AutoCloner

Multiple sequence alignment - TraesCS7A01G105500

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	TraesCS7A01G105500	chr7A	100.000	2414	0	0	1	2414	64201782	64199369	0.000000e+00	4458.0
1	TraesCS7A01G105500	chr7A	83.929	784	93	18	1	768	64313468	64314234	0.000000e+00	719.0
2	TraesCS7A01G105500	chr7A	88.774	579	56	4	811	1381	64314239	64314816	0.000000e+00	701.0
3	TraesCS7A01G105500	chr7A	91.593	226	18	1	1710	1935	64315252	64315476	6.480000e-81	311.0
4	TraesCS7A01G105500	chr7A	84.706	85	7	4	1932	2014	64315495	64315575	1.990000e-11	80.5
5	TraesCS7A01G105500	chr7B	95.063	1033	34	10	1383	2414	1753377	1754393	0.000000e+00	1609.0
6	TraesCS7A01G105500	chr7B	87.213	1392	132	17	4	1381	2326229	2324870	0.000000e+00	1543.0
7	TraesCS7A01G105500	chr7B	87.848	971	99	13	224	1185	1710915	1711875	0.000000e+00	1122.0
8	TraesCS7A01G105500	chr7B	88.988	672	57	9	1	666	1738895	1739555	0.000000e+00	815.0
9	TraesCS7A01G105500	chr7B	83.989	737	79	20	1710	2414	2324492	2323763	0.000000e+00	671.0
10	TraesCS7A01G105500	chr7B	91.481	270	12	4	1385	1654	2324838	2324580	6.340000e-96	361.0
11	TraesCS7A01G105500	chr7B	94.091	220	13	0	1162	1381	1753128	1753347	3.850000e-88	335.0
12	TraesCS7A01G105500	chr7B	90.955	199	17	1	1	199	1710720	1710917	1.420000e-67	267.0
13	TraesCS7A01G105500	chr7B	85.950	121	12	3	1	118	707431889	707431771	9.060000e-25	124.0
14	TraesCS7A01G105500	chr7B	84.615	104	13	2	22	123	1767513	1767411	1.530000e-17	100.0
15	TraesCS7A01G105500	chr3B	83.956	723	76	24	961	1668	33487291	33486594	0.000000e+00	656.0
16	TraesCS7A01G105500	chr3B	84.522	575	66	17	403	967	33496370	33495809	4.540000e-152	547.0
17	TraesCS7A01G105500	chr3B	89.222	334	34	2	961	1293	33468140	33467808	1.340000e-112	416.0
18	TraesCS7A01G105500	chr3B	85.442	419	36	10	1	398	33501153	33500739	1.730000e-111	412.0
19	TraesCS7A01G105500	chr3B	82.883	333	25	10	1710	2020	33467484	33467162	1.100000e-68	270.0
20	TraesCS7A01G105500	chr3B	92.135	89	5	1	1932	2020	33486296	33486210	9.060000e-25	124.0

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	TraesCS7A01G105500	chr7A	64199369	64201782	2413	True	4458.000000	4458	100.0000	1	2414	1	chr7A.!!$R1	2413
1	TraesCS7A01G105500	chr7A	64313468	64315575	2107	False	452.875000	719	87.2505	1	2014	4	chr7A.!!$F1	2013
2	TraesCS7A01G105500	chr7B	1753128	1754393	1265	False	972.000000	1609	94.5770	1162	2414	2	chr7B.!!$F3	1252
3	TraesCS7A01G105500	chr7B	2323763	2326229	2466	True	858.333333	1543	87.5610	4	2414	3	chr7B.!!$R3	2410
4	TraesCS7A01G105500	chr7B	1738895	1739555	660	False	815.000000	815	88.9880	1	666	1	chr7B.!!$F1	665
5	TraesCS7A01G105500	chr7B	1710720	1711875	1155	False	694.500000	1122	89.4015	1	1185	2	chr7B.!!$F2	1184
6	TraesCS7A01G105500	chr3B	33495809	33496370	561	True	547.000000	547	84.5220	403	967	1	chr3B.!!$R1	564
7	TraesCS7A01G105500	chr3B	33486210	33487291	1081	True	390.000000	656	88.0455	961	2020	2	chr3B.!!$R4	1059
8	TraesCS7A01G105500	chr3B	33467162	33468140	978	True	343.000000	416	86.0525	961	2020	2	chr3B.!!$R3	1059

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
987	1057	0.317799	AAATTGCTGATGTTGGCGCA	59.682	45.0	10.83	0.0	0.0	6.09	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1846	2036	3.635331	CAATGCTCTTGTGTGTTTCTGG	58.365	45.455	0.0	0.0	0.0	3.86	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
38	39	6.659242	AGTTGAACCCACCACAGAATTTATAG	59.341	38.462	0.00	0.00	0.00	1.31
57	58	3.938289	AGTCTCTAGAACGGTGTTTCC	57.062	47.619	0.00	0.00	0.00	3.13
63	64	3.893200	TCTAGAACGGTGTTTCCTTCTCA	59.107	43.478	0.00	0.00	36.18	3.27
258	294	0.707616	ACTAGAGCCTGACCCACTCT	59.292	55.000	0.00	0.00	43.12	3.24
398	435	6.043474	TGACAGGTTAAGGTACAGTAATTGGT	59.957	38.462	0.00	0.00	0.00	3.67
420	458	6.319405	TGGTACCTAAAGGGAAATTAAATCGC	59.681	38.462	14.36	1.77	40.27	4.58
445	483	5.065859	AGCCATCGAATAGAGATCTGATACG	59.934	44.000	0.00	0.00	0.00	3.06
448	486	4.907809	TCGAATAGAGATCTGATACGGGT	58.092	43.478	0.00	0.00	0.00	5.28
461	499	3.130516	TGATACGGGTTACTCTGCTTCAG	59.869	47.826	0.00	0.00	0.00	3.02
479	517	2.158871	TCAGTTCAGTTGGTACCGCTTT	60.159	45.455	7.57	0.00	0.00	3.51
515	553	2.233922	ACCGTTGATTCTCGAACTGGAT	59.766	45.455	0.00	0.00	0.00	3.41
526	571	4.220602	TCTCGAACTGGATGATCTTGTTGA	59.779	41.667	7.93	6.03	0.00	3.18
538	586	8.502387	GGATGATCTTGTTGATTGTAGCTATTC	58.498	37.037	0.00	0.00	35.14	1.75
607	655	2.602257	TGAGGCCTGACATGATAACG	57.398	50.000	12.00	0.00	0.00	3.18
620	668	7.247728	TGACATGATAACGTTAATCTTTTGGC	58.752	34.615	12.81	7.39	0.00	4.52
623	671	9.120538	ACATGATAACGTTAATCTTTTGGCTAT	57.879	29.630	12.81	0.00	0.00	2.97
624	672	9.599322	CATGATAACGTTAATCTTTTGGCTATC	57.401	33.333	12.81	2.16	0.00	2.08
632	680	8.562892	CGTTAATCTTTTGGCTATCTGATGAAT	58.437	33.333	0.00	0.00	0.00	2.57
685	738	1.135046	CAGTCTGTTGCTCTGTCGTG	58.865	55.000	0.00	0.00	0.00	4.35
715	768	9.555727	TCATACAGATTTTATGTTAAGGTAGCC	57.444	33.333	0.00	0.00	32.02	3.93
755	813	4.259810	CCGTATTTATTATCGATGGCAGCG	60.260	45.833	20.57	20.57	0.00	5.18
760	818	6.795098	TTTATTATCGATGGCAGCGTAAAT	57.205	33.333	25.32	23.92	0.00	1.40
774	832	5.681543	GCAGCGTAAATAAAGATAGTTTGGC	59.318	40.000	0.00	0.00	0.00	4.52
869	928	5.577835	TGAACAAAATTCCTCACAAAGTCG	58.422	37.500	0.00	0.00	0.00	4.18
881	940	3.685272	TCACAAAGTCGCACTTGTTGTTA	59.315	39.130	2.88	0.00	38.66	2.41
950	1009	3.044894	ACAATTGTGTTTCCCCATGGTT	58.955	40.909	11.07	0.00	32.58	3.67
959	1028	4.538490	TGTTTCCCCATGGTTGTACTATCT	59.462	41.667	11.73	0.00	0.00	1.98
984	1054	2.991190	CACTGAAATTGCTGATGTTGGC	59.009	45.455	0.00	0.00	0.00	4.52
987	1057	0.317799	AAATTGCTGATGTTGGCGCA	59.682	45.000	10.83	0.00	0.00	6.09
995	1065	1.199789	TGATGTTGGCGCACTCATTTC	59.800	47.619	10.83	0.98	0.00	2.17
1006	1076	2.486982	GCACTCATTTCACAGATGCAGT	59.513	45.455	0.00	0.00	0.00	4.40
1012	1082	5.065235	TCATTTCACAGATGCAGTTCTTCA	58.935	37.500	0.00	0.00	0.00	3.02
1041	1111	4.148825	GCGGGCAGGACGATCACT	62.149	66.667	0.00	0.00	0.00	3.41
1071	1141	2.625639	GATCCAGGGGACACCATCTAT	58.374	52.381	0.00	0.00	43.89	1.98
1098	1168	3.055167	TCAAGGCGAAGATTCAGGATCAA	60.055	43.478	0.00	0.00	37.22	2.57
1104	1174	2.322355	AGATTCAGGATCAACAGCGG	57.678	50.000	0.00	0.00	37.22	5.52
1164	1234	3.521560	TCTGGCTGATTACGACATTGAC	58.478	45.455	0.00	0.00	0.00	3.18
1219	1289	4.102210	CCCAGAGAAGGAAGATGCTAATCA	59.898	45.833	0.00	0.00	35.03	2.57
1299	1369	4.014406	TCGACAGTGTCAAGGCTAAGATA	58.986	43.478	22.66	0.00	32.09	1.98
1308	1378	5.932303	TGTCAAGGCTAAGATACAAGTTGAC	59.068	40.000	10.54	0.00	41.78	3.18
1381	1451	2.852075	ACTTTCGCACCCTGGGGA	60.852	61.111	18.88	1.33	38.96	4.81
1505	1605	2.432456	CCTGCGTAAGAGCGTGCA	60.432	61.111	0.00	0.00	40.67	4.57
1507	1607	2.432456	TGCGTAAGAGCGTGCAGG	60.432	61.111	1.01	1.01	40.67	4.85
1508	1608	3.854459	GCGTAAGAGCGTGCAGGC	61.854	66.667	23.37	23.37	43.02	4.85
1510	1610	1.138883	CGTAAGAGCGTGCAGGCTA	59.861	57.895	31.99	15.69	44.93	3.93
1511	1611	1.140407	CGTAAGAGCGTGCAGGCTAC	61.140	60.000	31.99	24.41	44.93	3.58
1512	1612	0.108804	GTAAGAGCGTGCAGGCTACA	60.109	55.000	31.99	17.65	44.93	2.74
1513	1613	0.606096	TAAGAGCGTGCAGGCTACAA	59.394	50.000	31.99	17.61	44.93	2.41
1514	1614	0.036010	AAGAGCGTGCAGGCTACAAT	60.036	50.000	31.99	16.33	44.93	2.71
1515	1615	0.460987	AGAGCGTGCAGGCTACAATC	60.461	55.000	31.99	19.71	44.93	2.67
1656	1758	4.667415	GCCGGTTAATGTTGTTCGAAGTAC	60.667	45.833	1.90	0.00	0.00	2.73
1657	1759	4.433283	CCGGTTAATGTTGTTCGAAGTACG	60.433	45.833	0.00	0.00	44.09	3.67
1658	1760	4.148696	CGGTTAATGTTGTTCGAAGTACGT	59.851	41.667	0.00	0.00	43.13	3.57
1659	1761	5.341993	CGGTTAATGTTGTTCGAAGTACGTA	59.658	40.000	0.00	0.00	43.13	3.57
1695	1797	6.246449	CACTCTGTTATCAAGAATCAAAGCG	58.754	40.000	0.00	0.00	0.00	4.68
1720	1910	4.885413	TGCTACTGCATTGCTGAAATTTT	58.115	34.783	20.66	1.53	45.31	1.82
1846	2036	8.125448	GCACATTACCAGATTTACTCAGAAATC	58.875	37.037	1.46	1.46	43.35	2.17
1975	2217	6.183360	GGAAACTTGGGAGACATTTTAGATCG	60.183	42.308	0.00	0.00	0.00	3.69
2087	2333	2.982744	GCAAAGAGCCCCGCAGAAC	61.983	63.158	0.00	0.00	37.23	3.01
2095	2341	0.750850	GCCCCGCAGAACTACAGATA	59.249	55.000	0.00	0.00	0.00	1.98
2101	2347	3.736252	CCGCAGAACTACAGATAAATCCG	59.264	47.826	0.00	0.00	0.00	4.18
2112	2359	8.857098	ACTACAGATAAATCCGCATACTCTTAA	58.143	33.333	0.00	0.00	0.00	1.85
2113	2360	9.862371	CTACAGATAAATCCGCATACTCTTAAT	57.138	33.333	0.00	0.00	0.00	1.40
2281	2529	4.339748	TGCTTTACAGGGTATCATTGCAA	58.660	39.130	0.00	0.00	0.00	4.08
2373	2621	1.425066	GGCCATGACCATATGAAGGGA	59.575	52.381	3.65	0.00	0.00	4.20
2398	2646	6.636562	AAGGAGTAGTTGATGGAGTATACG	57.363	41.667	0.00	0.00	0.00	3.06

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
38	39	3.938289	AGGAAACACCGTTCTAGAGAC	57.062	47.619	0.00	0.00	44.74	3.36
57	58	6.192234	ACTCTGCAGCAAATAAATGAGAAG	57.808	37.500	9.47	0.00	0.00	2.85
63	64	7.340232	TCTGGAAATACTCTGCAGCAAATAAAT	59.660	33.333	9.47	0.00	0.00	1.40
188	197	0.546598	CCCGCTCTGAATTAGGGGTT	59.453	55.000	8.53	0.00	43.66	4.11
258	294	1.690352	GATAAACCCTAGCCGCCACTA	59.310	52.381	0.00	0.00	0.00	2.74
368	405	5.937111	ACTGTACCTTAACCTGTCATGTTT	58.063	37.500	0.00	0.00	0.00	2.83
371	408	7.065803	CCAATTACTGTACCTTAACCTGTCATG	59.934	40.741	0.00	0.00	0.00	3.07
398	435	6.038936	GCTGCGATTTAATTTCCCTTTAGGTA	59.961	38.462	0.00	0.00	36.75	3.08
420	458	4.780275	TCAGATCTCTATTCGATGGCTG	57.220	45.455	0.00	0.00	0.00	4.85
445	483	3.244249	ACTGAACTGAAGCAGAGTAACCC	60.244	47.826	0.82	0.00	36.07	4.11
448	486	4.141711	ACCAACTGAACTGAAGCAGAGTAA	60.142	41.667	0.82	0.00	36.07	2.24
461	499	1.334689	GCAAAGCGGTACCAACTGAAC	60.335	52.381	13.54	0.00	33.42	3.18
515	553	7.436376	CGAGAATAGCTACAATCAACAAGATCA	59.564	37.037	0.00	0.00	35.39	2.92
526	571	5.871396	TCCCTTTCGAGAATAGCTACAAT	57.129	39.130	0.00	0.00	0.00	2.71
538	586	4.628074	TCAGTTACTGTTTCCCTTTCGAG	58.372	43.478	12.41	0.00	32.61	4.04
634	682	9.967346	CAGTTCTACCGATTAGATCATTTAAGA	57.033	33.333	0.00	0.00	36.65	2.10
635	683	9.751542	ACAGTTCTACCGATTAGATCATTTAAG	57.248	33.333	0.00	0.00	36.65	1.85
649	702	0.803117	CTGCTCGACAGTTCTACCGA	59.197	55.000	6.79	0.00	41.86	4.69
760	818	9.679661	TCAATATGAACAGCCAAACTATCTTTA	57.320	29.630	0.00	0.00	0.00	1.85
853	912	2.851195	AGTGCGACTTTGTGAGGAATT	58.149	42.857	0.00	0.00	0.00	2.17
869	928	9.724839	TTACAAAGACTAATTAACAACAAGTGC	57.275	29.630	0.00	0.00	0.00	4.40
950	1009	5.874810	GCAATTTCAGTGGACAGATAGTACA	59.125	40.000	0.00	0.00	39.29	2.90
959	1028	3.489355	ACATCAGCAATTTCAGTGGACA	58.511	40.909	0.00	0.00	0.00	4.02
984	1054	1.465777	TGCATCTGTGAAATGAGTGCG	59.534	47.619	0.00	0.00	34.06	5.34
987	1057	4.649692	AGAACTGCATCTGTGAAATGAGT	58.350	39.130	0.00	0.00	0.00	3.41
995	1065	4.694037	TCTTGATGAAGAACTGCATCTGTG	59.306	41.667	19.56	11.63	41.08	3.66
1006	1076	1.404181	CGCGAGGGTCTTGATGAAGAA	60.404	52.381	0.00	0.00	40.00	2.52
1041	1111	1.264749	CCCCTGGATCGACCTTGACA	61.265	60.000	0.00	0.00	39.86	3.58
1071	1141	4.081142	TCCTGAATCTTCGCCTTGACAATA	60.081	41.667	0.00	0.00	0.00	1.90
1098	1168	0.893270	TGCCAAACATAAGCCGCTGT	60.893	50.000	0.00	0.00	0.00	4.40
1104	1174	1.106285	CCTCCCTGCCAAACATAAGC	58.894	55.000	0.00	0.00	0.00	3.09
1164	1234	1.742761	AGTGAAGGGTGCATTCATCG	58.257	50.000	4.62	0.00	38.81	3.84
1219	1289	7.209471	TCTTGCCTGTCAACGTTTTAATTAT	57.791	32.000	0.00	0.00	0.00	1.28
1299	1369	1.523758	GAATGCCCTCGTCAACTTGT	58.476	50.000	0.00	0.00	0.00	3.16
1308	1378	1.450312	GTCCACAGGAATGCCCTCG	60.450	63.158	0.00	0.00	45.60	4.63
1400	1498	2.580867	CTCGCTAGTCAGGCACGC	60.581	66.667	0.00	0.00	0.00	5.34
1505	1605	5.423610	ACTTCTGACATACTGATTGTAGCCT	59.576	40.000	0.00	0.00	34.24	4.58
1506	1606	5.665459	ACTTCTGACATACTGATTGTAGCC	58.335	41.667	0.00	0.00	34.24	3.93
1507	1607	8.879342	AATACTTCTGACATACTGATTGTAGC	57.121	34.615	0.00	0.00	34.24	3.58
1509	1609	9.098355	GCAAATACTTCTGACATACTGATTGTA	57.902	33.333	0.00	0.00	35.37	2.41
1510	1610	7.826252	AGCAAATACTTCTGACATACTGATTGT	59.174	33.333	0.00	0.00	0.00	2.71
1511	1611	8.206325	AGCAAATACTTCTGACATACTGATTG	57.794	34.615	0.00	0.00	0.00	2.67
1512	1612	9.319143	GTAGCAAATACTTCTGACATACTGATT	57.681	33.333	0.00	0.00	0.00	2.57
1513	1613	7.928706	GGTAGCAAATACTTCTGACATACTGAT	59.071	37.037	0.00	0.00	34.56	2.90
1514	1614	7.124298	AGGTAGCAAATACTTCTGACATACTGA	59.876	37.037	0.00	0.00	34.56	3.41
1515	1615	7.223582	CAGGTAGCAAATACTTCTGACATACTG	59.776	40.741	0.00	0.00	34.56	2.74
1635	1737	4.148696	ACGTACTTCGAACAACATTAACCG	59.851	41.667	0.00	0.00	42.86	4.44
1720	1910	5.034852	TGCTATAAAGACATTAGCAGGCA	57.965	39.130	0.00	0.00	38.65	4.75
1846	2036	3.635331	CAATGCTCTTGTGTGTTTCTGG	58.365	45.455	0.00	0.00	0.00	3.86
2087	2333	9.862371	ATTAAGAGTATGCGGATTTATCTGTAG	57.138	33.333	0.00	0.00	35.60	2.74
2373	2621	7.341256	TCGTATACTCCATCAACTACTCCTTTT	59.659	37.037	0.56	0.00	0.00	2.27

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.