AutoCloner

Multiple sequence alignment - TraesCS7B01G292300

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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	TraesCS7B01G292300	chr7B	100.000	3029	0	0	1	3029	528870653	528873681	0.000000e+00	5594.0
1	TraesCS7B01G292300	chr7B	91.749	2036	99	25	637	2652	73173851	73175837	0.000000e+00	2765.0
2	TraesCS7B01G292300	chr7B	86.869	1447	169	11	942	2374	557257487	557256048	0.000000e+00	1600.0
3	TraesCS7B01G292300	chr7B	85.564	1427	188	15	912	2330	557460718	557459302	0.000000e+00	1478.0
4	TraesCS7B01G292300	chr7B	85.086	523	40	16	3	506	73173000	73173503	1.620000e-137	499.0
5	TraesCS7B01G292300	chr7B	85.323	402	26	6	2656	3029	73175891	73176287	4.740000e-103	385.0
6	TraesCS7B01G292300	chr7B	75.122	410	35	28	2675	3029	664399451	664399054	2.450000e-26	130.0
7	TraesCS7B01G292300	chr7B	89.216	102	6	2	2423	2524	664399641	664399545	4.100000e-24	122.0
8	TraesCS7B01G292300	chr7D	93.851	2667	121	14	1	2652	500772765	500775403	0.000000e+00	3976.0
9	TraesCS7B01G292300	chr7D	93.349	1654	85	13	637	2279	113581190	113582829	0.000000e+00	2422.0
10	TraesCS7B01G292300	chr7D	87.963	1404	148	16	993	2380	523057027	523055629	0.000000e+00	1637.0
11	TraesCS7B01G292300	chr7D	87.223	1401	166	10	938	2330	523128208	523126813	0.000000e+00	1583.0
12	TraesCS7B01G292300	chr7D	91.479	399	9	9	2656	3029	500775619	500776017	2.680000e-145	525.0
13	TraesCS7B01G292300	chr7D	85.851	523	36	16	3	506	113580237	113580740	3.460000e-144	521.0
14	TraesCS7B01G292300	chr7D	100.000	37	0	0	2993	3029	113582861	113582897	5.420000e-08	69.4
15	TraesCS7B01G292300	chr7A	93.735	2123	117	8	538	2652	566787791	566789905	0.000000e+00	3169.0
16	TraesCS7B01G292300	chr7A	87.518	1426	161	11	969	2380	603331692	603330270	0.000000e+00	1631.0
17	TraesCS7B01G292300	chr7A	85.437	515	48	14	1	506	566787213	566787709	7.490000e-141	510.0
18	TraesCS7B01G292300	chr7A	81.266	395	30	20	2656	3029	566789963	566790334	2.300000e-71	279.0
19	TraesCS7B01G292300	chr7A	78.174	449	53	18	2423	2850	566988828	566989252	8.390000e-61	244.0
20	TraesCS7B01G292300	chr7A	75.472	265	33	19	2673	2922	566909830	566910077	1.920000e-17	100.0
21	TraesCS7B01G292300	chr3D	87.943	987	73	13	715	1680	603682150	603683111	0.000000e+00	1122.0
22	TraesCS7B01G292300	chr3B	78.515	377	43	21	2488	2850	805812633	805812281	2.370000e-51	213.0
23	TraesCS7B01G292300	chr3B	87.692	130	5	6	2721	2850	810195314	810195196	1.130000e-29	141.0
24	TraesCS7B01G292300	chrUn	77.236	369	53	14	2673	3029	86611602	86611951	1.430000e-43	187.0
25	TraesCS7B01G292300	chrUn	91.176	102	4	2	2423	2524	86611297	86611393	1.890000e-27	134.0
26	TraesCS7B01G292300	chr3A	77.734	256	12	20	2721	2949	732405069	732404832	6.860000e-22	115.0

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	TraesCS7B01G292300	chr7B	528870653	528873681	3028	False	5594.000000	5594	100.000000	1	3029	1	chr7B.!!$F1	3028
1	TraesCS7B01G292300	chr7B	557256048	557257487	1439	True	1600.000000	1600	86.869000	942	2374	1	chr7B.!!$R1	1432
2	TraesCS7B01G292300	chr7B	557459302	557460718	1416	True	1478.000000	1478	85.564000	912	2330	1	chr7B.!!$R2	1418
3	TraesCS7B01G292300	chr7B	73173000	73176287	3287	False	1216.333333	2765	87.386000	3	3029	3	chr7B.!!$F2	3026
4	TraesCS7B01G292300	chr7D	500772765	500776017	3252	False	2250.500000	3976	92.665000	1	3029	2	chr7D.!!$F2	3028
5	TraesCS7B01G292300	chr7D	523055629	523057027	1398	True	1637.000000	1637	87.963000	993	2380	1	chr7D.!!$R1	1387
6	TraesCS7B01G292300	chr7D	523126813	523128208	1395	True	1583.000000	1583	87.223000	938	2330	1	chr7D.!!$R2	1392
7	TraesCS7B01G292300	chr7D	113580237	113582897	2660	False	1004.133333	2422	93.066667	3	3029	3	chr7D.!!$F1	3026
8	TraesCS7B01G292300	chr7A	603330270	603331692	1422	True	1631.000000	1631	87.518000	969	2380	1	chr7A.!!$R1	1411
9	TraesCS7B01G292300	chr7A	566787213	566790334	3121	False	1319.333333	3169	86.812667	1	3029	3	chr7A.!!$F3	3028
10	TraesCS7B01G292300	chr3D	603682150	603683111	961	False	1122.000000	1122	87.943000	715	1680	1	chr3D.!!$F1	965

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
799	1152	0.034896	AGTGCAAGTAGGACCAACCG	59.965	55.0	0.0	0.0	44.74	4.44	F
801	1154	0.250124	TGCAAGTAGGACCAACCGTG	60.250	55.0	0.0	0.0	44.74	4.94	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1852	2244	0.635009	TACCCAGTAGCTACCAGGCT	59.365	55.000	23.41	14.89	45.29	4.58	R
2683	3323	1.664302	GCTCTTCAAAACCGCAGCTTC	60.664	52.381	0.00	0.00	0.00	3.86	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
255	263	4.398319	TGGTTTCATCTCCAAAGAACCTC	58.602	43.478	0.00	0.00	34.49	3.85
402	419	9.199982	TCTAAGAACAACCATAACTTAACTTCG	57.800	33.333	0.00	0.00	0.00	3.79
445	464	8.861086	TCTTTACCATTTATTTTGTTACTGGCA	58.139	29.630	0.00	0.00	0.00	4.92
480	500	2.683362	GGTTAGTGCTCCCAACTTATGC	59.317	50.000	0.00	0.00	0.00	3.14
506	526	3.896888	TGGAGTGCATTTGAATCTGGTTT	59.103	39.130	0.00	0.00	0.00	3.27
507	527	4.344679	TGGAGTGCATTTGAATCTGGTTTT	59.655	37.500	0.00	0.00	0.00	2.43
508	528	5.538053	TGGAGTGCATTTGAATCTGGTTTTA	59.462	36.000	0.00	0.00	0.00	1.52
509	529	6.095377	GGAGTGCATTTGAATCTGGTTTTAG	58.905	40.000	0.00	0.00	0.00	1.85
510	530	5.473039	AGTGCATTTGAATCTGGTTTTAGC	58.527	37.500	0.00	0.00	0.00	3.09
581	670	2.551912	GGTTGTCACCAAGGCCACG	61.552	63.158	5.01	0.00	43.61	4.94
634	723	5.331902	CAAAGAGTGGGTACGCATAAATTG	58.668	41.667	16.34	14.32	0.00	2.32
649	995	5.769662	GCATAAATTGGATGTCACCTGGATA	59.230	40.000	0.00	0.00	0.00	2.59
705	1057	9.599866	AAATAATTTCGATCACATGTACAGAGA	57.400	29.630	0.00	0.00	0.00	3.10
706	1058	9.770097	AATAATTTCGATCACATGTACAGAGAT	57.230	29.630	0.00	4.48	0.00	2.75
797	1150	5.001232	TCAAATAGTGCAAGTAGGACCAAC	58.999	41.667	0.00	0.00	39.79	3.77
798	1151	3.629142	ATAGTGCAAGTAGGACCAACC	57.371	47.619	0.00	0.00	39.79	3.77
799	1152	0.034896	AGTGCAAGTAGGACCAACCG	59.965	55.000	0.00	0.00	44.74	4.44
800	1153	0.250166	GTGCAAGTAGGACCAACCGT	60.250	55.000	0.00	0.00	44.74	4.83
801	1154	0.250124	TGCAAGTAGGACCAACCGTG	60.250	55.000	0.00	0.00	44.74	4.94
802	1155	0.250166	GCAAGTAGGACCAACCGTGT	60.250	55.000	0.00	0.00	44.74	4.49
834	1187	1.959985	TGTGTGGTACCAAGGCAAATG	59.040	47.619	18.31	0.00	0.00	2.32
896	1249	9.574516	ACTTCTAATTTGGAGTGTTCTTATTGT	57.425	29.630	0.00	0.00	0.00	2.71
947	1304	1.372997	GAACTCTGAGCAACGCCGA	60.373	57.895	4.19	0.00	0.00	5.54
1077	1438	1.063006	CATGCTCCATTTCGCCACG	59.937	57.895	0.00	0.00	0.00	4.94
1197	1558	2.946988	CTATCCCTGACGGCCTCCCA	62.947	65.000	0.00	0.00	0.00	4.37
1289	1669	4.719369	GCTCTTGTCCGCCGACGT	62.719	66.667	0.00	0.00	42.37	4.34
1341	1725	2.461110	GCCGTTCGCCATCGACATT	61.461	57.895	0.00	0.00	45.43	2.71
1735	2127	2.115910	CAAGCCCAAGCCTGTGGA	59.884	61.111	0.28	0.00	41.65	4.02
1737	2129	2.156098	AAGCCCAAGCCTGTGGAGA	61.156	57.895	0.28	0.00	41.65	3.71
1852	2244	0.966920	GTTCACCGAGTTCCTCTCCA	59.033	55.000	0.00	0.00	39.84	3.86
1875	2267	0.033796	TGGTAGCTACTGGGTACGCT	60.034	55.000	22.74	3.78	46.41	5.07
1890	2282	2.360475	GCTTTCCTCTGGGCGCTT	60.360	61.111	7.64	0.00	0.00	4.68
1938	2330	3.832492	GCGCTCCTCCGAGAAGCT	61.832	66.667	4.99	0.00	38.52	3.74
2212	2618	2.692368	GGTGAGGGAGGCCATGGA	60.692	66.667	18.40	0.00	0.00	3.41
2218	2624	3.866582	GGAGGCCATGGAGTCCGG	61.867	72.222	18.40	0.00	0.00	5.14
2358	2769	1.528129	GTCCTGTTGAAGCCCAGAAG	58.472	55.000	0.00	0.00	0.00	2.85
2374	2785	5.355596	CCCAGAAGTAATGAAGACTAGCAG	58.644	45.833	0.00	0.00	0.00	4.24
2407	2818	6.539649	TGCACTACATGTTCAGTTTCTTAC	57.460	37.500	2.30	0.00	0.00	2.34
2408	2819	6.288294	TGCACTACATGTTCAGTTTCTTACT	58.712	36.000	2.30	0.00	37.68	2.24
2409	2820	6.765989	TGCACTACATGTTCAGTTTCTTACTT	59.234	34.615	2.30	0.00	33.85	2.24
2410	2821	7.929245	TGCACTACATGTTCAGTTTCTTACTTA	59.071	33.333	2.30	0.00	33.85	2.24
2411	2822	8.936864	GCACTACATGTTCAGTTTCTTACTTAT	58.063	33.333	2.30	0.00	33.85	1.73
2588	3016	5.464030	TTGGTAGTCACTTGGTTCTACTC	57.536	43.478	0.00	0.00	34.85	2.59
2627	3055	4.430007	TGCTTATTAGTACCAGCAAGTCG	58.570	43.478	0.00	0.00	39.32	4.18
2645	3073	3.255888	AGTCGTCATGAGAAACACAGCTA	59.744	43.478	0.00	0.00	0.00	3.32
2652	3080	6.591834	GTCATGAGAAACACAGCTACTTATGT	59.408	38.462	0.00	0.00	0.00	2.29
2653	3081	7.118390	GTCATGAGAAACACAGCTACTTATGTT	59.882	37.037	0.00	0.00	36.86	2.71
2662	3302	9.587772	AACACAGCTACTTATGTTCTATAGTTG	57.412	33.333	0.00	0.00	29.30	3.16
2683	3323	6.435904	AGTTGGAGGCTTAGAGCATATAGTAG	59.564	42.308	2.04	0.00	44.75	2.57
2824	3475	4.649705	TCCAACTGGGGCGGAGGA	62.650	66.667	0.00	0.00	37.22	3.71
2826	3477	2.190578	CAACTGGGGCGGAGGATC	59.809	66.667	0.00	0.00	0.00	3.36
2850	3501	0.400594	CAAAACCGGAGAGAACCCCT	59.599	55.000	9.46	0.00	0.00	4.79

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
81	82	7.811117	ACTTCTAGACGCACTTAGATTAGAT	57.189	36.000	0.00	0.00	0.00	1.98
82	83	8.775527	CATACTTCTAGACGCACTTAGATTAGA	58.224	37.037	0.00	0.00	0.00	2.10
83	84	7.535940	GCATACTTCTAGACGCACTTAGATTAG	59.464	40.741	0.00	0.00	0.00	1.73
84	85	7.228906	AGCATACTTCTAGACGCACTTAGATTA	59.771	37.037	0.00	0.00	0.00	1.75
85	86	6.039941	AGCATACTTCTAGACGCACTTAGATT	59.960	38.462	0.00	0.00	0.00	2.40
255	263	5.630680	GCTAATATTGTTTGCAATCATCCCG	59.369	40.000	10.87	0.80	43.61	5.14
480	500	0.813184	ATTCAAATGCACTCCAGCGG	59.187	50.000	0.00	0.00	37.31	5.52
510	530	4.450976	TGTGTTGGTTGCTATGGCTATAG	58.549	43.478	12.50	12.50	39.44	1.31
581	670	5.402270	CCAAACATGTTTTGCAGTTAGCTAC	59.598	40.000	21.10	0.00	45.94	3.58
634	723	4.101585	TCTCAACATATCCAGGTGACATCC	59.898	45.833	0.00	0.00	0.00	3.51
649	995	6.878317	TCTCCTTTATCATCGTTCTCAACAT	58.122	36.000	0.00	0.00	0.00	2.71
705	1057	2.756760	CCGTGGGTGTACTGTACTGTAT	59.243	50.000	17.98	0.00	0.00	2.29
706	1058	2.161855	CCGTGGGTGTACTGTACTGTA	58.838	52.381	17.98	8.40	0.00	2.74
797	1150	1.949133	CAGACACACACGGACACGG	60.949	63.158	0.00	0.00	46.48	4.94
799	1152	0.459585	ACACAGACACACACGGACAC	60.460	55.000	0.00	0.00	0.00	3.67
800	1153	0.459411	CACACAGACACACACGGACA	60.459	55.000	0.00	0.00	0.00	4.02
801	1154	1.151777	CCACACAGACACACACGGAC	61.152	60.000	0.00	0.00	0.00	4.79
802	1155	1.142965	CCACACAGACACACACGGA	59.857	57.895	0.00	0.00	0.00	4.69
834	1187	2.363683	AGCATCTTTCCAGTTAGCTGC	58.636	47.619	0.17	0.00	41.26	5.25
896	1249	4.722526	TGAAGGAGGAAGAAACCATTGA	57.277	40.909	0.00	0.00	0.00	2.57
947	1304	3.368739	GCAAATTTAATGGCAGCTCAGGT	60.369	43.478	0.00	0.00	0.00	4.00
1197	1558	3.374402	CTGCGAGGGTGGTCGTCT	61.374	66.667	0.00	0.00	42.17	4.18
1216	1584	1.836802	GGACTCCAAGAGCTCCAAGAT	59.163	52.381	10.93	0.00	33.38	2.40
1265	1633	2.270205	CGGACAAGAGCAGGGCAT	59.730	61.111	0.00	0.00	0.00	4.40
1289	1669	3.353029	CAACGCATGTCACCGGCA	61.353	61.111	0.00	0.00	0.00	5.69
1735	2127	3.063084	GCACCCGTCGTCCTCTCT	61.063	66.667	0.00	0.00	0.00	3.10
1737	2129	2.680352	ATGCACCCGTCGTCCTCT	60.680	61.111	0.00	0.00	0.00	3.69
1852	2244	0.635009	TACCCAGTAGCTACCAGGCT	59.365	55.000	23.41	14.89	45.29	4.58
1875	2267	2.047274	CGAAGCGCCCAGAGGAAA	60.047	61.111	2.29	0.00	33.47	3.13
2147	2546	1.903877	CGTCCTTCATGTCCAGCCCT	61.904	60.000	0.00	0.00	0.00	5.19
2212	2618	1.826054	CCTCTGATCTCGCCGGACT	60.826	63.158	5.05	0.00	0.00	3.85
2218	2624	2.818132	CCACCCCTCTGATCTCGC	59.182	66.667	0.00	0.00	0.00	5.03
2358	2769	4.340950	AGAGGCTCTGCTAGTCTTCATTAC	59.659	45.833	17.96	0.00	41.43	1.89
2374	2785	2.906691	ATGTAGTGCATGAGAGGCTC	57.093	50.000	6.34	6.34	36.26	4.70
2409	2820	9.190317	TGCTAGAATAAGTTCTGAGACTGAATA	57.810	33.333	0.00	0.00	44.27	1.75
2410	2821	8.072321	TGCTAGAATAAGTTCTGAGACTGAAT	57.928	34.615	0.00	0.00	44.27	2.57
2411	2822	7.468141	TGCTAGAATAAGTTCTGAGACTGAA	57.532	36.000	0.00	0.00	44.27	3.02
2412	2823	7.652524	ATGCTAGAATAAGTTCTGAGACTGA	57.347	36.000	0.00	0.00	44.27	3.41
2413	2824	8.715191	AAATGCTAGAATAAGTTCTGAGACTG	57.285	34.615	0.00	0.00	44.27	3.51
2627	3055	6.591834	ACATAAGTAGCTGTGTTTCTCATGAC	59.408	38.462	0.00	0.00	0.00	3.06
2645	3073	7.439108	AAGCCTCCAACTATAGAACATAAGT	57.561	36.000	6.78	0.00	0.00	2.24
2652	3080	5.208890	TGCTCTAAGCCTCCAACTATAGAA	58.791	41.667	6.78	0.00	41.51	2.10
2653	3081	4.804597	TGCTCTAAGCCTCCAACTATAGA	58.195	43.478	6.78	0.00	41.51	1.98
2662	3302	6.405397	GCTTCTACTATATGCTCTAAGCCTCC	60.405	46.154	0.00	0.00	41.51	4.30
2683	3323	1.664302	GCTCTTCAAAACCGCAGCTTC	60.664	52.381	0.00	0.00	0.00	3.86
2824	3475	1.347707	TCTCTCCGGTTTTGCTGTGAT	59.652	47.619	0.00	0.00	0.00	3.06
2826	3477	1.264288	GTTCTCTCCGGTTTTGCTGTG	59.736	52.381	0.00	0.00	0.00	3.66
2973	3660	1.007336	GTACGTCGTTCACTGGCCAG	61.007	60.000	31.60	31.60	0.00	4.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.