AutoCloner

Multiple sequence alignment - TraesCS1A01G100700

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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	TraesCS1A01G100700	chr1A	100.000	2699	0	0	1	2699	96746342	96749040	0.000000e+00	4985.0
1	TraesCS1A01G100700	chr1A	97.826	322	6	1	45	365	505878039	505878360	3.040000e-154	555.0
2	TraesCS1A01G100700	chr2A	97.525	2343	50	3	365	2699	214725815	214723473	0.000000e+00	3999.0
3	TraesCS1A01G100700	chr2A	86.068	768	55	26	388	1113	611698236	611697479	0.000000e+00	778.0
4	TraesCS1A01G100700	chr2A	98.438	320	4	1	47	365	177824834	177824515	1.810000e-156	562.0
5	TraesCS1A01G100700	chr2A	93.238	281	17	1	47	325	6456192	6455912	1.930000e-111	412.0
6	TraesCS1A01G100700	chr2A	86.385	213	26	2	1129	1339	611697313	611697102	2.090000e-56	230.0
7	TraesCS1A01G100700	chr2A	89.691	97	9	1	1423	1519	611696513	611696418	3.650000e-24	122.0
8	TraesCS1A01G100700	chr2A	93.671	79	4	1	1441	1519	611697103	611697026	1.700000e-22	117.0
9	TraesCS1A01G100700	chr5A	97.815	1556	33	1	1143	2698	648916133	648914579	0.000000e+00	2684.0
10	TraesCS1A01G100700	chr5A	94.415	949	37	3	1766	2699	219234258	219233311	0.000000e+00	1445.0
11	TraesCS1A01G100700	chr5A	97.972	789	9	2	365	1146	648944176	648943388	0.000000e+00	1362.0
12	TraesCS1A01G100700	chr2B	89.253	1405	67	30	365	1721	206742328	206743696	0.000000e+00	1681.0
13	TraesCS1A01G100700	chr2B	94.382	89	3	2	1670	1756	206743696	206743784	4.690000e-28	135.0
14	TraesCS1A01G100700	chr2B	100.000	53	0	0	1180	1232	206743169	206743117	6.150000e-17	99.0
15	TraesCS1A01G100700	chr6D	95.502	956	28	2	1759	2699	393957642	393956687	0.000000e+00	1513.0
16	TraesCS1A01G100700	chr6D	89.909	773	35	19	390	1121	143494314	143495084	0.000000e+00	955.0
17	TraesCS1A01G100700	chr6D	79.896	577	45	20	1129	1663	143495262	143495809	9.190000e-95	357.0
18	TraesCS1A01G100700	chr7A	94.416	985	46	7	365	1341	501994273	501993290	0.000000e+00	1506.0
19	TraesCS1A01G100700	chr7A	98.119	319	5	1	47	365	95923918	95923601	3.040000e-154	555.0
20	TraesCS1A01G100700	chr7A	87.755	147	4	5	1617	1750	501993292	501993147	2.780000e-35	159.0
21	TraesCS1A01G100700	chr2D	94.770	956	31	6	1759	2699	390622188	390621237	0.000000e+00	1471.0
22	TraesCS1A01G100700	chr2D	94.501	782	27	9	1759	2524	81631571	81632352	0.000000e+00	1192.0
23	TraesCS1A01G100700	chr7B	94.731	949	34	3	1766	2699	301889951	301889004	0.000000e+00	1461.0
24	TraesCS1A01G100700	chrUn	94.310	949	38	3	1766	2699	195345538	195344591	0.000000e+00	1439.0
25	TraesCS1A01G100700	chrUn	94.204	949	38	4	1766	2699	389615675	389616621	0.000000e+00	1432.0
26	TraesCS1A01G100700	chrUn	96.324	272	10	0	2428	2699	473251050	473251321	5.300000e-122	448.0
27	TraesCS1A01G100700	chr3D	89.193	768	42	19	390	1118	299072955	299072190	0.000000e+00	920.0
28	TraesCS1A01G100700	chr3D	87.353	767	50	17	390	1118	604603117	604602360	0.000000e+00	835.0
29	TraesCS1A01G100700	chr3D	94.681	282	9	3	47	325	32173645	32173367	1.480000e-117	433.0
30	TraesCS1A01G100700	chr3D	79.196	572	39	17	1142	1663	299072033	299071492	9.320000e-85	324.0
31	TraesCS1A01G100700	chr3D	95.238	42	1	1	325	365	32172391	32172350	6.240000e-07	65.8
32	TraesCS1A01G100700	chr3D	97.222	36	1	0	328	363	16448205	16448170	8.070000e-06	62.1
33	TraesCS1A01G100700	chr7D	87.891	768	52	11	390	1118	14254351	14255116	0.000000e+00	865.0
34	TraesCS1A01G100700	chr6A	87.139	762	41	20	390	1118	234190830	234191567	0.000000e+00	811.0
35	TraesCS1A01G100700	chr6A	84.252	254	20	4	1416	1663	234192069	234192308	2.090000e-56	230.0
36	TraesCS1A01G100700	chr6A	95.349	86	4	0	1129	1214	234191790	234191875	1.300000e-28	137.0
37	TraesCS1A01G100700	chr4A	98.746	319	4	0	47	365	16860090	16860408	3.900000e-158	568.0
38	TraesCS1A01G100700	chr6B	86.476	525	36	13	628	1118	385532062	385532585	6.570000e-151	544.0
39	TraesCS1A01G100700	chr6B	83.333	288	24	4	1129	1414	385532767	385533032	7.460000e-61	244.0
40	TraesCS1A01G100700	chr3B	96.032	252	7	2	77	325	685077141	685077392	9.000000e-110	407.0
41	TraesCS1A01G100700	chr3B	97.561	41	1	0	325	365	685078378	685078418	1.340000e-08	71.3
42	TraesCS1A01G100700	chr4B	97.222	36	1	0	328	363	16785648	16785613	8.070000e-06	62.1
43	TraesCS1A01G100700	chr1B	94.872	39	2	0	325	363	180409503	180409465	8.070000e-06	62.1

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	TraesCS1A01G100700	chr1A	96746342	96749040	2698	False	4985.000000	4985	100.000000	1	2699	1	chr1A.!!$F1	2698
1	TraesCS1A01G100700	chr2A	214723473	214725815	2342	True	3999.000000	3999	97.525000	365	2699	1	chr2A.!!$R3	2334
2	TraesCS1A01G100700	chr2A	611696418	611698236	1818	True	311.750000	778	88.953750	388	1519	4	chr2A.!!$R4	1131
3	TraesCS1A01G100700	chr5A	648914579	648916133	1554	True	2684.000000	2684	97.815000	1143	2698	1	chr5A.!!$R2	1555
4	TraesCS1A01G100700	chr5A	219233311	219234258	947	True	1445.000000	1445	94.415000	1766	2699	1	chr5A.!!$R1	933
5	TraesCS1A01G100700	chr5A	648943388	648944176	788	True	1362.000000	1362	97.972000	365	1146	1	chr5A.!!$R3	781
6	TraesCS1A01G100700	chr2B	206742328	206743784	1456	False	908.000000	1681	91.817500	365	1756	2	chr2B.!!$F1	1391
7	TraesCS1A01G100700	chr6D	393956687	393957642	955	True	1513.000000	1513	95.502000	1759	2699	1	chr6D.!!$R1	940
8	TraesCS1A01G100700	chr6D	143494314	143495809	1495	False	656.000000	955	84.902500	390	1663	2	chr6D.!!$F1	1273
9	TraesCS1A01G100700	chr7A	501993147	501994273	1126	True	832.500000	1506	91.085500	365	1750	2	chr7A.!!$R2	1385
10	TraesCS1A01G100700	chr2D	390621237	390622188	951	True	1471.000000	1471	94.770000	1759	2699	1	chr2D.!!$R1	940
11	TraesCS1A01G100700	chr2D	81631571	81632352	781	False	1192.000000	1192	94.501000	1759	2524	1	chr2D.!!$F1	765
12	TraesCS1A01G100700	chr7B	301889004	301889951	947	True	1461.000000	1461	94.731000	1766	2699	1	chr7B.!!$R1	933
13	TraesCS1A01G100700	chrUn	195344591	195345538	947	True	1439.000000	1439	94.310000	1766	2699	1	chrUn.!!$R1	933
14	TraesCS1A01G100700	chrUn	389615675	389616621	946	False	1432.000000	1432	94.204000	1766	2699	1	chrUn.!!$F1	933
15	TraesCS1A01G100700	chr3D	604602360	604603117	757	True	835.000000	835	87.353000	390	1118	1	chr3D.!!$R2	728
16	TraesCS1A01G100700	chr3D	299071492	299072955	1463	True	622.000000	920	84.194500	390	1663	2	chr3D.!!$R4	1273
17	TraesCS1A01G100700	chr3D	32172350	32173645	1295	True	249.400000	433	94.959500	47	365	2	chr3D.!!$R3	318
18	TraesCS1A01G100700	chr7D	14254351	14255116	765	False	865.000000	865	87.891000	390	1118	1	chr7D.!!$F1	728
19	TraesCS1A01G100700	chr6A	234190830	234192308	1478	False	392.666667	811	88.913333	390	1663	3	chr6A.!!$F1	1273
20	TraesCS1A01G100700	chr6B	385532062	385533032	970	False	394.000000	544	84.904500	628	1414	2	chr6B.!!$F1	786
21	TraesCS1A01G100700	chr3B	685077141	685078418	1277	False	239.150000	407	96.796500	77	365	2	chr3B.!!$F1	288

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
865	1913	1.89833	TAGCGTGGCAGCTTCCATCA	61.898	55.0	8.77	0.0	46.8	3.07	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2438	4430	3.068024	TGTTGGTTCTTGGTTCTTGCATC	59.932	43.478	0.0	0.0	0.0	3.91	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
23	24	3.977427	CAACTTGTTTGGGACTAAAGGC	58.023	45.455	0.00	0.00	0.00	4.35
24	25	3.595190	ACTTGTTTGGGACTAAAGGCT	57.405	42.857	0.00	0.00	0.00	4.58
25	26	3.910989	ACTTGTTTGGGACTAAAGGCTT	58.089	40.909	0.00	0.00	0.00	4.35
26	27	4.286707	ACTTGTTTGGGACTAAAGGCTTT	58.713	39.130	17.76	17.76	0.00	3.51
27	28	4.099419	ACTTGTTTGGGACTAAAGGCTTTG	59.901	41.667	22.32	13.97	0.00	2.77
28	29	3.637769	TGTTTGGGACTAAAGGCTTTGT	58.362	40.909	22.32	16.86	0.00	2.83
29	30	4.027437	TGTTTGGGACTAAAGGCTTTGTT	58.973	39.130	22.32	8.73	0.00	2.83
30	31	4.142049	TGTTTGGGACTAAAGGCTTTGTTG	60.142	41.667	22.32	13.85	0.00	3.33
31	32	3.306472	TGGGACTAAAGGCTTTGTTGT	57.694	42.857	22.32	16.69	0.00	3.32
32	33	3.637769	TGGGACTAAAGGCTTTGTTGTT	58.362	40.909	22.32	1.84	0.00	2.83
33	34	3.383185	TGGGACTAAAGGCTTTGTTGTTG	59.617	43.478	22.32	7.79	0.00	3.33
34	35	3.383505	GGGACTAAAGGCTTTGTTGTTGT	59.616	43.478	22.32	10.58	0.00	3.32
35	36	4.142026	GGGACTAAAGGCTTTGTTGTTGTT	60.142	41.667	22.32	0.00	0.00	2.83
36	37	4.803613	GGACTAAAGGCTTTGTTGTTGTTG	59.196	41.667	22.32	0.00	0.00	3.33
37	38	5.400066	ACTAAAGGCTTTGTTGTTGTTGT	57.600	34.783	22.32	0.00	0.00	3.32
38	39	5.789521	ACTAAAGGCTTTGTTGTTGTTGTT	58.210	33.333	22.32	0.00	0.00	2.83
39	40	5.637387	ACTAAAGGCTTTGTTGTTGTTGTTG	59.363	36.000	22.32	0.00	0.00	3.33
40	41	3.676291	AGGCTTTGTTGTTGTTGTTGT	57.324	38.095	0.00	0.00	0.00	3.32
41	42	4.001618	AGGCTTTGTTGTTGTTGTTGTT	57.998	36.364	0.00	0.00	0.00	2.83
42	43	3.745458	AGGCTTTGTTGTTGTTGTTGTTG	59.255	39.130	0.00	0.00	0.00	3.33
43	44	3.496507	GGCTTTGTTGTTGTTGTTGTTGT	59.503	39.130	0.00	0.00	0.00	3.32
44	45	4.024472	GGCTTTGTTGTTGTTGTTGTTGTT	60.024	37.500	0.00	0.00	0.00	2.83
45	46	4.903016	GCTTTGTTGTTGTTGTTGTTGTTG	59.097	37.500	0.00	0.00	0.00	3.33
46	47	5.503194	GCTTTGTTGTTGTTGTTGTTGTTGT	60.503	36.000	0.00	0.00	0.00	3.32
47	48	6.292381	GCTTTGTTGTTGTTGTTGTTGTTGTA	60.292	34.615	0.00	0.00	0.00	2.41
48	49	7.534085	TTTGTTGTTGTTGTTGTTGTTGTAA	57.466	28.000	0.00	0.00	0.00	2.41
49	50	7.715265	TTGTTGTTGTTGTTGTTGTTGTAAT	57.285	28.000	0.00	0.00	0.00	1.89
50	51	8.812147	TTGTTGTTGTTGTTGTTGTTGTAATA	57.188	26.923	0.00	0.00	0.00	0.98
209	210	7.867403	CAGTTATGTTTGTGAAATTTACTGGCT	59.133	33.333	0.00	0.00	0.00	4.75
247	251	9.651718	GTGAAATACCAAATTCTAAATAGCTCG	57.348	33.333	0.00	0.00	0.00	5.03
292	296	9.573166	CCTCATCATATATTGGGTCTTTAACAA	57.427	33.333	0.00	0.00	0.00	2.83
359	1357	8.951243	CATACATACTTGAGCTAGCTGATAGTA	58.049	37.037	24.99	23.32	33.65	1.82
462	1461	6.611613	AGTCATGGTCTCATTGAGTTTCTA	57.388	37.500	13.23	4.64	0.00	2.10
865	1913	1.898330	TAGCGTGGCAGCTTCCATCA	61.898	55.000	8.77	0.00	46.80	3.07
1092	2178	2.559840	GTCTCCGTCAAGCGTCGA	59.440	61.111	0.00	0.00	39.32	4.20
1113	2202	1.749063	CACCCTCGTACATGTCAGCTA	59.251	52.381	0.00	0.00	0.00	3.32
1419	3273	2.056906	GCAGGGGGCTGGATAACGAT	62.057	60.000	0.00	0.00	40.25	3.73
2204	4181	9.487790	GAATGTGAATAAAAATGGGAAGAACAA	57.512	29.630	0.00	0.00	0.00	2.83
2400	4377	3.689347	CTTCAATTGGACCAGGTGATGA	58.311	45.455	5.42	5.15	0.00	2.92
2403	4380	1.293062	ATTGGACCAGGTGATGAGCT	58.707	50.000	0.00	0.00	0.00	4.09
2438	4430	4.478843	CAATCCATAATTGCTCACCTCG	57.521	45.455	0.00	0.00	38.48	4.63
2464	4456	4.097286	GCAAGAACCAAGAACCAACACTTA	59.903	41.667	0.00	0.00	0.00	2.24

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
2	3	3.636764	AGCCTTTAGTCCCAAACAAGTTG	59.363	43.478	0.00	0.00	36.94	3.16
3	4	3.910989	AGCCTTTAGTCCCAAACAAGTT	58.089	40.909	0.00	0.00	0.00	2.66
4	5	3.595190	AGCCTTTAGTCCCAAACAAGT	57.405	42.857	0.00	0.00	0.00	3.16
5	6	4.099419	ACAAAGCCTTTAGTCCCAAACAAG	59.901	41.667	0.00	0.00	0.00	3.16
6	7	4.027437	ACAAAGCCTTTAGTCCCAAACAA	58.973	39.130	0.00	0.00	0.00	2.83
7	8	3.637769	ACAAAGCCTTTAGTCCCAAACA	58.362	40.909	0.00	0.00	0.00	2.83
8	9	4.142026	ACAACAAAGCCTTTAGTCCCAAAC	60.142	41.667	0.00	0.00	0.00	2.93
9	10	4.027437	ACAACAAAGCCTTTAGTCCCAAA	58.973	39.130	0.00	0.00	0.00	3.28
10	11	3.637769	ACAACAAAGCCTTTAGTCCCAA	58.362	40.909	0.00	0.00	0.00	4.12
11	12	3.306472	ACAACAAAGCCTTTAGTCCCA	57.694	42.857	0.00	0.00	0.00	4.37
12	13	3.383505	ACAACAACAAAGCCTTTAGTCCC	59.616	43.478	0.00	0.00	0.00	4.46
13	14	4.649088	ACAACAACAAAGCCTTTAGTCC	57.351	40.909	0.00	0.00	0.00	3.85
14	15	5.407502	ACAACAACAACAAAGCCTTTAGTC	58.592	37.500	0.00	0.00	0.00	2.59
15	16	5.400066	ACAACAACAACAAAGCCTTTAGT	57.600	34.783	0.00	0.00	0.00	2.24
16	17	5.637387	ACAACAACAACAACAAAGCCTTTAG	59.363	36.000	0.00	0.00	0.00	1.85
17	18	5.542779	ACAACAACAACAACAAAGCCTTTA	58.457	33.333	0.00	0.00	0.00	1.85
18	19	4.384940	ACAACAACAACAACAAAGCCTTT	58.615	34.783	0.00	0.00	0.00	3.11
19	20	4.001618	ACAACAACAACAACAAAGCCTT	57.998	36.364	0.00	0.00	0.00	4.35
20	21	3.676291	ACAACAACAACAACAAAGCCT	57.324	38.095	0.00	0.00	0.00	4.58
21	22	3.496507	ACAACAACAACAACAACAAAGCC	59.503	39.130	0.00	0.00	0.00	4.35
22	23	4.723879	ACAACAACAACAACAACAAAGC	57.276	36.364	0.00	0.00	0.00	3.51
23	24	6.042144	ACAACAACAACAACAACAACAAAG	57.958	33.333	0.00	0.00	0.00	2.77
24	25	7.534085	TTACAACAACAACAACAACAACAAA	57.466	28.000	0.00	0.00	0.00	2.83
25	26	7.715265	ATTACAACAACAACAACAACAACAA	57.285	28.000	0.00	0.00	0.00	2.83
26	27	8.812147	TTATTACAACAACAACAACAACAACA	57.188	26.923	0.00	0.00	0.00	3.33
47	48	8.760735	TGGACCATGATGAATCAACAATTTATT	58.239	29.630	0.00	0.00	40.69	1.40
48	49	8.308851	TGGACCATGATGAATCAACAATTTAT	57.691	30.769	0.00	0.00	40.69	1.40
49	50	7.631161	GCTGGACCATGATGAATCAACAATTTA	60.631	37.037	0.00	0.00	40.69	1.40
50	51	6.608539	TGGACCATGATGAATCAACAATTT	57.391	33.333	0.00	0.00	40.69	1.82
174	175	3.443329	CACAAACATAACTGCAGGCCATA	59.557	43.478	19.93	5.98	0.00	2.74
247	251	2.203181	GCTGCCTCTCCTGATGCC	60.203	66.667	0.00	0.00	33.73	4.40
462	1461	6.072948	TGACACGAACGATGGAAATTTAATGT	60.073	34.615	0.14	0.00	0.00	2.71
799	1845	1.129998	GATCATGCACGCATATGCTCC	59.870	52.381	24.56	12.98	46.28	4.70
865	1913	2.298661	CCCGGGGGTAAAGCTCAGT	61.299	63.158	14.71	0.00	0.00	3.41
1092	2178	0.246635	GCTGACATGTACGAGGGTGT	59.753	55.000	0.00	0.00	0.00	4.16
1176	2498	0.393944	AGGTCTCCGTGCTCATCGTA	60.394	55.000	0.00	0.00	0.00	3.43
1419	3273	3.153676	TCTTGACGTCTGTTTCGTTCA	57.846	42.857	17.92	0.00	41.64	3.18
2055	4032	9.140874	TCATAAATGACAATTATAATGGTGGCA	57.859	29.630	10.33	9.00	32.46	4.92
2420	4397	3.732212	CATCGAGGTGAGCAATTATGGA	58.268	45.455	0.00	0.00	0.00	3.41
2438	4430	3.068024	TGTTGGTTCTTGGTTCTTGCATC	59.932	43.478	0.00	0.00	0.00	3.91
2464	4456	7.812690	TGTACCGAGTAATGAGTATGTACAT	57.187	36.000	13.93	13.93	34.18	2.29

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.