AutoCloner

Multiple sequence alignment - TraesCS5D01G054000

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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	TraesCS5D01G054000	chr5D	100.000	2561	0	0	1	2561	51636469	51639029	0.000000e+00	4730.0
1	TraesCS5D01G054000	chr5D	87.108	861	61	27	693	1521	51851926	51852768	0.000000e+00	929.0
2	TraesCS5D01G054000	chr5D	86.652	884	64	33	693	1557	51860653	51861501	0.000000e+00	929.0
3	TraesCS5D01G054000	chr5D	89.212	723	40	16	693	1399	51697979	51698679	0.000000e+00	869.0
4	TraesCS5D01G054000	chr5D	87.027	740	50	29	693	1399	51674918	51675644	0.000000e+00	793.0
5	TraesCS5D01G054000	chr5D	81.672	622	102	11	58	675	6910424	6911037	8.180000e-140	507.0
6	TraesCS5D01G054000	chr5B	89.331	1659	122	26	1	1615	54507616	54509263	0.000000e+00	2032.0
7	TraesCS5D01G054000	chr5B	91.994	712	34	8	693	1399	54709942	54710635	0.000000e+00	977.0
8	TraesCS5D01G054000	chr5B	87.027	740	49	29	693	1399	54549121	54549846	0.000000e+00	791.0
9	TraesCS5D01G054000	chr5B	90.141	426	27	7	1097	1521	54850241	54850652	8.060000e-150	540.0
10	TraesCS5D01G054000	chr5B	76.322	435	43	33	2133	2547	54509276	54509670	7.280000e-41	178.0
11	TraesCS5D01G054000	chr5A	87.047	1490	133	33	1	1447	40627931	40629403	0.000000e+00	1628.0
12	TraesCS5D01G054000	chr5A	84.211	1102	106	32	1494	2547	40629400	40630481	0.000000e+00	1009.0
13	TraesCS5D01G054000	chr5A	92.636	679	28	6	694	1366	40812946	40813608	0.000000e+00	957.0
14	TraesCS5D01G054000	chr5A	86.152	881	71	30	693	1557	40934446	40935291	0.000000e+00	904.0
15	TraesCS5D01G054000	chr5A	86.152	881	71	30	693	1557	40968329	40969174	0.000000e+00	904.0
16	TraesCS5D01G054000	chr5A	86.152	881	71	30	693	1557	41005211	41006056	0.000000e+00	904.0
17	TraesCS5D01G054000	chr5A	85.012	854	80	28	679	1521	40925029	40925845	0.000000e+00	824.0
18	TraesCS5D01G054000	chr5A	85.695	734	57	32	693	1388	40684334	40685057	0.000000e+00	730.0
19	TraesCS5D01G054000	chr4D	83.221	596	97	3	85	678	745148	745742	6.230000e-151	544.0
20	TraesCS5D01G054000	chr2D	82.205	635	106	7	66	698	604075047	604074418	8.060000e-150	540.0
21	TraesCS5D01G054000	chr2D	82.353	595	94	9	85	674	625356367	625355779	8.180000e-140	507.0
22	TraesCS5D01G054000	chr2D	81.481	621	106	8	61	678	429082295	429081681	3.800000e-138	501.0
23	TraesCS5D01G054000	chr2B	81.804	632	102	10	66	693	5475511	5474889	3.780000e-143	518.0
24	TraesCS5D01G054000	chr1D	81.369	628	104	10	58	678	447368328	447367707	1.370000e-137	499.0
25	TraesCS5D01G054000	chr7A	81.141	631	108	10	58	679	30089225	30088597	1.770000e-136	496.0
26	TraesCS5D01G054000	chr7A	94.737	38	1	1	2308	2345	48885417	48885453	9.900000e-05	58.4
27	TraesCS5D01G054000	chr7A	96.875	32	1	0	2320	2351	690360059	690360028	1.000000e-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	TraesCS5D01G054000	chr5D	51636469	51639029	2560	False	4730.0	4730	100.0000	1	2561	1	chr5D.!!$F2	2560
1	TraesCS5D01G054000	chr5D	51851926	51852768	842	False	929.0	929	87.1080	693	1521	1	chr5D.!!$F5	828
2	TraesCS5D01G054000	chr5D	51860653	51861501	848	False	929.0	929	86.6520	693	1557	1	chr5D.!!$F6	864
3	TraesCS5D01G054000	chr5D	51697979	51698679	700	False	869.0	869	89.2120	693	1399	1	chr5D.!!$F4	706
4	TraesCS5D01G054000	chr5D	51674918	51675644	726	False	793.0	793	87.0270	693	1399	1	chr5D.!!$F3	706
5	TraesCS5D01G054000	chr5D	6910424	6911037	613	False	507.0	507	81.6720	58	675	1	chr5D.!!$F1	617
6	TraesCS5D01G054000	chr5B	54507616	54509670	2054	False	1105.0	2032	82.8265	1	2547	2	chr5B.!!$F4	2546
7	TraesCS5D01G054000	chr5B	54709942	54710635	693	False	977.0	977	91.9940	693	1399	1	chr5B.!!$F2	706
8	TraesCS5D01G054000	chr5B	54549121	54549846	725	False	791.0	791	87.0270	693	1399	1	chr5B.!!$F1	706
9	TraesCS5D01G054000	chr5A	40627931	40630481	2550	False	1318.5	1628	85.6290	1	2547	2	chr5A.!!$F7	2546
10	TraesCS5D01G054000	chr5A	40812946	40813608	662	False	957.0	957	92.6360	694	1366	1	chr5A.!!$F2	672
11	TraesCS5D01G054000	chr5A	40934446	40935291	845	False	904.0	904	86.1520	693	1557	1	chr5A.!!$F4	864
12	TraesCS5D01G054000	chr5A	40968329	40969174	845	False	904.0	904	86.1520	693	1557	1	chr5A.!!$F5	864
13	TraesCS5D01G054000	chr5A	41005211	41006056	845	False	904.0	904	86.1520	693	1557	1	chr5A.!!$F6	864
14	TraesCS5D01G054000	chr5A	40925029	40925845	816	False	824.0	824	85.0120	679	1521	1	chr5A.!!$F3	842
15	TraesCS5D01G054000	chr5A	40684334	40685057	723	False	730.0	730	85.6950	693	1388	1	chr5A.!!$F1	695
16	TraesCS5D01G054000	chr4D	745148	745742	594	False	544.0	544	83.2210	85	678	1	chr4D.!!$F1	593
17	TraesCS5D01G054000	chr2D	604074418	604075047	629	True	540.0	540	82.2050	66	698	1	chr2D.!!$R2	632
18	TraesCS5D01G054000	chr2D	625355779	625356367	588	True	507.0	507	82.3530	85	674	1	chr2D.!!$R3	589
19	TraesCS5D01G054000	chr2D	429081681	429082295	614	True	501.0	501	81.4810	61	678	1	chr2D.!!$R1	617
20	TraesCS5D01G054000	chr2B	5474889	5475511	622	True	518.0	518	81.8040	66	693	1	chr2B.!!$R1	627
21	TraesCS5D01G054000	chr1D	447367707	447368328	621	True	499.0	499	81.3690	58	678	1	chr1D.!!$R1	620
22	TraesCS5D01G054000	chr7A	30088597	30089225	628	True	496.0	496	81.1410	58	679	1	chr7A.!!$R1	621

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
462	485	0.317799	TGGCAACGACTACGGCTTTA	59.682	50.0	0.0	0.0	44.46	1.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2057	2358	0.036765	TACGTGAGGGGTCATTGTGC	60.037	55.0	0.0	0.0	0.0	4.57	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
53	56	9.399403	CAAAAAGAAGAGTAATGCTAAAAGACC	57.601	33.333	0.00	0.00	0.00	3.85
64	67	7.859325	AATGCTAAAAGACCGATAGCTTTTA	57.141	32.000	0.00	0.00	42.46	1.52
103	107	3.864921	GCGACTAGGAAAAGCTTTCCTCA	60.865	47.826	24.51	14.62	45.32	3.86
131	139	1.603455	CCACCAACGAGCCCATGTT	60.603	57.895	0.00	0.00	0.00	2.71
139	147	1.586154	CGAGCCCATGTTTTCGCCTT	61.586	55.000	0.00	0.00	0.00	4.35
190	210	0.411848	GGGGAGGGGATTTTTGGTGA	59.588	55.000	0.00	0.00	0.00	4.02
295	318	0.991920	TCTTTCGGGCTCCAATCCTT	59.008	50.000	0.00	0.00	0.00	3.36
382	405	1.777878	TGCCAAGGTTAGGGTTTCTCA	59.222	47.619	0.00	0.00	0.00	3.27
393	416	1.940613	GGGTTTCTCATCATGCGTACC	59.059	52.381	0.00	0.00	0.00	3.34
440	463	9.667107	AGGTTCTACAAATCGATTCAAGAATTA	57.333	29.630	22.26	7.57	0.00	1.40
447	470	8.034215	ACAAATCGATTCAAGAATTAAATGGCA	58.966	29.630	11.83	0.00	0.00	4.92
454	477	7.441890	TTCAAGAATTAAATGGCAACGACTA	57.558	32.000	0.00	0.00	42.51	2.59
462	485	0.317799	TGGCAACGACTACGGCTTTA	59.682	50.000	0.00	0.00	44.46	1.85
466	489	1.067354	CAACGACTACGGCTTTAGGGT	60.067	52.381	0.00	0.00	44.46	4.34
470	493	1.753073	GACTACGGCTTTAGGGTGCTA	59.247	52.381	0.00	0.00	0.00	3.49
487	510	2.025863	GCTAGTCCTTAGGGGCACGTA	61.026	57.143	0.00	0.00	40.27	3.57
514	537	2.431057	AGACTTTCCGGCTGTTATCGAT	59.569	45.455	2.16	2.16	0.00	3.59
552	575	2.782222	TATGGGAGCGACGACAGCC	61.782	63.158	0.00	0.00	34.64	4.85
598	621	1.024046	CGGCAATGGTCATTCGGTGA	61.024	55.000	0.00	0.00	0.00	4.02
608	631	1.836802	TCATTCGGTGATCCATGGACA	59.163	47.619	18.99	14.43	0.00	4.02
619	642	3.364889	TCCATGGACATCGACGTAATC	57.635	47.619	11.44	0.00	0.00	1.75
622	646	4.119862	CCATGGACATCGACGTAATCTTT	58.880	43.478	5.56	0.00	0.00	2.52
629	653	7.117454	GGACATCGACGTAATCTTTTTATGTG	58.883	38.462	0.00	0.00	0.00	3.21
636	660	7.274033	CGACGTAATCTTTTTATGTGTGAGGTA	59.726	37.037	0.00	0.00	0.00	3.08
648	672	9.787435	TTTATGTGTGAGGTATTTTGTACTTCT	57.213	29.630	0.00	0.00	0.00	2.85
650	674	6.822442	TGTGTGAGGTATTTTGTACTTCTGA	58.178	36.000	0.00	0.00	0.00	3.27
684	710	1.047002	AGATCTGATCCTTCCCGCAG	58.953	55.000	13.83	0.00	0.00	5.18
909	968	0.958822	CACCTTTTTCCCGGGTCAAG	59.041	55.000	22.86	19.39	0.00	3.02
1182	1290	1.378762	CCCGATGGTGGTGGAACTT	59.621	57.895	0.00	0.00	36.74	2.66
1771	2045	6.721571	TTTTCTGTATCCGTGATCAAACTC	57.278	37.500	0.00	0.00	0.00	3.01
1773	2047	3.116300	CTGTATCCGTGATCAAACTCCG	58.884	50.000	0.00	0.00	0.00	4.63
1777	2051	3.114668	TCCGTGATCAAACTCCGAAAA	57.885	42.857	0.00	0.00	0.00	2.29
1795	2069	8.665643	TCCGAAAATTTAGACTTAAGACAACA	57.334	30.769	10.09	0.00	0.00	3.33
1830	2127	4.653888	AGAACAAACGGGGCGGGG	62.654	66.667	0.00	0.00	0.00	5.73
1844	2141	2.375146	GGCGGGGACATGAACTTTAAT	58.625	47.619	0.00	0.00	0.00	1.40
1845	2142	2.758423	GGCGGGGACATGAACTTTAATT	59.242	45.455	0.00	0.00	0.00	1.40
1939	2240	6.932051	ACAAAATTGTAATGAACTTTGCACG	58.068	32.000	0.00	0.00	40.16	5.34
1956	2257	8.465999	ACTTTGCACGGAAATGAAATAATATGA	58.534	29.630	0.00	0.00	0.00	2.15
2003	2304	0.756294	TCCTCAGAAAAGCGTGTGGA	59.244	50.000	0.00	0.00	34.67	4.02
2004	2305	1.347707	TCCTCAGAAAAGCGTGTGGAT	59.652	47.619	0.00	0.00	32.64	3.41
2009	2310	2.527547	GAAAAGCGTGTGGATGCCCG	62.528	60.000	0.00	0.00	34.26	6.13
2013	2314	2.125147	CGTGTGGATGCCCGACAT	60.125	61.111	0.00	0.00	43.54	3.06
2039	2340	4.473520	CGCTTCCCCGACCAGCAT	62.474	66.667	0.00	0.00	32.71	3.79
2043	2344	0.390860	CTTCCCCGACCAGCATAGAG	59.609	60.000	0.00	0.00	0.00	2.43
2045	2346	1.043116	TCCCCGACCAGCATAGAGTG	61.043	60.000	0.00	0.00	0.00	3.51
2047	2348	0.387202	CCCGACCAGCATAGAGTGAG	59.613	60.000	0.00	0.00	0.00	3.51
2053	2354	2.093235	ACCAGCATAGAGTGAGCCTTTC	60.093	50.000	0.00	0.00	0.00	2.62
2057	2358	2.544685	CATAGAGTGAGCCTTTCCGTG	58.455	52.381	0.00	0.00	0.00	4.94
2061	2362	1.891919	GTGAGCCTTTCCGTGCACA	60.892	57.895	18.64	0.00	0.00	4.57
2073	2374	1.577328	CGTGCACAATGACCCCTCAC	61.577	60.000	18.64	0.00	0.00	3.51
2087	2388	2.091541	CCCTCACGTACATTGCCAATT	58.908	47.619	0.00	0.00	0.00	2.32
2110	2411	3.820590	CGGGCAAACGCATATGGA	58.179	55.556	4.56	0.00	0.00	3.41
2111	2412	2.102554	CGGGCAAACGCATATGGAA	58.897	52.632	4.56	0.00	0.00	3.53
2119	2420	4.523813	CAAACGCATATGGAACGATTACC	58.476	43.478	4.56	0.00	0.00	2.85
2128	2429	7.470009	GCATATGGAACGATTACCCTTTCATTT	60.470	37.037	4.56	0.00	0.00	2.32
2148	2449	7.447594	TCATTTTTCTAGTTTCCTAGTCGGTT	58.552	34.615	0.00	0.00	41.31	4.44
2220	2524	3.258123	GCCTTTTTCTTAGAATGGCCACA	59.742	43.478	8.16	0.00	39.89	4.17
2255	2559	8.422577	AAAAGGTTTGGCTATCTTAGAAATGT	57.577	30.769	0.00	0.00	0.00	2.71
2257	2561	9.528489	AAAGGTTTGGCTATCTTAGAAATGTTA	57.472	29.630	0.00	0.00	0.00	2.41
2468	2786	9.383519	TGATCACCTAAAATAGACAGATGAAAC	57.616	33.333	0.00	0.00	0.00	2.78
2479	2797	5.660460	AGACAGATGAAACAAAACAAACCC	58.340	37.500	0.00	0.00	0.00	4.11
2509	2827	3.821033	GTGTCTCCAAGCATTTAACTGGT	59.179	43.478	0.00	0.00	0.00	4.00
2547	2867	3.119459	TCTCTGAGCGTTTAGGTGACATC	60.119	47.826	0.00	0.00	0.00	3.06
2548	2868	2.826128	TCTGAGCGTTTAGGTGACATCT	59.174	45.455	0.00	0.00	0.00	2.90
2549	2869	3.258372	TCTGAGCGTTTAGGTGACATCTT	59.742	43.478	0.00	0.00	0.00	2.40
2550	2870	3.325870	TGAGCGTTTAGGTGACATCTTG	58.674	45.455	0.00	0.00	0.00	3.02
2551	2871	3.244078	TGAGCGTTTAGGTGACATCTTGT	60.244	43.478	0.00	0.00	0.00	3.16

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
53	56	5.117897	GCGAGAGGAGAAATAAAAGCTATCG	59.882	44.000	0.00	0.00	0.00	2.92
64	67	3.467776	GCCTTGCGAGAGGAGAAAT	57.532	52.632	1.22	0.00	39.25	2.17
103	107	0.611062	TCGTTGGTGGAGATCGAGGT	60.611	55.000	0.00	0.00	0.00	3.85
131	139	2.660802	GACGGAGGGAAGGCGAAA	59.339	61.111	0.00	0.00	0.00	3.46
190	210	0.763652	TCTACTAGCCGGATCCGAGT	59.236	55.000	35.42	29.38	42.83	4.18
295	318	1.663739	CCAACGGACGGACTTGAGA	59.336	57.895	0.00	0.00	0.00	3.27
366	389	4.273318	GCATGATGAGAAACCCTAACCTT	58.727	43.478	0.00	0.00	0.00	3.50
393	416	8.897872	AACCTAATACCAAATATAGTCGTTGG	57.102	34.615	2.18	2.18	46.05	3.77
411	434	9.667107	TTCTTGAATCGATTTGTAGAACCTAAT	57.333	29.630	12.81	0.00	0.00	1.73
421	444	8.034215	TGCCATTTAATTCTTGAATCGATTTGT	58.966	29.630	12.81	0.00	0.00	2.83
424	447	7.220683	CGTTGCCATTTAATTCTTGAATCGATT	59.779	33.333	11.20	11.20	0.00	3.34
440	463	0.321298	AGCCGTAGTCGTTGCCATTT	60.321	50.000	0.00	0.00	35.01	2.32
447	470	1.067354	CACCCTAAAGCCGTAGTCGTT	60.067	52.381	0.00	0.00	35.01	3.85
454	477	0.535797	GACTAGCACCCTAAAGCCGT	59.464	55.000	0.00	0.00	0.00	5.68
462	485	0.031010	CCCCTAAGGACTAGCACCCT	60.031	60.000	3.36	0.00	38.24	4.34
466	489	1.327690	CGTGCCCCTAAGGACTAGCA	61.328	60.000	0.00	0.00	38.24	3.49
470	493	0.251922	TGTACGTGCCCCTAAGGACT	60.252	55.000	0.00	0.00	38.24	3.85
487	510	0.600255	CAGCCGGAAAGTCTTCGTGT	60.600	55.000	5.05	0.00	31.77	4.49
514	537	2.038975	AGAGCCGGCCTGACCTTA	59.961	61.111	26.15	0.00	35.61	2.69
575	598	2.759560	AATGACCATTGCCGCCCC	60.760	61.111	0.00	0.00	0.00	5.80
578	601	2.406616	ACCGAATGACCATTGCCGC	61.407	57.895	0.00	0.00	0.00	6.53
579	602	1.024046	TCACCGAATGACCATTGCCG	61.024	55.000	0.00	0.00	29.99	5.69
590	613	2.548707	CGATGTCCATGGATCACCGAAT	60.549	50.000	19.62	2.64	39.42	3.34
598	621	3.574396	AGATTACGTCGATGTCCATGGAT	59.426	43.478	19.62	1.68	0.00	3.41
608	631	7.010183	CCTCACACATAAAAAGATTACGTCGAT	59.990	37.037	0.00	0.00	0.00	3.59
622	646	9.787435	AGAAGTACAAAATACCTCACACATAAA	57.213	29.630	0.00	0.00	0.00	1.40
629	653	8.547967	TTCATCAGAAGTACAAAATACCTCAC	57.452	34.615	0.00	0.00	0.00	3.51
703	730	5.049336	GCTCTGACTTTTTGTAAGTTCTCCC	60.049	44.000	0.00	0.00	0.00	4.30
909	968	1.005340	CAGGATGAGCTTCGAGCAAC	58.995	55.000	9.09	4.22	45.56	4.17
1032	1130	5.584253	TCAAGCTTAGTTCTAGTGCTAGG	57.416	43.478	0.00	0.00	34.06	3.02
1182	1290	2.687902	CCCCTAGGGTCCTCGTCA	59.312	66.667	26.66	0.00	38.25	4.35
1663	1937	8.415950	TCATGTTGTATTTGTTGGGTAATCTT	57.584	30.769	0.00	0.00	0.00	2.40
1666	1940	9.267084	GTTTTCATGTTGTATTTGTTGGGTAAT	57.733	29.630	0.00	0.00	0.00	1.89
1667	1941	8.258007	TGTTTTCATGTTGTATTTGTTGGGTAA	58.742	29.630	0.00	0.00	0.00	2.85
1757	2031	2.823924	TTTCGGAGTTTGATCACGGA	57.176	45.000	0.00	0.00	0.00	4.69
1760	2034	7.807680	AGTCTAAATTTTCGGAGTTTGATCAC	58.192	34.615	0.00	0.00	0.00	3.06
1771	2045	8.557029	AGTGTTGTCTTAAGTCTAAATTTTCGG	58.443	33.333	1.63	0.00	0.00	4.30
1801	2075	5.393678	CCCCGTTTGTTCTCAAAAGAAAGAA	60.394	40.000	7.84	0.00	43.04	2.52
1803	2077	4.359706	CCCCGTTTGTTCTCAAAAGAAAG	58.640	43.478	7.84	0.00	43.04	2.62
1805	2079	2.100087	GCCCCGTTTGTTCTCAAAAGAA	59.900	45.455	7.84	0.00	43.78	2.52
1809	2106	1.448922	CCGCCCCGTTTGTTCTCAAA	61.449	55.000	0.00	0.00	40.64	2.69
1822	2119	2.781431	AAAGTTCATGTCCCCGCCCC	62.781	60.000	0.00	0.00	0.00	5.80
1915	2216	6.019156	CCGTGCAAAGTTCATTACAATTTTGT	60.019	34.615	1.08	1.08	44.86	2.83
1917	2218	6.276847	TCCGTGCAAAGTTCATTACAATTTT	58.723	32.000	0.00	0.00	0.00	1.82
1924	2225	5.697473	TCATTTCCGTGCAAAGTTCATTA	57.303	34.783	0.00	0.00	0.00	1.90
1978	2279	0.321122	CGCTTTTCTGAGGAGCTGGT	60.321	55.000	0.00	0.00	34.33	4.00
2022	2323	2.978452	CTATGCTGGTCGGGGAAGCG	62.978	65.000	0.00	0.00	39.88	4.68
2026	2327	1.043116	CACTCTATGCTGGTCGGGGA	61.043	60.000	0.00	0.00	0.00	4.81
2030	2331	0.249238	GGCTCACTCTATGCTGGTCG	60.249	60.000	0.00	0.00	0.00	4.79
2039	2340	0.246635	GCACGGAAAGGCTCACTCTA	59.753	55.000	0.00	0.00	0.00	2.43
2043	2344	1.444119	TTGTGCACGGAAAGGCTCAC	61.444	55.000	13.13	0.00	33.76	3.51
2045	2346	0.109597	CATTGTGCACGGAAAGGCTC	60.110	55.000	13.13	0.00	0.00	4.70
2047	2348	0.387239	GTCATTGTGCACGGAAAGGC	60.387	55.000	13.13	0.00	0.00	4.35
2053	2354	2.034066	AGGGGTCATTGTGCACGG	59.966	61.111	13.13	4.42	0.00	4.94
2057	2358	0.036765	TACGTGAGGGGTCATTGTGC	60.037	55.000	0.00	0.00	0.00	4.57
2061	2362	2.939640	GCAATGTACGTGAGGGGTCATT	60.940	50.000	0.00	0.00	0.00	2.57
2094	2395	0.248458	CGTTCCATATGCGTTTGCCC	60.248	55.000	0.00	0.00	41.78	5.36
2107	2408	6.492087	AGAAAAATGAAAGGGTAATCGTTCCA	59.508	34.615	0.00	0.00	0.00	3.53
2110	2411	8.631480	ACTAGAAAAATGAAAGGGTAATCGTT	57.369	30.769	0.00	0.00	0.00	3.85
2111	2412	8.631480	AACTAGAAAAATGAAAGGGTAATCGT	57.369	30.769	0.00	0.00	0.00	3.73
2148	2449	5.221263	CCCGTAGCTAGCTTTTCTTGAGATA	60.221	44.000	24.88	0.00	0.00	1.98
2192	2496	6.295067	GGCCATTCTAAGAAAAAGGCTAAACA	60.295	38.462	0.00	0.00	40.40	2.83
2193	2497	6.100004	GGCCATTCTAAGAAAAAGGCTAAAC	58.900	40.000	0.00	0.00	40.40	2.01
2194	2498	5.777732	TGGCCATTCTAAGAAAAAGGCTAAA	59.222	36.000	0.00	0.73	40.40	1.85
2197	2501	3.511540	GTGGCCATTCTAAGAAAAAGGCT	59.488	43.478	9.72	0.00	40.40	4.58
2198	2502	3.258123	TGTGGCCATTCTAAGAAAAAGGC	59.742	43.478	9.72	0.00	39.86	4.35
2199	2503	5.467035	TTGTGGCCATTCTAAGAAAAAGG	57.533	39.130	9.72	0.00	0.00	3.11
2200	2504	7.967890	AATTTGTGGCCATTCTAAGAAAAAG	57.032	32.000	9.72	0.00	0.00	2.27
2201	2505	8.744568	AAAATTTGTGGCCATTCTAAGAAAAA	57.255	26.923	9.72	0.00	0.00	1.94
2202	2506	7.989741	TGAAAATTTGTGGCCATTCTAAGAAAA	59.010	29.630	9.72	0.65	0.00	2.29
2206	2510	7.727331	TTTGAAAATTTGTGGCCATTCTAAG	57.273	32.000	9.72	0.00	0.00	2.18
2442	2753	9.383519	GTTTCATCTGTCTATTTTAGGTGATCA	57.616	33.333	0.00	0.00	32.13	2.92
2461	2772	4.048241	TCGGGGTTTGTTTTGTTTCATC	57.952	40.909	0.00	0.00	0.00	2.92
2468	2786	1.135053	ACGGTTTCGGGGTTTGTTTTG	60.135	47.619	0.00	0.00	41.39	2.44
2473	2791	0.816421	AGACACGGTTTCGGGGTTTG	60.816	55.000	0.00	0.00	45.53	2.93
2474	2792	0.533531	GAGACACGGTTTCGGGGTTT	60.534	55.000	0.00	0.00	45.53	3.27
2476	2794	2.739132	GAGACACGGTTTCGGGGT	59.261	61.111	0.00	0.00	45.53	4.95
2479	2797	1.566018	GCTTGGAGACACGGTTTCGG	61.566	60.000	0.00	0.00	42.67	4.30

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.