AutoCloner

Multiple sequence alignment - TraesCS7A01G122500

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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	TraesCS7A01G122500	chr7A	100.000	2354	0	0	1	2354	78696267	78698620	0.000000e+00	4348.0
1	TraesCS7A01G122500	chr7A	95.299	1340	42	11	1035	2354	721854515	721855853	0.000000e+00	2106.0
2	TraesCS7A01G122500	chr7A	94.462	1300	48	9	1078	2354	711643387	711644685	0.000000e+00	1980.0
3	TraesCS7A01G122500	chr7A	93.866	1027	54	3	1	1019	721852806	721853831	0.000000e+00	1539.0
4	TraesCS7A01G122500	chr7A	93.402	773	45	6	1	770	711642318	711643087	0.000000e+00	1140.0
5	TraesCS7A01G122500	chr7A	92.290	441	26	2	581	1014	721853837	721854276	9.240000e-174	619.0
6	TraesCS7A01G122500	chr7A	91.167	317	21	1	717	1026	711643074	711643390	7.780000e-115	424.0
7	TraesCS7A01G122500	chr6B	93.589	1747	80	13	637	2354	684054862	684053119	0.000000e+00	2577.0
8	TraesCS7A01G122500	chr3B	93.582	1745	83	10	637	2354	752769058	752767316	0.000000e+00	2575.0
9	TraesCS7A01G122500	chr2A	94.911	1297	46	6	1078	2354	63985556	63986852	0.000000e+00	2012.0
10	TraesCS7A01G122500	chr2A	94.301	772	40	4	1	770	63984487	63985256	0.000000e+00	1179.0
11	TraesCS7A01G122500	chr2A	90.852	317	22	1	717	1026	63985243	63985559	3.620000e-113	418.0
12	TraesCS7A01G122500	chr2A	75.061	413	53	29	428	814	677826861	677826473	1.890000e-31	147.0
13	TraesCS7A01G122500	chr6A	91.644	1460	97	8	919	2354	2547320	2545862	0.000000e+00	1997.0
14	TraesCS7A01G122500	chr6A	76.000	300	37	19	428	715	604353109	604353385	3.180000e-24	122.0
15	TraesCS7A01G122500	chr3D	94.545	1265	49	7	1110	2354	605102624	605101360	0.000000e+00	1936.0
16	TraesCS7A01G122500	chr2B	90.136	882	57	9	625	1488	1500126	1499257	0.000000e+00	1120.0
17	TraesCS7A01G122500	chr2B	96.573	496	15	2	1860	2354	1499264	1498770	0.000000e+00	821.0
18	TraesCS7A01G122500	chr7D	87.572	346	37	5	1782	2124	553452304	553451962	1.700000e-106	396.0
19	TraesCS7A01G122500	chr3A	81.522	368	51	7	1224	1580	731655545	731655906	1.060000e-73	287.0
20	TraesCS7A01G122500	chr3A	75.743	404	47	28	438	814	26786334	26786713	3.130000e-34	156.0
21	TraesCS7A01G122500	chr4A	81.250	368	56	7	1224	1580	256234736	256235101	3.830000e-73	285.0
22	TraesCS7A01G122500	chr7B	92.857	168	11	1	2183	2349	148527299	148527466	2.340000e-60	243.0
23	TraesCS7A01G122500	chr5A	76.061	330	44	22	428	746	434793821	434794126	3.150000e-29	139.0
24	TraesCS7A01G122500	chr5B	96.875	32	0	1	203	234	23359237	23359267	4.000000e-03	52.8
25	TraesCS7A01G122500	chr5B	100.000	28	0	0	259	286	45205714	45205741	4.000000e-03	52.8

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	TraesCS7A01G122500	chr7A	78696267	78698620	2353	False	4348.000000	4348	100.000000	1	2354	1	chr7A.!!$F1	2353
1	TraesCS7A01G122500	chr7A	721852806	721855853	3047	False	1421.333333	2106	93.818333	1	2354	3	chr7A.!!$F3	2353
2	TraesCS7A01G122500	chr7A	711642318	711644685	2367	False	1181.333333	1980	93.010333	1	2354	3	chr7A.!!$F2	2353
3	TraesCS7A01G122500	chr6B	684053119	684054862	1743	True	2577.000000	2577	93.589000	637	2354	1	chr6B.!!$R1	1717
4	TraesCS7A01G122500	chr3B	752767316	752769058	1742	True	2575.000000	2575	93.582000	637	2354	1	chr3B.!!$R1	1717
5	TraesCS7A01G122500	chr2A	63984487	63986852	2365	False	1203.000000	2012	93.354667	1	2354	3	chr2A.!!$F1	2353
6	TraesCS7A01G122500	chr6A	2545862	2547320	1458	True	1997.000000	1997	91.644000	919	2354	1	chr6A.!!$R1	1435
7	TraesCS7A01G122500	chr3D	605101360	605102624	1264	True	1936.000000	1936	94.545000	1110	2354	1	chr3D.!!$R1	1244
8	TraesCS7A01G122500	chr2B	1498770	1500126	1356	True	970.500000	1120	93.354500	625	2354	2	chr2B.!!$R1	1729

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
453	456	1.27055	CCACCAATTTTTCAGCTCGCT	59.729	47.619	0.0	0.0	0.0	4.93	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1354	2095	0.736053	GCTGAAAACGGGTGACACAA	59.264	50.0	8.08	0.0	0.0	3.33	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
214	216	6.527057	AGTTTGCTACGTAATACTTCCTCT	57.473	37.500	0.00	0.00	0.00	3.69
254	256	6.019152	CGTCCCATAACGTAAGATGTTTTTG	58.981	40.000	0.00	0.00	43.62	2.44
255	257	5.798434	GTCCCATAACGTAAGATGTTTTTGC	59.202	40.000	0.00	0.00	43.62	3.68
363	366	6.775708	TGGCACTAGTAGTTTTTATGGAACT	58.224	36.000	0.00	0.00	40.28	3.01
380	383	6.022163	TGGAACTCACTAACTACTGCTAAC	57.978	41.667	0.00	0.00	0.00	2.34
403	406	4.581824	CCAGTTATATGCTCATGCCAACTT	59.418	41.667	0.00	0.00	38.71	2.66
453	456	1.270550	CCACCAATTTTTCAGCTCGCT	59.729	47.619	0.00	0.00	0.00	4.93
485	488	4.081531	CCCAGCCTATTTTTCTGCAAATCA	60.082	41.667	0.00	0.00	0.00	2.57
615	618	3.322466	CCCGGGTCTGGCACTCTT	61.322	66.667	14.18	0.00	0.00	2.85
628	631	1.837051	ACTCTTCCACGAGGCCACA	60.837	57.895	5.01	0.00	35.33	4.17
637	640	3.256960	GAGGCCACAACCCCCTCA	61.257	66.667	5.01	0.00	43.63	3.86
646	649	3.581141	AACCCCCTCACCTCCTCCC	62.581	68.421	0.00	0.00	0.00	4.30
887	1347	4.655527	CGAACTTGTCGCTGGACT	57.344	55.556	0.00	0.00	44.14	3.85
963	1423	3.928779	GGCGGCGATGAGGATCCA	61.929	66.667	15.82	0.00	0.00	3.41
1054	1787	2.348411	CCCCCAGGAATCATGTGTAC	57.652	55.000	0.00	0.00	33.47	2.90
1055	1788	1.475034	CCCCCAGGAATCATGTGTACG	60.475	57.143	0.00	0.00	33.47	3.67
1056	1789	1.209504	CCCCAGGAATCATGTGTACGT	59.790	52.381	0.00	0.00	0.00	3.57
1057	1790	2.279741	CCCAGGAATCATGTGTACGTG	58.720	52.381	0.00	0.00	0.00	4.49
1058	1791	2.279741	CCAGGAATCATGTGTACGTGG	58.720	52.381	0.00	0.00	33.80	4.94
1059	1792	1.665679	CAGGAATCATGTGTACGTGGC	59.334	52.381	0.00	0.00	33.80	5.01
1060	1793	1.014352	GGAATCATGTGTACGTGGCC	58.986	55.000	0.00	0.00	33.80	5.36
1061	1794	1.677518	GGAATCATGTGTACGTGGCCA	60.678	52.381	0.00	0.00	33.80	5.36
1062	1795	2.080693	GAATCATGTGTACGTGGCCAA	58.919	47.619	7.24	0.00	33.80	4.52
1063	1796	1.737838	ATCATGTGTACGTGGCCAAG	58.262	50.000	17.83	17.83	33.80	3.61
1064	1797	0.682292	TCATGTGTACGTGGCCAAGA	59.318	50.000	26.25	6.20	33.80	3.02
1065	1798	1.277842	TCATGTGTACGTGGCCAAGAT	59.722	47.619	26.25	11.87	33.80	2.40
1066	1799	1.398041	CATGTGTACGTGGCCAAGATG	59.602	52.381	26.25	13.67	0.00	2.90
1067	1800	0.682292	TGTGTACGTGGCCAAGATGA	59.318	50.000	26.25	7.12	0.00	2.92
1068	1801	1.076332	GTGTACGTGGCCAAGATGAC	58.924	55.000	26.25	18.41	0.00	3.06
1069	1802	0.036765	TGTACGTGGCCAAGATGACC	60.037	55.000	26.25	0.78	0.00	4.02
1070	1803	0.036765	GTACGTGGCCAAGATGACCA	60.037	55.000	26.25	0.10	0.00	4.02
1072	1805	3.578456	GTGGCCAAGATGACCACG	58.422	61.111	7.24	0.00	44.02	4.94
1073	1806	2.359850	TGGCCAAGATGACCACGC	60.360	61.111	0.61	0.00	0.00	5.34
1074	1807	3.499737	GGCCAAGATGACCACGCG	61.500	66.667	3.53	3.53	0.00	6.01
1155	1888	5.050023	CGGTCAGTCTCTTTCTTTTCTTTCC	60.050	44.000	0.00	0.00	0.00	3.13
1203	1944	4.870123	TGTGGCTGCTCAAATTAATGTT	57.130	36.364	0.00	0.00	0.00	2.71
1422	2163	0.389817	GCATGAGTAGTGCACGGACA	60.390	55.000	22.02	16.20	42.08	4.02
1453	2194	5.596361	AGTGTATCTTACCAGAGATGGACAG	59.404	44.000	0.31	0.00	37.01	3.51
1673	2428	9.859427	AGTCATAAACAATGTCAATAATGTTGG	57.141	29.630	0.00	0.00	36.23	3.77
1682	2437	5.321102	TGTCAATAATGTTGGTAAGTGCCT	58.679	37.500	0.00	0.00	0.00	4.75
1718	2473	1.741327	AAGCACCACAGCAGGCTTTG	61.741	55.000	0.51	0.51	43.56	2.77
1923	2679	5.534654	TGCTTTTGGCTGTGACTTACTATTT	59.465	36.000	0.00	0.00	42.39	1.40
1924	2680	5.858581	GCTTTTGGCTGTGACTTACTATTTG	59.141	40.000	0.00	0.00	38.06	2.32
2084	2840	9.063615	TGAATACTCTACTCTTTATATGTCGCA	57.936	33.333	0.00	0.00	0.00	5.10

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
214	216	3.770388	TGGGACGGTTACATTATGAGACA	59.230	43.478	0.00	0.00	0.00	3.41
298	301	7.296628	AGGTATTATGTTCTTGTTGGCAAAA	57.703	32.000	0.00	0.00	33.73	2.44
338	341	6.879458	AGTTCCATAAAAACTACTAGTGCCAG	59.121	38.462	5.39	0.00	35.25	4.85
358	361	5.047519	TGGTTAGCAGTAGTTAGTGAGTTCC	60.048	44.000	0.00	0.00	0.00	3.62
363	366	7.713734	ATAACTGGTTAGCAGTAGTTAGTGA	57.286	36.000	17.66	0.00	38.55	3.41
380	383	4.139786	AGTTGGCATGAGCATATAACTGG	58.860	43.478	0.00	0.00	44.61	4.00
453	456	5.784906	AGAAAAATAGGCTGGGAAATTTGGA	59.215	36.000	0.00	0.00	0.00	3.53
615	618	3.948719	GGGTTGTGGCCTCGTGGA	61.949	66.667	7.92	0.00	34.57	4.02
628	631	2.125225	GGAGGAGGTGAGGGGGTT	59.875	66.667	0.00	0.00	0.00	4.11
770	1223	0.874390	TTGGTGCAACAGCGATTCTC	59.126	50.000	3.79	0.00	39.98	2.87
798	1251	4.096003	CCCGCCCTCCGTTGTGAT	62.096	66.667	0.00	0.00	34.38	3.06
963	1423	4.129737	CACACGGGCCGATCGTCT	62.130	66.667	35.78	5.60	38.94	4.18
1000	1460	1.660560	GCACGCATCTCCTTTGCCAT	61.661	55.000	0.00	0.00	36.75	4.40
1035	1768	1.475034	CGTACACATGATTCCTGGGGG	60.475	57.143	0.00	0.00	0.00	5.40
1036	1769	1.209504	ACGTACACATGATTCCTGGGG	59.790	52.381	0.00	0.00	0.00	4.96
1037	1770	2.279741	CACGTACACATGATTCCTGGG	58.720	52.381	0.00	0.00	0.00	4.45
1038	1771	2.279741	CCACGTACACATGATTCCTGG	58.720	52.381	0.00	0.00	0.00	4.45
1039	1772	1.665679	GCCACGTACACATGATTCCTG	59.334	52.381	0.00	0.00	0.00	3.86
1040	1773	1.406887	GGCCACGTACACATGATTCCT	60.407	52.381	0.00	0.00	0.00	3.36
1041	1774	1.014352	GGCCACGTACACATGATTCC	58.986	55.000	0.00	0.00	0.00	3.01
1042	1775	1.732941	TGGCCACGTACACATGATTC	58.267	50.000	0.00	0.00	0.00	2.52
1043	1776	2.083774	CTTGGCCACGTACACATGATT	58.916	47.619	3.88	0.00	0.00	2.57
1044	1777	1.277842	TCTTGGCCACGTACACATGAT	59.722	47.619	3.88	0.00	0.00	2.45
1045	1778	0.682292	TCTTGGCCACGTACACATGA	59.318	50.000	3.88	0.00	0.00	3.07
1046	1779	1.398041	CATCTTGGCCACGTACACATG	59.602	52.381	3.88	0.00	0.00	3.21
1047	1780	1.277842	TCATCTTGGCCACGTACACAT	59.722	47.619	3.88	0.00	0.00	3.21
1048	1781	0.682292	TCATCTTGGCCACGTACACA	59.318	50.000	3.88	0.00	0.00	3.72
1049	1782	1.076332	GTCATCTTGGCCACGTACAC	58.924	55.000	3.88	0.00	0.00	2.90
1050	1783	0.036765	GGTCATCTTGGCCACGTACA	60.037	55.000	3.88	0.00	42.98	2.90
1051	1784	0.036765	TGGTCATCTTGGCCACGTAC	60.037	55.000	3.88	4.22	46.74	3.67
1052	1785	2.367529	TGGTCATCTTGGCCACGTA	58.632	52.632	3.88	0.00	46.74	3.57
1053	1786	3.156714	TGGTCATCTTGGCCACGT	58.843	55.556	3.88	0.00	46.74	4.49
1057	1790	3.499737	CGCGTGGTCATCTTGGCC	61.500	66.667	0.00	0.00	43.98	5.36
1058	1791	3.499737	CCGCGTGGTCATCTTGGC	61.500	66.667	6.91	0.00	0.00	4.52
1059	1792	3.499737	GCCGCGTGGTCATCTTGG	61.500	66.667	17.91	0.00	37.67	3.61
1060	1793	2.434884	AGCCGCGTGGTCATCTTG	60.435	61.111	17.91	0.00	37.67	3.02
1061	1794	2.125512	GAGCCGCGTGGTCATCTT	60.126	61.111	17.91	0.00	41.24	2.40
1062	1795	4.498520	CGAGCCGCGTGGTCATCT	62.499	66.667	17.91	4.53	41.69	2.90
1155	1888	2.654056	CGTCATCGATCAATAGTGCTCG	59.346	50.000	9.92	9.92	43.18	5.03
1175	1908	1.723608	TTGAGCAGCCACAAACACCG	61.724	55.000	0.81	0.00	0.00	4.94
1203	1944	5.543790	TCCTATACATAGCAGCAGATTTGGA	59.456	40.000	0.00	0.00	0.00	3.53
1354	2095	0.736053	GCTGAAAACGGGTGACACAA	59.264	50.000	8.08	0.00	0.00	3.33
1422	2163	7.956328	TCTCTGGTAAGATACACTAACATGT	57.044	36.000	0.00	0.00	36.56	3.21
1453	2194	5.739161	CAGGCATAATTACGCAAAAAGACTC	59.261	40.000	5.81	0.00	0.00	3.36
1532	2275	6.645790	AACAAGCTTTTTCTCAGTGATGAT	57.354	33.333	0.00	0.00	0.00	2.45
1584	2327	9.803315	GAAGTTGATTATACATGTCTGTGTAGA	57.197	33.333	0.00	0.00	37.93	2.59
1585	2328	9.809096	AGAAGTTGATTATACATGTCTGTGTAG	57.191	33.333	0.00	0.00	37.93	2.74
1701	2456	2.337532	CAAAGCCTGCTGTGGTGC	59.662	61.111	1.14	0.00	0.00	5.01
1718	2473	3.942130	AAAAGGACATTGCTACAAGGC	57.058	42.857	0.00	0.00	0.00	4.35
1770	2525	1.743958	CTCTAGCATACGGGGATACGG	59.256	57.143	0.00	0.00	38.39	4.02
1841	2597	3.198409	TGTGCTCACAGTTCAGAACAT	57.802	42.857	15.85	0.12	36.21	2.71
1844	2600	3.473923	TCATGTGCTCACAGTTCAGAA	57.526	42.857	8.74	0.00	45.48	3.02
1923	2679	7.303182	ACTAAGACATGCATATAGGCTAACA	57.697	36.000	11.14	0.00	34.04	2.41
1924	2680	9.706691	TTAACTAAGACATGCATATAGGCTAAC	57.293	33.333	11.14	0.32	34.04	2.34

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.