AutoCloner

Multiple sequence alignment - TraesCS6B01G106800

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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	TraesCS6B01G106800	chr6B	100.000	2309	0	0	1	2309	87503131	87500823	0.000000e+00	4265.0
1	TraesCS6B01G106800	chr6B	85.279	1345	184	7	1	1333	151387193	151385851	0.000000e+00	1375.0
2	TraesCS6B01G106800	chr4A	89.755	1347	118	12	1	1333	676915480	676914140	0.000000e+00	1705.0
3	TraesCS6B01G106800	chr4A	84.644	1348	188	12	1	1333	669052075	669050732	0.000000e+00	1325.0
4	TraesCS6B01G106800	chr7D	85.969	1347	171	10	1	1333	615912063	615910721	0.000000e+00	1424.0
5	TraesCS6B01G106800	chr7D	92.105	38	3	0	1370	1407	62194954	62194991	1.000000e-03	54.7
6	TraesCS6B01G106800	chr1D	85.587	1346	180	7	1	1334	475891460	475892803	0.000000e+00	1399.0
7	TraesCS6B01G106800	chr6D	91.800	1000	48	15	1333	2309	37414848	37413860	0.000000e+00	1362.0
8	TraesCS6B01G106800	chr7B	85.090	1328	185	6	1	1316	552747420	552746094	0.000000e+00	1343.0
9	TraesCS6B01G106800	chr7B	84.770	1346	189	9	1	1333	192798493	192797151	0.000000e+00	1336.0
10	TraesCS6B01G106800	chr7B	83.333	72	11	1	1337	1407	742664254	742664325	5.320000e-07	65.8
11	TraesCS6B01G106800	chr5A	84.062	1349	203	8	1	1338	71139704	71141051	0.000000e+00	1290.0
12	TraesCS6B01G106800	chr5A	80.503	159	29	2	1177	1333	600260021	600259863	1.120000e-23	121.0
13	TraesCS6B01G106800	chr1B	88.973	1052	102	6	294	1334	606431042	606429994	0.000000e+00	1288.0
14	TraesCS6B01G106800	chr5B	82.950	1349	211	10	1	1335	348576111	348574768	0.000000e+00	1199.0
15	TraesCS6B01G106800	chr6A	86.667	825	80	19	1504	2309	48651571	48650758	0.000000e+00	887.0
16	TraesCS6B01G106800	chr6A	74.114	1298	296	35	61	1333	511536433	511537715	1.230000e-137	499.0
17	TraesCS6B01G106800	chr2A	74.343	1103	245	33	255	1333	48221244	48222332	3.520000e-118	435.0
18	TraesCS6B01G106800	chr2A	78.534	191	39	2	1145	1333	751763205	751763015	8.660000e-25	124.0
19	TraesCS6B01G106800	chr5D	90.244	246	15	1	1041	1277	564909405	564909650	1.720000e-81	313.0
20	TraesCS6B01G106800	chr4B	75.430	407	83	10	941	1333	567009762	567009359	5.070000e-42	182.0

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	TraesCS6B01G106800	chr6B	87500823	87503131	2308	True	4265	4265	100.000	1	2309	1	chr6B.!!$R1	2308
1	TraesCS6B01G106800	chr6B	151385851	151387193	1342	True	1375	1375	85.279	1	1333	1	chr6B.!!$R2	1332
2	TraesCS6B01G106800	chr4A	676914140	676915480	1340	True	1705	1705	89.755	1	1333	1	chr4A.!!$R2	1332
3	TraesCS6B01G106800	chr4A	669050732	669052075	1343	True	1325	1325	84.644	1	1333	1	chr4A.!!$R1	1332
4	TraesCS6B01G106800	chr7D	615910721	615912063	1342	True	1424	1424	85.969	1	1333	1	chr7D.!!$R1	1332
5	TraesCS6B01G106800	chr1D	475891460	475892803	1343	False	1399	1399	85.587	1	1334	1	chr1D.!!$F1	1333
6	TraesCS6B01G106800	chr6D	37413860	37414848	988	True	1362	1362	91.800	1333	2309	1	chr6D.!!$R1	976
7	TraesCS6B01G106800	chr7B	552746094	552747420	1326	True	1343	1343	85.090	1	1316	1	chr7B.!!$R2	1315
8	TraesCS6B01G106800	chr7B	192797151	192798493	1342	True	1336	1336	84.770	1	1333	1	chr7B.!!$R1	1332
9	TraesCS6B01G106800	chr5A	71139704	71141051	1347	False	1290	1290	84.062	1	1338	1	chr5A.!!$F1	1337
10	TraesCS6B01G106800	chr1B	606429994	606431042	1048	True	1288	1288	88.973	294	1334	1	chr1B.!!$R1	1040
11	TraesCS6B01G106800	chr5B	348574768	348576111	1343	True	1199	1199	82.950	1	1335	1	chr5B.!!$R1	1334
12	TraesCS6B01G106800	chr6A	48650758	48651571	813	True	887	887	86.667	1504	2309	1	chr6A.!!$R1	805
13	TraesCS6B01G106800	chr6A	511536433	511537715	1282	False	499	499	74.114	61	1333	1	chr6A.!!$F1	1272
14	TraesCS6B01G106800	chr2A	48221244	48222332	1088	False	435	435	74.343	255	1333	1	chr2A.!!$F1	1078

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
919	924	0.403655	TGGCATGGTGCTTAGGAACA	59.596	50.0	0.0	0.0	44.28	3.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2245	2289	0.108709	CCAACCATCCGCAAACCATG	60.109	55.0	0.0	0.0	0.0	3.66	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
25	26	3.056107	TCTTTCCGACCTATCACACCAAG	60.056	47.826	0.00	0.00	0.00	3.61
28	29	1.762957	CCGACCTATCACACCAAGGAT	59.237	52.381	0.00	0.00	34.34	3.24
30	31	3.243771	CCGACCTATCACACCAAGGATAC	60.244	52.174	0.00	0.00	34.34	2.24
46	48	2.454055	GATACTTGCCGCTTCAATTGC	58.546	47.619	0.00	0.00	0.00	3.56
62	64	1.885560	TTGCGTTTCGGATTTCCTGA	58.114	45.000	0.00	0.00	0.00	3.86
179	181	1.680249	GGGATGACTTTCTGTCCTGGC	60.680	57.143	0.00	0.00	44.75	4.85
191	193	1.306141	TCCTGGCATCCGGAGAAGT	60.306	57.895	11.34	0.00	29.82	3.01
234	236	1.586154	GCATACAAACTGGCCACGCT	61.586	55.000	0.00	0.00	0.00	5.07
244	246	2.167861	GGCCACGCTCGATCAGAAC	61.168	63.158	0.00	0.00	0.00	3.01
245	247	1.446099	GCCACGCTCGATCAGAACA	60.446	57.895	0.00	0.00	0.00	3.18
246	248	1.687494	GCCACGCTCGATCAGAACAC	61.687	60.000	0.00	0.00	0.00	3.32
325	327	4.473520	ATCTGGAAGGCCGCGGTG	62.474	66.667	28.70	1.63	36.79	4.94
363	367	9.155975	GAAGATAAACGCATGGAGATGTATTAT	57.844	33.333	0.00	0.00	31.50	1.28
427	431	1.202580	GCGACAAGATCTACCTGCCAT	60.203	52.381	0.00	0.00	0.00	4.40
453	457	2.844348	GTGGGGTTGAGGAGGAAGATTA	59.156	50.000	0.00	0.00	0.00	1.75
454	458	3.459969	GTGGGGTTGAGGAGGAAGATTAT	59.540	47.826	0.00	0.00	0.00	1.28
455	459	3.459598	TGGGGTTGAGGAGGAAGATTATG	59.540	47.826	0.00	0.00	0.00	1.90
487	491	2.807045	GTCTGCACTCACGCGAGG	60.807	66.667	15.93	4.29	44.17	4.63
526	530	2.976840	GCGTCGCTGGCCATTTTCA	61.977	57.895	5.51	0.00	0.00	2.69
578	583	2.380064	ATGGTTTGCCTCACTTTGGA	57.620	45.000	0.00	0.00	35.27	3.53
597	602	5.999205	TGGAAAAATGTACGGTCTAGGTA	57.001	39.130	0.00	0.00	0.00	3.08
599	604	5.111989	GGAAAAATGTACGGTCTAGGTACC	58.888	45.833	2.73	2.73	39.55	3.34
615	620	4.610333	AGGTACCGGATATGCTCATCATA	58.390	43.478	9.46	0.00	41.52	2.15
721	726	4.051922	GGACAGCTACTACAAATCCATCG	58.948	47.826	0.00	0.00	0.00	3.84
882	887	1.139853	GATGGCTCGTTCCTTCAGGAT	59.860	52.381	0.00	0.00	44.98	3.24
915	920	1.610522	GCTATTGGCATGGTGCTTAGG	59.389	52.381	1.64	0.00	44.28	2.69
919	924	0.403655	TGGCATGGTGCTTAGGAACA	59.596	50.000	0.00	0.00	44.28	3.18
925	930	3.857157	TGGTGCTTAGGAACAAGAAGT	57.143	42.857	0.00	0.00	0.00	3.01
964	969	5.107298	GCAGCATATCGTTTCATCTTCTACC	60.107	44.000	0.00	0.00	0.00	3.18
1055	1061	2.600173	CCCGGTGGTGGTGCAAAT	60.600	61.111	0.00	0.00	0.00	2.32
1086	1092	2.598045	AGCGCTATCATGCTTGACG	58.402	52.632	8.99	5.66	38.57	4.35
1108	1114	0.179059	TGGTGCACTTCTTCGCTCAA	60.179	50.000	17.98	0.00	0.00	3.02
1253	1268	0.036294	GTTTGGCTAGGCTCGGTTCT	60.036	55.000	18.18	0.00	0.00	3.01
1286	1301	1.623811	GGACTTGTGGCCTCTTGACTA	59.376	52.381	3.32	0.00	0.00	2.59
1298	1313	7.449086	GTGGCCTCTTGACTATAACTCTATACT	59.551	40.741	3.32	0.00	0.00	2.12
1378	1393	8.873144	TGTAGATACCAAAGTACTACCTTTTGT	58.127	33.333	0.00	0.00	35.01	2.83
1437	1452	7.377766	TCAAAACTTTAAGTAGCAGGCTATG	57.622	36.000	4.06	0.00	0.00	2.23
1467	1482	5.570320	ACTGGTGGCTCATACAAAAGTTAT	58.430	37.500	0.00	0.00	0.00	1.89
1571	1590	4.743493	CAACCATAACAAAGGCATACCAC	58.257	43.478	0.00	0.00	39.06	4.16
1582	1602	2.509548	AGGCATACCACCAAGCATCTAA	59.490	45.455	0.00	0.00	39.06	2.10
1654	1675	3.066760	GCCCAAGTTTAGCGCTAAATCAT	59.933	43.478	37.14	25.60	37.37	2.45
1684	1705	5.191059	GTCTGCTATTAGCGACAAAATTCG	58.809	41.667	23.49	0.00	46.26	3.34
1700	1721	4.673534	AATTCGTTTAGCGTAAACCCAG	57.326	40.909	12.12	3.21	43.85	4.45
1760	1782	9.724839	GCAACATTATAGTCCGCTATTTAAAAA	57.275	29.630	0.00	0.00	38.71	1.94
1999	2031	5.279708	GGGAGAAATCCATGATCGATAGTGT	60.280	44.000	0.00	0.00	37.40	3.55
2023	2055	2.305635	ACCATTGTGTAGGTGATGCTCA	59.694	45.455	0.00	0.00	36.60	4.26
2041	2073	1.164411	CACAGGCGTTGCATTCCTTA	58.836	50.000	0.00	0.00	0.00	2.69
2069	2103	1.480789	GTCCAAGTCTCCCTCTCTCC	58.519	60.000	0.00	0.00	0.00	3.71
2088	2132	3.041211	TCCCTCTCTCTCTCTCTCTCTG	58.959	54.545	0.00	0.00	0.00	3.35
2103	2147	1.364678	TCTCTGTCCATCCTTACCCCA	59.635	52.381	0.00	0.00	0.00	4.96
2176	2220	2.717011	GGCAACAACGTTTATTGTGTCG	59.283	45.455	18.54	0.00	42.01	4.35
2195	2239	4.184629	GTCGTGTCATTCTTCTAGGCATT	58.815	43.478	0.00	0.00	0.00	3.56
2284	2328	1.067142	GTGGTGGTGCGATCTGAGTAA	60.067	52.381	0.00	0.00	0.00	2.24
2295	2339	4.499865	GCGATCTGAGTAATGCCTCTAACA	60.500	45.833	0.00	0.00	32.50	2.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
5	6	2.027561	CCTTGGTGTGATAGGTCGGAAA	60.028	50.000	0.00	0.00	0.00	3.13
11	12	4.384208	GCAAGTATCCTTGGTGTGATAGGT	60.384	45.833	0.00	0.00	46.72	3.08
25	26	2.796032	GCAATTGAAGCGGCAAGTATCC	60.796	50.000	10.34	0.00	0.00	2.59
46	48	3.435327	TGTCATTCAGGAAATCCGAAACG	59.565	43.478	9.59	0.00	42.08	3.60
62	64	2.662866	CCTCCATGCTCCATTGTCATT	58.337	47.619	0.00	0.00	0.00	2.57
107	109	1.371558	GGTCGACATCCATAGGCCC	59.628	63.158	18.91	0.00	0.00	5.80
179	181	1.270839	ACAACCACACTTCTCCGGATG	60.271	52.381	3.57	2.11	0.00	3.51
191	193	5.995282	CACTCCTCATAGTAAAACAACCACA	59.005	40.000	0.00	0.00	0.00	4.17
234	236	2.180769	CGGCGGTGTTCTGATCGA	59.819	61.111	0.00	0.00	0.00	3.59
325	327	5.030936	GCGTTTATCTTCATCTTTTGAGGC	58.969	41.667	0.00	0.00	35.27	4.70
363	367	1.746322	TTGTGTCGCCAACGTCCCTA	61.746	55.000	0.00	0.00	41.18	3.53
364	368	2.596553	TTTGTGTCGCCAACGTCCCT	62.597	55.000	0.00	0.00	41.18	4.20
427	431	0.545309	CCTCCTCAACCCCACAGAGA	60.545	60.000	0.00	0.00	0.00	3.10
453	457	3.119245	GCAGACAACCAAAGCATGATCAT	60.119	43.478	1.18	1.18	0.00	2.45
454	458	2.229543	GCAGACAACCAAAGCATGATCA	59.770	45.455	0.00	0.00	0.00	2.92
455	459	2.229543	TGCAGACAACCAAAGCATGATC	59.770	45.455	0.00	0.00	0.00	2.92
487	491	3.119708	GCCTCATGTTTGTCCACAGAATC	60.120	47.826	0.00	0.00	0.00	2.52
526	530	7.067859	CCATCATGTACAAGAAAATCATCACCT	59.932	37.037	4.69	0.00	0.00	4.00
597	602	5.682234	TCAATATGATGAGCATATCCGGT	57.318	39.130	3.43	0.00	46.84	5.28
599	604	6.424207	CCAGATCAATATGATGAGCATATCCG	59.576	42.308	3.43	0.00	46.84	4.18
721	726	1.201343	GAGTAACTTCCAGCGATCGC	58.799	55.000	32.15	32.15	42.33	4.58
841	846	0.108804	ACGGACAATGCCAGTCTACG	60.109	55.000	0.00	0.00	36.29	3.51
882	887	3.132111	TGCCAATAGCTATTGAGTCGTCA	59.868	43.478	37.00	23.29	44.40	4.35
892	897	2.965671	AGCACCATGCCAATAGCTAT	57.034	45.000	0.00	0.00	46.52	2.97
893	898	2.734755	AAGCACCATGCCAATAGCTA	57.265	45.000	0.00	0.00	46.52	3.32
915	920	3.322254	TGAGGACCTCTCACTTCTTGTTC	59.678	47.826	22.14	0.00	46.71	3.18
964	969	2.697425	CTCAAGCGGATCGTTGCG	59.303	61.111	2.75	2.75	40.02	4.85
1055	1061	2.831894	TAGCGCTTCCGAGGAGTCCA	62.832	60.000	18.68	0.00	36.29	4.02
1086	1092	1.129437	GAGCGAAGAAGTGCACCATTC	59.871	52.381	14.63	11.97	0.00	2.67
1253	1268	4.564821	GCCACAAGTCCTCAATACAAGGTA	60.565	45.833	0.00	0.00	35.29	3.08
1298	1313	7.127405	GGGGGTAAAGGGAGTTTATTTAATGA	58.873	38.462	0.00	0.00	33.11	2.57
1303	1318	3.878924	GCGGGGGTAAAGGGAGTTTATTT	60.879	47.826	0.00	0.00	33.11	1.40
1490	1505	7.561251	AGTTTAAGCAAAAACCCTAAATGTGT	58.439	30.769	9.54	0.00	39.66	3.72
1541	1560	3.306225	CCTTTGTTATGGTTGCATGCTGT	60.306	43.478	20.33	2.84	0.00	4.40
1571	1590	6.757897	TCTTTGTTATGGTTAGATGCTTGG	57.242	37.500	0.00	0.00	0.00	3.61
1582	1602	6.463995	TGTCAAGCTTTTCTTTGTTATGGT	57.536	33.333	0.00	0.00	31.27	3.55
1654	1675	4.202111	TGTCGCTAATAGCAGACAATAGCA	60.202	41.667	25.53	10.80	44.81	3.49
1684	1705	3.811497	AGTTGTCTGGGTTTACGCTAAAC	59.189	43.478	10.36	10.36	45.51	2.01
1999	2031	2.676750	GCATCACCTACACAATGGTCGA	60.677	50.000	0.00	0.00	33.75	4.20
2023	2055	2.128771	ATAAGGAATGCAACGCCTGT	57.871	45.000	6.18	1.21	31.06	4.00
2041	2073	1.757699	GGAGACTTGGACGAAGCCTAT	59.242	52.381	0.00	0.00	34.68	2.57
2069	2103	3.181461	GGACAGAGAGAGAGAGAGAGAGG	60.181	56.522	0.00	0.00	0.00	3.69
2088	2132	2.106684	GAGGAATGGGGTAAGGATGGAC	59.893	54.545	0.00	0.00	0.00	4.02
2103	2147	1.081174	TGGGAGACAAGAGGGAGGAAT	59.919	52.381	0.00	0.00	0.00	3.01
2176	2220	5.181748	AGACAATGCCTAGAAGAATGACAC	58.818	41.667	0.00	0.00	0.00	3.67
2195	2239	1.412361	CCCCCTTTTGTTCCCAAGACA	60.412	52.381	0.00	0.00	0.00	3.41
2245	2289	0.108709	CCAACCATCCGCAAACCATG	60.109	55.000	0.00	0.00	0.00	3.66
2284	2328	3.053395	ACCACCATCAATGTTAGAGGCAT	60.053	43.478	0.00	0.00	0.00	4.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.