AutoCloner

Multiple sequence alignment - TraesCS3D01G509500

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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	TraesCS3D01G509500	chr3D	100.000	2745	0	0	1	2745	594954199	594956943	0.000000e+00	5070.0
1	TraesCS3D01G509500	chr3D	95.541	314	14	0	408	721	590160053	590160366	1.130000e-138	503.0
2	TraesCS3D01G509500	chr3D	92.264	349	27	0	1404	1752	594893351	594893699	1.900000e-136	496.0
3	TraesCS3D01G509500	chr3D	94.888	313	15	1	409	721	594947433	594947122	3.180000e-134	488.0
4	TraesCS3D01G509500	chr3D	84.598	448	48	8	864	1302	594892914	594893349	2.530000e-115	425.0
5	TraesCS3D01G509500	chr3B	91.284	1262	65	19	753	1990	798403496	798404736	0.000000e+00	1679.0
6	TraesCS3D01G509500	chr3B	89.496	695	53	11	31	721	575260254	575259576	0.000000e+00	861.0
7	TraesCS3D01G509500	chr3B	86.612	732	73	12	4	727	13529884	13529170	0.000000e+00	785.0
8	TraesCS3D01G509500	chr3B	85.970	727	78	11	4	722	726425061	726424351	0.000000e+00	756.0
9	TraesCS3D01G509500	chr3B	88.889	432	32	6	1404	1831	798397597	798398016	4.050000e-143	518.0
10	TraesCS3D01G509500	chr3B	87.879	429	13	19	2031	2429	798404751	798405170	4.140000e-128	468.0
11	TraesCS3D01G509500	chr3B	93.194	191	7	6	2560	2745	798406487	798406676	2.690000e-70	276.0
12	TraesCS3D01G509500	chr3B	93.431	137	7	1	2431	2567	798405288	798405422	4.640000e-48	202.0
13	TraesCS3D01G509500	chr3B	85.577	208	13	12	2237	2427	798412570	798412777	4.640000e-48	202.0
14	TraesCS3D01G509500	chr3B	97.143	35	1	0	1883	1917	798404654	798404688	2.950000e-05	60.2
15	TraesCS3D01G509500	chr2D	95.146	721	23	3	1	721	380678823	380678115	0.000000e+00	1127.0
16	TraesCS3D01G509500	chr4D	94.751	724	28	6	1	722	108842938	108842223	0.000000e+00	1118.0
17	TraesCS3D01G509500	chr5D	93.767	722	32	5	1	722	406900184	406899476	0.000000e+00	1072.0
18	TraesCS3D01G509500	chr5D	93.930	313	18	1	409	721	406945054	406945365	3.200000e-129	472.0
19	TraesCS3D01G509500	chr3A	88.621	870	47	13	753	1598	725904330	725905171	0.000000e+00	1011.0
20	TraesCS3D01G509500	chr3A	86.243	945	92	16	1187	2114	725911406	725912329	0.000000e+00	990.0
21	TraesCS3D01G509500	chr3A	83.240	895	56	39	1587	2437	725905324	725906168	0.000000e+00	736.0
22	TraesCS3D01G509500	chr3A	90.394	406	29	5	1404	1807	725842717	725843114	2.420000e-145	525.0
23	TraesCS3D01G509500	chr3A	86.283	452	45	12	864	1302	725842268	725842715	2.470000e-130	475.0
24	TraesCS3D01G509500	chr3A	96.532	173	4	2	1578	1749	726714175	726714004	4.470000e-73	285.0
25	TraesCS3D01G509500	chr3A	86.932	176	19	4	1413	1587	726716032	726715860	7.760000e-46	195.0
26	TraesCS3D01G509500	chr1D	92.116	723	40	6	1	721	42896549	42897256	0.000000e+00	1003.0
27	TraesCS3D01G509500	chr1D	95.939	394	12	1	1	394	7181206	7180817	1.070000e-178	636.0
28	TraesCS3D01G509500	chr1D	95.812	382	10	2	1	380	4307620	4307997	1.810000e-171	612.0
29	TraesCS3D01G509500	chr7A	87.059	85	11	0	1619	1703	146951390	146951474	2.250000e-16	97.1
30	TraesCS3D01G509500	chr7D	85.882	85	12	0	1619	1703	146106565	146106649	1.050000e-14	91.6
31	TraesCS3D01G509500	chr7B	85.882	85	12	0	1619	1703	108286047	108286131	1.050000e-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	TraesCS3D01G509500	chr3D	594954199	594956943	2744	False	5070.00	5070	100.0000	1	2745	1	chr3D.!!$F2	2744
1	TraesCS3D01G509500	chr3D	594892914	594893699	785	False	460.50	496	88.4310	864	1752	2	chr3D.!!$F3	888
2	TraesCS3D01G509500	chr3B	575259576	575260254	678	True	861.00	861	89.4960	31	721	1	chr3B.!!$R2	690
3	TraesCS3D01G509500	chr3B	13529170	13529884	714	True	785.00	785	86.6120	4	727	1	chr3B.!!$R1	723
4	TraesCS3D01G509500	chr3B	726424351	726425061	710	True	756.00	756	85.9700	4	722	1	chr3B.!!$R3	718
5	TraesCS3D01G509500	chr3B	798403496	798406676	3180	False	537.04	1679	92.5862	753	2745	5	chr3B.!!$F3	1992
6	TraesCS3D01G509500	chr2D	380678115	380678823	708	True	1127.00	1127	95.1460	1	721	1	chr2D.!!$R1	720
7	TraesCS3D01G509500	chr4D	108842223	108842938	715	True	1118.00	1118	94.7510	1	722	1	chr4D.!!$R1	721
8	TraesCS3D01G509500	chr5D	406899476	406900184	708	True	1072.00	1072	93.7670	1	722	1	chr5D.!!$R1	721
9	TraesCS3D01G509500	chr3A	725911406	725912329	923	False	990.00	990	86.2430	1187	2114	1	chr3A.!!$F1	927
10	TraesCS3D01G509500	chr3A	725904330	725906168	1838	False	873.50	1011	85.9305	753	2437	2	chr3A.!!$F3	1684
11	TraesCS3D01G509500	chr3A	725842268	725843114	846	False	500.00	525	88.3385	864	1807	2	chr3A.!!$F2	943
12	TraesCS3D01G509500	chr3A	726714004	726716032	2028	True	240.00	285	91.7320	1413	1749	2	chr3A.!!$R1	336
13	TraesCS3D01G509500	chr1D	42896549	42897256	707	False	1003.00	1003	92.1160	1	721	1	chr1D.!!$F2	720

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	End Stability	Orientation
23	24	0.624500	ATTTGCCAGCCCTCTCCCTA	60.625	55.000	0.00	3.53	F
305	306	1.221840	CTCGTTGCTGTAGGGCCAT	59.778	57.895	6.18	4.40	F
1095	1135	0.105964	AAGACAACAGCACGCAGGTA	59.894	50.000	0.00	3.08	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1080	1117	0.038251	TCTCTACCTGCGTGCTGTTG	60.038	55.0	0.00	0.00	3.33	R
1708	3624	0.252057	TCCCGGAGAAGTCCATGTCA	60.252	55.0	0.73	44.18	3.58	R
2170	4174	0.318955	CCAGCGCCTGAAACCTTTTG	60.319	55.0	2.29	32.44	2.44	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
23	24	0.624500	ATTTGCCAGCCCTCTCCCTA	60.625	55.000	0.00	0.00	0.00	3.53
58	59	5.070446	ACCTACAGTCAGATTCAGTCACAAA	59.930	40.000	0.00	0.00	0.00	2.83
177	178	7.091811	TGGAGAAATCCCTATCCTTCTTCAAAT	60.092	37.037	0.00	0.00	31.81	2.32
196	197	2.484189	TCCTAACCCTAACCCTAGCC	57.516	55.000	0.00	0.00	0.00	3.93
298	299	1.540267	GTCAGAGGTCTCGTTGCTGTA	59.460	52.381	0.00	0.00	34.09	2.74
305	306	1.221840	CTCGTTGCTGTAGGGCCAT	59.778	57.895	6.18	0.00	0.00	4.40
354	360	1.476488	GCGAGAAGAAGAAGAGGAGCT	59.524	52.381	0.00	0.00	0.00	4.09
355	361	2.685897	GCGAGAAGAAGAAGAGGAGCTA	59.314	50.000	0.00	0.00	0.00	3.32
356	362	3.243068	GCGAGAAGAAGAAGAGGAGCTAG	60.243	52.174	0.00	0.00	0.00	3.42
357	363	3.243068	CGAGAAGAAGAAGAGGAGCTAGC	60.243	52.174	6.62	6.62	0.00	3.42
423	438	4.423209	AGGGGAGGGGGAGTGAGC	62.423	72.222	0.00	0.00	0.00	4.26
639	659	3.000041	TGTCACGAAATCAGCGCTAAAT	59.000	40.909	10.99	3.69	0.00	1.40
740	760	4.223556	TCTAATCAGAGACAGAGACGGT	57.776	45.455	0.00	0.00	0.00	4.83
741	761	4.193090	TCTAATCAGAGACAGAGACGGTC	58.807	47.826	0.00	0.00	35.50	4.79
743	763	3.916359	ATCAGAGACAGAGACGGTCTA	57.084	47.619	11.27	0.00	45.21	2.59
744	764	2.975266	TCAGAGACAGAGACGGTCTAC	58.025	52.381	11.27	5.16	45.21	2.59
745	765	1.661617	CAGAGACAGAGACGGTCTACG	59.338	57.143	11.27	7.64	45.21	3.51
746	766	1.549620	AGAGACAGAGACGGTCTACGA	59.450	52.381	11.27	0.00	45.21	3.43
747	767	1.928503	GAGACAGAGACGGTCTACGAG	59.071	57.143	11.27	4.06	45.21	4.18
748	768	2.417107	GAGACAGAGACGGTCTACGAGA	60.417	54.545	11.27	0.00	45.21	4.04
749	769	4.281013	GAGACAGAGACGGTCTACGAGAG	61.281	56.522	11.27	0.60	45.21	3.20
750	770	6.693626	GAGACAGAGACGGTCTACGAGAGT	62.694	54.167	11.27	3.76	45.21	3.24
751	771	7.390413	GAGACAGAGACGGTCTACGAGAGTA	62.390	52.000	11.27	0.00	45.21	2.59
802	824	3.549423	CGGACATAGTCGAAGCGGAATAA	60.549	47.826	0.00	0.00	32.65	1.40
1090	1130	0.654472	CGTGAAAGACAACAGCACGC	60.654	55.000	0.00	0.00	44.35	5.34
1095	1135	0.105964	AAGACAACAGCACGCAGGTA	59.894	50.000	0.00	0.00	0.00	3.08
1120	1160	0.744281	GAAGGAGAAGGAGGAGAGCG	59.256	60.000	0.00	0.00	0.00	5.03
1131	1171	1.682684	GGAGAGCGAGGGGAGACAA	60.683	63.158	0.00	0.00	0.00	3.18
1215	1255	4.541648	ATCTCCGTCCCCCTCCCG	62.542	72.222	0.00	0.00	0.00	5.14
1237	1277	3.872027	GAACGAAGGCGAGGTTCC	58.128	61.111	0.00	0.00	41.64	3.62
1312	1352	4.072839	TCCGATCATCGATGTAAGTAGCT	58.927	43.478	24.09	0.00	43.74	3.32
1318	1358	6.887376	TCATCGATGTAAGTAGCTTCAAAC	57.113	37.500	24.09	0.00	0.00	2.93
1319	1359	6.631016	TCATCGATGTAAGTAGCTTCAAACT	58.369	36.000	24.09	0.00	0.00	2.66
1320	1360	7.768240	TCATCGATGTAAGTAGCTTCAAACTA	58.232	34.615	24.09	0.00	0.00	2.24
1321	1361	8.414003	TCATCGATGTAAGTAGCTTCAAACTAT	58.586	33.333	24.09	0.00	0.00	2.12
1322	1362	8.695284	CATCGATGTAAGTAGCTTCAAACTATC	58.305	37.037	17.50	0.00	0.00	2.08
1323	1363	7.768240	TCGATGTAAGTAGCTTCAAACTATCA	58.232	34.615	0.00	0.00	0.00	2.15
1356	1396	3.443329	TGTGCACAACAGTTCATCTTGTT	59.557	39.130	19.28	0.00	33.78	2.83
1360	1411	4.736793	GCACAACAGTTCATCTTGTTTCTG	59.263	41.667	0.00	0.00	0.00	3.02
1362	1413	5.967674	CACAACAGTTCATCTTGTTTCTGTC	59.032	40.000	0.00	0.00	35.53	3.51
1708	3624	2.417719	AACTCAAGTCCCAGTACCCT	57.582	50.000	0.00	0.00	0.00	4.34
1794	3715	1.344438	TGAGGCGATAATGCGGAAGAT	59.656	47.619	0.00	0.00	35.06	2.40
1799	3720	3.975035	GGCGATAATGCGGAAGATTTTTC	59.025	43.478	0.00	0.00	35.06	2.29
1807	3728	2.032178	GCGGAAGATTTTTCGATGGAGG	59.968	50.000	0.00	0.00	37.49	4.30
1810	3731	4.394920	CGGAAGATTTTTCGATGGAGGAAA	59.605	41.667	0.00	0.00	37.49	3.13
1884	3808	2.780014	CTGTTTATGCGTCTACGTACCG	59.220	50.000	4.24	5.72	42.22	4.02
2025	4003	3.696281	TGTCGACGTTTTGAGTAGTCA	57.304	42.857	11.62	0.00	33.56	3.41
2034	4012	7.461546	CGACGTTTTGAGTAGTCATTCTATGTG	60.462	40.741	0.00	0.00	33.56	3.21
2170	4174	3.075148	GGGAAGTACAGTTTCAGAAGGC	58.925	50.000	0.00	0.00	0.00	4.35
2243	4247	3.477530	AGTTTGGGCTACACAGAAAGTC	58.522	45.455	0.00	0.00	0.00	3.01
2307	4320	6.469322	CACCAATAATGATACGATATGCACG	58.531	40.000	0.00	0.00	0.00	5.34
2323	4343	2.093625	TGCACGTATTTTTAGCAGAGCG	59.906	45.455	0.00	0.00	0.00	5.03
2389	4412	4.037923	TCTGAATTTGAGGTGTTTTGCTCC	59.962	41.667	0.00	0.00	0.00	4.70
2410	4433	7.916552	GCTCCTAAGCGTTCTTTGAATTAATA	58.083	34.615	0.00	0.00	39.10	0.98
2416	4439	8.620533	AAGCGTTCTTTGAATTAATATTGCTC	57.379	30.769	0.00	0.00	0.00	4.26
2469	4608	3.940209	TTTTGGATTGCTCACCACATC	57.060	42.857	0.00	0.00	35.81	3.06
2474	4613	2.616256	GGATTGCTCACCACATCTGTCA	60.616	50.000	0.00	0.00	0.00	3.58
2515	4654	5.762825	AATTGTTGCTGCTTCGATCATAT	57.237	34.783	0.00	0.00	0.00	1.78
2520	4659	0.441533	CTGCTTCGATCATATGGCGC	59.558	55.000	0.00	0.00	0.00	6.53
2582	5793	6.777213	TTTAGTTTTGGCCTTTGAAGTACA	57.223	33.333	3.32	0.00	0.00	2.90
2591	5802	7.589958	TGGCCTTTGAAGTACATTTTTCTAA	57.410	32.000	3.32	0.00	0.00	2.10
2635	5850	8.750298	TCTGTGGGTTTAATTTTTGTAGTGAAA	58.250	29.630	0.00	0.00	0.00	2.69
2644	5859	6.843069	ATTTTTGTAGTGAAAACATGCACC	57.157	33.333	0.00	0.00	35.67	5.01
2702	5918	5.006746	ACTGTCGCAGTTTTTCTTTACAGAG	59.993	40.000	0.00	0.00	42.59	3.35
2704	5920	5.353123	TGTCGCAGTTTTTCTTTACAGAGTT	59.647	36.000	0.00	0.00	0.00	3.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
40	41	3.136443	TGGGTTTGTGACTGAATCTGACT	59.864	43.478	0.00	0.00	0.00	3.41
58	59	4.228210	TGATAGATCCAAGCTTTTCTGGGT	59.772	41.667	0.00	0.00	37.18	4.51
177	178	1.412074	CGGCTAGGGTTAGGGTTAGGA	60.412	57.143	0.00	0.00	0.00	2.94
196	197	1.128200	TCTCTCCTCTCCTCTCCTCG	58.872	60.000	0.00	0.00	0.00	4.63
354	360	0.332972	TCCTCTGCTCTCCACTGCTA	59.667	55.000	0.00	0.00	0.00	3.49
355	361	0.971959	CTCCTCTGCTCTCCACTGCT	60.972	60.000	0.00	0.00	0.00	4.24
356	362	1.516892	CTCCTCTGCTCTCCACTGC	59.483	63.158	0.00	0.00	0.00	4.40
357	363	1.256361	TGCTCCTCTGCTCTCCACTG	61.256	60.000	0.00	0.00	0.00	3.66
411	426	2.608988	CACCAGCTCACTCCCCCT	60.609	66.667	0.00	0.00	0.00	4.79
412	427	3.721706	CCACCAGCTCACTCCCCC	61.722	72.222	0.00	0.00	0.00	5.40
413	428	3.721706	CCCACCAGCTCACTCCCC	61.722	72.222	0.00	0.00	0.00	4.81
414	429	2.607750	TCCCACCAGCTCACTCCC	60.608	66.667	0.00	0.00	0.00	4.30
423	438	4.778415	CGCTCGTCGTCCCACCAG	62.778	72.222	0.00	0.00	0.00	4.00
577	596	2.032377	TGATGACCGTTTCAAGCGTTTC	60.032	45.455	0.00	0.00	37.92	2.78
639	659	8.904099	TTTTAAAAACTGACCAAAAACTCCAA	57.096	26.923	0.00	0.00	0.00	3.53
722	742	3.080300	AGACCGTCTCTGTCTCTGATT	57.920	47.619	0.00	0.00	38.71	2.57
727	747	1.928503	CTCGTAGACCGTCTCTGTCTC	59.071	57.143	3.74	0.00	41.97	3.36
728	748	1.549620	TCTCGTAGACCGTCTCTGTCT	59.450	52.381	3.74	0.00	44.85	3.41
729	749	1.928503	CTCTCGTAGACCGTCTCTGTC	59.071	57.143	3.74	0.00	37.94	3.51
730	750	1.275856	ACTCTCGTAGACCGTCTCTGT	59.724	52.381	3.74	0.00	37.94	3.41
731	751	2.012937	ACTCTCGTAGACCGTCTCTG	57.987	55.000	3.74	0.00	37.94	3.35
732	752	3.520569	GTTACTCTCGTAGACCGTCTCT	58.479	50.000	3.74	0.00	37.94	3.10
733	753	2.281234	CGTTACTCTCGTAGACCGTCTC	59.719	54.545	3.74	0.00	37.94	3.36
734	754	2.094494	TCGTTACTCTCGTAGACCGTCT	60.094	50.000	6.25	6.25	37.94	4.18
735	755	2.263077	TCGTTACTCTCGTAGACCGTC	58.737	52.381	0.00	0.00	37.94	4.79
736	756	2.094494	TCTCGTTACTCTCGTAGACCGT	60.094	50.000	0.00	0.00	37.94	4.83
737	757	2.281234	GTCTCGTTACTCTCGTAGACCG	59.719	54.545	0.00	0.00	33.73	4.79
738	758	2.281234	CGTCTCGTTACTCTCGTAGACC	59.719	54.545	0.00	0.00	34.93	3.85
739	759	2.284969	GCGTCTCGTTACTCTCGTAGAC	60.285	54.545	0.00	0.00	34.99	2.59
740	760	1.923204	GCGTCTCGTTACTCTCGTAGA	59.077	52.381	0.00	0.00	0.00	2.59
741	761	1.005137	GGCGTCTCGTTACTCTCGTAG	60.005	57.143	0.00	0.00	0.00	3.51
742	762	1.002366	GGCGTCTCGTTACTCTCGTA	58.998	55.000	0.00	0.00	0.00	3.43
743	763	1.792941	GGCGTCTCGTTACTCTCGT	59.207	57.895	0.00	0.00	0.00	4.18
744	764	1.296722	CGGCGTCTCGTTACTCTCG	60.297	63.158	0.00	0.00	0.00	4.04
745	765	1.583194	GCGGCGTCTCGTTACTCTC	60.583	63.158	9.37	0.00	0.00	3.20
746	766	2.484203	GCGGCGTCTCGTTACTCT	59.516	61.111	9.37	0.00	0.00	3.24
747	767	2.943034	CGCGGCGTCTCGTTACTC	60.943	66.667	15.36	0.00	0.00	2.59
748	768	4.471726	CCGCGGCGTCTCGTTACT	62.472	66.667	22.00	0.00	0.00	2.24
749	769	3.951655	TTCCGCGGCGTCTCGTTAC	62.952	63.158	23.51	0.00	0.00	2.50
750	770	2.546645	AATTCCGCGGCGTCTCGTTA	62.547	55.000	23.51	0.00	0.00	3.18
751	771	3.927163	AATTCCGCGGCGTCTCGTT	62.927	57.895	23.51	3.96	0.00	3.85
881	908	3.580319	AGGCTTTGGGCTTCGGGT	61.580	61.111	0.00	0.00	46.62	5.28
1008	1045	1.764723	TGCATGATGTCCTCGGAGATT	59.235	47.619	6.58	0.00	33.89	2.40
1077	1114	0.319900	CTACCTGCGTGCTGTTGTCT	60.320	55.000	0.00	0.00	0.00	3.41
1080	1117	0.038251	TCTCTACCTGCGTGCTGTTG	60.038	55.000	0.00	0.00	0.00	3.33
1090	1130	4.605183	TCCTTCTCCTTCTTCTCTACCTG	58.395	47.826	0.00	0.00	0.00	4.00
1095	1135	3.596046	TCTCCTCCTTCTCCTTCTTCTCT	59.404	47.826	0.00	0.00	0.00	3.10
1120	1160	1.271434	GGAGTTTGGTTGTCTCCCCTC	60.271	57.143	0.00	0.00	41.09	4.30
1215	1255	1.448013	CCTCGCCTTCGTTCCTTCC	60.448	63.158	0.00	0.00	36.96	3.46
1312	1352	9.098355	GCACATAGTTGATAGTGATAGTTTGAA	57.902	33.333	0.00	0.00	33.99	2.69
1318	1358	7.492344	TGTTGTGCACATAGTTGATAGTGATAG	59.508	37.037	22.39	0.00	33.99	2.08
1319	1359	7.327214	TGTTGTGCACATAGTTGATAGTGATA	58.673	34.615	22.39	0.00	33.99	2.15
1320	1360	6.172630	TGTTGTGCACATAGTTGATAGTGAT	58.827	36.000	22.39	0.00	33.99	3.06
1321	1361	5.546526	TGTTGTGCACATAGTTGATAGTGA	58.453	37.500	22.39	0.00	33.99	3.41
1322	1362	5.409520	ACTGTTGTGCACATAGTTGATAGTG	59.590	40.000	22.39	1.34	33.76	2.74
1323	1363	5.551233	ACTGTTGTGCACATAGTTGATAGT	58.449	37.500	22.39	14.87	33.76	2.12
1337	1377	4.736793	CAGAAACAAGATGAACTGTTGTGC	59.263	41.667	0.00	0.00	40.24	4.57
1356	1396	4.155462	GCATCAGCAAGAGATTTGACAGAA	59.845	41.667	0.00	0.00	41.58	3.02
1360	1411	2.223203	CCGCATCAGCAAGAGATTTGAC	60.223	50.000	0.00	0.00	42.27	3.18
1362	1413	1.741706	ACCGCATCAGCAAGAGATTTG	59.258	47.619	0.00	0.00	42.27	2.32
1552	1610	0.604780	GCTTGCTGCTCTCAGGTTCA	60.605	55.000	0.00	0.00	40.65	3.18
1576	1634	1.753078	CGTCTCGGGGTCCAGATCA	60.753	63.158	0.00	0.00	0.00	2.92
1708	3624	0.252057	TCCCGGAGAAGTCCATGTCA	60.252	55.000	0.73	0.00	44.18	3.58
1775	3696	2.086054	ATCTTCCGCATTATCGCCTC	57.914	50.000	0.00	0.00	0.00	4.70
1794	3715	2.500229	AGCGTTTCCTCCATCGAAAAA	58.500	42.857	0.00	0.00	31.32	1.94
1799	3720	2.194271	GTAGAAGCGTTTCCTCCATCG	58.806	52.381	8.51	0.00	33.64	3.84
1884	3808	7.593825	AGTCATCCAAATAGCAAACTACAAAC	58.406	34.615	0.00	0.00	0.00	2.93
1992	3970	9.796062	TCAAAACGTCGACAATACTATTAAAAC	57.204	29.630	17.16	0.00	0.00	2.43
1994	3972	9.195411	ACTCAAAACGTCGACAATACTATTAAA	57.805	29.630	17.16	0.00	0.00	1.52
1995	3973	8.746922	ACTCAAAACGTCGACAATACTATTAA	57.253	30.769	17.16	0.00	0.00	1.40
1998	3976	7.533426	ACTACTCAAAACGTCGACAATACTAT	58.467	34.615	17.16	0.00	0.00	2.12
2001	3979	5.626543	TGACTACTCAAAACGTCGACAATAC	59.373	40.000	17.16	0.00	0.00	1.89
2008	3986	6.527023	ACATAGAATGACTACTCAAAACGTCG	59.473	38.462	0.00	0.00	33.62	5.12
2025	4003	6.579666	ATGCGCCATATTTTCACATAGAAT	57.420	33.333	4.18	0.00	35.83	2.40
2074	4056	5.470368	TCCACTTCTCTGTAAACTTGATCG	58.530	41.667	0.00	0.00	0.00	3.69
2170	4174	0.318955	CCAGCGCCTGAAACCTTTTG	60.319	55.000	2.29	0.00	32.44	2.44
2243	4247	5.308825	ACATCCAGGTTCTTGTTACTGAAG	58.691	41.667	0.00	0.00	32.86	3.02
2307	4320	3.757745	TTGGCGCTCTGCTAAAAATAC	57.242	42.857	7.64	0.00	41.53	1.89
2323	4343	3.189287	AGACATCATGACGTTTCTTTGGC	59.811	43.478	0.00	0.00	0.00	4.52
2389	4412	9.722056	AGCAATATTAATTCAAAGAACGCTTAG	57.278	29.630	0.00	0.00	32.98	2.18
2453	4592	2.012673	GACAGATGTGGTGAGCAATCC	58.987	52.381	0.00	0.00	0.00	3.01
2469	4608	4.743057	TTAGTCTGGATCCACATGACAG	57.257	45.455	26.08	10.99	0.00	3.51
2474	4613	8.906867	CAACAATTATTTAGTCTGGATCCACAT	58.093	33.333	11.44	1.84	0.00	3.21
2582	5793	7.269316	ACACCCGTTTGTTTCATTAGAAAAAT	58.731	30.769	0.00	0.00	44.75	1.82
2591	5802	4.215399	CACAGATACACCCGTTTGTTTCAT	59.785	41.667	6.79	0.00	31.82	2.57
2602	5813	6.599356	AAAATTAAACCCACAGATACACCC	57.401	37.500	0.00	0.00	0.00	4.61
2635	5850	6.763355	AGATAAGAGAATATCGGTGCATGTT	58.237	36.000	0.00	0.00	37.37	2.71
2669	5885	7.136772	AGAAAAACTGCGACAGTAAAATTACC	58.863	34.615	11.92	1.56	44.62	2.85
2673	5889	8.185505	TGTAAAGAAAAACTGCGACAGTAAAAT	58.814	29.630	11.92	1.57	44.62	1.82
2702	5918	1.212751	GAAGCACCGGCCAATGAAC	59.787	57.895	0.00	0.00	42.56	3.18
2704	5920	1.971167	GTGAAGCACCGGCCAATGA	60.971	57.895	0.00	0.00	42.56	2.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.