AutoCloner

Multiple sequence alignment - TraesCS7A01G076000

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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	TraesCS7A01G076000	chr7A	100.000	3103	0	0	1	3103	41625695	41628797	0.000000e+00	5731
1	TraesCS7A01G076000	chr7B	93.787	2897	161	10	210	3103	2564405	2561525	0.000000e+00	4335
2	TraesCS7A01G076000	chr7B	95.588	204	9	0	1	204	2564672	2564469	8.300000e-86	327
3	TraesCS7A01G076000	chr4A	93.388	2904	167	15	204	3103	657366735	657369617	0.000000e+00	4276
4	TraesCS7A01G076000	chr4A	93.287	2905	171	14	204	3103	657307041	657309926	0.000000e+00	4263
5	TraesCS7A01G076000	chr4A	93.049	2906	174	16	204	3098	649144568	649147456	0.000000e+00	4222
6	TraesCS7A01G076000	chr4A	93.368	1900	109	8	204	2099	649174043	649175929	0.000000e+00	2795
7	TraesCS7A01G076000	chr4A	95.588	204	9	0	1	204	649173782	649173985	8.300000e-86	327
8	TraesCS7A01G076000	chr4A	94.608	204	10	1	1	204	657306781	657306983	6.460000e-82	315
9	TraesCS7A01G076000	chr4A	94.608	204	9	1	1	204	657366476	657366677	6.460000e-82	315
10	TraesCS7A01G076000	chr4A	92.157	204	15	1	1	204	649144308	649144510	1.410000e-73	287
11	TraesCS7A01G076000	chr7D	92.384	2915	189	18	204	3103	42212392	42215288	0.000000e+00	4122
12	TraesCS7A01G076000	chr7D	92.289	2918	180	24	204	3103	42084631	42081741	0.000000e+00	4100
13	TraesCS7A01G076000	chr7D	91.864	2913	198	19	204	3102	41917241	41914354	0.000000e+00	4030
14	TraesCS7A01G076000	chr7D	92.299	2558	148	16	555	3103	42246216	42248733	0.000000e+00	3587
15	TraesCS7A01G076000	chr7D	91.234	2464	173	20	457	2913	567986933	567989360	0.000000e+00	3314
16	TraesCS7A01G076000	chr7D	92.105	266	21	0	204	469	42245772	42246037	2.920000e-100	375
17	TraesCS7A01G076000	chr7D	94.608	204	11	0	1	204	42212131	42212334	1.800000e-82	316
18	TraesCS7A01G076000	chr7D	93.627	204	13	0	1	204	41917502	41917299	3.890000e-79	305
19	TraesCS7A01G076000	chr7D	93.171	205	12	2	1	204	42084892	42084689	1.810000e-77	300
20	TraesCS7A01G076000	chr7D	91.667	204	17	0	1	204	42245511	42245714	1.820000e-72	283
21	TraesCS7A01G076000	chr7D	95.614	114	5	0	356	469	42246075	42246188	1.900000e-42	183
22	TraesCS7A01G076000	chr2B	89.942	2933	238	25	209	3103	784364955	784367868	0.000000e+00	3729
23	TraesCS7A01G076000	chr2B	90.928	1444	110	9	209	1636	784510020	784511458	0.000000e+00	1921
24	TraesCS7A01G076000	chr2B	90.251	1477	117	10	1634	3098	784511491	784512952	0.000000e+00	1905

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	TraesCS7A01G076000	chr7A	41625695	41628797	3102	False	5731.0	5731	100.00000	1	3103	1	chr7A.!!$F1	3102
1	TraesCS7A01G076000	chr7B	2561525	2564672	3147	True	2331.0	4335	94.68750	1	3103	2	chr7B.!!$R1	3102
2	TraesCS7A01G076000	chr4A	657366476	657369617	3141	False	2295.5	4276	93.99800	1	3103	2	chr4A.!!$F4	3102
3	TraesCS7A01G076000	chr4A	657306781	657309926	3145	False	2289.0	4263	93.94750	1	3103	2	chr4A.!!$F3	3102
4	TraesCS7A01G076000	chr4A	649144308	649147456	3148	False	2254.5	4222	92.60300	1	3098	2	chr4A.!!$F1	3097
5	TraesCS7A01G076000	chr4A	649173782	649175929	2147	False	1561.0	2795	94.47800	1	2099	2	chr4A.!!$F2	2098
6	TraesCS7A01G076000	chr7D	567986933	567989360	2427	False	3314.0	3314	91.23400	457	2913	1	chr7D.!!$F1	2456
7	TraesCS7A01G076000	chr7D	42212131	42215288	3157	False	2219.0	4122	93.49600	1	3103	2	chr7D.!!$F2	3102
8	TraesCS7A01G076000	chr7D	42081741	42084892	3151	True	2200.0	4100	92.73000	1	3103	2	chr7D.!!$R2	3102
9	TraesCS7A01G076000	chr7D	41914354	41917502	3148	True	2167.5	4030	92.74550	1	3102	2	chr7D.!!$R1	3101
10	TraesCS7A01G076000	chr7D	42245511	42248733	3222	False	1107.0	3587	92.92125	1	3103	4	chr7D.!!$F3	3102
11	TraesCS7A01G076000	chr2B	784364955	784367868	2913	False	3729.0	3729	89.94200	209	3103	1	chr2B.!!$F1	2894
12	TraesCS7A01G076000	chr2B	784510020	784512952	2932	False	1913.0	1921	90.58950	209	3098	2	chr2B.!!$F2	2889

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
207	268	0.598065	AGAACAAGCGGAACAATGGC	59.402	50.0	0.0	0.0	0.00	4.40	F
504	569	0.818296	CAAGTACTCCCTCGTCCAGG	59.182	60.0	0.0	0.0	43.01	4.45	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1434	1628	0.107214	TTTGCAGTCCGGGGATCATC	60.107	55.000	0.0	0.0	0.0	2.92	R
2353	2606	1.135689	GCGGTGCTTTTGTATCCAGTG	60.136	52.381	0.0	0.0	0.0	3.66	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
117	119	5.488919	AGGACCCAGATCTCAAAACAAGATA	59.511	40.000	0.00	0.00	33.64	1.98
165	168	2.902423	TTCACGGCAGCACAAAGGGT	62.902	55.000	0.00	0.00	0.00	4.34
177	180	2.957474	ACAAAGGGTGTGCCAAATAGT	58.043	42.857	0.00	0.00	39.72	2.12
207	268	0.598065	AGAACAAGCGGAACAATGGC	59.402	50.000	0.00	0.00	0.00	4.40
315	376	3.507622	CCATCCATGCTCGATCAGTACTA	59.492	47.826	0.00	0.00	0.00	1.82
335	396	3.112709	GCGTCGACAGCCCAGAAC	61.113	66.667	17.16	0.00	0.00	3.01
336	397	2.805353	CGTCGACAGCCCAGAACG	60.805	66.667	17.16	0.00	0.00	3.95
443	507	5.401550	TGCTTGCATAATACACAGAAAAGC	58.598	37.500	0.00	0.00	38.34	3.51
504	569	0.818296	CAAGTACTCCCTCGTCCAGG	59.182	60.000	0.00	0.00	43.01	4.45
601	780	2.754002	GGACGGAGGGAGTATATACTGC	59.246	54.545	22.44	22.44	43.00	4.40
623	802	7.288852	ACTGCACATATCCCTATCCTATATGAC	59.711	40.741	8.19	2.15	37.15	3.06
671	851	9.533253	TGGAAAGAAATTCAAAAGAGATTTCAC	57.467	29.630	9.78	2.83	39.98	3.18
708	891	3.081804	AGCCGGTTGATAAGTTTCCAAG	58.918	45.455	1.90	0.00	0.00	3.61
711	894	4.379499	GCCGGTTGATAAGTTTCCAAGAAG	60.379	45.833	1.90	0.00	0.00	2.85
712	895	4.379499	CCGGTTGATAAGTTTCCAAGAAGC	60.379	45.833	0.00	0.00	0.00	3.86
713	896	4.379499	CGGTTGATAAGTTTCCAAGAAGCC	60.379	45.833	0.00	0.00	0.00	4.35
723	907	2.123589	TCCAAGAAGCCCCAATCGATA	58.876	47.619	0.00	0.00	0.00	2.92
741	925	3.997021	CGATAAAGAGTGTGTTTCCTGCT	59.003	43.478	0.00	0.00	0.00	4.24
779	964	7.667219	CCCTATAATGTATCAGGACATGCTTTT	59.333	37.037	0.00	0.00	39.99	2.27
879	1067	9.481340	TCATTCCTCATTCTAAATAGATTGACG	57.519	33.333	9.75	7.51	37.62	4.35
917	1105	7.938490	CCAGTATATATATGCCCACATATGCAA	59.062	37.037	1.58	0.00	46.65	4.08
920	1108	1.603456	TATGCCCACATATGCAACCG	58.397	50.000	1.58	0.00	41.50	4.44
997	1187	5.127845	ACAACTCTGTCAACTCTTCTCTTCA	59.872	40.000	0.00	0.00	0.00	3.02
1037	1227	3.064324	GATTGTTGGCGCTGGGCT	61.064	61.111	16.51	0.00	42.94	5.19
1224	1414	1.194547	GATGCGCCAACATACATACCG	59.805	52.381	4.18	0.00	0.00	4.02
1242	1432	4.522722	ACCGAAAACCTTGTTTGTGAAA	57.477	36.364	0.00	0.00	0.00	2.69
1362	1552	3.910817	GGCACATGACATGGCAAAA	57.089	47.368	19.39	0.00	42.03	2.44
1434	1628	6.364706	GTGAGAATAGTGCAGAGAATATTCCG	59.635	42.308	11.92	2.62	35.96	4.30
1462	1656	0.882927	CGGACTGCAAAGTTTCCCGA	60.883	55.000	0.00	0.00	37.87	5.14
1508	1702	3.165875	ACAAGTCAGGCAAGAGCTACTA	58.834	45.455	0.00	0.00	41.70	1.82
1628	1830	2.480759	GCCCGGTATGTACACACACTAG	60.481	54.545	6.61	0.00	37.54	2.57
1664	1909	2.482494	CTGGAAACACTAGGGGATCCT	58.518	52.381	12.58	0.00	40.98	3.24
1711	1963	6.841781	ATATATTTTCAGTGGGTACAGGGT	57.158	37.500	0.00	0.00	0.00	4.34
1750	2002	5.295540	GTCTCCACTAGAAGGATGCAATTTC	59.704	44.000	8.72	0.00	35.47	2.17
1751	2003	5.190528	TCTCCACTAGAAGGATGCAATTTCT	59.809	40.000	13.16	13.16	33.99	2.52
1752	2004	5.431765	TCCACTAGAAGGATGCAATTTCTC	58.568	41.667	12.29	0.00	33.51	2.87
1753	2005	5.045651	TCCACTAGAAGGATGCAATTTCTCA	60.046	40.000	12.29	2.55	33.51	3.27
1754	2006	5.296283	CCACTAGAAGGATGCAATTTCTCAG	59.704	44.000	12.29	10.91	33.51	3.35
1755	2007	6.111382	CACTAGAAGGATGCAATTTCTCAGA	58.889	40.000	12.29	0.00	33.51	3.27
1756	2008	6.258287	CACTAGAAGGATGCAATTTCTCAGAG	59.742	42.308	12.29	8.56	33.51	3.35
1757	2009	5.176741	AGAAGGATGCAATTTCTCAGAGT	57.823	39.130	0.00	0.00	0.00	3.24
1758	2010	5.568392	AGAAGGATGCAATTTCTCAGAGTT	58.432	37.500	0.00	0.00	0.00	3.01
1759	2011	5.415077	AGAAGGATGCAATTTCTCAGAGTTG	59.585	40.000	0.00	0.00	0.00	3.16
1835	2087	9.685828	TTAATAACATGCACAAAGAACTAAACC	57.314	29.630	0.00	0.00	0.00	3.27
1857	2110	6.650120	ACCATTAGATGAACTACACCGAAAT	58.350	36.000	0.00	0.00	0.00	2.17
1928	2181	5.008019	GCAGACTTCAAAAGAGATGTGACAA	59.992	40.000	0.00	0.00	0.00	3.18
2035	2288	3.199946	GTGGATAACCTCCTTGTGATGGA	59.800	47.826	0.00	0.00	45.21	3.41
2062	2315	9.444600	GGCGAATTTAATATTTGGAGACCTATA	57.555	33.333	0.00	0.00	0.00	1.31
2240	2493	5.824904	ATGTTGTCTTCATATGCCAAGTC	57.175	39.130	0.00	0.00	0.00	3.01
2353	2606	2.483583	TTGACGTGATTGTGTTTGCC	57.516	45.000	0.00	0.00	0.00	4.52
2386	2639	2.586425	AGCACCGCAAATATATGGCTT	58.414	42.857	7.73	0.00	0.00	4.35
2451	2704	8.948631	TTTCTTGGTGCAACAATTGTTAAATA	57.051	26.923	22.87	7.55	39.98	1.40
2694	2949	6.549912	TCAAATCAGTGAATGTGTCTTCTG	57.450	37.500	0.00	0.00	33.38	3.02
2800	3055	1.620822	GGGTTGTTCTGCACCAATCT	58.379	50.000	0.00	0.00	0.00	2.40
2801	3056	2.790433	GGGTTGTTCTGCACCAATCTA	58.210	47.619	0.00	0.00	0.00	1.98
2816	3071	5.072329	CACCAATCTAGGGATGTCCACTTAT	59.928	44.000	0.86	0.00	38.24	1.73
2828	3083	7.255242	GGGATGTCCACTTATTTGTATGATGTG	60.255	40.741	0.86	0.00	37.91	3.21
2847	3102	8.677148	TGATGTGCTATAAAATTAACCTCCTC	57.323	34.615	0.00	0.00	0.00	3.71
2888	3144	4.439057	CCCATCCTTTCAATGCAATGAAG	58.561	43.478	16.32	10.96	40.21	3.02
2915	3172	7.306205	CAAAGGTCTTTTGCATTTTCTCAAA	57.694	32.000	0.00	0.00	39.71	2.69
2916	3173	7.750769	CAAAGGTCTTTTGCATTTTCTCAAAA	58.249	30.769	0.00	0.00	39.71	2.44

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
117	119	4.102681	AGTTAGTTGTGGTTCTGCTACCTT	59.897	41.667	0.00	0.00	39.04	3.50
165	168	3.694043	TGTCAGCTACTATTTGGCACA	57.306	42.857	0.00	0.00	0.00	4.57
171	174	7.363431	GCTTGTTCTTTTGTCAGCTACTATTT	58.637	34.615	0.00	0.00	0.00	1.40
177	180	2.548057	CCGCTTGTTCTTTTGTCAGCTA	59.452	45.455	0.00	0.00	0.00	3.32
207	268	4.806247	CCTCAAGTTGGCTATCTAGAAACG	59.194	45.833	2.34	0.00	31.03	3.60
335	396	1.812922	GATGGACTCTGCAGGTGCG	60.813	63.158	15.13	2.83	45.83	5.34
336	397	0.461693	GAGATGGACTCTGCAGGTGC	60.462	60.000	15.13	15.86	41.94	5.01
443	507	9.787532	TCAAGAAAGATTGTTAGTGTTTCTTTG	57.212	29.630	7.88	5.51	42.81	2.77
504	569	7.657761	AGATACATCCATTTTCAGGACGTAATC	59.342	37.037	0.00	0.00	37.37	1.75
601	780	8.865090	GGAAGTCATATAGGATAGGGATATGTG	58.135	40.741	0.00	0.00	35.78	3.21
623	802	5.393787	CCATTCCTGTTGTCATCAATGGAAG	60.394	44.000	16.46	11.58	43.99	3.46
669	849	4.273480	CCGGCTTTGGATATGTTTAGAGTG	59.727	45.833	0.00	0.00	0.00	3.51
671	851	4.451900	ACCGGCTTTGGATATGTTTAGAG	58.548	43.478	0.00	0.00	0.00	2.43
708	891	3.561725	CACTCTTTATCGATTGGGGCTTC	59.438	47.826	1.71	0.00	0.00	3.86
711	894	2.614057	CACACTCTTTATCGATTGGGGC	59.386	50.000	1.71	0.00	0.00	5.80
712	895	3.873910	ACACACTCTTTATCGATTGGGG	58.126	45.455	1.71	0.00	0.00	4.96
713	896	5.163754	GGAAACACACTCTTTATCGATTGGG	60.164	44.000	1.71	0.00	0.00	4.12
723	907	6.016777	CAGAATAAGCAGGAAACACACTCTTT	60.017	38.462	0.00	0.00	0.00	2.52
779	964	7.281324	CCATCTAAATATTGAACCGTTGGTGTA	59.719	37.037	0.00	0.00	35.34	2.90
917	1105	3.820467	TGTTTGCTTGATGAATCTTCGGT	59.180	39.130	0.00	0.00	0.00	4.69
920	1108	5.224888	TGCTTGTTTGCTTGATGAATCTTC	58.775	37.500	0.00	0.00	0.00	2.87
997	1187	7.581213	TCAACACTACAACATTCTCCATTTT	57.419	32.000	0.00	0.00	0.00	1.82
1140	1330	3.739209	CAAGATGTAGCTTGAGGCGATCA	60.739	47.826	3.93	0.00	46.31	2.92
1224	1414	7.762159	TCCAAGTATTTCACAAACAAGGTTTTC	59.238	33.333	0.00	0.00	0.00	2.29
1242	1432	5.163405	ACGCTCAACATAGTCATCCAAGTAT	60.163	40.000	0.00	0.00	0.00	2.12
1362	1552	2.224426	TGTGAACCCGACTATTGTGCTT	60.224	45.455	0.00	0.00	0.00	3.91
1375	1569	3.119137	ACAAGAAACTTTGCTGTGAACCC	60.119	43.478	0.00	0.00	0.00	4.11
1434	1628	0.107214	TTTGCAGTCCGGGGATCATC	60.107	55.000	0.00	0.00	0.00	2.92
1462	1656	2.825223	TGAGGAGTGGATGACATCACT	58.175	47.619	17.08	16.37	45.70	3.41
1508	1702	3.554934	ACGACCAATACATTCATGCCAT	58.445	40.909	0.00	0.00	0.00	4.40
1628	1830	8.749354	AGTGTTTCCAGGTCCAAAAATAATATC	58.251	33.333	0.00	0.00	0.00	1.63
1664	1909	3.666876	CCATAGGGTAAGGGTGGGA	57.333	57.895	0.00	0.00	0.00	4.37
1672	1918	9.118367	TGAAAATATATAGTGCCCATAGGGTAA	57.882	33.333	3.68	0.00	46.51	2.85
1673	1919	8.688222	TGAAAATATATAGTGCCCATAGGGTA	57.312	34.615	3.68	0.00	46.51	3.69
1751	2003	6.222038	AGTAACAACTCTGAACAACTCTGA	57.778	37.500	0.00	0.00	0.00	3.27
1752	2004	7.426410	TCTAGTAACAACTCTGAACAACTCTG	58.574	38.462	0.00	0.00	0.00	3.35
1753	2005	7.584122	TCTAGTAACAACTCTGAACAACTCT	57.416	36.000	0.00	0.00	0.00	3.24
1754	2006	8.644318	TTTCTAGTAACAACTCTGAACAACTC	57.356	34.615	0.00	0.00	0.00	3.01
1755	2007	8.258708	ACTTTCTAGTAACAACTCTGAACAACT	58.741	33.333	0.00	0.00	31.21	3.16
1756	2008	8.421673	ACTTTCTAGTAACAACTCTGAACAAC	57.578	34.615	0.00	0.00	31.21	3.32
1811	2063	7.721402	TGGTTTAGTTCTTTGTGCATGTTATT	58.279	30.769	0.00	0.00	0.00	1.40
1900	2153	5.856986	CACATCTCTTTTGAAGTCTGCATTG	59.143	40.000	0.00	0.00	0.00	2.82
1901	2154	5.766670	TCACATCTCTTTTGAAGTCTGCATT	59.233	36.000	0.00	0.00	0.00	3.56
1908	2161	7.396540	AAACTTGTCACATCTCTTTTGAAGT	57.603	32.000	0.00	0.00	0.00	3.01
1928	2181	4.099881	ACATGAATCTGCAACCACAAAACT	59.900	37.500	0.00	0.00	0.00	2.66
2035	2288	6.365520	AGGTCTCCAAATATTAAATTCGCCT	58.634	36.000	0.00	0.00	0.00	5.52
2062	2315	3.749954	GCCTTCTGATGCCATACCTTGAT	60.750	47.826	0.00	0.00	0.00	2.57
2063	2316	2.421952	GCCTTCTGATGCCATACCTTGA	60.422	50.000	0.00	0.00	0.00	3.02
2327	2580	6.032775	GCAAACACAATCACGTCAAATGATAG	59.967	38.462	0.00	0.00	35.72	2.08
2353	2606	1.135689	GCGGTGCTTTTGTATCCAGTG	60.136	52.381	0.00	0.00	0.00	3.66
2371	2624	7.197071	TGTTACCTTAAGCCATATATTTGCG	57.803	36.000	0.00	0.00	0.00	4.85
2413	2666	4.672409	CACCAAGAAAACAAACTCAGACC	58.328	43.478	0.00	0.00	0.00	3.85
2478	2733	4.760530	TGTTCTCACCATTCTGGGATAG	57.239	45.455	0.00	0.00	43.37	2.08
2694	2949	0.390209	AATGGAAGGCATTGCGTTGC	60.390	50.000	23.33	23.33	43.09	4.17
2800	3055	7.684317	TCATACAAATAAGTGGACATCCCTA	57.316	36.000	0.00	0.00	35.38	3.53
2801	3056	6.575244	TCATACAAATAAGTGGACATCCCT	57.425	37.500	0.00	0.00	35.38	4.20
2847	3102	2.614734	GGGGAAAAGTTACAGTCCTCCG	60.615	54.545	0.00	0.00	0.00	4.63
2945	3203	0.323542	ACCGTCTAGCACACTAGCCT	60.324	55.000	0.00	0.00	44.83	4.58
3033	3301	3.379372	CCTGGCACATATGAACCTTGAAG	59.621	47.826	10.38	3.75	38.20	3.02

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.