AutoCloner

Multiple sequence alignment - TraesCS2A01G162900

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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	TraesCS2A01G162900	chr2A	100.000	3830	0	0	1	3830	115143196	115139367	0.000000e+00	7073
1	TraesCS2A01G162900	chr2A	88.235	153	14	3	3095	3245	176673268	176673418	3.040000e-41	180
2	TraesCS2A01G162900	chr2A	87.097	155	17	2	3092	3245	141506470	141506318	5.090000e-39	172
3	TraesCS2A01G162900	chr2D	95.311	1834	57	14	2007	3830	113510312	113508498	0.000000e+00	2883
4	TraesCS2A01G162900	chr2D	91.495	823	62	3	1	821	113512212	113511396	0.000000e+00	1125
5	TraesCS2A01G162900	chr2D	92.284	648	44	1	851	1492	113511396	113510749	0.000000e+00	915
6	TraesCS2A01G162900	chr2D	94.393	428	16	3	1558	1978	113510733	113510307	0.000000e+00	651
7	TraesCS2A01G162900	chr2B	93.350	1579	65	14	1525	3093	164109012	164107464	0.000000e+00	2298
8	TraesCS2A01G162900	chr2B	93.051	590	32	4	881	1461	164109620	164109031	0.000000e+00	854
9	TraesCS2A01G162900	chr2B	84.688	529	45	22	3247	3759	164107463	164106955	2.660000e-136	496
10	TraesCS2A01G162900	chr1D	88.453	866	85	9	1	858	299695797	299694939	0.000000e+00	1031
11	TraesCS2A01G162900	chr1D	83.696	368	47	7	493	857	281396788	281397145	6.130000e-88	335
12	TraesCS2A01G162900	chr4B	87.182	866	96	12	1	862	94952046	94951192	0.000000e+00	970
13	TraesCS2A01G162900	chr4B	87.261	157	17	2	3090	3245	106227407	106227561	3.930000e-40	176
14	TraesCS2A01G162900	chr3D	86.574	864	87	15	1	858	575775793	575774953	0.000000e+00	926
15	TraesCS2A01G162900	chr3D	85.407	884	86	18	1	866	516967990	516967132	0.000000e+00	878
16	TraesCS2A01G162900	chr3D	87.462	654	64	13	209	858	83937826	83938465	0.000000e+00	737
17	TraesCS2A01G162900	chr6D	90.735	680	53	5	1	677	418532935	418532263	0.000000e+00	898
18	TraesCS2A01G162900	chr6D	87.742	155	16	2	3092	3245	392273074	392273226	1.090000e-40	178
19	TraesCS2A01G162900	chr6D	85.890	163	17	3	3088	3248	320698076	320698234	6.580000e-38	169
20	TraesCS2A01G162900	chr4D	85.867	842	69	25	1	818	44543784	44544599	0.000000e+00	850
21	TraesCS2A01G162900	chr1B	84.810	869	96	16	1	862	538721757	538720918	0.000000e+00	841
22	TraesCS2A01G162900	chr6B	88.314	676	67	8	1	673	630577057	630576391	0.000000e+00	800
23	TraesCS2A01G162900	chr7A	83.236	853	123	13	1	847	191279248	191278410	0.000000e+00	765
24	TraesCS2A01G162900	chr7A	86.335	161	15	5	3088	3245	421785002	421785158	6.580000e-38	169
25	TraesCS2A01G162900	chr7D	83.397	783	109	14	80	857	441980237	441981003	0.000000e+00	706
26	TraesCS2A01G162900	chr5D	89.071	549	57	3	1	547	337143178	337142631	0.000000e+00	678
27	TraesCS2A01G162900	chr7B	86.957	161	14	5	3088	3245	369872715	369872871	1.410000e-39	174
28	TraesCS2A01G162900	chr1A	86.624	157	17	3	3092	3246	155857706	155857860	1.830000e-38	171

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	TraesCS2A01G162900	chr2A	115139367	115143196	3829	True	7073.0	7073	100.00000	1	3830	1	chr2A.!!$R1	3829
1	TraesCS2A01G162900	chr2D	113508498	113512212	3714	True	1393.5	2883	93.37075	1	3830	4	chr2D.!!$R1	3829
2	TraesCS2A01G162900	chr2B	164106955	164109620	2665	True	1216.0	2298	90.36300	881	3759	3	chr2B.!!$R1	2878
3	TraesCS2A01G162900	chr1D	299694939	299695797	858	True	1031.0	1031	88.45300	1	858	1	chr1D.!!$R1	857
4	TraesCS2A01G162900	chr4B	94951192	94952046	854	True	970.0	970	87.18200	1	862	1	chr4B.!!$R1	861
5	TraesCS2A01G162900	chr3D	575774953	575775793	840	True	926.0	926	86.57400	1	858	1	chr3D.!!$R2	857
6	TraesCS2A01G162900	chr3D	516967132	516967990	858	True	878.0	878	85.40700	1	866	1	chr3D.!!$R1	865
7	TraesCS2A01G162900	chr3D	83937826	83938465	639	False	737.0	737	87.46200	209	858	1	chr3D.!!$F1	649
8	TraesCS2A01G162900	chr6D	418532263	418532935	672	True	898.0	898	90.73500	1	677	1	chr6D.!!$R1	676
9	TraesCS2A01G162900	chr4D	44543784	44544599	815	False	850.0	850	85.86700	1	818	1	chr4D.!!$F1	817
10	TraesCS2A01G162900	chr1B	538720918	538721757	839	True	841.0	841	84.81000	1	862	1	chr1B.!!$R1	861
11	TraesCS2A01G162900	chr6B	630576391	630577057	666	True	800.0	800	88.31400	1	673	1	chr6B.!!$R1	672
12	TraesCS2A01G162900	chr7A	191278410	191279248	838	True	765.0	765	83.23600	1	847	1	chr7A.!!$R1	846
13	TraesCS2A01G162900	chr7D	441980237	441981003	766	False	706.0	706	83.39700	80	857	1	chr7D.!!$F1	777
14	TraesCS2A01G162900	chr5D	337142631	337143178	547	True	678.0	678	89.07100	1	547	1	chr5D.!!$R1	546

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	End Stability	Orientation
563	599	0.185416	GACCTCTCCCATCCCTACGA	59.815	60.000	3.43	F
1054	1153	1.394151	CTCCCCTCTCCCTCCAAGT	59.606	63.158	3.16	F
2067	2174	0.167470	CAACCGCTGTCATCTTGCTG	59.833	55.000	4.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1469	1569	0.332632	TCCCCAGGGAAATGAAGCAG	59.667	55.0	7.25	42.05	4.24	R
2704	2811	0.478072	AACATGCTCAAGGACACCCA	59.522	50.0	0.00	33.88	4.51	R
3278	3394	0.249398	AGTTCAGCCGGACATACCAC	59.751	55.0	5.05	38.90	4.16	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
73	74	3.130160	CTCTCGCCAAGGCCAAGC	61.130	66.667	5.01	3.06	37.98	4.01
260	262	1.218316	GAAATCCGAGGCGAGGTGT	59.782	57.895	0.00	0.00	0.00	4.16
263	265	1.541310	AATCCGAGGCGAGGTGTTCA	61.541	55.000	0.00	0.00	0.00	3.18
294	296	0.319900	GAAGCAGGACGTCAAGCTCA	60.320	55.000	27.11	0.00	36.07	4.26
299	301	0.318762	AGGACGTCAAGCTCAACCTC	59.681	55.000	18.91	0.00	0.00	3.85
555	591	3.148279	GACGCCGACCTCTCCCAT	61.148	66.667	0.00	0.00	0.00	4.00
563	599	0.185416	GACCTCTCCCATCCCTACGA	59.815	60.000	0.00	0.00	0.00	3.43
730	815	4.216472	AGCGGGAAAGAGAACTTTGAATTC	59.784	41.667	0.00	0.00	44.97	2.17
741	827	8.956426	AGAGAACTTTGAATTCTGTTGTGTTTA	58.044	29.630	7.05	0.00	36.53	2.01
744	830	7.755582	ACTTTGAATTCTGTTGTGTTTAAGC	57.244	32.000	7.05	0.00	0.00	3.09
849	940	2.677875	GCTGAGGGGCCAAACAGG	60.678	66.667	19.71	7.18	41.84	4.00
859	950	1.598701	GCCAAACAGGTGGAGATGGC	61.599	60.000	0.00	0.00	45.54	4.40
873	964	2.500910	GAGATGGCTCCTATATGCTGCT	59.499	50.000	0.00	0.00	35.01	4.24
876	967	3.969287	TGGCTCCTATATGCTGCTTAG	57.031	47.619	0.00	0.00	0.00	2.18
966	1059	4.584874	TCGGATAAGCTCTCCTATCTCTG	58.415	47.826	12.18	1.01	0.00	3.35
967	1060	3.694072	CGGATAAGCTCTCCTATCTCTGG	59.306	52.174	12.18	0.00	0.00	3.86
969	1062	2.468301	AAGCTCTCCTATCTCTGGCA	57.532	50.000	0.00	0.00	0.00	4.92
995	1094	1.754226	GGAGACGGAGAAATCAGAGCT	59.246	52.381	0.00	0.00	0.00	4.09
1027	1126	5.988092	AGTCTACGCTAATCACGAGATTAC	58.012	41.667	10.73	7.76	42.54	1.89
1054	1153	1.394151	CTCCCCTCTCCCTCCAAGT	59.606	63.158	0.00	0.00	0.00	3.16
1059	1158	1.621672	CCTCTCCCTCCAAGTCCAGC	61.622	65.000	0.00	0.00	0.00	4.85
1072	1171	3.086600	CCAGCCCCCTCTCCTCAC	61.087	72.222	0.00	0.00	0.00	3.51
1224	1323	2.445845	CCCGGGTCTGAGGCCATA	60.446	66.667	14.18	0.00	0.00	2.74
1280	1379	5.794894	ACCACTAGTCTGAATTTCGAACAT	58.205	37.500	0.00	0.00	0.00	2.71
1431	1530	1.464734	AGCGGATTCTCGAGAGTCAA	58.535	50.000	31.35	12.97	33.10	3.18
1454	1554	4.951094	AGTAGCCGTCTCTCTTTCACTTAT	59.049	41.667	0.00	0.00	0.00	1.73
1456	1556	5.153950	AGCCGTCTCTCTTTCACTTATTT	57.846	39.130	0.00	0.00	0.00	1.40
1461	1561	7.220491	GCCGTCTCTCTTTCACTTATTTACTAC	59.780	40.741	0.00	0.00	0.00	2.73
1467	1567	8.038944	TCTCTTTCACTTATTTACTACCGCAAT	58.961	33.333	0.00	0.00	0.00	3.56
1469	1569	8.662141	TCTTTCACTTATTTACTACCGCAATTC	58.338	33.333	0.00	0.00	0.00	2.17
1484	1584	3.518590	GCAATTCTGCTTCATTTCCCTG	58.481	45.455	0.00	0.00	45.74	4.45
1498	1598	2.059756	TCCCTGGGGAAATCAGTTCT	57.940	50.000	14.00	0.00	42.05	3.01
1499	1599	1.916181	TCCCTGGGGAAATCAGTTCTC	59.084	52.381	14.00	0.00	42.05	2.87
1504	1604	2.496899	GGGAAATCAGTTCTCCTGCA	57.503	50.000	0.00	0.00	41.25	4.41
1505	1605	3.010200	GGGAAATCAGTTCTCCTGCAT	57.990	47.619	0.00	0.00	41.25	3.96
1506	1606	2.686915	GGGAAATCAGTTCTCCTGCATG	59.313	50.000	0.00	0.00	41.25	4.06
1507	1607	2.686915	GGAAATCAGTTCTCCTGCATGG	59.313	50.000	0.00	0.00	41.25	3.66
1508	1608	3.350833	GAAATCAGTTCTCCTGCATGGT	58.649	45.455	0.00	0.00	41.25	3.55
1509	1609	3.446442	AATCAGTTCTCCTGCATGGTT	57.554	42.857	0.00	0.00	41.25	3.67
1510	1610	2.479566	TCAGTTCTCCTGCATGGTTC	57.520	50.000	0.00	0.00	41.25	3.62
1511	1611	1.081892	CAGTTCTCCTGCATGGTTCG	58.918	55.000	0.00	0.00	33.59	3.95
1512	1612	0.976641	AGTTCTCCTGCATGGTTCGA	59.023	50.000	0.00	0.00	37.07	3.71
1513	1613	1.347707	AGTTCTCCTGCATGGTTCGAA	59.652	47.619	0.00	0.00	37.07	3.71
1514	1614	2.026822	AGTTCTCCTGCATGGTTCGAAT	60.027	45.455	0.00	0.00	37.07	3.34
1515	1615	2.749621	GTTCTCCTGCATGGTTCGAATT	59.250	45.455	0.00	0.00	37.07	2.17
1516	1616	3.071874	TCTCCTGCATGGTTCGAATTT	57.928	42.857	0.00	0.00	37.07	1.82
1517	1617	3.420893	TCTCCTGCATGGTTCGAATTTT	58.579	40.909	0.00	0.00	37.07	1.82
1518	1618	3.826157	TCTCCTGCATGGTTCGAATTTTT	59.174	39.130	0.00	0.00	37.07	1.94
1546	1646	6.528537	TTTATGTCTGATCAAACCAATGGG	57.471	37.500	3.55	0.00	41.29	4.00
1559	1659	2.513753	CCAATGGGTAGTTCAGCACAA	58.486	47.619	0.00	0.00	0.00	3.33
1564	1664	3.178046	TGGGTAGTTCAGCACAATAGGA	58.822	45.455	0.00	0.00	0.00	2.94
1578	1679	5.423015	CACAATAGGACAGTGCTGAACTAT	58.577	41.667	4.51	9.57	36.83	2.12
1586	1687	5.294552	GGACAGTGCTGAACTATGGTTAATC	59.705	44.000	6.17	0.00	36.83	1.75
1688	1795	6.863645	TGAAACAAAAAGAAACACAACATCGA	59.136	30.769	0.00	0.00	0.00	3.59
1693	1800	5.811399	AAAGAAACACAACATCGAACTGA	57.189	34.783	0.00	0.00	0.00	3.41
1810	1917	0.677731	TTGCCTGCCTTCAATCCGAG	60.678	55.000	0.00	0.00	0.00	4.63
2067	2174	0.167470	CAACCGCTGTCATCTTGCTG	59.833	55.000	0.00	0.00	0.00	4.41
2176	2283	7.557719	TGTTTTCTTCCTATCATTCCAGATTCC	59.442	37.037	0.00	0.00	0.00	3.01
2328	2435	1.000955	GTCGTGTGGACAACTCCTGAT	59.999	52.381	0.00	0.00	45.36	2.90
2373	2480	5.561725	GCAGAAACAATGTGGAGAGAAACTC	60.562	44.000	0.00	0.00	44.24	3.01
2539	2646	4.211164	CAGACACAGAAGCACGTCAAAATA	59.789	41.667	0.00	0.00	0.00	1.40
2548	2655	8.124823	CAGAAGCACGTCAAAATATTATCATGT	58.875	33.333	0.00	0.00	0.00	3.21
2550	2657	6.201517	AGCACGTCAAAATATTATCATGTGC	58.798	36.000	20.18	20.18	46.74	4.57
2572	2679	5.476254	TGCATCTCATGTAAACATTTGGTCA	59.524	36.000	0.00	0.00	33.61	4.02
2704	2811	1.628846	ACCAGGACCAAACTCGCTATT	59.371	47.619	0.00	0.00	0.00	1.73
2772	2879	5.557891	ATTTCTCCAGCTTTCTGAAATCG	57.442	39.130	2.88	0.00	42.95	3.34
2782	2889	5.751028	AGCTTTCTGAAATCGCAGTATCTAC	59.249	40.000	14.36	0.00	37.20	2.59
2860	2967	5.098893	CCTGATAAAGTCAACTCTGAGTCG	58.901	45.833	11.31	0.00	36.14	4.18
2912	3019	1.985159	TGATGTTAACCAGCAGAGGGT	59.015	47.619	2.48	0.00	41.41	4.34
3041	3151	1.067354	GCAATGTAGCTTGCCTTGCTT	60.067	47.619	17.25	0.00	44.56	3.91
3082	3192	6.056884	ACATTCCATCAAACAAATTGCAAGT	58.943	32.000	4.94	0.00	38.98	3.16
3205	3321	6.066032	TCAGTCCGTATGTAGTCCATATTGA	58.934	40.000	0.00	0.00	38.29	2.57
3209	3325	7.872993	AGTCCGTATGTAGTCCATATTGAAATG	59.127	37.037	0.00	0.00	38.29	2.32
3245	3361	5.505181	ACATTTGTGAACAGAGGGAGTAT	57.495	39.130	0.00	0.00	0.00	2.12
3254	3370	5.191722	TGAACAGAGGGAGTATTAAGCCAAT	59.808	40.000	0.00	0.00	0.00	3.16
3263	3379	6.547510	GGGAGTATTAAGCCAATCAGTTTGAT	59.452	38.462	0.00	0.00	39.09	2.57
3278	3394	7.856492	TCAGTTTGATGAAATGTTGAATTCG	57.144	32.000	0.04	0.00	35.00	3.34
3472	3593	5.069119	AGTCATCATAGTGTGGCGATAAGAA	59.931	40.000	0.00	0.00	0.00	2.52
3568	3689	3.265791	GTGCTTCTTCGGTCTGATCATT	58.734	45.455	0.00	0.00	0.00	2.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
73	74	1.373748	CCGGGTTGTAGACACCGTG	60.374	63.158	9.91	0.00	39.18	4.94
208	210	2.733218	CGTTGCTCTTGGCGTCGA	60.733	61.111	0.00	0.00	45.43	4.20
260	262	2.417586	CTGCTTCGTCATCAATGCTGAA	59.582	45.455	0.00	0.00	34.49	3.02
263	265	1.065926	TCCTGCTTCGTCATCAATGCT	60.066	47.619	0.00	0.00	0.00	3.79
294	296	0.763223	ACGTTGGTCCTGAGGAGGTT	60.763	55.000	0.00	0.00	40.76	3.50
299	301	2.432628	GCGACGTTGGTCCTGAGG	60.433	66.667	4.64	0.00	40.17	3.86
555	591	1.076923	GGCTCCTCTGTCGTAGGGA	60.077	63.158	0.00	0.00	34.66	4.20
563	599	0.323178	CAAATGGCAGGCTCCTCTGT	60.323	55.000	0.00	0.00	37.12	3.41
730	815	0.584396	TCGGCGCTTAAACACAACAG	59.416	50.000	7.64	0.00	0.00	3.16
762	851	3.842869	GTGGATCGAGTTTCCAGCT	57.157	52.632	6.48	0.00	43.78	4.24
836	926	2.780924	TCCACCTGTTTGGCCCCT	60.781	61.111	0.00	0.00	40.22	4.79
859	950	4.159506	GGAGTCCTAAGCAGCATATAGGAG	59.840	50.000	17.50	0.00	44.36	3.69
862	953	5.046735	ACATGGAGTCCTAAGCAGCATATAG	60.047	44.000	11.33	0.00	0.00	1.31
864	955	3.649981	ACATGGAGTCCTAAGCAGCATAT	59.350	43.478	11.33	0.00	0.00	1.78
967	1060	4.452733	CTCCGTCTCCCCCGTTGC	62.453	72.222	0.00	0.00	0.00	4.17
969	1062	0.908180	ATTTCTCCGTCTCCCCCGTT	60.908	55.000	0.00	0.00	0.00	4.44
995	1094	1.480789	TAGCGTAGACTCCATTGCCA	58.519	50.000	0.00	0.00	0.00	4.92
1054	1153	3.284251	TGAGGAGAGGGGGCTGGA	61.284	66.667	0.00	0.00	0.00	3.86
1059	1158	4.825679	GGGGGTGAGGAGAGGGGG	62.826	77.778	0.00	0.00	0.00	5.40
1224	1323	1.202855	AGCACCTGAACACTGAGCAAT	60.203	47.619	0.00	0.00	0.00	3.56
1280	1379	1.938585	AACAGAATGGAGAGTCGGGA	58.061	50.000	0.00	0.00	43.62	5.14
1404	1503	1.135373	TCGAGAATCCGCTTCACACTC	60.135	52.381	0.00	0.00	36.24	3.51
1431	1530	2.797786	AGTGAAAGAGAGACGGCTACT	58.202	47.619	0.00	0.00	0.00	2.57
1467	1567	1.272648	CCCCAGGGAAATGAAGCAGAA	60.273	52.381	7.25	0.00	37.50	3.02
1469	1569	0.332632	TCCCCAGGGAAATGAAGCAG	59.667	55.000	7.25	0.00	42.05	4.24
1481	1581	1.918957	AGGAGAACTGATTTCCCCAGG	59.081	52.381	0.00	0.00	34.43	4.45
1493	1593	0.976641	TCGAACCATGCAGGAGAACT	59.023	50.000	0.00	0.00	41.22	3.01
1494	1594	1.808411	TTCGAACCATGCAGGAGAAC	58.192	50.000	0.00	0.00	41.22	3.01
1495	1595	2.787473	ATTCGAACCATGCAGGAGAA	57.213	45.000	0.00	7.30	41.22	2.87
1496	1596	2.787473	AATTCGAACCATGCAGGAGA	57.213	45.000	0.00	0.00	41.22	3.71
1497	1597	3.855689	AAAATTCGAACCATGCAGGAG	57.144	42.857	0.00	0.00	41.22	3.69
1521	1621	7.016072	ACCCATTGGTTTGATCAGACATAAAAA	59.984	33.333	17.33	4.88	44.75	1.94
1522	1622	6.496565	ACCCATTGGTTTGATCAGACATAAAA	59.503	34.615	17.33	7.01	44.75	1.52
1523	1623	6.015918	ACCCATTGGTTTGATCAGACATAAA	58.984	36.000	17.33	9.17	44.75	1.40
1534	1634	3.153919	GCTGAACTACCCATTGGTTTGA	58.846	45.455	1.20	0.00	44.75	2.69
1546	1646	4.627467	CACTGTCCTATTGTGCTGAACTAC	59.373	45.833	0.00	0.00	0.00	2.73
1547	1647	4.820897	CACTGTCCTATTGTGCTGAACTA	58.179	43.478	0.00	0.00	0.00	2.24
1559	1659	4.033709	ACCATAGTTCAGCACTGTCCTAT	58.966	43.478	0.00	2.56	35.97	2.57
1564	1664	6.054860	AGATTAACCATAGTTCAGCACTGT	57.945	37.500	0.00	0.00	35.97	3.55
1578	1679	7.495901	TGCAATGAACAAAAGAAGATTAACCA	58.504	30.769	0.00	0.00	0.00	3.67
1600	1701	4.828387	TGAGCATAGGCATCAATTATTGCA	59.172	37.500	0.67	0.00	44.61	4.08
1688	1795	7.661437	TCTTACATTCTATGCACAAACTCAGTT	59.339	33.333	0.00	0.00	0.00	3.16
1693	1800	6.711277	TCCTCTTACATTCTATGCACAAACT	58.289	36.000	0.00	0.00	0.00	2.66
1810	1917	2.624838	CCCATATGGTTTCAGGTCATGC	59.375	50.000	20.46	0.00	0.00	4.06
1999	2106	0.968901	ACCCAGTCATTGCTGCCATG	60.969	55.000	7.35	7.35	35.28	3.66
2067	2174	5.126061	ACATCAACCATACATTTCCTTGCTC	59.874	40.000	0.00	0.00	0.00	4.26
2207	2314	4.689345	GCAGCAGCAAAAGATCAAAGAAAT	59.311	37.500	0.00	0.00	41.58	2.17
2208	2315	4.053295	GCAGCAGCAAAAGATCAAAGAAA	58.947	39.130	0.00	0.00	41.58	2.52
2328	2435	2.507484	CAATCTTCTGCCACCTTGACA	58.493	47.619	0.00	0.00	0.00	3.58
2486	2593	8.757982	ATAATTCACAAGCAGACAAGGAATAT	57.242	30.769	0.00	0.00	0.00	1.28
2503	2610	4.744570	TCTGTGTCTGGACGATAATTCAC	58.255	43.478	0.00	0.00	0.00	3.18
2539	2646	8.454570	TGTTTACATGAGATGCACATGATAAT	57.545	30.769	19.39	3.18	45.22	1.28
2548	2655	5.476254	TGACCAAATGTTTACATGAGATGCA	59.524	36.000	0.00	0.00	36.56	3.96
2550	2657	7.149569	ACTGACCAAATGTTTACATGAGATG	57.850	36.000	0.00	0.00	36.56	2.90
2704	2811	0.478072	AACATGCTCAAGGACACCCA	59.522	50.000	0.00	0.00	33.88	4.51
2707	2814	4.877823	TGATATGAACATGCTCAAGGACAC	59.122	41.667	2.34	0.00	0.00	3.67
2839	2946	5.707242	ACGACTCAGAGTTGACTTTATCA	57.293	39.130	22.92	0.00	33.76	2.15
2912	3019	5.104569	TCACACAAATATGGAGCATCAGGTA	60.105	40.000	0.00	0.00	36.25	3.08
2926	3033	4.058124	GCTCACACTGAGTCACACAAATA	58.942	43.478	1.37	0.00	45.94	1.40
3041	3151	4.338118	GGAATGTTCCAGTTGAAGTTCACA	59.662	41.667	4.68	0.00	46.76	3.58
3082	3192	5.128827	GTGAATGGAGGGAGTAGTAATGACA	59.871	44.000	0.00	0.00	0.00	3.58
3171	3282	9.309516	GACTACATACGGACTGAAATTAATGAA	57.690	33.333	0.00	0.00	0.00	2.57
3209	3325	9.243637	TGTTCACAAATGTAAGCTATTTTTGAC	57.756	29.630	14.55	8.84	35.28	3.18
3217	3333	5.012664	TCCCTCTGTTCACAAATGTAAGCTA	59.987	40.000	0.00	0.00	0.00	3.32
3226	3342	5.938125	GCTTAATACTCCCTCTGTTCACAAA	59.062	40.000	0.00	0.00	0.00	2.83
3245	3361	7.669427	ACATTTCATCAAACTGATTGGCTTAA	58.331	30.769	0.00	0.00	39.62	1.85
3254	3370	7.379262	CACGAATTCAACATTTCATCAAACTGA	59.621	33.333	6.22	0.00	0.00	3.41
3263	3379	6.348950	GGACATACCACGAATTCAACATTTCA	60.349	38.462	6.22	0.00	38.79	2.69
3278	3394	0.249398	AGTTCAGCCGGACATACCAC	59.751	55.000	5.05	0.00	38.90	4.16
3472	3593	3.175594	ACTGAAATCATGCCCCACAAAT	58.824	40.909	0.00	0.00	0.00	2.32
3518	3639	8.909708	TCTCTCCAATTGCAATAAAATTAACG	57.090	30.769	13.39	0.00	0.00	3.18
3529	3650	4.529897	AGCACATATCTCTCCAATTGCAA	58.470	39.130	0.00	0.00	0.00	4.08
3568	3689	6.516718	TGTAAATTTGCGAAAAATTCTCCCA	58.483	32.000	0.00	3.28	0.00	4.37
3779	3910	2.576615	GAGGGACCTGGTAATTCATGC	58.423	52.381	0.00	0.00	0.00	4.06

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.