AutoCloner

Multiple sequence alignment - TraesCS7D01G280100

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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	TraesCS7D01G280100	chr7D	100.000	2437	0	0	1	2437	272236474	272234038	0.000000e+00	4501.0
1	TraesCS7D01G280100	chr7D	96.179	1858	65	6	580	2433	272281420	272279565	0.000000e+00	3033.0
2	TraesCS7D01G280100	chr7D	96.943	458	14	0	1	458	272281878	272281421	0.000000e+00	769.0
3	TraesCS7D01G280100	chr7D	83.558	371	50	5	824	1186	110887803	110888170	1.080000e-88	337.0
4	TraesCS7D01G280100	chr4D	92.876	1853	96	15	588	2433	354987531	354985708	0.000000e+00	2658.0
5	TraesCS7D01G280100	chr4D	94.196	224	13	0	97	320	354987754	354987531	2.320000e-90	342.0
6	TraesCS7D01G280100	chr4D	91.473	129	11	0	190	318	354987885	354987757	6.920000e-41	178.0
7	TraesCS7D01G280100	chr3B	91.135	1895	138	12	542	2433	85807080	85805213	0.000000e+00	2542.0
8	TraesCS7D01G280100	chr3B	84.000	550	64	12	1904	2433	198128969	198129514	7.780000e-140	507.0
9	TraesCS7D01G280100	chr3B	93.171	205	14	0	1	205	85807294	85807090	3.940000e-78	302.0
10	TraesCS7D01G280100	chr5B	92.257	1653	90	12	787	2433	237125732	237124112	0.000000e+00	2309.0
11	TraesCS7D01G280100	chr5B	94.486	943	41	6	1492	2433	116641198	116642130	0.000000e+00	1443.0
12	TraesCS7D01G280100	chr5B	86.437	988	70	19	520	1498	116632928	116633860	0.000000e+00	1024.0
13	TraesCS7D01G280100	chr5B	90.789	380	34	1	1	379	116632494	116632873	7.780000e-140	507.0
14	TraesCS7D01G280100	chr5B	92.704	233	16	1	1	232	237128880	237128648	3.880000e-88	335.0
15	TraesCS7D01G280100	chr5B	94.898	196	9	1	609	803	237125945	237125750	3.040000e-79	305.0
16	TraesCS7D01G280100	chr5B	89.520	229	22	2	575	801	248649573	248649801	3.070000e-74	289.0
17	TraesCS7D01G280100	chr5B	92.000	75	6	0	542	616	237128563	237128489	3.310000e-19	106.0
18	TraesCS7D01G280100	chr5B	91.935	62	5	0	447	508	116632875	116632936	1.200000e-13	87.9
19	TraesCS7D01G280100	chr7B	87.234	1457	118	23	920	2346	70066521	70067939	0.000000e+00	1598.0
20	TraesCS7D01G280100	chr7B	87.997	1308	97	16	1071	2346	69830957	69832236	0.000000e+00	1491.0
21	TraesCS7D01G280100	chr7B	87.764	1087	87	18	1290	2346	69990371	69991441	0.000000e+00	1229.0
22	TraesCS7D01G280100	chr7B	85.000	380	37	8	920	1299	69986404	69986763	3.830000e-98	368.0
23	TraesCS7D01G280100	chr7B	91.855	221	17	1	582	801	205197869	205197649	8.460000e-80	307.0
24	TraesCS7D01G280100	chr7B	95.349	43	2	0	824	866	69986250	69986292	4.350000e-08	69.4
25	TraesCS7D01G280100	chr6B	86.416	1465	121	24	920	2346	549026422	549027846	0.000000e+00	1531.0
26	TraesCS7D01G280100	chr6B	88.385	1059	81	13	1315	2346	548946291	548947334	0.000000e+00	1236.0
27	TraesCS7D01G280100	chr6B	85.287	401	36	6	920	1320	548945483	548945860	2.270000e-105	392.0
28	TraesCS7D01G280100	chr6B	84.831	178	27	0	1	178	560665644	560665467	1.930000e-41	180.0
29	TraesCS7D01G280100	chr6B	95.349	43	2	0	824	866	549026261	549026303	4.350000e-08	69.4
30	TraesCS7D01G280100	chr7A	83.497	1527	118	42	824	2301	116015075	116016516	0.000000e+00	1301.0
31	TraesCS7D01G280100	chr7A	89.140	221	19	2	582	801	715756956	715757172	1.110000e-68	270.0
32	TraesCS7D01G280100	chr6A	83.700	1000	124	25	920	1894	596895414	596896399	0.000000e+00	907.0
33	TraesCS7D01G280100	chr4A	82.386	704	105	12	798	1489	127333050	127333746	1.610000e-166	595.0
34	TraesCS7D01G280100	chrUn	83.514	552	60	14	1904	2434	22424157	22424698	1.010000e-133	486.0
35	TraesCS7D01G280100	chr1B	91.855	221	17	1	582	801	633782284	633782504	8.460000e-80	307.0
36	TraesCS7D01G280100	chr4B	87.500	144	18	0	36	179	572620892	572620749	1.500000e-37	167.0

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	TraesCS7D01G280100	chr7D	272234038	272236474	2436	True	4501.000000	4501	100.000000	1	2437	1	chr7D.!!$R1	2436
1	TraesCS7D01G280100	chr7D	272279565	272281878	2313	True	1901.000000	3033	96.561000	1	2433	2	chr7D.!!$R2	2432
2	TraesCS7D01G280100	chr4D	354985708	354987885	2177	True	1059.333333	2658	92.848333	97	2433	3	chr4D.!!$R1	2336
3	TraesCS7D01G280100	chr3B	85805213	85807294	2081	True	1422.000000	2542	92.153000	1	2433	2	chr3B.!!$R1	2432
4	TraesCS7D01G280100	chr3B	198128969	198129514	545	False	507.000000	507	84.000000	1904	2433	1	chr3B.!!$F1	529
5	TraesCS7D01G280100	chr5B	116641198	116642130	932	False	1443.000000	1443	94.486000	1492	2433	1	chr5B.!!$F1	941
6	TraesCS7D01G280100	chr5B	237124112	237128880	4768	True	763.750000	2309	92.964750	1	2433	4	chr5B.!!$R1	2432
7	TraesCS7D01G280100	chr5B	116632494	116633860	1366	False	539.633333	1024	89.720333	1	1498	3	chr5B.!!$F3	1497
8	TraesCS7D01G280100	chr7B	70066521	70067939	1418	False	1598.000000	1598	87.234000	920	2346	1	chr7B.!!$F2	1426
9	TraesCS7D01G280100	chr7B	69830957	69832236	1279	False	1491.000000	1491	87.997000	1071	2346	1	chr7B.!!$F1	1275
10	TraesCS7D01G280100	chr7B	69986250	69991441	5191	False	555.466667	1229	89.371000	824	2346	3	chr7B.!!$F3	1522
11	TraesCS7D01G280100	chr6B	548945483	548947334	1851	False	814.000000	1236	86.836000	920	2346	2	chr6B.!!$F1	1426
12	TraesCS7D01G280100	chr6B	549026261	549027846	1585	False	800.200000	1531	90.882500	824	2346	2	chr6B.!!$F2	1522
13	TraesCS7D01G280100	chr7A	116015075	116016516	1441	False	1301.000000	1301	83.497000	824	2301	1	chr7A.!!$F1	1477
14	TraesCS7D01G280100	chr6A	596895414	596896399	985	False	907.000000	907	83.700000	920	1894	1	chr6A.!!$F1	974
15	TraesCS7D01G280100	chr4A	127333050	127333746	696	False	595.000000	595	82.386000	798	1489	1	chr4A.!!$F1	691
16	TraesCS7D01G280100	chrUn	22424157	22424698	541	False	486.000000	486	83.514000	1904	2434	1	chrUn.!!$F1	530

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
907	3614	0.526662	GCTGTAGAGTAGTGGCGTGT	59.473	55.0	0.0	0.0	0.0	4.49	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2374	9262	1.221414	GCTTGTCAGCGACTGAAACT	58.779	50.0	10.46	0.0	42.46	2.66	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
280	316	2.435938	CGCCGGCTGGTGTACAAT	60.436	61.111	26.68	0.00	41.05	2.71
397	434	1.800586	CCCACTGTTGTTCGTCATCTG	59.199	52.381	0.00	0.00	0.00	2.90
399	436	2.138320	CACTGTTGTTCGTCATCTGCT	58.862	47.619	0.00	0.00	0.00	4.24
441	478	2.257207	TCGGTCTCCATTCCTGTTCTT	58.743	47.619	0.00	0.00	0.00	2.52
461	498	1.053424	ACTCAAGAAGTAACCCGCCA	58.947	50.000	0.00	0.00	36.07	5.69
464	501	1.004200	AAGAAGTAACCCGCCACCG	60.004	57.895	0.00	0.00	0.00	4.94
508	545	9.426534	CTTCCCCCTCTATAATTTTCATTTTCT	57.573	33.333	0.00	0.00	0.00	2.52
540	577	8.742777	AGCTATTCATTTTCAATTGTAGCTCAA	58.257	29.630	14.03	0.00	39.34	3.02
569	606	3.055021	TGCATGACTGATTTAACCGGGTA	60.055	43.478	6.32	0.00	0.00	3.69
818	3441	4.926832	GCTTTGCCGTAACCATATTTTGTT	59.073	37.500	0.00	0.00	0.00	2.83
866	3489	0.687920	GGAGAAGCCCAGCCCTATAC	59.312	60.000	0.00	0.00	0.00	1.47
894	3601	3.488048	GCCGATAGCAGAGCTGTAG	57.512	57.895	0.00	0.00	40.10	2.74
897	3604	2.226330	CCGATAGCAGAGCTGTAGAGT	58.774	52.381	0.00	0.00	40.10	3.24
898	3605	3.403968	CCGATAGCAGAGCTGTAGAGTA	58.596	50.000	0.00	0.00	40.10	2.59
899	3606	3.435327	CCGATAGCAGAGCTGTAGAGTAG	59.565	52.174	0.00	0.00	40.10	2.57
900	3607	4.062293	CGATAGCAGAGCTGTAGAGTAGT	58.938	47.826	0.00	0.00	40.10	2.73
901	3608	4.084066	CGATAGCAGAGCTGTAGAGTAGTG	60.084	50.000	0.00	0.00	40.10	2.74
902	3609	2.374184	AGCAGAGCTGTAGAGTAGTGG	58.626	52.381	0.00	0.00	37.57	4.00
903	3610	1.202359	GCAGAGCTGTAGAGTAGTGGC	60.202	57.143	0.00	0.00	0.00	5.01
904	3611	1.064803	CAGAGCTGTAGAGTAGTGGCG	59.935	57.143	0.00	0.00	0.00	5.69
905	3612	1.096416	GAGCTGTAGAGTAGTGGCGT	58.904	55.000	0.00	0.00	0.00	5.68
906	3613	0.811915	AGCTGTAGAGTAGTGGCGTG	59.188	55.000	0.00	0.00	0.00	5.34
907	3614	0.526662	GCTGTAGAGTAGTGGCGTGT	59.473	55.000	0.00	0.00	0.00	4.49
908	3615	1.741706	GCTGTAGAGTAGTGGCGTGTA	59.258	52.381	0.00	0.00	0.00	2.90
909	3616	2.163010	GCTGTAGAGTAGTGGCGTGTAA	59.837	50.000	0.00	0.00	0.00	2.41
910	3617	3.756069	CTGTAGAGTAGTGGCGTGTAAC	58.244	50.000	0.00	0.00	0.00	2.50
911	3618	2.489329	TGTAGAGTAGTGGCGTGTAACC	59.511	50.000	0.00	0.00	0.00	2.85
912	3619	0.893447	AGAGTAGTGGCGTGTAACCC	59.107	55.000	0.00	0.00	0.00	4.11
913	3620	0.893447	GAGTAGTGGCGTGTAACCCT	59.107	55.000	0.00	0.00	0.00	4.34
914	3621	2.094675	GAGTAGTGGCGTGTAACCCTA	58.905	52.381	0.00	0.00	0.00	3.53
915	3622	2.493278	GAGTAGTGGCGTGTAACCCTAA	59.507	50.000	0.00	0.00	0.00	2.69
916	3623	2.899256	AGTAGTGGCGTGTAACCCTAAA	59.101	45.455	0.00	0.00	0.00	1.85
917	3624	2.934886	AGTGGCGTGTAACCCTAAAA	57.065	45.000	0.00	0.00	0.00	1.52
983	3727	1.082496	GCAAGTGAGTTGAGCGCAC	60.082	57.895	11.47	3.13	46.25	5.34
1214	3968	4.129737	CTCCGGCACCATCGTCGT	62.130	66.667	0.00	0.00	0.00	4.34
1543	8374	8.543774	TCCTTGTAAGAAAATCTCTCTTGCTAT	58.456	33.333	3.03	0.00	36.71	2.97
1544	8375	9.171877	CCTTGTAAGAAAATCTCTCTTGCTATT	57.828	33.333	3.03	0.00	36.71	1.73
1615	8452	4.024670	GCTTCTTCCTTGGACTAGGACTA	58.975	47.826	1.94	0.00	43.91	2.59
1620	8457	4.440826	TCCTTGGACTAGGACTAGCTAG	57.559	50.000	19.44	19.44	39.40	3.42
1860	8717	4.141413	CCATGGTGGATCTAGTGGAATCAA	60.141	45.833	2.57	0.00	40.96	2.57
1902	8759	3.564511	CAAAGCACCTTGGAAATGTACG	58.435	45.455	0.00	0.00	0.00	3.67
2041	8902	5.580998	ACAACATCTCTACCACTCTAGGAA	58.419	41.667	0.00	0.00	0.00	3.36
2078	8940	3.571590	TGCACCAACCTTTAGGAATTGT	58.428	40.909	2.06	0.00	38.94	2.71
2301	9188	6.262601	AGACCAATTTACACAAAAGTTCACG	58.737	36.000	0.00	0.00	0.00	4.35
2361	9249	5.864474	AGTATGTCTGCTAGTTCACTTTTCG	59.136	40.000	0.00	0.00	0.00	3.46
2374	9262	4.471548	TCACTTTTCGTAAATTTCCCCCA	58.528	39.130	0.00	0.00	0.00	4.96
2376	9264	4.279922	CACTTTTCGTAAATTTCCCCCAGT	59.720	41.667	0.00	0.00	0.00	4.00
2434	9322	7.986085	ACTAAATTTACAGACTTGATGCACT	57.014	32.000	0.00	0.00	0.00	4.40
2435	9323	8.396272	ACTAAATTTACAGACTTGATGCACTT	57.604	30.769	0.00	0.00	0.00	3.16
2436	9324	9.502091	ACTAAATTTACAGACTTGATGCACTTA	57.498	29.630	0.00	0.00	0.00	2.24

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
310	346	4.202315	ACATAATACAACATAGGAGCGGCA	60.202	41.667	1.45	0.00	0.00	5.69
397	434	3.181458	TGGACGGAGGGATATAAACAAGC	60.181	47.826	0.00	0.00	0.00	4.01
399	436	5.617252	GATTGGACGGAGGGATATAAACAA	58.383	41.667	0.00	0.00	0.00	2.83
441	478	2.028748	GTGGCGGGTTACTTCTTGAGTA	60.029	50.000	0.00	0.00	39.86	2.59
461	498	2.496470	GAGGACCAGAATAAGTGACGGT	59.504	50.000	0.00	0.00	0.00	4.83
464	501	4.383226	GGGAAGAGGACCAGAATAAGTGAC	60.383	50.000	0.00	0.00	0.00	3.67
511	548	9.401058	AGCTACAATTGAAAATGAATAGCTACT	57.599	29.630	13.59	0.00	41.67	2.57
512	549	9.657121	GAGCTACAATTGAAAATGAATAGCTAC	57.343	33.333	17.80	10.89	43.08	3.58
513	550	9.394767	TGAGCTACAATTGAAAATGAATAGCTA	57.605	29.630	17.80	0.00	43.08	3.32
514	551	8.284945	TGAGCTACAATTGAAAATGAATAGCT	57.715	30.769	17.81	17.81	45.09	3.32
515	552	8.801913	GTTGAGCTACAATTGAAAATGAATAGC	58.198	33.333	13.59	11.83	40.76	2.97
516	553	9.844790	TGTTGAGCTACAATTGAAAATGAATAG	57.155	29.630	13.59	1.86	40.76	1.73
518	555	9.362539	GATGTTGAGCTACAATTGAAAATGAAT	57.637	29.630	13.59	0.00	40.76	2.57
519	556	8.358895	TGATGTTGAGCTACAATTGAAAATGAA	58.641	29.630	13.59	0.00	40.76	2.57
520	557	7.884257	TGATGTTGAGCTACAATTGAAAATGA	58.116	30.769	13.59	0.00	40.76	2.57
521	558	7.811236	ACTGATGTTGAGCTACAATTGAAAATG	59.189	33.333	13.59	0.00	40.76	2.32
522	559	7.811236	CACTGATGTTGAGCTACAATTGAAAAT	59.189	33.333	13.59	0.00	40.76	1.82
523	560	7.140705	CACTGATGTTGAGCTACAATTGAAAA	58.859	34.615	13.59	0.00	40.76	2.29
524	561	6.671190	CACTGATGTTGAGCTACAATTGAAA	58.329	36.000	13.59	0.00	40.76	2.69
525	562	5.335113	GCACTGATGTTGAGCTACAATTGAA	60.335	40.000	13.59	0.00	40.76	2.69
526	563	4.154737	GCACTGATGTTGAGCTACAATTGA	59.845	41.667	13.59	0.00	40.76	2.57
527	564	4.083164	TGCACTGATGTTGAGCTACAATTG	60.083	41.667	3.24	3.24	40.76	2.32
531	568	2.837532	TGCACTGATGTTGAGCTACA	57.162	45.000	0.00	0.00	0.00	2.74
577	614	1.272369	TGCATTGGTGATGGGCTTACA	60.272	47.619	0.00	0.00	36.21	2.41
818	3441	0.821711	CGGCCCAAGAAAGTTGGACA	60.822	55.000	5.32	0.00	42.06	4.02
866	3489	0.827925	TGCTATCGGCTCTACCTGGG	60.828	60.000	0.00	0.00	42.39	4.45
890	3597	2.489329	GGTTACACGCCACTACTCTACA	59.511	50.000	0.00	0.00	0.00	2.74
894	3601	0.893447	AGGGTTACACGCCACTACTC	59.107	55.000	0.00	0.00	0.00	2.59
897	3604	4.348863	TTTTTAGGGTTACACGCCACTA	57.651	40.909	0.00	0.00	0.00	2.74
898	3605	2.934886	TTTTAGGGTTACACGCCACT	57.065	45.000	0.00	0.00	0.00	4.00
915	3622	1.064952	GTGTACACGCCACTGCTTTTT	59.935	47.619	10.84	0.00	34.43	1.94
916	3623	0.661020	GTGTACACGCCACTGCTTTT	59.339	50.000	10.84	0.00	34.43	2.27
917	3624	0.462937	TGTGTACACGCCACTGCTTT	60.463	50.000	20.61	0.00	33.92	3.51
1483	8313	1.677217	GGAGAGGTGACTGGCATGAAC	60.677	57.143	0.00	0.00	44.43	3.18
1615	8452	5.420421	TGCTCAGTGTAAGAGATTTCTAGCT	59.580	40.000	0.00	0.00	35.09	3.32
1620	8457	4.629200	CAGGTGCTCAGTGTAAGAGATTTC	59.371	45.833	0.00	0.00	35.09	2.17
1860	8717	8.562892	GCTTTGCATTCTGTATAGTGAATGTAT	58.437	33.333	19.98	0.00	46.51	2.29
1902	8759	7.081526	ACTTACAAAGAATGATGTCTCATGC	57.918	36.000	0.00	0.00	41.34	4.06
2031	8892	4.450419	CACTCAAAAGTGCTTCCTAGAGTG	59.550	45.833	0.00	0.00	46.01	3.51
2032	8893	4.636249	CACTCAAAAGTGCTTCCTAGAGT	58.364	43.478	0.00	0.00	46.01	3.24
2078	8940	2.736347	AGCTCTTCTTTAGCCCGACTA	58.264	47.619	0.00	0.00	41.02	2.59
2284	9170	3.377798	GTCCCCGTGAACTTTTGTGTAAA	59.622	43.478	0.00	0.00	0.00	2.01
2301	9188	7.368059	CCAGCTAATTTTATAAATTCGTCCCC	58.632	38.462	0.00	0.00	0.00	4.81
2340	9228	4.632153	ACGAAAAGTGAACTAGCAGACAT	58.368	39.130	0.00	0.00	0.00	3.06
2361	9249	4.082949	CGACTGAAACTGGGGGAAATTTAC	60.083	45.833	0.00	0.00	0.00	2.01
2374	9262	1.221414	GCTTGTCAGCGACTGAAACT	58.779	50.000	10.46	0.00	42.46	2.66

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.