AutoCloner

Multiple sequence alignment - TraesCS7B01G339600

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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	TraesCS7B01G339600	chr7B	100.000	3170	0	0	1	3170	594062817	594065986	0.000000e+00	5854.0
1	TraesCS7B01G339600	chr7B	81.266	1201	172	27	1069	2250	594024920	594026086	0.000000e+00	922.0
2	TraesCS7B01G339600	chr7B	86.072	359	45	3	283	637	594034819	594035176	6.420000e-102	381.0
3	TraesCS7B01G339600	chr7B	87.500	96	4	5	3049	3143	594026207	594026295	1.560000e-18	104.0
4	TraesCS7B01G339600	chr7D	96.383	3152	93	12	1	3146	549769740	549772876	0.000000e+00	5169.0
5	TraesCS7B01G339600	chr7D	84.327	1761	237	20	705	2453	549697257	549698990	0.000000e+00	1687.0
6	TraesCS7B01G339600	chr7D	83.463	1669	242	20	668	2321	549705282	549706931	0.000000e+00	1522.0
7	TraesCS7B01G339600	chr7D	81.240	1919	285	41	668	2555	549783147	549785021	0.000000e+00	1480.0
8	TraesCS7B01G339600	chr7D	79.217	332	45	13	321	639	549704847	549705167	3.200000e-50	209.0
9	TraesCS7B01G339600	chr7D	84.694	98	11	3	2953	3048	549699592	549699687	9.360000e-16	95.3
10	TraesCS7B01G339600	chr7A	96.561	2210	70	5	726	2933	635241129	635243334	0.000000e+00	3655.0
11	TraesCS7B01G339600	chr7A	85.690	1761	221	17	705	2453	635074711	635076452	0.000000e+00	1827.0
12	TraesCS7B01G339600	chr7A	84.072	1670	225	24	668	2321	635093988	635095632	0.000000e+00	1572.0
13	TraesCS7B01G339600	chr7A	83.171	1747	240	31	787	2510	635051461	635053176	0.000000e+00	1548.0
14	TraesCS7B01G339600	chr7A	82.222	1665	254	24	909	2555	635270772	635272412	0.000000e+00	1397.0
15	TraesCS7B01G339600	chr7A	93.349	421	18	5	193	608	635240704	635241119	5.810000e-172	614.0
16	TraesCS7B01G339600	chr7A	85.873	361	38	7	284	640	635074334	635074685	3.860000e-99	372.0
17	TraesCS7B01G339600	chr7A	84.058	207	25	4	378	584	635093749	635093947	3.230000e-45	193.0
18	TraesCS7B01G339600	chr7A	91.971	137	7	2	1	136	635240580	635240713	4.170000e-44	189.0
19	TraesCS7B01G339600	chr3A	94.548	697	28	5	2319	3014	370463831	370463144	0.000000e+00	1068.0
20	TraesCS7B01G339600	chr3A	93.840	698	33	6	2318	3014	590310800	590310112	0.000000e+00	1042.0
21	TraesCS7B01G339600	chr3A	93.696	698	32	7	2318	3014	404361093	404360407	0.000000e+00	1035.0
22	TraesCS7B01G339600	chr3A	93.123	698	37	6	2318	3014	722933098	722933785	0.000000e+00	1013.0
23	TraesCS7B01G339600	chrUn	94.413	698	28	6	2318	3014	1915267	1915954	0.000000e+00	1062.0
24	TraesCS7B01G339600	chr2A	94.413	698	28	6	2318	3014	566445884	566446571	0.000000e+00	1062.0
25	TraesCS7B01G339600	chr5A	93.983	698	31	5	2318	3014	417829731	417829044	0.000000e+00	1046.0

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	TraesCS7B01G339600	chr7B	594062817	594065986	3169	False	5854.00	5854	100.000000	1	3170	1	chr7B.!!$F2	3169
1	TraesCS7B01G339600	chr7B	594024920	594026295	1375	False	513.00	922	84.383000	1069	3143	2	chr7B.!!$F3	2074
2	TraesCS7B01G339600	chr7D	549769740	549772876	3136	False	5169.00	5169	96.383000	1	3146	1	chr7D.!!$F1	3145
3	TraesCS7B01G339600	chr7D	549783147	549785021	1874	False	1480.00	1480	81.240000	668	2555	1	chr7D.!!$F2	1887
4	TraesCS7B01G339600	chr7D	549697257	549699687	2430	False	891.15	1687	84.510500	705	3048	2	chr7D.!!$F3	2343
5	TraesCS7B01G339600	chr7D	549704847	549706931	2084	False	865.50	1522	81.340000	321	2321	2	chr7D.!!$F4	2000
6	TraesCS7B01G339600	chr7A	635051461	635053176	1715	False	1548.00	1548	83.171000	787	2510	1	chr7A.!!$F1	1723
7	TraesCS7B01G339600	chr7A	635240580	635243334	2754	False	1486.00	3655	93.960333	1	2933	3	chr7A.!!$F5	2932
8	TraesCS7B01G339600	chr7A	635270772	635272412	1640	False	1397.00	1397	82.222000	909	2555	1	chr7A.!!$F2	1646
9	TraesCS7B01G339600	chr7A	635074334	635076452	2118	False	1099.50	1827	85.781500	284	2453	2	chr7A.!!$F3	2169
10	TraesCS7B01G339600	chr7A	635093749	635095632	1883	False	882.50	1572	84.065000	378	2321	2	chr7A.!!$F4	1943
11	TraesCS7B01G339600	chr3A	370463144	370463831	687	True	1068.00	1068	94.548000	2319	3014	1	chr3A.!!$R1	695
12	TraesCS7B01G339600	chr3A	590310112	590310800	688	True	1042.00	1042	93.840000	2318	3014	1	chr3A.!!$R3	696
13	TraesCS7B01G339600	chr3A	404360407	404361093	686	True	1035.00	1035	93.696000	2318	3014	1	chr3A.!!$R2	696
14	TraesCS7B01G339600	chr3A	722933098	722933785	687	False	1013.00	1013	93.123000	2318	3014	1	chr3A.!!$F1	696
15	TraesCS7B01G339600	chrUn	1915267	1915954	687	False	1062.00	1062	94.413000	2318	3014	1	chrUn.!!$F1	696
16	TraesCS7B01G339600	chr2A	566445884	566446571	687	False	1062.00	1062	94.413000	2318	3014	1	chr2A.!!$F1	696
17	TraesCS7B01G339600	chr5A	417829044	417829731	687	True	1046.00	1046	93.983000	2318	3014	1	chr5A.!!$R1	696

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
167	172	1.208776	TGATCTCCTGCATGTCCTGTG	59.791	52.381	0.0	0.0	0.00	3.66	F
919	1043	2.159184	TGCGTTTGCCAGTTGAATTTCA	60.159	40.909	0.0	0.0	41.78	2.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1551	1693	0.591741	CTGACGGCCGACTAACGATC	60.592	60.0	35.9	17.03	45.77	3.69	R
2747	3006	0.030235	GAAAACCAACCTGCACGACC	59.970	55.0	0.0	0.00	0.00	4.79	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
82	87	4.393062	CGCCTTGTATTCATTTCAGACACT	59.607	41.667	0.00	0.00	0.00	3.55
84	89	6.092122	CGCCTTGTATTCATTTCAGACACTAA	59.908	38.462	0.00	0.00	0.00	2.24
87	92	9.778993	CCTTGTATTCATTTCAGACACTAATTG	57.221	33.333	0.00	0.00	0.00	2.32
107	112	9.775854	CTAATTGGAGATATGATTTGACAGTCT	57.224	33.333	1.31	0.00	0.00	3.24
162	167	2.548875	GACAGTGATCTCCTGCATGTC	58.451	52.381	11.44	5.84	33.09	3.06
165	170	1.485480	AGTGATCTCCTGCATGTCCTG	59.515	52.381	0.00	0.00	0.00	3.86
166	171	1.209019	GTGATCTCCTGCATGTCCTGT	59.791	52.381	0.00	0.00	0.00	4.00
167	172	1.208776	TGATCTCCTGCATGTCCTGTG	59.791	52.381	0.00	0.00	0.00	3.66
262	267	5.197451	ACACCCAGTTGAGTTTGAATGTTA	58.803	37.500	0.00	0.00	0.00	2.41
409	428	3.581024	GATGCAATCACAACACATGGT	57.419	42.857	0.00	0.00	44.70	3.55
751	864	4.152759	CGGCCGACAATTGTAAAACTCTAA	59.847	41.667	24.07	0.00	0.00	2.10
878	998	3.895232	AGCATCACGTTATCTCTTGGT	57.105	42.857	0.00	0.00	0.00	3.67
918	1042	2.468831	TGCGTTTGCCAGTTGAATTTC	58.531	42.857	0.00	0.00	41.78	2.17
919	1043	2.159184	TGCGTTTGCCAGTTGAATTTCA	60.159	40.909	0.00	0.00	41.78	2.69
946	1070	5.207110	ACAGATAACCTCAATCATCTCCG	57.793	43.478	0.00	0.00	0.00	4.63
1139	1269	2.670934	GCACAGTGCCACCTCCAG	60.671	66.667	15.27	0.00	37.42	3.86
1309	1439	7.473366	TCAGCACTCTAAGTTAAGTTATCTCG	58.527	38.462	3.23	0.00	0.00	4.04
1411	1541	4.147321	TCTACTACCACAACCTCGAGTTT	58.853	43.478	12.31	0.00	36.18	2.66
1551	1693	1.107538	TAGGATCCGACAAGCCGAGG	61.108	60.000	5.98	0.00	0.00	4.63
1696	1838	1.821753	CGGAGACTTCTGTGGACATCT	59.178	52.381	0.00	0.00	0.00	2.90
1875	2017	1.550130	CCTGGGCCTTGAAGTACCGA	61.550	60.000	4.53	0.00	0.00	4.69
1986	2140	1.448540	CACTGCATCGGAGTGTCCC	60.449	63.158	7.41	0.00	36.79	4.46
2329	2495	4.021807	TCTGGTGACGTTTGTGCTATCTTA	60.022	41.667	0.00	0.00	0.00	2.10
2333	2499	4.389077	GTGACGTTTGTGCTATCTTAAGCT	59.611	41.667	0.00	0.00	43.19	3.74
2364	2531	6.479436	CGATGTGTCGGAGTATCTATGATAC	58.521	44.000	9.06	9.06	44.00	2.24
2747	3006	7.921786	TCTTTTTATCAGGGATACTTGTGTG	57.078	36.000	0.00	0.00	45.47	3.82
2806	3164	7.625828	AGAAGTTGGCACTTTGGTTATATAC	57.374	36.000	0.00	0.00	43.79	1.47
2811	3169	6.425577	TGGCACTTTGGTTATATACGTTTC	57.574	37.500	0.00	0.00	0.00	2.78
2912	3271	3.879998	TCTTGTCTGTGGTTTAACTGCA	58.120	40.909	0.00	0.00	0.00	4.41
2936	3295	0.512952	CTGTTGGCGTTCTACACTGC	59.487	55.000	0.00	0.00	0.00	4.40
2937	3296	0.105964	TGTTGGCGTTCTACACTGCT	59.894	50.000	0.00	0.00	0.00	4.24
3021	3380	4.332828	TCGACTTGAACATCTACTCTCCA	58.667	43.478	0.00	0.00	0.00	3.86
3122	3517	1.338579	CCAGCACTCCTCTGAAACTCC	60.339	57.143	0.00	0.00	33.54	3.85
3136	3531	6.653989	TCTGAAACTCCTCTTCTTGAAGTTT	58.346	36.000	9.80	4.18	0.00	2.66
3149	3544	9.801873	TCTTCTTGAAGTTTAATGTTTTTCTGG	57.198	29.630	9.80	0.00	0.00	3.86
3150	3545	9.801873	CTTCTTGAAGTTTAATGTTTTTCTGGA	57.198	29.630	2.44	0.00	0.00	3.86
3155	3550	9.323985	TGAAGTTTAATGTTTTTCTGGAAATGG	57.676	29.630	0.00	0.00	0.00	3.16
3156	3551	9.325198	GAAGTTTAATGTTTTTCTGGAAATGGT	57.675	29.630	0.00	0.00	0.00	3.55
3157	3552	9.679661	AAGTTTAATGTTTTTCTGGAAATGGTT	57.320	25.926	0.00	0.00	0.00	3.67
3158	3553	9.108284	AGTTTAATGTTTTTCTGGAAATGGTTG	57.892	29.630	0.00	0.00	0.00	3.77
3159	3554	7.489574	TTAATGTTTTTCTGGAAATGGTTGC	57.510	32.000	0.00	0.00	0.00	4.17
3160	3555	4.478206	TGTTTTTCTGGAAATGGTTGCA	57.522	36.364	0.00	0.00	33.54	4.08
3161	3556	4.187694	TGTTTTTCTGGAAATGGTTGCAC	58.812	39.130	0.00	0.00	31.02	4.57
3162	3557	4.187694	GTTTTTCTGGAAATGGTTGCACA	58.812	39.130	0.00	0.00	31.02	4.57
3163	3558	3.731652	TTTCTGGAAATGGTTGCACAG	57.268	42.857	0.00	0.00	31.02	3.66
3164	3559	0.961019	TCTGGAAATGGTTGCACAGC	59.039	50.000	0.00	0.00	31.02	4.40
3165	3560	0.675083	CTGGAAATGGTTGCACAGCA	59.325	50.000	0.00	0.00	37.28	4.41
3166	3561	1.274167	CTGGAAATGGTTGCACAGCAT	59.726	47.619	7.47	7.47	46.04	3.79
3167	3562	1.001068	TGGAAATGGTTGCACAGCATG	59.999	47.619	12.24	0.00	43.13	4.06

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
84	89	8.051535	ACAAGACTGTCAAATCATATCTCCAAT	58.948	33.333	10.88	0.00	0.00	3.16
87	92	6.238320	GCACAAGACTGTCAAATCATATCTCC	60.238	42.308	10.88	0.00	31.64	3.71
162	167	1.873591	GGCTTGTTGTAGTGTCACAGG	59.126	52.381	5.62	0.00	0.00	4.00
165	170	3.684788	CCTATGGCTTGTTGTAGTGTCAC	59.315	47.826	0.00	0.00	0.00	3.67
166	171	3.580895	TCCTATGGCTTGTTGTAGTGTCA	59.419	43.478	0.00	0.00	0.00	3.58
167	172	4.202245	TCCTATGGCTTGTTGTAGTGTC	57.798	45.455	0.00	0.00	0.00	3.67
244	249	6.064846	ACAGCTAACATTCAAACTCAACTG	57.935	37.500	0.00	0.00	0.00	3.16
245	250	6.498304	CAACAGCTAACATTCAAACTCAACT	58.502	36.000	0.00	0.00	0.00	3.16
246	251	5.173854	GCAACAGCTAACATTCAAACTCAAC	59.826	40.000	0.00	0.00	0.00	3.18
247	252	5.163571	TGCAACAGCTAACATTCAAACTCAA	60.164	36.000	0.00	0.00	0.00	3.02
305	310	7.599998	GCTTTGTTTCTATCAATGGTGATGTTT	59.400	33.333	0.00	0.00	44.49	2.83
539	560	8.242729	TGTGATCACATCATAGTTCTAGTGAT	57.757	34.615	24.56	5.64	46.05	3.06
751	864	8.245195	ACCATAACTCAAAAGTGTAAATTGGT	57.755	30.769	0.00	0.00	35.36	3.67
876	996	6.438763	GCATAACAGTATTTGGCATAAGACC	58.561	40.000	0.00	0.00	0.00	3.85
878	998	5.820423	ACGCATAACAGTATTTGGCATAAGA	59.180	36.000	0.00	0.00	0.00	2.10
918	1042	5.614324	TGATTGAGGTTATCTGTACCCTG	57.386	43.478	0.00	0.00	36.27	4.45
919	1043	6.146760	AGATGATTGAGGTTATCTGTACCCT	58.853	40.000	0.00	0.00	36.27	4.34
1139	1269	1.264020	TGTCGAGCATGAACTTGTTGC	59.736	47.619	0.00	0.00	36.63	4.17
1309	1439	3.064324	GCCATCACAGGTGCCCAC	61.064	66.667	0.00	0.00	0.00	4.61
1411	1541	1.667154	CCCTCTGACGAAGGCGATGA	61.667	60.000	0.00	0.00	41.64	2.92
1551	1693	0.591741	CTGACGGCCGACTAACGATC	60.592	60.000	35.90	17.03	45.77	3.69
1555	1697	0.731855	GACACTGACGGCCGACTAAC	60.732	60.000	35.90	16.97	0.00	2.34
1875	2017	7.667043	TGTCTTCATCGCTAACAAGTTAATT	57.333	32.000	0.00	0.00	0.00	1.40
1986	2140	3.247411	TGTCACAGTGCAACATAAAGTCG	59.753	43.478	0.00	0.00	41.43	4.18
2258	2424	9.601217	AGCCATATAAAGTGTTTAGTTCTACAG	57.399	33.333	0.00	0.00	0.00	2.74
2259	2425	9.378551	CAGCCATATAAAGTGTTTAGTTCTACA	57.621	33.333	0.00	0.00	0.00	2.74
2313	2479	3.933332	GGAGCTTAAGATAGCACAAACGT	59.067	43.478	6.67	0.00	43.68	3.99
2329	2495	1.737029	CGACACATCGTGATGGAGCTT	60.737	52.381	13.95	0.00	43.66	3.74
2747	3006	0.030235	GAAAACCAACCTGCACGACC	59.970	55.000	0.00	0.00	0.00	4.79
2806	3164	8.628882	AACCAAAGTGATTCTAAAAAGAAACG	57.371	30.769	0.00	0.00	0.00	3.60
2912	3271	0.602905	GTAGAACGCCAACAGCCAGT	60.603	55.000	0.00	0.00	38.78	4.00
2936	3295	4.869297	CACCTTCAGATCTTAGCACAAGAG	59.131	45.833	0.00	0.00	0.00	2.85
2937	3296	4.528206	TCACCTTCAGATCTTAGCACAAGA	59.472	41.667	0.00	3.55	0.00	3.02
3021	3380	1.208165	ATCTTTCCAGGTTCCCGGCT	61.208	55.000	0.00	0.00	0.00	5.52
3136	3531	6.481644	GTGCAACCATTTCCAGAAAAACATTA	59.518	34.615	0.00	0.00	33.56	1.90
3146	3541	0.675083	TGCTGTGCAACCATTTCCAG	59.325	50.000	0.00	0.00	34.76	3.86
3147	3542	1.001068	CATGCTGTGCAACCATTTCCA	59.999	47.619	0.00	0.00	43.62	3.53
3148	3543	1.001181	ACATGCTGTGCAACCATTTCC	59.999	47.619	0.00	0.00	43.62	3.13
3149	3544	2.443887	ACATGCTGTGCAACCATTTC	57.556	45.000	0.00	0.00	43.62	2.17
3150	3545	2.914695	AACATGCTGTGCAACCATTT	57.085	40.000	0.00	0.00	43.62	2.32

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.