AutoCloner

Multiple sequence alignment - TraesCS5D01G394000

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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	TraesCS5D01G394000	chr5D	100.000	3906	0	0	1	3906	462073312	462077217	0.000000e+00	7214.0
1	TraesCS5D01G394000	chr5D	83.838	99	11	5	3381	3477	255076534	255076439	5.380000e-14	89.8
2	TraesCS5D01G394000	chr5D	92.593	54	4	0	3381	3434	428386327	428386380	1.160000e-10	78.7
3	TraesCS5D01G394000	chr5D	95.556	45	2	0	3553	3597	255076479	255076523	5.410000e-09	73.1
4	TraesCS5D01G394000	chr5D	87.931	58	5	1	3540	3597	126572375	126572430	2.520000e-07	67.6
5	TraesCS5D01G394000	chr5D	100.000	32	0	0	604	635	5426228	5426197	4.210000e-05	60.2
6	TraesCS5D01G394000	chr5A	95.094	2446	101	7	732	3161	582381350	582383792	0.000000e+00	3834.0
7	TraesCS5D01G394000	chr5A	93.923	543	17	5	3171	3705	582383761	582384295	0.000000e+00	806.0
8	TraesCS5D01G394000	chr5A	91.244	217	4	2	3704	3906	582384400	582384615	8.260000e-72	281.0
9	TraesCS5D01G394000	chr5A	82.828	99	12	5	3381	3477	338287883	338287788	2.500000e-12	84.2
10	TraesCS5D01G394000	chr5A	95.556	45	2	0	3553	3597	338287828	338287872	5.410000e-09	73.1
11	TraesCS5D01G394000	chr5A	87.097	62	6	1	3539	3600	667304819	667304878	7.000000e-08	69.4
12	TraesCS5D01G394000	chr5A	87.931	58	5	1	3540	3597	141880995	141881050	2.520000e-07	67.6
13	TraesCS5D01G394000	chr5B	95.321	2351	87	6	661	3009	568401319	568403648	0.000000e+00	3711.0
14	TraesCS5D01G394000	chr5B	94.033	972	38	5	2951	3906	568403647	568404614	0.000000e+00	1456.0
15	TraesCS5D01G394000	chr5B	95.000	40	2	0	3123	3162	568403860	568403899	3.260000e-06	63.9
16	TraesCS5D01G394000	chr2D	90.349	601	46	7	4	593	109741831	109741232	0.000000e+00	778.0
17	TraesCS5D01G394000	chr2D	90.374	561	48	3	1	557	398456065	398455507	0.000000e+00	732.0
18	TraesCS5D01G394000	chr2D	91.856	528	38	2	1	524	557170121	557169595	0.000000e+00	732.0
19	TraesCS5D01G394000	chr2D	89.831	59	4	1	3539	3597	394525140	394525196	1.510000e-09	75.0
20	TraesCS5D01G394000	chr7D	89.803	608	44	9	1	594	38739518	38740121	0.000000e+00	763.0
21	TraesCS5D01G394000	chr7D	89.840	561	51	3	1	557	528679411	528679969	0.000000e+00	715.0
22	TraesCS5D01G394000	chr7D	88.889	216	19	3	811	1021	21085034	21084819	1.080000e-65	261.0
23	TraesCS5D01G394000	chr7D	89.781	137	9	2	659	790	21085291	21085155	1.870000e-38	171.0
24	TraesCS5D01G394000	chr7D	80.537	149	25	2	3389	3537	175652620	175652476	1.150000e-20	111.0
25	TraesCS5D01G394000	chr2A	89.735	604	47	9	1	596	686011404	686012000	0.000000e+00	758.0
26	TraesCS5D01G394000	chr2A	89.362	611	49	7	1	596	585984183	585984792	0.000000e+00	754.0
27	TraesCS5D01G394000	chr2A	79.167	144	25	5	462	602	117844081	117843940	1.160000e-15	95.3
28	TraesCS5D01G394000	chr3D	89.327	609	44	10	1	594	532206874	532206272	0.000000e+00	745.0
29	TraesCS5D01G394000	chr3D	88.980	608	51	7	1	594	471962105	471961500	0.000000e+00	737.0
30	TraesCS5D01G394000	chr4D	86.517	623	42	16	1	594	363691996	363691387	0.000000e+00	647.0
31	TraesCS5D01G394000	chr4D	85.321	109	12	3	3381	3488	486932222	486932117	4.130000e-20	110.0
32	TraesCS5D01G394000	chr4D	80.992	121	14	8	3380	3495	67791793	67791909	1.930000e-13	87.9
33	TraesCS5D01G394000	chr4D	91.525	59	3	1	3541	3599	486932157	486932213	3.240000e-11	80.5
34	TraesCS5D01G394000	chr4D	78.704	108	23	0	3381	3488	301756564	301756457	5.410000e-09	73.1
35	TraesCS5D01G394000	chr4D	89.091	55	4	1	3539	3593	89432429	89432377	2.520000e-07	67.6
36	TraesCS5D01G394000	chr4D	94.595	37	2	0	3562	3598	317957582	317957618	1.520000e-04	58.4
37	TraesCS5D01G394000	chr1A	83.721	129	13	5	3380	3501	398461003	398460876	8.870000e-22	115.0
38	TraesCS5D01G394000	chr1A	100.000	36	0	0	3562	3597	398460956	398460991	2.520000e-07	67.6
39	TraesCS5D01G394000	chr1A	100.000	29	0	0	3409	3437	99002718	99002690	2.000000e-03	54.7
40	TraesCS5D01G394000	chr1D	83.594	128	14	6	3380	3501	317439607	317439481	3.190000e-21	113.0
41	TraesCS5D01G394000	chr1D	100.000	36	0	0	3562	3597	317439560	317439595	2.520000e-07	67.6
42	TraesCS5D01G394000	chr7A	79.866	149	26	2	3389	3537	177333672	177333528	5.340000e-19	106.0
43	TraesCS5D01G394000	chr4B	79.137	139	19	9	3380	3513	100314579	100314712	1.930000e-13	87.9
44	TraesCS5D01G394000	chr4B	78.899	109	21	2	3381	3488	376157970	376157863	5.410000e-09	73.1
45	TraesCS5D01G394000	chr1B	90.323	62	4	1	3539	3600	565664621	565664562	3.240000e-11	80.5
46	TraesCS5D01G394000	chr1B	97.222	36	1	0	3562	3597	429597317	429597352	1.170000e-05	62.1
47	TraesCS5D01G394000	chr4A	82.759	87	15	0	3378	3464	179057200	179057286	1.160000e-10	78.7
48	TraesCS5D01G394000	chr4A	86.364	66	6	2	3535	3600	501972654	501972592	7.000000e-08	69.4
49	TraesCS5D01G394000	chr2B	89.831	59	4	1	3539	3597	466165248	466165304	1.510000e-09	75.0
50	TraesCS5D01G394000	chr6B	94.872	39	2	0	3562	3600	451927267	451927229	1.170000e-05	62.1

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	TraesCS5D01G394000	chr5D	462073312	462077217	3905	False	7214.000000	7214	100.000000	1	3906	1	chr5D.!!$F4	3905
1	TraesCS5D01G394000	chr5A	582381350	582384615	3265	False	1640.333333	3834	93.420333	732	3906	3	chr5A.!!$F4	3174
2	TraesCS5D01G394000	chr5B	568401319	568404614	3295	False	1743.633333	3711	94.784667	661	3906	3	chr5B.!!$F1	3245
3	TraesCS5D01G394000	chr2D	109741232	109741831	599	True	778.000000	778	90.349000	4	593	1	chr2D.!!$R1	589
4	TraesCS5D01G394000	chr2D	398455507	398456065	558	True	732.000000	732	90.374000	1	557	1	chr2D.!!$R2	556
5	TraesCS5D01G394000	chr2D	557169595	557170121	526	True	732.000000	732	91.856000	1	524	1	chr2D.!!$R3	523
6	TraesCS5D01G394000	chr7D	38739518	38740121	603	False	763.000000	763	89.803000	1	594	1	chr7D.!!$F1	593
7	TraesCS5D01G394000	chr7D	528679411	528679969	558	False	715.000000	715	89.840000	1	557	1	chr7D.!!$F2	556
8	TraesCS5D01G394000	chr2A	686011404	686012000	596	False	758.000000	758	89.735000	1	596	1	chr2A.!!$F2	595
9	TraesCS5D01G394000	chr2A	585984183	585984792	609	False	754.000000	754	89.362000	1	596	1	chr2A.!!$F1	595
10	TraesCS5D01G394000	chr3D	532206272	532206874	602	True	745.000000	745	89.327000	1	594	1	chr3D.!!$R2	593
11	TraesCS5D01G394000	chr3D	471961500	471962105	605	True	737.000000	737	88.980000	1	594	1	chr3D.!!$R1	593
12	TraesCS5D01G394000	chr4D	363691387	363691996	609	True	647.000000	647	86.517000	1	594	1	chr4D.!!$R3	593

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	Hairpin	End Stability	Orientation
721	767	0.586802	GCGCTCGAGTCTTTGGTTTT	59.413	50.000	15.13	0.00	2.43	F
1449	1501	0.037326	ATTTCGACGAAGCCAGCAGA	60.037	50.000	10.61	0.00	4.26	F
2122	2174	1.480954	ACGCCATCCTAAACGAGATGT	59.519	47.619	0.00	38.57	3.06	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1547	1599	1.004044	CCCAATCACTGCTGAACCTCT	59.996	52.381	0.00	0.00	3.69	R
2478	2530	1.229428	TACAGCACAGCTTCAGCAAC	58.771	50.000	0.75	45.16	4.17	R
3042	3159	1.604378	CAGCTGGTAGGGGACTTGG	59.396	63.158	5.57	43.67	3.61	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
72	73	0.800631	ACTGCTTGTGTGATCATGCG	59.199	50.000	0.00	0.00	40.02	4.73
190	191	2.014128	ACGTTTGAACAGTTCACCCAG	58.986	47.619	15.93	9.95	39.87	4.45
203	204	2.698803	TCACCCAGTTTCATCATGACG	58.301	47.619	0.00	0.00	0.00	4.35
206	207	2.038426	ACCCAGTTTCATCATGACGTGA	59.962	45.455	0.00	0.00	42.06	4.35
596	640	1.065418	CCCGGTTGGAGTTGCTCTTAT	60.065	52.381	0.00	0.00	37.49	1.73
597	641	2.169769	CCCGGTTGGAGTTGCTCTTATA	59.830	50.000	0.00	0.00	37.49	0.98
598	642	3.181454	CCCGGTTGGAGTTGCTCTTATAT	60.181	47.826	0.00	0.00	37.49	0.86
599	643	4.451900	CCGGTTGGAGTTGCTCTTATATT	58.548	43.478	0.00	0.00	37.49	1.28
600	644	4.273480	CCGGTTGGAGTTGCTCTTATATTG	59.727	45.833	0.00	0.00	37.49	1.90
601	645	4.876107	CGGTTGGAGTTGCTCTTATATTGT	59.124	41.667	0.00	0.00	0.00	2.71
602	646	6.046593	CGGTTGGAGTTGCTCTTATATTGTA	58.953	40.000	0.00	0.00	0.00	2.41
603	647	6.018994	CGGTTGGAGTTGCTCTTATATTGTAC	60.019	42.308	0.00	0.00	0.00	2.90
604	648	7.048512	GGTTGGAGTTGCTCTTATATTGTACT	58.951	38.462	0.00	0.00	0.00	2.73
605	649	7.224949	GGTTGGAGTTGCTCTTATATTGTACTC	59.775	40.741	0.00	0.00	0.00	2.59
606	650	7.661536	TGGAGTTGCTCTTATATTGTACTCT	57.338	36.000	0.00	0.00	33.20	3.24
607	651	7.492524	TGGAGTTGCTCTTATATTGTACTCTG	58.507	38.462	0.00	0.00	33.20	3.35
608	652	7.124298	TGGAGTTGCTCTTATATTGTACTCTGT	59.876	37.037	0.00	0.00	33.20	3.41
609	653	7.982354	GGAGTTGCTCTTATATTGTACTCTGTT	59.018	37.037	0.00	0.00	33.20	3.16
610	654	9.372369	GAGTTGCTCTTATATTGTACTCTGTTT	57.628	33.333	0.00	0.00	0.00	2.83
611	655	9.372369	AGTTGCTCTTATATTGTACTCTGTTTC	57.628	33.333	0.00	0.00	0.00	2.78
612	656	9.372369	GTTGCTCTTATATTGTACTCTGTTTCT	57.628	33.333	0.00	0.00	0.00	2.52
644	688	5.584253	TCTTTCTAGAGATGAAACGGAGG	57.416	43.478	0.00	0.00	31.21	4.30
645	689	4.402793	TCTTTCTAGAGATGAAACGGAGGG	59.597	45.833	0.00	0.00	31.21	4.30
646	690	3.664551	TCTAGAGATGAAACGGAGGGA	57.335	47.619	0.00	0.00	0.00	4.20
647	691	3.556999	TCTAGAGATGAAACGGAGGGAG	58.443	50.000	0.00	0.00	0.00	4.30
648	692	2.239681	AGAGATGAAACGGAGGGAGT	57.760	50.000	0.00	0.00	0.00	3.85
649	693	3.383698	AGAGATGAAACGGAGGGAGTA	57.616	47.619	0.00	0.00	0.00	2.59
650	694	3.917300	AGAGATGAAACGGAGGGAGTAT	58.083	45.455	0.00	0.00	0.00	2.12
651	695	3.892588	AGAGATGAAACGGAGGGAGTATC	59.107	47.826	0.00	0.00	0.00	2.24
652	696	3.892588	GAGATGAAACGGAGGGAGTATCT	59.107	47.826	0.00	0.00	33.73	1.98
653	697	4.290942	AGATGAAACGGAGGGAGTATCTT	58.709	43.478	0.00	0.00	33.73	2.40
654	698	4.717280	AGATGAAACGGAGGGAGTATCTTT	59.283	41.667	0.00	0.00	33.73	2.52
655	699	4.903045	TGAAACGGAGGGAGTATCTTTT	57.097	40.909	0.00	0.00	33.73	2.27
656	700	4.575885	TGAAACGGAGGGAGTATCTTTTG	58.424	43.478	0.00	0.00	33.73	2.44
657	701	4.285003	TGAAACGGAGGGAGTATCTTTTGA	59.715	41.667	0.00	0.00	33.73	2.69
658	702	5.045869	TGAAACGGAGGGAGTATCTTTTGAT	60.046	40.000	0.00	0.00	42.66	2.57
659	703	4.674281	ACGGAGGGAGTATCTTTTGATC	57.326	45.455	0.00	0.00	40.19	2.92
721	767	0.586802	GCGCTCGAGTCTTTGGTTTT	59.413	50.000	15.13	0.00	0.00	2.43
1067	1119	2.280592	GCCGACGGTGTGTCCTTT	60.281	61.111	16.73	0.00	45.23	3.11
1282	1334	2.418669	TCAGGAACCCAAAGAAGGACT	58.581	47.619	0.00	0.00	0.00	3.85
1302	1354	2.606725	CTGCGACTCCTTTGATGATGAC	59.393	50.000	0.00	0.00	0.00	3.06
1308	1360	2.932614	CTCCTTTGATGATGACGACCAC	59.067	50.000	0.00	0.00	0.00	4.16
1358	1410	4.796231	CGTGGAGGAACGGAGCCG	62.796	72.222	7.48	7.48	46.03	5.52
1410	1462	3.248764	GAGGCTGCCTCCCATGAT	58.751	61.111	33.62	4.83	44.36	2.45
1413	1465	1.228184	GGCTGCCTCCCATGATGAG	60.228	63.158	12.43	0.00	0.00	2.90
1449	1501	0.037326	ATTTCGACGAAGCCAGCAGA	60.037	50.000	10.61	0.00	0.00	4.26
1476	1528	1.600636	CTCTTGCTTTGCGTCCCCA	60.601	57.895	0.00	0.00	0.00	4.96
1547	1599	3.490933	CGCATGGTCGAGAAGATCCTAAA	60.491	47.826	0.00	0.00	0.00	1.85
1554	1606	5.450826	GGTCGAGAAGATCCTAAAGAGGTTC	60.451	48.000	0.00	0.00	44.19	3.62
1555	1607	5.125739	GTCGAGAAGATCCTAAAGAGGTTCA	59.874	44.000	5.16	0.00	42.14	3.18
1569	1621	1.985159	AGGTTCAGCAGTGATTGGGTA	59.015	47.619	0.00	0.00	30.85	3.69
1641	1693	5.173664	CACTCTGCTGATTCATACAACTCA	58.826	41.667	0.00	0.00	0.00	3.41
1932	1984	1.542679	GAGGGGATCGGTACCTCCT	59.457	63.158	17.41	12.11	43.93	3.69
2122	2174	1.480954	ACGCCATCCTAAACGAGATGT	59.519	47.619	0.00	0.00	38.57	3.06
2259	2311	2.034221	GCCCCAGACGCTTCCTTT	59.966	61.111	0.00	0.00	0.00	3.11
2478	2530	0.245539	ACATCAAGACGTACACCCCG	59.754	55.000	0.00	0.00	0.00	5.73
2496	2548	1.779025	CGTTGCTGAAGCTGTGCTGT	61.779	55.000	3.61	0.00	39.62	4.40
2694	2746	6.316390	AGAAAGAAACGTTTGATCTTGTGACT	59.684	34.615	20.10	10.34	33.86	3.41
2788	2848	0.606673	GAAGCACACTGGTTCCCCTC	60.607	60.000	3.28	0.00	46.01	4.30
2961	3078	7.889589	TTACACTGTCATTGATCTGTTACAG	57.110	36.000	5.94	5.94	40.08	2.74
2991	3108	9.613428	TGTTGCTCTGCTACATTTAACTATATT	57.387	29.630	3.03	0.00	39.07	1.28
2999	3116	8.547894	TGCTACATTTAACTATATTCGCAACAG	58.452	33.333	0.00	0.00	0.00	3.16
3001	3118	7.315247	ACATTTAACTATATTCGCAACAGCA	57.685	32.000	0.00	0.00	0.00	4.41
3042	3159	2.880890	CCATAGCAGTAAGGACATTGGC	59.119	50.000	0.00	0.00	0.00	4.52
3083	3200	6.329496	TGCCGATTTTATTCCTTTTCATCAC	58.671	36.000	0.00	0.00	0.00	3.06
3176	3293	2.556622	CAAGCCGGTGAACCATTTTAGT	59.443	45.455	1.90	0.00	35.14	2.24
3180	3297	5.121105	AGCCGGTGAACCATTTTAGTATAC	58.879	41.667	1.90	0.00	35.14	1.47
3290	3407	7.408756	TCACAAAATCAGCAGCCTTATTTAT	57.591	32.000	0.00	0.00	27.74	1.40
3345	3462	8.292448	CACATTAATGCCTTTCTGATACCATAC	58.708	37.037	15.48	0.00	0.00	2.39
3348	3465	5.894298	ATGCCTTTCTGATACCATACAGA	57.106	39.130	0.00	0.00	40.66	3.41
3349	3466	5.282055	TGCCTTTCTGATACCATACAGAG	57.718	43.478	0.00	0.00	42.72	3.35
3350	3467	4.716784	TGCCTTTCTGATACCATACAGAGT	59.283	41.667	0.00	0.00	42.72	3.24
3351	3468	5.189736	TGCCTTTCTGATACCATACAGAGTT	59.810	40.000	0.00	0.00	42.72	3.01
3352	3469	6.382859	TGCCTTTCTGATACCATACAGAGTTA	59.617	38.462	0.00	0.00	42.72	2.24
3431	3548	6.706716	AGTTCTAGCTTTGTCCTAAGTCAAAC	59.293	38.462	0.00	0.00	29.74	2.93
3550	3667	8.842358	ACTGAAATTAATCGGTCAAACTTAGA	57.158	30.769	0.00	0.00	33.66	2.10

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
72	73	5.004251	CGCTCATCTTCTACGATCATATTGC	59.996	44.000	0.00	0.00	0.00	3.56
203	204	2.032799	TGCACGTGAGTTTTCCAATCAC	59.967	45.455	22.23	0.00	46.40	3.06
206	207	2.687935	AGTTGCACGTGAGTTTTCCAAT	59.312	40.909	22.23	0.16	46.40	3.16
207	208	2.088423	AGTTGCACGTGAGTTTTCCAA	58.912	42.857	22.23	9.11	46.40	3.53
354	361	9.619316	TCAAATAAACATAGTTTCAACCGAATG	57.381	29.630	0.00	0.00	0.00	2.67
469	502	1.300311	CAACGCGCCGACCCATATA	60.300	57.895	5.73	0.00	0.00	0.86
579	623	7.048512	AGTACAATATAAGAGCAACTCCAACC	58.951	38.462	0.00	0.00	0.00	3.77
622	666	4.402793	CCCTCCGTTTCATCTCTAGAAAGA	59.597	45.833	0.00	0.00	35.81	2.52
623	667	4.402793	TCCCTCCGTTTCATCTCTAGAAAG	59.597	45.833	0.00	0.00	35.81	2.62
624	668	4.350245	TCCCTCCGTTTCATCTCTAGAAA	58.650	43.478	0.00	0.00	32.93	2.52
625	669	3.954904	CTCCCTCCGTTTCATCTCTAGAA	59.045	47.826	0.00	0.00	0.00	2.10
626	670	3.053544	ACTCCCTCCGTTTCATCTCTAGA	60.054	47.826	0.00	0.00	0.00	2.43
627	671	3.292460	ACTCCCTCCGTTTCATCTCTAG	58.708	50.000	0.00	0.00	0.00	2.43
628	672	3.383698	ACTCCCTCCGTTTCATCTCTA	57.616	47.619	0.00	0.00	0.00	2.43
629	673	2.239681	ACTCCCTCCGTTTCATCTCT	57.760	50.000	0.00	0.00	0.00	3.10
630	674	3.892588	AGATACTCCCTCCGTTTCATCTC	59.107	47.826	0.00	0.00	0.00	2.75
631	675	3.917300	AGATACTCCCTCCGTTTCATCT	58.083	45.455	0.00	0.00	0.00	2.90
632	676	4.674281	AAGATACTCCCTCCGTTTCATC	57.326	45.455	0.00	0.00	0.00	2.92
633	677	5.045869	TCAAAAGATACTCCCTCCGTTTCAT	60.046	40.000	0.00	0.00	0.00	2.57
634	678	4.285003	TCAAAAGATACTCCCTCCGTTTCA	59.715	41.667	0.00	0.00	0.00	2.69
635	679	4.828829	TCAAAAGATACTCCCTCCGTTTC	58.171	43.478	0.00	0.00	0.00	2.78
636	680	4.903045	TCAAAAGATACTCCCTCCGTTT	57.097	40.909	0.00	0.00	0.00	3.60
637	681	4.717280	AGATCAAAAGATACTCCCTCCGTT	59.283	41.667	0.00	0.00	0.00	4.44
638	682	4.290942	AGATCAAAAGATACTCCCTCCGT	58.709	43.478	0.00	0.00	0.00	4.69
639	683	4.946478	AGATCAAAAGATACTCCCTCCG	57.054	45.455	0.00	0.00	0.00	4.63
640	684	6.732896	TGTAGATCAAAAGATACTCCCTCC	57.267	41.667	0.00	0.00	0.00	4.30
641	685	9.921637	CTATTGTAGATCAAAAGATACTCCCTC	57.078	37.037	0.00	0.00	39.62	4.30
642	686	8.371699	GCTATTGTAGATCAAAAGATACTCCCT	58.628	37.037	0.00	0.00	39.62	4.20
643	687	8.150945	TGCTATTGTAGATCAAAAGATACTCCC	58.849	37.037	0.00	0.00	39.62	4.30
644	688	8.983724	GTGCTATTGTAGATCAAAAGATACTCC	58.016	37.037	0.00	0.00	39.62	3.85
645	689	9.534565	TGTGCTATTGTAGATCAAAAGATACTC	57.465	33.333	0.00	0.00	39.62	2.59
648	692	9.836864	ACATGTGCTATTGTAGATCAAAAGATA	57.163	29.630	0.00	0.00	39.62	1.98
649	693	8.743085	ACATGTGCTATTGTAGATCAAAAGAT	57.257	30.769	0.00	0.00	39.62	2.40
650	694	8.043113	AGACATGTGCTATTGTAGATCAAAAGA	58.957	33.333	1.15	0.00	39.62	2.52
651	695	8.121086	CAGACATGTGCTATTGTAGATCAAAAG	58.879	37.037	1.15	0.00	39.62	2.27
652	696	7.607607	ACAGACATGTGCTATTGTAGATCAAAA	59.392	33.333	1.15	0.00	38.57	2.44
653	697	7.105588	ACAGACATGTGCTATTGTAGATCAAA	58.894	34.615	1.15	0.00	38.57	2.69
654	698	6.643388	ACAGACATGTGCTATTGTAGATCAA	58.357	36.000	1.15	0.00	38.57	2.57
655	699	6.225981	ACAGACATGTGCTATTGTAGATCA	57.774	37.500	1.15	0.00	38.57	2.92
721	767	1.259507	CCGAAGAAACGTTTTGCGAGA	59.740	47.619	23.39	0.00	44.77	4.04
1043	1095	2.098233	CACACCGTCGGCGCTAATT	61.098	57.895	12.28	0.00	36.67	1.40
1188	1240	1.705337	CTTTATGTGGCCGGAGCACG	61.705	60.000	5.05	0.00	42.56	5.34
1282	1334	2.621338	GTCATCATCAAAGGAGTCGCA	58.379	47.619	0.00	0.00	0.00	5.10
1302	1354	0.450482	GCACAAATTCGTCGTGGTCG	60.450	55.000	0.00	0.00	38.55	4.79
1308	1360	1.011968	TCGGGAGCACAAATTCGTCG	61.012	55.000	0.00	0.00	0.00	5.12
1407	1459	0.820226	CCTCGAACTCAGCCTCATCA	59.180	55.000	0.00	0.00	0.00	3.07
1410	1462	1.607756	AGCCTCGAACTCAGCCTCA	60.608	57.895	0.00	0.00	0.00	3.86
1413	1465	0.107945	AATCAGCCTCGAACTCAGCC	60.108	55.000	0.00	0.00	0.00	4.85
1416	1468	1.544246	TCGAAATCAGCCTCGAACTCA	59.456	47.619	0.00	0.00	40.89	3.41
1449	1501	2.165998	GCAAAGCAAGAGGTCAGGATT	58.834	47.619	0.00	0.00	0.00	3.01
1547	1599	1.004044	CCCAATCACTGCTGAACCTCT	59.996	52.381	0.00	0.00	0.00	3.69
1554	1606	1.091771	CCGCTACCCAATCACTGCTG	61.092	60.000	0.00	0.00	0.00	4.41
1555	1607	1.221840	CCGCTACCCAATCACTGCT	59.778	57.895	0.00	0.00	0.00	4.24
1569	1621	2.438951	TAAAGAACCCGAACGCCGCT	62.439	55.000	0.00	0.00	36.84	5.52
1641	1693	7.458397	TGAACTTTCCTAGTATGTCAACCATT	58.542	34.615	0.00	0.00	35.54	3.16
1902	1954	2.171448	CGATCCCCTCAACTCTTGGAAT	59.829	50.000	0.00	0.00	0.00	3.01
1932	1984	3.065786	ACGTGTTGAAACTACTCTCGTCA	59.934	43.478	0.00	0.00	0.00	4.35
2122	2174	1.221840	GAGGGCATCCTTTCGAGCA	59.778	57.895	0.00	0.00	45.05	4.26
2259	2311	9.000486	CCGAGTATGTATATGAGAGAGTTGTAA	58.000	37.037	0.00	0.00	0.00	2.41
2415	2467	3.118112	CCATCCTAACCAGCATCTTCAGT	60.118	47.826	0.00	0.00	0.00	3.41
2478	2530	1.229428	TACAGCACAGCTTCAGCAAC	58.771	50.000	0.75	0.00	45.16	4.17
2496	2548	7.066525	CGAAGTACCTTTATCCATTGCCTTTTA	59.933	37.037	0.00	0.00	0.00	1.52
2694	2746	3.610040	TTCGCCTTATCAAGCTTCTCA	57.390	42.857	0.00	0.00	0.00	3.27
2788	2848	3.581755	CAGCACCATCCTTGTTCAAATG	58.418	45.455	0.00	0.00	0.00	2.32
2961	3078	4.756084	AAATGTAGCAGAGCAACAGAAC	57.244	40.909	0.00	0.00	0.00	3.01
2991	3108	2.287915	GTCTTCTTTTCTGCTGTTGCGA	59.712	45.455	0.00	0.00	43.34	5.10
2999	3116	4.023622	GGAACTTCTGGTCTTCTTTTCTGC	60.024	45.833	0.00	0.00	0.00	4.26
3001	3118	5.373812	TGGAACTTCTGGTCTTCTTTTCT	57.626	39.130	0.00	0.00	0.00	2.52
3042	3159	1.604378	CAGCTGGTAGGGGACTTGG	59.396	63.158	5.57	0.00	43.67	3.61
3083	3200	7.011950	TCCACATACTTTTTATATTGCAGACGG	59.988	37.037	0.00	0.00	0.00	4.79
3290	3407	3.806949	ACTGTTGGAAATAAGGGAGCA	57.193	42.857	0.00	0.00	0.00	4.26
3345	3462	6.129393	CGATAATTTCCATGCGTTAACTCTG	58.871	40.000	3.71	0.00	0.00	3.35
3348	3465	5.583061	TGACGATAATTTCCATGCGTTAACT	59.417	36.000	3.71	0.00	31.58	2.24
3349	3466	5.802064	TGACGATAATTTCCATGCGTTAAC	58.198	37.500	0.00	0.00	31.58	2.01
3350	3467	6.612247	ATGACGATAATTTCCATGCGTTAA	57.388	33.333	0.00	0.00	31.58	2.01
3351	3468	6.037720	ACAATGACGATAATTTCCATGCGTTA	59.962	34.615	0.00	0.00	31.58	3.18
3352	3469	5.163663	ACAATGACGATAATTTCCATGCGTT	60.164	36.000	0.00	0.00	31.58	4.84
3496	3613	8.441312	TTCCTCATAAAATACGTTTCCATACC	57.559	34.615	0.00	0.00	0.00	2.73
3549	3666	6.913132	GCTTTGTCCTAAGTTGAACTTCTTTC	59.087	38.462	14.64	5.27	39.51	2.62
3550	3667	6.603599	AGCTTTGTCCTAAGTTGAACTTCTTT	59.396	34.615	14.64	0.00	39.51	2.52

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.