AutoCloner

Multiple sequence alignment - TraesCS3B01G443700

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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	TraesCS3B01G443700	chr3B	100.000	4756	0	0	1	4756	684138101	684133346	0.000000e+00	8783.0
1	TraesCS3B01G443700	chr3B	93.409	531	30	4	1	528	370891036	370890508	0.000000e+00	782.0
2	TraesCS3B01G443700	chr3D	93.419	3723	195	25	526	4223	519596358	519600055	0.000000e+00	5472.0
3	TraesCS3B01G443700	chr3D	85.897	2964	347	38	1291	4218	519644323	519641395	0.000000e+00	3092.0
4	TraesCS3B01G443700	chr3D	87.573	1030	107	13	2617	3634	519620583	519621603	0.000000e+00	1173.0
5	TraesCS3B01G443700	chr3D	94.518	529	27	2	1	528	478695888	478695361	0.000000e+00	815.0
6	TraesCS3B01G443700	chr3D	93.774	530	29	4	1	528	306270168	306270695	0.000000e+00	793.0
7	TraesCS3B01G443700	chr3D	93.195	529	34	2	1	528	358927518	358928045	0.000000e+00	776.0
8	TraesCS3B01G443700	chr3D	92.523	535	34	6	4223	4756	519600093	519600622	0.000000e+00	761.0
9	TraesCS3B01G443700	chr3D	96.970	33	1	0	4091	4123	475580012	475580044	6.650000e-04	56.5
10	TraesCS3B01G443700	chr3A	92.555	3640	231	22	526	4142	654517640	654521262	0.000000e+00	5184.0
11	TraesCS3B01G443700	chr3A	92.439	2870	183	15	632	3493	654498904	654501747	0.000000e+00	4067.0
12	TraesCS3B01G443700	chr3A	85.436	2973	355	42	1290	4218	654584759	654581821	0.000000e+00	3020.0
13	TraesCS3B01G443700	chr3A	90.909	726	52	4	3515	4227	654501739	654502463	0.000000e+00	963.0
14	TraesCS3B01G443700	chr3A	91.418	536	43	3	4223	4756	654541459	654541993	0.000000e+00	732.0
15	TraesCS3B01G443700	chr3A	90.892	538	44	5	4223	4756	654502495	654503031	0.000000e+00	717.0
16	TraesCS3B01G443700	chr3A	89.027	483	48	5	2621	3101	654559975	654560454	1.140000e-165	593.0
17	TraesCS3B01G443700	chr3A	86.774	499	52	9	3097	3589	654562133	654562623	1.160000e-150	544.0
18	TraesCS3B01G443700	chr3A	81.157	536	72	15	4222	4756	654581779	654581272	2.060000e-108	403.0
19	TraesCS3B01G443700	chrUn	91.563	3378	254	17	870	4223	101062265	101065635	0.000000e+00	4630.0
20	TraesCS3B01G443700	chrUn	89.591	538	52	4	4222	4756	101065672	101066208	0.000000e+00	680.0
21	TraesCS3B01G443700	chr6A	91.577	3158	216	26	873	3988	35564038	35560889	0.000000e+00	4313.0
22	TraesCS3B01G443700	chr7D	95.066	527	23	3	1	526	480013615	480013091	0.000000e+00	826.0
23	TraesCS3B01G443700	chr7D	73.381	1946	428	67	1421	3318	612711783	612713686	4.010000e-180	641.0
24	TraesCS3B01G443700	chr2D	93.750	528	30	3	1	527	368125273	368125798	0.000000e+00	789.0
25	TraesCS3B01G443700	chr2D	93.573	529	32	2	1	528	368067914	368068441	0.000000e+00	787.0
26	TraesCS3B01G443700	chr5B	93.750	528	27	6	1	526	445851277	445850754	0.000000e+00	787.0
27	TraesCS3B01G443700	chr5B	87.032	347	37	8	526	868	522854112	522853770	7.470000e-103	385.0
28	TraesCS3B01G443700	chr5D	93.409	531	30	5	1	528	398835632	398835104	0.000000e+00	782.0
29	TraesCS3B01G443700	chr5D	86.705	346	40	6	526	868	400401371	400401713	3.470000e-101	379.0
30	TraesCS3B01G443700	chr7B	74.111	1603	341	52	1766	3329	702196546	702194979	1.140000e-165	593.0
31	TraesCS3B01G443700	chr4D	87.069	348	36	9	526	868	128921556	128921213	7.470000e-103	385.0
32	TraesCS3B01G443700	chr5A	86.994	346	37	8	526	867	680906392	680906051	2.690000e-102	383.0
33	TraesCS3B01G443700	chr4B	87.106	349	32	11	526	867	565311186	565311528	2.690000e-102	383.0
34	TraesCS3B01G443700	chr2B	86.819	349	35	10	526	868	637789911	637789568	3.470000e-101	379.0
35	TraesCS3B01G443700	chr4A	86.705	346	39	6	526	868	546616004	546615663	1.250000e-100	377.0

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	TraesCS3B01G443700	chr3B	684133346	684138101	4755	True	8783.000000	8783	100.000000	1	4756	1	chr3B.!!$R2	4755
1	TraesCS3B01G443700	chr3B	370890508	370891036	528	True	782.000000	782	93.409000	1	528	1	chr3B.!!$R1	527
2	TraesCS3B01G443700	chr3D	519596358	519600622	4264	False	3116.500000	5472	92.971000	526	4756	2	chr3D.!!$F5	4230
3	TraesCS3B01G443700	chr3D	519641395	519644323	2928	True	3092.000000	3092	85.897000	1291	4218	1	chr3D.!!$R2	2927
4	TraesCS3B01G443700	chr3D	519620583	519621603	1020	False	1173.000000	1173	87.573000	2617	3634	1	chr3D.!!$F4	1017
5	TraesCS3B01G443700	chr3D	478695361	478695888	527	True	815.000000	815	94.518000	1	528	1	chr3D.!!$R1	527
6	TraesCS3B01G443700	chr3D	306270168	306270695	527	False	793.000000	793	93.774000	1	528	1	chr3D.!!$F1	527
7	TraesCS3B01G443700	chr3D	358927518	358928045	527	False	776.000000	776	93.195000	1	528	1	chr3D.!!$F2	527
8	TraesCS3B01G443700	chr3A	654517640	654521262	3622	False	5184.000000	5184	92.555000	526	4142	1	chr3A.!!$F1	3616
9	TraesCS3B01G443700	chr3A	654498904	654503031	4127	False	1915.666667	4067	91.413333	632	4756	3	chr3A.!!$F3	4124
10	TraesCS3B01G443700	chr3A	654581272	654584759	3487	True	1711.500000	3020	83.296500	1290	4756	2	chr3A.!!$R1	3466
11	TraesCS3B01G443700	chr3A	654541459	654541993	534	False	732.000000	732	91.418000	4223	4756	1	chr3A.!!$F2	533
12	TraesCS3B01G443700	chr3A	654559975	654562623	2648	False	568.500000	593	87.900500	2621	3589	2	chr3A.!!$F4	968
13	TraesCS3B01G443700	chrUn	101062265	101066208	3943	False	2655.000000	4630	90.577000	870	4756	2	chrUn.!!$F1	3886
14	TraesCS3B01G443700	chr6A	35560889	35564038	3149	True	4313.000000	4313	91.577000	873	3988	1	chr6A.!!$R1	3115
15	TraesCS3B01G443700	chr7D	480013091	480013615	524	True	826.000000	826	95.066000	1	526	1	chr7D.!!$R1	525
16	TraesCS3B01G443700	chr7D	612711783	612713686	1903	False	641.000000	641	73.381000	1421	3318	1	chr7D.!!$F1	1897
17	TraesCS3B01G443700	chr2D	368125273	368125798	525	False	789.000000	789	93.750000	1	527	1	chr2D.!!$F2	526
18	TraesCS3B01G443700	chr2D	368067914	368068441	527	False	787.000000	787	93.573000	1	528	1	chr2D.!!$F1	527
19	TraesCS3B01G443700	chr5B	445850754	445851277	523	True	787.000000	787	93.750000	1	526	1	chr5B.!!$R1	525
20	TraesCS3B01G443700	chr5D	398835104	398835632	528	True	782.000000	782	93.409000	1	528	1	chr5D.!!$R1	527
21	TraesCS3B01G443700	chr7B	702194979	702196546	1567	True	593.000000	593	74.111000	1766	3329	1	chr7B.!!$R1	1563

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
851	863	1.273606	CGGTAGATCGATGATGGCCTT	59.726	52.381	0.54	0.0	0.00	4.35	F
1647	1721	0.457035	CCCTGTTGGAAATCCATGCG	59.543	55.000	2.38	0.0	46.97	4.73	F
1650	1724	0.897401	TGTTGGAAATCCATGCGCCA	60.897	50.000	4.18	0.0	46.97	5.69	F
3257	5047	0.534203	TGGTCAAGCCCTCGTGTTTC	60.534	55.000	0.00	0.0	36.04	2.78	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1699	1773	0.468226	TTCGGCTCAAGTTCCACAGT	59.532	50.000	0.00	0.00	0.00	3.55	R
3113	4891	0.998928	ATATGAGGGTGTGGGCACAA	59.001	50.000	0.00	0.00	46.95	3.33	R
3331	5123	3.479489	ACATGAGTCAACAAGATGCACA	58.521	40.909	0.00	0.00	0.00	4.57	R
4275	6147	0.595567	GCAATGCATGGCCACATACG	60.596	55.000	15.73	4.46	34.99	3.06	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
37	38	5.103000	CAGAATCGTTTCGGTCTACTTGAT	58.897	41.667	0.72	0.00	36.93	2.57
53	54	3.118261	ACTTGATATGGACGTGATGCCTT	60.118	43.478	0.00	0.00	0.00	4.35
100	103	3.550561	TGTCATAACTTTGCGCTTTTCG	58.449	40.909	9.73	0.00	42.12	3.46
181	184	3.041946	CTCTAGTGAAACCTATGGCCCT	58.958	50.000	0.00	0.00	37.80	5.19
182	185	3.456277	CTCTAGTGAAACCTATGGCCCTT	59.544	47.826	0.00	0.00	37.80	3.95
394	403	6.257630	GTGTTTGATTGTTTGTGCAGGTATTT	59.742	34.615	0.00	0.00	0.00	1.40
404	413	5.289917	TGTGCAGGTATTTGTGATTTACG	57.710	39.130	0.00	0.00	0.00	3.18
423	432	3.354467	ACGGTGTTCTTCTCCTACTAGG	58.646	50.000	0.00	0.00	36.46	3.02
461	470	9.886132	GTTCTCAAACTGAGGGAAATACTTATA	57.114	33.333	3.92	0.00	44.39	0.98
528	537	2.873649	GCAAGCTCAAGAAGTAGCAGGT	60.874	50.000	0.00	0.00	41.32	4.00
529	538	3.406764	CAAGCTCAAGAAGTAGCAGGTT	58.593	45.455	0.00	0.00	41.32	3.50
530	539	4.569943	CAAGCTCAAGAAGTAGCAGGTTA	58.430	43.478	0.00	0.00	41.32	2.85
531	540	5.181748	CAAGCTCAAGAAGTAGCAGGTTAT	58.818	41.667	0.00	0.00	41.32	1.89
546	555	4.160626	GCAGGTTATAGTTGGACTCTGAGT	59.839	45.833	10.66	10.66	0.00	3.41
575	584	6.382087	TGGTGTGTAGATAGGATATGGAGTT	58.618	40.000	0.00	0.00	0.00	3.01
576	585	6.267699	TGGTGTGTAGATAGGATATGGAGTTG	59.732	42.308	0.00	0.00	0.00	3.16
630	642	7.994425	CTCTTATCTAATGAGAGGCTAGACA	57.006	40.000	0.00	0.00	38.83	3.41
643	655	3.774766	AGGCTAGACACATGATGTAACCA	59.225	43.478	0.00	0.00	43.56	3.67
664	676	4.500205	CCAATGCCAACATAATAGCACAGG	60.500	45.833	0.00	0.00	38.21	4.00
665	677	3.364460	TGCCAACATAATAGCACAGGT	57.636	42.857	0.00	0.00	0.00	4.00
668	680	4.196193	GCCAACATAATAGCACAGGTACA	58.804	43.478	0.00	0.00	0.00	2.90
670	682	5.182487	CCAACATAATAGCACAGGTACACA	58.818	41.667	0.00	0.00	0.00	3.72
681	693	2.356780	GGTACACAGGGGAGTCGGG	61.357	68.421	0.00	0.00	0.00	5.14
685	697	3.923645	ACAGGGGAGTCGGGGACA	61.924	66.667	0.00	0.00	34.60	4.02
697	709	4.101448	GGGACATGTGCCGGAGCT	62.101	66.667	21.48	0.00	40.80	4.09
760	772	3.178611	CCCCATAGTCAGGCCCCC	61.179	72.222	0.00	0.00	0.00	5.40
765	777	3.341469	ATAGTCAGGCCCCCGGGAA	62.341	63.158	26.32	0.00	37.50	3.97
851	863	1.273606	CGGTAGATCGATGATGGCCTT	59.726	52.381	0.54	0.00	0.00	4.35
1005	1017	1.302949	GCAGGGCTGGACCACATAA	59.697	57.895	0.00	0.00	42.05	1.90
1015	1027	1.548719	GGACCACATAAAACAAGGGGC	59.451	52.381	0.00	0.00	0.00	5.80
1022	1034	5.303971	CACATAAAACAAGGGGCAATTTCA	58.696	37.500	0.00	0.00	0.00	2.69
1032	1044	3.845398	AGGGGCAATTTCATCCATCAAAA	59.155	39.130	0.00	0.00	0.00	2.44
1237	1260	2.519063	CAAGCACCACCACTGCCA	60.519	61.111	0.00	0.00	35.01	4.92
1266	1308	3.368501	CTCCCTCCCCTCTCCCCA	61.369	72.222	0.00	0.00	0.00	4.96
1286	1347	2.359404	GTCCTCACCTCTCCCCGA	59.641	66.667	0.00	0.00	0.00	5.14
1287	1348	2.053277	GTCCTCACCTCTCCCCGAC	61.053	68.421	0.00	0.00	0.00	4.79
1288	1349	3.141488	CCTCACCTCTCCCCGACG	61.141	72.222	0.00	0.00	0.00	5.12
1289	1350	2.361357	CTCACCTCTCCCCGACGT	60.361	66.667	0.00	0.00	0.00	4.34
1294	1355	2.045242	CTCTCCCCGACGTCCTCA	60.045	66.667	10.58	0.00	0.00	3.86
1392	1463	2.622942	TGCAAAAGCTTCGATGGAGTTT	59.377	40.909	0.00	0.00	0.00	2.66
1401	1472	4.686972	CTTCGATGGAGTTTAGATCTGCA	58.313	43.478	5.18	0.00	37.63	4.41
1492	1563	2.013405	AGGCTCCCCTGCATCAAAT	58.987	52.632	0.00	0.00	40.94	2.32
1531	1602	1.363807	CTCTCACGGCGATGGCATA	59.636	57.895	16.62	0.00	42.47	3.14
1620	1691	1.198713	GCCAGATCTCTTGTCCTCCA	58.801	55.000	0.00	0.00	0.00	3.86
1647	1721	0.457035	CCCTGTTGGAAATCCATGCG	59.543	55.000	2.38	0.00	46.97	4.73
1650	1724	0.897401	TGTTGGAAATCCATGCGCCA	60.897	50.000	4.18	0.00	46.97	5.69
1699	1773	1.153329	AACTCGTTGTTGTCCGCCA	60.153	52.632	0.00	0.00	37.52	5.69
1703	1777	2.177580	CGTTGTTGTCCGCCACTGT	61.178	57.895	0.00	0.00	0.00	3.55
1826	1900	6.543465	ACCTACATCATGTTGGACAATGTATG	59.457	38.462	23.30	5.72	44.30	2.39
1995	2072	7.345653	TGTGATCTAAGGGTGAATTCACTATCT	59.654	37.037	31.81	23.83	45.73	1.98
2024	2101	4.276926	GGAGCTTGTTGTGAACTCATTCTT	59.723	41.667	0.00	0.00	35.69	2.52
2037	2114	6.543465	TGAACTCATTCTTGACAGAACATGTT	59.457	34.615	11.78	11.78	42.05	2.71
2176	2257	5.542635	ACAGAGGAGTCTATTGTGTTTGGTA	59.457	40.000	0.00	0.00	0.00	3.25
2191	2272	6.103997	GTGTTTGGTATTTGGTATCTCGAGA	58.896	40.000	19.19	19.19	0.00	4.04
2381	2464	1.131126	CTATGAGCCCAACTTTGCACG	59.869	52.381	0.00	0.00	0.00	5.34
2481	2564	4.451096	GCACTCGTGTTTTATCTCCTTCAA	59.549	41.667	0.00	0.00	0.00	2.69
2609	2694	7.156673	AGTAGCTTACATTTACTTTTCGGTCA	58.843	34.615	0.00	0.00	0.00	4.02
2652	2737	0.898320	AGATTGTCCCTGTGAGTCCG	59.102	55.000	0.00	0.00	0.00	4.79
2827	2912	6.010850	AGGTCTCATCAAGTAACACTAGACA	58.989	40.000	0.00	0.00	32.95	3.41
3027	3121	9.593134	TTTATATGTTTATGGTGGTTGAAATGC	57.407	29.630	0.00	0.00	0.00	3.56
3028	3122	4.264460	TGTTTATGGTGGTTGAAATGCC	57.736	40.909	0.00	0.00	0.00	4.40
3095	3190	8.848474	TCCATTAGTAGCTAATTCTAAATGCC	57.152	34.615	0.00	0.00	34.83	4.40
3113	4891	1.412343	GCCATATTCCCACGGCATTTT	59.588	47.619	0.00	0.00	44.25	1.82
3257	5047	0.534203	TGGTCAAGCCCTCGTGTTTC	60.534	55.000	0.00	0.00	36.04	2.78
3269	5059	4.272504	CCCTCGTGTTTCGCATATGTATTT	59.727	41.667	4.29	0.00	39.67	1.40
3277	5067	6.524933	TGTTTCGCATATGTATTTTGGTTTCG	59.475	34.615	4.29	0.00	0.00	3.46
3331	5123	9.589461	TGTCTAGCTAGAGTAGGCTATAATTTT	57.411	33.333	23.87	0.00	39.79	1.82
3356	5149	6.207221	TGTGCATCTTGTTGACTCATGTTAAT	59.793	34.615	0.00	0.00	0.00	1.40
3386	5180	3.196254	CCTCTATTGGGTGCATGCTTTTT	59.804	43.478	20.33	1.62	0.00	1.94
3483	5277	7.349859	TCATACCTAAATTGACTATCCTTGGGT	59.650	37.037	0.00	0.00	0.00	4.51
3680	5487	6.012113	AGAAGACATCCAAAATCAACCATCA	58.988	36.000	0.00	0.00	0.00	3.07
3720	5527	3.407698	TGCATATGTGGTTTCTCGTTGT	58.592	40.909	4.29	0.00	0.00	3.32
3728	5535	1.732259	GGTTTCTCGTTGTGCATCGAT	59.268	47.619	10.85	0.00	35.57	3.59
3865	5673	8.902540	AAGTTAATGTGTCAACTTATGTCAGA	57.097	30.769	0.00	0.00	41.86	3.27
3910	5718	4.096382	ACATGTTTCCACCGAATTATGCTC	59.904	41.667	0.00	0.00	30.54	4.26
4014	5823	7.859325	TTTCTAACTATTGCACCCTACAATC	57.141	36.000	0.00	0.00	38.62	2.67
4020	5829	5.951747	ACTATTGCACCCTACAATCAACAAT	59.048	36.000	0.00	0.00	38.62	2.71
4046	5863	7.206687	AGATGCATCTTCTGTTACTTAGCTAC	58.793	38.462	23.75	0.00	31.97	3.58
4047	5864	6.280855	TGCATCTTCTGTTACTTAGCTACA	57.719	37.500	0.00	0.00	0.00	2.74
4169	6003	0.462789	ACACCTTTGTCCGACGTCTT	59.537	50.000	14.70	0.00	0.00	3.01
4176	6010	3.235481	TCCGACGTCTTGGCCCAA	61.235	61.111	14.70	0.00	0.00	4.12
4218	6052	7.129425	AGGACTCAGAAGACTTGGAGTATATT	58.871	38.462	15.53	3.85	40.48	1.28
4275	6147	8.338259	CGCTTGCATCCTATATTATCCATAAAC	58.662	37.037	0.00	0.00	0.00	2.01
4347	6219	9.366216	GGACAAATCCTAAACAAATCCAATAAC	57.634	33.333	0.00	0.00	42.45	1.89
4348	6220	9.366216	GACAAATCCTAAACAAATCCAATAACC	57.634	33.333	0.00	0.00	0.00	2.85
4417	6296	9.277565	CTTTGACATAAGACATTTTAATGACCG	57.722	33.333	9.32	0.00	39.67	4.79
4422	6301	8.883731	ACATAAGACATTTTAATGACCGAAGAG	58.116	33.333	9.32	0.00	39.67	2.85
4511	6390	8.301002	TGCTCAAAATTTTATAGGTACAACCAC	58.699	33.333	2.44	0.00	41.95	4.16
4580	6459	7.475771	TCCATTTACAAACATGTTTCTTTGC	57.524	32.000	20.85	0.00	31.63	3.68
4590	6469	2.758130	TGTTTCTTTGCCCCCTCTTTT	58.242	42.857	0.00	0.00	0.00	2.27
4621	6500	9.590451	AAACCATTATTGCTTGAAGATAACATG	57.410	29.630	0.00	0.00	0.00	3.21
4632	6511	8.571336	GCTTGAAGATAACATGTTAGGCATAAT	58.429	33.333	22.03	6.00	35.74	1.28

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
37	38	3.563808	GCAATAAAGGCATCACGTCCATA	59.436	43.478	0.00	0.00	0.00	2.74
53	54	6.482898	ACCAAGGCAATGATTATGCAATAA	57.517	33.333	0.00	0.00	45.60	1.40
100	103	6.546395	ACAAATTACTGTCGAGCAATTGATC	58.454	36.000	13.73	13.73	0.00	2.92
394	403	4.039973	AGGAGAAGAACACCGTAAATCACA	59.960	41.667	0.00	0.00	34.46	3.58
404	413	4.771054	TCAACCTAGTAGGAGAAGAACACC	59.229	45.833	23.50	0.00	37.67	4.16
423	432	5.763204	TCAGTTTGAGAACCAAGGTATCAAC	59.237	40.000	15.46	11.96	35.28	3.18
461	470	2.240667	AGGGTGATGCAGCAAAGTAGAT	59.759	45.455	6.05	0.00	33.07	1.98
528	537	6.262496	CCATACGACTCAGAGTCCAACTATAA	59.738	42.308	22.65	2.49	42.12	0.98
529	538	5.763698	CCATACGACTCAGAGTCCAACTATA	59.236	44.000	22.65	7.99	42.12	1.31
530	539	4.580995	CCATACGACTCAGAGTCCAACTAT	59.419	45.833	22.65	10.68	42.12	2.12
531	540	3.945921	CCATACGACTCAGAGTCCAACTA	59.054	47.826	22.65	9.06	42.12	2.24
546	555	6.602009	CCATATCCTATCTACACACCATACGA	59.398	42.308	0.00	0.00	0.00	3.43
624	636	5.008019	GGCATTGGTTACATCATGTGTCTAG	59.992	44.000	0.00	0.00	42.29	2.43
630	642	3.831333	TGTTGGCATTGGTTACATCATGT	59.169	39.130	0.00	0.00	0.00	3.21
643	655	4.280819	ACCTGTGCTATTATGTTGGCATT	58.719	39.130	0.00	0.00	37.05	3.56
664	676	2.356780	CCCCGACTCCCCTGTGTAC	61.357	68.421	0.00	0.00	0.00	2.90
665	677	2.038329	CCCCGACTCCCCTGTGTA	59.962	66.667	0.00	0.00	0.00	2.90
668	680	3.254035	ATGTCCCCGACTCCCCTGT	62.254	63.158	0.00	0.00	33.15	4.00
670	682	2.365635	CATGTCCCCGACTCCCCT	60.366	66.667	0.00	0.00	33.15	4.79
681	693	2.512515	GAGCTCCGGCACATGTCC	60.513	66.667	0.87	0.00	41.70	4.02
707	719	1.143183	CGCTACAATACCGCACCCT	59.857	57.895	0.00	0.00	0.00	4.34
738	750	3.142393	CCTGACTATGGGGGCTCG	58.858	66.667	0.00	0.00	0.00	5.03
765	777	5.876612	GAGGTTACTCGATACGGATACAT	57.123	43.478	0.00	0.00	33.35	2.29
779	791	6.017400	TCGAGATTTGTTAACGAGGTTACT	57.983	37.500	0.26	0.00	0.00	2.24
784	796	4.862574	TGACATCGAGATTTGTTAACGAGG	59.137	41.667	0.26	0.00	39.86	4.63
795	807	3.373130	CACACAAGCATGACATCGAGATT	59.627	43.478	0.00	0.00	0.00	2.40
939	951	3.269381	TCTCCCAACTTTGCCTTATCCAT	59.731	43.478	0.00	0.00	0.00	3.41
1005	1017	2.978278	TGGATGAAATTGCCCCTTGTTT	59.022	40.909	0.00	0.00	0.00	2.83
1096	1119	8.881262	GGATTCCTTATTTGACCCTAGAGATTA	58.119	37.037	0.00	0.00	0.00	1.75
1167	1190	0.913205	TAGTGGTGTGTGGTGGTGTT	59.087	50.000	0.00	0.00	0.00	3.32
1237	1260	3.648660	AGGGAGGGGAATGGGGGT	61.649	66.667	0.00	0.00	0.00	4.95
1266	1308	2.363147	GGGAGAGGTGAGGACGCT	60.363	66.667	0.00	0.00	0.00	5.07
1286	1347	2.037527	GGGGAGAGGTGAGGACGT	59.962	66.667	0.00	0.00	0.00	4.34
1287	1348	3.141488	CGGGGAGAGGTGAGGACG	61.141	72.222	0.00	0.00	0.00	4.79
1288	1349	2.760385	CCGGGGAGAGGTGAGGAC	60.760	72.222	0.00	0.00	0.00	3.85
1289	1350	4.779733	GCCGGGGAGAGGTGAGGA	62.780	72.222	2.18	0.00	0.00	3.71
1392	1463	1.683385	CCCAGACGACATGCAGATCTA	59.317	52.381	0.00	0.00	0.00	1.98
1401	1472	2.816411	TCTAGGAAACCCAGACGACAT	58.184	47.619	0.00	0.00	0.00	3.06
1511	1582	4.899239	GCCATCGCCGTGAGAGGG	62.899	72.222	4.47	4.47	41.99	4.30
1599	1670	0.467804	GAGGACAAGAGATCTGGCCC	59.532	60.000	0.00	0.00	0.00	5.80
1647	1721	2.827642	GCCATGTCCTGCTCTGGC	60.828	66.667	0.00	0.00	46.54	4.85
1650	1724	2.996395	CTGGCCATGTCCTGCTCT	59.004	61.111	5.51	0.00	0.00	4.09
1699	1773	0.468226	TTCGGCTCAAGTTCCACAGT	59.532	50.000	0.00	0.00	0.00	3.55
1703	1777	1.416401	ACTCTTTCGGCTCAAGTTCCA	59.584	47.619	0.00	0.00	0.00	3.53
1851	1928	2.034685	CGTCTCGAGCATAGGGAATTCA	59.965	50.000	7.81	0.00	0.00	2.57
1995	2072	0.469494	TCACAACAAGCTCCTGCAGA	59.531	50.000	17.39	0.00	42.74	4.26
2024	2101	6.072728	GGCTACAATGTTAACATGTTCTGTCA	60.073	38.462	21.46	10.36	36.98	3.58
2037	2114	1.568597	AGCATGGGGGCTACAATGTTA	59.431	47.619	0.00	0.00	43.70	2.41
2176	2257	4.444876	CCCCAACATCTCGAGATACCAAAT	60.445	45.833	26.87	1.71	32.63	2.32
2191	2272	2.990967	CGCCTGCAACCCCAACAT	60.991	61.111	0.00	0.00	0.00	2.71
2381	2464	5.012561	ACAACCATATGCTTCTCTATCTCCC	59.987	44.000	0.00	0.00	0.00	4.30
2609	2694	8.502738	TCTATTGGGCATTCTTCTTTTACCTAT	58.497	33.333	0.00	0.00	0.00	2.57
2843	2928	3.089284	TGAAGCATAGGTCTCGAAGACA	58.911	45.455	14.26	0.00	46.79	3.41
2920	3012	5.211973	TCTACTTCATGTAGGAGGATGCTT	58.788	41.667	11.35	0.00	46.45	3.91
2950	3044	8.671028	TCAAAGAAACTTACAAGAAGTAACACC	58.329	33.333	0.00	0.00	37.77	4.16
3027	3121	2.053865	AATTGGGATGCCAGTGCGG	61.054	57.895	5.91	0.00	41.78	5.69
3028	3122	1.140161	CAATTGGGATGCCAGTGCG	59.860	57.895	5.91	0.00	41.78	5.34
3095	3190	3.864583	CACAAAAATGCCGTGGGAATATG	59.135	43.478	0.00	0.00	0.00	1.78
3113	4891	0.998928	ATATGAGGGTGTGGGCACAA	59.001	50.000	0.00	0.00	46.95	3.33
3219	5006	8.684386	TTGACCATTAGAGAACATTGTAAACA	57.316	30.769	0.00	0.00	0.00	2.83
3257	5047	5.204833	CCTCGAAACCAAAATACATATGCG	58.795	41.667	1.58	0.00	0.00	4.73
3269	5059	5.993441	CCTAGTTCTTTAACCTCGAAACCAA	59.007	40.000	0.00	0.00	36.15	3.67
3277	5067	6.174049	AGTTGATGCCTAGTTCTTTAACCTC	58.826	40.000	0.00	0.00	36.15	3.85
3331	5123	3.479489	ACATGAGTCAACAAGATGCACA	58.521	40.909	0.00	0.00	0.00	4.57
3386	5180	6.523840	CCCTTGATGGAACTTTTTGATGAAA	58.476	36.000	0.00	0.00	38.35	2.69
3459	5253	7.707467	ACCCAAGGATAGTCAATTTAGGTAT	57.293	36.000	0.00	0.00	0.00	2.73
3728	5535	5.414789	TTGACATGGAAAGGACGATCTTA	57.585	39.130	0.00	0.00	0.00	2.10
3810	5618	5.211174	TGAATTGCATCACAACCATTCAA	57.789	34.783	4.18	0.00	42.27	2.69
3972	5780	3.509184	AGAAAAGAGAGCAAATGGAAGGC	59.491	43.478	0.00	0.00	0.00	4.35
3983	5791	5.065346	GGGTGCAATAGTTAGAAAAGAGAGC	59.935	44.000	0.00	0.00	0.00	4.09
4014	5823	8.206325	AGTAACAGAAGATGCATCTATTGTTG	57.794	34.615	37.85	28.49	40.58	3.33
4020	5829	7.353414	AGCTAAGTAACAGAAGATGCATCTA	57.647	36.000	28.92	10.08	35.76	1.98
4086	5906	1.229272	ACCCCTAGGCCGTAACACA	60.229	57.895	2.05	0.00	36.11	3.72
4126	5960	0.766674	TGACCTAAGGTGCCACAGGT	60.767	55.000	5.11	5.11	44.11	4.00
4129	5963	1.136828	AACTGACCTAAGGTGCCACA	58.863	50.000	0.00	0.00	35.25	4.17
4218	6052	2.167693	CGCAGGATCCTAGTTGGTTGTA	59.832	50.000	15.67	0.00	37.07	2.41
4275	6147	0.595567	GCAATGCATGGCCACATACG	60.596	55.000	15.73	4.46	34.99	3.06
4365	6243	4.469657	TCACCAATTATGCTTCATACCCC	58.530	43.478	0.00	0.00	0.00	4.95
4485	6364	8.301002	GTGGTTGTACCTATAAAATTTTGAGCA	58.699	33.333	13.76	2.51	39.58	4.26
4535	6414	6.762333	TGGATCATAATGTTGTCTCGATCAT	58.238	36.000	0.00	0.00	31.52	2.45
4536	6415	6.160576	TGGATCATAATGTTGTCTCGATCA	57.839	37.500	0.00	0.00	31.52	2.92
4537	6416	7.664082	AATGGATCATAATGTTGTCTCGATC	57.336	36.000	0.00	0.00	0.00	3.69
4538	6417	8.993121	GTAAATGGATCATAATGTTGTCTCGAT	58.007	33.333	0.00	0.00	0.00	3.59

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.