AutoCloner

Multiple sequence alignment - TraesCS7D01G093100

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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	TraesCS7D01G093100	chr7D	100.000	2654	0	0	1	2654	55422648	55425301	0.000000e+00	4902.0
1	TraesCS7D01G093100	chr7A	90.899	1890	118	28	795	2653	59412485	59414351	0.000000e+00	2488.0
2	TraesCS7D01G093100	chr7A	88.409	440	36	5	257	695	6424409	6423984	1.410000e-142	516.0
3	TraesCS7D01G093100	chr7A	88.085	235	24	2	559	792	6424045	6423814	2.600000e-70	276.0
4	TraesCS7D01G093100	chr4A	88.285	1878	131	42	826	2654	671940243	671942080	0.000000e+00	2167.0
5	TraesCS7D01G093100	chr3D	91.621	919	60	10	1740	2654	601383431	601382526	0.000000e+00	1254.0
6	TraesCS7D01G093100	chr3D	88.419	544	56	4	29	568	416409571	416410111	0.000000e+00	649.0
7	TraesCS7D01G093100	chr1D	91.513	919	62	9	1740	2654	28628655	28629561	0.000000e+00	1251.0
8	TraesCS7D01G093100	chr5B	89.663	919	77	11	1740	2654	611768212	611769116	0.000000e+00	1155.0
9	TraesCS7D01G093100	chr5A	88.651	793	73	11	6	792	311003166	311003947	0.000000e+00	950.0
10	TraesCS7D01G093100	chr3A	88.110	799	78	8	8	792	13859058	13858263	0.000000e+00	933.0
11	TraesCS7D01G093100	chr6B	84.097	698	95	10	8	695	331017202	331017893	0.000000e+00	660.0
12	TraesCS7D01G093100	chr2D	88.315	445	36	6	257	700	58735630	58735201	1.090000e-143	520.0
13	TraesCS7D01G093100	chr2D	88.983	236	22	2	559	793	58735266	58735034	3.340000e-74	289.0
14	TraesCS7D01G093100	chr2D	86.735	98	10	2	1753	1850	58370340	58370434	3.610000e-19	106.0
15	TraesCS7D01G093100	chr2D	100.000	30	0	0	745	774	18236184	18236155	3.690000e-04	56.5
16	TraesCS7D01G093100	chr2D	81.429	70	10	2	595	661	600323521	600323452	1.000000e-03	54.7
17	TraesCS7D01G093100	chr7B	78.931	318	40	12	363	677	746987375	746987082	9.700000e-45	191.0
18	TraesCS7D01G093100	chr6D	83.333	96	14	2	443	537	466612973	466613067	1.310000e-13	87.9
19	TraesCS7D01G093100	chr6A	82.474	97	17	0	443	539	613076031	613076127	4.710000e-13	86.1
20	TraesCS7D01G093100	chr6A	88.710	62	4	3	430	490	601670247	601670306	3.660000e-09	73.1
21	TraesCS7D01G093100	chr2B	94.595	37	2	0	737	773	607070190	607070226	1.030000e-04	58.4
22	TraesCS7D01G093100	chrUn	100.000	30	0	0	745	774	178482720	178482749	3.690000e-04	56.5
23	TraesCS7D01G093100	chr4B	96.970	33	1	0	741	773	527593541	527593573	3.690000e-04	56.5
24	TraesCS7D01G093100	chr2A	100.000	30	0	0	745	774	19362523	19362494	3.690000e-04	56.5
25	TraesCS7D01G093100	chr2A	92.308	39	2	1	595	632	749854213	749854175	1.000000e-03	54.7

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	TraesCS7D01G093100	chr7D	55422648	55425301	2653	False	4902.0	4902	100.000	1	2654	1	chr7D.!!$F1	2653
1	TraesCS7D01G093100	chr7A	59412485	59414351	1866	False	2488.0	2488	90.899	795	2653	1	chr7A.!!$F1	1858
2	TraesCS7D01G093100	chr7A	6423814	6424409	595	True	396.0	516	88.247	257	792	2	chr7A.!!$R1	535
3	TraesCS7D01G093100	chr4A	671940243	671942080	1837	False	2167.0	2167	88.285	826	2654	1	chr4A.!!$F1	1828
4	TraesCS7D01G093100	chr3D	601382526	601383431	905	True	1254.0	1254	91.621	1740	2654	1	chr3D.!!$R1	914
5	TraesCS7D01G093100	chr3D	416409571	416410111	540	False	649.0	649	88.419	29	568	1	chr3D.!!$F1	539
6	TraesCS7D01G093100	chr1D	28628655	28629561	906	False	1251.0	1251	91.513	1740	2654	1	chr1D.!!$F1	914
7	TraesCS7D01G093100	chr5B	611768212	611769116	904	False	1155.0	1155	89.663	1740	2654	1	chr5B.!!$F1	914
8	TraesCS7D01G093100	chr5A	311003166	311003947	781	False	950.0	950	88.651	6	792	1	chr5A.!!$F1	786
9	TraesCS7D01G093100	chr3A	13858263	13859058	795	True	933.0	933	88.110	8	792	1	chr3A.!!$R1	784
10	TraesCS7D01G093100	chr6B	331017202	331017893	691	False	660.0	660	84.097	8	695	1	chr6B.!!$F1	687
11	TraesCS7D01G093100	chr2D	58735034	58735630	596	True	404.5	520	88.649	257	793	2	chr2D.!!$R3	536

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
60	61	0.037605	CTAAACGTCCACCGCCTTCT	60.038	55.0	0.0	0.0	41.42	2.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1748	1880	0.861837	AACTGAGCAACTCTTTCGCG	59.138	50.0	0.0	0.0	0.0	5.87	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
60	61	0.037605	CTAAACGTCCACCGCCTTCT	60.038	55.000	0.00	0.00	41.42	2.85
128	133	5.677319	TTCCTTATCTCCAACGAACAGAT	57.323	39.130	0.00	0.00	0.00	2.90
129	134	6.785337	TTCCTTATCTCCAACGAACAGATA	57.215	37.500	0.00	0.00	0.00	1.98
137	147	3.454447	TCCAACGAACAGATACCATCCAT	59.546	43.478	0.00	0.00	0.00	3.41
138	148	3.561310	CCAACGAACAGATACCATCCATG	59.439	47.826	0.00	0.00	0.00	3.66
149	160	1.216064	CCATCCATGTCTCCTTCCCA	58.784	55.000	0.00	0.00	0.00	4.37
164	179	3.173965	CTTCCCAACTTCTCCTACCTCA	58.826	50.000	0.00	0.00	0.00	3.86
241	256	3.177228	CCTCCTCCTTTCTCTCTTTCCA	58.823	50.000	0.00	0.00	0.00	3.53
305	320	2.347490	GAGCACCGGTGTGGACAT	59.653	61.111	33.92	14.32	42.99	3.06
343	358	1.526917	AAGGTCAGCTGCAAACGCT	60.527	52.632	9.47	0.00	38.49	5.07
355	370	1.302192	AAACGCTGGTACCGCATGT	60.302	52.632	22.55	13.53	0.00	3.21
405	421	0.108992	GTAATGGCGACTGGACACGA	60.109	55.000	0.00	0.00	35.56	4.35
483	499	4.109050	GCAGAAATACAGAGAAGAGGTCG	58.891	47.826	0.00	0.00	0.00	4.79
528	544	4.123497	ACAAGGGTCTTTTTGCAAGAAC	57.877	40.909	0.00	0.00	33.33	3.01
555	571	3.137913	AGAAGTGGCTGGAGATATTGCAT	59.862	43.478	0.00	0.00	0.00	3.96
574	590	4.553323	GCATGTTTTTGCAACTGAGATCT	58.447	39.130	0.00	0.00	42.31	2.75
575	591	4.986659	GCATGTTTTTGCAACTGAGATCTT	59.013	37.500	0.00	0.00	42.31	2.40
576	592	5.107607	GCATGTTTTTGCAACTGAGATCTTG	60.108	40.000	0.00	0.00	42.31	3.02
641	731	9.777575	CAGAAAAAGAAGAACAAATTTTGCAAT	57.222	25.926	9.04	0.00	0.00	3.56
661	751	5.574443	GCAATTAAGATCTTGTTGCAGGAAC	59.426	40.000	33.03	16.75	41.18	3.62
676	766	2.096248	AGGAACGAGGTTTGCAACAAA	58.904	42.857	0.00	0.00	0.00	2.83
681	771	0.752658	GAGGTTTGCAACAAAGGGCT	59.247	50.000	0.00	0.00	0.00	5.19
690	781	1.833934	ACAAAGGGCTTGTGGCAGG	60.834	57.895	0.00	0.00	46.80	4.85
710	801	5.411669	GCAGGAAAATAGAAAAGAGGAACGA	59.588	40.000	0.00	0.00	0.00	3.85
721	812	0.389948	GAGGAACGAACGGCTCATGT	60.390	55.000	0.00	0.00	0.00	3.21
736	827	3.795488	GCTCATGTCATACAATCGGACGA	60.795	47.826	0.00	0.00	34.32	4.20
745	836	0.716108	CAATCGGACGACTTGTGAGC	59.284	55.000	0.00	0.00	0.00	4.26
793	884	2.125512	GACGTGTAGCAGGCCCAG	60.126	66.667	0.00	0.00	0.00	4.45
872	963	9.890085	CTTATATCGAAATGCATTTTTGTTGTG	57.110	29.630	24.81	9.40	31.56	3.33
1027	1136	2.113139	CTCCACCACCACCACCAC	59.887	66.667	0.00	0.00	0.00	4.16
1028	1137	2.692741	TCCACCACCACCACCACA	60.693	61.111	0.00	0.00	0.00	4.17
1510	1622	3.154473	CCGATGGCGAGGGGAAGA	61.154	66.667	0.00	0.00	40.82	2.87
1638	1750	2.174349	CAGCGGCGCAAGTCTTTC	59.826	61.111	35.02	0.11	42.28	2.62
1700	1812	0.890683	CAGGGGTGCCTGATTTTGAC	59.109	55.000	0.00	0.00	39.96	3.18
1738	1870	3.690139	CCATGGCTTGCTAGATGATGATC	59.310	47.826	0.00	0.00	0.00	2.92
1748	1880	0.946221	GATGATGATCCACGGCGACC	60.946	60.000	16.62	0.00	0.00	4.79
1773	1905	4.508124	CGAAAGAGTTGCTCAGTTACTGTT	59.492	41.667	12.41	0.00	32.06	3.16
1776	1908	2.222027	AGTTGCTCAGTTACTGTTGCC	58.778	47.619	21.77	12.52	33.84	4.52
1777	1909	1.266989	GTTGCTCAGTTACTGTTGCCC	59.733	52.381	21.77	13.29	33.84	5.36
1778	1910	0.472044	TGCTCAGTTACTGTTGCCCA	59.528	50.000	21.77	8.80	33.84	5.36
1779	1911	0.875059	GCTCAGTTACTGTTGCCCAC	59.125	55.000	12.41	0.00	32.61	4.61
1780	1912	1.523758	CTCAGTTACTGTTGCCCACC	58.476	55.000	12.41	0.00	32.61	4.61
1781	1913	0.250124	TCAGTTACTGTTGCCCACCG	60.250	55.000	12.41	0.00	32.61	4.94
1782	1914	0.534203	CAGTTACTGTTGCCCACCGT	60.534	55.000	3.88	0.00	0.00	4.83
1803	1936	4.511826	CGTTGGTTTTGTAGCTCTCTTTCT	59.488	41.667	0.00	0.00	0.00	2.52
1806	1939	6.377327	TGGTTTTGTAGCTCTCTTTCTTTG	57.623	37.500	0.00	0.00	0.00	2.77
1819	1952	4.655963	TCTTTCTTTGGGTGAAGATCAGG	58.344	43.478	0.00	0.00	35.70	3.86
1871	2004	5.279456	GGTTTCTGTTTCATGTTAAGCCCAT	60.279	40.000	0.00	0.00	0.00	4.00
1872	2005	6.071616	GGTTTCTGTTTCATGTTAAGCCCATA	60.072	38.462	0.00	0.00	0.00	2.74
1873	2006	6.757897	TTCTGTTTCATGTTAAGCCCATAG	57.242	37.500	0.00	0.00	0.00	2.23
1928	2063	5.294552	GTGTTTGGTCAGAAGGTATGATAGC	59.705	44.000	0.00	0.00	0.00	2.97
1963	2099	0.790814	GAAGAAGCTCCGTTCCGTTG	59.209	55.000	0.00	0.00	0.00	4.10
1966	2102	0.721718	GAAGCTCCGTTCCGTTGATG	59.278	55.000	0.00	0.00	0.00	3.07
2005	2142	2.421424	CCTGTAGTTTTCAGATGCCAGC	59.579	50.000	0.00	0.00	35.20	4.85
2074	2232	1.512926	ATTATCGATGAACTGCGCCC	58.487	50.000	8.54	0.00	0.00	6.13
2076	2234	0.249447	TATCGATGAACTGCGCCCAG	60.249	55.000	8.54	0.00	44.80	4.45
2169	2340	6.399039	GCGAGATTGTGTTATGTACATCGATC	60.399	42.308	12.68	12.15	36.74	3.69
2338	2526	8.978874	TGTCCTTGTATGCTTCATTATGTTAT	57.021	30.769	0.00	0.00	0.00	1.89
2581	2771	6.013725	TCACAGATTCTAAAAAGGCTGTCCTA	60.014	38.462	0.00	0.00	43.40	2.94
2638	2828	7.839907	TCCAACTGATTTTGCTGCTAATTAAT	58.160	30.769	0.00	0.00	0.00	1.40
2639	2829	8.965819	TCCAACTGATTTTGCTGCTAATTAATA	58.034	29.630	0.00	0.00	0.00	0.98
2640	2830	9.585099	CCAACTGATTTTGCTGCTAATTAATAA	57.415	29.630	0.00	0.00	0.00	1.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	7.436933	GTGATCAGAATCTTTTCCCTTGTTTT	58.563	34.615	0.00	0.00	32.75	2.43
1	2	6.015095	GGTGATCAGAATCTTTTCCCTTGTTT	60.015	38.462	0.00	0.00	32.75	2.83
2	3	5.478332	GGTGATCAGAATCTTTTCCCTTGTT	59.522	40.000	0.00	0.00	32.75	2.83
3	4	5.012893	GGTGATCAGAATCTTTTCCCTTGT	58.987	41.667	0.00	0.00	32.75	3.16
81	82	4.363990	AGCGGTGGTGCAGACTCG	62.364	66.667	0.00	0.00	37.31	4.18
128	133	2.293519	TGGGAAGGAGACATGGATGGTA	60.294	50.000	0.00	0.00	0.00	3.25
129	134	1.216990	GGGAAGGAGACATGGATGGT	58.783	55.000	0.00	0.00	0.00	3.55
137	147	1.978580	GGAGAAGTTGGGAAGGAGACA	59.021	52.381	0.00	0.00	0.00	3.41
138	148	2.261729	AGGAGAAGTTGGGAAGGAGAC	58.738	52.381	0.00	0.00	0.00	3.36
149	160	2.972713	TGCACTTGAGGTAGGAGAAGTT	59.027	45.455	0.00	0.00	0.00	2.66
164	179	2.769893	GCCATTTGGTTTGATGCACTT	58.230	42.857	0.00	0.00	37.57	3.16
387	402	0.821517	ATCGTGTCCAGTCGCCATTA	59.178	50.000	0.00	0.00	0.00	1.90
452	468	7.931407	TCTTCTCTGTATTTCTGCAACAAACTA	59.069	33.333	0.00	0.00	0.00	2.24
483	499	3.861689	GCAAAATTTACAGCAGCATCTCC	59.138	43.478	0.00	0.00	0.00	3.71
528	544	2.260844	TCTCCAGCCACTTCTTTGTG	57.739	50.000	0.00	0.00	37.66	3.33
555	571	5.581126	ACAAGATCTCAGTTGCAAAAACA	57.419	34.783	0.00	0.00	0.00	2.83
574	590	5.355596	CAAACCTAATTCCTGCAACAACAA	58.644	37.500	0.00	0.00	0.00	2.83
575	591	4.739137	GCAAACCTAATTCCTGCAACAACA	60.739	41.667	0.00	0.00	33.19	3.33
576	592	3.740832	GCAAACCTAATTCCTGCAACAAC	59.259	43.478	0.00	0.00	33.19	3.32
641	731	4.637276	TCGTTCCTGCAACAAGATCTTAA	58.363	39.130	7.86	0.00	34.20	1.85
643	733	3.070018	CTCGTTCCTGCAACAAGATCTT	58.930	45.455	0.88	0.88	34.20	2.40
676	766	0.178924	ATTTTCCTGCCACAAGCCCT	60.179	50.000	0.00	0.00	42.71	5.19
681	771	5.243730	CCTCTTTTCTATTTTCCTGCCACAA	59.756	40.000	0.00	0.00	0.00	3.33
685	776	5.392057	CGTTCCTCTTTTCTATTTTCCTGCC	60.392	44.000	0.00	0.00	0.00	4.85
690	781	6.304882	CCGTTCGTTCCTCTTTTCTATTTTC	58.695	40.000	0.00	0.00	0.00	2.29
710	801	2.866156	CGATTGTATGACATGAGCCGTT	59.134	45.455	0.00	0.00	0.00	4.44
721	812	3.191791	TCACAAGTCGTCCGATTGTATGA	59.808	43.478	13.25	8.11	35.47	2.15
736	827	3.665675	GATCCGCCGGCTCACAAGT	62.666	63.158	26.68	2.74	0.00	3.16
745	836	4.598062	GATCTTTTAAAAAGATCCGCCGG	58.402	43.478	19.30	0.00	44.17	6.13
810	901	2.096248	AGTTTCGCACAAAGAACCCAA	58.904	42.857	0.00	0.00	0.00	4.12
811	902	1.757682	AGTTTCGCACAAAGAACCCA	58.242	45.000	0.00	0.00	0.00	4.51
812	903	4.499037	AATAGTTTCGCACAAAGAACCC	57.501	40.909	0.00	0.00	0.00	4.11
813	904	6.822073	AAAAATAGTTTCGCACAAAGAACC	57.178	33.333	0.00	0.00	0.00	3.62
867	958	7.322699	CGGACATTTTACACAATCTAACACAAC	59.677	37.037	0.00	0.00	0.00	3.32
872	963	5.329493	GCCGGACATTTTACACAATCTAAC	58.671	41.667	5.05	0.00	0.00	2.34
1700	1812	2.162208	CCATGGACGGTCTCAAAATGTG	59.838	50.000	5.56	0.34	0.00	3.21
1748	1880	0.861837	AACTGAGCAACTCTTTCGCG	59.138	50.000	0.00	0.00	0.00	5.87
1757	1889	1.266989	GGGCAACAGTAACTGAGCAAC	59.733	52.381	0.81	0.00	37.61	4.17
1777	1909	2.218603	AGAGCTACAAAACCAACGGTG	58.781	47.619	0.00	0.00	35.34	4.94
1778	1910	2.104281	AGAGAGCTACAAAACCAACGGT	59.896	45.455	0.00	0.00	37.65	4.83
1779	1911	2.767505	AGAGAGCTACAAAACCAACGG	58.232	47.619	0.00	0.00	0.00	4.44
1780	1912	4.511826	AGAAAGAGAGCTACAAAACCAACG	59.488	41.667	0.00	0.00	0.00	4.10
1781	1913	6.378710	AAGAAAGAGAGCTACAAAACCAAC	57.621	37.500	0.00	0.00	0.00	3.77
1782	1914	6.183360	CCAAAGAAAGAGAGCTACAAAACCAA	60.183	38.462	0.00	0.00	0.00	3.67
1803	1936	4.996793	TGAAATCCTGATCTTCACCCAAA	58.003	39.130	0.00	0.00	0.00	3.28
1806	1939	3.054065	ACCTGAAATCCTGATCTTCACCC	60.054	47.826	0.00	0.00	0.00	4.61
1819	1952	4.008074	TCAGTGACCAGAACCTGAAATC	57.992	45.455	0.00	0.00	32.44	2.17
1871	2004	7.177921	ACCACTAACATCAGCACTTAAGTACTA	59.822	37.037	8.04	0.00	0.00	1.82
1872	2005	6.014499	ACCACTAACATCAGCACTTAAGTACT	60.014	38.462	8.04	4.98	0.00	2.73
1873	2006	6.164176	ACCACTAACATCAGCACTTAAGTAC	58.836	40.000	8.04	2.17	0.00	2.73
1928	2063	2.569059	TCTTCCGACACCTAGATACCG	58.431	52.381	0.00	0.00	0.00	4.02
1963	2099	2.289002	GCTTACAGCAGCATACCACATC	59.711	50.000	0.00	0.00	41.89	3.06
1966	2102	1.017387	GGCTTACAGCAGCATACCAC	58.983	55.000	0.00	0.00	44.75	4.16
2063	2221	1.034838	AAACAACTGGGCGCAGTTCA	61.035	50.000	37.62	1.67	42.87	3.18
2074	2232	2.512485	TGCATCCAAGCAAACAACTG	57.488	45.000	0.00	0.00	42.46	3.16
2169	2340	0.244994	AGCTAGCAGGTCACAAGACG	59.755	55.000	18.83	0.00	45.92	4.18
2264	2452	7.566760	TCAACAGTAACATCATTCAAGTGTT	57.433	32.000	0.00	0.00	39.26	3.32
2567	2757	8.879427	AATACTAACAATAGGACAGCCTTTTT	57.121	30.769	0.00	0.00	43.90	1.94

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.