AutoCloner

Multiple sequence alignment - TraesCS3B01G076700

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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	TraesCS3B01G076700	chr3B	100.000	2727	0	0	579	3305	47261723	47264449	0.000000e+00	5036.0
1	TraesCS3B01G076700	chr3B	100.000	417	0	0	1	417	47261145	47261561	0.000000e+00	771.0
2	TraesCS3B01G076700	chr3B	75.626	439	84	13	1837	2270	46328856	46329276	2.600000e-46	196.0
3	TraesCS3B01G076700	chr3B	75.186	403	80	15	1832	2230	46305523	46305909	4.380000e-39	172.0
4	TraesCS3B01G076700	chr3B	82.456	171	28	2	1183	1352	46788458	46788289	7.390000e-32	148.0
5	TraesCS3B01G076700	chr3B	82.692	156	27	0	1196	1351	47256438	47256593	4.450000e-29	139.0
6	TraesCS3B01G076700	chr3D	96.459	2739	78	11	579	3305	28242267	28244998	0.000000e+00	4503.0
7	TraesCS3B01G076700	chr3D	82.343	1161	186	12	1165	2318	27890278	27889130	0.000000e+00	990.0
8	TraesCS3B01G076700	chr3D	82.260	885	137	13	1440	2318	28485519	28486389	0.000000e+00	747.0
9	TraesCS3B01G076700	chr3D	92.494	413	16	10	1	411	28241821	28242220	7.950000e-161	577.0
10	TraesCS3B01G076700	chr3D	73.556	450	94	14	1837	2280	28123722	28123292	7.390000e-32	148.0
11	TraesCS3B01G076700	chr3D	87.387	111	14	0	2653	2763	27889120	27889010	9.630000e-26	128.0
12	TraesCS3B01G076700	chr3D	81.410	156	29	0	1196	1351	28233435	28233590	9.630000e-26	128.0
13	TraesCS3B01G076700	chr3D	81.875	160	16	7	2615	2767	9675024	9674871	4.480000e-24	122.0
14	TraesCS3B01G076700	chr3D	81.098	164	17	8	3132	3288	28487700	28487856	5.790000e-23	119.0
15	TraesCS3B01G076700	chr3D	83.784	111	13	5	2653	2763	28486399	28486504	2.100000e-17	100.0
16	TraesCS3B01G076700	chr3A	91.688	1191	72	14	1152	2326	38208213	38209392	0.000000e+00	1626.0
17	TraesCS3B01G076700	chr3A	79.344	1433	249	25	908	2318	38238429	38239836	0.000000e+00	963.0
18	TraesCS3B01G076700	chr3A	93.468	444	26	3	2320	2762	38215310	38215751	0.000000e+00	656.0
19	TraesCS3B01G076700	chr3A	94.431	413	18	4	1	411	38207323	38207732	6.020000e-177	630.0
20	TraesCS3B01G076700	chr3A	89.095	431	38	4	579	1001	38207778	38208207	8.120000e-146	527.0
21	TraesCS3B01G076700	chr3A	82.051	156	27	1	1196	1351	38197793	38197947	7.440000e-27	132.0
22	TraesCS3B01G076700	chr3A	80.272	147	29	0	1196	1342	10416351	10416497	9.690000e-21	111.0
23	TraesCS3B01G076700	chr3A	100.000	31	0	0	204	234	38207495	38207525	1.280000e-04	58.4
24	TraesCS3B01G076700	chr2B	73.795	477	105	13	1839	2306	787034389	787033924	1.580000e-38	171.0
25	TraesCS3B01G076700	chr7B	83.784	148	23	1	1201	1348	746305451	746305597	4.450000e-29	139.0
26	TraesCS3B01G076700	chrUn	72.050	483	120	12	1196	1671	35802098	35801624	2.680000e-26	130.0
27	TraesCS3B01G076700	chrUn	71.784	482	123	10	1196	1671	324842387	324841913	1.250000e-24	124.0
28	TraesCS3B01G076700	chrUn	71.784	482	123	10	1196	1671	387902246	387902720	1.250000e-24	124.0
29	TraesCS3B01G076700	chr4B	80.240	167	31	2	1187	1352	99435803	99435968	1.250000e-24	124.0

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	TraesCS3B01G076700	chr3B	47261145	47264449	3304	False	2903.50	5036	100.000000	1	3305	2	chr3B.!!$F4	3304
1	TraesCS3B01G076700	chr3D	28241821	28244998	3177	False	2540.00	4503	94.476500	1	3305	2	chr3D.!!$F2	3304
2	TraesCS3B01G076700	chr3D	27889010	27890278	1268	True	559.00	990	84.865000	1165	2763	2	chr3D.!!$R3	1598
3	TraesCS3B01G076700	chr3D	28485519	28487856	2337	False	322.00	747	82.380667	1440	3288	3	chr3D.!!$F3	1848
4	TraesCS3B01G076700	chr3A	38238429	38239836	1407	False	963.00	963	79.344000	908	2318	1	chr3A.!!$F4	1410
5	TraesCS3B01G076700	chr3A	38207323	38209392	2069	False	710.35	1626	93.803500	1	2326	4	chr3A.!!$F5	2325

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
383	386	0.744281	AGAACAACTTGTTTGGCCCG	59.256	50.0	8.56	0.00	41.28	6.13	F
1092	1103	0.179015	TCTCTTCCGGGAGATCCTCG	60.179	60.0	14.44	0.47	37.43	4.63	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1577	1612	1.151777	CGCCGCACCGACAAATATCT	61.152	55.0	0.0	0.0	0.0	1.98	R
2660	2701	0.754957	CACTTGCAGGGGGTGTTCAA	60.755	55.0	0.0	0.0	0.0	2.69	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
27	28	3.402110	TGACTGTCTGGTTTATGTGCTG	58.598	45.455	9.51	0.00	0.00	4.41
161	164	7.043458	CGTTTAGATGTGCAATTCAACAGTTTT	60.043	33.333	0.00	0.00	0.00	2.43
199	202	2.806434	TGACATTGGTAAGCTGCCATT	58.194	42.857	10.62	5.37	35.71	3.16
233	236	3.489355	CATTGGTAAGCTGCCATGGATA	58.511	45.455	18.40	1.89	35.71	2.59
369	372	2.224378	CCAAACAGAGCCTGAGAGAACA	60.224	50.000	8.91	0.00	35.18	3.18
370	373	3.470709	CAAACAGAGCCTGAGAGAACAA	58.529	45.455	8.91	0.00	35.18	2.83
383	386	0.744281	AGAACAACTTGTTTGGCCCG	59.256	50.000	8.56	0.00	41.28	6.13
411	414	8.715191	TTGAAAATGATTATTTGGCGCTAAAT	57.285	26.923	30.46	30.46	36.65	1.40
412	415	8.715191	TGAAAATGATTATTTGGCGCTAAATT	57.285	26.923	32.30	18.49	36.65	1.82
413	416	8.816144	TGAAAATGATTATTTGGCGCTAAATTC	58.184	29.630	32.30	24.82	36.65	2.17
414	417	7.713764	AAATGATTATTTGGCGCTAAATTCC	57.286	32.000	32.30	21.75	35.26	3.01
415	418	5.195001	TGATTATTTGGCGCTAAATTCCC	57.805	39.130	32.30	21.46	32.79	3.97
416	419	4.038642	TGATTATTTGGCGCTAAATTCCCC	59.961	41.667	32.30	20.02	32.79	4.81
617	620	5.221303	CCATTTTCTCATCCAACGGCATTAT	60.221	40.000	0.00	0.00	0.00	1.28
624	627	3.558931	TCCAACGGCATTATCTGACAT	57.441	42.857	0.00	0.00	29.06	3.06
639	642	5.694231	TCTGACATGTGAAAAGACCATTG	57.306	39.130	1.15	0.00	0.00	2.82
762	765	5.825593	TTAGATAGAGTGCCAAATAGGGG	57.174	43.478	0.00	0.00	38.09	4.79
764	767	4.307259	AGATAGAGTGCCAAATAGGGGAA	58.693	43.478	0.00	0.00	38.09	3.97
804	814	7.365497	AGGGAAGCATATTTTGAAATAAGGG	57.635	36.000	0.73	0.00	34.79	3.95
805	815	7.132128	AGGGAAGCATATTTTGAAATAAGGGA	58.868	34.615	0.73	0.00	34.79	4.20
898	909	3.608316	ACAAAACAACAACCACATGCT	57.392	38.095	0.00	0.00	0.00	3.79
975	986	1.330521	CGAATCAAAATGTCCCGCGAT	59.669	47.619	8.23	0.00	0.00	4.58
1092	1103	0.179015	TCTCTTCCGGGAGATCCTCG	60.179	60.000	14.44	0.47	37.43	4.63
1118	1140	2.271800	GCCACGAAGATGATCTCGTTT	58.728	47.619	14.22	0.00	36.64	3.60
1125	1147	6.473778	CACGAAGATGATCTCGTTTGTATCTT	59.526	38.462	14.22	3.18	37.53	2.40
1308	1335	2.552373	CCCCAAGTTCTTCTACCGCTTT	60.552	50.000	0.00	0.00	0.00	3.51
1397	1432	1.133976	GTGAATCATGGACCCTCCCAG	60.134	57.143	0.00	0.00	39.97	4.45
1452	1487	2.047179	GGCGGCTTCCTCGAAAGT	60.047	61.111	0.00	0.00	0.00	2.66
1502	1537	2.149803	CTCGTCAAGTACCGGGTGCA	62.150	60.000	17.72	0.00	0.00	4.57
1577	1612	0.685097	CCACCGAAGTTCAGGAGGAA	59.315	55.000	18.46	0.00	40.13	3.36
1673	1708	4.080243	TCCTTTCAAGGTGGTCTTTGTGTA	60.080	41.667	5.48	0.00	46.54	2.90
1739	1776	5.564550	GGAGACTGGCATATGGTCAATATT	58.435	41.667	4.56	0.00	32.98	1.28
1903	1940	0.897621	GGGCCTCCTTTGACAAATGG	59.102	55.000	0.84	5.69	32.94	3.16
2247	2285	4.251103	TCCTTGCTACTATCCTCTCACA	57.749	45.455	0.00	0.00	0.00	3.58
2250	2288	4.646945	CCTTGCTACTATCCTCTCACAAGA	59.353	45.833	0.00	0.00	36.28	3.02
2446	2486	5.341196	GCCGTATTGTGTTTTGTGTTATCAC	59.659	40.000	0.00	0.00	44.08	3.06
2462	2502	6.254589	GTGTTATCACTCAATGTAGCTGTCTC	59.745	42.308	0.00	0.00	40.98	3.36
2550	2591	1.271543	TGGGCATGTTTGGACTCTCAG	60.272	52.381	0.00	0.00	0.00	3.35
2636	2677	7.775561	ACTCCATAATACCAACTTTCCTTGATC	59.224	37.037	0.00	0.00	0.00	2.92
2660	2701	7.514721	TCCCAATAGTTCTCTTTGTTAGTTGT	58.485	34.615	0.00	0.00	0.00	3.32
2670	2711	4.399934	TCTTTGTTAGTTGTTGAACACCCC	59.600	41.667	0.00	0.00	35.35	4.95
2795	3635	6.127479	ACAAATGTAGTGTCAAAAGGCTCAAA	60.127	34.615	0.00	0.00	0.00	2.69
2796	3636	6.655078	AATGTAGTGTCAAAAGGCTCAAAT	57.345	33.333	0.00	0.00	0.00	2.32
2801	3641	8.296713	TGTAGTGTCAAAAGGCTCAAATATTTC	58.703	33.333	0.00	0.00	0.00	2.17
2825	3665	6.543465	TCTTCTTTTGTCATCAGTGTTCACAT	59.457	34.615	5.74	0.00	0.00	3.21
2826	3666	6.698008	TCTTTTGTCATCAGTGTTCACATT	57.302	33.333	5.74	0.00	0.00	2.71
2930	3788	0.768622	TCACCGGGTTTGTTCCATCT	59.231	50.000	6.32	0.00	0.00	2.90
2966	3824	8.237267	GGTTGGCACTATTTATATGTTATCTGC	58.763	37.037	0.00	0.00	0.00	4.26
3027	3915	6.969043	TCTAATCCAGGGAATTTCAGCTTAA	58.031	36.000	0.00	0.00	0.00	1.85
3098	3986	0.541296	ATGCTTGTGCTTGGAGGCTT	60.541	50.000	0.00	0.00	40.48	4.35
3106	3994	1.143684	TGCTTGGAGGCTTGTCTCTTT	59.856	47.619	2.16	0.00	34.39	2.52
3168	4072	2.959516	TGTGTATTCTTCTCGGCTGTG	58.040	47.619	0.00	0.00	0.00	3.66
3212	4116	3.498397	AGTCGATGTTTTGTGTAAGCCAG	59.502	43.478	0.00	0.00	0.00	4.85
3297	4205	4.112716	TGAAAAGCATGTACGGTCGATA	57.887	40.909	0.00	0.00	0.00	2.92

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
10	11	2.158682	ACACCAGCACATAAACCAGACA	60.159	45.455	0.00	0.00	0.00	3.41
11	12	2.226437	CACACCAGCACATAAACCAGAC	59.774	50.000	0.00	0.00	0.00	3.51
27	28	0.671251	TTGAACCATTTCGGCACACC	59.329	50.000	0.00	0.00	39.03	4.16
127	130	6.589830	ATTGCACATCTAAACGAGTATGAC	57.410	37.500	0.00	0.00	0.00	3.06
141	144	5.982516	TGGTAAAACTGTTGAATTGCACATC	59.017	36.000	0.00	0.00	0.00	3.06
181	184	2.806434	TCAATGGCAGCTTACCAATGT	58.194	42.857	16.60	2.00	41.49	2.71
199	202	4.584325	GCTTACCAATGCCAAATCCTATCA	59.416	41.667	0.00	0.00	0.00	2.15
233	236	0.596082	GCGTGTATTTGGCACTTGGT	59.404	50.000	0.00	0.00	34.91	3.67
369	372	2.035632	TCAAATCGGGCCAAACAAGTT	58.964	42.857	4.39	0.00	0.00	2.66
370	373	1.698506	TCAAATCGGGCCAAACAAGT	58.301	45.000	4.39	0.00	0.00	3.16
383	386	7.237920	AGCGCCAAATAATCATTTTCAAATC	57.762	32.000	2.29	0.00	31.82	2.17
617	620	5.008911	CACAATGGTCTTTTCACATGTCAGA	59.991	40.000	0.00	0.00	0.00	3.27
624	627	1.686052	GGGCACAATGGTCTTTTCACA	59.314	47.619	0.00	0.00	0.00	3.58
639	642	5.185828	ACAAGGAAGAAATTATTGAGGGCAC	59.814	40.000	0.00	0.00	0.00	5.01
764	767	5.487131	TGCTTCCCTATTTTGCCCTATTTTT	59.513	36.000	0.00	0.00	0.00	1.94
768	771	3.971468	TGCTTCCCTATTTTGCCCTAT	57.029	42.857	0.00	0.00	0.00	2.57
898	909	1.422402	AGGGAAGAGGTTGGCGTTTTA	59.578	47.619	0.00	0.00	0.00	1.52
1032	1043	2.222886	CACGGACATACGAGGATCTCT	58.777	52.381	0.00	0.00	37.61	3.10
1092	1103	0.460284	ATCATCTTCGTGGCACCGAC	60.460	55.000	12.86	0.00	36.42	4.79
1118	1140	3.635433	GCGACTACGGCAAGATACA	57.365	52.632	0.00	0.00	40.15	2.29
1308	1335	1.383456	GCTTGCGATGGTGGGCATAA	61.383	55.000	0.00	0.00	39.21	1.90
1452	1487	2.965147	GCGGCAATCGAGCACAACA	61.965	57.895	0.00	0.00	42.43	3.33
1502	1537	2.167693	TCACACACAACGAACTCTTCCT	59.832	45.455	0.00	0.00	0.00	3.36
1577	1612	1.151777	CGCCGCACCGACAAATATCT	61.152	55.000	0.00	0.00	0.00	1.98
1673	1708	8.522830	CATGGGTTCTTATATCTTTTGTTGTGT	58.477	33.333	0.00	0.00	0.00	3.72
1903	1940	3.120511	CCGAAAGCTGCTCTTGTAGAAAC	60.121	47.826	1.00	0.00	34.67	2.78
2247	2285	5.300286	GCAATTACCTGGTGCATAGAATCTT	59.700	40.000	10.23	0.00	38.19	2.40
2250	2288	4.796606	AGCAATTACCTGGTGCATAGAAT	58.203	39.130	10.23	0.00	40.83	2.40
2462	2502	3.628942	TGATTTGGATCGCTCAAGAATGG	59.371	43.478	0.00	0.00	34.91	3.16
2518	2558	3.350219	ACATGCCCAACTAGTTACTGG	57.650	47.619	8.04	10.33	0.00	4.00
2636	2677	7.745620	ACAACTAACAAAGAGAACTATTGGG	57.254	36.000	0.00	0.00	0.00	4.12
2660	2701	0.754957	CACTTGCAGGGGGTGTTCAA	60.755	55.000	0.00	0.00	0.00	2.69
2670	2711	4.081972	ACAGATGTACTAGTCACTTGCAGG	60.082	45.833	0.00	0.00	0.00	4.85
2796	3636	9.119418	TGAACACTGATGACAAAAGAAGAAATA	57.881	29.630	0.00	0.00	0.00	1.40
2801	3641	6.122850	TGTGAACACTGATGACAAAAGAAG	57.877	37.500	6.51	0.00	0.00	2.85
2825	3665	6.759272	AGAAGAGCACTGTAACACAATCTAA	58.241	36.000	0.00	0.00	0.00	2.10
2826	3666	6.346477	AGAAGAGCACTGTAACACAATCTA	57.654	37.500	0.00	0.00	0.00	1.98
2930	3788	2.853159	GTGCCAACCACATCGATGA	58.147	52.632	31.33	3.59	44.06	2.92
2993	3851	3.054361	TCCCTGGATTAGAAACTTGGCTC	60.054	47.826	0.00	0.00	0.00	4.70
3027	3915	8.530804	ACCGACTTCAAATAATACTACTAGGT	57.469	34.615	0.00	0.00	0.00	3.08
3098	3986	4.016444	GTCATATTTGGGCCAAAGAGACA	58.984	43.478	33.28	19.90	36.76	3.41
3106	3994	4.601406	AGTTTAGGTCATATTTGGGCCA	57.399	40.909	0.00	0.00	0.00	5.36
3168	4072	6.051717	ACTGTAATGTCATGCTTCTCATACC	58.948	40.000	0.00	0.00	33.19	2.73
3212	4116	3.045601	TGCTTACTGCTGAAACTCTCC	57.954	47.619	0.00	0.00	43.37	3.71
3235	4139	7.549488	AGAATACACAACAATACAAGTCTAGGC	59.451	37.037	0.00	0.00	0.00	3.93

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.