AutoCloner

Multiple sequence alignment - TraesCS7B01G272300

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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	TraesCS7B01G272300	chr7B	100.000	2750	0	0	1	2750	499258174	499255425	0.000000e+00	5079.0
1	TraesCS7B01G272300	chr7B	100.000	28	0	0	94	121	36468675	36468702	5.000000e-03	52.8
2	TraesCS7B01G272300	chr7A	90.188	2283	141	33	1	2268	520562484	520564698	0.000000e+00	2898.0
3	TraesCS7B01G272300	chr7A	94.294	333	17	1	2418	2750	520565298	520565628	2.440000e-140	508.0
4	TraesCS7B01G272300	chr7A	95.556	45	1	1	2317	2361	520565222	520565265	1.370000e-08	71.3
5	TraesCS7B01G272300	chr7A	79.747	79	12	1	348	426	545513085	545513011	1.000000e-03	54.7
6	TraesCS7B01G272300	chr7D	94.794	1671	65	13	402	2064	475376434	475374778	0.000000e+00	2584.0
7	TraesCS7B01G272300	chr7D	94.321	405	16	3	2072	2470	475374408	475374005	5.030000e-172	614.0
8	TraesCS7B01G272300	chr7D	89.024	410	42	3	1	408	475377154	475376746	3.160000e-139	505.0
9	TraesCS7B01G272300	chr7D	96.181	288	11	0	2463	2750	475373984	475373697	3.210000e-129	472.0
10	TraesCS7B01G272300	chr7D	100.000	28	0	0	94	121	87485186	87485213	5.000000e-03	52.8
11	TraesCS7B01G272300	chr1B	85.600	250	25	9	1129	1371	418821471	418821716	4.550000e-63	252.0
12	TraesCS7B01G272300	chr1D	84.615	247	27	9	1129	1368	309088096	309088338	4.580000e-58	235.0
13	TraesCS7B01G272300	chr6A	78.644	295	51	11	1116	1402	465231904	465232194	4.680000e-43	185.0
14	TraesCS7B01G272300	chr6A	87.931	58	5	2	15	71	538093811	538093867	1.770000e-07	67.6
15	TraesCS7B01G272300	chr2A	80.000	250	42	8	1129	1374	672292457	672292212	7.830000e-41	178.0
16	TraesCS7B01G272300	chr2A	84.746	59	8	1	214	272	587166341	587166398	1.060000e-04	58.4
17	TraesCS7B01G272300	chr2D	82.812	192	29	4	1129	1318	527293783	527293594	4.710000e-38	169.0
18	TraesCS7B01G272300	chr2D	83.544	79	12	1	15	93	335119304	335119227	3.800000e-09	73.1
19	TraesCS7B01G272300	chr2B	82.812	192	29	4	1129	1318	624355484	624355295	4.710000e-38	169.0
20	TraesCS7B01G272300	chr6D	77.288	295	55	12	1116	1402	326540347	326540637	2.190000e-36	163.0
21	TraesCS7B01G272300	chr3D	80.952	210	34	5	178	383	64084892	64084685	7.880000e-36	161.0
22	TraesCS7B01G272300	chr5A	77.510	249	45	8	40	285	275115050	275114810	3.690000e-29	139.0
23	TraesCS7B01G272300	chr4A	76.154	260	52	10	15	268	118634299	118634554	7.990000e-26	128.0
24	TraesCS7B01G272300	chr4A	90.323	62	6	0	17	78	338716259	338716320	6.310000e-12	82.4
25	TraesCS7B01G272300	chr5B	77.439	164	34	3	223	384	679560418	679560580	8.110000e-16	95.3

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	TraesCS7B01G272300	chr7B	499255425	499258174	2749	True	5079.00	5079	100.000	1	2750	1	chr7B.!!$R1	2749
1	TraesCS7B01G272300	chr7A	520562484	520565628	3144	False	1159.10	2898	93.346	1	2750	3	chr7A.!!$F1	2749
2	TraesCS7B01G272300	chr7D	475373697	475377154	3457	True	1043.75	2584	93.580	1	2750	4	chr7D.!!$R1	2749

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
359	361	0.113972	TGAACATGGTTGGATGGCCA	59.886	50.0	8.56	8.56	44.17	5.36	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2214	2914	0.240411	AACACTCCTCTACGTGCGTC	59.76	55.0	0.0	0.0	34.58	5.19	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
93	94	2.111043	CACGACTGTTGTGGCCCT	59.889	61.111	18.52	0.00	33.69	5.19
141	142	0.726787	CCGATGACGACGACACGAAA	60.727	55.000	17.75	0.00	42.66	3.46
144	145	0.313043	ATGACGACGACACGAAAGGT	59.687	50.000	0.00	0.00	37.03	3.50
152	153	0.163146	GACACGAAAGGTTACAGCGC	59.837	55.000	0.00	0.00	0.00	5.92
191	192	3.695022	ATGCGTACGAGGTCACCGC	62.695	63.158	21.65	0.00	44.27	5.68
240	241	8.538409	TTTAGGGTTTTAGTTGAATAGACGAC	57.462	34.615	0.00	0.00	0.00	4.34
280	281	7.908827	TGTAAATTATGTCCGAGCTTTAACA	57.091	32.000	0.00	0.00	0.00	2.41
288	289	6.137794	TGTCCGAGCTTTAACAAATTTTGA	57.862	33.333	15.81	0.00	0.00	2.69
300	302	4.241681	ACAAATTTTGACGTGTTTGCTGT	58.758	34.783	15.81	0.00	35.53	4.40
305	307	7.532682	AATTTTGACGTGTTTGCTGTAATTT	57.467	28.000	0.00	0.00	0.00	1.82
309	311	4.334203	TGACGTGTTTGCTGTAATTTGTCT	59.666	37.500	0.00	0.00	0.00	3.41
311	313	3.421888	CGTGTTTGCTGTAATTTGTCTGC	59.578	43.478	0.00	0.00	0.00	4.26
318	320	4.701651	TGCTGTAATTTGTCTGCTATGCTT	59.298	37.500	0.00	0.00	0.00	3.91
359	361	0.113972	TGAACATGGTTGGATGGCCA	59.886	50.000	8.56	8.56	44.17	5.36
397	399	5.041940	GTCCGTGGACAAATATAGTGTCTC	58.958	45.833	14.10	8.95	44.02	3.36
411	732	2.490991	GTGTCTCTTTTAAGGCACGGT	58.509	47.619	0.00	0.00	41.58	4.83
415	736	2.875933	TCTCTTTTAAGGCACGGTGTTG	59.124	45.455	10.24	0.00	0.00	3.33
435	756	5.248477	TGTTGGAGATGCCCTAATATCCTAC	59.752	44.000	5.76	5.76	41.28	3.18
459	780	4.154918	CAGTCATTTCTACAACAGCTTCCC	59.845	45.833	0.00	0.00	0.00	3.97
464	785	1.207089	TCTACAACAGCTTCCCCGATG	59.793	52.381	0.00	0.00	0.00	3.84
468	790	2.515523	CAGCTTCCCCGATGGCAG	60.516	66.667	0.00	0.00	0.00	4.85
472	794	1.895707	CTTCCCCGATGGCAGATGC	60.896	63.158	0.00	0.00	41.14	3.91
614	937	4.394920	ACTGTGAAATTAATACGGTGGCAG	59.605	41.667	1.32	0.00	32.98	4.85
635	958	5.448438	CAGCAAGTTAAAAACGCACTCATA	58.552	37.500	0.00	0.00	36.23	2.15
639	962	6.249260	GCAAGTTAAAAACGCACTCATATCTG	59.751	38.462	0.00	0.00	36.23	2.90
640	963	7.298122	CAAGTTAAAAACGCACTCATATCTGT	58.702	34.615	0.00	0.00	36.23	3.41
641	964	7.061752	AGTTAAAAACGCACTCATATCTGTC	57.938	36.000	0.00	0.00	36.23	3.51
644	967	2.586258	ACGCACTCATATCTGTCCAC	57.414	50.000	0.00	0.00	0.00	4.02
645	968	1.824852	ACGCACTCATATCTGTCCACA	59.175	47.619	0.00	0.00	0.00	4.17
646	969	2.233676	ACGCACTCATATCTGTCCACAA	59.766	45.455	0.00	0.00	0.00	3.33
647	970	3.261580	CGCACTCATATCTGTCCACAAA	58.738	45.455	0.00	0.00	0.00	2.83
648	971	3.062639	CGCACTCATATCTGTCCACAAAC	59.937	47.826	0.00	0.00	0.00	2.93
649	972	4.002982	GCACTCATATCTGTCCACAAACA	58.997	43.478	0.00	0.00	0.00	2.83
650	973	4.455533	GCACTCATATCTGTCCACAAACAA	59.544	41.667	0.00	0.00	0.00	2.83
651	974	5.124457	GCACTCATATCTGTCCACAAACAAT	59.876	40.000	0.00	0.00	0.00	2.71
652	975	6.316140	GCACTCATATCTGTCCACAAACAATA	59.684	38.462	0.00	0.00	0.00	1.90
653	976	7.677276	GCACTCATATCTGTCCACAAACAATAC	60.677	40.741	0.00	0.00	0.00	1.89
654	977	6.535150	ACTCATATCTGTCCACAAACAATACG	59.465	38.462	0.00	0.00	0.00	3.06
655	978	6.403049	TCATATCTGTCCACAAACAATACGT	58.597	36.000	0.00	0.00	0.00	3.57
1288	1623	1.987855	CTCGTGGTGAAGGGCCCTA	60.988	63.158	28.96	7.70	0.00	3.53
1302	1637	1.221840	CCCTACAGCCGTGCTCAAT	59.778	57.895	0.00	0.00	36.40	2.57
1527	1862	1.005275	CGAGCTGCCATCCATCGAT	60.005	57.895	0.00	0.00	35.47	3.59
1620	1955	2.203294	GAACCAACGTGGCTGGGT	60.203	61.111	9.49	2.06	42.67	4.51
1782	2117	2.011122	TCCGTCACTCTCCCTCTTTT	57.989	50.000	0.00	0.00	0.00	2.27
1812	2147	9.300681	ACTTGTGAATATGGAATTTCTTTCTCA	57.699	29.630	0.00	1.18	34.56	3.27
1877	2213	2.484417	GGCTACCCATGACTGTGATCTG	60.484	54.545	0.00	0.00	0.00	2.90
1914	2252	7.967890	ACTGATGCACATTAATAATGATCGA	57.032	32.000	18.78	0.00	41.46	3.59
2008	2346	8.922676	CCAATATATGTACGTACCTGAATTGTC	58.077	37.037	22.43	0.00	0.00	3.18
2042	2380	7.972527	TCTCTTTCTAGTTCTACATGTCGTAC	58.027	38.462	0.00	0.00	0.00	3.67
2064	2402	4.202253	ACTCAGACACATACAGCTGTTCAA	60.202	41.667	27.06	7.61	0.00	2.69
2066	2404	5.122519	TCAGACACATACAGCTGTTCAAAA	58.877	37.500	27.06	6.71	0.00	2.44
2098	2798	3.253188	TGAAACGATTGGAGGCTGAAAAG	59.747	43.478	0.00	0.00	0.00	2.27
2214	2914	1.992667	TGTGCTTGCGAGAGAATAACG	59.007	47.619	4.70	0.00	0.00	3.18
2220	2920	0.566593	GCGAGAGAATAACGACGCAC	59.433	55.000	0.00	0.00	44.29	5.34
2237	2939	0.522180	CACGTAGAGGAGTGTTCGCT	59.478	55.000	0.00	0.00	33.97	4.93
2244	2946	1.160329	AGGAGTGTTCGCTTGTGTGC	61.160	55.000	0.00	0.00	0.00	4.57
2357	3537	1.314730	AGGTAACCACACGGCAAAAG	58.685	50.000	0.00	0.00	34.57	2.27
2396	3578	0.987294	ATAGAGTGCAAGTGGCTGGT	59.013	50.000	0.00	0.00	45.15	4.00
2425	3607	0.892755	CCAAGTAGGAGTACACGCCA	59.107	55.000	4.91	0.00	41.22	5.69
2701	3911	6.105397	ACATACGTCTGAGAAACCCTAAAA	57.895	37.500	8.06	0.00	0.00	1.52
2732	3942	5.003804	ACCGCTGAGAAAGAACAAATATGT	58.996	37.500	0.00	0.00	43.14	2.29

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
191	192	2.865343	CTACACTACCTTGTAGCGGG	57.135	55.000	1.28	0.00	41.88	6.13
217	218	7.230849	TGTCGTCTATTCAACTAAAACCCTA	57.769	36.000	0.00	0.00	0.00	3.53
249	250	8.500753	AGCTCGGACATAATTTACATAAAACA	57.499	30.769	0.00	0.00	0.00	2.83
279	280	4.838665	ACAGCAAACACGTCAAAATTTG	57.161	36.364	0.00	0.00	35.57	2.32
280	281	7.532682	AATTACAGCAAACACGTCAAAATTT	57.467	28.000	0.00	0.00	0.00	1.82
288	289	4.597079	CAGACAAATTACAGCAAACACGT	58.403	39.130	0.00	0.00	0.00	4.49
300	302	9.086336	GCAAATTTAAGCATAGCAGACAAATTA	57.914	29.630	0.00	0.00	0.00	1.40
305	307	5.902613	AGCAAATTTAAGCATAGCAGACA	57.097	34.783	3.62	0.00	0.00	3.41
309	311	7.959689	TTTCAAAGCAAATTTAAGCATAGCA	57.040	28.000	3.62	0.00	0.00	3.49
359	361	0.463295	CGGACATGAATGCAGGAGCT	60.463	55.000	0.00	0.00	42.74	4.09
397	399	1.950909	TCCAACACCGTGCCTTAAAAG	59.049	47.619	0.00	0.00	0.00	2.27
411	732	4.242811	AGGATATTAGGGCATCTCCAACA	58.757	43.478	0.00	0.00	36.21	3.33
415	736	4.362677	TGGTAGGATATTAGGGCATCTCC	58.637	47.826	0.00	0.00	0.00	3.71
435	756	4.154918	GGAAGCTGTTGTAGAAATGACTGG	59.845	45.833	0.00	0.00	0.00	4.00
459	780	0.536687	ATGGAAGCATCTGCCATCGG	60.537	55.000	0.40	0.00	46.41	4.18
464	785	1.162800	GGTCGATGGAAGCATCTGCC	61.163	60.000	0.00	0.00	43.38	4.85
468	790	2.890808	TGTAGGTCGATGGAAGCATC	57.109	50.000	0.00	0.00	0.00	3.91
614	937	6.249260	CAGATATGAGTGCGTTTTTAACTTGC	59.751	38.462	0.00	0.00	0.00	4.01
635	958	5.992829	TGTTACGTATTGTTTGTGGACAGAT	59.007	36.000	0.00	0.00	0.00	2.90
639	962	6.733280	CGTATTGTTACGTATTGTTTGTGGAC	59.267	38.462	0.00	0.00	44.84	4.02
640	963	6.819437	CGTATTGTTACGTATTGTTTGTGGA	58.181	36.000	0.00	0.00	44.84	4.02
842	1176	1.447489	CAGCAACGCTCCTCCTCTG	60.447	63.158	0.00	0.00	36.40	3.35
878	1213	2.262915	CTCACCAGCAGACGTCCC	59.737	66.667	13.01	3.59	0.00	4.46
982	1317	0.733566	ATTTCCAATGCAAGTGCGCG	60.734	50.000	0.00	0.00	45.83	6.86
983	1318	0.717224	CATTTCCAATGCAAGTGCGC	59.283	50.000	0.00	0.00	45.83	6.09
1064	1399	1.756950	ATAACTCCGCCTCTCGCCA	60.757	57.895	0.00	0.00	36.73	5.69
1081	1416	1.324014	TCCCTCCCTCTCTTCTCCAT	58.676	55.000	0.00	0.00	0.00	3.41
1288	1623	1.244019	GGGAAATTGAGCACGGCTGT	61.244	55.000	2.98	0.00	39.88	4.40
1302	1637	3.717294	GAGGCCAGCTCCGGGAAA	61.717	66.667	5.01	0.00	0.00	3.13
1468	1803	1.064946	CGACCTGGCTCGACATCTC	59.935	63.158	11.57	0.00	35.58	2.75
1812	2147	5.063880	ACGGAAAATTAGAAGCTGACAAGT	58.936	37.500	0.00	0.00	0.00	3.16
1877	2213	3.871594	GTGCATCAGTATCAACCACCTAC	59.128	47.826	0.00	0.00	0.00	3.18
1914	2252	1.219124	CAGGCGTGTACTGAGGCAT	59.781	57.895	0.00	0.00	38.20	4.40
2008	2346	9.635520	TGTAGAACTAGAAAGAGATTTTTACGG	57.364	33.333	0.00	0.00	0.00	4.02
2042	2380	3.917988	TGAACAGCTGTATGTGTCTGAG	58.082	45.455	22.01	0.00	32.52	3.35
2064	2402	6.568869	TCCAATCGTTTCACATGTTCTTTTT	58.431	32.000	0.00	0.00	0.00	1.94
2066	2404	5.278463	CCTCCAATCGTTTCACATGTTCTTT	60.278	40.000	0.00	0.00	0.00	2.52
2068	2406	3.753272	CCTCCAATCGTTTCACATGTTCT	59.247	43.478	0.00	0.00	0.00	3.01
2069	2407	3.670627	GCCTCCAATCGTTTCACATGTTC	60.671	47.826	0.00	0.00	0.00	3.18
2070	2408	2.228822	GCCTCCAATCGTTTCACATGTT	59.771	45.455	0.00	0.00	0.00	2.71
2075	2775	1.808411	TCAGCCTCCAATCGTTTCAC	58.192	50.000	0.00	0.00	0.00	3.18
2098	2798	2.098117	CAGAATCCGAGGCATCAAAACC	59.902	50.000	0.00	0.00	0.00	3.27
2214	2914	0.240411	AACACTCCTCTACGTGCGTC	59.760	55.000	0.00	0.00	34.58	5.19
2220	2920	1.068472	ACAAGCGAACACTCCTCTACG	60.068	52.381	0.00	0.00	0.00	3.51
2221	2921	2.288273	ACACAAGCGAACACTCCTCTAC	60.288	50.000	0.00	0.00	0.00	2.59
2224	2924	0.861837	CACACAAGCGAACACTCCTC	59.138	55.000	0.00	0.00	0.00	3.71
2237	2939	3.244044	TGCACTATAGACACAGCACACAA	60.244	43.478	6.78	0.00	0.00	3.33
2244	2946	3.516981	AGTGCTGCACTATAGACACAG	57.483	47.619	32.18	11.16	43.46	3.66
2357	3537	3.431922	TCGATCGTATCACCTGGTTTC	57.568	47.619	15.94	0.00	0.00	2.78
2396	3578	6.012113	TGTACTCCTACTTGGTACTTGCTAA	58.988	40.000	0.00	0.00	37.35	3.09
2404	3586	2.094675	GGCGTGTACTCCTACTTGGTA	58.905	52.381	0.00	0.00	37.07	3.25
2474	3684	1.802960	GATATTGAGCTGACCGCATGG	59.197	52.381	0.00	0.00	42.61	3.66
2651	3861	7.014038	AGACCCAATAATTTCTCAATGATCAGC	59.986	37.037	0.09	0.00	0.00	4.26
2701	3911	4.537135	TCTTTCTCAGCGGTATGTTTCT	57.463	40.909	0.00	0.00	0.00	2.52

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.