AutoCloner

Multiple sequence alignment - TraesCS2D01G106200

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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	TraesCS2D01G106200	chr2D	100.000	3201	0	0	1	3201	58637899	58641099	0.000000e+00	5912
1	TraesCS2D01G106200	chr2D	96.661	2216	39	9	997	3201	55249846	55247655	0.000000e+00	3650
2	TraesCS2D01G106200	chr2D	89.515	1669	115	30	1562	3201	55247086	55245449	0.000000e+00	2058
3	TraesCS2D01G106200	chr2D	97.647	255	6	0	721	975	55250160	55249906	3.790000e-119	438
4	TraesCS2D01G106200	chr2D	95.397	239	11	0	2963	3201	55242601	55242363	6.480000e-102	381
5	TraesCS2D01G106200	chr2B	91.580	1829	104	21	1235	3027	87530334	87528520	0.000000e+00	2479
6	TraesCS2D01G106200	chr2B	90.122	1144	71	17	2034	3160	87517212	87516094	0.000000e+00	1448
7	TraesCS2D01G106200	chr2B	90.126	1033	74	18	1563	2580	87423459	87422440	0.000000e+00	1317
8	TraesCS2D01G106200	chr2B	91.615	811	58	5	1235	2035	87518103	87517293	0.000000e+00	1112
9	TraesCS2D01G106200	chr2B	91.554	592	30	6	1	592	780665109	780665680	0.000000e+00	798
10	TraesCS2D01G106200	chr2B	89.509	591	37	4	997	1579	87424048	87423475	0.000000e+00	725
11	TraesCS2D01G106200	chr2B	90.508	295	18	4	2876	3160	87416215	87415921	6.480000e-102	381
12	TraesCS2D01G106200	chr2B	89.865	296	18	5	2579	2871	87422358	87422072	1.400000e-98	370
13	TraesCS2D01G106200	chr2B	93.035	201	14	0	997	1197	87518294	87518094	8.680000e-76	294
14	TraesCS2D01G106200	chr2B	90.047	211	20	1	997	1207	87530525	87530316	4.070000e-69	272
15	TraesCS2D01G106200	chr2B	82.305	243	43	0	1720	1962	155820575	155820817	9.000000e-51	211
16	TraesCS2D01G106200	chr2B	78.682	258	35	7	997	1243	87775981	87775733	1.540000e-33	154
17	TraesCS2D01G106200	chr2A	94.444	1458	67	6	588	2035	56108226	56106773	0.000000e+00	2231
18	TraesCS2D01G106200	chr2A	92.869	1192	53	16	2034	3201	56106691	56105508	0.000000e+00	1701
19	TraesCS2D01G106200	chr2A	90.520	1192	57	18	2034	3201	55972312	55971153	0.000000e+00	1524
20	TraesCS2D01G106200	chr2A	91.988	337	27	0	1699	2035	55972730	55972394	1.040000e-129	473
21	TraesCS2D01G106200	chr2A	82.917	240	41	0	1723	1962	109324640	109324401	1.930000e-52	217
22	TraesCS2D01G106200	chr2A	73.761	545	73	34	2183	2714	55971328	55970841	1.990000e-32	150
23	TraesCS2D01G106200	chr2A	86.792	106	11	1	2392	2494	56105510	56105405	7.260000e-22	115
24	TraesCS2D01G106200	chr6A	87.958	191	22	1	1	190	169504357	169504167	1.160000e-54	224
25	TraesCS2D01G106200	chr3B	87.500	192	22	2	1	190	762407326	762407517	1.490000e-53	220
26	TraesCS2D01G106200	chr4D	86.905	168	20	2	25	190	346275030	346274863	1.520000e-43	187
27	TraesCS2D01G106200	chr4D	85.629	167	22	2	26	190	346279533	346279367	1.180000e-39	174
28	TraesCS2D01G106200	chr4D	84.524	168	24	2	25	190	346278031	346277864	7.100000e-37	165
29	TraesCS2D01G106200	chrUn	84.615	169	23	3	25	190	124666216	124666384	7.100000e-37	165

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	TraesCS2D01G106200	chr2D	58637899	58641099	3200	False	5912.000000	5912	100.000000	1	3201	1	chr2D.!!$F1	3200
1	TraesCS2D01G106200	chr2D	55242363	55250160	7797	True	1631.750000	3650	94.805000	721	3201	4	chr2D.!!$R1	2480
2	TraesCS2D01G106200	chr2B	87528520	87530525	2005	True	1375.500000	2479	90.813500	997	3027	2	chr2B.!!$R5	2030
3	TraesCS2D01G106200	chr2B	87516094	87518294	2200	True	951.333333	1448	91.590667	997	3160	3	chr2B.!!$R4	2163
4	TraesCS2D01G106200	chr2B	87422072	87424048	1976	True	804.000000	1317	89.833333	997	2871	3	chr2B.!!$R3	1874
5	TraesCS2D01G106200	chr2B	780665109	780665680	571	False	798.000000	798	91.554000	1	592	1	chr2B.!!$F2	591
6	TraesCS2D01G106200	chr2A	56105405	56108226	2821	True	1349.000000	2231	91.368333	588	3201	3	chr2A.!!$R3	2613
7	TraesCS2D01G106200	chr2A	55970841	55972730	1889	True	715.666667	1524	85.423000	1699	3201	3	chr2A.!!$R2	1502

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
199	200	0.179137	CATCTCGTCCGCTTGTAGCA	60.179	55.0	0.00	0.0	42.58	3.49	F
1664	1797	0.319211	TACTGAACGGCAGACGGTTG	60.319	55.0	13.54	0.0	46.88	3.77	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1910	2046	0.971386	CATATCTGCAAATGGGCCCC	59.029	55.0	22.27	3.07	0.0	5.80	R
2926	5457	0.251341	ACCCCCAAAAGCTGCACTAG	60.251	55.0	1.02	0.00	0.0	2.57	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
146	147	6.603095	CAAACTAGTTGTAGCCAGAATTGTC	58.397	40.000	9.34	0.00	32.08	3.18
158	159	1.131883	AGAATTGTCGCAGATTGCAGC	59.868	47.619	1.69	0.00	45.36	5.25
168	169	1.447838	GATTGCAGCTCCCGTCGAA	60.448	57.895	0.00	0.00	0.00	3.71
199	200	0.179137	CATCTCGTCCGCTTGTAGCA	60.179	55.000	0.00	0.00	42.58	3.49
200	201	0.747255	ATCTCGTCCGCTTGTAGCAT	59.253	50.000	0.00	0.00	42.58	3.79
201	202	0.179137	TCTCGTCCGCTTGTAGCATG	60.179	55.000	0.00	0.00	42.58	4.06
265	266	2.735478	CAGTGCGGACGCGGTTTA	60.735	61.111	12.47	0.00	45.51	2.01
277	278	1.362406	GCGGTTTAGAGTGGCTGCTC	61.362	60.000	0.00	2.23	35.82	4.26
326	327	2.039974	TACGTTCGCCGGAGTAGCA	61.040	57.895	5.05	0.00	42.24	3.49
380	381	1.673920	AGCGTTGGTCGTGTTTGATTT	59.326	42.857	0.00	0.00	42.13	2.17
383	384	2.223386	CGTTGGTCGTGTTTGATTTGGT	60.223	45.455	0.00	0.00	34.52	3.67
384	385	3.732471	CGTTGGTCGTGTTTGATTTGGTT	60.732	43.478	0.00	0.00	34.52	3.67
390	391	6.127703	TGGTCGTGTTTGATTTGGTTAAAAGA	60.128	34.615	0.00	0.00	0.00	2.52
442	443	6.670027	ACTAGGCAAAAGAGATAAGGAAGAGA	59.330	38.462	0.00	0.00	0.00	3.10
460	461	2.818274	CCGAGCGGTTTGTAGGGC	60.818	66.667	0.00	0.00	0.00	5.19
461	462	2.818274	CGAGCGGTTTGTAGGGCC	60.818	66.667	0.00	0.00	0.00	5.80
462	463	2.437895	GAGCGGTTTGTAGGGCCC	60.438	66.667	16.46	16.46	0.00	5.80
463	464	3.253838	AGCGGTTTGTAGGGCCCA	61.254	61.111	27.56	7.27	0.00	5.36
464	465	2.750237	GCGGTTTGTAGGGCCCAG	60.750	66.667	27.56	5.37	0.00	4.45
465	466	2.045340	CGGTTTGTAGGGCCCAGG	60.045	66.667	27.56	0.00	0.00	4.45
466	467	2.598787	CGGTTTGTAGGGCCCAGGA	61.599	63.158	27.56	5.59	0.00	3.86
467	468	1.303282	GGTTTGTAGGGCCCAGGAG	59.697	63.158	27.56	0.00	0.00	3.69
468	469	1.303282	GTTTGTAGGGCCCAGGAGG	59.697	63.158	27.56	0.00	39.47	4.30
485	486	4.011517	GGACGCGTGGGGGAGAAA	62.012	66.667	20.70	0.00	0.00	2.52
490	491	2.742372	CGTGGGGGAGAAAGTGCG	60.742	66.667	0.00	0.00	0.00	5.34
537	538	1.792949	GATTAGGCGCAATCGAATCGT	59.207	47.619	10.83	0.00	38.10	3.73
600	601	5.557891	TCGAAACGTTTCCCTTGTTTTTA	57.442	34.783	29.95	2.46	36.06	1.52
613	614	7.116736	TCCCTTGTTTTTATCTATCAACCCTC	58.883	38.462	0.00	0.00	0.00	4.30
642	643	4.182339	GTTTATGACGAGGGGACTTCTTC	58.818	47.826	0.00	0.00	44.43	2.87
650	651	3.288092	GAGGGGACTTCTTCTCTCTCTC	58.712	54.545	0.00	0.00	44.43	3.20
660	661	8.661352	ACTTCTTCTCTCTCTCTTTTTCTTTG	57.339	34.615	0.00	0.00	0.00	2.77
681	684	4.803452	TGTTCTTTTGAGGTTCATTCCCT	58.197	39.130	0.00	0.00	34.11	4.20
1033	1074	2.110213	ACAAGCTCGTTCGGGCAA	59.890	55.556	19.00	0.00	0.00	4.52
1664	1797	0.319211	TACTGAACGGCAGACGGTTG	60.319	55.000	13.54	0.00	46.88	3.77
1910	2046	0.933047	TCGTCGCAAGTGTCTCAACG	60.933	55.000	0.00	0.00	39.48	4.10
2263	4687	0.105964	TCGAGCTGCTTAGATCCCCT	60.106	55.000	2.53	0.00	0.00	4.79
2298	4722	4.842574	TGAGCATTGCCAACAAGACTATA	58.157	39.130	4.70	0.00	39.69	1.31
2299	4723	5.439721	TGAGCATTGCCAACAAGACTATAT	58.560	37.500	4.70	0.00	39.69	0.86
2360	4784	2.530460	TTGCTCATATGGGTTTGGCT	57.470	45.000	4.11	0.00	0.00	4.75
2361	4785	2.530460	TGCTCATATGGGTTTGGCTT	57.470	45.000	4.11	0.00	0.00	4.35
2362	4786	2.818921	TGCTCATATGGGTTTGGCTTT	58.181	42.857	4.11	0.00	0.00	3.51
2363	4787	2.496871	TGCTCATATGGGTTTGGCTTTG	59.503	45.455	4.11	0.00	0.00	2.77
2364	4788	2.159057	GCTCATATGGGTTTGGCTTTGG	60.159	50.000	4.11	0.00	0.00	3.28
2365	4789	1.830477	TCATATGGGTTTGGCTTTGGC	59.170	47.619	2.13	0.00	37.82	4.52
2531	4955	9.710979	CATTTTAAATTTGCTCTAATTGCCATG	57.289	29.630	0.00	0.00	0.00	3.66
2783	5310	0.251341	CCTTTGGTCAGGTCCCAAGG	60.251	60.000	2.05	2.05	42.63	3.61
2922	5453	2.158842	GCTCTATGGTGCTTCTCATGGT	60.159	50.000	0.00	0.00	0.00	3.55
2923	5454	3.464907	CTCTATGGTGCTTCTCATGGTG	58.535	50.000	0.00	0.00	0.00	4.17
2924	5455	3.106827	TCTATGGTGCTTCTCATGGTGA	58.893	45.455	0.00	0.00	0.00	4.02
2926	5457	0.321919	TGGTGCTTCTCATGGTGAGC	60.322	55.000	2.13	7.79	43.95	4.26
3066	5614	9.736023	CTAAATTCTGTTATGAAAATGGTAGGC	57.264	33.333	0.00	0.00	0.00	3.93
3106	5654	2.414824	GGTCGAGCTGCTTATATCCTCG	60.415	54.545	7.51	0.00	44.76	4.63
3113	5661	6.348295	CGAGCTGCTTATATCCTCGTTACTAA	60.348	42.308	2.53	0.00	40.17	2.24
3186	5743	3.197983	TCCCTGATATGGTTTTGGGAGT	58.802	45.455	0.00	0.00	38.67	3.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
17	18	5.695851	ACCACTATCTCTTGTTTTTGCTG	57.304	39.130	0.00	0.00	0.00	4.41
158	159	1.446272	GAACCTGCTTCGACGGGAG	60.446	63.158	7.85	3.79	39.59	4.30
168	169	1.220206	CGAGATGCTGGAACCTGCT	59.780	57.895	19.95	8.66	40.75	4.24
199	200	0.541392	TGGAACAGCGCCTACATCAT	59.459	50.000	2.29	0.00	0.00	2.45
200	201	1.979262	TGGAACAGCGCCTACATCA	59.021	52.632	2.29	0.00	0.00	3.07
201	202	4.932789	TGGAACAGCGCCTACATC	57.067	55.556	2.29	0.00	0.00	3.06
259	260	1.078759	CGAGCAGCCACTCTAAACCG	61.079	60.000	2.45	0.00	34.35	4.44
368	369	7.763356	TCTTCTTTTAACCAAATCAAACACGA	58.237	30.769	0.00	0.00	0.00	4.35
380	381	5.735922	GCACACAAGCATCTTCTTTTAACCA	60.736	40.000	0.00	0.00	0.00	3.67
383	384	4.036262	ACGCACACAAGCATCTTCTTTTAA	59.964	37.500	0.00	0.00	0.00	1.52
384	385	3.563808	ACGCACACAAGCATCTTCTTTTA	59.436	39.130	0.00	0.00	0.00	1.52
390	391	1.265095	CTCAACGCACACAAGCATCTT	59.735	47.619	0.00	0.00	0.00	2.40
413	414	6.407202	TCCTTATCTCTTTTGCCTAGTCAAC	58.593	40.000	0.00	0.00	0.00	3.18
468	469	3.952628	CTTTCTCCCCCACGCGTCC	62.953	68.421	9.86	0.00	0.00	4.79
469	470	2.434359	CTTTCTCCCCCACGCGTC	60.434	66.667	9.86	0.00	0.00	5.19
470	471	3.239253	ACTTTCTCCCCCACGCGT	61.239	61.111	5.58	5.58	0.00	6.01
471	472	2.742372	CACTTTCTCCCCCACGCG	60.742	66.667	3.53	3.53	0.00	6.01
472	473	3.056328	GCACTTTCTCCCCCACGC	61.056	66.667	0.00	0.00	0.00	5.34
473	474	2.742372	CGCACTTTCTCCCCCACG	60.742	66.667	0.00	0.00	0.00	4.94
490	491	3.423154	CAGTTTCGCCACGCCCTC	61.423	66.667	0.00	0.00	0.00	4.30
508	509	1.301322	GCGCCTAATCTCCTGGCTC	60.301	63.158	0.00	0.00	44.09	4.70
521	522	0.928229	GTAACGATTCGATTGCGCCT	59.072	50.000	13.95	0.00	37.46	5.52
523	524	0.980596	GCGTAACGATTCGATTGCGC	60.981	55.000	26.07	26.07	37.46	6.09
552	553	2.668550	GCCGGCTGAACTTTCGGT	60.669	61.111	22.15	0.00	43.87	4.69
600	601	9.401058	CATAAACAAAAGAGAGGGTTGATAGAT	57.599	33.333	0.00	0.00	0.00	1.98
613	614	4.392138	GTCCCCTCGTCATAAACAAAAGAG	59.608	45.833	0.00	0.00	0.00	2.85
624	625	2.104170	GAGAAGAAGTCCCCTCGTCAT	58.896	52.381	0.00	0.00	0.00	3.06
642	643	9.500864	CAAAAGAACAAAGAAAAAGAGAGAGAG	57.499	33.333	0.00	0.00	0.00	3.20
650	651	8.532977	TGAACCTCAAAAGAACAAAGAAAAAG	57.467	30.769	0.00	0.00	0.00	2.27
660	661	4.559502	GCAGGGAATGAACCTCAAAAGAAC	60.560	45.833	0.00	0.00	35.78	3.01
692	695	8.106462	AGGGAATGAAAACCTCAAAAAGAAAAA	58.894	29.630	0.00	0.00	37.67	1.94
693	696	7.552330	CAGGGAATGAAAACCTCAAAAAGAAAA	59.448	33.333	0.00	0.00	37.67	2.29
906	909	1.902508	TCTCTTGAAGCCGTTGGATCT	59.097	47.619	0.00	0.00	0.00	2.75
1033	1074	3.480133	GGGGCGTGATGCTAGGGT	61.480	66.667	0.00	0.00	45.43	4.34
1687	1820	4.924305	TTATGTCCGCCGTAAAGACTAT	57.076	40.909	0.00	0.00	0.00	2.12
1910	2046	0.971386	CATATCTGCAAATGGGCCCC	59.029	55.000	22.27	3.07	0.00	5.80
2263	4687	5.947228	GCAATGCTCAGCCAAATAGTATA	57.053	39.130	0.00	0.00	0.00	1.47
2320	4744	8.162878	AGCAATGTATGGTTTCTCATGATAAG	57.837	34.615	0.00	0.00	35.94	1.73
2322	4746	7.281841	TGAGCAATGTATGGTTTCTCATGATA	58.718	34.615	0.00	0.00	40.59	2.15
2360	4784	2.865119	TGCATCTTCTCTCTGCCAAA	57.135	45.000	0.00	0.00	35.02	3.28
2361	4785	2.865119	TTGCATCTTCTCTCTGCCAA	57.135	45.000	0.00	0.00	35.02	4.52
2362	4786	3.361281	AATTGCATCTTCTCTCTGCCA	57.639	42.857	0.00	0.00	35.02	4.92
2363	4787	4.450053	ACTAATTGCATCTTCTCTCTGCC	58.550	43.478	0.00	0.00	35.02	4.85
2364	4788	6.292811	GCTAACTAATTGCATCTTCTCTCTGC	60.293	42.308	0.00	0.00	36.45	4.26
2365	4789	6.985645	AGCTAACTAATTGCATCTTCTCTCTG	59.014	38.462	0.00	0.00	0.00	3.35
2439	4863	1.838112	TTTTGAGCCTATGTGCAGGG	58.162	50.000	0.00	0.00	36.10	4.45
2531	4955	1.471684	CTGCCAAGCTTGTCAATCTCC	59.528	52.381	24.35	3.76	0.00	3.71
2926	5457	0.251341	ACCCCCAAAAGCTGCACTAG	60.251	55.000	1.02	0.00	0.00	2.57
3066	5614	4.388469	CGACCAAACAAATGGCTTTTATGG	59.612	41.667	16.31	16.31	44.75	2.74
3075	5623	1.666888	GCAGCTCGACCAAACAAATGG	60.667	52.381	0.00	0.00	46.38	3.16
3106	5654	5.598769	AGCCGATACTCACCAATTAGTAAC	58.401	41.667	0.00	0.00	32.24	2.50
3113	5661	4.519730	GTCTAGTAGCCGATACTCACCAAT	59.480	45.833	0.00	0.00	43.90	3.16
3177	5734	3.951680	GTGGTTTCTTCTCACTCCCAAAA	59.048	43.478	0.00	0.00	0.00	2.44

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.