AutoCloner

Multiple sequence alignment - TraesCS2B01G086600

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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	TraesCS2B01G086600	chr2B	100.000	2168	0	0	1	2168	48305124	48302957	0.000000e+00	4004
1	TraesCS2B01G086600	chr2B	92.038	1256	98	1	911	2166	48180325	48179072	0.000000e+00	1764
2	TraesCS2B01G086600	chr2B	94.731	892	47	0	1	892	48216535	48215644	0.000000e+00	1387
3	TraesCS2B01G086600	chr2B	93.638	896	51	3	1	892	48181203	48180310	0.000000e+00	1334
4	TraesCS2B01G086600	chr2B	92.282	894	67	2	1	892	48148735	48147842	0.000000e+00	1267
5	TraesCS2B01G086600	chr2B	92.126	889	66	4	1	886	49285316	49286203	0.000000e+00	1251
6	TraesCS2B01G086600	chr2B	87.292	960	91	9	908	1847	49116370	49117318	0.000000e+00	1068
7	TraesCS2B01G086600	chr2B	89.245	781	59	11	125	892	49115620	49116388	0.000000e+00	953
8	TraesCS2B01G086600	chr2B	88.889	540	39	6	1499	2019	49255445	49255982	0.000000e+00	645
9	TraesCS2B01G086600	chr2B	87.550	249	21	8	1775	2019	49286919	49287161	1.640000e-71	279
10	TraesCS2B01G086600	chr2B	87.413	143	15	3	2019	2160	364913381	364913241	6.190000e-36	161
11	TraesCS2B01G086600	chr2A	92.849	1720	111	5	1	1718	32101387	32099678	0.000000e+00	2484
12	TraesCS2B01G086600	chr2A	89.160	1393	111	26	391	1782	32017860	32016507	0.000000e+00	1700
13	TraesCS2B01G086600	chr2A	90.225	1023	79	5	955	1957	32026531	32025510	0.000000e+00	1315
14	TraesCS2B01G086600	chr2A	93.125	480	31	2	424	903	32026994	32026517	0.000000e+00	702
15	TraesCS2B01G086600	chr2A	93.926	461	28	0	422	882	32093674	32093214	0.000000e+00	697
16	TraesCS2B01G086600	chr2A	92.581	310	21	1	1	308	32094008	32093699	5.490000e-121	444
17	TraesCS2B01G086600	chr2A	93.950	281	17	0	1	281	32027326	32027046	1.990000e-115	425
18	TraesCS2B01G086600	chrUn	87.367	1132	115	12	908	2019	311531955	311533078	0.000000e+00	1273
19	TraesCS2B01G086600	chrUn	86.115	749	82	9	1291	2019	379450426	379449680	0.000000e+00	787
20	TraesCS2B01G086600	chrUn	96.032	126	5	0	1	126	311531110	311531235	2.820000e-49	206
21	TraesCS2B01G086600	chr2D	87.157	1129	117	11	911	2019	30158488	30157368	0.000000e+00	1256
22	TraesCS2B01G086600	chr2D	87.200	1125	111	16	915	2019	30238074	30236963	0.000000e+00	1249
23	TraesCS2B01G086600	chr2D	87.068	1129	114	17	911	2019	30230471	30229355	0.000000e+00	1247
24	TraesCS2B01G086600	chr2D	86.980	1129	118	12	911	2019	30096837	30095718	0.000000e+00	1243
25	TraesCS2B01G086600	chr2D	92.506	774	50	7	125	892	29885608	29884837	0.000000e+00	1101
26	TraesCS2B01G086600	chr2D	90.000	540	34	2	1499	2019	30047860	30047322	0.000000e+00	680
27	TraesCS2B01G086600	chr2D	91.667	240	18	2	1781	2019	29884121	29883883	4.460000e-87	331
28	TraesCS2B01G086600	chr2D	96.825	126	4	0	1	126	29885703	29885578	6.060000e-51	211
29	TraesCS2B01G086600	chr6D	89.041	146	15	1	2019	2164	323434663	323434807	1.710000e-41	180
30	TraesCS2B01G086600	chr6D	84.106	151	18	5	2019	2168	61433206	61433351	8.070000e-30	141
31	TraesCS2B01G086600	chr4D	86.842	152	17	3	2017	2168	65636187	65636335	1.330000e-37	167
32	TraesCS2B01G086600	chr4D	91.743	109	8	1	2019	2127	20685211	20685318	1.340000e-32	150
33	TraesCS2B01G086600	chr6B	93.578	109	6	1	2019	2127	231286736	231286629	6.190000e-36	161
34	TraesCS2B01G086600	chr4A	85.816	141	15	3	2019	2157	297157522	297157385	6.240000e-31	145
35	TraesCS2B01G086600	chr7D	88.288	111	11	1	2017	2127	480687548	480687656	4.860000e-27	132

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	TraesCS2B01G086600	chr2B	48302957	48305124	2167	True	4004.000000	4004	100.000000	1	2168	1	chr2B.!!$R3	2167
1	TraesCS2B01G086600	chr2B	48179072	48181203	2131	True	1549.000000	1764	92.838000	1	2166	2	chr2B.!!$R5	2165
2	TraesCS2B01G086600	chr2B	48215644	48216535	891	True	1387.000000	1387	94.731000	1	892	1	chr2B.!!$R2	891
3	TraesCS2B01G086600	chr2B	48147842	48148735	893	True	1267.000000	1267	92.282000	1	892	1	chr2B.!!$R1	891
4	TraesCS2B01G086600	chr2B	49115620	49117318	1698	False	1010.500000	1068	88.268500	125	1847	2	chr2B.!!$F2	1722
5	TraesCS2B01G086600	chr2B	49285316	49287161	1845	False	765.000000	1251	89.838000	1	2019	2	chr2B.!!$F3	2018
6	TraesCS2B01G086600	chr2B	49255445	49255982	537	False	645.000000	645	88.889000	1499	2019	1	chr2B.!!$F1	520
7	TraesCS2B01G086600	chr2A	32099678	32101387	1709	True	2484.000000	2484	92.849000	1	1718	1	chr2A.!!$R2	1717
8	TraesCS2B01G086600	chr2A	32016507	32017860	1353	True	1700.000000	1700	89.160000	391	1782	1	chr2A.!!$R1	1391
9	TraesCS2B01G086600	chr2A	32025510	32027326	1816	True	814.000000	1315	92.433333	1	1957	3	chr2A.!!$R3	1956
10	TraesCS2B01G086600	chr2A	32093214	32094008	794	True	570.500000	697	93.253500	1	882	2	chr2A.!!$R4	881
11	TraesCS2B01G086600	chrUn	379449680	379450426	746	True	787.000000	787	86.115000	1291	2019	1	chrUn.!!$R1	728
12	TraesCS2B01G086600	chrUn	311531110	311533078	1968	False	739.500000	1273	91.699500	1	2019	2	chrUn.!!$F1	2018
13	TraesCS2B01G086600	chr2D	30157368	30158488	1120	True	1256.000000	1256	87.157000	911	2019	1	chr2D.!!$R3	1108
14	TraesCS2B01G086600	chr2D	30236963	30238074	1111	True	1249.000000	1249	87.200000	915	2019	1	chr2D.!!$R5	1104
15	TraesCS2B01G086600	chr2D	30229355	30230471	1116	True	1247.000000	1247	87.068000	911	2019	1	chr2D.!!$R4	1108
16	TraesCS2B01G086600	chr2D	30095718	30096837	1119	True	1243.000000	1243	86.980000	911	2019	1	chr2D.!!$R2	1108
17	TraesCS2B01G086600	chr2D	30047322	30047860	538	True	680.000000	680	90.000000	1499	2019	1	chr2D.!!$R1	520
18	TraesCS2B01G086600	chr2D	29883883	29885703	1820	True	547.666667	1101	93.666000	1	2019	3	chr2D.!!$R6	2018

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
635	684	0.627451	TCATGGAGCTCAAGGCCAAT	59.373	50.0	17.19	0.0	43.05	3.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2053	2130	1.380785	ATCACTGGGCTGGCAATGG	60.381	57.895	2.88	0.0	0.0	3.16	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
50	51	2.030027	TCTCCTCCAACACCATCTGT	57.970	50.000	0.00	0.00	32.89	3.41
150	152	1.908619	TCATCAGGCTTCTGGTGCTTA	59.091	47.619	2.05	0.00	46.43	3.09
341	375	7.888021	TGTTTTCCATGTTGATGTTATCTAGGT	59.112	33.333	0.00	0.00	0.00	3.08
342	376	8.739972	GTTTTCCATGTTGATGTTATCTAGGTT	58.260	33.333	0.00	0.00	0.00	3.50
345	379	7.047891	TCCATGTTGATGTTATCTAGGTTCAC	58.952	38.462	0.00	0.00	0.00	3.18
413	450	4.196626	ACTTTGCATGCATAGCACAATT	57.803	36.364	30.54	12.98	43.04	2.32
443	482	7.112565	CGTTCTCTGTCATTGTTTCATTTGAAG	59.887	37.037	0.00	0.00	35.21	3.02
635	684	0.627451	TCATGGAGCTCAAGGCCAAT	59.373	50.000	17.19	0.00	43.05	3.16
658	707	1.357137	TCCACCACTATCAAGGCACA	58.643	50.000	0.00	0.00	0.00	4.57
689	738	9.281371	GTAGAGGACATTAAAGTTTGTAGGTTT	57.719	33.333	0.00	0.00	0.00	3.27
698	747	4.353383	AGTTTGTAGGTTTGTCCTCTCC	57.647	45.455	0.00	0.00	44.42	3.71
757	806	2.358267	CCATGAATGAGAAGGAAGCTGC	59.642	50.000	0.00	0.00	0.00	5.25
800	849	8.722394	GGGAAAAAGTTTGACATTGTTTTGTTA	58.278	29.630	0.00	0.00	0.00	2.41
835	884	0.835941	ATCATGACTGGTCCAGAGGC	59.164	55.000	26.18	13.90	35.18	4.70
1181	1234	3.609853	TGGTCTAGCGCAATTCATCTTT	58.390	40.909	11.47	0.00	0.00	2.52
1194	1247	6.976925	GCAATTCATCTTTCTTAAGTGATGGG	59.023	38.462	22.53	15.70	37.48	4.00
1196	1249	6.387192	TTCATCTTTCTTAAGTGATGGGGA	57.613	37.500	22.53	13.53	37.48	4.81
1287	1340	9.994432	AAATGTATCATTTGATTTCGAGAACTC	57.006	29.630	6.87	0.00	36.05	3.01
1388	1441	4.787551	TCTGTTTTTGGTCAAGGCTTCTA	58.212	39.130	0.00	0.00	0.00	2.10
1395	1448	4.281898	TGGTCAAGGCTTCTAACTAACC	57.718	45.455	0.00	0.00	0.00	2.85
1528	1582	8.995220	GTGTATCCAATTAATGACCGCTATTAA	58.005	33.333	0.00	0.00	35.26	1.40
1583	1637	9.543231	CTATTGGTAAACACCCCTATATCTCTA	57.457	37.037	0.00	0.00	0.00	2.43
1592	1646	4.675550	ACCCCTATATCTCTACCTTGTCCT	59.324	45.833	0.00	0.00	0.00	3.85
1632	1686	0.753848	CATGCACCCATCCATCTGCA	60.754	55.000	0.00	0.00	43.50	4.41
1633	1687	0.467474	ATGCACCCATCCATCTGCAG	60.467	55.000	7.63	7.63	42.66	4.41
1686	1740	0.662619	TGCAGCAAGGTTCAAAGACG	59.337	50.000	0.00	0.00	0.00	4.18
1805	1879	4.283337	TCCCTGGTGTCGATGAGTTATAA	58.717	43.478	0.00	0.00	0.00	0.98
1875	1952	1.204941	AGCGTTGTGTCATCTCCTACC	59.795	52.381	0.00	0.00	0.00	3.18
1947	2024	2.126071	GAAGGCACGTGCGAGCTA	60.126	61.111	32.35	0.00	43.26	3.32
1995	2072	2.991866	GAGAAGCTTGCTTTGGAAATGC	59.008	45.455	2.10	0.00	46.12	3.56
2030	2107	3.627332	TAGGGATGTGGCACCCCGA	62.627	63.158	21.61	16.09	46.64	5.14
2044	2121	2.636412	CCCGACTCAGAGCAACCGA	61.636	63.158	0.00	0.00	0.00	4.69
2053	2130	3.596214	TCAGAGCAACCGATTTACCTTC	58.404	45.455	0.00	0.00	0.00	3.46
2062	2139	2.358898	CCGATTTACCTTCCATTGCCAG	59.641	50.000	0.00	0.00	0.00	4.85
2068	2145	1.304713	CTTCCATTGCCAGCCCAGT	60.305	57.895	0.00	0.00	0.00	4.00
2073	2150	0.395311	CATTGCCAGCCCAGTGATCT	60.395	55.000	0.00	0.00	0.00	2.75
2094	2171	2.292267	AGTCTTCTGGCAACACACAAG	58.708	47.619	0.00	0.00	46.17	3.16
2096	2173	2.682856	GTCTTCTGGCAACACACAAGAA	59.317	45.455	0.00	0.00	46.17	2.52
2104	2181	3.243068	GGCAACACACAAGAACTTGGTAG	60.243	47.826	17.05	9.84	44.45	3.18
2117	2194	3.139077	ACTTGGTAGAGAAAAGCAACCG	58.861	45.455	0.00	0.00	32.69	4.44
2142	2219	7.189512	GCTTTATTGACATAAGCGAGAACATT	58.810	34.615	0.00	0.00	0.00	2.71
2143	2220	7.164826	GCTTTATTGACATAAGCGAGAACATTG	59.835	37.037	0.00	0.00	0.00	2.82
2166	2243	5.517411	TGGTTCGATATTACAACAAGTAGCG	59.483	40.000	0.00	0.00	33.43	4.26
2167	2244	5.745294	GGTTCGATATTACAACAAGTAGCGA	59.255	40.000	0.00	0.00	33.43	4.93

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
50	51	8.462804	ATGGAACATGTACCTGAAGGTTAGAGA	61.463	40.741	7.43	0.00	46.52	3.10
150	152	3.196901	TGGATGTAAAGCGTGGACACTAT	59.803	43.478	0.56	0.00	0.00	2.12
294	327	5.051816	ACAAACAATGAACATGCCAAGAAG	58.948	37.500	0.00	0.00	0.00	2.85
297	330	5.738118	AAACAAACAATGAACATGCCAAG	57.262	34.783	0.00	0.00	0.00	3.61
413	450	5.296748	TGAAACAATGACAGAGAACGATCA	58.703	37.500	0.00	0.00	0.00	2.92
635	684	1.490490	GCCTTGATAGTGGTGGATCCA	59.510	52.381	11.44	11.44	45.01	3.41
645	694	5.482908	CTCTACAAGTTGTGCCTTGATAGT	58.517	41.667	18.90	0.00	43.65	2.12
658	707	8.747538	ACAAACTTTAATGTCCTCTACAAGTT	57.252	30.769	0.00	0.00	42.70	2.66
689	738	1.980765	AGCAGAATTGTGGAGAGGACA	59.019	47.619	4.57	0.00	0.00	4.02
698	747	4.063689	AGTGAAGTCTGAGCAGAATTGTG	58.936	43.478	16.68	0.00	44.55	3.33
757	806	3.439857	TCCCCTCAAGGAACAAATCAG	57.560	47.619	0.00	0.00	38.24	2.90
800	849	7.110810	CAGTCATGATGGGCATATTCTTATCT	58.889	38.462	0.00	0.00	34.82	1.98
976	1029	3.126858	GCACGAATCTTCACAATTGCCTA	59.873	43.478	5.05	0.00	0.00	3.93
1228	1281	3.498397	CACAACAACGGAGACTAAAGCAT	59.502	43.478	0.00	0.00	0.00	3.79
1377	1430	3.263425	CCTGGGTTAGTTAGAAGCCTTGA	59.737	47.826	6.01	0.00	45.47	3.02
1388	1441	4.340950	CACAACATGAAACCTGGGTTAGTT	59.659	41.667	0.00	0.03	37.35	2.24
1395	1448	3.213506	TGACTCACAACATGAAACCTGG	58.786	45.455	0.00	0.00	36.69	4.45
1583	1637	9.636789	AGTTAATTTTACTTACAAGGACAAGGT	57.363	29.630	0.00	0.00	0.00	3.50
1592	1646	8.144478	TGCATGGCAAGTTAATTTTACTTACAA	58.856	29.630	0.00	0.00	34.76	2.41
1686	1740	9.334693	CATAAATGCTAGGATTTCGAATAAAGC	57.665	33.333	23.56	5.21	0.00	3.51
1726	1780	3.592865	AGAGGAGAAAGGTCAGGAAAGT	58.407	45.455	0.00	0.00	0.00	2.66
1733	1787	2.172505	TGTTGCAAGAGGAGAAAGGTCA	59.827	45.455	0.00	0.00	0.00	4.02
1839	1915	4.142138	ACAACGCTCCTCTATACTTCCTTG	60.142	45.833	0.00	0.00	0.00	3.61
1875	1952	4.269603	GTGTGTCGATCTCAATCATTGGAG	59.730	45.833	0.00	0.00	31.76	3.86
1969	2046	4.558226	TCCAAAGCAAGCTTCTCTCATA	57.442	40.909	7.88	0.00	34.84	2.15
1971	2048	2.936919	TCCAAAGCAAGCTTCTCTCA	57.063	45.000	7.88	0.00	34.84	3.27
1995	2072	8.936864	CACATCCCTAAACTAACTTTACTTCTG	58.063	37.037	0.00	0.00	0.00	3.02
2030	2107	2.567615	AGGTAAATCGGTTGCTCTGAGT	59.432	45.455	6.53	0.00	34.66	3.41
2044	2121	2.110578	GGCTGGCAATGGAAGGTAAAT	58.889	47.619	0.00	0.00	0.00	1.40
2053	2130	1.380785	ATCACTGGGCTGGCAATGG	60.381	57.895	2.88	0.00	0.00	3.16
2062	2139	2.102252	CCAGAAGACTAGATCACTGGGC	59.898	54.545	18.73	0.00	43.97	5.36
2068	2145	3.578282	TGTGTTGCCAGAAGACTAGATCA	59.422	43.478	0.00	0.00	0.00	2.92
2073	2150	3.133901	TCTTGTGTGTTGCCAGAAGACTA	59.866	43.478	0.00	0.00	39.13	2.59
2094	2171	4.319549	CGGTTGCTTTTCTCTACCAAGTTC	60.320	45.833	0.00	0.00	0.00	3.01
2096	2173	3.139077	CGGTTGCTTTTCTCTACCAAGT	58.861	45.455	0.00	0.00	0.00	3.16
2117	2194	6.106877	TGTTCTCGCTTATGTCAATAAAGC	57.893	37.500	7.52	7.52	0.00	3.51
2142	2219	5.517411	CGCTACTTGTTGTAATATCGAACCA	59.483	40.000	0.00	0.00	0.00	3.67
2143	2220	5.745294	TCGCTACTTGTTGTAATATCGAACC	59.255	40.000	0.00	0.00	0.00	3.62

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.