AutoCloner

Multiple sequence alignment - TraesCS4B01G388100

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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	TraesCS4B01G388100	chr4B	100.000	2708	0	0	1	2708	665434729	665437436	0.000000e+00	5001.0
1	TraesCS4B01G388100	chr4B	94.344	1998	81	13	1	1981	665385648	665383666	0.000000e+00	3035.0
2	TraesCS4B01G388100	chr4B	92.738	2093	111	18	636	2708	665382338	665380267	0.000000e+00	2985.0
3	TraesCS4B01G388100	chr4B	95.397	1347	47	3	636	1981	665383668	665382336	0.000000e+00	2130.0
4	TraesCS4B01G388100	chr5A	92.734	1913	102	18	805	2708	705407690	705409574	0.000000e+00	2728.0
5	TraesCS4B01G388100	chr5A	91.007	556	35	8	2079	2621	705382175	705381622	0.000000e+00	736.0
6	TraesCS4B01G388100	chr5A	81.561	602	97	11	1142	1737	705395169	705394576	4.050000e-133	484.0
7	TraesCS4B01G388100	chr5A	80.631	444	71	13	1273	1710	705322831	705323265	2.010000e-86	329.0
8	TraesCS4B01G388100	chrUn	93.696	1047	44	5	806	1851	108608076	108609101	0.000000e+00	1548.0
9	TraesCS4B01G388100	chrUn	82.173	589	93	9	1127	1710	108604181	108604762	1.870000e-136	496.0
10	TraesCS4B01G388100	chr7B	91.810	696	29	12	2014	2708	742235636	742236304	0.000000e+00	944.0
11	TraesCS4B01G388100	chr7B	89.938	487	42	3	289	773	436958536	436958055	2.960000e-174	621.0
12	TraesCS4B01G388100	chr7B	92.735	234	14	3	1	232	105938201	105937969	4.320000e-88	335.0
13	TraesCS4B01G388100	chr7B	92.275	233	13	4	1	232	72516076	72516304	2.600000e-85	326.0
14	TraesCS4B01G388100	chr5D	92.165	485	36	1	291	773	309120452	309119968	0.000000e+00	684.0
15	TraesCS4B01G388100	chr5D	90.329	486	43	2	289	772	481608002	481608485	3.800000e-178	634.0
16	TraesCS4B01G388100	chr5D	83.333	66	9	2	2352	2417	387847356	387847293	2.910000e-05	60.2
17	TraesCS4B01G388100	chr2D	90.349	487	43	3	289	773	481022683	481023167	1.060000e-178	636.0
18	TraesCS4B01G388100	chr2D	80.323	742	124	12	998	1722	577547523	577548259	2.370000e-150	542.0
19	TraesCS4B01G388100	chr2D	94.444	234	10	3	1	232	89922948	89922716	9.220000e-95	357.0
20	TraesCS4B01G388100	chr7A	90.144	487	44	2	289	773	343830710	343830226	4.920000e-177	630.0
21	TraesCS4B01G388100	chr7A	92.735	234	14	3	1	232	716410622	716410854	4.320000e-88	335.0
22	TraesCS4B01G388100	chr3B	90.164	488	43	4	289	773	489062171	489062656	4.920000e-177	630.0
23	TraesCS4B01G388100	chr3B	86.567	67	7	2	2349	2414	106700706	106700771	3.740000e-09	73.1
24	TraesCS4B01G388100	chr2B	90.184	489	41	5	289	773	150147090	150147575	4.920000e-177	630.0
25	TraesCS4B01G388100	chr5B	89.959	488	43	4	289	773	547011194	547011678	2.290000e-175	625.0
26	TraesCS4B01G388100	chr5B	90.909	44	4	0	2349	2392	472681651	472681694	2.910000e-05	60.2
27	TraesCS4B01G388100	chr3D	95.299	234	7	4	1	232	550190994	550190763	4.260000e-98	368.0
28	TraesCS4B01G388100	chr7D	93.162	234	13	3	1	232	420419927	420420159	9.290000e-90	340.0
29	TraesCS4B01G388100	chr4D	93.162	234	13	3	1	232	351728450	351728218	9.290000e-90	340.0
30	TraesCS4B01G388100	chr3A	91.880	234	16	3	1	232	717671687	717671919	9.350000e-85	324.0

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	TraesCS4B01G388100	chr4B	665434729	665437436	2707	False	5001.000000	5001	100.000000	1	2708	1	chr4B.!!$F1	2707
1	TraesCS4B01G388100	chr4B	665380267	665385648	5381	True	2716.666667	3035	94.159667	1	2708	3	chr4B.!!$R1	2707
2	TraesCS4B01G388100	chr5A	705407690	705409574	1884	False	2728.000000	2728	92.734000	805	2708	1	chr5A.!!$F2	1903
3	TraesCS4B01G388100	chr5A	705381622	705382175	553	True	736.000000	736	91.007000	2079	2621	1	chr5A.!!$R1	542
4	TraesCS4B01G388100	chr5A	705394576	705395169	593	True	484.000000	484	81.561000	1142	1737	1	chr5A.!!$R2	595
5	TraesCS4B01G388100	chrUn	108604181	108609101	4920	False	1022.000000	1548	87.934500	806	1851	2	chrUn.!!$F1	1045
6	TraesCS4B01G388100	chr7B	742235636	742236304	668	False	944.000000	944	91.810000	2014	2708	1	chr7B.!!$F2	694
7	TraesCS4B01G388100	chr2D	577547523	577548259	736	False	542.000000	542	80.323000	998	1722	1	chr2D.!!$F2	724

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
983	4080	0.674534	ATAAGAGATGGACCGACGCC	59.325	55.0	0.0	0.0	0.0	5.68	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1948	7723	3.548745	TGGACTGCAGATTGTCTATGG	57.451	47.619	23.35	0.0	34.01	2.74	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
28	29	6.910259	ATCACCCCCTATTACTCTCTTTTT	57.090	37.500	0.00	0.00	0.00	1.94
37	38	7.340487	CCCTATTACTCTCTTTTTCTTTGCCAT	59.660	37.037	0.00	0.00	0.00	4.40
120	121	6.183360	ACCTCTGAAAACAAACTTTCTCCATG	60.183	38.462	0.00	0.00	36.46	3.66
127	128	9.780413	GAAAACAAACTTTCTCCATGATCTATC	57.220	33.333	0.00	0.00	33.36	2.08
224	226	0.997196	GTCTCCCACGTTACATTCGC	59.003	55.000	0.00	0.00	0.00	4.70
226	228	1.418342	CTCCCACGTTACATTCGCCG	61.418	60.000	0.00	0.00	0.00	6.46
261	263	2.092375	GGGAAAAGCCTGGTAGTAGCAT	60.092	50.000	1.83	0.00	36.66	3.79
340	355	4.337274	TGCTATTCGTACTTAGCAGTAGCA	59.663	41.667	14.41	10.16	44.32	3.49
425	440	8.576936	AAAGAGCGCTACTACTATATTTTCAC	57.423	34.615	11.50	0.00	0.00	3.18
579	596	9.492973	AAATCATGTCGTCACATCATAATCATA	57.507	29.630	0.00	0.00	41.69	2.15
617	634	8.546244	CAAGTTACATGACATGTCTCATCATAC	58.454	37.037	24.04	14.33	43.67	2.39
643	660	1.826340	TAGCACTTCTTGAGGCGCCA	61.826	55.000	31.54	5.56	0.00	5.69
691	708	5.180680	GCGTGGACCTCAACTAACTATTTTT	59.819	40.000	0.00	0.00	0.00	1.94
692	709	6.620089	GCGTGGACCTCAACTAACTATTTTTC	60.620	42.308	0.00	0.00	0.00	2.29
776	793	3.343788	CTCCGGCCACTCGTCACTC	62.344	68.421	2.24	0.00	0.00	3.51
809	826	2.160417	CACTCTTTTTGACCGGCTGATC	59.840	50.000	0.00	0.00	0.00	2.92
844	3935	2.418976	CGTCTGATCGGTGTCACTCTTA	59.581	50.000	2.35	0.00	0.00	2.10
981	4078	1.954382	TCCATAAGAGATGGACCGACG	59.046	52.381	2.06	0.00	42.81	5.12
982	4079	1.603172	CCATAAGAGATGGACCGACGC	60.603	57.143	0.00	0.00	41.64	5.19
983	4080	0.674534	ATAAGAGATGGACCGACGCC	59.325	55.000	0.00	0.00	0.00	5.68
984	4081	1.721664	TAAGAGATGGACCGACGCCG	61.722	60.000	0.00	0.00	0.00	6.46
985	4082	3.515286	GAGATGGACCGACGCCGA	61.515	66.667	0.00	0.00	38.22	5.54
986	4083	3.753070	GAGATGGACCGACGCCGAC	62.753	68.421	0.00	0.00	38.22	4.79
1116	4216	2.092753	CCTTACCATCCTGACACTGCAT	60.093	50.000	0.00	0.00	0.00	3.96
1353	5784	1.828660	CCGTGTCCTCTCCGCCTAT	60.829	63.158	0.00	0.00	0.00	2.57
1447	7220	1.515020	CTGAAGCCCGTCAGAGAGG	59.485	63.158	5.45	0.00	46.76	3.69
1747	7521	1.333619	TGCAGCTCGTTTTGGACTTTC	59.666	47.619	0.00	0.00	0.00	2.62
1759	7533	7.601508	TCGTTTTGGACTTTCTTTAGGTCTATC	59.398	37.037	0.00	0.00	0.00	2.08
1760	7534	7.603024	CGTTTTGGACTTTCTTTAGGTCTATCT	59.397	37.037	0.00	0.00	0.00	1.98
1761	7535	8.937884	GTTTTGGACTTTCTTTAGGTCTATCTC	58.062	37.037	0.00	0.00	0.00	2.75
1762	7536	6.793505	TGGACTTTCTTTAGGTCTATCTCC	57.206	41.667	0.00	0.00	0.00	3.71
1763	7537	5.360144	TGGACTTTCTTTAGGTCTATCTCCG	59.640	44.000	0.00	0.00	0.00	4.63
1764	7538	5.265350	ACTTTCTTTAGGTCTATCTCCGC	57.735	43.478	0.00	0.00	0.00	5.54
1785	7559	3.050619	CCTCCGGTCGATATTTCTTTCG	58.949	50.000	0.00	0.00	36.72	3.46
1899	7674	2.154798	TTTCAGCCCCGACGTCTCAG	62.155	60.000	14.70	2.57	0.00	3.35
1948	7723	7.482654	AAGAAAAAGCTAAAACTTTGGCATC	57.517	32.000	12.30	5.73	45.69	3.91
2040	7818	6.986817	AGTGTAGAAATTATCCATCAACTCCG	59.013	38.462	0.00	0.00	0.00	4.63
2061	7840	3.242248	CGAAACCGGTAAATCTTAGAGCG	59.758	47.826	8.00	0.00	0.00	5.03
2150	7933	3.254657	TGGGGTGATTAAACTTTTGCTCG	59.745	43.478	0.00	0.00	0.00	5.03
2309	8095	7.565398	ACATCAGTAACAGTCCATTCCTACTAT	59.435	37.037	0.00	0.00	0.00	2.12

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
28	29	3.631250	GGAGTAATTGGGATGGCAAAGA	58.369	45.455	0.00	0.00	0.00	2.52
37	38	2.026641	CGTACCTCGGAGTAATTGGGA	58.973	52.381	4.02	0.00	35.71	4.37
120	121	4.070716	CAAGAAGGCACATGGGATAGATC	58.929	47.826	0.00	0.00	0.00	2.75
127	128	1.341080	AAACCAAGAAGGCACATGGG	58.659	50.000	0.00	0.00	43.14	4.00
152	153	2.631267	ACGGTAACCTTTGTGTTCGTT	58.369	42.857	0.00	0.00	28.10	3.85
224	226	4.730949	TTTCCCTAGTAGTGATGTTCGG	57.269	45.455	0.00	0.00	0.00	4.30
226	228	4.876679	GGCTTTTCCCTAGTAGTGATGTTC	59.123	45.833	0.00	0.00	0.00	3.18
261	263	3.000819	CAGTAGCGTGGGTCCCCA	61.001	66.667	5.13	0.00	45.02	4.96
318	333	4.676018	GTGCTACTGCTAAGTACGAATAGC	59.324	45.833	16.60	16.60	43.78	2.97
340	355	1.831736	AGTAGCGCTGGTATGGAAAGT	59.168	47.619	22.90	0.00	0.00	2.66
388	403	1.672881	GCGCTCTTTAATGCTGGACAT	59.327	47.619	0.00	0.00	42.30	3.06
617	634	5.163913	GCGCCTCAAGAAGTGCTATATTATG	60.164	44.000	0.00	0.00	0.00	1.90
627	644	0.886490	AACTGGCGCCTCAAGAAGTG	60.886	55.000	29.70	8.48	0.00	3.16
643	660	1.310904	GCGAGAGAGGGATACGAACT	58.689	55.000	0.00	0.00	37.60	3.01
671	688	5.642491	AGCGAAAAATAGTTAGTTGAGGTCC	59.358	40.000	0.00	0.00	0.00	4.46
672	689	6.723131	AGCGAAAAATAGTTAGTTGAGGTC	57.277	37.500	0.00	0.00	0.00	3.85
674	691	6.241385	CGAAGCGAAAAATAGTTAGTTGAGG	58.759	40.000	0.00	0.00	0.00	3.86
691	708	2.401967	GGTAGTAGAGCCGAAGCGA	58.598	57.895	0.00	0.00	46.67	4.93
776	793	6.851330	GGTCAAAAAGAGTGTTTCAATAGACG	59.149	38.462	0.00	0.00	0.00	4.18
809	826	3.793144	GACGAGGCGGCTGCTTTG	61.793	66.667	19.63	16.83	42.25	2.77
860	3951	3.287222	TGTTTAGCCAAGTGAAAGCAGT	58.713	40.909	0.00	0.00	0.00	4.40
984	4081	4.052518	ATGGCTGCTGGGTGGGTC	62.053	66.667	0.00	0.00	0.00	4.46
985	4082	4.371417	CATGGCTGCTGGGTGGGT	62.371	66.667	0.00	0.00	0.00	4.51
1116	4216	1.073548	GGTGTTTTCGGGGCTACCA	59.926	57.895	0.00	0.00	40.22	3.25
1341	5772	2.210711	GGGGTCATAGGCGGAGAGG	61.211	68.421	0.00	0.00	0.00	3.69
1438	7211	0.172352	CTTCTGACGGCCTCTCTGAC	59.828	60.000	0.00	0.00	0.00	3.51
1556	7329	1.304134	GGCCCGTCTTCCCATTTGT	60.304	57.895	0.00	0.00	0.00	2.83
1680	7453	2.513666	TTGATCGGGATGGCGTGC	60.514	61.111	0.00	0.00	0.00	5.34
1747	7521	2.559231	GGAGGCGGAGATAGACCTAAAG	59.441	54.545	0.00	0.00	30.95	1.85
1776	7550	4.516365	ACTAGACGGACACGAAAGAAAT	57.484	40.909	0.00	0.00	44.60	2.17
1785	7559	5.521372	ACAAACTAACAAACTAGACGGACAC	59.479	40.000	0.00	0.00	0.00	3.67
1918	7693	8.811378	CCAAAGTTTTAGCTTTTTCTTTCTGAG	58.189	33.333	0.00	0.00	36.64	3.35
1931	7706	5.358160	GTCTATGGATGCCAAAGTTTTAGCT	59.642	40.000	8.45	0.00	36.95	3.32
1948	7723	3.548745	TGGACTGCAGATTGTCTATGG	57.451	47.619	23.35	0.00	34.01	2.74
2040	7818	4.179298	ACGCTCTAAGATTTACCGGTTTC	58.821	43.478	15.04	8.18	0.00	2.78
2061	7840	9.664332	ATTATGTTTATGGCATCTGATAGAGAC	57.336	33.333	1.65	0.00	31.75	3.36
2287	8073	7.113658	ACATAGTAGGAATGGACTGTTACTG	57.886	40.000	0.00	0.00	0.00	2.74
2309	8095	7.822161	AATTATGCTATGTATGAGGCAAACA	57.178	32.000	0.00	0.00	38.21	2.83

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.