AutoCloner

Multiple sequence alignment - TraesCS6A01G105100

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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	TraesCS6A01G105100	chr6A	100.000	2648	0	0	1	2648	73683551	73680904	0.000000e+00	4891
1	TraesCS6A01G105100	chr6D	94.543	1741	59	11	916	2648	58462092	58460380	0.000000e+00	2656
2	TraesCS6A01G105100	chr6D	95.206	897	21	3	1	878	58463075	58462182	0.000000e+00	1399
3	TraesCS6A01G105100	chr6D	88.000	500	35	11	1431	1919	343522932	343523417	3.830000e-158	568
4	TraesCS6A01G105100	chr6B	92.184	1177	59	13	916	2091	131932193	131931049	0.000000e+00	1633
5	TraesCS6A01G105100	chr6B	95.165	393	18	1	2257	2648	131931013	131930621	1.040000e-173	619
6	TraesCS6A01G105100	chr6B	96.457	254	9	0	1107	1360	651661650	651661397	1.130000e-113	420
7	TraesCS6A01G105100	chr6B	84.188	234	21	8	663	895	131932482	131932264	2.060000e-51	213
8	TraesCS6A01G105100	chr6B	86.452	155	19	2	450	602	131932650	131932496	4.530000e-38	169
9	TraesCS6A01G105100	chr7D	89.936	934	68	15	997	1919	478414746	478415664	0.000000e+00	1181
10	TraesCS6A01G105100	chr7D	87.664	762	70	12	993	1745	223709334	223710080	0.000000e+00	865
11	TraesCS6A01G105100	chr2B	88.136	767	63	17	1164	1919	401017632	401018381	0.000000e+00	887
12	TraesCS6A01G105100	chr2B	88.525	549	38	14	1382	1919	86848818	86848284	2.220000e-180	641
13	TraesCS6A01G105100	chr2B	84.861	251	35	3	1	250	17877152	17877400	1.570000e-62	250
14	TraesCS6A01G105100	chr2B	88.679	106	12	0	2543	2648	640338629	640338734	2.140000e-26	130
15	TraesCS6A01G105100	chr7B	87.223	767	73	14	1164	1919	8676871	8676119	0.000000e+00	850
16	TraesCS6A01G105100	chr7B	88.235	136	12	3	2121	2254	733153350	733153217	2.730000e-35	159
17	TraesCS6A01G105100	chr1A	88.142	565	41	15	1367	1919	365222469	365223019	0.000000e+00	649
18	TraesCS6A01G105100	chr5B	88.525	549	38	10	1382	1919	290878565	290879099	2.220000e-180	641
19	TraesCS6A01G105100	chr5B	94.942	257	13	0	1104	1360	658346496	658346752	1.140000e-108	403
20	TraesCS6A01G105100	chr5B	84.615	247	37	1	4	250	705634749	705634504	7.320000e-61	244
21	TraesCS6A01G105100	chr2D	87.928	497	35	10	1434	1919	621170113	621169631	1.780000e-156	562
22	TraesCS6A01G105100	chr2D	88.679	106	12	0	2543	2648	537505226	537505331	2.140000e-26	130
23	TraesCS6A01G105100	chr1B	88.050	477	32	10	1452	1917	149121645	149121183	2.320000e-150	542
24	TraesCS6A01G105100	chr5D	86.600	500	42	12	1431	1919	170711797	170712282	1.810000e-146	529
25	TraesCS6A01G105100	chr3D	94.553	257	14	0	1104	1360	482588262	482588518	5.310000e-107	398
26	TraesCS6A01G105100	chr3D	84.959	246	37	0	5	250	58277470	58277715	1.570000e-62	250
27	TraesCS6A01G105100	chr3D	84.810	158	17	6	2122	2274	36839800	36839645	4.570000e-33	152
28	TraesCS6A01G105100	chr1D	86.179	246	32	1	4	247	455656324	455656079	5.620000e-67	265
29	TraesCS6A01G105100	chr1D	85.141	249	30	6	1	248	339566142	339566384	5.660000e-62	248
30	TraesCS6A01G105100	chr3A	84.211	247	38	1	4	250	493803912	493803667	3.410000e-59	239
31	TraesCS6A01G105100	chr4D	83.740	246	40	0	5	250	474693126	474693371	1.580000e-57	233
32	TraesCS6A01G105100	chr2A	82.927	246	34	4	5	247	413389420	413389660	5.740000e-52	215

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	TraesCS6A01G105100	chr6A	73680904	73683551	2647	True	4891.0	4891	100.00000	1	2648	1	chr6A.!!$R1	2647
1	TraesCS6A01G105100	chr6D	58460380	58463075	2695	True	2027.5	2656	94.87450	1	2648	2	chr6D.!!$R1	2647
2	TraesCS6A01G105100	chr6B	131930621	131932650	2029	True	658.5	1633	89.49725	450	2648	4	chr6B.!!$R2	2198
3	TraesCS6A01G105100	chr7D	478414746	478415664	918	False	1181.0	1181	89.93600	997	1919	1	chr7D.!!$F2	922
4	TraesCS6A01G105100	chr7D	223709334	223710080	746	False	865.0	865	87.66400	993	1745	1	chr7D.!!$F1	752
5	TraesCS6A01G105100	chr2B	401017632	401018381	749	False	887.0	887	88.13600	1164	1919	1	chr2B.!!$F2	755
6	TraesCS6A01G105100	chr2B	86848284	86848818	534	True	641.0	641	88.52500	1382	1919	1	chr2B.!!$R1	537
7	TraesCS6A01G105100	chr7B	8676119	8676871	752	True	850.0	850	87.22300	1164	1919	1	chr7B.!!$R1	755
8	TraesCS6A01G105100	chr1A	365222469	365223019	550	False	649.0	649	88.14200	1367	1919	1	chr1A.!!$F1	552
9	TraesCS6A01G105100	chr5B	290878565	290879099	534	False	641.0	641	88.52500	1382	1919	1	chr5B.!!$F1	537

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
924	1010	0.674895	CCTCTTCCTGAACCGCTTGG	60.675	60.0	0.0	0.0	39.35	3.61	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1772	1879	1.403323	GCTCAGCATTTGCCTAGAACC	59.597	52.381	0.0	0.0	43.38	3.62	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
82	83	9.887629	ACTAATCATGATCCATATGATGTCTTC	57.112	33.333	9.06	0.00	42.73	2.87
115	116	4.382040	CCATTAGTTCTCGAGGACATGTGT	60.382	45.833	25.58	7.20	0.00	3.72
121	122	3.418047	TCTCGAGGACATGTGTGAAGTA	58.582	45.455	13.56	0.00	0.00	2.24
122	123	3.824443	TCTCGAGGACATGTGTGAAGTAA	59.176	43.478	13.56	0.00	0.00	2.24
209	210	2.744202	CCTCTAGTGGTGTCATGCAAAC	59.256	50.000	2.47	0.00	0.00	2.93
494	514	8.913487	TTTAGGGGCTAACTATAGTATTTTGC	57.087	34.615	5.65	3.51	0.00	3.68
629	649	6.264744	AGAGTTCCAATGATATGCCATGAAAG	59.735	38.462	0.00	0.00	0.00	2.62
704	724	7.209471	AGTGCTTGAAAATTTCGGTGTAATA	57.791	32.000	0.97	0.00	0.00	0.98
745	765	5.477510	TGCCAAATGCTTACGAATTTCAAT	58.522	33.333	0.00	0.00	42.00	2.57
822	843	9.319143	AGATTGTACACTGAATATTAAGTGCTC	57.681	33.333	26.77	20.54	46.28	4.26
824	845	6.627243	TGTACACTGAATATTAAGTGCTCGT	58.373	36.000	26.77	13.78	46.28	4.18
836	857	1.344438	AGTGCTCGTGTGAATCCTGAA	59.656	47.619	0.00	0.00	0.00	3.02
855	876	3.932710	TGAACGTTGGATGTAGAATGAGC	59.067	43.478	5.00	0.00	0.00	4.26
861	882	1.506493	GATGTAGAATGAGCGGCTGG	58.494	55.000	7.50	0.00	0.00	4.85
872	893	2.203209	CGGCTGGTATTGGAGGCC	60.203	66.667	0.00	0.00	39.43	5.19
895	928	3.470567	GCGGCGTGAGTGACTTCG	61.471	66.667	9.37	6.73	0.00	3.79
896	929	2.050351	CGGCGTGAGTGACTTCGT	60.050	61.111	0.00	0.00	0.00	3.85
924	1010	0.674895	CCTCTTCCTGAACCGCTTGG	60.675	60.000	0.00	0.00	39.35	3.61
930	1016	2.282180	TGAACCGCTTGGCCCTTC	60.282	61.111	0.00	0.00	35.53	3.46
955	1041	1.735376	TAGCGAATCTCACCTCCCGC	61.735	60.000	0.00	0.00	42.52	6.13
1014	1103	2.583593	GCGATGGAGCTGTCGTCC	60.584	66.667	12.54	0.00	39.87	4.79
1105	1194	2.688666	AGATCCTGGCCGCCAAGA	60.689	61.111	14.45	13.78	30.80	3.02
1437	1528	1.563435	CTGTGTCTCAACTGCAGGCG	61.563	60.000	19.93	8.57	0.00	5.52
1555	1646	1.828768	CTGGATGAGACCCTGGCTC	59.171	63.158	0.00	0.00	0.00	4.70
1556	1647	0.979709	CTGGATGAGACCCTGGCTCA	60.980	60.000	1.47	1.47	45.52	4.26
1608	1702	2.744768	GCTCCAGAAAGCCTTCGCG	61.745	63.158	0.00	0.00	41.18	5.87
1609	1703	1.374758	CTCCAGAAAGCCTTCGCGT	60.375	57.895	5.77	0.00	41.18	6.01
1610	1704	1.355066	CTCCAGAAAGCCTTCGCGTC	61.355	60.000	5.77	0.00	41.18	5.19
1634	1728	3.010138	TCACAGGTTAGGGATCAAAAGGG	59.990	47.826	0.00	0.00	0.00	3.95
1635	1729	2.311841	ACAGGTTAGGGATCAAAAGGGG	59.688	50.000	0.00	0.00	0.00	4.79
1651	1745	1.202891	AGGGGGCACAAAACTGACTAC	60.203	52.381	0.00	0.00	0.00	2.73
1652	1746	0.872388	GGGGCACAAAACTGACTACG	59.128	55.000	0.00	0.00	0.00	3.51
1653	1747	1.589803	GGGCACAAAACTGACTACGT	58.410	50.000	0.00	0.00	0.00	3.57
1654	1748	2.548493	GGGGCACAAAACTGACTACGTA	60.548	50.000	0.00	0.00	0.00	3.57
1655	1749	2.735134	GGGCACAAAACTGACTACGTAG	59.265	50.000	20.97	20.97	0.00	3.51
1657	1751	4.549458	GGCACAAAACTGACTACGTAGTA	58.451	43.478	27.44	14.69	45.11	1.82
1658	1752	4.383948	GGCACAAAACTGACTACGTAGTAC	59.616	45.833	27.44	19.83	45.11	2.73
1659	1753	5.218139	GCACAAAACTGACTACGTAGTACT	58.782	41.667	27.44	10.45	45.11	2.73
1684	1780	2.289195	TGTGGTACTCCAAGCTAAACGG	60.289	50.000	0.00	0.00	46.15	4.44
1757	1864	4.380655	GGCTAGCGGACCATAACATAGTAG	60.381	50.000	9.00	0.00	0.00	2.57
1758	1865	4.217983	GCTAGCGGACCATAACATAGTAGT	59.782	45.833	0.00	0.00	0.00	2.73
1759	1866	5.413833	GCTAGCGGACCATAACATAGTAGTA	59.586	44.000	0.00	0.00	0.00	1.82
1760	1867	5.702349	AGCGGACCATAACATAGTAGTAC	57.298	43.478	0.00	0.00	0.00	2.73
1773	1880	8.997621	AACATAGTAGTACAATGTAGTGTTGG	57.002	34.615	10.78	0.42	33.59	3.77
1787	1894	2.558359	AGTGTTGGTTCTAGGCAAATGC	59.442	45.455	0.00	0.00	41.14	3.56
1802	1909	4.378046	GGCAAATGCTGAGCAAATTTTGAG	60.378	41.667	26.94	9.54	43.62	3.02
1870	1977	5.103000	CCCTACTACTGATGAAACGAACTG	58.897	45.833	0.00	0.00	0.00	3.16
1932	2045	7.282450	AGTCTTGTTTAGAACACCGAAATTCTT	59.718	33.333	1.22	0.00	41.97	2.52
1933	2046	7.376072	GTCTTGTTTAGAACACCGAAATTCTTG	59.624	37.037	1.22	0.00	41.97	3.02
1939	2052	4.832823	AGAACACCGAAATTCTTGGGATTT	59.167	37.500	0.00	0.00	34.62	2.17
2140	2268	1.480219	GGCGCTGCTATACACACGAC	61.480	60.000	7.64	0.00	0.00	4.34
2150	2278	2.428960	TACACACGACGCCTGCACAT	62.429	55.000	0.00	0.00	0.00	3.21
2156	2284	4.357947	ACGCCTGCACATCGACGT	62.358	61.111	0.00	0.00	0.00	4.34
2339	2467	2.354510	TGCAAACCAAAAGTCGTCTGAG	59.645	45.455	0.00	0.00	0.00	3.35
2597	2727	6.312180	GGAATGCTTTCTGGCTTATTTTCTTG	59.688	38.462	11.68	0.00	32.16	3.02
2619	2749	4.458989	TGCTTGCTAATTTAGTTCCACTGG	59.541	41.667	5.38	0.00	0.00	4.00

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
82	83	6.072728	CCTCGAGAACTAATGGATCTACTCAG	60.073	46.154	15.71	0.00	0.00	3.35
115	116	8.882736	CACATGATTACTAGCAACATTACTTCA	58.117	33.333	0.00	0.00	0.00	3.02
121	122	7.928307	ACTTCACATGATTACTAGCAACATT	57.072	32.000	0.00	0.00	0.00	2.71
122	123	7.607607	TCAACTTCACATGATTACTAGCAACAT	59.392	33.333	0.00	0.00	0.00	2.71
209	210	5.329493	TGATGAAGTGTTATGTACTCGACG	58.671	41.667	0.00	0.00	0.00	5.12
494	514	6.086222	CCATTTCATTCAAACACTTAGTCCG	58.914	40.000	0.00	0.00	0.00	4.79
611	631	7.937649	TCTTCTTCTTTCATGGCATATCATTG	58.062	34.615	0.00	0.00	0.00	2.82
629	649	7.437862	AGCATATCATTCGAACTCTTCTTCTTC	59.562	37.037	0.00	0.00	0.00	2.87
704	724	7.701539	TTTGGCATTCATACAACTCAATAGT	57.298	32.000	0.00	0.00	37.65	2.12
822	843	1.194547	CCAACGTTCAGGATTCACACG	59.805	52.381	0.00	0.00	36.91	4.49
824	845	2.920724	TCCAACGTTCAGGATTCACA	57.079	45.000	0.00	0.00	0.00	3.58
836	857	2.540515	CGCTCATTCTACATCCAACGT	58.459	47.619	0.00	0.00	0.00	3.99
855	876	2.203209	GGCCTCCAATACCAGCCG	60.203	66.667	0.00	0.00	33.18	5.52
861	882	2.481471	GCGCCTTGGCCTCCAATAC	61.481	63.158	3.32	0.00	43.07	1.89
880	901	0.388649	ATCACGAAGTCACTCACGCC	60.389	55.000	4.58	0.00	41.61	5.68
895	928	2.461695	TCAGGAAGAGGTCTCCATCAC	58.538	52.381	0.00	0.00	0.00	3.06
896	929	2.834549	GTTCAGGAAGAGGTCTCCATCA	59.165	50.000	0.00	0.00	0.00	3.07
924	1010	2.666098	TTCGCTACAGGGGAAGGGC	61.666	63.158	0.00	0.00	41.05	5.19
930	1016	0.105039	GGTGAGATTCGCTACAGGGG	59.895	60.000	0.00	0.00	0.00	4.79
1555	1646	2.032528	TCTGAACTGGCGGGCTTG	59.967	61.111	2.38	0.00	0.00	4.01
1556	1647	2.348998	CTCTGAACTGGCGGGCTT	59.651	61.111	2.38	0.00	0.00	4.35
1608	1702	1.822990	TGATCCCTAACCTGTGACGAC	59.177	52.381	0.00	0.00	0.00	4.34
1609	1703	2.225382	TGATCCCTAACCTGTGACGA	57.775	50.000	0.00	0.00	0.00	4.20
1610	1704	3.328382	TTTGATCCCTAACCTGTGACG	57.672	47.619	0.00	0.00	0.00	4.35
1634	1728	1.589803	ACGTAGTCAGTTTTGTGCCC	58.410	50.000	0.00	0.00	29.74	5.36
1635	1729	3.387397	ACTACGTAGTCAGTTTTGTGCC	58.613	45.455	22.45	0.00	43.93	5.01
1655	1749	4.159879	AGCTTGGAGTACCACATACAGTAC	59.840	45.833	0.00	0.00	46.80	2.73
1656	1750	4.350245	AGCTTGGAGTACCACATACAGTA	58.650	43.478	0.00	0.00	46.80	2.74
1657	1751	3.173965	AGCTTGGAGTACCACATACAGT	58.826	45.455	0.00	0.00	46.80	3.55
1658	1752	3.895232	AGCTTGGAGTACCACATACAG	57.105	47.619	0.00	0.00	46.80	2.74
1659	1753	5.484715	GTTTAGCTTGGAGTACCACATACA	58.515	41.667	0.00	0.00	46.80	2.29
1684	1780	3.431572	CGATTGAGCTAGCTAATGAAGGC	59.568	47.826	19.38	2.75	0.00	4.35
1757	1864	5.350640	GCCTAGAACCAACACTACATTGTAC	59.649	44.000	0.00	0.00	0.00	2.90
1758	1865	5.012251	TGCCTAGAACCAACACTACATTGTA	59.988	40.000	0.00	0.00	0.00	2.41
1759	1866	4.202419	TGCCTAGAACCAACACTACATTGT	60.202	41.667	0.00	0.00	0.00	2.71
1760	1867	4.323417	TGCCTAGAACCAACACTACATTG	58.677	43.478	0.00	0.00	0.00	2.82
1772	1879	1.403323	GCTCAGCATTTGCCTAGAACC	59.597	52.381	0.00	0.00	43.38	3.62
1773	1880	2.086869	TGCTCAGCATTTGCCTAGAAC	58.913	47.619	0.00	0.00	43.38	3.01
1787	1894	5.957798	TCCATTAGCTCAAAATTTGCTCAG	58.042	37.500	4.89	0.00	38.15	3.35
1802	1909	2.614057	CCCACGAAACTCATCCATTAGC	59.386	50.000	0.00	0.00	0.00	3.09
1870	1977	6.073548	GCATGTATCTGCCTGTAGACATTTAC	60.074	42.308	0.00	0.00	36.10	2.01
1932	2045	3.509442	AGTGGCAAAGATTGAAATCCCA	58.491	40.909	0.00	0.00	36.04	4.37
1933	2046	3.428045	CGAGTGGCAAAGATTGAAATCCC	60.428	47.826	0.00	0.00	36.04	3.85
2001	2114	7.428282	TCATCTAGCGTTTGAATTACAACAA	57.572	32.000	0.00	0.00	38.29	2.83
2140	2268	3.545481	GACGTCGATGTGCAGGCG	61.545	66.667	16.54	0.00	41.70	5.52
2156	2284	2.965147	GCTGTTGGCATTGCGACGA	61.965	57.895	0.00	0.00	41.35	4.20
2619	2749	6.473455	GCAATTGTCATTATTCTACTGGCAAC	59.527	38.462	7.40	0.00	37.32	4.17

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.