AutoCloner

Multiple sequence alignment - TraesCS4A01G216600

Loading Multiple Alignment...

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	TraesCS4A01G216600	chr4A	100.000	2342	0	0	1	2342	515559421	515557080	0.000000e+00	4325
1	TraesCS4A01G216600	chr4D	92.844	1621	66	23	108	1702	66565834	66564238	0.000000e+00	2305
2	TraesCS4A01G216600	chr4D	90.083	121	3	5	1	117	66565994	66565879	5.210000e-32	148
3	TraesCS4A01G216600	chr4B	90.993	1743	103	30	1	1702	97126730	97125001	0.000000e+00	2300
4	TraesCS4A01G216600	chr4B	91.549	639	49	4	1708	2342	64814955	64814318	0.000000e+00	876
5	TraesCS4A01G216600	chr1D	91.900	642	52	0	1701	2342	19558285	19557644	0.000000e+00	898
6	TraesCS4A01G216600	chr3B	91.783	645	48	5	1700	2342	125802174	125801533	0.000000e+00	893
7	TraesCS4A01G216600	chr7D	91.615	644	54	0	1699	2342	566011833	566011190	0.000000e+00	891
8	TraesCS4A01G216600	chr6D	91.420	641	55	0	1702	2342	239854979	239855619	0.000000e+00	880
9	TraesCS4A01G216600	chr6D	90.839	644	58	1	1700	2342	346250236	346249593	0.000000e+00	861
10	TraesCS4A01G216600	chr3D	91.654	635	52	1	1708	2342	156247825	156248458	0.000000e+00	878
11	TraesCS4A01G216600	chr3D	90.952	641	56	1	1702	2342	90195454	90194816	0.000000e+00	861
12	TraesCS4A01G216600	chr5D	90.952	641	58	0	1702	2342	553360685	553360045	0.000000e+00	863

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	TraesCS4A01G216600	chr4A	515557080	515559421	2341	True	4325.0	4325	100.0000	1	2342	1	chr4A.!!$R1	2341
1	TraesCS4A01G216600	chr4D	66564238	66565994	1756	True	1226.5	2305	91.4635	1	1702	2	chr4D.!!$R1	1701
2	TraesCS4A01G216600	chr4B	97125001	97126730	1729	True	2300.0	2300	90.9930	1	1702	1	chr4B.!!$R2	1701
3	TraesCS4A01G216600	chr4B	64814318	64814955	637	True	876.0	876	91.5490	1708	2342	1	chr4B.!!$R1	634
4	TraesCS4A01G216600	chr1D	19557644	19558285	641	True	898.0	898	91.9000	1701	2342	1	chr1D.!!$R1	641
5	TraesCS4A01G216600	chr3B	125801533	125802174	641	True	893.0	893	91.7830	1700	2342	1	chr3B.!!$R1	642
6	TraesCS4A01G216600	chr7D	566011190	566011833	643	True	891.0	891	91.6150	1699	2342	1	chr7D.!!$R1	643
7	TraesCS4A01G216600	chr6D	239854979	239855619	640	False	880.0	880	91.4200	1702	2342	1	chr6D.!!$F1	640
8	TraesCS4A01G216600	chr6D	346249593	346250236	643	True	861.0	861	90.8390	1700	2342	1	chr6D.!!$R1	642
9	TraesCS4A01G216600	chr3D	156247825	156248458	633	False	878.0	878	91.6540	1708	2342	1	chr3D.!!$F1	634
10	TraesCS4A01G216600	chr3D	90194816	90195454	638	True	861.0	861	90.9520	1702	2342	1	chr3D.!!$R1	640
11	TraesCS4A01G216600	chr5D	553360045	553360685	640	True	863.0	863	90.9520	1702	2342	1	chr5D.!!$R1	640

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
256	312	1.000171	GACCCAGAAAAGCAAGCCAAG	60.0	52.381	0.0	0.0	0.0	3.61	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1875	1959	0.179234	TGGTCCAGTCTTTGCGTCAA	59.821	50.0	0.0	0.0	0.0	3.18	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
57	58	6.713762	AACAATCACAAGGAGAATGTTCAA	57.286	33.333	0.00	0.00	29.80	2.69
84	85	7.838771	AAAATAAAAGAATCAGCAAGGCATC	57.161	32.000	0.00	0.00	0.00	3.91
85	86	6.534475	AATAAAAGAATCAGCAAGGCATCA	57.466	33.333	0.00	0.00	0.00	3.07
88	89	6.726490	AAAAGAATCAGCAAGGCATCATAT	57.274	33.333	0.00	0.00	0.00	1.78
92	93	7.828508	AGAATCAGCAAGGCATCATATAAAA	57.171	32.000	0.00	0.00	0.00	1.52
173	229	4.940046	CCATGAGCATATGTCCTATCCAAC	59.060	45.833	4.29	0.00	0.00	3.77
204	260	6.451393	CCATCAATCCTTGTCTAGCTAGTAC	58.549	44.000	20.10	16.16	0.00	2.73
205	261	6.266558	CCATCAATCCTTGTCTAGCTAGTACT	59.733	42.308	20.10	0.00	0.00	2.73
242	298	5.163163	TGGAGAGATGAATTATTGGACCCAG	60.163	44.000	0.00	0.00	0.00	4.45
256	312	1.000171	GACCCAGAAAAGCAAGCCAAG	60.000	52.381	0.00	0.00	0.00	3.61
340	396	2.532235	CAATGCGAAATGACCATGGTG	58.468	47.619	25.52	7.81	0.00	4.17
384	441	5.458015	CAAAGAACTAATCGTCCCCAAAAC	58.542	41.667	0.00	0.00	0.00	2.43
404	461	8.636213	CCAAAACCAAGCTGATATAAATCTGAT	58.364	33.333	0.00	0.00	33.98	2.90
444	501	6.056428	ACTAAATCCGACTGTCAAAACAAC	57.944	37.500	8.73	0.00	34.24	3.32
485	542	7.136822	AGAGGTCATAGTGCCAAATATTGTA	57.863	36.000	0.00	0.00	0.00	2.41
570	628	7.432350	TTTCACAAACCAAATCATATTTGCC	57.568	32.000	6.82	0.00	35.83	4.52
672	731	1.547372	AGGTTTTGCACATGGATGCTC	59.453	47.619	9.44	0.00	46.28	4.26
698	757	2.860136	GTGGCTTTTGTTTTGTCTCTGC	59.140	45.455	0.00	0.00	0.00	4.26
709	768	2.010145	TGTCTCTGCTCCGTTAATGC	57.990	50.000	0.00	0.00	0.00	3.56
725	787	6.027749	CGTTAATGCTTTGATAGTGAAACCC	58.972	40.000	0.00	0.00	37.80	4.11
776	838	8.601845	AAAATTAAAAAGCGCCAAGAAATACT	57.398	26.923	2.29	0.00	0.00	2.12
938	1003	2.198304	GATGGTCTCCTTTGCCCCGT	62.198	60.000	0.00	0.00	0.00	5.28
1048	1113	3.109547	GATCGGCGTGTGTTGCGA	61.110	61.111	6.85	0.00	0.00	5.10
1074	1139	1.152525	GATCTGCCTCCTCCCGGTA	60.153	63.158	0.00	0.00	0.00	4.02
1075	1140	0.543174	GATCTGCCTCCTCCCGGTAT	60.543	60.000	0.00	0.00	0.00	2.73
1173	1238	3.307339	GGAGAATGATGATGACTAGGGGC	60.307	52.174	0.00	0.00	0.00	5.80
1376	1441	2.167487	TGCTTTCTTGCCGGAAACTTTT	59.833	40.909	5.05	0.00	32.63	2.27
1448	1513	2.646175	TAGCAAGGCGCCGAGAACT	61.646	57.895	23.20	17.32	44.04	3.01
1464	1529	4.333095	CGAGAACTTCGTCTCCTGATTAGA	59.667	45.833	0.00	0.00	44.27	2.10
1572	1650	1.089920	GTTGGCGAGTCCGTCTACTA	58.910	55.000	0.00	0.00	41.53	1.82
1623	1702	6.942005	TCTGACAAATGAGACCATACAAATGT	59.058	34.615	0.00	0.00	31.59	2.71
1641	1720	6.751888	ACAAATGTACAAGTTGAGCAAGAAAC	59.248	34.615	22.63	0.00	0.00	2.78
1643	1722	4.185394	TGTACAAGTTGAGCAAGAAACGA	58.815	39.130	10.54	0.00	0.00	3.85
1676	1755	0.035820	GTGCTTAATCCCCGTCACCA	60.036	55.000	0.00	0.00	0.00	4.17
1685	1764	1.026718	CCCCGTCACCAATCTTGCTC	61.027	60.000	0.00	0.00	0.00	4.26
1692	1771	1.000896	CCAATCTTGCTCCCCGGTT	60.001	57.895	0.00	0.00	0.00	4.44
1739	1821	7.763985	TGATTTCATGAAGTATTGCTCTTCGTA	59.236	33.333	8.41	0.00	42.68	3.43
1780	1862	2.268298	GTACAAAGATGCGTCACGGAT	58.732	47.619	2.83	2.83	41.25	4.18
1807	1889	7.411808	TCAACTATACAAGGAACTAGGAGACT	58.588	38.462	0.00	0.00	38.49	3.24
1812	1894	0.413832	AGGAACTAGGAGACTGGCCA	59.586	55.000	4.71	4.71	43.94	5.36
1831	1913	4.984161	GGCCAAATACACAATATGCACATC	59.016	41.667	0.00	0.00	0.00	3.06
1901	1985	2.224402	GCAAAGACTGGACCAGAACTCT	60.224	50.000	28.56	17.02	35.18	3.24
1940	2024	3.152341	CAAGCCCTTGGTCATGATATCC	58.848	50.000	0.00	0.00	36.95	2.59
1966	2050	2.307496	TGTTGGGAAGTAGGGACGTA	57.693	50.000	0.00	0.00	0.00	3.57
2040	2124	2.632377	ACTCAATATGCTTGGTCCGTG	58.368	47.619	0.00	0.00	0.00	4.94
2087	2171	1.173444	AGACCGCTGAGACGTTGTCT	61.173	55.000	0.00	0.00	46.42	3.41
2135	2219	1.834263	GGGCAAGAGAGCTCCTAAAGA	59.166	52.381	10.93	0.00	34.17	2.52
2194	2278	1.141881	CCGCACGATACTCAGCCTT	59.858	57.895	0.00	0.00	0.00	4.35
2204	2288	0.901124	ACTCAGCCTTAGCACTGGAG	59.099	55.000	1.63	0.00	43.56	3.86
2217	2301	0.107116	ACTGGAGCGAGAGACCGTAT	60.107	55.000	0.00	0.00	33.07	3.06
2219	2303	0.107361	TGGAGCGAGAGACCGTATGA	60.107	55.000	0.00	0.00	33.07	2.15
2226	2310	1.333931	GAGAGACCGTATGATGTCGCA	59.666	52.381	0.00	0.00	36.61	5.10
2229	2313	1.681264	AGACCGTATGATGTCGCATGA	59.319	47.619	0.00	0.00	36.61	3.07
2237	2321	2.921821	TGATGTCGCATGAATGACCAT	58.078	42.857	0.00	0.00	34.18	3.55
2283	2367	1.066143	CACAATAGCCCGAAGTGGAGT	60.066	52.381	0.00	0.00	42.00	3.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
64	65	7.828508	ATATGATGCCTTGCTGATTCTTTTA	57.171	32.000	0.00	0.00	0.00	1.52
67	68	7.828508	TTTATATGATGCCTTGCTGATTCTT	57.171	32.000	0.00	0.00	0.00	2.52
68	69	7.828508	TTTTATATGATGCCTTGCTGATTCT	57.171	32.000	0.00	0.00	0.00	2.40
156	212	3.788227	TGGGTTGGATAGGACATATGC	57.212	47.619	1.58	0.00	33.03	3.14
256	312	5.959652	AACCAAACAAAACAATACGAAGC	57.040	34.783	0.00	0.00	0.00	3.86
340	396	4.832248	TGGTGACTGTAGGATTTGATGAC	58.168	43.478	0.00	0.00	0.00	3.06
347	403	5.568620	AGTTCTTTGGTGACTGTAGGATT	57.431	39.130	0.00	0.00	0.00	3.01
384	441	7.974482	TCACATCAGATTTATATCAGCTTGG	57.026	36.000	0.00	0.00	32.95	3.61
404	461	7.706607	CGGATTTAGTATTCACTTCTGATCACA	59.293	37.037	0.00	0.00	36.14	3.58
416	473	7.658167	TGTTTTGACAGTCGGATTTAGTATTCA	59.342	33.333	0.00	0.00	0.00	2.57
417	474	8.025243	TGTTTTGACAGTCGGATTTAGTATTC	57.975	34.615	0.00	0.00	0.00	1.75
418	475	7.972832	TGTTTTGACAGTCGGATTTAGTATT	57.027	32.000	0.00	0.00	0.00	1.89
419	476	7.442969	TGTTGTTTTGACAGTCGGATTTAGTAT	59.557	33.333	0.00	0.00	0.00	2.12
444	501	3.244353	ACCTCTCAAGAACCACAGATGTG	60.244	47.826	5.97	5.97	45.23	3.21
453	510	3.526534	GCACTATGACCTCTCAAGAACC	58.473	50.000	0.00	0.00	0.00	3.62
533	590	3.791973	TTGTGAAAACGGCAGTTCATT	57.208	38.095	1.78	0.00	40.18	2.57
543	600	7.530190	GCAAATATGATTTGGTTTGTGAAAACG	59.470	33.333	12.53	0.00	34.82	3.60
544	601	7.802720	GGCAAATATGATTTGGTTTGTGAAAAC	59.197	33.333	12.53	0.00	34.82	2.43
672	731	1.136110	ACAAAACAAAAGCCACGAGGG	59.864	47.619	0.00	0.00	40.85	4.30
698	757	6.662414	TTCACTATCAAAGCATTAACGGAG	57.338	37.500	0.00	0.00	0.00	4.63
709	768	4.513442	TGGATCGGGTTTCACTATCAAAG	58.487	43.478	0.00	0.00	0.00	2.77
725	787	3.002656	CGTCCCATCAAGAAAATGGATCG	59.997	47.826	3.72	4.62	45.51	3.69
763	825	2.009774	CACCTCCAGTATTTCTTGGCG	58.990	52.381	0.00	0.00	0.00	5.69
766	828	3.557595	GCGATCACCTCCAGTATTTCTTG	59.442	47.826	0.00	0.00	0.00	3.02
776	838	0.684535	TGTTTCTGCGATCACCTCCA	59.315	50.000	0.00	0.00	0.00	3.86
938	1003	0.902984	TCGGGTTGCTCTGCTTCCTA	60.903	55.000	0.00	0.00	0.00	2.94
944	1009	2.743928	CTGGTCGGGTTGCTCTGC	60.744	66.667	0.00	0.00	0.00	4.26
1032	1097	3.411351	GTCGCAACACACGCCGAT	61.411	61.111	0.00	0.00	31.96	4.18
1173	1238	4.093952	CCGTGAAAGCAGCAGCCG	62.094	66.667	0.00	0.00	43.56	5.52
1376	1441	1.477685	AAGTCGAGCGAAAAGGGGGA	61.478	55.000	0.00	0.00	0.00	4.81
1386	1451	1.355066	GGAGCCAGAAAAGTCGAGCG	61.355	60.000	0.00	0.00	33.38	5.03
1448	1513	4.087182	ACAACCTCTAATCAGGAGACGAA	58.913	43.478	0.00	0.00	36.96	3.85
1464	1529	6.319658	CAGCTAACATATCAATCCAACAACCT	59.680	38.462	0.00	0.00	0.00	3.50
1556	1634	1.799994	GAGATAGTAGACGGACTCGCC	59.200	57.143	0.00	0.00	40.63	5.54
1572	1650	6.024563	TGAGAGGAGAAATACTGAGGAGAT	57.975	41.667	0.00	0.00	0.00	2.75
1623	1702	4.814234	ACATCGTTTCTTGCTCAACTTGTA	59.186	37.500	0.00	0.00	0.00	2.41
1641	1720	0.725784	GCACGACCAAAAGCACATCG	60.726	55.000	0.00	0.00	38.71	3.84
1643	1722	1.032014	AAGCACGACCAAAAGCACAT	58.968	45.000	0.00	0.00	0.00	3.21
1676	1755	0.322546	GACAACCGGGGAGCAAGATT	60.323	55.000	6.32	0.00	0.00	2.40
1685	1764	2.483014	TACAATTCTGACAACCGGGG	57.517	50.000	6.32	0.00	0.00	5.73
1718	1800	5.961272	TGTACGAAGAGCAATACTTCATGA	58.039	37.500	0.00	0.00	42.39	3.07
1724	1806	6.496571	GTGTCTATGTACGAAGAGCAATACT	58.503	40.000	0.00	0.00	0.00	2.12
1771	1853	4.547406	TGTATAGTTGAGATCCGTGACG	57.453	45.455	0.00	0.00	0.00	4.35
1780	1862	7.556996	GTCTCCTAGTTCCTTGTATAGTTGAGA	59.443	40.741	0.00	0.00	0.00	3.27
1807	1889	3.766051	TGTGCATATTGTGTATTTGGCCA	59.234	39.130	0.00	0.00	0.00	5.36
1812	1894	7.155655	TGTGTGATGTGCATATTGTGTATTT	57.844	32.000	0.00	0.00	0.00	1.40
1831	1913	3.541632	GGGGGTGTTGAGTATATGTGTG	58.458	50.000	0.00	0.00	0.00	3.82
1875	1959	0.179234	TGGTCCAGTCTTTGCGTCAA	59.821	50.000	0.00	0.00	0.00	3.18
1940	2024	2.094752	CCCTACTTCCCAACAATTTGCG	60.095	50.000	0.00	0.00	0.00	4.85
1966	2050	4.340950	CCCTTGGCCATATTCGTGTTTTAT	59.659	41.667	6.09	0.00	0.00	1.40
2040	2124	1.166531	GCTAACCCGGTGCATCATCC	61.167	60.000	0.00	0.00	0.00	3.51
2087	2171	1.255882	GTGCCATGGTGGTCAATTGA	58.744	50.000	14.67	3.38	40.46	2.57
2090	2174	1.678635	CCGTGCCATGGTGGTCAAT	60.679	57.895	14.67	0.00	40.46	2.57
2092	2176	3.565214	ACCGTGCCATGGTGGTCA	61.565	61.111	14.67	0.00	40.46	4.02
2114	2198	0.912486	TTTAGGAGCTCTCTTGCCCC	59.088	55.000	14.64	0.00	0.00	5.80
2171	2255	2.557059	CTGAGTATCGTGCGGTGGCA	62.557	60.000	0.00	0.00	43.42	4.92
2194	2278	1.032657	GGTCTCTCGCTCCAGTGCTA	61.033	60.000	0.00	0.00	0.00	3.49
2204	2288	1.660614	CGACATCATACGGTCTCTCGC	60.661	57.143	0.00	0.00	31.88	5.03
2217	2301	2.399916	TGGTCATTCATGCGACATCA	57.600	45.000	10.60	0.56	33.66	3.07
2219	2303	2.876550	CTCATGGTCATTCATGCGACAT	59.123	45.455	10.60	0.00	42.96	3.06
2226	2310	6.465464	CCCTCACTTATCTCATGGTCATTCAT	60.465	42.308	0.00	0.00	0.00	2.57
2229	2313	4.723789	ACCCTCACTTATCTCATGGTCATT	59.276	41.667	0.00	0.00	0.00	2.57
2237	2321	4.061131	TCTTGGACCCTCACTTATCTCA	57.939	45.455	0.00	0.00	0.00	3.27
2305	2389	1.393603	CTACTCCGATGCAGACTGGA	58.606	55.000	4.26	0.73	0.00	3.86

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.