AutoCloner

Multiple sequence alignment - TraesCS4B01G086700

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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	TraesCS4B01G086700	chr4B	100.000	2595	0	0	392	2986	86748530	86745936	0.000000e+00	4793.0
1	TraesCS4B01G086700	chr4B	100.000	42	0	0	1	42	86748921	86748880	8.870000e-11	78.7
2	TraesCS4B01G086700	chr4B	82.353	68	8	4	400	465	484763843	484763778	4.160000e-04	56.5
3	TraesCS4B01G086700	chr1B	93.463	2371	138	12	631	2986	515932428	515930060	0.000000e+00	3504.0
4	TraesCS4B01G086700	chr4A	93.158	2353	143	13	649	2986	651988110	651990459	0.000000e+00	3437.0
5	TraesCS4B01G086700	chr2B	91.771	2467	179	17	534	2986	504790086	504792542	0.000000e+00	3410.0
6	TraesCS4B01G086700	chr2B	90.351	2539	215	21	463	2986	250745413	250747936	0.000000e+00	3304.0
7	TraesCS4B01G086700	chr6D	91.548	2449	194	13	548	2986	454863211	454865656	0.000000e+00	3363.0
8	TraesCS4B01G086700	chr5D	91.649	2371	180	13	631	2986	106512649	106515016	0.000000e+00	3265.0
9	TraesCS4B01G086700	chr7A	91.558	2369	192	8	624	2986	183363010	183365376	0.000000e+00	3260.0
10	TraesCS4B01G086700	chr7A	88.139	2504	255	29	414	2882	82954347	82956843	0.000000e+00	2940.0
11	TraesCS4B01G086700	chr7A	89.091	55	4	2	466	520	455582088	455582036	1.920000e-07	67.6
12	TraesCS4B01G086700	chr3D	91.066	2373	192	16	631	2986	1970314	1972683	0.000000e+00	3190.0
13	TraesCS4B01G086700	chr2D	91.001	2378	193	13	620	2986	387951013	387953380	0.000000e+00	3186.0
14	TraesCS4B01G086700	chr1D	89.984	1228	97	20	431	1643	280711697	280710481	0.000000e+00	1563.0

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	TraesCS4B01G086700	chr4B	86745936	86748921	2985	True	2435.85	4793	100.000	1	2986	2	chr4B.!!$R2	2985
1	TraesCS4B01G086700	chr1B	515930060	515932428	2368	True	3504.00	3504	93.463	631	2986	1	chr1B.!!$R1	2355
2	TraesCS4B01G086700	chr4A	651988110	651990459	2349	False	3437.00	3437	93.158	649	2986	1	chr4A.!!$F1	2337
3	TraesCS4B01G086700	chr2B	504790086	504792542	2456	False	3410.00	3410	91.771	534	2986	1	chr2B.!!$F2	2452
4	TraesCS4B01G086700	chr2B	250745413	250747936	2523	False	3304.00	3304	90.351	463	2986	1	chr2B.!!$F1	2523
5	TraesCS4B01G086700	chr6D	454863211	454865656	2445	False	3363.00	3363	91.548	548	2986	1	chr6D.!!$F1	2438
6	TraesCS4B01G086700	chr5D	106512649	106515016	2367	False	3265.00	3265	91.649	631	2986	1	chr5D.!!$F1	2355
7	TraesCS4B01G086700	chr7A	183363010	183365376	2366	False	3260.00	3260	91.558	624	2986	1	chr7A.!!$F2	2362
8	TraesCS4B01G086700	chr7A	82954347	82956843	2496	False	2940.00	2940	88.139	414	2882	1	chr7A.!!$F1	2468
9	TraesCS4B01G086700	chr3D	1970314	1972683	2369	False	3190.00	3190	91.066	631	2986	1	chr3D.!!$F1	2355
10	TraesCS4B01G086700	chr2D	387951013	387953380	2367	False	3186.00	3186	91.001	620	2986	1	chr2D.!!$F1	2366
11	TraesCS4B01G086700	chr1D	280710481	280711697	1216	True	1563.00	1563	89.984	431	1643	1	chr1D.!!$R1	1212

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
505	521	1.384082	TAGGAACCCTAGCCTGCCC	60.384	63.158	0.0	0.0	35.73	5.36	F
1339	1374	0.108804	GATCCGTCTGAGGTTTGCGA	60.109	55.000	0.0	0.0	0.00	5.10	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1656	1692	0.03889	GCCCTTCTTCTTGCCCTTCT	59.961	55.0	0.0	0.0	0.00	2.85	R
2938	3015	1.50714	TGAGGGGCGATGTCCTAATT	58.493	50.0	0.0	0.0	32.74	1.40	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
505	521	1.384082	TAGGAACCCTAGCCTGCCC	60.384	63.158	0.00	0.00	35.73	5.36
571	587	1.604593	CTGTTGGGCCTTGACTGGG	60.605	63.158	4.53	0.00	0.00	4.45
679	708	9.332301	CTTGTTTTTACGCGAATTTTATTCCTA	57.668	29.630	15.93	0.00	0.00	2.94
714	743	2.224450	CGTAGAACCCCCTGAAACTGTT	60.224	50.000	0.00	0.00	0.00	3.16
715	744	2.658807	AGAACCCCCTGAAACTGTTC	57.341	50.000	0.00	0.00	36.45	3.18
716	745	1.850345	AGAACCCCCTGAAACTGTTCA	59.150	47.619	0.00	0.00	41.57	3.18
723	752	3.317993	CCCCTGAAACTGTTCATTTTCGT	59.682	43.478	9.74	0.00	42.85	3.85
1095	1130	1.115467	GCGAGATCTTTCTCCAGGGA	58.885	55.000	0.00	0.00	44.76	4.20
1170	1205	3.250762	CCAAGTTCGAAACTGAGAATGCA	59.749	43.478	0.00	0.00	41.91	3.96
1172	1207	2.476619	AGTTCGAAACTGAGAATGCACG	59.523	45.455	0.00	0.00	41.01	5.34
1225	1260	7.148000	TGTCACCTACTCTGAAAGATGAGTATG	60.148	40.741	0.00	0.00	45.62	2.39
1235	1270	2.113807	AGATGAGTATGTGGCTGAGCA	58.886	47.619	6.82	0.00	0.00	4.26
1238	1273	1.338105	TGAGTATGTGGCTGAGCACAC	60.338	52.381	15.94	15.94	38.08	3.82
1280	1315	0.874390	CTTAAGCAGCGGTTTGAGCA	59.126	50.000	0.00	0.00	37.01	4.26
1339	1374	0.108804	GATCCGTCTGAGGTTTGCGA	60.109	55.000	0.00	0.00	0.00	5.10
1362	1397	1.946984	TCAAGACGGTTGGGGAGTAT	58.053	50.000	0.49	0.00	0.00	2.12
1419	1454	5.538813	TCAGTTGTGTGGTACTGAGATTACT	59.461	40.000	0.00	0.00	44.20	2.24
1489	1524	0.170561	CCAGTCCTCACGGAACTACG	59.829	60.000	0.00	0.00	42.08	3.51
1571	1607	4.757149	CAGGACGAGGTTCTCAAAAAGAAT	59.243	41.667	0.00	0.00	45.57	2.40
1654	1690	1.948144	GCCTCAACAGAAGAAGAGGGC	60.948	57.143	9.16	0.00	46.08	5.19
1656	1692	1.349026	CTCAACAGAAGAAGAGGGCCA	59.651	52.381	6.18	0.00	0.00	5.36
1707	1746	1.271597	CCCCAGCTAAGCAGAACAAGT	60.272	52.381	0.00	0.00	0.00	3.16
1739	1783	2.289532	GCAGAGGCCTCAGGACTGT	61.290	63.158	33.90	0.00	43.92	3.55
1780	1824	2.905996	ATTTCTCCCGCCAGTGCCA	61.906	57.895	0.00	0.00	0.00	4.92
1983	2027	3.876589	GACACCCACGTCGCCATGT	62.877	63.158	0.00	0.00	0.00	3.21
2106	2158	2.159599	GCTGAAGTGAATGGCTTCTTCG	60.160	50.000	6.61	0.00	41.94	3.79
2230	2292	4.196626	ACTTTGGCAATTGGATGACATG	57.803	40.909	7.72	0.00	38.36	3.21
2350	2422	6.112734	AGATGCCATATTTTAGAACACGTGA	58.887	36.000	25.01	0.00	0.00	4.35
2383	2455	2.251371	GAAACGTGCCTTGCCGAC	59.749	61.111	0.00	0.00	0.00	4.79
2502	2577	0.683504	ATAGTTGGCTCCGGACGAGT	60.684	55.000	0.00	0.00	41.10	4.18
2779	2856	3.751698	CCCTCAAGACCGTTTTTAGAAGG	59.248	47.826	0.00	0.00	0.00	3.46
2869	2946	5.637006	TTAACAACTCACATGGCCATAAC	57.363	39.130	20.30	0.00	0.00	1.89
2875	2952	4.523083	ACTCACATGGCCATAACGTTAAT	58.477	39.130	20.30	0.00	0.00	1.40
2877	2954	3.066064	TCACATGGCCATAACGTTAATGC	59.934	43.478	20.30	16.51	0.00	3.56
2888	2965	6.401688	CCATAACGTTAATGCGAAGAACTTCA	60.402	38.462	12.81	0.00	39.46	3.02
2889	2966	5.412526	AACGTTAATGCGAAGAACTTCAA	57.587	34.783	0.00	3.13	39.46	2.69
2897	2974	2.420372	GCGAAGAACTTCAAGAATCCCC	59.580	50.000	13.72	0.00	39.46	4.81
2904	2981	7.416101	GAAGAACTTCAAGAATCCCCATGATTC	60.416	40.741	9.33	6.78	46.21	2.52
2938	3015	2.459644	TGCGCTAAGGGGAAGTTAGTA	58.540	47.619	9.73	0.00	31.22	1.82
2945	3022	6.041296	CGCTAAGGGGAAGTTAGTAATTAGGA	59.959	42.308	0.00	0.00	31.22	2.94

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
518	534	4.530857	CATCCGACCGGCTCACCC	62.531	72.222	0.00	0.00	34.68	4.61
520	536	4.530857	CCCATCCGACCGGCTCAC	62.531	72.222	0.00	0.00	34.68	3.51
626	654	7.944729	ACTATAGGGGCTAAAATGCAATATG	57.055	36.000	4.43	0.00	34.04	1.78
679	708	3.308866	GGTTCTACGCGAAATATTGCTGT	59.691	43.478	15.93	0.00	33.43	4.40
723	752	1.609555	AGCCCAAATACGCGTTTTCAA	59.390	42.857	20.78	0.00	0.00	2.69
996	1031	0.327924	TGACAATTCCGGCCATCTGT	59.672	50.000	2.24	0.00	0.00	3.41
1170	1205	1.004440	GAGAAAGTGCAGAGCCCGT	60.004	57.895	0.00	0.00	0.00	5.28
1172	1207	1.743252	CGGAGAAAGTGCAGAGCCC	60.743	63.158	0.00	0.00	0.00	5.19
1235	1270	1.374190	CAGAGGCCAGAAGCAGTGT	59.626	57.895	5.01	0.00	46.50	3.55
1238	1273	1.078567	GTCCAGAGGCCAGAAGCAG	60.079	63.158	5.01	0.00	46.50	4.24
1280	1315	2.548920	GGCTTCACAGTGTACTTCAGCT	60.549	50.000	0.00	0.00	0.00	4.24
1339	1374	0.841289	TCCCCAACCGTCTTGAAGTT	59.159	50.000	0.00	0.00	0.00	2.66
1362	1397	0.750249	TCCGATGCAGAGCCGAATTA	59.250	50.000	0.00	0.00	0.00	1.40
1419	1454	6.295916	GGGTTTTCTCAATCTTCTAGGAGTCA	60.296	42.308	0.00	0.00	0.00	3.41
1489	1524	2.682494	TCGTGTAGTCCCCTGGCC	60.682	66.667	0.00	0.00	0.00	5.36
1571	1607	0.524392	CAAGTGGTTGCGCGACAAAA	60.524	50.000	28.27	11.23	40.82	2.44
1603	1639	1.587933	GAGAGCGTTCACCTCCTCGT	61.588	60.000	1.01	0.00	0.00	4.18
1605	1641	0.603569	TTGAGAGCGTTCACCTCCTC	59.396	55.000	1.01	0.00	0.00	3.71
1654	1690	1.615384	CCCTTCTTCTTGCCCTTCTGG	60.615	57.143	0.00	0.00	37.09	3.86
1656	1692	0.038890	GCCCTTCTTCTTGCCCTTCT	59.961	55.000	0.00	0.00	0.00	2.85
1707	1746	3.983420	CTGCCCTCCCTTGCCCAA	61.983	66.667	0.00	0.00	0.00	4.12
1910	1954	2.122989	GGGGTCGCCTCTATGGGA	60.123	66.667	0.00	0.00	36.00	4.37
2106	2158	1.538419	GGTATGCTAAGTGGACTCGGC	60.538	57.143	0.00	0.00	0.00	5.54
2331	2403	4.260212	CGCCTCACGTGTTCTAAAATATGG	60.260	45.833	16.51	3.43	36.87	2.74
2383	2455	1.815421	GGTATGAGTGGTGGCGCTG	60.815	63.158	7.64	0.00	0.00	5.18
2779	2856	2.810852	CCAGAGGCAGAAGAGTTCAAAC	59.189	50.000	0.00	0.00	0.00	2.93
2869	2946	5.264060	TCTTGAAGTTCTTCGCATTAACG	57.736	39.130	4.17	0.00	0.00	3.18
2875	2952	3.074412	GGGATTCTTGAAGTTCTTCGCA	58.926	45.455	4.17	0.00	0.00	5.10
2877	2954	3.674997	TGGGGATTCTTGAAGTTCTTCG	58.325	45.455	4.17	0.00	0.00	3.79
2897	2974	2.009108	CGGAGCACACGGAATCATG	58.991	57.895	0.00	0.00	0.00	3.07
2938	3015	1.507140	TGAGGGGCGATGTCCTAATT	58.493	50.000	0.00	0.00	32.74	1.40
2945	3022	1.903877	CTCACCTTGAGGGGCGATGT	61.904	60.000	1.54	0.00	40.71	3.06

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.