AutoCloner

Multiple sequence alignment - TraesCS7D01G127900

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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	TraesCS7D01G127900	chr7D	100.000	2801	0	0	1	2801	80299743	80296943	0.000000e+00	5173.0
1	TraesCS7D01G127900	chr7D	87.625	1705	165	26	1113	2801	80198716	80197042	0.000000e+00	1938.0
2	TraesCS7D01G127900	chr7D	88.147	1333	122	17	1476	2801	80383075	80381772	0.000000e+00	1554.0
3	TraesCS7D01G127900	chr7D	84.509	1162	127	31	1590	2744	80384333	80383218	0.000000e+00	1099.0
4	TraesCS7D01G127900	chr7D	85.950	726	53	25	1113	1801	80462653	80461940	0.000000e+00	730.0
5	TraesCS7D01G127900	chr7D	80.213	844	113	33	1296	2110	80417335	80416517	4.020000e-163	584.0
6	TraesCS7D01G127900	chr7D	89.390	377	25	4	692	1068	80199218	80198857	7.070000e-126	460.0
7	TraesCS7D01G127900	chr7D	89.958	239	12	5	883	1115	112411240	112411472	5.870000e-77	298.0
8	TraesCS7D01G127900	chr7D	92.500	80	6	0	1497	1576	80470374	80470295	6.340000e-22	115.0
9	TraesCS7D01G127900	chr7D	96.875	32	1	0	1073	1104	80198819	80198788	1.000000e-03	54.7
10	TraesCS7D01G127900	chr7B	93.636	880	51	4	1925	2801	27485577	27484700	0.000000e+00	1310.0
11	TraesCS7D01G127900	chr7B	90.436	826	42	17	1113	1933	27486919	27486126	0.000000e+00	1053.0
12	TraesCS7D01G127900	chr7B	93.522	247	12	2	1257	1499	27594992	27594746	5.700000e-97	364.0
13	TraesCS7D01G127900	chr7B	84.688	320	30	10	692	1007	27487414	27487110	4.530000e-78	302.0
14	TraesCS7D01G127900	chr7B	94.231	52	1	2	1065	1115	27487036	27486986	8.320000e-11	78.7
15	TraesCS7D01G127900	chr7B	92.308	39	3	0	1078	1116	27595211	27595173	3.900000e-04	56.5
16	TraesCS7D01G127900	chr7A	86.574	1080	107	20	1283	2349	83157748	83156694	0.000000e+00	1157.0
17	TraesCS7D01G127900	chr7A	87.243	682	52	16	1141	1805	83106605	83105942	0.000000e+00	745.0
18	TraesCS7D01G127900	chr7A	84.659	704	51	30	1112	1786	83142326	83141651	0.000000e+00	649.0
19	TraesCS7D01G127900	chr7A	88.664	494	43	7	9	499	680912089	680911606	8.640000e-165	590.0
20	TraesCS7D01G127900	chr7A	86.740	543	40	13	9	537	608532256	608531732	2.420000e-160	575.0
21	TraesCS7D01G127900	chr7A	87.830	493	48	6	9	499	671403810	671403328	4.050000e-158	568.0
22	TraesCS7D01G127900	chr7A	83.919	541	51	14	9	537	559550807	559550291	4.190000e-133	484.0
23	TraesCS7D01G127900	chr7A	85.584	437	54	6	2372	2801	83156468	83156034	1.530000e-122	449.0
24	TraesCS7D01G127900	chr7A	83.246	382	35	12	694	1073	83170315	83169961	9.680000e-85	324.0
25	TraesCS7D01G127900	chr7A	87.940	199	14	5	923	1115	83142586	83142392	2.810000e-55	226.0
26	TraesCS7D01G127900	chr7A	86.010	193	19	2	812	1004	83107008	83106824	1.700000e-47	200.0
27	TraesCS7D01G127900	chr7A	81.481	135	11	1	569	689	680911430	680911296	6.390000e-17	99.0
28	TraesCS7D01G127900	chr7A	97.674	43	1	0	1073	1115	83106751	83106709	1.080000e-09	75.0
29	TraesCS7D01G127900	chr4A	87.956	548	47	11	2	537	648314241	648314781	1.830000e-176	628.0
30	TraesCS7D01G127900	chr3B	87.298	496	45	9	9	499	31125976	31126458	4.080000e-153	551.0
31	TraesCS7D01G127900	chr3B	81.734	542	46	16	9	537	43056412	43055911	1.210000e-108	403.0
32	TraesCS7D01G127900	chr3B	80.899	178	9	5	536	689	43055826	43055650	1.760000e-22	117.0
33	TraesCS7D01G127900	chr5B	88.571	455	44	6	9	461	572132896	572133344	1.900000e-151	545.0
34	TraesCS7D01G127900	chr5B	81.884	138	11	1	570	693	572133395	572133532	1.370000e-18	104.0
35	TraesCS7D01G127900	chr5B	93.651	63	4	0	566	628	587446663	587446725	8.260000e-16	95.3
36	TraesCS7D01G127900	chr2B	85.370	540	49	17	9	537	637862968	637863488	1.480000e-147	532.0
37	TraesCS7D01G127900	chr2B	87.209	86	8	3	566	649	16306028	16305944	8.260000e-16	95.3
38	TraesCS7D01G127900	chr2B	79.310	145	16	7	559	689	63163959	63164103	3.840000e-14	89.8
39	TraesCS7D01G127900	chr6B	84.715	543	55	14	9	537	154396665	154397193	4.140000e-143	518.0
40	TraesCS7D01G127900	chr6B	92.308	65	5	0	566	630	154397316	154397380	2.970000e-15	93.5
41	TraesCS7D01G127900	chr3A	89.474	76	7	1	566	641	467120375	467120301	8.260000e-16	95.3
42	TraesCS7D01G127900	chr4D	88.158	76	8	1	566	641	8826395	8826469	3.840000e-14	89.8
43	TraesCS7D01G127900	chr4D	85.542	83	9	3	560	641	6765456	6765536	1.790000e-12	84.2
44	TraesCS7D01G127900	chr6A	91.489	47	4	0	645	691	52402968	52402922	6.480000e-07	65.8

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	TraesCS7D01G127900	chr7D	80296943	80299743	2800	True	5173.000000	5173	100.000000	1	2801	1	chr7D.!!$R1	2800
1	TraesCS7D01G127900	chr7D	80381772	80384333	2561	True	1326.500000	1554	86.328000	1476	2801	2	chr7D.!!$R6	1325
2	TraesCS7D01G127900	chr7D	80197042	80199218	2176	True	817.566667	1938	91.296667	692	2801	3	chr7D.!!$R5	2109
3	TraesCS7D01G127900	chr7D	80461940	80462653	713	True	730.000000	730	85.950000	1113	1801	1	chr7D.!!$R3	688
4	TraesCS7D01G127900	chr7D	80416517	80417335	818	True	584.000000	584	80.213000	1296	2110	1	chr7D.!!$R2	814
5	TraesCS7D01G127900	chr7B	27484700	27487414	2714	True	685.925000	1310	90.747750	692	2801	4	chr7B.!!$R1	2109
6	TraesCS7D01G127900	chr7A	83156034	83157748	1714	True	803.000000	1157	86.079000	1283	2801	2	chr7A.!!$R7	1518
7	TraesCS7D01G127900	chr7A	608531732	608532256	524	True	575.000000	575	86.740000	9	537	1	chr7A.!!$R3	528
8	TraesCS7D01G127900	chr7A	559550291	559550807	516	True	484.000000	484	83.919000	9	537	1	chr7A.!!$R2	528
9	TraesCS7D01G127900	chr7A	83141651	83142586	935	True	437.500000	649	86.299500	923	1786	2	chr7A.!!$R6	863
10	TraesCS7D01G127900	chr7A	680911296	680912089	793	True	344.500000	590	85.072500	9	689	2	chr7A.!!$R8	680
11	TraesCS7D01G127900	chr7A	83105942	83107008	1066	True	340.000000	745	90.309000	812	1805	3	chr7A.!!$R5	993
12	TraesCS7D01G127900	chr4A	648314241	648314781	540	False	628.000000	628	87.956000	2	537	1	chr4A.!!$F1	535
13	TraesCS7D01G127900	chr3B	43055650	43056412	762	True	260.000000	403	81.316500	9	689	2	chr3B.!!$R1	680
14	TraesCS7D01G127900	chr5B	572132896	572133532	636	False	324.500000	545	85.227500	9	693	2	chr5B.!!$F2	684
15	TraesCS7D01G127900	chr2B	637862968	637863488	520	False	532.000000	532	85.370000	9	537	1	chr2B.!!$F2	528
16	TraesCS7D01G127900	chr6B	154396665	154397380	715	False	305.750000	518	88.511500	9	630	2	chr6B.!!$F1	621

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
921	1067	0.684479	CAGATCGACCTCCCCTGTCA	60.684	60.0	0.0	0.0	32.91	3.58	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2610	3805	0.038892	CCAGCACACACCAAATCAGC	60.039	55.0	0.0	0.0	0.0	4.26	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
338	351	7.730364	TCAGGAACACTTCTATCAGTTTTTC	57.270	36.000	0.00	0.00	0.00	2.29
395	408	4.259292	CGGCGCGCTATTTATAATCACTAC	60.259	45.833	32.29	6.50	0.00	2.73
466	479	3.262135	GAGATCGAGTCTCCTTAAGCG	57.738	52.381	11.57	0.00	46.35	4.68
467	480	2.873472	GAGATCGAGTCTCCTTAAGCGA	59.127	50.000	11.57	0.00	46.35	4.93
499	512	6.697019	ACTTAATTTTGCGGCTGCTTATATTG	59.303	34.615	20.27	5.60	43.34	1.90
551	666	3.571590	ACTGTGCCCAATTTGTCCTAAA	58.428	40.909	0.00	0.00	0.00	1.85
644	784	1.211703	TGTGCTCAAGTTCAGGGTTCA	59.788	47.619	0.00	0.00	0.00	3.18
662	802	4.395231	GGTTCAATTTAGCTTTCGCCTACT	59.605	41.667	0.00	0.00	36.60	2.57
680	820	8.313292	TCGCCTACTAGTTCAAGGTTTATTTTA	58.687	33.333	11.10	0.00	32.67	1.52
681	821	8.938906	CGCCTACTAGTTCAAGGTTTATTTTAA	58.061	33.333	11.10	0.00	32.67	1.52
748	894	3.072184	AGGGTCCGTGTCGATATACTACT	59.928	47.826	0.00	0.00	0.00	2.57
749	895	4.284490	AGGGTCCGTGTCGATATACTACTA	59.716	45.833	0.00	0.00	0.00	1.82
854	1000	1.686325	CCCCTACACCATGTCTCCCG	61.686	65.000	0.00	0.00	0.00	5.14
893	1039	2.049433	CGAGCCCACGACGAGTTT	60.049	61.111	0.00	0.00	35.09	2.66
920	1066	1.395826	CCAGATCGACCTCCCCTGTC	61.396	65.000	0.00	0.00	0.00	3.51
921	1067	0.684479	CAGATCGACCTCCCCTGTCA	60.684	60.000	0.00	0.00	32.91	3.58
1024	1170	0.820226	CTGCCAGAGTGCACTAGCTA	59.180	55.000	26.86	16.79	42.74	3.32
1027	1173	2.025155	GCCAGAGTGCACTAGCTAGTA	58.975	52.381	25.63	9.22	42.74	1.82
1052	1203	2.949447	ACTCCCAGCACAAGTTTTCAT	58.051	42.857	0.00	0.00	0.00	2.57
1055	1212	3.149196	TCCCAGCACAAGTTTTCATCTC	58.851	45.455	0.00	0.00	0.00	2.75
1133	1436	2.811317	GTCACTCTTCCTGCGCGG	60.811	66.667	9.96	9.96	0.00	6.46
1222	1540	5.368145	AGATGAGCAACAAGTGAGTGTTTA	58.632	37.500	0.00	0.00	39.73	2.01
1223	1541	6.000219	AGATGAGCAACAAGTGAGTGTTTAT	59.000	36.000	0.00	0.00	39.73	1.40
1224	1542	5.673337	TGAGCAACAAGTGAGTGTTTATC	57.327	39.130	0.00	0.00	39.73	1.75
1225	1543	4.211164	TGAGCAACAAGTGAGTGTTTATCG	59.789	41.667	0.00	0.00	39.73	2.92
1226	1544	4.377021	AGCAACAAGTGAGTGTTTATCGA	58.623	39.130	0.00	0.00	39.73	3.59
1588	1941	8.712228	AAGTTGTGGATTCTTAATTTCTTCCT	57.288	30.769	0.00	0.00	0.00	3.36
1696	2064	1.405933	CGGCTCAACATCCTCATGTCA	60.406	52.381	0.00	0.00	42.89	3.58
1714	2107	0.033504	CACCACCGACTACACTTGCT	59.966	55.000	0.00	0.00	0.00	3.91
1883	2295	8.341892	AGTTTATTTCTCTTGTCCAGGATTTC	57.658	34.615	0.00	0.00	0.00	2.17
2134	3114	5.358725	ACTGTTTTACAACACTAAACCCCTG	59.641	40.000	0.00	0.00	38.03	4.45
2226	3209	3.646715	CCCCTCCCCTTCGCAACA	61.647	66.667	0.00	0.00	0.00	3.33
2290	3274	1.224592	GACAGTGGCGATGGGGAAT	59.775	57.895	0.00	0.00	0.00	3.01
2297	3281	1.146930	GCGATGGGGAATGCTCTCA	59.853	57.895	0.00	0.00	0.00	3.27
2370	3557	2.250741	GAGCCCTCCCTCAGAGTTGC	62.251	65.000	0.00	0.00	41.47	4.17
2409	3596	1.649390	CGACGCAGAGCTACTCCTGT	61.649	60.000	2.48	0.00	0.00	4.00
2514	3703	2.970324	GTTGGTGACGCGCCTCAA	60.970	61.111	10.74	3.09	34.70	3.02
2518	3707	3.112709	GTGACGCGCCTCAACTCC	61.113	66.667	10.74	0.00	0.00	3.85
2561	3750	3.628646	GAGCGATGGCCCACCTTGT	62.629	63.158	0.00	0.00	41.24	3.16
2616	3811	2.557805	CAACGTGCGCTGCTGATT	59.442	55.556	9.73	0.00	0.00	2.57
2693	3888	1.769465	TGTTGGTGGTAGTGTAGGCAA	59.231	47.619	0.00	0.00	0.00	4.52

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
171	179	9.248291	GCCAAATACCTGTATCACATTTTATTG	57.752	33.333	0.00	0.00	0.00	1.90
182	190	7.704899	GGTAACATTTTGCCAAATACCTGTATC	59.295	37.037	9.45	2.02	37.43	2.24
188	196	4.623595	CACGGTAACATTTTGCCAAATACC	59.376	41.667	7.38	7.38	37.33	2.73
338	351	9.988350	AAAACTGTTAGAAGCGTTCATATATTG	57.012	29.630	0.00	0.00	0.00	1.90
463	476	3.668656	GCAAAATTAAGTTTCGCTTCGCT	59.331	39.130	12.41	0.00	38.57	4.93
464	477	3.478125	CGCAAAATTAAGTTTCGCTTCGC	60.478	43.478	15.51	8.02	38.57	4.70
465	478	3.057609	CCGCAAAATTAAGTTTCGCTTCG	59.942	43.478	15.51	8.05	38.57	3.79
466	479	3.181544	GCCGCAAAATTAAGTTTCGCTTC	60.182	43.478	15.51	7.63	38.57	3.86
467	480	2.729360	GCCGCAAAATTAAGTTTCGCTT	59.271	40.909	15.51	0.00	41.05	4.68
507	533	4.259356	TGCTCGCTTACTCTACTCTGTAA	58.741	43.478	0.00	0.00	0.00	2.41
551	666	4.479993	GCTGGGCTGGCTCGACAT	62.480	66.667	0.00	0.00	0.00	3.06
702	842	4.388499	GCCTGCGAAGGAACGGGA	62.388	66.667	15.89	0.00	0.00	5.14
703	843	4.697756	TGCCTGCGAAGGAACGGG	62.698	66.667	15.89	0.00	0.00	5.28
748	894	1.028330	CGTGTGCCGAGGTAGAGGTA	61.028	60.000	0.00	0.00	39.56	3.08
749	895	2.341101	CGTGTGCCGAGGTAGAGGT	61.341	63.158	0.00	0.00	39.56	3.85
873	1019	4.778415	CTCGTCGTGGGCTCGTGG	62.778	72.222	0.00	0.00	0.00	4.94
874	1020	3.553437	AACTCGTCGTGGGCTCGTG	62.553	63.158	0.00	0.00	0.00	4.35
875	1021	1.518056	TAAACTCGTCGTGGGCTCGT	61.518	55.000	0.00	0.00	0.00	4.18
893	1039	2.105134	GGAGGTCGATCTGGAGAGAGTA	59.895	54.545	0.91	0.00	0.00	2.59
920	1066	1.324435	CTACGTTCGATGCATGGTGTG	59.676	52.381	2.46	0.00	0.00	3.82
921	1067	1.640428	CTACGTTCGATGCATGGTGT	58.360	50.000	2.46	6.58	0.00	4.16
1024	1170	1.938585	TGTGCTGGGAGTAGCTTACT	58.061	50.000	0.00	0.00	44.01	2.24
1027	1173	1.059913	ACTTGTGCTGGGAGTAGCTT	58.940	50.000	0.00	0.00	44.01	3.74
1052	1203	4.443621	CTCCTGTACTACGTGATCAGAGA	58.556	47.826	0.00	1.68	0.00	3.10
1055	1212	2.946329	AGCTCCTGTACTACGTGATCAG	59.054	50.000	0.00	1.65	0.00	2.90
1117	1420	4.742201	GCCGCGCAGGAAGAGTGA	62.742	66.667	20.06	0.00	45.00	3.41
1197	1509	3.181462	ACACTCACTTGTTGCTCATCTCA	60.181	43.478	0.00	0.00	0.00	3.27
1222	1540	2.159338	GCATTGCATTGAACACCTCGAT	60.159	45.455	12.66	0.00	0.00	3.59
1223	1541	1.199789	GCATTGCATTGAACACCTCGA	59.800	47.619	12.66	0.00	0.00	4.04
1224	1542	1.068402	TGCATTGCATTGAACACCTCG	60.068	47.619	7.38	0.00	31.71	4.63
1225	1543	2.331194	GTGCATTGCATTGAACACCTC	58.669	47.619	15.49	0.00	41.91	3.85
1226	1544	1.336148	CGTGCATTGCATTGAACACCT	60.336	47.619	15.49	0.00	41.91	4.00
1588	1941	2.535485	AATGACAGGGGAATGCGCGA	62.535	55.000	12.10	0.00	0.00	5.87
1696	2064	1.624336	TAGCAAGTGTAGTCGGTGGT	58.376	50.000	0.00	0.00	0.00	4.16
1714	2107	3.245229	ACTCCCACATTCAACCAGCAATA	60.245	43.478	0.00	0.00	0.00	1.90
1805	2208	7.335924	ACGCCAACATTATACTAACATTGTTCT	59.664	33.333	5.07	0.00	0.00	3.01
1806	2209	7.469260	ACGCCAACATTATACTAACATTGTTC	58.531	34.615	5.07	0.00	0.00	3.18
1807	2210	7.119992	TGACGCCAACATTATACTAACATTGTT	59.880	33.333	7.30	7.30	0.00	2.83
1809	2212	6.905076	GTGACGCCAACATTATACTAACATTG	59.095	38.462	0.00	0.00	0.00	2.82
1820	2230	1.527736	GTTGACGTGACGCCAACATTA	59.472	47.619	27.56	0.00	46.27	1.90
1828	2238	2.475519	CCCATATTTGTTGACGTGACGC	60.476	50.000	4.25	0.00	0.00	5.19
2151	3131	3.936203	TGGGAGCAACGCGAGGTT	61.936	61.111	15.93	0.99	40.22	3.50
2290	3274	4.362279	GTGCAAGAAAAATTGTGAGAGCA	58.638	39.130	0.00	0.00	32.56	4.26
2297	3281	3.791973	TCACCGTGCAAGAAAAATTGT	57.208	38.095	0.00	0.00	32.56	2.71
2388	3575	0.107800	AGGAGTAGCTCTGCGTCGTA	60.108	55.000	0.00	0.00	39.54	3.43
2409	3596	3.243805	TGAAATCCCACGTCTCGTTGTTA	60.244	43.478	0.00	0.00	38.32	2.41
2561	3750	1.813859	CTGGTAATCGAGGTCGCCA	59.186	57.895	0.00	0.00	39.60	5.69
2610	3805	0.038892	CCAGCACACACCAAATCAGC	60.039	55.000	0.00	0.00	0.00	4.26
2616	3811	1.151221	ATCAGCCAGCACACACCAA	59.849	52.632	0.00	0.00	0.00	3.67

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.