AutoCloner

Multiple sequence alignment - TraesCS5B01G123800

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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	TraesCS5B01G123800	chr5B	100.000	4706	0	0	1	4706	223127741	223123036	0.000000e+00	8691.0
1	TraesCS5B01G123800	chr5B	86.420	81	7	4	1605	1684	69134890	69134813	8.390000e-13	86.1
2	TraesCS5B01G123800	chr5B	82.418	91	14	2	294	383	551516402	551516313	1.400000e-10	78.7
3	TraesCS5B01G123800	chr5B	97.059	34	1	0	621	654	397957741	397957708	1.830000e-04	58.4
4	TraesCS5B01G123800	chr5D	97.596	3827	79	9	1	3820	209646524	209642704	0.000000e+00	6545.0
5	TraesCS5B01G123800	chr5D	97.166	247	6	1	3885	4130	209642358	209642112	2.620000e-112	416.0
6	TraesCS5B01G123800	chr5D	96.970	33	1	0	621	653	4029931	4029899	6.580000e-04	56.5
7	TraesCS5B01G123800	chr5A	97.526	3193	63	9	649	3831	271050733	271047547	0.000000e+00	5445.0
8	TraesCS5B01G123800	chr5A	96.099	282	5	1	3849	4130	271047155	271046880	5.550000e-124	455.0
9	TraesCS5B01G123800	chr5A	94.000	300	14	1	1	296	271051033	271050734	7.180000e-123	451.0
10	TraesCS5B01G123800	chr4D	91.161	577	48	3	4131	4706	91056884	91057458	0.000000e+00	780.0
11	TraesCS5B01G123800	chr4A	87.414	580	64	6	4131	4706	699614644	699615218	0.000000e+00	658.0
12	TraesCS5B01G123800	chr4A	86.897	580	65	8	4131	4706	144632348	144631776	1.430000e-179	640.0
13	TraesCS5B01G123800	chr4A	100.000	30	0	0	621	650	648259215	648259244	6.580000e-04	56.5
14	TraesCS5B01G123800	chr4A	100.000	30	0	0	621	650	734244322	734244351	6.580000e-04	56.5
15	TraesCS5B01G123800	chr1B	87.241	580	65	7	4131	4706	259785033	259785607	0.000000e+00	652.0
16	TraesCS5B01G123800	chr7A	87.219	579	65	8	4132	4706	173130576	173131149	0.000000e+00	651.0
17	TraesCS5B01G123800	chr7A	86.792	583	68	7	4128	4706	619191444	619192021	3.970000e-180	641.0
18	TraesCS5B01G123800	chr7A	86.621	583	67	9	4129	4706	188886429	188887005	6.640000e-178	634.0
19	TraesCS5B01G123800	chrUn	87.024	578	70	4	4131	4706	29316610	29317184	0.000000e+00	647.0
20	TraesCS5B01G123800	chr2A	86.792	583	68	7	4128	4706	689766941	689767518	3.970000e-180	641.0
21	TraesCS5B01G123800	chr2A	100.000	31	0	0	620	650	331181162	331181192	1.830000e-04	58.4
22	TraesCS5B01G123800	chr2B	90.397	302	24	3	301	597	583920987	583921288	4.410000e-105	392.0
23	TraesCS5B01G123800	chr6A	87.081	209	21	5	454	657	595770552	595770345	1.020000e-56	231.0
24	TraesCS5B01G123800	chr6A	88.889	162	18	0	294	455	595770788	595770627	2.870000e-47	200.0
25	TraesCS5B01G123800	chr2D	93.056	72	5	0	295	366	650064166	650064095	6.440000e-19	106.0
26	TraesCS5B01G123800	chr7B	86.957	92	6	4	295	383	647817865	647817777	1.080000e-16	99.0
27	TraesCS5B01G123800	chr7B	84.783	92	8	4	295	383	647818290	647818202	2.330000e-13	87.9
28	TraesCS5B01G123800	chr3D	83.146	89	15	0	295	383	102231544	102231456	1.090000e-11	82.4
29	TraesCS5B01G123800	chr3B	82.418	91	14	2	294	383	25662351	25662262	1.400000e-10	78.7
30	TraesCS5B01G123800	chr4B	94.595	37	1	1	621	656	183813084	183813120	6.580000e-04	56.5
31	TraesCS5B01G123800	chr3A	96.970	33	0	1	622	654	519765837	519765806	2.000000e-03	54.7

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	TraesCS5B01G123800	chr5B	223123036	223127741	4705	True	8691.0	8691	100.000	1	4706	1	chr5B.!!$R2	4705
1	TraesCS5B01G123800	chr5D	209642112	209646524	4412	True	3480.5	6545	97.381	1	4130	2	chr5D.!!$R2	4129
2	TraesCS5B01G123800	chr5A	271046880	271051033	4153	True	2117.0	5445	95.875	1	4130	3	chr5A.!!$R1	4129
3	TraesCS5B01G123800	chr4D	91056884	91057458	574	False	780.0	780	91.161	4131	4706	1	chr4D.!!$F1	575
4	TraesCS5B01G123800	chr4A	699614644	699615218	574	False	658.0	658	87.414	4131	4706	1	chr4A.!!$F2	575
5	TraesCS5B01G123800	chr4A	144631776	144632348	572	True	640.0	640	86.897	4131	4706	1	chr4A.!!$R1	575
6	TraesCS5B01G123800	chr1B	259785033	259785607	574	False	652.0	652	87.241	4131	4706	1	chr1B.!!$F1	575
7	TraesCS5B01G123800	chr7A	173130576	173131149	573	False	651.0	651	87.219	4132	4706	1	chr7A.!!$F1	574
8	TraesCS5B01G123800	chr7A	619191444	619192021	577	False	641.0	641	86.792	4128	4706	1	chr7A.!!$F3	578
9	TraesCS5B01G123800	chr7A	188886429	188887005	576	False	634.0	634	86.621	4129	4706	1	chr7A.!!$F2	577
10	TraesCS5B01G123800	chrUn	29316610	29317184	574	False	647.0	647	87.024	4131	4706	1	chrUn.!!$F1	575
11	TraesCS5B01G123800	chr2A	689766941	689767518	577	False	641.0	641	86.792	4128	4706	1	chr2A.!!$F2	578

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
428	436	0.545171	AGTAGTCATGGCATGCAGCT	59.455	50.000	22.56	19.77	44.79	4.24	F
467	475	1.070843	CGTATTTAGCCAATCACGCGG	60.071	52.381	12.47	0.00	0.00	6.46	F
534	542	1.202076	GCCTCTTCGCATGCAACTAAC	60.202	52.381	19.57	0.00	0.00	2.34	F
2343	2364	1.271871	TGGTCCGCATTTGGTCAAGAT	60.272	47.619	0.00	0.00	0.00	2.40	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
2366	2387	1.829222	CAGCCCCATGAAGCTCAAAAT	59.171	47.619	6.48	37.18	1.82	R
2554	2575	3.262420	GTGCCCATATATGTTAGCCTCG	58.738	50.000	11.73	0.00	4.63	R
2568	2589	1.966845	AGTTACTGGTAGGTGCCCAT	58.033	50.000	0.00	0.00	4.00	R
4412	4810	0.248539	GTCGACGATCACCTACAGCC	60.249	60.000	0.00	0.00	4.85	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
72	77	6.428385	TTTTGGTAAAAGCCACACAAATTG	57.572	33.333	0.00	0.00	38.42	2.32
163	170	3.321968	GGTTTGGTCTTTTCCAGCATTCT	59.678	43.478	0.00	0.00	38.80	2.40
199	207	4.081752	TGAAGTTGTCTTGCACCATTTGTT	60.082	37.500	0.00	0.00	33.64	2.83
200	208	4.470334	AGTTGTCTTGCACCATTTGTTT	57.530	36.364	0.00	0.00	0.00	2.83
255	263	6.255950	GGCATAGAAGTTGGACGAAAATAAC	58.744	40.000	0.00	0.00	0.00	1.89
303	311	5.071115	GGATGGATTGCTATATACTCCCTCC	59.929	48.000	0.00	0.00	34.86	4.30
383	391	1.821216	ATGGCGTTTGATTTCCGAGT	58.179	45.000	0.00	0.00	0.00	4.18
403	411	0.899717	GGGGCAGCAACCAATCAGAA	60.900	55.000	0.00	0.00	0.00	3.02
428	436	0.545171	AGTAGTCATGGCATGCAGCT	59.455	50.000	22.56	19.77	44.79	4.24
467	475	1.070843	CGTATTTAGCCAATCACGCGG	60.071	52.381	12.47	0.00	0.00	6.46
494	502	3.814049	GCGCTAGCAGCAGTTATTG	57.186	52.632	21.32	1.34	42.58	1.90
534	542	1.202076	GCCTCTTCGCATGCAACTAAC	60.202	52.381	19.57	0.00	0.00	2.34
544	552	3.740590	CATGCAACTAACTGCGAGAAAG	58.259	45.455	0.00	0.00	45.74	2.62
545	553	2.833794	TGCAACTAACTGCGAGAAAGT	58.166	42.857	0.00	0.00	45.74	2.66
606	616	4.321675	GGGGCCTTATAAAAACATATGCGG	60.322	45.833	0.84	0.00	0.00	5.69
614	624	6.693315	ATAAAAACATATGCGGCTAGTTGT	57.307	33.333	1.58	0.00	0.00	3.32
660	670	4.139786	CGGAGGTAGTAGTATGTAAGCCA	58.860	47.826	0.00	0.00	0.00	4.75
679	689	2.497273	CCACAAAATGGGAAGGGTGATC	59.503	50.000	0.00	0.00	45.95	2.92
805	815	1.979809	TGGGGTGATGGAATGTAGGT	58.020	50.000	0.00	0.00	0.00	3.08
871	881	7.391554	TCATGGGCTAATATCAGCTAAACATTC	59.608	37.037	0.00	0.00	41.50	2.67
1143	1155	2.219458	CATGATCCAGCACCTGTGATC	58.781	52.381	0.51	12.65	37.99	2.92
1201	1213	2.299993	TCACGATGTGATTGAGAGGC	57.700	50.000	0.00	0.00	37.67	4.70
1278	1290	1.887198	GTCTGTCGAACCTGGAGAGAA	59.113	52.381	0.00	0.00	35.84	2.87
1360	1372	2.349590	TGAAGCAGGTGATGATGTTCG	58.650	47.619	0.00	0.00	0.00	3.95
1595	1610	6.959671	AGTGGTTTTGTTTTGTACATGTTG	57.040	33.333	2.30	0.00	36.44	3.33
1596	1611	6.459923	AGTGGTTTTGTTTTGTACATGTTGT	58.540	32.000	2.30	0.00	36.44	3.32
1597	1612	6.931840	AGTGGTTTTGTTTTGTACATGTTGTT	59.068	30.769	2.30	0.00	36.44	2.83
1679	1694	1.406903	CATTTTGGGATGGAGGGAGC	58.593	55.000	0.00	0.00	0.00	4.70
1924	1945	4.276678	TCACTTTCCTTGTGAAGAATGCAG	59.723	41.667	0.00	0.00	40.89	4.41
2012	2033	3.985008	TGCATGAATTATTGCAGGCATC	58.015	40.909	9.98	0.00	45.39	3.91
2026	2047	5.070001	TGCAGGCATCTAATTAACCATACC	58.930	41.667	0.00	0.00	0.00	2.73
2157	2178	3.372954	GCTGATGTATACGTCGCTCTTT	58.627	45.455	23.09	0.00	34.69	2.52
2163	2184	5.244785	TGTATACGTCGCTCTTTTCTCAT	57.755	39.130	0.00	0.00	0.00	2.90
2251	2272	6.841601	AGATATAATAGCCCAAGTTGCAGAA	58.158	36.000	0.00	0.00	0.00	3.02
2343	2364	1.271871	TGGTCCGCATTTGGTCAAGAT	60.272	47.619	0.00	0.00	0.00	2.40
2365	2386	7.605449	AGATGCTAACACAACTTGCATTTTAT	58.395	30.769	0.00	0.00	43.28	1.40
2366	2387	8.739039	AGATGCTAACACAACTTGCATTTTATA	58.261	29.630	0.00	0.00	43.28	0.98
2529	2550	2.051105	TGCACCACAGCAAATGCAT	58.949	47.368	8.28	0.00	42.92	3.96
2568	2589	2.299013	CAGCACCCGAGGCTAACATATA	59.701	50.000	0.00	0.00	40.23	0.86
2745	2766	2.102578	ACTTTTTCTGCAGCTGTGGTT	58.897	42.857	16.64	0.00	0.00	3.67
2970	2993	4.567747	GGCTTTAGGTCAAATCTCCTTGGA	60.568	45.833	0.00	0.00	35.51	3.53
3030	3053	4.701956	CATACCCAATGTTTCACAGTCC	57.298	45.455	0.00	0.00	0.00	3.85
3191	3214	1.492176	CATACCTGCCTCATCCCTTGT	59.508	52.381	0.00	0.00	0.00	3.16
3396	3419	2.743928	GAGTGCAAGGAGTGGCCG	60.744	66.667	0.00	0.00	43.43	6.13
3831	3854	5.365619	AGTTGTCACTAGAAAACCGTTGAT	58.634	37.500	0.00	0.00	41.98	2.57
3832	3855	5.820947	AGTTGTCACTAGAAAACCGTTGATT	59.179	36.000	0.00	0.00	41.98	2.57
3833	3856	6.987992	AGTTGTCACTAGAAAACCGTTGATTA	59.012	34.615	0.00	0.00	41.98	1.75
3834	3857	7.170998	AGTTGTCACTAGAAAACCGTTGATTAG	59.829	37.037	0.00	0.00	41.98	1.73
3835	3858	5.407387	TGTCACTAGAAAACCGTTGATTAGC	59.593	40.000	0.00	0.00	0.00	3.09
3836	3859	4.933400	TCACTAGAAAACCGTTGATTAGCC	59.067	41.667	0.00	0.00	0.00	3.93
3837	3860	4.935808	CACTAGAAAACCGTTGATTAGCCT	59.064	41.667	0.00	0.00	0.00	4.58
3838	3861	5.411669	CACTAGAAAACCGTTGATTAGCCTT	59.588	40.000	0.00	0.00	0.00	4.35
3839	3862	6.002082	ACTAGAAAACCGTTGATTAGCCTTT	58.998	36.000	0.00	0.00	0.00	3.11
3840	3863	5.784578	AGAAAACCGTTGATTAGCCTTTT	57.215	34.783	0.00	0.00	0.00	2.27
3841	3864	5.769367	AGAAAACCGTTGATTAGCCTTTTC	58.231	37.500	0.00	0.00	0.00	2.29
3842	3865	4.514781	AAACCGTTGATTAGCCTTTTCC	57.485	40.909	0.00	0.00	0.00	3.13
3843	3866	2.443416	ACCGTTGATTAGCCTTTTCCC	58.557	47.619	0.00	0.00	0.00	3.97
3844	3867	1.749063	CCGTTGATTAGCCTTTTCCCC	59.251	52.381	0.00	0.00	0.00	4.81
3845	3868	1.749063	CGTTGATTAGCCTTTTCCCCC	59.251	52.381	0.00	0.00	0.00	5.40
4034	4431	9.965824	CATCTGTGGTTAAGTTACAAATTTTCT	57.034	29.630	0.00	0.00	0.00	2.52
4104	4502	2.480419	GGTGAATCGTTGGAACACTGAG	59.520	50.000	0.00	0.00	39.29	3.35
4195	4593	1.342819	AAGCAGAAGAGAGTTGCTCGT	59.657	47.619	0.00	0.00	46.72	4.18
4199	4597	6.527788	AAGCAGAAGAGAGTTGCTCGTTTAC	61.528	44.000	0.00	0.00	46.72	2.01
4229	4627	1.156736	CCGAGCGAAAACCAGATTGT	58.843	50.000	0.00	0.00	0.00	2.71
4264	4662	0.885879	GAACCGGGTGAAAACCATCC	59.114	55.000	6.32	0.00	42.82	3.51
4325	4723	2.203938	TCCAAAGAGGGCCTCGGT	60.204	61.111	27.11	16.84	38.24	4.69
4335	4733	2.581354	GCCTCGGTGAGACAGCAT	59.419	61.111	0.00	0.00	0.00	3.79
4401	4799	2.609747	TCCCTACACTCTGAGCAAACT	58.390	47.619	4.19	0.00	0.00	2.66
4405	4803	4.021016	CCCTACACTCTGAGCAAACTACTT	60.021	45.833	4.19	0.00	0.00	2.24
4406	4804	5.511545	CCCTACACTCTGAGCAAACTACTTT	60.512	44.000	4.19	0.00	0.00	2.66
4412	4810	5.525378	ACTCTGAGCAAACTACTTTGACTTG	59.475	40.000	4.19	0.00	39.43	3.16
4415	4813	3.555966	AGCAAACTACTTTGACTTGGCT	58.444	40.909	0.00	0.00	39.43	4.75
4421	4819	3.646637	ACTACTTTGACTTGGCTGTAGGT	59.353	43.478	0.00	0.00	33.73	3.08
4442	4840	0.599558	ATCGTCGACTCAACCCGAAA	59.400	50.000	14.70	0.00	36.50	3.46
4452	4850	3.055094	ACTCAACCCGAAATGTAGCAGAT	60.055	43.478	0.00	0.00	0.00	2.90
4553	4953	1.341482	TGAAGGACAAAACCAGGCACA	60.341	47.619	0.00	0.00	0.00	4.57
4555	4955	0.258774	AGGACAAAACCAGGCACAGT	59.741	50.000	0.00	0.00	0.00	3.55
4574	4974	0.676466	TTGGCGCCACGAAAGATCAT	60.676	50.000	32.95	0.00	0.00	2.45
4579	4979	1.860950	CGCCACGAAAGATCATCGAAT	59.139	47.619	22.69	3.72	42.76	3.34
4581	4982	2.866156	GCCACGAAAGATCATCGAATGA	59.134	45.455	22.69	0.00	42.76	2.57
4586	4987	4.115516	CGAAAGATCATCGAATGACCACT	58.884	43.478	13.79	0.00	43.01	4.00
4641	5042	1.278238	CCGCAACTTCGACTCCATAC	58.722	55.000	0.00	0.00	0.00	2.39
4686	5087	1.582968	GGACACGCCGTACAAGAGA	59.417	57.895	0.00	0.00	0.00	3.10
4687	5088	0.456312	GGACACGCCGTACAAGAGAG	60.456	60.000	0.00	0.00	0.00	3.20
4688	5089	0.240411	GACACGCCGTACAAGAGAGT	59.760	55.000	0.00	0.00	0.00	3.24
4697	5098	2.998670	CGTACAAGAGAGTCGACTACCA	59.001	50.000	20.09	0.00	0.00	3.25

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
24	25	3.270027	TGAGCGGTAACTGATCAATTGG	58.730	45.455	5.42	0.00	33.81	3.16
115	122	2.290260	TGTCCTGCACCCATCTTAACAG	60.290	50.000	0.00	0.00	0.00	3.16
163	170	7.461107	CAAGACAACTTCAGTTACGAAGAAAA	58.539	34.615	18.31	0.00	44.32	2.29
303	311	2.116533	GGCCCAATAAACCCGGACG	61.117	63.158	0.73	0.00	0.00	4.79
383	391	1.607178	CTGATTGGTTGCTGCCCCA	60.607	57.895	4.23	4.23	0.00	4.96
395	403	8.461222	TGCCATGACTACTTTAAATTCTGATTG	58.539	33.333	0.00	0.00	0.00	2.67
403	411	5.450965	GCTGCATGCCATGACTACTTTAAAT	60.451	40.000	16.68	0.00	35.15	1.40
428	436	0.899717	GAAGGGGAAATGTGCAGCCA	60.900	55.000	0.00	0.00	0.00	4.75
534	542	4.690748	TCAATTGGTTAGACTTTCTCGCAG	59.309	41.667	5.42	0.00	0.00	5.18
544	552	4.495844	GGCTATGCGTTCAATTGGTTAGAC	60.496	45.833	5.42	0.00	0.00	2.59
545	553	3.625764	GGCTATGCGTTCAATTGGTTAGA	59.374	43.478	5.42	0.00	0.00	2.10
606	616	1.448013	GGCCCACGAGACAACTAGC	60.448	63.158	0.00	0.00	0.00	3.42
614	624	0.034863	GGTTTATTGGGCCCACGAGA	60.035	55.000	28.70	11.05	0.00	4.04
660	670	3.833559	AGATCACCCTTCCCATTTTGT	57.166	42.857	0.00	0.00	0.00	2.83
679	689	3.254411	GTGCTTGGAAGAGGGAAGAAAAG	59.746	47.826	0.00	0.00	0.00	2.27
751	761	8.250332	GCCAAAACATATCTCCAAGAAATACAA	58.750	33.333	0.00	0.00	0.00	2.41
752	762	7.395772	TGCCAAAACATATCTCCAAGAAATACA	59.604	33.333	0.00	0.00	0.00	2.29
831	841	3.711190	AGCCCATGAAAGTTCTTTTTGGT	59.289	39.130	18.14	6.54	0.00	3.67
871	881	0.947244	ACACGAAGAGCCTGCAAAAG	59.053	50.000	0.00	0.00	0.00	2.27
1278	1290	7.040409	GGGTTCTTAACAATCTCTTGACACATT	60.040	37.037	0.00	0.00	36.20	2.71
1457	1469	5.589050	AGAAAACAGTTTGACTTAGGGACAC	59.411	40.000	0.00	0.00	0.00	3.67
1679	1694	8.081633	TCTACTGTGCTATTTCAAAACCAAATG	58.918	33.333	0.00	0.00	0.00	2.32
1924	1945	5.163513	CAGTAAAAAGCATGGTTGTGATCC	58.836	41.667	11.56	0.00	0.00	3.36
2026	2047	6.182039	AGACAACACCAAATACAATGATCG	57.818	37.500	0.00	0.00	0.00	3.69
2343	2364	9.703892	AAATATAAAATGCAAGTTGTGTTAGCA	57.296	25.926	4.48	0.00	39.79	3.49
2365	2386	3.025978	CAGCCCCATGAAGCTCAAAATA	58.974	45.455	6.48	0.00	37.18	1.40
2366	2387	1.829222	CAGCCCCATGAAGCTCAAAAT	59.171	47.619	6.48	0.00	37.18	1.82
2554	2575	3.262420	GTGCCCATATATGTTAGCCTCG	58.738	50.000	11.73	0.00	0.00	4.63
2568	2589	1.966845	AGTTACTGGTAGGTGCCCAT	58.033	50.000	0.00	0.00	0.00	4.00
2745	2766	4.099881	AGAAGAAACTTGCCATTTTCAGCA	59.900	37.500	3.89	0.00	34.68	4.41
2835	2856	5.222079	TGTACATGTTGCTTGACCTAGAA	57.778	39.130	2.30	0.00	0.00	2.10
3030	3053	0.604511	ACCTACGGCTTGTTTTCCCG	60.605	55.000	0.00	0.00	46.97	5.14
3191	3214	1.414866	TAGAACAGTGCCACCAGCCA	61.415	55.000	0.00	0.00	42.71	4.75
3396	3419	1.294659	CCTTGTTGCGGAGAGTCAGC	61.295	60.000	0.00	0.00	38.08	4.26
3609	3632	4.323417	GGTAGTCCATTGTGAACATGTCA	58.677	43.478	0.00	0.00	0.00	3.58
3842	3865	3.152341	CAGCAGCTATAAAATCAGGGGG	58.848	50.000	0.00	0.00	0.00	5.40
3843	3866	2.555757	GCAGCAGCTATAAAATCAGGGG	59.444	50.000	0.00	0.00	37.91	4.79
3844	3867	2.555757	GGCAGCAGCTATAAAATCAGGG	59.444	50.000	0.00	0.00	41.70	4.45
3845	3868	2.555757	GGGCAGCAGCTATAAAATCAGG	59.444	50.000	0.00	0.00	41.70	3.86
3846	3869	3.004106	GTGGGCAGCAGCTATAAAATCAG	59.996	47.826	0.00	0.00	41.70	2.90
3847	3870	2.951642	GTGGGCAGCAGCTATAAAATCA	59.048	45.455	0.00	0.00	41.70	2.57
4034	4431	3.701205	TTGCTGAGACAAGGCAAGATA	57.299	42.857	0.00	0.00	40.38	1.98
4035	4432	2.574006	TTGCTGAGACAAGGCAAGAT	57.426	45.000	0.00	0.00	40.38	2.40
4195	4593	3.055963	TCGCTCGGTTTTCCATAGGTAAA	60.056	43.478	0.00	0.00	40.70	2.01
4199	4597	2.018542	TTCGCTCGGTTTTCCATAGG	57.981	50.000	0.00	0.00	40.70	2.57
4200	4598	3.425758	GGTTTTCGCTCGGTTTTCCATAG	60.426	47.826	0.00	0.00	40.70	2.23
4203	4601	0.664224	GGTTTTCGCTCGGTTTTCCA	59.336	50.000	0.00	0.00	40.70	3.53
4229	4627	4.141574	CCCGGTTCTCCATAATTAACTGGA	60.142	45.833	13.69	10.67	46.80	3.86
4335	4733	1.600485	GTGATGATGATGACGCATGCA	59.400	47.619	19.57	0.00	0.00	3.96
4348	4746	3.541242	CTCTAGGGGAGGAGTGATGAT	57.459	52.381	0.00	0.00	38.35	2.45
4401	4799	3.644265	TCACCTACAGCCAAGTCAAAGTA	59.356	43.478	0.00	0.00	0.00	2.24
4405	4803	2.353704	CGATCACCTACAGCCAAGTCAA	60.354	50.000	0.00	0.00	0.00	3.18
4406	4804	1.204704	CGATCACCTACAGCCAAGTCA	59.795	52.381	0.00	0.00	0.00	3.41
4412	4810	0.248539	GTCGACGATCACCTACAGCC	60.249	60.000	0.00	0.00	0.00	4.85
4415	4813	2.103537	TGAGTCGACGATCACCTACA	57.896	50.000	10.46	0.00	0.00	2.74
4421	4819	0.956902	TCGGGTTGAGTCGACGATCA	60.957	55.000	10.46	6.66	0.00	2.92
4442	4840	1.134580	AGCTTCACGCATCTGCTACAT	60.135	47.619	0.09	0.00	42.61	2.29
4452	4850	2.741759	TCTTCATGTAGCTTCACGCA	57.258	45.000	0.00	0.00	42.61	5.24
4499	4899	1.135139	GATTCGAGGCTGCACTGTCTA	59.865	52.381	0.50	0.00	0.00	2.59
4513	4913	2.420372	CAGAGTTCTCCGTCAGATTCGA	59.580	50.000	0.00	0.00	0.00	3.71
4553	4953	1.298859	GATCTTTCGTGGCGCCAACT	61.299	55.000	34.66	10.58	0.00	3.16
4555	4955	0.676466	ATGATCTTTCGTGGCGCCAA	60.676	50.000	34.66	15.23	0.00	4.52
4574	4974	0.955428	GGCTGCAAGTGGTCATTCGA	60.955	55.000	0.50	0.00	35.30	3.71
4579	4979	1.227943	GACTGGCTGCAAGTGGTCA	60.228	57.895	15.75	0.00	35.30	4.02
4581	4982	0.607489	GATGACTGGCTGCAAGTGGT	60.607	55.000	15.75	2.25	35.30	4.16
4586	4987	2.483013	GGTATACGATGACTGGCTGCAA	60.483	50.000	0.50	0.00	0.00	4.08
4627	5028	4.062991	GTTTGTTGGTATGGAGTCGAAGT	58.937	43.478	0.00	0.00	0.00	3.01
4641	5042	1.281656	GCCTCGGTTCGTTTGTTGG	59.718	57.895	0.00	0.00	0.00	3.77
4678	5079	4.011966	TGTGGTAGTCGACTCTCTTGTA	57.988	45.455	23.89	0.00	0.00	2.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.