AutoCloner

Multiple sequence alignment - TraesCS1B01G112100

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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	TraesCS1B01G112100	chr1B	100.000	2318	0	0	1	2318	130034532	130032215	0.000000e+00	4281
1	TraesCS1B01G112100	chr1B	97.460	866	20	2	1453	2318	130026044	130025181	0.000000e+00	1476
2	TraesCS1B01G112100	chr1B	96.647	865	26	2	1454	2318	528519903	528520764	0.000000e+00	1434
3	TraesCS1B01G112100	chr1B	99.285	699	5	0	1	699	109358546	109357848	0.000000e+00	1264
4	TraesCS1B01G112100	chr1B	99.142	699	6	0	1	699	130041297	130040599	0.000000e+00	1258
5	TraesCS1B01G112100	chr1B	98.999	699	7	0	1	699	288516992	288516294	0.000000e+00	1253
6	TraesCS1B01G112100	chr7A	96.532	865	26	2	1454	2318	594537984	594537124	0.000000e+00	1428
7	TraesCS1B01G112100	chr7A	96.069	865	30	3	1454	2318	554906035	554905175	0.000000e+00	1406
8	TraesCS1B01G112100	chr7A	74.021	281	73	0	1026	1306	708361502	708361782	5.230000e-22	115
9	TraesCS1B01G112100	chr1A	96.424	867	25	5	1454	2318	427438210	427437348	0.000000e+00	1424
10	TraesCS1B01G112100	chr1A	99.283	697	4	1	4	699	13397774	13398470	0.000000e+00	1258
11	TraesCS1B01G112100	chr1A	91.053	760	59	8	708	1459	97810188	97809430	0.000000e+00	1018
12	TraesCS1B01G112100	chrUn	96.185	865	30	2	1454	2318	255614969	255615830	0.000000e+00	1411
13	TraesCS1B01G112100	chrUn	99.139	697	5	1	4	699	444331843	444331147	0.000000e+00	1253
14	TraesCS1B01G112100	chr2B	96.296	864	25	6	1456	2318	139087777	139086920	0.000000e+00	1411
15	TraesCS1B01G112100	chr5B	96.074	866	30	3	1453	2318	138302600	138303461	0.000000e+00	1408
16	TraesCS1B01G112100	chr5A	96.069	865	31	2	1454	2318	523637993	523637132	0.000000e+00	1406
17	TraesCS1B01G112100	chr3B	99.285	699	5	0	1	699	195688035	195688733	0.000000e+00	1264
18	TraesCS1B01G112100	chr2A	99.285	699	4	1	1	699	621554399	621555096	0.000000e+00	1262
19	TraesCS1B01G112100	chr6B	99.142	699	6	0	1	699	24324968	24324270	0.000000e+00	1258
20	TraesCS1B01G112100	chr6B	98.999	699	7	0	1	699	24394079	24393381	0.000000e+00	1253

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	TraesCS1B01G112100	chr1B	130032215	130034532	2317	True	4281	4281	100.000	1	2318	1	chr1B.!!$R3	2317
1	TraesCS1B01G112100	chr1B	130025181	130026044	863	True	1476	1476	97.460	1453	2318	1	chr1B.!!$R2	865
2	TraesCS1B01G112100	chr1B	528519903	528520764	861	False	1434	1434	96.647	1454	2318	1	chr1B.!!$F1	864
3	TraesCS1B01G112100	chr1B	109357848	109358546	698	True	1264	1264	99.285	1	699	1	chr1B.!!$R1	698
4	TraesCS1B01G112100	chr1B	130040599	130041297	698	True	1258	1258	99.142	1	699	1	chr1B.!!$R4	698
5	TraesCS1B01G112100	chr1B	288516294	288516992	698	True	1253	1253	98.999	1	699	1	chr1B.!!$R5	698
6	TraesCS1B01G112100	chr7A	594537124	594537984	860	True	1428	1428	96.532	1454	2318	1	chr7A.!!$R2	864
7	TraesCS1B01G112100	chr7A	554905175	554906035	860	True	1406	1406	96.069	1454	2318	1	chr7A.!!$R1	864
8	TraesCS1B01G112100	chr1A	427437348	427438210	862	True	1424	1424	96.424	1454	2318	1	chr1A.!!$R2	864
9	TraesCS1B01G112100	chr1A	13397774	13398470	696	False	1258	1258	99.283	4	699	1	chr1A.!!$F1	695
10	TraesCS1B01G112100	chr1A	97809430	97810188	758	True	1018	1018	91.053	708	1459	1	chr1A.!!$R1	751
11	TraesCS1B01G112100	chrUn	255614969	255615830	861	False	1411	1411	96.185	1454	2318	1	chrUn.!!$F1	864
12	TraesCS1B01G112100	chrUn	444331147	444331843	696	True	1253	1253	99.139	4	699	1	chrUn.!!$R1	695
13	TraesCS1B01G112100	chr2B	139086920	139087777	857	True	1411	1411	96.296	1456	2318	1	chr2B.!!$R1	862
14	TraesCS1B01G112100	chr5B	138302600	138303461	861	False	1408	1408	96.074	1453	2318	1	chr5B.!!$F1	865
15	TraesCS1B01G112100	chr5A	523637132	523637993	861	True	1406	1406	96.069	1454	2318	1	chr5A.!!$R1	864
16	TraesCS1B01G112100	chr3B	195688035	195688733	698	False	1264	1264	99.285	1	699	1	chr3B.!!$F1	698
17	TraesCS1B01G112100	chr2A	621554399	621555096	697	False	1262	1262	99.285	1	699	1	chr2A.!!$F1	698
18	TraesCS1B01G112100	chr6B	24324270	24324968	698	True	1258	1258	99.142	1	699	1	chr6B.!!$R1	698
19	TraesCS1B01G112100	chr6B	24393381	24394079	698	True	1253	1253	98.999	1	699	1	chr6B.!!$R2	698

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
729	730	1.468127	TGCGCCTACACACATTTCATG	59.532	47.619	4.18	0.0	0.0	3.07	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2249	2258	0.608308	TGAGATCCTGGACGTCACGT	60.608	55.0	18.91	0.09	45.1	4.49	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
457	458	4.525912	AAAGGGTTACGTCGATACAAGT	57.474	40.909	0.00	0.00	0.00	3.16
729	730	1.468127	TGCGCCTACACACATTTCATG	59.532	47.619	4.18	0.00	0.00	3.07
738	739	5.108187	ACACACATTTCATGCCTCTCTAT	57.892	39.130	0.00	0.00	0.00	1.98
746	747	8.168725	ACATTTCATGCCTCTCTATTCCAATAT	58.831	33.333	0.00	0.00	0.00	1.28
747	748	9.676861	CATTTCATGCCTCTCTATTCCAATATA	57.323	33.333	0.00	0.00	0.00	0.86
748	749	9.902684	ATTTCATGCCTCTCTATTCCAATATAG	57.097	33.333	0.00	0.00	0.00	1.31
749	750	8.441311	TTCATGCCTCTCTATTCCAATATAGT	57.559	34.615	0.00	0.00	31.44	2.12
889	894	5.918608	AGGTTCGTATCAGTAATTCAGCAT	58.081	37.500	0.00	0.00	0.00	3.79
901	906	3.795623	ATTCAGCATGCACATCTTTCC	57.204	42.857	21.98	0.00	34.76	3.13
926	931	4.844349	AGTTTATGCTCCTTCAGGCTAA	57.156	40.909	0.00	0.00	34.44	3.09
958	963	5.008619	TGCAACAAACAATTGACATCACT	57.991	34.783	13.59	0.00	38.94	3.41
959	964	4.804665	TGCAACAAACAATTGACATCACTG	59.195	37.500	13.59	1.87	38.94	3.66
960	965	4.805192	GCAACAAACAATTGACATCACTGT	59.195	37.500	13.59	1.77	38.94	3.55
961	966	5.976534	GCAACAAACAATTGACATCACTGTA	59.023	36.000	13.59	0.00	38.94	2.74
962	967	6.074888	GCAACAAACAATTGACATCACTGTAC	60.075	38.462	13.59	0.00	38.94	2.90
963	968	6.942532	ACAAACAATTGACATCACTGTACT	57.057	33.333	13.59	0.00	38.94	2.73
964	969	7.333528	ACAAACAATTGACATCACTGTACTT	57.666	32.000	13.59	0.00	38.94	2.24
965	970	7.195646	ACAAACAATTGACATCACTGTACTTG	58.804	34.615	13.59	0.00	38.94	3.16
1014	1020	2.100631	CACCATGGACTTCGCCGTC	61.101	63.158	21.47	0.00	0.00	4.79
1015	1021	2.264480	CCATGGACTTCGCCGTCA	59.736	61.111	5.56	0.00	35.63	4.35
1041	1047	2.859981	GCTGTGGGTGGTTGGCAAG	61.860	63.158	0.00	0.00	0.00	4.01
1071	1077	2.031163	GTCACAGACGGCCTGCTT	59.969	61.111	0.00	0.00	46.81	3.91
1080	1086	2.110967	CGGCCTGCTTGAGTCATGG	61.111	63.158	0.00	3.48	0.00	3.66
1082	1088	1.001641	GCCTGCTTGAGTCATGGGT	60.002	57.895	8.02	0.00	0.00	4.51
1086	1092	1.001641	GCTTGAGTCATGGGTGGCT	60.002	57.895	8.02	0.00	44.61	4.75
1090	1096	1.227380	GAGTCATGGGTGGCTAGCG	60.227	63.158	9.00	0.00	41.25	4.26
1092	1098	3.083349	TCATGGGTGGCTAGCGCT	61.083	61.111	17.26	17.26	36.09	5.92
1094	1100	4.181010	ATGGGTGGCTAGCGCTGG	62.181	66.667	22.90	20.11	36.09	4.85
1128	1134	2.169789	CGACGCCCTCAAGATGCAG	61.170	63.158	0.00	0.00	0.00	4.41
1139	1145	0.749649	AAGATGCAGCTCCTCTACGG	59.250	55.000	4.22	0.00	0.00	4.02
1158	1164	1.407437	GGACAAGGGATGCTCGACAAT	60.407	52.381	0.00	0.00	0.00	2.71
1161	1167	0.035152	AAGGGATGCTCGACAATGCA	60.035	50.000	0.00	0.00	43.67	3.96
1179	1185	1.382695	ACAGGGTAGGGACATCCGG	60.383	63.158	0.00	0.00	41.52	5.14
1241	1247	1.226859	CATATGGTGCCGACGACGT	60.227	57.895	0.00	0.00	37.88	4.34
1245	1251	4.409218	GGTGCCGACGACGTGCTA	62.409	66.667	4.58	0.00	36.92	3.49
1278	1284	2.125552	TTCTGCATCCAGGACGCG	60.126	61.111	3.53	3.53	39.61	6.01
1281	1287	4.819761	TGCATCCAGGACGCGCTC	62.820	66.667	5.73	2.64	0.00	5.03
1284	1290	3.893763	ATCCAGGACGCGCTCGAG	61.894	66.667	5.73	8.45	39.41	4.04
1312	1318	0.031585	CCATGCTGCCGATTTGGATG	59.968	55.000	0.00	0.00	42.00	3.51
1315	1321	2.123428	GCTGCCGATTTGGATGCCT	61.123	57.895	0.00	0.00	42.00	4.75
1332	1338	0.244994	CCTAGAGCTGCGTTGACAGT	59.755	55.000	0.00	0.00	39.96	3.55
1333	1339	1.623359	CTAGAGCTGCGTTGACAGTC	58.377	55.000	0.00	0.00	39.96	3.51
1337	1343	1.661821	GCTGCGTTGACAGTCTCGT	60.662	57.895	15.96	0.00	39.96	4.18
1347	1353	1.929836	GACAGTCTCGTCATCAATGCC	59.070	52.381	0.00	0.00	35.88	4.40
1349	1355	0.179100	AGTCTCGTCATCAATGCCCG	60.179	55.000	0.00	0.00	0.00	6.13
1356	1362	2.048023	CATCAATGCCCGCCACACT	61.048	57.895	0.00	0.00	0.00	3.55
1377	1383	1.838112	CCAAGGCTGTGGCTGATAAA	58.162	50.000	0.00	0.00	38.81	1.40
1380	1386	3.609853	CAAGGCTGTGGCTGATAAACTA	58.390	45.455	0.00	0.00	38.81	2.24
1404	1410	1.333177	GCTCATCATCCTCTACCCGT	58.667	55.000	0.00	0.00	0.00	5.28
1506	1512	3.170717	TCCTACGGTTTCACCAAGATCT	58.829	45.455	0.00	0.00	38.47	2.75
1659	1665	0.107410	ACCAAGTGCTGAACGGACAA	60.107	50.000	0.00	0.00	36.26	3.18
1684	1690	1.481019	CCGCGTTCAACACACGTACA	61.481	55.000	4.92	0.00	39.92	2.90
2194	2203	0.322187	CCCCGAATTCTTCCGGTGTT	60.322	55.000	0.00	0.00	43.93	3.32
2249	2258	0.838554	TGGACCATTCCGGAACTCCA	60.839	55.000	25.92	25.92	46.37	3.86
2260	2269	1.361271	GAACTCCACGTGACGTCCA	59.639	57.895	19.30	0.00	38.32	4.02
2291	2300	2.545537	GGGACTCCGAACAACTTTCT	57.454	50.000	0.00	0.00	0.00	2.52

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
31	32	6.881065	TGCTCAATGTTCAAGTAGCTTAATCT	59.119	34.615	0.00	0.00	0.00	2.40
294	295	0.963962	CTCATGGCAAGGCACACTTT	59.036	50.000	0.00	0.00	37.29	2.66
699	700	2.081462	GTGTAGGCGCAGGTTTATGTT	58.919	47.619	10.83	0.00	0.00	2.71
700	701	1.002659	TGTGTAGGCGCAGGTTTATGT	59.997	47.619	10.83	0.00	0.00	2.29
701	702	1.396996	GTGTGTAGGCGCAGGTTTATG	59.603	52.381	10.83	0.00	35.58	1.90
702	703	1.002659	TGTGTGTAGGCGCAGGTTTAT	59.997	47.619	10.83	0.00	35.58	1.40
703	704	0.393448	TGTGTGTAGGCGCAGGTTTA	59.607	50.000	10.83	0.00	35.58	2.01
704	705	0.250727	ATGTGTGTAGGCGCAGGTTT	60.251	50.000	10.83	0.00	35.58	3.27
705	706	0.250727	AATGTGTGTAGGCGCAGGTT	60.251	50.000	10.83	0.00	35.58	3.50
706	707	0.250727	AAATGTGTGTAGGCGCAGGT	60.251	50.000	10.83	0.00	35.58	4.00
729	730	7.846066	ACATGACTATATTGGAATAGAGAGGC	58.154	38.462	0.00	0.00	34.63	4.70
738	739	8.078060	TGTGAAGAGACATGACTATATTGGAA	57.922	34.615	0.00	0.00	0.00	3.53
746	747	4.160439	GGTGGATGTGAAGAGACATGACTA	59.840	45.833	0.00	0.00	36.67	2.59
747	748	3.055530	GGTGGATGTGAAGAGACATGACT	60.056	47.826	0.00	0.00	36.67	3.41
748	749	3.265791	GGTGGATGTGAAGAGACATGAC	58.734	50.000	0.00	0.00	36.67	3.06
749	750	2.905736	TGGTGGATGTGAAGAGACATGA	59.094	45.455	0.00	0.00	36.67	3.07
759	763	1.297689	GCAGAGCTGGTGGATGTGA	59.702	57.895	0.00	0.00	0.00	3.58
803	808	4.035684	GTGGTCGTTTTCTCTTCTTTTGC	58.964	43.478	0.00	0.00	0.00	3.68
889	894	5.335897	GCATAAACTTGAGGAAAGATGTGCA	60.336	40.000	10.13	0.00	40.03	4.57
901	906	3.376546	GCCTGAAGGAGCATAAACTTGAG	59.623	47.826	0.00	0.00	37.39	3.02
926	931	3.228188	TGTTTGTTGCAAGAGGAGGAT	57.772	42.857	0.00	0.00	0.00	3.24
958	963	0.758734	AGTCACCTGCAGCAAGTACA	59.241	50.000	8.66	0.00	0.00	2.90
959	964	1.884235	AAGTCACCTGCAGCAAGTAC	58.116	50.000	8.66	1.54	0.00	2.73
960	965	3.981071	ATAAGTCACCTGCAGCAAGTA	57.019	42.857	8.66	0.00	0.00	2.24
961	966	2.867109	ATAAGTCACCTGCAGCAAGT	57.133	45.000	8.66	0.00	0.00	3.16
962	967	4.697352	AGTTAATAAGTCACCTGCAGCAAG	59.303	41.667	8.66	0.00	0.00	4.01
963	968	4.455533	CAGTTAATAAGTCACCTGCAGCAA	59.544	41.667	8.66	0.00	0.00	3.91
964	969	4.002982	CAGTTAATAAGTCACCTGCAGCA	58.997	43.478	8.66	0.00	0.00	4.41
965	970	3.181506	GCAGTTAATAAGTCACCTGCAGC	60.182	47.826	8.66	0.00	43.54	5.25
1045	1051	2.110213	GTCTGTGACGGGTGCCAA	59.890	61.111	0.00	0.00	0.00	4.52
1059	1065	1.548357	ATGACTCAAGCAGGCCGTCT	61.548	55.000	0.00	0.00	0.00	4.18
1071	1077	1.907739	GCTAGCCACCCATGACTCA	59.092	57.895	2.29	0.00	0.00	3.41
1090	1096	2.124529	GTTAGCTCCCAGCCCAGC	60.125	66.667	0.00	0.00	43.77	4.85
1092	1098	1.915228	GATGTTAGCTCCCAGCCCA	59.085	57.895	0.00	0.00	43.77	5.36
1094	1100	0.530870	GTCGATGTTAGCTCCCAGCC	60.531	60.000	0.00	0.00	43.77	4.85
1098	1104	1.591863	GGCGTCGATGTTAGCTCCC	60.592	63.158	6.48	0.00	0.00	4.30
1101	1107	1.320344	TGAGGGCGTCGATGTTAGCT	61.320	55.000	6.48	0.00	0.00	3.32
1102	1108	0.459585	TTGAGGGCGTCGATGTTAGC	60.460	55.000	6.48	0.00	0.00	3.09
1103	1109	1.134367	TCTTGAGGGCGTCGATGTTAG	59.866	52.381	6.48	0.00	0.00	2.34
1104	1110	1.179152	TCTTGAGGGCGTCGATGTTA	58.821	50.000	6.48	0.00	0.00	2.41
1139	1145	1.667724	CATTGTCGAGCATCCCTTGTC	59.332	52.381	0.00	0.00	0.00	3.18
1158	1164	1.271840	GGATGTCCCTACCCTGTGCA	61.272	60.000	0.00	0.00	0.00	4.57
1161	1167	1.382695	CCGGATGTCCCTACCCTGT	60.383	63.158	0.00	0.00	0.00	4.00
1224	1230	1.226859	CACGTCGTCGGCACCATAT	60.227	57.895	7.05	0.00	41.85	1.78
1228	1234	4.409218	TAGCACGTCGTCGGCACC	62.409	66.667	14.96	0.00	41.85	5.01
1245	1251	2.430332	GCAGAAGTAGTCCAGCTCATCT	59.570	50.000	0.00	0.00	0.00	2.90
1254	1260	2.111384	TCCTGGATGCAGAAGTAGTCC	58.889	52.381	16.85	0.00	0.00	3.85
1264	1270	4.819761	GAGCGCGTCCTGGATGCA	62.820	66.667	33.40	0.00	43.95	3.96
1299	1305	0.836606	TCTAGGCATCCAAATCGGCA	59.163	50.000	0.00	0.00	33.14	5.69
1303	1309	1.878734	GCAGCTCTAGGCATCCAAATC	59.121	52.381	6.07	0.00	44.79	2.17
1312	1318	1.079819	TGTCAACGCAGCTCTAGGC	60.080	57.895	0.00	0.00	42.19	3.93
1315	1321	1.200252	GAGACTGTCAACGCAGCTCTA	59.800	52.381	10.88	0.00	39.96	2.43
1332	1338	1.521457	GCGGGCATTGATGACGAGA	60.521	57.895	11.05	0.00	36.40	4.04
1333	1339	2.537560	GGCGGGCATTGATGACGAG	61.538	63.158	11.05	0.97	36.40	4.18
1337	1343	2.045708	GTGTGGCGGGCATTGATGA	61.046	57.895	7.75	0.00	0.00	2.92
1349	1355	3.677648	CAGCCTTGGCAGTGTGGC	61.678	66.667	14.54	12.71	45.21	5.01
1367	1373	4.905429	TGAGCACTTTAGTTTATCAGCCA	58.095	39.130	0.00	0.00	0.00	4.75
1371	1377	7.568349	AGGATGATGAGCACTTTAGTTTATCA	58.432	34.615	0.00	0.00	0.00	2.15
1372	1378	7.930865	AGAGGATGATGAGCACTTTAGTTTATC	59.069	37.037	0.00	0.00	0.00	1.75
1377	1383	5.069781	GGTAGAGGATGATGAGCACTTTAGT	59.930	44.000	0.00	0.00	0.00	2.24
1380	1386	3.135530	GGGTAGAGGATGATGAGCACTTT	59.864	47.826	0.00	0.00	0.00	2.66
1506	1512	8.166422	TCGTTGCTTAGATGAACTCATAGATA	57.834	34.615	0.00	0.00	36.57	1.98
1659	1665	1.885850	GTGTTGAACGCGGAGGTGT	60.886	57.895	12.47	0.00	38.89	4.16
1959	1965	2.366972	GCAAGCCTCCCCTCCCTA	60.367	66.667	0.00	0.00	0.00	3.53
2014	2020	1.077787	CATGCGCCTAGGGTTTGGA	60.078	57.895	11.72	0.00	0.00	3.53
2249	2258	0.608308	TGAGATCCTGGACGTCACGT	60.608	55.000	18.91	0.09	45.10	4.49

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.