AutoCloner

Multiple sequence alignment - TraesCS1B01G143900

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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	TraesCS1B01G143900	chr1B	100.000	1308	0	0	369	1676	195588251	195589558	0.000000e+00	2416
1	TraesCS1B01G143900	chr1B	100.000	391	0	0	2006	2396	195589888	195590278	0.000000e+00	723
2	TraesCS1B01G143900	chr1B	87.279	566	39	9	369	904	195579900	195580462	1.220000e-172	616
3	TraesCS1B01G143900	chr1B	100.000	215	0	0	1	215	195587883	195588097	4.800000e-107	398
4	TraesCS1B01G143900	chr1B	93.488	215	12	1	1	215	195579623	195579835	3.840000e-83	318
5	TraesCS1B01G143900	chr1D	95.141	782	34	4	899	1676	141703616	141704397	0.000000e+00	1230
6	TraesCS1B01G143900	chr1D	94.490	363	20	0	543	905	361145370	361145732	5.780000e-156	560
7	TraesCS1B01G143900	chr1D	92.063	378	11	5	2007	2384	141704435	141704793	4.570000e-142	514
8	TraesCS1B01G143900	chr1D	93.488	215	12	2	1	215	64003958	64003746	3.840000e-83	318
9	TraesCS1B01G143900	chr6D	88.752	569	29	9	369	905	377231800	377231235	0.000000e+00	664
10	TraesCS1B01G143900	chr5D	88.556	568	28	10	369	904	160073125	160073687	0.000000e+00	654
11	TraesCS1B01G143900	chr5D	86.796	568	39	9	369	904	557995125	557994562	3.410000e-168	601
12	TraesCS1B01G143900	chr5D	86.467	569	41	16	369	904	509453191	509453756	2.050000e-165	592
13	TraesCS1B01G143900	chr5D	94.737	361	18	1	543	903	387072880	387072521	5.780000e-156	560
14	TraesCS1B01G143900	chr3D	88.787	544	48	11	369	904	434835033	434834495	0.000000e+00	654
15	TraesCS1B01G143900	chr3D	94.247	365	21	0	543	907	114031613	114031249	2.080000e-155	558
16	TraesCS1B01G143900	chr3D	95.349	215	10	0	1	215	186442896	186442682	2.280000e-90	342
17	TraesCS1B01G143900	chr7D	87.698	569	33	11	369	903	90487552	90488117	1.560000e-176	628
18	TraesCS1B01G143900	chr7D	94.022	368	19	2	543	910	559387720	559388084	2.690000e-154	555
19	TraesCS1B01G143900	chr7D	94.495	218	9	2	1	215	373535135	373535352	1.370000e-87	333
20	TraesCS1B01G143900	chr7D	93.488	215	11	2	1	215	263535297	263535508	1.380000e-82	316
21	TraesCS1B01G143900	chr7B	87.823	542	42	16	373	904	31254920	31255447	4.380000e-172	614
22	TraesCS1B01G143900	chr1A	92.891	422	26	4	899	1317	148961485	148961065	5.660000e-171	610
23	TraesCS1B01G143900	chr1A	88.442	398	23	1	2022	2396	148960464	148960067	2.170000e-125	459
24	TraesCS1B01G143900	chr1A	86.053	337	33	5	1346	1676	148961067	148960739	1.360000e-92	350
25	TraesCS1B01G143900	chr3B	86.268	568	42	19	369	904	432362838	432363401	3.430000e-163	584
26	TraesCS1B01G143900	chr2D	95.304	362	16	1	543	904	195232422	195232062	7.430000e-160	573
27	TraesCS1B01G143900	chr4D	95.278	360	16	1	543	902	292920308	292920666	9.610000e-159	569
28	TraesCS1B01G143900	chr4D	86.242	487	33	6	369	822	387543819	387543334	4.600000e-137	497
29	TraesCS1B01G143900	chr4A	94.931	217	9	1	1	215	681085106	681084890	2.950000e-89	339
30	TraesCS1B01G143900	chr7A	93.519	216	12	2	1	215	518562873	518562659	1.070000e-83	320
31	TraesCS1B01G143900	chr3A	93.519	216	12	2	1	215	472856774	472856560	1.070000e-83	320
32	TraesCS1B01G143900	chr2A	93.088	217	13	2	1	215	502365223	502365007	1.380000e-82	316

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	TraesCS1B01G143900	chr1B	195587883	195590278	2395	False	1179	2416	100.000000	1	2396	3	chr1B.!!$F2	2395
1	TraesCS1B01G143900	chr1B	195579623	195580462	839	False	467	616	90.383500	1	904	2	chr1B.!!$F1	903
2	TraesCS1B01G143900	chr1D	141703616	141704793	1177	False	872	1230	93.602000	899	2384	2	chr1D.!!$F2	1485
3	TraesCS1B01G143900	chr6D	377231235	377231800	565	True	664	664	88.752000	369	905	1	chr6D.!!$R1	536
4	TraesCS1B01G143900	chr5D	160073125	160073687	562	False	654	654	88.556000	369	904	1	chr5D.!!$F1	535
5	TraesCS1B01G143900	chr5D	557994562	557995125	563	True	601	601	86.796000	369	904	1	chr5D.!!$R2	535
6	TraesCS1B01G143900	chr5D	509453191	509453756	565	False	592	592	86.467000	369	904	1	chr5D.!!$F2	535
7	TraesCS1B01G143900	chr3D	434834495	434835033	538	True	654	654	88.787000	369	904	1	chr3D.!!$R3	535
8	TraesCS1B01G143900	chr7D	90487552	90488117	565	False	628	628	87.698000	369	903	1	chr7D.!!$F1	534
9	TraesCS1B01G143900	chr7B	31254920	31255447	527	False	614	614	87.823000	373	904	1	chr7B.!!$F1	531
10	TraesCS1B01G143900	chr1A	148960067	148961485	1418	True	473	610	89.128667	899	2396	3	chr1A.!!$R1	1497
11	TraesCS1B01G143900	chr3B	432362838	432363401	563	False	584	584	86.268000	369	904	1	chr3B.!!$F1	535

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
159	160	0.113776	AGAGTGTCGGAGGGTTACCA	59.886	55.0	2.98	0.0	40.13	3.25	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1451	1500	0.249868	TGTCCTCAGGCGTGAAACAG	60.25	55.0	16.17	3.91	35.74	3.16	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
38	39	1.269102	GGTGTACCGGATGAGATCACG	60.269	57.143	9.46	0.00	0.00	4.35
39	40	1.029681	TGTACCGGATGAGATCACGG	58.970	55.000	9.46	9.58	43.85	4.94
129	130	3.060602	CAGAAGTGTTCCGGAGAGTTTC	58.939	50.000	3.34	8.37	0.00	2.78
158	159	0.531200	CAGAGTGTCGGAGGGTTACC	59.469	60.000	0.00	0.00	0.00	2.85
159	160	0.113776	AGAGTGTCGGAGGGTTACCA	59.886	55.000	2.98	0.00	40.13	3.25
164	165	0.248565	GTCGGAGGGTTACCAGAACC	59.751	60.000	2.98	0.00	40.13	3.62
510	520	5.015924	TCCTCCTCCCATCCTTTATATACGA	59.984	44.000	0.00	0.00	0.00	3.43
649	686	1.895798	TCATGCTGACGAAACTCTCCT	59.104	47.619	0.00	0.00	0.00	3.69
772	810	2.555325	AGACGTTCGACTACATCAACCA	59.445	45.455	0.00	0.00	0.00	3.67
783	821	6.363088	CGACTACATCAACCACGTTACTAAAA	59.637	38.462	0.00	0.00	0.00	1.52
790	828	5.585445	TCAACCACGTTACTAAAAGCTTTCA	59.415	36.000	13.10	0.00	0.00	2.69
797	835	6.256321	ACGTTACTAAAAGCTTTCACTTTCGA	59.744	34.615	13.10	0.00	38.92	3.71
872	913	4.998033	AGATAGATCTTGCGTGATCGTAGA	59.002	41.667	0.00	0.00	45.35	2.59
905	947	4.040706	TGAAATACTACGTTCCCCAACACT	59.959	41.667	0.00	0.00	32.14	3.55
906	948	5.245751	TGAAATACTACGTTCCCCAACACTA	59.754	40.000	0.00	0.00	32.14	2.74
907	949	5.945144	AATACTACGTTCCCCAACACTAT	57.055	39.130	0.00	0.00	32.14	2.12
908	950	5.945144	ATACTACGTTCCCCAACACTATT	57.055	39.130	0.00	0.00	32.14	1.73
909	951	4.628963	ACTACGTTCCCCAACACTATTT	57.371	40.909	0.00	0.00	32.14	1.40
910	952	4.320870	ACTACGTTCCCCAACACTATTTG	58.679	43.478	0.00	0.00	32.14	2.32
981	1024	5.472137	TCGGGAAGTAACCAAAGAGAATTTG	59.528	40.000	0.00	0.00	0.00	2.32
1011	1054	6.150140	AGGCACAAGAGAGAATGAAACATTAC	59.850	38.462	0.00	0.00	0.00	1.89
1125	1169	5.068198	ACACATGTTTCTGAAACTGCATTCT	59.932	36.000	27.75	9.57	41.90	2.40
1143	1187	5.360999	GCATTCTAAGTTCTATGGCCCTTTT	59.639	40.000	0.00	0.00	0.00	2.27
1246	1290	8.725405	TGTTAGTCAACTGAAGAAACACATTA	57.275	30.769	0.00	0.00	35.56	1.90
1282	1326	6.584185	TTCCTACAAAATACCTTCCTTTGC	57.416	37.500	0.00	0.00	34.15	3.68
1351	1395	5.506708	AGAGAAAATTAATACCTTGGCCGT	58.493	37.500	0.00	0.00	0.00	5.68
1441	1490	1.281899	GAAGATTCGGCCTTCACTCG	58.718	55.000	0.00	0.00	39.70	4.18
1462	1511	2.543031	GGAAGGTTTTCTGTTTCACGCC	60.543	50.000	0.00	0.00	33.68	5.68
1477	1526	2.565391	TCACGCCTGAGGACAAAATCTA	59.435	45.455	0.65	0.00	0.00	1.98
1533	1583	4.743151	TGTTAACTCAAGAACTACACGCTG	59.257	41.667	7.22	0.00	0.00	5.18
1549	1599	1.168407	GCTGCTCACCTGTTTCTGCA	61.168	55.000	0.00	0.00	0.00	4.41
1616	1666	0.899720	TGAAGATACCGGTTCGCCTT	59.100	50.000	15.04	11.24	34.30	4.35
2138	2211	1.131638	TTCTATGGCCGATGCTCCTT	58.868	50.000	0.00	0.00	37.74	3.36
2148	2221	1.474143	CGATGCTCCTTCCTTTCCTCC	60.474	57.143	0.00	0.00	0.00	4.30
2150	2223	0.475632	TGCTCCTTCCTTTCCTCCCA	60.476	55.000	0.00	0.00	0.00	4.37
2230	2303	2.711922	GGAGACGGTGAGATGGCGT	61.712	63.158	0.00	0.00	0.00	5.68
2323	2396	3.766591	TCCTTGCAAGTTTCAAGAACCAA	59.233	39.130	24.35	0.00	42.52	3.67

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
20	21	1.029681	CCGTGATCTCATCCGGTACA	58.970	55.000	0.00	0.00	37.91	2.90
23	24	0.683179	TGTCCGTGATCTCATCCGGT	60.683	55.000	0.00	0.00	41.11	5.28
129	130	2.094390	TCCGACACTCTGGTTTTATCCG	60.094	50.000	0.00	0.00	0.00	4.18
172	173	2.194868	GGCCCATTAACCTCGGGG	59.805	66.667	0.00	0.00	43.72	5.73
173	174	1.453197	GTGGCCCATTAACCTCGGG	60.453	63.158	0.00	0.00	43.42	5.14
174	175	1.453197	GGTGGCCCATTAACCTCGG	60.453	63.158	0.00	0.00	0.00	4.63
175	176	1.301623	TGGTGGCCCATTAACCTCG	59.698	57.895	10.34	0.00	35.17	4.63
496	506	4.574390	CCCCCTCCCTCGTATATAAAGGAT	60.574	50.000	12.16	0.00	31.44	3.24
649	686	0.397114	TAGATCCAGCTGAGGCCGAA	60.397	55.000	17.39	0.00	39.73	4.30
772	810	6.256321	TCGAAAGTGAAAGCTTTTAGTAACGT	59.744	34.615	23.06	11.70	38.64	3.99
783	821	4.436242	TCGTAGATCGAAAGTGAAAGCT	57.564	40.909	0.00	0.00	45.98	3.74
797	835	2.957006	GTGTCCACATACCCTCGTAGAT	59.043	50.000	0.00	0.00	33.89	1.98
810	848	2.207229	CGGGGAGAGTGTGTCCACA	61.207	63.158	0.00	0.00	44.39	4.17
905	947	1.346395	AGTGTCACTGTCGGGCAAATA	59.654	47.619	4.21	0.00	0.00	1.40
906	948	0.108585	AGTGTCACTGTCGGGCAAAT	59.891	50.000	4.21	0.00	0.00	2.32
907	949	0.107410	AAGTGTCACTGTCGGGCAAA	60.107	50.000	6.18	0.00	0.00	3.68
908	950	0.107410	AAAGTGTCACTGTCGGGCAA	60.107	50.000	6.18	0.00	0.00	4.52
909	951	0.753867	TAAAGTGTCACTGTCGGGCA	59.246	50.000	6.18	0.00	0.00	5.36
910	952	1.145803	GTAAAGTGTCACTGTCGGGC	58.854	55.000	6.18	0.00	0.00	6.13
948	991	1.067364	GTTACTTCCCGAGCTAGCTCC	59.933	57.143	33.57	18.82	39.77	4.70
959	1002	6.650427	ACAAATTCTCTTTGGTTACTTCCC	57.350	37.500	3.09	0.00	33.92	3.97
981	1024	4.067896	TCATTCTCTCTTGTGCCTTCAAC	58.932	43.478	0.00	0.00	0.00	3.18
1011	1054	9.698309	TCTATATCTTTCCTTTTCTTATCAGCG	57.302	33.333	0.00	0.00	0.00	5.18
1082	1125	8.040727	ACATGTGTAAGCTCAAGAATGTATGTA	58.959	33.333	0.00	0.00	0.00	2.29
1125	1169	6.886178	ACTCTAAAAGGGCCATAGAACTTA	57.114	37.500	6.18	0.00	0.00	2.24
1143	1187	5.818678	TGCCAACCTTTTCTAGAACTCTA	57.181	39.130	4.18	0.00	0.00	2.43
1246	1290	5.426689	TTTGTAGGAATGACATGAGAGCT	57.573	39.130	0.00	0.00	0.00	4.09
1282	1326	2.286872	GATGAGTCCAGTTGCATCCAG	58.713	52.381	0.00	0.00	32.93	3.86
1351	1395	1.459158	AATGCTGGTGTTGCCCCAA	60.459	52.632	0.00	0.00	36.04	4.12
1441	1490	2.543031	GGCGTGAAACAGAAAACCTTCC	60.543	50.000	0.00	0.00	35.74	3.46
1451	1500	0.249868	TGTCCTCAGGCGTGAAACAG	60.250	55.000	16.17	3.91	35.74	3.16
1462	1511	7.412853	CCGAATGAAATAGATTTTGTCCTCAG	58.587	38.462	0.00	0.00	0.00	3.35
1497	1546	4.780815	TGAGTTAACATTATGGAGCCTGG	58.219	43.478	8.61	0.00	0.00	4.45
1533	1583	1.198637	GACATGCAGAAACAGGTGAGC	59.801	52.381	0.00	0.00	34.14	4.26
1549	1599	0.749649	GCTGGAGAGTCATCCGACAT	59.250	55.000	0.00	0.00	45.23	3.06
1616	1666	3.741075	CGATGGGTAATAGCAGCTCACAA	60.741	47.826	0.00	0.00	0.00	3.33
2005	2055	7.590689	CGATCGAGTTCTAGGGTTTATAACTTC	59.409	40.741	10.26	0.00	30.83	3.01
2110	2160	1.758280	TCGGCCATAGAATACGTTGGT	59.242	47.619	2.24	0.00	0.00	3.67
2138	2211	1.423921	GGAACTGTTGGGAGGAAAGGA	59.576	52.381	0.00	0.00	0.00	3.36
2148	2221	2.104963	GCCTCCCTATAGGAACTGTTGG	59.895	54.545	21.07	11.18	46.94	3.77
2150	2223	3.041946	CTGCCTCCCTATAGGAACTGTT	58.958	50.000	21.07	0.00	46.94	3.16
2222	2295	3.766691	ACGCCGGTTACGCCATCT	61.767	61.111	1.90	0.00	39.22	2.90

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.