AutoCloner

Multiple sequence alignment - TraesCS1B01G122100

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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	TraesCS1B01G122100	chr1B	100.000	3332	0	0	1	3332	145717217	145720548	0.000000e+00	6154
1	TraesCS1B01G122100	chr1B	100.000	447	0	0	3685	4131	145720901	145721347	0.000000e+00	826
2	TraesCS1B01G122100	chr1B	78.756	579	99	22	56	623	469945843	469946408	2.350000e-97	366
3	TraesCS1B01G122100	chr1B	80.972	247	35	11	1	238	469945542	469945785	7.050000e-43	185
4	TraesCS1B01G122100	chr1A	98.048	1588	20	6	1722	3302	87199015	87200598	0.000000e+00	2750
5	TraesCS1B01G122100	chr1A	96.570	962	24	5	728	1683	87198057	87199015	0.000000e+00	1585
6	TraesCS1B01G122100	chr1A	97.528	445	11	0	3685	4129	87200614	87201058	0.000000e+00	761
7	TraesCS1B01G122100	chr1D	97.732	1587	33	2	1723	3309	91231507	91233090	0.000000e+00	2728
8	TraesCS1B01G122100	chr1D	97.694	1084	24	1	626	1709	91230439	91231521	0.000000e+00	1862
9	TraesCS1B01G122100	chr1D	97.763	447	10	0	3685	4131	91233107	91233553	0.000000e+00	771
10	TraesCS1B01G122100	chr6D	91.707	627	48	2	1	625	53612317	53611693	0.000000e+00	867
11	TraesCS1B01G122100	chr3D	91.626	621	43	5	8	626	436230882	436230269	0.000000e+00	850
12	TraesCS1B01G122100	chr4B	90.143	629	45	8	1	626	115392387	115393001	0.000000e+00	802
13	TraesCS1B01G122100	chr5B	80.885	633	90	20	1	625	487910795	487910186	1.740000e-128	470
14	TraesCS1B01G122100	chr5B	78.045	583	102	22	56	623	710491937	710492508	1.100000e-90	344
15	TraesCS1B01G122100	chr5D	78.905	621	88	32	18	625	406834120	406833530	8.380000e-102	381
16	TraesCS1B01G122100	chr3B	75.920	652	96	34	16	625	789481243	789480611	1.130000e-70	278
17	TraesCS1B01G122100	chr3B	79.699	266	42	12	8	263	119417433	119417170	9.120000e-42	182
18	TraesCS1B01G122100	chrUn	75.688	654	96	34	16	625	41739976	41739342	6.810000e-68	268
19	TraesCS1B01G122100	chrUn	75.665	489	77	22	1	477	102841124	102840666	5.410000e-49	206
20	TraesCS1B01G122100	chr7B	85.772	246	24	9	1	238	28633038	28632796	2.470000e-62	250
21	TraesCS1B01G122100	chr5A	84.082	245	31	7	1	239	69316354	69316596	3.210000e-56	230
22	TraesCS1B01G122100	chr6B	83.740	246	28	10	1	238	516559200	516558959	5.370000e-54	222

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	TraesCS1B01G122100	chr1B	145717217	145721347	4130	False	3490.000000	6154	100.000000	1	4131	2	chr1B.!!$F1	4130
1	TraesCS1B01G122100	chr1B	469945542	469946408	866	False	275.500000	366	79.864000	1	623	2	chr1B.!!$F2	622
2	TraesCS1B01G122100	chr1A	87198057	87201058	3001	False	1698.666667	2750	97.382000	728	4129	3	chr1A.!!$F1	3401
3	TraesCS1B01G122100	chr1D	91230439	91233553	3114	False	1787.000000	2728	97.729667	626	4131	3	chr1D.!!$F1	3505
4	TraesCS1B01G122100	chr6D	53611693	53612317	624	True	867.000000	867	91.707000	1	625	1	chr6D.!!$R1	624
5	TraesCS1B01G122100	chr3D	436230269	436230882	613	True	850.000000	850	91.626000	8	626	1	chr3D.!!$R1	618
6	TraesCS1B01G122100	chr4B	115392387	115393001	614	False	802.000000	802	90.143000	1	626	1	chr4B.!!$F1	625
7	TraesCS1B01G122100	chr5B	487910186	487910795	609	True	470.000000	470	80.885000	1	625	1	chr5B.!!$R1	624
8	TraesCS1B01G122100	chr5B	710491937	710492508	571	False	344.000000	344	78.045000	56	623	1	chr5B.!!$F1	567
9	TraesCS1B01G122100	chr5D	406833530	406834120	590	True	381.000000	381	78.905000	18	625	1	chr5D.!!$R1	607
10	TraesCS1B01G122100	chr3B	789480611	789481243	632	True	278.000000	278	75.920000	16	625	1	chr3B.!!$R2	609
11	TraesCS1B01G122100	chrUn	41739342	41739976	634	True	268.000000	268	75.688000	16	625	1	chrUn.!!$R1	609

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	Hairpin	End Stability	Orientation
630	1062	1.112113	GAACAGGAGCTCCCGACATA	58.888	55.0	29.54	40.87	2.29	F
1524	1961	0.324943	CCGACTGGGACTGGTTCATT	59.675	55.0	0.00	38.47	2.57	F
1717	2154	0.885879	ACATCCTCTAACACGCGTCA	59.114	50.0	9.86	0.00	4.35	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1698	2135	0.885879	TGACGCGTGTTAGAGGATGT	59.114	50.000	20.7	0.00	3.06	R
2867	3312	0.746659	GCAAAAGGCTGTCCACTGTT	59.253	50.000	0.0	40.25	3.16	R
3309	3754	1.975680	GCCGATATTAAGGGTGGGAGA	59.024	52.381	0.0	0.00	3.71	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
53	178	8.783833	TGAACTTTTTCAAATTCAATGAACCA	57.216	26.923	0.00	0.00	38.87	3.67
73	220	8.084073	TGAACCATTTTCAAATCTGATGAACTC	58.916	33.333	0.00	0.00	36.57	3.01
74	221	7.771927	ACCATTTTCAAATCTGATGAACTCT	57.228	32.000	0.00	0.00	36.57	3.24
75	222	8.186709	ACCATTTTCAAATCTGATGAACTCTT	57.813	30.769	0.00	0.00	36.57	2.85
76	223	8.645110	ACCATTTTCAAATCTGATGAACTCTTT	58.355	29.630	0.00	0.00	36.57	2.52
77	224	9.485206	CCATTTTCAAATCTGATGAACTCTTTT	57.515	29.630	0.00	0.00	36.57	2.27
82	229	9.520204	TTCAAATCTGATGAACTCTTTTCAAAC	57.480	29.630	0.00	0.00	32.10	2.93
83	230	8.137437	TCAAATCTGATGAACTCTTTTCAAACC	58.863	33.333	0.00	0.00	31.55	3.27
84	231	6.581171	ATCTGATGAACTCTTTTCAAACCC	57.419	37.500	0.00	0.00	31.55	4.11
85	232	4.515191	TCTGATGAACTCTTTTCAAACCCG	59.485	41.667	0.00	0.00	31.55	5.28
86	233	4.456535	TGATGAACTCTTTTCAAACCCGA	58.543	39.130	0.00	0.00	31.55	5.14
87	234	5.070001	TGATGAACTCTTTTCAAACCCGAT	58.930	37.500	0.00	0.00	31.55	4.18
88	235	4.829064	TGAACTCTTTTCAAACCCGATG	57.171	40.909	0.00	0.00	0.00	3.84
89	236	4.456535	TGAACTCTTTTCAAACCCGATGA	58.543	39.130	0.00	0.00	0.00	2.92
90	237	4.884744	TGAACTCTTTTCAAACCCGATGAA	59.115	37.500	0.00	0.00	35.11	2.57
91	238	4.830826	ACTCTTTTCAAACCCGATGAAC	57.169	40.909	0.00	0.00	36.57	3.18
92	239	4.461198	ACTCTTTTCAAACCCGATGAACT	58.539	39.130	0.00	0.00	36.57	3.01
169	319	6.801862	GGTGAACTAATTTTCAAACTCGATGG	59.198	38.462	0.00	0.00	37.24	3.51
323	721	8.632679	TCTTCTAAAATGATGAACTTTTGCTGT	58.367	29.630	0.00	0.00	0.00	4.40
330	728	5.964758	TGATGAACTTTTGCTGTGAAGTTT	58.035	33.333	3.35	0.00	43.88	2.66
367	768	7.584847	TCGATTTCACGTTTAAACAAATCTGAC	59.415	33.333	25.00	11.47	31.73	3.51
438	867	2.880890	AGCAAAGCACAAGTCTTCGATT	59.119	40.909	0.00	0.00	0.00	3.34
626	1058	3.068691	CCGAACAGGAGCTCCCGA	61.069	66.667	29.54	0.00	45.00	5.14
627	1059	2.182030	CGAACAGGAGCTCCCGAC	59.818	66.667	29.54	16.60	40.87	4.79
628	1060	2.636412	CGAACAGGAGCTCCCGACA	61.636	63.158	29.54	0.00	40.87	4.35
629	1061	1.901085	GAACAGGAGCTCCCGACAT	59.099	57.895	29.54	11.39	40.87	3.06
630	1062	1.112113	GAACAGGAGCTCCCGACATA	58.888	55.000	29.54	0.00	40.87	2.29
631	1063	1.689273	GAACAGGAGCTCCCGACATAT	59.311	52.381	29.54	5.79	40.87	1.78
632	1064	1.794714	ACAGGAGCTCCCGACATATT	58.205	50.000	29.54	4.94	40.87	1.28
633	1065	2.958818	ACAGGAGCTCCCGACATATTA	58.041	47.619	29.54	0.00	40.87	0.98
791	1228	1.142748	CAGATGGCGAGGTCTGGTC	59.857	63.158	0.00	0.00	38.50	4.02
815	1252	2.608261	CCAGTCACTTCTCCGACAACTC	60.608	54.545	0.00	0.00	34.48	3.01
828	1265	4.309950	AACTCCCACCGACACGCC	62.310	66.667	0.00	0.00	0.00	5.68
1369	1806	3.650950	GGGACCTTGCTGCTGGGA	61.651	66.667	15.84	0.00	0.00	4.37
1374	1811	2.124819	CTTGCTGCTGGGATCGCT	60.125	61.111	11.46	0.00	0.00	4.93
1524	1961	0.324943	CCGACTGGGACTGGTTCATT	59.675	55.000	0.00	0.00	38.47	2.57
1602	2039	3.585862	TGTCTTCGTACTCATGGCTTTC	58.414	45.455	0.00	0.00	0.00	2.62
1698	2135	5.538849	TTCGGCAGGTACATGTTCATATA	57.461	39.130	2.30	0.00	0.00	0.86
1699	2136	4.878439	TCGGCAGGTACATGTTCATATAC	58.122	43.478	2.30	0.00	0.00	1.47
1700	2137	4.342665	TCGGCAGGTACATGTTCATATACA	59.657	41.667	2.30	0.00	0.00	2.29
1701	2138	5.011635	TCGGCAGGTACATGTTCATATACAT	59.988	40.000	2.30	0.00	39.27	2.29
1702	2139	5.348724	CGGCAGGTACATGTTCATATACATC	59.651	44.000	2.30	0.00	36.64	3.06
1703	2140	5.643777	GGCAGGTACATGTTCATATACATCC	59.356	44.000	2.30	0.00	36.64	3.51
1704	2141	6.467677	GCAGGTACATGTTCATATACATCCT	58.532	40.000	2.30	0.00	36.64	3.24
1705	2142	6.591834	GCAGGTACATGTTCATATACATCCTC	59.408	42.308	2.30	0.00	36.64	3.71
1706	2143	7.526192	GCAGGTACATGTTCATATACATCCTCT	60.526	40.741	2.30	0.00	36.64	3.69
1707	2144	9.025041	CAGGTACATGTTCATATACATCCTCTA	57.975	37.037	2.30	0.00	36.64	2.43
1708	2145	9.601810	AGGTACATGTTCATATACATCCTCTAA	57.398	33.333	2.30	0.00	36.64	2.10
1709	2146	9.640963	GGTACATGTTCATATACATCCTCTAAC	57.359	37.037	2.30	0.00	36.64	2.34
1712	2149	7.867909	ACATGTTCATATACATCCTCTAACACG	59.132	37.037	0.00	0.00	36.64	4.49
1713	2150	6.213677	TGTTCATATACATCCTCTAACACGC	58.786	40.000	0.00	0.00	0.00	5.34
1714	2151	5.043189	TCATATACATCCTCTAACACGCG	57.957	43.478	3.53	3.53	0.00	6.01
1715	2152	4.517832	TCATATACATCCTCTAACACGCGT	59.482	41.667	5.58	5.58	0.00	6.01
1716	2153	2.838386	TACATCCTCTAACACGCGTC	57.162	50.000	9.86	0.00	0.00	5.19
1717	2154	0.885879	ACATCCTCTAACACGCGTCA	59.114	50.000	9.86	0.00	0.00	4.35
1718	2155	1.271379	ACATCCTCTAACACGCGTCAA	59.729	47.619	9.86	0.00	0.00	3.18
1719	2156	2.288579	ACATCCTCTAACACGCGTCAAA	60.289	45.455	9.86	0.00	0.00	2.69
1720	2157	2.512485	TCCTCTAACACGCGTCAAAA	57.488	45.000	9.86	0.00	0.00	2.44
1721	2158	2.823984	TCCTCTAACACGCGTCAAAAA	58.176	42.857	9.86	0.00	0.00	1.94
1780	2217	4.466567	TCATGTTGAATTGTGTCACGAC	57.533	40.909	0.00	0.00	0.00	4.34
2353	2797	4.837093	TTGGACGGAAAGAGTATGGATT	57.163	40.909	0.00	0.00	0.00	3.01
2387	2832	2.749621	AGAGAATTTTAGCAGCCAACGG	59.250	45.455	0.00	0.00	0.00	4.44
2422	2867	7.617041	AATAAAACTACTCACTTGCAGATCC	57.383	36.000	0.00	0.00	0.00	3.36
2567	3012	9.635520	ATTGTTCTCTGCTCTGATTTAATTTTG	57.364	29.630	0.00	0.00	0.00	2.44
2841	3286	2.155279	GACAGAGCCCCTTTTTCTCAC	58.845	52.381	0.00	0.00	0.00	3.51
2867	3312	5.939447	TGGCACATTATGATAAGATGGTGA	58.061	37.500	0.00	0.00	0.00	4.02
3071	3516	2.224606	CTCAAGCCTTGAAGTTGCAGA	58.775	47.619	8.74	0.00	39.58	4.26
3288	3733	3.672867	GCATATCGAGTGCTCTTTCTAGC	59.327	47.826	15.93	0.00	43.08	3.42
3289	3734	2.483583	ATCGAGTGCTCTTTCTAGCG	57.516	50.000	0.00	0.00	45.85	4.26
3292	3737	3.801129	GTGCTCTTTCTAGCGCCC	58.199	61.111	2.29	0.00	45.26	6.13
3293	3738	1.815840	GTGCTCTTTCTAGCGCCCC	60.816	63.158	2.29	0.00	45.26	5.80
3294	3739	2.203084	GCTCTTTCTAGCGCCCCC	60.203	66.667	2.29	0.00	31.76	5.40
3326	3771	2.913617	CCCCTCTCCCACCCTTAATATC	59.086	54.545	0.00	0.00	0.00	1.63
3730	4175	7.024345	TCTATATTTGTGGCTCCATCATGAT	57.976	36.000	1.18	1.18	0.00	2.45
3866	4311	5.003804	GGAGAGGAAAAAGCAGAACATGTA	58.996	41.667	0.00	0.00	0.00	2.29
3882	4327	6.434652	AGAACATGTAGTCTGTTACTAGCACT	59.565	38.462	0.00	0.00	41.42	4.40
3910	4355	3.870274	TCATCACTGGAATGAGCTTCTG	58.130	45.455	0.00	0.00	34.08	3.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
6	7	9.612620	GTTCATCGTATTTGAAAAGAGTTCATT	57.387	29.630	0.00	0.00	35.03	2.57
24	46	8.870160	TCATTGAATTTGAAAAAGTTCATCGT	57.130	26.923	0.00	0.00	43.29	3.73
73	220	6.902224	AAAAAGTTCATCGGGTTTGAAAAG	57.098	33.333	0.00	0.00	35.03	2.27
330	728	9.932699	TTAAACGTGAAATCGAAAAAGTTCATA	57.067	25.926	0.00	0.00	32.93	2.15
343	741	8.782533	AGTCAGATTTGTTTAAACGTGAAATC	57.217	30.769	22.74	22.74	32.96	2.17
367	768	7.221452	AGTGTGACCGCGTTATTTACTAATAAG	59.779	37.037	4.92	0.00	37.00	1.73
381	790	0.461339	AAGAACAAGTGTGACCGCGT	60.461	50.000	4.92	0.00	0.00	6.01
418	827	2.975851	CAATCGAAGACTTGTGCTTTGC	59.024	45.455	0.00	0.00	42.51	3.68
423	852	4.686554	ACTAGAACAATCGAAGACTTGTGC	59.313	41.667	3.04	1.52	42.51	4.57
438	867	1.278127	GCTGGGCTAACCACTAGAACA	59.722	52.381	0.00	0.00	46.80	3.18
495	924	5.746245	AGAAAAATCGCAAAATCGTTGTTGA	59.254	32.000	0.39	0.00	0.00	3.18
497	926	5.051106	CCAGAAAAATCGCAAAATCGTTGTT	60.051	36.000	0.00	0.00	0.00	2.83
791	1228	1.609501	TCGGAGAAGTGACTGGGGG	60.610	63.158	0.00	0.00	0.00	5.40
815	1252	4.920112	TTGTGGCGTGTCGGTGGG	62.920	66.667	0.00	0.00	0.00	4.61
1524	1961	1.958902	AATCGGCGGCGTTAAGGGTA	61.959	55.000	31.06	9.62	0.00	3.69
1530	1967	1.005867	GGGATAATCGGCGGCGTTA	60.006	57.895	31.06	25.35	0.00	3.18
1602	2039	4.330250	GGGTCAATGAGATACCATCATGG	58.670	47.826	0.54	0.54	45.02	3.66
1698	2135	0.885879	TGACGCGTGTTAGAGGATGT	59.114	50.000	20.70	0.00	0.00	3.06
1699	2136	1.990799	TTGACGCGTGTTAGAGGATG	58.009	50.000	20.70	0.00	0.00	3.51
1700	2137	2.736144	TTTGACGCGTGTTAGAGGAT	57.264	45.000	20.70	0.00	0.00	3.24
1701	2138	2.512485	TTTTGACGCGTGTTAGAGGA	57.488	45.000	20.70	0.00	0.00	3.71
1737	2174	6.148948	TGAAAACTCGGCAATTTGATGTTAG	58.851	36.000	0.00	0.00	0.00	2.34
1780	2217	7.391148	AAGCTGTAAACCATTGTTACTATGG	57.609	36.000	20.90	20.90	46.48	2.74
2353	2797	7.068103	TGCTAAAATTCTCTCCAAGTTCAAACA	59.932	33.333	0.00	0.00	0.00	2.83
2422	2867	5.674148	CACTATCATCGATTGCACTTTTTCG	59.326	40.000	0.00	0.00	0.00	3.46
2566	3011	8.112822	TGGATAAGGAAATGATCTAAACCAACA	58.887	33.333	0.00	0.00	0.00	3.33
2567	3012	8.519799	TGGATAAGGAAATGATCTAAACCAAC	57.480	34.615	0.00	0.00	0.00	3.77
2841	3286	5.713389	ACCATCTTATCATAATGTGCCATGG	59.287	40.000	7.63	7.63	0.00	3.66
2867	3312	0.746659	GCAAAAGGCTGTCCACTGTT	59.253	50.000	0.00	0.00	40.25	3.16
3071	3516	7.745717	TCTTCCAAGGTCCGATTGATATATTT	58.254	34.615	0.00	0.00	0.00	1.40
3309	3754	1.975680	GCCGATATTAAGGGTGGGAGA	59.024	52.381	0.00	0.00	0.00	3.71
3730	4175	5.541484	TGCTCTCATCTCTATGCCTTCAATA	59.459	40.000	0.00	0.00	32.76	1.90
3813	4258	3.755905	TCAAATATGAACTCAGCGCCAAA	59.244	39.130	2.29	0.00	30.99	3.28
3814	4259	3.126858	GTCAAATATGAACTCAGCGCCAA	59.873	43.478	2.29	0.00	37.30	4.52
3866	4311	4.585162	AGAACACAGTGCTAGTAACAGACT	59.415	41.667	0.00	0.00	42.69	3.24
3882	4327	4.572909	CTCATTCCAGTGATGAGAACACA	58.427	43.478	13.98	0.00	43.18	3.72
3910	4355	3.855858	GTCCTGAAGAGAATGGACAGAC	58.144	50.000	6.18	0.00	45.87	3.51
4086	4531	5.643379	TGCATAGCTTTTAACCTCCTTTG	57.357	39.130	0.00	0.00	0.00	2.77

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.