AutoCloner

Multiple sequence alignment - TraesCS1D01G334500

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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	TraesCS1D01G334500	chr1D	100.000	2567	0	0	1	2567	424732116	424734682	0.000000e+00	4741.0
1	TraesCS1D01G334500	chr1D	88.060	2010	193	22	68	2042	58566461	58564464	0.000000e+00	2338.0
2	TraesCS1D01G334500	chr1D	79.938	324	50	11	2253	2567	204795655	204795338	9.240000e-55	224.0
3	TraesCS1D01G334500	chr7D	85.384	2511	282	43	118	2564	536462739	536460250	0.000000e+00	2525.0
4	TraesCS1D01G334500	chr7D	85.637	2033	226	29	31	2042	4240311	4238324	0.000000e+00	2076.0
5	TraesCS1D01G334500	chr7D	86.203	1638	194	21	31	1639	406522231	406520597	0.000000e+00	1744.0
6	TraesCS1D01G334500	chr7D	86.720	994	96	20	1406	2371	488777396	488778381	0.000000e+00	1072.0
7	TraesCS1D01G334500	chr1A	84.298	2522	324	27	69	2537	555932493	555934995	0.000000e+00	2398.0
8	TraesCS1D01G334500	chr1A	90.770	1636	124	11	431	2042	520576393	520578025	0.000000e+00	2159.0
9	TraesCS1D01G334500	chr1A	84.727	2069	243	32	28	2042	251944321	251946370	0.000000e+00	2002.0
10	TraesCS1D01G334500	chr3D	83.750	2597	307	48	31	2567	551004184	551001643	0.000000e+00	2351.0
11	TraesCS1D01G334500	chr3D	85.694	1384	151	30	96	1463	105108360	105107008	0.000000e+00	1415.0
12	TraesCS1D01G334500	chr3D	84.859	568	61	17	1984	2536	297490687	297491244	1.340000e-152	549.0
13	TraesCS1D01G334500	chr5A	83.780	2386	299	47	127	2466	440669687	440672030	0.000000e+00	2182.0
14	TraesCS1D01G334500	chr5A	80.761	1918	255	64	693	2550	504238596	504236733	0.000000e+00	1393.0
15	TraesCS1D01G334500	chr5A	85.468	1101	140	10	429	1521	654845572	654844484	0.000000e+00	1129.0
16	TraesCS1D01G334500	chrUn	83.375	2400	296	58	28	2384	286002929	286005268	0.000000e+00	2126.0
17	TraesCS1D01G334500	chr3B	84.496	2064	247	32	539	2567	547564373	547562348	0.000000e+00	1971.0
18	TraesCS1D01G334500	chr3B	89.215	1057	89	14	1337	2369	697196788	697195733	0.000000e+00	1297.0
19	TraesCS1D01G334500	chr3B	84.848	99	15	0	2464	2562	387213391	387213489	1.630000e-17	100.0
20	TraesCS1D01G334500	chr5B	87.107	1590	169	19	993	2551	289034306	289032722	0.000000e+00	1768.0
21	TraesCS1D01G334500	chr5B	82.039	206	33	4	2364	2567	242196881	242196678	3.400000e-39	172.0
22	TraesCS1D01G334500	chr7A	85.933	1500	185	18	561	2042	292816268	292817759	0.000000e+00	1578.0
23	TraesCS1D01G334500	chr7A	78.309	1277	199	43	694	1939	56842340	56843569	0.000000e+00	752.0
24	TraesCS1D01G334500	chr1B	84.648	1407	177	25	106	1492	647050303	647051690	0.000000e+00	1365.0
25	TraesCS1D01G334500	chr7B	82.883	555	81	11	1990	2534	203887938	203888488	1.070000e-133	486.0
26	TraesCS1D01G334500	chr7B	78.495	186	35	3	2355	2539	448797488	448797669	1.610000e-22	117.0
27	TraesCS1D01G334500	chr7B	90.000	50	5	0	2517	2566	516875129	516875080	5.930000e-07	65.8
28	TraesCS1D01G334500	chr6D	82.211	579	73	16	1992	2567	450134213	450134764	2.990000e-129	472.0
29	TraesCS1D01G334500	chr2B	82.111	559	67	21	1999	2544	376148294	376148832	5.040000e-122	448.0
30	TraesCS1D01G334500	chr2D	82.957	487	50	12	1992	2454	630544030	630544507	2.380000e-110	409.0

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	TraesCS1D01G334500	chr1D	424732116	424734682	2566	False	4741	4741	100.000	1	2567	1	chr1D.!!$F1	2566
1	TraesCS1D01G334500	chr1D	58564464	58566461	1997	True	2338	2338	88.060	68	2042	1	chr1D.!!$R1	1974
2	TraesCS1D01G334500	chr7D	536460250	536462739	2489	True	2525	2525	85.384	118	2564	1	chr7D.!!$R3	2446
3	TraesCS1D01G334500	chr7D	4238324	4240311	1987	True	2076	2076	85.637	31	2042	1	chr7D.!!$R1	2011
4	TraesCS1D01G334500	chr7D	406520597	406522231	1634	True	1744	1744	86.203	31	1639	1	chr7D.!!$R2	1608
5	TraesCS1D01G334500	chr7D	488777396	488778381	985	False	1072	1072	86.720	1406	2371	1	chr7D.!!$F1	965
6	TraesCS1D01G334500	chr1A	555932493	555934995	2502	False	2398	2398	84.298	69	2537	1	chr1A.!!$F3	2468
7	TraesCS1D01G334500	chr1A	520576393	520578025	1632	False	2159	2159	90.770	431	2042	1	chr1A.!!$F2	1611
8	TraesCS1D01G334500	chr1A	251944321	251946370	2049	False	2002	2002	84.727	28	2042	1	chr1A.!!$F1	2014
9	TraesCS1D01G334500	chr3D	551001643	551004184	2541	True	2351	2351	83.750	31	2567	1	chr3D.!!$R2	2536
10	TraesCS1D01G334500	chr3D	105107008	105108360	1352	True	1415	1415	85.694	96	1463	1	chr3D.!!$R1	1367
11	TraesCS1D01G334500	chr3D	297490687	297491244	557	False	549	549	84.859	1984	2536	1	chr3D.!!$F1	552
12	TraesCS1D01G334500	chr5A	440669687	440672030	2343	False	2182	2182	83.780	127	2466	1	chr5A.!!$F1	2339
13	TraesCS1D01G334500	chr5A	504236733	504238596	1863	True	1393	1393	80.761	693	2550	1	chr5A.!!$R1	1857
14	TraesCS1D01G334500	chr5A	654844484	654845572	1088	True	1129	1129	85.468	429	1521	1	chr5A.!!$R2	1092
15	TraesCS1D01G334500	chrUn	286002929	286005268	2339	False	2126	2126	83.375	28	2384	1	chrUn.!!$F1	2356
16	TraesCS1D01G334500	chr3B	547562348	547564373	2025	True	1971	1971	84.496	539	2567	1	chr3B.!!$R1	2028
17	TraesCS1D01G334500	chr3B	697195733	697196788	1055	True	1297	1297	89.215	1337	2369	1	chr3B.!!$R2	1032
18	TraesCS1D01G334500	chr5B	289032722	289034306	1584	True	1768	1768	87.107	993	2551	1	chr5B.!!$R2	1558
19	TraesCS1D01G334500	chr7A	292816268	292817759	1491	False	1578	1578	85.933	561	2042	1	chr7A.!!$F2	1481
20	TraesCS1D01G334500	chr7A	56842340	56843569	1229	False	752	752	78.309	694	1939	1	chr7A.!!$F1	1245
21	TraesCS1D01G334500	chr1B	647050303	647051690	1387	False	1365	1365	84.648	106	1492	1	chr1B.!!$F1	1386
22	TraesCS1D01G334500	chr7B	203887938	203888488	550	False	486	486	82.883	1990	2534	1	chr7B.!!$F1	544
23	TraesCS1D01G334500	chr6D	450134213	450134764	551	False	472	472	82.211	1992	2567	1	chr6D.!!$F1	575
24	TraesCS1D01G334500	chr2B	376148294	376148832	538	False	448	448	82.111	1999	2544	1	chr2B.!!$F1	545

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
23	24	0.683973	ACCACTTCTCAGTCAGCCAG	59.316	55.0	0.00	0.00	0.00	4.85	F
1191	1278	0.393537	GGACTACGACCTCGAGGGAA	60.394	60.0	34.04	15.54	43.02	3.97	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1291	1379	0.378257	GTTCTCGGCCGTCGTGTATA	59.622	55.0	27.15	1.04	40.32	1.47	R
2184	2317	1.015109	GCCAGAGATCACTCGTCGTA	58.985	55.0	0.00	0.00	46.64	3.43	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
20	21	3.669251	ACTAACCACTTCTCAGTCAGC	57.331	47.619	0.00	0.00	0.00	4.26
21	22	2.300437	ACTAACCACTTCTCAGTCAGCC	59.700	50.000	0.00	0.00	0.00	4.85
22	23	1.131638	AACCACTTCTCAGTCAGCCA	58.868	50.000	0.00	0.00	0.00	4.75
23	24	0.683973	ACCACTTCTCAGTCAGCCAG	59.316	55.000	0.00	0.00	0.00	4.85
24	25	0.683973	CCACTTCTCAGTCAGCCAGT	59.316	55.000	0.00	0.00	0.00	4.00
25	26	1.337635	CCACTTCTCAGTCAGCCAGTC	60.338	57.143	0.00	0.00	0.00	3.51
26	27	1.342496	CACTTCTCAGTCAGCCAGTCA	59.658	52.381	0.00	0.00	0.00	3.41
29	30	1.709578	TCTCAGTCAGCCAGTCAACT	58.290	50.000	0.00	0.00	0.00	3.16
45	46	3.913573	CTCATTTCGTCCGCGCGG	61.914	66.667	42.13	42.13	38.14	6.46
58	59	1.419874	CGCGCGGGTCCGTTTAAATA	61.420	55.000	24.84	0.00	42.09	1.40
77	78	4.866508	ATAGTGACGGTCAGAAAAGTCA	57.133	40.909	11.83	1.05	40.77	3.41
79	80	2.431057	AGTGACGGTCAGAAAAGTCAGT	59.569	45.455	11.83	5.32	43.22	3.41
264	273	2.228822	CCACCATTTTCCTCCACTTTCG	59.771	50.000	0.00	0.00	0.00	3.46
375	388	2.597340	CATCATGACCGCCCCCTT	59.403	61.111	0.00	0.00	0.00	3.95
437	461	2.699954	CGCCCTAGCAAAAGAAGAAGA	58.300	47.619	0.00	0.00	39.83	2.87
446	470	3.498397	GCAAAAGAAGAAGATGACGGTCA	59.502	43.478	14.01	14.01	0.00	4.02
677	744	0.737219	ATCGTCTACGTTTCCTCGGG	59.263	55.000	0.00	0.00	40.80	5.14
750	818	2.264794	CGTCTACCCGCAAGCCTT	59.735	61.111	0.00	0.00	0.00	4.35
820	894	4.169696	CCCGCGCCCATCAACCTA	62.170	66.667	0.00	0.00	0.00	3.08
821	895	2.588877	CCGCGCCCATCAACCTAG	60.589	66.667	0.00	0.00	0.00	3.02
825	899	1.515954	CGCCCATCAACCTAGACGT	59.484	57.895	0.00	0.00	0.00	4.34
1189	1276	0.814812	GAGGACTACGACCTCGAGGG	60.815	65.000	34.04	20.19	43.25	4.30
1191	1278	0.393537	GGACTACGACCTCGAGGGAA	60.394	60.000	34.04	15.54	43.02	3.97
1231	1318	1.377333	GGGAGCCTTTGTTCGAGGG	60.377	63.158	0.00	0.00	34.75	4.30
1291	1379	1.122019	AAGAGCAGGTGGACGAAGGT	61.122	55.000	0.00	0.00	0.00	3.50
1308	1396	1.439353	GGTATACACGACGGCCGAGA	61.439	60.000	35.90	10.05	41.76	4.04
1321	1409	0.799393	GCCGAGAACAAGCTCCTTTC	59.201	55.000	0.00	0.00	0.00	2.62
1335	1423	2.634940	CTCCTTTCTGAGTGTTGGAGGA	59.365	50.000	0.00	0.00	37.87	3.71
1427	1515	3.251004	AGTTCCATGAACGCAAGAAGTTC	59.749	43.478	0.00	0.00	45.96	3.01
1650	1762	2.744741	TGCTTGCATGCAATTCATTTGG	59.255	40.909	31.96	18.77	40.29	3.28
1740	1853	1.646189	GAGGGTCATCAAAGACGAGC	58.354	55.000	0.00	0.00	39.42	5.03
2043	2171	1.202989	AGATGCTAGAGATCGAGGCCA	60.203	52.381	5.01	0.00	0.00	5.36
2094	2223	1.265365	CTCTCGCTAGCATGATGACGA	59.735	52.381	16.45	9.34	0.00	4.20
2175	2308	0.745845	GAAGATGCAGGCCGACATGT	60.746	55.000	17.07	11.03	0.00	3.21
2184	2317	1.072331	AGGCCGACATGTTCAAGTTCT	59.928	47.619	0.00	0.00	0.00	3.01
2199	2332	4.093115	TCAAGTTCTACGACGAGTGATCTC	59.907	45.833	0.00	0.00	37.35	2.75
2434	2616	2.229302	CCGCGGACCTTTTCCAAATTTA	59.771	45.455	24.07	0.00	46.29	1.40
2499	2682	3.482436	ACTCAAATGTTAAACAGGGCGA	58.518	40.909	0.00	0.00	0.00	5.54
2545	2728	3.576648	ACGGACAAAAAGCGAACAAAAA	58.423	36.364	0.00	0.00	0.00	1.94
2552	2735	2.217429	AAGCGAACAAAAATGCCGTT	57.783	40.000	0.00	0.00	0.00	4.44
2553	2736	2.217429	AGCGAACAAAAATGCCGTTT	57.783	40.000	0.00	0.00	0.00	3.60

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	2.300437	GGCTGACTGAGAAGTGGTTAGT	59.700	50.000	0.00	0.00	0.00	2.24
1	2	2.300152	TGGCTGACTGAGAAGTGGTTAG	59.700	50.000	0.00	0.00	0.00	2.34
2	3	2.300152	CTGGCTGACTGAGAAGTGGTTA	59.700	50.000	0.00	0.00	0.00	2.85
3	4	1.071385	CTGGCTGACTGAGAAGTGGTT	59.929	52.381	0.00	0.00	0.00	3.67
4	5	0.683973	CTGGCTGACTGAGAAGTGGT	59.316	55.000	0.00	0.00	0.00	4.16
5	6	0.683973	ACTGGCTGACTGAGAAGTGG	59.316	55.000	0.00	0.00	0.00	4.00
6	7	1.342496	TGACTGGCTGACTGAGAAGTG	59.658	52.381	0.00	0.00	0.00	3.16
7	8	1.709578	TGACTGGCTGACTGAGAAGT	58.290	50.000	0.00	0.00	0.00	3.01
8	9	2.036992	AGTTGACTGGCTGACTGAGAAG	59.963	50.000	0.00	0.00	0.00	2.85
9	10	2.036475	GAGTTGACTGGCTGACTGAGAA	59.964	50.000	0.00	0.00	0.00	2.87
10	11	1.615883	GAGTTGACTGGCTGACTGAGA	59.384	52.381	0.00	0.00	0.00	3.27
11	12	1.342496	TGAGTTGACTGGCTGACTGAG	59.658	52.381	0.00	0.00	0.00	3.35
12	13	1.413118	TGAGTTGACTGGCTGACTGA	58.587	50.000	0.00	0.00	0.00	3.41
13	14	2.469274	ATGAGTTGACTGGCTGACTG	57.531	50.000	0.00	0.00	0.00	3.51
14	15	3.406764	GAAATGAGTTGACTGGCTGACT	58.593	45.455	0.00	0.00	0.00	3.41
15	16	2.158449	CGAAATGAGTTGACTGGCTGAC	59.842	50.000	0.00	0.00	0.00	3.51
16	17	2.224281	ACGAAATGAGTTGACTGGCTGA	60.224	45.455	0.00	0.00	0.00	4.26
17	18	2.146342	ACGAAATGAGTTGACTGGCTG	58.854	47.619	0.00	0.00	0.00	4.85
18	19	2.417719	GACGAAATGAGTTGACTGGCT	58.582	47.619	0.00	0.00	0.00	4.75
19	20	1.464997	GGACGAAATGAGTTGACTGGC	59.535	52.381	0.00	0.00	0.00	4.85
20	21	1.726791	CGGACGAAATGAGTTGACTGG	59.273	52.381	0.00	0.00	0.00	4.00
21	22	1.126846	GCGGACGAAATGAGTTGACTG	59.873	52.381	0.00	0.00	0.00	3.51
22	23	1.429463	GCGGACGAAATGAGTTGACT	58.571	50.000	0.00	0.00	0.00	3.41
23	24	0.093026	CGCGGACGAAATGAGTTGAC	59.907	55.000	0.00	0.00	43.93	3.18
24	25	1.623081	GCGCGGACGAAATGAGTTGA	61.623	55.000	8.83	0.00	43.93	3.18
25	26	1.225745	GCGCGGACGAAATGAGTTG	60.226	57.895	8.83	0.00	43.93	3.16
26	27	2.726691	CGCGCGGACGAAATGAGTT	61.727	57.895	24.84	0.00	43.93	3.01
54	55	5.607477	TGACTTTTCTGACCGTCACTATTT	58.393	37.500	0.00	0.00	32.00	1.40
55	56	5.209818	TGACTTTTCTGACCGTCACTATT	57.790	39.130	0.00	0.00	32.00	1.73
58	59	2.431057	ACTGACTTTTCTGACCGTCACT	59.569	45.455	0.00	0.00	33.32	3.41
66	67	2.210116	GCGTTGGACTGACTTTTCTGA	58.790	47.619	0.00	0.00	0.00	3.27
200	204	2.511600	GGAGTAGTTGGCGCGCAT	60.512	61.111	34.42	17.58	0.00	4.73
201	205	4.752879	GGGAGTAGTTGGCGCGCA	62.753	66.667	34.42	16.55	0.00	6.09
208	212	4.157120	CGGGCCGGGGAGTAGTTG	62.157	72.222	20.56	0.00	0.00	3.16
264	273	3.691342	GGCGGGAGGGTTTTTGGC	61.691	66.667	0.00	0.00	0.00	4.52
298	310	3.060000	TCGTCGTCCATGGCGAGT	61.060	61.111	25.06	0.00	39.14	4.18
422	443	4.894784	ACCGTCATCTTCTTCTTTTGCTA	58.105	39.130	0.00	0.00	0.00	3.49
437	461	2.579201	CCGCTCCTTGACCGTCAT	59.421	61.111	1.09	0.00	0.00	3.06
455	479	4.148825	CTTCGCCGACTCCCTGGG	62.149	72.222	6.33	6.33	0.00	4.45
658	725	0.737219	CCCGAGGAAACGTAGACGAT	59.263	55.000	9.41	0.00	43.02	3.73
677	744	1.446272	GCGACTCTGGTAGCACCAC	60.446	63.158	4.16	0.00	44.79	4.16
776	844	4.988598	CGCCACCACGCTCACCTT	62.989	66.667	0.00	0.00	0.00	3.50
820	894	2.633509	GGCTACCGGTGTGACGTCT	61.634	63.158	19.93	0.00	0.00	4.18
821	895	2.126189	GGCTACCGGTGTGACGTC	60.126	66.667	19.93	9.11	0.00	4.34
945	1020	3.804036	TGAAACAGTTGGTCGTCTCATT	58.196	40.909	0.00	0.00	0.00	2.57
1189	1276	4.267928	CGTCGATGTCCAACTTATCCTTTC	59.732	45.833	0.00	0.00	0.00	2.62
1191	1278	3.430374	CCGTCGATGTCCAACTTATCCTT	60.430	47.826	3.52	0.00	0.00	3.36
1291	1379	0.378257	GTTCTCGGCCGTCGTGTATA	59.622	55.000	27.15	1.04	40.32	1.47
1308	1396	3.567478	ACACTCAGAAAGGAGCTTGTT	57.433	42.857	0.00	0.00	38.50	2.83
1390	1478	1.337821	GAACTCACGATGGACACGAC	58.662	55.000	0.00	0.00	34.70	4.34
1427	1515	1.867919	TTTGCATTTGGTACGGCGGG	61.868	55.000	13.24	0.00	0.00	6.13
1833	1961	5.772169	CCTTCTTCTTGAAATTGGTCTTCCT	59.228	40.000	0.00	0.00	33.79	3.36
2043	2171	3.056213	CCTTGGTCTTGGCATTGGT	57.944	52.632	0.00	0.00	0.00	3.67
2094	2223	2.240667	CCACCTTCATGATCTTCACCCT	59.759	50.000	0.00	0.00	0.00	4.34
2175	2308	4.454847	AGATCACTCGTCGTAGAACTTGAA	59.545	41.667	0.00	0.00	39.69	2.69
2184	2317	1.015109	GCCAGAGATCACTCGTCGTA	58.985	55.000	0.00	0.00	46.64	3.43
2402	2582	3.896133	TCCGCGGCCGTAGATCAC	61.896	66.667	28.70	6.83	0.00	3.06
2434	2616	1.134487	CCATTTCATGTTCGCGCGT	59.866	52.632	30.98	7.39	0.00	6.01
2471	2653	3.252215	TGTTTAACATTTGAGTCGGCAGG	59.748	43.478	0.00	0.00	0.00	4.85
2480	2662	3.304123	CGTTCGCCCTGTTTAACATTTGA	60.304	43.478	0.00	0.00	0.00	2.69
2515	2698	1.671845	CTTTTTGTCCGTTTGGGTCGA	59.328	47.619	0.00	0.00	37.00	4.20
2545	2728	1.657556	CGACCCAAACAAACGGCAT	59.342	52.632	0.00	0.00	0.00	4.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.