AutoCloner

Multiple sequence alignment - TraesCS5D01G066600

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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	TraesCS5D01G066600	chr5D	100.000	2831	0	0	1	2831	62109225	62106395	0.000000e+00	5228.0
1	TraesCS5D01G066600	chr5B	94.171	1973	76	17	895	2831	68843890	68845859	0.000000e+00	2970.0
2	TraesCS5D01G066600	chr5B	93.648	1952	73	18	901	2831	68377473	68379394	0.000000e+00	2870.0
3	TraesCS5D01G066600	chr5A	95.394	1650	56	11	1014	2643	51899657	51898008	0.000000e+00	2608.0
4	TraesCS5D01G066600	chr5A	94.574	129	6	1	241	369	51905192	51905065	6.190000e-47	198.0
5	TraesCS5D01G066600	chr5A	95.522	67	3	0	175	241	51905636	51905570	1.070000e-19	108.0
6	TraesCS5D01G066600	chr4A	90.924	628	36	10	1	609	708565396	708564771	0.000000e+00	824.0
7	TraesCS5D01G066600	chr4A	93.684	285	15	1	615	896	708564715	708564431	9.380000e-115	424.0
8	TraesCS5D01G066600	chr3B	93.658	473	26	4	1	472	12767725	12768194	0.000000e+00	704.0
9	TraesCS5D01G066600	chr3B	93.065	447	28	3	1	446	2017691	2017247	0.000000e+00	651.0
10	TraesCS5D01G066600	chr3B	93.972	282	17	0	615	896	12768423	12768704	7.250000e-116	427.0
11	TraesCS5D01G066600	chr3B	93.333	285	16	1	615	896	2017072	2016788	4.360000e-113	418.0
12	TraesCS5D01G066600	chr3B	94.444	144	8	0	466	609	12768224	12768367	3.670000e-54	222.0
13	TraesCS5D01G066600	chr3B	72.714	689	148	26	1075	1729	728486636	728485954	8.000000e-46	195.0
14	TraesCS5D01G066600	chr3B	93.966	116	7	0	494	609	2017243	2017128	2.900000e-40	176.0
15	TraesCS5D01G066600	chr3B	85.417	96	14	0	1633	1728	728258914	728258819	1.790000e-17	100.0
16	TraesCS5D01G066600	chr3A	93.736	447	25	3	1	446	628225366	628224922	0.000000e+00	667.0
17	TraesCS5D01G066600	chr3A	92.982	285	17	1	615	896	628224747	628224463	2.030000e-111	412.0
18	TraesCS5D01G066600	chr3A	93.966	116	7	0	494	609	628224918	628224803	2.900000e-40	176.0
19	TraesCS5D01G066600	chr3A	82.474	97	17	0	1633	1729	686260394	686260298	5.020000e-13	86.1
20	TraesCS5D01G066600	chrUn	72.714	689	148	26	1075	1729	295941902	295941220	8.000000e-46	195.0
21	TraesCS5D01G066600	chr3D	72.464	690	148	28	1075	1729	549046395	549045713	1.730000e-42	183.0
22	TraesCS5D01G066600	chr2B	81.000	100	19	0	1630	1729	781198685	781198784	2.340000e-11	80.5
23	TraesCS5D01G066600	chr1A	97.436	39	1	0	403	441	207134496	207134534	1.820000e-07	67.6

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	TraesCS5D01G066600	chr5D	62106395	62109225	2830	True	5228.000000	5228	100.000000	1	2831	1	chr5D.!!$R1	2830
1	TraesCS5D01G066600	chr5B	68843890	68845859	1969	False	2970.000000	2970	94.171000	895	2831	1	chr5B.!!$F2	1936
2	TraesCS5D01G066600	chr5B	68377473	68379394	1921	False	2870.000000	2870	93.648000	901	2831	1	chr5B.!!$F1	1930
3	TraesCS5D01G066600	chr5A	51898008	51899657	1649	True	2608.000000	2608	95.394000	1014	2643	1	chr5A.!!$R1	1629
4	TraesCS5D01G066600	chr4A	708564431	708565396	965	True	624.000000	824	92.304000	1	896	2	chr4A.!!$R1	895
5	TraesCS5D01G066600	chr3B	12767725	12768704	979	False	451.000000	704	94.024667	1	896	3	chr3B.!!$F1	895
6	TraesCS5D01G066600	chr3B	2016788	2017691	903	True	415.000000	651	93.454667	1	896	3	chr3B.!!$R3	895
7	TraesCS5D01G066600	chr3A	628224463	628225366	903	True	418.333333	667	93.561333	1	896	3	chr3A.!!$R2	895

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
772	859	0.03601	CGCACCAGATCCAGACCTTT	60.036	55.0	0.0	0.0	0.0	3.11	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1908	2031	0.608308	GTGTAGGAAACAGGGGTGGC	60.608	60.0	0.0	0.0	39.29	5.01	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
41	42	9.952188	GGGATAGTTTAAACTGAAGCAATATTC	57.048	33.333	27.40	11.16	40.07	1.75
48	49	9.601971	TTTAAACTGAAGCAATATTCGTACAAC	57.398	29.630	0.00	0.00	31.52	3.32
72	73	5.387855	CGAAAAGTTGACATTCTCGACTCTG	60.388	44.000	0.00	0.00	42.21	3.35
88	89	3.658709	ACTCTGTGTAGCTCTTTTCAGC	58.341	45.455	0.00	0.00	39.99	4.26
101	102	5.924825	GCTCTTTTCAGCACAGAAAAATCAT	59.075	36.000	11.24	0.00	44.27	2.45
153	154	5.865552	GCTTGCTGAACATTGAACAATACAT	59.134	36.000	0.00	0.00	0.00	2.29
189	190	7.428020	TCGTGCTACGATTTTAGGTATACAAT	58.572	34.615	5.01	0.00	46.73	2.71
192	193	8.485591	GTGCTACGATTTTAGGTATACAATGAC	58.514	37.037	5.01	0.00	0.00	3.06
232	233	6.317642	TGTTTATGTACCAGTGCACCATAATC	59.682	38.462	19.52	18.59	30.55	1.75
277	278	4.518970	ACGTCCAATTTTGTAGTTGAGCAT	59.481	37.500	0.00	0.00	0.00	3.79
294	295	1.401552	GCATATTTTGCGAGGAGTGCA	59.598	47.619	0.00	0.00	42.54	4.57
295	296	2.033801	GCATATTTTGCGAGGAGTGCAT	59.966	45.455	0.00	0.00	42.54	3.96
307	308	0.240945	GAGTGCATCCCCACGTTTTG	59.759	55.000	0.00	0.00	40.59	2.44
323	324	4.901123	TGGTGTGCCCACGACACG	62.901	66.667	0.00	0.00	43.95	4.49
335	336	2.096614	CCACGACACGTTATGAACCAAC	60.097	50.000	0.00	0.00	38.32	3.77
341	342	0.167251	CGTTATGAACCAACCGCCAC	59.833	55.000	0.00	0.00	0.00	5.01
354	355	1.129809	CGCCACGTTCATGTTCGTC	59.870	57.895	12.98	5.11	38.23	4.20
360	361	2.915463	CACGTTCATGTTCGTCCTACTC	59.085	50.000	12.98	0.00	38.23	2.59
364	365	4.495422	GTTCATGTTCGTCCTACTCATGT	58.505	43.478	0.00	0.00	37.64	3.21
399	400	1.151668	CACTTTGGCGTTCCTCTCAG	58.848	55.000	0.00	0.00	0.00	3.35
402	403	0.319555	TTTGGCGTTCCTCTCAGTCG	60.320	55.000	0.00	0.00	0.00	4.18
507	544	3.117663	AGAACAAAACTGGAGCCAACCTA	60.118	43.478	0.00	0.00	0.00	3.08
509	546	3.844640	ACAAAACTGGAGCCAACCTAAT	58.155	40.909	0.00	0.00	0.00	1.73
538	575	9.582431	CTGATTGCAGAAAATAACTGATCAAAT	57.418	29.630	0.00	0.00	45.17	2.32
595	632	7.707624	AGTAAATCAAATCTGATGCTTGGAA	57.292	32.000	0.00	0.00	41.66	3.53
654	741	7.444183	TCTTAGTCCTATCAAACACCACAAAAG	59.556	37.037	0.00	0.00	0.00	2.27
659	746	6.657541	TCCTATCAAACACCACAAAAGTATCC	59.342	38.462	0.00	0.00	0.00	2.59
694	781	7.041098	GCTCAAATCCTGAACTAAAAAGAGTGA	60.041	37.037	0.00	0.00	32.17	3.41
703	790	6.323739	TGAACTAAAAAGAGTGAATTGCCCTT	59.676	34.615	0.00	0.00	0.00	3.95
714	801	3.582208	TGAATTGCCCTTAGCCACAAATT	59.418	39.130	0.00	0.00	42.71	1.82
762	849	7.309377	CCCAATAAATTATGAATCGCACCAGAT	60.309	37.037	0.00	0.00	0.00	2.90
765	852	3.836365	TTATGAATCGCACCAGATCCA	57.164	42.857	0.00	0.00	0.00	3.41
766	853	2.251409	ATGAATCGCACCAGATCCAG	57.749	50.000	0.00	0.00	0.00	3.86
772	859	0.036010	CGCACCAGATCCAGACCTTT	60.036	55.000	0.00	0.00	0.00	3.11
868	958	0.753848	GGGAGGAGGAGGAGAACGAG	60.754	65.000	0.00	0.00	0.00	4.18
903	993	1.375013	TCGTTCGCTACCCAAAGGC	60.375	57.895	0.00	0.00	36.11	4.35
972	1064	4.193893	TGCTGCCATCCCATCCCG	62.194	66.667	0.00	0.00	0.00	5.14
1089	1210	1.614824	CTCAGGCCTGGTCCTCCTT	60.615	63.158	32.23	0.00	33.25	3.36
1247	1368	0.449388	CTGGAATTCCGCAGAACAGC	59.551	55.000	19.57	0.00	39.43	4.40
1461	1583	2.070890	CTTGCTATGTCGTCGCTGCG	62.071	60.000	17.25	17.25	0.00	5.18
1488	1610	1.168714	ACGGTAACTCCCTGTACGAC	58.831	55.000	0.00	0.00	0.00	4.34
1492	1614	0.608856	TAACTCCCTGTACGACGGCA	60.609	55.000	0.00	0.00	0.00	5.69
1517	1639	2.353704	CGCTCATTAGGTGTGAGTTCCA	60.354	50.000	5.19	0.00	43.86	3.53
1536	1658	2.624293	CCACCTCCACCTCTACAGATCA	60.624	54.545	0.00	0.00	0.00	2.92
1653	1775	3.362262	CACGAGACGGGGAAGACA	58.638	61.111	0.00	0.00	0.00	3.41
1788	1911	1.065418	CCGGCAAGGTCTAACTGGATT	60.065	52.381	0.00	0.00	34.51	3.01
1931	2054	2.305927	CACCCCTGTTTCCTACACTGAT	59.694	50.000	0.00	0.00	32.10	2.90
2213	2348	2.158534	ACCCAAGCACATGGACAAGTTA	60.159	45.455	0.00	0.00	43.54	2.24
2315	2450	1.273606	TCCAGCTTCTGCACTAGTGAC	59.726	52.381	27.08	17.20	42.74	3.67
2406	2544	9.705290	TTTATGTGCGACTATATGTATGAATGT	57.295	29.630	0.00	0.00	0.00	2.71
2706	2850	0.320374	TGGAAGTAGACAAGGCCACG	59.680	55.000	5.01	0.00	0.00	4.94
2707	2851	0.391263	GGAAGTAGACAAGGCCACGG	60.391	60.000	5.01	0.00	0.00	4.94

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
5	6	9.391006	TCAGTTTAAACTATCCCACATGATTAC	57.609	33.333	20.15	0.00	37.08	1.89
48	49	4.681942	AGAGTCGAGAATGTCAACTTTTCG	59.318	41.667	0.00	0.00	0.00	3.46
72	73	3.393800	TCTGTGCTGAAAAGAGCTACAC	58.606	45.455	0.00	0.00	39.90	2.90
123	124	2.036217	TCAATGTTCAGCAAGCAAAGGG	59.964	45.455	0.00	0.00	0.00	3.95
153	154	1.198408	CGTAGCACGACTCTGGTGTTA	59.802	52.381	3.04	0.00	46.05	2.41
232	233	6.253727	ACGTTCTCTGCTTCGTATTTTCATAG	59.746	38.462	0.00	0.00	34.78	2.23
277	278	2.288666	GGATGCACTCCTCGCAAAATA	58.711	47.619	7.65	0.00	43.84	1.40
307	308	2.974935	TAACGTGTCGTGGGCACACC	62.975	60.000	14.84	0.02	44.86	4.16
323	324	0.167251	CGTGGCGGTTGGTTCATAAC	59.833	55.000	0.00	0.00	0.00	1.89
335	336	2.222953	GACGAACATGAACGTGGCGG	62.223	60.000	21.28	0.00	42.74	6.13
341	342	3.211803	TGAGTAGGACGAACATGAACG	57.788	47.619	0.00	7.24	0.00	3.95
360	361	0.745845	GCTGGCACTCCTACCACATG	60.746	60.000	0.00	0.00	0.00	3.21
364	365	2.203922	TGGCTGGCACTCCTACCA	60.204	61.111	0.00	0.00	36.23	3.25
399	400	7.667043	TGGCTAATGATATTTATGTTCCGAC	57.333	36.000	0.00	0.00	0.00	4.79
459	461	3.140325	TGGCCAAGAAGAGTGGTAAAG	57.860	47.619	0.61	0.00	38.50	1.85
507	544	8.114331	TCAGTTATTTTCTGCAATCAGTGATT	57.886	30.769	12.75	12.75	41.10	2.57
509	546	7.391275	TGATCAGTTATTTTCTGCAATCAGTGA	59.609	33.333	0.00	0.00	41.10	3.41
605	642	5.869579	AGCATCTGAGTCCTTACTTTTGAA	58.130	37.500	0.00	0.00	35.56	2.69
654	741	6.037610	CAGGATTTGAGCAAACTGTAGGATAC	59.962	42.308	0.00	0.00	36.11	2.24
659	746	5.471456	AGTTCAGGATTTGAGCAAACTGTAG	59.529	40.000	11.12	0.00	39.29	2.74
703	790	5.104693	TGGCTAGTTAGCTAATTTGTGGCTA	60.105	40.000	9.88	3.77	43.34	3.93
762	849	5.304686	ACTGTTAATGTCAAAGGTCTGGA	57.695	39.130	0.00	0.00	0.00	3.86
765	852	5.865085	TGCTACTGTTAATGTCAAAGGTCT	58.135	37.500	0.00	0.00	0.00	3.85
766	853	5.932303	TCTGCTACTGTTAATGTCAAAGGTC	59.068	40.000	0.00	0.00	0.00	3.85
772	859	5.304778	TGCTTTCTGCTACTGTTAATGTCA	58.695	37.500	0.00	0.00	43.37	3.58
800	887	1.210155	GGTCTGGTTGTTGATGCGC	59.790	57.895	0.00	0.00	0.00	6.09
850	937	0.753848	CCTCGTTCTCCTCCTCCTCC	60.754	65.000	0.00	0.00	0.00	4.30
892	982	0.906775	TAGGGTTCGCCTTTGGGTAG	59.093	55.000	0.00	0.00	37.45	3.18
1089	1210	0.246360	CGATGTAGCACCACCTGTCA	59.754	55.000	0.00	0.00	0.00	3.58
1247	1368	2.745884	TGGCGACAATCTTGGGCG	60.746	61.111	0.00	0.00	37.44	6.13
1461	1583	2.098831	GGAGTTACCGTTGCCGAGC	61.099	63.158	0.00	0.00	35.63	5.03
1467	1589	1.541147	TCGTACAGGGAGTTACCGTTG	59.459	52.381	0.00	0.00	40.11	4.10
1468	1590	1.541588	GTCGTACAGGGAGTTACCGTT	59.458	52.381	0.00	0.00	40.11	4.44
1472	1594	0.179153	GCCGTCGTACAGGGAGTTAC	60.179	60.000	7.84	0.00	30.71	2.50
1492	1614	0.037697	TCACACCTAATGAGCGCGTT	60.038	50.000	8.43	0.00	0.00	4.84
1517	1639	3.052566	TGATGATCTGTAGAGGTGGAGGT	60.053	47.826	0.00	0.00	0.00	3.85
1536	1658	8.763984	AGATCCAAGCTTTAGAATTTGATGAT	57.236	30.769	0.00	0.00	0.00	2.45
1742	1864	2.124695	GTGGAACATCCCGGAGCC	60.125	66.667	0.73	0.00	44.52	4.70
1788	1911	1.003580	GTCACCATTTCTGAGGAGGCA	59.996	52.381	0.00	0.00	0.00	4.75
1908	2031	0.608308	GTGTAGGAAACAGGGGTGGC	60.608	60.000	0.00	0.00	39.29	5.01
1931	2054	2.421388	CCTTGAGATATTCCGCACCCAA	60.421	50.000	0.00	0.00	0.00	4.12
2139	2274	1.140312	TCCATGCTTAGGATGGGGTC	58.860	55.000	28.11	0.00	40.84	4.46
2406	2544	4.081406	ACTAGTTTTCATGGCAAGCATGA	58.919	39.130	0.00	0.00	37.29	3.07
2795	2941	7.821652	TGTATGGACGATTCAAGCAAAATAAA	58.178	30.769	0.00	0.00	0.00	1.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.