AutoCloner

Multiple sequence alignment - TraesCS7D01G536500

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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	TraesCS7D01G536500	chr7D	100.000	4006	0	0	1	4006	628215999	628211994	0.000000e+00	7398.0
1	TraesCS7D01G536500	chr7D	95.000	40	2	0	3013	3052	418918987	418919026	3.340000e-06	63.9
2	TraesCS7D01G536500	chr7A	92.949	2879	129	42	630	3455	724963307	724966164	0.000000e+00	4124.0
3	TraesCS7D01G536500	chr7A	94.216	657	20	6	1	651	724962511	724963155	0.000000e+00	987.0
4	TraesCS7D01G536500	chr7A	91.256	446	39	0	3561	4006	724966339	724966784	3.420000e-170	608.0
5	TraesCS7D01G536500	chr7A	100.000	28	0	0	3491	3518	724966236	724966263	7.000000e-03	52.8
6	TraesCS7D01G536500	chr7B	97.234	2061	44	6	1131	3181	730814181	730816238	0.000000e+00	3478.0
7	TraesCS7D01G536500	chr7B	95.716	1097	34	6	28	1124	730813062	730814145	0.000000e+00	1753.0
8	TraesCS7D01G536500	chr7B	94.224	831	31	2	3181	4006	730816668	730817486	0.000000e+00	1253.0
9	TraesCS7D01G536500	chr3D	91.894	1283	75	15	2196	3455	29707392	29706116	0.000000e+00	1766.0
10	TraesCS7D01G536500	chr3D	89.888	445	45	0	3561	4005	29705926	29705482	1.250000e-159	573.0
11	TraesCS7D01G536500	chr3D	94.595	222	12	0	1969	2190	29707725	29707504	1.070000e-90	344.0
12	TraesCS7D01G536500	chr3D	86.957	322	20	7	1436	1737	29708212	29707893	3.830000e-90	342.0
13	TraesCS7D01G536500	chr3D	83.750	80	6	4	3483	3562	29706042	29705970	7.180000e-08	69.4
14	TraesCS7D01G536500	chr3B	90.718	1282	75	24	2196	3455	50938689	50937430	0.000000e+00	1668.0
15	TraesCS7D01G536500	chr3B	89.732	448	43	1	3561	4005	50933349	50932902	1.620000e-158	569.0
16	TraesCS7D01G536500	chr3B	84.959	492	39	22	2976	3455	50933958	50933490	2.180000e-127	466.0
17	TraesCS7D01G536500	chr3B	86.816	402	31	3	2577	2978	50937041	50936662	2.860000e-116	429.0
18	TraesCS7D01G536500	chr3B	95.113	266	13	0	1925	2190	50939066	50938801	1.720000e-113	420.0
19	TraesCS7D01G536500	chr3B	91.121	214	16	2	3561	3771	50937251	50937038	1.820000e-73	287.0
20	TraesCS7D01G536500	chr3B	79.427	384	52	15	1466	1841	50939458	50939094	3.090000e-61	246.0
21	TraesCS7D01G536500	chr3B	100.000	37	0	0	3482	3518	50937363	50937327	7.180000e-08	69.4
22	TraesCS7D01G536500	chr3A	89.216	1289	81	24	2196	3455	40365114	40363855	0.000000e+00	1557.0
23	TraesCS7D01G536500	chr3A	89.888	445	45	0	3561	4005	40363676	40363232	1.250000e-159	573.0
24	TraesCS7D01G536500	chr3A	85.000	480	38	13	1385	1841	40365992	40365524	1.310000e-124	457.0
25	TraesCS7D01G536500	chr3A	92.164	268	19	2	1925	2190	40365496	40365229	1.050000e-100	377.0

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	TraesCS7D01G536500	chr7D	628211994	628215999	4005	True	7398.000000	7398	100.000000	1	4006	1	chr7D.!!$R1	4005
1	TraesCS7D01G536500	chr7A	724962511	724966784	4273	False	1442.950000	4124	94.605250	1	4006	4	chr7A.!!$F1	4005
2	TraesCS7D01G536500	chr7B	730813062	730817486	4424	False	2161.333333	3478	95.724667	28	4006	3	chr7B.!!$F1	3978
3	TraesCS7D01G536500	chr3D	29705482	29708212	2730	True	618.880000	1766	89.416800	1436	4005	5	chr3D.!!$R1	2569
4	TraesCS7D01G536500	chr3B	50932902	50939458	6556	True	519.300000	1668	89.735750	1466	4005	8	chr3B.!!$R1	2539
5	TraesCS7D01G536500	chr3A	40363232	40365992	2760	True	741.000000	1557	89.067000	1385	4005	4	chr3A.!!$R1	2620

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
966	1153	0.591236	CACGGTTGCGAAACAAGTGG	60.591	55.0	20.25	7.36	39.50	4.00	F
1903	2177	0.957395	AAGGGTGAGCACAATCAGCG	60.957	55.0	2.75	0.00	46.29	5.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1972	2284	0.595095	CTTCAGTTGCAACCTCCAGC	59.405	55.000	25.62	0.0	0.0	4.85	R
3518	4456	3.630168	ACAAATGGTGCATACATAGCCA	58.370	40.909	7.20	0.0	0.0	4.75	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
60	61	5.105554	ACTCCACTTGACATGTCTATCTCAC	60.106	44.000	25.55	0.00	0.00	3.51
122	123	2.430465	AGTATGTTGCTGCACAGGAAG	58.570	47.619	0.00	0.00	39.44	3.46
153	154	1.487976	CTTGCCTGGAAGCAGATAGGA	59.512	52.381	0.00	0.00	45.13	2.94
274	275	2.780643	CAACGGCGCAGAGTCATG	59.219	61.111	16.26	0.94	0.00	3.07
361	367	3.450457	AGTGATCCAGTCAAGATCTCACC	59.550	47.826	0.00	0.00	40.69	4.02
363	369	3.450096	TGATCCAGTCAAGATCTCACCTG	59.550	47.826	0.00	2.16	40.69	4.00
408	414	8.369424	CAAGATCATTCTCCAGAATCTACAGAT	58.631	37.037	0.00	0.00	42.41	2.90
409	415	8.495160	AGATCATTCTCCAGAATCTACAGATT	57.505	34.615	4.13	4.13	46.54	2.40
410	416	8.936787	AGATCATTCTCCAGAATCTACAGATTT	58.063	33.333	5.95	0.00	44.14	2.17
452	458	5.763698	CCTGCTGATCACTCATTGTATGAAT	59.236	40.000	0.00	0.00	39.11	2.57
453	459	6.073167	CCTGCTGATCACTCATTGTATGAATC	60.073	42.308	0.00	0.00	39.11	2.52
752	935	2.636893	CCAGAGATGCCAGGTAATAGCT	59.363	50.000	0.00	0.00	0.00	3.32
851	1035	0.978146	TAAGGCTCTCTGTGGGCTCC	60.978	60.000	1.23	0.00	37.36	4.70
900	1087	6.293462	GCCTTCTTCCTATAAATACAAAGGCG	60.293	42.308	6.55	0.00	44.58	5.52
928	1115	4.101119	CGGGGAGAAGTATCAGGTAAACAT	59.899	45.833	0.00	0.00	0.00	2.71
964	1151	1.063488	GCACGGTTGCGAAACAAGT	59.937	52.632	8.91	4.66	39.50	3.16
966	1153	0.591236	CACGGTTGCGAAACAAGTGG	60.591	55.000	20.25	7.36	39.50	4.00
1105	1297	5.944007	AGGTACAGGATTGTTCATTTGGTAC	59.056	40.000	0.00	0.00	38.76	3.34
1125	1317	5.163374	GGTACCACTGATCCTTACGGTATTT	60.163	44.000	7.15	0.00	32.01	1.40
1128	1320	4.049186	CACTGATCCTTACGGTATTTCGG	58.951	47.826	0.00	0.00	0.00	4.30
1129	1321	3.956199	ACTGATCCTTACGGTATTTCGGA	59.044	43.478	0.00	0.00	0.00	4.55
1132	1353	5.535333	TGATCCTTACGGTATTTCGGATTC	58.465	41.667	8.96	5.41	31.80	2.52
1540	1786	6.783708	AATCAAAACTCAAGTTGGTGGTTA	57.216	33.333	2.34	0.00	38.44	2.85
1551	1797	5.514500	AGTTGGTGGTTATCAATGTAGGT	57.486	39.130	0.00	0.00	0.00	3.08
1809	2081	1.493772	TGTTAAACTGCTGTCGTCCG	58.506	50.000	0.00	0.00	0.00	4.79
1903	2177	0.957395	AAGGGTGAGCACAATCAGCG	60.957	55.000	2.75	0.00	46.29	5.18
2210	2633	6.464892	CCAATAGCTAGAATGTCCAATGAGGA	60.465	42.308	0.00	0.00	46.75	3.71
2313	2737	3.813166	TGAAAGCCTTTCAAGTACTTCCG	59.187	43.478	17.22	0.00	45.94	4.30
2342	2766	1.398390	GAGGGCAGTGCATTTAACTCG	59.602	52.381	18.61	0.00	0.00	4.18
2412	2855	1.736681	GATTGCAAGCCACTCTGTCTC	59.263	52.381	2.49	0.00	0.00	3.36
2459	2906	0.957395	CCAAGGAACGCAGTGCAGAT	60.957	55.000	16.83	2.59	45.00	2.90
2589	3036	4.160736	TGACAGACTAATGACTGACACG	57.839	45.455	0.00	0.00	38.85	4.49
2598	3045	3.628280	GACTGACACGACGAGGGCC	62.628	68.421	0.00	0.00	0.00	5.80
2800	3247	6.666417	ACACGTAGTTGTTCTAGTACAGAAG	58.334	40.000	2.27	0.00	41.43	2.85
2824	3271	5.689514	GCCTATATCGATACTGCAATGCTAG	59.310	44.000	7.41	4.98	0.00	3.42
3075	3522	4.559300	GCATGCTGTTATTTCCACAGTTGT	60.559	41.667	11.37	0.00	43.21	3.32
3252	4131	6.629128	CCACCTCTGTCTATGATCATACATC	58.371	44.000	11.49	5.86	0.00	3.06
3311	4193	9.290988	ACAGTAGATATCGACTCTGATGTTTAT	57.709	33.333	14.81	0.00	29.21	1.40
3422	4314	7.159372	TCTGGTGTACCTCTTTTCTTCAATAC	58.841	38.462	2.32	0.00	36.82	1.89
3521	4459	7.824289	ACAGTTGTATGGATATATGTATGTGGC	59.176	37.037	0.00	0.00	0.00	5.01
3522	4460	8.043113	CAGTTGTATGGATATATGTATGTGGCT	58.957	37.037	0.00	0.00	0.00	4.75
3523	4461	9.267071	AGTTGTATGGATATATGTATGTGGCTA	57.733	33.333	0.00	0.00	0.00	3.93
3526	4464	9.212593	TGTATGGATATATGTATGTGGCTATGT	57.787	33.333	0.00	0.00	0.00	2.29
3538	4481	3.380954	TGTGGCTATGTATGCACCATTTG	59.619	43.478	6.06	2.46	31.99	2.32
3551	4494	5.698832	TGCACCATTTGTAGAAATCTTTCG	58.301	37.500	0.00	0.00	41.92	3.46
3663	8553	6.387513	TGAAGCCTAGTATTACACCCCAATAA	59.612	38.462	0.00	0.00	0.00	1.40
3702	8592	3.653344	TCTTGTGTGATCCTGTTCTTCG	58.347	45.455	0.00	0.00	0.00	3.79
3990	8883	3.749064	GAGTGGACGAGCGCTGGA	61.749	66.667	26.95	0.00	0.00	3.86

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
79	80	1.542915	TCTTCTTTGCCTTGCTCATGC	59.457	47.619	0.00	0.00	40.20	4.06
80	81	3.928727	TTCTTCTTTGCCTTGCTCATG	57.071	42.857	0.00	0.00	0.00	3.07
81	82	4.343239	ACTTTTCTTCTTTGCCTTGCTCAT	59.657	37.500	0.00	0.00	0.00	2.90
82	83	3.701040	ACTTTTCTTCTTTGCCTTGCTCA	59.299	39.130	0.00	0.00	0.00	4.26
83	84	4.313277	ACTTTTCTTCTTTGCCTTGCTC	57.687	40.909	0.00	0.00	0.00	4.26
84	85	5.302823	ACATACTTTTCTTCTTTGCCTTGCT	59.697	36.000	0.00	0.00	0.00	3.91
85	86	5.532557	ACATACTTTTCTTCTTTGCCTTGC	58.467	37.500	0.00	0.00	0.00	4.01
122	123	4.301628	CTTCCAGGCAAGTCAATTTTGTC	58.698	43.478	0.00	0.00	0.00	3.18
153	154	5.615289	GCCTTTCAGGTATACATCATCTGT	58.385	41.667	5.01	0.00	38.67	3.41
361	367	6.653740	TCTTGCTGATCCATATCTTAATGCAG	59.346	38.462	0.00	0.00	32.93	4.41
363	369	7.627298	ATCTTGCTGATCCATATCTTAATGC	57.373	36.000	0.00	0.00	32.93	3.56
434	440	7.816995	GGGTAGAGATTCATACAATGAGTGATC	59.183	40.741	0.00	0.00	40.94	2.92
452	458	4.454847	CGTGAATCGCTATTAGGGTAGAGA	59.545	45.833	7.54	0.00	35.47	3.10
453	459	4.215827	ACGTGAATCGCTATTAGGGTAGAG	59.784	45.833	7.54	0.38	44.19	2.43
752	935	2.265367	TCCATCCTGCTCACTTACCAA	58.735	47.619	0.00	0.00	0.00	3.67
851	1035	1.106944	GGGGAGAGAGAAGAGGAGCG	61.107	65.000	0.00	0.00	0.00	5.03
900	1087	2.361438	CCTGATACTTCTCCCCGTACAC	59.639	54.545	0.00	0.00	0.00	2.90
928	1115	0.378962	GCGCCTTGTGTGTTTGTGTA	59.621	50.000	0.00	0.00	0.00	2.90
964	1151	7.888021	TGTTCCTTCTTGCTTCTAAATAATCCA	59.112	33.333	0.00	0.00	0.00	3.41
966	1153	8.184848	GGTGTTCCTTCTTGCTTCTAAATAATC	58.815	37.037	0.00	0.00	0.00	1.75
1125	1317	2.550606	CCAAACTCCAAAACGAATCCGA	59.449	45.455	0.00	0.00	39.50	4.55
1128	1320	2.609491	GGGCCAAACTCCAAAACGAATC	60.609	50.000	4.39	0.00	0.00	2.52
1129	1321	1.343142	GGGCCAAACTCCAAAACGAAT	59.657	47.619	4.39	0.00	0.00	3.34
1132	1353	0.750249	AAGGGCCAAACTCCAAAACG	59.250	50.000	6.18	0.00	0.00	3.60
1881	2155	2.616510	GCTGATTGTGCTCACCCTTAGT	60.617	50.000	0.00	0.00	0.00	2.24
1903	2177	5.545658	TGTTTGGAGCAAGATAATTCGAC	57.454	39.130	0.00	0.00	0.00	4.20
1972	2284	0.595095	CTTCAGTTGCAACCTCCAGC	59.405	55.000	25.62	0.00	0.00	4.85
2210	2633	8.621286	CAGTACAAGTAAAATCAACAAAGGACT	58.379	33.333	0.00	0.00	0.00	3.85
2313	2737	4.608948	ATGCACTGCCCTCTATAACTAC	57.391	45.455	0.00	0.00	0.00	2.73
2342	2766	6.138761	GCTTGTACATGCAGTGCTATTAATC	58.861	40.000	24.45	1.95	33.54	1.75
2412	2855	8.816894	ACATTATAGTATACTGAATGGTCCCTG	58.183	37.037	28.34	15.10	36.11	4.45
2589	3036	2.094649	CCTATCTTTATCGGCCCTCGTC	60.095	54.545	0.00	0.00	40.32	4.20
2598	3045	3.876914	TGTTTGGCAGCCTATCTTTATCG	59.123	43.478	14.15	0.00	0.00	2.92
2756	3203	5.924825	CGTGTTACTTTAGTGGTTAAGAGCT	59.075	40.000	0.00	0.00	0.00	4.09
2757	3204	5.693555	ACGTGTTACTTTAGTGGTTAAGAGC	59.306	40.000	0.00	0.00	0.00	4.09
2760	3207	8.482429	CAACTACGTGTTACTTTAGTGGTTAAG	58.518	37.037	0.00	0.00	35.35	1.85
2773	3220	7.576236	TCTGTACTAGAACAACTACGTGTTAC	58.424	38.462	0.00	0.00	41.78	2.50
2784	3231	7.718314	TCGATATAGGCTTCTGTACTAGAACAA	59.282	37.037	0.00	0.00	40.43	2.83
2800	3247	4.437239	AGCATTGCAGTATCGATATAGGC	58.563	43.478	11.91	12.66	0.00	3.93
2973	3420	6.515531	CGCATTGGCAATTCTATCTGGTAATT	60.516	38.462	10.65	0.00	41.24	1.40
3252	4131	6.231211	ACTGAAGGTACAATGTCTGTAAAGG	58.769	40.000	0.00	0.00	42.23	3.11
3311	4193	9.914834	ACATTCAGGCCTTAAGTATACATTTAA	57.085	29.630	0.00	1.81	0.00	1.52
3400	4292	6.935208	AGTGTATTGAAGAAAAGAGGTACACC	59.065	38.462	8.26	0.00	40.71	4.16
3434	4326	6.183347	CCTTTAGAAACCTCTGAATGACCAT	58.817	40.000	0.00	0.00	32.70	3.55
3518	4456	3.630168	ACAAATGGTGCATACATAGCCA	58.370	40.909	7.20	0.00	0.00	4.75
3519	4457	5.063204	TCTACAAATGGTGCATACATAGCC	58.937	41.667	7.20	0.00	0.00	3.93
3520	4458	6.618287	TTCTACAAATGGTGCATACATAGC	57.382	37.500	7.20	0.00	0.00	2.97
3521	4459	9.060347	AGATTTCTACAAATGGTGCATACATAG	57.940	33.333	7.20	6.32	31.94	2.23
3522	4460	8.978874	AGATTTCTACAAATGGTGCATACATA	57.021	30.769	7.20	0.00	31.94	2.29
3523	4461	7.886629	AGATTTCTACAAATGGTGCATACAT	57.113	32.000	0.00	0.00	31.94	2.29
3524	4462	7.701539	AAGATTTCTACAAATGGTGCATACA	57.298	32.000	0.00	0.00	31.94	2.29
3525	4463	7.429340	CGAAAGATTTCTACAAATGGTGCATAC	59.571	37.037	0.00	0.00	31.94	2.39
3526	4464	7.335673	TCGAAAGATTTCTACAAATGGTGCATA	59.664	33.333	0.00	0.00	31.94	3.14
3527	4465	6.150976	TCGAAAGATTTCTACAAATGGTGCAT	59.849	34.615	0.00	0.00	31.94	3.96
3528	4466	5.471797	TCGAAAGATTTCTACAAATGGTGCA	59.528	36.000	3.98	0.00	31.94	4.57
3529	4467	5.938322	TCGAAAGATTTCTACAAATGGTGC	58.062	37.500	3.98	0.00	31.94	5.01
3538	4481	6.305638	GGTGTGCATTTTCGAAAGATTTCTAC	59.694	38.462	10.98	6.64	41.60	2.59
3551	4494	5.414454	TGTACTCCTATTGGTGTGCATTTTC	59.586	40.000	13.32	0.00	43.73	2.29
3702	8592	4.093556	CCGTCCAGAGAAGAAGCAAATAAC	59.906	45.833	0.00	0.00	0.00	1.89

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.