AutoCloner

Multiple sequence alignment - TraesCS7A01G000600

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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	TraesCS7A01G000600	chr7A	100.000	2805	0	0	1	2805	330413	333217	0.000000e+00	5180
1	TraesCS7A01G000600	chr7A	87.000	1500	172	10	523	2012	634009	635495	0.000000e+00	1668
2	TraesCS7A01G000600	chr7A	84.127	126	13	5	128	250	623412	623533	6.350000e-22	115
3	TraesCS7A01G000600	chr4A	96.494	2624	76	10	167	2787	744380444	744377834	0.000000e+00	4322
4	TraesCS7A01G000600	chr4A	94.196	2550	126	13	249	2787	744032408	744029870	0.000000e+00	3869
5	TraesCS7A01G000600	chr4A	87.744	1844	187	22	261	2086	744415967	744417789	0.000000e+00	2117
6	TraesCS7A01G000600	chr4A	85.871	1734	206	26	249	1955	743674764	743676485	0.000000e+00	1808
7	TraesCS7A01G000600	chr4A	83.451	1849	228	41	523	2344	743345791	743347588	0.000000e+00	1648
8	TraesCS7A01G000600	chr4A	84.691	405	55	6	2387	2787	470799689	470799288	5.630000e-107	398
9	TraesCS7A01G000600	chr4A	88.500	200	12	4	52	251	744032635	744032447	6.040000e-57	231
10	TraesCS7A01G000600	chr4A	90.968	155	2	3	29	179	744380610	744380464	6.130000e-47	198
11	TraesCS7A01G000600	chr4A	87.097	93	9	2	132	223	743345189	743345279	4.940000e-18	102
12	TraesCS7A01G000600	chr7D	88.086	1343	145	9	673	2007	1236103	1234768	0.000000e+00	1580
13	TraesCS7A01G000600	chr7D	82.944	428	62	10	2363	2787	139300017	139299598	2.640000e-100	375
14	TraesCS7A01G000600	chr7D	83.582	134	15	7	121	250	1237338	1237208	4.910000e-23	119
15	TraesCS7A01G000600	chr3D	82.385	1845	247	48	249	2064	18908255	18910050	0.000000e+00	1535
16	TraesCS7A01G000600	chrUn	88.765	1255	136	3	686	1939	51384689	51385939	0.000000e+00	1531
17	TraesCS7A01G000600	chrUn	83.465	127	14	6	128	250	51390596	51390719	8.210000e-21	111
18	TraesCS7A01G000600	chr3A	82.236	1610	238	35	282	1876	26489108	26490684	0.000000e+00	1345
19	TraesCS7A01G000600	chr3A	83.632	1393	209	9	673	2064	26481477	26482851	0.000000e+00	1291
20	TraesCS7A01G000600	chr3A	82.558	430	66	8	2362	2787	523306039	523305615	1.230000e-98	370
21	TraesCS7A01G000600	chr2D	84.742	426	60	4	2363	2787	309090783	309090362	3.340000e-114	422
22	TraesCS7A01G000600	chr1B	82.910	433	58	10	2365	2787	387937954	387938380	2.640000e-100	375
23	TraesCS7A01G000600	chr5A	82.558	430	60	10	2359	2786	678589193	678589609	5.710000e-97	364
24	TraesCS7A01G000600	chr2B	82.009	428	65	10	2362	2787	439560688	439560271	1.240000e-93	353

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	TraesCS7A01G000600	chr7A	330413	333217	2804	False	5180.0	5180	100.000	1	2805	1	chr7A.!!$F1	2804
1	TraesCS7A01G000600	chr7A	634009	635495	1486	False	1668.0	1668	87.000	523	2012	1	chr7A.!!$F3	1489
2	TraesCS7A01G000600	chr4A	744377834	744380610	2776	True	2260.0	4322	93.731	29	2787	2	chr4A.!!$R3	2758
3	TraesCS7A01G000600	chr4A	744415967	744417789	1822	False	2117.0	2117	87.744	261	2086	1	chr4A.!!$F2	1825
4	TraesCS7A01G000600	chr4A	744029870	744032635	2765	True	2050.0	3869	91.348	52	2787	2	chr4A.!!$R2	2735
5	TraesCS7A01G000600	chr4A	743674764	743676485	1721	False	1808.0	1808	85.871	249	1955	1	chr4A.!!$F1	1706
6	TraesCS7A01G000600	chr4A	743345189	743347588	2399	False	875.0	1648	85.274	132	2344	2	chr4A.!!$F3	2212
7	TraesCS7A01G000600	chr7D	1234768	1237338	2570	True	849.5	1580	85.834	121	2007	2	chr7D.!!$R2	1886
8	TraesCS7A01G000600	chr3D	18908255	18910050	1795	False	1535.0	1535	82.385	249	2064	1	chr3D.!!$F1	1815
9	TraesCS7A01G000600	chrUn	51384689	51385939	1250	False	1531.0	1531	88.765	686	1939	1	chrUn.!!$F1	1253
10	TraesCS7A01G000600	chr3A	26489108	26490684	1576	False	1345.0	1345	82.236	282	1876	1	chr3A.!!$F2	1594
11	TraesCS7A01G000600	chr3A	26481477	26482851	1374	False	1291.0	1291	83.632	673	2064	1	chr3A.!!$F1	1391

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
684	1534	1.230635	TTTCTTCGACAGCAGCAGCC	61.231	55.0	0.0	0.0	43.56	4.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2611	3495	0.388649	AGCACTGACGGATCGTGAAC	60.389	55.0	0.0	0.0	41.37	3.18	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
20	21	2.703416	GATGATTGATATCGCCTGGCA	58.297	47.619	20.29	6.38	33.23	4.92
21	22	2.865119	TGATTGATATCGCCTGGCAT	57.135	45.000	20.29	13.36	33.23	4.40
22	23	3.144657	TGATTGATATCGCCTGGCATT	57.855	42.857	20.29	7.56	33.23	3.56
23	24	2.815503	TGATTGATATCGCCTGGCATTG	59.184	45.455	20.29	2.22	33.23	2.82
24	25	2.346766	TTGATATCGCCTGGCATTGT	57.653	45.000	20.29	2.96	0.00	2.71
25	26	2.346766	TGATATCGCCTGGCATTGTT	57.653	45.000	20.29	0.00	0.00	2.83
26	27	1.948834	TGATATCGCCTGGCATTGTTG	59.051	47.619	20.29	0.58	0.00	3.33
125	130	2.557924	TGAGAGATGCGCCACAATTTTT	59.442	40.909	4.18	0.00	0.00	1.94
302	472	8.365210	GTGTTTACTCATAAATGCGATGTTTTG	58.635	33.333	0.00	0.00	32.91	2.44
597	1432	9.095700	TGCATAAAGGGAAATTTAAACTACCTT	57.904	29.630	9.09	9.09	38.41	3.50
684	1534	1.230635	TTTCTTCGACAGCAGCAGCC	61.231	55.000	0.00	0.00	43.56	4.85
1117	1974	4.392138	CGAACAGTTCCTTGGATAAGTTCC	59.608	45.833	7.76	0.00	45.69	3.62
1393	2250	4.018506	TCATTGCCCCAGAAGTTCATTCTA	60.019	41.667	5.50	0.00	46.91	2.10
1693	2550	6.998074	TCTGGAAATGTTTGAGAGAAGCTTAA	59.002	34.615	0.00	0.00	0.00	1.85
2112	2993	3.774959	ATCGGTCCGATGTCAGCGC	62.775	63.158	25.86	0.00	45.24	5.92
2186	3068	0.459489	TTGTGTTGCAAGCTCCAACC	59.541	50.000	20.85	14.85	41.33	3.77
2323	3207	6.183360	TGTGGCAATATATTTCAATTCGCTGT	60.183	34.615	0.00	0.00	0.00	4.40
2346	3230	4.243007	AGCAAACTAATTGTGGAAGTGC	57.757	40.909	0.00	0.00	41.32	4.40
2521	3405	2.938956	ACTTGGAGTCCCTCAAACTG	57.061	50.000	6.74	0.00	31.08	3.16
2545	3429	6.876789	TGTAGATGAATGATTACACAAACCGT	59.123	34.615	0.00	0.00	0.00	4.83
2558	3442	2.158813	ACAAACCGTCCATGAACAGTCT	60.159	45.455	0.00	0.00	0.00	3.24
2611	3495	0.095245	CGAGTTGCAAGCATACGGTG	59.905	55.000	0.00	0.00	0.00	4.94
2627	3511	0.038526	GGTGTTCACGATCCGTCAGT	60.039	55.000	0.00	0.00	38.32	3.41
2669	3553	2.364324	TCGTCCCCGAAGAATTAGATGG	59.636	50.000	0.00	0.00	40.86	3.51
2787	3671	2.567615	GACTAGAGGAGGCTCCAAAACA	59.432	50.000	33.86	13.68	39.61	2.83
2788	3672	2.979678	ACTAGAGGAGGCTCCAAAACAA	59.020	45.455	33.86	12.64	39.61	2.83
2789	3673	2.575805	AGAGGAGGCTCCAAAACAAG	57.424	50.000	33.86	0.00	39.61	3.16
2790	3674	1.074566	AGAGGAGGCTCCAAAACAAGG	59.925	52.381	33.86	0.00	39.61	3.61
2791	3675	1.073923	GAGGAGGCTCCAAAACAAGGA	59.926	52.381	33.86	0.00	39.61	3.36
2798	3682	2.579410	TCCAAAACAAGGAGGTAGCC	57.421	50.000	0.00	0.00	0.00	3.93
2799	3683	1.777878	TCCAAAACAAGGAGGTAGCCA	59.222	47.619	0.00	0.00	0.00	4.75
2800	3684	1.886542	CCAAAACAAGGAGGTAGCCAC	59.113	52.381	0.00	0.00	0.00	5.01
2801	3685	1.886542	CAAAACAAGGAGGTAGCCACC	59.113	52.381	0.00	0.00	46.19	4.61

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	2.703416	TGCCAGGCGATATCAATCATC	58.297	47.619	7.03	0.00	31.93	2.92
1	2	2.865119	TGCCAGGCGATATCAATCAT	57.135	45.000	7.03	0.00	31.93	2.45
2	3	2.815503	CAATGCCAGGCGATATCAATCA	59.184	45.455	7.03	0.00	31.93	2.57
3	4	2.816087	ACAATGCCAGGCGATATCAATC	59.184	45.455	7.03	0.00	0.00	2.67
4	5	2.867624	ACAATGCCAGGCGATATCAAT	58.132	42.857	7.03	0.00	0.00	2.57
5	6	2.346766	ACAATGCCAGGCGATATCAA	57.653	45.000	7.03	0.00	0.00	2.57
6	7	1.948834	CAACAATGCCAGGCGATATCA	59.051	47.619	7.03	0.00	0.00	2.15
7	8	2.693797	CAACAATGCCAGGCGATATC	57.306	50.000	7.03	0.00	0.00	1.63
19	20	1.303236	TGGGGACTCGGCAACAATG	60.303	57.895	0.00	0.00	0.00	2.82
20	21	1.002134	CTGGGGACTCGGCAACAAT	60.002	57.895	0.00	0.00	0.00	2.71
21	22	2.429930	CTGGGGACTCGGCAACAA	59.570	61.111	0.00	0.00	0.00	2.83
22	23	4.329545	GCTGGGGACTCGGCAACA	62.330	66.667	0.00	0.00	38.79	3.33
23	24	3.553095	AAGCTGGGGACTCGGCAAC	62.553	63.158	5.70	0.00	41.26	4.17
24	25	3.249189	AAGCTGGGGACTCGGCAA	61.249	61.111	5.70	0.00	41.26	4.52
25	26	3.706373	GAAGCTGGGGACTCGGCA	61.706	66.667	5.70	0.00	41.26	5.69
26	27	3.672295	CTGAAGCTGGGGACTCGGC	62.672	68.421	0.00	0.00	39.22	5.54
27	28	2.581354	CTGAAGCTGGGGACTCGG	59.419	66.667	0.00	0.00	0.00	4.63
232	271	5.704978	ACATTGGTTCATTATTTTGCCAACC	59.295	36.000	0.00	0.00	38.58	3.77
302	472	0.393132	GCCCTCTTGCTACCTGGAAC	60.393	60.000	0.00	0.00	0.00	3.62
438	619	9.165035	CAATGATTACAGGCATGGTAAATTTTT	57.835	29.630	2.31	0.00	34.67	1.94
636	1478	7.916914	ATGTTACTTCCTTGCGTAAACTAAT	57.083	32.000	0.00	0.00	0.00	1.73
637	1479	8.875803	CATATGTTACTTCCTTGCGTAAACTAA	58.124	33.333	0.00	0.00	0.00	2.24
638	1480	7.010738	GCATATGTTACTTCCTTGCGTAAACTA	59.989	37.037	4.29	0.00	0.00	2.24
639	1481	6.183360	GCATATGTTACTTCCTTGCGTAAACT	60.183	38.462	4.29	0.00	0.00	2.66
1117	1974	5.228945	TCTTTGGGGTTCTCTGAGTAAAG	57.771	43.478	4.32	7.46	0.00	1.85
1756	2616	7.183580	TCACACAAAAACAAAGGAACAAAAG	57.816	32.000	0.00	0.00	0.00	2.27
1806	2667	5.241949	ACTGAAACGAGAGACAAGTGAGTAT	59.758	40.000	0.00	0.00	0.00	2.12
2112	2993	1.880027	GCTTGGACAGTAACTTGTGGG	59.120	52.381	0.00	0.00	0.00	4.61
2186	3068	6.728200	TCTTAAAGATCCATGCATTTTAGCG	58.272	36.000	0.00	0.00	37.31	4.26
2323	3207	5.300539	TGCACTTCCACAATTAGTTTGCTTA	59.699	36.000	0.00	0.00	39.03	3.09
2346	3230	4.997395	ACTCAACACTAAGTATGCACCTTG	59.003	41.667	10.03	4.16	0.00	3.61
2391	3275	6.138967	TCCTGGTTGATCATAGAGAGAATCA	58.861	40.000	0.00	0.00	37.82	2.57
2392	3276	6.662865	TCCTGGTTGATCATAGAGAGAATC	57.337	41.667	0.00	0.00	0.00	2.52
2394	3278	5.721480	TGTTCCTGGTTGATCATAGAGAGAA	59.279	40.000	0.00	0.00	0.00	2.87
2521	3405	7.303634	ACGGTTTGTGTAATCATTCATCTAC	57.696	36.000	0.00	0.00	0.00	2.59
2545	3429	2.095212	CGTTCGAGAGACTGTTCATGGA	60.095	50.000	0.00	0.00	41.84	3.41
2611	3495	0.388649	AGCACTGACGGATCGTGAAC	60.389	55.000	0.00	0.00	41.37	3.18
2627	3511	0.898326	TAGCTCTGGACGGTGAAGCA	60.898	55.000	0.00	0.00	0.00	3.91
2667	3551	5.104527	CCCAGTGTGTTTATAATCTCCTCCA	60.105	44.000	0.00	0.00	0.00	3.86
2669	3553	4.816925	GCCCAGTGTGTTTATAATCTCCTC	59.183	45.833	0.00	0.00	0.00	3.71

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.