AutoCloner

Multiple sequence alignment - TraesCS2D01G401800

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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	TraesCS2D01G401800	chr2D	100.000	7094	0	0	1	7094	516703120	516710213	0.000000e+00	13101.0
1	TraesCS2D01G401800	chr2D	91.000	100	9	0	6653	6752	516811880	516811979	1.240000e-27	135.0
2	TraesCS2D01G401800	chr2A	94.056	4559	148	29	673	5194	660509227	660513699	0.000000e+00	6804.0
3	TraesCS2D01G401800	chr2A	90.056	1780	106	31	5356	7091	660513698	660515450	0.000000e+00	2241.0
4	TraesCS2D01G401800	chr2A	96.757	185	5	1	5182	5365	746756979	746757163	2.490000e-79	307.0
5	TraesCS2D01G401800	chr2B	93.123	2792	109	20	686	3427	608444292	608447050	0.000000e+00	4015.0
6	TraesCS2D01G401800	chr2B	96.472	1559	40	6	3645	5194	608447044	608448596	0.000000e+00	2560.0
7	TraesCS2D01G401800	chr2B	91.818	1320	67	21	5356	6653	608448595	608449895	0.000000e+00	1801.0
8	TraesCS2D01G401800	chr2B	84.375	672	98	5	1	670	504316596	504317262	0.000000e+00	652.0
9	TraesCS2D01G401800	chr2B	89.083	458	22	10	6652	7091	608449960	608450407	1.740000e-150	544.0
10	TraesCS2D01G401800	chr1A	89.866	671	66	2	1	670	533320665	533321334	0.000000e+00	861.0
11	TraesCS2D01G401800	chr1A	86.720	497	65	1	176	671	460292860	460292364	1.040000e-152	551.0
12	TraesCS2D01G401800	chr1A	88.492	252	28	1	426	676	58839300	58839049	3.220000e-78	303.0
13	TraesCS2D01G401800	chr4B	89.568	671	70	0	1	671	562362751	562362081	0.000000e+00	852.0
14	TraesCS2D01G401800	chr6B	89.286	672	69	3	1	670	666776548	666777218	0.000000e+00	839.0
15	TraesCS2D01G401800	chr6B	88.276	145	13	4	529	671	51384412	51384554	3.400000e-38	171.0
16	TraesCS2D01G401800	chr6B	97.561	41	1	0	678	718	195277492	195277452	3.550000e-08	71.3
17	TraesCS2D01G401800	chr6B	88.462	52	5	1	3663	3713	451927500	451927449	2.140000e-05	62.1
18	TraesCS2D01G401800	chr6A	89.185	601	59	2	1	598	101431256	101430659	0.000000e+00	745.0
19	TraesCS2D01G401800	chr6A	97.561	41	1	0	678	718	131937843	131937803	3.550000e-08	71.3
20	TraesCS2D01G401800	chr5B	81.990	583	98	7	96	675	586471748	586472326	8.270000e-134	488.0
21	TraesCS2D01G401800	chr5A	100.000	169	0	0	5190	5358	651496989	651496821	5.340000e-81	313.0
22	TraesCS2D01G401800	chr4D	98.837	172	2	0	5193	5364	75782217	75782046	2.490000e-79	307.0
23	TraesCS2D01G401800	chr4A	97.222	180	4	1	5188	5366	362067906	362068085	3.220000e-78	303.0
24	TraesCS2D01G401800	chr4A	95.187	187	8	1	5174	5360	582530159	582529974	1.940000e-75	294.0
25	TraesCS2D01G401800	chr7A	97.207	179	4	1	5180	5357	324925209	324925031	1.160000e-77	302.0
26	TraesCS2D01G401800	chr7A	92.683	41	2	1	688	728	176417739	176417778	2.760000e-04	58.4
27	TraesCS2D01G401800	chr7D	95.676	185	6	2	5175	5358	381797774	381797957	5.380000e-76	296.0
28	TraesCS2D01G401800	chr7D	78.491	265	44	8	4639	4892	619630720	619630982	2.050000e-35	161.0
29	TraesCS2D01G401800	chr1D	95.699	186	5	3	5175	5358	331539448	331539264	5.380000e-76	296.0
30	TraesCS2D01G401800	chr1B	94.764	191	8	2	5179	5367	336774398	336774588	5.380000e-76	296.0
31	TraesCS2D01G401800	chr3B	84.906	265	32	5	4497	4759	778446712	778446454	1.960000e-65	261.0
32	TraesCS2D01G401800	chrUn	88.780	205	22	1	469	672	29597483	29597279	4.250000e-62	250.0

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	TraesCS2D01G401800	chr2D	516703120	516710213	7093	False	13101.0	13101	100.000	1	7094	1	chr2D.!!$F1	7093
1	TraesCS2D01G401800	chr2A	660509227	660515450	6223	False	4522.5	6804	92.056	673	7091	2	chr2A.!!$F2	6418
2	TraesCS2D01G401800	chr2B	608444292	608450407	6115	False	2230.0	4015	92.624	686	7091	4	chr2B.!!$F2	6405
3	TraesCS2D01G401800	chr2B	504316596	504317262	666	False	652.0	652	84.375	1	670	1	chr2B.!!$F1	669
4	TraesCS2D01G401800	chr1A	533320665	533321334	669	False	861.0	861	89.866	1	670	1	chr1A.!!$F1	669
5	TraesCS2D01G401800	chr4B	562362081	562362751	670	True	852.0	852	89.568	1	671	1	chr4B.!!$R1	670
6	TraesCS2D01G401800	chr6B	666776548	666777218	670	False	839.0	839	89.286	1	670	1	chr6B.!!$F2	669
7	TraesCS2D01G401800	chr6A	101430659	101431256	597	True	745.0	745	89.185	1	598	1	chr6A.!!$R1	597
8	TraesCS2D01G401800	chr5B	586471748	586472326	578	False	488.0	488	81.990	96	675	1	chr5B.!!$F1	579

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
359	367	0.678048	GTCGAGAAGCAATGGCCCTT	60.678	55.0	0.00	0.00	42.56	3.95	F
604	615	1.029947	GTGTGGCTCATAAACCCCCG	61.030	60.0	0.00	0.00	0.00	5.73	F
1389	1435	0.958876	CCCCAGGTTTTGCGTCTACC	60.959	60.0	0.00	0.00	0.00	3.18	F
2482	2548	0.387929	GTGGAATGGATGCTGCATGG	59.612	55.0	21.53	0.00	0.00	3.66	F
2545	2611	2.620627	GGGGTGGGTTTCTCAATCGATT	60.621	50.0	4.39	4.39	0.00	3.34	F
3464	3536	0.376152	GCTGCCACATCGATTCACTG	59.624	55.0	0.00	0.00	0.00	3.66	F
3472	3544	0.460311	ATCGATTCACTGTCGGGTCC	59.540	55.0	0.00	0.00	39.45	4.46	F
5204	5289	0.041386	AGGCTTCTACTCCCTCCGTT	59.959	55.0	0.00	0.00	0.00	4.44	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1389	1435	0.247736	AAGTGAGAGCAACTAGGCCG	59.752	55.000	0.00	0.00	6.13	R
1845	1910	1.084018	ATGGAGAGGGAAAGGGCAAA	58.916	50.000	0.00	0.00	3.68	R
3164	3232	0.324552	ATATGCACTGGGCTTGGCAA	60.325	50.000	2.50	45.15	4.52	R
3436	3508	0.250234	GATGTGGCAGCTACTGGTCA	59.750	55.000	10.64	31.21	4.02	R
3661	3733	0.460635	TGCGTGCTCCCGGTATTTAC	60.461	55.000	0.00	0.00	2.01	R
5187	5272	0.460722	GGAACGGAGGGAGTAGAAGC	59.539	60.000	0.00	0.00	3.86	R
5341	5426	3.716431	TGTTAATACTCCCTCCGTTCCT	58.284	45.455	0.00	0.00	3.36	R
6541	6651	0.036765	TTTATGCGGCAAGACGAGGT	60.037	50.000	6.82	35.47	3.85	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
21	22	2.676471	GGGCCATCTGGTTTGCGT	60.676	61.111	4.39	0.00	37.57	5.24
114	116	1.749634	GAGAGCTGGCTGATTGCAAAT	59.250	47.619	1.71	0.00	45.15	2.32
211	216	2.899256	CAAAAATCAGGGTGGATGGTGT	59.101	45.455	0.00	0.00	0.00	4.16
271	279	2.650116	GCAGAGACCAGAGCGGGAA	61.650	63.158	0.00	0.00	40.22	3.97
281	289	1.146263	GAGCGGGAAGTACATGGGG	59.854	63.158	0.00	0.00	0.00	4.96
287	295	1.202651	GGGAAGTACATGGGGTCATCG	60.203	57.143	0.00	0.00	0.00	3.84
359	367	0.678048	GTCGAGAAGCAATGGCCCTT	60.678	55.000	0.00	0.00	42.56	3.95
438	447	3.585289	TCAGGACATAAACCTTGGCACTA	59.415	43.478	0.00	0.00	35.35	2.74
450	459	3.307691	CCTTGGCACTAGAGGAATGAACA	60.308	47.826	0.00	0.00	32.11	3.18
458	467	2.898705	AGAGGAATGAACACGAGCATC	58.101	47.619	0.00	0.00	0.00	3.91
507	516	7.121974	ACTCAATTTCATAGTTGTGTCTTCG	57.878	36.000	0.00	0.00	29.08	3.79
533	543	3.329386	TGAAGGCAGAGTTTCGAATCAG	58.671	45.455	8.83	0.00	0.00	2.90
604	615	1.029947	GTGTGGCTCATAAACCCCCG	61.030	60.000	0.00	0.00	0.00	5.73
723	735	4.095932	GCTTAAGGCGCCAAATAGTAACTT	59.904	41.667	31.54	12.46	0.00	2.66
724	736	5.554822	TTAAGGCGCCAAATAGTAACTTG	57.445	39.130	31.54	0.00	0.00	3.16
891	920	6.302615	CGATTTGCTTTCAACACAACAAAAA	58.697	32.000	0.00	0.00	31.52	1.94
892	921	6.960431	CGATTTGCTTTCAACACAACAAAAAT	59.040	30.769	0.00	0.00	31.52	1.82
947	979	5.175859	TCTAAGACAGCCGGTTAAATCTTG	58.824	41.667	16.89	9.99	0.00	3.02
1354	1400	2.190538	GGTACTTGGGTAGGTTGGCTA	58.809	52.381	0.00	0.00	0.00	3.93
1356	1402	2.040342	ACTTGGGTAGGTTGGCTACT	57.960	50.000	0.00	0.00	0.00	2.57
1365	1411	1.630878	AGGTTGGCTACTCCCTCTTTG	59.369	52.381	0.00	0.00	0.00	2.77
1385	1431	1.815817	ATTGCCCCAGGTTTTGCGTC	61.816	55.000	0.00	0.00	0.00	5.19
1387	1433	1.302993	GCCCCAGGTTTTGCGTCTA	60.303	57.895	0.00	0.00	0.00	2.59
1389	1435	0.958876	CCCCAGGTTTTGCGTCTACC	60.959	60.000	0.00	0.00	0.00	3.18
1483	1532	2.124570	CAGATTGGGGCTGTCGGG	60.125	66.667	0.00	0.00	0.00	5.14

Showing 1 to 25 of 222 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
21	22	3.329889	ATGGAGGGCTTGCCGTCA	61.330	61.111	28.07	17.85	0.00	4.35
67	68	7.013750	TGAGGTATTTTGTGACAAACATAAGCA	59.986	33.333	10.72	3.33	38.99	3.91
70	71	8.684386	TCTGAGGTATTTTGTGACAAACATAA	57.316	30.769	10.72	0.00	38.99	1.90
114	116	4.186136	ACGGGTCGTCTCCTTTGA	57.814	55.556	0.00	0.00	33.69	2.69
173	178	3.737559	TTTGCATAACCATGAGGAGGT	57.262	42.857	0.00	0.00	42.34	3.85
211	216	1.295792	GTCGTTGGCTCTGTTGACAA	58.704	50.000	0.00	0.00	0.00	3.18
271	279	0.691078	AGCCGATGACCCCATGTACT	60.691	55.000	0.00	0.00	32.09	2.73
281	289	1.683917	ACACTCCTGATAGCCGATGAC	59.316	52.381	0.00	0.00	0.00	3.06
287	295	0.181350	CCCCAACACTCCTGATAGCC	59.819	60.000	0.00	0.00	0.00	3.93
359	367	4.041567	TGAGTTAATGAGAGGTCCAAAGCA	59.958	41.667	0.00	0.00	0.00	3.91
438	447	2.736719	CGATGCTCGTGTTCATTCCTCT	60.737	50.000	0.00	0.00	34.72	3.69
458	467	4.791411	GCAGTAGCTCTAATCTCCTTCACG	60.791	50.000	0.00	0.00	37.91	4.35
507	516	3.131396	TCGAAACTCTGCCTTCAAAGAC	58.869	45.455	0.00	0.00	0.00	3.01
604	615	6.672266	TCATAGGGATACAATTCAGGTCTC	57.328	41.667	0.00	0.00	39.74	3.36
671	683	9.003658	CATTTATAGGCTATTCTGTTAACTGGG	57.996	37.037	13.08	0.90	0.00	4.45
1168	1214	2.156917	TGCTTGCACAGAGGATTTGAG	58.843	47.619	0.00	0.00	0.00	3.02
1354	1400	0.332972	GGGGCAATCAAAGAGGGAGT	59.667	55.000	0.00	0.00	0.00	3.85
1356	1402	0.332632	CTGGGGCAATCAAAGAGGGA	59.667	55.000	0.00	0.00	0.00	4.20
1365	1411	1.079888	CGCAAAACCTGGGGCAATC	60.080	57.895	0.00	0.00	34.37	2.67
1385	1431	0.386113	GAGAGCAACTAGGCCGGTAG	59.614	60.000	1.90	0.00	0.00	3.18
1387	1433	1.609501	TGAGAGCAACTAGGCCGGT	60.610	57.895	1.90	0.00	0.00	5.28
1389	1435	0.247736	AAGTGAGAGCAACTAGGCCG	59.752	55.000	0.00	0.00	0.00	6.13
1483	1532	7.857569	TCGATTATCCGAAAACAACATAATCC	58.142	34.615	0.00	0.00	34.79	3.01
1511	1561	3.006110	CCTGTCACTGATGCCAAACAATT	59.994	43.478	0.00	0.00	0.00	2.32
1521	1571	4.000331	AGTTCTGAACCTGTCACTGATG	58.000	45.455	16.48	0.00	31.13	3.07

Showing 1 to 25 of 224 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.