AutoCloner

Multiple sequence alignment - TraesCS1B01G471000

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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	TraesCS1B01G471000	chr1B	100.000	2561	0	0	1	2561	679248861	679251421	0.000000e+00	4730
1	TraesCS1B01G471000	chr1B	97.071	1434	41	1	457	1889	679173936	679175369	0.000000e+00	2414
2	TraesCS1B01G471000	chr1B	95.982	1344	34	6	457	1797	679225220	679226546	0.000000e+00	2165
3	TraesCS1B01G471000	chr1B	85.714	917	120	9	903	1813	679255504	679256415	0.000000e+00	957
4	TraesCS1B01G471000	chr1B	84.951	917	127	9	903	1813	679194738	679195649	0.000000e+00	918
5	TraesCS1B01G471000	chr1B	85.509	697	71	22	1879	2561	679235907	679236587	0.000000e+00	701
6	TraesCS1B01G471000	chr1B	97.661	342	7	1	1	341	679173157	679173498	1.020000e-163	586
7	TraesCS1B01G471000	chr1B	97.329	337	6	3	1	336	679224416	679224750	1.030000e-158	569
8	TraesCS1B01G471000	chr1B	85.854	205	20	6	2336	2539	679185364	679185560	2.580000e-50	209
9	TraesCS1B01G471000	chr1B	87.255	102	3	3	1788	1889	679228539	679228630	9.690000e-20	108
10	TraesCS1B01G471000	chr1D	92.981	1382	67	8	511	1889	487614224	487615578	0.000000e+00	1988
11	TraesCS1B01G471000	chr1D	86.611	717	83	8	903	1617	487624105	487624810	0.000000e+00	780
12	TraesCS1B01G471000	chr1D	79.104	402	40	19	115	513	487611052	487611412	1.180000e-58	237
13	TraesCS1B01G471000	chr1D	96.667	120	4	0	1	120	487610237	487610356	1.550000e-47	200
14	TraesCS1B01G471000	chr1A	91.858	1437	69	18	462	1889	585690111	585691508	0.000000e+00	1962
15	TraesCS1B01G471000	chr1A	83.687	1177	171	18	557	1727	585742687	585743848	0.000000e+00	1090
16	TraesCS1B01G471000	chr1A	83.965	343	19	17	3	344	585689293	585689600	1.930000e-76	296
17	TraesCS1B01G471000	chr1A	87.556	225	21	6	2336	2559	585726667	585726885	1.180000e-63	254

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	TraesCS1B01G471000	chr1B	679248861	679251421	2560	False	4730.000000	4730	100.0000	1	2561	1	chr1B.!!$F4	2560
1	TraesCS1B01G471000	chr1B	679173157	679175369	2212	False	1500.000000	2414	97.3660	1	1889	2	chr1B.!!$F6	1888
2	TraesCS1B01G471000	chr1B	679255504	679256415	911	False	957.000000	957	85.7140	903	1813	1	chr1B.!!$F5	910
3	TraesCS1B01G471000	chr1B	679224416	679228630	4214	False	947.333333	2165	93.5220	1	1889	3	chr1B.!!$F7	1888
4	TraesCS1B01G471000	chr1B	679194738	679195649	911	False	918.000000	918	84.9510	903	1813	1	chr1B.!!$F2	910
5	TraesCS1B01G471000	chr1B	679235907	679236587	680	False	701.000000	701	85.5090	1879	2561	1	chr1B.!!$F3	682
6	TraesCS1B01G471000	chr1D	487610237	487615578	5341	False	808.333333	1988	89.5840	1	1889	3	chr1D.!!$F2	1888
7	TraesCS1B01G471000	chr1D	487624105	487624810	705	False	780.000000	780	86.6110	903	1617	1	chr1D.!!$F1	714
8	TraesCS1B01G471000	chr1A	585689293	585691508	2215	False	1129.000000	1962	87.9115	3	1889	2	chr1A.!!$F3	1886
9	TraesCS1B01G471000	chr1A	585742687	585743848	1161	False	1090.000000	1090	83.6870	557	1727	1	chr1A.!!$F2	1170

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
305	1018	0.395862	TTGGGCCGAAAAGTTGGACA	60.396	50.000	0.00	0.00	33.70	4.02	F
908	4834	1.612442	ATGGACCGGCCGGCTATAT	60.612	57.895	43.58	27.94	40.66	0.86	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1357	5291	0.768221	ACACAGAAGGCCTCCTCCAA	60.768	55.0	5.23	0.00	30.89	3.53	R
2507	8467	0.107703	TGCTTACAGCGGGATGGAAG	60.108	55.0	4.55	4.55	46.26	3.46	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
205	907	3.350219	AAGCGGGTCAATTATGTGAGT	57.650	42.857	0.00	0.00	0.00	3.41
305	1018	0.395862	TTGGGCCGAAAAGTTGGACA	60.396	50.000	0.00	0.00	33.70	4.02
358	1394	2.482336	TGAGTTTCACACACACACACAC	59.518	45.455	0.00	0.00	0.00	3.82
437	1516	5.765182	TCTTTTTCCTTCTTCTGTGATGGAC	59.235	40.000	0.00	0.00	39.16	4.02
882	4805	5.014860	TGATCTTCCAATGATGCATATCCCT	59.985	40.000	0.00	0.00	32.09	4.20
907	4833	2.203728	ATGGACCGGCCGGCTATA	60.204	61.111	43.58	26.98	40.66	1.31
908	4834	1.612442	ATGGACCGGCCGGCTATAT	60.612	57.895	43.58	27.94	40.66	0.86
1315	5249	3.910627	AGGGTGTGAAGGAATTAGTGTCT	59.089	43.478	0.00	0.00	0.00	3.41
1417	5351	1.887242	TTCATATGCGCCGGTGAGC	60.887	57.895	21.76	15.40	37.86	4.26
1505	5439	1.748329	CGCCCCTTCGATGAGGATGA	61.748	60.000	4.64	0.00	39.25	2.92
1638	5581	4.858935	ACTGTTGTATGAACAATGTGTGC	58.141	39.130	0.00	0.00	46.84	4.57
1831	7781	2.029623	GTCTCGATAGCCCCAGTTACA	58.970	52.381	0.00	0.00	0.00	2.41
1833	7783	3.825014	GTCTCGATAGCCCCAGTTACATA	59.175	47.826	0.00	0.00	0.00	2.29
1844	7794	5.013547	CCCCAGTTACATATGGTTTTGTCA	58.986	41.667	7.80	0.00	34.58	3.58
1932	7882	8.842358	AAATGTTCTTGATGCATCTGAAAAAT	57.158	26.923	26.32	20.34	0.00	1.82
1941	7891	7.379750	TGATGCATCTGAAAAATGACATCAAA	58.620	30.769	26.32	0.00	40.50	2.69
1944	7894	8.610248	TGCATCTGAAAAATGACATCAAAAAT	57.390	26.923	0.00	0.00	0.00	1.82
2066	8016	8.428063	TGAGGAAAAATGATAAAACCAACACAT	58.572	29.630	0.00	0.00	0.00	3.21
2067	8017	9.921637	GAGGAAAAATGATAAAACCAACACATA	57.078	29.630	0.00	0.00	0.00	2.29
2068	8018	9.927668	AGGAAAAATGATAAAACCAACACATAG	57.072	29.630	0.00	0.00	0.00	2.23
2069	8019	9.921637	GGAAAAATGATAAAACCAACACATAGA	57.078	29.630	0.00	0.00	0.00	1.98
2102	8052	7.576861	AAGGTCAATCGAAAAGGTTCTAAAA	57.423	32.000	0.00	0.00	0.00	1.52
2126	8076	6.993079	ACCAAAGAAAAACTGATGAATACCC	58.007	36.000	0.00	0.00	0.00	3.69
2171	8121	5.405331	AGAGAGAAAACCGAAGAAAAACG	57.595	39.130	0.00	0.00	0.00	3.60
2172	8122	3.948851	AGAGAAAACCGAAGAAAAACGC	58.051	40.909	0.00	0.00	0.00	4.84
2173	8123	3.626217	AGAGAAAACCGAAGAAAAACGCT	59.374	39.130	0.00	0.00	0.00	5.07
2174	8124	3.691498	AGAAAACCGAAGAAAAACGCTG	58.309	40.909	0.00	0.00	0.00	5.18
2177	8127	3.982576	AACCGAAGAAAAACGCTGAAT	57.017	38.095	0.00	0.00	0.00	2.57
2188	8138	7.801752	AGAAAAACGCTGAATAGAAAGAGAAG	58.198	34.615	0.00	0.00	0.00	2.85
2190	8140	6.473397	AAACGCTGAATAGAAAGAGAAGTG	57.527	37.500	0.00	0.00	0.00	3.16
2209	8160	6.651225	AGAAGTGAAGAAAACTAGGGAAATCG	59.349	38.462	0.00	0.00	0.00	3.34
2229	8180	9.185192	GAAATCGATGAAAACAGAAGAACAAAT	57.815	29.630	0.00	0.00	0.00	2.32
2283	8243	6.951062	AGAGAAAACAGAAGGAAAGAAAGG	57.049	37.500	0.00	0.00	0.00	3.11
2286	8246	7.067615	AGAGAAAACAGAAGGAAAGAAAGGAAC	59.932	37.037	0.00	0.00	0.00	3.62
2288	8248	4.417426	ACAGAAGGAAAGAAAGGAACGA	57.583	40.909	0.00	0.00	0.00	3.85
2321	8281	8.477256	AGTGAAATCAAGAAATCAGGAAAACAA	58.523	29.630	0.00	0.00	0.00	2.83
2337	8297	9.810545	CAGGAAAACAAAAGTTATAACAAAGGA	57.189	29.630	17.65	0.00	0.00	3.36
2365	8325	9.936759	AAAAGAAAAACTGAATAAAACTGGTGA	57.063	25.926	0.00	0.00	0.00	4.02
2401	8361	8.906636	AAGAACCGAAGAAAACTAAAAGAAAC	57.093	30.769	0.00	0.00	0.00	2.78
2402	8362	8.277490	AGAACCGAAGAAAACTAAAAGAAACT	57.723	30.769	0.00	0.00	0.00	2.66
2477	8437	3.936203	CCCGCTAATAGGCCGGCA	61.936	66.667	30.85	9.36	0.00	5.69
2479	8439	1.741770	CCGCTAATAGGCCGGCATC	60.742	63.158	30.85	12.35	0.00	3.91
2484	8444	1.198759	TAATAGGCCGGCATCCTCCC	61.199	60.000	30.85	8.87	35.21	4.30
2510	8470	2.117910	GCCTGACGCGATAACTACTTC	58.882	52.381	15.93	0.00	0.00	3.01
2520	8480	3.654414	GATAACTACTTCCATCCCGCTG	58.346	50.000	0.00	0.00	0.00	5.18
2541	8501	3.865745	TGTAAGCAAGATAAAGCTCTCGC	59.134	43.478	0.00	0.00	40.90	5.03

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
205	907	5.551305	TTCAGAGTCTTCAACCTTGATGA	57.449	39.130	0.00	0.63	38.53	2.92
305	1018	2.736670	AACAAGCTGGGTGAAACTCT	57.263	45.000	0.00	0.00	38.97	3.24
358	1394	2.752354	TCTCCTTTGTGTGTGTGTTTGG	59.248	45.455	0.00	0.00	0.00	3.28
412	1491	6.432472	GTCCATCACAGAAGAAGGAAAAAGAT	59.568	38.462	0.00	0.00	37.17	2.40
437	1516	1.561643	TGTAGAGGGCAAGACTCCAG	58.438	55.000	0.00	0.00	35.58	3.86
882	4805	1.105167	CGGCCGGTCCATGACTACTA	61.105	60.000	20.10	0.00	32.47	1.82
907	4833	4.741837	GCTCATAGGCATCGGCATGTATAT	60.742	45.833	0.00	0.00	43.71	0.86
908	4834	3.430790	GCTCATAGGCATCGGCATGTATA	60.431	47.826	0.00	0.00	43.71	1.47
1315	5249	5.681437	GCTTACCGTCCATCAACTCATCTAA	60.681	44.000	0.00	0.00	0.00	2.10
1357	5291	0.768221	ACACAGAAGGCCTCCTCCAA	60.768	55.000	5.23	0.00	30.89	3.53
1417	5351	1.404717	CCTCCTCATCACGTTCCACAG	60.405	57.143	0.00	0.00	0.00	3.66
1505	5439	2.241685	AGGAAGCTGATCTTGCCATCTT	59.758	45.455	7.48	0.00	43.29	2.40
1638	5581	4.989279	ATGCCAAAAAGTAGCATACCAG	57.011	40.909	0.00	0.00	45.10	4.00
1668	5612	6.770785	TGCTAACAAATAGTGAGGTCAAAACT	59.229	34.615	0.00	0.00	33.87	2.66
1690	5634	2.060980	TTTGGCCCAAAACGGTGCT	61.061	52.632	6.40	0.00	32.99	4.40
1831	7781	8.704668	GGAGGGATTAAATTGACAAAACCATAT	58.295	33.333	0.00	0.00	0.00	1.78
1833	7783	6.500049	TGGAGGGATTAAATTGACAAAACCAT	59.500	34.615	0.00	0.00	0.00	3.55
1851	7801	3.855599	TCCCATATTTGAACTTGGAGGGA	59.144	43.478	0.00	0.00	40.31	4.20
1905	7855	8.665643	TTTTCAGATGCATCAAGAACATTTTT	57.334	26.923	27.81	0.00	0.00	1.94
1907	7857	8.717821	CATTTTTCAGATGCATCAAGAACATTT	58.282	29.630	27.81	12.51	0.00	2.32
1908	7858	8.092068	TCATTTTTCAGATGCATCAAGAACATT	58.908	29.630	27.81	16.09	0.00	2.71
1987	7937	9.906660	ACGTGAAACAATATTTTGATACATGTT	57.093	25.926	2.30	0.00	35.74	2.71
2027	7977	9.927081	ATCATTTTTCCTCAGTTTCCTATGTAT	57.073	29.630	0.00	0.00	0.00	2.29
2039	7989	7.925483	TGTGTTGGTTTTATCATTTTTCCTCAG	59.075	33.333	0.00	0.00	0.00	3.35
2040	7990	7.786030	TGTGTTGGTTTTATCATTTTTCCTCA	58.214	30.769	0.00	0.00	0.00	3.86
2075	8025	6.465439	AGAACCTTTTCGATTGACCTTTTT	57.535	33.333	0.00	0.00	36.78	1.94
2102	8052	6.553100	TGGGTATTCATCAGTTTTTCTTTGGT	59.447	34.615	0.00	0.00	0.00	3.67
2143	8093	5.291905	TCTTCGGTTTTCTCTCTTCCTTT	57.708	39.130	0.00	0.00	0.00	3.11
2147	8097	5.902432	CGTTTTTCTTCGGTTTTCTCTCTTC	59.098	40.000	0.00	0.00	0.00	2.87
2158	8108	4.312443	TCTATTCAGCGTTTTTCTTCGGT	58.688	39.130	0.00	0.00	38.29	4.69
2171	8121	7.897575	TTCTTCACTTCTCTTTCTATTCAGC	57.102	36.000	0.00	0.00	0.00	4.26
2173	8123	9.838339	AGTTTTCTTCACTTCTCTTTCTATTCA	57.162	29.630	0.00	0.00	0.00	2.57
2177	8127	8.368668	CCCTAGTTTTCTTCACTTCTCTTTCTA	58.631	37.037	0.00	0.00	0.00	2.10
2188	8138	6.594159	TCATCGATTTCCCTAGTTTTCTTCAC	59.406	38.462	0.00	0.00	0.00	3.18
2190	8140	7.611213	TTCATCGATTTCCCTAGTTTTCTTC	57.389	36.000	0.00	0.00	0.00	2.87
2258	8209	7.615757	TCCTTTCTTTCCTTCTGTTTTCTCTTT	59.384	33.333	0.00	0.00	0.00	2.52
2342	8302	9.936759	TTTTCACCAGTTTTATTCAGTTTTTCT	57.063	25.926	0.00	0.00	0.00	2.52
2375	8335	9.350357	GTTTCTTTTAGTTTTCTTCGGTTCTTT	57.650	29.630	0.00	0.00	0.00	2.52
2421	8381	1.021920	GCTCTGCTCCGGTTTTCTCC	61.022	60.000	0.00	0.00	0.00	3.71
2431	8391	1.731720	CTGTAGGTTTGCTCTGCTCC	58.268	55.000	0.00	0.00	0.00	4.70
2437	8397	1.871039	TCGTTTGCTGTAGGTTTGCTC	59.129	47.619	0.00	0.00	0.00	4.26
2438	8398	1.961793	TCGTTTGCTGTAGGTTTGCT	58.038	45.000	0.00	0.00	0.00	3.91
2477	8437	0.468400	GTCAGGCGTAGAGGGAGGAT	60.468	60.000	0.00	0.00	0.00	3.24
2479	8439	2.482333	CGTCAGGCGTAGAGGGAGG	61.482	68.421	0.00	0.00	35.54	4.30
2499	8459	3.069729	ACAGCGGGATGGAAGTAGTTATC	59.930	47.826	0.00	0.00	0.00	1.75
2503	8463	2.154567	TACAGCGGGATGGAAGTAGT	57.845	50.000	0.00	0.00	0.00	2.73
2505	8465	1.138266	GCTTACAGCGGGATGGAAGTA	59.862	52.381	10.31	0.00	42.26	2.24
2507	8467	0.107703	TGCTTACAGCGGGATGGAAG	60.108	55.000	4.55	4.55	46.26	3.46
2510	8470	0.107703	TCTTGCTTACAGCGGGATGG	60.108	55.000	0.00	0.00	46.26	3.51
2541	8501	2.550699	TAATTGCCGGTGCCCAGGAG	62.551	60.000	1.90	0.00	36.33	3.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.