AutoCloner

Multiple sequence alignment - TraesCS1A01G435100

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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	TraesCS1A01G435100	chr1A	100.000	2325	0	0	413	2737	585689982	585692306	0.000000e+00	4294.0
1	TraesCS1A01G435100	chr1A	83.421	1140	145	26	667	1776	585742717	585743842	0.000000e+00	1018.0
2	TraesCS1A01G435100	chr1A	100.000	40	0	0	1	40	585689570	585689609	1.050000e-09	75.0
3	TraesCS1A01G435100	chr1D	92.617	2167	119	19	591	2736	487614224	487616370	0.000000e+00	3077.0
4	TraesCS1A01G435100	chr1D	88.485	660	69	4	970	1628	487624105	487624758	0.000000e+00	791.0
5	TraesCS1A01G435100	chr1D	79.328	387	53	17	472	851	487623635	487624001	2.110000e-61	246.0
6	TraesCS1A01G435100	chr1D	90.580	138	9	3	456	593	487611279	487611412	2.170000e-41	180.0
7	TraesCS1A01G435100	chr1B	91.610	1621	84	18	436	2017	679173836	679175443	0.000000e+00	2193.0
8	TraesCS1A01G435100	chr1B	92.055	1460	85	14	413	1855	679225101	679226546	0.000000e+00	2025.0
9	TraesCS1A01G435100	chr1B	91.858	1437	69	18	542	1939	679249322	679250749	0.000000e+00	1962.0
10	TraesCS1A01G435100	chr1B	91.934	905	49	14	1844	2737	679228537	679229428	0.000000e+00	1245.0
11	TraesCS1A01G435100	chr1B	84.967	918	113	15	970	1870	679255504	679256413	0.000000e+00	907.0
12	TraesCS1A01G435100	chr1B	84.205	918	120	16	970	1870	679194738	679195647	0.000000e+00	869.0
13	TraesCS1A01G435100	chr1B	88.967	707	68	9	2038	2737	679175432	679176135	0.000000e+00	865.0
14	TraesCS1A01G435100	chr1B	78.947	475	59	16	468	921	679255030	679255484	4.460000e-73	285.0
15	TraesCS1A01G435100	chr1B	80.938	320	40	8	619	921	679194403	679194718	1.640000e-57	233.0
16	TraesCS1A01G435100	chr2B	85.938	64	8	1	2576	2638	358047210	358047147	1.760000e-07	67.6
17	TraesCS1A01G435100	chr2D	91.111	45	3	1	2595	2638	302424603	302424559	2.940000e-05	60.2

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	TraesCS1A01G435100	chr1A	585689570	585692306	2736	False	2184.5	4294	100.0000	1	2737	2	chr1A.!!$F2	2736
1	TraesCS1A01G435100	chr1A	585742717	585743842	1125	False	1018.0	1018	83.4210	667	1776	1	chr1A.!!$F1	1109
2	TraesCS1A01G435100	chr1D	487611279	487616370	5091	False	1628.5	3077	91.5985	456	2736	2	chr1D.!!$F1	2280
3	TraesCS1A01G435100	chr1D	487623635	487624758	1123	False	518.5	791	83.9065	472	1628	2	chr1D.!!$F2	1156
4	TraesCS1A01G435100	chr1B	679249322	679250749	1427	False	1962.0	1962	91.8580	542	1939	1	chr1B.!!$F1	1397
5	TraesCS1A01G435100	chr1B	679225101	679229428	4327	False	1635.0	2025	91.9945	413	2737	2	chr1B.!!$F4	2324
6	TraesCS1A01G435100	chr1B	679173836	679176135	2299	False	1529.0	2193	90.2885	436	2737	2	chr1B.!!$F2	2301
7	TraesCS1A01G435100	chr1B	679255030	679256413	1383	False	596.0	907	81.9570	468	1870	2	chr1B.!!$F5	1402
8	TraesCS1A01G435100	chr1B	679194403	679195647	1244	False	551.0	869	82.5715	619	1870	2	chr1B.!!$F3	1251

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
735	3562	0.248866	CCAACAACTTTCGGTGGTGC	60.249	55.0	0.00	0.0	31.41	5.01	F
1356	4243	0.910088	AGGTCTTACCAGGTGGAGGC	60.910	60.0	0.76	1.3	41.95	4.70	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1555	4442	0.031111	TCCATCCTCATCGAAGGGGT	60.031	55.0	6.43	0.0	37.02	4.95	R
2601	7529	0.045008	TGGCCCAACTCCCCTATACA	59.955	55.0	0.00	0.0	0.00	2.29	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
18	19	2.747855	CCCGGCCTGTTTCTGAGC	60.748	66.667	0.00	0.00	0.00	4.26
19	20	2.032528	CCGGCCTGTTTCTGAGCA	59.967	61.111	0.00	0.00	0.00	4.26
20	21	1.600636	CCGGCCTGTTTCTGAGCAA	60.601	57.895	0.00	0.00	0.00	3.91
21	22	0.962356	CCGGCCTGTTTCTGAGCAAT	60.962	55.000	0.00	0.00	0.00	3.56
22	23	0.883833	CGGCCTGTTTCTGAGCAATT	59.116	50.000	0.00	0.00	0.00	2.32
23	24	2.083774	CGGCCTGTTTCTGAGCAATTA	58.916	47.619	0.00	0.00	0.00	1.40
24	25	2.159517	CGGCCTGTTTCTGAGCAATTAC	60.160	50.000	0.00	0.00	0.00	1.89
25	26	2.159517	GGCCTGTTTCTGAGCAATTACG	60.160	50.000	0.00	0.00	0.00	3.18
26	27	2.742053	GCCTGTTTCTGAGCAATTACGA	59.258	45.455	0.00	0.00	0.00	3.43
27	28	3.181516	GCCTGTTTCTGAGCAATTACGAG	60.182	47.826	0.00	0.00	0.00	4.18
28	29	3.997021	CCTGTTTCTGAGCAATTACGAGT	59.003	43.478	0.00	0.00	0.00	4.18
29	30	4.452455	CCTGTTTCTGAGCAATTACGAGTT	59.548	41.667	0.00	0.00	0.00	3.01
30	31	5.049405	CCTGTTTCTGAGCAATTACGAGTTT	60.049	40.000	0.00	0.00	0.00	2.66
31	32	6.147164	CCTGTTTCTGAGCAATTACGAGTTTA	59.853	38.462	0.00	0.00	0.00	2.01
32	33	6.884187	TGTTTCTGAGCAATTACGAGTTTAC	58.116	36.000	0.00	0.00	0.00	2.01
33	34	6.704493	TGTTTCTGAGCAATTACGAGTTTACT	59.296	34.615	0.00	0.00	0.00	2.24
34	35	7.225931	TGTTTCTGAGCAATTACGAGTTTACTT	59.774	33.333	0.00	0.00	0.00	2.24
35	36	8.706035	GTTTCTGAGCAATTACGAGTTTACTTA	58.294	33.333	0.00	0.00	0.00	2.24
36	37	8.821147	TTCTGAGCAATTACGAGTTTACTTAA	57.179	30.769	0.00	0.00	0.00	1.85
37	38	8.997621	TCTGAGCAATTACGAGTTTACTTAAT	57.002	30.769	0.00	0.00	0.00	1.40
38	39	9.084164	TCTGAGCAATTACGAGTTTACTTAATC	57.916	33.333	0.00	0.00	0.00	1.75
39	40	7.891782	TGAGCAATTACGAGTTTACTTAATCG	58.108	34.615	0.00	0.00	40.86	3.34
436	437	6.030228	CACACACAAAAAGGAGAAACTCTTC	58.970	40.000	0.00	0.00	0.00	2.87
437	438	5.946377	ACACACAAAAAGGAGAAACTCTTCT	59.054	36.000	0.00	0.00	44.93	2.85
438	439	6.434340	ACACACAAAAAGGAGAAACTCTTCTT	59.566	34.615	0.00	0.00	44.00	2.52
518	523	3.428532	TGTACCCTCTACAAGTGGACTC	58.571	50.000	0.00	0.00	30.66	3.36
607	3430	9.476202	CATGATCACTACATTTTATTCTCGGTA	57.524	33.333	0.00	0.00	0.00	4.02
669	3492	4.370364	AAACGCTATGGCCATTAGTTTG	57.630	40.909	29.00	16.70	34.44	2.93
735	3562	0.248866	CCAACAACTTTCGGTGGTGC	60.249	55.000	0.00	0.00	31.41	5.01
758	3585	5.567423	GCCCTATATGCCATGAAATTTCCAC	60.567	44.000	15.48	3.25	0.00	4.02
787	3615	4.707105	TCATTGGTGCTGTCCTATATGTG	58.293	43.478	0.00	0.00	0.00	3.21
820	3650	1.871676	GGAAGTTTCGTTCAGGGTCAC	59.128	52.381	0.00	0.00	0.00	3.67
827	3657	1.342174	TCGTTCAGGGTCACACCTTAC	59.658	52.381	0.00	0.00	39.34	2.34
925	3773	9.609346	GAATTTCTCCCAATTGATGATGAAATT	57.391	29.630	24.22	24.22	40.40	1.82
949	3801	4.780815	TCTTCCAATGACACATATCCCAC	58.219	43.478	0.00	0.00	0.00	4.61
965	3817	1.141019	CACGTAGTCATGGACCGGG	59.859	63.158	6.32	0.00	41.61	5.73
1057	3940	7.568349	TCAACCTACATAGATTGCATTCTCTT	58.432	34.615	14.14	1.83	0.00	2.85
1103	3990	6.260714	TGATGATGGATCAAAACGTCCTAATG	59.739	38.462	0.00	0.00	38.19	1.90
1150	4037	1.959282	GATCTTGGGGCCATTGATCAC	59.041	52.381	19.82	0.00	36.84	3.06
1269	4156	3.813240	GCTTGATGATAGCCCCACATCAT	60.813	47.826	0.00	0.00	45.88	2.45
1270	4157	4.404640	CTTGATGATAGCCCCACATCATT	58.595	43.478	0.00	0.00	45.88	2.57
1271	4158	3.758425	TGATGATAGCCCCACATCATTG	58.242	45.455	0.00	0.00	43.17	2.82
1347	4234	1.041447	GGCGAGGCTAGGTCTTACCA	61.041	60.000	0.00	0.00	41.95	3.25
1356	4243	0.910088	AGGTCTTACCAGGTGGAGGC	60.910	60.000	0.76	1.30	41.95	4.70
1516	4403	1.566298	ATGAGGAGGCTTGGGTGGAC	61.566	60.000	0.00	0.00	0.00	4.02
1555	4442	1.833630	GGACTGTGTGAGGATGATCCA	59.166	52.381	14.90	0.00	39.61	3.41
1622	4509	5.901413	TTAGAAGGATGATGGAGAATGCT	57.099	39.130	0.00	0.00	0.00	3.79
1712	4619	3.998341	GTGTCGGTATGCTACTTTTTGGA	59.002	43.478	0.00	0.00	0.00	3.53
1733	4640	9.562408	TTTGGAATTTAATTAAGGTTTTGACCC	57.438	29.630	0.00	0.00	0.00	4.46
1843	4750	6.183360	ATACATAAAGTAGGAAAACGCCAACG	60.183	38.462	0.00	0.00	39.94	4.10
1857	4764	4.977741	CGCCAACGTTTTACTCTCTAAA	57.022	40.909	0.00	0.00	33.53	1.85
1858	4765	4.942765	CGCCAACGTTTTACTCTCTAAAG	58.057	43.478	0.00	0.00	33.53	1.85
1900	6818	5.622346	AGCCTTTGGTTTTGTCCATTTAA	57.378	34.783	0.00	0.00	37.33	1.52
1966	6884	3.449018	ACTGTCAGAACTAGTGCCATAGG	59.551	47.826	6.91	0.00	0.00	2.57
1985	6903	3.705051	AGGTTGATGTGATCTGGCATTT	58.295	40.909	0.00	0.00	0.00	2.32
1998	6916	6.550481	TGATCTGGCATTTATAATTTGCAGGA	59.450	34.615	17.70	14.93	38.12	3.86
2033	6955	5.134202	AGCAAAAGGGTAGTTTATGTTGC	57.866	39.130	0.00	0.00	40.24	4.17
2145	7067	1.970917	GCATGAGTATATGCGGCGCC	61.971	60.000	30.82	19.07	43.36	6.53
2150	7074	0.243907	AGTATATGCGGCGCCTACAG	59.756	55.000	30.82	10.13	0.00	2.74
2287	7213	2.723124	ATGCCAAACGTGTCAATTCC	57.277	45.000	0.00	0.00	0.00	3.01
2320	7247	3.894759	ACTTTGCTCTACATGCATCCAT	58.105	40.909	0.00	0.00	40.34	3.41
2327	7254	6.714278	TGCTCTACATGCATCCATTGTATAT	58.286	36.000	0.00	0.00	35.31	0.86
2359	7286	9.652114	AAAAGAAGGAAATGAAGCTATGGATAT	57.348	29.630	0.00	0.00	0.00	1.63
2520	7448	6.090493	GGTCAATCGTCTTACTAGGACAAAAC	59.910	42.308	0.00	0.00	33.73	2.43
2535	7463	6.405538	AGGACAAAACAAACATGTGTCAAAT	58.594	32.000	0.00	0.00	40.28	2.32
2540	7468	8.816144	ACAAAACAAACATGTGTCAAATGATAC	58.184	29.630	10.12	3.62	36.80	2.24
2542	7470	8.801715	AAACAAACATGTGTCAAATGATACTC	57.198	30.769	10.12	0.00	37.13	2.59
2560	7488	4.942761	ACTCAAAGTGAAATGTGCCATT	57.057	36.364	0.00	0.00	0.00	3.16
2586	7514	7.117285	GAGCATCTTCAATAAATCCCCTTTT	57.883	36.000	0.00	0.00	0.00	2.27
2600	7528	6.620877	ATCCCCTTTTCCTGATTAAAAACC	57.379	37.500	0.00	0.00	0.00	3.27
2601	7529	5.722290	TCCCCTTTTCCTGATTAAAAACCT	58.278	37.500	0.00	0.00	0.00	3.50
2654	7583	4.941263	TCCAACAAATCCCATAAACGAGAG	59.059	41.667	0.00	0.00	0.00	3.20
2704	7635	2.252714	CCCAAGCTCCCCTCTATCTAC	58.747	57.143	0.00	0.00	0.00	2.59
2720	7651	2.175035	CTACGGGAAAAGGGCCGTCA	62.175	60.000	0.00	0.00	39.60	4.35
2727	7658	2.422479	GGAAAAGGGCCGTCAATAACTC	59.578	50.000	0.00	0.00	0.00	3.01
2728	7659	2.124277	AAAGGGCCGTCAATAACTCC	57.876	50.000	0.00	0.00	0.00	3.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	2.750350	CTCAGAAACAGGCCGGGT	59.250	61.111	8.08	0.00	0.00	5.28
2	3	0.962356	ATTGCTCAGAAACAGGCCGG	60.962	55.000	0.00	0.00	0.00	6.13
3	4	0.883833	AATTGCTCAGAAACAGGCCG	59.116	50.000	0.00	0.00	0.00	6.13
4	5	2.159517	CGTAATTGCTCAGAAACAGGCC	60.160	50.000	0.00	0.00	0.00	5.19
5	6	2.742053	TCGTAATTGCTCAGAAACAGGC	59.258	45.455	0.00	0.00	0.00	4.85
6	7	3.997021	ACTCGTAATTGCTCAGAAACAGG	59.003	43.478	0.00	0.00	0.00	4.00
9	10	7.118422	AGTAAACTCGTAATTGCTCAGAAAC	57.882	36.000	0.00	0.00	0.00	2.78
11	12	8.821147	TTAAGTAAACTCGTAATTGCTCAGAA	57.179	30.769	0.00	0.00	0.00	3.02
13	14	8.050750	CGATTAAGTAAACTCGTAATTGCTCAG	58.949	37.037	0.00	0.00	0.00	3.35
473	474	4.533707	ACTCCATTCCATCACAGAAGAAGA	59.466	41.667	0.00	0.00	0.00	2.87
539	548	1.302033	GCACCACTCACCTGGTCAG	60.302	63.158	0.00	0.00	43.15	3.51
540	549	2.818169	GGCACCACTCACCTGGTCA	61.818	63.158	0.00	0.00	43.15	4.02
575	584	9.337396	GAATAAAATGTAGTGATCATGGTACCA	57.663	33.333	18.99	18.99	0.00	3.25
580	589	7.442364	ACCGAGAATAAAATGTAGTGATCATGG	59.558	37.037	0.00	0.00	0.00	3.66
650	3473	2.297701	CCAAACTAATGGCCATAGCGT	58.702	47.619	21.15	13.43	41.24	5.07
651	3474	2.297701	ACCAAACTAATGGCCATAGCG	58.702	47.619	21.15	12.75	44.75	4.26
669	3492	4.700700	ACGTTGGGAGTATTAATGCTACC	58.299	43.478	24.11	24.11	43.18	3.18
735	3562	5.335897	CGTGGAAATTTCATGGCATATAGGG	60.336	44.000	19.49	0.00	0.00	3.53
758	3585	2.350772	GGACAGCACCAATGAAACTTCG	60.351	50.000	0.00	0.00	0.00	3.79
787	3615	4.998033	ACGAAACTTCCTGGAAATCTCTTC	59.002	41.667	10.86	7.77	0.00	2.87
820	3650	4.223923	AGATGACTTCAGAAGGGTAAGGTG	59.776	45.833	14.90	0.00	0.00	4.00
827	3657	6.494491	AGATATCAGAGATGACTTCAGAAGGG	59.506	42.308	14.90	0.00	0.00	3.95
925	3773	6.533730	GTGGGATATGTGTCATTGGAAGATA	58.466	40.000	0.00	0.00	0.00	1.98
938	3790	3.653344	CCATGACTACGTGGGATATGTG	58.347	50.000	3.26	0.00	46.26	3.21
949	3801	2.106332	GCCCGGTCCATGACTACG	59.894	66.667	0.00	0.00	32.47	3.51
1072	3959	4.336153	CGTTTTGATCCATCATCACCATCA	59.664	41.667	0.00	0.00	41.56	3.07
1103	3990	1.520342	GAGAGATGACACCAGCGCC	60.520	63.158	2.29	0.00	33.13	6.53
1150	4037	3.548745	TGCTTACCAGGATGACATCTG	57.451	47.619	14.95	10.67	39.69	2.90
1516	4403	1.202855	CCTCATACATGGCCCCTTCTG	60.203	57.143	0.00	0.00	0.00	3.02
1555	4442	0.031111	TCCATCCTCATCGAAGGGGT	60.031	55.000	6.43	0.00	37.02	4.95
1712	4619	8.270137	AGTGGGGTCAAAACCTTAATTAAATT	57.730	30.769	0.00	0.00	45.66	1.82
1733	4640	1.153353	ACGGTGCGAACAAATAGTGG	58.847	50.000	0.00	0.00	0.00	4.00
1779	4686	6.966632	GCGAGATGCAATGTTTGATACTTTTA	59.033	34.615	0.00	0.00	45.45	1.52
1870	6778	4.003648	ACAAAACCAAAGGCTATCGAGAG	58.996	43.478	1.78	1.78	0.00	3.20
1900	6818	3.309848	CCCATATTTGAACTTGGAGGGGT	60.310	47.826	0.00	0.00	0.00	4.95
1939	6857	3.877508	GGCACTAGTTCTGACAGTGTTTT	59.122	43.478	0.00	0.00	37.30	2.43
1940	6858	3.118408	TGGCACTAGTTCTGACAGTGTTT	60.118	43.478	0.00	0.00	37.30	2.83
1941	6859	2.434336	TGGCACTAGTTCTGACAGTGTT	59.566	45.455	0.00	0.00	37.30	3.32
1942	6860	2.039418	TGGCACTAGTTCTGACAGTGT	58.961	47.619	0.00	0.00	37.30	3.55
1966	6884	9.754382	AAATTATAAATGCCAGATCACATCAAC	57.246	29.630	0.00	0.00	0.00	3.18
1998	6916	9.700831	ACTACCCTTTTGCTTCATTAGATTTAT	57.299	29.630	0.00	0.00	0.00	1.40
2033	6955	5.773239	TCCGCAGTTTACTTCTTTATTCG	57.227	39.130	0.00	0.00	0.00	3.34
2145	7067	3.686726	GCATGTCCTTTTCTGGTCTGTAG	59.313	47.826	0.00	0.00	0.00	2.74
2150	7074	4.240096	CAAATGCATGTCCTTTTCTGGTC	58.760	43.478	0.00	0.00	0.00	4.02
2287	7213	9.941664	CATGTAGAGCAAAGTTTTCCATATAAG	57.058	33.333	0.00	0.00	0.00	1.73
2335	7262	9.652114	AAATATCCATAGCTTCATTTCCTTCTT	57.348	29.630	0.00	0.00	0.00	2.52
2350	7277	6.938596	TCATTGTCCTGCTGAAATATCCATAG	59.061	38.462	0.00	0.00	0.00	2.23
2359	7286	3.436704	GTCGATTCATTGTCCTGCTGAAA	59.563	43.478	0.00	0.00	33.03	2.69
2560	7488	6.770286	AGGGGATTTATTGAAGATGCTCTA	57.230	37.500	0.00	0.00	0.00	2.43
2586	7514	6.679303	TCCCCTATACAGGTTTTTAATCAGGA	59.321	38.462	0.00	0.00	40.79	3.86
2600	7528	0.765510	GGCCCAACTCCCCTATACAG	59.234	60.000	0.00	0.00	0.00	2.74
2601	7529	0.045008	TGGCCCAACTCCCCTATACA	59.955	55.000	0.00	0.00	0.00	2.29
2665	7596	6.485648	GCTTGGGTTGATTATACGTTATCCTT	59.514	38.462	0.00	0.00	0.00	3.36
2670	7601	5.362263	GGAGCTTGGGTTGATTATACGTTA	58.638	41.667	0.00	0.00	0.00	3.18
2671	7602	4.196971	GGAGCTTGGGTTGATTATACGTT	58.803	43.478	0.00	0.00	0.00	3.99

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.