AutoCloner

Multiple sequence alignment - TraesCS7D01G391200

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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	TraesCS7D01G391200	chr7D	100.000	2375	0	0	1	2375	506664416	506662042	0.000000e+00	4386
1	TraesCS7D01G391200	chr7D	89.839	2234	169	26	169	2375	506642952	506640750	0.000000e+00	2815
2	TraesCS7D01G391200	chr7D	86.094	1165	122	15	1219	2375	506640290	506639158	0.000000e+00	1218
3	TraesCS7D01G391200	chr7D	87.076	472	49	10	1875	2338	506638702	506638235	7.520000e-145	523
4	TraesCS7D01G391200	chr7D	92.683	123	8	1	1	122	506651000	506650878	2.430000e-40	176
5	TraesCS7D01G391200	chr7D	92.857	70	3	2	108	177	506650862	506650795	1.500000e-17	100
6	TraesCS7D01G391200	chr7A	90.890	2415	164	30	1	2374	574089132	574086733	0.000000e+00	3190
7	TraesCS7D01G391200	chr7A	90.713	743	59	5	1202	1944	574086255	574085523	0.000000e+00	981
8	TraesCS7D01G391200	chr7A	91.076	437	21	9	1942	2375	574085400	574084979	2.050000e-160	575
9	TraesCS7D01G391200	chr7B	91.661	1391	77	22	13	1369	534822824	534821439	0.000000e+00	1890
10	TraesCS7D01G391200	chr7B	93.373	1177	73	5	1202	2375	534820038	534818864	0.000000e+00	1736
11	TraesCS7D01G391200	chr7B	85.046	983	93	29	1414	2374	534821442	534820492	0.000000e+00	952
12	TraesCS7D01G391200	chr7B	84.343	677	74	20	1714	2375	534818361	534817702	3.330000e-178	634
13	TraesCS7D01G391200	chr3D	77.529	2234	336	102	197	2375	567301991	567299869	0.000000e+00	1192
14	TraesCS7D01G391200	chr3D	76.487	1446	220	58	231	1611	568007093	568005703	0.000000e+00	676
15	TraesCS7D01G391200	chr3D	75.437	1486	254	66	215	1625	7594478	7595927	9.330000e-174	619
16	TraesCS7D01G391200	chr3D	77.000	1100	151	42	932	1992	569676429	569675393	9.660000e-149	536
17	TraesCS7D01G391200	chr3D	75.990	833	115	45	1178	2001	604304660	604305416	3.760000e-93	351
18	TraesCS7D01G391200	chr3D	82.713	376	54	8	1631	2001	568005710	568005341	8.190000e-85	324
19	TraesCS7D01G391200	chr3D	78.828	529	69	27	1802	2327	94647741	94647253	1.370000e-82	316
20	TraesCS7D01G391200	chr3D	78.841	345	57	12	197	536	564341576	564341243	3.970000e-53	219
21	TraesCS7D01G391200	chr3D	81.119	143	19	3	2120	2261	569646759	569646624	8.980000e-20	108
22	TraesCS7D01G391200	chr3B	78.220	1708	264	73	269	1939	754948309	754949945	0.000000e+00	994
23	TraesCS7D01G391200	chr3B	79.639	1331	191	37	904	2224	755250666	755249406	0.000000e+00	883
24	TraesCS7D01G391200	chr3B	85.096	208	31	0	197	404	753672736	753672943	1.850000e-51	213
25	TraesCS7D01G391200	chr3B	84.615	208	32	0	198	405	752973257	752973050	8.600000e-50	207
26	TraesCS7D01G391200	chr3A	77.717	1095	155	46	926	1992	700639969	700638936	2.630000e-164	588
27	TraesCS7D01G391200	chr3A	82.180	578	88	9	1076	1649	700635406	700634840	1.280000e-132	483
28	TraesCS7D01G391200	chr3A	79.916	478	61	15	1690	2149	700634679	700634219	3.810000e-83	318
29	TraesCS7D01G391200	chr3A	72.829	1071	199	53	197	1222	699540243	699541266	5.000000e-72	281
30	TraesCS7D01G391200	chr3A	83.451	284	33	10	1738	2014	12745730	12746006	3.920000e-63	252
31	TraesCS7D01G391200	chr3A	80.909	330	48	11	1682	2001	12810733	12810409	1.820000e-61	246
32	TraesCS7D01G391200	chr3A	80.058	346	56	11	2038	2375	701765806	701766146	6.560000e-61	244
33	TraesCS7D01G391200	chr3A	83.333	222	32	4	187	405	699533364	699533583	1.440000e-47	200
34	TraesCS7D01G391200	chr6B	83.654	208	34	0	197	404	565398517	565398724	1.860000e-46	196

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	TraesCS7D01G391200	chr7D	506662042	506664416	2374	True	4386.000000	4386	100.000000	1	2375	1	chr7D.!!$R1	2374
1	TraesCS7D01G391200	chr7D	506638235	506642952	4717	True	1518.666667	2815	87.669667	169	2375	3	chr7D.!!$R2	2206
2	TraesCS7D01G391200	chr7A	574084979	574089132	4153	True	1582.000000	3190	90.893000	1	2375	3	chr7A.!!$R1	2374
3	TraesCS7D01G391200	chr7B	534817702	534822824	5122	True	1303.000000	1890	88.605750	13	2375	4	chr7B.!!$R1	2362
4	TraesCS7D01G391200	chr3D	567299869	567301991	2122	True	1192.000000	1192	77.529000	197	2375	1	chr3D.!!$R3	2178
5	TraesCS7D01G391200	chr3D	7594478	7595927	1449	False	619.000000	619	75.437000	215	1625	1	chr3D.!!$F1	1410
6	TraesCS7D01G391200	chr3D	569675393	569676429	1036	True	536.000000	536	77.000000	932	1992	1	chr3D.!!$R5	1060
7	TraesCS7D01G391200	chr3D	568005341	568007093	1752	True	500.000000	676	79.600000	231	2001	2	chr3D.!!$R6	1770
8	TraesCS7D01G391200	chr3D	604304660	604305416	756	False	351.000000	351	75.990000	1178	2001	1	chr3D.!!$F2	823
9	TraesCS7D01G391200	chr3B	754948309	754949945	1636	False	994.000000	994	78.220000	269	1939	1	chr3B.!!$F2	1670
10	TraesCS7D01G391200	chr3B	755249406	755250666	1260	True	883.000000	883	79.639000	904	2224	1	chr3B.!!$R2	1320
11	TraesCS7D01G391200	chr3A	700634219	700639969	5750	True	463.000000	588	79.937667	926	2149	3	chr3A.!!$R2	1223
12	TraesCS7D01G391200	chr3A	699540243	699541266	1023	False	281.000000	281	72.829000	197	1222	1	chr3A.!!$F3	1025

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
878	980	0.03759	TGGTGCCTGTTTTATCGCCT	59.962	50.0	0.0	0.0	0.0	5.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2026	12725	3.52156	ACCAGCAATACATACAGTCACG	58.478	45.455	0.0	0.0	0.0	4.35	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	114	0.393537	CCACAGCCCAGAGTTCCATC	60.394	60.000	0.00	0.00	0.00	3.51
111	116	1.833630	CACAGCCCAGAGTTCCATCTA	59.166	52.381	0.00	0.00	0.00	1.98
161	183	5.645497	CAGAAAAATCTCCATTCCGACTCTT	59.355	40.000	0.00	0.00	0.00	2.85
184	206	0.666374	CCACCGAAACAGAAACACCC	59.334	55.000	0.00	0.00	0.00	4.61
190	213	1.602377	GAAACAGAAACACCCACCTCG	59.398	52.381	0.00	0.00	0.00	4.63
255	284	2.282958	TCTCCTCCGCAACGTCCT	60.283	61.111	0.00	0.00	0.00	3.85
281	310	0.878416	GATCGTCCTCTGGGAGATCG	59.122	60.000	0.00	1.61	43.12	3.69
313	342	1.460305	CCCCAGATCCCTCATCCGT	60.460	63.158	0.00	0.00	30.71	4.69
439	504	2.358737	CGCACCTTCCTCGCCTTT	60.359	61.111	0.00	0.00	0.00	3.11
546	619	4.180946	CCTCCTCGTCGTCTGGCG	62.181	72.222	0.00	0.00	43.01	5.69
771	855	0.391130	TCTTTGCGTTGGGATCCGAG	60.391	55.000	5.45	0.00	0.00	4.63
878	980	0.037590	TGGTGCCTGTTTTATCGCCT	59.962	50.000	0.00	0.00	0.00	5.52
1018	1162	0.309922	GATGGATGACATGCTTGGCG	59.690	55.000	8.51	0.00	40.72	5.69
1102	1252	3.714798	TGAGGTTTGGGACTTGAAGTACT	59.285	43.478	7.60	0.00	0.00	2.73
1333	5928	5.856126	TGTTCCGTATGATTTCTTCACAC	57.144	39.130	0.00	0.00	37.11	3.82
1407	7585	1.375013	GGCGGTGCTTCTTAACGGA	60.375	57.895	0.00	0.00	0.00	4.69
1434	7612	2.492019	TCGTATCCTCATGAGTTGCG	57.508	50.000	21.11	20.51	0.00	4.85
1488	7693	6.397272	TGCTGATTTCTTCTTTTTGTGTTGT	58.603	32.000	0.00	0.00	0.00	3.32
1575	7792	3.265791	GGATGAAGTGACTACTGCTTGG	58.734	50.000	0.00	0.00	37.19	3.61
1634	9507	9.474920	TGCTTTTGAAATATTTTCGAACTGATT	57.525	25.926	0.00	0.00	0.00	2.57
1664	9537	5.441718	TGTCTCTATTTTCTTGGGCTGAT	57.558	39.130	0.00	0.00	0.00	2.90
1682	11287	5.936372	GGCTGATGACATGCTTCATTCTATA	59.064	40.000	0.00	0.00	36.30	1.31
1838	11452	4.885325	CCTGTTTGTACCCTTTGTTGTAGT	59.115	41.667	0.00	0.00	0.00	2.73
1892	11507	1.072806	TGACTTGAAGCTGCACCTGAT	59.927	47.619	0.00	0.00	0.00	2.90
2026	12725	3.906720	TTGCATCTACCACCTTCTACC	57.093	47.619	0.00	0.00	0.00	3.18
2042	12743	5.977725	CCTTCTACCGTGACTGTATGTATTG	59.022	44.000	0.00	0.00	0.00	1.90
2053	12754	6.593770	TGACTGTATGTATTGCTGGTTGTAAG	59.406	38.462	0.00	0.00	0.00	2.34
2090	12795	7.147966	TGCAGATTGTGATGCTCTCATAAAATT	60.148	33.333	3.87	0.00	42.98	1.82
2091	12796	7.167635	GCAGATTGTGATGCTCTCATAAAATTG	59.832	37.037	3.87	4.56	38.32	2.32
2169	12887	0.324645	GATGGTCAAATGTGGGGCCT	60.325	55.000	0.84	0.00	0.00	5.19
2176	12894	2.109128	TCAAATGTGGGGCCTTCTTACA	59.891	45.455	0.84	1.46	0.00	2.41
2338	13057	2.030805	GCCCTTTGCCGAATAGCTAATG	60.031	50.000	0.00	0.00	0.00	1.90
2342	13063	4.335315	CCTTTGCCGAATAGCTAATGTCAA	59.665	41.667	0.00	0.00	0.00	3.18
2347	13068	5.064707	TGCCGAATAGCTAATGTCAAAGAAC	59.935	40.000	0.00	0.00	0.00	3.01
2350	13071	6.313905	CCGAATAGCTAATGTCAAAGAACTGT	59.686	38.462	0.00	0.00	0.00	3.55

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
65	70	2.521958	TAGCAGCTCTCAAACGGGCC	62.522	60.000	0.00	0.00	0.00	5.80
109	114	7.164230	AGGAATGGAGATAAGCGTAGAATAG	57.836	40.000	0.00	0.00	0.00	1.73
111	116	7.726033	ATAGGAATGGAGATAAGCGTAGAAT	57.274	36.000	0.00	0.00	0.00	2.40
161	183	2.940410	GTGTTTCTGTTTCGGTGGAGAA	59.060	45.455	0.00	0.00	0.00	2.87
424	489	0.955919	GGTCAAAGGCGAGGAAGGTG	60.956	60.000	0.00	0.00	0.00	4.00
612	691	3.056328	GTTGAAGTCCGGCAGGGC	61.056	66.667	0.00	0.00	44.17	5.19
771	855	1.521681	GATGTACCTCGGTGGCTGC	60.522	63.158	0.00	0.00	40.22	5.25
878	980	0.970937	CTCCAGTGGGTTCTCGCCTA	60.971	60.000	9.92	0.00	34.93	3.93
1018	1162	3.181506	GCAGCCTTGTTACAGCAATAGAC	60.182	47.826	0.00	0.00	0.00	2.59
1102	1252	1.383456	GCTATCGGCAATGCAACCCA	61.383	55.000	7.79	0.00	41.35	4.51
1318	5913	7.038302	ACCTTCTACTGGTGTGAAGAAATCATA	60.038	37.037	14.77	0.00	40.97	2.15
1333	5928	2.736719	CGACAGCATGACCTTCTACTGG	60.737	54.545	0.00	0.00	39.69	4.00
1407	7585	6.777213	ACTCATGAGGATACGAAAACTAGT	57.223	37.500	26.08	0.00	46.39	2.57
1434	7612	9.376075	CCATACTTGATCCAATACATAGACATC	57.624	37.037	0.00	0.00	0.00	3.06
1488	7693	3.134623	ACCACATGACAGTCACTTCTGAA	59.865	43.478	5.05	0.00	38.63	3.02
1575	7792	5.109210	GGCTTGGTAATTTTAGCATCAACC	58.891	41.667	3.30	0.00	40.41	3.77
1634	9507	5.111989	CAAGAAAATAGAGACATCAGGCGA	58.888	41.667	0.00	0.00	0.00	5.54
1640	9513	5.431765	TCAGCCCAAGAAAATAGAGACATC	58.568	41.667	0.00	0.00	0.00	3.06
1682	11287	9.647918	TCAAGTATGGAGAAGAACACTAGATAT	57.352	33.333	0.00	0.00	0.00	1.63
1838	11452	4.564782	ATCTGCCTCTTCTCATTGTCAA	57.435	40.909	0.00	0.00	0.00	3.18
1892	11507	5.975988	AATGCTCCAAGGTATCCTAGAAA	57.024	39.130	0.00	0.00	31.13	2.52
2026	12725	3.521560	ACCAGCAATACATACAGTCACG	58.478	45.455	0.00	0.00	0.00	4.35
2042	12743	5.409826	GCATCATATCCTACTTACAACCAGC	59.590	44.000	0.00	0.00	0.00	4.85
2053	12754	6.183360	GCATCACAATCTGCATCATATCCTAC	60.183	42.308	0.00	0.00	38.28	3.18
2090	12795	5.591472	CAGAATCCTACATGAGCCAAATTCA	59.409	40.000	0.00	0.00	0.00	2.57
2091	12796	5.591877	ACAGAATCCTACATGAGCCAAATTC	59.408	40.000	0.00	1.38	0.00	2.17
2169	12887	4.284829	TCATGGCAGACACATGTAAGAA	57.715	40.909	0.00	0.00	44.57	2.52
2176	12894	3.548770	CAACCTATCATGGCAGACACAT	58.451	45.455	0.00	0.00	0.00	3.21
2289	13008	6.377327	AATATGACATTGAAACTTAGCCCG	57.623	37.500	0.00	0.00	0.00	6.13
2327	13046	7.965107	CCAACAGTTCTTTGACATTAGCTATTC	59.035	37.037	0.00	0.00	0.00	1.75
2338	13057	4.137543	ACCATCTCCAACAGTTCTTTGAC	58.862	43.478	0.00	0.00	0.00	3.18
2342	13063	4.351111	ACCTAACCATCTCCAACAGTTCTT	59.649	41.667	0.00	0.00	0.00	2.52
2347	13068	3.775316	ACCTACCTAACCATCTCCAACAG	59.225	47.826	0.00	0.00	0.00	3.16
2350	13071	4.348020	AGACCTACCTAACCATCTCCAA	57.652	45.455	0.00	0.00	0.00	3.53

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.