AutoCloner

Multiple sequence alignment - TraesCS5D01G086100

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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	TraesCS5D01G086100	chr5D	100.000	3275	0	0	1	3275	91551701	91554975	0.000000e+00	6048.0
1	TraesCS5D01G086100	chr5D	88.435	147	14	2	2794	2940	528717285	528717428	1.210000e-39	174.0
2	TraesCS5D01G086100	chr5D	88.435	147	10	3	3122	3261	424787839	424787693	1.560000e-38	171.0
3	TraesCS5D01G086100	chr5D	95.238	42	2	0	665	706	91403257	91403298	2.110000e-07	67.6
4	TraesCS5D01G086100	chr5A	93.002	2015	85	18	540	2532	85254780	85256760	0.000000e+00	2889.0
5	TraesCS5D01G086100	chr5A	94.216	536	23	6	1	536	85178347	85178874	0.000000e+00	811.0
6	TraesCS5D01G086100	chr5A	88.462	182	14	2	2619	2793	85256880	85257061	2.560000e-51	213.0
7	TraesCS5D01G086100	chr5A	84.409	186	21	4	37	220	28435881	28436060	3.360000e-40	176.0
8	TraesCS5D01G086100	chr5B	93.865	1744	56	16	635	2367	96850330	96852033	0.000000e+00	2580.0
9	TraesCS5D01G086100	chr5B	97.359	871	12	4	2413	3275	96852047	96852914	0.000000e+00	1471.0
10	TraesCS5D01G086100	chr5B	95.468	684	25	6	1	680	96849665	96850346	0.000000e+00	1086.0
11	TraesCS5D01G086100	chr5B	88.435	147	14	2	2794	2940	665744476	665744619	1.210000e-39	174.0
12	TraesCS5D01G086100	chr7D	88.591	149	16	1	2794	2942	34757011	34756864	2.600000e-41	180.0
13	TraesCS5D01G086100	chr7D	87.013	154	17	3	2794	2947	436459770	436459620	1.560000e-38	171.0
14	TraesCS5D01G086100	chr7D	86.250	160	18	4	2784	2940	535326655	535326813	1.560000e-38	171.0
15	TraesCS5D01G086100	chr7D	83.673	147	16	4	3120	3258	475155619	475155473	7.370000e-27	132.0
16	TraesCS5D01G086100	chr4B	84.574	188	21	5	33	217	321280884	321281066	2.600000e-41	180.0
17	TraesCS5D01G086100	chr4B	84.146	164	20	5	37	197	424246868	424247028	1.570000e-33	154.0
18	TraesCS5D01G086100	chr2B	86.228	167	17	3	37	201	443416166	443416328	3.360000e-40	176.0
19	TraesCS5D01G086100	chr2B	100.000	29	0	0	2002	2030	632989201	632989229	2.000000e-03	54.7
20	TraesCS5D01G086100	chr1B	87.662	154	16	3	2788	2940	632021078	632020927	3.360000e-40	176.0
21	TraesCS5D01G086100	chr3A	87.417	151	18	1	2794	2944	582283222	582283371	4.340000e-39	172.0
22	TraesCS5D01G086100	chr3D	86.335	161	17	4	2783	2939	315480419	315480578	1.560000e-38	171.0
23	TraesCS5D01G086100	chr4A	85.616	146	15	3	37	180	227972180	227972321	7.320000e-32	148.0
24	TraesCS5D01G086100	chr4A	82.927	164	22	3	39	201	209746990	209747148	3.410000e-30	143.0
25	TraesCS5D01G086100	chr2D	81.522	184	26	6	17	197	477376159	477376337	9.470000e-31	145.0
26	TraesCS5D01G086100	chr2D	100.000	29	0	0	2002	2030	533166294	533166322	2.000000e-03	54.7
27	TraesCS5D01G086100	chrUn	87.500	112	5	2	3122	3226	42246236	42246345	1.600000e-23	121.0
28	TraesCS5D01G086100	chr2A	92.500	40	3	0	1991	2030	677547133	677547172	1.270000e-04	58.4

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	TraesCS5D01G086100	chr5D	91551701	91554975	3274	False	6048.000000	6048	100.000	1	3275	1	chr5D.!!$F2	3274
1	TraesCS5D01G086100	chr5A	85254780	85257061	2281	False	1551.000000	2889	90.732	540	2793	2	chr5A.!!$F3	2253
2	TraesCS5D01G086100	chr5A	85178347	85178874	527	False	811.000000	811	94.216	1	536	1	chr5A.!!$F2	535
3	TraesCS5D01G086100	chr5B	96849665	96852914	3249	False	1712.333333	2580	95.564	1	3275	3	chr5B.!!$F2	3274

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
935	979	0.461548	TCGCAATCCTCTCTCGCATT	59.538	50.0	0.0	0.0	0.0	3.56	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2394	2466	0.181114	TGTCTCAACTGCCTTGCACT	59.819	50.0	0.0	0.0	33.79	4.4	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
92	93	1.600636	CCTCGTTTGCCCTCAAGCA	60.601	57.895	0.00	0.00	42.17	3.91
342	344	9.511144	GTATACAAAAACATAACTTACCATGGC	57.489	33.333	13.04	0.00	0.00	4.40
468	471	8.490311	TCATGTTTTAGAAACCCAAAAATCCTT	58.510	29.630	0.00	0.00	0.00	3.36
536	539	5.295431	TGATATATAAACTTGCCATGCGC	57.705	39.130	0.00	0.00	38.31	6.09
537	540	2.686558	ATATAAACTTGCCATGCGCG	57.313	45.000	0.00	0.00	42.08	6.86
538	541	0.660488	TATAAACTTGCCATGCGCGG	59.340	50.000	8.83	0.00	42.08	6.46
562	565	7.570324	CGGCGTTGGAAAATTCATAAAATTGTT	60.570	33.333	0.00	0.00	0.00	2.83
648	653	6.071952	CCATGACAATTAACTATATGTGGGCC	60.072	42.308	0.00	0.00	0.00	5.80
661	666	1.001393	TGGGCCGCTTCCCTAAAAG	60.001	57.895	10.91	0.00	46.67	2.27
698	732	1.786937	CAGCATCTCCTAGTCCTGGT	58.213	55.000	0.00	0.00	0.00	4.00
709	743	4.540906	TCCTAGTCCTGGTCTTTAGACTCT	59.459	45.833	9.56	4.42	44.20	3.24
729	769	1.001269	AAAAACCTAGCCGGCCTCC	60.001	57.895	26.15	0.00	35.61	4.30
730	770	1.498176	AAAAACCTAGCCGGCCTCCT	61.498	55.000	26.15	7.06	35.61	3.69
733	773	1.946063	AACCTAGCCGGCCTCCTCTA	61.946	60.000	26.15	6.75	35.61	2.43
735	775	0.759436	CCTAGCCGGCCTCCTCTAAA	60.759	60.000	26.15	0.00	0.00	1.85
736	776	1.120530	CTAGCCGGCCTCCTCTAAAA	58.879	55.000	26.15	0.00	0.00	1.52
737	777	1.485066	CTAGCCGGCCTCCTCTAAAAA	59.515	52.381	26.15	0.00	0.00	1.94
861	905	4.530857	CCGCCCACCTCGACCATC	62.531	72.222	0.00	0.00	0.00	3.51
862	906	3.461773	CGCCCACCTCGACCATCT	61.462	66.667	0.00	0.00	0.00	2.90
863	907	2.501610	GCCCACCTCGACCATCTC	59.498	66.667	0.00	0.00	0.00	2.75
864	908	3.095347	GCCCACCTCGACCATCTCC	62.095	68.421	0.00	0.00	0.00	3.71
865	909	2.786495	CCCACCTCGACCATCTCCG	61.786	68.421	0.00	0.00	0.00	4.63
866	910	2.105128	CACCTCGACCATCTCCGC	59.895	66.667	0.00	0.00	0.00	5.54
867	911	3.148279	ACCTCGACCATCTCCGCC	61.148	66.667	0.00	0.00	0.00	6.13
868	912	3.917760	CCTCGACCATCTCCGCCC	61.918	72.222	0.00	0.00	0.00	6.13
869	913	3.147595	CTCGACCATCTCCGCCCA	61.148	66.667	0.00	0.00	0.00	5.36
870	914	3.432051	CTCGACCATCTCCGCCCAC	62.432	68.421	0.00	0.00	0.00	4.61
871	915	4.530857	CGACCATCTCCGCCCACC	62.531	72.222	0.00	0.00	0.00	4.61
872	916	3.083997	GACCATCTCCGCCCACCT	61.084	66.667	0.00	0.00	0.00	4.00
873	917	3.083997	ACCATCTCCGCCCACCTC	61.084	66.667	0.00	0.00	0.00	3.85
874	918	4.227134	CCATCTCCGCCCACCTCG	62.227	72.222	0.00	0.00	0.00	4.63
875	919	3.147595	CATCTCCGCCCACCTCGA	61.148	66.667	0.00	0.00	0.00	4.04
876	920	3.148279	ATCTCCGCCCACCTCGAC	61.148	66.667	0.00	0.00	0.00	4.20
921	965	1.380515	CCCCTCTCTCTCCTCGCAA	60.381	63.158	0.00	0.00	0.00	4.85
925	969	1.691196	CTCTCTCTCCTCGCAATCCT	58.309	55.000	0.00	0.00	0.00	3.24
935	979	0.461548	TCGCAATCCTCTCTCGCATT	59.538	50.000	0.00	0.00	0.00	3.56
942	986	0.883814	CCTCTCTCGCATTGCATCCC	60.884	60.000	9.69	0.00	0.00	3.85
1142	1189	0.397816	CTCATCGAAGACCCCCTCCT	60.398	60.000	0.00	0.00	42.51	3.69
1152	1199	2.586792	CCCCTCCTCCGCAAGAAG	59.413	66.667	0.00	0.00	43.02	2.85
1383	1430	5.104527	GCCATATGACCTATTGGGCTATGTA	60.105	44.000	3.65	0.00	43.49	2.29
1564	1614	2.408565	TGGTGAAGTTTGAGGAGGAGT	58.591	47.619	0.00	0.00	0.00	3.85
1593	1643	5.181433	GGTTGGTCATGATGATGATGATGAG	59.819	44.000	0.00	0.00	40.78	2.90
1597	1647	5.179533	GTCATGATGATGATGATGAGGAGG	58.820	45.833	0.00	0.00	40.78	4.30
1598	1648	5.046520	GTCATGATGATGATGATGAGGAGGA	60.047	44.000	0.00	0.00	40.78	3.71
1599	1649	5.187967	TCATGATGATGATGATGAGGAGGAG	59.812	44.000	0.00	0.00	33.40	3.69
1600	1650	3.838903	TGATGATGATGATGAGGAGGAGG	59.161	47.826	0.00	0.00	0.00	4.30
1601	1651	3.625252	TGATGATGATGAGGAGGAGGA	57.375	47.619	0.00	0.00	0.00	3.71
1602	1652	3.508426	TGATGATGATGAGGAGGAGGAG	58.492	50.000	0.00	0.00	0.00	3.69
1603	1653	2.395336	TGATGATGAGGAGGAGGAGG	57.605	55.000	0.00	0.00	0.00	4.30
1604	1654	1.862242	TGATGATGAGGAGGAGGAGGA	59.138	52.381	0.00	0.00	0.00	3.71
1605	1655	2.158340	TGATGATGAGGAGGAGGAGGAG	60.158	54.545	0.00	0.00	0.00	3.69
1606	1656	0.560193	TGATGAGGAGGAGGAGGAGG	59.440	60.000	0.00	0.00	0.00	4.30
1607	1657	0.178935	GATGAGGAGGAGGAGGAGGG	60.179	65.000	0.00	0.00	0.00	4.30
1608	1658	2.123033	GAGGAGGAGGAGGAGGGC	60.123	72.222	0.00	0.00	0.00	5.19
1611	1661	2.200092	GAGGAGGAGGAGGGCGAT	59.800	66.667	0.00	0.00	0.00	4.58
1711	1782	2.158475	TGGAGTCAAATCCAAAGTGGCT	60.158	45.455	0.00	0.00	46.45	4.75
1740	1811	2.026641	CATGATTTGGAAGGATGGCGT	58.973	47.619	0.00	0.00	0.00	5.68
1845	1916	0.956633	CTGCTGTTGACATGCAAGGT	59.043	50.000	0.00	0.00	37.12	3.50
1852	1923	2.049888	TGACATGCAAGGTGTGACAA	57.950	45.000	0.00	0.00	0.00	3.18
2260	2331	2.738521	CCGAGTCACCGGCACTTG	60.739	66.667	0.00	7.96	43.25	3.16
2386	2458	7.020827	TGTATCCTTCTCATTCTTTTGGTCT	57.979	36.000	0.00	0.00	0.00	3.85
2480	2552	5.929058	TGCCCAAGTTGCATATAATTTCA	57.071	34.783	0.00	0.00	32.85	2.69
2486	2558	9.868277	CCCAAGTTGCATATAATTTCAAAGTTA	57.132	29.630	0.00	0.00	0.00	2.24
2522	2594	5.012239	TCAAATGCTGCCTTTTATGTCTCT	58.988	37.500	0.00	0.00	0.00	3.10
2559	2695	6.973474	CGTACATAGTACCTTCCTTTTGAGAG	59.027	42.308	2.06	0.00	0.00	3.20
2628	2764	9.881649	CATATCTTCTATAGCATGGTGTATGTT	57.118	33.333	7.89	0.00	39.08	2.71
3112	3256	9.869844	CTTGACAACATTGTAAAAGTTCTAGAG	57.130	33.333	0.00	0.00	42.43	2.43
3166	3310	4.061596	CCGCTCCCAGAAATCTAAGAATC	58.938	47.826	0.00	0.00	0.00	2.52
3167	3311	4.202305	CCGCTCCCAGAAATCTAAGAATCT	60.202	45.833	0.00	0.00	0.00	2.40
3180	3324	5.580998	TCTAAGAATCTGTGGAGTACCTGT	58.419	41.667	0.00	0.00	37.04	4.00
3185	3329	2.815158	TCTGTGGAGTACCTGTATGCA	58.185	47.619	0.00	0.00	37.04	3.96

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
23	24	7.498900	TCCATTTTGCATCACGATATCTTACTT	59.501	33.333	0.34	0.00	0.00	2.24
35	36	4.614555	TGATACGTCCATTTTGCATCAC	57.385	40.909	0.00	0.00	0.00	3.06
92	93	6.018180	GGTCATATTTATCGAGTTCGGCTTTT	60.018	38.462	1.26	0.00	40.29	2.27
93	94	5.465724	GGTCATATTTATCGAGTTCGGCTTT	59.534	40.000	1.26	0.00	40.29	3.51
136	138	6.498304	TCGTATTTAGTTTATCGACACCTCC	58.502	40.000	0.00	0.00	0.00	4.30
465	468	5.247507	TGTTCACATGTCAAGTTTCAAGG	57.752	39.130	0.00	0.00	0.00	3.61
468	471	7.326968	TGTAATGTTCACATGTCAAGTTTCA	57.673	32.000	0.00	0.00	36.56	2.69
536	539	6.128688	ACAATTTTATGAATTTTCCAACGCCG	60.129	34.615	0.00	0.00	0.00	6.46
537	540	7.127917	ACAATTTTATGAATTTTCCAACGCC	57.872	32.000	0.00	0.00	0.00	5.68
610	614	6.971726	AATTGTCATGGCAGATCATAACAT	57.028	33.333	0.00	0.00	26.68	2.71
611	615	7.557358	AGTTAATTGTCATGGCAGATCATAACA	59.443	33.333	17.25	0.85	0.00	2.41
648	653	7.254795	CCACATATAGTTTCTTTTAGGGAAGCG	60.255	40.741	0.00	0.00	0.00	4.68
661	666	2.291741	GCTGCAGCCCACATATAGTTTC	59.708	50.000	28.76	0.00	34.31	2.78
735	775	6.930722	CCTGGAAACAACAGAATAGCATTTTT	59.069	34.615	0.00	0.00	42.06	1.94
736	776	6.458210	CCTGGAAACAACAGAATAGCATTTT	58.542	36.000	0.00	0.00	42.06	1.82
737	777	5.567423	GCCTGGAAACAACAGAATAGCATTT	60.567	40.000	0.00	0.00	42.06	2.32
744	788	2.158475	TGGAGCCTGGAAACAACAGAAT	60.158	45.455	0.00	0.00	42.06	2.40
863	907	4.530857	GATGGTCGAGGTGGGCGG	62.531	72.222	0.00	0.00	0.00	6.13
864	908	3.432051	GAGATGGTCGAGGTGGGCG	62.432	68.421	0.00	0.00	0.00	6.13
865	909	2.501610	GAGATGGTCGAGGTGGGC	59.498	66.667	0.00	0.00	0.00	5.36
866	910	1.381872	AGGAGATGGTCGAGGTGGG	60.382	63.158	0.00	0.00	0.00	4.61
867	911	1.819229	CAGGAGATGGTCGAGGTGG	59.181	63.158	0.00	0.00	0.00	4.61
868	912	1.142748	GCAGGAGATGGTCGAGGTG	59.857	63.158	0.00	0.00	0.00	4.00
869	913	2.418910	CGCAGGAGATGGTCGAGGT	61.419	63.158	0.00	0.00	0.00	3.85
870	914	2.415010	CGCAGGAGATGGTCGAGG	59.585	66.667	0.00	0.00	0.00	4.63
909	953	1.214175	AGAGAGGATTGCGAGGAGAGA	59.786	52.381	0.00	0.00	0.00	3.10
921	965	1.270732	GGATGCAATGCGAGAGAGGAT	60.271	52.381	0.00	0.00	0.00	3.24
925	969	1.146930	GGGGATGCAATGCGAGAGA	59.853	57.895	0.00	0.00	34.31	3.10
935	979	1.550524	GTAGCGATATCAGGGGATGCA	59.449	52.381	3.12	0.00	34.89	3.96
1031	1078	0.614979	CAAGGAGTCTTCGGGGAGGA	60.615	60.000	0.00	0.00	0.00	3.71
1134	1181	3.009115	TTCTTGCGGAGGAGGGGG	61.009	66.667	0.00	0.00	0.00	5.40
1152	1199	0.323451	CTTGTAGGGTTTGGGGGAGC	60.323	60.000	0.00	0.00	0.00	4.70
1383	1430	2.123897	GTGGTGGGGTTGCACACT	60.124	61.111	5.30	0.00	37.72	3.55
1564	1614	5.434182	TCATCATCATGACCAACCACTAA	57.566	39.130	0.00	0.00	33.80	2.24
1593	1643	3.460478	ATCGCCCTCCTCCTCCTCC	62.460	68.421	0.00	0.00	0.00	4.30
1597	1647	2.206536	CCTCATCGCCCTCCTCCTC	61.207	68.421	0.00	0.00	0.00	3.71
1598	1648	2.123077	CCTCATCGCCCTCCTCCT	60.123	66.667	0.00	0.00	0.00	3.69
1599	1649	2.123251	TCCTCATCGCCCTCCTCC	60.123	66.667	0.00	0.00	0.00	4.30
1600	1650	2.206536	CCTCCTCATCGCCCTCCTC	61.207	68.421	0.00	0.00	0.00	3.71
1601	1651	2.123077	CCTCCTCATCGCCCTCCT	60.123	66.667	0.00	0.00	0.00	3.69
1602	1652	2.123251	TCCTCCTCATCGCCCTCC	60.123	66.667	0.00	0.00	0.00	4.30
1603	1653	2.206536	CCTCCTCCTCATCGCCCTC	61.207	68.421	0.00	0.00	0.00	4.30
1604	1654	2.123077	CCTCCTCCTCATCGCCCT	60.123	66.667	0.00	0.00	0.00	5.19
1605	1655	2.123251	TCCTCCTCCTCATCGCCC	60.123	66.667	0.00	0.00	0.00	6.13
1606	1656	1.045911	AACTCCTCCTCCTCATCGCC	61.046	60.000	0.00	0.00	0.00	5.54
1607	1657	0.103937	CAACTCCTCCTCCTCATCGC	59.896	60.000	0.00	0.00	0.00	4.58
1608	1658	1.407258	GACAACTCCTCCTCCTCATCG	59.593	57.143	0.00	0.00	0.00	3.84
1611	1661	0.252284	GGGACAACTCCTCCTCCTCA	60.252	60.000	0.00	0.00	36.68	3.86
1711	1782	3.258872	CCTTCCAAATCATGCTTGTTCCA	59.741	43.478	0.00	0.00	0.00	3.53
1845	1916	4.042062	ACTGGGATGATCTTTCTTGTCACA	59.958	41.667	0.00	0.00	0.00	3.58
1852	1923	1.134280	CGGCACTGGGATGATCTTTCT	60.134	52.381	0.00	0.00	0.00	2.52
2329	2401	6.664816	CCAACCATGGGCATAATATATCACTT	59.335	38.462	18.09	0.00	43.51	3.16
2386	2458	5.800296	TCAACTGCCTTGCACTATTACTTA	58.200	37.500	0.00	0.00	33.79	2.24
2394	2466	0.181114	TGTCTCAACTGCCTTGCACT	59.819	50.000	0.00	0.00	33.79	4.40
2480	2552	8.764287	GCATTTGAAGCATTAACACTTAACTTT	58.236	29.630	0.00	0.00	0.00	2.66
2486	2558	4.687483	GCAGCATTTGAAGCATTAACACTT	59.313	37.500	0.00	0.00	0.00	3.16
2559	2695	7.881775	ATAAACATAATCAGGACCAAGTTCC	57.118	36.000	0.00	0.00	35.66	3.62
3112	3256	4.989168	CCGAACAGCTCCTTAATACCATAC	59.011	45.833	0.00	0.00	0.00	2.39
3166	3310	2.735444	CGTGCATACAGGTACTCCACAG	60.735	54.545	0.00	0.00	34.60	3.66
3167	3311	1.203758	CGTGCATACAGGTACTCCACA	59.796	52.381	0.00	0.00	34.60	4.17
3180	3324	4.215399	AGTTTCAGCTAAAAAGCGTGCATA	59.785	37.500	0.00	0.00	40.27	3.14
3185	3329	2.223377	CGGAGTTTCAGCTAAAAAGCGT	59.777	45.455	0.00	0.00	40.27	5.07
3249	3400	1.749063	GCATTGTTACAGTTAGGGCCC	59.251	52.381	16.46	16.46	0.00	5.80

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.