AutoCloner

Multiple sequence alignment - TraesCS4B01G096300

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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	TraesCS4B01G096300	chr4B	100.000	2549	0	0	1	2549	100012187	100009639	0.000000e+00	4708
1	TraesCS4B01G096300	chr4B	96.068	1653	56	6	901	2549	656537850	656536203	0.000000e+00	2684
2	TraesCS4B01G096300	chr4B	95.431	788	33	3	101	886	74702324	74703110	0.000000e+00	1253
3	TraesCS4B01G096300	chr4B	95.426	787	31	5	101	884	100001405	100000621	0.000000e+00	1249
4	TraesCS4B01G096300	chr4B	90.146	893	79	8	1	886	416370662	416369772	0.000000e+00	1153
5	TraesCS4B01G096300	chr5B	96.249	1653	55	5	901	2549	518021607	518019958	0.000000e+00	2702
6	TraesCS4B01G096300	chr5B	94.804	789	34	5	101	886	7832489	7833273	0.000000e+00	1223
7	TraesCS4B01G096300	chr5B	82.594	293	32	17	7	295	350610969	350610692	9.110000e-60	241
8	TraesCS4B01G096300	chr2B	96.010	1654	56	6	901	2549	666075441	666073793	0.000000e+00	2680
9	TraesCS4B01G096300	chr2B	94.550	789	38	4	101	886	481616347	481615561	0.000000e+00	1214
10	TraesCS4B01G096300	chr3B	95.949	1654	59	3	901	2549	723101861	723103511	0.000000e+00	2676
11	TraesCS4B01G096300	chr3B	95.048	1656	66	6	901	2549	804661364	804663010	0.000000e+00	2590
12	TraesCS4B01G096300	chr3B	94.571	792	34	7	99	886	718305033	718305819	0.000000e+00	1216
13	TraesCS4B01G096300	chr1B	95.952	1655	58	8	901	2549	575860024	575858373	0.000000e+00	2676
14	TraesCS4B01G096300	chr1B	94.810	790	34	6	100	886	70147375	70148160	0.000000e+00	1225
15	TraesCS4B01G096300	chr1B	90.428	888	71	13	7	886	237329516	237328635	0.000000e+00	1157
16	TraesCS4B01G096300	chr1B	91.096	146	9	3	1	143	468026769	468026913	7.200000e-46	195
17	TraesCS4B01G096300	chr7B	95.681	1644	57	8	912	2549	503449843	503451478	0.000000e+00	2630
18	TraesCS4B01G096300	chr7B	95.674	1618	57	8	937	2549	54520360	54518751	0.000000e+00	2588
19	TraesCS4B01G096300	chr2D	94.715	1665	62	11	901	2549	64509030	64510684	0.000000e+00	2564
20	TraesCS4B01G096300	chr2D	88.372	172	13	5	1	167	63637016	63637185	1.550000e-47	200
21	TraesCS4B01G096300	chr4A	95.311	789	33	4	101	886	661161126	661160339	0.000000e+00	1249
22	TraesCS4B01G096300	chr3D	88.757	169	16	3	1	167	273990969	273990802	1.200000e-48	204
23	TraesCS4B01G096300	chr6B	91.156	147	11	1	7	153	386201553	386201409	5.560000e-47	198
24	TraesCS4B01G096300	chr5A	89.744	156	11	4	1	153	382705318	382705165	7.200000e-46	195
25	TraesCS4B01G096300	chr3A	82.743	226	25	14	3	219	115024627	115024407	3.350000e-44	189

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	TraesCS4B01G096300	chr4B	100009639	100012187	2548	True	4708	4708	100.000	1	2549	1	chr4B.!!$R2	2548
1	TraesCS4B01G096300	chr4B	656536203	656537850	1647	True	2684	2684	96.068	901	2549	1	chr4B.!!$R4	1648
2	TraesCS4B01G096300	chr4B	74702324	74703110	786	False	1253	1253	95.431	101	886	1	chr4B.!!$F1	785
3	TraesCS4B01G096300	chr4B	100000621	100001405	784	True	1249	1249	95.426	101	884	1	chr4B.!!$R1	783
4	TraesCS4B01G096300	chr4B	416369772	416370662	890	True	1153	1153	90.146	1	886	1	chr4B.!!$R3	885
5	TraesCS4B01G096300	chr5B	518019958	518021607	1649	True	2702	2702	96.249	901	2549	1	chr5B.!!$R2	1648
6	TraesCS4B01G096300	chr5B	7832489	7833273	784	False	1223	1223	94.804	101	886	1	chr5B.!!$F1	785
7	TraesCS4B01G096300	chr2B	666073793	666075441	1648	True	2680	2680	96.010	901	2549	1	chr2B.!!$R2	1648
8	TraesCS4B01G096300	chr2B	481615561	481616347	786	True	1214	1214	94.550	101	886	1	chr2B.!!$R1	785
9	TraesCS4B01G096300	chr3B	723101861	723103511	1650	False	2676	2676	95.949	901	2549	1	chr3B.!!$F2	1648
10	TraesCS4B01G096300	chr3B	804661364	804663010	1646	False	2590	2590	95.048	901	2549	1	chr3B.!!$F3	1648
11	TraesCS4B01G096300	chr3B	718305033	718305819	786	False	1216	1216	94.571	99	886	1	chr3B.!!$F1	787
12	TraesCS4B01G096300	chr1B	575858373	575860024	1651	True	2676	2676	95.952	901	2549	1	chr1B.!!$R2	1648
13	TraesCS4B01G096300	chr1B	70147375	70148160	785	False	1225	1225	94.810	100	886	1	chr1B.!!$F1	786
14	TraesCS4B01G096300	chr1B	237328635	237329516	881	True	1157	1157	90.428	7	886	1	chr1B.!!$R1	879
15	TraesCS4B01G096300	chr7B	503449843	503451478	1635	False	2630	2630	95.681	912	2549	1	chr7B.!!$F1	1637
16	TraesCS4B01G096300	chr7B	54518751	54520360	1609	True	2588	2588	95.674	937	2549	1	chr7B.!!$R1	1612
17	TraesCS4B01G096300	chr2D	64509030	64510684	1654	False	2564	2564	94.715	901	2549	1	chr2D.!!$F2	1648
18	TraesCS4B01G096300	chr4A	661160339	661161126	787	True	1249	1249	95.311	101	886	1	chr4A.!!$R1	785

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
890	907	0.034896	TTGCAAGTCTCTTCGGGTCC	59.965	55.0	0.0	0.0	0.0	4.46	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2031	2058	0.466124	GCCATCTCTCCTAGCGGTTT	59.534	55.0	0.0	0.0	0.0	3.27	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
83	84	5.751142	AAAGGAGGCCTTAATATCCCTTT	57.249	39.130	21.11	21.11	43.92	3.11
159	161	9.502091	TGTTCCATGCTATTATATTACCTGTTC	57.498	33.333	0.00	0.00	0.00	3.18
167	169	9.155975	GCTATTATATTACCTGTTCTGGATGTG	57.844	37.037	2.86	0.00	0.00	3.21
475	486	7.336427	CCGACGTACTTCTTCCTCCTATATAAT	59.664	40.741	0.00	0.00	0.00	1.28
646	657	0.613260	CCCCTCCGATGAGTTGTGAA	59.387	55.000	0.00	0.00	36.86	3.18
681	693	7.016268	ACAGACATTCGGGTCCATAGTTATTAT	59.984	37.037	0.00	0.00	38.59	1.28
788	801	1.604438	CGGTGTGTTTGTCGAGATCCA	60.604	52.381	0.00	0.00	0.00	3.41
886	903	4.932200	AGTTATCTTTGCAAGTCTCTTCGG	59.068	41.667	0.00	0.00	0.00	4.30
887	904	2.169832	TCTTTGCAAGTCTCTTCGGG	57.830	50.000	0.00	0.00	0.00	5.14
888	905	1.416401	TCTTTGCAAGTCTCTTCGGGT	59.584	47.619	0.00	0.00	0.00	5.28
889	906	1.801178	CTTTGCAAGTCTCTTCGGGTC	59.199	52.381	0.00	0.00	0.00	4.46
890	907	0.034896	TTGCAAGTCTCTTCGGGTCC	59.965	55.000	0.00	0.00	0.00	4.46
891	908	1.118965	TGCAAGTCTCTTCGGGTCCA	61.119	55.000	0.00	0.00	0.00	4.02
892	909	0.250513	GCAAGTCTCTTCGGGTCCAT	59.749	55.000	0.00	0.00	0.00	3.41
893	910	1.480954	GCAAGTCTCTTCGGGTCCATA	59.519	52.381	0.00	0.00	0.00	2.74
894	911	2.482142	GCAAGTCTCTTCGGGTCCATAG	60.482	54.545	0.00	0.00	0.00	2.23
895	912	2.761208	CAAGTCTCTTCGGGTCCATAGT	59.239	50.000	0.00	0.00	0.00	2.12
896	913	3.103080	AGTCTCTTCGGGTCCATAGTT	57.897	47.619	0.00	0.00	0.00	2.24
897	914	4.246712	AGTCTCTTCGGGTCCATAGTTA	57.753	45.455	0.00	0.00	0.00	2.24
898	915	4.805744	AGTCTCTTCGGGTCCATAGTTAT	58.194	43.478	0.00	0.00	0.00	1.89
899	916	5.209659	AGTCTCTTCGGGTCCATAGTTATT	58.790	41.667	0.00	0.00	0.00	1.40
933	950	1.153269	GGAAGCTAGCTGTGGAGGC	60.153	63.158	20.16	2.06	0.00	4.70
953	970	3.771160	CGGCGGTGGGAAGCTAGT	61.771	66.667	0.00	0.00	0.00	2.57
988	1005	1.007336	GGCGTTGAGATCACGTTCGT	61.007	55.000	6.02	0.00	0.00	3.85
1003	1020	0.458543	TTCGTCTTCGAGCTCCATGC	60.459	55.000	8.47	0.00	46.81	4.06
1063	1082	2.494445	CGCGTGTGGAGATGCCTA	59.506	61.111	0.00	0.00	37.63	3.93
1251	1270	1.913778	TCATGCAGGTGACATGCTTT	58.086	45.000	23.05	8.04	43.71	3.51
1321	1340	4.660168	AGAAGAGCATGAAGAATGGTTGT	58.340	39.130	0.00	0.00	46.95	3.32
1329	1348	2.629137	TGAAGAATGGTTGTGCATGCTT	59.371	40.909	20.33	2.06	29.75	3.91
1351	1370	1.743623	CGAACCATAGTGGCCGCAA	60.744	57.895	20.59	0.00	42.67	4.85
1538	1557	8.637986	ACTGGTTGTAATGTTGAAAATGTATGT	58.362	29.630	0.00	0.00	0.00	2.29
1724	1749	7.548967	TGATCAATGAAATGCAGCTAATGAAA	58.451	30.769	0.00	0.00	0.00	2.69
2031	2058	2.046314	GTTTAGGGCTGCGCTGGA	60.046	61.111	27.01	13.86	0.00	3.86
2141	2169	2.226437	GTGAGACCGTGAATGTTTGCAT	59.774	45.455	0.00	0.00	36.80	3.96
2285	2318	7.375834	CACTTGGTTTAGGATTTAAAGGGAAC	58.624	38.462	0.00	0.00	0.00	3.62
2386	2425	2.693069	ACAAGTTCTCGAGCTTCATGG	58.307	47.619	7.81	0.00	29.11	3.66
2427	2467	9.328845	GAAATTATATGTTTGGGCATGAACATT	57.671	29.630	13.75	6.78	42.18	2.71
2484	2524	9.502091	AACTTAGATAAGATGCAACACAAGTAA	57.498	29.630	6.61	0.00	37.08	2.24
2520	2560	5.231568	GGATAATAAGTTCACGGACAGTTCG	59.768	44.000	0.00	0.00	0.00	3.95

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
47	48	4.141779	GGCCTCCTTTTAATAGAGAACCGA	60.142	45.833	0.00	0.00	0.00	4.69
159	161	6.469782	AAAATAAAGCCCATACACATCCAG	57.530	37.500	0.00	0.00	0.00	3.86
197	199	5.936372	CCAGTTAGTAGGTTAGTCCCAAAAC	59.064	44.000	0.00	0.00	36.75	2.43
475	486	4.292571	TGGATGTTTTTGGGGTATGTAGGA	59.707	41.667	0.00	0.00	0.00	2.94
646	657	5.416271	ACCCGAATGTCTGTGTAAACTAT	57.584	39.130	0.00	0.00	0.00	2.12
681	693	6.865834	AAAAGAGAGAAGAAGCCATCTAGA	57.134	37.500	0.00	0.00	37.42	2.43
788	801	8.137745	ACTTGATCATAAACCCACAATTCATT	57.862	30.769	0.00	0.00	0.00	2.57
886	903	3.979495	CGTCGTGCTAATAACTATGGACC	59.021	47.826	0.00	0.00	0.00	4.46
887	904	4.674211	GTCGTCGTGCTAATAACTATGGAC	59.326	45.833	0.00	0.00	0.00	4.02
888	905	4.553351	CGTCGTCGTGCTAATAACTATGGA	60.553	45.833	0.00	0.00	0.00	3.41
889	906	3.662645	CGTCGTCGTGCTAATAACTATGG	59.337	47.826	0.00	0.00	0.00	2.74
890	907	3.662645	CCGTCGTCGTGCTAATAACTATG	59.337	47.826	0.71	0.00	35.01	2.23
891	908	3.313526	ACCGTCGTCGTGCTAATAACTAT	59.686	43.478	0.71	0.00	35.01	2.12
892	909	2.677836	ACCGTCGTCGTGCTAATAACTA	59.322	45.455	0.71	0.00	35.01	2.24
893	910	1.470098	ACCGTCGTCGTGCTAATAACT	59.530	47.619	0.71	0.00	35.01	2.24
894	911	1.580704	CACCGTCGTCGTGCTAATAAC	59.419	52.381	0.71	0.00	35.01	1.89
895	912	1.467883	CCACCGTCGTCGTGCTAATAA	60.468	52.381	0.71	0.00	35.01	1.40
896	913	0.099259	CCACCGTCGTCGTGCTAATA	59.901	55.000	0.71	0.00	35.01	0.98
897	914	1.153901	CCACCGTCGTCGTGCTAAT	60.154	57.895	0.71	0.00	35.01	1.73
898	915	2.256158	CCACCGTCGTCGTGCTAA	59.744	61.111	0.71	0.00	35.01	3.09
899	916	3.740397	CCCACCGTCGTCGTGCTA	61.740	66.667	0.71	0.00	35.01	3.49
953	970	4.308458	CCGTCGTGCCCTCCACAA	62.308	66.667	0.00	0.00	44.91	3.33
988	1005	0.176680	GAAGGCATGGAGCTCGAAGA	59.823	55.000	7.83	0.00	44.79	2.87
1063	1082	2.341101	ACCGCGGACAGACGAAGAT	61.341	57.895	35.90	0.00	35.47	2.40
1251	1270	2.096268	CAGAGCATCGACGCAAAGAAAA	60.096	45.455	6.14	0.00	42.67	2.29
1260	1279	2.125552	TTGGCCAGAGCATCGACG	60.126	61.111	5.11	0.00	42.67	5.12
1321	1340	2.361104	GGTTCGGGGAAGCATGCA	60.361	61.111	21.98	0.00	39.49	3.96
1329	1348	2.372074	GGCCACTATGGTTCGGGGA	61.372	63.158	0.00	0.00	40.46	4.81
1351	1370	0.894184	TCTTCTTCCGGAGCTCGTGT	60.894	55.000	3.34	0.00	37.11	4.49
1538	1557	8.423349	CAAATTCCTCCATAATTCATGCCTTTA	58.577	33.333	0.00	0.00	32.84	1.85
1724	1749	6.897413	ACCTTAATTGTTTGGCTCTGGAATAT	59.103	34.615	0.00	0.00	0.00	1.28
1936	1962	6.484977	GTGCATTTTCCACCCTTCATTTTTAA	59.515	34.615	0.00	0.00	0.00	1.52
2031	2058	0.466124	GCCATCTCTCCTAGCGGTTT	59.534	55.000	0.00	0.00	0.00	3.27
2114	2142	6.037172	GCAAACATTCACGGTCTCACTATTAT	59.963	38.462	0.00	0.00	0.00	1.28
2115	2143	5.350365	GCAAACATTCACGGTCTCACTATTA	59.650	40.000	0.00	0.00	0.00	0.98
2141	2169	1.603678	GGAAAACCACTCTCACGCGTA	60.604	52.381	13.44	0.00	0.00	4.42
2285	2318	7.878477	AGTCATGAACTAACATGCAAATTTG	57.122	32.000	14.03	14.03	44.79	2.32
2365	2404	3.070018	CCATGAAGCTCGAGAACTTGTT	58.930	45.455	18.75	0.00	0.00	2.83
2386	2425	8.914011	ACATATAATTTCTTCCCTAAACCAAGC	58.086	33.333	0.00	0.00	0.00	4.01
2520	2560	1.061131	CATGTTTCGTCATGAGTCCGC	59.939	52.381	0.00	0.00	45.41	5.54

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.