AutoCloner

Multiple sequence alignment - TraesCS5D01G054400

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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	TraesCS5D01G054400	chr5D	100.000	2312	0	0	1	2312	51697338	51699649	0.000000e+00	4270.0
1	TraesCS5D01G054400	chr5D	85.614	994	69	31	601	1538	51674877	51675852	0.000000e+00	976.0
2	TraesCS5D01G054400	chr5D	89.212	723	40	17	642	1342	51637161	51637867	0.000000e+00	869.0
3	TraesCS5D01G054400	chr5D	85.314	892	71	38	597	1445	51851882	51852756	0.000000e+00	867.0
4	TraesCS5D01G054400	chr5D	86.441	767	65	23	597	1341	51860609	51861358	0.000000e+00	804.0
5	TraesCS5D01G054400	chr5D	91.095	539	32	3	1432	1970	565811846	565812368	0.000000e+00	715.0
6	TraesCS5D01G054400	chr5D	94.760	229	12	0	1529	1757	51676261	51676489	7.860000e-95	357.0
7	TraesCS5D01G054400	chr5D	90.875	263	19	2	2052	2309	565812366	565812628	4.730000e-92	348.0
8	TraesCS5D01G054400	chr5D	84.426	122	13	6	537	653	51611178	51611298	5.220000e-22	115.0
9	TraesCS5D01G054400	chr5D	97.368	38	1	0	395	432	51611062	51611099	5.330000e-07	65.8
10	TraesCS5D01G054400	chr5B	93.999	1783	75	20	1	1779	54709303	54711057	0.000000e+00	2671.0
11	TraesCS5D01G054400	chr5B	86.136	880	73	29	597	1439	54549077	54549944	0.000000e+00	904.0
12	TraesCS5D01G054400	chr5B	86.292	766	69	21	597	1342	54859867	54860616	0.000000e+00	800.0
13	TraesCS5D01G054400	chr5B	86.152	751	47	18	643	1342	54508304	54509048	0.000000e+00	758.0
14	TraesCS5D01G054400	chr5B	90.598	351	27	5	1467	1815	54550019	54550365	5.820000e-126	460.0
15	TraesCS5D01G054400	chr5B	96.774	93	3	0	1963	2055	676928098	676928190	3.080000e-34	156.0
16	TraesCS5D01G054400	chr5B	83.832	167	10	12	499	653	54507043	54507204	2.390000e-30	143.0
17	TraesCS5D01G054400	chr5A	92.750	1531	73	14	1	1524	40812317	40813816	0.000000e+00	2178.0
18	TraesCS5D01G054400	chr5A	87.027	740	50	12	642	1342	40628623	40629355	0.000000e+00	793.0
19	TraesCS5D01G054400	chr5A	86.126	764	73	22	597	1341	40934402	40935151	0.000000e+00	793.0
20	TraesCS5D01G054400	chr5A	86.126	764	73	22	597	1341	40968285	40969034	0.000000e+00	793.0
21	TraesCS5D01G054400	chr5A	86.126	764	73	22	597	1341	41005167	41005916	0.000000e+00	793.0
22	TraesCS5D01G054400	chr5A	89.474	456	38	4	1523	1970	40813981	40814434	3.330000e-158	568.0
23	TraesCS5D01G054400	chr5A	93.436	259	12	1	2052	2305	40814432	40814690	1.680000e-101	379.0
24	TraesCS5D01G054400	chr5A	93.258	178	12	0	1529	1706	40687325	40687502	1.760000e-66	263.0
25	TraesCS5D01G054400	chr7A	98.901	91	1	0	1965	2055	435835175	435835265	1.840000e-36	163.0
26	TraesCS5D01G054400	chr3B	97.849	93	2	0	1963	2055	793269110	793269202	6.610000e-36	161.0
27	TraesCS5D01G054400	chr2B	95.833	96	4	0	1959	2054	297438929	297439024	3.080000e-34	156.0
28	TraesCS5D01G054400	chr4B	95.833	96	3	1	1965	2060	250706577	250706483	1.110000e-33	154.0
29	TraesCS5D01G054400	chr2A	94.949	99	4	1	1969	2067	68249092	68248995	1.110000e-33	154.0
30	TraesCS5D01G054400	chrUn	95.789	95	3	1	1961	2055	31480462	31480555	3.980000e-33	152.0
31	TraesCS5D01G054400	chrUn	91.743	109	7	2	1958	2065	17270432	17270325	1.430000e-32	150.0
32	TraesCS5D01G054400	chr4A	92.453	106	7	1	1950	2054	697942097	697941992	1.430000e-32	150.0

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	TraesCS5D01G054400	chr5D	51697338	51699649	2311	False	4270.000000	4270	100.000000	1	2312	1	chr5D.!!$F2	2311
1	TraesCS5D01G054400	chr5D	51637161	51637867	706	False	869.000000	869	89.212000	642	1342	1	chr5D.!!$F1	700
2	TraesCS5D01G054400	chr5D	51851882	51852756	874	False	867.000000	867	85.314000	597	1445	1	chr5D.!!$F3	848
3	TraesCS5D01G054400	chr5D	51860609	51861358	749	False	804.000000	804	86.441000	597	1341	1	chr5D.!!$F4	744
4	TraesCS5D01G054400	chr5D	51674877	51676489	1612	False	666.500000	976	90.187000	601	1757	2	chr5D.!!$F6	1156
5	TraesCS5D01G054400	chr5D	565811846	565812628	782	False	531.500000	715	90.985000	1432	2309	2	chr5D.!!$F7	877
6	TraesCS5D01G054400	chr5B	54709303	54711057	1754	False	2671.000000	2671	93.999000	1	1779	1	chr5B.!!$F1	1778
7	TraesCS5D01G054400	chr5B	54859867	54860616	749	False	800.000000	800	86.292000	597	1342	1	chr5B.!!$F2	745
8	TraesCS5D01G054400	chr5B	54549077	54550365	1288	False	682.000000	904	88.367000	597	1815	2	chr5B.!!$F5	1218
9	TraesCS5D01G054400	chr5B	54507043	54509048	2005	False	450.500000	758	84.992000	499	1342	2	chr5B.!!$F4	843
10	TraesCS5D01G054400	chr5A	40812317	40814690	2373	False	1041.666667	2178	91.886667	1	2305	3	chr5A.!!$F6	2304
11	TraesCS5D01G054400	chr5A	40628623	40629355	732	False	793.000000	793	87.027000	642	1342	1	chr5A.!!$F1	700
12	TraesCS5D01G054400	chr5A	40934402	40935151	749	False	793.000000	793	86.126000	597	1341	1	chr5A.!!$F3	744
13	TraesCS5D01G054400	chr5A	40968285	40969034	749	False	793.000000	793	86.126000	597	1341	1	chr5A.!!$F4	744
14	TraesCS5D01G054400	chr5A	41005167	41005916	749	False	793.000000	793	86.126000	597	1341	1	chr5A.!!$F5	744

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
96	97	0.669077	GGGCGATATGACGAGTCTGT	59.331	55.0	4.78	0.0	35.09	3.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2037	3899	0.038744	ACCTACTCCCTCCGTTTCGA	59.961	55.0	0.0	0.0	0.0	3.71	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
45	46	7.120051	TCTACTAGAGTAGTCTTTCAGCCAAT	58.880	38.462	14.79	0.00	46.08	3.16
96	97	0.669077	GGGCGATATGACGAGTCTGT	59.331	55.000	4.78	0.00	35.09	3.41
129	130	6.352308	GCTCTAAGAGGGTGGACTTTCTAAAT	60.352	42.308	0.00	0.00	0.00	1.40
158	159	2.706190	AGGTACAGCCCTCCATTATGTC	59.294	50.000	0.00	0.00	38.26	3.06
170	171	7.628234	CCCTCCATTATGTCTGATAGCTAAAT	58.372	38.462	0.00	0.00	0.00	1.40
207	208	9.123709	CAAAATCTAAGATCTACGCTAGCTTAG	57.876	37.037	19.53	19.53	39.38	2.18
547	549	2.299867	GTGCACAAAATGGATGGACCTT	59.700	45.455	13.17	0.00	39.86	3.50
569	571	1.907255	AGCTCCACCCTGGTTAGTTAC	59.093	52.381	0.00	0.00	39.03	2.50
678	1796	7.727181	AGAGAACTTACAAAAAGTCAGAGCTA	58.273	34.615	0.00	0.00	0.00	3.32
680	1798	6.421202	AGAACTTACAAAAAGTCAGAGCTACG	59.579	38.462	0.00	0.00	0.00	3.51
949	2110	0.887836	CAGCACAGCTCAAAGCCTCA	60.888	55.000	0.00	0.00	43.77	3.86
1050	2256	2.264794	GCGGTGGTGATCTTCGGT	59.735	61.111	0.00	0.00	0.00	4.69
1179	2385	1.356124	AGGCACTGGTGAGACTCATT	58.644	50.000	8.73	0.00	37.18	2.57
1344	2553	2.755650	CTTTGTAGATATTCGGCCGCT	58.244	47.619	23.51	14.28	0.00	5.52
1377	2591	4.621460	CACGGGAGAATAATATACACGCAG	59.379	45.833	0.00	0.00	0.00	5.18
1407	2626	4.062991	GTTCCGTGTTCCTGTTATCTTGT	58.937	43.478	0.00	0.00	0.00	3.16
1408	2627	5.221481	TGTTCCGTGTTCCTGTTATCTTGTA	60.221	40.000	0.00	0.00	0.00	2.41
1420	2639	9.292195	TCCTGTTATCTTGTATATCACGTGATA	57.708	33.333	33.83	33.83	40.85	2.15
1625	3478	6.765905	TCGATAGTGCACCAAAAAGTGGAAG	61.766	44.000	14.63	0.00	44.29	3.46
1665	3519	3.701542	AGCATCCTTGATCTCTTGTACGA	59.298	43.478	0.00	0.00	0.00	3.43
1830	3692	6.428295	CCAACTTGGTATGGGGTTCTTATTA	58.572	40.000	0.00	0.00	32.87	0.98
1834	3696	7.705700	ACTTGGTATGGGGTTCTTATTACTTT	58.294	34.615	0.00	0.00	0.00	2.66
1910	3772	5.592104	TGAGAACTAGATAATCCGTTGCA	57.408	39.130	0.00	0.00	0.00	4.08
1915	3777	3.391296	ACTAGATAATCCGTTGCACCCAT	59.609	43.478	0.00	0.00	0.00	4.00
1945	3807	2.100991	CAAATGCGGCCGAGAAGC	59.899	61.111	33.48	11.66	0.00	3.86
1970	3832	6.018994	CGAGGGCAACTATAAGAAACATGTAC	60.019	42.308	0.00	0.00	0.00	2.90
1971	3833	6.958767	AGGGCAACTATAAGAAACATGTACT	58.041	36.000	0.00	0.00	0.00	2.73
1972	3834	7.048512	AGGGCAACTATAAGAAACATGTACTC	58.951	38.462	0.00	0.00	0.00	2.59
1973	3835	6.260271	GGGCAACTATAAGAAACATGTACTCC	59.740	42.308	0.00	0.00	0.00	3.85
1974	3836	6.260271	GGCAACTATAAGAAACATGTACTCCC	59.740	42.308	0.00	0.00	0.00	4.30
1975	3837	7.048512	GCAACTATAAGAAACATGTACTCCCT	58.951	38.462	0.00	0.00	0.00	4.20
1976	3838	7.224949	GCAACTATAAGAAACATGTACTCCCTC	59.775	40.741	0.00	0.00	0.00	4.30
1977	3839	7.362802	ACTATAAGAAACATGTACTCCCTCC	57.637	40.000	0.00	0.00	0.00	4.30
1978	3840	3.611766	AAGAAACATGTACTCCCTCCG	57.388	47.619	0.00	0.00	0.00	4.63
1979	3841	2.537143	AGAAACATGTACTCCCTCCGT	58.463	47.619	0.00	0.00	0.00	4.69
1980	3842	2.904434	AGAAACATGTACTCCCTCCGTT	59.096	45.455	0.00	0.00	0.00	4.44
1981	3843	3.056035	AGAAACATGTACTCCCTCCGTTC	60.056	47.826	0.00	0.00	0.00	3.95
1982	3844	2.233305	ACATGTACTCCCTCCGTTCT	57.767	50.000	0.00	0.00	0.00	3.01
1983	3845	1.825474	ACATGTACTCCCTCCGTTCTG	59.175	52.381	0.00	0.00	0.00	3.02
1984	3846	2.100197	CATGTACTCCCTCCGTTCTGA	58.900	52.381	0.00	0.00	0.00	3.27
1985	3847	2.526888	TGTACTCCCTCCGTTCTGAT	57.473	50.000	0.00	0.00	0.00	2.90
1986	3848	2.816411	TGTACTCCCTCCGTTCTGATT	58.184	47.619	0.00	0.00	0.00	2.57
1987	3849	3.170717	TGTACTCCCTCCGTTCTGATTT	58.829	45.455	0.00	0.00	0.00	2.17
1988	3850	4.346730	TGTACTCCCTCCGTTCTGATTTA	58.653	43.478	0.00	0.00	0.00	1.40
1989	3851	3.889520	ACTCCCTCCGTTCTGATTTAC	57.110	47.619	0.00	0.00	0.00	2.01
1990	3852	3.442076	ACTCCCTCCGTTCTGATTTACT	58.558	45.455	0.00	0.00	0.00	2.24
1991	3853	3.447944	ACTCCCTCCGTTCTGATTTACTC	59.552	47.826	0.00	0.00	0.00	2.59
1992	3854	2.426024	TCCCTCCGTTCTGATTTACTCG	59.574	50.000	0.00	0.00	0.00	4.18
1993	3855	2.165845	CCCTCCGTTCTGATTTACTCGT	59.834	50.000	0.00	0.00	0.00	4.18
1994	3856	3.436496	CCTCCGTTCTGATTTACTCGTC	58.564	50.000	0.00	0.00	0.00	4.20
1995	3857	3.099362	CTCCGTTCTGATTTACTCGTCG	58.901	50.000	0.00	0.00	0.00	5.12
1996	3858	2.485426	TCCGTTCTGATTTACTCGTCGT	59.515	45.455	0.00	0.00	0.00	4.34
1997	3859	2.592897	CCGTTCTGATTTACTCGTCGTG	59.407	50.000	0.00	0.00	0.00	4.35
1998	3860	2.592897	CGTTCTGATTTACTCGTCGTGG	59.407	50.000	0.00	0.00	0.00	4.94
1999	3861	3.572584	GTTCTGATTTACTCGTCGTGGT	58.427	45.455	0.00	0.00	0.00	4.16
2000	3862	3.928727	TCTGATTTACTCGTCGTGGTT	57.071	42.857	0.00	0.00	0.00	3.67
2001	3863	4.247267	TCTGATTTACTCGTCGTGGTTT	57.753	40.909	0.00	0.00	0.00	3.27
2002	3864	4.624015	TCTGATTTACTCGTCGTGGTTTT	58.376	39.130	0.00	0.00	0.00	2.43
2003	3865	5.771469	TCTGATTTACTCGTCGTGGTTTTA	58.229	37.500	0.00	0.00	0.00	1.52
2004	3866	5.860182	TCTGATTTACTCGTCGTGGTTTTAG	59.140	40.000	0.00	0.00	0.00	1.85
2005	3867	5.531634	TGATTTACTCGTCGTGGTTTTAGT	58.468	37.500	0.00	0.00	0.00	2.24
2006	3868	5.984926	TGATTTACTCGTCGTGGTTTTAGTT	59.015	36.000	0.00	0.00	0.00	2.24
2007	3869	5.888412	TTTACTCGTCGTGGTTTTAGTTC	57.112	39.130	0.00	0.00	0.00	3.01
2008	3870	3.441496	ACTCGTCGTGGTTTTAGTTCA	57.559	42.857	0.00	0.00	0.00	3.18
2009	3871	3.784338	ACTCGTCGTGGTTTTAGTTCAA	58.216	40.909	0.00	0.00	0.00	2.69
2010	3872	4.183101	ACTCGTCGTGGTTTTAGTTCAAA	58.817	39.130	0.00	0.00	0.00	2.69
2011	3873	4.812626	ACTCGTCGTGGTTTTAGTTCAAAT	59.187	37.500	0.00	0.00	0.00	2.32
2012	3874	5.295045	ACTCGTCGTGGTTTTAGTTCAAATT	59.705	36.000	0.00	0.00	0.00	1.82
2013	3875	6.121613	TCGTCGTGGTTTTAGTTCAAATTT	57.878	33.333	0.00	0.00	0.00	1.82
2014	3876	5.966503	TCGTCGTGGTTTTAGTTCAAATTTG	59.033	36.000	12.15	12.15	0.00	2.32
2015	3877	5.966503	CGTCGTGGTTTTAGTTCAAATTTGA	59.033	36.000	16.91	16.91	34.92	2.69
2016	3878	6.469595	CGTCGTGGTTTTAGTTCAAATTTGAA	59.530	34.615	26.01	26.01	44.31	2.69
2029	3891	7.743520	TTCAAATTTGAACTAAAACCACGAC	57.256	32.000	26.01	0.00	41.88	4.34
2030	3892	5.966503	TCAAATTTGAACTAAAACCACGACG	59.033	36.000	18.45	0.00	33.55	5.12
2031	3893	5.738118	AATTTGAACTAAAACCACGACGA	57.262	34.783	0.00	0.00	0.00	4.20
2032	3894	4.782252	TTTGAACTAAAACCACGACGAG	57.218	40.909	0.00	0.00	0.00	4.18
2033	3895	3.441496	TGAACTAAAACCACGACGAGT	57.559	42.857	0.00	0.00	0.00	4.18
2034	3896	4.566545	TGAACTAAAACCACGACGAGTA	57.433	40.909	0.00	0.00	0.00	2.59
2035	3897	4.930963	TGAACTAAAACCACGACGAGTAA	58.069	39.130	0.00	0.00	0.00	2.24
2036	3898	5.347342	TGAACTAAAACCACGACGAGTAAA	58.653	37.500	0.00	0.00	0.00	2.01
2037	3899	5.984926	TGAACTAAAACCACGACGAGTAAAT	59.015	36.000	0.00	0.00	0.00	1.40
2038	3900	6.144402	TGAACTAAAACCACGACGAGTAAATC	59.856	38.462	0.00	0.00	0.00	2.17
2050	3912	3.515330	GAGTAAATCGAAACGGAGGGA	57.485	47.619	0.00	0.00	0.00	4.20
2051	3913	3.445857	GAGTAAATCGAAACGGAGGGAG	58.554	50.000	0.00	0.00	0.00	4.30
2052	3914	2.830321	AGTAAATCGAAACGGAGGGAGT	59.170	45.455	0.00	0.00	0.00	3.85
2053	3915	4.019174	AGTAAATCGAAACGGAGGGAGTA	58.981	43.478	0.00	0.00	0.00	2.59
2159	4021	2.111043	AGTGGGCCAACACAGTCG	59.889	61.111	14.26	0.00	43.72	4.18
2202	4064	3.846405	TTGGGAGCCGGAGAGGTGT	62.846	63.158	5.05	0.00	43.70	4.16
2254	4121	2.353958	CTGTGGCAGCATGGACCT	59.646	61.111	0.00	0.00	35.86	3.85
2256	4123	2.352422	GTGGCAGCATGGACCTGA	59.648	61.111	3.29	0.00	35.86	3.86
2263	4130	2.681976	GCAGCATGGACCTGACTATGTT	60.682	50.000	3.29	0.00	35.86	2.71
2309	4176	4.685169	ACGATGTCGCTTTGATTTTGAT	57.315	36.364	1.77	0.00	44.43	2.57
2310	4177	5.046910	ACGATGTCGCTTTGATTTTGATT	57.953	34.783	1.77	0.00	44.43	2.57
2311	4178	5.460646	ACGATGTCGCTTTGATTTTGATTT	58.539	33.333	1.77	0.00	44.43	2.17

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
96	97	2.828520	CACCCTCTTAGAGCAACTCTCA	59.171	50.000	3.26	0.00	44.35	3.27
129	130	3.702048	GGCTGTACCTGCACCCGA	61.702	66.667	9.62	0.00	34.51	5.14
158	159	2.300152	TGCTCCCGGATTTAGCTATCAG	59.700	50.000	0.73	0.00	37.16	2.90
170	171	3.454447	TCTTAGATTTTGATGCTCCCGGA	59.546	43.478	0.73	0.00	0.00	5.14
547	549	2.337359	ACTAACCAGGGTGGAGCTAA	57.663	50.000	0.00	0.00	40.96	3.09
569	571	5.277490	CCATATGTTCTTGTGTATTCTGGCG	60.277	44.000	1.24	0.00	0.00	5.69
678	1796	1.488812	TGTATTGCTGATAAGGCCCGT	59.511	47.619	0.00	0.00	0.00	5.28
680	1798	3.507622	GGAATGTATTGCTGATAAGGCCC	59.492	47.826	0.00	0.00	0.00	5.80
929	2084	0.604780	GAGGCTTTGAGCTGTGCTGA	60.605	55.000	0.00	0.00	41.99	4.26
949	2110	5.941058	TCGCTTCTAGCTAGCTCTTGTATAT	59.059	40.000	23.26	0.00	39.60	0.86
1344	2553	2.031012	CTCCCGTGTCAGCTGCAA	59.969	61.111	9.47	0.00	0.00	4.08
1395	2609	9.908152	TTATCACGTGATATACAAGATAACAGG	57.092	33.333	32.72	0.00	36.94	4.00
1420	2639	3.202829	TGGTTTGCCTTAGTCTTCGTT	57.797	42.857	0.00	0.00	35.27	3.85
1665	3519	3.314357	GCTACAAAGTGTTCGGAAAAGGT	59.686	43.478	0.00	0.00	0.00	3.50
1768	3622	9.434420	ACAGAGAGATAGCATCTATTTTATTGC	57.566	33.333	0.00	0.00	40.38	3.56
1819	3681	7.769044	TCTCATAGTGCAAAGTAATAAGAACCC	59.231	37.037	0.00	0.00	0.00	4.11
1830	3692	5.013183	AGGTTACCTTCTCATAGTGCAAAGT	59.987	40.000	0.00	0.00	0.00	2.66
1834	3696	3.838317	ACAGGTTACCTTCTCATAGTGCA	59.162	43.478	0.00	0.00	0.00	4.57
1861	3723	1.064357	GCTAGTCTGTACGCACTCCTC	59.936	57.143	0.00	0.00	0.00	3.71
1910	3772	5.481105	CATTTGCTTATTGTGTCAATGGGT	58.519	37.500	5.40	0.00	0.00	4.51
1915	3777	3.573598	CCGCATTTGCTTATTGTGTCAA	58.426	40.909	0.51	0.00	39.32	3.18
1945	3807	4.876107	ACATGTTTCTTATAGTTGCCCTCG	59.124	41.667	0.00	0.00	0.00	4.63
1970	3832	3.489398	CGAGTAAATCAGAACGGAGGGAG	60.489	52.174	0.00	0.00	0.00	4.30
1971	3833	2.426024	CGAGTAAATCAGAACGGAGGGA	59.574	50.000	0.00	0.00	0.00	4.20
1972	3834	2.165845	ACGAGTAAATCAGAACGGAGGG	59.834	50.000	0.00	0.00	0.00	4.30
1973	3835	3.436496	GACGAGTAAATCAGAACGGAGG	58.564	50.000	0.00	0.00	0.00	4.30
1974	3836	3.099362	CGACGAGTAAATCAGAACGGAG	58.901	50.000	0.00	0.00	0.00	4.63
1975	3837	2.485426	ACGACGAGTAAATCAGAACGGA	59.515	45.455	0.00	0.00	0.00	4.69
1976	3838	2.592897	CACGACGAGTAAATCAGAACGG	59.407	50.000	0.00	0.00	0.00	4.44
1977	3839	2.592897	CCACGACGAGTAAATCAGAACG	59.407	50.000	0.00	0.00	0.00	3.95
1978	3840	3.572584	ACCACGACGAGTAAATCAGAAC	58.427	45.455	0.00	0.00	0.00	3.01
1979	3841	3.928727	ACCACGACGAGTAAATCAGAA	57.071	42.857	0.00	0.00	0.00	3.02
1980	3842	3.928727	AACCACGACGAGTAAATCAGA	57.071	42.857	0.00	0.00	0.00	3.27
1981	3843	4.985044	AAAACCACGACGAGTAAATCAG	57.015	40.909	0.00	0.00	0.00	2.90
1982	3844	5.531634	ACTAAAACCACGACGAGTAAATCA	58.468	37.500	0.00	0.00	0.00	2.57
1983	3845	6.144402	TGAACTAAAACCACGACGAGTAAATC	59.856	38.462	0.00	0.00	0.00	2.17
1984	3846	5.984926	TGAACTAAAACCACGACGAGTAAAT	59.015	36.000	0.00	0.00	0.00	1.40
1985	3847	5.347342	TGAACTAAAACCACGACGAGTAAA	58.653	37.500	0.00	0.00	0.00	2.01
1986	3848	4.930963	TGAACTAAAACCACGACGAGTAA	58.069	39.130	0.00	0.00	0.00	2.24
1987	3849	4.566545	TGAACTAAAACCACGACGAGTA	57.433	40.909	0.00	0.00	0.00	2.59
1988	3850	3.441496	TGAACTAAAACCACGACGAGT	57.559	42.857	0.00	0.00	0.00	4.18
1989	3851	4.782252	TTTGAACTAAAACCACGACGAG	57.218	40.909	0.00	0.00	0.00	4.18
1990	3852	5.738118	AATTTGAACTAAAACCACGACGA	57.262	34.783	0.00	0.00	0.00	4.20
1991	3853	5.966503	TCAAATTTGAACTAAAACCACGACG	59.033	36.000	18.45	0.00	33.55	5.12
1992	3854	7.743520	TTCAAATTTGAACTAAAACCACGAC	57.256	32.000	26.01	0.00	41.88	4.34
2005	3867	6.469595	CGTCGTGGTTTTAGTTCAAATTTGAA	59.530	34.615	26.01	26.01	44.31	2.69
2006	3868	5.966503	CGTCGTGGTTTTAGTTCAAATTTGA	59.033	36.000	16.91	16.91	34.92	2.69
2007	3869	5.966503	TCGTCGTGGTTTTAGTTCAAATTTG	59.033	36.000	12.15	12.15	0.00	2.32
2008	3870	6.121613	TCGTCGTGGTTTTAGTTCAAATTT	57.878	33.333	0.00	0.00	0.00	1.82
2009	3871	5.295045	ACTCGTCGTGGTTTTAGTTCAAATT	59.705	36.000	0.00	0.00	0.00	1.82
2010	3872	4.812626	ACTCGTCGTGGTTTTAGTTCAAAT	59.187	37.500	0.00	0.00	0.00	2.32
2011	3873	4.183101	ACTCGTCGTGGTTTTAGTTCAAA	58.817	39.130	0.00	0.00	0.00	2.69
2012	3874	3.784338	ACTCGTCGTGGTTTTAGTTCAA	58.216	40.909	0.00	0.00	0.00	2.69
2013	3875	3.441496	ACTCGTCGTGGTTTTAGTTCA	57.559	42.857	0.00	0.00	0.00	3.18
2014	3876	5.888412	TTTACTCGTCGTGGTTTTAGTTC	57.112	39.130	0.00	0.00	0.00	3.01
2015	3877	5.117592	CGATTTACTCGTCGTGGTTTTAGTT	59.882	40.000	0.00	0.00	42.56	2.24
2016	3878	4.618489	CGATTTACTCGTCGTGGTTTTAGT	59.382	41.667	0.00	0.00	42.56	2.24
2017	3879	5.109815	CGATTTACTCGTCGTGGTTTTAG	57.890	43.478	0.00	0.00	42.56	1.85
2030	3892	3.119209	ACTCCCTCCGTTTCGATTTACTC	60.119	47.826	0.00	0.00	0.00	2.59
2031	3893	2.830321	ACTCCCTCCGTTTCGATTTACT	59.170	45.455	0.00	0.00	0.00	2.24
2032	3894	3.242549	ACTCCCTCCGTTTCGATTTAC	57.757	47.619	0.00	0.00	0.00	2.01
2033	3895	3.382546	CCTACTCCCTCCGTTTCGATTTA	59.617	47.826	0.00	0.00	0.00	1.40
2034	3896	2.167900	CCTACTCCCTCCGTTTCGATTT	59.832	50.000	0.00	0.00	0.00	2.17
2035	3897	1.755380	CCTACTCCCTCCGTTTCGATT	59.245	52.381	0.00	0.00	0.00	3.34
2036	3898	1.341778	ACCTACTCCCTCCGTTTCGAT	60.342	52.381	0.00	0.00	0.00	3.59
2037	3899	0.038744	ACCTACTCCCTCCGTTTCGA	59.961	55.000	0.00	0.00	0.00	3.71
2038	3900	1.755179	TACCTACTCCCTCCGTTTCG	58.245	55.000	0.00	0.00	0.00	3.46
2039	3901	6.944862	TCTTATATACCTACTCCCTCCGTTTC	59.055	42.308	0.00	0.00	0.00	2.78
2040	3902	6.856757	TCTTATATACCTACTCCCTCCGTTT	58.143	40.000	0.00	0.00	0.00	3.60
2041	3903	6.460103	TCTTATATACCTACTCCCTCCGTT	57.540	41.667	0.00	0.00	0.00	4.44
2042	3904	6.655376	ATCTTATATACCTACTCCCTCCGT	57.345	41.667	0.00	0.00	0.00	4.69
2043	3905	7.147337	ACCTATCTTATATACCTACTCCCTCCG	60.147	44.444	0.00	0.00	0.00	4.63
2044	3906	8.116679	ACCTATCTTATATACCTACTCCCTCC	57.883	42.308	0.00	0.00	0.00	4.30
2045	3907	9.994017	AAACCTATCTTATATACCTACTCCCTC	57.006	37.037	0.00	0.00	0.00	4.30
2153	4015	2.319890	AAAAGCCCGACCACGACTGT	62.320	55.000	0.00	0.00	42.66	3.55
2254	4121	6.259167	ACAACGCTTTACAAAGAACATAGTCA	59.741	34.615	5.89	0.00	38.28	3.41
2256	4123	6.293244	GGACAACGCTTTACAAAGAACATAGT	60.293	38.462	5.89	0.00	38.28	2.12
2263	4130	3.799366	TCTGGACAACGCTTTACAAAGA	58.201	40.909	5.89	0.00	38.28	2.52

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.