AutoCloner

Multiple sequence alignment - TraesCS5D01G046000

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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	TraesCS5D01G046000	chr5D	100.000	2219	0	0	1	2219	45126232	45124014	0.000000e+00	4098.0
1	TraesCS5D01G046000	chr5D	95.893	560	23	0	1	560	118999496	118998937	0.000000e+00	907.0
2	TraesCS5D01G046000	chr3B	93.622	831	44	2	1398	2219	754616758	754615928	0.000000e+00	1232.0
3	TraesCS5D01G046000	chr3B	86.005	836	99	9	1397	2219	642210399	642209569	0.000000e+00	880.0
4	TraesCS5D01G046000	chr3B	85.366	246	34	2	314	558	432337383	432337627	1.020000e-63	254.0
5	TraesCS5D01G046000	chr6D	91.947	832	55	5	1394	2216	21809073	21809901	0.000000e+00	1155.0
6	TraesCS5D01G046000	chr6D	100.000	48	0	0	569	616	283804950	283804903	3.030000e-14	89.8
7	TraesCS5D01G046000	chr6D	92.727	55	4	0	569	623	34582503	34582449	1.830000e-11	80.5
8	TraesCS5D01G046000	chr2B	91.466	832	61	6	1397	2219	63187355	63188185	0.000000e+00	1134.0
9	TraesCS5D01G046000	chr2B	85.921	831	96	14	1398	2215	103415686	103416508	0.000000e+00	867.0
10	TraesCS5D01G046000	chr7D	89.759	830	70	14	1401	2219	522879700	522878875	0.000000e+00	1048.0
11	TraesCS5D01G046000	chr7D	96.064	559	22	0	1	559	378893802	378893244	0.000000e+00	911.0
12	TraesCS5D01G046000	chr7D	94.172	326	16	2	1	325	392751325	392751648	5.500000e-136	494.0
13	TraesCS5D01G046000	chr7D	96.923	260	8	0	294	553	575614861	575614602	9.410000e-119	436.0
14	TraesCS5D01G046000	chr7D	94.141	256	13	2	1	255	575615108	575614854	2.670000e-104	388.0
15	TraesCS5D01G046000	chr7D	100.000	46	0	0	569	614	25055145	25055190	3.930000e-13	86.1
16	TraesCS5D01G046000	chr7D	97.826	46	1	0	569	614	443425632	443425677	1.830000e-11	80.5
17	TraesCS5D01G046000	chr5A	89.186	823	84	5	1398	2216	635913841	635914662	0.000000e+00	1022.0
18	TraesCS5D01G046000	chr5A	90.038	793	29	24	629	1397	35740183	35739417	0.000000e+00	981.0
19	TraesCS5D01G046000	chr6A	87.711	830	84	13	1398	2216	61868871	61869693	0.000000e+00	952.0
20	TraesCS5D01G046000	chr6A	91.786	560	35	2	1	560	518824641	518824093	0.000000e+00	769.0
21	TraesCS5D01G046000	chr5B	89.286	756	25	12	612	1359	45031364	45030657	0.000000e+00	896.0
22	TraesCS5D01G046000	chr5B	86.330	812	88	14	1425	2219	86125708	86124903	0.000000e+00	863.0
23	TraesCS5D01G046000	chr4B	95.691	557	21	1	1	557	474481841	474482394	0.000000e+00	893.0
24	TraesCS5D01G046000	chr4B	95.512	557	25	0	1	557	60323071	60322515	0.000000e+00	891.0
25	TraesCS5D01G046000	chr4B	94.231	52	2	1	569	620	188176859	188176809	6.570000e-11	78.7
26	TraesCS5D01G046000	chr1B	95.818	550	23	0	1	550	39307967	39308516	0.000000e+00	889.0
27	TraesCS5D01G046000	chr3A	84.000	275	37	5	286	558	712399925	712399656	7.860000e-65	257.0
28	TraesCS5D01G046000	chr3A	94.444	54	1	2	568	620	697244733	697244681	5.080000e-12	82.4
29	TraesCS5D01G046000	chr4A	81.752	274	47	3	285	557	434735158	434734887	2.220000e-55	226.0
30	TraesCS5D01G046000	chr4A	100.000	46	0	0	569	614	64138823	64138778	3.930000e-13	86.1
31	TraesCS5D01G046000	chr2D	79.751	321	52	7	3	321	318445312	318445621	1.030000e-53	220.0
32	TraesCS5D01G046000	chr2D	96.154	52	2	0	569	620	154158849	154158900	3.930000e-13	86.1
33	TraesCS5D01G046000	chr4D	94.340	53	2	1	569	620	175088851	175088799	1.830000e-11	80.5

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	TraesCS5D01G046000	chr5D	45124014	45126232	2218	True	4098	4098	100.000	1	2219	1	chr5D.!!$R1	2218
1	TraesCS5D01G046000	chr5D	118998937	118999496	559	True	907	907	95.893	1	560	1	chr5D.!!$R2	559
2	TraesCS5D01G046000	chr3B	754615928	754616758	830	True	1232	1232	93.622	1398	2219	1	chr3B.!!$R2	821
3	TraesCS5D01G046000	chr3B	642209569	642210399	830	True	880	880	86.005	1397	2219	1	chr3B.!!$R1	822
4	TraesCS5D01G046000	chr6D	21809073	21809901	828	False	1155	1155	91.947	1394	2216	1	chr6D.!!$F1	822
5	TraesCS5D01G046000	chr2B	63187355	63188185	830	False	1134	1134	91.466	1397	2219	1	chr2B.!!$F1	822
6	TraesCS5D01G046000	chr2B	103415686	103416508	822	False	867	867	85.921	1398	2215	1	chr2B.!!$F2	817
7	TraesCS5D01G046000	chr7D	522878875	522879700	825	True	1048	1048	89.759	1401	2219	1	chr7D.!!$R2	818
8	TraesCS5D01G046000	chr7D	378893244	378893802	558	True	911	911	96.064	1	559	1	chr7D.!!$R1	558
9	TraesCS5D01G046000	chr7D	575614602	575615108	506	True	412	436	95.532	1	553	2	chr7D.!!$R3	552
10	TraesCS5D01G046000	chr5A	635913841	635914662	821	False	1022	1022	89.186	1398	2216	1	chr5A.!!$F1	818
11	TraesCS5D01G046000	chr5A	35739417	35740183	766	True	981	981	90.038	629	1397	1	chr5A.!!$R1	768
12	TraesCS5D01G046000	chr6A	61868871	61869693	822	False	952	952	87.711	1398	2216	1	chr6A.!!$F1	818
13	TraesCS5D01G046000	chr6A	518824093	518824641	548	True	769	769	91.786	1	560	1	chr6A.!!$R1	559
14	TraesCS5D01G046000	chr5B	45030657	45031364	707	True	896	896	89.286	612	1359	1	chr5B.!!$R1	747
15	TraesCS5D01G046000	chr5B	86124903	86125708	805	True	863	863	86.330	1425	2219	1	chr5B.!!$R2	794
16	TraesCS5D01G046000	chr4B	474481841	474482394	553	False	893	893	95.691	1	557	1	chr4B.!!$F1	556
17	TraesCS5D01G046000	chr4B	60322515	60323071	556	True	891	891	95.512	1	557	1	chr4B.!!$R1	556
18	TraesCS5D01G046000	chr1B	39307967	39308516	549	False	889	889	95.818	1	550	1	chr1B.!!$F1	549

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
577	581	0.60864	CTCGAGGGGCAAGTTGTACT	59.391	55.0	3.91	0.36	0.0	2.73	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1472	1522	0.042731	TGTACCTCCTCCCTGGGAAG	59.957	60.0	17.81	11.33	34.66	3.46	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
189	190	4.740822	GCCCATGCCCGACACCTT	62.741	66.667	0.00	0.00	0.00	3.50
207	208	2.902423	TTCTTGCACAACCAGGCCGT	62.902	55.000	0.00	0.00	0.00	5.68
562	566	3.429141	GACACGGGAGTCGCTCGA	61.429	66.667	1.78	0.00	44.67	4.04
563	567	3.384014	GACACGGGAGTCGCTCGAG	62.384	68.421	8.45	8.45	44.67	4.04
564	568	4.180946	CACGGGAGTCGCTCGAGG	62.181	72.222	15.58	4.50	44.67	4.63
569	573	3.760035	GAGTCGCTCGAGGGGCAA	61.760	66.667	32.07	10.85	34.81	4.52
570	574	3.708220	GAGTCGCTCGAGGGGCAAG	62.708	68.421	32.07	0.00	34.81	4.01
571	575	4.070552	GTCGCTCGAGGGGCAAGT	62.071	66.667	27.10	0.00	32.43	3.16
572	576	3.311110	TCGCTCGAGGGGCAAGTT	61.311	61.111	27.01	0.00	0.00	2.66
573	577	3.121030	CGCTCGAGGGGCAAGTTG	61.121	66.667	21.06	0.00	0.00	3.16
574	578	2.032681	GCTCGAGGGGCAAGTTGT	59.967	61.111	15.58	0.00	0.00	3.32
575	579	1.295423	GCTCGAGGGGCAAGTTGTA	59.705	57.895	15.58	0.00	0.00	2.41
576	580	1.019805	GCTCGAGGGGCAAGTTGTAC	61.020	60.000	15.58	0.00	0.00	2.90
577	581	0.608640	CTCGAGGGGCAAGTTGTACT	59.391	55.000	3.91	0.36	0.00	2.73
578	582	1.822990	CTCGAGGGGCAAGTTGTACTA	59.177	52.381	3.91	0.00	0.00	1.82
579	583	1.822990	TCGAGGGGCAAGTTGTACTAG	59.177	52.381	4.48	1.73	0.00	2.57
580	584	1.822990	CGAGGGGCAAGTTGTACTAGA	59.177	52.381	4.48	0.00	0.00	2.43
581	585	2.159226	CGAGGGGCAAGTTGTACTAGAG	60.159	54.545	4.48	0.00	0.00	2.43
582	586	2.832733	GAGGGGCAAGTTGTACTAGAGT	59.167	50.000	4.48	0.00	0.00	3.24
583	587	3.248888	AGGGGCAAGTTGTACTAGAGTT	58.751	45.455	4.48	0.00	0.00	3.01
584	588	3.008049	AGGGGCAAGTTGTACTAGAGTTG	59.992	47.826	4.48	1.55	0.00	3.16
585	589	3.007614	GGGGCAAGTTGTACTAGAGTTGA	59.992	47.826	4.48	0.00	0.00	3.18
586	590	4.246458	GGGCAAGTTGTACTAGAGTTGAG	58.754	47.826	4.48	0.00	0.00	3.02
587	591	4.021368	GGGCAAGTTGTACTAGAGTTGAGA	60.021	45.833	4.48	0.00	0.00	3.27
588	592	4.924462	GGCAAGTTGTACTAGAGTTGAGAC	59.076	45.833	4.48	3.19	0.00	3.36
589	593	5.509163	GGCAAGTTGTACTAGAGTTGAGACA	60.509	44.000	4.48	0.00	0.00	3.41
590	594	5.402867	GCAAGTTGTACTAGAGTTGAGACAC	59.597	44.000	4.48	0.00	0.00	3.67
591	595	6.736243	GCAAGTTGTACTAGAGTTGAGACACT	60.736	42.308	4.48	0.00	0.00	3.55
592	596	6.963083	AGTTGTACTAGAGTTGAGACACTT	57.037	37.500	0.00	0.00	0.00	3.16
593	597	8.350722	CAAGTTGTACTAGAGTTGAGACACTTA	58.649	37.037	0.00	0.00	0.00	2.24
594	598	8.638629	AGTTGTACTAGAGTTGAGACACTTAT	57.361	34.615	0.00	0.00	0.00	1.73
595	599	9.080097	AGTTGTACTAGAGTTGAGACACTTATT	57.920	33.333	0.00	0.00	0.00	1.40
596	600	9.694137	GTTGTACTAGAGTTGAGACACTTATTT	57.306	33.333	0.00	0.00	0.00	1.40
598	602	9.692749	TGTACTAGAGTTGAGACACTTATTTTG	57.307	33.333	0.00	0.00	0.00	2.44
599	603	9.909644	GTACTAGAGTTGAGACACTTATTTTGA	57.090	33.333	0.00	0.00	0.00	2.69
601	605	8.861086	ACTAGAGTTGAGACACTTATTTTGAGA	58.139	33.333	0.00	0.00	0.00	3.27
602	606	7.954788	AGAGTTGAGACACTTATTTTGAGAC	57.045	36.000	0.00	0.00	0.00	3.36
603	607	6.642950	AGAGTTGAGACACTTATTTTGAGACG	59.357	38.462	0.00	0.00	0.00	4.18
604	608	5.696724	AGTTGAGACACTTATTTTGAGACGG	59.303	40.000	0.00	0.00	0.00	4.79
605	609	5.462530	TGAGACACTTATTTTGAGACGGA	57.537	39.130	0.00	0.00	0.00	4.69
606	610	5.470368	TGAGACACTTATTTTGAGACGGAG	58.530	41.667	0.00	0.00	0.00	4.63
607	611	4.822026	AGACACTTATTTTGAGACGGAGG	58.178	43.478	0.00	0.00	0.00	4.30
608	612	3.933332	GACACTTATTTTGAGACGGAGGG	59.067	47.826	0.00	0.00	0.00	4.30
609	613	3.581332	ACACTTATTTTGAGACGGAGGGA	59.419	43.478	0.00	0.00	0.00	4.20
610	614	4.184629	CACTTATTTTGAGACGGAGGGAG	58.815	47.826	0.00	0.00	0.00	4.30
726	730	3.966006	AGAGCCATGTAGACATCATCACT	59.034	43.478	0.00	0.00	33.61	3.41
810	814	4.444024	CACAACGATGGCCACGCG	62.444	66.667	23.76	23.76	0.00	6.01
811	815	4.673298	ACAACGATGGCCACGCGA	62.673	61.111	29.91	0.00	0.00	5.87
812	816	3.418913	CAACGATGGCCACGCGAA	61.419	61.111	29.91	0.00	0.00	4.70
813	817	2.435938	AACGATGGCCACGCGAAT	60.436	55.556	29.91	17.91	0.00	3.34
814	818	2.461110	AACGATGGCCACGCGAATC	61.461	57.895	29.91	13.48	0.00	2.52
815	819	3.988385	CGATGGCCACGCGAATCG	61.988	66.667	21.69	15.86	45.38	3.34
816	820	3.640000	GATGGCCACGCGAATCGG	61.640	66.667	15.93	8.81	43.86	4.18
817	821	4.155733	ATGGCCACGCGAATCGGA	62.156	61.111	15.93	0.00	43.86	4.55
818	822	4.812476	TGGCCACGCGAATCGGAG	62.812	66.667	15.93	0.00	43.86	4.63
821	825	3.257561	CCACGCGAATCGGAGCTG	61.258	66.667	15.93	0.00	43.86	4.24
822	826	3.918220	CACGCGAATCGGAGCTGC	61.918	66.667	15.93	0.00	43.86	5.25
825	829	4.838152	GCGAATCGGAGCTGCCCA	62.838	66.667	4.35	0.00	0.00	5.36
826	830	2.587194	CGAATCGGAGCTGCCCAG	60.587	66.667	0.00	0.00	0.00	4.45
827	831	2.203126	GAATCGGAGCTGCCCAGG	60.203	66.667	0.00	0.00	0.00	4.45
828	832	3.764160	GAATCGGAGCTGCCCAGGG	62.764	68.421	0.00	0.00	0.00	4.45
910	936	4.202080	CCAATGAATAACGACGACCCTCTA	60.202	45.833	0.00	0.00	0.00	2.43
985	1025	2.290367	CACAACAGGAGTGCAAAATCGA	59.710	45.455	0.00	0.00	0.00	3.59
986	1026	2.290641	ACAACAGGAGTGCAAAATCGAC	59.709	45.455	0.00	0.00	0.00	4.20
1161	1201	3.753434	CTCGTCCTGCCGCTCACT	61.753	66.667	0.00	0.00	0.00	3.41
1225	1265	7.277981	GCTCTTTGAGATACCGATGAAAACTTA	59.722	37.037	0.00	0.00	0.00	2.24
1226	1266	8.475331	TCTTTGAGATACCGATGAAAACTTAC	57.525	34.615	0.00	0.00	0.00	2.34
1242	1287	7.653713	TGAAAACTTACATCTCAGTTCTCTCAC	59.346	37.037	0.00	0.00	31.79	3.51
1246	1291	7.995289	ACTTACATCTCAGTTCTCTCACATAG	58.005	38.462	0.00	0.00	0.00	2.23
1247	1292	7.613801	ACTTACATCTCAGTTCTCTCACATAGT	59.386	37.037	0.00	0.00	0.00	2.12
1252	1297	6.480763	TCTCAGTTCTCTCACATAGTCTCTT	58.519	40.000	0.00	0.00	0.00	2.85
1253	1298	6.374053	TCTCAGTTCTCTCACATAGTCTCTTG	59.626	42.308	0.00	0.00	0.00	3.02
1254	1299	6.241645	TCAGTTCTCTCACATAGTCTCTTGA	58.758	40.000	0.00	0.00	0.00	3.02
1255	1300	6.717084	TCAGTTCTCTCACATAGTCTCTTGAA	59.283	38.462	0.00	0.00	0.00	2.69
1315	1364	6.814644	CGTGGTTCTGGTATGTAAAGAATGTA	59.185	38.462	0.00	0.00	32.85	2.29
1316	1365	7.494625	CGTGGTTCTGGTATGTAAAGAATGTAT	59.505	37.037	0.00	0.00	32.85	2.29
1317	1366	8.827677	GTGGTTCTGGTATGTAAAGAATGTATC	58.172	37.037	0.00	0.00	32.85	2.24
1318	1367	8.544622	TGGTTCTGGTATGTAAAGAATGTATCA	58.455	33.333	0.00	0.00	32.85	2.15
1319	1368	9.391006	GGTTCTGGTATGTAAAGAATGTATCAA	57.609	33.333	0.00	0.00	32.85	2.57
1360	1409	2.987821	GGTTCTTCGTAGTTCTCACTGC	59.012	50.000	0.00	0.00	34.06	4.40
1367	1416	2.731027	CGTAGTTCTCACTGCATGCGTA	60.731	50.000	14.09	0.00	35.42	4.42
1386	1435	4.728595	GCGTACGGTTTTGTTCTGAAACTT	60.729	41.667	18.39	0.00	37.22	2.66
1407	1456	2.933906	TGTTCACTTTCTGTCACGAACC	59.066	45.455	0.00	0.00	31.83	3.62
1472	1522	2.235155	GAGACTTGGGAGAGAAGGTTCC	59.765	54.545	0.00	0.00	0.00	3.62
1477	1527	0.913205	GGGAGAGAAGGTTCCTTCCC	59.087	60.000	23.02	16.41	42.30	3.97
1676	1740	0.323725	GCAGGTGTGACATTCCCCAT	60.324	55.000	0.00	0.00	0.00	4.00
1702	1766	2.665185	AACGGGCGCTGTCTTCAC	60.665	61.111	7.64	0.00	0.00	3.18
1990	2061	0.828022	TGGGACACGTGAAAGACTGT	59.172	50.000	25.01	0.00	0.00	3.55
2044	2115	2.377628	TACGCCATCTTGCCGATCCC	62.378	60.000	0.00	0.00	0.00	3.85
2151	2222	1.269831	GCTTGAGGAGAACACTGTCGT	60.270	52.381	0.00	0.00	0.00	4.34
2158	2229	1.068741	GAGAACACTGTCGTCCACCTT	59.931	52.381	0.00	0.00	0.00	3.50

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
174	175	1.002134	AAGAAGGTGTCGGGCATGG	60.002	57.895	0.00	0.00	0.00	3.66
189	190	2.594303	CGGCCTGGTTGTGCAAGA	60.594	61.111	0.00	0.00	0.00	3.02
509	513	2.600439	GGGAGTAAACCCTAGCCGT	58.400	57.895	0.00	0.00	45.90	5.68
560	564	1.822990	TCTAGTACAACTTGCCCCTCG	59.177	52.381	0.00	0.00	0.00	4.63
561	565	2.832733	ACTCTAGTACAACTTGCCCCTC	59.167	50.000	0.00	0.00	0.00	4.30
562	566	2.903926	ACTCTAGTACAACTTGCCCCT	58.096	47.619	0.00	0.00	0.00	4.79
563	567	3.007614	TCAACTCTAGTACAACTTGCCCC	59.992	47.826	0.00	0.00	0.00	5.80
564	568	4.021368	TCTCAACTCTAGTACAACTTGCCC	60.021	45.833	0.00	0.00	0.00	5.36
565	569	4.924462	GTCTCAACTCTAGTACAACTTGCC	59.076	45.833	0.00	0.00	0.00	4.52
566	570	5.402867	GTGTCTCAACTCTAGTACAACTTGC	59.597	44.000	0.00	0.00	0.00	4.01
567	571	6.740110	AGTGTCTCAACTCTAGTACAACTTG	58.260	40.000	0.00	0.00	0.00	3.16
568	572	6.963083	AGTGTCTCAACTCTAGTACAACTT	57.037	37.500	0.00	0.00	0.00	2.66
569	573	6.963083	AAGTGTCTCAACTCTAGTACAACT	57.037	37.500	0.00	0.00	0.00	3.16
570	574	9.694137	AAATAAGTGTCTCAACTCTAGTACAAC	57.306	33.333	0.00	0.00	0.00	3.32
572	576	9.692749	CAAAATAAGTGTCTCAACTCTAGTACA	57.307	33.333	0.00	0.00	0.00	2.90
573	577	9.909644	TCAAAATAAGTGTCTCAACTCTAGTAC	57.090	33.333	0.00	0.00	0.00	2.73
575	579	8.861086	TCTCAAAATAAGTGTCTCAACTCTAGT	58.139	33.333	0.00	0.00	0.00	2.57
576	580	9.134734	GTCTCAAAATAAGTGTCTCAACTCTAG	57.865	37.037	0.00	0.00	0.00	2.43
577	581	7.808381	CGTCTCAAAATAAGTGTCTCAACTCTA	59.192	37.037	0.00	0.00	0.00	2.43
578	582	6.642950	CGTCTCAAAATAAGTGTCTCAACTCT	59.357	38.462	0.00	0.00	0.00	3.24
579	583	6.128795	CCGTCTCAAAATAAGTGTCTCAACTC	60.129	42.308	0.00	0.00	0.00	3.01
580	584	5.696724	CCGTCTCAAAATAAGTGTCTCAACT	59.303	40.000	0.00	0.00	0.00	3.16
581	585	5.694910	TCCGTCTCAAAATAAGTGTCTCAAC	59.305	40.000	0.00	0.00	0.00	3.18
582	586	5.849510	TCCGTCTCAAAATAAGTGTCTCAA	58.150	37.500	0.00	0.00	0.00	3.02
583	587	5.462530	TCCGTCTCAAAATAAGTGTCTCA	57.537	39.130	0.00	0.00	0.00	3.27
584	588	4.865365	CCTCCGTCTCAAAATAAGTGTCTC	59.135	45.833	0.00	0.00	0.00	3.36
585	589	4.322801	CCCTCCGTCTCAAAATAAGTGTCT	60.323	45.833	0.00	0.00	0.00	3.41
586	590	3.933332	CCCTCCGTCTCAAAATAAGTGTC	59.067	47.826	0.00	0.00	0.00	3.67
587	591	3.581332	TCCCTCCGTCTCAAAATAAGTGT	59.419	43.478	0.00	0.00	0.00	3.55
588	592	4.184629	CTCCCTCCGTCTCAAAATAAGTG	58.815	47.826	0.00	0.00	0.00	3.16
589	593	3.838903	ACTCCCTCCGTCTCAAAATAAGT	59.161	43.478	0.00	0.00	0.00	2.24
590	594	4.473477	ACTCCCTCCGTCTCAAAATAAG	57.527	45.455	0.00	0.00	0.00	1.73
591	595	5.897824	AGATACTCCCTCCGTCTCAAAATAA	59.102	40.000	0.00	0.00	0.00	1.40
592	596	5.455872	AGATACTCCCTCCGTCTCAAAATA	58.544	41.667	0.00	0.00	0.00	1.40
593	597	4.290942	AGATACTCCCTCCGTCTCAAAAT	58.709	43.478	0.00	0.00	0.00	1.82
594	598	3.709587	AGATACTCCCTCCGTCTCAAAA	58.290	45.455	0.00	0.00	0.00	2.44
595	599	3.383698	AGATACTCCCTCCGTCTCAAA	57.616	47.619	0.00	0.00	0.00	2.69
596	600	3.383698	AAGATACTCCCTCCGTCTCAA	57.616	47.619	0.00	0.00	0.00	3.02
597	601	3.383698	AAAGATACTCCCTCCGTCTCA	57.616	47.619	0.00	0.00	0.00	3.27
598	602	4.441773	GGAAAAAGATACTCCCTCCGTCTC	60.442	50.000	0.00	0.00	0.00	3.36
599	603	3.451540	GGAAAAAGATACTCCCTCCGTCT	59.548	47.826	0.00	0.00	0.00	4.18
600	604	3.197116	TGGAAAAAGATACTCCCTCCGTC	59.803	47.826	0.00	0.00	0.00	4.79
601	605	3.178865	TGGAAAAAGATACTCCCTCCGT	58.821	45.455	0.00	0.00	0.00	4.69
602	606	3.906720	TGGAAAAAGATACTCCCTCCG	57.093	47.619	0.00	0.00	0.00	4.63
603	607	4.816925	CGAATGGAAAAAGATACTCCCTCC	59.183	45.833	0.00	0.00	0.00	4.30
604	608	4.273724	GCGAATGGAAAAAGATACTCCCTC	59.726	45.833	0.00	0.00	0.00	4.30
605	609	4.200092	GCGAATGGAAAAAGATACTCCCT	58.800	43.478	0.00	0.00	0.00	4.20
606	610	3.945285	TGCGAATGGAAAAAGATACTCCC	59.055	43.478	0.00	0.00	0.00	4.30
607	611	5.560966	TTGCGAATGGAAAAAGATACTCC	57.439	39.130	0.00	0.00	0.00	3.85
608	612	7.867445	TTTTTGCGAATGGAAAAAGATACTC	57.133	32.000	3.75	0.00	46.28	2.59
639	643	4.280436	TCTTATGCAACGGAAAAGGAGA	57.720	40.909	0.00	0.00	0.00	3.71
640	644	5.154222	GTTTCTTATGCAACGGAAAAGGAG	58.846	41.667	11.13	0.00	30.98	3.69
711	715	7.229506	CACCAGAGTATAGTGATGATGTCTACA	59.770	40.741	0.00	0.00	33.21	2.74
715	719	6.398234	ACACCAGAGTATAGTGATGATGTC	57.602	41.667	0.00	0.00	35.47	3.06
716	720	6.798427	AACACCAGAGTATAGTGATGATGT	57.202	37.500	0.00	0.00	35.47	3.06
717	721	7.946207	AGTAACACCAGAGTATAGTGATGATG	58.054	38.462	0.00	0.00	35.47	3.07
718	722	9.815306	ATAGTAACACCAGAGTATAGTGATGAT	57.185	33.333	0.00	0.00	35.47	2.45
719	723	9.286170	GATAGTAACACCAGAGTATAGTGATGA	57.714	37.037	0.00	0.00	35.47	2.92
810	814	2.203126	CCTGGGCAGCTCCGATTC	60.203	66.667	0.00	0.00	34.94	2.52
811	815	3.801997	CCCTGGGCAGCTCCGATT	61.802	66.667	0.00	0.00	34.94	3.34
822	826	2.755469	CGTTTCATGGGCCCTGGG	60.755	66.667	25.70	8.86	0.00	4.45
823	827	3.451894	GCGTTTCATGGGCCCTGG	61.452	66.667	25.70	15.44	0.00	4.45
824	828	2.676121	TGCGTTTCATGGGCCCTG	60.676	61.111	25.70	18.57	0.00	4.45
825	829	2.361610	CTGCGTTTCATGGGCCCT	60.362	61.111	25.70	5.48	0.00	5.19
826	830	4.133796	GCTGCGTTTCATGGGCCC	62.134	66.667	17.59	17.59	0.00	5.80
827	831	1.312371	TTAGCTGCGTTTCATGGGCC	61.312	55.000	0.00	0.00	0.00	5.80
828	832	0.179163	GTTAGCTGCGTTTCATGGGC	60.179	55.000	0.00	0.00	0.00	5.36
829	833	1.453155	AGTTAGCTGCGTTTCATGGG	58.547	50.000	0.00	0.00	0.00	4.00
830	834	3.189287	AGAAAGTTAGCTGCGTTTCATGG	59.811	43.478	15.02	0.00	32.38	3.66
831	835	4.398247	GAGAAAGTTAGCTGCGTTTCATG	58.602	43.478	15.02	0.00	32.38	3.07
832	836	3.437049	GGAGAAAGTTAGCTGCGTTTCAT	59.563	43.478	15.02	4.71	32.38	2.57
833	837	2.806244	GGAGAAAGTTAGCTGCGTTTCA	59.194	45.455	15.02	0.00	32.38	2.69
910	936	8.361139	GCAATCAGTGTGTAGTATATAGAGGTT	58.639	37.037	0.00	0.00	0.00	3.50
1074	1114	2.281070	AGCAGTGCGGTGAGGTTG	60.281	61.111	10.00	0.00	0.00	3.77
1225	1265	6.186957	AGACTATGTGAGAGAACTGAGATGT	58.813	40.000	0.00	0.00	0.00	3.06
1226	1266	6.543465	AGAGACTATGTGAGAGAACTGAGATG	59.457	42.308	0.00	0.00	0.00	2.90
1242	1287	8.200120	TCATACATCCAAGTTCAAGAGACTATG	58.800	37.037	0.00	0.00	0.00	2.23
1246	1291	7.856145	AATCATACATCCAAGTTCAAGAGAC	57.144	36.000	0.00	0.00	0.00	3.36
1247	1292	9.551734	CATAATCATACATCCAAGTTCAAGAGA	57.448	33.333	0.00	0.00	0.00	3.10
1252	1297	6.827762	TGCACATAATCATACATCCAAGTTCA	59.172	34.615	0.00	0.00	0.00	3.18
1253	1298	7.263100	TGCACATAATCATACATCCAAGTTC	57.737	36.000	0.00	0.00	0.00	3.01
1254	1299	7.503230	TCATGCACATAATCATACATCCAAGTT	59.497	33.333	0.00	0.00	0.00	2.66
1255	1300	6.999871	TCATGCACATAATCATACATCCAAGT	59.000	34.615	0.00	0.00	0.00	3.16
1315	1364	8.752187	ACCAATTACTAGCACATTTGATTTGAT	58.248	29.630	0.00	0.00	0.00	2.57
1316	1365	8.121305	ACCAATTACTAGCACATTTGATTTGA	57.879	30.769	0.00	0.00	0.00	2.69
1317	1366	8.761575	AACCAATTACTAGCACATTTGATTTG	57.238	30.769	0.00	0.00	0.00	2.32
1318	1367	8.806146	AGAACCAATTACTAGCACATTTGATTT	58.194	29.630	0.00	0.00	0.00	2.17
1319	1368	8.353423	AGAACCAATTACTAGCACATTTGATT	57.647	30.769	0.00	0.00	0.00	2.57
1360	1409	2.222213	TCAGAACAAAACCGTACGCATG	59.778	45.455	10.49	7.91	0.00	4.06
1367	1416	4.776795	ACAAGTTTCAGAACAAAACCGT	57.223	36.364	0.00	0.00	37.33	4.83
1386	1435	2.933906	GGTTCGTGACAGAAAGTGAACA	59.066	45.455	5.42	0.00	37.91	3.18
1407	1456	2.149578	GATCCAATTCTGCGAGGATGG	58.850	52.381	0.00	0.00	40.80	3.51
1472	1522	0.042731	TGTACCTCCTCCCTGGGAAG	59.957	60.000	17.81	11.33	34.66	3.46
1477	1527	3.235200	CCTAATCTGTACCTCCTCCCTG	58.765	54.545	0.00	0.00	0.00	4.45
1655	1719	1.244019	GGGGAATGTCACACCTGCAC	61.244	60.000	0.00	0.00	0.00	4.57
1676	1740	2.358247	GCGCCCGTTCTGAAGGAA	60.358	61.111	11.39	0.00	0.00	3.36
2044	2115	2.202492	CCTTCTCGGTGCTCGACG	60.202	66.667	0.00	0.00	43.74	5.12
2151	2222	2.172483	GAGCGCTCCTTCAAGGTGGA	62.172	60.000	27.22	0.00	36.53	4.02

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.