AutoCloner

Multiple sequence alignment - TraesCS1D01G261700

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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	TraesCS1D01G261700	chr1D	100.000	3488	0	0	1	3488	355667380	355670867	0.000000e+00	6442
1	TraesCS1D01G261700	chr1D	91.767	583	42	4	2907	3488	440869106	440868529	0.000000e+00	806
2	TraesCS1D01G261700	chr1A	92.801	2403	117	21	521	2909	456242905	456245265	0.000000e+00	3428
3	TraesCS1D01G261700	chr1A	90.291	515	39	8	1	511	456242091	456242598	0.000000e+00	664
4	TraesCS1D01G261700	chr1A	81.314	487	52	19	2914	3388	381319290	381319749	3.310000e-95	359
5	TraesCS1D01G261700	chr1B	91.969	2092	111	25	842	2909	478560499	478562557	0.000000e+00	2880
6	TraesCS1D01G261700	chr1B	88.715	319	32	4	149	464	478557131	478557448	1.520000e-103	387
7	TraesCS1D01G261700	chr1B	92.748	262	16	2	590	848	478557749	478558010	3.290000e-100	375
8	TraesCS1D01G261700	chr1B	92.035	113	7	2	1	111	478557026	478557138	1.300000e-34	158
9	TraesCS1D01G261700	chr2B	87.394	1531	169	14	951	2480	682258486	682259993	0.000000e+00	1736
10	TraesCS1D01G261700	chr2A	86.971	1535	172	18	948	2480	709173342	709174850	0.000000e+00	1701
11	TraesCS1D01G261700	chr2A	88.488	582	64	3	2907	3487	102114982	102115561	0.000000e+00	701
12	TraesCS1D01G261700	chr5B	86.195	1456	176	12	1030	2480	610282405	610280970	0.000000e+00	1552
13	TraesCS1D01G261700	chr5B	83.568	1491	188	32	984	2454	684085152	684086605	0.000000e+00	1343
14	TraesCS1D01G261700	chr5D	85.783	1463	185	12	1022	2480	493912454	493913897	0.000000e+00	1528
15	TraesCS1D01G261700	chr5D	85.302	1456	189	11	1030	2480	494079147	494077712	0.000000e+00	1480
16	TraesCS1D01G261700	chr5D	84.270	1494	190	26	984	2457	542106114	542107582	0.000000e+00	1415
17	TraesCS1D01G261700	chr5D	90.985	477	40	3	3009	3483	361569675	361569200	1.060000e-179	640
18	TraesCS1D01G261700	chr5A	85.488	1454	186	12	1032	2480	617097304	617095871	0.000000e+00	1493
19	TraesCS1D01G261700	chr5A	85.175	1457	189	13	1030	2480	617123660	617122225	0.000000e+00	1469
20	TraesCS1D01G261700	chr5A	89.583	576	58	2	2914	3488	624197050	624196476	0.000000e+00	730
21	TraesCS1D01G261700	chr4A	84.401	1468	181	27	1030	2476	713605996	713604556	0.000000e+00	1399
22	TraesCS1D01G261700	chr4A	84.083	1489	193	25	990	2457	626954615	626953150	0.000000e+00	1397
23	TraesCS1D01G261700	chr7B	86.851	578	63	4	2913	3488	576676547	576675981	4.910000e-178	634
24	TraesCS1D01G261700	chr7D	88.152	422	45	5	2908	3326	7523136	7523555	6.720000e-137	497
25	TraesCS1D01G261700	chr7D	81.867	375	48	14	2909	3274	227559923	227560286	7.320000e-77	298
26	TraesCS1D01G261700	chr7D	89.344	122	13	0	3362	3483	7523548	7523669	1.680000e-33	154
27	TraesCS1D01G261700	chr2D	82.083	480	73	12	2914	3388	556922579	556922108	7.010000e-107	398
28	TraesCS1D01G261700	chr7A	79.722	360	56	12	2911	3267	237526299	237526644	9.670000e-61	244
29	TraesCS1D01G261700	chr3A	78.533	368	60	15	2911	3274	366631908	366632260	1.260000e-54	224

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	TraesCS1D01G261700	chr1D	355667380	355670867	3487	False	6442.0	6442	100.00000	1	3488	1	chr1D.!!$F1	3487
1	TraesCS1D01G261700	chr1D	440868529	440869106	577	True	806.0	806	91.76700	2907	3488	1	chr1D.!!$R1	581
2	TraesCS1D01G261700	chr1A	456242091	456245265	3174	False	2046.0	3428	91.54600	1	2909	2	chr1A.!!$F2	2908
3	TraesCS1D01G261700	chr1B	478557026	478562557	5531	False	950.0	2880	91.36675	1	2909	4	chr1B.!!$F1	2908
4	TraesCS1D01G261700	chr2B	682258486	682259993	1507	False	1736.0	1736	87.39400	951	2480	1	chr2B.!!$F1	1529
5	TraesCS1D01G261700	chr2A	709173342	709174850	1508	False	1701.0	1701	86.97100	948	2480	1	chr2A.!!$F2	1532
6	TraesCS1D01G261700	chr2A	102114982	102115561	579	False	701.0	701	88.48800	2907	3487	1	chr2A.!!$F1	580
7	TraesCS1D01G261700	chr5B	610280970	610282405	1435	True	1552.0	1552	86.19500	1030	2480	1	chr5B.!!$R1	1450
8	TraesCS1D01G261700	chr5B	684085152	684086605	1453	False	1343.0	1343	83.56800	984	2454	1	chr5B.!!$F1	1470
9	TraesCS1D01G261700	chr5D	493912454	493913897	1443	False	1528.0	1528	85.78300	1022	2480	1	chr5D.!!$F1	1458
10	TraesCS1D01G261700	chr5D	494077712	494079147	1435	True	1480.0	1480	85.30200	1030	2480	1	chr5D.!!$R2	1450
11	TraesCS1D01G261700	chr5D	542106114	542107582	1468	False	1415.0	1415	84.27000	984	2457	1	chr5D.!!$F2	1473
12	TraesCS1D01G261700	chr5A	617095871	617097304	1433	True	1493.0	1493	85.48800	1032	2480	1	chr5A.!!$R1	1448
13	TraesCS1D01G261700	chr5A	617122225	617123660	1435	True	1469.0	1469	85.17500	1030	2480	1	chr5A.!!$R2	1450
14	TraesCS1D01G261700	chr5A	624196476	624197050	574	True	730.0	730	89.58300	2914	3488	1	chr5A.!!$R3	574
15	TraesCS1D01G261700	chr4A	713604556	713605996	1440	True	1399.0	1399	84.40100	1030	2476	1	chr4A.!!$R2	1446
16	TraesCS1D01G261700	chr4A	626953150	626954615	1465	True	1397.0	1397	84.08300	990	2457	1	chr4A.!!$R1	1467
17	TraesCS1D01G261700	chr7B	576675981	576676547	566	True	634.0	634	86.85100	2913	3488	1	chr7B.!!$R1	575
18	TraesCS1D01G261700	chr7D	7523136	7523669	533	False	325.5	497	88.74800	2908	3483	2	chr7D.!!$F2	575

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
515	521	0.099613	CATGAGACACGGTCGAGAGG	59.900	60.0	0.0	0.0	37.67	3.69	F
526	829	0.394565	GTCGAGAGGGGATGGATTGG	59.605	60.0	0.0	0.0	0.00	3.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1501	4464	2.737376	GACAGTCGCCAACGGGTC	60.737	66.667	0.00	0.00	40.63	4.46	R
2518	5514	0.171903	GGCATGACATGAGTTGTGCC	59.828	55.000	19.76	8.89	45.13	5.01	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
89	91	2.359214	TCGGCAACTTGTGTATTTGCAA	59.641	40.909	0.00	0.00	46.12	4.08
135	137	3.261643	TCACATCCTCAGCTTTGCTAAGA	59.738	43.478	12.29	0.00	36.40	2.10
136	138	4.080695	TCACATCCTCAGCTTTGCTAAGAT	60.081	41.667	12.29	1.88	36.40	2.40
147	149	4.442706	CTTTGCTAAGATGTCGTATGGGT	58.557	43.478	1.23	0.00	32.92	4.51
186	188	0.113580	TCTTAACAACCAAGGGCCCC	59.886	55.000	21.43	0.00	0.00	5.80
318	322	2.047274	GTGAACGCAGCCTGGCTA	60.047	61.111	22.90	0.76	36.40	3.93
329	333	3.506067	GCAGCCTGGCTAAAAGTTTTCTA	59.494	43.478	22.90	0.00	36.40	2.10
365	370	1.112950	AGGGTTAGCCTTAGACGCTC	58.887	55.000	0.00	0.00	37.79	5.03
376	381	5.712446	AGCCTTAGACGCTCTCATTGATATA	59.288	40.000	0.00	0.00	0.00	0.86
378	383	7.038659	GCCTTAGACGCTCTCATTGATATAAT	58.961	38.462	0.00	0.00	0.00	1.28
466	471	1.519455	CCAGATCGGTCTTGACGGC	60.519	63.158	0.00	0.00	30.42	5.68
467	472	1.874019	CAGATCGGTCTTGACGGCG	60.874	63.158	4.80	4.80	30.42	6.46
468	473	2.044555	AGATCGGTCTTGACGGCGA	61.045	57.895	16.62	5.03	0.00	5.54
511	517	2.571757	GGCATGAGACACGGTCGA	59.428	61.111	0.00	0.00	37.67	4.20
512	518	1.517257	GGCATGAGACACGGTCGAG	60.517	63.158	0.00	0.00	37.67	4.04
514	520	0.524392	GCATGAGACACGGTCGAGAG	60.524	60.000	0.00	0.00	37.67	3.20
515	521	0.099613	CATGAGACACGGTCGAGAGG	59.900	60.000	0.00	0.00	37.67	3.69
516	522	1.032657	ATGAGACACGGTCGAGAGGG	61.033	60.000	0.00	0.00	37.67	4.30
518	524	2.360852	GACACGGTCGAGAGGGGA	60.361	66.667	0.00	0.00	0.00	4.81
519	525	1.753463	GACACGGTCGAGAGGGGAT	60.753	63.158	0.00	0.00	0.00	3.85
526	829	0.394565	GTCGAGAGGGGATGGATTGG	59.605	60.000	0.00	0.00	0.00	3.16
533	836	1.466526	GGGATGGATTGGGGATGGG	59.533	63.158	0.00	0.00	0.00	4.00
568	871	0.465824	CGGGGTATCGTCAGAGAGGT	60.466	60.000	0.00	0.00	0.00	3.85
588	1025	3.685643	TAAAACCCTAGGCGCGGGC	62.686	63.158	17.31	17.31	46.04	6.13
603	1040	0.814010	CGGGCGTAAGGGAATCTTGG	60.814	60.000	0.00	0.00	36.93	3.61
605	1042	1.340697	GGGCGTAAGGGAATCTTGGTT	60.341	52.381	0.00	0.00	36.93	3.67
650	1087	8.433421	ACTTTTTCTTTCAACGAGACAGATAA	57.567	30.769	0.00	0.00	33.31	1.75
793	1236	2.034001	GGTATCAAAATCTCGAACGGCG	60.034	50.000	4.80	4.80	42.69	6.46
895	3837	7.103641	TCTTCTTAATTGCTCCGAAACTATGT	58.896	34.615	0.00	0.00	0.00	2.29
896	3838	8.255206	TCTTCTTAATTGCTCCGAAACTATGTA	58.745	33.333	0.00	0.00	0.00	2.29
897	3839	7.766219	TCTTAATTGCTCCGAAACTATGTAC	57.234	36.000	0.00	0.00	0.00	2.90
1017	3965	1.522668	CCATGGCAGTCAAAGACGAA	58.477	50.000	0.00	0.00	37.67	3.85
1232	4192	0.858135	GCGATCGATATCTCCGTCGC	60.858	60.000	21.57	18.22	43.16	5.19
1521	4484	4.308458	CCGTTGGCGACTGTCCCA	62.308	66.667	12.23	12.23	41.33	4.37
1647	4616	1.687368	GCATTCTTCCAGGGCCTGAAT	60.687	52.381	34.84	21.99	32.44	2.57
1689	4658	2.084546	GGCGAGGTGTTCAATAGCTTT	58.915	47.619	0.00	0.00	0.00	3.51
1690	4659	2.159517	GGCGAGGTGTTCAATAGCTTTG	60.160	50.000	0.00	0.00	0.00	2.77
1836	4808	4.487412	GCGGACAGCTGCATTGGC	62.487	66.667	15.27	6.85	45.91	4.52
1845	4817	1.756950	CTGCATTGGCTGGCTGGAT	60.757	57.895	2.00	0.00	41.91	3.41
2480	5467	1.070289	GAGTTCCGTGAAGGTTGGAGT	59.930	52.381	0.00	0.00	41.99	3.85
2481	5468	1.489230	AGTTCCGTGAAGGTTGGAGTT	59.511	47.619	0.00	0.00	41.99	3.01
2482	5469	1.871676	GTTCCGTGAAGGTTGGAGTTC	59.128	52.381	0.00	0.00	41.99	3.01
2483	5470	0.395312	TCCGTGAAGGTTGGAGTTCC	59.605	55.000	0.00	0.00	41.99	3.62
2489	5476	3.497262	GTGAAGGTTGGAGTTCCGTAAAG	59.503	47.826	0.00	0.00	39.43	1.85
2491	5478	3.679824	AGGTTGGAGTTCCGTAAAGAG	57.320	47.619	0.00	0.00	39.43	2.85
2517	5513	0.900182	TTGCTCTCTGCTTCTCGGGA	60.900	55.000	0.00	0.00	43.37	5.14
2518	5514	1.318886	TGCTCTCTGCTTCTCGGGAG	61.319	60.000	0.00	0.00	43.37	4.30
2583	5588	5.474532	CCAAACATGATACATACCATGGAGG	59.525	44.000	21.47	9.64	43.16	4.30
2603	5609	2.032681	GTCCAAGTCTTGCCGGCT	59.967	61.111	29.70	2.88	0.00	5.52
2623	5633	4.481112	GCCTGCCGCCATGTTTCG	62.481	66.667	0.00	0.00	0.00	3.46
2624	5634	3.055719	CCTGCCGCCATGTTTCGT	61.056	61.111	0.00	0.00	0.00	3.85
2625	5635	2.625823	CCTGCCGCCATGTTTCGTT	61.626	57.895	0.00	0.00	0.00	3.85
2626	5636	1.302383	CCTGCCGCCATGTTTCGTTA	61.302	55.000	0.00	0.00	0.00	3.18
2627	5637	0.179200	CTGCCGCCATGTTTCGTTAC	60.179	55.000	0.00	0.00	0.00	2.50
2628	5638	0.885150	TGCCGCCATGTTTCGTTACA	60.885	50.000	0.00	0.00	0.00	2.41
2629	5639	0.450184	GCCGCCATGTTTCGTTACAT	59.550	50.000	0.00	0.38	39.27	2.29
2680	5690	4.207891	ACAGACTTGTGACACTGAAACT	57.792	40.909	7.20	0.00	35.83	2.66
2681	5691	4.184629	ACAGACTTGTGACACTGAAACTC	58.815	43.478	7.20	0.00	35.83	3.01
2682	5692	4.081420	ACAGACTTGTGACACTGAAACTCT	60.081	41.667	7.20	0.00	35.83	3.24
2683	5693	4.872691	CAGACTTGTGACACTGAAACTCTT	59.127	41.667	7.20	0.00	32.90	2.85
2684	5694	5.006165	CAGACTTGTGACACTGAAACTCTTC	59.994	44.000	7.20	0.00	32.90	2.87
2685	5695	5.091261	ACTTGTGACACTGAAACTCTTCT	57.909	39.130	7.20	0.00	32.33	2.85
2686	5696	5.491982	ACTTGTGACACTGAAACTCTTCTT	58.508	37.500	7.20	0.00	32.33	2.52
2757	5772	9.447040	GTAATGAAACTCTACACTTTTGTTTCC	57.553	33.333	12.36	0.00	43.11	3.13
2813	5838	7.421530	GTGAATCTACTCACAAACTTGCTAA	57.578	36.000	0.00	0.00	44.32	3.09
2814	5839	7.291567	GTGAATCTACTCACAAACTTGCTAAC	58.708	38.462	0.00	0.00	44.32	2.34
2815	5840	6.426937	TGAATCTACTCACAAACTTGCTAACC	59.573	38.462	0.00	0.00	0.00	2.85
2816	5841	5.546621	TCTACTCACAAACTTGCTAACCT	57.453	39.130	0.00	0.00	0.00	3.50
2817	5842	5.297547	TCTACTCACAAACTTGCTAACCTG	58.702	41.667	0.00	0.00	0.00	4.00
2818	5843	2.618709	ACTCACAAACTTGCTAACCTGC	59.381	45.455	0.00	0.00	0.00	4.85
2819	5844	1.953686	TCACAAACTTGCTAACCTGCC	59.046	47.619	0.00	0.00	0.00	4.85
2820	5845	1.680735	CACAAACTTGCTAACCTGCCA	59.319	47.619	0.00	0.00	0.00	4.92
2821	5846	2.297033	CACAAACTTGCTAACCTGCCAT	59.703	45.455	0.00	0.00	0.00	4.40
2909	5934	9.515020	CTCTGAAGTCTGAAGTCATTATCTTAC	57.485	37.037	0.00	0.00	0.00	2.34
3131	6158	1.379642	CGCTTCTGGATTTGGGAGGC	61.380	60.000	0.00	0.00	0.00	4.70
3177	6204	1.152963	GCAACCGGGCATATCCAGT	60.153	57.895	6.32	0.00	36.21	4.00
3238	6265	3.501349	GACTCCAGCAGGTATGGATCTA	58.499	50.000	0.00	0.00	45.64	1.98
3292	6320	2.481276	CGATTCTGTAGGCGTTCATGGA	60.481	50.000	0.00	0.00	0.00	3.41
3350	6379	2.047002	TATCCACCGAGATGACGACA	57.953	50.000	0.00	0.00	35.09	4.35
3364	6393	0.952497	ACGACAACGGCGAGACTAGA	60.952	55.000	16.62	0.00	44.46	2.43
3410	6439	2.220586	TGTCAACGAGCCATCCCCA	61.221	57.895	0.00	0.00	0.00	4.96
3424	6453	0.695924	TCCCCAACCATCATCAACGT	59.304	50.000	0.00	0.00	0.00	3.99
3427	6456	1.438651	CCAACCATCATCAACGTCGT	58.561	50.000	0.00	0.00	0.00	4.34
3467	6496	1.153429	GGAGCCGTATCTGCCGTTT	60.153	57.895	0.00	0.00	0.00	3.60
3474	6503	1.466866	CGTATCTGCCGTTTCTCGTCA	60.467	52.381	0.00	0.00	37.94	4.35
3479	6508	1.126846	CTGCCGTTTCTCGTCATTCAC	59.873	52.381	0.00	0.00	37.94	3.18
3483	6512	2.800544	CCGTTTCTCGTCATTCACTGTT	59.199	45.455	0.00	0.00	37.94	3.16

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
89	91	6.233434	AGCATTATGTTCATGTCGATATGGT	58.767	36.000	20.34	8.40	0.00	3.55
135	137	5.449107	GTACTGATGTACCCATACGACAT	57.551	43.478	0.00	0.00	42.25	3.06
136	138	4.906065	GTACTGATGTACCCATACGACA	57.094	45.455	0.00	0.00	42.25	4.35
147	149	5.772393	AGAAATTGGGTGGTACTGATGTA	57.228	39.130	0.00	0.00	0.00	2.29
186	188	5.289675	GGCGATTGGAAGAGAATATGTATCG	59.710	44.000	0.00	0.00	36.41	2.92
224	226	3.316868	GTCCAAATCTTTTCGTTGTCCCA	59.683	43.478	0.00	0.00	0.00	4.37
226	228	3.316868	TGGTCCAAATCTTTTCGTTGTCC	59.683	43.478	0.00	0.00	0.00	4.02
318	322	7.201794	GCTAGGGTTCACACTTAGAAAACTTTT	60.202	37.037	0.00	0.00	0.00	2.27
357	362	8.960591	TGATCATTATATCAATGAGAGCGTCTA	58.039	33.333	5.94	0.00	39.69	2.59
376	381	7.190501	TCTGGAGATAGATGAGGATGATCATT	58.809	38.462	10.14	0.00	27.93	2.57
378	383	6.150034	TCTGGAGATAGATGAGGATGATCA	57.850	41.667	0.00	0.00	27.93	2.92
487	493	0.460109	CGTGTCTCATGCCCAATCGA	60.460	55.000	0.00	0.00	0.00	3.59
511	517	0.276277	ATCCCCAATCCATCCCCTCT	59.724	55.000	0.00	0.00	0.00	3.69
512	518	0.407139	CATCCCCAATCCATCCCCTC	59.593	60.000	0.00	0.00	0.00	4.30
514	520	1.466526	CCATCCCCAATCCATCCCC	59.533	63.158	0.00	0.00	0.00	4.81
515	521	1.466526	CCCATCCCCAATCCATCCC	59.533	63.158	0.00	0.00	0.00	3.85
516	522	1.466526	CCCCATCCCCAATCCATCC	59.533	63.158	0.00	0.00	0.00	3.51
518	524	0.027058	TACCCCCATCCCCAATCCAT	60.027	55.000	0.00	0.00	0.00	3.41
519	525	0.254347	TTACCCCCATCCCCAATCCA	60.254	55.000	0.00	0.00	0.00	3.41
526	829	0.750546	GCGAGTTTTACCCCCATCCC	60.751	60.000	0.00	0.00	0.00	3.85
533	836	2.396157	CCGCCAGCGAGTTTTACCC	61.396	63.158	14.67	0.00	42.83	3.69
559	862	4.094476	CCTAGGGTTTTACACCTCTCTGA	58.906	47.826	0.00	0.00	46.38	3.27
568	871	1.078988	CCGCGCCTAGGGTTTTACA	60.079	57.895	11.72	0.00	0.00	2.41
588	1025	3.818773	ACAACAACCAAGATTCCCTTACG	59.181	43.478	0.00	0.00	32.86	3.18
603	1040	7.016361	AGTCACTCAACAAAGATACAACAAC	57.984	36.000	0.00	0.00	0.00	3.32
605	1042	7.624360	AAAGTCACTCAACAAAGATACAACA	57.376	32.000	0.00	0.00	0.00	3.33
662	1099	8.663025	GTGCAATCGTTCAGATAATATCATGAT	58.337	33.333	13.81	13.81	38.98	2.45
742	1182	4.992688	ACATGCAAGAGTTCGAACAAAAA	58.007	34.783	28.78	10.43	0.00	1.94
750	1190	2.324860	TCACGTACATGCAAGAGTTCG	58.675	47.619	12.35	12.35	35.17	3.95
758	1198	3.878160	TGATACCTTCACGTACATGCA	57.122	42.857	0.00	0.00	0.00	3.96
895	3837	5.047021	AGGCTATAGGAGTGATACGTACGTA	60.047	44.000	28.62	28.62	34.87	3.57
896	3838	3.999663	GGCTATAGGAGTGATACGTACGT	59.000	47.826	25.98	25.98	0.00	3.57
897	3839	4.252073	AGGCTATAGGAGTGATACGTACG	58.748	47.826	15.01	15.01	0.00	3.67
1232	4192	2.809601	CGACGTCAGGGAAAGGCG	60.810	66.667	17.16	0.00	0.00	5.52
1501	4464	2.737376	GACAGTCGCCAACGGGTC	60.737	66.667	0.00	0.00	40.63	4.46
1690	4659	4.500116	GTCCGGCTCCAGCTCGTC	62.500	72.222	0.00	0.00	41.70	4.20
2517	5513	1.171308	GCATGACATGAGTTGTGCCT	58.829	50.000	19.76	0.00	39.18	4.75
2518	5514	0.171903	GGCATGACATGAGTTGTGCC	59.828	55.000	19.76	8.89	45.13	5.01
2583	5588	2.027625	CCGGCAAGACTTGGACGTC	61.028	63.158	16.80	7.13	0.00	4.34
2622	5632	5.063944	CAGAAAACTCCATCTCCATGTAACG	59.936	44.000	0.00	0.00	0.00	3.18
2623	5633	5.940470	ACAGAAAACTCCATCTCCATGTAAC	59.060	40.000	0.00	0.00	0.00	2.50
2624	5634	6.126863	ACAGAAAACTCCATCTCCATGTAA	57.873	37.500	0.00	0.00	0.00	2.41
2625	5635	5.762179	ACAGAAAACTCCATCTCCATGTA	57.238	39.130	0.00	0.00	0.00	2.29
2626	5636	4.647564	ACAGAAAACTCCATCTCCATGT	57.352	40.909	0.00	0.00	0.00	3.21
2627	5637	5.391310	CGAAACAGAAAACTCCATCTCCATG	60.391	44.000	0.00	0.00	0.00	3.66
2628	5638	4.697352	CGAAACAGAAAACTCCATCTCCAT	59.303	41.667	0.00	0.00	0.00	3.41
2629	5639	4.065088	CGAAACAGAAAACTCCATCTCCA	58.935	43.478	0.00	0.00	0.00	3.86
2630	5640	3.437049	CCGAAACAGAAAACTCCATCTCC	59.563	47.826	0.00	0.00	0.00	3.71
2631	5641	3.120165	GCCGAAACAGAAAACTCCATCTC	60.120	47.826	0.00	0.00	0.00	2.75
2632	5642	2.814336	GCCGAAACAGAAAACTCCATCT	59.186	45.455	0.00	0.00	0.00	2.90
2633	5643	2.552315	TGCCGAAACAGAAAACTCCATC	59.448	45.455	0.00	0.00	0.00	3.51
2771	5786	8.853077	AGATTCACATGATCAGAAGTACAAAA	57.147	30.769	0.00	0.00	0.00	2.44
2772	5787	9.371136	GTAGATTCACATGATCAGAAGTACAAA	57.629	33.333	0.00	0.00	0.00	2.83
2805	5820	4.235079	TGAATATGGCAGGTTAGCAAGT	57.765	40.909	0.00	0.00	35.83	3.16
2812	5837	9.074576	CATATATATGCATGAATATGGCAGGTT	57.925	33.333	23.02	0.00	34.79	3.50
2813	5838	7.668469	CCATATATATGCATGAATATGGCAGGT	59.332	37.037	29.98	5.82	42.50	4.00
2814	5839	7.886446	TCCATATATATGCATGAATATGGCAGG	59.114	37.037	32.77	21.50	45.79	4.85
2815	5840	8.857694	TCCATATATATGCATGAATATGGCAG	57.142	34.615	32.77	21.36	45.79	4.85
2816	5841	7.392393	GCTCCATATATATGCATGAATATGGCA	59.608	37.037	32.77	25.61	45.79	4.92
2817	5842	7.392393	TGCTCCATATATATGCATGAATATGGC	59.608	37.037	32.77	26.98	45.79	4.40
2818	5843	8.857694	TGCTCCATATATATGCATGAATATGG	57.142	34.615	32.31	32.31	46.81	2.74
2872	5897	7.340487	ACTTCAGACTTCAGAGTTCCAATTTTT	59.660	33.333	0.00	0.00	35.88	1.94
2873	5898	6.830838	ACTTCAGACTTCAGAGTTCCAATTTT	59.169	34.615	0.00	0.00	35.88	1.82
2880	5905	8.250332	AGATAATGACTTCAGACTTCAGAGTTC	58.750	37.037	0.00	0.00	35.88	3.01
2886	5911	7.122204	TCCGTAAGATAATGACTTCAGACTTCA	59.878	37.037	0.00	0.00	43.02	3.02
2909	5934	2.228103	GGGTGAAGGTAAGCTTTTTCCG	59.772	50.000	3.20	0.00	0.00	4.30
2965	5990	2.925724	TCAACAAACGATCCAACAGGT	58.074	42.857	0.00	0.00	0.00	4.00
3086	6113	0.035343	TCCCAGAGACACGAGACGAT	60.035	55.000	0.00	0.00	0.00	3.73
3161	6188	1.152963	GCACTGGATATGCCCGGTT	60.153	57.895	0.00	0.00	42.98	4.44
3238	6265	1.235756	GGAAAGGGATGGGGGATCTT	58.764	55.000	0.00	0.00	0.00	2.40
3350	6379	0.323178	TCCCTTCTAGTCTCGCCGTT	60.323	55.000	0.00	0.00	0.00	4.44
3364	6393	1.073199	CAAACCAGCCGTCTCCCTT	59.927	57.895	0.00	0.00	0.00	3.95
3410	6439	1.275291	AGGACGACGTTGATGATGGTT	59.725	47.619	10.51	0.00	0.00	3.67
3424	6453	3.247442	CGTAACAAATGCTACAGGACGA	58.753	45.455	0.00	0.00	0.00	4.20
3427	6456	2.027561	AGCCGTAACAAATGCTACAGGA	60.028	45.455	8.18	0.00	30.97	3.86
3467	6496	1.795768	GGCAACAGTGAATGACGAGA	58.204	50.000	0.00	0.00	0.00	4.04

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.