AutoCloner

Multiple sequence alignment - TraesCS6B01G052600

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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	TraesCS6B01G052600	chr6B	100.000	2448	0	0	1	2448	32023494	32025941	0.000000e+00	4521
1	TraesCS6B01G052600	chr6B	95.979	1517	51	7	777	2290	31793112	31794621	0.000000e+00	2455
2	TraesCS6B01G052600	chr6B	92.491	1092	60	7	512	1582	32171659	32172749	0.000000e+00	1543
3	TraesCS6B01G052600	chr6B	94.707	869	36	4	1585	2448	567464475	567463612	0.000000e+00	1341
4	TraesCS6B01G052600	chr6B	94.502	873	38	4	1582	2448	699405914	699406782	0.000000e+00	1338
5	TraesCS6B01G052600	chr6B	91.939	521	42	0	948	1468	32075907	32076427	0.000000e+00	730
6	TraesCS6B01G052600	chr6B	91.363	521	45	0	948	1468	31844251	31844771	0.000000e+00	713
7	TraesCS6B01G052600	chr6B	88.378	413	30	6	3	414	31783390	31783785	4.730000e-132	481
8	TraesCS6B01G052600	chr6B	88.649	370	23	7	427	777	31783770	31784139	1.340000e-117	433
9	TraesCS6B01G052600	chr6B	96.522	115	4	0	1468	1582	32087057	32087171	8.930000e-45	191
10	TraesCS6B01G052600	chr6B	94.783	115	6	0	1468	1582	31869197	31869311	1.930000e-41	180
11	TraesCS6B01G052600	chr6B	84.270	178	15	8	216	389	32171383	32171551	7.010000e-36	161
12	TraesCS6B01G052600	chr6A	90.295	1391	73	16	215	1582	18624364	18625715	0.000000e+00	1764
13	TraesCS6B01G052600	chr6A	89.744	195	13	6	1	190	18583906	18584098	2.430000e-60	243
14	TraesCS6B01G052600	chr6D	91.908	1174	70	4	427	1582	17891912	17893078	0.000000e+00	1618
15	TraesCS6B01G052600	chr6D	80.769	390	38	13	1	389	17891492	17891845	1.120000e-68	270
16	TraesCS6B01G052600	chr7B	94.822	869	35	4	1585	2448	29159191	29158328	0.000000e+00	1347
17	TraesCS6B01G052600	chr1B	94.616	873	37	4	1581	2448	206440807	206441674	0.000000e+00	1343
18	TraesCS6B01G052600	chr1B	76.835	436	79	14	908	1325	623851682	623852113	2.450000e-55	226
19	TraesCS6B01G052600	chr4B	94.616	873	36	5	1582	2448	633608817	633607950	0.000000e+00	1341
20	TraesCS6B01G052600	chr1D	94.591	869	38	3	1585	2448	205417366	205418230	0.000000e+00	1336
21	TraesCS6B01G052600	chr2B	94.489	871	39	3	1583	2448	654847001	654846135	0.000000e+00	1334
22	TraesCS6B01G052600	chr2B	94.091	880	40	6	1576	2448	404634457	404633583	0.000000e+00	1327

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	TraesCS6B01G052600	chr6B	32023494	32025941	2447	False	4521	4521	100.0000	1	2448	1	chr6B.!!$F4	2447
1	TraesCS6B01G052600	chr6B	31793112	31794621	1509	False	2455	2455	95.9790	777	2290	1	chr6B.!!$F1	1513
2	TraesCS6B01G052600	chr6B	567463612	567464475	863	True	1341	1341	94.7070	1585	2448	1	chr6B.!!$R1	863
3	TraesCS6B01G052600	chr6B	699405914	699406782	868	False	1338	1338	94.5020	1582	2448	1	chr6B.!!$F7	866
4	TraesCS6B01G052600	chr6B	32171383	32172749	1366	False	852	1543	88.3805	216	1582	2	chr6B.!!$F9	1366
5	TraesCS6B01G052600	chr6B	32075907	32076427	520	False	730	730	91.9390	948	1468	1	chr6B.!!$F5	520
6	TraesCS6B01G052600	chr6B	31844251	31844771	520	False	713	713	91.3630	948	1468	1	chr6B.!!$F2	520
7	TraesCS6B01G052600	chr6B	31783390	31784139	749	False	457	481	88.5135	3	777	2	chr6B.!!$F8	774
8	TraesCS6B01G052600	chr6A	18624364	18625715	1351	False	1764	1764	90.2950	215	1582	1	chr6A.!!$F2	1367
9	TraesCS6B01G052600	chr6D	17891492	17893078	1586	False	944	1618	86.3385	1	1582	2	chr6D.!!$F1	1581
10	TraesCS6B01G052600	chr7B	29158328	29159191	863	True	1347	1347	94.8220	1585	2448	1	chr7B.!!$R1	863
11	TraesCS6B01G052600	chr1B	206440807	206441674	867	False	1343	1343	94.6160	1581	2448	1	chr1B.!!$F1	867
12	TraesCS6B01G052600	chr4B	633607950	633608817	867	True	1341	1341	94.6160	1582	2448	1	chr4B.!!$R1	866
13	TraesCS6B01G052600	chr1D	205417366	205418230	864	False	1336	1336	94.5910	1585	2448	1	chr1D.!!$F1	863
14	TraesCS6B01G052600	chr2B	654846135	654847001	866	True	1334	1334	94.4890	1583	2448	1	chr2B.!!$R2	865
15	TraesCS6B01G052600	chr2B	404633583	404634457	874	True	1327	1327	94.0910	1576	2448	1	chr2B.!!$R1	872

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
311	316	0.032678	ATCCGATGACTCATGTCGCC	59.967	55.0	0.0	0.0	45.7	5.54	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2207	2296	0.474079	TACCTGGGCCGGCCATTATA	60.474	55.0	44.46	27.81	37.98	0.98	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
46	47	2.487265	GCGATGGGACCATAGGAATGTT	60.487	50.000	12.41	0.00	36.70	2.71
52	53	4.017591	TGGGACCATAGGAATGTTGAATGT	60.018	41.667	0.00	0.00	0.00	2.71
69	70	2.195411	TGGCTGCTGGCAAGACAA	59.805	55.556	17.61	0.00	46.03	3.18
95	100	0.528684	CGAATCGCTGGAGAGGAACC	60.529	60.000	0.00	0.00	0.00	3.62
97	102	0.618968	AATCGCTGGAGAGGAACCCT	60.619	55.000	0.00	0.00	36.03	4.34
127	132	2.781158	GGAGAGGACGAGGCAGAGC	61.781	68.421	0.00	0.00	0.00	4.09
145	150	0.394352	GCGGGGAAATGAGACATGGT	60.394	55.000	0.00	0.00	0.00	3.55
213	218	3.645975	CACCGGTCGTGTGGTTGC	61.646	66.667	2.59	0.00	35.96	4.17
271	276	1.902918	GATGTGGCAGCACACCCAA	60.903	57.895	10.46	0.00	40.62	4.12
285	290	1.741401	CCCAACGCAGAGATTCGCA	60.741	57.895	0.00	0.00	0.00	5.10
311	316	0.032678	ATCCGATGACTCATGTCGCC	59.967	55.000	0.00	0.00	45.70	5.54
342	347	5.065988	GCTTGAAATATTCCTGGCGAACTAA	59.934	40.000	0.00	0.00	31.79	2.24
343	348	6.238759	GCTTGAAATATTCCTGGCGAACTAAT	60.239	38.462	0.00	0.00	31.79	1.73
344	349	7.639113	TTGAAATATTCCTGGCGAACTAATT	57.361	32.000	0.00	0.00	31.79	1.40
413	475	9.640963	ATGATAATGGTAATTACTAAGCTCGTC	57.359	33.333	15.05	4.91	31.07	4.20
414	476	8.635328	TGATAATGGTAATTACTAAGCTCGTCA	58.365	33.333	15.05	7.03	31.07	4.35
415	477	8.813643	ATAATGGTAATTACTAAGCTCGTCAC	57.186	34.615	15.05	0.00	31.07	3.67
416	478	5.002464	TGGTAATTACTAAGCTCGTCACC	57.998	43.478	15.05	0.00	0.00	4.02
417	479	4.142093	TGGTAATTACTAAGCTCGTCACCC	60.142	45.833	15.05	0.00	0.00	4.61
418	480	2.865343	ATTACTAAGCTCGTCACCCG	57.135	50.000	0.00	0.00	38.13	5.28
419	481	0.171903	TTACTAAGCTCGTCACCCGC	59.828	55.000	0.00	0.00	36.19	6.13
420	482	0.961857	TACTAAGCTCGTCACCCGCA	60.962	55.000	0.00	0.00	36.19	5.69
421	483	1.080093	CTAAGCTCGTCACCCGCAA	60.080	57.895	0.00	0.00	36.19	4.85
422	484	0.669318	CTAAGCTCGTCACCCGCAAA	60.669	55.000	0.00	0.00	36.19	3.68
423	485	0.249953	TAAGCTCGTCACCCGCAAAA	60.250	50.000	0.00	0.00	36.19	2.44
424	486	1.098712	AAGCTCGTCACCCGCAAAAA	61.099	50.000	0.00	0.00	36.19	1.94
425	487	1.370051	GCTCGTCACCCGCAAAAAC	60.370	57.895	0.00	0.00	36.19	2.43
426	488	2.018544	CTCGTCACCCGCAAAAACA	58.981	52.632	0.00	0.00	36.19	2.83
427	489	0.378962	CTCGTCACCCGCAAAAACAA	59.621	50.000	0.00	0.00	36.19	2.83
428	490	1.001815	CTCGTCACCCGCAAAAACAAT	60.002	47.619	0.00	0.00	36.19	2.71
429	491	1.405821	TCGTCACCCGCAAAAACAATT	59.594	42.857	0.00	0.00	36.19	2.32
430	492	2.617308	TCGTCACCCGCAAAAACAATTA	59.383	40.909	0.00	0.00	36.19	1.40
431	493	2.722116	CGTCACCCGCAAAAACAATTAC	59.278	45.455	0.00	0.00	0.00	1.89
432	494	3.549221	CGTCACCCGCAAAAACAATTACT	60.549	43.478	0.00	0.00	0.00	2.24
433	495	3.978855	GTCACCCGCAAAAACAATTACTC	59.021	43.478	0.00	0.00	0.00	2.59
434	496	3.632604	TCACCCGCAAAAACAATTACTCA	59.367	39.130	0.00	0.00	0.00	3.41
435	497	3.733727	CACCCGCAAAAACAATTACTCAC	59.266	43.478	0.00	0.00	0.00	3.51
436	498	3.243602	ACCCGCAAAAACAATTACTCACC	60.244	43.478	0.00	0.00	0.00	4.02
445	507	4.451629	ACAATTACTCACCTCGTCGATT	57.548	40.909	0.00	0.00	0.00	3.34
459	521	6.481644	ACCTCGTCGATTAGTACCTAAACTAG	59.518	42.308	0.00	0.00	33.62	2.57
466	528	6.461231	CGATTAGTACCTAAACTAGCCTTGCT	60.461	42.308	0.00	0.00	34.62	3.91
492	554	2.837498	CACGCATGGGAATATCTCACA	58.163	47.619	17.76	0.00	43.31	3.58
524	586	5.961272	TCGATATCGTGCATGTATGGTAAT	58.039	37.500	23.61	0.00	40.80	1.89
558	620	3.976015	TGTTTTTCCTTGAGTTGGACCT	58.024	40.909	0.00	0.00	32.65	3.85
593	655	5.741982	CGCCATGGTTATTTTTAGTTGCTAC	59.258	40.000	14.67	0.00	0.00	3.58
596	661	5.883503	TGGTTATTTTTAGTTGCTACCCG	57.116	39.130	0.00	0.00	0.00	5.28
806	890	3.623060	GTGATCTGCAAACCGTATCACAT	59.377	43.478	8.47	0.00	43.70	3.21
894	980	2.216488	CACATTGACAGCGCGTATCTAC	59.784	50.000	8.43	0.00	0.00	2.59
1051	1137	2.154462	CTCTTTTGTTCATCGGGTGCT	58.846	47.619	0.00	0.00	0.00	4.40
1084	1170	4.009675	TGGACAATGTAAGCACATCTTCC	58.990	43.478	8.84	8.84	44.83	3.46
1085	1171	3.063997	GGACAATGTAAGCACATCTTCCG	59.936	47.826	0.00	0.00	44.83	4.30
1235	1323	2.125753	CTGAGCCCGAGAGCACAC	60.126	66.667	0.00	0.00	34.23	3.82
1414	1502	7.390440	TGTTTTAATTCGAGAGTGGAATGTCAT	59.610	33.333	0.00	0.00	34.50	3.06
1454	1542	4.202631	TGCTACCAGGAAAATAAGGGTGTT	60.203	41.667	0.00	0.00	33.14	3.32
1593	1682	7.042335	CCTTAAGACCACCTATCACTACAAAG	58.958	42.308	3.36	0.00	0.00	2.77
1683	1772	8.344831	CGTACATCCATGACAAATTTATGACAT	58.655	33.333	0.00	0.00	36.39	3.06
1860	1949	0.938168	CGTTAAGCTATCGGGTCGGC	60.938	60.000	0.00	0.00	0.00	5.54
1907	1996	1.567357	CCCGACCAATGGGGATTTTT	58.433	50.000	3.55	0.00	46.95	1.94
2088	2177	2.515901	GACCATAATGGGCCGGCT	59.484	61.111	28.56	9.11	40.64	5.52
2207	2296	3.205338	GCCCACAAGATTTTTGTTTGCT	58.795	40.909	0.00	0.00	0.00	3.91
2291	2381	0.539438	AAGGCCCACGAGATTTTGCA	60.539	50.000	0.00	0.00	0.00	4.08
2332	2426	1.615392	GCTGCCCACAAGAATTTGAGT	59.385	47.619	0.00	0.00	37.73	3.41
2427	2521	4.243008	TGGCCTGCCACGTTTCGA	62.243	61.111	6.80	0.00	41.89	3.71

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
46	47	1.529152	CTTGCCAGCAGCCACATTCA	61.529	55.000	0.00	0.00	42.71	2.57
52	53	1.455402	TTTGTCTTGCCAGCAGCCA	60.455	52.632	0.00	0.00	42.71	4.75
95	100	4.135153	CTCCTCCCGCGTGTCAGG	62.135	72.222	4.92	4.37	0.00	3.86
97	102	3.062466	CTCTCCTCCCGCGTGTCA	61.062	66.667	4.92	0.00	0.00	3.58
127	132	1.065491	TCACCATGTCTCATTTCCCCG	60.065	52.381	0.00	0.00	0.00	5.73
145	150	3.442273	GGGTATTTTCGTCATTTGGCTCA	59.558	43.478	0.00	0.00	0.00	4.26
153	158	5.116882	GTCTTAGCAGGGTATTTTCGTCAT	58.883	41.667	0.00	0.00	0.00	3.06
204	209	2.411504	AACCACACGGCAACCACAC	61.412	57.895	0.00	0.00	34.57	3.82
205	210	2.044848	AACCACACGGCAACCACA	60.045	55.556	0.00	0.00	34.57	4.17
206	211	2.411290	CAACCACACGGCAACCAC	59.589	61.111	0.00	0.00	34.57	4.16
207	212	3.522731	GCAACCACACGGCAACCA	61.523	61.111	0.00	0.00	34.57	3.67
208	213	4.279043	GGCAACCACACGGCAACC	62.279	66.667	0.00	0.00	34.57	3.77
209	214	4.622456	CGGCAACCACACGGCAAC	62.622	66.667	0.00	0.00	34.57	4.17
213	218	3.345808	CAGACGGCAACCACACGG	61.346	66.667	0.00	0.00	38.77	4.94
271	276	0.108186	TTCCATGCGAATCTCTGCGT	60.108	50.000	0.00	0.00	0.00	5.24
285	290	3.645212	ACATGAGTCATCGGATCTTCCAT	59.355	43.478	1.56	0.00	35.91	3.41
311	316	2.609459	AGGAATATTTCAAGCGCGTGAG	59.391	45.455	24.46	5.64	0.00	3.51
320	325	7.639113	AATTAGTTCGCCAGGAATATTTCAA	57.361	32.000	0.00	0.00	36.92	2.69
356	361	2.711542	CTAACAATCGCCAGAAACCCT	58.288	47.619	0.00	0.00	0.00	4.34
411	473	3.972403	AGTAATTGTTTTTGCGGGTGAC	58.028	40.909	0.00	0.00	0.00	3.67
412	474	3.632604	TGAGTAATTGTTTTTGCGGGTGA	59.367	39.130	0.00	0.00	0.00	4.02
413	475	3.733727	GTGAGTAATTGTTTTTGCGGGTG	59.266	43.478	0.00	0.00	0.00	4.61
414	476	3.243602	GGTGAGTAATTGTTTTTGCGGGT	60.244	43.478	0.00	0.00	0.00	5.28
415	477	3.005367	AGGTGAGTAATTGTTTTTGCGGG	59.995	43.478	0.00	0.00	0.00	6.13
416	478	4.226761	GAGGTGAGTAATTGTTTTTGCGG	58.773	43.478	0.00	0.00	0.00	5.69
417	479	3.906008	CGAGGTGAGTAATTGTTTTTGCG	59.094	43.478	0.00	0.00	0.00	4.85
418	480	4.855531	ACGAGGTGAGTAATTGTTTTTGC	58.144	39.130	0.00	0.00	0.00	3.68
419	481	5.050634	TCGACGAGGTGAGTAATTGTTTTTG	60.051	40.000	0.00	0.00	0.00	2.44
420	482	5.051816	TCGACGAGGTGAGTAATTGTTTTT	58.948	37.500	0.00	0.00	0.00	1.94
421	483	4.624015	TCGACGAGGTGAGTAATTGTTTT	58.376	39.130	0.00	0.00	0.00	2.43
422	484	4.247267	TCGACGAGGTGAGTAATTGTTT	57.753	40.909	0.00	0.00	0.00	2.83
423	485	3.928727	TCGACGAGGTGAGTAATTGTT	57.071	42.857	0.00	0.00	0.00	2.83
424	486	4.451629	AATCGACGAGGTGAGTAATTGT	57.548	40.909	3.01	0.00	0.00	2.71
425	487	5.579718	ACTAATCGACGAGGTGAGTAATTG	58.420	41.667	3.01	0.00	0.00	2.32
426	488	5.831702	ACTAATCGACGAGGTGAGTAATT	57.168	39.130	3.01	0.00	0.00	1.40
427	489	5.238214	GGTACTAATCGACGAGGTGAGTAAT	59.762	44.000	3.01	0.00	0.00	1.89
428	490	4.572389	GGTACTAATCGACGAGGTGAGTAA	59.428	45.833	3.01	0.00	0.00	2.24
429	491	4.122776	GGTACTAATCGACGAGGTGAGTA	58.877	47.826	3.01	5.42	0.00	2.59
430	492	2.941720	GGTACTAATCGACGAGGTGAGT	59.058	50.000	3.01	6.36	0.00	3.41
431	493	3.204526	AGGTACTAATCGACGAGGTGAG	58.795	50.000	3.01	0.32	36.02	3.51
432	494	3.272574	AGGTACTAATCGACGAGGTGA	57.727	47.619	3.01	0.00	36.02	4.02
445	507	5.266788	TCAGCAAGGCTAGTTTAGGTACTA	58.733	41.667	0.00	0.00	36.83	1.82
466	528	2.049888	TATTCCCATGCGTGCAATCA	57.950	45.000	0.00	0.00	0.00	2.57
492	554	1.869754	GCACGATATCGATGCACCAGT	60.870	52.381	30.37	9.61	41.97	4.00
524	586	8.243961	TCAAGGAAAAACATCCACAAGATTTA	57.756	30.769	0.00	0.00	42.27	1.40
558	620	8.862325	AAAATAACCATGGCGAGATATGATAA	57.138	30.769	13.04	0.00	0.00	1.75
593	655	2.817834	CCACGTGGTATGTGCGGG	60.818	66.667	26.95	0.00	33.88	6.13
666	731	1.133513	TGTGCTCCTGGTTTGGAATGT	60.134	47.619	0.00	0.00	35.43	2.71
806	890	1.717032	ACAAGCTAGGACCACAGACA	58.283	50.000	0.00	0.00	0.00	3.41
894	980	9.244799	TGCTGTACAAAATAAGTATCAGATACG	57.755	33.333	13.89	2.18	40.64	3.06
898	984	6.821665	GGGTGCTGTACAAAATAAGTATCAGA	59.178	38.462	0.00	0.00	0.00	3.27
1019	1105	7.148573	CGATGAACAAAAGAGCAACTGTATACT	60.149	37.037	4.17	0.00	0.00	2.12
1051	1137	5.414454	GCTTACATTGTCCAACCATGACTAA	59.586	40.000	0.00	0.00	33.83	2.24
1085	1171	9.994432	GCTGCAAGGATATAAACAATATGATAC	57.006	33.333	0.00	0.00	30.53	2.24
1235	1323	1.061131	GTTGCGATGTCCATCTTCGTG	59.939	52.381	5.79	0.00	42.88	4.35
1414	1502	5.070001	GGTAGCATACTTGGGCATTGAATA	58.930	41.667	0.00	0.00	42.51	1.75
1487	1575	3.181488	CGCCCATGACTCAAATTGCATAA	60.181	43.478	0.00	0.00	0.00	1.90
1654	1743	8.822855	TCATAAATTTGTCATGGATGTACGTAC	58.177	33.333	18.90	18.90	0.00	3.67
1655	1744	8.822855	GTCATAAATTTGTCATGGATGTACGTA	58.177	33.333	0.00	0.00	0.00	3.57
1656	1745	7.335673	TGTCATAAATTTGTCATGGATGTACGT	59.664	33.333	0.00	0.00	0.00	3.57
1657	1746	7.693020	TGTCATAAATTTGTCATGGATGTACG	58.307	34.615	0.00	0.00	0.00	3.67
1683	1772	7.069950	ACAGCACAGGTATGACTATCTTGATTA	59.930	37.037	0.00	0.00	0.00	1.75
1860	1949	2.914059	ACGGGTTATCGGATCCAAAAG	58.086	47.619	13.41	0.00	0.00	2.27
1907	1996	6.406065	CCAGCCAATGATGATTTTACATGTGA	60.406	38.462	9.11	0.00	0.00	3.58
2088	2177	1.583556	TCTCATGGGCCTTTAGCTGA	58.416	50.000	4.53	0.00	43.05	4.26
2207	2296	0.474079	TACCTGGGCCGGCCATTATA	60.474	55.000	44.46	27.81	37.98	0.98
2291	2381	2.124860	GCCGGCCCGTTAATGTCT	60.125	61.111	18.11	0.00	0.00	3.41
2387	2481	7.686438	CATTAATGGACCGGATCAAATATGA	57.314	36.000	9.46	0.00	40.57	2.15

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.