.022	363	52	5	1423	1785	290125103	290125459	1.170000e-90	344.0
52	TraesCS1B01G180100	chr1A	80.872	413	55	15	1	401	338596475	338596075	1.990000e-78	303.0
53	TraesCS1B01G180100	chr1A	79.851	268	44	8	3616	3880	580438356	580438096	2.090000e-43	187.0
54	TraesCS1B01G180100	chr1A	84.615	104	12	3	438	539	338596070	338595969	2.800000e-17	100.0
55	TraesCS1B01G180100	chr3A	87.636	461	51	4	3916	4372	685360924	685361382	8.380000e-147	531.0
56	TraesCS1B01G180100	chr5B	86.768	461	55	4	3916	4372	446878981	446878523	3.930000e-140	508.0
57	TraesCS1B01G180100	chrUn	86.534	453	53	8	3923	4370	115044127	115044576	3.950000e-135	492.0
58	TraesCS1B01G180100	chrUn	79.545	220	36	8	3664	3880	29316703	29316916	9.860000e-32	148.0
59	TraesCS1B01G180100	chr7B	86.334	461	52	5	3916	4372	69538691	69539144	3.950000e-135	492.0
60	TraesCS1B01G180100	chr7B	75.627	279	58	9	3608	3880	641169402	641169128	3.570000e-26	130.0
61	TraesCS1B01G180100	chr7D	79.730	740	89	31	2711	3446	90410250	90410932	3.080000e-131	479.0
62	TraesCS1B01G180100	chr7D	79.927	274	44	8	3614	3883	572758630	572758896	1.620000e-44	191.0
63	TraesCS1B01G180100	chr7D	75.986	279	54	12	3609	3880	13620137	13620409	9.930000e-27	132.0
64	TraesCS1B01G180100	chr2B	83.807	457	70	3	3919	4371	26242915	26242459	8.740000e-117	431.0
65	TraesCS1B01G180100	chr2B	83.117	462	71	5	3919	4374	26245456	26244996	8.800000e-112	414.0
66	TraesCS1B01G180100	chr4D	77.528	356	67	11	4023	4371	485381364	485381015	7.460000e-48	202.0
67	TraesCS1B01G180100	chr2D	80.216	278	44	6	3610	3879	617544092	617544366	9.650000e-47	198.0
68	TraesCS1B01G180100	chr2D	76.190	189	42	3	3962	4149	616359714	616359528	3.620000e-16	97.1
69	TraesCS1B01G180100	chr4A	89.109	101	10	1	3628	3728	166302837	166302936	1.660000e-24	124.0
70	TraesCS1B01G180100	chr5D	88.000	75	8	1	3627	3701	26712930	26713003	2.180000e-13	87.9

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	TraesCS1B01G180100	chr1B	326911448	326915847	4399	False	8126.000000	8126	100.000000	1	4400	1	chr1B.!!$F1	4399
1	TraesCS1B01G180100	chr1B	327226855	327230515	3660	False	1093.500000	1327	88.038000	1	3604	4	chr1B.!!$F3	3603
2	TraesCS1B01G180100	chr1B	322473546	322476353	2807	False	592.000000	822	84.346667	759	3561	3	chr1B.!!$F2	2802
3	TraesCS1B01G180100	chr1B	327339079	327343695	4616	False	540.250000	784	86.769250	527	2495	4	chr1B.!!$F4	1968
4	TraesCS1B01G180100	chr1B	350442283	350444478	2195	True	452.000000	621	84.352000	1	2471	2	chr1B.!!$R2	2470
5	TraesCS1B01G180100	chr1D	226942360	226946782	4422	False	2260.666667	3840	94.295000	1	4372	3	chr1D.!!$F4	4371
6	TraesCS1B01G180100	chr1D	227372765	227376541	3776	False	1110.500000	2165	88.164750	1	3604	4	chr1D.!!$F5	3603
7	TraesCS1B01G180100	chr1D	223164293	223165167	874	False	955.000000	955	86.674000	2700	3573	1	chr1D.!!$F1	873
8	TraesCS1B01G180100	chr1D	226824469	226828384	3915	False	666.800000	968	88.329600	91	3604	5	chr1D.!!$F3	3513
9	TraesCS1B01G180100	chr1D	226469232	226469816	584	False	623.000000	623	86.519000	2895	3457	1	chr1D.!!$F2	562
10	TraesCS1B01G180100	chr1D	208412317	208418390	6073	True	550.833333	1166	85.849167	59	3604	6	chr1D.!!$R2	3545
11	TraesCS1B01G180100	chr1D	261722142	261724365	2223	False	492.666667	673	85.444000	1	2472	3	chr1D.!!$F7	2471
12	TraesCS1B01G180100	chr1D	227646583	227649238	2655	False	408.800000	649	87.845800	279	2478	5	chr1D.!!$F6	2199
13	TraesCS1B01G180100	chr1A	294038649	294042287	3638	False	1012.000000	1229	86.784250	1	3604	4	chr1A.!!$F2	3603
14	TraesCS1B01G180100	chr1A	290124481	290127291	2810	False	592.000000	811	84.337333	758	3579	3	chr1A.!!$F1	2821
15	TraesCS1B01G180100	chr1A	338594157	338596475	2318	True	343.333333	627	84.893667	1	2478	3	chr1A.!!$R2	2477
16	TraesCS1B01G180100	chr7D	90410250	90410932	682	False	479.000000	479	79.730000	2711	3446	1	chr7D.!!$F2	735
17	TraesCS1B01G180100	chr2B	26242459	26245456	2997	True	422.500000	431	83.462000	3919	4374	2	chr2B.!!$R1	455

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	Hairpin	End Stability	Orientation
250	286	2.143925	GTGTGCCTACTGTGGTTCTTC	58.856	52.381	0.00	2.87	F
621	1109	2.740981	GTGCTGGTCTTGATGTCTTCTG	59.259	50.000	0.00	3.02	F
1408	3516	1.110518	GGAAGTGTCCCCCGCAAAAA	61.111	55.000	38.08	1.94	F
2526	6430	0.104671	TTCTTTGTGCAAGGCAAGGC	59.895	50.000	41.47	4.35	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1389	3497	1.110518	TTTTTGCGGGGGACACTTCC	61.111	55.0	0.00	0.00	41.95	3.46	R
2046	5867	2.160417	CCAAAGTTGTAGCTAGCTGCAC	59.840	50.0	31.79	24.86	45.94	4.57	R
3253	9165	1.508632	CGTCCACCTGTAAACACCAG	58.491	55.0	0.00	0.00	0.00	4.00	R
3685	9617	0.102663	TGGTTTTTCGCCCGGTTTTC	59.897	50.0	0.00	0.00	0.00	2.29	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
159	189	5.574082	TGCCGTGGTAATTATTTTTCATCG	58.426	37.500	0.00	0.00	0.00	3.84
250	286	2.143925	GTGTGCCTACTGTGGTTCTTC	58.856	52.381	0.00	0.00	0.00	2.87
325	695	5.348724	TGATTTAATCTCACTTGCAGACGAC	59.651	40.000	6.50	0.00	0.00	4.34
401	786	7.817478	TGTATGTCTAGTCAATCGTGATGTTTT	59.183	33.333	0.00	0.00	35.80	2.43
621	1109	2.740981	GTGCTGGTCTTGATGTCTTCTG	59.259	50.000	0.00	0.00	0.00	3.02
737	1346	7.011482	ACCTAGTATGCGTTCAAGATTTTGATC	59.989	37.037	0.00	0.00	42.60	2.92
849	1612	7.571080	TGCACATGAATTTTCTCATAGCATA	57.429	32.000	0.00	0.00	39.31	3.14
1111	1905	4.199432	TGCAAAAGGAAGTCTGCAAAAA	57.801	36.364	0.00	0.00	41.61	1.94
1317	3425	6.017933	GTGCATGAAGTGAAGAAATTAGACG	58.982	40.000	0.00	0.00	0.00	4.18
1384	3492	6.959639	TTCCTATGATTTCATTTACCAGGC	57.040	37.500	0.00	0.00	37.76	4.85
1385	3493	6.012337	TCCTATGATTTCATTTACCAGGCA	57.988	37.500	0.00	0.00	37.76	4.75
1386	3494	5.827797	TCCTATGATTTCATTTACCAGGCAC	59.172	40.000	0.00	0.00	37.76	5.01
1387	3495	5.010012	CCTATGATTTCATTTACCAGGCACC	59.990	44.000	0.00	0.00	37.76	5.01
1388	3496	4.046286	TGATTTCATTTACCAGGCACCT	57.954	40.909	0.00	0.00	0.00	4.00
1389	3497	3.763360	TGATTTCATTTACCAGGCACCTG	59.237	43.478	9.87	9.87	43.26	4.00
1397	3505	4.386413	CAGGCACCTGGAAGTGTC	57.614	61.111	8.93	0.00	42.82	3.67
1398	3506	1.302832	CAGGCACCTGGAAGTGTCC	60.303	63.158	8.93	0.00	43.55	4.02
1399	3507	2.034221	GGCACCTGGAAGTGTCCC	59.966	66.667	0.00	0.00	44.23	4.46
1400	3508	2.034221	GCACCTGGAAGTGTCCCC	59.966	66.667	0.00	0.00	44.23	4.81
1401	3509	2.757077	CACCTGGAAGTGTCCCCC	59.243	66.667	0.00	0.00	44.23	5.40
1402	3510	2.928396	ACCTGGAAGTGTCCCCCG	60.928	66.667	0.00	0.00	44.23	5.73
1403	3511	4.410400	CCTGGAAGTGTCCCCCGC	62.410	72.222	0.00	0.00	44.23	6.13
1404	3512	3.636231	CTGGAAGTGTCCCCCGCA	61.636	66.667	0.00	0.00	44.23	5.69
1405	3513	3.172106	TGGAAGTGTCCCCCGCAA	61.172	61.111	0.00	0.00	44.23	4.85
1406	3514	2.114411	GGAAGTGTCCCCCGCAAA	59.886	61.111	0.00	0.00	38.08	3.68

Showing 1 to 25 of 105 entries

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Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
80	97	4.284746	AGAACAAGAAGTAGAAGTCCCTGG	59.715	45.833	0.00	0.00	0.00	4.45
159	189	1.194781	TGAGGGGCAGAGTCAACCTC	61.195	60.000	12.72	12.72	46.14	3.85
325	695	2.736826	GCCCCTTCCTCTTCTCCCG	61.737	68.421	0.00	0.00	0.00	5.14
621	1109	2.030451	CCCGTACTACCGCTTCTAATCC	60.030	54.545	0.00	0.00	0.00	3.01
676	1277	2.561478	TCAGGGGTAGAACAAAGCAC	57.439	50.000	0.00	0.00	0.00	4.40
1114	1908	8.902540	CCAGATGGTATTTACAGCTAATACAA	57.097	34.615	16.13	8.30	39.24	2.41
1317	3425	7.573968	AATTCATAATTGAAGTAGGAGTGCC	57.426	36.000	0.00	0.00	44.75	5.01
1381	3489	2.529744	GGGACACTTCCAGGTGCCT	61.530	63.158	0.00	0.00	44.98	4.75
1382	3490	2.034221	GGGACACTTCCAGGTGCC	59.966	66.667	0.00	0.00	44.98	5.01
1383	3491	2.034221	GGGGACACTTCCAGGTGC	59.966	66.667	0.00	0.00	44.98	5.01
1384	3492	2.757077	GGGGGACACTTCCAGGTG	59.243	66.667	0.00	0.00	44.98	4.00
1385	3493	2.928396	CGGGGGACACTTCCAGGT	60.928	66.667	0.00	0.00	44.98	4.00
1386	3494	4.410400	GCGGGGGACACTTCCAGG	62.410	72.222	0.00	0.00	44.98	4.45
1387	3495	2.690653	TTTGCGGGGGACACTTCCAG	62.691	60.000	0.00	0.00	44.98	3.86
1388	3496	2.285889	TTTTGCGGGGGACACTTCCA	62.286	55.000	0.00	0.00	44.98	3.53
1389	3497	1.110518	TTTTTGCGGGGGACACTTCC	61.111	55.000	0.00	0.00	41.95	3.46
1390	3498	2.421220	TTTTTGCGGGGGACACTTC	58.579	52.632	0.00	0.00	0.00	3.01
1391	3499	4.688770	TTTTTGCGGGGGACACTT	57.311	50.000	0.00	0.00	0.00	3.16
1408	3516	2.452600	TCACTTCCAGGTGCCTTTTT	57.547	45.000	0.00	0.00	37.16	1.94
1409	3517	2.430694	GTTTCACTTCCAGGTGCCTTTT	59.569	45.455	0.00	0.00	37.16	2.27
1410	3518	2.031870	GTTTCACTTCCAGGTGCCTTT	58.968	47.619	0.00	0.00	37.16	3.11
1411	3519	1.692411	GTTTCACTTCCAGGTGCCTT	58.308	50.000	0.00	0.00	37.16	4.35
1453	3561	2.923121	AGAGCAACATATGGCGTTGAT	58.077	42.857	7.80	1.19	45.05	2.57
1454	3562	2.401583	AGAGCAACATATGGCGTTGA	57.598	45.000	7.80	0.00	45.30	3.18
1523	3631	5.410132	TGTATATTGACAACTCAAACACCGG	59.590	40.000	0.00	0.00	39.90	5.28

Showing 1 to 25 of 105 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.