AutoCloner

Multiple sequence alignment - TraesCS4D01G131800

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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	TraesCS4D01G131800	chr4D	100.000	2762	0	0	1	2762	118552033	118549272	0.000000e+00	5101
1	TraesCS4D01G131800	chr4D	88.095	126	13	1	321	444	391733460	391733585	6.160000e-32	148
2	TraesCS4D01G131800	chr4B	95.858	2028	70	6	181	2201	332574329	332576349	0.000000e+00	3267
3	TraesCS4D01G131800	chr4B	91.234	308	18	4	2457	2762	45479942	45479642	7.120000e-111	411
4	TraesCS4D01G131800	chr4B	90.654	214	18	1	1989	2202	362064503	362064292	1.620000e-72	283
5	TraesCS4D01G131800	chr4B	92.778	180	13	0	1	180	332574049	332574228	7.590000e-66	261
6	TraesCS4D01G131800	chr4A	93.652	1276	46	8	181	1455	615222361	615221120	0.000000e+00	1875
7	TraesCS4D01G131800	chr4A	96.044	455	14	4	1459	1912	615219174	615218723	0.000000e+00	737
8	TraesCS4D01G131800	chr4A	96.949	295	7	1	1907	2201	615218696	615218404	6.870000e-136	494
9	TraesCS4D01G131800	chr4A	93.296	179	6	2	2	180	615222628	615222456	2.730000e-65	259
10	TraesCS4D01G131800	chr4A	88.235	85	9	1	341	424	261879038	261879122	1.750000e-17	100
11	TraesCS4D01G131800	chr2A	94.518	1204	45	6	253	1455	604627150	604625967	0.000000e+00	1838
12	TraesCS4D01G131800	chr2A	95.604	455	16	4	1459	1912	604624021	604623570	0.000000e+00	726
13	TraesCS4D01G131800	chr2A	87.766	564	51	8	2202	2759	1843352	1843903	0.000000e+00	643
14	TraesCS4D01G131800	chr2A	96.610	295	7	3	1907	2201	604623543	604623252	1.150000e-133	486
15	TraesCS4D01G131800	chr2A	91.531	307	19	3	2457	2761	202537286	202537587	1.530000e-112	416
16	TraesCS4D01G131800	chr2A	94.972	179	9	0	2	180	604627474	604627296	5.820000e-72	281
17	TraesCS4D01G131800	chr5A	94.298	1210	47	10	253	1455	482741277	482740083	0.000000e+00	1832
18	TraesCS4D01G131800	chr5A	95.385	455	17	4	1462	1915	482738135	482737684	0.000000e+00	721
19	TraesCS4D01G131800	chr5A	91.803	305	19	2	2457	2759	154884735	154885035	1.180000e-113	420
20	TraesCS4D01G131800	chr5A	93.296	179	9	1	2	180	482741601	482741426	7.590000e-66	261
21	TraesCS4D01G131800	chr5B	94.025	1205	56	6	252	1455	24175412	24176601	0.000000e+00	1812
22	TraesCS4D01G131800	chr5B	95.604	455	15	5	1459	1912	24178544	24178994	0.000000e+00	725
23	TraesCS4D01G131800	chr5B	87.011	562	50	8	2213	2762	137388143	137387593	1.820000e-171	612
24	TraesCS4D01G131800	chr5B	97.288	295	6	1	1907	2201	24179021	24179313	1.480000e-137	499
25	TraesCS4D01G131800	chr5B	95.531	179	8	0	2	180	24175102	24175280	1.250000e-73	287
26	TraesCS4D01G131800	chr3A	92.572	1279	64	16	181	1455	322330074	322328823	0.000000e+00	1807
27	TraesCS4D01G131800	chr3A	95.207	772	35	2	685	1455	238190195	238189425	0.000000e+00	1219
28	TraesCS4D01G131800	chr3A	93.419	775	36	5	253	1027	180127850	180127091	0.000000e+00	1134
29	TraesCS4D01G131800	chr3A	96.044	455	14	4	1459	1912	180126824	180126373	0.000000e+00	737
30	TraesCS4D01G131800	chr3A	95.385	455	16	5	1459	1912	322326880	322326430	0.000000e+00	719
31	TraesCS4D01G131800	chr3A	96.990	299	7	1	1907	2205	180126346	180126050	4.110000e-138	501
32	TraesCS4D01G131800	chr3A	96.678	301	8	1	1907	2207	322326403	322326105	1.480000e-137	499
33	TraesCS4D01G131800	chr3A	92.208	308	19	3	2457	2762	222007819	222008123	5.460000e-117	431
34	TraesCS4D01G131800	chr3A	93.962	265	13	2	1648	1912	238187591	238187330	5.540000e-107	398
35	TraesCS4D01G131800	chr3A	93.574	249	13	2	1953	2201	238186914	238186669	4.350000e-98	368
36	TraesCS4D01G131800	chr3A	95.531	179	8	0	2	180	180128172	180127994	1.250000e-73	287
37	TraesCS4D01G131800	chr3A	94.444	180	10	0	2	181	322330337	322330158	7.530000e-71	278
38	TraesCS4D01G131800	chr3A	93.296	179	12	0	2	180	238190393	238190215	5.870000e-67	265
39	TraesCS4D01G131800	chr7A	93.548	775	35	5	253	1027	577148188	577147429	0.000000e+00	1140
40	TraesCS4D01G131800	chr7A	95.824	455	15	4	1459	1912	577147162	577146711	0.000000e+00	732
41	TraesCS4D01G131800	chr7A	96.949	295	7	1	1907	2201	577146684	577146392	6.870000e-136	494
42	TraesCS4D01G131800	chr7A	96.648	179	6	0	2	180	577148510	577148332	5.780000e-77	298
43	TraesCS4D01G131800	chr7D	93.182	308	13	3	2457	2762	557563283	557562982	1.950000e-121	446
44	TraesCS4D01G131800	chr7D	92.182	307	16	3	2457	2761	14287230	14286930	7.070000e-116	427
45	TraesCS4D01G131800	chr1A	91.234	308	20	3	2457	2762	69480089	69479787	1.980000e-111	412
46	TraesCS4D01G131800	chr1D	94.595	259	11	3	2204	2459	43428648	43428390	5.540000e-107	398
47	TraesCS4D01G131800	chr1D	93.822	259	15	1	2202	2459	55600939	55601197	3.340000e-104	388
48	TraesCS4D01G131800	chr1D	93.822	259	14	2	2202	2459	315181742	315181485	3.340000e-104	388
49	TraesCS4D01G131800	chr2D	94.231	260	13	2	2202	2459	354422077	354421818	1.990000e-106	396
50	TraesCS4D01G131800	chrUn	93.822	259	14	2	2202	2459	271120510	271120253	3.340000e-104	388
51	TraesCS4D01G131800	chrUn	95.614	114	1	4	1459	1571	480551244	480551354	2.190000e-41	180
52	TraesCS4D01G131800	chr6D	93.822	259	15	1	2202	2459	252746605	252746347	3.340000e-104	388
53	TraesCS4D01G131800	chr6D	85.088	114	14	3	321	431	100688803	100688916	2.250000e-21	113
54	TraesCS4D01G131800	chr3D	93.822	259	15	1	2202	2459	295933349	295933607	3.340000e-104	388
55	TraesCS4D01G131800	chr2B	88.889	126	12	1	321	444	232789544	232789669	1.320000e-33	154

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	TraesCS4D01G131800	chr4D	118549272	118552033	2761	True	5101.00	5101	100.000000	1	2762	1	chr4D.!!$R1	2761
1	TraesCS4D01G131800	chr4B	332574049	332576349	2300	False	1764.00	3267	94.318000	1	2201	2	chr4B.!!$F1	2200
2	TraesCS4D01G131800	chr4A	615218404	615222628	4224	True	841.25	1875	94.985250	2	2201	4	chr4A.!!$R1	2199
3	TraesCS4D01G131800	chr2A	604623252	604627474	4222	True	832.75	1838	95.426000	2	2201	4	chr2A.!!$R1	2199
4	TraesCS4D01G131800	chr2A	1843352	1843903	551	False	643.00	643	87.766000	2202	2759	1	chr2A.!!$F1	557
5	TraesCS4D01G131800	chr5A	482737684	482741601	3917	True	938.00	1832	94.326333	2	1915	3	chr5A.!!$R1	1913
6	TraesCS4D01G131800	chr5B	24175102	24179313	4211	False	830.75	1812	95.612000	2	2201	4	chr5B.!!$F1	2199
7	TraesCS4D01G131800	chr5B	137387593	137388143	550	True	612.00	612	87.011000	2213	2762	1	chr5B.!!$R1	549
8	TraesCS4D01G131800	chr3A	322326105	322330337	4232	True	825.75	1807	94.769750	2	2207	4	chr3A.!!$R3	2205
9	TraesCS4D01G131800	chr3A	180126050	180128172	2122	True	664.75	1134	95.496000	2	2205	4	chr3A.!!$R1	2203
10	TraesCS4D01G131800	chr3A	238186669	238190393	3724	True	562.50	1219	94.009750	2	2201	4	chr3A.!!$R2	2199
11	TraesCS4D01G131800	chr7A	577146392	577148510	2118	True	666.00	1140	95.742250	2	2201	4	chr7A.!!$R1	2199

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
108	109	2.357034	GGAGAAGCACAACGCCGA	60.357	61.111	0.0	0.0	44.04	5.54	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2102	4589	1.211949	CCCATCCCCGTTTACATGACT	59.788	52.381	0.0	0.0	0.0	3.41	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
108	109	2.357034	GGAGAAGCACAACGCCGA	60.357	61.111	0.00	0.00	44.04	5.54
450	596	2.573009	TGGACATCTTCTGCTGATGGAA	59.427	45.455	8.32	0.00	43.88	3.53
538	684	5.131067	AGTATCTTGTAGTACTGATCGGCA	58.869	41.667	5.39	0.00	30.35	5.69
998	1153	9.467258	AATCAACGCATATCCATTTATTCTTTG	57.533	29.630	0.00	0.00	0.00	2.77
1148	1306	3.775654	AGCAGCCTAGTCACCGCC	61.776	66.667	0.00	0.00	0.00	6.13
1167	1325	1.344496	CCCCTACTCTGACATCCCCTT	60.344	57.143	0.00	0.00	0.00	3.95
1399	1560	2.224606	CTGGTGCTCAAAGAAGCTTGA	58.775	47.619	2.10	0.00	42.94	3.02
1486	3597	6.937392	AGGTTTAGAGGTGAGTCAATCTAAC	58.063	40.000	20.74	16.69	34.78	2.34
1588	3699	2.159114	TCTGCAGCGCATCACACTATAA	60.159	45.455	11.47	0.00	38.13	0.98
1867	3978	5.769662	TGGTGTTTGCATTGATACTCTCTTT	59.230	36.000	0.00	0.00	0.00	2.52
1939	4082	4.019792	TGGTGCATACAACATCTTGTCT	57.980	40.909	0.00	0.00	39.04	3.41
2160	4647	1.591768	AGATGGGTACGGGGATGTTT	58.408	50.000	0.00	0.00	0.00	2.83
2290	4782	3.731652	TGGTGTTGATTCTTTTGCCAG	57.268	42.857	0.00	0.00	0.00	4.85
2324	4816	7.384439	TGTATTCCAAAAATATTCTGCGTGA	57.616	32.000	0.00	0.00	0.00	4.35
2326	4818	7.967854	TGTATTCCAAAAATATTCTGCGTGAAG	59.032	33.333	0.00	0.00	38.18	3.02
2340	4832	2.411547	GCGTGAAGTTTCAGGTCATTCG	60.412	50.000	13.97	5.70	43.08	3.34
2360	4852	5.607119	TCGGAGAACTTTTATTTCTGCAC	57.393	39.130	4.76	0.00	40.45	4.57
2406	4900	0.599204	GAAAACAGCGTCAGTCCGGA	60.599	55.000	0.00	0.00	0.00	5.14
2453	4947	2.310538	AGAGTCCAAAACAAGGGCAAG	58.689	47.619	0.00	0.00	31.65	4.01
2478	4976	3.565482	TGTCCTCAAGCAATTCAGTTGAC	59.435	43.478	0.00	0.00	40.37	3.18
2482	4980	4.741676	CCTCAAGCAATTCAGTTGACAAAC	59.258	41.667	0.00	0.00	40.37	2.93
2526	5024	9.841880	AACTTTTACAAACTCTGTTTTCTCTTC	57.158	29.630	0.00	0.00	39.64	2.87
2577	5077	7.867403	TCAAGTTTTCAGCAAAGATTATGAACC	59.133	33.333	0.00	0.00	31.72	3.62
2607	5107	8.755941	CATATTCACAATAACACTTAGGTCTCG	58.244	37.037	0.00	0.00	0.00	4.04
2634	5134	8.720562	TGTTTACTCATATCAATGGCATAATCG	58.279	33.333	0.00	0.00	33.61	3.34
2677	5177	5.712152	AATCTTGGATGACAACACTTTCC	57.288	39.130	0.00	0.00	34.76	3.13
2692	5192	7.494298	ACAACACTTTCCCAAAACAATCATAAC	59.506	33.333	0.00	0.00	0.00	1.89
2693	5193	7.360113	ACACTTTCCCAAAACAATCATAACT	57.640	32.000	0.00	0.00	0.00	2.24

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
108	109	3.056035	CGTTACCTAGGAACCTTGAGCTT	60.056	47.826	17.98	0.00	0.00	3.74
234	347	3.626924	GACTCCGTGGTGGTGGCT	61.627	66.667	0.00	0.00	36.26	4.75
235	348	4.699522	GGACTCCGTGGTGGTGGC	62.700	72.222	0.00	0.00	38.62	5.01
236	349	4.373116	CGGACTCCGTGGTGGTGG	62.373	72.222	9.51	0.00	42.73	4.61
237	350	4.373116	CCGGACTCCGTGGTGGTG	62.373	72.222	16.35	0.00	46.80	4.17
240	353	4.742201	CTGCCGGACTCCGTGGTG	62.742	72.222	16.35	2.08	46.80	4.17
277	409	4.459089	GCGGGGAGTGTCTCAGGC	62.459	72.222	0.00	0.00	31.08	4.85
284	416	3.402681	CTCCATGGCGGGGAGTGT	61.403	66.667	6.96	0.00	45.59	3.55
349	485	1.132500	GGCTAGGTGTGGCTAAGGAT	58.868	55.000	0.00	0.00	0.00	3.24
388	524	1.817209	GACTAGAAGAGGTGCGGGG	59.183	63.158	0.00	0.00	0.00	5.73
389	525	1.030488	TCGACTAGAAGAGGTGCGGG	61.030	60.000	0.00	0.00	0.00	6.13
390	526	1.025812	ATCGACTAGAAGAGGTGCGG	58.974	55.000	0.00	0.00	0.00	5.69
391	527	2.455032	CAATCGACTAGAAGAGGTGCG	58.545	52.381	0.00	0.00	0.00	5.34
392	528	2.815478	CCAATCGACTAGAAGAGGTGC	58.185	52.381	0.00	0.00	0.00	5.01
393	529	2.482142	GGCCAATCGACTAGAAGAGGTG	60.482	54.545	0.00	0.00	0.00	4.00
394	530	1.757699	GGCCAATCGACTAGAAGAGGT	59.242	52.381	0.00	0.00	0.00	3.85
395	531	1.069358	GGGCCAATCGACTAGAAGAGG	59.931	57.143	4.39	0.00	0.00	3.69
396	532	2.035321	GAGGGCCAATCGACTAGAAGAG	59.965	54.545	6.18	0.00	0.00	2.85
397	533	2.032620	GAGGGCCAATCGACTAGAAGA	58.967	52.381	6.18	0.00	0.00	2.87
538	684	8.324306	TCATGACTGAATCTAAAAAGTCTGGAT	58.676	33.333	0.00	0.00	39.80	3.41
998	1153	3.550436	GCTACTTATCTCCCACTACGTGC	60.550	52.174	0.00	0.00	31.34	5.34
1148	1306	2.182516	AAGGGGATGTCAGAGTAGGG	57.817	55.000	0.00	0.00	0.00	3.53
1167	1325	4.469586	TGGTACCTCATCAGCTTCATGTTA	59.530	41.667	14.36	0.00	0.00	2.41
1399	1560	3.239449	GTTCCATTTCTTGGTTCCCCTT	58.761	45.455	0.00	0.00	46.52	3.95
1486	3597	5.236282	TGAAAAATGGTGCCATGTACAATG	58.764	37.500	0.00	0.00	36.68	2.82
1559	3670	1.398041	GATGCGCTGCAGAAACACATA	59.602	47.619	20.43	0.00	43.65	2.29
1588	3699	9.794983	TGTAGTAAGTACAGAAGGAACCCCCTT	62.795	44.444	0.00	0.00	46.15	3.95
1683	3794	2.616376	TCGTGCACAAAAGTATTGCAGT	59.384	40.909	18.64	0.00	46.57	4.40
2020	4506	5.606329	CCCATCCCCATAAACAAATAACCAT	59.394	40.000	0.00	0.00	0.00	3.55
2021	4507	4.965532	CCCATCCCCATAAACAAATAACCA	59.034	41.667	0.00	0.00	0.00	3.67
2022	4508	4.346709	CCCCATCCCCATAAACAAATAACC	59.653	45.833	0.00	0.00	0.00	2.85
2023	4509	5.069914	GTCCCCATCCCCATAAACAAATAAC	59.930	44.000	0.00	0.00	0.00	1.89
2102	4589	1.211949	CCCATCCCCGTTTACATGACT	59.788	52.381	0.00	0.00	0.00	3.41
2259	4751	2.113139	AACACCAAGAGGCCCACG	59.887	61.111	0.00	0.00	39.06	4.94
2267	4759	3.703556	TGGCAAAAGAATCAACACCAAGA	59.296	39.130	0.00	0.00	0.00	3.02
2270	4762	3.030291	ACTGGCAAAAGAATCAACACCA	58.970	40.909	0.00	0.00	0.00	4.17
2272	4764	7.713764	AAAATACTGGCAAAAGAATCAACAC	57.286	32.000	0.00	0.00	0.00	3.32
2301	4793	7.968405	ACTTCACGCAGAATATTTTTGGAATAC	59.032	33.333	0.00	0.00	35.25	1.89
2319	4811	2.411547	CGAATGACCTGAAACTTCACGC	60.412	50.000	0.00	0.00	32.90	5.34
2324	4816	4.065789	GTTCTCCGAATGACCTGAAACTT	58.934	43.478	0.00	0.00	0.00	2.66
2326	4818	3.665190	AGTTCTCCGAATGACCTGAAAC	58.335	45.455	0.00	0.00	0.00	2.78
2340	4832	8.419076	TTTTTGTGCAGAAATAAAAGTTCTCC	57.581	30.769	10.13	0.00	32.96	3.71
2360	4852	6.621164	GCAGAATTGCCATGGTGTTATTTTTG	60.621	38.462	14.67	10.79	44.74	2.44
2406	4900	7.844009	ACTTGCATGATTTGAATGGAACTAAT	58.156	30.769	6.60	0.00	32.71	1.73
2453	4947	3.406764	ACTGAATTGCTTGAGGACACTC	58.593	45.455	0.00	0.00	44.23	3.51
2520	5018	9.878667	TGGATTTACATATTTACAACGAAGAGA	57.121	29.630	0.00	0.00	0.00	3.10
2526	5024	9.169468	GAATGCTGGATTTACATATTTACAACG	57.831	33.333	0.00	0.00	0.00	4.10
2543	5043	2.957680	TGCTGAAAACTTGAATGCTGGA	59.042	40.909	0.00	0.00	0.00	3.86
2577	5077	8.956426	ACCTAAGTGTTATTGTGAATATGGTTG	58.044	33.333	0.00	0.00	0.00	3.77
2607	5107	9.831737	GATTATGCCATTGATATGAGTAAACAC	57.168	33.333	0.00	0.00	33.37	3.32
2660	5160	3.304911	TTGGGAAAGTGTTGTCATCCA	57.695	42.857	0.00	0.00	31.63	3.41
2693	5193	9.559732	CCATCTTGTACCATCTTGTTATATCAA	57.440	33.333	0.00	0.00	0.00	2.57
2713	5213	1.896465	GGGCTAGCGAGATACCATCTT	59.104	52.381	9.00	0.00	40.38	2.40
2714	5214	1.076350	AGGGCTAGCGAGATACCATCT	59.924	52.381	9.00	0.00	43.70	2.90
2715	5215	1.551452	AGGGCTAGCGAGATACCATC	58.449	55.000	9.00	0.00	0.00	3.51
2716	5216	2.016905	AAGGGCTAGCGAGATACCAT	57.983	50.000	9.00	0.00	0.00	3.55
2717	5217	1.687123	GAAAGGGCTAGCGAGATACCA	59.313	52.381	9.00	0.00	0.00	3.25
2718	5218	1.964933	AGAAAGGGCTAGCGAGATACC	59.035	52.381	9.00	2.74	0.00	2.73
2719	5219	2.623889	TCAGAAAGGGCTAGCGAGATAC	59.376	50.000	9.00	0.00	0.00	2.24
2720	5220	2.887783	CTCAGAAAGGGCTAGCGAGATA	59.112	50.000	9.00	0.00	0.00	1.98
2721	5221	1.686052	CTCAGAAAGGGCTAGCGAGAT	59.314	52.381	9.00	0.00	0.00	2.75
2722	5222	1.107114	CTCAGAAAGGGCTAGCGAGA	58.893	55.000	9.00	0.00	0.00	4.04

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.