AutoCloner

Multiple sequence alignment - TraesCS5B01G193700

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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	TraesCS5B01G193700	chr5B	100.000	4574	0	0	1	4574	350367208	350371781	0.000000e+00	8447.0
1	TraesCS5B01G193700	chr5B	92.920	339	24	0	4051	4389	399398931	399398593	1.140000e-135	494.0
2	TraesCS5B01G193700	chr5B	90.625	288	26	1	1020	1307	350485442	350485728	9.290000e-102	381.0
3	TraesCS5B01G193700	chr5B	89.547	287	26	4	1013	1296	350392284	350392569	1.210000e-95	361.0
4	TraesCS5B01G193700	chr5A	93.347	2450	108	22	1615	4031	392037260	392034833	0.000000e+00	3570.0
5	TraesCS5B01G193700	chr5A	94.135	1040	38	8	591	1611	392038434	392037399	0.000000e+00	1561.0
6	TraesCS5B01G193700	chr5A	88.552	297	28	6	1016	1307	392000553	392000258	5.630000e-94	355.0
7	TraesCS5B01G193700	chr5A	88.194	288	29	2	1020	1307	391990144	391989862	5.670000e-89	339.0
8	TraesCS5B01G193700	chr5D	95.010	1944	88	4	2059	3999	305710831	305712768	0.000000e+00	3044.0
9	TraesCS5B01G193700	chr5D	90.134	1490	75	25	590	2058	305709365	305710803	0.000000e+00	1871.0
10	TraesCS5B01G193700	chr5D	90.972	288	25	1	1020	1307	305763099	305763385	2.000000e-103	387.0
11	TraesCS5B01G193700	chr5D	88.235	289	31	3	1010	1296	305715048	305715335	4.380000e-90	342.0
12	TraesCS5B01G193700	chr5D	79.596	495	68	15	85	569	20981175	20980704	1.590000e-84	324.0
13	TraesCS5B01G193700	chr6B	95.986	573	23	0	1	573	299044186	299043614	0.000000e+00	931.0
14	TraesCS5B01G193700	chr6B	83.162	582	80	8	2	577	107880460	107879891	2.440000e-142	516.0
15	TraesCS5B01G193700	chr6B	82.759	87	15	0	492	578	56546291	56546377	1.360000e-10	78.7
16	TraesCS5B01G193700	chr2B	93.064	519	36	0	4056	4574	544711908	544712426	0.000000e+00	760.0
17	TraesCS5B01G193700	chr7A	92.678	519	37	1	4056	4574	567442405	567441888	0.000000e+00	747.0
18	TraesCS5B01G193700	chr7A	92.958	355	24	1	1	354	32687287	32686933	2.440000e-142	516.0
19	TraesCS5B01G193700	chr7A	90.431	209	20	0	363	571	32686955	32686747	4.510000e-70	276.0
20	TraesCS5B01G193700	chr3D	89.231	520	29	8	4055	4574	11782755	11783247	3.890000e-175	625.0
21	TraesCS5B01G193700	chr3D	75.292	514	70	26	85	588	380976815	380976349	4.670000e-45	193.0
22	TraesCS5B01G193700	chr3D	86.207	145	16	3	1907	2049	138078862	138079004	2.200000e-33	154.0
23	TraesCS5B01G193700	chr3D	96.739	92	1	2	3926	4017	570803527	570803438	7.930000e-33	152.0
24	TraesCS5B01G193700	chr3D	94.792	96	4	1	3920	4014	612302308	612302403	1.030000e-31	148.0
25	TraesCS5B01G193700	chr3D	92.308	104	5	3	3915	4017	520219097	520218996	1.330000e-30	145.0
26	TraesCS5B01G193700	chr3D	81.379	145	14	5	18	162	606303454	606303585	6.260000e-19	106.0
27	TraesCS5B01G193700	chr7B	90.476	252	23	1	4056	4307	750142553	750142303	9.490000e-87	331.0
28	TraesCS5B01G193700	chr7B	86.099	223	26	2	4333	4551	537798773	537798994	7.650000e-58	235.0
29	TraesCS5B01G193700	chr6A	91.250	240	21	0	4057	4296	73446845	73447084	1.230000e-85	327.0
30	TraesCS5B01G193700	chr1D	82.333	300	47	5	1003	1296	457531713	457531414	5.870000e-64	255.0
31	TraesCS5B01G193700	chr4B	85.185	162	16	6	1887	2048	658773063	658773216	4.740000e-35	159.0
32	TraesCS5B01G193700	chr4B	86.713	143	16	3	1910	2051	526931208	526931348	6.130000e-34	156.0
33	TraesCS5B01G193700	chr4B	82.184	174	21	9	1879	2051	155374406	155374570	1.720000e-29	141.0
34	TraesCS5B01G193700	chr1A	84.242	165	22	4	5	168	561757275	561757114	1.700000e-34	158.0
35	TraesCS5B01G193700	chr1A	93.000	100	3	3	3925	4021	121132423	121132325	4.770000e-30	143.0
36	TraesCS5B01G193700	chr1A	80.814	172	27	3	398	569	367013048	367013213	3.710000e-26	130.0
37	TraesCS5B01G193700	chr1B	86.093	151	13	4	1898	2048	442177125	442177267	6.130000e-34	156.0
38	TraesCS5B01G193700	chr4A	93.269	104	3	3	3917	4017	628924500	628924398	2.850000e-32	150.0
39	TraesCS5B01G193700	chr4A	83.537	164	19	4	1888	2051	363744703	363744548	3.690000e-31	147.0
40	TraesCS5B01G193700	chr4A	90.411	73	7	0	4274	4346	727745364	727745436	3.770000e-16	97.1
41	TraesCS5B01G193700	chr4D	84.277	159	17	4	1893	2051	168219332	168219182	1.030000e-31	148.0
42	TraesCS5B01G193700	chr3A	93.137	102	3	4	3920	4018	655646770	655646670	3.690000e-31	147.0
43	TraesCS5B01G193700	chr3B	91.509	106	5	4	3921	4025	685061561	685061459	4.770000e-30	143.0
44	TraesCS5B01G193700	chr3B	84.270	89	14	0	492	580	97824785	97824873	2.270000e-13	87.9
45	TraesCS5B01G193700	chr2D	86.555	119	15	1	452	569	523159582	523159464	3.710000e-26	130.0

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	TraesCS5B01G193700	chr5B	350367208	350371781	4573	False	8447.000000	8447	100.000000	1	4574	1	chr5B.!!$F1	4573
1	TraesCS5B01G193700	chr5A	392034833	392038434	3601	True	2565.500000	3570	93.741000	591	4031	2	chr5A.!!$R3	3440
2	TraesCS5B01G193700	chr5D	305709365	305715335	5970	False	1752.333333	3044	91.126333	590	3999	3	chr5D.!!$F2	3409
3	TraesCS5B01G193700	chr6B	299043614	299044186	572	True	931.000000	931	95.986000	1	573	1	chr6B.!!$R2	572
4	TraesCS5B01G193700	chr6B	107879891	107880460	569	True	516.000000	516	83.162000	2	577	1	chr6B.!!$R1	575
5	TraesCS5B01G193700	chr2B	544711908	544712426	518	False	760.000000	760	93.064000	4056	4574	1	chr2B.!!$F1	518
6	TraesCS5B01G193700	chr7A	567441888	567442405	517	True	747.000000	747	92.678000	4056	4574	1	chr7A.!!$R1	518
7	TraesCS5B01G193700	chr7A	32686747	32687287	540	True	396.000000	516	91.694500	1	571	2	chr7A.!!$R2	570

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
750	781	0.609131	CAACCCAAGCCATCGTCCTT	60.609	55.0	0.00	0.00	0.00	3.36	F
1468	1517	0.606401	AAGCTGGTGTACGCTTGCAT	60.606	50.0	20.02	10.15	44.18	3.96	F
3385	3612	0.106819	CAGGGAGAGGGCAAGAATGG	60.107	60.0	0.00	0.00	0.00	3.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2677	2901	0.772124	TTCCACCAAAGAGCCCTCCT	60.772	55.0	0.00	0.0	0.0	3.69	R
3461	3688	0.531532	GATCACAGTGGCATCCTCCG	60.532	60.0	0.00	0.0	0.0	4.63	R
4235	4564	0.461339	TATCTTTGGACTTCGCGGCC	60.461	55.0	6.13	3.6	0.0	6.13	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
107	108	0.821301	TTGCTGCAACCATTGTCGGA	60.821	50.000	11.69	0.00	0.00	4.55
314	320	1.079127	CGAGAAACGCATGGGAGGT	60.079	57.895	17.76	0.39	34.51	3.85
441	468	0.683973	CCACTGCTCCTGTTCTCTGT	59.316	55.000	0.00	0.00	0.00	3.41
500	529	4.429854	GGAGAAGCCTAAATCTGATGGT	57.570	45.455	0.00	0.00	0.00	3.55
573	602	2.928361	CGCCGGCGCTTATTACTG	59.072	61.111	38.48	5.99	0.00	2.74
577	606	1.522806	CGGCGCTTATTACTGCCCA	60.523	57.895	7.64	0.00	44.71	5.36
578	607	0.884704	CGGCGCTTATTACTGCCCAT	60.885	55.000	7.64	0.00	44.71	4.00
579	608	0.875059	GGCGCTTATTACTGCCCATC	59.125	55.000	7.64	0.00	41.70	3.51
580	609	1.543429	GGCGCTTATTACTGCCCATCT	60.543	52.381	7.64	0.00	41.70	2.90
581	610	2.289444	GGCGCTTATTACTGCCCATCTA	60.289	50.000	7.64	0.00	41.70	1.98
582	611	3.399330	GCGCTTATTACTGCCCATCTAA	58.601	45.455	0.00	0.00	0.00	2.10
583	612	3.813166	GCGCTTATTACTGCCCATCTAAA	59.187	43.478	0.00	0.00	0.00	1.85
584	613	4.274950	GCGCTTATTACTGCCCATCTAAAA	59.725	41.667	0.00	0.00	0.00	1.52
585	614	5.220970	GCGCTTATTACTGCCCATCTAAAAA	60.221	40.000	0.00	0.00	0.00	1.94
678	709	1.002792	GCGTTGAATATTCCGGCTTCC	60.003	52.381	12.90	0.00	0.00	3.46
750	781	0.609131	CAACCCAAGCCATCGTCCTT	60.609	55.000	0.00	0.00	0.00	3.36
752	783	1.815421	CCCAAGCCATCGTCCTTCG	60.815	63.158	0.00	0.00	41.41	3.79
826	857	3.866910	TCAATTATAGACGAACGGTTGCC	59.133	43.478	0.00	0.00	0.00	4.52
862	893	2.906354	CTCTCCATAACCACGGGAAAG	58.094	52.381	0.00	0.00	0.00	2.62
896	927	3.744719	CCCGCGAAGGAGACGACA	61.745	66.667	8.23	0.00	45.00	4.35
1361	1410	3.469899	TTGTCGATCCAATTTTGCGAG	57.530	42.857	0.00	0.00	0.00	5.03
1393	1442	4.532126	TGGATCATCTCGGGTATATGCTTT	59.468	41.667	0.00	0.00	0.00	3.51
1416	1465	3.813724	GGTTTATCCGCAGATCCCTTAAC	59.186	47.826	0.00	0.00	33.67	2.01
1422	1471	4.703897	TCCGCAGATCCCTTAACTATTTG	58.296	43.478	0.00	0.00	0.00	2.32
1427	1476	5.504173	GCAGATCCCTTAACTATTTGCGTTC	60.504	44.000	0.00	0.00	0.00	3.95
1468	1517	0.606401	AAGCTGGTGTACGCTTGCAT	60.606	50.000	20.02	10.15	44.18	3.96
1469	1518	1.021390	AGCTGGTGTACGCTTGCATC	61.021	55.000	20.02	2.98	31.17	3.91
1538	1587	2.930040	CGAAGCAAATCACGTGGACTAT	59.070	45.455	17.00	0.00	0.00	2.12
1539	1588	4.109766	CGAAGCAAATCACGTGGACTATA	58.890	43.478	17.00	0.00	0.00	1.31
1540	1589	4.745125	CGAAGCAAATCACGTGGACTATAT	59.255	41.667	17.00	0.00	0.00	0.86
1579	1628	9.319143	GGAGTAGCATATTCGCATCTAAAATAT	57.681	33.333	0.00	0.00	0.00	1.28
1597	1646	5.843019	AATATGATCCCCGAATGGTAGTT	57.157	39.130	0.00	0.00	0.00	2.24
1616	1665	6.590677	GGTAGTTGACCTTTATCTGTCTGAAC	59.409	42.308	0.00	0.00	45.89	3.18
1617	1666	6.174720	AGTTGACCTTTATCTGTCTGAACA	57.825	37.500	0.00	0.00	32.67	3.18
1659	1843	5.211266	TGTGAAATAACCAAATACTCGCG	57.789	39.130	0.00	0.00	0.00	5.87
1661	1845	3.242155	TGAAATAACCAAATACTCGCGCG	60.242	43.478	26.76	26.76	0.00	6.86
1830	2026	1.469917	GCATCCAATGTGCGAATTCG	58.530	50.000	23.34	23.34	43.27	3.34
1895	2091	4.154802	TGGGATTGCTAGATACCCCATA	57.845	45.455	8.69	0.00	38.79	2.74
1903	2099	4.219944	TGCTAGATACCCCATACGTTCATC	59.780	45.833	0.00	0.00	0.00	2.92
1913	2109	7.918076	ACCCCATACGTTCATCATTATAAGAT	58.082	34.615	0.00	0.00	0.00	2.40
1953	2149	8.495949	CAATATGGACTACATACGGATTGAAAC	58.504	37.037	0.00	0.00	44.41	2.78
1959	2155	3.259064	ACATACGGATTGAAACGAGTGG	58.741	45.455	0.00	0.00	0.00	4.00
1961	2157	2.080286	ACGGATTGAAACGAGTGGAG	57.920	50.000	0.00	0.00	0.00	3.86
2078	2302	6.169800	TGCAGCCAATAATAATGCTACGATA	58.830	36.000	0.00	0.00	37.76	2.92
2224	2448	4.222588	GCTATCCAATCTCTAGTGGCAGAT	59.777	45.833	0.00	0.00	40.76	2.90
2387	2611	4.392047	TCACATTGTTGCTCTCATCAGTT	58.608	39.130	0.00	0.00	0.00	3.16
2450	2674	5.213891	TCATTTCTGCAACAGTGAGAGTA	57.786	39.130	0.00	0.00	32.61	2.59
2533	2757	3.264193	AGGCTGTTGTGAAGATACCATCA	59.736	43.478	0.00	0.00	0.00	3.07
2713	2937	4.140924	GGTGGAAAGATGGGGGATTATCTT	60.141	45.833	0.00	0.00	43.49	2.40
2718	2942	6.596869	AAAGATGGGGGATTATCTTTCTGA	57.403	37.500	6.43	0.00	45.58	3.27
2824	3048	5.133941	GGACTACCTGATGACTCATCTACA	58.866	45.833	18.01	0.55	41.06	2.74
2831	3055	3.701542	TGATGACTCATCTACAGGTGTCC	59.298	47.826	18.01	0.00	41.06	4.02
3040	3267	6.253746	CACAAACTGCTGATAAGCTATGAAC	58.746	40.000	3.06	0.00	35.49	3.18
3104	3331	4.129380	CCCATATTTGCAGAGATCGTTCA	58.871	43.478	0.00	0.00	0.00	3.18
3220	3447	0.107897	TGCATACGGCTACAACCCTG	60.108	55.000	0.00	0.00	45.15	4.45
3242	3469	1.071385	CTCATATGGGGCTGGAGTGAC	59.929	57.143	2.13	0.00	0.00	3.67
3255	3482	0.249489	GAGTGACCAGTGTTGCGAGT	60.249	55.000	0.00	0.00	0.00	4.18
3273	3500	2.045926	GACAGGTCCAATGCCGCT	60.046	61.111	0.00	0.00	0.00	5.52
3348	3575	4.142160	TGCTTCATCTACTCGCTGTTGTAT	60.142	41.667	0.00	0.00	0.00	2.29
3385	3612	0.106819	CAGGGAGAGGGCAAGAATGG	60.107	60.000	0.00	0.00	0.00	3.16
3390	3617	0.915364	AGAGGGCAAGAATGGACTCC	59.085	55.000	0.00	0.00	0.00	3.85
3421	3648	1.536922	CGGAGTTGCAGCATATCGAGT	60.537	52.381	2.55	0.00	0.00	4.18
3461	3688	0.179142	GGAGACTTCTACGCGGGAAC	60.179	60.000	12.47	4.00	0.00	3.62
3511	3738	4.472833	AGTATGGTGAGGAAGAGCTTGATT	59.527	41.667	0.00	0.00	0.00	2.57
3555	3782	3.253921	TGATGCATCACCAAGTTGAACAG	59.746	43.478	25.42	0.00	0.00	3.16
3602	3829	4.267928	GCGTGATATGTACAGGAAGTTGTC	59.732	45.833	0.33	0.00	32.56	3.18
3605	3832	2.762535	ATGTACAGGAAGTTGTCGGG	57.237	50.000	0.33	0.00	32.56	5.14
3667	3894	4.209538	TGCATATTTTCAGGGGATCAGTG	58.790	43.478	0.00	0.00	0.00	3.66
3791	4018	2.295349	AGCAGCAATCAGAAGTGTTTGG	59.705	45.455	0.00	0.00	34.96	3.28
3855	4082	8.154856	ACAGTTACCAGTTCAAGCTTTATCTAA	58.845	33.333	0.00	0.00	0.00	2.10
3857	4084	7.606839	AGTTACCAGTTCAAGCTTTATCTAACC	59.393	37.037	0.00	0.00	0.00	2.85
3880	4107	4.391216	CGAAAGTGCATGAGAAATGAGACT	59.609	41.667	0.00	0.00	0.00	3.24
3890	4117	8.306038	GCATGAGAAATGAGACTCAGTATATCT	58.694	37.037	11.52	8.19	44.50	1.98
3917	4144	6.427300	CATGCATGCAAAATTTCAACAAAC	57.573	33.333	26.68	0.00	0.00	2.93
4100	4429	8.608844	ACTTTATTCCTCAAATAATAGCGAGG	57.391	34.615	0.00	0.00	45.40	4.63
4163	4492	9.178758	ACAGAATCCCAAAACATAGAAGAATAC	57.821	33.333	0.00	0.00	0.00	1.89
4198	4527	2.238144	AGTGTGCTAACTCATGAGCCAT	59.762	45.455	22.83	11.60	37.94	4.40
4212	4541	5.240844	TCATGAGCCATCATATTTGCTTCAG	59.759	40.000	0.00	0.00	44.58	3.02
4235	4564	4.201930	GGTAGACAGTGAGAATACTCCACG	60.202	50.000	0.00	0.00	41.99	4.94
4237	4566	1.204941	ACAGTGAGAATACTCCACGGC	59.795	52.381	0.00	0.00	41.99	5.68
4241	4673	2.960129	GAATACTCCACGGCCGCG	60.960	66.667	28.58	17.55	0.00	6.46
4288	4821	2.287970	CCAGTACAGTAGCAACGTCACA	60.288	50.000	0.00	0.00	0.00	3.58
4349	5592	4.406003	ACAAAGCTATTATCCGACTCCACT	59.594	41.667	0.00	0.00	0.00	4.00
4351	5594	5.968528	AAGCTATTATCCGACTCCACTAG	57.031	43.478	0.00	0.00	0.00	2.57
4374	6198	4.512571	GCACTTTGTTGCATCCAATTTTCT	59.487	37.500	0.00	0.00	42.49	2.52
4404	6228	1.985473	TAGCCCGTTCCTAATCGCTA	58.015	50.000	0.00	0.00	0.00	4.26
4415	6239	2.480416	CCTAATCGCTATCATCTCCGCC	60.480	54.545	0.00	0.00	0.00	6.13
4416	6240	0.969149	AATCGCTATCATCTCCGCCA	59.031	50.000	0.00	0.00	0.00	5.69
4427	6251	3.055458	TCATCTCCGCCAAATCAACACTA	60.055	43.478	0.00	0.00	0.00	2.74

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
99	100	2.736144	TCGTAGCAAACTCCGACAAT	57.264	45.000	0.00	0.00	28.23	2.71
107	108	1.374252	CTGCCGGTCGTAGCAAACT	60.374	57.895	1.90	0.00	38.82	2.66
381	387	3.717294	GACCACCTCCCACGCCAT	61.717	66.667	0.00	0.00	0.00	4.40
479	508	4.429854	ACCATCAGATTTAGGCTTCTCC	57.570	45.455	0.00	0.00	0.00	3.71
490	519	3.007506	TGTCCACGTACAACCATCAGATT	59.992	43.478	0.00	0.00	0.00	2.40
584	613	3.523972	GGTCAGATAGGGGAGGTCTTTTT	59.476	47.826	0.00	0.00	0.00	1.94
585	614	3.116174	GGTCAGATAGGGGAGGTCTTTT	58.884	50.000	0.00	0.00	0.00	2.27
586	615	2.319438	AGGTCAGATAGGGGAGGTCTTT	59.681	50.000	0.00	0.00	0.00	2.52
587	616	1.940957	AGGTCAGATAGGGGAGGTCTT	59.059	52.381	0.00	0.00	0.00	3.01
588	617	1.219213	CAGGTCAGATAGGGGAGGTCT	59.781	57.143	0.00	0.00	0.00	3.85
649	680	0.539986	ATATTCAACGCGTGGACCCT	59.460	50.000	17.75	6.80	0.00	4.34
651	682	1.329599	GGAATATTCAACGCGTGGACC	59.670	52.381	17.75	10.32	0.00	4.46
750	781	1.613437	TGTCAGATCAGTTGACTGCGA	59.387	47.619	13.05	0.00	44.08	5.10
752	783	2.759191	TGTGTCAGATCAGTTGACTGC	58.241	47.619	13.05	7.88	44.08	4.40
826	857	2.500442	GAGCGACTGACGTGCGATG	61.500	63.158	0.00	0.00	44.60	3.84
896	927	3.692406	GAACGAGGAGGGCGGTGT	61.692	66.667	0.00	0.00	0.00	4.16
937	968	1.810755	CTTTTGGTCTTTCGCCTACCC	59.189	52.381	0.00	0.00	31.97	3.69
939	970	2.742589	CCTCTTTTGGTCTTTCGCCTAC	59.257	50.000	0.00	0.00	0.00	3.18
940	971	2.874457	GCCTCTTTTGGTCTTTCGCCTA	60.874	50.000	0.00	0.00	0.00	3.93
948	992	2.034221	GGCGGCCTCTTTTGGTCT	59.966	61.111	12.87	0.00	0.00	3.85
993	1042	4.552365	GCCTCTGCCATAGCGCCA	62.552	66.667	2.29	0.00	44.31	5.69
1361	1410	0.608582	GAGATGATCCATGCCCCAGC	60.609	60.000	0.00	0.00	40.48	4.85
1393	1442	1.507140	AGGGATCTGCGGATAAACCA	58.493	50.000	19.78	0.00	38.90	3.67
1416	1465	1.061131	CGTGAGCCAGAACGCAAATAG	59.939	52.381	0.00	0.00	32.40	1.73
1468	1517	6.932400	TCAGATTTCGCACCTTTTACTTAAGA	59.068	34.615	10.09	0.00	0.00	2.10
1469	1518	7.129109	TCAGATTTCGCACCTTTTACTTAAG	57.871	36.000	0.00	0.00	0.00	1.85
1579	1628	2.169769	GTCAACTACCATTCGGGGATCA	59.830	50.000	0.00	0.00	42.91	2.92
1659	1843	6.017933	CAGAAATCAAACATAACTGTCTCGC	58.982	40.000	0.00	0.00	33.36	5.03
1661	1845	8.316640	AGTCAGAAATCAAACATAACTGTCTC	57.683	34.615	0.00	0.00	33.36	3.36
1849	2045	4.323104	CCCAGATTTTTAATCCCCGCAAAA	60.323	41.667	0.00	0.00	0.00	2.44
1855	2051	3.454447	CCCAACCCAGATTTTTAATCCCC	59.546	47.826	0.00	0.00	0.00	4.81
1895	2091	9.173021	TCCAAAACATCTTATAATGATGAACGT	57.827	29.630	21.61	0.00	42.68	3.99
1953	2149	4.095610	GTTTTTGTGTGTTTCTCCACTCG	58.904	43.478	0.00	0.00	36.30	4.18
2224	2448	5.419788	ACCCCGCGTATTATCATCAGTATAA	59.580	40.000	4.92	0.00	0.00	0.98
2387	2611	2.359354	CAACGCCCCGACCATCAA	60.359	61.111	0.00	0.00	0.00	2.57
2533	2757	3.464907	CTGAGCCACGATGATCTGAAAT	58.535	45.455	0.00	0.00	0.00	2.17
2677	2901	0.772124	TTCCACCAAAGAGCCCTCCT	60.772	55.000	0.00	0.00	0.00	3.69
2831	3055	7.087409	TGATAAACATTACAAGTCCATGCAG	57.913	36.000	0.00	0.00	0.00	4.41
2845	3069	4.545678	TGCTTAGCCCCATGATAAACATT	58.454	39.130	0.29	0.00	37.07	2.71
3066	3293	1.079612	GGGGCTGCACATGAAAAGC	60.080	57.895	3.46	4.68	34.86	3.51
3104	3331	4.906664	AGATACTTGCCCTTGATCTCTCAT	59.093	41.667	0.00	0.00	0.00	2.90
3220	3447	1.071385	CACTCCAGCCCCATATGAGAC	59.929	57.143	3.65	0.00	0.00	3.36
3242	3469	1.224069	CCTGTCACTCGCAACACTGG	61.224	60.000	0.00	0.00	0.00	4.00
3255	3482	2.359850	GCGGCATTGGACCTGTCA	60.360	61.111	0.00	0.00	0.00	3.58
3385	3612	3.651803	CTCCGATGTGATAAGGGAGTC	57.348	52.381	0.00	0.00	39.51	3.36
3390	3617	2.868583	CTGCAACTCCGATGTGATAAGG	59.131	50.000	0.00	0.00	0.00	2.69
3421	3648	3.009033	CCTACTCCATGACACCTTTCCAA	59.991	47.826	0.00	0.00	0.00	3.53
3461	3688	0.531532	GATCACAGTGGCATCCTCCG	60.532	60.000	0.00	0.00	0.00	4.63
3511	3738	5.407084	TCAACGCTTTTTCATCGTCATTAGA	59.593	36.000	0.00	0.00	35.18	2.10
3555	3782	5.194432	TCTAATCACCTGAGACTACCACTC	58.806	45.833	0.00	0.00	35.26	3.51
3602	3829	1.417890	AGCATAATCCTGAACTCCCCG	59.582	52.381	0.00	0.00	0.00	5.73
3605	3832	3.696051	TGCAAAGCATAATCCTGAACTCC	59.304	43.478	0.00	0.00	31.71	3.85
3667	3894	2.415426	CAAACAACACCCGGGCAC	59.585	61.111	24.08	0.00	0.00	5.01
3791	4018	5.628130	ACCCCCAAAAAGTTACTACTTCTC	58.372	41.667	0.00	0.00	43.74	2.87
3855	4082	3.411446	TCATTTCTCATGCACTTTCGGT	58.589	40.909	0.00	0.00	0.00	4.69
3857	4084	4.391216	AGTCTCATTTCTCATGCACTTTCG	59.609	41.667	0.00	0.00	0.00	3.46
3894	4121	6.202937	AGTTTGTTGAAATTTTGCATGCATG	58.797	32.000	23.37	22.70	0.00	4.06
3898	4125	8.173775	TGTTGTAGTTTGTTGAAATTTTGCATG	58.826	29.630	0.00	0.00	0.00	4.06
3907	4134	4.675671	CGGGCTTGTTGTAGTTTGTTGAAA	60.676	41.667	0.00	0.00	0.00	2.69
3912	4139	1.944709	GACGGGCTTGTTGTAGTTTGT	59.055	47.619	0.00	0.00	0.00	2.83
3917	4144	1.204941	AGCTAGACGGGCTTGTTGTAG	59.795	52.381	0.00	0.00	36.56	2.74
4010	4245	3.140144	ACAAAATGGGAGAGGGAGAAACA	59.860	43.478	0.00	0.00	0.00	2.83
4011	4246	3.767711	ACAAAATGGGAGAGGGAGAAAC	58.232	45.455	0.00	0.00	0.00	2.78
4163	4492	8.371770	AGTTAGCACACTTTTCTTTTAGAGAG	57.628	34.615	0.00	0.00	35.37	3.20
4176	4505	2.038952	TGGCTCATGAGTTAGCACACTT	59.961	45.455	23.38	0.00	40.61	3.16
4178	4507	2.099141	TGGCTCATGAGTTAGCACAC	57.901	50.000	23.38	4.50	40.61	3.82
4198	4527	6.070824	TCACTGTCTACCTGAAGCAAATATGA	60.071	38.462	0.00	0.00	0.00	2.15
4212	4541	4.201930	CGTGGAGTATTCTCACTGTCTACC	60.202	50.000	1.51	0.00	42.05	3.18
4235	4564	0.461339	TATCTTTGGACTTCGCGGCC	60.461	55.000	6.13	3.60	0.00	6.13
4237	4566	3.788797	GCAATTATCTTTGGACTTCGCGG	60.789	47.826	6.13	0.00	0.00	6.46
4241	4673	5.713025	TGCAAGCAATTATCTTTGGACTTC	58.287	37.500	0.00	0.00	0.00	3.01
4288	4821	1.521764	TCCAGATGCATATGTGGGGT	58.478	50.000	19.36	0.00	45.41	4.95
4349	5592	4.870123	AATTGGATGCAACAAAGTGCTA	57.130	36.364	0.12	0.00	45.17	3.49
4351	5594	4.512571	AGAAAATTGGATGCAACAAAGTGC	59.487	37.500	0.12	2.16	45.15	4.40
4391	6215	4.416620	CGGAGATGATAGCGATTAGGAAC	58.583	47.826	0.00	0.00	0.00	3.62
4397	6221	0.969149	TGGCGGAGATGATAGCGATT	59.031	50.000	0.00	0.00	0.00	3.34
4404	6228	2.684881	GTGTTGATTTGGCGGAGATGAT	59.315	45.455	0.00	0.00	0.00	2.45
4427	6251	5.145564	ACATGGTATATACCTCAACTCGGT	58.854	41.667	28.12	13.66	46.58	4.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.