AutoCloner

Multiple sequence alignment - TraesCS1D01G252000

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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	TraesCS1D01G252000	chr1D	100.000	3946	0	0	1	3946	344589295	344593240	0.000000e+00	7287.0
1	TraesCS1D01G252000	chr1B	95.625	2903	79	16	1077	3946	466094524	466091637	0.000000e+00	4614.0
2	TraesCS1D01G252000	chr1B	93.955	1340	72	5	1320	2656	682437250	682438583	0.000000e+00	2017.0
3	TraesCS1D01G252000	chr1B	90.766	509	32	5	1	508	466119186	466118692	0.000000e+00	665.0
4	TraesCS1D01G252000	chr1B	91.325	415	16	10	758	1161	466095013	466094608	2.070000e-152	549.0
5	TraesCS1D01G252000	chr1B	93.237	207	13	1	502	708	466108706	466108501	1.780000e-78	303.0
6	TraesCS1D01G252000	chr1B	94.737	57	3	0	703	759	466095231	466095175	5.430000e-14	89.8
7	TraesCS1D01G252000	chr1A	97.779	1306	26	1	1244	2546	444122300	444123605	0.000000e+00	2248.0
8	TraesCS1D01G252000	chr1A	90.014	711	52	6	1	710	444120473	444121165	0.000000e+00	902.0
9	TraesCS1D01G252000	chr1A	85.792	739	47	31	3227	3946	444124214	444124913	0.000000e+00	730.0
10	TraesCS1D01G252000	chr1A	89.414	444	14	15	707	1124	444121580	444122016	2.700000e-146	529.0
11	TraesCS1D01G252000	chr1A	85.470	234	17	1	2545	2778	444123709	444123925	1.100000e-55	228.0
12	TraesCS1D01G252000	chr2A	95.575	565	24	1	2312	2875	476213898	476213334	0.000000e+00	904.0
13	TraesCS1D01G252000	chr2A	81.419	775	117	14	12	782	691400845	691400094	3.370000e-170	608.0
14	TraesCS1D01G252000	chr2A	97.531	324	8	0	1322	1645	476214251	476213928	4.460000e-154	555.0
15	TraesCS1D01G252000	chr2A	96.012	326	13	0	1320	1645	476212096	476212421	7.510000e-147	531.0
16	TraesCS1D01G252000	chr2A	91.343	335	14	9	2856	3178	476213250	476212919	1.010000e-120	444.0
17	TraesCS1D01G252000	chr2A	87.562	402	19	10	3208	3588	476212831	476212440	1.680000e-118	436.0
18	TraesCS1D01G252000	chr3D	82.850	793	113	13	1	788	588843867	588843093	0.000000e+00	689.0
19	TraesCS1D01G252000	chr3D	97.613	377	2	2	1341	1711	284206928	284206553	1.200000e-179	640.0
20	TraesCS1D01G252000	chr5A	83.903	702	98	11	1	699	427836410	427835721	0.000000e+00	656.0
21	TraesCS1D01G252000	chr4A	81.646	790	117	15	1	787	601200924	601201688	7.200000e-177	630.0
22	TraesCS1D01G252000	chr5D	83.204	643	94	11	1	642	328703121	328703750	9.510000e-161	577.0
23	TraesCS1D01G252000	chr5D	84.328	134	13	4	642	775	312433666	312433791	1.490000e-24	124.0
24	TraesCS1D01G252000	chr7B	93.664	363	13	2	1334	1695	221893234	221892881	5.800000e-148	534.0
25	TraesCS1D01G252000	chr7B	98.734	79	1	0	1633	1711	29687351	29687429	1.480000e-29	141.0
26	TraesCS1D01G252000	chr3B	93.611	360	13	2	1334	1692	492742384	492742734	2.700000e-146	529.0
27	TraesCS1D01G252000	chr3B	86.207	377	23	17	1341	1711	245923633	245923280	8.000000e-102	381.0
28	TraesCS1D01G252000	chr2B	93.333	360	14	2	1334	1692	113193319	113193669	1.260000e-144	523.0
29	TraesCS1D01G252000	chr7D	81.395	301	44	8	309	607	20505193	20504903	6.590000e-58	235.0
30	TraesCS1D01G252000	chr5B	87.317	205	17	4	581	785	343824114	343823919	3.970000e-55	226.0

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	TraesCS1D01G252000	chr1D	344589295	344593240	3945	False	7287.000000	7287	100.000000	1	3946	1	chr1D.!!$F1	3945
1	TraesCS1D01G252000	chr1B	682437250	682438583	1333	False	2017.000000	2017	93.955000	1320	2656	1	chr1B.!!$F1	1336
2	TraesCS1D01G252000	chr1B	466091637	466095231	3594	True	1750.933333	4614	93.895667	703	3946	3	chr1B.!!$R3	3243
3	TraesCS1D01G252000	chr1A	444120473	444124913	4440	False	927.400000	2248	89.693800	1	3946	5	chr1A.!!$F1	3945
4	TraesCS1D01G252000	chr2A	691400094	691400845	751	True	608.000000	608	81.419000	12	782	1	chr2A.!!$R1	770
5	TraesCS1D01G252000	chr2A	476212440	476214251	1811	True	584.750000	904	93.002750	1322	3588	4	chr2A.!!$R2	2266
6	TraesCS1D01G252000	chr3D	588843093	588843867	774	True	689.000000	689	82.850000	1	788	1	chr3D.!!$R2	787
7	TraesCS1D01G252000	chr5A	427835721	427836410	689	True	656.000000	656	83.903000	1	699	1	chr5A.!!$R1	698
8	TraesCS1D01G252000	chr4A	601200924	601201688	764	False	630.000000	630	81.646000	1	787	1	chr4A.!!$F1	786
9	TraesCS1D01G252000	chr5D	328703121	328703750	629	False	577.000000	577	83.204000	1	642	1	chr5D.!!$F2	641

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
959	1548	0.254638	TCTTCCCCTCCCTCTCCCTA	60.255	60.0	0.0	0.0	0.0	3.53	F
1006	1608	0.253207	CCCAAACCCCTACCTCTCCT	60.253	60.0	0.0	0.0	0.0	3.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2289	3231	0.179048	TAGCCACAATCTCATGCCGG	60.179	55.000	0.0	0.0	0.0	6.13	R
2981	4136	1.281867	CAGGTGGCATTAACAGGAGGA	59.718	52.381	0.0	0.0	0.0	3.71	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
115	116	1.188863	ACCTCCATTGCCAAATCTGC	58.811	50.000	0.00	0.00	0.00	4.26
125	126	5.480642	TTGCCAAATCTGCCATTTTCTTA	57.519	34.783	0.00	0.00	0.00	2.10
199	200	1.416030	GGGCAAAAGTCCATTGGTTGT	59.584	47.619	1.86	0.00	0.00	3.32
211	212	6.215636	AGTCCATTGGTTGTAATTCCTAGAGT	59.784	38.462	1.86	0.00	0.00	3.24
288	289	6.801575	TGGTTTTGTGAAGGTAAATTCAGAC	58.198	36.000	0.00	0.00	39.78	3.51
337	339	2.202932	CGGCCGGAGTCATTGGAG	60.203	66.667	20.10	0.00	0.00	3.86
338	340	2.721167	CGGCCGGAGTCATTGGAGA	61.721	63.158	20.10	0.00	0.00	3.71
424	426	1.980772	GCTGAAGGGCAGGCAATGT	60.981	57.895	0.00	0.00	45.03	2.71
434	436	2.549778	GGCAGGCAATGTTTTTAGGCAA	60.550	45.455	0.00	0.00	0.00	4.52
449	451	2.334946	GCAAGCATGCGAACCCTGA	61.335	57.895	13.01	0.00	43.83	3.86
450	452	1.865788	GCAAGCATGCGAACCCTGAA	61.866	55.000	13.01	0.00	43.83	3.02
451	453	0.597568	CAAGCATGCGAACCCTGAAA	59.402	50.000	13.01	0.00	0.00	2.69
452	454	1.000385	CAAGCATGCGAACCCTGAAAA	60.000	47.619	13.01	0.00	0.00	2.29
453	455	1.549203	AGCATGCGAACCCTGAAAAT	58.451	45.000	13.01	0.00	0.00	1.82
454	456	2.722094	AGCATGCGAACCCTGAAAATA	58.278	42.857	13.01	0.00	0.00	1.40
455	457	2.684881	AGCATGCGAACCCTGAAAATAG	59.315	45.455	13.01	0.00	0.00	1.73
456	458	2.423538	GCATGCGAACCCTGAAAATAGT	59.576	45.455	0.00	0.00	0.00	2.12
458	460	4.275936	GCATGCGAACCCTGAAAATAGTAT	59.724	41.667	0.00	0.00	0.00	2.12
500	502	1.089112	TTGAGACAGATTGCATGGCG	58.911	50.000	0.00	0.00	0.00	5.69
561	563	2.172717	AGATGGCGGGCTACTTACAATT	59.827	45.455	2.38	0.00	0.00	2.32
566	568	4.131596	GGCGGGCTACTTACAATTATTCA	58.868	43.478	0.00	0.00	0.00	2.57
611	613	7.504238	TCTCCATCCTAGAGAGTAACAAAGATC	59.496	40.741	0.00	0.00	35.46	2.75
818	1406	1.602377	CGCACGAGGTTTTCTCCTTTT	59.398	47.619	0.00	0.00	39.30	2.27
835	1423	3.884693	CCTTTTGGGCTCATTTTGCTTTT	59.115	39.130	0.00	0.00	35.46	2.27
836	1424	4.023792	CCTTTTGGGCTCATTTTGCTTTTC	60.024	41.667	0.00	0.00	35.46	2.29
837	1425	3.834489	TTGGGCTCATTTTGCTTTTCA	57.166	38.095	0.00	0.00	0.00	2.69
880	1468	2.383527	CGGAGGCGCTGTCTTCAAC	61.384	63.158	7.64	0.00	0.00	3.18
940	1529	0.321021	CTGGCAGTCTCAGCACTCTT	59.679	55.000	6.28	0.00	0.00	2.85
954	1543	1.097722	ACTCTTCTTCCCCTCCCTCT	58.902	55.000	0.00	0.00	0.00	3.69
956	1545	0.340208	TCTTCTTCCCCTCCCTCTCC	59.660	60.000	0.00	0.00	0.00	3.71
959	1548	0.254638	TCTTCCCCTCCCTCTCCCTA	60.255	60.000	0.00	0.00	0.00	3.53
972	1566	2.108601	CTCTCCCTACCCCGAACTATCT	59.891	54.545	0.00	0.00	0.00	1.98
1006	1608	0.253207	CCCAAACCCCTACCTCTCCT	60.253	60.000	0.00	0.00	0.00	3.69
2029	2971	0.652592	CAGCGGTGATGATTTCGGAC	59.347	55.000	9.50	0.00	0.00	4.79
2169	3111	2.409870	CCCCCAATTGCTCGCACTC	61.410	63.158	0.00	0.00	0.00	3.51
2262	3204	1.664151	GAGTTCCCGGCATTCTTTACG	59.336	52.381	0.00	0.00	0.00	3.18
2289	3231	5.185249	TGGCCTCGAATCCACTATAAGATAC	59.815	44.000	3.32	0.00	0.00	2.24
2316	3258	4.380843	TGAGATTGTGGCTAAAAAGGGA	57.619	40.909	0.00	0.00	0.00	4.20
2400	3342	6.427853	TGAAGTATGACACAATTGGAGTTGAG	59.572	38.462	10.83	0.00	33.37	3.02
2565	3615	9.119329	GTATCTAGTATCAATTGTTAGCTGACG	57.881	37.037	5.13	0.00	0.00	4.35
2981	4136	7.017353	ACATCCCAGTCAGAATTGAGATATGAT	59.983	37.037	0.00	0.00	32.98	2.45
3166	4333	6.012658	TGTTGGCATCAAGATTTTGACTAC	57.987	37.500	0.00	0.00	45.54	2.73
3173	4357	6.565811	GCATCAAGATTTTGACTACGTTGTCA	60.566	38.462	25.49	25.49	45.54	3.58
3213	4445	0.588252	CCGCAATGCATACTAGGTGC	59.412	55.000	5.91	13.61	42.81	5.01
3251	4483	3.013921	TGTCTCCTGTTGAACACCAAAC	58.986	45.455	0.00	0.00	36.36	2.93
3295	4530	0.610687	CTGGAGAGAAGTCCACCACC	59.389	60.000	0.00	0.00	41.99	4.61
3446	4697	4.286032	ACATTTCAGTTCCAGTAGCCACTA	59.714	41.667	0.00	0.00	32.21	2.74
3447	4698	3.955650	TTCAGTTCCAGTAGCCACTAC	57.044	47.619	0.00	0.00	37.23	2.73
3484	4735	2.281484	GCCAAGTGCCAACCGAGA	60.281	61.111	0.00	0.00	0.00	4.04
3500	4751	2.436824	GAAGAGCTGGCCCGTTCC	60.437	66.667	7.40	0.00	0.00	3.62
3522	4773	4.081309	CCATGTGAAATTCCTGCCTTTCAT	60.081	41.667	1.55	0.00	41.80	2.57
3556	4826	6.035112	GCTACAGAACCTTATCAGAAAACGAG	59.965	42.308	0.00	0.00	0.00	4.18
3652	4922	2.169789	CAAGCTGAGGATGGCGTCG	61.170	63.158	0.00	0.00	0.00	5.12
3848	5127	1.518572	GTGGTGGCTATGTCGTCGG	60.519	63.158	0.00	0.00	0.00	4.79

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
9	10	3.516981	ATCTCTGGAGATGTTGTCACG	57.483	47.619	11.74	0.00	45.77	4.35
125	126	9.853177	CCCTTAAGACAATTCCAGTAATTAGAT	57.147	33.333	3.36	0.00	35.54	1.98
199	200	5.248477	ACTTCAGGTTGCACTCTAGGAATTA	59.752	40.000	0.00	0.00	0.00	1.40
288	289	4.260620	CCCGAACCAACTATAAAAGATGCG	60.261	45.833	0.00	0.00	0.00	4.73
337	339	1.905449	ACCTCGTCGTCGCTATTTTC	58.095	50.000	0.00	0.00	36.96	2.29
338	340	2.358939	AACCTCGTCGTCGCTATTTT	57.641	45.000	0.00	0.00	36.96	1.82
424	426	2.609244	GGTTCGCATGCTTGCCTAAAAA	60.609	45.455	17.13	3.57	46.57	1.94
434	436	1.549203	ATTTTCAGGGTTCGCATGCT	58.451	45.000	17.13	0.00	0.00	3.79
475	477	4.157105	CCATGCAATCTGTCTCAAACATCA	59.843	41.667	0.00	0.00	37.23	3.07
500	502	4.920828	TTGAGGGCCTCAACAACC	57.079	55.556	38.53	11.94	44.27	3.77
546	548	5.181245	CCCATGAATAATTGTAAGTAGCCCG	59.819	44.000	0.00	0.00	0.00	6.13
561	563	2.241941	TCTTCAGCAAGGCCCATGAATA	59.758	45.455	10.23	1.37	31.69	1.75
566	568	2.105766	GAATTCTTCAGCAAGGCCCAT	58.894	47.619	0.00	0.00	0.00	4.00
611	613	2.064762	CACAAGTTGCTCTCTCTTCCG	58.935	52.381	1.81	0.00	0.00	4.30
700	706	7.509318	AGATTACATCAGTTATACTAGGTGGCA	59.491	37.037	0.00	0.00	0.00	4.92
782	1370	4.387936	TCGTGCGATTTAACGTGATTTTC	58.612	39.130	0.00	0.00	40.61	2.29
784	1372	3.181524	CCTCGTGCGATTTAACGTGATTT	60.182	43.478	0.00	0.00	40.61	2.17
818	1406	3.324268	TGATGAAAAGCAAAATGAGCCCA	59.676	39.130	0.00	0.00	0.00	5.36
835	1423	4.502171	TGCTTCGCTTTGATTTTGATGA	57.498	36.364	0.00	0.00	0.00	2.92
836	1424	4.445052	TGTTGCTTCGCTTTGATTTTGATG	59.555	37.500	0.00	0.00	0.00	3.07
837	1425	4.619973	TGTTGCTTCGCTTTGATTTTGAT	58.380	34.783	0.00	0.00	0.00	2.57
940	1529	0.254638	TAGGGAGAGGGAGGGGAAGA	60.255	60.000	0.00	0.00	0.00	2.87
954	1543	1.854939	TGAGATAGTTCGGGGTAGGGA	59.145	52.381	0.00	0.00	0.00	4.20
956	1545	2.488545	CGATGAGATAGTTCGGGGTAGG	59.511	54.545	0.00	0.00	0.00	3.18
959	1548	0.674534	GCGATGAGATAGTTCGGGGT	59.325	55.000	0.00	0.00	33.62	4.95
1006	1608	1.268992	ATCATTTCCGGTCGGGGTGA	61.269	55.000	9.68	11.10	36.01	4.02
2076	3018	4.452455	AGGAAGTTGACATGCTTTAGAACG	59.548	41.667	0.00	0.00	0.00	3.95
2205	3147	6.406624	CCAAATCCCTCTCCATTTCATTCTTG	60.407	42.308	0.00	0.00	0.00	3.02
2262	3204	3.963428	ATAGTGGATTCGAGGCCATAC	57.037	47.619	5.01	0.00	36.41	2.39
2289	3231	0.179048	TAGCCACAATCTCATGCCGG	60.179	55.000	0.00	0.00	0.00	6.13
2400	3342	7.506938	TCAAAGGAATTATCATCCTCCATTTCC	59.493	37.037	0.00	0.00	46.65	3.13
2565	3615	5.947443	AGCTCAAGACATAAATGCAAGTTC	58.053	37.500	0.00	0.00	0.00	3.01
2981	4136	1.281867	CAGGTGGCATTAACAGGAGGA	59.718	52.381	0.00	0.00	0.00	3.71
3166	4333	1.800805	AAGCCATCTCTGTGACAACG	58.199	50.000	0.00	0.00	0.00	4.10
3173	4357	4.455877	CGGACTTTTTAAAGCCATCTCTGT	59.544	41.667	2.23	0.00	39.63	3.41
3213	4445	5.940470	AGGAGACAAGTTTTATAAGCCACAG	59.060	40.000	0.00	0.00	0.00	3.66
3251	4483	2.109181	GAAAGGGGGATCCGCGAG	59.891	66.667	21.47	0.00	41.60	5.03
3295	4530	2.461300	TCCACTATCTGGAGACTGGG	57.539	55.000	0.00	0.00	44.99	4.45
3484	4735	2.606587	ATGGAACGGGCCAGCTCTT	61.607	57.895	4.39	0.00	42.15	2.85
3500	4751	4.524316	TGAAAGGCAGGAATTTCACATG	57.476	40.909	0.00	0.00	39.76	3.21
3522	4773	1.203187	AGGTTCTGTAGCCTCCTGACA	60.203	52.381	0.00	0.00	0.00	3.58
3534	4791	4.691216	GCTCGTTTTCTGATAAGGTTCTGT	59.309	41.667	1.59	0.00	0.00	3.41
3592	4862	4.021104	CCCATTTCCCTTTCTCCTTTTCAC	60.021	45.833	0.00	0.00	0.00	3.18
3593	4863	4.159557	CCCATTTCCCTTTCTCCTTTTCA	58.840	43.478	0.00	0.00	0.00	2.69
3685	4955	4.144727	AGGAGGGACGGGAGCGAT	62.145	66.667	0.00	0.00	0.00	4.58
3686	4956	4.816984	GAGGAGGGACGGGAGCGA	62.817	72.222	0.00	0.00	0.00	4.93

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.