AutoCloner

Multiple sequence alignment - TraesCS7D01G273500

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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	TraesCS7D01G273500	chr7D	100.000	2432	0	0	1	2432	263959741	263957310	0.000000e+00	4492
1	TraesCS7D01G273500	chr7D	80.334	778	130	15	776	1542	263952837	263952072	3.510000e-158	568
2	TraesCS7D01G273500	chr7D	88.193	415	39	6	340	745	353804083	353803670	1.010000e-133	486
3	TraesCS7D01G273500	chr7D	84.841	409	57	4	339	745	629516715	629516310	8.100000e-110	407
4	TraesCS7D01G273500	chr7A	94.808	1695	62	13	746	2432	287215521	287213845	0.000000e+00	2619
5	TraesCS7D01G273500	chr7A	89.125	423	30	4	340	746	398920418	398920840	1.670000e-141	512
6	TraesCS7D01G273500	chr7A	88.498	426	35	4	334	745	283148523	283148948	1.000000e-138	503
7	TraesCS7D01G273500	chr7A	96.226	106	4	0	1	106	287216411	287216306	8.940000e-40	174
8	TraesCS7D01G273500	chr7B	95.611	1162	34	8	746	1894	244270132	244268975	0.000000e+00	1847
9	TraesCS7D01G273500	chr7B	96.042	480	18	1	1954	2432	244266504	244266025	0.000000e+00	780
10	TraesCS7D01G273500	chr7B	95.588	340	12	2	1	339	244270460	244270123	2.130000e-150	542
11	TraesCS7D01G273500	chr7B	85.545	422	41	12	339	746	615223341	615223756	8.040000e-115	424
12	TraesCS7D01G273500	chr7B	87.037	270	20	7	490	745	558264133	558264401	8.510000e-75	291
13	TraesCS7D01G273500	chr7B	79.479	307	49	10	936	1231	244219171	244218868	3.170000e-49	206
14	TraesCS7D01G273500	chr5B	89.176	425	30	5	335	745	697520166	697520588	1.290000e-142	516
15	TraesCS7D01G273500	chr5B	78.868	265	54	2	1103	1366	528537672	528537935	6.910000e-41	178
16	TraesCS7D01G273500	chr5B	78.358	268	50	8	1103	1366	528524850	528525113	1.500000e-37	167
17	TraesCS7D01G273500	chr6B	89.311	421	28	5	340	745	487204244	487203826	1.670000e-141	512
18	TraesCS7D01G273500	chr6B	89.260	419	28	5	341	745	487207491	487207076	2.160000e-140	508
19	TraesCS7D01G273500	chr6B	88.222	433	35	4	331	750	39335224	39335653	1.000000e-138	503
20	TraesCS7D01G273500	chr5D	88.124	421	36	4	340	746	423244539	423244119	2.810000e-134	488
21	TraesCS7D01G273500	chr5D	82.540	126	14	4	1151	1269	434656979	434656855	1.190000e-18	104
22	TraesCS7D01G273500	chr5D	81.538	130	18	3	1146	1269	434679122	434678993	4.280000e-18	102
23	TraesCS7D01G273500	chr2A	88.180	423	31	12	340	746	59937391	59936972	1.010000e-133	486
24	TraesCS7D01G273500	chr4A	85.511	421	46	7	340	745	716103550	716103970	2.230000e-115	425
25	TraesCS7D01G273500	chr1A	83.373	421	50	14	340	747	552144120	552144533	2.950000e-99	372
26	TraesCS7D01G273500	chr5A	78.030	264	58	0	1103	1366	549153940	549154203	1.500000e-37	167
27	TraesCS7D01G273500	chr5A	77.733	247	53	2	1121	1366	549214942	549214697	1.510000e-32	150

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	TraesCS7D01G273500	chr7D	263957310	263959741	2431	True	4492.000000	4492	100.0000	1	2432	1	chr7D.!!$R2	2431
1	TraesCS7D01G273500	chr7D	263952072	263952837	765	True	568.000000	568	80.3340	776	1542	1	chr7D.!!$R1	766
2	TraesCS7D01G273500	chr7A	287213845	287216411	2566	True	1396.500000	2619	95.5170	1	2432	2	chr7A.!!$R1	2431
3	TraesCS7D01G273500	chr7B	244266025	244270460	4435	True	1056.333333	1847	95.7470	1	2432	3	chr7B.!!$R2	2431
4	TraesCS7D01G273500	chr6B	487203826	487207491	3665	True	510.000000	512	89.2855	340	745	2	chr6B.!!$R1	405

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
748	4589	0.179056	CACCGGATACTTTCCCGCAT	60.179	55.0	9.46	0.0	44.07	4.73	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1990	8309	1.807142	GGTTTACAGAAGCAGCACCTC	59.193	52.381	0.0	0.0	0.0	3.85	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
69	70	0.471780	AACAAAAAGGGGCAGGAGGG	60.472	55.000	0.00	0.00	0.00	4.30
93	94	7.094677	GGGAAATCAGCAAAAGCAACATAAAAT	60.095	33.333	0.00	0.00	0.00	1.82
133	204	3.936564	ACTGGAAAAACAAAAGCTGCAA	58.063	36.364	1.02	0.00	0.00	4.08
144	215	2.791383	AAGCTGCAAAATAACGCACA	57.209	40.000	1.02	0.00	33.75	4.57
260	332	9.672086	CTACTATCTTGTACAGCTATCTCAAAC	57.328	37.037	0.00	0.00	0.00	2.93
263	335	5.724328	TCTTGTACAGCTATCTCAAACCTG	58.276	41.667	0.00	0.00	0.00	4.00
339	917	3.804325	CAGTGGTCCTATGCATTTAGTCG	59.196	47.826	3.54	0.00	0.00	4.18
340	918	3.131396	GTGGTCCTATGCATTTAGTCGG	58.869	50.000	3.54	0.00	0.00	4.79
341	919	2.104111	TGGTCCTATGCATTTAGTCGGG	59.896	50.000	3.54	0.00	0.00	5.14
342	920	2.367567	GGTCCTATGCATTTAGTCGGGA	59.632	50.000	3.54	0.00	0.00	5.14
343	921	3.181458	GGTCCTATGCATTTAGTCGGGAA	60.181	47.826	3.54	0.00	0.00	3.97
344	922	4.448210	GTCCTATGCATTTAGTCGGGAAA	58.552	43.478	3.54	0.00	0.00	3.13
375	953	2.998949	CCAGCCTTGGGGTACTCC	59.001	66.667	4.21	4.21	41.05	3.85
386	964	3.788672	GGTACTCCCAATGCTCCAG	57.211	57.895	0.00	0.00	0.00	3.86
395	973	2.029649	CCCAATGCTCCAGTGTCAAAAG	60.030	50.000	0.00	0.00	0.00	2.27
397	975	2.886523	CAATGCTCCAGTGTCAAAAGGA	59.113	45.455	0.00	0.00	0.00	3.36
407	985	9.546428	CTCCAGTGTCAAAAGGAATTTTTAAAT	57.454	29.630	0.00	0.00	36.87	1.40
425	1003	9.788960	TTTTTAAATGTTTCAAAAATTTCCGGG	57.211	25.926	1.23	0.00	0.00	5.73
463	1041	5.482163	TCACAAGGAATGTCACTACATCA	57.518	39.130	0.00	0.00	45.79	3.07
598	4425	9.683069	GCTAGATTTCACATTTTTCTTTCTCAA	57.317	29.630	0.00	0.00	0.00	3.02
632	4459	8.299990	TCAAGTTTGGACCTGAAATTTTTAGA	57.700	30.769	2.68	0.00	0.00	2.10
650	4490	7.900782	TTTTAGAGCTTGTAGGTACATTCAC	57.099	36.000	0.00	0.00	35.89	3.18
652	4492	5.078411	AGAGCTTGTAGGTACATTCACAG	57.922	43.478	0.00	0.00	35.89	3.66
745	4586	0.529992	GAGCACCGGATACTTTCCCG	60.530	60.000	9.46	0.00	42.06	5.14
746	4587	2.178235	GCACCGGATACTTTCCCGC	61.178	63.158	9.46	0.00	44.07	6.13
747	4588	1.219664	CACCGGATACTTTCCCGCA	59.780	57.895	9.46	0.00	44.07	5.69
748	4589	0.179056	CACCGGATACTTTCCCGCAT	60.179	55.000	9.46	0.00	44.07	4.73
749	4590	0.544697	ACCGGATACTTTCCCGCATT	59.455	50.000	9.46	0.00	44.07	3.56
750	4591	1.064979	ACCGGATACTTTCCCGCATTT	60.065	47.619	9.46	0.00	44.07	2.32
751	4592	2.171027	ACCGGATACTTTCCCGCATTTA	59.829	45.455	9.46	0.00	44.07	1.40
752	4593	2.806244	CCGGATACTTTCCCGCATTTAG	59.194	50.000	0.00	0.00	44.07	1.85
753	4594	3.463944	CGGATACTTTCCCGCATTTAGT	58.536	45.455	0.00	0.00	42.06	2.24
754	4595	3.493503	CGGATACTTTCCCGCATTTAGTC	59.506	47.826	0.00	0.00	42.06	2.59
920	4763	1.234821	GGCACAAACCATCGACAGAA	58.765	50.000	0.00	0.00	0.00	3.02
1113	4969	0.107312	ACCCATCATGCAGCTCAGTC	60.107	55.000	0.00	0.00	0.00	3.51
1277	5133	1.128692	GCTGCCTTGTGATACAACGAC	59.871	52.381	0.00	0.00	33.96	4.34
1278	5134	2.412870	CTGCCTTGTGATACAACGACA	58.587	47.619	0.00	0.00	33.96	4.35
1284	5140	4.454161	CCTTGTGATACAACGACAATGGAA	59.546	41.667	0.00	0.00	33.96	3.53
1448	5304	5.300969	TCCTGAAAAATGAAGATCTTGCG	57.699	39.130	14.00	0.00	0.00	4.85
1660	5516	6.319658	TCTTTCTCATTCCCAAATGCATCTAC	59.680	38.462	0.00	0.00	41.76	2.59
1746	5609	4.087956	GCAAAAAGGCAAAACAAACGAAG	58.912	39.130	0.00	0.00	0.00	3.79
1850	5713	7.894753	TTCTTTTATGTATGGATGCCATCAA	57.105	32.000	7.06	0.00	40.74	2.57
1862	5725	4.380233	GGATGCCATCAAAGAAGTGAGTTG	60.380	45.833	7.06	0.00	0.00	3.16
1921	5784	4.520492	GCTTGAATCAAGAAAGACCTTCCA	59.480	41.667	25.54	0.00	43.42	3.53
1923	5786	6.391227	TTGAATCAAGAAAGACCTTCCAAC	57.609	37.500	0.00	0.00	34.21	3.77
1924	5787	5.694995	TGAATCAAGAAAGACCTTCCAACT	58.305	37.500	0.00	0.00	34.21	3.16
1925	5788	5.532406	TGAATCAAGAAAGACCTTCCAACTG	59.468	40.000	0.00	0.00	34.21	3.16
1927	5790	3.458118	TCAAGAAAGACCTTCCAACTGGA	59.542	43.478	0.00	0.00	43.73	3.86
1928	5791	4.104738	TCAAGAAAGACCTTCCAACTGGAT	59.895	41.667	0.00	0.00	44.98	3.41
2164	8483	4.142093	TGCGGAACATCCTAAGTAACCTAC	60.142	45.833	0.00	0.00	33.30	3.18
2300	8619	1.064505	CACATTGCCTCCATTGTAGCG	59.935	52.381	0.00	0.00	34.71	4.26
2312	8631	2.261037	TTGTAGCGAACAATGCATGC	57.739	45.000	11.82	11.82	43.22	4.06
2383	8702	2.747446	GCGTAAGTCATGGACCATTTGT	59.253	45.455	3.52	0.00	41.68	2.83

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
133	204	1.173913	GCCCCTTCTGTGCGTTATTT	58.826	50.000	0.00	0.00	0.00	1.40
144	215	1.068121	ACTAACTTGCTGCCCCTTCT	58.932	50.000	0.00	0.00	0.00	2.85
185	256	4.190001	TGTGTTTGAAGCAACGTACCTTA	58.810	39.130	0.00	0.00	0.00	2.69
260	332	2.159142	GGTACGTGATAGTGGGTTCAGG	60.159	54.545	0.00	0.00	34.71	3.86
263	335	3.518590	CTTGGTACGTGATAGTGGGTTC	58.481	50.000	0.00	0.00	0.00	3.62
339	917	1.134068	GGGAGCACTGGATACTTTCCC	60.134	57.143	0.00	0.00	44.77	3.97
340	918	1.559682	TGGGAGCACTGGATACTTTCC	59.440	52.381	0.00	0.00	45.69	3.13
341	919	2.911484	CTGGGAGCACTGGATACTTTC	58.089	52.381	0.00	0.00	37.61	2.62
342	920	1.065126	GCTGGGAGCACTGGATACTTT	60.065	52.381	0.00	0.00	41.89	2.66
343	921	0.543749	GCTGGGAGCACTGGATACTT	59.456	55.000	0.00	0.00	41.89	2.24
344	922	1.341156	GGCTGGGAGCACTGGATACT	61.341	60.000	0.00	0.00	44.75	2.12
375	953	2.029649	CCTTTTGACACTGGAGCATTGG	60.030	50.000	0.00	0.00	0.00	3.16
378	956	2.957402	TCCTTTTGACACTGGAGCAT	57.043	45.000	0.00	0.00	0.00	3.79
431	1009	6.005823	TGACATTCCTTGTGAACATTCTCAT	58.994	36.000	0.00	0.00	39.18	2.90
432	1010	5.239306	GTGACATTCCTTGTGAACATTCTCA	59.761	40.000	0.00	0.00	39.18	3.27
433	1011	5.471456	AGTGACATTCCTTGTGAACATTCTC	59.529	40.000	0.00	0.00	39.18	2.87
439	1017	5.700832	TGATGTAGTGACATTCCTTGTGAAC	59.299	40.000	0.00	0.00	46.64	3.18
477	1055	7.824289	TCTCAATCTACATTTCGATTTTGGACT	59.176	33.333	0.00	0.00	0.00	3.85
517	1095	9.539825	AACATTGACACTATTCAGATCTGTATC	57.460	33.333	21.92	7.64	0.00	2.24
590	4417	7.168637	CCAAACTTGAATCACACATTGAGAAAG	59.831	37.037	0.00	0.00	37.77	2.62
598	4425	4.279169	CAGGTCCAAACTTGAATCACACAT	59.721	41.667	0.00	0.00	34.53	3.21
632	4459	4.891992	ACTGTGAATGTACCTACAAGCT	57.108	40.909	0.00	0.00	39.99	3.74
693	4534	1.652947	ACTCCCGGTACTCCAATGTT	58.347	50.000	0.00	0.00	0.00	2.71
920	4763	2.396590	AAAGTCGGTCTGTGTGTGTT	57.603	45.000	0.00	0.00	0.00	3.32
1077	4930	2.771943	TGGGTGGATATCCTTGTCTGAC	59.228	50.000	22.35	10.08	36.82	3.51
1277	5133	6.334989	AGCAAACACATCACATATTCCATTG	58.665	36.000	0.00	0.00	0.00	2.82
1278	5134	6.534475	AGCAAACACATCACATATTCCATT	57.466	33.333	0.00	0.00	0.00	3.16
1284	5140	6.653020	TCTCCTTAGCAAACACATCACATAT	58.347	36.000	0.00	0.00	0.00	1.78
1631	5487	6.590068	TGCATTTGGGAATGAGAAAGAAAAA	58.410	32.000	3.47	0.00	44.37	1.94
1636	5492	5.593679	AGATGCATTTGGGAATGAGAAAG	57.406	39.130	0.00	0.00	44.37	2.62
1689	5549	2.870411	ACTCTAAAACGTGTGTCTTGGC	59.130	45.455	0.00	0.00	0.00	4.52
1791	5654	6.082707	TCTAAAACAGTACTCCCTTCTTCCT	58.917	40.000	0.00	0.00	0.00	3.36
1797	5660	7.008941	TGTAGACTCTAAAACAGTACTCCCTT	58.991	38.462	0.00	0.00	0.00	3.95
1850	5713	6.449698	CATTTGGTATTGCAACTCACTTCTT	58.550	36.000	0.00	0.00	0.00	2.52
1862	5725	7.278424	ACAATTTCATACAGCATTTGGTATTGC	59.722	33.333	0.00	0.00	39.17	3.56
1921	5784	5.754543	TTTTTCCGACGTTAAATCCAGTT	57.245	34.783	0.00	0.00	0.00	3.16
1990	8309	1.807142	GGTTTACAGAAGCAGCACCTC	59.193	52.381	0.00	0.00	0.00	3.85
2300	8619	4.888038	TGAGTCTATGCATGCATTGTTC	57.112	40.909	36.23	29.59	37.82	3.18
2312	8631	3.181493	GCAAACAAGGCCATGAGTCTATG	60.181	47.826	16.33	5.21	0.00	2.23

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.