AutoCloner

Multiple sequence alignment - TraesCS1A01G076800

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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	TraesCS1A01G076800	chr1A	100.000	2347	0	0	1	2347	59509803	59512149	0.000000e+00	4335
1	TraesCS1A01G076800	chr1D	88.209	1128	79	13	405	1527	82333634	82334712	0.000000e+00	1297
2	TraesCS1A01G076800	chr1D	90.238	840	56	8	1534	2347	19460191	19461030	0.000000e+00	1074
3	TraesCS1A01G076800	chr1D	92.202	654	31	4	869	1522	61351618	61352251	0.000000e+00	907
4	TraesCS1A01G076800	chr1D	96.250	400	10	1	1	395	60941008	60941407	0.000000e+00	651
5	TraesCS1A01G076800	chr1D	89.439	303	27	2	498	799	60949678	60949976	6.120000e-101	377
6	TraesCS1A01G076800	chr1D	94.737	133	7	0	1534	1666	462299322	462299454	8.500000e-50	207
7	TraesCS1A01G076800	chr1D	93.407	91	5	1	405	495	60941493	60941582	1.460000e-27	134
8	TraesCS1A01G076800	chr1D	88.119	101	9	2	1430	1527	196447936	196448036	1.470000e-22	117
9	TraesCS1A01G076800	chr7D	94.509	692	34	3	1660	2347	205947894	205948585	0.000000e+00	1064
10	TraesCS1A01G076800	chr7D	93.488	691	42	1	1660	2347	580896133	580896823	0.000000e+00	1024
11	TraesCS1A01G076800	chr1B	94.067	691	37	2	1660	2347	520360779	520360090	0.000000e+00	1046
12	TraesCS1A01G076800	chr3D	93.922	691	39	2	1658	2345	327464910	327465600	0.000000e+00	1040
13	TraesCS1A01G076800	chr3D	87.963	108	10	2	1422	1528	535459697	535459592	8.810000e-25	124
14	TraesCS1A01G076800	chr3A	93.786	692	41	1	1658	2347	13349157	13348466	0.000000e+00	1038
15	TraesCS1A01G076800	chr3A	93.750	688	41	1	1660	2347	640676674	640677359	0.000000e+00	1031
16	TraesCS1A01G076800	chr5A	93.023	688	45	2	1660	2347	708708131	708707447	0.000000e+00	1002
17	TraesCS1A01G076800	chr2D	92.909	691	46	1	1660	2347	66155690	66155000	0.000000e+00	1002
18	TraesCS1A01G076800	chr2D	94.615	130	7	0	1537	1666	54603451	54603322	3.950000e-48	202
19	TraesCS1A01G076800	chr6A	93.985	133	8	0	1534	1666	603765287	603765419	3.950000e-48	202
20	TraesCS1A01G076800	chr3B	93.985	133	8	0	1534	1666	688150610	688150742	3.950000e-48	202
21	TraesCS1A01G076800	chrUn	93.846	130	8	0	1537	1666	89713778	89713649	1.840000e-46	196
22	TraesCS1A01G076800	chr7A	93.846	130	8	0	1537	1666	682909250	682909121	1.840000e-46	196
23	TraesCS1A01G076800	chr5B	93.233	133	9	0	1534	1666	704318599	704318731	1.840000e-46	196
24	TraesCS1A01G076800	chr4A	93.846	130	8	0	1537	1666	677465835	677465706	1.840000e-46	196
25	TraesCS1A01G076800	chr2B	93.233	133	9	0	1534	1666	470493882	470494014	1.840000e-46	196

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	TraesCS1A01G076800	chr1A	59509803	59512149	2346	False	4335.0	4335	100.0000	1	2347	1	chr1A.!!$F1	2346
1	TraesCS1A01G076800	chr1D	82333634	82334712	1078	False	1297.0	1297	88.2090	405	1527	1	chr1D.!!$F4	1122
2	TraesCS1A01G076800	chr1D	19460191	19461030	839	False	1074.0	1074	90.2380	1534	2347	1	chr1D.!!$F1	813
3	TraesCS1A01G076800	chr1D	61351618	61352251	633	False	907.0	907	92.2020	869	1522	1	chr1D.!!$F3	653
4	TraesCS1A01G076800	chr1D	60941008	60941582	574	False	392.5	651	94.8285	1	495	2	chr1D.!!$F7	494
5	TraesCS1A01G076800	chr7D	205947894	205948585	691	False	1064.0	1064	94.5090	1660	2347	1	chr7D.!!$F1	687
6	TraesCS1A01G076800	chr7D	580896133	580896823	690	False	1024.0	1024	93.4880	1660	2347	1	chr7D.!!$F2	687
7	TraesCS1A01G076800	chr1B	520360090	520360779	689	True	1046.0	1046	94.0670	1660	2347	1	chr1B.!!$R1	687
8	TraesCS1A01G076800	chr3D	327464910	327465600	690	False	1040.0	1040	93.9220	1658	2345	1	chr3D.!!$F1	687
9	TraesCS1A01G076800	chr3A	13348466	13349157	691	True	1038.0	1038	93.7860	1658	2347	1	chr3A.!!$R1	689
10	TraesCS1A01G076800	chr3A	640676674	640677359	685	False	1031.0	1031	93.7500	1660	2347	1	chr3A.!!$F1	687
11	TraesCS1A01G076800	chr5A	708707447	708708131	684	True	1002.0	1002	93.0230	1660	2347	1	chr5A.!!$R1	687
12	TraesCS1A01G076800	chr2D	66155000	66155690	690	True	1002.0	1002	92.9090	1660	2347	1	chr2D.!!$R2	687

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
530	613	0.094046	CACGCGTATCCGACAAAACC	59.906	55.0	13.44	0.0	35.63	3.27	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2166	2281	0.387929	AGAGAGAAACGACACCGCAA	59.612	50.0	0.0	0.0	39.95	4.85	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
193	194	0.107312	TCGAGGAGGTTACCGAGGAG	60.107	60.000	0.00	0.00	34.73	3.69
329	330	2.176273	CATCTCTTGCTTCCGGGCG	61.176	63.158	0.00	0.00	34.52	6.13
349	350	0.318699	GACCAGTTTTCCGGCTTTGC	60.319	55.000	0.00	0.00	0.00	3.68
375	381	4.379243	AGAGCGCAACCTCACCGG	62.379	66.667	11.47	0.00	34.26	5.28
387	393	3.381335	ACCTCACCGGTCCATTTATAGT	58.619	45.455	2.59	0.00	44.93	2.12
395	401	3.386726	CGGTCCATTTATAGTGTCCCAGA	59.613	47.826	0.00	0.00	0.00	3.86
396	402	4.501571	CGGTCCATTTATAGTGTCCCAGAG	60.502	50.000	0.00	0.00	0.00	3.35
399	405	4.654262	TCCATTTATAGTGTCCCAGAGACC	59.346	45.833	0.00	0.00	45.68	3.85
400	406	4.202367	CCATTTATAGTGTCCCAGAGACCC	60.202	50.000	0.00	0.00	45.68	4.46
401	407	3.769189	TTATAGTGTCCCAGAGACCCA	57.231	47.619	0.00	0.00	45.68	4.51
402	408	2.166907	ATAGTGTCCCAGAGACCCAG	57.833	55.000	0.00	0.00	45.68	4.45
403	409	1.081481	TAGTGTCCCAGAGACCCAGA	58.919	55.000	0.00	0.00	45.68	3.86
487	569	1.869690	GAGCGCCAAGTGTTTCCTC	59.130	57.895	2.29	0.00	0.00	3.71
495	577	2.726822	AAGTGTTTCCTCGTCGGGGC	62.727	60.000	6.17	0.00	0.00	5.80
496	578	3.235481	TGTTTCCTCGTCGGGGCA	61.235	61.111	6.17	0.00	0.00	5.36
500	582	2.444700	TTTCCTCGTCGGGGCAAGAC	62.445	60.000	6.17	2.06	35.41	3.01
530	613	0.094046	CACGCGTATCCGACAAAACC	59.906	55.000	13.44	0.00	35.63	3.27
534	617	1.673626	GCGTATCCGACAAAACCCAGA	60.674	52.381	0.00	0.00	35.63	3.86
540	623	1.841663	CGACAAAACCCAGAGCCACG	61.842	60.000	0.00	0.00	0.00	4.94
541	624	2.130073	GACAAAACCCAGAGCCACGC	62.130	60.000	0.00	0.00	0.00	5.34
559	642	4.626081	CCCGCGCCTTATCCCCAG	62.626	72.222	0.00	0.00	0.00	4.45
564	647	4.235762	GCCTTATCCCCAGCGCGA	62.236	66.667	12.10	0.00	0.00	5.87
565	648	2.743718	CCTTATCCCCAGCGCGAT	59.256	61.111	12.10	0.00	0.00	4.58
566	649	1.669115	CCTTATCCCCAGCGCGATG	60.669	63.158	19.16	19.16	0.00	3.84
567	650	2.280797	TTATCCCCAGCGCGATGC	60.281	61.111	20.85	0.00	46.98	3.91
578	661	4.802051	GCGATGCCCTGCCTCCAA	62.802	66.667	0.00	0.00	0.00	3.53
594	677	2.361230	AACAGCGCCCCTTTAGCC	60.361	61.111	2.29	0.00	0.00	3.93
698	781	3.134127	GGATGCAACCCCGTGCTC	61.134	66.667	0.47	0.00	45.17	4.26
704	787	3.647771	AACCCCGTGCTCTTCCCC	61.648	66.667	0.00	0.00	0.00	4.81
705	788	4.974438	ACCCCGTGCTCTTCCCCA	62.974	66.667	0.00	0.00	0.00	4.96
768	851	2.050350	CCGCGACCCTGTTCTCCTA	61.050	63.158	8.23	0.00	0.00	2.94
793	876	3.227276	CCGCTATCCGCCTCTGGT	61.227	66.667	0.00	0.00	35.03	4.00
822	905	1.447314	GTGTGAACCCGGACGGATC	60.447	63.158	13.13	10.54	37.50	3.36
837	920	1.668101	GGATCCGAGGAGCTTCACGT	61.668	60.000	11.06	0.00	0.00	4.49
842	925	1.009389	CGAGGAGCTTCACGTTGGAC	61.009	60.000	3.36	0.00	0.00	4.02
953	1036	3.283684	CGAGGCTCGGATCTCGCT	61.284	66.667	28.52	0.00	44.68	4.93
1019	1102	1.289066	TGGAGCTCCACGTCTTTCG	59.711	57.895	32.00	0.00	42.01	3.46
1079	1162	3.047877	GTTCACGGGGAAGCACGG	61.048	66.667	0.00	0.00	35.82	4.94
1087	1170	4.021925	GGAAGCACGGCAGGACCT	62.022	66.667	0.00	0.00	35.61	3.85
1233	1316	2.486966	GCCTTGTCATGGAAGCGC	59.513	61.111	8.93	0.00	0.00	5.92
1235	1318	1.377725	CCTTGTCATGGAAGCGCCT	60.378	57.895	2.29	0.00	37.63	5.52
1238	1321	2.045926	GTCATGGAAGCGCCTGGT	60.046	61.111	2.29	0.00	37.63	4.00
1302	1385	7.308229	GGTGATCCTTTCGATTTGGATATCAAG	60.308	40.741	12.38	0.00	40.33	3.02
1324	1407	3.054655	GGTGAGTATTTAGTGCCCAGGAA	60.055	47.826	0.00	0.00	0.00	3.36
1392	1476	1.804372	GCTCTCAATGTCCTACTGCCG	60.804	57.143	0.00	0.00	0.00	5.69
1441	1525	1.945662	CACGGCTGCACAACAAAGC	60.946	57.895	0.50	0.00	36.17	3.51
1473	1558	7.707035	GTCTTGGTTGAATATCACGATCTTACT	59.293	37.037	0.00	0.00	0.00	2.24
1479	1564	9.000018	GTTGAATATCACGATCTTACTTTTTGC	58.000	33.333	0.00	0.00	0.00	3.68
1485	1570	3.815401	ACGATCTTACTTTTTGCAGTGCT	59.185	39.130	17.60	0.00	0.00	4.40
1529	1614	8.785329	TCAAATAGTTGTAGTTGCACATATGA	57.215	30.769	10.38	0.00	34.79	2.15
1530	1615	9.225436	TCAAATAGTTGTAGTTGCACATATGAA	57.775	29.630	10.38	0.00	34.79	2.57
1531	1616	9.494479	CAAATAGTTGTAGTTGCACATATGAAG	57.506	33.333	10.38	2.58	28.20	3.02
1532	1617	7.792374	ATAGTTGTAGTTGCACATATGAAGG	57.208	36.000	10.38	0.00	0.00	3.46
1533	1618	4.943705	AGTTGTAGTTGCACATATGAAGGG	59.056	41.667	10.38	0.00	0.00	3.95
1534	1619	3.278574	TGTAGTTGCACATATGAAGGGC	58.721	45.455	10.38	7.95	0.00	5.19
1535	1620	2.512692	AGTTGCACATATGAAGGGCA	57.487	45.000	10.38	10.42	0.00	5.36
1541	1626	2.837498	CACATATGAAGGGCATCGTCA	58.163	47.619	10.38	0.00	38.44	4.35
1582	1667	4.659172	CCAGAAACCTGGGCGCCA	62.659	66.667	30.85	13.75	45.86	5.69
1583	1668	3.365265	CAGAAACCTGGGCGCCAC	61.365	66.667	30.85	18.39	0.00	5.01
1603	1688	2.960688	GCCGCAAACTCCCTCCTCT	61.961	63.158	0.00	0.00	0.00	3.69
1616	1701	3.532155	CCTCTTCTCCCTCCGCCG	61.532	72.222	0.00	0.00	0.00	6.46
1685	1796	1.738346	CGACCGATCTGGGATCTGCA	61.738	60.000	8.20	0.00	44.64	4.41
1838	1953	2.366590	TGCATGCTATCTTCAGATCGGT	59.633	45.455	20.33	0.00	36.05	4.69
1896	2011	2.419297	GCACCTCCGATCAGATCTGTTT	60.419	50.000	21.92	11.21	0.00	2.83
1936	2051	0.179134	GGTGGTCATCTCTTCCGTCG	60.179	60.000	0.00	0.00	0.00	5.12
2120	2235	1.674441	CGACCCACTCGTATTGCTCTA	59.326	52.381	0.00	0.00	37.64	2.43
2155	2270	4.225860	TGGTGTTCCAGACCGGAT	57.774	55.556	9.46	0.00	45.80	4.18
2221	2336	3.184683	GAGCAGCGCTGGAAGTCG	61.185	66.667	36.47	12.02	39.88	4.18

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
28	29	0.030638	GCAGAAAAAGAACGCCAGCA	59.969	50.000	0.00	0.00	0.00	4.41
176	177	1.726533	CGCTCCTCGGTAACCTCCTC	61.727	65.000	0.00	0.00	33.78	3.71
239	240	1.076533	CCTACGCGCTACAACCACTG	61.077	60.000	5.73	0.00	0.00	3.66
329	330	0.313987	CAAAGCCGGAAAACTGGTCC	59.686	55.000	5.05	0.00	0.00	4.46
375	381	5.453480	GGTCTCTGGGACACTATAAATGGAC	60.453	48.000	10.30	0.00	46.16	4.02
387	393	0.832135	GTGTCTGGGTCTCTGGGACA	60.832	60.000	10.30	0.00	46.16	4.02
395	401	0.389948	GCGAAATCGTGTCTGGGTCT	60.390	55.000	4.59	0.00	42.22	3.85
396	402	0.389948	AGCGAAATCGTGTCTGGGTC	60.390	55.000	4.59	0.00	42.22	4.46
399	405	2.093783	GGTTTAGCGAAATCGTGTCTGG	59.906	50.000	4.59	0.00	42.22	3.86
400	406	2.222508	CGGTTTAGCGAAATCGTGTCTG	60.223	50.000	15.72	0.00	42.92	3.51
401	407	1.990563	CGGTTTAGCGAAATCGTGTCT	59.009	47.619	15.72	0.00	42.92	3.41
402	408	1.987770	TCGGTTTAGCGAAATCGTGTC	59.012	47.619	21.68	0.00	46.94	3.67
403	409	1.990563	CTCGGTTTAGCGAAATCGTGT	59.009	47.619	21.68	0.00	46.94	4.49
495	577	1.056103	CGTGAGAGAACTGCGTCTTG	58.944	55.000	0.00	0.00	0.00	3.02
496	578	0.664767	GCGTGAGAGAACTGCGTCTT	60.665	55.000	0.00	0.00	0.00	3.01
561	644	4.802051	TTGGAGGCAGGGCATCGC	62.802	66.667	0.00	0.00	40.46	4.58
562	645	2.825836	GTTGGAGGCAGGGCATCG	60.826	66.667	0.00	0.00	40.46	3.84
563	646	1.751927	CTGTTGGAGGCAGGGCATC	60.752	63.158	0.00	0.00	38.72	3.91
564	647	2.357836	CTGTTGGAGGCAGGGCAT	59.642	61.111	0.00	0.00	0.00	4.40
565	648	4.666253	GCTGTTGGAGGCAGGGCA	62.666	66.667	0.00	0.00	34.73	5.36
572	655	2.478335	TAAAGGGGCGCTGTTGGAGG	62.478	60.000	7.64	0.00	0.00	4.30
573	656	1.002624	TAAAGGGGCGCTGTTGGAG	60.003	57.895	7.64	0.00	0.00	3.86
574	657	1.002624	CTAAAGGGGCGCTGTTGGA	60.003	57.895	7.64	0.00	0.00	3.53
575	658	2.700773	GCTAAAGGGGCGCTGTTGG	61.701	63.158	7.64	5.31	0.00	3.77
576	659	2.700773	GGCTAAAGGGGCGCTGTTG	61.701	63.158	7.64	1.17	0.00	3.33
577	660	2.361230	GGCTAAAGGGGCGCTGTT	60.361	61.111	7.64	4.66	0.00	3.16
759	842	1.592400	CGGCGGTCAGTAGGAGAACA	61.592	60.000	0.00	0.00	0.00	3.18
762	845	2.261430	TAGCGGCGGTCAGTAGGAGA	62.261	60.000	17.55	0.00	0.00	3.71
768	851	3.900892	CGGATAGCGGCGGTCAGT	61.901	66.667	17.55	2.52	0.00	3.41
803	886	3.291101	ATCCGTCCGGGTTCACACG	62.291	63.158	0.00	2.23	43.52	4.49
805	888	2.652095	GGATCCGTCCGGGTTCACA	61.652	63.158	0.00	0.00	36.40	3.58
815	898	1.360911	GAAGCTCCTCGGATCCGTC	59.639	63.158	32.15	17.47	40.74	4.79
818	901	1.066587	CGTGAAGCTCCTCGGATCC	59.933	63.158	0.00	0.00	0.00	3.36
822	905	1.738099	CCAACGTGAAGCTCCTCGG	60.738	63.158	0.00	0.00	0.00	4.63
849	932	4.675404	CACAGGAAGACGTGGGAC	57.325	61.111	0.00	0.00	37.48	4.46
857	940	1.671742	GCGGAGTTCCACAGGAAGA	59.328	57.895	0.00	0.00	42.88	2.87
953	1036	0.683179	ATGGATGGTGTCGAGACGGA	60.683	55.000	6.62	0.00	0.00	4.69
1044	1127	0.842030	ACCCAGAAGCCTCCACATGA	60.842	55.000	0.00	0.00	0.00	3.07
1085	1168	3.636231	TCACGGCCACCCTGAAGG	61.636	66.667	2.24	0.00	43.78	3.46
1086	1169	2.358737	GTCACGGCCACCCTGAAG	60.359	66.667	2.24	0.00	0.00	3.02
1087	1170	4.308458	CGTCACGGCCACCCTGAA	62.308	66.667	2.24	0.00	0.00	3.02
1233	1316	2.435422	TGATAATGCACACACACCAGG	58.565	47.619	0.00	0.00	0.00	4.45
1235	1318	4.522022	TGATTTGATAATGCACACACACCA	59.478	37.500	0.00	0.00	0.00	4.17
1238	1321	5.472820	TGTCTGATTTGATAATGCACACACA	59.527	36.000	0.00	0.00	0.00	3.72
1302	1385	2.504175	TCCTGGGCACTAAATACTCACC	59.496	50.000	0.00	0.00	0.00	4.02
1324	1407	1.028330	CATTCTGGCGAGCACCATGT	61.028	55.000	0.00	0.00	39.54	3.21
1437	1521	5.796424	ATTCAACCAAGACTGAATGCTTT	57.204	34.783	0.00	0.00	40.06	3.51
1441	1525	6.313658	TCGTGATATTCAACCAAGACTGAATG	59.686	38.462	7.40	0.00	41.30	2.67
1525	1610	1.347707	GGGATGACGATGCCCTTCATA	59.652	52.381	0.00	0.00	38.85	2.15
1528	1613	4.464262	GGGATGACGATGCCCTTC	57.536	61.111	0.00	0.00	38.85	3.46
1532	1617	1.674057	CTAGGGGGATGACGATGCC	59.326	63.158	0.00	0.00	39.38	4.40
1533	1618	1.674057	CCTAGGGGGATGACGATGC	59.326	63.158	0.00	0.00	37.23	3.91
1582	1667	4.699522	GAGGGAGTTTGCGGCGGT	62.700	66.667	9.78	0.00	0.00	5.68
1936	2051	3.775654	CTCAGGCCGACCACCTCC	61.776	72.222	0.00	0.00	39.06	4.30
2155	2270	2.046411	ACCGCAATGTCGCCATCA	60.046	55.556	0.00	0.00	0.00	3.07
2166	2281	0.387929	AGAGAGAAACGACACCGCAA	59.612	50.000	0.00	0.00	39.95	4.85
2221	2336	3.791586	GCTCCACCTCCTGCCTCC	61.792	72.222	0.00	0.00	0.00	4.30
2255	2370	1.153549	GACATCTCCGCCGAAGCTT	60.154	57.895	0.00	0.00	36.60	3.74
2264	2379	1.134580	AGGCATGACTTGACATCTCCG	60.135	52.381	0.00	0.00	34.87	4.63
2327	2442	0.669077	GGAGGATCTGTCGTGCGTAT	59.331	55.000	0.00	0.00	33.73	3.06

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.