AutoCloner

Multiple sequence alignment - TraesCS5B01G499300

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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	TraesCS5B01G499300	chr5B	100.000	2306	0	0	1	2306	665937590	665939895	0.000000e+00	4259
1	TraesCS5B01G499300	chr5B	87.410	1382	127	17	942	2306	665958156	665959507	0.000000e+00	1544
2	TraesCS5B01G499300	chr5B	86.288	598	67	14	3	589	573405490	573406083	8.990000e-179	636
3	TraesCS5B01G499300	chr5B	86.905	168	14	6	428	591	541079912	541079749	5.060000e-42	182
4	TraesCS5B01G499300	chr5B	80.892	157	13	9	795	948	665912772	665912914	8.710000e-20	108
5	TraesCS5B01G499300	chr5D	93.057	821	43	6	1493	2306	528762730	528763543	0.000000e+00	1188
6	TraesCS5B01G499300	chr5D	92.535	777	48	6	591	1363	528761820	528762590	0.000000e+00	1105
7	TraesCS5B01G499300	chr5D	86.643	846	86	12	1481	2306	528803240	528804078	0.000000e+00	911
8	TraesCS5B01G499300	chr5D	82.816	966	133	18	1360	2306	528747679	528748630	0.000000e+00	833
9	TraesCS5B01G499300	chr5D	90.203	592	53	4	3	589	63482465	63483056	0.000000e+00	767
10	TraesCS5B01G499300	chr5D	85.895	631	55	18	672	1293	528745475	528746080	1.930000e-180	641
11	TraesCS5B01G499300	chr5D	85.622	619	59	16	3	593	503842008	503842624	7.000000e-175	623
12	TraesCS5B01G499300	chr5D	87.654	405	36	2	956	1360	528802717	528803107	2.090000e-125	459
13	TraesCS5B01G499300	chr5D	79.008	262	19	15	699	937	528760908	528761156	1.850000e-31	147
14	TraesCS5B01G499300	chr3B	92.348	575	36	3	3	570	139193134	139193707	0.000000e+00	811
15	TraesCS5B01G499300	chr3B	85.460	619	57	19	3	589	13018155	13017538	4.210000e-172	614
16	TraesCS5B01G499300	chr3D	89.786	607	42	2	3	589	591143392	591143998	0.000000e+00	760
17	TraesCS5B01G499300	chr4D	88.689	610	46	4	3	589	4049483	4050092	0.000000e+00	723
18	TraesCS5B01G499300	chr2D	88.091	613	48	9	6	593	631831596	631830984	0.000000e+00	704
19	TraesCS5B01G499300	chrUn	87.175	616	50	12	3	589	114973779	114974394	0.000000e+00	673
20	TraesCS5B01G499300	chrUn	80.485	825	131	16	1504	2306	97782359	97783175	2.530000e-169	604
21	TraesCS5B01G499300	chr6B	81.522	828	129	12	1498	2306	106509354	106510176	0.000000e+00	660
22	TraesCS5B01G499300	chr6B	86.949	544	46	6	69	587	2979229	2979772	2.550000e-164	588
23	TraesCS5B01G499300	chr1D	93.548	434	28	0	3	436	405808750	405808317	0.000000e+00	647
24	TraesCS5B01G499300	chr1D	82.923	568	87	6	1747	2306	476570488	476569923	9.510000e-139	503
25	TraesCS5B01G499300	chr1B	84.774	486	68	2	1827	2306	662843672	662843187	1.240000e-132	483
26	TraesCS5B01G499300	chr7B	87.349	166	11	6	428	590	698875724	698875566	5.060000e-42	182
27	TraesCS5B01G499300	chr1A	82.323	198	31	4	1820	2015	584840466	584840661	3.940000e-38	169

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	TraesCS5B01G499300	chr5B	665937590	665939895	2305	False	4259.000000	4259	100.0000	1	2306	1	chr5B.!!$F3	2305
1	TraesCS5B01G499300	chr5B	665958156	665959507	1351	False	1544.000000	1544	87.4100	942	2306	1	chr5B.!!$F4	1364
2	TraesCS5B01G499300	chr5B	573405490	573406083	593	False	636.000000	636	86.2880	3	589	1	chr5B.!!$F1	586
3	TraesCS5B01G499300	chr5D	528760908	528763543	2635	False	813.333333	1188	88.2000	591	2306	3	chr5D.!!$F4	1715
4	TraesCS5B01G499300	chr5D	63482465	63483056	591	False	767.000000	767	90.2030	3	589	1	chr5D.!!$F1	586
5	TraesCS5B01G499300	chr5D	528745475	528748630	3155	False	737.000000	833	84.3555	672	2306	2	chr5D.!!$F3	1634
6	TraesCS5B01G499300	chr5D	528802717	528804078	1361	False	685.000000	911	87.1485	956	2306	2	chr5D.!!$F5	1350
7	TraesCS5B01G499300	chr5D	503842008	503842624	616	False	623.000000	623	85.6220	3	593	1	chr5D.!!$F2	590
8	TraesCS5B01G499300	chr3B	139193134	139193707	573	False	811.000000	811	92.3480	3	570	1	chr3B.!!$F1	567
9	TraesCS5B01G499300	chr3B	13017538	13018155	617	True	614.000000	614	85.4600	3	589	1	chr3B.!!$R1	586
10	TraesCS5B01G499300	chr3D	591143392	591143998	606	False	760.000000	760	89.7860	3	589	1	chr3D.!!$F1	586
11	TraesCS5B01G499300	chr4D	4049483	4050092	609	False	723.000000	723	88.6890	3	589	1	chr4D.!!$F1	586
12	TraesCS5B01G499300	chr2D	631830984	631831596	612	True	704.000000	704	88.0910	6	593	1	chr2D.!!$R1	587
13	TraesCS5B01G499300	chrUn	114973779	114974394	615	False	673.000000	673	87.1750	3	589	1	chrUn.!!$F2	586
14	TraesCS5B01G499300	chrUn	97782359	97783175	816	False	604.000000	604	80.4850	1504	2306	1	chrUn.!!$F1	802
15	TraesCS5B01G499300	chr6B	106509354	106510176	822	False	660.000000	660	81.5220	1498	2306	1	chr6B.!!$F2	808
16	TraesCS5B01G499300	chr6B	2979229	2979772	543	False	588.000000	588	86.9490	69	587	1	chr6B.!!$F1	518
17	TraesCS5B01G499300	chr1D	476569923	476570488	565	True	503.000000	503	82.9230	1747	2306	1	chr1D.!!$R2	559

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
609	932	0.464452	AGATCCCCTAAAACGAGCCG	59.536	55.0	0.0	0.0	0.0	5.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1719	3621	1.135575	GCGAGGGACATTTTCTTGCAG	60.136	52.381	0.0	0.0	37.73	4.41	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
64	65	1.066422	GAGATCTCGGCGTGCATCA	59.934	57.895	7.04	0.00	0.00	3.07
84	85	0.909610	AACCGAGGAGATGCCCAAGA	60.910	55.000	0.00	0.00	37.37	3.02
90	91	2.505819	GAGGAGATGCCCAAGAACCTTA	59.494	50.000	0.00	0.00	37.37	2.69
234	240	3.702048	CCGGCGAAGTTGGGGAGA	61.702	66.667	9.30	0.00	0.00	3.71
376	382	3.391382	CGGAGGAGGTGGTGGACC	61.391	72.222	0.00	0.00	46.58	4.46
515	577	1.751351	CAATGCCTCTCCACGTCTCTA	59.249	52.381	0.00	0.00	0.00	2.43
593	657	8.639761	ACACGCTAGACCTATTTTAACATAGAT	58.360	33.333	9.74	0.00	0.00	1.98
594	658	9.130312	CACGCTAGACCTATTTTAACATAGATC	57.870	37.037	9.74	2.92	0.00	2.75
609	932	0.464452	AGATCCCCTAAAACGAGCCG	59.536	55.000	0.00	0.00	0.00	5.52
746	1069	3.193479	AGATGCTTTAAGGGCCTTTTTCG	59.807	43.478	26.29	11.69	0.00	3.46
816	1147	1.150827	GTACCCACCAACTTGTACGC	58.849	55.000	0.00	0.00	0.00	4.42
829	1160	6.453396	CCAACTTGTACGCGTACTTTATTCTC	60.453	42.308	39.69	18.41	37.00	2.87
832	1163	4.414852	TGTACGCGTACTTTATTCTCACC	58.585	43.478	39.69	17.10	37.00	4.02
837	1168	3.302699	GCGTACTTTATTCTCACCGTCAC	59.697	47.826	0.00	0.00	0.00	3.67
859	1190	2.224426	TGATAGGCAGTTGTTGACCGTT	60.224	45.455	0.00	0.00	34.24	4.44
937	1268	1.380112	ACCAGGAGCTCGTCTACCC	60.380	63.158	5.82	0.00	0.00	3.69
948	1279	1.189524	CGTCTACCCCTTCACCCACA	61.190	60.000	0.00	0.00	0.00	4.17
965	1297	1.597302	CATCCTCGCAGCCATCAGG	60.597	63.158	0.00	0.00	38.23	3.86
1036	1368	0.250166	CATCATCGCCTCTGCCATCA	60.250	55.000	0.00	0.00	0.00	3.07
1039	1371	0.250166	CATCGCCTCTGCCATCATCA	60.250	55.000	0.00	0.00	0.00	3.07
1074	1406	2.501261	CAGATCATGTCCGCCATCAAT	58.499	47.619	0.00	0.00	0.00	2.57
1135	1467	1.336440	AGAAGATGAGATCGTCGCTGG	59.664	52.381	0.00	0.00	41.70	4.85
1149	1481	2.681778	CTGGAGACGGTGGAGGCT	60.682	66.667	0.00	0.00	0.00	4.58
1156	1488	3.385384	CGGTGGAGGCTCTGCTCA	61.385	66.667	15.23	0.25	0.00	4.26
1169	1501	1.066914	CTGCTCAAAGACGCTGAGAC	58.933	55.000	10.11	3.80	42.51	3.36
1172	1504	0.664466	CTCAAAGACGCTGAGACGCA	60.664	55.000	1.68	0.00	42.51	5.24
1294	1626	1.270274	CTGCTGCACAAAAGGTATGCA	59.730	47.619	0.00	0.00	46.73	3.96
1302	1634	3.069443	CACAAAAGGTATGCAAACCCAGT	59.931	43.478	0.00	0.00	40.71	4.00
1308	1640	2.890945	GGTATGCAAACCCAGTTGACTT	59.109	45.455	0.00	0.00	33.02	3.01
1325	1657	7.376072	CAGTTGACTTAACCAAGACGAAATTTC	59.624	37.037	8.20	8.20	40.24	2.17
1329	1661	5.178809	ACTTAACCAAGACGAAATTTCTCCG	59.821	40.000	15.92	6.43	35.60	4.63
1382	3268	6.141844	GCTTTTTGCGTCCTTAGTAAGAAAAC	59.858	38.462	11.66	5.87	0.00	2.43
1388	3274	6.316890	TGCGTCCTTAGTAAGAAAACAAACTT	59.683	34.615	11.66	0.00	0.00	2.66
1391	3277	7.165318	CGTCCTTAGTAAGAAAACAAACTTTGC	59.835	37.037	11.66	0.00	0.00	3.68
1393	3279	8.188139	TCCTTAGTAAGAAAACAAACTTTGCTG	58.812	33.333	11.66	0.00	0.00	4.41
1394	3280	7.043391	CCTTAGTAAGAAAACAAACTTTGCTGC	60.043	37.037	11.66	0.00	0.00	5.25
1395	3281	5.965922	AGTAAGAAAACAAACTTTGCTGCT	58.034	33.333	0.00	0.00	0.00	4.24
1396	3282	6.036470	AGTAAGAAAACAAACTTTGCTGCTC	58.964	36.000	0.00	0.00	0.00	4.26
1398	3284	4.676546	AGAAAACAAACTTTGCTGCTCTC	58.323	39.130	0.00	0.00	0.00	3.20
1447	3336	0.171007	GTGTTGGCCATCATGTTCCG	59.829	55.000	19.23	0.00	0.00	4.30
1474	3363	9.389570	GACCACCGCATATTTACATTATAAAAC	57.610	33.333	0.00	0.00	0.00	2.43
1478	3367	7.801315	ACCGCATATTTACATTATAAAACAGCG	59.199	33.333	0.00	0.00	35.56	5.18
1516	3405	5.144100	TGTGTTGGGGTGTTTGATTTCTAT	58.856	37.500	0.00	0.00	0.00	1.98
1618	3520	6.402222	TGAAATTGTTGCCTTTGTAGTGTTT	58.598	32.000	0.00	0.00	0.00	2.83
1654	3556	2.323999	TCCAGGTTGAAAATGGCCAT	57.676	45.000	14.09	14.09	33.92	4.40
1719	3621	1.886542	ACCGCATTCCTTTCACTTTCC	59.113	47.619	0.00	0.00	0.00	3.13
1752	3663	0.107456	CCCTCGCATGCAGGATAACT	59.893	55.000	27.62	0.00	31.91	2.24
1782	3693	2.253758	GCGGCTGTGACAGAAGCAA	61.254	57.895	18.18	0.00	41.36	3.91
1818	3729	4.816925	GGGATAAGGAAAAACAGGAGATCG	59.183	45.833	0.00	0.00	0.00	3.69
1833	3744	4.885907	AGGAGATCGTGGTTCGTTTATCTA	59.114	41.667	0.00	0.00	40.80	1.98
1933	3844	5.009911	TGGTTTTCAATGATCCACAGTTCAG	59.990	40.000	0.00	0.00	0.00	3.02
1964	3875	1.276622	GGGTGTGGGTCTATGTGTCT	58.723	55.000	0.00	0.00	0.00	3.41
2272	4190	3.760684	GCTCCCTTGACAGATGACATTTT	59.239	43.478	0.00	0.00	0.00	1.82

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
55	56	1.970917	CTCCTCGGTTTGATGCACGC	61.971	60.000	0.00	0.00	0.00	5.34
64	65	0.035056	CTTGGGCATCTCCTCGGTTT	60.035	55.000	0.00	0.00	34.39	3.27
84	85	4.536090	TGGTGGACTCTTGATCATAAGGTT	59.464	41.667	0.00	0.00	0.00	3.50
90	91	2.355513	GCAGTGGTGGACTCTTGATCAT	60.356	50.000	0.00	0.00	29.75	2.45
194	200	1.198094	TCGCCTCCATGGTTTCCTCA	61.198	55.000	12.58	0.00	38.35	3.86
234	240	2.206536	GCTATGGAGGGCTCTCGCT	61.207	63.158	7.70	0.00	40.85	4.93
342	348	3.755628	GCGCTCACCCTCACCGTA	61.756	66.667	0.00	0.00	0.00	4.02
593	657	1.891722	GACCGGCTCGTTTTAGGGGA	61.892	60.000	0.00	0.00	0.00	4.81
594	658	1.449070	GACCGGCTCGTTTTAGGGG	60.449	63.158	0.00	0.00	0.00	4.79
694	1017	8.102047	TCGGGTGGAGTTTATTTACTTATGAAA	58.898	33.333	0.00	0.00	0.00	2.69
707	1030	3.681594	GCATCTTCATCGGGTGGAGTTTA	60.682	47.826	0.00	0.00	34.78	2.01
746	1069	4.929808	CCTACGCCAGAATATCATTACCAC	59.070	45.833	0.00	0.00	0.00	4.16
816	1147	4.557690	CAGTGACGGTGAGAATAAAGTACG	59.442	45.833	0.00	0.00	0.00	3.67
829	1160	3.352447	CTGCCTATCAGTGACGGTG	57.648	57.895	10.95	2.92	38.02	4.94
847	1178	1.533129	GCCAAGTCAACGGTCAACAAC	60.533	52.381	0.00	0.00	0.00	3.32
856	1187	2.051345	GGTTGCGCCAAGTCAACG	60.051	61.111	4.18	0.00	42.42	4.10
937	1268	1.450312	GCGAGGATGTGGGTGAAGG	60.450	63.158	0.00	0.00	0.00	3.46
948	1279	2.827423	CCTGATGGCTGCGAGGAT	59.173	61.111	0.00	0.00	0.00	3.24
965	1297	2.419851	CCTCTCTCAACTCCTCAATGGC	60.420	54.545	0.00	0.00	35.26	4.40
1036	1368	1.878088	CTGCTTGCTCACAACACTGAT	59.122	47.619	0.00	0.00	0.00	2.90
1039	1371	2.149578	GATCTGCTTGCTCACAACACT	58.850	47.619	0.00	0.00	0.00	3.55
1074	1406	0.329261	ACTGCAGCTTAATCTGGCCA	59.671	50.000	15.27	4.71	34.74	5.36
1083	1415	1.070134	ACGAAGTTCCACTGCAGCTTA	59.930	47.619	15.27	0.00	37.78	3.09
1106	1438	3.562141	CGATCTCATCTTCTGTAGGTCGT	59.438	47.826	0.00	0.00	0.00	4.34
1135	1467	2.888863	CAGAGCCTCCACCGTCTC	59.111	66.667	0.00	0.00	0.00	3.36
1149	1481	0.961753	TCTCAGCGTCTTTGAGCAGA	59.038	50.000	0.00	0.00	41.41	4.26
1156	1488	0.664767	GACTGCGTCTCAGCGTCTTT	60.665	55.000	2.10	0.00	46.76	2.52
1294	1626	4.643334	GTCTTGGTTAAGTCAACTGGGTTT	59.357	41.667	0.00	0.00	37.30	3.27
1295	1627	4.204799	GTCTTGGTTAAGTCAACTGGGTT	58.795	43.478	0.00	0.00	37.30	4.11
1302	1634	7.255001	GGAGAAATTTCGTCTTGGTTAAGTCAA	60.255	37.037	12.42	0.00	35.38	3.18
1308	1640	3.998341	CCGGAGAAATTTCGTCTTGGTTA	59.002	43.478	12.42	0.00	0.00	2.85
1325	1657	0.532573	TTAGAGCTCAAGCACCGGAG	59.467	55.000	17.77	0.00	45.16	4.63
1329	1661	4.006319	AGAACAATTAGAGCTCAAGCACC	58.994	43.478	17.77	0.00	45.16	5.01
1373	3259	6.036470	AGAGCAGCAAAGTTTGTTTTCTTAC	58.964	36.000	16.70	0.00	0.00	2.34
1414	3303	2.290641	GCCAACACTACCAACTCTTGTG	59.709	50.000	0.00	0.00	35.09	3.33
1416	3305	1.880027	GGCCAACACTACCAACTCTTG	59.120	52.381	0.00	0.00	0.00	3.02
1447	3336	7.675962	TTATAATGTAAATATGCGGTGGTCC	57.324	36.000	0.00	0.00	0.00	4.46
1474	3363	6.991485	ACACAATGAACTTATTTTTCGCTG	57.009	33.333	0.00	0.00	0.00	5.18
1478	3367	6.989759	ACCCCAACACAATGAACTTATTTTTC	59.010	34.615	0.00	0.00	0.00	2.29
1595	3489	6.019075	GGAAACACTACAAAGGCAACAATTTC	60.019	38.462	0.00	0.00	41.41	2.17
1618	3520	3.498481	CCTGGAAACACTGATTTGAGGGA	60.498	47.826	0.00	0.00	35.60	4.20
1654	3556	7.379059	TGCCCTCTCATATTCTTCATCTTAA	57.621	36.000	0.00	0.00	0.00	1.85
1719	3621	1.135575	GCGAGGGACATTTTCTTGCAG	60.136	52.381	0.00	0.00	37.73	4.41
1752	3663	2.192861	CAGCCGCTGTTGTTTCCCA	61.193	57.895	12.54	0.00	0.00	4.37
1782	3693	5.171541	TCCTTATCCCTCCCTATGACTTT	57.828	43.478	0.00	0.00	0.00	2.66
1818	3729	4.119442	TGCTCCTAGATAAACGAACCAC	57.881	45.455	0.00	0.00	0.00	4.16
1833	3744	4.260170	GTGATCTCTTTTGTGATGCTCCT	58.740	43.478	0.00	0.00	33.36	3.69
1964	3875	7.434897	CCAATTTTCTTCAAATCAAACGTCTCA	59.565	33.333	0.00	0.00	33.60	3.27
2073	3985	6.708285	TGATTAGGACCTTCTTACCAGAAAC	58.292	40.000	0.00	0.00	38.63	2.78

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.