AutoCloner

Multiple sequence alignment - TraesCS3B01G149700

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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	TraesCS3B01G149700	chr3B	100.000	2785	0	0	1	2785	141004490	141001706	0.000000e+00	5144.0
1	TraesCS3B01G149700	chr3B	85.806	155	22	0	1511	1665	71173110	71172956	6.170000e-37	165.0
2	TraesCS3B01G149700	chr3A	93.728	1403	57	15	748	2135	107566990	107565604	0.000000e+00	2074.0
3	TraesCS3B01G149700	chr3A	91.721	616	47	2	2174	2785	107557848	107557233	0.000000e+00	852.0
4	TraesCS3B01G149700	chr3D	94.714	1135	45	7	748	1871	91387411	91386281	0.000000e+00	1749.0
5	TraesCS3B01G149700	chr3D	87.500	432	33	11	2174	2589	91384772	91384346	1.940000e-131	479.0
6	TraesCS3B01G149700	chr2D	89.946	746	49	10	1	721	621853617	621852873	0.000000e+00	939.0
7	TraesCS3B01G149700	chr2D	86.275	459	60	2	265	721	180454632	180454175	1.930000e-136	496.0
8	TraesCS3B01G149700	chr7B	89.257	754	49	14	1	725	714212606	714213356	0.000000e+00	915.0
9	TraesCS3B01G149700	chr7B	89.037	748	54	11	1	721	648196882	648197628	0.000000e+00	902.0
10	TraesCS3B01G149700	chr7B	88.874	746	57	9	1	721	685965125	685965869	0.000000e+00	894.0
11	TraesCS3B01G149700	chr7B	85.985	264	13	7	484	723	567538700	567538963	7.650000e-66	261.0
12	TraesCS3B01G149700	chr7B	88.199	161	19	0	1507	1667	594179386	594179226	2.830000e-45	193.0
13	TraesCS3B01G149700	chr4A	88.993	745	55	11	2	721	738840694	738841436	0.000000e+00	896.0
14	TraesCS3B01G149700	chr2B	88.800	750	57	6	1	724	196663553	196662805	0.000000e+00	894.0
15	TraesCS3B01G149700	chr2B	88.800	750	55	5	1	722	740843829	740843081	0.000000e+00	893.0
16	TraesCS3B01G149700	chr2B	93.651	126	8	0	600	725	765227444	765227319	3.660000e-44	189.0
17	TraesCS3B01G149700	chr1B	88.755	747	59	9	1	723	12149270	12150015	0.000000e+00	891.0
18	TraesCS3B01G149700	chr6B	88.514	740	59	10	1	715	692121101	692120363	0.000000e+00	872.0
19	TraesCS3B01G149700	chr6B	88.060	737	61	12	1	712	691936310	691937044	0.000000e+00	848.0
20	TraesCS3B01G149700	chr6B	90.893	560	46	5	170	725	30945401	30944843	0.000000e+00	747.0
21	TraesCS3B01G149700	chr6B	87.914	513	51	7	210	721	701358249	701357747	6.640000e-166	593.0
22	TraesCS3B01G149700	chr5B	85.515	573	47	13	187	723	700431033	700431605	1.450000e-157	566.0
23	TraesCS3B01G149700	chr7D	85.435	460	63	3	265	721	100253774	100254232	2.510000e-130	475.0
24	TraesCS3B01G149700	chr7D	79.556	225	43	3	1050	1274	549960502	549960281	1.030000e-34	158.0
25	TraesCS3B01G149700	chr7D	77.091	275	58	3	1048	1321	549881853	549881583	1.340000e-33	154.0
26	TraesCS3B01G149700	chr5D	83.047	466	62	15	265	722	37807943	37807487	9.290000e-110	407.0
27	TraesCS3B01G149700	chrUn	79.556	225	43	3	1050	1274	282920513	282920734	1.030000e-34	158.0
28	TraesCS3B01G149700	chrUn	89.908	109	10	1	2322	2429	199871356	199871248	3.740000e-29	139.0
29	TraesCS3B01G149700	chrUn	89.908	109	10	1	2322	2429	199901276	199901168	3.740000e-29	139.0
30	TraesCS3B01G149700	chrUn	89.908	109	10	1	2322	2429	220754744	220754852	3.740000e-29	139.0
31	TraesCS3B01G149700	chrUn	89.908	109	10	1	2322	2429	260641809	260641917	3.740000e-29	139.0
32	TraesCS3B01G149700	chrUn	89.908	109	10	1	2322	2429	282092575	282092683	3.740000e-29	139.0
33	TraesCS3B01G149700	chrUn	89.908	109	10	1	2322	2429	293587378	293587270	3.740000e-29	139.0
34	TraesCS3B01G149700	chrUn	89.908	109	10	1	2322	2429	293589142	293589034	3.740000e-29	139.0
35	TraesCS3B01G149700	chrUn	89.908	109	10	1	2322	2429	370055970	370055862	3.740000e-29	139.0
36	TraesCS3B01G149700	chrUn	89.908	109	10	1	2322	2429	384489453	384489345	3.740000e-29	139.0
37	TraesCS3B01G149700	chr4D	88.158	76	9	0	1763	1838	10744802	10744877	1.060000e-14	91.6

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	TraesCS3B01G149700	chr3B	141001706	141004490	2784	True	5144	5144	100.000	1	2785	1	chr3B.!!$R2	2784
1	TraesCS3B01G149700	chr3A	107565604	107566990	1386	True	2074	2074	93.728	748	2135	1	chr3A.!!$R2	1387
2	TraesCS3B01G149700	chr3A	107557233	107557848	615	True	852	852	91.721	2174	2785	1	chr3A.!!$R1	611
3	TraesCS3B01G149700	chr3D	91384346	91387411	3065	True	1114	1749	91.107	748	2589	2	chr3D.!!$R1	1841
4	TraesCS3B01G149700	chr2D	621852873	621853617	744	True	939	939	89.946	1	721	1	chr2D.!!$R2	720
5	TraesCS3B01G149700	chr7B	714212606	714213356	750	False	915	915	89.257	1	725	1	chr7B.!!$F4	724
6	TraesCS3B01G149700	chr7B	648196882	648197628	746	False	902	902	89.037	1	721	1	chr7B.!!$F2	720
7	TraesCS3B01G149700	chr7B	685965125	685965869	744	False	894	894	88.874	1	721	1	chr7B.!!$F3	720
8	TraesCS3B01G149700	chr4A	738840694	738841436	742	False	896	896	88.993	2	721	1	chr4A.!!$F1	719
9	TraesCS3B01G149700	chr2B	196662805	196663553	748	True	894	894	88.800	1	724	1	chr2B.!!$R1	723
10	TraesCS3B01G149700	chr2B	740843081	740843829	748	True	893	893	88.800	1	722	1	chr2B.!!$R2	721
11	TraesCS3B01G149700	chr1B	12149270	12150015	745	False	891	891	88.755	1	723	1	chr1B.!!$F1	722
12	TraesCS3B01G149700	chr6B	692120363	692121101	738	True	872	872	88.514	1	715	1	chr6B.!!$R2	714
13	TraesCS3B01G149700	chr6B	691936310	691937044	734	False	848	848	88.060	1	712	1	chr6B.!!$F1	711
14	TraesCS3B01G149700	chr6B	30944843	30945401	558	True	747	747	90.893	170	725	1	chr6B.!!$R1	555
15	TraesCS3B01G149700	chr6B	701357747	701358249	502	True	593	593	87.914	210	721	1	chr6B.!!$R3	511
16	TraesCS3B01G149700	chr5B	700431033	700431605	572	False	566	566	85.515	187	723	1	chr5B.!!$F1	536

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
763	806	0.036294	CCCCAGAGAAACCGGACTTC	60.036	60.0	9.46	10.88	0.0	3.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1831	1894	0.110486	TTGAGGCCTTCCGCTTCTTT	59.89	50.0	6.77	0.0	43.82	2.52	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
54	55	6.331369	AGTTGATGACGTGGATTTGAATTT	57.669	33.333	0.00	0.00	0.00	1.82
63	64	4.327898	CGTGGATTTGAATTTTGCATCTGG	59.672	41.667	0.00	0.00	0.00	3.86
179	184	1.616865	AGATTGTCCAGTTCGAACCGA	59.383	47.619	24.22	16.92	0.00	4.69
183	188	0.388263	GTCCAGTTCGAACCGACTCC	60.388	60.000	26.90	10.75	34.89	3.85
185	190	1.171308	CCAGTTCGAACCGACTCCTA	58.829	55.000	24.22	0.00	34.89	2.94
251	257	0.663688	TTTCAGCCAAAACGCGCTAA	59.336	45.000	5.73	0.00	32.92	3.09
399	408	9.778741	TTCTACACATAGAGTTCAATGAAAACT	57.221	29.630	0.00	3.03	38.69	2.66
400	409	9.778741	TCTACACATAGAGTTCAATGAAAACTT	57.221	29.630	0.00	0.00	37.10	2.66
430	439	8.230486	GGTTGTGATAGTTTGAGAAGTAACATG	58.770	37.037	0.00	0.00	29.66	3.21
478	487	2.347731	GAGCGAGGTGGGACTAAAAAG	58.652	52.381	0.00	0.00	0.00	2.27
480	489	1.610886	GCGAGGTGGGACTAAAAAGCT	60.611	52.381	0.00	0.00	0.00	3.74
502	520	5.418209	GCTACTGTCAACTAGGAACCTCTAA	59.582	44.000	0.00	0.00	0.00	2.10
508	526	5.359292	GTCAACTAGGAACCTCTAATACCGT	59.641	44.000	0.00	0.00	0.00	4.83
510	528	6.096001	TCAACTAGGAACCTCTAATACCGTTC	59.904	42.308	0.00	0.00	35.05	3.95
537	555	3.674138	GCACGAACCGATACTAAAGGTGA	60.674	47.826	0.00	0.00	38.44	4.02
589	607	3.391506	ACAACCACTTTAGTACCGGTC	57.608	47.619	12.40	2.55	0.00	4.79
654	697	1.557371	TGGACCGGCACTAATGATCAA	59.443	47.619	0.00	0.00	0.00	2.57
667	710	6.588204	ACTAATGATCAAATTAGTGCCGGTA	58.412	36.000	17.16	0.00	46.64	4.02
703	746	5.045942	TGGGACTATTGTGCTTCACATTAGA	60.046	40.000	24.01	8.68	44.33	2.10
735	778	9.687210	TTTCTACTAGTGTATGTTTGTACTGTG	57.313	33.333	5.39	0.00	0.00	3.66
736	779	8.400184	TCTACTAGTGTATGTTTGTACTGTGT	57.600	34.615	5.39	0.00	0.00	3.72
737	780	8.853126	TCTACTAGTGTATGTTTGTACTGTGTT	58.147	33.333	5.39	0.00	0.00	3.32
740	783	9.820725	ACTAGTGTATGTTTGTACTGTGTTAAA	57.179	29.630	0.00	0.00	0.00	1.52
743	786	9.777575	AGTGTATGTTTGTACTGTGTTAAAAAC	57.222	29.630	0.00	0.00	0.00	2.43
744	787	9.012448	GTGTATGTTTGTACTGTGTTAAAAACC	57.988	33.333	0.00	0.00	0.00	3.27
745	788	8.189460	TGTATGTTTGTACTGTGTTAAAAACCC	58.811	33.333	0.00	0.00	0.00	4.11
746	789	5.963594	TGTTTGTACTGTGTTAAAAACCCC	58.036	37.500	0.00	0.00	0.00	4.95
763	806	0.036294	CCCCAGAGAAACCGGACTTC	60.036	60.000	9.46	10.88	0.00	3.01
812	856	2.063541	AACGCTCAACTTGCCAGTGC	62.064	55.000	0.00	0.00	31.60	4.40
882	928	8.564574	TGTTGTAATCTGTAAATTTGTCCTGTC	58.435	33.333	0.00	0.00	0.00	3.51
884	930	8.684386	TGTAATCTGTAAATTTGTCCTGTCAA	57.316	30.769	0.00	0.00	0.00	3.18
1098	1146	4.436998	GTGCTGTACGCCGAGGCT	62.437	66.667	12.70	0.00	39.32	4.58
1113	1161	2.432628	GCTGGGAAGGACGTCGTG	60.433	66.667	12.13	0.00	0.00	4.35
1122	1170	2.559785	GGACGTCGTGGACTTCCTA	58.440	57.895	9.92	0.00	44.34	2.94
1223	1271	0.109735	CTCTACAGCAGCGTCGACAA	60.110	55.000	17.16	0.00	0.00	3.18
1361	1409	0.454600	CTGCAAATCTTCCGCTGCAT	59.545	50.000	0.00	0.00	43.42	3.96
1403	1451	0.614979	AGGAGCTACGTGACCATGGT	60.615	55.000	19.89	19.89	0.00	3.55
1414	1462	0.899720	GACCATGGTAAGTGGGACGA	59.100	55.000	19.80	0.00	41.14	4.20
1548	1599	1.135199	GTGACGTACACGGTGATGGAT	60.135	52.381	16.29	0.00	44.95	3.41
1572	1623	2.586079	AAGATCGCGCCCATGTCG	60.586	61.111	0.00	0.00	0.00	4.35
1651	1702	0.603975	GGAGAAGACCGTGCAGCTTT	60.604	55.000	0.00	0.00	0.00	3.51
1707	1763	7.005380	GCAAATTGATCGTTCAGTTGATTTTG	58.995	34.615	18.75	13.14	32.68	2.44
1708	1764	7.306749	GCAAATTGATCGTTCAGTTGATTTTGT	60.307	33.333	18.75	0.00	32.68	2.83
1831	1894	0.824595	TCACCGACGTCTTCCTTGGA	60.825	55.000	14.70	0.00	0.00	3.53
1888	1953	3.550233	TAGTTGTCACTGCAGTCGAAGAC	60.550	47.826	18.64	20.73	46.07	3.01
1931	2994	0.036306	TCCTTGGGAAGAAGCGGAAC	59.964	55.000	0.00	0.00	0.00	3.62
1974	3188	1.577328	CTGCGGCGTCCTTGTTGATT	61.577	55.000	9.37	0.00	0.00	2.57
1976	3190	0.039527	GCGGCGTCCTTGTTGATTTT	60.040	50.000	9.37	0.00	0.00	1.82
2051	3266	7.925483	CAGGAAACAAAAACATGAATCCTGTTA	59.075	33.333	17.18	0.00	43.56	2.41
2055	3270	9.442047	AAACAAAAACATGAATCCTGTTAAACA	57.558	25.926	0.00	0.00	35.84	2.83
2079	3294	4.430407	CGTTTTCGTGGAAATGGTTTTG	57.570	40.909	0.00	0.00	38.65	2.44
2103	3318	5.295292	GTGAGGGAACATTCTATGATGTGTG	59.705	44.000	0.00	0.00	40.03	3.82
2104	3319	5.045651	TGAGGGAACATTCTATGATGTGTGT	60.046	40.000	0.00	0.00	40.03	3.72
2135	3350	2.031683	CGCCTAAATCTTAAAGCGGTGG	59.968	50.000	0.00	0.00	39.89	4.61
2140	3355	1.024579	ATCTTAAAGCGGTGGCACGG	61.025	55.000	19.64	19.64	43.41	4.94
2161	3376	1.534163	CCGCATGTAGCAATCCTCATG	59.466	52.381	0.00	0.00	46.13	3.07
2167	3382	0.394192	TAGCAATCCTCATGGGCTCG	59.606	55.000	0.00	0.00	36.10	5.03
2169	3384	1.153107	CAATCCTCATGGGCTCGCA	60.153	57.895	0.00	0.00	34.39	5.10
2170	3385	1.147824	AATCCTCATGGGCTCGCAG	59.852	57.895	0.00	0.00	34.39	5.18
2172	3387	0.760567	ATCCTCATGGGCTCGCAGTA	60.761	55.000	0.00	0.00	34.39	2.74
2207	3482	5.969423	AGCATGTATGACAAATTTTCCTGG	58.031	37.500	0.00	0.00	0.00	4.45
2227	3502	0.116940	ACATGTGGGCAATTTCCCCT	59.883	50.000	10.95	0.00	45.97	4.79
2230	3505	0.039618	TGTGGGCAATTTCCCCTCTC	59.960	55.000	10.95	0.00	45.97	3.20
2298	3573	3.243877	CGAGGATTGAAATGTCTACGCAG	59.756	47.826	0.00	0.00	0.00	5.18
2338	3623	3.108847	TCCCCTGTTTTGGTTGTTCTT	57.891	42.857	0.00	0.00	0.00	2.52
2373	3658	3.998672	GTCGGGTCGAGGCAACCA	61.999	66.667	6.14	0.00	38.62	3.67
2416	3701	3.187700	GTTAGCAACATCCGAGACGAAT	58.812	45.455	0.00	0.00	0.00	3.34
2506	3793	5.047847	AGTCGATACAACCGTAATGAATGG	58.952	41.667	0.00	0.00	40.50	3.16
2532	3819	7.061673	GCTCAGTGATAAGTCTAATCGCTTATG	59.938	40.741	0.00	0.00	41.16	1.90
2590	3877	1.209261	AGCCCAAAACACACCAAAAGG	59.791	47.619	0.00	0.00	0.00	3.11
2594	3881	3.055458	CCCAAAACACACCAAAAGGTTCT	60.055	43.478	0.00	0.00	0.00	3.01
2645	3932	5.890985	TCATACAACATATTGGAAACAGGGG	59.109	40.000	0.00	0.00	44.54	4.79
2693	3981	4.858692	CCTTAAACATGTCGAAAATGGCAG	59.141	41.667	0.00	4.34	0.00	4.85
2696	3984	1.820519	ACATGTCGAAAATGGCAGCAT	59.179	42.857	12.56	0.00	0.00	3.79
2713	4001	2.489329	AGCATGACCAAATTTGAGACCG	59.511	45.455	19.86	4.87	0.00	4.79
2737	4025	1.146041	GCCCTATGCACCGACATGA	59.854	57.895	0.00	0.00	40.77	3.07
2742	4030	2.223021	CCTATGCACCGACATGAAAACG	60.223	50.000	0.00	0.00	0.00	3.60
2746	4034	2.041244	GCACCGACATGAAAACGTTTC	58.959	47.619	15.01	8.59	0.00	2.78
2780	4068	8.624019	TGCTATATAAGGGTATTAGAGGCATT	57.376	34.615	0.00	0.00	0.00	3.56

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
73	75	6.847421	ATAACTTAGTACAACTCCGGACTT	57.153	37.500	0.00	0.00	0.00	3.01
114	117	4.748102	GGACGAAAACTCATCTGTTACACA	59.252	41.667	0.00	0.00	0.00	3.72
396	405	7.506114	TCTCAAACTATCACAACCACTAAGTT	58.494	34.615	0.00	0.00	0.00	2.66
399	408	7.506114	ACTTCTCAAACTATCACAACCACTAA	58.494	34.615	0.00	0.00	0.00	2.24
400	409	7.062749	ACTTCTCAAACTATCACAACCACTA	57.937	36.000	0.00	0.00	0.00	2.74
430	439	7.859377	GCTAACAGAGTTTTTACCACCTTAAAC	59.141	37.037	0.00	0.00	0.00	2.01
478	487	3.764972	AGAGGTTCCTAGTTGACAGTAGC	59.235	47.826	0.00	0.00	0.00	3.58
480	489	7.559170	GGTATTAGAGGTTCCTAGTTGACAGTA	59.441	40.741	0.00	0.00	0.00	2.74
502	520	0.319083	TTCGTGCCACAGAACGGTAT	59.681	50.000	0.00	0.00	40.18	2.73
508	526	0.604073	TATCGGTTCGTGCCACAGAA	59.396	50.000	0.00	0.00	0.00	3.02
510	528	0.108804	AGTATCGGTTCGTGCCACAG	60.109	55.000	0.00	0.00	0.00	3.66
553	571	0.682532	TTGTTGCAGGCTGTGGACAA	60.683	50.000	17.16	19.26	0.00	3.18
556	574	1.827789	GGTTGTTGCAGGCTGTGGA	60.828	57.895	17.16	0.00	0.00	4.02
654	697	6.431852	AGTTTGTAACAATACCGGCACTAATT	59.568	34.615	0.00	0.00	0.00	1.40
667	710	6.294508	GCACAATAGTCCCAGTTTGTAACAAT	60.295	38.462	0.00	0.00	31.45	2.71
724	767	5.105432	TGGGGGTTTTTAACACAGTACAAAC	60.105	40.000	0.00	0.00	36.19	2.93
725	768	5.021458	TGGGGGTTTTTAACACAGTACAAA	58.979	37.500	0.00	0.00	36.19	2.83
726	769	4.607239	TGGGGGTTTTTAACACAGTACAA	58.393	39.130	0.00	0.00	36.19	2.41
727	770	4.079901	TCTGGGGGTTTTTAACACAGTACA	60.080	41.667	0.00	0.00	36.19	2.90
728	771	4.463070	TCTGGGGGTTTTTAACACAGTAC	58.537	43.478	0.00	0.00	36.19	2.73
729	772	4.412858	TCTCTGGGGGTTTTTAACACAGTA	59.587	41.667	0.00	0.00	36.19	2.74
730	773	3.203487	TCTCTGGGGGTTTTTAACACAGT	59.797	43.478	0.00	0.00	36.19	3.55
731	774	3.827722	TCTCTGGGGGTTTTTAACACAG	58.172	45.455	0.00	0.00	36.19	3.66
732	775	3.955524	TCTCTGGGGGTTTTTAACACA	57.044	42.857	0.00	0.00	36.19	3.72
733	776	4.202182	GGTTTCTCTGGGGGTTTTTAACAC	60.202	45.833	0.00	0.00	0.00	3.32
734	777	3.962063	GGTTTCTCTGGGGGTTTTTAACA	59.038	43.478	0.00	0.00	0.00	2.41
735	778	3.005050	CGGTTTCTCTGGGGGTTTTTAAC	59.995	47.826	0.00	0.00	0.00	2.01
736	779	3.224269	CGGTTTCTCTGGGGGTTTTTAA	58.776	45.455	0.00	0.00	0.00	1.52
737	780	2.489437	CCGGTTTCTCTGGGGGTTTTTA	60.489	50.000	0.00	0.00	38.86	1.52
738	781	1.699730	CGGTTTCTCTGGGGGTTTTT	58.300	50.000	0.00	0.00	0.00	1.94
739	782	0.178973	CCGGTTTCTCTGGGGGTTTT	60.179	55.000	0.00	0.00	38.86	2.43
740	783	1.063654	TCCGGTTTCTCTGGGGGTTT	61.064	55.000	0.00	0.00	42.62	3.27
741	784	1.462627	TCCGGTTTCTCTGGGGGTT	60.463	57.895	0.00	0.00	42.62	4.11
742	785	2.206036	TCCGGTTTCTCTGGGGGT	59.794	61.111	0.00	0.00	42.62	4.95
743	786	1.489560	AAGTCCGGTTTCTCTGGGGG	61.490	60.000	0.00	0.00	42.62	5.40
744	787	0.036294	GAAGTCCGGTTTCTCTGGGG	60.036	60.000	0.00	0.00	42.62	4.96
745	788	0.977395	AGAAGTCCGGTTTCTCTGGG	59.023	55.000	15.25	0.00	42.62	4.45
746	789	2.224305	ACAAGAAGTCCGGTTTCTCTGG	60.224	50.000	19.38	15.18	43.70	3.86
763	806	4.264253	TGATTCCCAGTGCAGATTACAAG	58.736	43.478	0.00	0.00	0.00	3.16
812	856	3.784701	ACGCGGGATATAGCTAGATTG	57.215	47.619	12.47	0.00	0.00	2.67
875	921	9.477484	AACGATAATACAAGATATTGACAGGAC	57.523	33.333	7.16	0.00	0.00	3.85
925	971	3.623060	GCATTGCCATGTATATACGAGGG	59.377	47.826	19.32	15.33	32.28	4.30
1098	1146	2.203523	TCCACGACGTCCTTCCCA	60.204	61.111	10.58	0.00	0.00	4.37
1113	1161	3.236047	GAGGAGGGAGAATAGGAAGTCC	58.764	54.545	0.00	0.00	0.00	3.85
1122	1170	1.965754	GCAGCGTGAGGAGGGAGAAT	61.966	60.000	0.00	0.00	0.00	2.40
1223	1271	0.733729	GATGTAGGTGTCGTCGAGCT	59.266	55.000	0.00	0.00	0.00	4.09
1372	1420	0.902531	TAGCTCCTGCAGTTGGGTAC	59.097	55.000	13.81	0.00	42.74	3.34
1403	1451	0.822944	TCCACACGTCGTCCCACTTA	60.823	55.000	0.00	0.00	0.00	2.24
1548	1599	2.184322	GGCGCGATCTTGAGGTCA	59.816	61.111	12.10	0.00	0.00	4.02
1572	1623	1.048724	TGGTGATCCCGGAGATGGTC	61.049	60.000	0.73	0.00	34.42	4.02
1707	1763	5.010617	TGCAGTCCTAATGAAAGGGAAAAAC	59.989	40.000	0.00	0.00	37.24	2.43
1708	1764	5.144100	TGCAGTCCTAATGAAAGGGAAAAA	58.856	37.500	0.00	0.00	37.24	1.94
1764	1827	4.326826	CTTCAGCATCTCCAAACCTTACA	58.673	43.478	0.00	0.00	0.00	2.41
1768	1831	1.615384	GCCTTCAGCATCTCCAAACCT	60.615	52.381	0.00	0.00	42.97	3.50
1807	1870	0.313043	GGAAGACGTCGGTGAGAACA	59.687	55.000	10.46	0.00	0.00	3.18
1831	1894	0.110486	TTGAGGCCTTCCGCTTCTTT	59.890	50.000	6.77	0.00	43.82	2.52
1891	1956	4.442706	GAAGTTGGTGAGAACAGTCAGAA	58.557	43.478	0.00	0.00	0.00	3.02
1892	1957	3.181465	GGAAGTTGGTGAGAACAGTCAGA	60.181	47.826	0.00	0.00	0.00	3.27
1894	1959	2.771943	AGGAAGTTGGTGAGAACAGTCA	59.228	45.455	0.00	0.00	0.00	3.41
1974	3188	5.008019	TGTTCAACAAAGCAAAGCAAACAAA	59.992	32.000	0.00	0.00	0.00	2.83
1976	3190	4.060900	TGTTCAACAAAGCAAAGCAAACA	58.939	34.783	0.00	0.00	0.00	2.83
2055	3270	3.786516	ACCATTTCCACGAAAACGTTT	57.213	38.095	7.96	7.96	35.11	3.60
2071	3286	4.482990	AGAATGTTCCCTCACAAAACCAT	58.517	39.130	0.00	0.00	0.00	3.55
2079	3294	5.295292	CACACATCATAGAATGTTCCCTCAC	59.705	44.000	0.00	0.00	37.78	3.51
2103	3318	3.279434	AGATTTAGGCGTGGGATCAAAC	58.721	45.455	0.00	0.00	0.00	2.93
2104	3319	3.644966	AGATTTAGGCGTGGGATCAAA	57.355	42.857	0.00	0.00	0.00	2.69
2140	3355	0.815213	TGAGGATTGCTACATGCGGC	60.815	55.000	0.00	0.00	46.63	6.53
2149	3364	1.147824	CGAGCCCATGAGGATTGCT	59.852	57.895	0.00	0.00	38.24	3.91
2150	3365	3.741860	CGAGCCCATGAGGATTGC	58.258	61.111	0.00	0.00	38.24	3.56
2161	3376	1.142097	GAGTTCCTACTGCGAGCCC	59.858	63.158	0.00	0.00	33.84	5.19
2167	3382	1.276421	TGCTTCCAGAGTTCCTACTGC	59.724	52.381	0.00	0.00	33.84	4.40
2169	3384	3.177228	ACATGCTTCCAGAGTTCCTACT	58.823	45.455	0.00	0.00	37.31	2.57
2170	3385	3.618690	ACATGCTTCCAGAGTTCCTAC	57.381	47.619	0.00	0.00	0.00	3.18
2172	3387	3.776969	TCATACATGCTTCCAGAGTTCCT	59.223	43.478	0.00	0.00	0.00	3.36
2227	3502	3.168292	TGGAGCAGAGAGAATTGTGAGA	58.832	45.455	0.00	0.00	0.00	3.27
2230	3505	3.405831	TGTTGGAGCAGAGAGAATTGTG	58.594	45.455	0.00	0.00	0.00	3.33
2328	3613	3.554337	GCTCTCCGAACTAAGAACAACCA	60.554	47.826	0.00	0.00	0.00	3.67
2338	3623	1.549170	GACCCAAAGCTCTCCGAACTA	59.451	52.381	0.00	0.00	0.00	2.24
2416	3701	1.073373	ATCTAGCCTCGCTCCGCTA	59.927	57.895	0.00	0.00	40.44	4.26
2486	3773	3.807622	AGCCATTCATTACGGTTGTATCG	59.192	43.478	0.00	0.00	0.00	2.92
2506	3793	4.865776	AGCGATTAGACTTATCACTGAGC	58.134	43.478	2.63	0.00	0.00	4.26
2532	3819	1.009829	CAGCGAAGGAAGGCATGTAC	58.990	55.000	0.00	0.00	0.00	2.90
2590	3877	0.390472	CTCCTGAGGCGGTCAAGAAC	60.390	60.000	0.00	0.00	33.60	3.01
2604	3891	4.350816	TGTATGATGATAAACCCCCTCCTG	59.649	45.833	0.00	0.00	0.00	3.86
2618	3905	7.285172	CCCTGTTTCCAATATGTTGTATGATGA	59.715	37.037	1.26	0.00	33.36	2.92
2619	3906	7.428020	CCCTGTTTCCAATATGTTGTATGATG	58.572	38.462	1.26	0.00	33.36	3.07
2640	3927	6.730977	TCTCCATATTCTTATAGTTCCCCCTG	59.269	42.308	0.00	0.00	0.00	4.45
2645	3932	7.106890	GCCCTTCTCCATATTCTTATAGTTCC	58.893	42.308	0.00	0.00	0.00	3.62
2693	3981	2.228822	ACGGTCTCAAATTTGGTCATGC	59.771	45.455	17.90	3.58	0.00	4.06
2696	3984	1.606668	GCACGGTCTCAAATTTGGTCA	59.393	47.619	17.90	0.00	0.00	4.02
2707	3995	3.077519	ATAGGGCGTGCACGGTCTC	62.078	63.158	37.47	23.37	40.23	3.36

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.