AutoCloner

Multiple sequence alignment - TraesCS7B01G481700

Loading Multiple Alignment...

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	TraesCS7B01G481700	chr7B	100.000	2396	0	0	1	2396	738143659	738146054	0.000000e+00	4425.0
1	TraesCS7B01G481700	chr7A	92.973	925	60	4	1476	2396	712681056	712681979	0.000000e+00	1343.0
2	TraesCS7B01G481700	chr7A	91.775	924	64	10	1476	2396	22081057	22080143	0.000000e+00	1275.0
3	TraesCS7B01G481700	chr7A	100.000	30	0	0	1447	1476	728282702	728282731	3.330000e-04	56.5
4	TraesCS7B01G481700	chr2A	91.429	875	38	17	558	1403	561554891	561554025	0.000000e+00	1166.0
5	TraesCS7B01G481700	chr2A	89.531	554	29	14	1	526	561555544	561554992	0.000000e+00	675.0
6	TraesCS7B01G481700	chr2A	80.145	413	80	2	1477	1887	554021112	554021524	8.320000e-80	307.0
7	TraesCS7B01G481700	chr2A	97.619	42	1	0	514	555	561554968	561554927	3.300000e-09	73.1
8	TraesCS7B01G481700	chr2A	97.059	34	1	0	1342	1375	563919128	563919161	9.250000e-05	58.4
9	TraesCS7B01G481700	chr2D	91.166	883	39	20	558	1410	426944107	426944980	0.000000e+00	1162.0
10	TraesCS7B01G481700	chr2D	87.906	554	38	14	1	526	426943454	426944006	2.020000e-175	625.0
11	TraesCS7B01G481700	chr2D	97.222	36	1	0	1340	1375	424678722	424678687	7.150000e-06	62.1
12	TraesCS7B01G481700	chr2B	91.170	872	40	18	558	1400	503772381	503773244	0.000000e+00	1149.0
13	TraesCS7B01G481700	chr2B	87.726	554	39	14	1	526	503771728	503772280	9.410000e-174	619.0
14	TraesCS7B01G481700	chr2B	97.561	41	1	0	515	555	503772305	503772345	1.190000e-08	71.3
15	TraesCS7B01G481700	chr2B	97.222	36	1	0	1340	1375	499560880	499560845	7.150000e-06	62.1
16	TraesCS7B01G481700	chr1D	88.095	924	106	4	1476	2396	483473670	483474592	0.000000e+00	1094.0
17	TraesCS7B01G481700	chr1B	87.657	875	101	5	1494	2364	673713988	673714859	0.000000e+00	1011.0
18	TraesCS7B01G481700	chr4A	87.069	232	27	2	1477	1707	744510935	744511164	2.360000e-65	259.0

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	TraesCS7B01G481700	chr7B	738143659	738146054	2395	False	4425.000000	4425	100.000000	1	2396	1	chr7B.!!$F1	2395
1	TraesCS7B01G481700	chr7A	712681056	712681979	923	False	1343.000000	1343	92.973000	1476	2396	1	chr7A.!!$F1	920
2	TraesCS7B01G481700	chr7A	22080143	22081057	914	True	1275.000000	1275	91.775000	1476	2396	1	chr7A.!!$R1	920
3	TraesCS7B01G481700	chr2A	561554025	561555544	1519	True	638.033333	1166	92.859667	1	1403	3	chr2A.!!$R1	1402
4	TraesCS7B01G481700	chr2D	426943454	426944980	1526	False	893.500000	1162	89.536000	1	1410	2	chr2D.!!$F1	1409
5	TraesCS7B01G481700	chr2B	503771728	503773244	1516	False	613.100000	1149	92.152333	1	1400	3	chr2B.!!$F1	1399
6	TraesCS7B01G481700	chr1D	483473670	483474592	922	False	1094.000000	1094	88.095000	1476	2396	1	chr1D.!!$F1	920
7	TraesCS7B01G481700	chr1B	673713988	673714859	871	False	1011.000000	1011	87.657000	1494	2364	1	chr1B.!!$F1	870

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
465	494	0.81361	TGTTCGACAACTGCCACCTG	60.814	55.0	0.0	0.0	33.17	4.0	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1977	2140	0.251297	CATGGACCAACCCTTCAGCA	60.251	55.0	0.0	0.0	38.0	4.41	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
61	62	1.299468	GCCGCTCACGATCTTCGAT	60.299	57.895	3.62	0.00	43.74	3.59
113	114	4.785453	GGTTCAGCCTGGAGCCGG	62.785	72.222	0.00	0.00	45.47	6.13
198	199	4.747529	GGGCCCGTACCACGTCAC	62.748	72.222	5.69	0.00	40.58	3.67
283	285	4.357947	GTGTGCTCGAGGTCGGCA	62.358	66.667	15.58	2.94	40.97	5.69
363	380	0.974010	CCTACGGGCAGAAGTGGGTA	60.974	60.000	0.00	0.00	34.76	3.69
390	407	1.298863	CACCGTTGTCGACTCGTGT	60.299	57.895	23.48	19.16	39.71	4.49
412	429	4.760047	CCCGGTGGAACGAGCAGG	62.760	72.222	0.00	0.00	38.12	4.85
413	430	4.760047	CCGGTGGAACGAGCAGGG	62.760	72.222	0.00	0.00	38.12	4.45
465	494	0.813610	TGTTCGACAACTGCCACCTG	60.814	55.000	0.00	0.00	33.17	4.00
555	620	4.111016	CACCCGCTCGTCGTGCTA	62.111	66.667	16.37	0.00	36.19	3.49
613	712	1.334992	CGTCGTGTGCTTGTACGGAG	61.335	60.000	0.00	0.00	40.48	4.63
778	933	3.058160	CGGAGCAAGGCCAAGTGG	61.058	66.667	5.01	0.00	38.53	4.00
793	948	1.228154	GTGGCCAACTTCTTCCGGT	60.228	57.895	7.24	0.00	0.00	5.28
795	950	0.821711	TGGCCAACTTCTTCCGGTTG	60.822	55.000	0.61	0.00	41.46	3.77
880	1035	4.662961	CGGTGACCGCTGTGCTCA	62.663	66.667	12.53	0.00	41.17	4.26
904	1059	1.669158	CTTGCTCTTCGTCACGCTCG	61.669	60.000	0.00	0.00	0.00	5.03
1261	1416	2.049526	CTGCCGTGTCGCTGTACA	60.050	61.111	0.00	0.00	0.00	2.90
1263	1418	1.686566	CTGCCGTGTCGCTGTACATG	61.687	60.000	0.00	0.00	36.36	3.21
1392	1547	3.650950	AGGGCCGACACCATGCTT	61.651	61.111	0.00	0.00	0.00	3.91
1412	1567	6.337853	GCTTTAGCATGTACTGTGTTCTAG	57.662	41.667	0.00	0.00	41.59	2.43
1413	1568	5.869888	GCTTTAGCATGTACTGTGTTCTAGT	59.130	40.000	0.00	0.00	41.59	2.57
1414	1569	7.033791	GCTTTAGCATGTACTGTGTTCTAGTA	58.966	38.462	0.00	0.00	41.59	1.82
1415	1570	7.221067	GCTTTAGCATGTACTGTGTTCTAGTAG	59.779	40.741	0.00	0.00	41.59	2.57
1416	1571	7.698506	TTAGCATGTACTGTGTTCTAGTAGT	57.301	36.000	0.00	0.00	31.72	2.73
1417	1572	8.797350	TTAGCATGTACTGTGTTCTAGTAGTA	57.203	34.615	0.00	0.00	31.72	1.82
1418	1573	7.883391	AGCATGTACTGTGTTCTAGTAGTAT	57.117	36.000	0.00	0.00	31.72	2.12
1419	1574	8.975663	AGCATGTACTGTGTTCTAGTAGTATA	57.024	34.615	0.00	0.00	31.72	1.47
1420	1575	9.404848	AGCATGTACTGTGTTCTAGTAGTATAA	57.595	33.333	0.00	0.00	31.72	0.98
1421	1576	9.448294	GCATGTACTGTGTTCTAGTAGTATAAC	57.552	37.037	0.00	0.08	31.72	1.89
1456	1611	9.598517	AAAAGCAATTGTAAGAAAAACATGAGA	57.401	25.926	7.40	0.00	0.00	3.27
1457	1612	9.768662	AAAGCAATTGTAAGAAAAACATGAGAT	57.231	25.926	7.40	0.00	0.00	2.75
1506	1663	8.719560	TTGCGAAAAAGTTAGGGTTTTTATTT	57.280	26.923	0.00	0.00	37.25	1.40
1597	1756	3.388308	GCTGTGCTATCACCACATCTAG	58.612	50.000	0.00	0.00	41.84	2.43
1621	1780	3.542712	AGTTCGCTAAACAATGTGCAG	57.457	42.857	0.00	0.00	40.56	4.41
1623	1782	1.522668	TCGCTAAACAATGTGCAGCT	58.477	45.000	14.76	0.00	0.00	4.24
1709	1870	2.692557	CCGAAACCAAATGGCCATATGA	59.307	45.455	21.15	0.00	39.32	2.15
1711	1872	4.522405	CCGAAACCAAATGGCCATATGATA	59.478	41.667	21.15	0.00	39.32	2.15
1760	1921	3.213506	TCTTGAGGGTCACAACACAATG	58.786	45.455	0.00	0.00	0.00	2.82
1770	1931	5.009010	GGTCACAACACAATGAGATTGAAGT	59.991	40.000	3.35	0.00	42.83	3.01
1780	1941	9.166173	CACAATGAGATTGAAGTAGGATTGTAA	57.834	33.333	3.35	0.00	42.83	2.41
1824	1987	1.510492	TGAGCCCTTCCATCATAGCA	58.490	50.000	0.00	0.00	0.00	3.49
1845	2008	2.536066	TGTAGTTCTGCTTCTAGGGCA	58.464	47.619	10.06	10.06	38.10	5.36
1894	2057	3.119955	GGACGCAAAAATAACTCCACCTC	60.120	47.826	0.00	0.00	0.00	3.85
1910	2073	6.775629	ACTCCACCTCTATCATCTCTTAGAAC	59.224	42.308	0.00	0.00	0.00	3.01
2003	2166	2.283101	GTTGGTCCATGGCCTGCA	60.283	61.111	21.23	7.26	0.00	4.41
2025	2188	4.919770	ACAGGGGGCTCTGTATGT	57.080	55.556	11.18	0.00	45.18	2.29
2031	2194	1.472728	GGGGGCTCTGTATGTTGTACG	60.473	57.143	0.00	0.00	0.00	3.67
2046	2209	5.110598	TGTTGTACGTGTGTGTGTATTTCT	58.889	37.500	0.00	0.00	0.00	2.52
2048	2211	4.684877	TGTACGTGTGTGTGTATTTCTGT	58.315	39.130	0.00	0.00	0.00	3.41
2056	2219	5.819901	TGTGTGTGTATTTCTGTTGTCATCA	59.180	36.000	0.00	0.00	0.00	3.07
2104	2267	4.512944	CCATACTCACCGAGATTTGATTGG	59.487	45.833	0.00	0.00	33.32	3.16
2107	2270	4.651778	ACTCACCGAGATTTGATTGGAAA	58.348	39.130	0.00	0.00	33.32	3.13
2123	2286	9.461312	TTGATTGGAAATGTTGTAATAGCTAGT	57.539	29.630	0.00	0.00	0.00	2.57
2172	2335	3.576550	GTGGGATTGGTTTACCATGTGTT	59.423	43.478	1.81	0.00	46.97	3.32
2226	2389	5.912149	AAACCATAATGATCCTGCTCCTA	57.088	39.130	0.00	0.00	0.00	2.94
2227	2390	5.912149	AACCATAATGATCCTGCTCCTAA	57.088	39.130	0.00	0.00	0.00	2.69
2228	2391	6.460103	AACCATAATGATCCTGCTCCTAAT	57.540	37.500	0.00	0.00	0.00	1.73
2250	2414	5.771153	TTTGTTCATGTGATTCAGCAAGA	57.229	34.783	0.00	0.00	0.00	3.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
9	10	2.490217	CGATCTCGTCCTTGCCGT	59.510	61.111	0.00	0.00	34.11	5.68
198	199	0.525668	GTACATGGTCAGCTCGTCCG	60.526	60.000	0.00	0.00	0.00	4.79
207	208	0.109458	GTCGCTGACGTACATGGTCA	60.109	55.000	0.00	0.05	41.82	4.02
378	395	2.338015	GGGGCTACACGAGTCGACA	61.338	63.158	21.50	2.37	0.00	4.35
390	407	4.700448	TCGTTCCACCGGGGGCTA	62.700	66.667	21.49	5.34	37.22	3.93
418	435	1.442769	GTGAGCACCATGTCGAACAT	58.557	50.000	0.00	0.00	39.91	2.71
419	436	0.943835	CGTGAGCACCATGTCGAACA	60.944	55.000	0.00	0.00	0.00	3.18
421	438	4.260194	CGTGAGCACCATGTCGAA	57.740	55.556	0.00	0.00	0.00	3.71
490	519	0.894184	TGGTCTCTGAGGACGGTGTC	60.894	60.000	4.59	0.00	37.12	3.67
493	522	1.304547	CCTGGTCTCTGAGGACGGT	60.305	63.158	4.59	0.00	37.12	4.83
613	712	4.798682	TCTTCGGGAGGAGGGGCC	62.799	72.222	0.00	0.00	35.64	5.80
710	865	1.066858	CAGCATGTACTCCACGACCTT	60.067	52.381	0.00	0.00	0.00	3.50
774	929	1.073199	CCGGAAGAAGTTGGCCACT	59.927	57.895	3.88	2.92	37.30	4.00
775	930	0.822121	AACCGGAAGAAGTTGGCCAC	60.822	55.000	9.46	0.00	0.00	5.01
776	931	0.821711	CAACCGGAAGAAGTTGGCCA	60.822	55.000	9.46	0.00	39.73	5.36
777	932	0.536460	TCAACCGGAAGAAGTTGGCC	60.536	55.000	9.46	0.00	42.87	5.36
778	933	0.591659	GTCAACCGGAAGAAGTTGGC	59.408	55.000	9.46	0.00	42.87	4.52
779	934	0.865769	CGTCAACCGGAAGAAGTTGG	59.134	55.000	9.46	0.00	42.87	3.77
793	948	2.202878	GGATAGCAGCGCCGTCAA	60.203	61.111	2.29	0.00	0.00	3.18
879	1034	1.136141	GTGACGAAGAGCAAGTGCATG	60.136	52.381	6.00	0.00	45.16	4.06
880	1035	1.151668	GTGACGAAGAGCAAGTGCAT	58.848	50.000	6.00	0.00	45.16	3.96
904	1059	2.435059	GAGCTCCGGGAAGCACAC	60.435	66.667	16.73	4.93	45.00	3.82
930	1085	2.549349	GGACATGTACAGGAACACGGTT	60.549	50.000	15.54	0.00	30.75	4.44
998	1153	3.069980	GAGAGCCTCGCGTCCATGT	62.070	63.158	5.77	0.00	0.00	3.21
1045	1200	2.333417	TGTCCAGCTCCTCGTCGAC	61.333	63.158	5.18	5.18	0.00	4.20
1078	1233	3.103911	CACCACGTCGTTCGGCTC	61.104	66.667	0.00	0.00	44.69	4.70
1245	1400	1.736282	CATGTACAGCGACACGGCA	60.736	57.895	0.33	0.00	34.64	5.69
1252	1407	2.202557	CGGCGTCATGTACAGCGA	60.203	61.111	17.53	7.42	0.00	4.93
1392	1547	7.698506	ACTACTAGAACACAGTACATGCTAA	57.301	36.000	0.00	0.00	0.00	3.09
1430	1585	9.598517	TCTCATGTTTTTCTTACAATTGCTTTT	57.401	25.926	5.05	0.00	0.00	2.27
1431	1586	9.768662	ATCTCATGTTTTTCTTACAATTGCTTT	57.231	25.926	5.05	0.00	0.00	3.51
1452	1607	9.878667	AAAATGTTGATGCATGATTTTATCTCA	57.121	25.926	2.46	0.00	0.00	3.27
1597	1756	3.121362	GCACATTGTTTAGCGAACTTTGC	60.121	43.478	7.38	0.00	39.08	3.68
1621	1780	4.111375	TCCTTCGTGAACAGAATAGAGC	57.889	45.455	0.00	0.00	0.00	4.09
1623	1782	8.932791	GTTAAAATCCTTCGTGAACAGAATAGA	58.067	33.333	0.00	0.00	0.00	1.98
1711	1872	8.374743	GCTCTCTCAGGATTCCTTTAATAGATT	58.625	37.037	1.28	0.00	0.00	2.40
1730	1891	2.106566	TGACCCTCAAGATGCTCTCTC	58.893	52.381	0.00	0.00	31.03	3.20
1748	1909	6.427853	CCTACTTCAATCTCATTGTGTTGTGA	59.572	38.462	0.00	0.00	41.02	3.58
1760	1921	9.039870	CAGATGTTACAATCCTACTTCAATCTC	57.960	37.037	0.00	0.00	0.00	2.75
1824	1987	3.107601	TGCCCTAGAAGCAGAACTACAT	58.892	45.455	3.55	0.00	34.69	2.29
1887	2050	6.071984	GGTTCTAAGAGATGATAGAGGTGGA	58.928	44.000	0.00	0.00	0.00	4.02
1894	2057	6.164876	CAGGCATGGTTCTAAGAGATGATAG	58.835	44.000	0.00	0.00	0.00	2.08
1938	2101	2.438954	CGACGGCTCGTTTAACCCG	61.439	63.158	9.15	9.15	41.37	5.28
1977	2140	0.251297	CATGGACCAACCCTTCAGCA	60.251	55.000	0.00	0.00	38.00	4.41
1991	2154	2.286045	TACCCTGCAGGCCATGGA	60.286	61.111	28.39	7.48	40.58	3.41
2003	2166	1.524720	TACAGAGCCCCCTGTACCCT	61.525	60.000	7.01	0.00	44.82	4.34
2014	2177	2.666508	CACACGTACAACATACAGAGCC	59.333	50.000	0.00	0.00	0.00	4.70
2025	2188	5.110598	ACAGAAATACACACACACGTACAA	58.889	37.500	0.00	0.00	0.00	2.41
2031	2194	5.478233	TGACAACAGAAATACACACACAC	57.522	39.130	0.00	0.00	0.00	3.82
2046	2209	2.158475	AGGAAAAGCCCTGATGACAACA	60.158	45.455	0.00	0.00	37.37	3.33
2048	2211	2.978156	AGGAAAAGCCCTGATGACAA	57.022	45.000	0.00	0.00	37.37	3.18
2056	2219	6.986391	AGGAGATTATTAAAGGAAAAGCCCT	58.014	36.000	0.00	0.00	38.42	5.19
2107	2270	9.865321	TTCGTTTCTAACTAGCTATTACAACAT	57.135	29.630	0.00	0.00	0.00	2.71
2123	2286	4.342951	TGGAAGTCTCCTGTTCGTTTCTAA	59.657	41.667	0.00	0.00	42.94	2.10
2172	2335	1.002201	TGGCACCTCCGAAACGAAATA	59.998	47.619	0.00	0.00	37.80	1.40
2226	2389	6.751157	TCTTGCTGAATCACATGAACAAATT	58.249	32.000	0.00	0.00	0.00	1.82
2227	2390	6.335471	TCTTGCTGAATCACATGAACAAAT	57.665	33.333	0.00	0.00	0.00	2.32
2228	2391	5.771153	TCTTGCTGAATCACATGAACAAA	57.229	34.783	0.00	0.00	0.00	2.83
2250	2414	2.503356	AGACGAATGGCTCCTTCATCTT	59.497	45.455	0.00	0.00	0.00	2.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.