AutoCloner

Multiple sequence alignment - TraesCS2D01G025200

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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	TraesCS2D01G025200	chr2D	100.000	2379	0	0	1	2379	10985657	10988035	0.000000e+00	4394.0
1	TraesCS2D01G025200	chr2D	81.540	948	86	24	784	1674	11029932	11030847	0.000000e+00	699.0
2	TraesCS2D01G025200	chr2D	89.397	481	27	9	1181	1655	11023141	11023603	3.410000e-163	584.0
3	TraesCS2D01G025200	chr2D	84.783	230	19	8	840	1055	11022764	11022991	1.430000e-52	217.0
4	TraesCS2D01G025200	chr2D	88.430	121	12	1	780	900	10986320	10986438	6.850000e-31	145.0
5	TraesCS2D01G025200	chr2D	88.430	121	12	1	664	782	10986436	10986556	6.850000e-31	145.0
6	TraesCS2D01G025200	chr2D	91.860	86	6	1	1084	1168	11022987	11023072	4.150000e-23	119.0
7	TraesCS2D01G025200	chr2D	86.905	84	11	0	691	774	11028076	11028159	7.000000e-16	95.3
8	TraesCS2D01G025200	chr2A	89.536	1510	95	19	27	1498	11649000	11650484	0.000000e+00	1855.0
9	TraesCS2D01G025200	chr2A	88.868	1051	68	16	482	1498	11690500	11691535	0.000000e+00	1247.0
10	TraesCS2D01G025200	chr2A	89.667	871	64	10	1511	2379	11695662	11696508	0.000000e+00	1086.0
11	TraesCS2D01G025200	chr2A	91.810	464	30	6	27	487	11665374	11665832	7.170000e-180	640.0
12	TraesCS2D01G025200	chr2A	95.484	155	7	0	1469	1623	11933366	11933212	5.080000e-62	248.0
13	TraesCS2D01G025200	chr2A	87.395	119	11	1	664	782	11649740	11649854	1.480000e-27	134.0
14	TraesCS2D01G025200	chr2A	87.395	119	11	1	664	782	11690791	11690905	1.480000e-27	134.0
15	TraesCS2D01G025200	chr2A	95.122	41	2	0	291	331	761516885	761516925	5.490000e-07	65.8
16	TraesCS2D01G025200	chr2B	90.657	685	38	7	993	1655	16828870	16829550	0.000000e+00	887.0
17	TraesCS2D01G025200	chr2B	82.730	608	62	24	993	1587	16847684	16848261	3.530000e-138	501.0
18	TraesCS2D01G025200	chr2B	84.959	246	28	3	737	979	16828580	16828819	8.500000e-60	241.0
19	TraesCS2D01G025200	chr2B	87.923	207	22	2	780	986	16847446	16847649	8.500000e-60	241.0
20	TraesCS2D01G025200	chr2B	86.000	100	12	1	805	904	16847032	16847129	3.230000e-19	106.0
21	TraesCS2D01G025200	chr2B	85.294	68	9	1	290	357	24701575	24701509	4.240000e-08	69.4
22	TraesCS2D01G025200	chr2B	97.059	34	1	0	673	706	16846949	16846982	9.180000e-05	58.4
23	TraesCS2D01G025200	chr2B	96.875	32	1	0	2139	2170	77179693	77179662	1.000000e-03	54.7
24	TraesCS2D01G025200	chrUn	84.642	866	62	29	840	1655	12171136	12171980	0.000000e+00	797.0
25	TraesCS2D01G025200	chrUn	82.848	927	94	25	692	1570	12174227	12175136	0.000000e+00	771.0
26	TraesCS2D01G025200	chrUn	89.397	481	38	9	1181	1655	470920957	470920484	5.660000e-166	593.0
27	TraesCS2D01G025200	chrUn	84.036	332	20	13	840	1149	467992735	467993055	2.990000e-74	289.0
28	TraesCS2D01G025200	chrUn	89.916	119	12	0	664	782	12174314	12174432	1.140000e-33	154.0
29	TraesCS2D01G025200	chr1D	78.906	128	19	8	236	357	414742450	414742575	1.960000e-11	80.5
30	TraesCS2D01G025200	chr3B	86.957	69	9	0	345	413	571791796	571791864	7.050000e-11	78.7
31	TraesCS2D01G025200	chr5B	88.889	63	6	1	291	353	145473411	145473350	2.540000e-10	76.8
32	TraesCS2D01G025200	chr3A	97.368	38	0	1	2136	2172	422461104	422461067	1.970000e-06	63.9
33	TraesCS2D01G025200	chr3A	85.484	62	5	4	296	355	738948253	738948194	7.100000e-06	62.1
34	TraesCS2D01G025200	chr6B	97.059	34	1	0	380	413	35773802	35773769	9.180000e-05	58.4
35	TraesCS2D01G025200	chr5D	97.059	34	1	0	1870	1903	260847668	260847635	9.180000e-05	58.4
36	TraesCS2D01G025200	chr6A	100.000	30	0	0	2140	2169	322685174	322685203	3.300000e-04	56.5
37	TraesCS2D01G025200	chr4D	100.000	28	0	0	386	413	426620016	426619989	4.000000e-03	52.8

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	TraesCS2D01G025200	chr2D	10985657	10988035	2378	False	1561.333333	4394	92.286667	1	2379	3	chr2D.!!$F1	2378
1	TraesCS2D01G025200	chr2D	11028076	11030847	2771	False	397.150000	699	84.222500	691	1674	2	chr2D.!!$F3	983
2	TraesCS2D01G025200	chr2D	11022764	11023603	839	False	306.666667	584	88.680000	840	1655	3	chr2D.!!$F2	815
3	TraesCS2D01G025200	chr2A	11695662	11696508	846	False	1086.000000	1086	89.667000	1511	2379	1	chr2A.!!$F2	868
4	TraesCS2D01G025200	chr2A	11649000	11650484	1484	False	994.500000	1855	88.465500	27	1498	2	chr2A.!!$F4	1471
5	TraesCS2D01G025200	chr2A	11690500	11691535	1035	False	690.500000	1247	88.131500	482	1498	2	chr2A.!!$F5	1016
6	TraesCS2D01G025200	chr2B	16828580	16829550	970	False	564.000000	887	87.808000	737	1655	2	chr2B.!!$F1	918
7	TraesCS2D01G025200	chr2B	16846949	16848261	1312	False	226.600000	501	88.428000	673	1587	4	chr2B.!!$F2	914
8	TraesCS2D01G025200	chrUn	12171136	12175136	4000	False	574.000000	797	85.802000	664	1655	3	chrUn.!!$F2	991

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
398	401	1.394917	CTCGTGTAGGCACAGATTTGC	59.605	52.381	0.0	0.0	45.5	3.68	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1833	6846	0.322366	TGATGCAAATGTCTCCGGCA	60.322	50.0	0.0	0.0	39.03	5.69	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
84	85	6.633500	TTCAATGACGGATTTCAAGAAGTT	57.367	33.333	0.00	0.00	0.00	2.66
86	87	5.762711	TCAATGACGGATTTCAAGAAGTTCA	59.237	36.000	5.50	0.00	0.00	3.18
286	289	3.796717	CGCATATTTACTCTTCGTGCAGA	59.203	43.478	0.00	0.00	0.00	4.26
287	290	4.445718	CGCATATTTACTCTTCGTGCAGAT	59.554	41.667	0.00	0.00	0.00	2.90
337	340	2.810400	CGTGCCTCTCAGAAAAGGGAAA	60.810	50.000	1.54	0.00	34.51	3.13
338	341	3.222603	GTGCCTCTCAGAAAAGGGAAAA	58.777	45.455	1.54	0.00	34.51	2.29
339	342	3.004839	GTGCCTCTCAGAAAAGGGAAAAC	59.995	47.826	1.54	0.00	34.51	2.43
340	343	3.222603	GCCTCTCAGAAAAGGGAAAACA	58.777	45.455	1.54	0.00	32.98	2.83
341	344	3.636764	GCCTCTCAGAAAAGGGAAAACAA	59.363	43.478	1.54	0.00	32.98	2.83
342	345	4.281941	GCCTCTCAGAAAAGGGAAAACAAT	59.718	41.667	1.54	0.00	32.98	2.71
343	346	5.565637	GCCTCTCAGAAAAGGGAAAACAATC	60.566	44.000	1.54	0.00	32.98	2.67
398	401	1.394917	CTCGTGTAGGCACAGATTTGC	59.605	52.381	0.00	0.00	45.50	3.68
476	481	4.219725	TGCCAACTAATTTAGACCCTTTGC	59.780	41.667	10.39	2.86	0.00	3.68
649	654	5.163405	ACAGATAAACACCGACATGAGCTAT	60.163	40.000	0.00	0.00	0.00	2.97
725	797	7.383102	AGGATAAGACATCACAATGTTGAAC	57.617	36.000	0.00	0.00	46.20	3.18
766	838	6.316390	AGACGTTTGGATAAGAATTGATGACC	59.684	38.462	0.00	0.00	0.00	4.02
812	5682	9.799106	ATATCTAGCATTGGCACTAAAATTAGT	57.201	29.630	0.00	0.00	44.42	2.24
830	5700	7.730364	AATTAGTTGTTAGGATAAGGCATCG	57.270	36.000	0.00	0.00	34.12	3.84
867	5737	5.008316	GTGGAAGTAAATCAAGACGTTTGGT	59.992	40.000	9.54	1.71	0.00	3.67
988	5861	2.930682	GGATCAGTTTCAGTTAGGACGC	59.069	50.000	0.00	0.00	0.00	5.19
989	5862	3.585862	GATCAGTTTCAGTTAGGACGCA	58.414	45.455	0.00	0.00	0.00	5.24
991	5864	4.794278	TCAGTTTCAGTTAGGACGCATA	57.206	40.909	0.00	0.00	0.00	3.14
1171	6133	9.575783	TTTAGTTTTTGTTTTTGCGAGTAGAAT	57.424	25.926	0.00	0.00	0.00	2.40
1172	6134	7.449934	AGTTTTTGTTTTTGCGAGTAGAATG	57.550	32.000	0.00	0.00	0.00	2.67
1173	6135	7.254852	AGTTTTTGTTTTTGCGAGTAGAATGA	58.745	30.769	0.00	0.00	0.00	2.57
1174	6136	7.920682	AGTTTTTGTTTTTGCGAGTAGAATGAT	59.079	29.630	0.00	0.00	0.00	2.45
1175	6137	7.851822	TTTTGTTTTTGCGAGTAGAATGATC	57.148	32.000	0.00	0.00	0.00	2.92
1176	6138	6.552859	TTGTTTTTGCGAGTAGAATGATCA	57.447	33.333	0.00	0.00	0.00	2.92
1177	6139	6.169419	TGTTTTTGCGAGTAGAATGATCAG	57.831	37.500	0.09	0.00	0.00	2.90
1178	6140	5.122239	TGTTTTTGCGAGTAGAATGATCAGG	59.878	40.000	0.09	0.00	0.00	3.86
1192	6171	7.331026	AGAATGATCAGGAGTATTGTTTTCGA	58.669	34.615	0.09	0.00	0.00	3.71
1235	6214	2.101415	TCGGATGCCTGTGATAGACAAG	59.899	50.000	0.00	0.00	32.80	3.16
1387	6380	7.846311	ACCACTGAATCCATCTAGCCATATATA	59.154	37.037	0.00	0.00	0.00	0.86
1543	6543	5.519927	GGGCAATGTTCATTTGCTACAATAC	59.480	40.000	8.15	0.00	46.74	1.89
1658	6671	1.635487	TCATCCTGTTGCCTAAGCCTT	59.365	47.619	0.00	0.00	38.69	4.35
1674	6687	7.501844	CCTAAGCCTTAGCAAAGTCTAACTAT	58.498	38.462	5.94	0.00	43.56	2.12
1675	6688	7.439655	CCTAAGCCTTAGCAAAGTCTAACTATG	59.560	40.741	5.94	0.00	43.56	2.23
1692	6705	6.796705	AACTATGGTAGTTGTGTTTAGTGC	57.203	37.500	1.81	0.00	46.58	4.40
1700	6713	5.852282	AGTTGTGTTTAGTGCTTTTCCAT	57.148	34.783	0.00	0.00	0.00	3.41
1713	6726	8.635765	AGTGCTTTTCCATCTAAACTATTTCA	57.364	30.769	0.00	0.00	0.00	2.69
1730	6743	9.435688	AACTATTTCATCAAACCTTTATTTGCC	57.564	29.630	0.00	0.00	39.08	4.52
1757	6770	7.880713	TGTAGTATTTCAATGTAGTTTGCCAGA	59.119	33.333	0.00	0.00	0.00	3.86
1763	6776	0.466543	TGTAGTTTGCCAGACGGTGT	59.533	50.000	0.00	0.00	33.28	4.16
1778	6791	1.598962	GTGTGAAGCAGCTGGAGCA	60.599	57.895	17.12	0.00	45.16	4.26
1811	6824	3.508840	CCGCCCGGAGACATTTGC	61.509	66.667	0.73	0.00	37.50	3.68
1812	6825	2.745884	CGCCCGGAGACATTTGCA	60.746	61.111	0.73	0.00	0.00	4.08
1814	6827	1.729881	GCCCGGAGACATTTGCATC	59.270	57.895	0.73	0.00	0.00	3.91
1815	6828	1.031571	GCCCGGAGACATTTGCATCA	61.032	55.000	0.73	0.00	0.00	3.07
1824	6837	4.445452	GACATTTGCATCATGTCCAACT	57.555	40.909	21.28	0.00	43.29	3.16
1825	6838	4.418392	GACATTTGCATCATGTCCAACTC	58.582	43.478	21.28	4.03	43.29	3.01
1826	6839	3.194116	ACATTTGCATCATGTCCAACTCC	59.806	43.478	6.27	0.00	27.99	3.85
1827	6840	1.452110	TTGCATCATGTCCAACTCCG	58.548	50.000	0.00	0.00	0.00	4.63
1828	6841	0.612744	TGCATCATGTCCAACTCCGA	59.387	50.000	0.00	0.00	0.00	4.55
1829	6842	1.009829	GCATCATGTCCAACTCCGAC	58.990	55.000	0.00	0.00	0.00	4.79
1830	6843	1.675714	GCATCATGTCCAACTCCGACA	60.676	52.381	0.00	0.00	44.00	4.35
1832	6845	3.273434	CATCATGTCCAACTCCGACATT	58.727	45.455	0.80	0.00	46.36	2.71
1833	6846	3.417069	TCATGTCCAACTCCGACATTT	57.583	42.857	0.80	0.00	46.36	2.32
1834	6847	3.073678	TCATGTCCAACTCCGACATTTG	58.926	45.455	0.80	0.00	46.36	2.32
1835	6848	1.234821	TGTCCAACTCCGACATTTGC	58.765	50.000	0.00	0.00	35.35	3.68
1836	6849	0.521735	GTCCAACTCCGACATTTGCC	59.478	55.000	0.00	0.00	0.00	4.52
1837	6850	0.953471	TCCAACTCCGACATTTGCCG	60.953	55.000	0.00	0.00	0.00	5.69
1838	6851	1.501741	CAACTCCGACATTTGCCGG	59.498	57.895	0.00	0.00	46.57	6.13
1843	6856	4.277239	CGACATTTGCCGGAGACA	57.723	55.556	5.05	0.00	0.00	3.41
1844	6857	2.767536	CGACATTTGCCGGAGACAT	58.232	52.632	5.05	0.00	0.00	3.06
1845	6858	1.086696	CGACATTTGCCGGAGACATT	58.913	50.000	5.05	0.00	0.00	2.71
1846	6859	1.468520	CGACATTTGCCGGAGACATTT	59.531	47.619	5.05	0.00	0.00	2.32
1847	6860	2.728846	CGACATTTGCCGGAGACATTTG	60.729	50.000	5.05	0.00	0.00	2.32
1848	6861	1.067635	ACATTTGCCGGAGACATTTGC	60.068	47.619	5.05	0.00	0.00	3.68
1849	6862	1.067706	CATTTGCCGGAGACATTTGCA	60.068	47.619	5.05	0.00	0.00	4.08
1850	6863	1.255882	TTTGCCGGAGACATTTGCAT	58.744	45.000	5.05	0.00	0.00	3.96
1862	6875	5.961395	GACATTTGCATCATGTCCAAATC	57.039	39.130	21.28	4.03	43.29	2.17
1875	6888	1.198867	TCCAAATCCGACACGCAAATG	59.801	47.619	0.00	0.00	0.00	2.32
1880	6893	0.317160	TCCGACACGCAAATGTCTCT	59.683	50.000	10.12	0.00	45.73	3.10
1921	6934	1.890979	GGCAGACATGATGCGGGAG	60.891	63.158	17.32	0.00	44.80	4.30
1931	6944	2.631012	GATGCGGGAGGGAGCCATTT	62.631	60.000	0.00	0.00	0.00	2.32
1949	6962	4.512571	CCATTTAGATCATGCATGTGACGA	59.487	41.667	25.43	7.04	0.00	4.20
2019	7033	1.521681	GCATGTGCGTAGGGAGGAC	60.522	63.158	0.00	0.00	0.00	3.85
2022	7036	0.324368	ATGTGCGTAGGGAGGACAGA	60.324	55.000	0.00	0.00	42.87	3.41
2044	7058	2.489722	GAGAGAAAAAGGGACCATGCAC	59.510	50.000	0.00	0.00	0.00	4.57
2054	7068	1.203052	GGACCATGCACTTGATTGGTG	59.797	52.381	12.04	0.00	42.41	4.17
2087	7101	3.865700	CCTCCGGCAAAAGTGAAAC	57.134	52.632	0.00	0.00	0.00	2.78
2098	7112	4.448732	GCAAAAGTGAAACCATTGGATGAC	59.551	41.667	10.37	2.32	37.80	3.06
2103	7117	5.846203	AGTGAAACCATTGGATGACAAAAG	58.154	37.500	10.37	0.00	39.58	2.27
2105	7119	5.463061	GTGAAACCATTGGATGACAAAAGTG	59.537	40.000	10.37	0.00	43.46	3.16
2115	7129	3.478857	TGACAAAAGTGGTCCGTACAT	57.521	42.857	0.00	0.00	34.36	2.29
2123	7137	2.433239	AGTGGTCCGTACATTATGGTCC	59.567	50.000	0.00	1.87	41.60	4.46
2133	7147	8.030692	TCCGTACATTATGGTCCGAAAATATAG	58.969	37.037	0.00	0.00	36.23	1.31
2162	7176	1.079127	AGGGTTCGCGTTGGAGATG	60.079	57.895	5.77	0.00	0.00	2.90
2222	7236	6.438425	AGAGGTCATTTGTTAGCCATCATTTT	59.562	34.615	0.00	0.00	0.00	1.82
2270	7284	6.071108	TGTTATTCCATACCCAACATGTTTGG	60.071	38.462	23.58	23.58	36.51	3.28
2287	7301	1.838112	TGGCTGTCATGGAATTGGAC	58.162	50.000	0.00	0.00	0.00	4.02
2288	7302	1.075212	TGGCTGTCATGGAATTGGACA	59.925	47.619	0.00	0.00	39.09	4.02
2289	7303	2.291735	TGGCTGTCATGGAATTGGACAT	60.292	45.455	0.00	0.00	40.44	3.06
2290	7304	2.100252	GGCTGTCATGGAATTGGACATG	59.900	50.000	7.65	7.65	44.40	3.21
2326	7340	5.789643	AATTCCAGCAAATGTGTGTTACT	57.210	34.783	0.00	0.00	0.00	2.24
2372	7386	0.680618	TCACTTGCCTTGCCAAATGG	59.319	50.000	0.00	0.00	38.53	3.16

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
63	64	6.000891	TGAACTTCTTGAAATCCGTCATTG	57.999	37.500	0.00	0.00	0.00	2.82
67	68	5.862924	TCATGAACTTCTTGAAATCCGTC	57.137	39.130	0.00	0.00	29.14	4.79
265	268	5.694006	AGATCTGCACGAAGAGTAAATATGC	59.306	40.000	0.00	0.00	0.00	3.14
266	269	6.145209	CCAGATCTGCACGAAGAGTAAATATG	59.855	42.308	17.76	0.00	0.00	1.78
286	289	2.093288	TCTCGCTGAAGCAAATCCAGAT	60.093	45.455	2.79	0.00	42.21	2.90
287	290	1.276138	TCTCGCTGAAGCAAATCCAGA	59.724	47.619	2.79	0.00	42.21	3.86
315	318	0.674895	CCCTTTTCTGAGAGGCACGG	60.675	60.000	4.20	0.00	0.00	4.94
317	320	2.568623	TTCCCTTTTCTGAGAGGCAC	57.431	50.000	4.20	0.00	0.00	5.01
367	370	2.543238	GCCTACACGAGAGGTAAATCGG	60.543	54.545	0.00	0.00	43.12	4.18
368	371	2.098607	TGCCTACACGAGAGGTAAATCG	59.901	50.000	0.00	0.00	44.36	3.34
398	401	2.872245	TCAAAAGTGCCTCTCGTGAAAG	59.128	45.455	0.00	0.00	0.00	2.62
476	481	9.132521	CAAAACTTTCATGATAACTAAAGGCTG	57.867	33.333	0.00	0.00	34.07	4.85
716	788	7.581213	TGATTTACTTCCACTGTTCAACATT	57.419	32.000	0.00	0.00	0.00	2.71
725	797	5.924475	AACGTCTTGATTTACTTCCACTG	57.076	39.130	0.00	0.00	0.00	3.66
812	5682	2.846193	GGCGATGCCTTATCCTAACAA	58.154	47.619	0.00	0.00	46.69	2.83
830	5700	1.615392	ACTTCCACTTTTGAGCATGGC	59.385	47.619	0.00	0.00	31.87	4.40
900	5773	7.751732	TGCTTAATGCTGACACTATTACTTTG	58.248	34.615	0.00	0.00	43.37	2.77
908	5781	6.633500	AAAGTTTGCTTAATGCTGACACTA	57.367	33.333	0.00	0.00	43.37	2.74
988	5861	2.741517	TGTTCTTCATGCACCGTGTATG	59.258	45.455	20.17	20.17	41.03	2.39
989	5862	3.052455	TGTTCTTCATGCACCGTGTAT	57.948	42.857	0.00	0.00	0.00	2.29
991	5864	1.806542	GATGTTCTTCATGCACCGTGT	59.193	47.619	0.00	0.00	36.83	4.49
1171	6133	5.347635	CGTTCGAAAACAATACTCCTGATCA	59.652	40.000	0.00	0.00	34.93	2.92
1172	6134	5.347907	ACGTTCGAAAACAATACTCCTGATC	59.652	40.000	0.00	0.00	34.93	2.92
1173	6135	5.235516	ACGTTCGAAAACAATACTCCTGAT	58.764	37.500	0.00	0.00	34.93	2.90
1174	6136	4.624015	ACGTTCGAAAACAATACTCCTGA	58.376	39.130	0.00	0.00	34.93	3.86
1175	6137	4.985044	ACGTTCGAAAACAATACTCCTG	57.015	40.909	0.00	0.00	34.93	3.86
1176	6138	5.063060	GCATACGTTCGAAAACAATACTCCT	59.937	40.000	0.00	0.00	34.93	3.69
1177	6139	5.163933	TGCATACGTTCGAAAACAATACTCC	60.164	40.000	0.00	0.00	34.93	3.85
1178	6140	5.849858	TGCATACGTTCGAAAACAATACTC	58.150	37.500	0.00	0.00	34.93	2.59
1192	6171	3.950397	TCCCATCTTTTCTGCATACGTT	58.050	40.909	0.00	0.00	0.00	3.99
1235	6214	1.202348	GTTGGGCCATGTCTTGCTAAC	59.798	52.381	7.26	0.00	0.00	2.34
1543	6543	3.056607	AGCATTCGGAACAATGGGAAAAG	60.057	43.478	0.00	0.00	34.75	2.27
1658	6671	8.033038	CACAACTACCATAGTTAGACTTTGCTA	58.967	37.037	1.05	0.00	46.66	3.49
1674	6687	5.066764	GGAAAAGCACTAAACACAACTACCA	59.933	40.000	0.00	0.00	0.00	3.25
1675	6688	5.066764	TGGAAAAGCACTAAACACAACTACC	59.933	40.000	0.00	0.00	0.00	3.18
1713	6726	8.823220	ATACTACAGGCAAATAAAGGTTTGAT	57.177	30.769	3.74	0.00	40.64	2.57
1730	6743	8.039603	TGGCAAACTACATTGAAATACTACAG	57.960	34.615	0.00	0.00	31.84	2.74
1746	6759	0.753867	TCACACCGTCTGGCAAACTA	59.246	50.000	0.00	0.00	39.70	2.24
1757	6770	2.281070	CCAGCTGCTTCACACCGT	60.281	61.111	8.66	0.00	0.00	4.83
1763	6776	1.004080	GAGTGCTCCAGCTGCTTCA	60.004	57.895	8.66	1.84	42.66	3.02
1799	6812	3.329743	GACATGATGCAAATGTCTCCG	57.670	47.619	26.74	3.98	46.81	4.63
1808	6821	1.003003	TCGGAGTTGGACATGATGCAA	59.997	47.619	0.00	0.00	36.08	4.08
1809	6822	0.612744	TCGGAGTTGGACATGATGCA	59.387	50.000	0.00	0.00	0.00	3.96
1811	6824	2.385013	TGTCGGAGTTGGACATGATG	57.615	50.000	0.00	0.00	39.36	3.07
1819	6832	1.501741	CGGCAAATGTCGGAGTTGG	59.498	57.895	0.00	0.00	39.84	3.77
1826	6839	1.086696	AATGTCTCCGGCAAATGTCG	58.913	50.000	0.00	0.00	43.72	4.35
1827	6840	2.867429	CAAATGTCTCCGGCAAATGTC	58.133	47.619	0.00	0.00	0.00	3.06
1828	6841	1.067635	GCAAATGTCTCCGGCAAATGT	60.068	47.619	0.00	0.00	0.00	2.71
1829	6842	1.067706	TGCAAATGTCTCCGGCAAATG	60.068	47.619	0.00	0.00	0.00	2.32
1830	6843	1.255882	TGCAAATGTCTCCGGCAAAT	58.744	45.000	0.00	0.00	0.00	2.32
1831	6844	1.202114	GATGCAAATGTCTCCGGCAAA	59.798	47.619	0.00	0.00	38.08	3.68
1832	6845	0.810648	GATGCAAATGTCTCCGGCAA	59.189	50.000	0.00	0.00	38.08	4.52
1833	6846	0.322366	TGATGCAAATGTCTCCGGCA	60.322	50.000	0.00	0.00	39.03	5.69
1834	6847	1.027357	ATGATGCAAATGTCTCCGGC	58.973	50.000	0.00	0.00	0.00	6.13
1835	6848	2.019249	ACATGATGCAAATGTCTCCGG	58.981	47.619	11.53	0.00	32.83	5.14
1836	6849	3.329743	GACATGATGCAAATGTCTCCG	57.670	47.619	26.74	3.98	46.81	4.63
1845	6858	2.423185	GTCGGATTTGGACATGATGCAA	59.577	45.455	0.00	0.00	36.76	4.08
1846	6859	2.016318	GTCGGATTTGGACATGATGCA	58.984	47.619	0.00	0.00	34.56	3.96
1847	6860	2.016318	TGTCGGATTTGGACATGATGC	58.984	47.619	0.00	0.00	39.36	3.91
1848	6861	3.680642	GTGTCGGATTTGGACATGATG	57.319	47.619	0.00	0.00	45.29	3.07
1875	6888	7.709613	ACATAAAAACGGACATATACCAGAGAC	59.290	37.037	0.00	0.00	0.00	3.36
1880	6893	6.831727	CGACATAAAAACGGACATATACCA	57.168	37.500	0.00	0.00	0.00	3.25
1921	6934	2.867624	TGCATGATCTAAATGGCTCCC	58.132	47.619	0.00	0.00	0.00	4.30
1931	6944	4.861102	ATCTCGTCACATGCATGATCTA	57.139	40.909	32.75	11.74	0.00	1.98
1949	6962	7.497909	CCAACCGAACACTAAACCATAATATCT	59.502	37.037	0.00	0.00	0.00	1.98
2009	7023	3.655615	TTCTCTCTCTGTCCTCCCTAC	57.344	52.381	0.00	0.00	0.00	3.18
2019	7033	4.260170	CATGGTCCCTTTTTCTCTCTCTG	58.740	47.826	0.00	0.00	0.00	3.35
2022	7036	2.376518	TGCATGGTCCCTTTTTCTCTCT	59.623	45.455	0.00	0.00	0.00	3.10
2044	7058	3.366679	GGACATGCACTTCACCAATCAAG	60.367	47.826	0.00	0.00	0.00	3.02
2054	7068	1.028868	GGAGGCTGGACATGCACTTC	61.029	60.000	0.00	0.00	0.00	3.01
2084	7098	4.408596	ACCACTTTTGTCATCCAATGGTTT	59.591	37.500	0.00	0.00	35.70	3.27
2087	7101	3.056607	GGACCACTTTTGTCATCCAATGG	60.057	47.826	0.00	0.00	34.92	3.16
2098	7112	4.698304	ACCATAATGTACGGACCACTTTTG	59.302	41.667	0.00	0.00	0.00	2.44
2103	7117	2.800629	CGGACCATAATGTACGGACCAC	60.801	54.545	0.00	0.00	38.93	4.16
2105	7119	1.682854	TCGGACCATAATGTACGGACC	59.317	52.381	0.00	0.00	42.88	4.46
2115	7129	6.328148	ACCTCCACTATATTTTCGGACCATAA	59.672	38.462	0.00	0.00	0.00	1.90
2123	7137	5.527582	CCCTCAAACCTCCACTATATTTTCG	59.472	44.000	0.00	0.00	0.00	3.46
2133	7147	1.235281	GCGAACCCTCAAACCTCCAC	61.235	60.000	0.00	0.00	0.00	4.02
2162	7176	5.722021	TTTCTTTGGTTTCTCATAAGGGC	57.278	39.130	0.00	0.00	0.00	5.19
2204	7218	6.040209	TGCTCAAAATGATGGCTAACAAAT	57.960	33.333	0.00	0.00	0.00	2.32
2222	7236	7.162761	ACAATGAATTCCATGATTTTTGCTCA	58.837	30.769	12.90	0.00	35.24	4.26
2270	7284	2.756760	ACATGTCCAATTCCATGACAGC	59.243	45.455	13.46	0.00	41.84	4.40
2326	7340	6.577103	TGACAAGGTTGAATTTGCATAACAA	58.423	32.000	0.00	0.00	36.13	2.83

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.