AutoCloner

Multiple sequence alignment - TraesCS3D01G415500

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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	TraesCS3D01G415500	chr3D	100.000	2857	0	0	1	2857	527146092	527148948	0.000000e+00	5276
1	TraesCS3D01G415500	chr3D	92.073	164	12	1	2675	2838	45491604	45491766	2.210000e-56	230
2	TraesCS3D01G415500	chr3D	90.196	102	5	4	2146	2244	37760915	37760816	8.310000e-26	128
3	TraesCS3D01G415500	chr3B	94.118	2890	101	31	4	2857	696977019	696979875	0.000000e+00	4331
4	TraesCS3D01G415500	chr3B	91.463	164	13	1	2675	2838	736416002	736415840	1.030000e-54	224
5	TraesCS3D01G415500	chr3B	91.837	98	6	2	2146	2242	60259751	60259655	4.970000e-28	135
6	TraesCS3D01G415500	chr3A	93.565	2875	117	20	1	2854	661790509	661793336	0.000000e+00	4222
7	TraesCS3D01G415500	chr4B	91.463	164	13	1	2675	2838	16556495	16556333	1.030000e-54	224
8	TraesCS3D01G415500	chr4B	90.000	100	6	3	2145	2244	30730987	30731082	2.990000e-25	126
9	TraesCS3D01G415500	chr2B	91.463	164	13	1	2675	2838	793489067	793489229	1.030000e-54	224
10	TraesCS3D01G415500	chr2B	89.080	174	17	2	2675	2848	785241769	785241940	6.200000e-52	215
11	TraesCS3D01G415500	chr7A	90.854	164	15	0	2675	2838	291825843	291825680	1.330000e-53	220
12	TraesCS3D01G415500	chr6A	90.854	164	14	1	2675	2838	60154254	60154416	4.790000e-53	219
13	TraesCS3D01G415500	chr1A	89.796	98	8	2	2147	2243	481924517	481924421	1.070000e-24	124
14	TraesCS3D01G415500	chr1A	87.963	108	6	4	2140	2243	481924413	481924517	1.390000e-23	121
15	TraesCS3D01G415500	chr1D	87.736	106	9	4	2141	2243	446426970	446426866	1.390000e-23	121
16	TraesCS3D01G415500	chr1D	88.776	98	9	2	2147	2243	381307088	381306992	5.000000e-23	119

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	TraesCS3D01G415500	chr3D	527146092	527148948	2856	False	5276	5276	100.000	1	2857	1	chr3D.!!$F2	2856
1	TraesCS3D01G415500	chr3B	696977019	696979875	2856	False	4331	4331	94.118	4	2857	1	chr3B.!!$F1	2853
2	TraesCS3D01G415500	chr3A	661790509	661793336	2827	False	4222	4222	93.565	1	2854	1	chr3A.!!$F1	2853

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
181	190	0.252012	ACACCCTCCTCTCAGTCCTG	60.252	60.0	0.00	0.0	0.0	3.86	F
712	737	0.441921	CGTGTGTGCGTGCATATGAA	59.558	50.0	6.97	0.0	0.0	2.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1013	1051	0.539986	GCTCGAGGTTATTGTGGGGA	59.46	55.0	15.58	0.0	0.00	4.81	R
2469	2520	0.109723	ACCGGTGGTTGTTGCAGTAT	59.89	50.0	6.12	0.0	27.29	2.12	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
35	36	2.512286	CCATGCCGTCGTGCTCAT	60.512	61.111	7.14	0.00	0.00	2.90
175	184	0.836400	GTTCCCACACCCTCCTCTCA	60.836	60.000	0.00	0.00	0.00	3.27
181	190	0.252012	ACACCCTCCTCTCAGTCCTG	60.252	60.000	0.00	0.00	0.00	3.86
244	260	2.310538	CCATAAATCTGTGCTTCCCCC	58.689	52.381	0.00	0.00	0.00	5.40
309	330	3.571401	AGTTCCTTGAAGCATGTCCTTTG	59.429	43.478	0.00	0.00	0.00	2.77
327	348	6.262273	GTCCTTTGACTGAACATAAGTTTCCA	59.738	38.462	0.00	0.00	36.98	3.53
409	430	2.441410	TCCCACATAGATTTTGCGCAA	58.559	42.857	21.02	21.02	0.00	4.85
469	490	6.352137	GCAAATAATTGACCCATCTTCCCTTT	60.352	38.462	0.00	0.00	38.94	3.11
488	509	0.694444	TCCCTCCATAACCTCTGGCC	60.694	60.000	0.00	0.00	33.56	5.36
557	578	9.866655	ATGAAGCATATTATTGGACTCCTTAAA	57.133	29.630	0.00	0.00	0.00	1.52
712	737	0.441921	CGTGTGTGCGTGCATATGAA	59.558	50.000	6.97	0.00	0.00	2.57
719	744	2.286294	GTGCGTGCATATGAAAGAGAGG	59.714	50.000	6.97	0.00	0.00	3.69
720	745	1.262683	GCGTGCATATGAAAGAGAGGC	59.737	52.381	6.97	0.00	0.00	4.70
721	746	2.554142	CGTGCATATGAAAGAGAGGCA	58.446	47.619	6.97	0.00	0.00	4.75
776	801	1.600023	CGCCCCTCTCTACAGTCTAG	58.400	60.000	0.00	0.00	0.00	2.43
988	1026	5.075493	CCCTATCCATCTTCTCATTTTGGG	58.925	45.833	0.00	0.00	0.00	4.12
990	1028	2.738743	TCCATCTTCTCATTTTGGGGC	58.261	47.619	0.00	0.00	0.00	5.80
1013	1051	0.850784	GGGGTTATGGCCAGTGGTAT	59.149	55.000	13.05	8.55	0.00	2.73
1213	1251	6.726258	TCTTTAGTGTGCATATGTTCACTG	57.274	37.500	28.22	18.95	40.61	3.66
1238	1276	9.990360	TGTGTATTCACTAGTTTCACTTCAATA	57.010	29.630	4.01	0.00	44.14	1.90
1305	1343	7.387643	GGGATTACCTGAAGAACATATAGACC	58.612	42.308	0.00	0.00	35.85	3.85
1355	1393	5.068723	GCCATCTAGTTAGTACTAAGTGCCA	59.931	44.000	26.52	13.96	36.46	4.92
1483	1521	2.483106	GGAGTTTTTGGTAAGCGGACTC	59.517	50.000	0.00	0.00	33.19	3.36
1541	1582	7.335422	CCTTACTCCTACAGTTAGTACGAGAAA	59.665	40.741	7.82	0.00	37.79	2.52
1653	1695	8.289618	TCTGAAAGCAACAATAACTAACATGAC	58.710	33.333	0.00	0.00	0.00	3.06
2196	2239	7.382218	GTCGCTGGTTTAGTACAAAGTTAGTAA	59.618	37.037	0.00	0.00	0.00	2.24
2224	2267	6.939551	TTGTACTAAATCAGCGACACTTAC	57.060	37.500	0.00	0.00	0.00	2.34
2297	2340	1.344438	TCGATGTGGTCTTCTGCTTGT	59.656	47.619	0.00	0.00	0.00	3.16
2316	2359	5.755861	GCTTGTATAGGCTTAGAACTTCAGG	59.244	44.000	0.00	0.00	0.00	3.86
2413	2463	4.957327	AGTTGACAGTATCTTCTCTACCCC	59.043	45.833	0.00	0.00	0.00	4.95
2415	2465	3.201487	TGACAGTATCTTCTCTACCCCGA	59.799	47.826	0.00	0.00	0.00	5.14
2469	2520	4.283978	TCCCTCTTTCCATGTAACAACGTA	59.716	41.667	0.00	0.00	0.00	3.57
2470	2521	5.046159	TCCCTCTTTCCATGTAACAACGTAT	60.046	40.000	0.00	0.00	0.00	3.06
2471	2522	6.154877	TCCCTCTTTCCATGTAACAACGTATA	59.845	38.462	0.00	0.00	0.00	1.47
2472	2523	6.257193	CCCTCTTTCCATGTAACAACGTATAC	59.743	42.308	0.00	0.00	0.00	1.47
2473	2524	7.039882	CCTCTTTCCATGTAACAACGTATACT	58.960	38.462	0.56	0.00	0.00	2.12
2474	2525	7.010183	CCTCTTTCCATGTAACAACGTATACTG	59.990	40.741	0.56	0.00	0.00	2.74
2475	2526	6.311935	TCTTTCCATGTAACAACGTATACTGC	59.688	38.462	0.56	0.00	0.00	4.40
2486	2537	1.392168	CGTATACTGCAACAACCACCG	59.608	52.381	0.56	0.00	0.00	4.94
2489	2540	0.816018	TACTGCAACAACCACCGGTG	60.816	55.000	28.26	28.26	35.34	4.94
2587	2638	0.741574	CTCAGCAGAGCAGGCTTCAG	60.742	60.000	0.00	0.00	40.23	3.02
2640	2692	9.057365	GTTTCATGTATGTACCACATTTTTACG	57.943	33.333	7.32	0.00	39.88	3.18
2641	2693	6.777101	TCATGTATGTACCACATTTTTACGC	58.223	36.000	7.32	0.00	39.88	4.42
2642	2694	6.371825	TCATGTATGTACCACATTTTTACGCA	59.628	34.615	7.32	0.00	39.88	5.24

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
21	22	3.647649	CTCCATGAGCACGACGGCA	62.648	63.158	10.28	0.00	35.83	5.69
35	36	2.628178	TGTTTTCTTCTCTCGCTCTCCA	59.372	45.455	0.00	0.00	0.00	3.86
181	190	1.156736	GGTGTGTGTCTGTATGCCAC	58.843	55.000	0.00	0.00	0.00	5.01
195	206	2.174363	TCTGAACATGCAGAGGTGTG	57.826	50.000	0.00	0.00	39.84	3.82
244	260	0.798776	GTGATGACGGTGAAAGCCAG	59.201	55.000	0.00	0.00	0.00	4.85
309	330	6.147985	GGAGAAGTGGAAACTTATGTTCAGTC	59.852	42.308	0.00	0.00	34.96	3.51
409	430	1.079405	ATCGAAACGGCGGACACAT	60.079	52.632	13.24	0.00	0.00	3.21
469	490	0.694444	GGCCAGAGGTTATGGAGGGA	60.694	60.000	0.00	0.00	40.51	4.20
573	598	7.226325	CCTTCTCTGCACCTATCTTATTTTCTG	59.774	40.741	0.00	0.00	0.00	3.02
611	636	3.686016	GCATCACCTTTGTCCCTTCTTA	58.314	45.455	0.00	0.00	0.00	2.10
824	857	1.893808	CTTGTGGCTCCGCTGTTGT	60.894	57.895	0.86	0.00	0.00	3.32
1013	1051	0.539986	GCTCGAGGTTATTGTGGGGA	59.460	55.000	15.58	0.00	0.00	4.81
1022	1060	3.617368	GCAGGGAGCTCGAGGTTA	58.383	61.111	19.66	0.00	41.15	2.85
1238	1276	0.979665	AGTCTGCACCTGTACAGCAT	59.020	50.000	17.86	4.67	37.68	3.79
1240	1278	2.544685	CATAGTCTGCACCTGTACAGC	58.455	52.381	17.86	8.01	33.80	4.40
1301	1339	3.558746	CCTTGATGTTCTCTTGCAGGTCT	60.559	47.826	0.00	0.00	0.00	3.85
1305	1343	4.318332	TGTACCTTGATGTTCTCTTGCAG	58.682	43.478	0.00	0.00	0.00	4.41
1380	1418	9.037737	GCATAATTTATCATGTGCTGAAAACAT	57.962	29.630	0.00	0.00	38.81	2.71
1414	1452	7.195839	AGCAAGTTGAAGTTTACAGAATCTC	57.804	36.000	7.16	0.00	0.00	2.75
1483	1521	5.080337	TGGCTACTGTATCCTCTTCCTATG	58.920	45.833	8.96	0.00	0.00	2.23
1541	1582	5.048434	GCTGTTTTGCTCTTGGTCTTAGAAT	60.048	40.000	0.00	0.00	0.00	2.40
1550	1591	1.337447	CCCATGCTGTTTTGCTCTTGG	60.337	52.381	0.00	0.00	0.00	3.61
1653	1695	0.587768	TGCTGTGAAGCATGTGAACG	59.412	50.000	0.00	0.00	40.23	3.95
2196	2239	4.994852	TGTCGCTGATTTAGTACAAAGCTT	59.005	37.500	0.00	0.00	0.00	3.74
2224	2267	5.533482	CAATATACTCCCTCCGTCTCAAAG	58.467	45.833	0.00	0.00	0.00	2.77
2297	2340	4.345257	CCAGCCTGAAGTTCTAAGCCTATA	59.655	45.833	4.17	0.00	0.00	1.31
2316	2359	1.467734	CAACAGTGCAGAAGATCCAGC	59.532	52.381	0.00	0.00	0.00	4.85
2415	2465	0.175302	CCACGAGAGCTGAAGATGCT	59.825	55.000	0.00	0.00	44.24	3.79
2469	2520	0.109723	ACCGGTGGTTGTTGCAGTAT	59.890	50.000	6.12	0.00	27.29	2.12
2470	2521	0.816018	CACCGGTGGTTGTTGCAGTA	60.816	55.000	27.57	0.00	31.02	2.74
2471	2522	2.118404	CACCGGTGGTTGTTGCAGT	61.118	57.895	27.57	0.00	31.02	4.40
2472	2523	2.721231	CACCGGTGGTTGTTGCAG	59.279	61.111	27.57	0.00	31.02	4.41
2473	2524	3.522731	GCACCGGTGGTTGTTGCA	61.523	61.111	34.58	0.00	31.02	4.08
2474	2525	3.216292	AGCACCGGTGGTTGTTGC	61.216	61.111	32.82	17.94	38.24	4.17
2475	2526	0.816018	TACAGCACCGGTGGTTGTTG	60.816	55.000	35.55	25.60	39.58	3.33
2486	2537	0.674895	CTGCTCCCTTGTACAGCACC	60.675	60.000	2.83	0.00	38.25	5.01
2489	2540	1.825474	TCTACTGCTCCCTTGTACAGC	59.175	52.381	0.00	0.00	33.35	4.40
2587	2638	4.306600	CCTGGTTGGTTAAATTCAACAGC	58.693	43.478	15.06	0.00	43.44	4.40
2640	2692	5.560966	TTACCTATGCTACAGCTTTTTGC	57.439	39.130	2.44	0.00	42.66	3.68
2641	2693	9.503427	GTTTATTACCTATGCTACAGCTTTTTG	57.497	33.333	2.44	0.00	42.66	2.44
2642	2694	9.238368	TGTTTATTACCTATGCTACAGCTTTTT	57.762	29.630	2.44	0.00	42.66	1.94

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.