AutoCloner

Multiple sequence alignment - TraesCS3D01G365500

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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	TraesCS3D01G365500	chr3D	100.000	3514	0	0	1	3514	479915658	479912145	0.000000e+00	6490
1	TraesCS3D01G365500	chr3D	91.490	2738	205	8	796	3514	479450282	479453010	0.000000e+00	3740
2	TraesCS3D01G365500	chr3D	93.484	2118	121	11	1400	3514	479894849	479892746	0.000000e+00	3131
3	TraesCS3D01G365500	chr3D	85.267	2776	300	52	796	3506	478738416	478741147	0.000000e+00	2760
4	TraesCS3D01G365500	chr3D	85.723	1660	180	32	1863	3514	479213666	479215276	0.000000e+00	1700
5	TraesCS3D01G365500	chr3D	82.618	1933	268	38	1457	3359	478755902	478757796	0.000000e+00	1646
6	TraesCS3D01G365500	chr3D	82.732	1911	255	32	1517	3384	478751505	478753383	0.000000e+00	1631
7	TraesCS3D01G365500	chr3D	85.981	1498	166	17	2020	3514	479962061	479960605	0.000000e+00	1563
8	TraesCS3D01G365500	chr3D	87.729	1092	116	14	2432	3514	479122403	479123485	0.000000e+00	1258
9	TraesCS3D01G365500	chr3A	91.198	1886	151	8	1634	3514	622710636	622712511	0.000000e+00	2549
10	TraesCS3D01G365500	chr3A	90.069	1883	152	8	1635	3514	622719359	622721209	0.000000e+00	2409
11	TraesCS3D01G365500	chr3A	89.862	1884	158	6	1634	3514	622819043	622820896	0.000000e+00	2390
12	TraesCS3D01G365500	chr3A	89.474	1881	164	7	1637	3514	622900263	622902112	0.000000e+00	2346
13	TraesCS3D01G365500	chr3A	90.554	1715	151	7	1802	3513	622891720	622893426	0.000000e+00	2259
14	TraesCS3D01G365500	chr3A	91.802	1171	91	4	1802	2969	622801595	622802763	0.000000e+00	1626
15	TraesCS3D01G365500	chr3A	93.992	799	44	4	1	797	521604458	521603662	0.000000e+00	1206
16	TraesCS3D01G365500	chr3A	88.793	812	76	7	796	1592	622709825	622710636	0.000000e+00	981
17	TraesCS3D01G365500	chr3A	87.546	811	86	7	796	1591	622718547	622719357	0.000000e+00	924
18	TraesCS3D01G365500	chr3A	87.423	811	87	7	796	1591	622899449	622900259	0.000000e+00	918
19	TraesCS3D01G365500	chr3A	87.192	812	88	8	796	1592	622818233	622819043	0.000000e+00	909
20	TraesCS3D01G365500	chr3B	83.541	2412	309	45	796	3168	639553429	639555791	0.000000e+00	2174
21	TraesCS3D01G365500	chr3B	85.401	2055	238	32	796	2813	638960276	638962305	0.000000e+00	2076
22	TraesCS3D01G365500	chr3B	86.527	1915	191	35	796	2692	639754053	639755918	0.000000e+00	2045
23	TraesCS3D01G365500	chr3B	85.032	2031	252	26	796	2794	639398964	639400974	0.000000e+00	2019
24	TraesCS3D01G365500	chr3B	77.789	968	153	39	2575	3492	639780990	639781945	1.110000e-149	540
25	TraesCS3D01G365500	chr3B	80.463	691	84	28	2862	3514	639774298	639774975	6.820000e-132	481
26	TraesCS3D01G365500	chr1D	96.638	803	21	5	1	800	470857123	470857922	0.000000e+00	1328
27	TraesCS3D01G365500	chr7A	95.392	803	29	6	1	797	711576876	711577676	0.000000e+00	1271
28	TraesCS3D01G365500	chr7A	94.757	801	37	4	1	797	688023861	688024660	0.000000e+00	1242
29	TraesCS3D01G365500	chr5A	94.534	805	40	3	1	801	702258901	702259705	0.000000e+00	1240
30	TraesCS3D01G365500	chr6A	96.395	749	24	3	1	747	47889835	47890582	0.000000e+00	1230
31	TraesCS3D01G365500	chr2B	96.138	751	27	2	1	750	340547616	340546867	0.000000e+00	1225
32	TraesCS3D01G365500	chr2B	96.133	750	28	1	1	750	245972307	245971559	0.000000e+00	1223
33	TraesCS3D01G365500	chr1B	94.161	805	35	10	1	797	474677857	474677057	0.000000e+00	1216
34	TraesCS3D01G365500	chr7D	88.889	99	5	4	705	797	537212367	537212465	2.220000e-22	117
35	TraesCS3D01G365500	chr7D	88.776	98	4	5	707	797	66451286	66451383	2.870000e-21	113
36	TraesCS3D01G365500	chr2D	86.667	105	7	3	705	802	207537222	207537118	3.710000e-20	110

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	TraesCS3D01G365500	chr3D	479912145	479915658	3513	True	6490.0	6490	100.0000	1	3514	1	chr3D.!!$R2	3513
1	TraesCS3D01G365500	chr3D	479450282	479453010	2728	False	3740.0	3740	91.4900	796	3514	1	chr3D.!!$F4	2718
2	TraesCS3D01G365500	chr3D	479892746	479894849	2103	True	3131.0	3131	93.4840	1400	3514	1	chr3D.!!$R1	2114
3	TraesCS3D01G365500	chr3D	478738416	478741147	2731	False	2760.0	2760	85.2670	796	3506	1	chr3D.!!$F1	2710
4	TraesCS3D01G365500	chr3D	479213666	479215276	1610	False	1700.0	1700	85.7230	1863	3514	1	chr3D.!!$F3	1651
5	TraesCS3D01G365500	chr3D	478751505	478757796	6291	False	1638.5	1646	82.6750	1457	3384	2	chr3D.!!$F5	1927
6	TraesCS3D01G365500	chr3D	479960605	479962061	1456	True	1563.0	1563	85.9810	2020	3514	1	chr3D.!!$R3	1494
7	TraesCS3D01G365500	chr3D	479122403	479123485	1082	False	1258.0	1258	87.7290	2432	3514	1	chr3D.!!$F2	1082
8	TraesCS3D01G365500	chr3A	622891720	622893426	1706	False	2259.0	2259	90.5540	1802	3513	1	chr3A.!!$F2	1711
9	TraesCS3D01G365500	chr3A	622709825	622712511	2686	False	1765.0	2549	89.9955	796	3514	2	chr3A.!!$F3	2718
10	TraesCS3D01G365500	chr3A	622718547	622721209	2662	False	1666.5	2409	88.8075	796	3514	2	chr3A.!!$F4	2718
11	TraesCS3D01G365500	chr3A	622818233	622820896	2663	False	1649.5	2390	88.5270	796	3514	2	chr3A.!!$F5	2718
12	TraesCS3D01G365500	chr3A	622899449	622902112	2663	False	1632.0	2346	88.4485	796	3514	2	chr3A.!!$F6	2718
13	TraesCS3D01G365500	chr3A	622801595	622802763	1168	False	1626.0	1626	91.8020	1802	2969	1	chr3A.!!$F1	1167
14	TraesCS3D01G365500	chr3A	521603662	521604458	796	True	1206.0	1206	93.9920	1	797	1	chr3A.!!$R1	796
15	TraesCS3D01G365500	chr3B	639553429	639555791	2362	False	2174.0	2174	83.5410	796	3168	1	chr3B.!!$F3	2372
16	TraesCS3D01G365500	chr3B	638960276	638962305	2029	False	2076.0	2076	85.4010	796	2813	1	chr3B.!!$F1	2017
17	TraesCS3D01G365500	chr3B	639754053	639755918	1865	False	2045.0	2045	86.5270	796	2692	1	chr3B.!!$F4	1896
18	TraesCS3D01G365500	chr3B	639398964	639400974	2010	False	2019.0	2019	85.0320	796	2794	1	chr3B.!!$F2	1998
19	TraesCS3D01G365500	chr3B	639780990	639781945	955	False	540.0	540	77.7890	2575	3492	1	chr3B.!!$F6	917
20	TraesCS3D01G365500	chr3B	639774298	639774975	677	False	481.0	481	80.4630	2862	3514	1	chr3B.!!$F5	652
21	TraesCS3D01G365500	chr1D	470857123	470857922	799	False	1328.0	1328	96.6380	1	800	1	chr1D.!!$F1	799
22	TraesCS3D01G365500	chr7A	711576876	711577676	800	False	1271.0	1271	95.3920	1	797	1	chr7A.!!$F2	796
23	TraesCS3D01G365500	chr7A	688023861	688024660	799	False	1242.0	1242	94.7570	1	797	1	chr7A.!!$F1	796
24	TraesCS3D01G365500	chr5A	702258901	702259705	804	False	1240.0	1240	94.5340	1	801	1	chr5A.!!$F1	800
25	TraesCS3D01G365500	chr6A	47889835	47890582	747	False	1230.0	1230	96.3950	1	747	1	chr6A.!!$F1	746
26	TraesCS3D01G365500	chr2B	340546867	340547616	749	True	1225.0	1225	96.1380	1	750	1	chr2B.!!$R2	749
27	TraesCS3D01G365500	chr2B	245971559	245972307	748	True	1223.0	1223	96.1330	1	750	1	chr2B.!!$R1	749
28	TraesCS3D01G365500	chr1B	474677057	474677857	800	True	1216.0	1216	94.1610	1	797	1	chr1B.!!$R1	796

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
943	977	0.602905	ACCCACAAGCAAGAGTACGC	60.603	55.0	0.0	0.0	0.0	4.42	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2657	2805	0.109342	AGTCCACTTGCTTGACCAGG	59.891	55.0	0.0	0.0	0.0	4.45	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
338	340	7.217906	GGGTAAGGAAAGATAGATTCGTGATT	58.782	38.462	0.00	0.00	0.00	2.57
371	373	6.547880	TGTTAGGAAATTACTGGTTTGCAAGA	59.452	34.615	0.00	0.00	30.42	3.02
816	831	5.685728	AGATCTATAGCCCACCTTTTTCAC	58.314	41.667	0.00	0.00	0.00	3.18
894	909	2.305927	GCTGCAGGCTATAAATAGGGGA	59.694	50.000	17.12	0.00	38.06	4.81
943	977	0.602905	ACCCACAAGCAAGAGTACGC	60.603	55.000	0.00	0.00	0.00	4.42
1000	1034	0.532573	GTCGGAGATGAGCAAGGACA	59.467	55.000	0.00	0.00	40.67	4.02
1028	1062	3.850752	TCTCTGAGGAAGAAGTCACCTT	58.149	45.455	4.59	0.00	33.37	3.50
1034	1068	1.202818	GGAAGAAGTCACCTTGCACCT	60.203	52.381	0.00	0.00	33.06	4.00
1053	1087	1.227380	GCGCATTCTCGGAGGTGAT	60.227	57.895	0.30	0.00	0.00	3.06
1056	1090	1.471501	CGCATTCTCGGAGGTGATGAA	60.472	52.381	15.95	0.78	0.00	2.57
1058	1092	2.196749	CATTCTCGGAGGTGATGAACG	58.803	52.381	4.96	0.00	0.00	3.95
1098	1138	0.179124	AGTCTTCCATCTTCGCGCTC	60.179	55.000	5.56	0.00	0.00	5.03
1128	1168	0.673644	GGCTGCAATACTCGGTGTGT	60.674	55.000	0.50	0.00	0.00	3.72
1137	1177	2.842462	TCGGTGTGTGAGGCAGGT	60.842	61.111	0.00	0.00	0.00	4.00
1273	1313	2.363795	CTGGTGGAGGCGGAGGTA	60.364	66.667	0.00	0.00	0.00	3.08
1296	1336	2.015587	GAAGATGCAGGAGGAAGCAAG	58.984	52.381	0.00	0.00	44.88	4.01
1308	1348	1.652167	GAAGCAAGCTAGCCTGGCAC	61.652	60.000	22.65	9.89	43.40	5.01
1366	1406	1.612442	GTGGAGGAGGTGTGGGCTA	60.612	63.158	0.00	0.00	0.00	3.93
1780	1878	2.835431	CATCGGACGGGAGGAGCT	60.835	66.667	0.00	0.00	0.00	4.09
1887	1985	3.626930	GGATCAGTCCTGTGAGAGTAGT	58.373	50.000	0.00	0.00	41.60	2.73
1895	1993	4.399618	GTCCTGTGAGAGTAGTAATGAGCA	59.600	45.833	0.00	0.00	0.00	4.26
1898	1996	4.086457	TGTGAGAGTAGTAATGAGCACCA	58.914	43.478	0.00	0.00	0.00	4.17
2091	2190	3.267483	GCTTATACCGTGGAGCTTGAAA	58.733	45.455	0.00	0.00	32.54	2.69
2126	2225	0.320771	TCAAGGAGGAGAACGCTTGC	60.321	55.000	0.00	0.00	0.00	4.01
2129	2228	1.448717	GGAGGAGAACGCTTGCCTC	60.449	63.158	0.00	0.00	44.84	4.70
2228	2327	5.027293	ACCGTTACTAAACTGTTTCACCT	57.973	39.130	9.38	0.00	29.80	4.00
2395	2504	2.361757	TGTGCTGATGAAAACACCTTGG	59.638	45.455	0.00	0.00	31.98	3.61
2465	2583	0.443869	CCAAGGAGAATGTGAACGCG	59.556	55.000	3.53	3.53	0.00	6.01
2525	2643	0.040646	TCTGGTGATAGGTGACCCGT	59.959	55.000	0.00	0.00	35.12	5.28
2532	2653	2.167693	TGATAGGTGACCCGTCATTCAC	59.832	50.000	0.00	0.00	42.18	3.18
2536	2657	2.754946	GTGACCCGTCATTCACCTTA	57.245	50.000	0.03	0.00	42.18	2.69
2657	2805	6.644248	AAGGACCCAAATGTTACTGTTTAC	57.356	37.500	0.00	0.00	0.00	2.01
3064	3303	2.819595	CACCGCTTGATGGTCCGG	60.820	66.667	0.00	0.00	45.80	5.14
3065	3304	4.778143	ACCGCTTGATGGTCCGGC	62.778	66.667	0.00	0.00	44.29	6.13
3086	3325	1.095600	GGCTAGCCTTTAGTTGTGCC	58.904	55.000	27.17	0.00	0.00	5.01
3122	3361	2.539476	CATGACGTCGATCATCAACCA	58.461	47.619	11.62	0.00	37.20	3.67
3218	3483	3.598019	ACCAGTATTTGCCAATTGCTG	57.402	42.857	9.56	9.56	42.00	4.41
3287	3564	1.093496	GTAACACCCTATGGCCGTGC	61.093	60.000	8.05	0.00	33.59	5.34
3343	3628	4.773674	TCAAAGGAGAACATCAATGCCAAT	59.226	37.500	0.00	0.00	0.00	3.16

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
737	745	3.414269	GGTTTATTTTCGTCCCACCTCA	58.586	45.455	0.00	0.00	0.00	3.86
773	786	5.381184	TCTCTACTCCTAATGTCTCAGCT	57.619	43.478	0.00	0.00	0.00	4.24
774	787	6.003950	AGATCTCTACTCCTAATGTCTCAGC	58.996	44.000	0.00	0.00	0.00	4.26
816	831	8.993121	AGATAGCTATTAAATTCACGTGATTGG	58.007	33.333	20.80	5.41	0.00	3.16
894	909	4.961511	TTCAGTCTTGCGCCGCGT	62.962	61.111	15.34	0.00	0.00	6.01
943	977	1.665916	CCACAGTGGTCACGCTCTG	60.666	63.158	11.99	0.00	34.61	3.35
957	991	3.570540	CATCCTATCTCTCCTCACCACA	58.429	50.000	0.00	0.00	0.00	4.17
1000	1034	5.541868	TGACTTCTTCCTCAGAGAACTTCAT	59.458	40.000	0.00	0.00	31.12	2.57
1034	1068	1.960040	ATCACCTCCGAGAATGCGCA	61.960	55.000	14.96	14.96	0.00	6.09
1109	1149	0.673644	ACACACCGAGTATTGCAGCC	60.674	55.000	0.00	0.00	0.00	4.85
1128	1168	1.148273	AAAGTTGCGACCTGCCTCA	59.852	52.632	0.00	0.00	45.60	3.86
1137	1177	0.109532	TCATGGACCCAAAGTTGCGA	59.890	50.000	0.00	0.00	0.00	5.10
1172	1212	1.948834	TGGCATTCCATATGTTGCTCG	59.051	47.619	17.07	0.00	37.47	5.03
1248	1288	3.569210	CCTCCACCAGCACCCACA	61.569	66.667	0.00	0.00	0.00	4.17
1273	1313	0.177604	CTTCCTCCTGCATCTTCGCT	59.822	55.000	0.00	0.00	0.00	4.93
1296	1336	2.202810	GACTCGTGCCAGGCTAGC	60.203	66.667	14.15	6.04	0.00	3.42
1308	1348	0.456995	GAGGCAAGGAGAACGACTCG	60.457	60.000	0.00	0.00	45.76	4.18
1366	1406	0.846427	TGGGGCTCCCTGTTGATCTT	60.846	55.000	0.00	0.00	45.70	2.40
1385	1425	4.740822	GCCGGGAATGCACTGGGT	62.741	66.667	2.18	0.00	34.85	4.51
1437	1492	4.622456	GCAACCGCACCACCGTTG	62.622	66.667	0.00	0.00	38.36	4.10
1477	1532	1.205655	CTCCAGCGTCATCTCTCCAAA	59.794	52.381	0.00	0.00	0.00	3.28
1649	1746	2.819595	CGCCCATCACCAGGAACG	60.820	66.667	0.00	0.00	0.00	3.95
1655	1752	2.655073	ATGTCGTCGCCCATCACCA	61.655	57.895	0.00	0.00	0.00	4.17
1780	1878	2.781923	CATGTCAACCTGTGTCATGGA	58.218	47.619	5.88	0.00	44.94	3.41
1884	1982	1.206132	CGGTGGTGGTGCTCATTACTA	59.794	52.381	0.00	0.00	0.00	1.82
1887	1985	1.376683	GCGGTGGTGGTGCTCATTA	60.377	57.895	0.00	0.00	0.00	1.90
1898	1996	3.620419	TTGATCATGCGGCGGTGGT	62.620	57.895	9.78	0.00	0.00	4.16
1944	2042	3.022406	AGTAAGTACCTACTTCCTGGCG	58.978	50.000	0.00	0.00	44.77	5.69
2039	2138	6.362820	CGGTTAAGAAAGACAGAGAGTGTAAC	59.637	42.308	0.00	0.00	40.56	2.50
2091	2190	0.834612	TTGAGGTGGTTCAGTTCGGT	59.165	50.000	0.00	0.00	0.00	4.69
2129	2228	2.028930	ACTTCGTACCTCCTCAGCTTTG	60.029	50.000	0.00	0.00	0.00	2.77
2228	2327	5.220378	GCAAAATCGTCTTCTGCAACAAAAA	60.220	36.000	0.00	0.00	33.19	1.94
2413	2522	5.265191	TCATCTTCTCCACTAGCTGTAAGT	58.735	41.667	0.00	0.00	35.30	2.24
2414	2523	5.843673	TCATCTTCTCCACTAGCTGTAAG	57.156	43.478	0.00	0.00	0.00	2.34
2525	2643	4.159693	AGCACGACTATGTAAGGTGAATGA	59.840	41.667	0.00	0.00	0.00	2.57
2532	2653	1.134818	TGCCAGCACGACTATGTAAGG	60.135	52.381	0.00	0.00	0.00	2.69
2536	2657	1.219124	CCTGCCAGCACGACTATGT	59.781	57.895	0.00	0.00	0.00	2.29
2629	2774	4.644685	CAGTAACATTTGGGTCCTTATGGG	59.355	45.833	0.00	0.00	0.00	4.00
2657	2805	0.109342	AGTCCACTTGCTTGACCAGG	59.891	55.000	0.00	0.00	0.00	4.45
2712	2863	6.038603	TGTTCCATTTGTCTGAAGTTTCTGAG	59.961	38.462	2.21	0.00	36.11	3.35
2747	2898	6.346120	CGCTAGTACACATCAACATATTGCTC	60.346	42.308	0.00	0.00	35.63	4.26
2953	3141	3.048337	TCCCGTGTGACCACTTATTTC	57.952	47.619	1.62	0.00	39.55	2.17
3064	3303	0.392595	ACAACTAAAGGCTAGCCGGC	60.393	55.000	27.83	21.89	41.95	6.13
3065	3304	1.369625	CACAACTAAAGGCTAGCCGG	58.630	55.000	27.83	19.96	41.95	6.13
3066	3305	0.727398	GCACAACTAAAGGCTAGCCG	59.273	55.000	27.83	16.04	41.95	5.52
3067	3306	1.095600	GGCACAACTAAAGGCTAGCC	58.904	55.000	27.19	27.19	0.00	3.93
3122	3361	4.465632	TGCACAACCGTAAGAGTATGAT	57.534	40.909	0.00	0.00	43.02	2.45
3183	3431	5.728937	ATACTGGTAAGTGTAGGAGAGGA	57.271	43.478	0.00	0.00	37.19	3.71
3184	3432	6.574350	CAAATACTGGTAAGTGTAGGAGAGG	58.426	44.000	0.00	0.00	37.19	3.69
3185	3433	6.043411	GCAAATACTGGTAAGTGTAGGAGAG	58.957	44.000	0.00	0.00	37.19	3.20
3287	3564	9.831737	CATCTTCTTCACCAGTTGTAAAAATAG	57.168	33.333	0.00	0.00	0.00	1.73

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.