AutoCloner

Multiple sequence alignment - TraesCS7D01G112400

Loading Multiple Alignment...

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	TraesCS7D01G112400	chr7D	100.000	2258	0	0	1	2258	68925140	68922883	0.000000e+00	4170.0
1	TraesCS7D01G112400	chr7D	89.218	473	40	6	28	491	636341334	636341804	4.180000e-162	580.0
2	TraesCS7D01G112400	chr7D	87.945	506	41	8	1	491	4740155	4739655	1.500000e-161	579.0
3	TraesCS7D01G112400	chr7D	88.795	473	42	6	28	491	635666511	635666041	9.050000e-159	569.0
4	TraesCS7D01G112400	chr7D	86.774	499	34	18	765	1243	66484559	66485045	5.520000e-146	527.0
5	TraesCS7D01G112400	chr7D	86.526	475	34	20	789	1243	68935346	68934882	1.560000e-136	496.0
6	TraesCS7D01G112400	chr7D	86.889	450	17	20	794	1242	68914199	68913791	1.220000e-127	466.0
7	TraesCS7D01G112400	chr7D	85.155	485	25	23	772	1243	68806170	68805720	9.510000e-124	453.0
8	TraesCS7D01G112400	chr7D	83.613	476	41	24	765	1235	66513325	66513768	1.610000e-111	412.0
9	TraesCS7D01G112400	chr7D	97.778	90	2	0	2169	2258	68804658	68804569	3.000000e-34	156.0
10	TraesCS7D01G112400	chr7D	87.023	131	10	4	2004	2128	68804784	68804655	8.410000e-30	141.0
11	TraesCS7D01G112400	chr7D	87.387	111	13	1	1725	1834	68911869	68911759	2.350000e-25	126.0
12	TraesCS7D01G112400	chr7D	95.833	48	2	0	491	538	4739636	4739589	6.690000e-11	78.7
13	TraesCS7D01G112400	chr7A	90.058	865	44	17	488	1329	71118219	71119064	0.000000e+00	1083.0
14	TraesCS7D01G112400	chr7A	95.503	467	13	5	770	1235	70893988	70894447	0.000000e+00	739.0
15	TraesCS7D01G112400	chr7A	90.428	397	22	14	858	1243	74596605	74596214	2.000000e-140	508.0
16	TraesCS7D01G112400	chr7A	85.801	493	33	19	770	1235	74611002	74610520	2.610000e-134	488.0
17	TraesCS7D01G112400	chr7A	84.100	478	19	24	1370	1816	71119220	71119671	2.090000e-110	409.0
18	TraesCS7D01G112400	chr7A	97.000	100	3	0	2159	2258	71119723	71119822	3.860000e-38	169.0
19	TraesCS7D01G112400	chr7A	85.714	70	10	0	1763	1832	632586326	632586395	8.650000e-10	75.0
20	TraesCS7D01G112400	chr7A	97.500	40	1	0	1795	1834	71120603	71120642	4.020000e-08	69.4
21	TraesCS7D01G112400	chr7B	86.769	650	41	17	1365	1975	10105611	10104968	0.000000e+00	682.0
22	TraesCS7D01G112400	chr7B	92.734	289	19	1	955	1243	7727879	7728165	1.250000e-112	416.0
23	TraesCS7D01G112400	chr7B	91.736	242	16	2	1128	1369	10152090	10151853	1.290000e-87	333.0
24	TraesCS7D01G112400	chr7B	95.213	188	9	0	2071	2258	10104928	10104741	4.710000e-77	298.0
25	TraesCS7D01G112400	chr7B	84.727	275	21	10	771	1025	8445978	8446251	2.880000e-64	255.0
26	TraesCS7D01G112400	chr7B	81.507	146	13	7	777	915	10241767	10241629	8.530000e-20	108.0
27	TraesCS7D01G112400	chr7B	84.848	99	15	0	1856	1954	10210784	10210686	1.430000e-17	100.0
28	TraesCS7D01G112400	chr7B	87.838	74	3	3	781	854	10190834	10190767	5.170000e-12	82.4
29	TraesCS7D01G112400	chr7B	95.000	40	2	0	1795	1834	9813822	9813783	1.870000e-06	63.9
30	TraesCS7D01G112400	chr7B	95.000	40	2	0	1795	1834	10104001	10103962	1.870000e-06	63.9
31	TraesCS7D01G112400	chr3A	89.897	485	36	5	1	476	154028556	154028076	1.480000e-171	612.0
32	TraesCS7D01G112400	chr3A	85.448	591	59	11	1	569	42446160	42446745	6.950000e-165	590.0
33	TraesCS7D01G112400	chr2A	88.911	496	43	5	3	491	708392931	708392441	3.210000e-168	601.0
34	TraesCS7D01G112400	chr2A	86.922	497	53	5	1	491	6132007	6131517	4.240000e-152	547.0
35	TraesCS7D01G112400	chr4B	88.400	500	43	8	3	491	17032332	17032827	2.500000e-164	588.0
36	TraesCS7D01G112400	chr3B	89.348	460	36	7	1	452	10736236	10735782	1.170000e-157	566.0
37	TraesCS7D01G112400	chr1D	84.162	543	51	26	706	1235	486922207	486922727	5.600000e-136	494.0
38	TraesCS7D01G112400	chr1D	85.455	110	16	0	1856	1965	486924244	486924353	5.100000e-22	115.0
39	TraesCS7D01G112400	chr1B	83.898	118	14	5	714	829	678107467	678107581	8.530000e-20	108.0

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	TraesCS7D01G112400	chr7D	68922883	68925140	2257	True	4170.000000	4170	100.000000	1	2258	1	chr7D.!!$R1	2257
1	TraesCS7D01G112400	chr7D	4739589	4740155	566	True	328.850000	579	91.889000	1	538	2	chr7D.!!$R4	537
2	TraesCS7D01G112400	chr7D	68911759	68914199	2440	True	296.000000	466	87.138000	794	1834	2	chr7D.!!$R6	1040
3	TraesCS7D01G112400	chr7D	68804569	68806170	1601	True	250.000000	453	89.985333	772	2258	3	chr7D.!!$R5	1486
4	TraesCS7D01G112400	chr7A	71118219	71120642	2423	False	432.600000	1083	92.164500	488	2258	4	chr7A.!!$F3	1770
5	TraesCS7D01G112400	chr7B	10103962	10105611	1649	True	347.966667	682	92.327333	1365	2258	3	chr7B.!!$R6	893
6	TraesCS7D01G112400	chr3A	42446160	42446745	585	False	590.000000	590	85.448000	1	569	1	chr3A.!!$F1	568
7	TraesCS7D01G112400	chr1D	486922207	486924353	2146	False	304.500000	494	84.808500	706	1965	2	chr1D.!!$F1	1259

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
867	953	0.17668	AATGCAGTCGGAGTAGGCAG	59.823	55.0	0.0	0.0	37.96	4.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1990	3907	0.040058	TGGCTGCCACCTGATTCAAT	59.96	50.0	19.3	0.0	0.0	2.57	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
83	84	2.920912	ACGCCTCCTCCGAACCAA	60.921	61.111	0.00	0.00	0.00	3.67
91	92	3.894547	CTCCGAACCAACACCCCGG	62.895	68.421	0.00	0.00	41.36	5.73
95	96	3.879180	GAACCAACACCCCGGGCAT	62.879	63.158	17.73	1.11	0.00	4.40
126	127	1.418373	TCAGCACGACAACGATGAAG	58.582	50.000	0.00	0.00	42.66	3.02
130	131	1.125021	GCACGACAACGATGAAGTCTG	59.875	52.381	0.00	0.00	42.66	3.51
247	255	2.116736	TTCTGCGCTTTCTGCAACCG	62.117	55.000	9.73	0.00	42.70	4.44
255	263	0.393808	TTTCTGCAACCGGGGCTATC	60.394	55.000	19.32	0.00	0.00	2.08
265	273	2.509964	ACCGGGGCTATCTTTCTGAAAT	59.490	45.455	6.32	0.00	0.00	2.17
279	287	7.826690	TCTTTCTGAAATAATACCCTTGTTGC	58.173	34.615	2.88	0.00	0.00	4.17
281	289	7.531857	TTCTGAAATAATACCCTTGTTGCAA	57.468	32.000	0.00	0.00	0.00	4.08
283	291	7.957002	TCTGAAATAATACCCTTGTTGCAAAA	58.043	30.769	0.00	0.00	0.00	2.44
286	294	8.424918	TGAAATAATACCCTTGTTGCAAAAGAA	58.575	29.630	17.53	5.20	0.00	2.52
370	378	2.972713	TCTGAAACTAGACCCTGTTGCT	59.027	45.455	0.00	0.00	0.00	3.91
462	475	1.202245	TGAAACAAGACGCTTGTTGCC	60.202	47.619	27.04	22.63	41.30	4.52
467	480	2.266554	CAAGACGCTTGTTGCCAAAAA	58.733	42.857	10.30	0.00	38.78	1.94
538	573	4.759096	GCGGATGTTGTGCGTGCC	62.759	66.667	0.00	0.00	44.26	5.01
559	602	3.506067	CCTTGAAGGTTAGCGTTTTCCAT	59.494	43.478	2.25	0.00	0.00	3.41
588	631	7.961326	AAAATGGCCAAATACTAGTGAATCT	57.039	32.000	10.96	0.00	0.00	2.40
591	634	9.646522	AAATGGCCAAATACTAGTGAATCTATT	57.353	29.630	10.96	0.00	0.00	1.73
726	769	2.723746	CGCCAATGCATAGCCCAC	59.276	61.111	14.21	0.00	37.32	4.61
743	786	2.249896	CGCGGACTAGCTAGCTCG	59.750	66.667	23.26	22.55	34.40	5.03
745	788	2.640421	CGGACTAGCTAGCTCGCC	59.360	66.667	23.26	19.01	0.00	5.54
747	790	1.657556	GGACTAGCTAGCTCGCCTG	59.342	63.158	23.26	9.98	0.00	4.85
748	791	1.657556	GACTAGCTAGCTCGCCTGG	59.342	63.158	23.26	8.19	0.00	4.45
752	795	4.154347	GCTAGCTCGCCTGGCTGT	62.154	66.667	17.92	0.62	43.98	4.40
753	796	2.581354	CTAGCTCGCCTGGCTGTT	59.419	61.111	17.92	9.84	40.52	3.16
754	797	1.078848	CTAGCTCGCCTGGCTGTTT	60.079	57.895	17.92	2.57	40.52	2.83
769	838	2.105528	TTTCGCGATACGGCTCCC	59.894	61.111	10.88	0.00	43.89	4.30
867	953	0.176680	AATGCAGTCGGAGTAGGCAG	59.823	55.000	0.00	0.00	37.96	4.85
868	954	0.684479	ATGCAGTCGGAGTAGGCAGA	60.684	55.000	0.00	0.00	37.96	4.26
869	955	1.139947	GCAGTCGGAGTAGGCAGAC	59.860	63.158	0.00	0.00	0.00	3.51
895	981	5.242838	CAGAACCTTTATAAGCACACCCAAA	59.757	40.000	0.00	0.00	0.00	3.28
1017	1117	0.179065	CGATGAGCTCCAAGATGGCA	60.179	55.000	12.15	0.00	37.47	4.92
1124	1224	0.109272	CTCAAGCTCTACGTCGCCAA	60.109	55.000	0.00	0.00	0.00	4.52
1245	1345	1.884235	CCAACCAAGAAGTCGAAGCT	58.116	50.000	0.00	0.00	0.00	3.74
1246	1346	1.532868	CCAACCAAGAAGTCGAAGCTG	59.467	52.381	0.00	0.00	0.00	4.24
1247	1347	2.213499	CAACCAAGAAGTCGAAGCTGT	58.787	47.619	0.00	0.00	0.00	4.40
1314	1442	1.734465	GTTGGCTTCAGACAAGGATCG	59.266	52.381	0.00	0.00	44.94	3.69
1333	1461	0.522180	GATCGATCGATACGCCCAGT	59.478	55.000	29.45	6.16	34.60	4.00
1334	1462	0.241213	ATCGATCGATACGCCCAGTG	59.759	55.000	28.45	0.00	32.36	3.66
1339	1467	2.452813	CGATACGCCCAGTGTGTGC	61.453	63.158	0.00	0.00	38.41	4.57
1340	1468	2.046314	ATACGCCCAGTGTGTGCC	60.046	61.111	0.00	0.00	38.41	5.01
1341	1469	2.521958	GATACGCCCAGTGTGTGCCT	62.522	60.000	0.00	0.00	38.41	4.75
1346	1481	1.376086	CCCAGTGTGTGCCTGATGA	59.624	57.895	0.00	0.00	31.38	2.92
1354	1489	0.321919	TGTGCCTGATGAGTCCTTGC	60.322	55.000	0.00	0.00	0.00	4.01
1360	1495	1.829849	CTGATGAGTCCTTGCCTCTGA	59.170	52.381	0.00	0.00	0.00	3.27
1362	1497	2.842496	TGATGAGTCCTTGCCTCTGAAT	59.158	45.455	0.00	0.00	0.00	2.57
1366	1501	3.822735	TGAGTCCTTGCCTCTGAATTTTG	59.177	43.478	0.00	0.00	0.00	2.44
1368	1503	1.895131	TCCTTGCCTCTGAATTTTGGC	59.105	47.619	0.00	0.00	45.10	4.52
1393	2259	7.270151	GCTAAAATTCTCTTCTTCGCTTCTTTG	59.730	37.037	0.00	0.00	0.00	2.77
1437	3167	6.462073	TTGTCTTGTAAGCGAAACATACTC	57.538	37.500	0.00	0.00	0.00	2.59
1448	3178	6.398918	AGCGAAACATACTCTTTACTGACAT	58.601	36.000	0.00	0.00	0.00	3.06
1510	3240	0.030504	TGAAGTTGTTGGCATGCACG	59.969	50.000	21.36	0.00	0.00	5.34
1618	3421	5.367945	TCGAGGCAGATAAAAACCCTTAT	57.632	39.130	0.00	0.00	0.00	1.73
1748	3647	1.971167	GCCGGCATCACTTGTCCAA	60.971	57.895	24.80	0.00	0.00	3.53
1853	3770	4.846509	GCATCTAAGAGAAATGCTTCTGC	58.153	43.478	0.00	0.00	42.19	4.26
1854	3771	4.575645	GCATCTAAGAGAAATGCTTCTGCT	59.424	41.667	0.00	0.00	42.19	4.24
1856	3773	6.259608	GCATCTAAGAGAAATGCTTCTGCTAA	59.740	38.462	0.00	0.00	42.19	3.09
1857	3774	7.041235	GCATCTAAGAGAAATGCTTCTGCTAAT	60.041	37.037	0.00	0.00	42.19	1.73
1863	3780	4.888239	AGAAATGCTTCTGCTAATGCTGAT	59.112	37.500	0.00	0.00	44.51	2.90
1868	3785	3.059051	GCTTCTGCTAATGCTGATGTAGC	60.059	47.826	10.57	0.00	44.51	3.58
1887	3804	5.412594	TGTAGCAGCCAGAATAAGAAAACAG	59.587	40.000	0.00	0.00	0.00	3.16
1898	3815	9.643693	CAGAATAAGAAAACAGCCATTACAAAT	57.356	29.630	0.00	0.00	0.00	2.32
1909	3826	6.127111	ACAGCCATTACAAATCAATGCCATTA	60.127	34.615	0.00	0.00	33.00	1.90
1911	3828	6.762661	AGCCATTACAAATCAATGCCATTAAC	59.237	34.615	0.00	0.00	33.00	2.01
1925	3842	3.127030	GCCATTAACTACCTGTTGACAGC	59.873	47.826	5.62	0.00	42.47	4.40
1971	3888	3.034030	GCACCTGGCAACACAGAC	58.966	61.111	0.00	0.00	46.17	3.51
1972	3889	1.823470	GCACCTGGCAACACAGACA	60.823	57.895	0.00	0.00	46.17	3.41
1973	3890	1.789078	GCACCTGGCAACACAGACAG	61.789	60.000	0.00	0.00	46.17	3.51
1974	3891	0.464373	CACCTGGCAACACAGACAGT	60.464	55.000	0.00	0.00	46.17	3.55
1975	3892	0.255890	ACCTGGCAACACAGACAGTT	59.744	50.000	0.00	0.00	46.17	3.16
1976	3893	0.947244	CCTGGCAACACAGACAGTTC	59.053	55.000	0.00	0.00	46.17	3.01
1977	3894	0.947244	CTGGCAACACAGACAGTTCC	59.053	55.000	0.00	0.00	46.17	3.62
1978	3895	0.546122	TGGCAACACAGACAGTTCCT	59.454	50.000	0.00	0.00	46.17	3.36
1979	3896	1.230324	GGCAACACAGACAGTTCCTC	58.770	55.000	0.00	0.00	0.00	3.71
1980	3897	1.230324	GCAACACAGACAGTTCCTCC	58.770	55.000	0.00	0.00	0.00	4.30
1981	3898	1.202698	GCAACACAGACAGTTCCTCCT	60.203	52.381	0.00	0.00	0.00	3.69
1982	3899	2.487934	CAACACAGACAGTTCCTCCTG	58.512	52.381	0.00	0.00	38.45	3.86
1984	3901	2.160822	CACAGACAGTTCCTCCTGTG	57.839	55.000	0.00	0.00	45.46	3.66
1985	3902	1.414181	CACAGACAGTTCCTCCTGTGT	59.586	52.381	11.82	0.00	45.46	3.72
1986	3903	2.160822	CAGACAGTTCCTCCTGTGTG	57.839	55.000	4.40	4.40	46.20	3.82
1987	3904	1.051812	AGACAGTTCCTCCTGTGTGG	58.948	55.000	0.00	0.00	45.46	4.17
1988	3905	1.048601	GACAGTTCCTCCTGTGTGGA	58.951	55.000	0.00	0.00	45.46	4.02
1999	3916	4.212143	TCCTGTGTGGAGATTGAATCAG	57.788	45.455	8.03	0.00	40.56	2.90
2025	3942	3.428045	GCAGCCAGAATAAGAACGCAATT	60.428	43.478	0.00	0.00	0.00	2.32
2043	3965	5.048083	CGCAATTATTACAGGCCAATGGTAT	60.048	40.000	5.01	0.00	0.00	2.73
2044	3966	6.516527	CGCAATTATTACAGGCCAATGGTATT	60.517	38.462	5.01	1.37	0.00	1.89
2045	3967	6.646240	GCAATTATTACAGGCCAATGGTATTG	59.354	38.462	5.01	7.69	0.00	1.90
2047	3969	8.855110	CAATTATTACAGGCCAATGGTATTGTA	58.145	33.333	5.01	4.99	0.00	2.41
2134	4057	4.252878	CAAAAGGCAAAACAGACAGGTTT	58.747	39.130	0.00	0.00	42.49	3.27

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
12	13	4.324471	GCACTCATGCCATGGTGA	57.676	55.556	22.44	9.27	46.97	4.02
66	67	2.920912	TTGGTTCGGAGGAGGCGT	60.921	61.111	0.00	0.00	0.00	5.68
95	96	0.528017	CGTGCTGAAGTAGAGGCAGA	59.472	55.000	0.00	0.00	35.29	4.26
107	108	1.269569	ACTTCATCGTTGTCGTGCTGA	60.270	47.619	0.00	0.00	38.33	4.26
247	255	6.659668	GGGTATTATTTCAGAAAGATAGCCCC	59.340	42.308	24.11	17.04	36.27	5.80
255	263	7.601856	TGCAACAAGGGTATTATTTCAGAAAG	58.398	34.615	1.28	0.00	0.00	2.62
298	306	6.542370	TCAGAAAGAAGAAAAATGGTTCGACT	59.458	34.615	0.00	0.00	32.50	4.18
370	378	2.755655	TGGCGGTGAAGTTTTTCTTTCA	59.244	40.909	0.00	0.00	36.40	2.69
403	411	6.705381	ACAGAGAGAGATCTTGTTTCACAAAG	59.295	38.462	0.00	0.00	37.69	2.77
407	416	5.107143	GCAACAGAGAGAGATCTTGTTTCAC	60.107	44.000	6.94	0.00	0.00	3.18
409	418	4.993584	TGCAACAGAGAGAGATCTTGTTTC	59.006	41.667	6.94	4.03	0.00	2.78
418	431	2.632028	AGCTTTCTGCAACAGAGAGAGA	59.368	45.455	16.75	0.00	42.86	3.10
419	432	3.042871	AGCTTTCTGCAACAGAGAGAG	57.957	47.619	16.75	8.99	42.86	3.20
420	433	3.070734	AGAAGCTTTCTGCAACAGAGAGA	59.929	43.478	16.75	0.00	42.86	3.10
421	434	3.401182	AGAAGCTTTCTGCAACAGAGAG	58.599	45.455	0.00	10.02	43.01	3.20
467	480	4.026356	AGTCCTGTGCAGCTATTTCTTT	57.974	40.909	0.00	0.00	0.00	2.52
470	483	3.338249	TCAAGTCCTGTGCAGCTATTTC	58.662	45.455	0.00	0.00	0.00	2.17
483	499	5.355350	GTCGGATTGATTTTGATCAAGTCCT	59.645	40.000	8.41	2.35	42.96	3.85
538	573	4.766404	ATGGAAAACGCTAACCTTCAAG	57.234	40.909	0.00	0.00	0.00	3.02
588	631	9.391006	GTGTGTTCTGGATTACCTCATTTAATA	57.609	33.333	0.00	0.00	37.04	0.98
591	634	6.653320	GTGTGTGTTCTGGATTACCTCATTTA	59.347	38.462	0.00	0.00	37.04	1.40
624	667	5.080337	TGTCTGAGTTGGTAGATCTTGAGT	58.920	41.667	0.00	0.00	0.00	3.41
726	769	2.249896	CGAGCTAGCTAGTCCGCG	59.750	66.667	19.38	12.15	34.40	6.46
743	786	1.813753	TATCGCGAAACAGCCAGGC	60.814	57.895	15.24	1.84	0.00	4.85
745	788	1.631072	CGTATCGCGAAACAGCCAG	59.369	57.895	15.24	0.00	44.77	4.85
747	790	3.003478	CCGTATCGCGAAACAGCC	58.997	61.111	15.24	0.00	44.77	4.85
748	791	2.078958	GAGCCGTATCGCGAAACAGC	62.079	60.000	15.24	14.70	44.77	4.40
749	792	1.480219	GGAGCCGTATCGCGAAACAG	61.480	60.000	15.24	3.79	44.77	3.16
750	793	1.517694	GGAGCCGTATCGCGAAACA	60.518	57.895	15.24	0.00	44.77	2.83
751	794	2.235699	GGGAGCCGTATCGCGAAAC	61.236	63.158	15.24	0.40	44.77	2.78
752	795	2.105528	GGGAGCCGTATCGCGAAA	59.894	61.111	15.24	0.00	44.77	3.46
769	838	3.864686	CCAGTCGAAATGGCCGCG	61.865	66.667	0.00	0.00	0.00	6.46
867	953	3.682858	TGTGCTTATAAAGGTTCTGCGTC	59.317	43.478	0.00	0.00	0.00	5.19
868	954	3.435671	GTGTGCTTATAAAGGTTCTGCGT	59.564	43.478	0.00	0.00	0.00	5.24
869	955	3.181510	GGTGTGCTTATAAAGGTTCTGCG	60.182	47.826	0.00	0.00	0.00	5.18
895	981	1.493022	TGTGTGTTGGTAGGGAAAGCT	59.507	47.619	0.00	0.00	0.00	3.74
941	1039	1.973812	GCAGGTGGGTTCTTCTGGC	60.974	63.158	0.00	0.00	0.00	4.85
1017	1117	2.501610	GCCGGCTTCTTCCTCGAT	59.498	61.111	22.15	0.00	0.00	3.59
1245	1345	1.906333	TGCCGACTAGCAGTCCACA	60.906	57.895	9.71	6.37	42.12	4.17
1246	1346	2.970639	TGCCGACTAGCAGTCCAC	59.029	61.111	9.71	4.39	42.12	4.02
1287	1415	1.003580	TGTCTGAAGCCAACTGGATCC	59.996	52.381	4.20	4.20	37.39	3.36
1292	1420	2.260844	TCCTTGTCTGAAGCCAACTG	57.739	50.000	0.00	0.00	0.00	3.16
1314	1442	0.522180	ACTGGGCGTATCGATCGATC	59.478	55.000	32.50	21.71	36.17	3.69
1329	1457	0.035881	ACTCATCAGGCACACACTGG	59.964	55.000	0.00	0.00	36.62	4.00
1331	1459	0.322975	GGACTCATCAGGCACACACT	59.677	55.000	0.00	0.00	0.00	3.55
1333	1461	1.059098	AAGGACTCATCAGGCACACA	58.941	50.000	0.00	0.00	0.00	3.72
1334	1462	1.446907	CAAGGACTCATCAGGCACAC	58.553	55.000	0.00	0.00	0.00	3.82
1339	1467	1.134461	CAGAGGCAAGGACTCATCAGG	60.134	57.143	1.39	0.00	40.81	3.86
1340	1468	1.829849	TCAGAGGCAAGGACTCATCAG	59.170	52.381	1.39	0.00	40.81	2.90
1341	1469	1.942776	TCAGAGGCAAGGACTCATCA	58.057	50.000	1.39	0.00	40.81	3.07
1346	1481	3.160269	CCAAAATTCAGAGGCAAGGACT	58.840	45.455	0.00	0.00	0.00	3.85
1362	1497	6.016276	AGCGAAGAAGAGAATTTTAGCCAAAA	60.016	34.615	0.00	0.00	38.00	2.44
1366	1501	5.352846	AGAAGCGAAGAAGAGAATTTTAGCC	59.647	40.000	0.00	0.00	0.00	3.93
1368	1503	7.270151	GCAAAGAAGCGAAGAAGAGAATTTTAG	59.730	37.037	0.00	0.00	0.00	1.85
1448	3178	7.931407	AGACAGTAAAACATTGACATGTCACTA	59.069	33.333	27.88	15.22	43.34	2.74
1510	3240	4.664188	TGTTTTTCTCTGGTTTTGTACGC	58.336	39.130	0.00	0.00	0.00	4.42
1643	3460	6.233434	AGTTTCTGCACATTACATTCTCAGA	58.767	36.000	0.00	0.00	0.00	3.27
1748	3647	3.055021	TGAACATGGCCATTTCAATGCAT	60.055	39.130	27.08	9.59	35.08	3.96
1863	3780	5.312895	TGTTTTCTTATTCTGGCTGCTACA	58.687	37.500	0.00	0.00	0.00	2.74
1868	3785	3.507233	TGGCTGTTTTCTTATTCTGGCTG	59.493	43.478	0.00	0.00	0.00	4.85
1870	3787	4.725790	ATGGCTGTTTTCTTATTCTGGC	57.274	40.909	0.00	0.00	0.00	4.85
1898	3815	5.414454	GTCAACAGGTAGTTAATGGCATTGA	59.586	40.000	22.57	12.01	38.74	2.57
1909	3826	0.756903	ACCGCTGTCAACAGGTAGTT	59.243	50.000	11.87	0.00	43.94	2.24
1911	3828	1.000955	AGAACCGCTGTCAACAGGTAG	59.999	52.381	11.87	0.00	43.94	3.18
1925	3842	1.247567	AGGTGCCAATTTGAGAACCG	58.752	50.000	0.00	0.00	32.83	4.44
1978	3895	3.054875	CCTGATTCAATCTCCACACAGGA	60.055	47.826	0.00	0.00	46.75	3.86
1979	3896	3.276857	CCTGATTCAATCTCCACACAGG	58.723	50.000	0.00	0.00	37.81	4.00
1980	3897	3.688185	CACCTGATTCAATCTCCACACAG	59.312	47.826	0.00	0.00	0.00	3.66
1981	3898	3.559811	CCACCTGATTCAATCTCCACACA	60.560	47.826	0.00	0.00	0.00	3.72
1982	3899	3.012518	CCACCTGATTCAATCTCCACAC	58.987	50.000	0.00	0.00	0.00	3.82
1983	3900	2.618816	GCCACCTGATTCAATCTCCACA	60.619	50.000	0.00	0.00	0.00	4.17
1984	3901	2.019984	GCCACCTGATTCAATCTCCAC	58.980	52.381	0.00	0.00	0.00	4.02
1985	3902	1.634973	TGCCACCTGATTCAATCTCCA	59.365	47.619	0.00	0.00	0.00	3.86
1986	3903	2.295885	CTGCCACCTGATTCAATCTCC	58.704	52.381	0.00	0.00	0.00	3.71
1987	3904	1.674962	GCTGCCACCTGATTCAATCTC	59.325	52.381	0.00	0.00	0.00	2.75
1988	3905	1.684248	GGCTGCCACCTGATTCAATCT	60.684	52.381	15.17	0.00	0.00	2.40
1989	3906	0.743097	GGCTGCCACCTGATTCAATC	59.257	55.000	15.17	0.00	0.00	2.67
1990	3907	0.040058	TGGCTGCCACCTGATTCAAT	59.960	50.000	19.30	0.00	0.00	2.57
1991	3908	0.609957	CTGGCTGCCACCTGATTCAA	60.610	55.000	19.30	0.00	0.00	2.69
1992	3909	1.001764	CTGGCTGCCACCTGATTCA	60.002	57.895	19.30	0.00	0.00	2.57
1993	3910	0.322816	TTCTGGCTGCCACCTGATTC	60.323	55.000	19.30	0.00	37.49	2.52
1994	3911	0.333993	ATTCTGGCTGCCACCTGATT	59.666	50.000	19.30	7.58	37.49	2.57
1995	3912	1.216064	TATTCTGGCTGCCACCTGAT	58.784	50.000	19.30	11.31	37.49	2.90
1996	3913	0.991146	TTATTCTGGCTGCCACCTGA	59.009	50.000	19.30	11.37	36.03	3.86
1997	3914	1.065199	TCTTATTCTGGCTGCCACCTG	60.065	52.381	19.30	8.83	0.00	4.00
1998	3915	1.289160	TCTTATTCTGGCTGCCACCT	58.711	50.000	19.30	7.68	0.00	4.00
1999	3916	1.745653	GTTCTTATTCTGGCTGCCACC	59.254	52.381	19.30	0.00	0.00	4.61

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.