AutoCloner

Multiple sequence alignment - TraesCS1A01G063000

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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	TraesCS1A01G063000	chr1A	100.000	2300	0	0	1	2300	42887135	42889434	0.000000e+00	4248
1	TraesCS1A01G063000	chr1A	95.671	693	28	2	1	691	97155062	97155754	0.000000e+00	1112
2	TraesCS1A01G063000	chr1A	95.665	692	27	3	1	690	178909363	178910053	0.000000e+00	1109
3	TraesCS1A01G063000	chr1A	95.389	694	28	3	1	690	97142925	97143618	0.000000e+00	1101
4	TraesCS1A01G063000	chr1A	95.376	692	30	2	1	690	178902005	178902696	0.000000e+00	1099
5	TraesCS1A01G063000	chr1A	95.376	692	30	2	1	690	429643375	429642684	0.000000e+00	1099
6	TraesCS1A01G063000	chr4A	95.929	1007	37	3	1296	2300	37361227	37362231	0.000000e+00	1629
7	TraesCS1A01G063000	chr4A	95.829	1007	38	3	1295	2300	485348520	485347517	0.000000e+00	1624
8	TraesCS1A01G063000	chr4A	96.126	697	25	2	1	696	121238860	121239555	0.000000e+00	1136
9	TraesCS1A01G063000	chr4A	95.376	692	30	2	1	690	407423643	407424334	0.000000e+00	1099
10	TraesCS1A01G063000	chr4A	95.369	691	31	1	1	690	45266534	45265844	0.000000e+00	1098
11	TraesCS1A01G063000	chr2A	95.829	1007	39	2	1295	2300	574983775	574982771	0.000000e+00	1624
12	TraesCS1A01G063000	chr2A	95.730	1007	38	4	1295	2300	447212050	447213052	0.000000e+00	1616
13	TraesCS1A01G063000	chr2A	95.553	1012	40	4	1291	2300	752387000	752385992	0.000000e+00	1615
14	TraesCS1A01G063000	chr2A	95.635	1008	38	4	1296	2300	532186273	532187277	0.000000e+00	1613
15	TraesCS1A01G063000	chr6A	95.726	1006	39	3	1295	2297	206129184	206130188	0.000000e+00	1616
16	TraesCS1A01G063000	chr6A	95.631	1007	40	3	1295	2300	83394728	83395731	0.000000e+00	1613
17	TraesCS1A01G063000	chr5A	95.626	1006	40	3	1296	2300	123315642	123316644	0.000000e+00	1611
18	TraesCS1A01G063000	chr5A	96.040	606	19	2	691	1295	672816565	672815964	0.000000e+00	981
19	TraesCS1A01G063000	chrUn	95.376	692	30	2	1	690	220401563	220402254	0.000000e+00	1099
20	TraesCS1A01G063000	chrUn	97.181	603	13	1	693	1295	75467278	75467876	0.000000e+00	1016
21	TraesCS1A01G063000	chr7A	96.198	605	19	1	691	1295	450568757	450568157	0.000000e+00	987
22	TraesCS1A01G063000	chr6B	96.198	605	19	1	691	1295	139444007	139444607	0.000000e+00	987
23	TraesCS1A01G063000	chr3D	96.192	604	19	1	692	1295	166289352	166289951	0.000000e+00	985
24	TraesCS1A01G063000	chr2D	95.868	605	20	2	691	1295	121213908	121213309	0.000000e+00	974
25	TraesCS1A01G063000	chr6D	95.082	610	17	7	691	1295	59413125	59412524	0.000000e+00	948
26	TraesCS1A01G063000	chr7B	95.194	541	21	3	756	1295	515049126	515049662	0.000000e+00	850
27	TraesCS1A01G063000	chr3B	95.167	538	22	2	756	1293	62880256	62879723	0.000000e+00	846
28	TraesCS1A01G063000	chr3B	94.937	79	3	1	691	769	62880289	62880212	3.100000e-24	122
29	TraesCS1A01G063000	chr3B	94.872	78	3	1	692	769	15742956	15742880	1.120000e-23	121

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	TraesCS1A01G063000	chr1A	42887135	42889434	2299	False	4248	4248	100.000	1	2300	1	chr1A.!!$F1	2299
1	TraesCS1A01G063000	chr1A	97155062	97155754	692	False	1112	1112	95.671	1	691	1	chr1A.!!$F3	690
2	TraesCS1A01G063000	chr1A	178909363	178910053	690	False	1109	1109	95.665	1	690	1	chr1A.!!$F5	689
3	TraesCS1A01G063000	chr1A	97142925	97143618	693	False	1101	1101	95.389	1	690	1	chr1A.!!$F2	689
4	TraesCS1A01G063000	chr1A	178902005	178902696	691	False	1099	1099	95.376	1	690	1	chr1A.!!$F4	689
5	TraesCS1A01G063000	chr1A	429642684	429643375	691	True	1099	1099	95.376	1	690	1	chr1A.!!$R1	689
6	TraesCS1A01G063000	chr4A	37361227	37362231	1004	False	1629	1629	95.929	1296	2300	1	chr4A.!!$F1	1004
7	TraesCS1A01G063000	chr4A	485347517	485348520	1003	True	1624	1624	95.829	1295	2300	1	chr4A.!!$R2	1005
8	TraesCS1A01G063000	chr4A	121238860	121239555	695	False	1136	1136	96.126	1	696	1	chr4A.!!$F2	695
9	TraesCS1A01G063000	chr4A	407423643	407424334	691	False	1099	1099	95.376	1	690	1	chr4A.!!$F3	689
10	TraesCS1A01G063000	chr4A	45265844	45266534	690	True	1098	1098	95.369	1	690	1	chr4A.!!$R1	689
11	TraesCS1A01G063000	chr2A	574982771	574983775	1004	True	1624	1624	95.829	1295	2300	1	chr2A.!!$R1	1005
12	TraesCS1A01G063000	chr2A	447212050	447213052	1002	False	1616	1616	95.730	1295	2300	1	chr2A.!!$F1	1005
13	TraesCS1A01G063000	chr2A	752385992	752387000	1008	True	1615	1615	95.553	1291	2300	1	chr2A.!!$R2	1009
14	TraesCS1A01G063000	chr2A	532186273	532187277	1004	False	1613	1613	95.635	1296	2300	1	chr2A.!!$F2	1004
15	TraesCS1A01G063000	chr6A	206129184	206130188	1004	False	1616	1616	95.726	1295	2297	1	chr6A.!!$F2	1002
16	TraesCS1A01G063000	chr6A	83394728	83395731	1003	False	1613	1613	95.631	1295	2300	1	chr6A.!!$F1	1005
17	TraesCS1A01G063000	chr5A	123315642	123316644	1002	False	1611	1611	95.626	1296	2300	1	chr5A.!!$F1	1004
18	TraesCS1A01G063000	chr5A	672815964	672816565	601	True	981	981	96.040	691	1295	1	chr5A.!!$R1	604
19	TraesCS1A01G063000	chrUn	220401563	220402254	691	False	1099	1099	95.376	1	690	1	chrUn.!!$F2	689
20	TraesCS1A01G063000	chrUn	75467278	75467876	598	False	1016	1016	97.181	693	1295	1	chrUn.!!$F1	602
21	TraesCS1A01G063000	chr7A	450568157	450568757	600	True	987	987	96.198	691	1295	1	chr7A.!!$R1	604
22	TraesCS1A01G063000	chr6B	139444007	139444607	600	False	987	987	96.198	691	1295	1	chr6B.!!$F1	604
23	TraesCS1A01G063000	chr3D	166289352	166289951	599	False	985	985	96.192	692	1295	1	chr3D.!!$F1	603
24	TraesCS1A01G063000	chr2D	121213309	121213908	599	True	974	974	95.868	691	1295	1	chr2D.!!$R1	604
25	TraesCS1A01G063000	chr6D	59412524	59413125	601	True	948	948	95.082	691	1295	1	chr6D.!!$R1	604
26	TraesCS1A01G063000	chr7B	515049126	515049662	536	False	850	850	95.194	756	1295	1	chr7B.!!$F1	539
27	TraesCS1A01G063000	chr3B	62879723	62880289	566	True	484	846	95.052	691	1293	2	chr3B.!!$R2	602

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
779	784	0.110295	TGGGTGGTGGTTGTCTCATG	59.89	55.0	0.0	0.0	0.0	3.07	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2235	2278	0.460987	CGAGTTGCATCTCAGTCCCC	60.461	60.0	21.58	0.0	34.46	4.81	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
44	45	2.579400	GGGTTTGGTAGGGTGGACTATT	59.421	50.000	0.00	0.00	0.00	1.73
51	52	1.807814	AGGGTGGACTATTAGCAGGG	58.192	55.000	0.00	0.00	0.00	4.45
86	87	5.880887	GGGCACTAGAGCAAAATAAACTAGT	59.119	40.000	14.31	0.00	42.58	2.57
133	134	2.373169	ACCAGTGAGCAAAAGAGGATGA	59.627	45.455	0.00	0.00	0.00	2.92
158	159	9.213819	GATTTGCTCAAATTTTTCAAAGAACAC	57.786	29.630	8.98	0.00	40.77	3.32
159	160	6.660887	TGCTCAAATTTTTCAAAGAACACC	57.339	33.333	0.00	0.00	0.00	4.16
284	285	5.660460	ACAAACTGGACCAGATTTGAAAAC	58.340	37.500	33.07	0.00	36.72	2.43
538	542	6.607019	AGAGGGTAAACAAGTCCAACAATAA	58.393	36.000	0.00	0.00	0.00	1.40
582	586	5.245075	GGGGTGAAAACTCCACAATATCAAA	59.755	40.000	0.00	0.00	36.31	2.69
613	617	9.354673	AGAGTGGTTCTGAAATCAAAAGATAAA	57.645	29.630	0.00	0.00	33.93	1.40
720	725	6.374417	AGTTGATGGTGGATTAGTTAGTGT	57.626	37.500	0.00	0.00	0.00	3.55
723	728	7.987458	AGTTGATGGTGGATTAGTTAGTGTATG	59.013	37.037	0.00	0.00	0.00	2.39
724	729	7.432148	TGATGGTGGATTAGTTAGTGTATGT	57.568	36.000	0.00	0.00	0.00	2.29
725	730	7.272244	TGATGGTGGATTAGTTAGTGTATGTG	58.728	38.462	0.00	0.00	0.00	3.21
726	731	5.424757	TGGTGGATTAGTTAGTGTATGTGC	58.575	41.667	0.00	0.00	0.00	4.57
727	732	4.814771	GGTGGATTAGTTAGTGTATGTGCC	59.185	45.833	0.00	0.00	0.00	5.01
728	733	5.396436	GGTGGATTAGTTAGTGTATGTGCCT	60.396	44.000	0.00	0.00	0.00	4.75
729	734	6.183360	GGTGGATTAGTTAGTGTATGTGCCTA	60.183	42.308	0.00	0.00	0.00	3.93
730	735	6.924060	GTGGATTAGTTAGTGTATGTGCCTAG	59.076	42.308	0.00	0.00	0.00	3.02
731	736	6.041637	TGGATTAGTTAGTGTATGTGCCTAGG	59.958	42.308	3.67	3.67	0.00	3.02
732	737	6.041751	GGATTAGTTAGTGTATGTGCCTAGGT	59.958	42.308	11.31	0.00	0.00	3.08
733	738	4.737855	AGTTAGTGTATGTGCCTAGGTG	57.262	45.455	11.31	0.00	0.00	4.00
734	739	3.451178	AGTTAGTGTATGTGCCTAGGTGG	59.549	47.826	11.31	0.00	39.35	4.61
735	740	1.952621	AGTGTATGTGCCTAGGTGGT	58.047	50.000	11.31	0.00	38.35	4.16
736	741	1.555075	AGTGTATGTGCCTAGGTGGTG	59.445	52.381	11.31	0.00	38.35	4.17
737	742	0.908910	TGTATGTGCCTAGGTGGTGG	59.091	55.000	11.31	0.00	38.35	4.61
738	743	0.909623	GTATGTGCCTAGGTGGTGGT	59.090	55.000	11.31	0.00	38.35	4.16
739	744	1.280998	GTATGTGCCTAGGTGGTGGTT	59.719	52.381	11.31	0.00	38.35	3.67
761	766	3.814842	TGTCTCATTTTGTGTAGTGCCTG	59.185	43.478	0.00	0.00	0.00	4.85
779	784	0.110295	TGGGTGGTGGTTGTCTCATG	59.890	55.000	0.00	0.00	0.00	3.07
807	840	2.700897	GGTAGTGCCTAGGTGATGATGT	59.299	50.000	11.31	0.00	0.00	3.06
965	1000	7.644157	GCATTTATTTGACCCGAAATACTTCTC	59.356	37.037	0.00	0.00	29.41	2.87
1027	1063	5.279556	GCTGAAGGAACTAGTACTGGAAAGT	60.280	44.000	13.86	1.36	38.49	2.66
1202	1238	7.867909	GGATATCACGAAGAACAACATATCAGA	59.132	37.037	4.83	0.00	0.00	3.27
1236	1272	8.143835	AGGACTTTCGACAATCAATTTGAAATT	58.856	29.630	2.68	0.00	38.76	1.82
1404	1442	8.267894	TCTTTGGCAGATTTTAGCTATCTTAGT	58.732	33.333	0.00	0.00	30.05	2.24
1528	1566	5.486735	TGGAGAATTCAAATGCAATTGGT	57.513	34.783	14.37	1.45	36.10	3.67
1533	1571	6.469410	AGAATTCAAATGCAATTGGTGACAT	58.531	32.000	14.37	0.00	42.32	3.06
1612	1650	2.038557	ACTTCAACGCACAGAGGGTAAT	59.961	45.455	0.00	0.00	43.40	1.89
1748	1786	2.100989	ACGAAGTAGGCGATCTCCTTT	58.899	47.619	10.08	0.00	41.94	3.11
1774	1812	6.059484	CCTTACAAACTCCTTGGTTCAACTA	58.941	40.000	0.00	0.00	39.56	2.24
1859	1897	6.131544	AGAAGTAACAAATGGTGTGTTGAC	57.868	37.500	0.18	0.00	40.60	3.18
1910	1948	4.104086	TGATAGTCTCCCCAACACTCAAT	58.896	43.478	0.00	0.00	0.00	2.57
1981	2019	1.574263	ACTTGGGGAAGGCTAGAGAC	58.426	55.000	0.00	0.00	0.00	3.36
1995	2033	6.080682	AGGCTAGAGACCAAGATTCATATGA	58.919	40.000	0.00	0.00	0.00	2.15
2054	2092	7.979786	AGGTGGTTCTCTCTCAGAAAATATA	57.020	36.000	0.00	0.00	43.10	0.86
2116	2158	0.252558	GAAGAGTGGGTGGAGGGGTA	60.253	60.000	0.00	0.00	0.00	3.69
2117	2159	0.421904	AAGAGTGGGTGGAGGGGTAT	59.578	55.000	0.00	0.00	0.00	2.73
2198	2240	1.393883	GAATTGAGAAACTCGGTCGGC	59.606	52.381	0.00	0.00	32.35	5.54
2199	2241	0.608640	ATTGAGAAACTCGGTCGGCT	59.391	50.000	0.00	0.00	32.35	5.52
2235	2278	3.886123	AGTGACCATTAGGATTTTCGGG	58.114	45.455	0.00	0.00	38.69	5.14

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
44	45	1.064463	CCCATGAGCTTTTCCCTGCTA	60.064	52.381	0.00	0.00	39.91	3.49
51	52	2.941720	CTCTAGTGCCCATGAGCTTTTC	59.058	50.000	0.00	0.00	0.00	2.29
86	87	4.099266	AGTTTGGCATTTTCTACTGCAACA	59.901	37.500	0.00	0.00	40.18	3.33
133	134	8.183536	GGTGTTCTTTGAAAAATTTGAGCAAAT	58.816	29.630	11.41	2.74	42.35	2.32
158	159	5.709164	TCATTTTTATGCAAAACCCCATTGG	59.291	36.000	0.00	0.00	37.18	3.16
159	160	6.814506	TCATTTTTATGCAAAACCCCATTG	57.185	33.333	0.00	0.00	37.18	2.82
284	285	4.158579	GGAAATTTTGAGCTCTACCCCAAG	59.841	45.833	16.19	0.00	0.00	3.61
334	336	1.386533	GGATGCTCCCACATCACTTG	58.613	55.000	6.82	0.00	46.81	3.16
538	542	6.480763	ACCCCAAGTGAAAACTTTTCAAAAT	58.519	32.000	16.79	5.55	0.00	1.82
582	586	7.645058	TTTGATTTCAGAACCACTCTTTTCT	57.355	32.000	0.00	0.00	32.02	2.52
720	725	1.280710	CAACCACCACCTAGGCACATA	59.719	52.381	9.30	0.00	43.14	2.29
723	728	0.605589	GACAACCACCACCTAGGCAC	60.606	60.000	9.30	0.00	43.14	5.01
724	729	0.766674	AGACAACCACCACCTAGGCA	60.767	55.000	9.30	0.00	43.14	4.75
725	730	0.036294	GAGACAACCACCACCTAGGC	60.036	60.000	9.30	0.00	43.14	3.93
726	731	1.348064	TGAGACAACCACCACCTAGG	58.652	55.000	7.41	7.41	45.67	3.02
727	732	3.703001	AATGAGACAACCACCACCTAG	57.297	47.619	0.00	0.00	0.00	3.02
728	733	4.141287	CAAAATGAGACAACCACCACCTA	58.859	43.478	0.00	0.00	0.00	3.08
729	734	2.958355	CAAAATGAGACAACCACCACCT	59.042	45.455	0.00	0.00	0.00	4.00
730	735	2.693074	ACAAAATGAGACAACCACCACC	59.307	45.455	0.00	0.00	0.00	4.61
731	736	3.130340	ACACAAAATGAGACAACCACCAC	59.870	43.478	0.00	0.00	0.00	4.16
732	737	3.360867	ACACAAAATGAGACAACCACCA	58.639	40.909	0.00	0.00	0.00	4.17
733	738	4.578928	ACTACACAAAATGAGACAACCACC	59.421	41.667	0.00	0.00	0.00	4.61
734	739	5.510671	CACTACACAAAATGAGACAACCAC	58.489	41.667	0.00	0.00	0.00	4.16
735	740	4.036262	GCACTACACAAAATGAGACAACCA	59.964	41.667	0.00	0.00	0.00	3.67
736	741	4.537015	GCACTACACAAAATGAGACAACC	58.463	43.478	0.00	0.00	0.00	3.77
737	742	4.275936	AGGCACTACACAAAATGAGACAAC	59.724	41.667	0.00	0.00	36.02	3.32
738	743	4.275689	CAGGCACTACACAAAATGAGACAA	59.724	41.667	0.00	0.00	36.02	3.18
739	744	3.814842	CAGGCACTACACAAAATGAGACA	59.185	43.478	0.00	0.00	36.02	3.41
761	766	1.244019	GCATGAGACAACCACCACCC	61.244	60.000	0.00	0.00	0.00	4.61
779	784	3.071023	TCACCTAGGCACTACCAATATGC	59.929	47.826	9.30	0.00	43.14	3.14
807	840	5.067674	ACACAAAAGACAATCAGCAAGCTAA	59.932	36.000	0.00	0.00	0.00	3.09
965	1000	7.951530	AGAATAACAATTTTGCACAAAGGAG	57.048	32.000	0.00	0.00	0.00	3.69
1015	1051	5.542635	TGACATAAGTCCACTTTCCAGTACT	59.457	40.000	0.00	0.00	44.33	2.73
1027	1063	3.779738	TCATCCCATGTGACATAAGTCCA	59.220	43.478	0.00	0.00	44.33	4.02
1202	1238	3.764237	TGTCGAAAGTCCTAAGCCTTT	57.236	42.857	0.00	0.00	33.74	3.11
1236	1272	9.672673	CCTCTTTGAGAAAGGATCTTGTTAATA	57.327	33.333	0.00	0.00	38.96	0.98
1260	1296	1.061735	ACCCAATCCCAACCAAAACCT	60.062	47.619	0.00	0.00	0.00	3.50
1360	1398	5.700832	CCAAAGACTAAAATTGGGAAAAGGC	59.299	40.000	0.00	0.00	39.92	4.35
1404	1442	7.561021	TTGTGTTAAGATTGCTTGACTTGTA	57.439	32.000	0.00	0.00	40.27	2.41
1454	1492	2.985896	TGCTTTACTTTCCGCTGCTAT	58.014	42.857	0.00	0.00	0.00	2.97
1455	1493	2.465860	TGCTTTACTTTCCGCTGCTA	57.534	45.000	0.00	0.00	0.00	3.49
1528	1566	3.004210	CCACGACAAAAACATCCATGTCA	59.996	43.478	5.71	0.00	41.69	3.58
1533	1571	2.359531	GGAACCACGACAAAAACATCCA	59.640	45.455	0.00	0.00	0.00	3.41
1599	1637	0.811281	GCAACCATTACCCTCTGTGC	59.189	55.000	0.00	0.00	0.00	4.57
1748	1786	3.460340	TGAACCAAGGAGTTTGTAAGGGA	59.540	43.478	0.00	0.00	34.87	4.20
1774	1812	1.072331	AGCCTCCGACAAAGATTGTGT	59.928	47.619	0.00	0.00	45.52	3.72
1859	1897	2.414481	CACAAGAGCAAGGAGTTCATCG	59.586	50.000	0.00	0.00	0.00	3.84
1910	1948	6.183361	CCAAATCCATATCCTGTGAGAGAGAA	60.183	42.308	0.00	0.00	0.00	2.87
1981	2019	6.250711	TCCATTCCCATCATATGAATCTTGG	58.749	40.000	9.99	12.36	0.00	3.61
1995	2033	5.373555	TGAGACCAAGATATTCCATTCCCAT	59.626	40.000	0.00	0.00	0.00	4.00
2054	2092	8.319057	TCAGAACATACCTACACTTCCAATAT	57.681	34.615	0.00	0.00	0.00	1.28
2198	2240	5.245531	TGGTCACTAGGTTTGCTAAATCAG	58.754	41.667	0.00	0.00	0.00	2.90
2199	2241	5.235850	TGGTCACTAGGTTTGCTAAATCA	57.764	39.130	0.00	0.00	0.00	2.57
2235	2278	0.460987	CGAGTTGCATCTCAGTCCCC	60.461	60.000	21.58	0.00	34.46	4.81

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.