AutoCloner

Multiple sequence alignment - TraesCS4A01G200300

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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	TraesCS4A01G200300	chr4A	100.000	2567	0	0	1	2567	488534721	488537287	0.000000e+00	4741
1	TraesCS4A01G200300	chr4A	96.231	743	27	1	1826	2567	319827909	319828651	0.000000e+00	1216
2	TraesCS4A01G200300	chr4A	92.730	729	46	3	1828	2555	538887877	538888599	0.000000e+00	1046
3	TraesCS4A01G200300	chr4B	93.563	1507	72	12	326	1831	131706831	131705349	0.000000e+00	2222
4	TraesCS4A01G200300	chr4B	92.035	339	11	4	1	330	131707285	131706954	1.800000e-126	462
5	TraesCS4A01G200300	chr4D	93.794	1289	61	9	543	1831	93439404	93438135	0.000000e+00	1919
6	TraesCS4A01G200300	chr4D	92.879	323	12	6	1	314	93450811	93450491	2.330000e-125	459
7	TraesCS4A01G200300	chr4D	92.262	168	13	0	381	548	93441873	93441706	3.300000e-59	239
8	TraesCS4A01G200300	chr4D	98.734	79	0	1	306	384	93447582	93447505	3.440000e-29	139
9	TraesCS4A01G200300	chr2A	97.581	744	16	2	1825	2567	733339075	733338333	0.000000e+00	1273
10	TraesCS4A01G200300	chr3A	97.439	742	19	0	1826	2567	25379097	25379838	0.000000e+00	1266
11	TraesCS4A01G200300	chr3A	97.439	742	19	0	1826	2567	25394252	25394993	0.000000e+00	1266
12	TraesCS4A01G200300	chr7A	95.687	742	31	1	1826	2567	439794579	439795319	0.000000e+00	1192
13	TraesCS4A01G200300	chr7A	95.506	445	20	0	1826	2270	206586234	206585790	0.000000e+00	712
14	TraesCS4A01G200300	chr6B	92.613	731	41	5	1826	2555	616933518	616934236	0.000000e+00	1038
15	TraesCS4A01G200300	chr6A	92.961	483	31	2	1825	2307	326819829	326819350	0.000000e+00	701
16	TraesCS4A01G200300	chr5A	91.185	329	29	0	2239	2567	322879844	322880172	5.040000e-122	448
17	TraesCS4A01G200300	chr5B	90.274	329	31	1	2239	2567	24683035	24682708	1.820000e-116	429

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	TraesCS4A01G200300	chr4A	488534721	488537287	2566	False	4741	4741	100.0000	1	2567	1	chr4A.!!$F2	2566
1	TraesCS4A01G200300	chr4A	319827909	319828651	742	False	1216	1216	96.2310	1826	2567	1	chr4A.!!$F1	741
2	TraesCS4A01G200300	chr4A	538887877	538888599	722	False	1046	1046	92.7300	1828	2555	1	chr4A.!!$F3	727
3	TraesCS4A01G200300	chr4B	131705349	131707285	1936	True	1342	2222	92.7990	1	1831	2	chr4B.!!$R1	1830
4	TraesCS4A01G200300	chr4D	93438135	93441873	3738	True	1079	1919	93.0280	381	1831	2	chr4D.!!$R1	1450
5	TraesCS4A01G200300	chr4D	93447505	93450811	3306	True	299	459	95.8065	1	384	2	chr4D.!!$R2	383
6	TraesCS4A01G200300	chr2A	733338333	733339075	742	True	1273	1273	97.5810	1825	2567	1	chr2A.!!$R1	742
7	TraesCS4A01G200300	chr3A	25379097	25379838	741	False	1266	1266	97.4390	1826	2567	1	chr3A.!!$F1	741
8	TraesCS4A01G200300	chr3A	25394252	25394993	741	False	1266	1266	97.4390	1826	2567	1	chr3A.!!$F2	741
9	TraesCS4A01G200300	chr7A	439794579	439795319	740	False	1192	1192	95.6870	1826	2567	1	chr7A.!!$F1	741
10	TraesCS4A01G200300	chr6B	616933518	616934236	718	False	1038	1038	92.6130	1826	2555	1	chr6B.!!$F1	729

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
522	3576	0.954452	CAGTTTCCTGTGGAACTGCC	59.046	55.0	1.06	0.0	41.87	4.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1670	7032	0.462759	CTTCTGAATCTGACGGGGGC	60.463	60.0	0.0	0.0	0.0	5.8	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
33	34	1.804151	GCTACAACAACGGAAGATGCA	59.196	47.619	0.00	0.00	37.40	3.96
42	43	3.340814	ACGGAAGATGCAGAAACAGAT	57.659	42.857	0.00	0.00	0.00	2.90
49	50	6.183360	GGAAGATGCAGAAACAGATTAGTGAC	60.183	42.308	0.00	0.00	0.00	3.67
69	70	4.688879	TGACGTTGTTAATCCATGACTGTC	59.311	41.667	0.00	0.00	0.00	3.51
144	154	3.304829	AGGCTGGCAAAAGTTTTCCTTA	58.695	40.909	3.38	0.48	31.48	2.69
422	3476	8.206867	CCTCTATGTAAGATGATTGAAGGACAA	58.793	37.037	0.00	0.00	36.91	3.18
496	3550	1.266989	CTTTTCCCAGTTCTTGCGGTC	59.733	52.381	0.00	0.00	0.00	4.79
522	3576	0.954452	CAGTTTCCTGTGGAACTGCC	59.046	55.000	1.06	0.00	41.87	4.85
580	5941	1.429463	CCGACTTCTTTCTCCAACCG	58.571	55.000	0.00	0.00	0.00	4.44
651	6012	5.157940	ACACATGCACTTCTCAATCTACT	57.842	39.130	0.00	0.00	0.00	2.57
653	6014	6.882656	ACACATGCACTTCTCAATCTACTAT	58.117	36.000	0.00	0.00	0.00	2.12
659	6020	5.069781	GCACTTCTCAATCTACTATCCCTGT	59.930	44.000	0.00	0.00	0.00	4.00
755	6117	1.019278	TGGCCGATTTCTTGAGACGC	61.019	55.000	0.00	0.00	0.00	5.19
762	6124	4.512657	CGATTTCTTGAGACGCATCAATC	58.487	43.478	3.62	0.00	38.47	2.67
778	6140	1.545582	CAATCGTTTGGTGCCAATCCT	59.454	47.619	4.32	0.00	35.70	3.24
845	6207	1.677576	CAGCTTGCACCTGAAGTTTCA	59.322	47.619	7.61	0.00	35.57	2.69
938	6300	1.987807	ATCTCATTCCCCCACCTGCG	61.988	60.000	0.00	0.00	0.00	5.18
968	6330	0.978907	TCATGAGAGCAGCCTGTCAA	59.021	50.000	0.00	0.00	43.58	3.18
1176	6538	3.147595	CCTCCCTCGCCGTCATCA	61.148	66.667	0.00	0.00	0.00	3.07
1182	6544	0.032540	CCTCGCCGTCATCATCATCA	59.967	55.000	0.00	0.00	0.00	3.07
1185	6547	1.615392	TCGCCGTCATCATCATCATCT	59.385	47.619	0.00	0.00	0.00	2.90
1218	6580	1.064134	CTCGCCGTCATCGTCATCA	59.936	57.895	0.00	0.00	35.01	3.07
1264	6626	4.933064	CGTCGATCCTCCCGCTGC	62.933	72.222	0.00	0.00	0.00	5.25
1331	6693	2.792599	GTCATCGTCGACGGAGCT	59.207	61.111	35.05	16.33	40.29	4.09
1392	6754	1.582937	CGGGTCGTCATCGTCTTCG	60.583	63.158	0.00	0.00	38.33	3.79
1396	6758	1.135746	GGTCGTCATCGTCTTCGTCTT	60.136	52.381	0.00	0.00	38.33	3.01
1479	6841	5.296748	CCGTACTACTACTTCTACCTCTCC	58.703	50.000	0.00	0.00	0.00	3.71
1574	6936	2.307098	CCTTTTGGAGGTGAGATGAGGT	59.693	50.000	0.00	0.00	44.07	3.85
1576	6938	2.030027	TTGGAGGTGAGATGAGGTGT	57.970	50.000	0.00	0.00	0.00	4.16
1578	6940	1.625315	TGGAGGTGAGATGAGGTGTTG	59.375	52.381	0.00	0.00	0.00	3.33
1579	6941	1.065854	GGAGGTGAGATGAGGTGTTGG	60.066	57.143	0.00	0.00	0.00	3.77
1580	6942	1.902508	GAGGTGAGATGAGGTGTTGGA	59.097	52.381	0.00	0.00	0.00	3.53
1581	6943	1.625818	AGGTGAGATGAGGTGTTGGAC	59.374	52.381	0.00	0.00	0.00	4.02
1582	6944	1.673033	GGTGAGATGAGGTGTTGGACG	60.673	57.143	0.00	0.00	0.00	4.79
1583	6945	1.000955	GTGAGATGAGGTGTTGGACGT	59.999	52.381	0.00	0.00	0.00	4.34
1584	6946	1.691976	TGAGATGAGGTGTTGGACGTT	59.308	47.619	0.00	0.00	0.00	3.99
1585	6947	2.069273	GAGATGAGGTGTTGGACGTTG	58.931	52.381	0.00	0.00	0.00	4.10
1586	6948	1.416401	AGATGAGGTGTTGGACGTTGT	59.584	47.619	0.00	0.00	0.00	3.32
1599	6961	4.696172	GTTGTCGTTGCGTCGCCG	62.696	66.667	15.88	12.17	37.07	6.46
1611	6973	4.015406	TCGCCGTGTGCCCATTCT	62.015	61.111	0.00	0.00	36.24	2.40
1621	6983	0.038166	TGCCCATTCTGGTGAACTCC	59.962	55.000	0.00	0.00	35.17	3.85
1639	7001	6.432162	TGAACTCCTCGTGTGTTTATAGTACT	59.568	38.462	0.00	0.00	31.12	2.73
1640	7002	7.607607	TGAACTCCTCGTGTGTTTATAGTACTA	59.392	37.037	4.77	4.77	31.12	1.82
1641	7003	7.313951	ACTCCTCGTGTGTTTATAGTACTAC	57.686	40.000	4.31	0.00	0.00	2.73
1642	7004	6.881065	ACTCCTCGTGTGTTTATAGTACTACA	59.119	38.462	4.31	0.00	0.00	2.74
1666	7028	5.612351	AGTACTGTCACTTCTTTTCCCTTC	58.388	41.667	0.00	0.00	0.00	3.46
1669	7031	2.152016	GTCACTTCTTTTCCCTTCCCG	58.848	52.381	0.00	0.00	0.00	5.14
1670	7032	1.073284	TCACTTCTTTTCCCTTCCCGG	59.927	52.381	0.00	0.00	0.00	5.73
1671	7033	0.251209	ACTTCTTTTCCCTTCCCGGC	60.251	55.000	0.00	0.00	0.00	6.13
1672	7034	0.965866	CTTCTTTTCCCTTCCCGGCC	60.966	60.000	0.00	0.00	0.00	6.13
1673	7035	2.362503	CTTTTCCCTTCCCGGCCC	60.363	66.667	0.00	0.00	0.00	5.80
1674	7036	3.957435	CTTTTCCCTTCCCGGCCCC	62.957	68.421	0.00	0.00	0.00	5.80
1693	7055	2.223923	CCCCGTCAGATTCAGAAGCTAG	60.224	54.545	0.00	0.00	0.00	3.42
1722	7084	6.967767	CACTTCCACTGTCTAGTAGTAATTCG	59.032	42.308	0.00	0.00	34.74	3.34
1728	7090	8.433126	CCACTGTCTAGTAGTAATTCGTTTTTG	58.567	37.037	0.00	0.00	34.74	2.44
1739	7101	8.397215	AGTAATTCGTTTTTGTTGTTGTAACC	57.603	30.769	0.00	0.00	0.00	2.85
1756	7118	6.199937	TGTAACCCTGTCTAGTAATTCGTC	57.800	41.667	0.00	0.00	0.00	4.20
1760	7122	3.705072	CCCTGTCTAGTAATTCGTCCCTT	59.295	47.826	0.00	0.00	0.00	3.95
1769	7131	5.801380	AGTAATTCGTCCCTTGTGTAATGT	58.199	37.500	0.00	0.00	0.00	2.71
1800	7162	9.651718	GCTGATTATTAACTATTACAAGTGCAC	57.348	33.333	9.40	9.40	0.00	4.57
2022	7385	9.826574	ATTTGAAGATGAAACCATCCAAATATG	57.173	29.630	14.84	0.00	40.95	1.78
2078	7442	4.700268	TGTTCGCAGCAAACATCAATAT	57.300	36.364	0.00	0.00	31.90	1.28
2152	7516	6.757947	ACATTGGAAAACTGAAAACATGTCTG	59.242	34.615	0.00	0.00	0.00	3.51
2527	7896	7.014808	TGGACATGTAAATCAGGTATCGACATA	59.985	37.037	0.00	0.00	41.28	2.29

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
33	34	8.603242	ATTAACAACGTCACTAATCTGTTTCT	57.397	30.769	3.59	0.00	0.00	2.52
42	43	6.367695	CAGTCATGGATTAACAACGTCACTAA	59.632	38.462	0.00	0.00	0.00	2.24
49	50	4.253685	AGGACAGTCATGGATTAACAACG	58.746	43.478	2.17	0.00	0.00	4.10
69	70	3.343617	TGGGAAGCGAAGTATCAAAAGG	58.656	45.455	0.00	0.00	0.00	3.11
144	154	3.868619	TGTACAAAAGGCTAACCCTGT	57.131	42.857	0.00	0.00	45.62	4.00
180	190	6.434596	CATGTCAATAAACAACCGACAAAGA	58.565	36.000	0.00	0.00	39.80	2.52
565	5926	2.417719	CTGGTCGGTTGGAGAAAGAAG	58.582	52.381	0.00	0.00	0.00	2.85
580	5941	1.375098	GCATCTGCAGAAGCCTGGTC	61.375	60.000	29.06	4.60	40.72	4.02
624	5985	6.175471	AGATTGAGAAGTGCATGTGTAATGA	58.825	36.000	0.00	0.00	0.00	2.57
651	6012	8.603898	TTTTGTAAGATAGAGTGACAGGGATA	57.396	34.615	0.00	0.00	0.00	2.59
653	6014	6.497259	ACTTTTGTAAGATAGAGTGACAGGGA	59.503	38.462	0.00	0.00	35.30	4.20
659	6020	6.995686	TGGCAAACTTTTGTAAGATAGAGTGA	59.004	34.615	3.74	0.00	40.24	3.41
755	6117	2.721274	TTGGCACCAAACGATTGATG	57.279	45.000	7.03	0.39	38.94	3.07
762	6124	0.893270	TCCAGGATTGGCACCAAACG	60.893	55.000	6.14	0.00	44.63	3.60
778	6140	2.844654	AGAGAAGATGCTCCTCTCCA	57.155	50.000	7.68	0.00	35.49	3.86
845	6207	1.610102	GCAGTGCAGGAGAAGATGTGT	60.610	52.381	11.09	0.00	0.00	3.72
902	6264	2.985512	GATTCCTGCGATCGGCTGCT	62.986	60.000	18.30	1.70	44.05	4.24
938	6300	0.733729	CTCTCATGAGCTTGCTTGGC	59.266	55.000	18.36	0.00	33.12	4.52
968	6330	2.616458	GGTCCCTCCATTGCCACCT	61.616	63.158	0.00	0.00	35.97	4.00
1176	6538	1.000163	GGCGACGGTGTAGATGATGAT	60.000	52.381	0.00	0.00	0.00	2.45
1182	6544	2.125961	GGGAGGCGACGGTGTAGAT	61.126	63.158	0.00	0.00	0.00	1.98
1185	6547	2.753043	GAGGGAGGCGACGGTGTA	60.753	66.667	0.00	0.00	0.00	2.90
1218	6580	2.264794	GGAGGCGACGGTGTTGAT	59.735	61.111	0.00	0.00	0.00	2.57
1392	6754	2.490685	GACGGAGCCGAGGAAGAC	59.509	66.667	16.83	0.00	42.83	3.01
1568	6930	1.872237	CGACAACGTCCAACACCTCAT	60.872	52.381	0.00	0.00	34.56	2.90
1571	6933	4.431035	CGACAACGTCCAACACCT	57.569	55.556	0.00	0.00	34.56	4.00
1581	6943	4.696172	GGCGACGCAACGACAACG	62.696	66.667	23.09	0.00	41.34	4.10
1611	6973	0.828022	AACACACGAGGAGTTCACCA	59.172	50.000	0.00	0.00	0.00	4.17
1621	6983	9.483062	GTACTTGTAGTACTATAAACACACGAG	57.517	37.037	12.48	8.28	45.70	4.18
1639	7001	6.099269	AGGGAAAAGAAGTGACAGTACTTGTA	59.901	38.462	0.00	0.00	40.78	2.41
1640	7002	5.104485	AGGGAAAAGAAGTGACAGTACTTGT	60.104	40.000	0.00	0.00	40.78	3.16
1641	7003	5.368989	AGGGAAAAGAAGTGACAGTACTTG	58.631	41.667	0.00	0.00	40.78	3.16
1642	7004	5.632034	AGGGAAAAGAAGTGACAGTACTT	57.368	39.130	0.00	0.00	43.24	2.24
1657	7019	3.987360	GGGGCCGGGAAGGGAAAA	61.987	66.667	2.18	0.00	41.48	2.29
1669	7031	1.910580	TTCTGAATCTGACGGGGGCC	61.911	60.000	0.00	0.00	0.00	5.80
1670	7032	0.462759	CTTCTGAATCTGACGGGGGC	60.463	60.000	0.00	0.00	0.00	5.80
1671	7033	0.462759	GCTTCTGAATCTGACGGGGG	60.463	60.000	0.00	0.00	0.00	5.40
1672	7034	0.539051	AGCTTCTGAATCTGACGGGG	59.461	55.000	0.00	0.00	0.00	5.73
1673	7035	2.801342	GCTAGCTTCTGAATCTGACGGG	60.801	54.545	7.70	0.00	0.00	5.28
1674	7036	2.159184	TGCTAGCTTCTGAATCTGACGG	60.159	50.000	17.23	0.00	0.00	4.79
1693	7055	1.001406	ACTAGACAGTGGAAGTGCTGC	59.999	52.381	0.00	0.00	42.38	5.25
1722	7084	5.716094	AGACAGGGTTACAACAACAAAAAC	58.284	37.500	0.00	0.00	0.00	2.43
1728	7090	7.148689	CGAATTACTAGACAGGGTTACAACAAC	60.149	40.741	0.00	0.00	0.00	3.32
1739	7101	4.159879	ACAAGGGACGAATTACTAGACAGG	59.840	45.833	0.00	0.00	0.00	4.00
1756	7118	4.323417	TCAGCAGTAACATTACACAAGGG	58.677	43.478	4.67	0.00	36.12	3.95
1800	7162	6.295039	ACGACCAAAATAAACAGTAGTGTG	57.705	37.500	3.39	0.00	36.84	3.82
1804	7166	9.415544	ACTAGTTACGACCAAAATAAACAGTAG	57.584	33.333	0.00	0.00	0.00	2.57
2057	7421	4.155644	TCATATTGATGTTTGCTGCGAACA	59.844	37.500	31.27	31.27	41.27	3.18
2062	7426	7.330208	AGAGTTTTTCATATTGATGTTTGCTGC	59.670	33.333	0.00	0.00	34.41	5.25
2152	7516	8.557029	GGTATTGTAAGTCAACCATATAAGCAC	58.443	37.037	0.00	0.00	38.97	4.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.