AutoCloner

Multiple sequence alignment - TraesCS1B01G434700

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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	TraesCS1B01G434700	chr1B	100.000	2267	0	0	1	2267	658968182	658970448	0.000000e+00	4187.0
1	TraesCS1B01G434700	chr1B	88.622	1995	105	44	214	2143	659072847	659074784	0.000000e+00	2314.0
2	TraesCS1B01G434700	chr1B	88.725	1898	98	41	449	2261	659033250	659035116	0.000000e+00	2213.0
3	TraesCS1B01G434700	chr1B	90.814	1633	80	24	685	2256	659294395	659296018	0.000000e+00	2121.0
4	TraesCS1B01G434700	chr1B	89.020	1357	61	31	847	2150	659285893	659287214	0.000000e+00	1600.0
5	TraesCS1B01G434700	chr1B	99.175	848	7	0	1420	2267	659003184	659004031	0.000000e+00	1528.0
6	TraesCS1B01G434700	chr1B	91.089	606	29	4	849	1429	659002553	659003158	0.000000e+00	797.0
7	TraesCS1B01G434700	chr1B	87.007	608	45	15	214	804	659181762	659182352	0.000000e+00	654.0
8	TraesCS1B01G434700	chr1B	85.759	632	68	8	1638	2259	659327172	659327791	0.000000e+00	649.0
9	TraesCS1B01G434700	chr1B	86.557	610	46	16	214	804	659285303	659285895	6.830000e-180	640.0
10	TraesCS1B01G434700	chr1B	87.845	543	46	11	847	1374	659182350	659182887	8.900000e-174	619.0
11	TraesCS1B01G434700	chr1B	84.186	645	49	20	756	1371	659316613	659317233	5.430000e-161	577.0
12	TraesCS1B01G434700	chr1B	79.621	898	95	36	1424	2259	659317674	659318545	4.230000e-157	564.0
13	TraesCS1B01G434700	chr1B	86.728	437	31	15	214	639	659293973	659294393	5.710000e-126	460.0
14	TraesCS1B01G434700	chr1B	97.328	262	6	1	2007	2267	659190872	659191133	5.750000e-121	444.0
15	TraesCS1B01G434700	chr1B	96.947	262	7	1	2007	2267	659083060	659083321	2.670000e-119	438.0
16	TraesCS1B01G434700	chr1B	95.288	191	9	0	1	191	659072430	659072620	1.020000e-78	303.0
17	TraesCS1B01G434700	chr1B	85.859	198	20	8	1	191	659293587	659293783	1.060000e-48	204.0
18	TraesCS1B01G434700	chr1B	85.000	140	10	6	54	191	659284983	659285113	5.080000e-27	132.0
19	TraesCS1B01G434700	chr1B	83.478	115	8	6	79	191	659181467	659181572	1.850000e-16	97.1
20	TraesCS1B01G434700	chr1B	100.000	29	0	0	188	216	646055237	646055209	1.000000e-03	54.7
21	TraesCS1B01G434700	chr1D	87.846	1119	72	25	233	1324	473960472	473961553	0.000000e+00	1254.0
22	TraesCS1B01G434700	chr1D	86.932	880	41	28	1420	2267	473961667	473962504	0.000000e+00	920.0
23	TraesCS1B01G434700	chr1D	83.281	634	72	18	1638	2259	473966754	473967365	9.150000e-154	553.0
24	TraesCS1B01G434700	chr1D	90.524	401	30	4	975	1374	473879802	473880195	7.170000e-145	523.0
25	TraesCS1B01G434700	chr1D	84.557	531	64	9	1737	2259	473998118	473998638	5.590000e-141	510.0
26	TraesCS1B01G434700	chr1D	87.398	246	18	6	1638	1883	473997879	473998111	1.030000e-68	270.0
27	TraesCS1B01G434700	chr1D	88.288	111	6	4	1422	1532	473880298	473880401	2.360000e-25	126.0
28	TraesCS1B01G434700	chr1D	80.368	163	14	14	1	155	473964935	473965087	8.560000e-20	108.0
29	TraesCS1B01G434700	chr1D	87.234	94	5	3	1343	1429	473961549	473961642	1.430000e-17	100.0
30	TraesCS1B01G434700	chr1D	100.000	32	0	0	188	219	432405227	432405258	2.430000e-05	60.2
31	TraesCS1B01G434700	chr1D	100.000	31	0	0	184	214	176391975	176392005	8.750000e-05	58.4
32	TraesCS1B01G434700	chr1A	87.829	797	60	17	603	1374	568327615	568328399	0.000000e+00	900.0
33	TraesCS1B01G434700	chr1A	91.554	592	35	10	853	1429	568265903	568266494	0.000000e+00	802.0
34	TraesCS1B01G434700	chr1A	86.371	631	63	9	1640	2259	568399455	568400073	0.000000e+00	667.0
35	TraesCS1B01G434700	chr1A	92.809	445	31	1	1610	2053	568266926	568267370	0.000000e+00	643.0
36	TraesCS1B01G434700	chr1A	85.786	598	50	14	233	818	568265325	568265899	3.220000e-168	601.0
37	TraesCS1B01G434700	chr1A	91.811	403	30	2	975	1374	568388967	568389369	1.970000e-155	558.0
38	TraesCS1B01G434700	chr1A	82.547	636	74	20	1638	2259	568384182	568384794	1.990000e-145	525.0
39	TraesCS1B01G434700	chr1A	84.749	459	33	14	214	660	568327170	568327603	2.080000e-115	425.0
40	TraesCS1B01G434700	chr1A	94.815	135	1	1	1	135	568326883	568327011	2.950000e-49	206.0
41	TraesCS1B01G434700	chr1A	91.156	147	5	3	1420	1565	568266516	568266655	2.300000e-45	193.0
42	TraesCS1B01G434700	chr1A	91.964	112	5	1	1420	1531	568383877	568383984	1.080000e-33	154.0
43	TraesCS1B01G434700	chr1A	92.308	78	6	0	32	109	568118360	568118437	6.620000e-21	111.0
44	TraesCS1B01G434700	chr1A	83.178	107	13	5	1	107	568382241	568382342	2.400000e-15	93.5
45	TraesCS1B01G434700	chr1A	88.732	71	5	1	759	826	568388151	568388221	1.440000e-12	84.2
46	TraesCS1B01G434700	chr3A	100.000	30	0	0	187	216	697283694	697283665	3.150000e-04	56.5
47	TraesCS1B01G434700	chr7D	100.000	29	0	0	188	216	618809241	618809213	1.000000e-03	54.7
48	TraesCS1B01G434700	chr7A	100.000	29	0	0	188	216	22166091	22166119	1.000000e-03	54.7
49	TraesCS1B01G434700	chr7A	100.000	29	0	0	188	216	97021651	97021679	1.000000e-03	54.7
50	TraesCS1B01G434700	chr4D	100.000	29	0	0	188	216	486315544	486315516	1.000000e-03	54.7
51	TraesCS1B01G434700	chr2D	100.000	29	0	0	188	216	619479372	619479400	1.000000e-03	54.7

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	TraesCS1B01G434700	chr1B	658968182	658970448	2266	False	4187.000000	4187	100.000000	1	2267	1	chr1B.!!$F1	2266
1	TraesCS1B01G434700	chr1B	659033250	659035116	1866	False	2213.000000	2213	88.725000	449	2261	1	chr1B.!!$F2	1812
2	TraesCS1B01G434700	chr1B	659072430	659074784	2354	False	1308.500000	2314	91.955000	1	2143	2	chr1B.!!$F7	2142
3	TraesCS1B01G434700	chr1B	659002553	659004031	1478	False	1162.500000	1528	95.132000	849	2267	2	chr1B.!!$F6	1418
4	TraesCS1B01G434700	chr1B	659293587	659296018	2431	False	928.333333	2121	87.800333	1	2256	3	chr1B.!!$F10	2255
5	TraesCS1B01G434700	chr1B	659284983	659287214	2231	False	790.666667	1600	86.859000	54	2150	3	chr1B.!!$F9	2096
6	TraesCS1B01G434700	chr1B	659327172	659327791	619	False	649.000000	649	85.759000	1638	2259	1	chr1B.!!$F5	621
7	TraesCS1B01G434700	chr1B	659316613	659318545	1932	False	570.500000	577	81.903500	756	2259	2	chr1B.!!$F11	1503
8	TraesCS1B01G434700	chr1B	659181467	659182887	1420	False	456.700000	654	86.110000	79	1374	3	chr1B.!!$F8	1295
9	TraesCS1B01G434700	chr1D	473960472	473967365	6893	False	587.000000	1254	85.132200	1	2267	5	chr1D.!!$F4	2266
10	TraesCS1B01G434700	chr1D	473997879	473998638	759	False	390.000000	510	85.977500	1638	2259	2	chr1D.!!$F5	621
11	TraesCS1B01G434700	chr1D	473879802	473880401	599	False	324.500000	523	89.406000	975	1532	2	chr1D.!!$F3	557
12	TraesCS1B01G434700	chr1A	568399455	568400073	618	False	667.000000	667	86.371000	1640	2259	1	chr1A.!!$F2	619
13	TraesCS1B01G434700	chr1A	568265325	568267370	2045	False	559.750000	802	90.326250	233	2053	4	chr1A.!!$F3	1820
14	TraesCS1B01G434700	chr1A	568326883	568328399	1516	False	510.333333	900	89.131000	1	1374	3	chr1A.!!$F4	1373
15	TraesCS1B01G434700	chr1A	568382241	568389369	7128	False	282.940000	558	87.646400	1	2259	5	chr1A.!!$F5	2258

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
597	1185	0.318445	CGGATTTAGCTACGACGGGG	60.318	60.0	0.0	0.0	0.0	5.73	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1834	3384	6.569179	AACCATACTTTGTCCACACAATAC	57.431	37.5	0.0	0.0	42.28	1.89	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
109	115	1.225704	GGAGCAAGGCCAGCTACAT	59.774	57.895	23.38	3.74	42.63	2.29
155	164	1.304381	GAGCTGGAACCAATGGCCA	60.304	57.895	8.56	8.56	0.00	5.36
156	165	0.685458	GAGCTGGAACCAATGGCCAT	60.685	55.000	14.09	14.09	0.00	4.40
191	202	3.449018	TCCAGATTCCAGAGCACTTACTC	59.551	47.826	0.00	0.00	36.91	2.59
193	204	2.769095	AGATTCCAGAGCACTTACTCCC	59.231	50.000	0.00	0.00	37.39	4.30
195	206	1.853963	TCCAGAGCACTTACTCCCTC	58.146	55.000	0.00	0.00	37.39	4.30
197	208	0.457851	CAGAGCACTTACTCCCTCCG	59.542	60.000	0.00	0.00	37.39	4.63
199	210	0.456628	GAGCACTTACTCCCTCCGTC	59.543	60.000	0.00	0.00	0.00	4.79
200	211	0.971447	AGCACTTACTCCCTCCGTCC	60.971	60.000	0.00	0.00	0.00	4.79
201	212	0.971447	GCACTTACTCCCTCCGTCCT	60.971	60.000	0.00	0.00	0.00	3.85
202	213	1.684248	GCACTTACTCCCTCCGTCCTA	60.684	57.143	0.00	0.00	0.00	2.94
203	214	2.946785	CACTTACTCCCTCCGTCCTAT	58.053	52.381	0.00	0.00	0.00	2.57
204	215	3.749954	GCACTTACTCCCTCCGTCCTATA	60.750	52.174	0.00	0.00	0.00	1.31
205	216	4.467769	CACTTACTCCCTCCGTCCTATAA	58.532	47.826	0.00	0.00	0.00	0.98
207	218	6.243900	CACTTACTCCCTCCGTCCTATAATA	58.756	44.000	0.00	0.00	0.00	0.98
209	220	8.051535	CACTTACTCCCTCCGTCCTATAATATA	58.948	40.741	0.00	0.00	0.00	0.86
211	222	9.122779	CTTACTCCCTCCGTCCTATAATATAAG	57.877	40.741	0.00	0.00	0.00	1.73
371	910	7.527457	AGTTCAAGTTCAAAAACAGTACAGAC	58.473	34.615	0.00	0.00	37.88	3.51
429	970	4.754322	TGAATAGTGACGAATAGCAAGCA	58.246	39.130	0.00	0.00	0.00	3.91
436	979	0.379669	CGAATAGCAAGCAAGGGCAG	59.620	55.000	0.00	0.00	44.61	4.85
437	980	1.755179	GAATAGCAAGCAAGGGCAGA	58.245	50.000	0.00	0.00	44.61	4.26
439	982	2.449137	ATAGCAAGCAAGGGCAGAAT	57.551	45.000	0.00	0.00	44.61	2.40
440	983	3.582998	ATAGCAAGCAAGGGCAGAATA	57.417	42.857	0.00	0.00	44.61	1.75
441	984	1.467920	AGCAAGCAAGGGCAGAATAC	58.532	50.000	0.00	0.00	44.61	1.89
579	1166	4.142902	ACATCAAACCGAAGCACTAATTCG	60.143	41.667	1.29	1.29	46.94	3.34
596	1184	0.664761	TCGGATTTAGCTACGACGGG	59.335	55.000	0.00	0.00	0.00	5.28
597	1185	0.318445	CGGATTTAGCTACGACGGGG	60.318	60.000	0.00	0.00	0.00	5.73
620	1216	6.592607	GGGTTCGAGAGTTATGTGTTAATTCA	59.407	38.462	0.00	0.00	30.90	2.57
621	1217	7.201530	GGGTTCGAGAGTTATGTGTTAATTCAG	60.202	40.741	0.00	0.00	30.90	3.02
712	1375	5.420725	AATGGACCCAAAAGGCTTAATTC	57.579	39.130	0.00	0.00	40.58	2.17
764	1450	7.007116	TCATGTCTGATACTGATACCTAGCTT	58.993	38.462	0.00	0.00	0.00	3.74
825	1521	2.224769	CCTTTTAACCCACAGCCAGAGA	60.225	50.000	0.00	0.00	0.00	3.10
826	1522	2.859165	TTTAACCCACAGCCAGAGAG	57.141	50.000	0.00	0.00	0.00	3.20
919	1632	1.215423	ACCAAACCACCAGAGCTTCTT	59.785	47.619	0.00	0.00	0.00	2.52
1019	1756	2.126580	GTCTTCCGGGTCGTCGTG	60.127	66.667	0.00	0.00	0.00	4.35
1137	1874	2.121963	TGGGAGAAGGTGGCCAGT	60.122	61.111	5.11	0.00	0.00	4.00
1391	2176	2.031333	GGGACTGCGTCGTTAGTATAGG	60.031	54.545	4.62	0.00	32.65	2.57
1834	3384	4.848357	ACAGGAAGGAATGGAGTATTGTG	58.152	43.478	0.00	0.00	0.00	3.33

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
109	115	7.173562	GCTCAGTTATTACACTAGCTAGCTAGA	59.826	40.741	43.93	28.77	46.56	2.43
155	164	5.545335	TGGAATCTGGATGTATGCACTCTAT	59.455	40.000	0.00	0.00	0.00	1.98
156	165	4.901250	TGGAATCTGGATGTATGCACTCTA	59.099	41.667	0.00	0.00	0.00	2.43
191	202	6.183360	GCACTCTTATATTATAGGACGGAGGG	60.183	46.154	0.00	0.00	0.00	4.30
193	204	6.183360	GGGCACTCTTATATTATAGGACGGAG	60.183	46.154	0.00	0.00	0.00	4.63
195	206	5.421056	TGGGCACTCTTATATTATAGGACGG	59.579	44.000	0.00	0.00	0.00	4.79
197	208	7.097834	GTGTGGGCACTCTTATATTATAGGAC	58.902	42.308	0.00	0.00	42.13	3.85
199	210	6.407202	GGTGTGGGCACTCTTATATTATAGG	58.593	44.000	0.00	0.00	44.65	2.57
200	211	6.013725	TGGGTGTGGGCACTCTTATATTATAG	60.014	42.308	0.00	0.00	46.03	1.31
201	212	5.847265	TGGGTGTGGGCACTCTTATATTATA	59.153	40.000	0.00	0.00	46.03	0.98
202	213	4.663120	TGGGTGTGGGCACTCTTATATTAT	59.337	41.667	0.00	0.00	46.03	1.28
203	214	4.041464	TGGGTGTGGGCACTCTTATATTA	58.959	43.478	0.00	0.00	46.03	0.98
204	215	2.849943	TGGGTGTGGGCACTCTTATATT	59.150	45.455	0.00	0.00	46.03	1.28
205	216	2.439507	CTGGGTGTGGGCACTCTTATAT	59.560	50.000	0.00	0.00	46.03	0.86
207	218	0.620556	CTGGGTGTGGGCACTCTTAT	59.379	55.000	0.00	0.00	46.03	1.73
209	220	2.839098	CTGGGTGTGGGCACTCTT	59.161	61.111	0.00	0.00	46.03	2.85
231	453	2.558795	CAGGTATAGATGGAGGTGACCG	59.441	54.545	0.00	0.00	0.00	4.79
371	910	5.404466	TTTTCCCATGCCTTGTAAATGAG	57.596	39.130	0.00	0.00	0.00	2.90
417	958	0.379669	CTGCCCTTGCTTGCTATTCG	59.620	55.000	0.00	0.00	38.71	3.34
429	970	2.189521	CGCGGGTATTCTGCCCTT	59.810	61.111	0.00	0.00	44.74	3.95
436	979	4.218478	GTGTGCGCGCGGGTATTC	62.218	66.667	33.06	14.22	0.00	1.75
445	988	2.099254	TTTGTGTGTGTGTGCGCG	59.901	55.556	0.00	0.00	0.00	6.86
446	989	0.525242	ATGTTTGTGTGTGTGTGCGC	60.525	50.000	0.00	0.00	0.00	6.09
479	1036	4.713321	AGCTGCATCACAAAGGGAAATTAT	59.287	37.500	1.02	0.00	0.00	1.28
493	1050	0.620030	TTCCTGGCTAAGCTGCATCA	59.380	50.000	1.02	0.00	34.04	3.07
579	1166	0.749049	ACCCCGTCGTAGCTAAATCC	59.251	55.000	0.00	0.00	0.00	3.01
596	1184	7.544566	TCTGAATTAACACATAACTCTCGAACC	59.455	37.037	0.00	0.00	0.00	3.62
597	1185	8.462143	TCTGAATTAACACATAACTCTCGAAC	57.538	34.615	0.00	0.00	0.00	3.95
620	1216	7.671302	ACACTACACACATCAACTTAATCTCT	58.329	34.615	0.00	0.00	0.00	3.10
621	1217	7.891183	ACACTACACACATCAACTTAATCTC	57.109	36.000	0.00	0.00	0.00	2.75
712	1375	1.972872	AAGTGACAGCCTGTTTGAGG	58.027	50.000	0.00	0.00	46.13	3.86
764	1450	2.289444	CCAGGTTCTCGCAGGTTTTCTA	60.289	50.000	0.00	0.00	0.00	2.10
825	1521	0.969917	AGCGTGCCATGTCTCTCTCT	60.970	55.000	0.00	0.00	0.00	3.10
826	1522	0.527385	GAGCGTGCCATGTCTCTCTC	60.527	60.000	0.00	0.00	0.00	3.20
919	1632	4.348168	AGTTAGGAAGTCCTTTGCTCTTGA	59.652	41.667	4.91	0.00	46.09	3.02
939	1652	1.214305	TGCTGGGGGCTATGGAAGTT	61.214	55.000	0.00	0.00	42.39	2.66
1083	1820	3.528370	CCGTAGTAGGCCAGCGCT	61.528	66.667	2.64	2.64	34.44	5.92
1350	2110	2.816087	CCAGCAAGCAGACAAATACAGT	59.184	45.455	0.00	0.00	0.00	3.55
1391	2176	4.040445	TGTGCCTTTTGAGTTAAAGCAC	57.960	40.909	14.26	14.26	39.64	4.40
1834	3384	6.569179	AACCATACTTTGTCCACACAATAC	57.431	37.500	0.00	0.00	42.28	1.89

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.