AutoCloner

Multiple sequence alignment - TraesCS7A01G111000

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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	TraesCS7A01G111000	chr7A	100.000	5211	0	0	1	5211	68028184	68033394	0.000000e+00	9624
1	TraesCS7A01G111000	chr7A	89.820	3340	311	18	797	4126	67984928	67988248	0.000000e+00	4257
2	TraesCS7A01G111000	chr7A	86.306	3162	396	24	986	4135	68043122	68046258	0.000000e+00	3406
3	TraesCS7A01G111000	chr7A	91.416	2027	156	8	2112	4136	68083599	68085609	0.000000e+00	2763
4	TraesCS7A01G111000	chr7A	88.902	1721	179	9	977	2690	67593008	67591293	0.000000e+00	2109
5	TraesCS7A01G111000	chr7D	90.978	3170	244	23	977	4135	64265789	64268927	0.000000e+00	4231
6	TraesCS7A01G111000	chr7D	89.321	3165	302	29	978	4128	64245415	64248557	0.000000e+00	3940
7	TraesCS7A01G111000	chr7D	87.054	3167	363	37	1000	4135	63943731	63940581	0.000000e+00	3533
8	TraesCS7A01G111000	chr7D	90.355	2167	186	16	1970	4128	59938408	59936257	0.000000e+00	2822
9	TraesCS7A01G111000	chr7D	88.601	2281	242	14	998	3268	64222841	64225113	0.000000e+00	2756
10	TraesCS7A01G111000	chr7D	90.918	969	85	3	977	1943	59939562	59938595	0.000000e+00	1299
11	TraesCS7A01G111000	chr7D	93.413	501	24	4	1	501	59940575	59940084	0.000000e+00	734
12	TraesCS7A01G111000	chr7D	93.089	463	6	6	522	984	59940026	59939590	0.000000e+00	654
13	TraesCS7A01G111000	chr7B	90.268	3134	298	5	998	4128	5282138	5285267	0.000000e+00	4091
14	TraesCS7A01G111000	chr7B	88.124	3427	348	20	711	4131	5502930	5506303	0.000000e+00	4019
15	TraesCS7A01G111000	chr7B	89.965	1973	191	7	2163	4131	5338212	5340181	0.000000e+00	2540
16	TraesCS7A01G111000	chr7B	81.570	1427	180	44	543	1913	5267136	5268535	0.000000e+00	1101
17	TraesCS7A01G111000	chr7B	79.741	464	60	23	543	985	5195234	5195684	6.560000e-79	305
18	TraesCS7A01G111000	chr4B	98.577	1054	14	1	4159	5211	34044506	34043453	0.000000e+00	1862
19	TraesCS7A01G111000	chr4B	94.476	1050	53	1	4162	5211	453733853	453734897	0.000000e+00	1613
20	TraesCS7A01G111000	chr4B	94.168	1046	55	2	4166	5211	619087827	619086788	0.000000e+00	1589
21	TraesCS7A01G111000	chr5A	98.571	1050	13	1	4162	5211	328813397	328814444	0.000000e+00	1855
22	TraesCS7A01G111000	chr5A	99.206	252	1	1	4159	4409	328818397	328818648	2.210000e-123	453
23	TraesCS7A01G111000	chr3B	98.104	1055	19	1	4157	5211	153626747	153625694	0.000000e+00	1836
24	TraesCS7A01G111000	chr2A	97.714	1050	24	0	4162	5211	39686733	39687782	0.000000e+00	1807
25	TraesCS7A01G111000	chr2A	92.439	1058	67	2	4162	5211	754131913	754130861	0.000000e+00	1498
26	TraesCS7A01G111000	chr4A	93.732	1053	55	5	4162	5211	707837973	707836929	0.000000e+00	1568
27	TraesCS7A01G111000	chr6A	98.109	846	16	0	4366	5211	73453130	73452285	0.000000e+00	1474

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	TraesCS7A01G111000	chr7A	68028184	68033394	5210	False	9624.00	9624	100.00000	1	5211	1	chr7A.!!$F2	5210
1	TraesCS7A01G111000	chr7A	67984928	67988248	3320	False	4257.00	4257	89.82000	797	4126	1	chr7A.!!$F1	3329
2	TraesCS7A01G111000	chr7A	68043122	68046258	3136	False	3406.00	3406	86.30600	986	4135	1	chr7A.!!$F3	3149
3	TraesCS7A01G111000	chr7A	68083599	68085609	2010	False	2763.00	2763	91.41600	2112	4136	1	chr7A.!!$F4	2024
4	TraesCS7A01G111000	chr7A	67591293	67593008	1715	True	2109.00	2109	88.90200	977	2690	1	chr7A.!!$R1	1713
5	TraesCS7A01G111000	chr7D	64265789	64268927	3138	False	4231.00	4231	90.97800	977	4135	1	chr7D.!!$F3	3158
6	TraesCS7A01G111000	chr7D	64245415	64248557	3142	False	3940.00	3940	89.32100	978	4128	1	chr7D.!!$F2	3150
7	TraesCS7A01G111000	chr7D	63940581	63943731	3150	True	3533.00	3533	87.05400	1000	4135	1	chr7D.!!$R1	3135
8	TraesCS7A01G111000	chr7D	64222841	64225113	2272	False	2756.00	2756	88.60100	998	3268	1	chr7D.!!$F1	2270
9	TraesCS7A01G111000	chr7D	59936257	59940575	4318	True	1377.25	2822	91.94375	1	4128	4	chr7D.!!$R2	4127
10	TraesCS7A01G111000	chr7B	5282138	5285267	3129	False	4091.00	4091	90.26800	998	4128	1	chr7B.!!$F3	3130
11	TraesCS7A01G111000	chr7B	5502930	5506303	3373	False	4019.00	4019	88.12400	711	4131	1	chr7B.!!$F5	3420
12	TraesCS7A01G111000	chr7B	5338212	5340181	1969	False	2540.00	2540	89.96500	2163	4131	1	chr7B.!!$F4	1968
13	TraesCS7A01G111000	chr7B	5267136	5268535	1399	False	1101.00	1101	81.57000	543	1913	1	chr7B.!!$F2	1370
14	TraesCS7A01G111000	chr4B	34043453	34044506	1053	True	1862.00	1862	98.57700	4159	5211	1	chr4B.!!$R1	1052
15	TraesCS7A01G111000	chr4B	453733853	453734897	1044	False	1613.00	1613	94.47600	4162	5211	1	chr4B.!!$F1	1049
16	TraesCS7A01G111000	chr4B	619086788	619087827	1039	True	1589.00	1589	94.16800	4166	5211	1	chr4B.!!$R2	1045
17	TraesCS7A01G111000	chr5A	328813397	328818648	5251	False	1154.00	1855	98.88850	4159	5211	2	chr5A.!!$F1	1052
18	TraesCS7A01G111000	chr3B	153625694	153626747	1053	True	1836.00	1836	98.10400	4157	5211	1	chr3B.!!$R1	1054
19	TraesCS7A01G111000	chr2A	39686733	39687782	1049	False	1807.00	1807	97.71400	4162	5211	1	chr2A.!!$F1	1049
20	TraesCS7A01G111000	chr2A	754130861	754131913	1052	True	1498.00	1498	92.43900	4162	5211	1	chr2A.!!$R1	1049
21	TraesCS7A01G111000	chr4A	707836929	707837973	1044	True	1568.00	1568	93.73200	4162	5211	1	chr4A.!!$R1	1049
22	TraesCS7A01G111000	chr6A	73452285	73453130	845	True	1474.00	1474	98.10900	4366	5211	1	chr6A.!!$R1	845

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
217	218	0.532862	ACTTGTGCCACCTGAGAACG	60.533	55.000	0.00	0.00	0.00	3.95	F
270	271	0.536260	CAGAGCAAGGAGAGGGTCAG	59.464	60.000	0.00	0.00	34.11	3.51	F
474	475	1.072965	CCTATCCATGTTCTGAGGGCC	59.927	57.143	0.00	0.00	0.00	5.80	F
910	998	1.148310	CTGTTACTCGCACCAACCAG	58.852	55.000	0.00	0.00	0.00	4.00	F
1692	1816	1.454847	TGCAGCTTTTGTCCCCGTT	60.455	52.632	0.00	0.00	0.00	4.44	F
2315	2628	1.013596	CGTGAGTGTGTCCAAAGCAA	58.986	50.000	0.00	0.00	0.00	3.91	F
3877	4199	0.248094	CTGCGAGATGCTGCATGTTG	60.248	55.000	21.53	20.46	46.63	3.33	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1557	1681	0.179000	CCTTGGAACTCCCATCCTCG	59.821	60.000	0.00	46.10	4.63	R
1660	1784	2.250031	AGCTGCACAATCAAATTGGGA	58.750	42.857	6.11	46.53	4.37	R
2296	2609	1.003545	CTTGCTTTGGACACACTCACG	60.004	52.381	0.00	0.00	4.35	R
2308	2621	3.497640	CACTGGAAGAGAGACTTGCTTTG	59.502	47.826	0.00	45.18	2.77	R
3648	3967	0.393537	CGCAGGAGAAAAGAGGCCAT	60.394	55.000	5.01	0.00	4.40	R
4152	4486	0.108585	GTTCCTCCACAGGTTGCTCA	59.891	55.000	0.00	41.28	4.26	R
4829	5172	0.528017	GATGACAGACGCTCCACTGA	59.472	55.000	0.00	37.54	3.41	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
58	59	5.525745	CAGTTGAGCTCTCGATCTAGTTAGA	59.474	44.000	16.19	0.00	36.65	2.10
98	99	2.939103	CCTGTTCTGATTTGGATCCGTC	59.061	50.000	7.39	5.98	0.00	4.79
104	105	2.016318	TGATTTGGATCCGTCATGTGC	58.984	47.619	7.39	0.00	0.00	4.57
184	185	4.512944	CAGAGTTGCTGTGTAGTGTTGAAT	59.487	41.667	0.00	0.00	39.85	2.57
212	213	1.211703	TCTTCAACTTGTGCCACCTGA	59.788	47.619	0.00	0.00	0.00	3.86
214	215	0.836606	TCAACTTGTGCCACCTGAGA	59.163	50.000	0.00	0.00	0.00	3.27
215	216	1.211703	TCAACTTGTGCCACCTGAGAA	59.788	47.619	0.00	0.00	0.00	2.87
216	217	1.334869	CAACTTGTGCCACCTGAGAAC	59.665	52.381	0.00	0.00	0.00	3.01
217	218	0.532862	ACTTGTGCCACCTGAGAACG	60.533	55.000	0.00	0.00	0.00	3.95
218	219	1.227823	TTGTGCCACCTGAGAACGG	60.228	57.895	0.00	0.00	0.00	4.44
219	220	1.978455	TTGTGCCACCTGAGAACGGT	61.978	55.000	0.00	0.00	34.38	4.83
270	271	0.536260	CAGAGCAAGGAGAGGGTCAG	59.464	60.000	0.00	0.00	34.11	3.51
277	278	1.220477	GGAGAGGGTCAGCTCTTGC	59.780	63.158	0.00	0.00	40.05	4.01
437	438	4.341366	AAAGCAAAGGGAAAATGGTCAG	57.659	40.909	0.00	0.00	0.00	3.51
444	445	2.162681	GGGAAAATGGTCAGTGGTCAG	58.837	52.381	0.00	0.00	0.00	3.51
446	447	2.814336	GGAAAATGGTCAGTGGTCAGAC	59.186	50.000	0.00	0.00	0.00	3.51
473	474	1.771255	ACCTATCCATGTTCTGAGGGC	59.229	52.381	0.00	0.00	0.00	5.19
474	475	1.072965	CCTATCCATGTTCTGAGGGCC	59.927	57.143	0.00	0.00	0.00	5.80
515	573	8.413229	CCTTTTCACTCTTTAGTTTCATTCCAA	58.587	33.333	0.00	0.00	31.97	3.53
516	574	9.455847	CTTTTCACTCTTTAGTTTCATTCCAAG	57.544	33.333	0.00	0.00	31.97	3.61
517	575	8.746052	TTTCACTCTTTAGTTTCATTCCAAGA	57.254	30.769	0.00	0.00	31.97	3.02
518	576	7.969536	TCACTCTTTAGTTTCATTCCAAGAG	57.030	36.000	5.40	5.40	41.95	2.85
519	577	6.428159	TCACTCTTTAGTTTCATTCCAAGAGC	59.572	38.462	6.64	0.00	40.55	4.09
520	578	5.707764	ACTCTTTAGTTTCATTCCAAGAGCC	59.292	40.000	6.64	0.00	40.55	4.70
521	579	5.010282	TCTTTAGTTTCATTCCAAGAGCCC	58.990	41.667	0.00	0.00	0.00	5.19
522	580	4.657814	TTAGTTTCATTCCAAGAGCCCT	57.342	40.909	0.00	0.00	0.00	5.19
523	581	3.532641	AGTTTCATTCCAAGAGCCCTT	57.467	42.857	0.00	0.00	0.00	3.95
524	582	3.849527	AGTTTCATTCCAAGAGCCCTTT	58.150	40.909	0.00	0.00	0.00	3.11
525	583	4.998051	AGTTTCATTCCAAGAGCCCTTTA	58.002	39.130	0.00	0.00	0.00	1.85
526	584	5.012893	AGTTTCATTCCAAGAGCCCTTTAG	58.987	41.667	0.00	0.00	0.00	1.85
527	585	4.657814	TTCATTCCAAGAGCCCTTTAGT	57.342	40.909	0.00	0.00	0.00	2.24
528	586	4.657814	TCATTCCAAGAGCCCTTTAGTT	57.342	40.909	0.00	0.00	0.00	2.24
529	587	4.998051	TCATTCCAAGAGCCCTTTAGTTT	58.002	39.130	0.00	0.00	0.00	2.66
530	588	5.010282	TCATTCCAAGAGCCCTTTAGTTTC	58.990	41.667	0.00	0.00	0.00	2.78
531	589	4.447138	TTCCAAGAGCCCTTTAGTTTCA	57.553	40.909	0.00	0.00	0.00	2.69
532	590	4.657814	TCCAAGAGCCCTTTAGTTTCAT	57.342	40.909	0.00	0.00	0.00	2.57
533	591	4.998051	TCCAAGAGCCCTTTAGTTTCATT	58.002	39.130	0.00	0.00	0.00	2.57
534	592	5.010282	TCCAAGAGCCCTTTAGTTTCATTC	58.990	41.667	0.00	0.00	0.00	2.67
535	593	4.158579	CCAAGAGCCCTTTAGTTTCATTCC	59.841	45.833	0.00	0.00	0.00	3.01
536	594	4.657814	AGAGCCCTTTAGTTTCATTCCA	57.342	40.909	0.00	0.00	0.00	3.53
648	709	5.246981	TCATCCAGTGGTTCTCTGAAAAT	57.753	39.130	9.54	0.00	35.20	1.82
656	717	7.118390	CCAGTGGTTCTCTGAAAATAGTTAGTG	59.882	40.741	0.00	0.00	35.20	2.74
671	732	9.463902	AAATAGTTAGTGTCTTCTAGCTGTCTA	57.536	33.333	0.00	0.00	34.35	2.59
675	736	5.174037	AGTGTCTTCTAGCTGTCTACTCT	57.826	43.478	0.00	0.00	0.00	3.24
910	998	1.148310	CTGTTACTCGCACCAACCAG	58.852	55.000	0.00	0.00	0.00	4.00
1325	1449	7.038659	CGAGTCAATAAGTTCCTCAAGAAGAT	58.961	38.462	0.00	0.00	34.29	2.40
1494	1618	2.543848	TCGTGTGTTAGCTCTGCAAAAG	59.456	45.455	0.00	0.00	0.00	2.27
1614	1738	3.392947	TCTCTATTGTTGGTGTTGGTGGA	59.607	43.478	0.00	0.00	0.00	4.02
1692	1816	1.454847	TGCAGCTTTTGTCCCCGTT	60.455	52.632	0.00	0.00	0.00	4.44
1734	1858	9.847224	ATCAAGAAAGTTTTCAAGGACTTACTA	57.153	29.630	7.30	0.00	39.61	1.82
1749	1873	7.736893	AGGACTTACTATATGGCCTTAACAAG	58.263	38.462	3.32	7.22	38.10	3.16
1794	1918	2.787994	ACAGCAAGGGATGAGAAACTG	58.212	47.619	0.00	0.00	33.73	3.16
1818	1942	5.126707	GCTCATGGAGGAAATCAGTGAATTT	59.873	40.000	0.00	0.00	0.00	1.82
1832	1961	8.868522	ATCAGTGAATTTCTTGTGGATAAGAA	57.131	30.769	0.00	0.00	43.02	2.52
1896	2027	5.585820	TTATGTGTGACGTAGCCAGATAA	57.414	39.130	0.00	0.00	0.00	1.75
2010	2316	5.746307	TCTTGTGCATGCATCTTATCTTC	57.254	39.130	25.64	7.97	0.00	2.87
2011	2317	4.271776	TCTTGTGCATGCATCTTATCTTCG	59.728	41.667	25.64	3.97	0.00	3.79
2012	2318	3.534554	TGTGCATGCATCTTATCTTCGT	58.465	40.909	25.64	0.00	0.00	3.85
2013	2319	3.940852	TGTGCATGCATCTTATCTTCGTT	59.059	39.130	25.64	0.00	0.00	3.85
2014	2320	5.115480	TGTGCATGCATCTTATCTTCGTTA	58.885	37.500	25.64	0.00	0.00	3.18
2015	2321	5.234972	TGTGCATGCATCTTATCTTCGTTAG	59.765	40.000	25.64	0.00	0.00	2.34
2016	2322	5.235186	GTGCATGCATCTTATCTTCGTTAGT	59.765	40.000	25.64	0.00	0.00	2.24
2017	2323	6.420903	GTGCATGCATCTTATCTTCGTTAGTA	59.579	38.462	25.64	0.00	0.00	1.82
2018	2324	7.116948	GTGCATGCATCTTATCTTCGTTAGTAT	59.883	37.037	25.64	0.00	0.00	2.12
2019	2325	7.657354	TGCATGCATCTTATCTTCGTTAGTATT	59.343	33.333	18.46	0.00	0.00	1.89
2020	2326	8.499162	GCATGCATCTTATCTTCGTTAGTATTT	58.501	33.333	14.21	0.00	0.00	1.40
2097	2405	7.538575	AGTTAGTGGTTGAATAATTCATGTGC	58.461	34.615	0.00	0.00	39.84	4.57
2113	2421	4.455533	TCATGTGCTTTGCTTAGTACCTTG	59.544	41.667	0.00	3.79	30.71	3.61
2128	2437	6.759497	AGTACCTTGCAATTATCCTTGTTC	57.241	37.500	0.00	0.00	0.00	3.18
2296	2609	3.551551	GGTAATCACAACAACTCGCAAC	58.448	45.455	0.00	0.00	0.00	4.17
2315	2628	1.013596	CGTGAGTGTGTCCAAAGCAA	58.986	50.000	0.00	0.00	0.00	3.91
2638	2951	4.751600	TCACTCAGCTATTATGATTTGCCG	59.248	41.667	0.00	0.00	0.00	5.69
3093	3406	4.343526	TGTTACTTGTGATTGGTTGCCATT	59.656	37.500	0.00	0.00	31.53	3.16
3285	3598	5.573146	GCTTTTGCAGACACTGGATATAAC	58.427	41.667	0.00	0.00	46.58	1.89
3388	3701	1.551883	CTGCCAAAAGGAATGGGGAAG	59.448	52.381	0.00	0.00	38.44	3.46
3393	3706	3.645687	CCAAAAGGAATGGGGAAGTTGAA	59.354	43.478	0.00	0.00	34.15	2.69
3406	3719	3.257624	GGAAGTTGAAGTCCCTCGAAGTA	59.742	47.826	0.00	0.00	0.00	2.24
3412	3725	4.087182	TGAAGTCCCTCGAAGTACTGAAT	58.913	43.478	0.00	0.00	0.00	2.57
3603	3922	5.410746	GTGTCAGATTGATGGATCGCATATT	59.589	40.000	0.00	0.00	0.00	1.28
3648	3967	3.283751	ACCTCCGTTGTTTTGATTCACA	58.716	40.909	0.00	0.00	0.00	3.58
3649	3968	3.888930	ACCTCCGTTGTTTTGATTCACAT	59.111	39.130	0.00	0.00	0.00	3.21
3730	4052	0.916358	CCCACCTCTCCACCCTGAAT	60.916	60.000	0.00	0.00	0.00	2.57
3807	4129	3.825160	TTCGGTTTCTGCGGCTGCT	62.825	57.895	20.27	0.00	43.34	4.24
3877	4199	0.248094	CTGCGAGATGCTGCATGTTG	60.248	55.000	21.53	20.46	46.63	3.33
4121	4455	1.582610	CCATCCAAAACGTCCCACCG	61.583	60.000	0.00	0.00	0.00	4.94
4128	4462	4.129757	ACGTCCCACCGTTGAAAC	57.870	55.556	0.00	0.00	37.96	2.78
4129	4463	1.221293	ACGTCCCACCGTTGAAACA	59.779	52.632	0.00	0.00	37.96	2.83
4131	4465	0.515564	CGTCCCACCGTTGAAACATC	59.484	55.000	0.00	0.00	0.00	3.06
4133	4467	2.610976	CGTCCCACCGTTGAAACATCTA	60.611	50.000	0.00	0.00	0.00	1.98
4134	4468	3.606687	GTCCCACCGTTGAAACATCTAT	58.393	45.455	0.00	0.00	0.00	1.98
4135	4469	3.374058	GTCCCACCGTTGAAACATCTATG	59.626	47.826	0.00	0.00	0.00	2.23
4136	4470	3.262151	TCCCACCGTTGAAACATCTATGA	59.738	43.478	0.00	0.00	0.00	2.15
4137	4471	4.080582	TCCCACCGTTGAAACATCTATGAT	60.081	41.667	0.00	0.00	0.00	2.45
4138	4472	5.129650	TCCCACCGTTGAAACATCTATGATA	59.870	40.000	0.00	0.00	0.00	2.15
4139	4473	5.997746	CCCACCGTTGAAACATCTATGATAT	59.002	40.000	0.00	0.00	0.00	1.63
4140	4474	6.073058	CCCACCGTTGAAACATCTATGATATG	60.073	42.308	0.00	0.00	0.00	1.78
4141	4475	6.073058	CCACCGTTGAAACATCTATGATATGG	60.073	42.308	0.00	0.00	0.00	2.74
4142	4476	6.483307	CACCGTTGAAACATCTATGATATGGT	59.517	38.462	0.00	0.00	0.00	3.55
4143	4477	7.655732	CACCGTTGAAACATCTATGATATGGTA	59.344	37.037	0.00	0.00	0.00	3.25
4144	4478	8.375506	ACCGTTGAAACATCTATGATATGGTAT	58.624	33.333	0.00	0.00	0.00	2.73
4145	4479	9.219603	CCGTTGAAACATCTATGATATGGTATT	57.780	33.333	0.00	0.00	0.00	1.89
4156	4490	8.911965	TCTATGATATGGTATTCTCATCTGAGC	58.088	37.037	2.21	0.00	41.80	4.26
4157	4491	6.923199	TGATATGGTATTCTCATCTGAGCA	57.077	37.500	2.21	0.00	41.80	4.26
4158	4492	7.307131	TGATATGGTATTCTCATCTGAGCAA	57.693	36.000	2.21	0.00	41.80	3.91
4159	4493	7.157347	TGATATGGTATTCTCATCTGAGCAAC	58.843	38.462	2.21	1.20	41.80	4.17
4160	4494	4.142609	TGGTATTCTCATCTGAGCAACC	57.857	45.455	13.87	13.87	41.80	3.77
4554	4896	2.987413	TGCTTATTGGCAACTCGTTG	57.013	45.000	0.00	5.45	43.14	4.10
4716	5058	4.566488	GGACTGAACCCAAATGATCTCAGT	60.566	45.833	9.09	9.09	44.59	3.41
4760	5103	3.969287	ACTCAGCTTCTGTGCTTGATA	57.031	42.857	0.00	0.00	41.98	2.15
4761	5104	4.277515	ACTCAGCTTCTGTGCTTGATAA	57.722	40.909	0.00	0.00	41.98	1.75
4829	5172	2.102925	CCAAAGAACACTGCAAACCCAT	59.897	45.455	0.00	0.00	0.00	4.00
5005	5348	3.759581	AGGTGCATGAAGAAACTGACAT	58.240	40.909	0.00	0.00	0.00	3.06
5080	5423	3.107601	TGCTCCTACCAAGCTTCTGTAT	58.892	45.455	0.00	0.00	40.50	2.29
5143	5488	6.305693	AGTGACAATTTTTCTGTGCTAGAC	57.694	37.500	0.00	0.00	34.43	2.59

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
58	59	2.713708	AGGAAAAGGAGAGAGGTTTGCT	59.286	45.455	0.00	0.00	0.00	3.91
62	63	3.977326	AGAACAGGAAAAGGAGAGAGGTT	59.023	43.478	0.00	0.00	0.00	3.50
64	65	3.580458	TCAGAACAGGAAAAGGAGAGAGG	59.420	47.826	0.00	0.00	0.00	3.69
71	72	5.105595	GGATCCAAATCAGAACAGGAAAAGG	60.106	44.000	6.95	0.00	33.21	3.11
98	99	2.708051	ACAGATCCAACTCTGCACATG	58.292	47.619	1.14	0.00	45.37	3.21
104	105	4.384056	AGTGTTCAACAGATCCAACTCTG	58.616	43.478	0.00	0.00	46.59	3.35
117	118	0.787183	GCTGAGCGAGAGTGTTCAAC	59.213	55.000	0.00	0.00	0.00	3.18
184	185	2.355756	GCACAAGTTGAAGAAGAGCACA	59.644	45.455	10.54	0.00	0.00	4.57
270	271	2.278854	GAGAACAGATGGAGCAAGAGC	58.721	52.381	0.00	0.00	42.56	4.09
277	278	1.127343	GGAGGGGAGAACAGATGGAG	58.873	60.000	0.00	0.00	0.00	3.86
487	488	8.630037	GGAATGAAACTAAAGAGTGAAAAGGAA	58.370	33.333	0.00	0.00	35.52	3.36
488	489	7.777910	TGGAATGAAACTAAAGAGTGAAAAGGA	59.222	33.333	0.00	0.00	35.52	3.36
489	490	7.940850	TGGAATGAAACTAAAGAGTGAAAAGG	58.059	34.615	0.00	0.00	35.52	3.11
490	491	9.455847	CTTGGAATGAAACTAAAGAGTGAAAAG	57.544	33.333	0.00	0.00	35.52	2.27
515	573	4.657814	TGGAATGAAACTAAAGGGCTCT	57.342	40.909	0.00	0.00	0.00	4.09
516	574	4.949856	TGATGGAATGAAACTAAAGGGCTC	59.050	41.667	0.00	0.00	0.00	4.70
517	575	4.706962	GTGATGGAATGAAACTAAAGGGCT	59.293	41.667	0.00	0.00	0.00	5.19
518	576	4.438744	CGTGATGGAATGAAACTAAAGGGC	60.439	45.833	0.00	0.00	0.00	5.19
519	577	4.700213	ACGTGATGGAATGAAACTAAAGGG	59.300	41.667	0.00	0.00	0.00	3.95
520	578	5.181245	ACACGTGATGGAATGAAACTAAAGG	59.819	40.000	25.01	0.00	0.00	3.11
521	579	6.241207	ACACGTGATGGAATGAAACTAAAG	57.759	37.500	25.01	0.00	0.00	1.85
522	580	6.038825	ACAACACGTGATGGAATGAAACTAAA	59.961	34.615	26.72	0.00	0.00	1.85
523	581	5.529430	ACAACACGTGATGGAATGAAACTAA	59.471	36.000	26.72	0.00	0.00	2.24
524	582	5.060506	ACAACACGTGATGGAATGAAACTA	58.939	37.500	26.72	0.00	0.00	2.24
525	583	3.882888	ACAACACGTGATGGAATGAAACT	59.117	39.130	26.72	2.68	0.00	2.66
526	584	4.223320	ACAACACGTGATGGAATGAAAC	57.777	40.909	26.72	0.00	0.00	2.78
527	585	4.909696	AACAACACGTGATGGAATGAAA	57.090	36.364	26.72	0.00	0.00	2.69
528	586	6.348950	GGAATAACAACACGTGATGGAATGAA	60.349	38.462	26.72	8.23	0.00	2.57
529	587	5.123186	GGAATAACAACACGTGATGGAATGA	59.877	40.000	26.72	9.61	0.00	2.57
530	588	5.106357	TGGAATAACAACACGTGATGGAATG	60.106	40.000	26.72	14.96	0.00	2.67
531	589	5.007034	TGGAATAACAACACGTGATGGAAT	58.993	37.500	26.72	17.21	0.00	3.01
532	590	4.390264	TGGAATAACAACACGTGATGGAA	58.610	39.130	26.72	15.84	0.00	3.53
533	591	4.009370	TGGAATAACAACACGTGATGGA	57.991	40.909	26.72	16.04	0.00	3.41
534	592	4.963276	ATGGAATAACAACACGTGATGG	57.037	40.909	26.72	15.61	0.00	3.51
535	593	8.797215	CAATAAATGGAATAACAACACGTGATG	58.203	33.333	25.01	23.64	0.00	3.07
536	594	8.909708	CAATAAATGGAATAACAACACGTGAT	57.090	30.769	25.01	7.78	0.00	3.06
648	709	7.622713	AGTAGACAGCTAGAAGACACTAACTA	58.377	38.462	0.00	0.00	0.00	2.24
656	717	5.190677	AGGAAGAGTAGACAGCTAGAAGAC	58.809	45.833	0.00	0.00	0.00	3.01
671	732	4.120946	AGTTGTACAGAGGAGGAAGAGT	57.879	45.455	0.00	0.00	0.00	3.24
675	736	5.221661	GGAAGAAAGTTGTACAGAGGAGGAA	60.222	44.000	0.00	0.00	0.00	3.36
910	998	2.869233	TGAGCAAAACCTGAACTTGC	57.131	45.000	0.00	0.00	44.61	4.01
1061	1185	3.581332	TCGGTTCTCCAGGTTGTATTCTT	59.419	43.478	0.00	0.00	0.00	2.52
1185	1309	1.678635	CTTGCCAGCCCAAATCCGA	60.679	57.895	0.00	0.00	0.00	4.55
1494	1618	1.408822	CCAACAAGCTCCCCTACATCC	60.409	57.143	0.00	0.00	0.00	3.51
1557	1681	0.179000	CCTTGGAACTCCCATCCTCG	59.821	60.000	0.00	0.00	46.10	4.63
1660	1784	2.250031	AGCTGCACAATCAAATTGGGA	58.750	42.857	6.11	0.00	46.53	4.37
1749	1873	9.736023	GTATTATGAATGTCATTGAACTTTCCC	57.264	33.333	1.88	0.00	38.26	3.97
1794	1918	3.272574	TCACTGATTTCCTCCATGAGC	57.727	47.619	0.00	0.00	0.00	4.26
1818	1942	6.763135	GTGATGCATACTTCTTATCCACAAGA	59.237	38.462	0.00	0.00	32.71	3.02
1832	1961	4.774124	ACAAGCACTATGTGATGCATACT	58.226	39.130	0.00	0.00	44.59	2.12
1874	2005	5.585820	TTATCTGGCTACGTCACACATAA	57.414	39.130	0.00	0.00	0.00	1.90
1952	2244	5.940470	AGAATTTGCTTACGGAGAAACAGAT	59.060	36.000	0.00	0.00	0.00	2.90
2019	2325	8.883731	GCAGCAGAAATAAGTCATAAGTCTAAA	58.116	33.333	0.00	0.00	0.00	1.85
2020	2326	8.040727	TGCAGCAGAAATAAGTCATAAGTCTAA	58.959	33.333	0.00	0.00	0.00	2.10
2021	2327	7.555965	TGCAGCAGAAATAAGTCATAAGTCTA	58.444	34.615	0.00	0.00	0.00	2.59
2296	2609	1.003545	CTTGCTTTGGACACACTCACG	60.004	52.381	0.00	0.00	0.00	4.35
2308	2621	3.497640	CACTGGAAGAGAGACTTGCTTTG	59.502	47.826	0.00	0.00	45.18	2.77
2315	2628	3.772387	TGTCATCACTGGAAGAGAGACT	58.228	45.455	0.00	0.00	36.87	3.24
2638	2951	5.344207	ACAAACAAGTCTTTAGATGCGAC	57.656	39.130	0.00	0.00	0.00	5.19
3093	3406	5.459762	CGCAAAAATTGAAAGCTTGAGAGAA	59.540	36.000	0.00	0.00	0.00	2.87
3360	3673	1.898574	CCTTTTGGCAGCCTCACGT	60.899	57.895	14.15	0.00	0.00	4.49
3388	3701	3.255149	TCAGTACTTCGAGGGACTTCAAC	59.745	47.826	10.19	0.00	41.55	3.18
3648	3967	0.393537	CGCAGGAGAAAAGAGGCCAT	60.394	55.000	5.01	0.00	0.00	4.40
3649	3968	1.003355	CGCAGGAGAAAAGAGGCCA	60.003	57.895	5.01	0.00	0.00	5.36
3730	4052	6.122277	CCCTTGCAATTCTTCCACTTCTATA	58.878	40.000	0.00	0.00	0.00	1.31
3807	4129	2.324330	CCCATCACGCGACTTGCAA	61.324	57.895	15.93	0.00	46.97	4.08
3877	4199	2.125633	GCCGTCGGAAACCCTCTC	60.126	66.667	17.49	0.00	0.00	3.20
4131	4465	8.693625	TGCTCAGATGAGAATACCATATCATAG	58.306	37.037	13.98	0.00	44.74	2.23
4133	4467	7.492077	TGCTCAGATGAGAATACCATATCAT	57.508	36.000	13.98	0.00	44.74	2.45
4134	4468	6.923199	TGCTCAGATGAGAATACCATATCA	57.077	37.500	13.98	0.00	44.74	2.15
4135	4469	6.593382	GGTTGCTCAGATGAGAATACCATATC	59.407	42.308	13.98	0.00	44.74	1.63
4136	4470	6.271857	AGGTTGCTCAGATGAGAATACCATAT	59.728	38.462	20.75	6.88	44.74	1.78
4137	4471	5.604231	AGGTTGCTCAGATGAGAATACCATA	59.396	40.000	20.75	0.00	44.74	2.74
4138	4472	4.411540	AGGTTGCTCAGATGAGAATACCAT	59.588	41.667	20.75	10.22	44.74	3.55
4139	4473	3.776969	AGGTTGCTCAGATGAGAATACCA	59.223	43.478	20.75	6.97	44.74	3.25
4140	4474	4.125703	CAGGTTGCTCAGATGAGAATACC	58.874	47.826	13.98	14.72	44.74	2.73
4141	4475	4.569966	CACAGGTTGCTCAGATGAGAATAC	59.430	45.833	13.98	7.30	44.74	1.89
4142	4476	4.383444	CCACAGGTTGCTCAGATGAGAATA	60.383	45.833	13.98	0.00	44.74	1.75
4143	4477	3.607741	CACAGGTTGCTCAGATGAGAAT	58.392	45.455	13.98	0.00	44.74	2.40
4144	4478	2.289882	CCACAGGTTGCTCAGATGAGAA	60.290	50.000	13.98	0.00	44.74	2.87
4145	4479	1.277273	CCACAGGTTGCTCAGATGAGA	59.723	52.381	13.98	0.00	44.74	3.27
4146	4480	1.277273	TCCACAGGTTGCTCAGATGAG	59.723	52.381	5.45	5.45	44.75	2.90
4147	4481	1.277273	CTCCACAGGTTGCTCAGATGA	59.723	52.381	0.00	0.00	0.00	2.92
4148	4482	1.678123	CCTCCACAGGTTGCTCAGATG	60.678	57.143	0.00	0.00	34.60	2.90
4149	4483	0.617413	CCTCCACAGGTTGCTCAGAT	59.383	55.000	0.00	0.00	34.60	2.90
4150	4484	0.471780	TCCTCCACAGGTTGCTCAGA	60.472	55.000	0.00	0.00	41.28	3.27
4151	4485	0.397941	TTCCTCCACAGGTTGCTCAG	59.602	55.000	0.00	0.00	41.28	3.35
4152	4486	0.108585	GTTCCTCCACAGGTTGCTCA	59.891	55.000	0.00	0.00	41.28	4.26
4153	4487	0.951040	CGTTCCTCCACAGGTTGCTC	60.951	60.000	0.00	0.00	41.28	4.26
4154	4488	1.071471	CGTTCCTCCACAGGTTGCT	59.929	57.895	0.00	0.00	41.28	3.91
4155	4489	1.227853	ACGTTCCTCCACAGGTTGC	60.228	57.895	0.00	0.00	41.28	4.17
4156	4490	0.944311	CGACGTTCCTCCACAGGTTG	60.944	60.000	0.00	0.00	41.28	3.77
4157	4491	1.366366	CGACGTTCCTCCACAGGTT	59.634	57.895	0.00	0.00	41.28	3.50
4158	4492	0.538057	TACGACGTTCCTCCACAGGT	60.538	55.000	5.50	0.00	41.28	4.00
4159	4493	0.109412	GTACGACGTTCCTCCACAGG	60.109	60.000	5.50	0.00	42.01	4.00
4160	4494	0.109412	GGTACGACGTTCCTCCACAG	60.109	60.000	15.63	0.00	0.00	3.66
4681	5023	3.244561	GGGTTCAGTCCATGTTGAGAGAA	60.245	47.826	0.00	0.00	0.00	2.87
4716	5058	1.682005	GCCCTAGCCAATGCCACAA	60.682	57.895	0.00	0.00	38.69	3.33
4760	5103	3.740115	AGAAACAAGCTACCGTGTCATT	58.260	40.909	0.00	0.00	32.39	2.57
4761	5104	3.402628	AGAAACAAGCTACCGTGTCAT	57.597	42.857	0.00	0.00	32.39	3.06
4829	5172	0.528017	GATGACAGACGCTCCACTGA	59.472	55.000	0.00	0.00	37.54	3.41
5080	5423	2.961741	GAGTCCTGATGATAGCACCAGA	59.038	50.000	3.18	0.00	0.00	3.86
5143	5488	1.675552	AACCTTCACCAACTCCGTTG	58.324	50.000	0.00	0.00	42.49	4.10

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.