AutoCloner

Multiple sequence alignment - TraesCS5D01G476800

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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	TraesCS5D01G476800	chr5D	100.000	2488	0	0	1	2488	515643061	515640574	0.000000e+00	4595
1	TraesCS5D01G476800	chr5A	88.152	1131	65	28	742	1819	643865265	643864151	0.000000e+00	1282
2	TraesCS5D01G476800	chr5A	93.557	714	31	9	1	707	471513433	471514138	0.000000e+00	1050
3	TraesCS5D01G476800	chr5A	89.216	306	19	7	2195	2488	643860190	643859887	1.090000e-98	370
4	TraesCS5D01G476800	chr7A	96.503	715	18	5	1	710	459207538	459206826	0.000000e+00	1175
5	TraesCS5D01G476800	chr7A	95.531	716	28	4	1	713	163375052	163374338	0.000000e+00	1142
6	TraesCS5D01G476800	chr1A	96.218	714	21	4	1	710	535412193	535412904	0.000000e+00	1164
7	TraesCS5D01G476800	chr1A	85.496	131	7	5	2370	2488	568534014	568533884	2.600000e-25	126
8	TraesCS5D01G476800	chr1B	95.512	713	28	4	1	710	491698713	491698002	0.000000e+00	1136
9	TraesCS5D01G476800	chr1B	75.986	279	34	15	2240	2488	659549456	659549181	2.020000e-21	113
10	TraesCS5D01G476800	chr7D	95.372	713	30	3	1	710	635392799	635393511	0.000000e+00	1131
11	TraesCS5D01G476800	chr4B	94.398	714	35	5	1	710	150733477	150732765	0.000000e+00	1092
12	TraesCS5D01G476800	chr5B	86.783	1029	63	28	713	1689	648279087	648278080	0.000000e+00	1079
13	TraesCS5D01G476800	chr5B	88.058	896	50	27	717	1572	648338133	648339011	0.000000e+00	1009
14	TraesCS5D01G476800	chr5B	88.018	893	50	27	720	1572	648317059	648316184	0.000000e+00	1003
15	TraesCS5D01G476800	chr5B	90.349	373	22	7	1865	2232	648312954	648312591	6.230000e-131	477
16	TraesCS5D01G476800	chr5B	90.160	376	23	7	1862	2232	648342239	648342605	6.230000e-131	477
17	TraesCS5D01G476800	chr5B	92.042	289	18	2	2205	2488	648266196	648265908	3.850000e-108	401
18	TraesCS5D01G476800	chr5B	91.608	286	19	2	2208	2488	648307951	648307666	8.340000e-105	390
19	TraesCS5D01G476800	chr5B	86.328	256	20	9	1948	2196	648270555	648270308	5.280000e-67	265
20	TraesCS5D01G476800	chr5B	87.387	222	16	8	1605	1819	648313252	648313036	6.870000e-61	244
21	TraesCS5D01G476800	chr5B	86.937	222	17	8	1605	1819	648341944	648342160	3.200000e-59	239
22	TraesCS5D01G476800	chr5B	96.639	119	4	0	1872	1990	648310518	648310400	5.430000e-47	198
23	TraesCS5D01G476800	chr5B	95.495	111	4	1	1694	1804	648277950	648277841	2.540000e-40	176
24	TraesCS5D01G476800	chr5B	90.441	136	8	3	1827	1962	648270815	648270685	9.150000e-40	174
25	TraesCS5D01G476800	chr2A	93.961	712	37	5	1	708	733218378	733217669	0.000000e+00	1072
26	TraesCS5D01G476800	chr7B	91.725	713	50	8	1	707	658118396	658119105	0.000000e+00	981

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	TraesCS5D01G476800	chr5D	515640574	515643061	2487	True	4595.0	4595	100.0000	1	2488	1	chr5D.!!$R1	2487
1	TraesCS5D01G476800	chr5A	471513433	471514138	705	False	1050.0	1050	93.5570	1	707	1	chr5A.!!$F1	706
2	TraesCS5D01G476800	chr5A	643859887	643865265	5378	True	826.0	1282	88.6840	742	2488	2	chr5A.!!$R1	1746
3	TraesCS5D01G476800	chr7A	459206826	459207538	712	True	1175.0	1175	96.5030	1	710	1	chr7A.!!$R2	709
4	TraesCS5D01G476800	chr7A	163374338	163375052	714	True	1142.0	1142	95.5310	1	713	1	chr7A.!!$R1	712
5	TraesCS5D01G476800	chr1A	535412193	535412904	711	False	1164.0	1164	96.2180	1	710	1	chr1A.!!$F1	709
6	TraesCS5D01G476800	chr1B	491698002	491698713	711	True	1136.0	1136	95.5120	1	710	1	chr1B.!!$R1	709
7	TraesCS5D01G476800	chr7D	635392799	635393511	712	False	1131.0	1131	95.3720	1	710	1	chr7D.!!$F1	709
8	TraesCS5D01G476800	chr4B	150732765	150733477	712	True	1092.0	1092	94.3980	1	710	1	chr4B.!!$R1	709
9	TraesCS5D01G476800	chr5B	648277841	648279087	1246	True	627.5	1079	91.1390	713	1804	2	chr5B.!!$R3	1091
10	TraesCS5D01G476800	chr5B	648338133	648342605	4472	False	575.0	1009	88.3850	717	2232	3	chr5B.!!$F1	1515
11	TraesCS5D01G476800	chr5B	648307666	648317059	9393	True	462.4	1003	90.8002	720	2488	5	chr5B.!!$R4	1768
12	TraesCS5D01G476800	chr5B	648270308	648270815	507	True	219.5	265	88.3845	1827	2196	2	chr5B.!!$R2	369
13	TraesCS5D01G476800	chr2A	733217669	733218378	709	True	1072.0	1072	93.9610	1	708	1	chr2A.!!$R1	707
14	TraesCS5D01G476800	chr7B	658118396	658119105	709	False	981.0	981	91.7250	1	707	1	chr7B.!!$F1	706

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
793	811	0.249073	CATTGAGTAGTCCGGCGAGG	60.249	60.0	9.3	0.0	42.97	4.63	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1830	4968	0.672401	AAACCACCTGCCGTATGTCG	60.672	55.0	0.0	0.0	39.52	4.35	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
398	402	5.946377	AGGTCTTATCACCCTGAATTCAAAC	59.054	40.000	9.88	0.00	37.09	2.93
402	406	7.118680	GTCTTATCACCCTGAATTCAAACGTAA	59.881	37.037	9.88	4.13	0.00	3.18
560	568	2.211250	AAAGCTGCCACACATCTGAT	57.789	45.000	0.00	0.00	0.00	2.90
647	655	1.896220	AAAGCTGGCACGAATCTCAA	58.104	45.000	0.00	0.00	0.00	3.02
730	740	1.028868	GCCCCTGACAGCAGATCAAC	61.029	60.000	0.00	0.00	45.17	3.18
732	742	1.678123	CCCCTGACAGCAGATCAACTG	60.678	57.143	12.12	12.12	45.17	3.16
784	802	2.100631	GTGCGGCGCATTGAGTAGT	61.101	57.895	38.43	0.00	41.91	2.73
793	811	0.249073	CATTGAGTAGTCCGGCGAGG	60.249	60.000	9.30	0.00	42.97	4.63
805	823	3.942601	GCGAGGGCCTTCTACTCT	58.057	61.111	7.89	0.00	0.00	3.24
928	948	1.699634	CCAACTTTCCTGACCTCCTCA	59.300	52.381	0.00	0.00	0.00	3.86
930	950	0.969894	ACTTTCCTGACCTCCTCACG	59.030	55.000	0.00	0.00	0.00	4.35
933	953	0.832135	TTCCTGACCTCCTCACGCTT	60.832	55.000	0.00	0.00	0.00	4.68
974	999	0.747644	CACCAGCCCACGCATCATTA	60.748	55.000	0.00	0.00	37.52	1.90
976	1001	1.650912	CAGCCCACGCATCATTAGC	59.349	57.895	0.00	0.00	37.52	3.09
984	1010	1.950216	ACGCATCATTAGCTCGAGAGA	59.050	47.619	18.75	5.54	39.12	3.10
1107	1148	4.357947	GCTGAGGTGTCGTGCGGA	62.358	66.667	0.00	0.00	0.00	5.54
1393	1436	0.249699	CACACCACTTGCGGAGTACA	60.250	55.000	0.00	0.00	36.65	2.90
1394	1437	0.249741	ACACCACTTGCGGAGTACAC	60.250	55.000	0.00	0.00	36.65	2.90
1395	1438	0.033504	CACCACTTGCGGAGTACACT	59.966	55.000	0.00	0.00	36.65	3.55
1396	1439	0.033504	ACCACTTGCGGAGTACACTG	59.966	55.000	0.00	0.00	36.65	3.66
1397	1440	1.291877	CCACTTGCGGAGTACACTGC	61.292	60.000	16.27	16.27	41.89	4.40
1400	1443	3.455152	TGCGGAGTACACTGCACT	58.545	55.556	21.05	0.00	45.49	4.40
1423	1489	3.686726	AGGAAAAATGCTAGCTCGTCAAG	59.313	43.478	17.23	0.00	0.00	3.02
1436	1502	3.759418	CTCGTCAAGCTCGTTGATTCTA	58.241	45.455	0.00	0.00	46.99	2.10
1514	1585	4.090588	GGGGCGAACCGATGGTGA	62.091	66.667	0.00	0.00	41.60	4.02
1515	1586	2.189521	GGGCGAACCGATGGTGAT	59.810	61.111	0.00	0.00	35.34	3.06
1516	1587	1.887707	GGGCGAACCGATGGTGATC	60.888	63.158	0.00	0.00	35.34	2.92
1541	1618	1.003839	GGGTGGCGTGAAGTGATGA	60.004	57.895	0.00	0.00	0.00	2.92
1572	1651	1.153349	GACGGAGGAGTTCATGGCC	60.153	63.158	0.00	0.00	0.00	5.36
1574	1653	2.190578	GGAGGAGTTCATGGCCGG	59.809	66.667	0.00	0.00	0.00	6.13
1575	1654	2.514824	GAGGAGTTCATGGCCGGC	60.515	66.667	21.18	21.18	0.00	6.13
1577	1656	2.825836	GGAGTTCATGGCCGGCTG	60.826	66.667	28.56	18.46	0.00	4.85
1580	1659	0.749454	GAGTTCATGGCCGGCTGAAT	60.749	55.000	27.74	18.62	34.18	2.57
1581	1660	0.546122	AGTTCATGGCCGGCTGAATA	59.454	50.000	27.74	9.68	34.18	1.75
1582	1661	1.064758	AGTTCATGGCCGGCTGAATAA	60.065	47.619	27.74	14.18	34.18	1.40
1583	1662	1.748493	GTTCATGGCCGGCTGAATAAA	59.252	47.619	27.74	13.23	34.18	1.40
1584	1663	2.362077	GTTCATGGCCGGCTGAATAAAT	59.638	45.455	27.74	9.33	34.18	1.40
1585	1664	3.500448	TCATGGCCGGCTGAATAAATA	57.500	42.857	28.56	0.00	0.00	1.40
1586	1665	3.411446	TCATGGCCGGCTGAATAAATAG	58.589	45.455	28.56	5.90	0.00	1.73
1612	4598	6.222389	ACTACTGTAGCTACGATACCTGTAG	58.778	44.000	18.74	19.14	41.75	2.74
1628	4614	3.315142	TAGTTCGCCTGCCCTGCTG	62.315	63.158	0.00	0.00	0.00	4.41
1634	4620	2.673523	CCTGCCCTGCTGCTACTT	59.326	61.111	0.00	0.00	0.00	2.24
1635	4621	1.451028	CCTGCCCTGCTGCTACTTC	60.451	63.158	0.00	0.00	0.00	3.01
1636	4622	1.297689	CTGCCCTGCTGCTACTTCA	59.702	57.895	0.00	0.00	0.00	3.02
1662	4648	9.277783	AGTAGTCATGCTTGAATAATAATGGTC	57.722	33.333	10.85	0.00	34.48	4.02
1686	4675	5.974300	TCAGTATTAATCTTTCGCATTCGC	58.026	37.500	0.00	0.00	35.26	4.70
1766	4881	3.551551	GAATTACCACAACTCGCACAAC	58.448	45.455	0.00	0.00	0.00	3.32
1819	4935	4.971830	GCGACACATCACATTCATATTTGG	59.028	41.667	0.00	0.00	0.00	3.28
1830	4968	2.004017	TCATATTTGGGCGTCGACAAC	58.996	47.619	17.16	6.70	0.00	3.32
1847	4985	2.577059	CGACATACGGCAGGTGGT	59.423	61.111	0.00	0.00	38.46	4.16
1849	4987	0.672401	CGACATACGGCAGGTGGTTT	60.672	55.000	0.00	0.00	38.46	3.27
1850	4988	0.802494	GACATACGGCAGGTGGTTTG	59.198	55.000	0.00	0.00	0.00	2.93
1851	4989	1.241315	ACATACGGCAGGTGGTTTGC	61.241	55.000	0.00	0.00	40.80	3.68
1871	5023	3.084579	CTAAGCGGCGCACTTCAG	58.915	61.111	35.02	17.93	0.00	3.02
2010	5307	3.862991	TTTGCCGGTGGTCGACCA	61.863	61.111	33.23	33.23	46.55	4.02
2018	5315	4.771127	TGGTCGACCACTTCTTGC	57.229	55.556	33.23	4.36	42.01	4.01
2020	5317	2.027625	GGTCGACCACTTCTTGCCG	61.028	63.158	29.75	0.00	35.64	5.69
2055	5361	0.264955	GAGAGGGGTGAGATGGGGTA	59.735	60.000	0.00	0.00	0.00	3.69
2058	5364	1.421646	GAGGGGTGAGATGGGGTAATG	59.578	57.143	0.00	0.00	0.00	1.90
2233	9285	3.504863	ACGTAAACTACAACGCGATCAT	58.495	40.909	15.93	0.00	42.74	2.45
2234	9286	3.545078	ACGTAAACTACAACGCGATCATC	59.455	43.478	15.93	0.00	42.74	2.92
2254	13975	3.101437	TCGCCTCTCAAACCCTAATACA	58.899	45.455	0.00	0.00	0.00	2.29
2260	13981	5.080969	TCTCAAACCCTAATACACCGAAG	57.919	43.478	0.00	0.00	0.00	3.79
2327	14048	2.647158	GCCGATCTATCCCCGTCCC	61.647	68.421	0.00	0.00	0.00	4.46
2332	14053	3.616721	CTATCCCCGTCCCCTGCG	61.617	72.222	0.00	0.00	0.00	5.18
2354	14075	2.682494	TCCACCTACTGGTCCGCC	60.682	66.667	0.00	0.00	46.60	6.13
2472	14193	4.020617	CGCTGAGGGCCAACTCCA	62.021	66.667	6.18	0.00	36.66	3.86

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
248	252	7.745620	ACAGAGTTTACTCATTCCGAAAAAT	57.254	32.000	12.10	0.00	45.21	1.82
418	424	8.088365	GGTTAACAGCTTATGAACCAAATTTCT	58.912	33.333	8.10	0.00	36.33	2.52
458	464	6.710692	AAGTAGTTGCATTTTATTTGCTGC	57.289	33.333	0.00	0.00	40.77	5.25
560	568	6.653020	AGACAAAGGAATACATCTGTGCATA	58.347	36.000	0.00	0.00	0.00	3.14
647	655	2.622942	TCTGCCGTTCAATTGCTTTCTT	59.377	40.909	0.00	0.00	0.00	2.52
713	723	1.277273	TCAGTTGATCTGCTGTCAGGG	59.723	52.381	13.87	0.00	43.32	4.45
714	724	2.619147	CTCAGTTGATCTGCTGTCAGG	58.381	52.381	13.87	0.00	43.32	3.86
715	725	2.001159	GCTCAGTTGATCTGCTGTCAG	58.999	52.381	13.87	0.00	43.32	3.51
718	728	0.689055	TGGCTCAGTTGATCTGCTGT	59.311	50.000	13.87	0.00	43.32	4.40
738	748	4.781959	CAACTGCAATGCCCGCCG	62.782	66.667	1.53	0.00	0.00	6.46
793	811	2.894765	GACCCTGATAGAGTAGAAGGCC	59.105	54.545	0.00	0.00	0.00	5.19
805	823	4.202388	GGCTTATTAAACCGGACCCTGATA	60.202	45.833	9.46	0.00	0.00	2.15
913	933	0.832135	AGCGTGAGGAGGTCAGGAAA	60.832	55.000	0.00	0.00	42.69	3.13
956	981	0.464373	CTAATGATGCGTGGGCTGGT	60.464	55.000	0.00	0.00	40.82	4.00
971	996	3.813166	GCACTCTACTCTCTCGAGCTAAT	59.187	47.826	7.81	0.00	41.09	1.73
974	999	1.065782	TGCACTCTACTCTCTCGAGCT	60.066	52.381	7.81	0.00	41.09	4.09
976	1001	1.330521	GCTGCACTCTACTCTCTCGAG	59.669	57.143	5.93	5.93	43.10	4.04
984	1010	0.174389	CCATCGTGCTGCACTCTACT	59.826	55.000	28.04	7.30	31.34	2.57
1008	1034	1.091771	CATTGGCCCTACGAGTGCTG	61.092	60.000	0.00	0.00	0.00	4.41
1393	1436	3.691609	GCTAGCATTTTTCCTAGTGCAGT	59.308	43.478	10.63	0.00	39.94	4.40
1394	1437	3.944015	AGCTAGCATTTTTCCTAGTGCAG	59.056	43.478	18.83	1.38	39.94	4.41
1395	1438	3.941483	GAGCTAGCATTTTTCCTAGTGCA	59.059	43.478	18.83	0.00	39.94	4.57
1396	1439	3.001736	CGAGCTAGCATTTTTCCTAGTGC	59.998	47.826	18.83	0.00	34.81	4.40
1397	1440	4.184629	ACGAGCTAGCATTTTTCCTAGTG	58.815	43.478	18.83	0.00	34.81	2.74
1398	1441	4.081642	TGACGAGCTAGCATTTTTCCTAGT	60.082	41.667	18.83	0.00	34.81	2.57
1399	1442	4.433615	TGACGAGCTAGCATTTTTCCTAG	58.566	43.478	18.83	0.00	35.31	3.02
1400	1443	4.465632	TGACGAGCTAGCATTTTTCCTA	57.534	40.909	18.83	0.00	0.00	2.94
1423	1489	1.333258	GCGCCATTAGAATCAACGAGC	60.333	52.381	0.00	0.00	0.00	5.03
1436	1502	3.802507	GCATGCAAATGCGCCATT	58.197	50.000	14.21	1.64	45.83	3.16
1459	1525	1.884464	CTGCGATAGTGCCATGCGT	60.884	57.895	0.00	0.00	39.35	5.24
1460	1526	2.601398	CCTGCGATAGTGCCATGCG	61.601	63.158	0.00	0.00	39.35	4.73
1551	1630	0.179134	CCATGAACTCCTCCGTCGAC	60.179	60.000	5.18	5.18	0.00	4.20
1572	1651	7.537991	GCTACAGTAGTACTATTTATTCAGCCG	59.462	40.741	5.75	0.00	0.00	5.52
1581	1660	9.213799	GGTATCGTAGCTACAGTAGTACTATTT	57.786	37.037	23.21	0.00	0.00	1.40
1582	1661	8.592809	AGGTATCGTAGCTACAGTAGTACTATT	58.407	37.037	23.21	0.00	34.21	1.73
1583	1662	8.034215	CAGGTATCGTAGCTACAGTAGTACTAT	58.966	40.741	23.21	9.74	34.67	2.12
1584	1663	7.014711	ACAGGTATCGTAGCTACAGTAGTACTA	59.985	40.741	23.21	0.00	34.67	1.82
1585	1664	6.183360	ACAGGTATCGTAGCTACAGTAGTACT	60.183	42.308	23.21	0.00	34.67	2.73
1586	1665	5.988561	ACAGGTATCGTAGCTACAGTAGTAC	59.011	44.000	23.21	15.53	34.67	2.73
1634	4620	9.276590	CCATTATTATTCAAGCATGACTACTGA	57.723	33.333	0.00	0.00	34.61	3.41
1635	4621	9.060347	ACCATTATTATTCAAGCATGACTACTG	57.940	33.333	0.00	0.00	34.61	2.74
1636	4622	9.277783	GACCATTATTATTCAAGCATGACTACT	57.722	33.333	0.00	0.00	34.61	2.57
1662	4648	6.067669	GCGAATGCGAAAGATTAATACTGAG	58.932	40.000	0.00	0.00	40.82	3.35
1766	4881	2.104622	ACTGTTTGGGGGAGCAAAATTG	59.895	45.455	0.00	0.00	0.00	2.32
1830	4968	0.672401	AAACCACCTGCCGTATGTCG	60.672	55.000	0.00	0.00	39.52	4.35
1851	4989	3.088500	GAAGTGCGCCGCTTAGCAG	62.089	63.158	11.67	0.00	44.70	4.24
1863	5015	5.048434	AGGAGATTTTTAGCAACTGAAGTGC	60.048	40.000	0.00	0.00	0.00	4.40
1871	5023	7.359514	GCATTTGTTCAGGAGATTTTTAGCAAC	60.360	37.037	0.00	0.00	0.00	4.17
2010	5307	2.750350	CTCCCACCGGCAAGAAGT	59.250	61.111	0.00	0.00	0.00	3.01
2011	5308	2.045926	CCTCCCACCGGCAAGAAG	60.046	66.667	0.00	0.00	0.00	2.85
2114	5420	2.279517	GCGTCGGCCAATCGATCT	60.280	61.111	13.94	0.00	41.40	2.75
2147	5454	1.081708	GTAACGCAAACGGCAAGGG	60.082	57.895	0.00	0.00	46.04	3.95
2203	9255	4.971830	CGTTGTAGTTTACGTCTTGAGACA	59.028	41.667	11.36	0.00	44.99	3.41
2233	9285	3.101437	TGTATTAGGGTTTGAGAGGCGA	58.899	45.455	0.00	0.00	0.00	5.54
2234	9286	3.195661	GTGTATTAGGGTTTGAGAGGCG	58.804	50.000	0.00	0.00	0.00	5.52
2237	9289	4.730949	TCGGTGTATTAGGGTTTGAGAG	57.269	45.455	0.00	0.00	0.00	3.20
2238	9290	4.529377	ACTTCGGTGTATTAGGGTTTGAGA	59.471	41.667	0.00	0.00	0.00	3.27

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.