AutoCloner

Multiple sequence alignment - TraesCS1B01G152600

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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	TraesCS1B01G152600	chr1B	100.000	2462	0	0	1	2462	245960329	245962790	0.000000e+00	4547
1	TraesCS1B01G152600	chr1B	93.778	450	28	0	2010	2459	139330384	139330833	0.000000e+00	676
2	TraesCS1B01G152600	chr5B	93.329	1469	98	0	1	1469	511693508	511692040	0.000000e+00	2170
3	TraesCS1B01G152600	chr5B	90.570	1474	124	11	1	1469	345850836	345852299	0.000000e+00	1938
4	TraesCS1B01G152600	chr5B	95.212	543	26	0	1467	2009	381735609	381736151	0.000000e+00	859
5	TraesCS1B01G152600	chr5B	83.088	544	69	18	1813	2344	472179899	472180431	7.970000e-130	473
6	TraesCS1B01G152600	chr7B	93.169	1464	95	3	10	1469	637347405	637345943	0.000000e+00	2145
7	TraesCS1B01G152600	chr7B	95.018	542	27	0	1468	2009	295804735	295805276	0.000000e+00	852
8	TraesCS1B01G152600	chr7B	93.407	455	27	3	2010	2462	71108548	71108095	0.000000e+00	671
9	TraesCS1B01G152600	chr7B	93.392	454	26	4	2010	2462	71126054	71125604	0.000000e+00	669
10	TraesCS1B01G152600	chr2B	92.730	1458	106	0	12	1469	503342285	503343742	0.000000e+00	2106
11	TraesCS1B01G152600	chr2B	95.203	542	26	0	1468	2009	405055469	405054928	0.000000e+00	857
12	TraesCS1B01G152600	chr2B	95.203	542	26	0	1468	2009	428719325	428719866	0.000000e+00	857
13	TraesCS1B01G152600	chr2B	93.640	456	24	4	2010	2462	206306642	206306189	0.000000e+00	676
14	TraesCS1B01G152600	chr2B	93.598	453	25	4	2010	2459	368398433	368398884	0.000000e+00	673
15	TraesCS1B01G152600	chrUn	92.449	1470	109	2	1	1469	22043798	22045266	0.000000e+00	2098
16	TraesCS1B01G152600	chr5D	92.302	1481	93	13	1	1469	58529650	58531121	0.000000e+00	2084
17	TraesCS1B01G152600	chr5D	82.527	641	75	22	1819	2450	384112261	384112873	1.680000e-146	529
18	TraesCS1B01G152600	chr3D	92.100	1481	100	12	1	1469	543499163	543500638	0.000000e+00	2071
19	TraesCS1B01G152600	chr3D	91.762	1493	89	19	1	1469	518967232	518965750	0.000000e+00	2045
20	TraesCS1B01G152600	chr3D	94.659	543	28	1	1468	2009	30497973	30498515	0.000000e+00	841
21	TraesCS1B01G152600	chr3D	93.435	457	25	5	2010	2462	31675253	31674798	0.000000e+00	673
22	TraesCS1B01G152600	chr3D	94.613	297	16	0	1	297	519069045	519068749	6.200000e-126	460
23	TraesCS1B01G152600	chr2D	90.199	1510	97	32	1	1469	408330785	408329286	0.000000e+00	1921
24	TraesCS1B01G152600	chr2D	95.548	292	13	0	1	292	9608553	9608844	3.710000e-128	468
25	TraesCS1B01G152600	chr1D	92.003	1288	83	13	194	1469	396011779	396010500	0.000000e+00	1790
26	TraesCS1B01G152600	chr3A	94.834	542	28	0	1468	2009	149491555	149492096	0.000000e+00	846
27	TraesCS1B01G152600	chr3A	94.834	542	28	0	1468	2009	149510499	149511040	0.000000e+00	846
28	TraesCS1B01G152600	chr6D	94.649	542	29	0	1468	2009	422277167	422277708	0.000000e+00	841
29	TraesCS1B01G152600	chr4B	94.203	552	31	1	1459	2009	82909487	82908936	0.000000e+00	841
30	TraesCS1B01G152600	chr3B	94.053	454	22	3	2010	2459	24507967	24508419	0.000000e+00	684
31	TraesCS1B01G152600	chr3B	94.102	373	22	0	1	373	499366370	499366742	3.550000e-158	568
32	TraesCS1B01G152600	chr6B	93.392	454	26	4	2007	2459	396476709	396477159	0.000000e+00	669
33	TraesCS1B01G152600	chr7A	82.669	652	88	18	1819	2458	480865392	480866030	2.770000e-154	555
34	TraesCS1B01G152600	chr2A	81.459	658	95	24	1819	2459	751685126	751685773	4.690000e-142	514
35	TraesCS1B01G152600	chr7D	81.279	657	89	24	1820	2459	361246462	361247101	3.660000e-138	501

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	TraesCS1B01G152600	chr1B	245960329	245962790	2461	False	4547	4547	100.000	1	2462	1	chr1B.!!$F2	2461
1	TraesCS1B01G152600	chr5B	511692040	511693508	1468	True	2170	2170	93.329	1	1469	1	chr5B.!!$R1	1468
2	TraesCS1B01G152600	chr5B	345850836	345852299	1463	False	1938	1938	90.570	1	1469	1	chr5B.!!$F1	1468
3	TraesCS1B01G152600	chr5B	381735609	381736151	542	False	859	859	95.212	1467	2009	1	chr5B.!!$F2	542
4	TraesCS1B01G152600	chr5B	472179899	472180431	532	False	473	473	83.088	1813	2344	1	chr5B.!!$F3	531
5	TraesCS1B01G152600	chr7B	637345943	637347405	1462	True	2145	2145	93.169	10	1469	1	chr7B.!!$R3	1459
6	TraesCS1B01G152600	chr7B	295804735	295805276	541	False	852	852	95.018	1468	2009	1	chr7B.!!$F1	541
7	TraesCS1B01G152600	chr2B	503342285	503343742	1457	False	2106	2106	92.730	12	1469	1	chr2B.!!$F3	1457
8	TraesCS1B01G152600	chr2B	405054928	405055469	541	True	857	857	95.203	1468	2009	1	chr2B.!!$R2	541
9	TraesCS1B01G152600	chr2B	428719325	428719866	541	False	857	857	95.203	1468	2009	1	chr2B.!!$F2	541
10	TraesCS1B01G152600	chrUn	22043798	22045266	1468	False	2098	2098	92.449	1	1469	1	chrUn.!!$F1	1468
11	TraesCS1B01G152600	chr5D	58529650	58531121	1471	False	2084	2084	92.302	1	1469	1	chr5D.!!$F1	1468
12	TraesCS1B01G152600	chr5D	384112261	384112873	612	False	529	529	82.527	1819	2450	1	chr5D.!!$F2	631
13	TraesCS1B01G152600	chr3D	543499163	543500638	1475	False	2071	2071	92.100	1	1469	1	chr3D.!!$F2	1468
14	TraesCS1B01G152600	chr3D	518965750	518967232	1482	True	2045	2045	91.762	1	1469	1	chr3D.!!$R2	1468
15	TraesCS1B01G152600	chr3D	30497973	30498515	542	False	841	841	94.659	1468	2009	1	chr3D.!!$F1	541
16	TraesCS1B01G152600	chr2D	408329286	408330785	1499	True	1921	1921	90.199	1	1469	1	chr2D.!!$R1	1468
17	TraesCS1B01G152600	chr1D	396010500	396011779	1279	True	1790	1790	92.003	194	1469	1	chr1D.!!$R1	1275
18	TraesCS1B01G152600	chr3A	149491555	149492096	541	False	846	846	94.834	1468	2009	1	chr3A.!!$F1	541
19	TraesCS1B01G152600	chr3A	149510499	149511040	541	False	846	846	94.834	1468	2009	1	chr3A.!!$F2	541
20	TraesCS1B01G152600	chr6D	422277167	422277708	541	False	841	841	94.649	1468	2009	1	chr6D.!!$F1	541
21	TraesCS1B01G152600	chr4B	82908936	82909487	551	True	841	841	94.203	1459	2009	1	chr4B.!!$R1	550
22	TraesCS1B01G152600	chr7A	480865392	480866030	638	False	555	555	82.669	1819	2458	1	chr7A.!!$F1	639
23	TraesCS1B01G152600	chr2A	751685126	751685773	647	False	514	514	81.459	1819	2459	1	chr2A.!!$F1	640
24	TraesCS1B01G152600	chr7D	361246462	361247101	639	False	501	501	81.279	1820	2459	1	chr7D.!!$F1	639

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
678	753	0.248458	GTGCACTTGAACACCGTTGG	60.248	55.0	10.32	0.0	0.0	3.77	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1631	1709	0.469494	AACCCCTTTAACACGTCGGT	59.531	50.0	0.0	0.0	0.0	4.69	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
27	28	4.897140	ACTACGGTTGCAATTAGTGGTAA	58.103	39.130	15.32	0.00	0.00	2.85
160	163	7.336975	GTTCATTTGTAGCATGTTGTTTGTTC	58.663	34.615	0.00	0.00	0.00	3.18
187	190	7.886338	AGATGTATGTTCGTGCTCATAGATTA	58.114	34.615	0.00	0.00	33.02	1.75
194	197	3.057526	TCGTGCTCATAGATTATCCGGTG	60.058	47.826	0.00	0.00	0.00	4.94
272	275	7.254488	GCATATGCTTGCTATGATAGTGATGAG	60.254	40.741	20.64	0.00	39.57	2.90
292	363	1.800586	GCCATGTACATGTATGCTCCG	59.199	52.381	29.25	15.30	37.11	4.63
358	429	1.827969	ACGCAAGATCTTAGTCAGGCT	59.172	47.619	7.86	0.00	43.62	4.58
588	662	0.823356	AAGTGGCAGCCGTTCATGTT	60.823	50.000	7.03	0.00	0.00	2.71
614	688	5.137970	GCTCGTGCTGAACAAGATGTGTT	62.138	47.826	1.41	0.00	43.93	3.32
640	714	5.441500	CTCATCTCTAGTGGAGTTAGGACA	58.558	45.833	3.16	0.00	42.40	4.02
678	753	0.248458	GTGCACTTGAACACCGTTGG	60.248	55.000	10.32	0.00	0.00	3.77
702	777	1.806623	GCAGGTGTTCGAGTTCTGTGT	60.807	52.381	8.26	0.00	0.00	3.72
872	947	1.080705	GTCGCGGTTAGCTCACAGT	60.081	57.895	6.13	0.00	45.59	3.55
953	1029	4.062991	GTGTTTCATTCTTACGACCACCT	58.937	43.478	0.00	0.00	0.00	4.00
983	1059	1.562008	TGAGTTCCTCAACACACCCAA	59.438	47.619	0.00	0.00	37.57	4.12
985	1061	1.564348	AGTTCCTCAACACACCCAACT	59.436	47.619	0.00	0.00	34.60	3.16
1035	1111	3.551496	CTTCGGGCTGGCAACTGGA	62.551	63.158	2.88	0.00	35.79	3.86
1075	1153	1.219393	GAGCCTCTTGGTTCTCCCG	59.781	63.158	0.00	0.00	39.99	5.14
1086	1164	0.250338	GTTCTCCCGTGCCAGAGTTT	60.250	55.000	0.00	0.00	0.00	2.66
1151	1229	0.319555	TTCGTGAAGCCCTTCGACAG	60.320	55.000	3.81	0.00	42.28	3.51
1195	1273	1.342975	GGAAGAGGAAGAGAGGAGGCT	60.343	57.143	0.00	0.00	0.00	4.58
1203	1281	2.260639	AGAGAGGAGGCTTGATGGAA	57.739	50.000	0.00	0.00	0.00	3.53
1294	1372	1.611261	CCCCTTGACGTCCACCCTA	60.611	63.158	14.12	0.00	0.00	3.53
1303	1381	4.343231	TGACGTCCACCCTAACTTGTATA	58.657	43.478	14.12	0.00	0.00	1.47
1315	1393	6.036735	CCCTAACTTGTATAACGTTGTCATGG	59.963	42.308	11.99	6.21	0.00	3.66
1416	1494	4.402851	GCCATGGCAGACACTCAA	57.597	55.556	32.08	0.00	41.49	3.02
1554	1632	6.206042	AGGTATTTCCCTTAGTGATGAGACT	58.794	40.000	0.00	0.00	36.75	3.24
1631	1709	6.143118	GCACACAAATAACAAATACTCGCAAA	59.857	34.615	0.00	0.00	0.00	3.68
1652	1730	0.236449	CGACGTGTTAAAGGGGTTGC	59.764	55.000	0.00	0.00	0.00	4.17
1746	1825	5.343249	AGATCGCAGAACAAATAAATTGCC	58.657	37.500	0.00	0.00	43.58	4.52
1805	1884	9.651913	TCTGAAAATAAATGCAAGGGAAAATAC	57.348	29.630	0.00	0.00	0.00	1.89
1883	1965	4.269844	GGCTTCTCTCGAGAAAAATAGCAG	59.730	45.833	17.36	4.58	45.75	4.24
1995	2082	4.496010	CGTCCAAGATTAGTAGACCGACTG	60.496	50.000	0.00	0.00	0.00	3.51
2074	2161	4.274705	TGCATTATGGGCTGTTATTACACG	59.725	41.667	0.00	0.00	0.00	4.49
2170	2258	2.095461	GGATTCTGGCTGGAAAAGGAC	58.905	52.381	0.00	0.00	0.00	3.85
2172	2260	0.250727	TTCTGGCTGGAAAAGGACCG	60.251	55.000	0.00	0.00	0.00	4.79
2199	2287	3.961849	TGGAAACCTATTATGCACAGCA	58.038	40.909	0.00	0.00	44.86	4.41
2206	2294	4.526262	ACCTATTATGCACAGCACCAAAAA	59.474	37.500	0.00	0.00	43.04	1.94
2221	2309	5.452636	GCACCAAAAATCCTAAAACTCCACA	60.453	40.000	0.00	0.00	0.00	4.17
2344	2436	4.748798	CCCTGTCTCCTGGGCCCT	62.749	72.222	25.70	0.00	42.26	5.19
2366	2459	4.828296	GGCCCTCCAGTGCCCATG	62.828	72.222	0.00	0.00	41.97	3.66
2382	2475	3.755378	GCCCATGTTCTGCTATATGAAGG	59.245	47.826	0.00	0.00	0.00	3.46
2387	2480	6.040166	CCATGTTCTGCTATATGAAGGCTTTT	59.960	38.462	0.00	0.00	0.00	2.27
2389	2482	7.553881	TGTTCTGCTATATGAAGGCTTTTAC	57.446	36.000	0.00	0.00	0.00	2.01
2459	2552	2.981350	GCGGAACCTTGGCGGAAA	60.981	61.111	0.00	0.00	36.31	3.13
2460	2553	2.951458	CGGAACCTTGGCGGAAAC	59.049	61.111	0.00	0.00	36.31	2.78
2461	2554	1.894756	CGGAACCTTGGCGGAAACA	60.895	57.895	0.00	0.00	36.31	2.83

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
5	6	3.412237	ACCACTAATTGCAACCGTAGT	57.588	42.857	0.00	7.37	0.00	2.73
8	9	3.078837	CCTTACCACTAATTGCAACCGT	58.921	45.455	0.00	0.00	0.00	4.83
27	28	3.276857	CACATGCTTGAACATCTAGCCT	58.723	45.455	6.60	0.00	43.03	4.58
137	140	6.804677	AGAACAAACAACATGCTACAAATGA	58.195	32.000	0.00	0.00	0.00	2.57
160	163	6.903419	TCTATGAGCACGAACATACATCTAG	58.097	40.000	0.00	0.00	0.00	2.43
187	190	4.322049	GCTATCATACTAAGCACACCGGAT	60.322	45.833	9.46	0.00	36.26	4.18
194	197	5.346281	GGTTCATCGCTATCATACTAAGCAC	59.654	44.000	0.00	0.00	35.98	4.40
272	275	1.800586	CGGAGCATACATGTACATGGC	59.199	52.381	33.32	26.94	42.91	4.40
292	363	1.133025	AGCACGCATTGACAATAAGCC	59.867	47.619	0.00	0.00	0.00	4.35
358	429	1.666011	GCTGTCGGACAGGACAAGA	59.334	57.895	32.63	0.62	46.01	3.02
494	565	2.908940	GGCAACAGCAGCACCAGT	60.909	61.111	0.00	0.00	0.00	4.00
614	688	5.369993	TCCTAACTCCACTAGAGATGAGCTA	59.630	44.000	0.00	0.00	46.50	3.32
640	714	0.695347	CCTCCTTGAAGCCCTTGTCT	59.305	55.000	0.00	0.00	0.00	3.41
678	753	2.221981	CAGAACTCGAACACCTGCTTTC	59.778	50.000	0.00	0.00	0.00	2.62
702	777	2.362242	GTGGTAGACACCTCCTGCA	58.638	57.895	0.00	0.00	45.98	4.41
739	814	1.827969	CATCGACCTCTCCACTTCCTT	59.172	52.381	0.00	0.00	0.00	3.36
872	947	6.099845	GGTGGATAGTATGAAAAGGAAGAGGA	59.900	42.308	0.00	0.00	0.00	3.71
953	1029	3.376082	AGGAACTCAGCGTCCCTTA	57.624	52.632	0.00	0.00	0.00	2.69
983	1059	3.099905	TGCATCTGGCTGTAGTTCTAGT	58.900	45.455	0.00	0.00	45.15	2.57
985	1061	2.159043	GCTGCATCTGGCTGTAGTTCTA	60.159	50.000	0.00	0.00	45.15	2.10
1151	1229	2.754254	GGACGGGGTCAAATGGCC	60.754	66.667	0.00	0.00	39.63	5.36
1195	1273	5.427806	AGACATTGATCTCCTCTTCCATCAA	59.572	40.000	0.00	0.00	39.09	2.57
1203	1281	4.914983	TGCAAAAGACATTGATCTCCTCT	58.085	39.130	0.00	0.00	31.84	3.69
1281	1359	1.416243	ACAAGTTAGGGTGGACGTCA	58.584	50.000	18.91	0.27	0.00	4.35
1294	1372	4.155280	GGCCATGACAACGTTATACAAGTT	59.845	41.667	0.00	0.00	0.00	2.66
1303	1381	1.603455	CCTGGGCCATGACAACGTT	60.603	57.895	6.72	0.00	0.00	3.99
1416	1494	1.151450	CCTGAGCCACAACACCCTT	59.849	57.895	0.00	0.00	0.00	3.95
1579	1657	2.033372	TGTTTACGTGGTGTGAGGAGA	58.967	47.619	0.00	0.00	0.00	3.71
1631	1709	0.469494	AACCCCTTTAACACGTCGGT	59.531	50.000	0.00	0.00	0.00	4.69
1746	1825	7.414814	ACCAAAAATACAAAAATACCTTGCG	57.585	32.000	0.00	0.00	0.00	4.85
1853	1933	3.908643	TCTCGAGAGAAGCCACTAGTA	57.091	47.619	12.08	0.00	41.32	1.82
1883	1965	5.767816	ACAGTAATTGTTTTCCCACTGTC	57.232	39.130	1.43	0.00	42.01	3.51
1995	2082	1.998315	CGTATCATAGATGCAGGCAGC	59.002	52.381	0.42	0.42	45.96	5.25
2109	2196	7.338710	TCCCTCTTCATGATAAACCTTGTAAG	58.661	38.462	0.00	0.00	0.00	2.34
2122	2209	1.139654	CGGCATTCTCCCTCTTCATGA	59.860	52.381	0.00	0.00	0.00	3.07
2147	2234	2.528564	CTTTTCCAGCCAGAATCCCAA	58.471	47.619	0.00	0.00	0.00	4.12
2170	2258	7.040755	TGTGCATAATAGGTTTCCAATATTCGG	60.041	37.037	0.00	0.00	0.00	4.30
2172	2260	7.809806	GCTGTGCATAATAGGTTTCCAATATTC	59.190	37.037	0.00	0.00	0.00	1.75
2199	2287	6.133356	TCTGTGGAGTTTTAGGATTTTTGGT	58.867	36.000	0.00	0.00	0.00	3.67
2206	2294	5.825593	TGACTTCTGTGGAGTTTTAGGAT	57.174	39.130	0.00	0.00	0.00	3.24
2257	2345	4.231890	TGGGCCCTCTATGGTATTTTCTTT	59.768	41.667	25.70	0.00	0.00	2.52
2344	2436	3.640407	GCACTGGAGGGCCACAGA	61.640	66.667	28.05	3.79	39.92	3.41
2366	2459	6.017026	GGGTAAAAGCCTTCATATAGCAGAAC	60.017	42.308	0.00	0.00	31.81	3.01
2416	2509	2.739132	GGTGGAGTTTCGTCCCGT	59.261	61.111	0.00	0.00	35.49	5.28

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.