AutoCloner

Multiple sequence alignment - TraesCS2A01G449900

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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	TraesCS2A01G449900	chr2A	100.000	3641	0	0	1	3641	699607452	699603812	0.000000e+00	6724.0
1	TraesCS2A01G449900	chr2A	88.156	743	56	12	1620	2358	699641767	699641053	0.000000e+00	856.0
2	TraesCS2A01G449900	chr2A	82.723	382	28	20	1278	1623	699642185	699641806	4.570000e-79	305.0
3	TraesCS2A01G449900	chr2A	78.758	499	64	26	2460	2927	391843761	391844248	2.750000e-76	296.0
4	TraesCS2A01G449900	chr2A	80.233	344	44	15	1045	1382	699772638	699772313	1.690000e-58	237.0
5	TraesCS2A01G449900	chr1B	95.161	1054	51	0	1	1054	629507427	629506374	0.000000e+00	1664.0
6	TraesCS2A01G449900	chrUn	94.867	1052	54	0	1	1052	294994349	294993298	0.000000e+00	1644.0
7	TraesCS2A01G449900	chrUn	94.867	1052	54	0	1	1052	327367842	327368893	0.000000e+00	1644.0
8	TraesCS2A01G449900	chrUn	94.867	1052	54	0	1	1052	327370849	327371900	0.000000e+00	1644.0
9	TraesCS2A01G449900	chr6B	94.867	1052	54	0	1	1052	79342183	79343234	0.000000e+00	1644.0
10	TraesCS2A01G449900	chr4B	94.782	1054	54	1	1	1053	351456081	351457134	0.000000e+00	1640.0
11	TraesCS2A01G449900	chr3D	94.772	1052	55	0	1	1052	11607934	11608985	0.000000e+00	1639.0
12	TraesCS2A01G449900	chr3D	85.666	1193	146	13	2465	3641	575932735	575931552	0.000000e+00	1232.0
13	TraesCS2A01G449900	chr3D	83.777	1202	140	20	2486	3641	400273209	400272017	0.000000e+00	1088.0
14	TraesCS2A01G449900	chr3D	88.591	745	83	2	2896	3639	51027084	51026341	0.000000e+00	904.0
15	TraesCS2A01G449900	chr3D	87.379	412	49	2	2463	2874	23169287	23168879	1.530000e-128	470.0
16	TraesCS2A01G449900	chr7D	94.677	1052	55	1	1	1052	557053402	557052352	0.000000e+00	1631.0
17	TraesCS2A01G449900	chr7D	89.386	782	80	3	2862	3641	126464958	126464178	0.000000e+00	981.0
18	TraesCS2A01G449900	chr7D	89.826	747	71	4	2896	3641	252068655	252069397	0.000000e+00	953.0
19	TraesCS2A01G449900	chr7D	84.890	867	121	8	2778	3641	510582910	510582051	0.000000e+00	867.0
20	TraesCS2A01G449900	chr7D	87.200	125	16	0	1422	1546	184536779	184536903	3.790000e-30	143.0
21	TraesCS2A01G449900	chr7D	86.076	79	9	2	2837	2915	252068577	252068653	2.330000e-12	84.2
22	TraesCS2A01G449900	chr7A	94.518	1058	55	3	1	1058	35603947	35602893	0.000000e+00	1629.0
23	TraesCS2A01G449900	chr7A	88.621	747	84	1	2896	3641	183646744	183645998	0.000000e+00	907.0
24	TraesCS2A01G449900	chr2D	95.844	794	28	2	1620	2411	558977623	558976833	0.000000e+00	1279.0
25	TraesCS2A01G449900	chr2D	89.651	773	65	10	1620	2386	559001986	559001223	0.000000e+00	970.0
26	TraesCS2A01G449900	chr2D	87.915	753	83	4	2896	3641	375253945	375253194	0.000000e+00	880.0
27	TraesCS2A01G449900	chr2D	91.468	586	24	10	1045	1623	558978228	558977662	0.000000e+00	782.0
28	TraesCS2A01G449900	chr2D	87.229	415	45	6	2460	2874	11025493	11025899	1.980000e-127	466.0
29	TraesCS2A01G449900	chr2D	87.379	412	44	5	2463	2874	118408132	118407729	1.980000e-127	466.0
30	TraesCS2A01G449900	chr2D	87.081	418	44	7	2461	2874	129834752	129835163	7.120000e-127	464.0
31	TraesCS2A01G449900	chr2D	86.534	401	44	4	2477	2874	340282083	340281690	2.010000e-117	433.0
32	TraesCS2A01G449900	chr2D	83.060	366	39	13	1278	1623	559002387	559002025	9.820000e-81	311.0
33	TraesCS2A01G449900	chr2D	82.216	343	40	12	1045	1382	559207797	559207471	3.580000e-70	276.0
34	TraesCS2A01G449900	chr2D	98.214	56	1	0	2408	2463	558976797	558976742	8.320000e-17	99.0
35	TraesCS2A01G449900	chr7B	84.375	1216	128	24	2463	3641	105831854	105833044	0.000000e+00	1136.0
36	TraesCS2A01G449900	chr7B	83.897	739	95	12	2922	3640	67902984	67902250	0.000000e+00	684.0
37	TraesCS2A01G449900	chr7B	79.914	463	62	11	2839	3295	25633926	25633489	9.820000e-81	311.0
38	TraesCS2A01G449900	chr2B	91.069	795	63	6	1620	2411	668052291	668051502	0.000000e+00	1068.0
39	TraesCS2A01G449900	chr2B	89.536	755	56	12	1620	2355	668171620	668170870	0.000000e+00	935.0
40	TraesCS2A01G449900	chr2B	83.717	608	53	26	1045	1623	668172249	668171659	1.920000e-147	532.0
41	TraesCS2A01G449900	chr2B	92.140	229	11	3	1396	1623	668052552	668052330	2.110000e-82	316.0
42	TraesCS2A01G449900	chr5D	89.130	736	78	2	2907	3641	127884463	127883729	0.000000e+00	915.0
43	TraesCS2A01G449900	chr5D	86.232	414	51	5	2459	2872	208513859	208514266	9.280000e-121	444.0
44	TraesCS2A01G449900	chr5D	85.952	420	45	8	2460	2876	127884941	127884533	1.550000e-118	436.0
45	TraesCS2A01G449900	chr6D	85.817	416	56	3	2461	2876	58439587	58439175	4.320000e-119	438.0

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	TraesCS2A01G449900	chr2A	699603812	699607452	3640	True	6724.0	6724	100.000000	1	3641	1	chr2A.!!$R1	3640
1	TraesCS2A01G449900	chr2A	699641053	699642185	1132	True	580.5	856	85.439500	1278	2358	2	chr2A.!!$R3	1080
2	TraesCS2A01G449900	chr1B	629506374	629507427	1053	True	1664.0	1664	95.161000	1	1054	1	chr1B.!!$R1	1053
3	TraesCS2A01G449900	chrUn	294993298	294994349	1051	True	1644.0	1644	94.867000	1	1052	1	chrUn.!!$R1	1051
4	TraesCS2A01G449900	chrUn	327367842	327371900	4058	False	1644.0	1644	94.867000	1	1052	2	chrUn.!!$F1	1051
5	TraesCS2A01G449900	chr6B	79342183	79343234	1051	False	1644.0	1644	94.867000	1	1052	1	chr6B.!!$F1	1051
6	TraesCS2A01G449900	chr4B	351456081	351457134	1053	False	1640.0	1640	94.782000	1	1053	1	chr4B.!!$F1	1052
7	TraesCS2A01G449900	chr3D	11607934	11608985	1051	False	1639.0	1639	94.772000	1	1052	1	chr3D.!!$F1	1051
8	TraesCS2A01G449900	chr3D	575931552	575932735	1183	True	1232.0	1232	85.666000	2465	3641	1	chr3D.!!$R4	1176
9	TraesCS2A01G449900	chr3D	400272017	400273209	1192	True	1088.0	1088	83.777000	2486	3641	1	chr3D.!!$R3	1155
10	TraesCS2A01G449900	chr3D	51026341	51027084	743	True	904.0	904	88.591000	2896	3639	1	chr3D.!!$R2	743
11	TraesCS2A01G449900	chr7D	557052352	557053402	1050	True	1631.0	1631	94.677000	1	1052	1	chr7D.!!$R3	1051
12	TraesCS2A01G449900	chr7D	126464178	126464958	780	True	981.0	981	89.386000	2862	3641	1	chr7D.!!$R1	779
13	TraesCS2A01G449900	chr7D	510582051	510582910	859	True	867.0	867	84.890000	2778	3641	1	chr7D.!!$R2	863
14	TraesCS2A01G449900	chr7D	252068577	252069397	820	False	518.6	953	87.951000	2837	3641	2	chr7D.!!$F2	804
15	TraesCS2A01G449900	chr7A	35602893	35603947	1054	True	1629.0	1629	94.518000	1	1058	1	chr7A.!!$R1	1057
16	TraesCS2A01G449900	chr7A	183645998	183646744	746	True	907.0	907	88.621000	2896	3641	1	chr7A.!!$R2	745
17	TraesCS2A01G449900	chr2D	375253194	375253945	751	True	880.0	880	87.915000	2896	3641	1	chr2D.!!$R3	745
18	TraesCS2A01G449900	chr2D	558976742	558978228	1486	True	720.0	1279	95.175333	1045	2463	3	chr2D.!!$R5	1418
19	TraesCS2A01G449900	chr2D	559001223	559002387	1164	True	640.5	970	86.355500	1278	2386	2	chr2D.!!$R6	1108
20	TraesCS2A01G449900	chr7B	105831854	105833044	1190	False	1136.0	1136	84.375000	2463	3641	1	chr7B.!!$F1	1178
21	TraesCS2A01G449900	chr7B	67902250	67902984	734	True	684.0	684	83.897000	2922	3640	1	chr7B.!!$R2	718
22	TraesCS2A01G449900	chr2B	668170870	668172249	1379	True	733.5	935	86.626500	1045	2355	2	chr2B.!!$R2	1310
23	TraesCS2A01G449900	chr2B	668051502	668052552	1050	True	692.0	1068	91.604500	1396	2411	2	chr2B.!!$R1	1015
24	TraesCS2A01G449900	chr5D	127883729	127884941	1212	True	675.5	915	87.541000	2460	3641	2	chr5D.!!$R1	1181

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
993	995	0.382515	CGTGGTTTTCTCCCGCAAAA	59.617	50.0	0.00	0.0	32.61	2.44	F
1200	1210	0.106149	ACGAACTTCGGCTGAACCTT	59.894	50.0	15.42	0.0	45.59	3.50	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2480	4522	0.400213	ATTGCCGTCCCTTTGAGTCA	59.600	50.0	0.0	0.0	0.0	3.41	R
3018	5127	0.255890	CCACCGATTTGGATGGAGGT	59.744	55.0	0.0	0.0	42.0	3.85	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
52	53	1.890876	CCATGGTTTGTTCTCGTCCA	58.109	50.000	2.57	0.00	0.00	4.02
102	103	6.209589	GTCAGTAGATACATGGCTAATCCTGA	59.790	42.308	0.00	3.13	35.26	3.86
124	125	2.399916	AAGAGCATTGGAGAGCAGTC	57.600	50.000	0.00	0.00	0.00	3.51
147	148	4.264253	CAGTGGATTTTCAGATACCTGCA	58.736	43.478	0.00	0.00	40.20	4.41
149	150	5.359009	CAGTGGATTTTCAGATACCTGCAAT	59.641	40.000	0.00	0.00	40.20	3.56
161	162	9.143155	TCAGATACCTGCAATGTACTTCTAATA	57.857	33.333	0.00	0.00	40.20	0.98
250	251	7.772757	GGTGATTTGGATAAGAGAAGATCACTT	59.227	37.037	11.47	0.00	40.96	3.16
472	473	9.862371	AGTGCTATATATCTTACAAAGAATCCG	57.138	33.333	0.00	0.00	41.63	4.18
489	490	7.479352	AGAATCCGATGTATCATGAGAGAAT	57.521	36.000	0.09	0.00	0.00	2.40
504	505	6.127810	TGAGAGAATAAAGCACATTGATGC	57.872	37.500	0.00	0.00	46.50	3.91
642	643	2.154462	GCTTTGCTCAGGCTTAGTTGA	58.846	47.619	0.00	0.00	39.59	3.18
710	711	6.131264	TGCTGATTTGGATGGAGTTATTCAT	58.869	36.000	0.00	0.00	0.00	2.57
747	748	4.202663	TGGAGGAAATTTGGATCAAGGTGA	60.203	41.667	0.00	0.00	0.00	4.02
860	862	5.910614	AGTACAACTCGTTTACTTGTCCTT	58.089	37.500	0.00	0.00	30.76	3.36
942	944	4.164294	GTCGTCTCGTGCTTGTAATACTT	58.836	43.478	0.00	0.00	0.00	2.24
949	951	5.109210	TCGTGCTTGTAATACTTCTCCATG	58.891	41.667	0.00	0.00	0.00	3.66
953	955	7.438160	CGTGCTTGTAATACTTCTCCATGATAA	59.562	37.037	0.00	0.00	0.00	1.75
962	964	9.507329	AATACTTCTCCATGATAATAATTGCGT	57.493	29.630	0.00	0.00	0.00	5.24
992	994	1.448922	CCGTGGTTTTCTCCCGCAAA	61.449	55.000	0.00	0.00	32.61	3.68
993	995	0.382515	CGTGGTTTTCTCCCGCAAAA	59.617	50.000	0.00	0.00	32.61	2.44
1026	1028	7.228706	ACATAAAAATCCGTGTCTCTTTGTCTT	59.771	33.333	0.00	0.00	0.00	3.01
1188	1196	1.453015	TGGCAACTGGCACGAACTT	60.453	52.632	1.18	0.00	46.12	2.66
1189	1197	1.444119	TGGCAACTGGCACGAACTTC	61.444	55.000	1.18	0.00	46.12	3.01
1190	1198	1.082756	GCAACTGGCACGAACTTCG	60.083	57.895	9.68	9.68	46.93	3.79
1191	1199	1.569493	CAACTGGCACGAACTTCGG	59.431	57.895	15.42	5.84	45.59	4.30
1193	1201	2.357517	CTGGCACGAACTTCGGCT	60.358	61.111	15.42	0.00	45.59	5.52
1198	1208	1.860078	CACGAACTTCGGCTGAACC	59.140	57.895	15.42	0.00	45.59	3.62
1200	1210	0.106149	ACGAACTTCGGCTGAACCTT	59.894	50.000	15.42	0.00	45.59	3.50
1258	1274	4.555709	AAGCGGCGTGTTGACCCA	62.556	61.111	9.37	0.00	0.00	4.51
1266	1283	4.182433	TGTTGACCCACGCCAGCA	62.182	61.111	0.00	0.00	0.00	4.41
1268	1285	1.376683	GTTGACCCACGCCAGCATA	60.377	57.895	0.00	0.00	0.00	3.14
1269	1286	1.376683	TTGACCCACGCCAGCATAC	60.377	57.895	0.00	0.00	0.00	2.39
1270	1287	2.890474	GACCCACGCCAGCATACG	60.890	66.667	0.00	0.00	0.00	3.06
1271	1288	3.659089	GACCCACGCCAGCATACGT	62.659	63.158	0.00	0.00	44.75	3.57
1272	1289	2.435938	CCCACGCCAGCATACGTT	60.436	61.111	0.00	0.00	41.32	3.99
1273	1290	2.749865	CCCACGCCAGCATACGTTG	61.750	63.158	0.00	0.00	41.32	4.10
1767	1996	2.951745	CGCGTCATCGAGCAGGTC	60.952	66.667	0.00	0.00	39.71	3.85
1839	2068	4.754667	GTGTTCCTCGGGCCCGAC	62.755	72.222	42.66	32.01	44.01	4.79
1902	2131	4.385405	ACGCTGTGCCAGAGCCTC	62.385	66.667	8.41	0.00	38.69	4.70
1989	2218	1.515954	CGCGGTGACCAAGGTCTAT	59.484	57.895	19.20	0.00	44.80	1.98
2159	3878	2.548057	ACATCGCCAACAACTACACTTG	59.452	45.455	0.00	0.00	0.00	3.16
2194	3913	5.394333	GGAGCCTACTTGTACTGTTCCTAAG	60.394	48.000	0.00	0.00	0.00	2.18
2394	4140	5.351458	AGGAACAAATGTTTCAAACTCTGC	58.649	37.500	7.30	0.00	38.56	4.26
2475	4517	8.239998	CCTTATTTTTCTTAGAGCAACTCCAAG	58.760	37.037	0.00	0.00	32.12	3.61
2480	4522	0.547712	TAGAGCAACTCCAAGGGGCT	60.548	55.000	0.00	0.00	37.56	5.19
2484	4526	1.763770	CAACTCCAAGGGGCTGACT	59.236	57.895	0.00	0.00	0.00	3.41
2489	4531	0.401738	TCCAAGGGGCTGACTCAAAG	59.598	55.000	0.00	0.00	0.00	2.77
2497	4539	1.371183	CTGACTCAAAGGGACGGCA	59.629	57.895	0.00	0.00	0.00	5.69
2505	4547	2.432510	TCAAAGGGACGGCAATTTTGTT	59.567	40.909	10.05	0.00	32.22	2.83
2513	4555	2.538037	ACGGCAATTTTGTTCGCTTTTC	59.462	40.909	7.65	0.00	33.02	2.29
2516	4558	3.000825	GGCAATTTTGTTCGCTTTTCGTT	59.999	39.130	0.00	0.00	39.67	3.85
2524	4566	1.288350	TCGCTTTTCGTTCGTTTGGA	58.712	45.000	0.00	0.00	39.67	3.53
2532	4574	3.100658	TCGTTCGTTTGGATCAGTCAA	57.899	42.857	0.00	0.00	0.00	3.18
2533	4575	3.459145	TCGTTCGTTTGGATCAGTCAAA	58.541	40.909	0.00	0.00	0.00	2.69
2581	4623	1.579084	GGTTGACGTATGCGCCCAAA	61.579	55.000	4.18	0.00	42.83	3.28
2607	4649	2.322081	CGACCCATTTTGACGGCGT	61.322	57.895	14.65	14.65	0.00	5.68
2617	4661	2.181426	TTGACGGCGTTGACAAAAAG	57.819	45.000	16.19	0.00	0.00	2.27
2618	4662	1.370609	TGACGGCGTTGACAAAAAGA	58.629	45.000	16.19	0.00	0.00	2.52
2677	4723	8.371699	ACTTAATTAAACATTAAAGCCAGCCAA	58.628	29.630	0.00	0.00	0.00	4.52
2681	4727	4.953940	AACATTAAAGCCAGCCAAGAAA	57.046	36.364	0.00	0.00	0.00	2.52
2715	4761	0.726827	ACGCGTCCACATTAGCATTG	59.273	50.000	5.58	0.00	0.00	2.82
2783	4835	0.109919	CGTTGTCATCGTCGTCCTCA	60.110	55.000	0.00	0.00	0.00	3.86
2927	5036	2.989253	TCCTCGAGGTTGCGCTCA	60.989	61.111	30.17	6.22	36.34	4.26
2938	5047	1.297689	TGCGCTCAAGCATCTCCTT	59.702	52.632	9.73	0.00	42.92	3.36
2997	5106	1.807226	CGCCACATCTCGAGGTACA	59.193	57.895	13.56	0.00	0.00	2.90
3070	5179	2.786495	CGCGCACTACTCCCATCCT	61.786	63.158	8.75	0.00	0.00	3.24
3195	5341	4.161295	CCGCGGAGAGGGCAATGA	62.161	66.667	24.07	0.00	46.30	2.57
3202	5348	1.112113	GAGAGGGCAATGACCTACGA	58.888	55.000	8.09	0.00	43.92	3.43
3247	5393	2.285368	TTCCTCCACCGCCTCCAT	60.285	61.111	0.00	0.00	0.00	3.41
3570	5717	0.681733	TTCCGGATCTAGATGCCAGC	59.318	55.000	17.57	0.00	0.00	4.85
3596	5743	2.768344	AGGGTGGCATCGGGGTAG	60.768	66.667	0.00	0.00	0.00	3.18
3627	5775	2.032528	GTGCTGCCAGTGCCACTA	59.967	61.111	0.00	0.00	36.33	2.74

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
52	53	9.128404	ACAACACTCAATGCATATGATAAATCT	57.872	29.630	6.97	0.00	0.00	2.40
102	103	3.494332	ACTGCTCTCCAATGCTCTTTTT	58.506	40.909	0.00	0.00	0.00	1.94
124	125	3.629398	GCAGGTATCTGAAAATCCACTGG	59.371	47.826	7.33	0.00	43.49	4.00
250	251	6.071984	ACCAATGGTGAAAACATAACCTGTA	58.928	36.000	3.09	0.00	33.10	2.74
472	473	8.599055	TGTGCTTTATTCTCTCATGATACATC	57.401	34.615	0.00	0.00	0.00	3.06
489	490	6.016860	GTGATATCTGGCATCAATGTGCTTTA	60.017	38.462	3.98	0.00	44.45	1.85
504	505	9.513727	CAACATCTCGAATATAGTGATATCTGG	57.486	37.037	3.98	0.00	0.00	3.86
577	578	3.252701	GCTTTGTCATCATATCAGCAGGG	59.747	47.826	0.00	0.00	0.00	4.45
670	671	2.724403	GCATAAACACCTTGTGCGC	58.276	52.632	0.00	0.00	41.54	6.09
710	711	8.413229	CAAATTTCCTCCAGTAGTCAAAGAAAA	58.587	33.333	0.00	0.00	0.00	2.29
717	718	5.250543	TGATCCAAATTTCCTCCAGTAGTCA	59.749	40.000	0.00	0.00	0.00	3.41
860	862	4.166725	AGGGCAATACATGAGATTCCTTGA	59.833	41.667	0.00	0.00	0.00	3.02
867	869	8.709308	GGTATATAAGAGGGCAATACATGAGAT	58.291	37.037	0.00	0.00	0.00	2.75
942	944	6.366061	CGAAGACGCAATTATTATCATGGAGA	59.634	38.462	0.00	0.00	0.00	3.71
949	951	4.134546	CGCACGAAGACGCAATTATTATC	58.865	43.478	0.00	0.00	43.96	1.75
953	955	1.323534	GACGCACGAAGACGCAATTAT	59.676	47.619	0.00	0.00	43.96	1.28
955	957	1.491563	GACGCACGAAGACGCAATT	59.508	52.632	0.00	0.00	43.96	2.32
962	964	2.632136	AAACCACGGACGCACGAAGA	62.632	55.000	6.34	0.00	37.61	2.87
992	994	6.264518	AGACACGGATTTTTATGTGGAAACTT	59.735	34.615	0.00	0.00	36.67	2.66
993	995	5.768164	AGACACGGATTTTTATGTGGAAACT	59.232	36.000	0.00	0.00	36.67	2.66
1177	1185	2.652382	TTCAGCCGAAGTTCGTGCCA	62.652	55.000	25.27	15.17	38.40	4.92
1188	1196	2.431057	GGAGAAGATAAGGTTCAGCCGA	59.569	50.000	0.00	0.00	43.70	5.54
1189	1197	2.799917	CGGAGAAGATAAGGTTCAGCCG	60.800	54.545	0.00	0.00	43.70	5.52
1190	1198	2.827652	CGGAGAAGATAAGGTTCAGCC	58.172	52.381	0.00	0.00	37.58	4.85
1191	1199	2.205911	GCGGAGAAGATAAGGTTCAGC	58.794	52.381	0.00	0.00	0.00	4.26
1193	1201	2.418746	GCTGCGGAGAAGATAAGGTTCA	60.419	50.000	8.65	0.00	0.00	3.18
1198	1208	1.539929	CCTGGCTGCGGAGAAGATAAG	60.540	57.143	8.65	0.00	0.00	1.73
1200	1210	2.032860	GCCTGGCTGCGGAGAAGATA	62.033	60.000	12.43	0.00	0.00	1.98
1266	1283	2.330440	TGGCTGATGATGCAACGTAT	57.670	45.000	0.00	0.00	0.00	3.06
1268	1285	0.736636	CATGGCTGATGATGCAACGT	59.263	50.000	0.00	0.00	33.31	3.99
1269	1286	1.018910	TCATGGCTGATGATGCAACG	58.981	50.000	0.00	0.00	36.06	4.10
1270	1287	1.746787	TGTCATGGCTGATGATGCAAC	59.253	47.619	0.00	0.00	43.20	4.17
1271	1288	2.131776	TGTCATGGCTGATGATGCAA	57.868	45.000	0.00	0.00	43.20	4.08
1272	1289	2.131776	TTGTCATGGCTGATGATGCA	57.868	45.000	0.00	0.00	43.20	3.96
1273	1290	3.057736	GGTATTGTCATGGCTGATGATGC	60.058	47.826	0.00	0.00	43.20	3.91
1274	1291	3.504906	GGGTATTGTCATGGCTGATGATG	59.495	47.826	0.00	0.00	43.20	3.07
1275	1292	3.499202	GGGGTATTGTCATGGCTGATGAT	60.499	47.826	0.00	0.00	43.20	2.45
1276	1293	2.158623	GGGGTATTGTCATGGCTGATGA	60.159	50.000	0.00	0.00	38.87	2.92
1415	1489	2.420890	CGCAGAGGAGGAGGATGC	59.579	66.667	0.00	0.00	0.00	3.91
1598	1757	1.601419	TAGTCCTCGAAGGTTGGCGG	61.601	60.000	0.00	0.00	36.53	6.13
1603	1762	0.526662	CGCTGTAGTCCTCGAAGGTT	59.473	55.000	0.00	0.00	36.53	3.50
1767	1996	3.075005	ATCCAGTCGGACACGGGG	61.075	66.667	11.27	6.39	46.79	5.73
1989	2218	0.895100	GGTCCTGCTTGGCAATCACA	60.895	55.000	0.00	0.00	38.41	3.58
2159	3878	1.140816	GTAGGCTCCGCAAATCGATC	58.859	55.000	0.00	0.00	41.67	3.69
2181	3900	6.956299	TGCGTTTTATCTTAGGAACAGTAC	57.044	37.500	0.00	0.00	0.00	2.73
2237	3966	7.821846	ACTCACATTTCAGTAGATTTCTTCCTC	59.178	37.037	0.00	0.00	0.00	3.71
2239	3968	7.065204	GGACTCACATTTCAGTAGATTTCTTCC	59.935	40.741	0.00	0.00	0.00	3.46
2394	4140	6.045318	GGGTATCATAGGATGACGATCAATG	58.955	44.000	0.00	0.00	43.01	2.82
2445	4487	9.780413	GAGTTGCTCTAAGAAAAATAAGGAATG	57.220	33.333	0.00	0.00	0.00	2.67
2475	4517	1.002011	GTCCCTTTGAGTCAGCCCC	60.002	63.158	0.00	0.00	0.00	5.80
2480	4522	0.400213	ATTGCCGTCCCTTTGAGTCA	59.600	50.000	0.00	0.00	0.00	3.41
2484	4526	2.035632	ACAAAATTGCCGTCCCTTTGA	58.964	42.857	0.00	0.00	32.57	2.69
2489	4531	1.006825	GCGAACAAAATTGCCGTCCC	61.007	55.000	9.26	0.00	32.56	4.46
2497	4539	4.099824	ACGAACGAAAAGCGAACAAAATT	58.900	34.783	0.14	0.00	44.57	1.82
2505	4547	1.288350	TCCAAACGAACGAAAAGCGA	58.712	45.000	0.14	0.00	44.57	4.93
2513	4555	3.541711	GTTTGACTGATCCAAACGAACG	58.458	45.455	9.39	0.00	42.32	3.95
2524	4566	4.806330	ACGTCTATGTTCGTTTGACTGAT	58.194	39.130	0.00	0.00	36.93	2.90
2532	4574	0.524862	AGCGGACGTCTATGTTCGTT	59.475	50.000	16.46	4.31	42.88	3.85
2533	4575	0.524862	AAGCGGACGTCTATGTTCGT	59.475	50.000	16.46	0.00	42.88	3.85
2581	4623	3.268103	AAAATGGGTCGGGCGAGCT	62.268	57.895	0.00	0.00	41.80	4.09
2607	4649	6.760298	TGCATGCACTATTTTCTTTTTGTCAA	59.240	30.769	18.46	0.00	0.00	3.18
2648	4694	9.203421	GCTGGCTTTAATGTTTAATTAAGTTGT	57.797	29.630	0.00	0.00	0.00	3.32
2672	4718	4.329545	TCGCCGGCTTTCTTGGCT	62.330	61.111	26.68	0.00	46.67	4.75
2677	4723	2.574399	GACTCTCGCCGGCTTTCT	59.426	61.111	26.68	2.06	0.00	2.52
2767	4813	1.313091	CCCTGAGGACGACGATGACA	61.313	60.000	0.00	0.00	33.47	3.58
2771	4817	3.921521	GACCCTGAGGACGACGAT	58.078	61.111	0.00	0.00	36.73	3.73
2783	4835	2.052690	CATCGACCTCACCGACCCT	61.053	63.158	0.00	0.00	38.97	4.34
2852	4904	2.434884	CTGCCCGCGACTGACATT	60.435	61.111	8.23	0.00	0.00	2.71
2920	5029	1.022982	CAAGGAGATGCTTGAGCGCA	61.023	55.000	11.47	0.00	45.83	6.09
2927	5036	1.134670	GGCGAGTACAAGGAGATGCTT	60.135	52.381	0.00	0.00	0.00	3.91
3014	5123	1.065491	CCGATTTGGATGGAGGTGACA	60.065	52.381	0.00	0.00	42.00	3.58
3018	5127	0.255890	CCACCGATTTGGATGGAGGT	59.744	55.000	0.00	0.00	42.00	3.85
3070	5179	1.522092	CCCATCAAGCGCTACTCCA	59.478	57.895	12.05	0.00	0.00	3.86
3195	5341	4.157120	GGCGGCCATGTCGTAGGT	62.157	66.667	15.62	0.00	31.29	3.08
3202	5348	4.157120	GGTACGAGGCGGCCATGT	62.157	66.667	23.09	20.26	0.00	3.21
3587	5734	1.049289	GTGCCTCTTCCTACCCCGAT	61.049	60.000	0.00	0.00	0.00	4.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.