AutoCloner

Multiple sequence alignment - TraesCS5B01G436900

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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	TraesCS5B01G436900	chr5B	100.000	3183	0	0	1	3183	610303775	610306957	0.000000e+00	5879
1	TraesCS5B01G436900	chr5B	96.662	779	25	1	1	778	617597171	617597949	0.000000e+00	1293
2	TraesCS5B01G436900	chr5B	95.652	782	31	3	1	779	609105085	609105866	0.000000e+00	1253
3	TraesCS5B01G436900	chr5B	95.432	613	18	3	1763	2375	610499593	610500195	0.000000e+00	968
4	TraesCS5B01G436900	chr5B	88.492	252	10	5	873	1105	610499282	610499533	1.440000e-73	287
5	TraesCS5B01G436900	chr5A	91.429	1540	102	17	840	2375	617205962	617207475	0.000000e+00	2085
6	TraesCS5B01G436900	chr5A	89.651	802	77	6	2386	3182	572024744	572025544	0.000000e+00	1016
7	TraesCS5B01G436900	chr5D	92.703	1439	65	15	946	2375	494214929	494216336	0.000000e+00	2039
8	TraesCS5B01G436900	chr6B	96.277	779	28	1	1	778	717700124	717700902	0.000000e+00	1277
9	TraesCS5B01G436900	chr1B	95.892	779	30	2	1	778	449989229	449988452	0.000000e+00	1260
10	TraesCS5B01G436900	chrUn	95.780	782	29	2	1	778	6853444	6854225	0.000000e+00	1258
11	TraesCS5B01G436900	chrUn	91.261	801	66	4	2386	3183	122326540	122327339	0.000000e+00	1088
12	TraesCS5B01G436900	chr3B	95.780	782	28	2	1	777	14989065	14989846	0.000000e+00	1256
13	TraesCS5B01G436900	chr3B	95.764	779	32	1	1	778	48017937	48017159	0.000000e+00	1254
14	TraesCS5B01G436900	chr3B	95.764	779	31	2	1	778	683034954	683035731	0.000000e+00	1254
15	TraesCS5B01G436900	chr3B	95.764	779	30	3	1	778	829474706	829475482	0.000000e+00	1253
16	TraesCS5B01G436900	chr3B	89.987	799	78	2	2386	3182	166660430	166659632	0.000000e+00	1031
17	TraesCS5B01G436900	chr2B	92.875	800	55	2	2386	3183	653907924	653908723	0.000000e+00	1160
18	TraesCS5B01G436900	chr2B	91.635	801	63	4	2386	3183	736967889	736968688	0.000000e+00	1105
19	TraesCS5B01G436900	chr2B	91.375	800	67	2	2386	3183	65681437	65680638	0.000000e+00	1094
20	TraesCS5B01G436900	chr3A	91.034	803	68	4	2383	3182	107055061	107055862	0.000000e+00	1081
21	TraesCS5B01G436900	chr7A	90.488	799	71	4	2386	3182	150085237	150084442	0.000000e+00	1050
22	TraesCS5B01G436900	chr1A	89.677	804	72	10	2385	3182	576791697	576792495	0.000000e+00	1014
23	TraesCS5B01G436900	chr4B	76.707	498	81	23	1614	2101	109222407	109222879	8.820000e-61	244
24	TraesCS5B01G436900	chr4A	76.295	502	77	24	1614	2101	508274503	508274030	2.470000e-56	230
25	TraesCS5B01G436900	chr4A	76.946	334	60	13	1780	2101	508494458	508494130	1.170000e-39	174

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	TraesCS5B01G436900	chr5B	610303775	610306957	3182	False	5879.0	5879	100.000	1	3183	1	chr5B.!!$F2	3182
1	TraesCS5B01G436900	chr5B	617597171	617597949	778	False	1293.0	1293	96.662	1	778	1	chr5B.!!$F3	777
2	TraesCS5B01G436900	chr5B	609105085	609105866	781	False	1253.0	1253	95.652	1	779	1	chr5B.!!$F1	778
3	TraesCS5B01G436900	chr5B	610499282	610500195	913	False	627.5	968	91.962	873	2375	2	chr5B.!!$F4	1502
4	TraesCS5B01G436900	chr5A	617205962	617207475	1513	False	2085.0	2085	91.429	840	2375	1	chr5A.!!$F2	1535
5	TraesCS5B01G436900	chr5A	572024744	572025544	800	False	1016.0	1016	89.651	2386	3182	1	chr5A.!!$F1	796
6	TraesCS5B01G436900	chr5D	494214929	494216336	1407	False	2039.0	2039	92.703	946	2375	1	chr5D.!!$F1	1429
7	TraesCS5B01G436900	chr6B	717700124	717700902	778	False	1277.0	1277	96.277	1	778	1	chr6B.!!$F1	777
8	TraesCS5B01G436900	chr1B	449988452	449989229	777	True	1260.0	1260	95.892	1	778	1	chr1B.!!$R1	777
9	TraesCS5B01G436900	chrUn	6853444	6854225	781	False	1258.0	1258	95.780	1	778	1	chrUn.!!$F1	777
10	TraesCS5B01G436900	chrUn	122326540	122327339	799	False	1088.0	1088	91.261	2386	3183	1	chrUn.!!$F2	797
11	TraesCS5B01G436900	chr3B	14989065	14989846	781	False	1256.0	1256	95.780	1	777	1	chr3B.!!$F1	776
12	TraesCS5B01G436900	chr3B	48017159	48017937	778	True	1254.0	1254	95.764	1	778	1	chr3B.!!$R1	777
13	TraesCS5B01G436900	chr3B	683034954	683035731	777	False	1254.0	1254	95.764	1	778	1	chr3B.!!$F2	777
14	TraesCS5B01G436900	chr3B	829474706	829475482	776	False	1253.0	1253	95.764	1	778	1	chr3B.!!$F3	777
15	TraesCS5B01G436900	chr3B	166659632	166660430	798	True	1031.0	1031	89.987	2386	3182	1	chr3B.!!$R2	796
16	TraesCS5B01G436900	chr2B	653907924	653908723	799	False	1160.0	1160	92.875	2386	3183	1	chr2B.!!$F1	797
17	TraesCS5B01G436900	chr2B	736967889	736968688	799	False	1105.0	1105	91.635	2386	3183	1	chr2B.!!$F2	797
18	TraesCS5B01G436900	chr2B	65680638	65681437	799	True	1094.0	1094	91.375	2386	3183	1	chr2B.!!$R1	797
19	TraesCS5B01G436900	chr3A	107055061	107055862	801	False	1081.0	1081	91.034	2383	3182	1	chr3A.!!$F1	799
20	TraesCS5B01G436900	chr7A	150084442	150085237	795	True	1050.0	1050	90.488	2386	3182	1	chr7A.!!$R1	796
21	TraesCS5B01G436900	chr1A	576791697	576792495	798	False	1014.0	1014	89.677	2385	3182	1	chr1A.!!$F1	797

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
798	809	0.037697	CTTACCACCACTGCACGCTA	60.038	55.0	0.0	0.0	0.0	4.26	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2621	2662	0.107459	GAAGATTGAGAAGGGCGGCT	60.107	55.0	9.56	0.0	0.0	5.52	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
315	316	2.623763	TAGAGGGAGGGGCTGGGA	60.624	66.667	0.00	0.00	0.00	4.37
540	550	3.595758	CATTGATTCCCCGCGGGC	61.596	66.667	39.46	25.12	43.94	6.13
710	721	2.046285	CCGGCAAAAATCGGGCTCT	61.046	57.895	0.00	0.00	42.32	4.09
716	727	1.892474	CAAAAATCGGGCTCTTGGGAA	59.108	47.619	0.00	0.00	0.00	3.97
784	795	2.275748	GCCTTCCTGGGCCTTACC	59.724	66.667	4.53	0.00	45.92	2.85
785	796	2.612493	GCCTTCCTGGGCCTTACCA	61.612	63.158	4.53	0.00	45.92	3.25
786	797	1.303282	CCTTCCTGGGCCTTACCAC	59.697	63.158	4.53	0.00	42.05	4.16
787	798	1.303282	CTTCCTGGGCCTTACCACC	59.697	63.158	4.53	0.00	42.05	4.61
788	799	1.464395	TTCCTGGGCCTTACCACCA	60.464	57.895	4.53	0.00	42.05	4.17
789	800	1.785353	TTCCTGGGCCTTACCACCAC	61.785	60.000	4.53	0.00	42.05	4.16
790	801	2.231380	CCTGGGCCTTACCACCACT	61.231	63.158	4.53	0.00	42.05	4.00
791	802	1.002134	CTGGGCCTTACCACCACTG	60.002	63.158	4.53	0.00	42.05	3.66
792	803	2.361230	GGGCCTTACCACCACTGC	60.361	66.667	0.84	0.00	42.05	4.40
793	804	2.434331	GGCCTTACCACCACTGCA	59.566	61.111	0.00	0.00	38.86	4.41
794	805	1.971695	GGCCTTACCACCACTGCAC	60.972	63.158	0.00	0.00	38.86	4.57
795	806	2.325082	GCCTTACCACCACTGCACG	61.325	63.158	0.00	0.00	0.00	5.34
796	807	2.325082	CCTTACCACCACTGCACGC	61.325	63.158	0.00	0.00	0.00	5.34
797	808	1.301716	CTTACCACCACTGCACGCT	60.302	57.895	0.00	0.00	0.00	5.07
798	809	0.037697	CTTACCACCACTGCACGCTA	60.038	55.000	0.00	0.00	0.00	4.26
799	810	0.037697	TTACCACCACTGCACGCTAG	60.038	55.000	0.00	0.00	0.00	3.42
800	811	1.884075	TACCACCACTGCACGCTAGG	61.884	60.000	0.00	0.00	0.00	3.02
801	812	2.343758	CACCACTGCACGCTAGGT	59.656	61.111	0.00	0.00	0.00	3.08
802	813	1.589630	CACCACTGCACGCTAGGTA	59.410	57.895	0.00	0.00	0.00	3.08
803	814	0.458543	CACCACTGCACGCTAGGTAG	60.459	60.000	0.00	0.00	0.00	3.18
804	815	1.519455	CCACTGCACGCTAGGTAGC	60.519	63.158	0.00	0.00	45.62	3.58
805	816	1.519455	CACTGCACGCTAGGTAGCC	60.519	63.158	3.39	0.00	46.34	3.93
806	817	2.278857	CTGCACGCTAGGTAGCCG	60.279	66.667	3.39	2.07	46.34	5.52
807	818	3.774959	CTGCACGCTAGGTAGCCGG	62.775	68.421	0.00	0.00	46.34	6.13
809	820	4.587189	CACGCTAGGTAGCCGGCC	62.587	72.222	26.15	8.83	46.34	6.13
812	823	3.930012	GCTAGGTAGCCGGCCCAG	61.930	72.222	26.15	17.71	43.39	4.45
813	824	3.930012	CTAGGTAGCCGGCCCAGC	61.930	72.222	26.15	21.14	0.00	4.85
814	825	4.475444	TAGGTAGCCGGCCCAGCT	62.475	66.667	27.33	27.33	44.49	4.24
815	826	3.995809	TAGGTAGCCGGCCCAGCTT	62.996	63.158	28.78	11.88	41.83	3.74
821	832	3.399181	CCGGCCCAGCTTGGTCTA	61.399	66.667	6.89	0.00	35.17	2.59
822	833	2.746375	CCGGCCCAGCTTGGTCTAT	61.746	63.158	6.89	0.00	35.17	1.98
823	834	1.407656	CCGGCCCAGCTTGGTCTATA	61.408	60.000	6.89	0.00	35.17	1.31
824	835	0.687354	CGGCCCAGCTTGGTCTATAT	59.313	55.000	6.89	0.00	35.17	0.86
825	836	1.899814	CGGCCCAGCTTGGTCTATATA	59.100	52.381	6.89	0.00	35.17	0.86
826	837	2.353803	CGGCCCAGCTTGGTCTATATAC	60.354	54.545	6.89	0.00	35.17	1.47
827	838	2.907042	GGCCCAGCTTGGTCTATATACT	59.093	50.000	5.61	0.00	35.17	2.12
828	839	3.307059	GGCCCAGCTTGGTCTATATACTG	60.307	52.174	5.61	0.00	35.17	2.74
829	840	3.325135	GCCCAGCTTGGTCTATATACTGT	59.675	47.826	5.61	0.00	35.17	3.55
830	841	4.527038	GCCCAGCTTGGTCTATATACTGTA	59.473	45.833	5.61	0.00	35.17	2.74
831	842	5.187967	GCCCAGCTTGGTCTATATACTGTAT	59.812	44.000	5.61	5.53	35.17	2.29
832	843	6.634805	CCCAGCTTGGTCTATATACTGTATG	58.365	44.000	10.51	0.00	35.17	2.39
833	844	6.437477	CCCAGCTTGGTCTATATACTGTATGA	59.563	42.308	10.51	0.00	35.17	2.15
834	845	7.363355	CCCAGCTTGGTCTATATACTGTATGAG	60.363	44.444	10.51	7.68	35.17	2.90
835	846	7.177568	CCAGCTTGGTCTATATACTGTATGAGT	59.822	40.741	10.51	0.00	33.83	3.41
836	847	9.232473	CAGCTTGGTCTATATACTGTATGAGTA	57.768	37.037	10.51	0.00	41.57	2.59
852	863	7.139392	TGTATGAGTATATCTTGCACTCGTTC	58.861	38.462	3.28	0.36	41.29	3.95
856	867	1.891178	TATCTTGCACTCGTTCGTCG	58.109	50.000	0.00	0.00	41.41	5.12
858	869	1.660575	CTTGCACTCGTTCGTCGGT	60.661	57.895	0.00	0.00	40.32	4.69
895	906	4.389077	CACTACTTTCCGAGTCACCATTTC	59.611	45.833	0.00	0.00	39.86	2.17
901	912	3.138304	TCCGAGTCACCATTTCTGTTTG	58.862	45.455	0.00	0.00	0.00	2.93
934	953	2.167662	TGTCGTTGATCTAGTGGCTGA	58.832	47.619	0.00	0.00	0.00	4.26
949	968	2.031120	GGCTGAGCACTGATCTCTACT	58.969	52.381	6.82	0.00	0.00	2.57
1524	1558	2.362889	CCCTTGCCCCCATCACAC	60.363	66.667	0.00	0.00	0.00	3.82
1553	1587	2.043252	AGGTAGGTAAGCCACTCACTCT	59.957	50.000	0.00	0.00	37.19	3.24
1554	1588	2.166664	GGTAGGTAAGCCACTCACTCTG	59.833	54.545	0.00	0.00	37.19	3.35
1555	1589	2.016905	AGGTAAGCCACTCACTCTGT	57.983	50.000	0.00	0.00	37.19	3.41
1556	1590	1.896465	AGGTAAGCCACTCACTCTGTC	59.104	52.381	0.00	0.00	37.19	3.51
1557	1591	1.618837	GGTAAGCCACTCACTCTGTCA	59.381	52.381	0.00	0.00	34.09	3.58
1558	1592	2.610727	GGTAAGCCACTCACTCTGTCAC	60.611	54.545	0.00	0.00	34.09	3.67
1559	1593	1.418334	AAGCCACTCACTCTGTCACT	58.582	50.000	0.00	0.00	0.00	3.41
1561	1595	0.676184	GCCACTCACTCTGTCACTCA	59.324	55.000	0.00	0.00	0.00	3.41
1563	1597	1.000283	CCACTCACTCTGTCACTCACC	60.000	57.143	0.00	0.00	0.00	4.02
1564	1598	1.959985	CACTCACTCTGTCACTCACCT	59.040	52.381	0.00	0.00	0.00	4.00
1565	1599	2.363680	CACTCACTCTGTCACTCACCTT	59.636	50.000	0.00	0.00	0.00	3.50
1566	1600	2.625790	ACTCACTCTGTCACTCACCTTC	59.374	50.000	0.00	0.00	0.00	3.46
1567	1601	1.964223	TCACTCTGTCACTCACCTTCC	59.036	52.381	0.00	0.00	0.00	3.46
1568	1602	1.967066	CACTCTGTCACTCACCTTCCT	59.033	52.381	0.00	0.00	0.00	3.36
1569	1603	2.366916	CACTCTGTCACTCACCTTCCTT	59.633	50.000	0.00	0.00	0.00	3.36
1570	1604	2.630580	ACTCTGTCACTCACCTTCCTTC	59.369	50.000	0.00	0.00	0.00	3.46
1571	1605	1.613925	TCTGTCACTCACCTTCCTTCG	59.386	52.381	0.00	0.00	0.00	3.79
1572	1606	1.341531	CTGTCACTCACCTTCCTTCGT	59.658	52.381	0.00	0.00	0.00	3.85
1573	1607	1.760613	TGTCACTCACCTTCCTTCGTT	59.239	47.619	0.00	0.00	0.00	3.85
1583	1617	2.159226	CCTTCCTTCGTTAGCGTCTCAT	60.159	50.000	0.00	0.00	39.49	2.90
1585	1619	2.876091	TCCTTCGTTAGCGTCTCATTG	58.124	47.619	0.00	0.00	39.49	2.82
1590	1624	1.317611	CGTTAGCGTCTCATTGTGTCG	59.682	52.381	0.00	1.87	0.00	4.35
1607	1641	0.457035	TCGAACGAATTAGGGTCGGG	59.543	55.000	14.30	0.00	42.82	5.14
1608	1642	0.457035	CGAACGAATTAGGGTCGGGA	59.543	55.000	8.20	0.00	42.82	5.14
1620	1654	3.948702	TCGGGAATCGATGGAGCA	58.051	55.556	0.00	0.00	43.74	4.26
1738	1772	2.446435	GAACACCCCGTACTAGTACCA	58.554	52.381	24.06	0.00	32.61	3.25
1748	1782	0.749454	ACTAGTACCACCTACGGCCG	60.749	60.000	26.86	26.86	0.00	6.13
1894	1928	3.862124	GTGTCGCGCACAGAAGAT	58.138	55.556	22.75	0.00	46.91	2.40
2140	2174	0.817654	TGGTCGTCTACAGCCTCATG	59.182	55.000	0.00	0.00	0.00	3.07
2176	2210	1.137086	CCACTCATCGACTTACCCAGG	59.863	57.143	0.00	0.00	0.00	4.45
2235	2272	5.051039	GCGATGCTAATAAAATCGACTCACA	60.051	40.000	8.35	0.00	44.57	3.58
2236	2273	6.347881	CGATGCTAATAAAATCGACTCACAC	58.652	40.000	0.00	0.00	44.57	3.82
2237	2274	6.199154	CGATGCTAATAAAATCGACTCACACT	59.801	38.462	0.00	0.00	44.57	3.55
2238	2275	6.887376	TGCTAATAAAATCGACTCACACTC	57.113	37.500	0.00	0.00	0.00	3.51
2239	2276	6.394809	TGCTAATAAAATCGACTCACACTCA	58.605	36.000	0.00	0.00	0.00	3.41
2240	2277	6.310467	TGCTAATAAAATCGACTCACACTCAC	59.690	38.462	0.00	0.00	0.00	3.51
2257	2294	3.115554	CTCACGCATCATCAACACGATA	58.884	45.455	0.00	0.00	31.20	2.92
2329	2367	2.618053	CCGCGGATTACAAGAAGAAGT	58.382	47.619	24.07	0.00	0.00	3.01
2332	2370	3.678072	CGCGGATTACAAGAAGAAGTTGA	59.322	43.478	0.00	0.00	0.00	3.18
2379	2417	2.993545	CGAGAGATCGGAGCTTGTTAG	58.006	52.381	0.00	0.00	0.00	2.34
2380	2418	2.614520	CGAGAGATCGGAGCTTGTTAGA	59.385	50.000	0.00	0.00	0.00	2.10
2381	2419	3.547214	CGAGAGATCGGAGCTTGTTAGAC	60.547	52.174	0.00	0.00	0.00	2.59
2382	2420	3.626930	AGAGATCGGAGCTTGTTAGACT	58.373	45.455	0.00	0.00	0.00	3.24
2383	2421	4.020543	AGAGATCGGAGCTTGTTAGACTT	58.979	43.478	0.00	0.00	0.00	3.01
2384	2422	4.464597	AGAGATCGGAGCTTGTTAGACTTT	59.535	41.667	0.00	0.00	0.00	2.66
2712	2753	0.883370	GGGTTCGTTGTTCTCGGCTT	60.883	55.000	0.00	0.00	0.00	4.35
2886	2927	2.363795	CCCCTGCGGTCTCCACTA	60.364	66.667	0.00	0.00	0.00	2.74
2924	2965	1.153168	CATGATCTCCGGGCCGTTT	60.153	57.895	26.32	5.99	0.00	3.60
2943	2984	4.684703	CGTTTCACTTCGACAACCTAATCT	59.315	41.667	0.00	0.00	0.00	2.40
2999	3040	1.810030	CGCCAAGGTTCTACCGCTC	60.810	63.158	0.00	0.00	44.90	5.03
3153	3194	1.048724	CGCTATCCAGGGTTCCCTCA	61.049	60.000	7.52	0.00	33.50	3.86

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
688	699	1.291906	CCCGATTTTTGCCGGCTTT	59.708	52.632	29.70	7.47	44.07	3.51
697	708	1.893137	GTTCCCAAGAGCCCGATTTTT	59.107	47.619	0.00	0.00	0.00	1.94
716	727	4.922026	AAAACGGCCCAGTCGCGT	62.922	61.111	5.77	0.00	32.11	6.01
778	789	2.325082	GCGTGCAGTGGTGGTAAGG	61.325	63.158	0.00	0.00	0.00	2.69
780	791	0.037697	CTAGCGTGCAGTGGTGGTAA	60.038	55.000	0.00	0.00	0.00	2.85
781	792	1.589630	CTAGCGTGCAGTGGTGGTA	59.410	57.895	0.00	0.00	0.00	3.25
782	793	2.343758	CTAGCGTGCAGTGGTGGT	59.656	61.111	0.00	0.00	0.00	4.16
783	794	1.884075	TACCTAGCGTGCAGTGGTGG	61.884	60.000	11.72	0.00	32.74	4.61
784	795	0.458543	CTACCTAGCGTGCAGTGGTG	60.459	60.000	11.72	2.00	32.74	4.17
785	796	1.890894	CTACCTAGCGTGCAGTGGT	59.109	57.895	0.00	8.13	35.05	4.16
786	797	1.519455	GCTACCTAGCGTGCAGTGG	60.519	63.158	0.00	0.00	39.82	4.00
787	798	4.094684	GCTACCTAGCGTGCAGTG	57.905	61.111	0.00	0.00	39.82	3.66
796	807	3.930012	GCTGGGCCGGCTACCTAG	61.930	72.222	30.08	17.93	38.73	3.02
797	808	3.995809	AAGCTGGGCCGGCTACCTA	62.996	63.158	38.63	6.74	46.32	3.08
808	819	6.437477	TCATACAGTATATAGACCAAGCTGGG	59.563	42.308	5.25	5.25	43.37	4.45
809	820	7.177568	ACTCATACAGTATATAGACCAAGCTGG	59.822	40.741	8.47	0.00	37.24	4.85
810	821	8.116651	ACTCATACAGTATATAGACCAAGCTG	57.883	38.462	8.47	0.00	31.37	4.24
811	822	9.983024	ATACTCATACAGTATATAGACCAAGCT	57.017	33.333	8.47	0.00	45.22	3.74
824	835	7.444487	ACGAGTGCAAGATATACTCATACAGTA	59.556	37.037	0.00	0.00	42.09	2.74
825	836	6.263392	ACGAGTGCAAGATATACTCATACAGT	59.737	38.462	0.00	0.00	40.57	3.55
826	837	6.673106	ACGAGTGCAAGATATACTCATACAG	58.327	40.000	0.00	0.00	40.57	2.74
827	838	6.635030	ACGAGTGCAAGATATACTCATACA	57.365	37.500	0.00	0.00	40.57	2.29
828	839	6.303496	CGAACGAGTGCAAGATATACTCATAC	59.697	42.308	0.00	0.00	40.57	2.39
829	840	6.017357	ACGAACGAGTGCAAGATATACTCATA	60.017	38.462	0.14	0.00	40.57	2.15
830	841	5.215903	CGAACGAGTGCAAGATATACTCAT	58.784	41.667	0.00	0.00	40.57	2.90
831	842	4.095932	ACGAACGAGTGCAAGATATACTCA	59.904	41.667	0.14	0.00	40.57	3.41
832	843	4.599047	ACGAACGAGTGCAAGATATACTC	58.401	43.478	0.14	0.00	37.93	2.59
833	844	4.599047	GACGAACGAGTGCAAGATATACT	58.401	43.478	0.14	0.00	0.00	2.12
834	845	3.417969	CGACGAACGAGTGCAAGATATAC	59.582	47.826	0.14	0.00	45.77	1.47
835	846	3.547413	CCGACGAACGAGTGCAAGATATA	60.547	47.826	0.00	0.00	45.77	0.86
836	847	2.451132	CGACGAACGAGTGCAAGATAT	58.549	47.619	0.14	0.00	45.77	1.63
837	848	1.466866	CCGACGAACGAGTGCAAGATA	60.467	52.381	0.00	0.00	45.77	1.98
838	849	0.732880	CCGACGAACGAGTGCAAGAT	60.733	55.000	0.00	0.00	45.77	2.40
843	854	3.164011	CGACCGACGAACGAGTGC	61.164	66.667	0.00	0.00	45.77	4.40
895	906	3.249917	ACAACGCAGGAAAAACAAACAG	58.750	40.909	0.00	0.00	0.00	3.16
901	912	1.843753	CAACGACAACGCAGGAAAAAC	59.156	47.619	0.00	0.00	43.96	2.43
934	953	3.095332	TGAGCAAGTAGAGATCAGTGCT	58.905	45.455	0.00	0.00	44.62	4.40
949	968	3.677148	GCAGCTACAGTAGTGATGAGCAA	60.677	47.826	19.08	0.00	32.95	3.91
1020	1054	4.856607	GAGAGGTCGAAGCGGCGG	62.857	72.222	9.78	0.00	29.52	6.13
1524	1558	1.614413	GGCTTACCTACCTCATCCTCG	59.386	57.143	0.00	0.00	0.00	4.63
1553	1587	1.410004	ACGAAGGAAGGTGAGTGACA	58.590	50.000	0.00	0.00	0.00	3.58
1554	1588	2.528041	AACGAAGGAAGGTGAGTGAC	57.472	50.000	0.00	0.00	0.00	3.67
1555	1589	2.029290	GCTAACGAAGGAAGGTGAGTGA	60.029	50.000	0.00	0.00	0.00	3.41
1556	1590	2.338500	GCTAACGAAGGAAGGTGAGTG	58.662	52.381	0.00	0.00	0.00	3.51
1557	1591	1.067776	CGCTAACGAAGGAAGGTGAGT	60.068	52.381	0.00	0.00	43.93	3.41
1558	1592	1.067776	ACGCTAACGAAGGAAGGTGAG	60.068	52.381	0.00	0.00	43.93	3.51
1559	1593	0.963962	ACGCTAACGAAGGAAGGTGA	59.036	50.000	0.00	0.00	43.93	4.02
1561	1595	1.201880	GAGACGCTAACGAAGGAAGGT	59.798	52.381	0.00	0.00	43.93	3.50
1563	1597	2.631418	TGAGACGCTAACGAAGGAAG	57.369	50.000	0.00	0.00	43.93	3.46
1564	1598	3.250744	CAATGAGACGCTAACGAAGGAA	58.749	45.455	0.00	0.00	43.93	3.36
1565	1599	2.230508	ACAATGAGACGCTAACGAAGGA	59.769	45.455	0.00	0.00	43.93	3.36
1566	1600	2.345641	CACAATGAGACGCTAACGAAGG	59.654	50.000	0.00	0.00	43.93	3.46
1567	1601	2.987149	ACACAATGAGACGCTAACGAAG	59.013	45.455	0.00	0.00	43.93	3.79
1568	1602	2.984471	GACACAATGAGACGCTAACGAA	59.016	45.455	0.00	0.00	43.93	3.85
1569	1603	2.592194	GACACAATGAGACGCTAACGA	58.408	47.619	0.00	0.00	43.93	3.85
1571	1605	2.592194	TCGACACAATGAGACGCTAAC	58.408	47.619	0.00	0.00	0.00	2.34
1572	1606	2.984471	GTTCGACACAATGAGACGCTAA	59.016	45.455	0.00	0.00	0.00	3.09
1573	1607	2.592194	GTTCGACACAATGAGACGCTA	58.408	47.619	0.00	0.00	0.00	4.26
1583	1617	3.319755	GACCCTAATTCGTTCGACACAA	58.680	45.455	0.00	0.00	0.00	3.33
1585	1619	1.916000	CGACCCTAATTCGTTCGACAC	59.084	52.381	0.00	0.00	0.00	3.67
1590	1624	2.678471	TTCCCGACCCTAATTCGTTC	57.322	50.000	0.00	0.00	34.56	3.95
1607	1641	1.260033	CGCTTCTTGCTCCATCGATTC	59.740	52.381	0.00	0.00	40.11	2.52
1608	1642	1.293924	CGCTTCTTGCTCCATCGATT	58.706	50.000	0.00	0.00	40.11	3.34
2140	2174	4.410743	GGGTCGTCGTCGGTGGAC	62.411	72.222	1.55	0.00	39.89	4.02
2235	2272	1.070821	CGTGTTGATGATGCGTGAGT	58.929	50.000	0.00	0.00	0.00	3.41
2236	2273	1.349234	TCGTGTTGATGATGCGTGAG	58.651	50.000	0.00	0.00	0.00	3.51
2237	2274	2.008752	ATCGTGTTGATGATGCGTGA	57.991	45.000	0.00	0.00	35.45	4.35
2238	2275	3.923827	TTATCGTGTTGATGATGCGTG	57.076	42.857	0.00	0.00	37.99	5.34
2239	2276	4.937696	TTTTATCGTGTTGATGATGCGT	57.062	36.364	0.00	0.00	37.99	5.24
2240	2277	5.265477	ACATTTTATCGTGTTGATGATGCG	58.735	37.500	0.00	0.00	37.99	4.73
2280	2318	6.488006	AGAGTGAAACACAGCAATGTAATTCT	59.512	34.615	4.75	0.00	41.43	2.40
2329	2367	2.079158	GCAGAACAGTAGCAGCATCAA	58.921	47.619	0.00	0.00	0.00	2.57
2332	2370	0.742281	CGGCAGAACAGTAGCAGCAT	60.742	55.000	0.00	0.00	0.00	3.79
2360	2398	3.630312	AGTCTAACAAGCTCCGATCTCTC	59.370	47.826	0.00	0.00	0.00	3.20
2497	2537	0.546747	CTGGGGTGGAGGTGGAGTAA	60.547	60.000	0.00	0.00	0.00	2.24
2595	2636	3.551407	GGGGATGGTCTCGGAGCC	61.551	72.222	0.00	5.87	0.00	4.70
2621	2662	0.107459	GAAGATTGAGAAGGGCGGCT	60.107	55.000	9.56	0.00	0.00	5.52
2750	2791	4.891727	ATCATCGCGGCGGTGGAC	62.892	66.667	32.41	0.00	38.63	4.02
2827	2868	2.849162	GATCATCGGAGGCCCCCA	60.849	66.667	3.33	0.00	0.00	4.96
2883	2924	0.179119	GCGTCGGTGGTAGCAATAGT	60.179	55.000	0.00	0.00	0.00	2.12
2886	2927	2.125269	GGCGTCGGTGGTAGCAAT	60.125	61.111	0.00	0.00	0.00	3.56
2924	2965	3.754850	TCGAGATTAGGTTGTCGAAGTGA	59.245	43.478	0.00	0.00	38.44	3.41
3056	3097	0.038067	CGTGGACGGTGTGGATAACA	60.038	55.000	0.00	0.00	34.00	2.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.