AutoCloner

Multiple sequence alignment - TraesCS7B01G031200

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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	TraesCS7B01G031200	chr7B	100.000	2398	0	0	1	2398	30075425	30073028	0.000000e+00	4429
1	TraesCS7B01G031200	chr7B	87.054	224	14	8	2190	2398	18358453	18358676	3.080000e-59	239
2	TraesCS7B01G031200	chr7D	94.717	1893	98	2	1	1892	180439623	180441514	0.000000e+00	2940
3	TraesCS7B01G031200	chr7D	93.071	534	21	8	1881	2398	180441638	180442171	0.000000e+00	767
4	TraesCS7B01G031200	chr3A	94.506	1893	103	1	1	1892	703853571	703851679	0.000000e+00	2918
5	TraesCS7B01G031200	chr3A	94.969	1113	55	1	655	1767	171150785	171151896	0.000000e+00	1744
6	TraesCS7B01G031200	chr3A	93.702	524	25	6	1878	2398	703851559	703851041	0.000000e+00	778
7	TraesCS7B01G031200	chr6D	94.453	1893	100	2	1	1892	150886678	150884790	0.000000e+00	2909
8	TraesCS7B01G031200	chr6D	92.509	534	24	8	1881	2398	150884666	150884133	0.000000e+00	750
9	TraesCS7B01G031200	chr6D	93.151	73	5	0	1759	1831	85565796	85565868	9.060000e-20	108
10	TraesCS7B01G031200	chr3D	94.348	1893	103	4	1	1892	86081406	86079517	0.000000e+00	2900
11	TraesCS7B01G031200	chr3D	92.322	534	24	9	1881	2398	86079392	86078860	0.000000e+00	743
12	TraesCS7B01G031200	chr4A	92.344	1894	126	4	1	1892	644923844	644921968	0.000000e+00	2676
13	TraesCS7B01G031200	chr2B	93.094	1781	118	5	102	1880	696855918	696857695	0.000000e+00	2603
14	TraesCS7B01G031200	chr2B	90.093	535	36	8	1881	2398	696857832	696858366	0.000000e+00	678
15	TraesCS7B01G031200	chr5A	92.831	1618	85	8	146	1763	241459561	241457975	0.000000e+00	2316
16	TraesCS7B01G031200	chr5A	92.883	829	57	1	1	829	667547779	667548605	0.000000e+00	1203
17	TraesCS7B01G031200	chr2A	92.213	1618	91	5	146	1763	111272867	111271285	0.000000e+00	2257
18	TraesCS7B01G031200	chr4B	93.071	534	21	8	1881	2398	145028669	145029202	0.000000e+00	767
19	TraesCS7B01G031200	chr4B	90.824	534	32	9	1881	2398	20175999	20176531	0.000000e+00	699
20	TraesCS7B01G031200	chr2D	92.529	522	23	8	1893	2398	91715460	91715981	0.000000e+00	734
21	TraesCS7B01G031200	chr2D	92.176	524	25	8	1891	2398	105779029	105778506	0.000000e+00	726
22	TraesCS7B01G031200	chr1A	89.608	510	48	3	1	508	548669993	548670499	0.000000e+00	643
23	TraesCS7B01G031200	chrUn	87.330	221	13	8	2193	2398	219487384	219487164	3.080000e-59	239
24	TraesCS7B01G031200	chrUn	87.330	221	13	8	2193	2398	237805729	237805509	3.080000e-59	239
25	TraesCS7B01G031200	chrUn	87.850	214	11	8	2200	2398	384535106	384535319	1.110000e-58	237
26	TraesCS7B01G031200	chr5D	82.772	267	21	3	1598	1841	483324111	483324375	5.190000e-52	215

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	TraesCS7B01G031200	chr7B	30073028	30075425	2397	True	4429.0	4429	100.0000	1	2398	1	chr7B.!!$R1	2397
1	TraesCS7B01G031200	chr7D	180439623	180442171	2548	False	1853.5	2940	93.8940	1	2398	2	chr7D.!!$F1	2397
2	TraesCS7B01G031200	chr3A	703851041	703853571	2530	True	1848.0	2918	94.1040	1	2398	2	chr3A.!!$R1	2397
3	TraesCS7B01G031200	chr3A	171150785	171151896	1111	False	1744.0	1744	94.9690	655	1767	1	chr3A.!!$F1	1112
4	TraesCS7B01G031200	chr6D	150884133	150886678	2545	True	1829.5	2909	93.4810	1	2398	2	chr6D.!!$R1	2397
5	TraesCS7B01G031200	chr3D	86078860	86081406	2546	True	1821.5	2900	93.3350	1	2398	2	chr3D.!!$R1	2397
6	TraesCS7B01G031200	chr4A	644921968	644923844	1876	True	2676.0	2676	92.3440	1	1892	1	chr4A.!!$R1	1891
7	TraesCS7B01G031200	chr2B	696855918	696858366	2448	False	1640.5	2603	91.5935	102	2398	2	chr2B.!!$F1	2296
8	TraesCS7B01G031200	chr5A	241457975	241459561	1586	True	2316.0	2316	92.8310	146	1763	1	chr5A.!!$R1	1617
9	TraesCS7B01G031200	chr5A	667547779	667548605	826	False	1203.0	1203	92.8830	1	829	1	chr5A.!!$F1	828
10	TraesCS7B01G031200	chr2A	111271285	111272867	1582	True	2257.0	2257	92.2130	146	1763	1	chr2A.!!$R1	1617
11	TraesCS7B01G031200	chr4B	145028669	145029202	533	False	767.0	767	93.0710	1881	2398	1	chr4B.!!$F2	517
12	TraesCS7B01G031200	chr4B	20175999	20176531	532	False	699.0	699	90.8240	1881	2398	1	chr4B.!!$F1	517
13	TraesCS7B01G031200	chr2D	91715460	91715981	521	False	734.0	734	92.5290	1893	2398	1	chr2D.!!$F1	505
14	TraesCS7B01G031200	chr2D	105778506	105779029	523	True	726.0	726	92.1760	1891	2398	1	chr2D.!!$R1	507
15	TraesCS7B01G031200	chr1A	548669993	548670499	506	False	643.0	643	89.6080	1	508	1	chr1A.!!$F1	507

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
530	533	0.625683	AGATGGGGTTCAGATGCCCT	60.626	55.0	9.7	0.0	44.25	5.19	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2272	2428	0.036105	CATGCACAGACACAGGGCTA	60.036	55.0	0.0	0.0	0.0	3.93	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
71	72	2.032681	GGCTGTTCGTTGGGCTCT	59.967	61.111	0.00	0.00	0.00	4.09
113	114	2.433664	GGACCCGCCACAACGTAG	60.434	66.667	0.00	0.00	36.34	3.51
114	115	3.230522	GGACCCGCCACAACGTAGT	62.231	63.158	0.00	0.00	38.94	2.73
120	121	1.404449	CCGCCACAACGTAGTATTCCA	60.404	52.381	0.00	0.00	45.00	3.53
129	130	1.202371	CGTAGTATTCCAGCGCTCCAA	60.202	52.381	7.13	2.84	0.00	3.53
211	212	4.304110	TGTCGACTGTCCAAGTTAATCAC	58.696	43.478	17.92	0.00	40.07	3.06
215	216	5.124297	TCGACTGTCCAAGTTAATCACGATA	59.876	40.000	1.55	0.00	40.07	2.92
242	243	9.314321	CAATTCATAAATCCGACTAGTAGTTGT	57.686	33.333	15.15	1.08	0.00	3.32
269	270	7.664758	AGAAATTACTGCAATTTTCTGAAGCT	58.335	30.769	10.36	0.00	44.98	3.74
278	279	6.257630	TGCAATTTTCTGAAGCTGTTTTAACC	59.742	34.615	0.00	0.00	0.00	2.85
376	379	6.463360	AGGTGTTATATTTTTGGTTGCTTGG	58.537	36.000	0.00	0.00	0.00	3.61
450	453	8.687242	TGTGATTAGTTGAACTATACTCTGGAG	58.313	37.037	5.81	0.00	29.64	3.86
525	528	3.117738	GGTTGATGAGATGGGGTTCAGAT	60.118	47.826	0.00	0.00	0.00	2.90
530	533	0.625683	AGATGGGGTTCAGATGCCCT	60.626	55.000	9.70	0.00	44.25	5.19
544	547	2.532854	GCCCTAGCAAGATCCAGGA	58.467	57.895	0.00	0.00	39.53	3.86
694	698	3.248764	GGCCATCTGGATCTGCCT	58.751	61.111	0.00	0.00	39.05	4.75
829	833	4.052922	TGGACCTCCTGTCTAGTATAGGT	58.947	47.826	0.00	0.00	43.89	3.08
932	936	8.442632	TGTTAATTCATCAGATAGCAGGAAAG	57.557	34.615	0.00	0.00	0.00	2.62
952	956	2.258013	CCGCCCTGCTTTGTCGAAA	61.258	57.895	0.00	0.00	0.00	3.46
988	992	2.212812	TGCCCACATTGCATGTTCTA	57.787	45.000	0.00	0.00	42.70	2.10
1183	1189	2.480037	GTGATGAGTTGTTCGATGTGCA	59.520	45.455	0.00	0.00	0.00	4.57
1225	1231	2.678190	GCTAGGTTGAAGAAGATGGCGT	60.678	50.000	0.00	0.00	0.00	5.68
1238	1244	1.264749	ATGGCGTGTAAGGAGGAGCA	61.265	55.000	0.00	0.00	0.00	4.26
1315	1321	7.042335	CACCTCGGTATTATTCACTTTCTCTT	58.958	38.462	0.00	0.00	0.00	2.85
1317	1323	7.764901	ACCTCGGTATTATTCACTTTCTCTTTC	59.235	37.037	0.00	0.00	0.00	2.62
1327	1333	3.633986	CACTTTCTCTTTCCTGCTGGTTT	59.366	43.478	9.73	0.00	34.23	3.27
1368	1374	3.446873	TGTGTTTTGCCTTGATTCTGTGT	59.553	39.130	0.00	0.00	0.00	3.72
1430	1436	9.612066	TGTGTGCTATGATTGTGAATTATAGAA	57.388	29.630	10.67	0.22	38.87	2.10
1452	1458	7.899973	AGAACAGACATTTGCATATTTCCTTT	58.100	30.769	0.36	0.00	0.00	3.11
1570	1576	5.421056	TGGTGTTGAGAAATCGATAGGTAGT	59.579	40.000	0.00	0.00	0.00	2.73
1656	1673	8.910944	CATGGTCTTTTCTGATAATGGAAGAAT	58.089	33.333	0.00	0.00	30.41	2.40
1710	1727	6.062258	TGTACTCCCTCCTTAATTCAAAGG	57.938	41.667	1.07	1.07	46.35	3.11
1712	1729	5.600669	ACTCCCTCCTTAATTCAAAGGTT	57.399	39.130	6.85	0.00	45.37	3.50
1720	1737	7.334671	CCTCCTTAATTCAAAGGTTAGACACTC	59.665	40.741	6.85	0.00	45.37	3.51
1802	1819	5.550403	TCAGATAGAAACTACCTTTTGGGGT	59.450	40.000	0.00	0.00	46.08	4.95
1815	1832	3.756082	TTTGGGGTGCCTTCTATTCAT	57.244	42.857	0.00	0.00	0.00	2.57
1872	1889	5.808030	CCGTGTTTTTCAGGTACAAAATTGT	59.192	36.000	4.01	4.01	44.86	2.71
1889	2043	3.415457	TTGTCCATAGTGTGCACATCA	57.585	42.857	24.69	14.27	0.00	3.07
1974	2128	0.544357	TCCCAGGTCGTCTCCAACAT	60.544	55.000	0.00	0.00	0.00	2.71
2132	2286	4.162131	TGCACTTCATATCAGGACTAGCAA	59.838	41.667	0.00	0.00	0.00	3.91
2197	2352	5.346181	AGCTAGGGTTGTTGATAGACTTC	57.654	43.478	0.00	0.00	0.00	3.01
2247	2402	6.655078	AAACACTAGAATGCCTGAAATGTT	57.345	33.333	0.00	0.00	0.00	2.71
2251	2406	6.115446	CACTAGAATGCCTGAAATGTTAGGA	58.885	40.000	0.00	0.00	36.11	2.94
2266	2422	6.978674	ATGTTAGGATAGCAAGTACTAGCA	57.021	37.500	0.00	0.00	34.78	3.49
2269	2425	6.380274	TGTTAGGATAGCAAGTACTAGCAAGT	59.620	38.462	0.00	0.00	39.91	3.16
2270	2426	7.558807	TGTTAGGATAGCAAGTACTAGCAAGTA	59.441	37.037	0.00	0.00	37.15	2.24
2310	2481	4.734695	GCATGTATGGGCTAGCTTTTTGTC	60.735	45.833	15.72	0.00	0.00	3.18
2357	2528	9.890629	TCTTTCTACAGAAATACAGCATGTTAT	57.109	29.630	4.93	0.00	44.86	1.89
2385	2556	8.682710	TCTATGGATGTTTATTTACTTGCAACC	58.317	33.333	0.00	0.00	29.82	3.77
2389	2560	7.885922	TGGATGTTTATTTACTTGCAACCTCTA	59.114	33.333	0.00	0.00	0.00	2.43

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
71	72	0.252330	TACATCCTGTCGGGGTTCCA	60.252	55.000	0.00	0.00	35.33	3.53
113	114	1.739067	AAGTTGGAGCGCTGGAATAC	58.261	50.000	18.48	5.59	0.00	1.89
114	115	2.027192	AGAAAGTTGGAGCGCTGGAATA	60.027	45.455	18.48	0.00	0.00	1.75
120	121	1.754745	TCCAGAAAGTTGGAGCGCT	59.245	52.632	11.27	11.27	42.24	5.92
129	130	1.537202	GCAAAGCGTGATCCAGAAAGT	59.463	47.619	0.00	0.00	0.00	2.66
211	212	8.744008	ACTAGTCGGATTTATGAATTGTATCG	57.256	34.615	0.00	0.00	0.00	2.92
215	216	9.314321	CAACTACTAGTCGGATTTATGAATTGT	57.686	33.333	0.00	0.00	0.00	2.71
230	231	9.635520	TGCAGTAATTTCTAACAACTACTAGTC	57.364	33.333	0.00	0.00	0.00	2.59
242	243	9.410556	GCTTCAGAAAATTGCAGTAATTTCTAA	57.589	29.630	9.39	2.63	45.74	2.10
269	270	7.337184	TCAGTGTTTGTAGACATGGTTAAAACA	59.663	33.333	0.00	4.92	34.62	2.83
278	279	5.207768	GCAACTTCAGTGTTTGTAGACATG	58.792	41.667	0.00	0.00	0.00	3.21
376	379	5.758784	ACTGAAAGCCAAGAGTTTGTAGTAC	59.241	40.000	0.00	0.00	37.60	2.73
530	533	1.476891	GTGACGTCCTGGATCTTGCTA	59.523	52.381	14.12	0.00	0.00	3.49
544	547	0.460284	GATCATGGGAAGCGTGACGT	60.460	55.000	6.91	0.00	0.00	4.34
613	617	0.249911	GACGAAGCAGGTGGTCTTGT	60.250	55.000	0.00	0.00	0.00	3.16
686	690	0.107643	GCTCCCTGGTAAGGCAGATC	59.892	60.000	0.00	0.00	42.96	2.75
829	833	6.101997	CACATACTAGCATTCACTGACTTGA	58.898	40.000	0.00	0.00	0.00	3.02
932	936	3.423154	CGACAAAGCAGGGCGGAC	61.423	66.667	0.00	0.00	0.00	4.79
952	956	2.299867	GGGCAAACATGGTCAGAAACAT	59.700	45.455	0.00	0.00	0.00	2.71
988	992	1.601419	GCCTGCATCAACACCTGCAT	61.601	55.000	0.00	0.00	46.48	3.96
1183	1189	0.313987	TGACACTTCATCGACGCTGT	59.686	50.000	0.00	0.00	0.00	4.40
1225	1231	2.906389	ACTCAACATGCTCCTCCTTACA	59.094	45.455	0.00	0.00	0.00	2.41
1238	1244	1.003580	CCAGGCACCAGTACTCAACAT	59.996	52.381	0.00	0.00	0.00	2.71
1315	1321	2.300956	TAATGCCAAACCAGCAGGAA	57.699	45.000	0.35	0.00	44.90	3.36
1317	1323	1.826720	ACATAATGCCAAACCAGCAGG	59.173	47.619	0.00	0.00	44.90	4.85
1327	1333	2.092267	ACATCCAGCAGACATAATGCCA	60.092	45.455	0.00	0.00	44.97	4.92
1430	1436	6.869913	CACAAAGGAAATATGCAAATGTCTGT	59.130	34.615	0.00	0.00	0.00	3.41
1452	1458	5.659440	TCAGTTCATACAGCAGATACACA	57.341	39.130	0.00	0.00	0.00	3.72
1520	1526	6.605594	ACAAACAGTCCTCAATTGGAAGTAAA	59.394	34.615	5.42	0.00	37.93	2.01
1608	1614	4.582656	TGAAACAGACATTCCGAAACCAAT	59.417	37.500	0.00	0.00	0.00	3.16
1617	1623	5.712152	AAAGACCATGAAACAGACATTCC	57.288	39.130	0.00	0.00	0.00	3.01
1679	1696	8.625467	AATTAAGGAGGGAGTACATAGAAACT	57.375	34.615	0.00	0.00	0.00	2.66
1802	1819	7.712639	GTCAAGTCTATGAATGAATAGAAGGCA	59.287	37.037	0.37	0.00	40.10	4.75
1815	1832	4.381612	GGTCGACCATGTCAAGTCTATGAA	60.382	45.833	29.75	0.00	35.64	2.57
1889	2043	2.972505	CACCTTGAACTGGCGCGT	60.973	61.111	8.43	0.00	0.00	6.01
1974	2128	1.338105	CCCTGAGCTTCATGTCGACAA	60.338	52.381	24.13	3.63	0.00	3.18
2132	2286	3.788227	TCTACCAGGCAAGACACAAAT	57.212	42.857	0.00	0.00	0.00	2.32
2197	2352	6.022163	AGATTTGACTTCCAGCAGAAAATG	57.978	37.500	0.00	0.00	32.88	2.32
2266	2422	2.563179	CACAGACACAGGGCTAGTACTT	59.437	50.000	0.00	0.00	0.00	2.24
2269	2425	0.895530	GCACAGACACAGGGCTAGTA	59.104	55.000	0.00	0.00	0.00	1.82
2270	2426	1.121407	TGCACAGACACAGGGCTAGT	61.121	55.000	0.00	0.00	0.00	2.57
2271	2427	0.251354	ATGCACAGACACAGGGCTAG	59.749	55.000	0.00	0.00	0.00	3.42
2272	2428	0.036105	CATGCACAGACACAGGGCTA	60.036	55.000	0.00	0.00	0.00	3.93
2273	2429	1.303074	CATGCACAGACACAGGGCT	60.303	57.895	0.00	0.00	0.00	5.19
2274	2430	0.321564	TACATGCACAGACACAGGGC	60.322	55.000	0.00	0.00	0.00	5.19
2276	2432	2.011947	CCATACATGCACAGACACAGG	58.988	52.381	0.00	0.00	0.00	4.00
2277	2433	2.011947	CCCATACATGCACAGACACAG	58.988	52.381	0.00	0.00	0.00	3.66
2310	2481	8.715191	AAAGAAGCATCAACTCACTATTCTAG	57.285	34.615	0.00	0.00	0.00	2.43
2357	2528	9.679661	TTGCAAGTAAATAAACATCCATAGAGA	57.320	29.630	0.00	0.00	0.00	3.10
2378	2549	1.352083	AGAGCTGGTAGAGGTTGCAA	58.648	50.000	0.00	0.00	30.42	4.08

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.