AutoCloner

Multiple sequence alignment - TraesCS1A01G445300

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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	TraesCS1A01G445300	chr1A	100.000	2465	0	0	1	2465	592977024	592979488	0.000000e+00	4553
1	TraesCS1A01G445300	chr1A	85.044	1023	113	19	778	1777	593214584	593215589	0.000000e+00	1005
2	TraesCS1A01G445300	chr1A	83.105	1024	128	21	778	1777	593217682	593218684	0.000000e+00	891
3	TraesCS1A01G445300	chr1A	86.991	761	58	11	788	1524	592851868	592852611	0.000000e+00	819
4	TraesCS1A01G445300	chr1A	81.317	562	74	11	938	1469	592994266	592994826	6.300000e-116	427
5	TraesCS1A01G445300	chr1A	83.544	474	54	14	25	481	593213800	593214266	2.930000e-114	422
6	TraesCS1A01G445300	chr1A	91.279	172	12	2	34	203	592923910	592924080	5.300000e-57	231
7	TraesCS1A01G445300	chr1A	86.697	218	13	8	34	235	592992740	592992957	6.860000e-56	228
8	TraesCS1A01G445300	chr1A	85.532	235	13	9	24	237	592851302	592851536	2.470000e-55	226
9	TraesCS1A01G445300	chr1D	90.800	2489	116	41	1	2446	494327150	494329568	0.000000e+00	3223
10	TraesCS1A01G445300	chr1D	85.044	1023	122	16	776	1777	494423981	494424993	0.000000e+00	1013
11	TraesCS1A01G445300	chr1D	88.817	617	45	9	931	1524	494169048	494169663	0.000000e+00	736
12	TraesCS1A01G445300	chr1D	80.995	563	73	18	938	1470	494349693	494350251	1.360000e-112	416
13	TraesCS1A01G445300	chr1D	82.218	523	43	20	24	497	494423167	494423688	2.950000e-109	405
14	TraesCS1A01G445300	chr1D	85.948	306	29	10	24	319	494168165	494168466	5.120000e-82	315
15	TraesCS1A01G445300	chr1D	77.519	516	49	42	34	502	494348372	494348867	5.260000e-62	248
16	TraesCS1A01G445300	chr1D	91.279	172	10	3	34	203	494305672	494305840	1.910000e-56	230
17	TraesCS1A01G445300	chr1D	79.573	328	28	14	318	632	494168628	494168929	5.380000e-47	198
18	TraesCS1A01G445300	chrUn	93.221	1490	71	16	1	1468	358968857	358967376	0.000000e+00	2165
19	TraesCS1A01G445300	chr1B	91.829	1028	50	11	1470	2465	687517610	687518635	0.000000e+00	1402
20	TraesCS1A01G445300	chr1B	84.623	1021	121	13	778	1777	687650802	687651807	0.000000e+00	983
21	TraesCS1A01G445300	chr1B	88.204	763	62	9	788	1524	687422956	687423716	0.000000e+00	885
22	TraesCS1A01G445300	chr1B	81.719	640	55	32	29	621	687422191	687422815	6.170000e-131	477
23	TraesCS1A01G445300	chr1B	81.883	563	70	15	938	1470	687531410	687531970	1.740000e-121	446
24	TraesCS1A01G445300	chr1B	79.487	624	78	27	1846	2447	687651856	687652451	4.940000e-107	398
25	TraesCS1A01G445300	chr1B	79.233	626	85	22	927	1515	686853885	686853268	6.390000e-106	394
26	TraesCS1A01G445300	chr1B	85.393	356	35	12	24	365	687650025	687650377	1.080000e-93	353

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	TraesCS1A01G445300	chr1A	592977024	592979488	2464	False	4553.000000	4553	100.000000	1	2465	1	chr1A.!!$F2	2464
1	TraesCS1A01G445300	chr1A	593213800	593218684	4884	False	772.666667	1005	83.897667	25	1777	3	chr1A.!!$F5	1752
2	TraesCS1A01G445300	chr1A	592851302	592852611	1309	False	522.500000	819	86.261500	24	1524	2	chr1A.!!$F3	1500
3	TraesCS1A01G445300	chr1A	592992740	592994826	2086	False	327.500000	427	84.007000	34	1469	2	chr1A.!!$F4	1435
4	TraesCS1A01G445300	chr1D	494327150	494329568	2418	False	3223.000000	3223	90.800000	1	2446	1	chr1D.!!$F2	2445
5	TraesCS1A01G445300	chr1D	494423167	494424993	1826	False	709.000000	1013	83.631000	24	1777	2	chr1D.!!$F5	1753
6	TraesCS1A01G445300	chr1D	494168165	494169663	1498	False	416.333333	736	84.779333	24	1524	3	chr1D.!!$F3	1500
7	TraesCS1A01G445300	chr1D	494348372	494350251	1879	False	332.000000	416	79.257000	34	1470	2	chr1D.!!$F4	1436
8	TraesCS1A01G445300	chrUn	358967376	358968857	1481	True	2165.000000	2165	93.221000	1	1468	1	chrUn.!!$R1	1467
9	TraesCS1A01G445300	chr1B	687517610	687518635	1025	False	1402.000000	1402	91.829000	1470	2465	1	chr1B.!!$F1	995
10	TraesCS1A01G445300	chr1B	687422191	687423716	1525	False	681.000000	885	84.961500	29	1524	2	chr1B.!!$F3	1495
11	TraesCS1A01G445300	chr1B	687650025	687652451	2426	False	578.000000	983	83.167667	24	2447	3	chr1B.!!$F4	2423
12	TraesCS1A01G445300	chr1B	687531410	687531970	560	False	446.000000	446	81.883000	938	1470	1	chr1B.!!$F2	532
13	TraesCS1A01G445300	chr1B	686853268	686853885	617	True	394.000000	394	79.233000	927	1515	1	chr1B.!!$R1	588

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
712	1251	0.453793	TGTTGAACTTGTTGGCACGG	59.546	50.0	0.0	0.0	0.0	4.94	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1942	3170	0.393132	GGAGGGTTGCTTGCTCCTAC	60.393	60.0	0.0	0.0	0.0	3.18	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
100	103	3.420893	TGGTGGAATTAGAAAGCAGTGG	58.579	45.455	0.00	0.00	0.00	4.00
198	209	3.006728	CCCTGTACCTTGGCCGGA	61.007	66.667	5.05	0.00	0.00	5.14
577	966	4.565166	TGCAACAACAGCTACGTACATATC	59.435	41.667	0.00	0.00	0.00	1.63
603	1004	8.166422	TCTGTTCCTTCCTTAATTTGTTTCTC	57.834	34.615	0.00	0.00	0.00	2.87
604	1005	7.998964	TCTGTTCCTTCCTTAATTTGTTTCTCT	59.001	33.333	0.00	0.00	0.00	3.10
605	1006	7.940850	TGTTCCTTCCTTAATTTGTTTCTCTG	58.059	34.615	0.00	0.00	0.00	3.35
606	1007	6.575162	TCCTTCCTTAATTTGTTTCTCTGC	57.425	37.500	0.00	0.00	0.00	4.26
608	1009	5.478332	CCTTCCTTAATTTGTTTCTCTGCCT	59.522	40.000	0.00	0.00	0.00	4.75
712	1251	0.453793	TGTTGAACTTGTTGGCACGG	59.546	50.000	0.00	0.00	0.00	4.94
1081	2196	4.099419	TCTCCTTCATGCTACGCAGATTTA	59.901	41.667	0.00	0.00	43.65	1.40
1146	2261	6.785076	TGATATGTTCCTTGAGGGTAACAAA	58.215	36.000	7.98	0.00	38.03	2.83
1213	2341	3.504906	TCCTGAGGTACGTACTTGAGTTG	59.495	47.826	24.07	9.47	0.00	3.16
1222	2352	4.613944	ACGTACTTGAGTTGATTTGACGA	58.386	39.130	7.20	0.00	0.00	4.20
1223	2353	5.045215	ACGTACTTGAGTTGATTTGACGAA	58.955	37.500	7.20	0.00	0.00	3.85
1227	2357	6.002062	ACTTGAGTTGATTTGACGAATTCC	57.998	37.500	0.00	0.00	0.00	3.01
1246	2397	8.850156	CGAATTCCTTCTTTTCCATATATTGGT	58.150	33.333	0.00	0.00	46.52	3.67
1377	2539	1.078848	GGAGGCGTTCATGAGTGCT	60.079	57.895	17.47	6.94	0.00	4.40
1465	2631	8.971073	AGGTCATCAACAGGAAAAATAATTAGG	58.029	33.333	0.00	0.00	0.00	2.69
1485	2651	0.249238	GACGCTTGCTCGATCCATCT	60.249	55.000	0.00	0.00	0.00	2.90
1562	2728	6.238211	GCTATGCATCATATTATTGTCGGGTC	60.238	42.308	0.19	0.00	0.00	4.46
1567	2733	5.265350	TCATATTATTGTCGGGTCGTCAA	57.735	39.130	3.01	3.01	38.87	3.18
1578	2744	2.286536	CGGGTCGTCAATTTGTTTTCGT	60.287	45.455	0.00	0.00	0.00	3.85
1594	2760	0.539669	TCGTGGTCAAGCAGAGAGGA	60.540	55.000	0.00	0.00	0.00	3.71
1602	2768	2.702478	TCAAGCAGAGAGGATACCCATG	59.298	50.000	0.00	0.00	33.88	3.66
1889	3104	4.989279	AAAAAGCGGTGCAGATTGATAT	57.011	36.364	0.00	0.00	0.00	1.63
1942	3170	4.564406	GCATCAACCTCCCATCCTACATAG	60.564	50.000	0.00	0.00	0.00	2.23
1969	3215	2.019984	CAAGCAACCCTCCATAAGCTC	58.980	52.381	0.00	0.00	0.00	4.09
1996	3242	6.621514	AGGTTCACAATTCCCTCCTTATCTAT	59.378	38.462	0.00	0.00	0.00	1.98
2034	3287	4.431416	TTCGAAATGGGTAGGCATACAT	57.569	40.909	11.12	0.00	33.21	2.29
2220	3491	0.462375	CGTCCGGATGTGTCCCATAA	59.538	55.000	15.98	0.00	41.83	1.90
2231	3502	3.263681	TGTGTCCCATAAAACACCGGATA	59.736	43.478	9.46	0.00	44.06	2.59
2265	3536	0.991355	TTCCCAGACAACCACACCCT	60.991	55.000	0.00	0.00	0.00	4.34
2281	3552	5.505780	CACACCCTTCATATCAAAACCCTA	58.494	41.667	0.00	0.00	0.00	3.53
2283	3554	6.095440	CACACCCTTCATATCAAAACCCTAAG	59.905	42.308	0.00	0.00	0.00	2.18
2288	3559	7.041098	CCCTTCATATCAAAACCCTAAGAATCG	60.041	40.741	0.00	0.00	0.00	3.34
2322	3593	5.733226	TCATATAGCACAAATTCACCACG	57.267	39.130	0.00	0.00	0.00	4.94
2338	3609	7.447374	TTCACCACGAATTCAATAGTTCAAT	57.553	32.000	6.22	0.00	0.00	2.57
2388	3661	6.594937	ACAATTCAATAATTCAACACATGCCC	59.405	34.615	0.00	0.00	32.87	5.36
2459	3737	1.812214	CGCTCGTCGCTCTATTTGCC	61.812	60.000	0.00	0.00	36.13	4.52

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
100	103	2.032549	ACGCATGCAAATATCGAGCTTC	60.033	45.455	19.57	0.00	0.00	3.86
198	209	0.485099	TTGGGGCTTTGGTGGTGTAT	59.515	50.000	0.00	0.00	0.00	2.29
458	709	7.781056	AGTAAAGAAAGCAAAGAAAACATCCA	58.219	30.769	0.00	0.00	0.00	3.41
460	711	9.301153	TGAAGTAAAGAAAGCAAAGAAAACATC	57.699	29.630	0.00	0.00	0.00	3.06
461	712	9.822185	ATGAAGTAAAGAAAGCAAAGAAAACAT	57.178	25.926	0.00	0.00	0.00	2.71
577	966	8.171164	AGAAACAAATTAAGGAAGGAACAGAG	57.829	34.615	0.00	0.00	0.00	3.35
972	2080	5.734498	CAGCTAGCTAAAATAACTGCAAACG	59.266	40.000	18.86	0.00	0.00	3.60
1146	2261	7.040755	TCCTTATCACACAAAACAATGTCGAAT	60.041	33.333	0.00	0.00	0.00	3.34
1213	2341	6.677913	TGGAAAAGAAGGAATTCGTCAAATC	58.322	36.000	0.30	0.00	0.00	2.17
1279	2439	1.669779	GATCTTCATGACTGCCTGTGC	59.330	52.381	0.00	0.00	38.26	4.57
1377	2539	0.953727	GCACAAAGTCATCAGCACCA	59.046	50.000	0.00	0.00	0.00	4.17
1465	2631	1.218230	GATGGATCGAGCAAGCGTCC	61.218	60.000	1.84	0.00	34.38	4.79
1485	2651	6.485171	AGCTAGCTTAATTTCTTCCTCCAAA	58.515	36.000	12.68	0.00	0.00	3.28
1562	2728	3.686128	TGACCACGAAAACAAATTGACG	58.314	40.909	0.00	2.90	0.00	4.35
1567	2733	3.380004	TCTGCTTGACCACGAAAACAAAT	59.620	39.130	0.00	0.00	0.00	2.32
1578	2744	2.111384	GGTATCCTCTCTGCTTGACCA	58.889	52.381	0.00	0.00	0.00	4.02
1602	2768	9.778993	CATTACATCGATCCCAATGATTTAATC	57.221	33.333	13.95	0.00	32.41	1.75
1665	2831	4.272018	CCCTGAAGCATAAATCAACGAGAG	59.728	45.833	0.00	0.00	0.00	3.20
1796	3011	9.869844	GATTAAATGCGCCATTCATATAGTATC	57.130	33.333	4.18	0.00	32.43	2.24
1889	3104	4.439426	CCATTTGAAGTCACGTTGGTCAAA	60.439	41.667	12.97	12.97	41.12	2.69
1942	3170	0.393132	GGAGGGTTGCTTGCTCCTAC	60.393	60.000	0.00	0.00	0.00	3.18
1969	3215	3.160679	AGGAGGGAATTGTGAACCTTG	57.839	47.619	0.00	0.00	32.42	3.61
1996	3242	7.812191	CCATTTCGAAATATCTTGTGGTTTTGA	59.188	33.333	22.33	0.00	0.00	2.69
2145	3411	6.050432	AGTCTGGTCGTAGATACTCTAACAG	58.950	44.000	0.00	0.00	40.67	3.16
2154	3420	2.029623	GGCCAAGTCTGGTCGTAGATA	58.970	52.381	0.00	0.00	45.53	1.98
2220	3491	3.845781	ATGAGATGCTATCCGGTGTTT	57.154	42.857	0.00	0.00	0.00	2.83
2231	3502	3.265221	TCTGGGAAGACAAATGAGATGCT	59.735	43.478	0.00	0.00	0.00	3.79
2265	3536	9.056005	CATCGATTCTTAGGGTTTTGATATGAA	57.944	33.333	0.00	0.00	0.00	2.57
2281	3552	2.171237	TGATGGAGGTGCATCGATTCTT	59.829	45.455	0.00	0.00	0.00	2.52
2283	3554	2.245159	TGATGGAGGTGCATCGATTC	57.755	50.000	0.00	0.00	0.00	2.52
2288	3559	3.937706	GTGCTATATGATGGAGGTGCATC	59.062	47.826	4.61	4.61	0.00	3.91

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.