AutoCloner

Multiple sequence alignment - TraesCS1B01G281200

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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	TraesCS1B01G281200	chr1B	100.000	3039	0	0	1	3039	489544214	489547252	0.000000e+00	5613
1	TraesCS1B01G281200	chr1B	83.019	689	69	26	1229	1898	489629109	489629768	5.650000e-162	580
2	TraesCS1B01G281200	chr1B	86.867	533	37	14	1659	2186	489576185	489576689	1.580000e-157	566
3	TraesCS1B01G281200	chr1B	80.813	615	109	7	1222	1833	489809183	489809791	9.860000e-130	473
4	TraesCS1B01G281200	chr1B	80.952	546	84	14	1210	1745	489787455	489787990	6.060000e-112	414
5	TraesCS1B01G281200	chr1B	91.189	227	10	8	922	1145	489808842	489809061	1.770000e-77	300
6	TraesCS1B01G281200	chr1B	81.707	328	41	15	788	1110	489628715	489629028	3.890000e-64	255
7	TraesCS1B01G281200	chr1B	91.667	96	5	2	2245	2340	489576672	489576764	2.460000e-26	130
8	TraesCS1B01G281200	chr1D	93.001	1686	78	15	671	2340	365790289	365791950	0.000000e+00	2423
9	TraesCS1B01G281200	chr1D	94.012	668	35	5	5	669	365789583	365790248	0.000000e+00	1007
10	TraesCS1B01G281200	chr1D	82.080	1144	124	54	788	1898	365794453	365795548	0.000000e+00	902
11	TraesCS1B01G281200	chr1D	82.210	534	72	15	1223	1745	365846154	365846675	3.600000e-119	438
12	TraesCS1B01G281200	chr1D	90.625	224	17	4	922	1145	365894190	365894409	8.240000e-76	294
13	TraesCS1B01G281200	chr1D	80.926	367	47	15	789	1146	365850636	365850988	4.990000e-68	268
14	TraesCS1B01G281200	chr1D	78.086	397	42	25	1520	1898	365851461	365851830	3.070000e-50	209
15	TraesCS1B01G281200	chr5B	92.297	714	40	5	2338	3038	439691588	439692299	0.000000e+00	1000
16	TraesCS1B01G281200	chr1A	90.694	677	50	9	1	669	464900113	464900784	0.000000e+00	889
17	TraesCS1B01G281200	chr1A	90.409	636	34	7	1201	1835	464907711	464908320	0.000000e+00	811
18	TraesCS1B01G281200	chr1A	80.037	1082	152	42	922	1967	465105128	465106181	0.000000e+00	743
19	TraesCS1B01G281200	chr1A	91.925	483	32	5	1863	2340	464908303	464908783	0.000000e+00	669
20	TraesCS1B01G281200	chr1A	84.682	692	72	22	1229	1898	464911618	464912297	0.000000e+00	660
21	TraesCS1B01G281200	chr1A	90.946	497	27	7	669	1149	464900831	464901325	0.000000e+00	652
22	TraesCS1B01G281200	chr1A	79.242	660	91	29	1210	1835	465074542	465075189	4.690000e-113	418
23	TraesCS1B01G281200	chr1A	80.781	333	48	13	788	1109	464911211	464911538	2.340000e-61	246
24	TraesCS1B01G281200	chr3D	81.983	716	98	22	2341	3039	387535921	387536622	2.030000e-161	579

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	TraesCS1B01G281200	chr1B	489544214	489547252	3038	False	5613.0	5613	100.000000	1	3039	1	chr1B.!!$F1	3038
1	TraesCS1B01G281200	chr1B	489628715	489629768	1053	False	417.5	580	82.363000	788	1898	2	chr1B.!!$F4	1110
2	TraesCS1B01G281200	chr1B	489787455	489787990	535	False	414.0	414	80.952000	1210	1745	1	chr1B.!!$F2	535
3	TraesCS1B01G281200	chr1B	489808842	489809791	949	False	386.5	473	86.001000	922	1833	2	chr1B.!!$F5	911
4	TraesCS1B01G281200	chr1B	489576185	489576764	579	False	348.0	566	89.267000	1659	2340	2	chr1B.!!$F3	681
5	TraesCS1B01G281200	chr1D	365789583	365795548	5965	False	1444.0	2423	89.697667	5	2340	3	chr1D.!!$F2	2335
6	TraesCS1B01G281200	chr1D	365846154	365851830	5676	False	305.0	438	80.407333	789	1898	3	chr1D.!!$F3	1109
7	TraesCS1B01G281200	chr5B	439691588	439692299	711	False	1000.0	1000	92.297000	2338	3038	1	chr5B.!!$F1	700
8	TraesCS1B01G281200	chr1A	464900113	464901325	1212	False	770.5	889	90.820000	1	1149	2	chr1A.!!$F3	1148
9	TraesCS1B01G281200	chr1A	465105128	465106181	1053	False	743.0	743	80.037000	922	1967	1	chr1A.!!$F2	1045
10	TraesCS1B01G281200	chr1A	464907711	464912297	4586	False	596.5	811	86.949250	788	2340	4	chr1A.!!$F4	1552
11	TraesCS1B01G281200	chr1A	465074542	465075189	647	False	418.0	418	79.242000	1210	1835	1	chr1A.!!$F1	625
12	TraesCS1B01G281200	chr3D	387535921	387536622	701	False	579.0	579	81.983000	2341	3039	1	chr3D.!!$F1	698

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
845	6053	0.447801	GGCGACCGTCGTAGAAGTTA	59.552	55.0	21.37	0.0	42.81	2.24	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2563	11281	0.249741	GTTGGTACTGCAGTCACCGT	60.25	55.0	25.56	0.0	34.94	4.83	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
61	62	2.869801	TCGTCATGAAACGCTTCAAACT	59.130	40.909	5.19	0.00	44.64	2.66
193	194	8.152898	CACATGGAGAATCATATTGGACTTCTA	58.847	37.037	0.00	0.00	36.25	2.10
203	204	4.946478	ATTGGACTTCTATCTCCTTCGG	57.054	45.455	0.00	0.00	0.00	4.30
254	256	2.352388	ACATCGAACCAACAATACGGG	58.648	47.619	0.00	0.00	0.00	5.28
255	257	2.027929	ACATCGAACCAACAATACGGGA	60.028	45.455	0.00	0.00	0.00	5.14
256	258	2.373540	TCGAACCAACAATACGGGAG	57.626	50.000	0.00	0.00	0.00	4.30
258	260	1.997606	CGAACCAACAATACGGGAGAC	59.002	52.381	0.00	0.00	0.00	3.36
302	304	5.351465	CGCCATACTATGTTTTGAAGACTGT	59.649	40.000	0.00	0.00	0.00	3.55
325	327	5.527582	GTGATAACCATTCACCGCTAGAAAT	59.472	40.000	0.00	0.00	38.00	2.17
334	336	5.440234	TCACCGCTAGAAATGAGATCTAC	57.560	43.478	0.00	0.00	0.00	2.59
434	439	3.572196	TACGCAAACCCCGGTCGAC	62.572	63.158	7.13	7.13	0.00	4.20
510	516	1.303236	CGACTGGCCATTTGTGGGA	60.303	57.895	5.51	0.00	0.00	4.37
523	529	0.895530	TGTGGGATCAGAAGTCGTCC	59.104	55.000	0.00	0.00	0.00	4.79
740	798	3.600388	CTGTCTACCATGTCAACTTCCC	58.400	50.000	0.00	0.00	0.00	3.97
845	6053	0.447801	GGCGACCGTCGTAGAAGTTA	59.552	55.000	21.37	0.00	42.81	2.24
862	6072	3.891049	AGTTATGCCCTTCCTTGACATC	58.109	45.455	0.00	0.00	0.00	3.06
957	6185	4.760047	GGGTGCACGCCAGTCGAT	62.760	66.667	22.50	0.00	41.67	3.59
1153	6400	1.400113	CCTTGCGTACTGTTGTGCATG	60.400	52.381	0.00	0.00	37.17	4.06
1175	6435	2.124903	GTGTCTGTGAACTGTGGTACG	58.875	52.381	0.00	0.00	0.00	3.67
1208	6513	7.043920	CGCATTTGTACATGTACACGTCTTATA	60.044	37.037	33.03	16.58	44.81	0.98
1444	6763	3.381590	CCGTCTTCTCATGGTGAGTGATA	59.618	47.826	6.83	0.00	44.58	2.15
1445	6764	4.038522	CCGTCTTCTCATGGTGAGTGATAT	59.961	45.833	6.83	0.00	44.58	1.63
1446	6765	4.981054	CGTCTTCTCATGGTGAGTGATATG	59.019	45.833	6.83	0.00	44.58	1.78
1453	6775	4.021981	TCATGGTGAGTGATATGTCGATCC	60.022	45.833	0.00	0.00	0.00	3.36
1454	6776	3.566351	TGGTGAGTGATATGTCGATCCT	58.434	45.455	0.00	0.00	0.00	3.24
1455	6777	3.570125	TGGTGAGTGATATGTCGATCCTC	59.430	47.826	0.00	0.00	0.00	3.71
1456	6778	3.057174	GGTGAGTGATATGTCGATCCTCC	60.057	52.174	0.00	0.00	0.00	4.30
1457	6779	3.570125	GTGAGTGATATGTCGATCCTCCA	59.430	47.826	0.00	0.00	0.00	3.86
1458	6780	4.219507	GTGAGTGATATGTCGATCCTCCAT	59.780	45.833	0.00	0.00	0.00	3.41
1459	6781	4.219288	TGAGTGATATGTCGATCCTCCATG	59.781	45.833	0.00	0.00	0.00	3.66
1460	6782	3.513119	AGTGATATGTCGATCCTCCATGG	59.487	47.826	4.97	4.97	37.10	3.66
1500	6930	2.460918	CTAGGCGGATCACTGTTTACG	58.539	52.381	0.00	0.00	0.00	3.18
1505	6935	2.259618	CGGATCACTGTTTACGGACTG	58.740	52.381	0.00	0.00	0.00	3.51
1564	6996	4.299547	TTCGCGCTGCTGGTGACT	62.300	61.111	5.56	0.00	0.00	3.41
1853	7285	2.108278	GACACCCAACTACCCGCAGT	62.108	60.000	0.00	0.00	0.00	4.40
1861	7293	0.330604	ACTACCCGCAGTACTCTCCA	59.669	55.000	0.00	0.00	0.00	3.86
1904	7336	4.324991	AACCGCCGAACCCTCACC	62.325	66.667	0.00	0.00	0.00	4.02
2118	7552	5.284188	CGTTTTTGTGAATGTAACGTGTGTT	59.716	36.000	0.00	0.00	42.19	3.32
2153	7587	3.611766	CGGAGGACCTGTATTCTTGTT	57.388	47.619	0.00	0.00	0.00	2.83
2219	7653	7.268586	GTTTGCAGTTGAGATCTCTCCTATAA	58.731	38.462	22.95	12.79	42.20	0.98
2243	7677	1.470494	TCAGAGAGTCAGCAACGCTAG	59.530	52.381	0.00	0.00	38.23	3.42
2246	7680	2.163412	AGAGAGTCAGCAACGCTAGAAG	59.837	50.000	0.00	0.00	38.23	2.85
2258	7692	3.600388	ACGCTAGAAGTAATGCTTGCTT	58.400	40.909	3.18	0.00	37.59	3.91
2273	7707	2.132740	TGCTTTGCCATCGTGTTTTC	57.867	45.000	0.00	0.00	0.00	2.29
2283	7717	5.088739	GCCATCGTGTTTTCAGTTTAGATG	58.911	41.667	0.00	0.00	35.38	2.90
2290	7724	7.065324	TCGTGTTTTCAGTTTAGATGTCAAGTT	59.935	33.333	0.00	0.00	0.00	2.66
2377	10847	9.667107	ACAAATCTACCGAATGATTTCTCTAAA	57.333	29.630	0.00	0.00	39.85	1.85
2526	11242	2.406616	ACAAAATAGCAGCGCCCCG	61.407	57.895	2.29	0.00	0.00	5.73
2554	11270	3.197790	CTTCCCGCACCGCATCTG	61.198	66.667	0.00	0.00	0.00	2.90
2581	11299	0.032952	GACGGTGACTGCAGTACCAA	59.967	55.000	29.08	13.76	34.10	3.67
2603	11321	2.756283	CTTCCCGGCGACTCTCCT	60.756	66.667	9.30	0.00	0.00	3.69
2626	11344	3.583383	GCTGGATCGCAGCACTTT	58.417	55.556	23.33	0.00	44.49	2.66
2759	11895	2.409870	CCAACGAAGCTCCATGGCC	61.410	63.158	6.96	0.00	0.00	5.36
2760	11896	2.436646	AACGAAGCTCCATGGCCG	60.437	61.111	6.96	7.73	0.00	6.13
2815	11954	0.883370	GACAAACTCCCCGACGCTTT	60.883	55.000	0.00	0.00	0.00	3.51
2869	12008	0.791983	CAAAGCTTCATCGCAGCACG	60.792	55.000	0.00	0.00	39.99	5.34
3011	12162	2.502510	CCATCGCAGCAACAACGC	60.503	61.111	0.00	0.00	0.00	4.84
3012	12163	2.502510	CATCGCAGCAACAACGCC	60.503	61.111	0.00	0.00	0.00	5.68

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
3	4	8.457261	AGTTTTCTTGCAGATGATGTATTCTTC	58.543	33.333	0.00	0.00	0.00	2.87
203	204	3.832981	CGACGGACGGTGTACAAC	58.167	61.111	0.00	0.00	38.46	3.32
302	304	4.746535	TTCTAGCGGTGAATGGTTATCA	57.253	40.909	0.00	0.00	0.00	2.15
334	336	8.733458	TGGTCTTCATTGTTCTTTGATGATTAG	58.267	33.333	0.00	0.00	31.32	1.73
343	345	6.122277	TGTCTCTTGGTCTTCATTGTTCTTT	58.878	36.000	0.00	0.00	0.00	2.52
434	439	2.725203	TTTGGTTCCGTCGCTCCCAG	62.725	60.000	0.00	0.00	0.00	4.45
443	448	1.768112	CGTGCTCGTTTTGGTTCCGT	61.768	55.000	0.00	0.00	0.00	4.69
444	449	1.083015	CGTGCTCGTTTTGGTTCCG	60.083	57.895	0.00	0.00	0.00	4.30
510	516	2.722201	GGCCCGGACGACTTCTGAT	61.722	63.158	0.73	0.00	31.20	2.90
575	582	5.121768	CGAAATGTCTCTTGGTTTTATCGGT	59.878	40.000	0.00	0.00	0.00	4.69
576	583	5.447279	CCGAAATGTCTCTTGGTTTTATCGG	60.447	44.000	0.00	0.00	38.92	4.18
612	622	4.180057	GGATCTCTAGCATGCTAATTCCG	58.820	47.826	26.71	15.47	0.00	4.30
740	798	6.747280	CGTAATCAAGAAAGTTATTGCCCTTG	59.253	38.462	0.00	0.00	34.11	3.61
831	6039	1.407979	AGGGCATAACTTCTACGACGG	59.592	52.381	0.00	0.00	0.00	4.79
845	6053	0.107017	CCGATGTCAAGGAAGGGCAT	60.107	55.000	0.00	0.00	0.00	4.40
862	6072	3.283684	TTCGGTTGGTGCAAGCCG	61.284	61.111	7.30	7.30	38.44	5.52
927	6154	2.540931	CGTGCACCCGTGGTTTATATAC	59.459	50.000	12.15	0.00	31.02	1.47
957	6185	1.487142	TCGACCTCTTTTGGGTTGTGA	59.513	47.619	0.00	0.00	38.87	3.58
1153	6400	2.024176	ACCACAGTTCACAGACACAC	57.976	50.000	0.00	0.00	0.00	3.82
1453	6775	3.750130	CGCTTCCTGATTTATCCATGGAG	59.250	47.826	21.33	4.18	0.00	3.86
1454	6776	3.743521	CGCTTCCTGATTTATCCATGGA	58.256	45.455	18.88	18.88	0.00	3.41
1455	6777	2.227388	GCGCTTCCTGATTTATCCATGG	59.773	50.000	4.97	4.97	0.00	3.66
1456	6778	3.144506	AGCGCTTCCTGATTTATCCATG	58.855	45.455	2.64	0.00	0.00	3.66
1457	6779	3.406764	GAGCGCTTCCTGATTTATCCAT	58.593	45.455	13.26	0.00	0.00	3.41
1458	6780	2.803133	CGAGCGCTTCCTGATTTATCCA	60.803	50.000	13.26	0.00	0.00	3.41
1459	6781	1.795286	CGAGCGCTTCCTGATTTATCC	59.205	52.381	13.26	0.00	0.00	2.59
1460	6782	1.193426	GCGAGCGCTTCCTGATTTATC	59.807	52.381	13.26	0.00	38.26	1.75
1461	6783	1.221414	GCGAGCGCTTCCTGATTTAT	58.779	50.000	13.26	0.00	38.26	1.40
1463	6785	3.490890	GCGAGCGCTTCCTGATTT	58.509	55.556	13.26	0.00	38.26	2.17
1482	6805	0.108329	CCGTAAACAGTGATCCGCCT	60.108	55.000	0.00	0.00	0.00	5.52
1484	6807	0.997196	GTCCGTAAACAGTGATCCGC	59.003	55.000	0.00	0.00	0.00	5.54
1489	6812	3.117794	CGTTTCAGTCCGTAAACAGTGA	58.882	45.455	0.00	0.00	35.74	3.41
1500	6930	0.523072	ATGCATGCACGTTTCAGTCC	59.477	50.000	25.37	0.00	0.00	3.85
1612	7044	2.522185	TCCTTAAGGACGTAGCACAGT	58.478	47.619	20.72	0.00	39.78	3.55
1833	7265	2.046604	GCGGGTAGTTGGGTGTCC	60.047	66.667	0.00	0.00	0.00	4.02
1835	7267	0.832983	TACTGCGGGTAGTTGGGTGT	60.833	55.000	0.00	0.00	32.19	4.16
1853	7285	2.363795	CTGGGGCGGTGGAGAGTA	60.364	66.667	0.00	0.00	0.00	2.59
2017	7449	2.240493	ACACCTGTTCGTCTCCTTTG	57.760	50.000	0.00	0.00	0.00	2.77
2059	7491	3.763902	AGTATAGCACGATCGATGCATC	58.236	45.455	30.35	17.10	45.92	3.91
2118	7552	3.744719	CCGGTGAGGTCGAGCGAA	61.745	66.667	9.28	0.00	36.43	4.70
2151	7585	9.989869	GCATTACTGATCCTCTAAAAGTAAAAC	57.010	33.333	4.30	0.00	37.02	2.43
2152	7586	9.959721	AGCATTACTGATCCTCTAAAAGTAAAA	57.040	29.630	4.30	0.00	37.02	1.52
2153	7587	9.959721	AAGCATTACTGATCCTCTAAAAGTAAA	57.040	29.630	4.30	0.00	37.02	2.01
2173	7607	3.052036	CGTAAAGCAGCAAACAAGCATT	58.948	40.909	0.00	0.00	36.85	3.56
2201	7635	9.295825	TCTGAAGATTATAGGAGAGATCTCAAC	57.704	37.037	24.39	15.77	44.60	3.18
2219	7653	2.673610	GCGTTGCTGACTCTCTGAAGAT	60.674	50.000	0.00	0.00	0.00	2.40
2243	7677	3.302365	TGGCAAAGCAAGCATTACTTC	57.698	42.857	0.00	0.00	36.04	3.01
2246	7680	2.187707	CGATGGCAAAGCAAGCATTAC	58.812	47.619	0.00	0.00	0.00	1.89
2258	7692	3.791973	AAACTGAAAACACGATGGCAA	57.208	38.095	0.00	0.00	0.00	4.52
2283	7717	6.492254	ACCGTCTTTTTCAACATAACTTGAC	58.508	36.000	0.00	0.00	29.62	3.18
2290	7724	5.293814	TCGTGAAACCGTCTTTTTCAACATA	59.706	36.000	0.00	0.00	42.98	2.29
2318	7752	1.235724	AGTTTTAGCGTTGCTGACCC	58.764	50.000	0.70	0.00	40.10	4.46
2376	10846	3.026694	GCAGGCTAGGTGGATGATTTTT	58.973	45.455	0.00	0.00	0.00	1.94
2377	10847	2.659428	GCAGGCTAGGTGGATGATTTT	58.341	47.619	0.00	0.00	0.00	1.82
2526	11242	3.798511	CGGGAAGGGAAGAGGGCC	61.799	72.222	0.00	0.00	0.00	5.80
2528	11244	3.009115	TGCGGGAAGGGAAGAGGG	61.009	66.667	0.00	0.00	0.00	4.30
2563	11281	0.249741	GTTGGTACTGCAGTCACCGT	60.250	55.000	25.56	0.00	34.94	4.83
2566	11284	2.135933	GAGTGTTGGTACTGCAGTCAC	58.864	52.381	25.56	23.24	34.89	3.67
2581	11299	2.600769	AGTCGCCGGGAAGAGTGT	60.601	61.111	2.18	0.00	0.00	3.55
2603	11321	2.580815	CTGCGATCCAGCTCACCA	59.419	61.111	0.00	0.00	38.13	4.17
2626	11344	3.333899	ATCGGTGGCAGCATCAGCA	62.334	57.895	17.80	0.00	45.49	4.41
2631	11349	2.515523	GAGCATCGGTGGCAGCAT	60.516	61.111	17.80	6.65	0.00	3.79
2687	11482	4.441695	CTTGCCGGAGAGAGCGCA	62.442	66.667	11.47	0.00	0.00	6.09
2737	11565	3.645268	ATGGAGCTTCGTTGGGGGC	62.645	63.158	0.00	0.00	0.00	5.80
2815	11954	1.795768	GCTGCCATAGCGCTACAATA	58.204	50.000	21.49	6.20	43.63	1.90
2841	11980	3.050275	GAAGCTTTGGTCGCGCCT	61.050	61.111	18.14	0.00	38.35	5.52
2869	12008	3.917760	CATCTCCGGGGCTCGTCC	61.918	72.222	5.83	0.00	37.11	4.79
3019	12170	0.674895	GAGGTGCAATGGAGCTTCGT	60.675	55.000	8.06	0.00	34.99	3.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.