AutoCloner

Multiple sequence alignment - TraesCS5B01G415500

Loading Multiple Alignment...

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	TraesCS5B01G415500	chr5B	100.000	3861	0	0	1	3861	589807174	589811034	0.000000e+00	7131
1	TraesCS5B01G415500	chr5B	87.391	230	16	9	1	224	650018466	650018244	6.400000e-63	252
2	TraesCS5B01G415500	chr7B	98.155	2764	50	1	1099	3861	152475663	152478426	0.000000e+00	4820
3	TraesCS5B01G415500	chr7B	98.154	2762	49	1	1100	3861	291563686	291560927	0.000000e+00	4817
4	TraesCS5B01G415500	chr7B	98.009	2762	51	4	1100	3861	255049877	255047120	0.000000e+00	4793
5	TraesCS5B01G415500	chr7B	97.828	2762	56	3	1100	3861	155733867	155731110	0.000000e+00	4765
6	TraesCS5B01G415500	chr7B	95.860	2174	82	4	1693	3861	418741987	418744157	0.000000e+00	3509
7	TraesCS5B01G415500	chr4A	98.117	2762	50	2	1100	3861	611029043	611031802	0.000000e+00	4811
8	TraesCS5B01G415500	chr1A	97.647	2762	51	4	1100	3861	440449531	440452278	0.000000e+00	4728
9	TraesCS5B01G415500	chr1A	97.679	474	8	2	1	471	372634934	372634461	0.000000e+00	811
10	TraesCS5B01G415500	chr1A	84.113	812	76	21	312	1096	97850290	97851075	0.000000e+00	736
11	TraesCS5B01G415500	chr1A	83.136	759	70	21	308	1036	441823967	441823237	1.170000e-179	640
12	TraesCS5B01G415500	chr1A	85.052	582	55	14	521	1096	463227543	463228098	7.240000e-157	564
13	TraesCS5B01G415500	chr1A	84.598	435	42	12	308	720	418096275	418095844	3.590000e-110	409
14	TraesCS5B01G415500	chr2B	97.647	2763	47	9	1100	3861	309475988	309478733	0.000000e+00	4726
15	TraesCS5B01G415500	chr3B	95.722	2174	84	5	1693	3861	470053067	470050898	0.000000e+00	3491
16	TraesCS5B01G415500	chr3B	97.386	1186	27	3	1097	2282	700380489	700381670	0.000000e+00	2015
17	TraesCS5B01G415500	chr2A	90.925	1113	71	9	1	1099	52420991	52419895	0.000000e+00	1469
18	TraesCS5B01G415500	chr2D	96.098	897	31	2	203	1096	29520345	29521240	0.000000e+00	1459
19	TraesCS5B01G415500	chr2D	92.201	718	48	4	385	1099	51074021	51073309	0.000000e+00	1009
20	TraesCS5B01G415500	chr2D	93.060	317	21	1	70	386	51074460	51074145	2.720000e-126	462
21	TraesCS5B01G415500	chr2D	85.550	436	37	13	308	720	582497134	582497566	2.130000e-117	433
22	TraesCS5B01G415500	chr5A	97.046	474	11	2	1	471	493617615	493617142	0.000000e+00	795
23	TraesCS5B01G415500	chr5A	93.725	494	29	2	1096	1589	246822544	246822053	0.000000e+00	739
24	TraesCS5B01G415500	chr5A	91.613	155	6	7	1	152	644814601	644814451	1.410000e-49	207
25	TraesCS5B01G415500	chr7A	84.540	815	74	17	308	1096	677932626	677933414	0.000000e+00	760
26	TraesCS5B01G415500	chr7A	78.462	325	45	14	788	1096	66768946	66769261	5.090000e-44	189
27	TraesCS5B01G415500	chrUn	83.966	817	75	20	308	1099	194086339	194085554	0.000000e+00	732
28	TraesCS5B01G415500	chr3A	84.149	429	43	12	314	720	36320134	36320559	3.620000e-105	392
29	TraesCS5B01G415500	chr5D	87.826	230	16	8	1	224	517431025	517430802	3.830000e-65	259

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	TraesCS5B01G415500	chr5B	589807174	589811034	3860	False	7131.0	7131	100.0000	1	3861	1	chr5B.!!$F1	3860
1	TraesCS5B01G415500	chr7B	152475663	152478426	2763	False	4820.0	4820	98.1550	1099	3861	1	chr7B.!!$F1	2762
2	TraesCS5B01G415500	chr7B	291560927	291563686	2759	True	4817.0	4817	98.1540	1100	3861	1	chr7B.!!$R3	2761
3	TraesCS5B01G415500	chr7B	255047120	255049877	2757	True	4793.0	4793	98.0090	1100	3861	1	chr7B.!!$R2	2761
4	TraesCS5B01G415500	chr7B	155731110	155733867	2757	True	4765.0	4765	97.8280	1100	3861	1	chr7B.!!$R1	2761
5	TraesCS5B01G415500	chr7B	418741987	418744157	2170	False	3509.0	3509	95.8600	1693	3861	1	chr7B.!!$F2	2168
6	TraesCS5B01G415500	chr4A	611029043	611031802	2759	False	4811.0	4811	98.1170	1100	3861	1	chr4A.!!$F1	2761
7	TraesCS5B01G415500	chr1A	440449531	440452278	2747	False	4728.0	4728	97.6470	1100	3861	1	chr1A.!!$F2	2761
8	TraesCS5B01G415500	chr1A	97850290	97851075	785	False	736.0	736	84.1130	312	1096	1	chr1A.!!$F1	784
9	TraesCS5B01G415500	chr1A	441823237	441823967	730	True	640.0	640	83.1360	308	1036	1	chr1A.!!$R3	728
10	TraesCS5B01G415500	chr1A	463227543	463228098	555	False	564.0	564	85.0520	521	1096	1	chr1A.!!$F3	575
11	TraesCS5B01G415500	chr2B	309475988	309478733	2745	False	4726.0	4726	97.6470	1100	3861	1	chr2B.!!$F1	2761
12	TraesCS5B01G415500	chr3B	470050898	470053067	2169	True	3491.0	3491	95.7220	1693	3861	1	chr3B.!!$R1	2168
13	TraesCS5B01G415500	chr3B	700380489	700381670	1181	False	2015.0	2015	97.3860	1097	2282	1	chr3B.!!$F1	1185
14	TraesCS5B01G415500	chr2A	52419895	52420991	1096	True	1469.0	1469	90.9250	1	1099	1	chr2A.!!$R1	1098
15	TraesCS5B01G415500	chr2D	29520345	29521240	895	False	1459.0	1459	96.0980	203	1096	1	chr2D.!!$F1	893
16	TraesCS5B01G415500	chr2D	51073309	51074460	1151	True	735.5	1009	92.6305	70	1099	2	chr2D.!!$R1	1029
17	TraesCS5B01G415500	chr7A	677932626	677933414	788	False	760.0	760	84.5400	308	1096	1	chr7A.!!$F2	788
18	TraesCS5B01G415500	chrUn	194085554	194086339	785	True	732.0	732	83.9660	308	1099	1	chrUn.!!$R1	791

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	Hairpin	End Stability	Orientation
442	611	1.114722	TGCCCCAACTGCCAAAGAAG	61.115	55.0	0.00	2.85	F
1247	1433	0.107116	GGCTACCGAGAGAGAGGTGA	60.107	60.0	41.51	4.02	F
1657	1853	0.193574	TGAGGAAGGAGAAGTGGGGT	59.806	55.0	0.00	4.95	F

Position	MSA Position	Penalty	Sequence	TM	GC	End Stability	Orientation
1703	1899	0.767375	AGCCACACACATTCCTCTGT	59.233	50.0	3.41	R
2736	2937	0.326904	ATGTGAGCCCTCTGATCCCA	60.327	55.0	4.37	R
3158	3360	1.448985	GCTCCTAAATCACGCAACCA	58.551	50.0	3.67	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
34	35	4.536489	GCAGTACCTGGAGGGGAAATATAT	59.464	45.833	0.00	0.00	40.27	0.86
87	89	2.857186	TATGTTTGTGCAGCAGAGGA	57.143	45.000	0.00	0.00	0.00	3.71
88	90	1.242076	ATGTTTGTGCAGCAGAGGAC	58.758	50.000	0.00	0.00	0.00	3.85
137	146	8.701895	ACAAGCCTATGTTTGCTACTATACTAA	58.298	33.333	0.00	0.00	36.66	2.24
150	159	8.967918	TGCTACTATACTAACTTGTTCACTCAT	58.032	33.333	0.00	0.00	0.00	2.90
198	207	5.163874	ACAATGACAAAACACATGCACAAAC	60.164	36.000	0.00	0.00	0.00	2.93
207	216	5.835113	ACACATGCACAAACTTTAGAACT	57.165	34.783	0.00	0.00	0.00	3.01
240	263	8.697846	AAATCATAAGCACATTTGACATGAAG	57.302	30.769	0.00	0.00	0.00	3.02
241	264	7.634671	ATCATAAGCACATTTGACATGAAGA	57.365	32.000	0.00	0.00	0.00	2.87
242	265	7.451501	TCATAAGCACATTTGACATGAAGAA	57.548	32.000	0.00	0.00	0.00	2.52
243	266	7.884257	TCATAAGCACATTTGACATGAAGAAA	58.116	30.769	0.00	0.00	0.00	2.52
244	267	8.525316	TCATAAGCACATTTGACATGAAGAAAT	58.475	29.630	0.00	0.00	0.00	2.17
245	268	9.791820	CATAAGCACATTTGACATGAAGAAATA	57.208	29.630	0.00	0.00	0.00	1.40
246	269	9.793252	ATAAGCACATTTGACATGAAGAAATAC	57.207	29.630	0.00	0.00	0.00	1.89
247	270	7.218228	AGCACATTTGACATGAAGAAATACA	57.782	32.000	0.00	0.00	0.00	2.29
248	271	7.086376	AGCACATTTGACATGAAGAAATACAC	58.914	34.615	0.00	0.00	0.00	2.90
249	272	6.862608	GCACATTTGACATGAAGAAATACACA	59.137	34.615	0.00	0.00	0.00	3.72
250	273	7.061441	GCACATTTGACATGAAGAAATACACAG	59.939	37.037	0.00	0.00	0.00	3.66
251	274	7.061441	CACATTTGACATGAAGAAATACACAGC	59.939	37.037	0.00	0.00	0.00	4.40
252	275	6.631971	TTTGACATGAAGAAATACACAGCA	57.368	33.333	0.00	0.00	0.00	4.41
253	276	6.631971	TTGACATGAAGAAATACACAGCAA	57.368	33.333	0.00	0.00	0.00	3.91
340	365	5.479306	TCGTGAGTTTGGATCCTCTTTTAG	58.521	41.667	14.23	0.00	0.00	1.85
344	369	7.255139	CGTGAGTTTGGATCCTCTTTTAGTTTT	60.255	37.037	14.23	0.00	0.00	2.43
376	401	9.936759	ATTAGCATAAGTAGATCCTCTTTTAGC	57.063	33.333	5.52	7.45	0.00	3.09
436	604	3.908904	ATGCATGCCCCAACTGCCA	62.909	57.895	16.68	0.00	35.02	4.92
442	611	1.114722	TGCCCCAACTGCCAAAGAAG	61.115	55.000	0.00	0.00	0.00	2.85
492	661	7.482654	GCAACTGCATCTATACATAGAACAA	57.517	36.000	3.16	0.00	42.20	2.83
559	733	5.323581	TGAACAAAGATGGAATGGTGATGA	58.676	37.500	0.00	0.00	0.00	2.92
617	792	4.130118	GTCAATCCTAGGACGAAATGCAT	58.870	43.478	15.42	0.00	0.00	3.96
694	873	2.190981	GCAACGAACGACCGAGAATAT	58.809	47.619	8.04	0.00	0.00	1.28
759	938	1.859427	CTTGTGCAAGCATGGCGTCT	61.859	55.000	0.00	0.00	38.51	4.18
782	961	9.601217	GTCTTACATGATTTATCCAGTAACAGT	57.399	33.333	0.00	0.00	0.00	3.55
879	1058	5.223382	TCTCGTTCAGTCTGAAAACAGATC	58.777	41.667	16.86	2.31	38.22	2.75
1096	1282	4.456280	TGTACGATCTTCAGTCTTGCAT	57.544	40.909	0.00	0.00	0.00	3.96
1167	1353	1.207488	AAGCCCATGTGGAGGTGCTA	61.207	55.000	0.00	0.00	37.39	3.49
1247	1433	0.107116	GGCTACCGAGAGAGAGGTGA	60.107	60.000	0.00	0.00	41.51	4.02
1313	1499	4.368003	CCTAACGGGAGTAGGGCA	57.632	61.111	0.00	0.00	46.69	5.36
1352	1538	2.680352	GGAGTGGGCTCACCTCGA	60.680	66.667	14.62	0.00	44.64	4.04
1557	1743	2.932663	GCTGTTGGAACTGCTGCTA	58.067	52.632	12.61	0.00	46.38	3.49
1634	1830	1.103398	GCTGTTGGTTGCTGTCCTGT	61.103	55.000	0.00	0.00	0.00	4.00
1657	1853	0.193574	TGAGGAAGGAGAAGTGGGGT	59.806	55.000	0.00	0.00	0.00	4.95
1689	1885	1.821136	GCTGATTGAAAGGGAACTGGG	59.179	52.381	0.00	0.00	42.68	4.45
1703	1899	2.254152	ACTGGGGACTGCTGATTCTA	57.746	50.000	0.00	0.00	0.00	2.10
1711	1907	3.449018	GGACTGCTGATTCTACAGAGGAA	59.551	47.826	11.79	0.00	39.94	3.36
1718	1914	5.728471	CTGATTCTACAGAGGAATGTGTGT	58.272	41.667	0.00	0.00	39.94	3.72
1820	2021	4.465886	AGAAGCTAGCTAAGATCCTCGAA	58.534	43.478	19.70	0.00	0.00	3.71
2131	2332	0.610174	ACATCCGCTGCGATATGGAT	59.390	50.000	28.23	18.65	41.85	3.41
2325	2526	1.078848	GCTTGCATCGAGTCAGGGT	60.079	57.895	0.00	0.00	0.00	4.34
2451	2652	1.028130	TGAGGAGACTATCGCTGCAG	58.972	55.000	10.11	10.11	44.43	4.41
2577	2778	4.228210	ACAAATGTCATATCTGTGGGGAGT	59.772	41.667	0.00	0.00	0.00	3.85
2618	2819	2.743718	CCAACTCGTGGCAGAGGT	59.256	61.111	15.26	8.33	41.72	3.85
2682	2883	2.111384	GAGGCAGAGGTGGATACTCAA	58.889	52.381	0.00	0.00	37.43	3.02
2736	2937	2.766828	GGTGGCTACTCAGGACACTTAT	59.233	50.000	0.00	0.00	32.88	1.73
2830	3031	5.510430	TGACTATGGAGACTTTGCTCTCTA	58.490	41.667	1.24	0.00	37.44	2.43
2841	3042	0.927029	TGCTCTCTAGGCCTCCACTA	59.073	55.000	9.68	0.00	0.00	2.74
3050	3252	3.384816	CACAGTCAAGTGCACTCCA	57.615	52.632	21.95	6.72	32.04	3.86
3158	3360	4.578516	TGTCGTGTGATCCTTGACAAATTT	59.421	37.500	5.12	0.00	36.69	1.82
3171	3373	4.437239	TGACAAATTTGGTTGCGTGATTT	58.563	34.783	21.74	0.00	31.29	2.17
3195	3397	3.749064	GCCAGACGAGCCAGACGA	61.749	66.667	0.00	0.00	34.70	4.20
3585	3788	5.177511	ACTTGGATTTATATGATGCGTCACG	59.822	40.000	11.65	0.00	37.14	4.35
3636	3839	3.173953	TCCATGCCTTGGTGAAGAATT	57.826	42.857	2.98	0.00	46.52	2.17
3725	3928	2.620585	GGCCTATTTGTCTGATCAAGGC	59.379	50.000	19.72	19.72	36.26	4.35

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
21	22	9.588096	AACATAGGTTGAAATATATTTCCCCTC	57.412	33.333	30.73	20.14	44.16	4.30
34	35	6.488344	TCATGTGCTGTTAACATAGGTTGAAA	59.512	34.615	9.13	0.00	36.10	2.69
137	146	8.561738	ACGGATTAAAATATGAGTGAACAAGT	57.438	30.769	0.00	0.00	0.00	3.16
181	190	6.884096	TCTAAAGTTTGTGCATGTGTTTTG	57.116	33.333	0.00	0.00	0.00	2.44
183	192	6.630071	AGTTCTAAAGTTTGTGCATGTGTTT	58.370	32.000	0.00	0.00	0.00	2.83
344	369	8.582657	GAGGATCTACTTATGCTAATAGTGGA	57.417	38.462	0.00	0.00	0.00	4.02
436	604	5.225642	GCTGCAGCAACTATTTTCTTCTTT	58.774	37.500	33.36	0.00	41.59	2.52
442	611	2.900122	TCGCTGCAGCAACTATTTTC	57.100	45.000	36.03	5.05	42.21	2.29
517	686	2.298446	TCAGTTTGAGGAGAGCTGAGTG	59.702	50.000	0.00	0.00	33.05	3.51
559	733	5.765182	CCTGTTAATCGGGAAAAGATATGCT	59.235	40.000	0.00	0.00	45.09	3.79
617	792	5.245751	ACAACTATTGGCATGAATTTGTCCA	59.754	36.000	0.00	0.00	34.12	4.02
694	873	4.551702	TTCACAGGAGTATTTGCAGCTA	57.448	40.909	0.00	0.00	0.00	3.32
759	938	9.173021	CCAACTGTTACTGGATAAATCATGTAA	57.827	33.333	0.00	0.00	34.35	2.41
782	961	8.383175	AGAATTCAGAATAAGTTCCTACACCAA	58.617	33.333	8.44	0.00	34.81	3.67
892	1071	8.002459	TCCCTCTGTACTGATACATATGTGTTA	58.998	37.037	18.81	7.74	40.57	2.41
1000	1183	9.750125	GTTCCCTTTATCATCCATTTTATTGTC	57.250	33.333	0.00	0.00	0.00	3.18
1043	1229	6.599445	ACTTTGCTCAAGGATCTTATAGCAT	58.401	36.000	12.82	0.00	39.50	3.79
1088	1274	1.664016	CGGTTCAACAGCATGCAAGAC	60.664	52.381	21.98	9.03	42.53	3.01
1096	1282	0.322098	CCCATACCGGTTCAACAGCA	60.322	55.000	15.04	0.00	0.00	4.41
1167	1353	2.769095	GACTGATGCCTCCTTCTAGGTT	59.231	50.000	0.00	0.00	39.02	3.50
1299	1485	3.771160	CGCTGCCCTACTCCCGTT	61.771	66.667	0.00	0.00	0.00	4.44
1334	1520	2.997315	CGAGGTGAGCCCACTCCA	60.997	66.667	0.00	0.00	42.74	3.86
1543	1729	1.167851	GCACATAGCAGCAGTTCCAA	58.832	50.000	0.00	0.00	44.79	3.53
1557	1743	1.625315	TCTGACTTAGCCACTGCACAT	59.375	47.619	0.00	0.00	41.13	3.21
1565	1751	3.245443	ACTTCTCTCCTCTGACTTAGCCA	60.245	47.826	0.00	0.00	0.00	4.75
1634	1830	1.349026	CCACTTCTCCTTCCTCAGCAA	59.651	52.381	0.00	0.00	0.00	3.91
1657	1853	3.124578	TCAATCAGCAGCACAACACTA	57.875	42.857	0.00	0.00	0.00	2.74
1689	1885	3.027412	TCCTCTGTAGAATCAGCAGTCC	58.973	50.000	4.54	0.00	35.63	3.85
1703	1899	0.767375	AGCCACACACATTCCTCTGT	59.233	50.000	0.00	0.00	0.00	3.41
1711	1907	2.035421	CAAGCACAGCCACACACAT	58.965	52.632	0.00	0.00	0.00	3.21
1820	2021	0.909610	TGGCCCCAGATTTCGACTCT	60.910	55.000	0.00	0.00	0.00	3.24
2131	2332	2.891580	GAGTACAAGGTGGACAGAGTCA	59.108	50.000	0.00	0.00	32.29	3.41
2444	2645	1.013005	CCTCTTGAGACACTGCAGCG	61.013	60.000	15.27	6.98	0.00	5.18
2451	2652	0.389166	CGCACCTCCTCTTGAGACAC	60.389	60.000	0.00	0.00	44.42	3.67
2618	2819	0.481567	CCCCTCTGTCGTATCCCCTA	59.518	60.000	0.00	0.00	0.00	3.53
2736	2937	0.326904	ATGTGAGCCCTCTGATCCCA	60.327	55.000	0.00	0.00	0.00	4.37
2841	3042	3.496870	GCCTCATCCGGATTACCTTCATT	60.497	47.826	16.19	0.00	0.00	2.57
3050	3252	3.310954	ACACTGAGGATAGGGAGATGGTT	60.311	47.826	0.00	0.00	0.00	3.67
3158	3360	1.448985	GCTCCTAAATCACGCAACCA	58.551	50.000	0.00	0.00	0.00	3.67
3171	3373	3.518998	GCTCGTCTGGCGCTCCTA	61.519	66.667	7.64	0.00	41.07	2.94
3195	3397	2.765969	CCTGGTGCCAGTCCCAAT	59.234	61.111	16.15	0.00	42.15	3.16
3585	3788	5.948992	AAACAGCTAAACACCTCATCTTC	57.051	39.130	0.00	0.00	0.00	2.87
3636	3839	3.322514	GCACCTGCACCTGAAACTA	57.677	52.632	0.00	0.00	41.59	2.24
3725	3928	5.125900	TGGGCATGTAGTTTGATGAAGAATG	59.874	40.000	0.00	0.00	0.00	2.67

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.