AutoCloner

Multiple sequence alignment - TraesCS6D01G230100

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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	TraesCS6D01G230100	chr6D	100.000	3185	0	0	1	3185	322587939	322584755	0.000000e+00	5882
1	TraesCS6D01G230100	chr6D	91.804	1635	102	14	943	2551	322572298	322570670	0.000000e+00	2248
2	TraesCS6D01G230100	chr6D	88.693	566	58	5	2622	3184	20193450	20194012	0.000000e+00	686
3	TraesCS6D01G230100	chr6D	84.013	638	77	16	2555	3185	289501075	289501694	9.840000e-165	590
4	TraesCS6D01G230100	chr6D	89.532	363	35	3	2557	2918	20199254	20198894	1.040000e-124	457
5	TraesCS6D01G230100	chr6B	94.097	2592	68	28	1	2556	500893283	500895825	0.000000e+00	3860
6	TraesCS6D01G230100	chr6B	90.528	1552	119	12	943	2466	501062655	501064206	0.000000e+00	2026
7	TraesCS6D01G230100	chr6A	97.320	1940	40	5	625	2556	460006745	460004810	0.000000e+00	3284
8	TraesCS6D01G230100	chr6A	91.195	1556	110	12	943	2475	459878438	459876887	0.000000e+00	2089
9	TraesCS6D01G230100	chr6A	93.060	634	27	6	1	626	460007406	460006782	0.000000e+00	911
10	TraesCS6D01G230100	chr2D	90.076	1189	107	7	997	2181	15133811	15134992	0.000000e+00	1531
11	TraesCS6D01G230100	chr3D	88.107	1194	140	2	996	2188	213996921	213998113	0.000000e+00	1417
12	TraesCS6D01G230100	chr3D	91.176	340	28	2	2557	2896	424341967	424341630	8.050000e-126	460
13	TraesCS6D01G230100	chr3D	87.172	343	29	3	2556	2883	424340013	424339671	3.000000e-100	375
14	TraesCS6D01G230100	chr3B	88.013	1193	141	2	996	2187	330800921	330799730	0.000000e+00	1410
15	TraesCS6D01G230100	chr3A	87.907	1199	143	2	991	2188	279436896	279435699	0.000000e+00	1410
16	TraesCS6D01G230100	chr5D	92.114	634	47	3	2553	3185	387112400	387111769	0.000000e+00	891
17	TraesCS6D01G230100	chr5D	91.318	645	40	4	2557	3185	414096731	414096087	0.000000e+00	867
18	TraesCS6D01G230100	chr5D	89.602	327	30	2	2556	2882	387110362	387110040	2.290000e-111	412
19	TraesCS6D01G230100	chr7D	90.853	645	43	4	2557	3185	350139283	350139927	0.000000e+00	850
20	TraesCS6D01G230100	chrUn	89.767	645	41	8	2557	3185	26911264	26910629	0.000000e+00	802
21	TraesCS6D01G230100	chr2A	91.504	565	45	3	2622	3185	628732133	628732695	0.000000e+00	774
22	TraesCS6D01G230100	chr7A	88.514	592	48	7	2613	3185	269963530	269962940	0.000000e+00	699
23	TraesCS6D01G230100	chr4D	88.621	580	48	5	2622	3185	455184140	455184717	0.000000e+00	689

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	TraesCS6D01G230100	chr6D	322584755	322587939	3184	True	5882.0	5882	100.000	1	3185	1	chr6D.!!$R3	3184
1	TraesCS6D01G230100	chr6D	322570670	322572298	1628	True	2248.0	2248	91.804	943	2551	1	chr6D.!!$R2	1608
2	TraesCS6D01G230100	chr6D	20193450	20194012	562	False	686.0	686	88.693	2622	3184	1	chr6D.!!$F1	562
3	TraesCS6D01G230100	chr6D	289501075	289501694	619	False	590.0	590	84.013	2555	3185	1	chr6D.!!$F2	630
4	TraesCS6D01G230100	chr6B	500893283	500895825	2542	False	3860.0	3860	94.097	1	2556	1	chr6B.!!$F1	2555
5	TraesCS6D01G230100	chr6B	501062655	501064206	1551	False	2026.0	2026	90.528	943	2466	1	chr6B.!!$F2	1523
6	TraesCS6D01G230100	chr6A	460004810	460007406	2596	True	2097.5	3284	95.190	1	2556	2	chr6A.!!$R2	2555
7	TraesCS6D01G230100	chr6A	459876887	459878438	1551	True	2089.0	2089	91.195	943	2475	1	chr6A.!!$R1	1532
8	TraesCS6D01G230100	chr2D	15133811	15134992	1181	False	1531.0	1531	90.076	997	2181	1	chr2D.!!$F1	1184
9	TraesCS6D01G230100	chr3D	213996921	213998113	1192	False	1417.0	1417	88.107	996	2188	1	chr3D.!!$F1	1192
10	TraesCS6D01G230100	chr3D	424339671	424341967	2296	True	417.5	460	89.174	2556	2896	2	chr3D.!!$R1	340
11	TraesCS6D01G230100	chr3B	330799730	330800921	1191	True	1410.0	1410	88.013	996	2187	1	chr3B.!!$R1	1191
12	TraesCS6D01G230100	chr3A	279435699	279436896	1197	True	1410.0	1410	87.907	991	2188	1	chr3A.!!$R1	1197
13	TraesCS6D01G230100	chr5D	414096087	414096731	644	True	867.0	867	91.318	2557	3185	1	chr5D.!!$R1	628
14	TraesCS6D01G230100	chr5D	387110040	387112400	2360	True	651.5	891	90.858	2553	3185	2	chr5D.!!$R2	632
15	TraesCS6D01G230100	chr7D	350139283	350139927	644	False	850.0	850	90.853	2557	3185	1	chr7D.!!$F1	628
16	TraesCS6D01G230100	chrUn	26910629	26911264	635	True	802.0	802	89.767	2557	3185	1	chrUn.!!$R1	628
17	TraesCS6D01G230100	chr2A	628732133	628732695	562	False	774.0	774	91.504	2622	3185	1	chr2A.!!$F1	563
18	TraesCS6D01G230100	chr7A	269962940	269963530	590	True	699.0	699	88.514	2613	3185	1	chr7A.!!$R1	572
19	TraesCS6D01G230100	chr4D	455184140	455184717	577	False	689.0	689	88.621	2622	3185	1	chr4D.!!$F1	563

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
88	89	0.723414	CGTGATGCGAAGAACATGCT	59.277	50.0	0.0	0.0	44.77	3.79	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2256	2341	5.576895	GCTTCAATGTCTAATGCTTCTTCC	58.423	41.667	0.0	0.0	0.0	3.46	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
54	55	4.363138	GTGGGTGGCGTAATTACTAGTAC	58.637	47.826	13.56	7.18	0.00	2.73
55	56	4.022603	TGGGTGGCGTAATTACTAGTACA	58.977	43.478	13.56	3.47	0.00	2.90
87	88	3.209429	CGTGATGCGAAGAACATGC	57.791	52.632	0.00	0.00	44.77	4.06
88	89	0.723414	CGTGATGCGAAGAACATGCT	59.277	50.000	0.00	0.00	44.77	3.79
89	90	1.926510	CGTGATGCGAAGAACATGCTA	59.073	47.619	0.00	0.00	44.77	3.49
90	91	2.034254	CGTGATGCGAAGAACATGCTAG	60.034	50.000	0.00	0.00	44.77	3.42
91	92	2.932614	GTGATGCGAAGAACATGCTAGT	59.067	45.455	0.00	0.00	0.00	2.57
93	94	4.566759	GTGATGCGAAGAACATGCTAGTTA	59.433	41.667	0.00	0.00	0.00	2.24
94	95	4.805719	TGATGCGAAGAACATGCTAGTTAG	59.194	41.667	0.00	0.00	0.00	2.34
95	96	4.188247	TGCGAAGAACATGCTAGTTAGT	57.812	40.909	0.00	0.00	0.00	2.24
96	97	5.319140	TGCGAAGAACATGCTAGTTAGTA	57.681	39.130	0.00	0.00	0.00	1.82
97	98	5.340803	TGCGAAGAACATGCTAGTTAGTAG	58.659	41.667	0.00	0.00	0.00	2.57
98	99	5.105877	TGCGAAGAACATGCTAGTTAGTAGT	60.106	40.000	0.00	0.00	0.00	2.73
99	100	5.805994	GCGAAGAACATGCTAGTTAGTAGTT	59.194	40.000	0.00	0.00	0.00	2.24
100	101	6.971184	GCGAAGAACATGCTAGTTAGTAGTTA	59.029	38.462	0.00	0.00	0.00	2.24
101	102	7.648510	GCGAAGAACATGCTAGTTAGTAGTTAT	59.351	37.037	0.00	0.00	0.00	1.89
102	103	8.959058	CGAAGAACATGCTAGTTAGTAGTTATG	58.041	37.037	0.00	9.98	34.34	1.90
154	165	3.577649	ATATTAGTCTGTCATCGGCGG	57.422	47.619	7.21	0.00	0.00	6.13
299	317	2.933573	CCGGTGTGTAGAGAGTAGGAT	58.066	52.381	0.00	0.00	0.00	3.24
314	332	2.344093	AGGATTAGGTGTGTGGGTCT	57.656	50.000	0.00	0.00	0.00	3.85
392	410	0.739813	GCGAGCTTTGTGTATCCGGT	60.740	55.000	0.00	0.00	0.00	5.28
421	439	3.901290	CGTAGTCGACTTCGCTATTGATC	59.099	47.826	27.58	1.40	39.71	2.92
471	489	2.919494	CGGTTGTTGGCTCTTGGGC	61.919	63.158	0.00	0.00	41.27	5.36
563	581	1.302033	CTTCTGTTCTGGCGCAGGT	60.302	57.895	10.83	0.00	33.81	4.00
791	851	6.961360	TTTTTCTTGTTTTGGGGTGTTTTT	57.039	29.167	0.00	0.00	0.00	1.94
847	910	3.303329	GCGTGTGCTGTATATTGGTCATG	60.303	47.826	0.00	0.00	38.39	3.07
856	919	2.890808	TATTGGTCATGAGAGCGTCC	57.109	50.000	0.00	0.00	45.10	4.79
894	958	5.562635	TGGGACAATACCGTGATTTTAGTT	58.437	37.500	0.00	0.00	31.92	2.24
912	976	8.458573	TTTTAGTTGCCTTTTCTGACTAATGA	57.541	30.769	0.00	0.00	34.06	2.57
2256	2341	0.038744	ATGTTGCTCCTGGGAAGTGG	59.961	55.000	0.00	0.00	0.00	4.00
2454	2564	7.724305	TTCTTTGTTGTGTAGTTCCTCATAC	57.276	36.000	0.00	0.00	0.00	2.39
2524	2634	5.441718	AATTCTATTGCTCTGTTCTCCCA	57.558	39.130	0.00	0.00	0.00	4.37
2580	2692	7.988599	TGTGTTATGACCGGTTTAGCTTATAAT	59.011	33.333	9.42	0.00	0.00	1.28
2601	2713	4.974438	AGGAGGCCCACCGGTCAA	62.974	66.667	2.59	0.00	42.76	3.18
2609	2721	1.949465	CCCACCGGTCAATAGTTAGC	58.051	55.000	2.59	0.00	0.00	3.09
2618	2730	1.209504	TCAATAGTTAGCGGCTTGGCT	59.790	47.619	8.26	6.84	46.88	4.75
2773	2936	4.235762	GCCGCCGCCATCTTCCTA	62.236	66.667	0.00	0.00	0.00	2.94
2836	2999	2.770048	CCCCGCTCCATCCTTCCT	60.770	66.667	0.00	0.00	0.00	3.36
2994	3158	1.048724	ATGACGTCCACCCCGATGAT	61.049	55.000	14.12	0.00	0.00	2.45
3002	3166	3.860605	CCCCGATGATCACCGCCA	61.861	66.667	3.13	0.00	0.00	5.69
3071	3235	3.727258	CGGCCCCCATCACTTCCA	61.727	66.667	0.00	0.00	0.00	3.53

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
15	16	5.125417	CCACCCACGTATGATGAAGAAAAAT	59.875	40.000	0.00	0.00	0.00	1.82
87	88	7.773149	ACTGCCAACTCATAACTACTAACTAG	58.227	38.462	0.00	0.00	0.00	2.57
88	89	7.713734	ACTGCCAACTCATAACTACTAACTA	57.286	36.000	0.00	0.00	0.00	2.24
89	90	6.607004	ACTGCCAACTCATAACTACTAACT	57.393	37.500	0.00	0.00	0.00	2.24
90	91	6.476053	GCTACTGCCAACTCATAACTACTAAC	59.524	42.308	0.00	0.00	0.00	2.34
91	92	6.153851	TGCTACTGCCAACTCATAACTACTAA	59.846	38.462	0.00	0.00	38.71	2.24
93	94	4.466370	TGCTACTGCCAACTCATAACTACT	59.534	41.667	0.00	0.00	38.71	2.57
94	95	4.567159	GTGCTACTGCCAACTCATAACTAC	59.433	45.833	0.00	0.00	38.71	2.73
95	96	4.676986	CGTGCTACTGCCAACTCATAACTA	60.677	45.833	0.00	0.00	38.71	2.24
96	97	3.600388	GTGCTACTGCCAACTCATAACT	58.400	45.455	0.00	0.00	38.71	2.24
97	98	2.348666	CGTGCTACTGCCAACTCATAAC	59.651	50.000	0.00	0.00	38.71	1.89
98	99	2.028476	ACGTGCTACTGCCAACTCATAA	60.028	45.455	0.00	0.00	38.71	1.90
99	100	1.548719	ACGTGCTACTGCCAACTCATA	59.451	47.619	0.00	0.00	38.71	2.15
100	101	0.321671	ACGTGCTACTGCCAACTCAT	59.678	50.000	0.00	0.00	38.71	2.90
101	102	0.319555	GACGTGCTACTGCCAACTCA	60.320	55.000	0.00	0.00	38.71	3.41
102	103	1.014564	GGACGTGCTACTGCCAACTC	61.015	60.000	0.00	0.00	38.71	3.01
103	104	1.004918	GGACGTGCTACTGCCAACT	60.005	57.895	0.00	0.00	38.71	3.16
104	105	1.004918	AGGACGTGCTACTGCCAAC	60.005	57.895	8.23	0.00	38.71	3.77
154	165	2.270527	GCCTCTCTTGGGGACTGC	59.729	66.667	0.00	0.00	0.00	4.40
181	192	3.278592	AACGAGGAAGACGCGGTCC	62.279	63.158	12.47	14.40	38.06	4.46
299	317	0.830444	AGCGAGACCCACACACCTAA	60.830	55.000	0.00	0.00	0.00	2.69
392	410	1.926511	GAAGTCGACTACGCCCGGAA	61.927	60.000	20.39	0.00	39.58	4.30
403	421	5.062308	ACAAAAGATCAATAGCGAAGTCGAC	59.938	40.000	7.70	7.70	43.02	4.20
456	474	1.228552	GGAGCCCAAGAGCCAACAA	60.229	57.895	0.00	0.00	0.00	2.83
471	489	4.704833	CACCCGGCCACACAGGAG	62.705	72.222	2.24	0.00	41.22	3.69
563	581	2.004583	CCTGCCGACGACTAATCAAA	57.995	50.000	0.00	0.00	0.00	2.69
619	637	2.919859	CTCACTGTAGCACATCGAAGTG	59.080	50.000	16.15	16.15	42.37	3.16
632	688	0.530744	GCGGGACACATCTCACTGTA	59.469	55.000	0.00	0.00	0.00	2.74
791	851	4.559153	GAAATAAGCCAGAGCAGCAAAAA	58.441	39.130	0.00	0.00	43.56	1.94
792	852	3.056607	GGAAATAAGCCAGAGCAGCAAAA	60.057	43.478	0.00	0.00	43.56	2.44
793	853	2.493278	GGAAATAAGCCAGAGCAGCAAA	59.507	45.455	0.00	0.00	43.56	3.68
847	910	4.517453	AGTACAGAGAATATGGACGCTCTC	59.483	45.833	0.00	0.00	36.56	3.20
856	919	7.657761	GGTATTGTCCCAAGTACAGAGAATATG	59.342	40.741	0.00	0.00	31.09	1.78
925	989	7.661847	AGAATGAAACTCCAACGAGAAATTACT	59.338	33.333	0.00	0.00	38.52	2.24
2256	2341	5.576895	GCTTCAATGTCTAATGCTTCTTCC	58.423	41.667	0.00	0.00	0.00	3.46
2454	2564	3.673052	CGAGACTCAGGAAGAAAGAGCAG	60.673	52.174	2.82	0.00	32.71	4.24
2598	2710	1.209504	AGCCAAGCCGCTAACTATTGA	59.790	47.619	0.00	0.00	37.32	2.57
2601	2713	0.830648	TGAGCCAAGCCGCTAACTAT	59.169	50.000	0.00	0.00	39.87	2.12
2743	2855	4.151582	GCGGCGGCTAGGGTTGTA	62.152	66.667	9.78	0.00	35.83	2.41
2836	2999	3.116096	ACCTGCTCCATAGGTTGTAGA	57.884	47.619	0.00	0.00	46.13	2.59

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.