AutoCloner

Multiple sequence alignment - TraesCS2A01G225800

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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	TraesCS2A01G225800	chr2A	100.000	3473	0	0	1	3473	232358619	232362091	0.000000e+00	6414
1	TraesCS2A01G225800	chr2A	95.819	3420	118	3	1	3396	772492537	772489119	0.000000e+00	5500
2	TraesCS2A01G225800	chr2A	95.711	3427	124	1	1	3404	505944176	505947602	0.000000e+00	5493
3	TraesCS2A01G225800	chr2A	95.444	3424	130	4	1	3401	719113875	719117295	0.000000e+00	5435
4	TraesCS2A01G225800	chr2A	95.408	3419	121	4	1	3396	52613558	52610153	0.000000e+00	5411
5	TraesCS2A01G225800	chr2A	97.520	766	17	2	2633	3397	24825820	24826584	0.000000e+00	1308
6	TraesCS2A01G225800	chr3A	96.110	3419	108	3	1	3396	695820810	695817394	0.000000e+00	5553
7	TraesCS2A01G225800	chr3A	95.203	3419	113	3	1	3396	746704534	746707924	0.000000e+00	5358
8	TraesCS2A01G225800	chr3A	95.387	1149	29	2	2270	3395	701107601	701106454	0.000000e+00	1807
9	TraesCS2A01G225800	chr3A	95.238	84	3	1	3390	3473	47205275	47205357	7.820000e-27	132
10	TraesCS2A01G225800	chr6A	95.994	3420	111	5	1	3397	158445266	158441850	0.000000e+00	5533
11	TraesCS2A01G225800	chr6A	95.106	3433	129	5	2	3397	585368446	585365016	0.000000e+00	5373
12	TraesCS2A01G225800	chr6A	94.240	3420	160	8	1	3396	82613174	82616580	0.000000e+00	5190
13	TraesCS2A01G225800	chr6A	94.920	1929	72	2	1491	3396	225413752	225415677	0.000000e+00	2996
14	TraesCS2A01G225800	chr6A	97.436	78	2	0	3396	3473	234275821	234275898	2.170000e-27	134
15	TraesCS2A01G225800	chr6A	97.436	78	2	0	3396	3473	288374187	288374264	2.170000e-27	134
16	TraesCS2A01G225800	chr6A	97.436	78	2	0	3396	3473	400245748	400245825	2.170000e-27	134
17	TraesCS2A01G225800	chr5A	95.905	3419	117	1	1	3396	276240596	276237178	0.000000e+00	5517
18	TraesCS2A01G225800	chr5A	95.700	3419	124	3	1	3396	38337519	38334101	0.000000e+00	5478
19	TraesCS2A01G225800	chr5A	95.613	3419	127	1	1	3396	690295291	690291873	0.000000e+00	5461
20	TraesCS2A01G225800	chr5A	95.582	3418	117	6	3	3397	534609020	534605614	0.000000e+00	5445
21	TraesCS2A01G225800	chrUn	95.350	3419	107	4	1	3396	33388356	33391745	0.000000e+00	5385
22	TraesCS2A01G225800	chrUn	95.203	3419	113	3	1	3396	33681090	33684480	0.000000e+00	5358
23	TraesCS2A01G225800	chr1A	98.684	76	1	0	3398	3473	437393815	437393740	6.050000e-28	135
24	TraesCS2A01G225800	chr1A	96.341	82	2	1	3392	3473	193928218	193928298	2.170000e-27	134
25	TraesCS2A01G225800	chr1A	97.436	78	2	0	3396	3473	245806713	245806790	2.170000e-27	134
26	TraesCS2A01G225800	chr7A	97.436	78	2	0	3396	3473	118224181	118224258	2.170000e-27	134
27	TraesCS2A01G225800	chr7A	95.238	84	3	1	3390	3473	157713823	157713741	7.820000e-27	132

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	TraesCS2A01G225800	chr2A	232358619	232362091	3472	False	6414	6414	100.000	1	3473	1	chr2A.!!$F2	3472
1	TraesCS2A01G225800	chr2A	772489119	772492537	3418	True	5500	5500	95.819	1	3396	1	chr2A.!!$R2	3395
2	TraesCS2A01G225800	chr2A	505944176	505947602	3426	False	5493	5493	95.711	1	3404	1	chr2A.!!$F3	3403
3	TraesCS2A01G225800	chr2A	719113875	719117295	3420	False	5435	5435	95.444	1	3401	1	chr2A.!!$F4	3400
4	TraesCS2A01G225800	chr2A	52610153	52613558	3405	True	5411	5411	95.408	1	3396	1	chr2A.!!$R1	3395
5	TraesCS2A01G225800	chr2A	24825820	24826584	764	False	1308	1308	97.520	2633	3397	1	chr2A.!!$F1	764
6	TraesCS2A01G225800	chr3A	695817394	695820810	3416	True	5553	5553	96.110	1	3396	1	chr3A.!!$R1	3395
7	TraesCS2A01G225800	chr3A	746704534	746707924	3390	False	5358	5358	95.203	1	3396	1	chr3A.!!$F2	3395
8	TraesCS2A01G225800	chr3A	701106454	701107601	1147	True	1807	1807	95.387	2270	3395	1	chr3A.!!$R2	1125
9	TraesCS2A01G225800	chr6A	158441850	158445266	3416	True	5533	5533	95.994	1	3397	1	chr6A.!!$R1	3396
10	TraesCS2A01G225800	chr6A	585365016	585368446	3430	True	5373	5373	95.106	2	3397	1	chr6A.!!$R2	3395
11	TraesCS2A01G225800	chr6A	82613174	82616580	3406	False	5190	5190	94.240	1	3396	1	chr6A.!!$F1	3395
12	TraesCS2A01G225800	chr6A	225413752	225415677	1925	False	2996	2996	94.920	1491	3396	1	chr6A.!!$F2	1905
13	TraesCS2A01G225800	chr5A	276237178	276240596	3418	True	5517	5517	95.905	1	3396	1	chr5A.!!$R2	3395
14	TraesCS2A01G225800	chr5A	38334101	38337519	3418	True	5478	5478	95.700	1	3396	1	chr5A.!!$R1	3395
15	TraesCS2A01G225800	chr5A	690291873	690295291	3418	True	5461	5461	95.613	1	3396	1	chr5A.!!$R4	3395
16	TraesCS2A01G225800	chr5A	534605614	534609020	3406	True	5445	5445	95.582	3	3397	1	chr5A.!!$R3	3394
17	TraesCS2A01G225800	chrUn	33388356	33391745	3389	False	5385	5385	95.350	1	3396	1	chrUn.!!$F1	3395
18	TraesCS2A01G225800	chrUn	33681090	33684480	3390	False	5358	5358	95.203	1	3396	1	chrUn.!!$F2	3395

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
578	591	0.107993	TCATCTTTGGCTGAGCTCGG	60.108	55.0	18.77	18.77	0.0	4.63	F
1827	1843	0.105778	GCGCTGCTATCCTTCCTTCT	59.894	55.0	0.00	0.00	0.0	2.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2041	2057	0.250513	CCCCTTCTCTTCTTGTCCCG	59.749	60.0	0.00	0.0	0.0	5.14	R
3181	3224	1.078759	GACGCGCTACTGACAATGCT	61.079	55.0	5.73	0.0	0.0	3.79	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
419	420	1.069358	GGCCGTTTTCAATTGGACCAA	59.931	47.619	9.92	9.92	0.00	3.67
578	591	0.107993	TCATCTTTGGCTGAGCTCGG	60.108	55.000	18.77	18.77	0.00	4.63
685	699	1.959282	CAGACTTTTCTTTGCAGGCCT	59.041	47.619	0.00	0.00	0.00	5.19
692	706	2.489938	TCTTTGCAGGCCTACGAAAT	57.510	45.000	3.98	0.00	0.00	2.17
747	761	3.637273	GTGGACGTGGGGAAGGCT	61.637	66.667	0.00	0.00	0.00	4.58
766	780	2.288273	GCTACGATAATGGAGCCGAAGT	60.288	50.000	0.00	0.00	0.00	3.01
835	849	1.525077	GTGGCCAGTGTCAAACCGA	60.525	57.895	5.11	0.00	0.00	4.69
877	891	2.747177	CAGTACTACTGGGGGATGACA	58.253	52.381	8.19	0.00	42.35	3.58
930	944	3.626222	GCAATGTTGGGTGGGTCCTATTA	60.626	47.826	0.00	0.00	36.25	0.98
963	977	3.764466	CTTCGTCTGGAGGCGGCT	61.764	66.667	13.09	13.09	0.00	5.52
1017	1031	2.014128	GGTATGAACATCAACACCCCG	58.986	52.381	0.00	0.00	0.00	5.73
1228	1242	3.893200	ACATATTATGGACGACCTTCCGA	59.107	43.478	5.33	0.00	38.69	4.55
1449	1463	2.168728	GCGGGTAGAGAAAGACCTCATT	59.831	50.000	0.00	0.00	35.91	2.57
1597	1613	6.206498	GTGAAGAAGCTGGATTTTACGTTTT	58.794	36.000	0.00	0.00	0.00	2.43
1764	1780	2.708216	TCATGCTCGCCAATAAGGAA	57.292	45.000	0.00	0.00	41.22	3.36
1827	1843	0.105778	GCGCTGCTATCCTTCCTTCT	59.894	55.000	0.00	0.00	0.00	2.85
1950	1966	2.288825	CCACGCTCTTTACTTGGACTCA	60.289	50.000	0.00	0.00	0.00	3.41
2041	2057	1.002011	GCAAGGGGTGGAGAGGTTC	60.002	63.158	0.00	0.00	0.00	3.62
2104	2121	0.874390	GACCGACTTTTGCTGCATCA	59.126	50.000	1.84	0.00	0.00	3.07
2332	2349	1.139455	AGGAGGTCGTCGGAAAAACAA	59.861	47.619	0.00	0.00	0.00	2.83
2690	2730	8.773645	TGTTGCTCAACTATATATGTTGCATAC	58.226	33.333	13.16	13.74	43.00	2.39
2784	2826	1.003355	CAAGTGGCCGGAGTGTCAT	60.003	57.895	5.05	0.00	0.00	3.06
2883	2925	7.840931	TCATGTTCTCAAAGTGATAGCTCTTA	58.159	34.615	0.00	0.00	0.00	2.10
2928	2970	7.609146	AGATGGATGACGATGTATTTGCATATT	59.391	33.333	0.00	0.00	0.00	1.28
2947	2989	6.308041	GCATATTATTCGAGACTTGTATCGCA	59.692	38.462	12.19	2.95	38.79	5.10
3232	3275	6.280643	ACAGCGTTGCAGATAATATCAGTAA	58.719	36.000	0.00	0.00	0.00	2.24
3371	3414	2.193087	GAGGCCCAAAACCCTCGCTA	62.193	60.000	0.00	0.00	38.38	4.26
3404	3447	2.176889	TCCCTAGTAGTGTGGTCTTGC	58.823	52.381	0.00	0.00	0.00	4.01
3405	3448	2.180276	CCCTAGTAGTGTGGTCTTGCT	58.820	52.381	0.00	0.00	0.00	3.91
3406	3449	2.093973	CCCTAGTAGTGTGGTCTTGCTG	60.094	54.545	0.00	0.00	0.00	4.41
3407	3450	2.093973	CCTAGTAGTGTGGTCTTGCTGG	60.094	54.545	0.00	0.00	0.00	4.85
3408	3451	1.717032	AGTAGTGTGGTCTTGCTGGA	58.283	50.000	0.00	0.00	0.00	3.86
3409	3452	1.344763	AGTAGTGTGGTCTTGCTGGAC	59.655	52.381	1.89	1.89	35.66	4.02
3410	3453	1.344763	GTAGTGTGGTCTTGCTGGACT	59.655	52.381	8.91	0.00	36.55	3.85
3411	3454	0.839946	AGTGTGGTCTTGCTGGACTT	59.160	50.000	8.91	0.00	36.55	3.01
3412	3455	0.947244	GTGTGGTCTTGCTGGACTTG	59.053	55.000	8.91	0.00	36.55	3.16
3413	3456	0.546122	TGTGGTCTTGCTGGACTTGT	59.454	50.000	8.91	0.00	36.55	3.16
3414	3457	1.064758	TGTGGTCTTGCTGGACTTGTT	60.065	47.619	8.91	0.00	36.55	2.83
3415	3458	2.024414	GTGGTCTTGCTGGACTTGTTT	58.976	47.619	8.91	0.00	36.55	2.83
3416	3459	2.427095	GTGGTCTTGCTGGACTTGTTTT	59.573	45.455	8.91	0.00	36.55	2.43
3417	3460	3.630312	GTGGTCTTGCTGGACTTGTTTTA	59.370	43.478	8.91	0.00	36.55	1.52
3418	3461	3.630312	TGGTCTTGCTGGACTTGTTTTAC	59.370	43.478	8.91	0.00	36.55	2.01
3419	3462	3.004419	GGTCTTGCTGGACTTGTTTTACC	59.996	47.826	8.91	0.00	36.55	2.85
3420	3463	3.630312	GTCTTGCTGGACTTGTTTTACCA	59.370	43.478	0.00	0.00	33.81	3.25
3421	3464	4.278419	GTCTTGCTGGACTTGTTTTACCAT	59.722	41.667	0.00	0.00	33.81	3.55
3422	3465	4.892934	TCTTGCTGGACTTGTTTTACCATT	59.107	37.500	0.00	0.00	0.00	3.16
3423	3466	6.016610	GTCTTGCTGGACTTGTTTTACCATTA	60.017	38.462	0.00	0.00	33.81	1.90
3424	3467	6.719370	TCTTGCTGGACTTGTTTTACCATTAT	59.281	34.615	0.00	0.00	0.00	1.28
3425	3468	6.509418	TGCTGGACTTGTTTTACCATTATC	57.491	37.500	0.00	0.00	0.00	1.75
3426	3469	5.123186	TGCTGGACTTGTTTTACCATTATCG	59.877	40.000	0.00	0.00	0.00	2.92
3427	3470	5.353123	GCTGGACTTGTTTTACCATTATCGA	59.647	40.000	0.00	0.00	0.00	3.59
3428	3471	6.456988	GCTGGACTTGTTTTACCATTATCGAG	60.457	42.308	0.00	0.00	0.00	4.04
3429	3472	5.878116	TGGACTTGTTTTACCATTATCGAGG	59.122	40.000	0.00	0.00	0.00	4.63
3430	3473	6.110707	GGACTTGTTTTACCATTATCGAGGA	58.889	40.000	0.00	0.00	0.00	3.71
3431	3474	6.766467	GGACTTGTTTTACCATTATCGAGGAT	59.234	38.462	0.00	0.00	0.00	3.24
3432	3475	7.254795	GGACTTGTTTTACCATTATCGAGGATG	60.255	40.741	0.00	0.00	0.00	3.51
3433	3476	7.110155	ACTTGTTTTACCATTATCGAGGATGT	58.890	34.615	9.22	0.00	0.00	3.06
3434	3477	7.280205	ACTTGTTTTACCATTATCGAGGATGTC	59.720	37.037	9.22	0.00	0.00	3.06
3435	3478	6.884832	TGTTTTACCATTATCGAGGATGTCT	58.115	36.000	9.22	0.00	0.00	3.41
3436	3479	7.335627	TGTTTTACCATTATCGAGGATGTCTT	58.664	34.615	9.22	0.00	0.00	3.01
3437	3480	7.279981	TGTTTTACCATTATCGAGGATGTCTTG	59.720	37.037	9.22	0.00	0.00	3.02
3438	3481	6.479972	TTACCATTATCGAGGATGTCTTGT	57.520	37.500	9.22	3.95	0.00	3.16
3439	3482	7.591421	TTACCATTATCGAGGATGTCTTGTA	57.409	36.000	9.22	3.22	0.00	2.41
3440	3483	6.479972	ACCATTATCGAGGATGTCTTGTAA	57.520	37.500	9.22	0.00	0.00	2.41
3441	3484	6.281405	ACCATTATCGAGGATGTCTTGTAAC	58.719	40.000	9.22	0.00	0.00	2.50
3442	3485	5.696724	CCATTATCGAGGATGTCTTGTAACC	59.303	44.000	9.22	0.00	0.00	2.85
3443	3486	2.933495	TCGAGGATGTCTTGTAACCG	57.067	50.000	0.00	0.00	0.00	4.44
3444	3487	1.475280	TCGAGGATGTCTTGTAACCGG	59.525	52.381	0.00	0.00	0.00	5.28
3445	3488	1.470979	CGAGGATGTCTTGTAACCGGG	60.471	57.143	6.32	0.00	0.00	5.73
3446	3489	1.829222	GAGGATGTCTTGTAACCGGGA	59.171	52.381	6.32	0.00	0.00	5.14
3447	3490	2.434702	GAGGATGTCTTGTAACCGGGAT	59.565	50.000	6.32	0.00	0.00	3.85
3448	3491	2.844348	AGGATGTCTTGTAACCGGGATT	59.156	45.455	6.32	0.00	0.00	3.01
3449	3492	3.118371	AGGATGTCTTGTAACCGGGATTC	60.118	47.826	6.32	0.00	0.00	2.52
3450	3493	2.773993	TGTCTTGTAACCGGGATTCC	57.226	50.000	6.32	0.00	0.00	3.01
3461	3504	3.875838	GGGATTCCGAGTCTGATCG	57.124	57.895	0.00	3.54	42.36	3.69
3462	3505	1.319541	GGGATTCCGAGTCTGATCGA	58.680	55.000	9.87	0.00	45.56	3.59
3463	3506	1.681793	GGGATTCCGAGTCTGATCGAA	59.318	52.381	9.87	4.89	45.56	3.71
3464	3507	2.297597	GGGATTCCGAGTCTGATCGAAT	59.702	50.000	9.87	8.08	45.56	3.34
3465	3508	3.243907	GGGATTCCGAGTCTGATCGAATT	60.244	47.826	9.87	0.00	45.56	2.17
3466	3509	3.738282	GGATTCCGAGTCTGATCGAATTG	59.262	47.826	9.87	0.00	45.56	2.32
3467	3510	3.868757	TTCCGAGTCTGATCGAATTGT	57.131	42.857	9.87	0.00	45.56	2.71
3468	3511	3.422417	TCCGAGTCTGATCGAATTGTC	57.578	47.619	9.87	0.00	45.56	3.18
3469	3512	3.017442	TCCGAGTCTGATCGAATTGTCT	58.983	45.455	9.87	0.00	45.56	3.41
3470	3513	3.444034	TCCGAGTCTGATCGAATTGTCTT	59.556	43.478	9.87	0.00	45.56	3.01
3471	3514	3.549471	CCGAGTCTGATCGAATTGTCTTG	59.451	47.826	9.87	0.00	45.56	3.02
3472	3515	3.549471	CGAGTCTGATCGAATTGTCTTGG	59.451	47.826	0.00	0.00	45.56	3.61

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
64	65	1.450134	CTGCCGCAATCCTGTGCTA	60.450	57.895	0.00	0.00	42.62	3.49
81	82	2.048127	GACGGCGAGTGGCTTTCT	60.048	61.111	16.62	0.00	42.94	2.52
505	506	4.341783	GGGAGCAGGTGCAGCTGT	62.342	66.667	37.97	27.42	43.58	4.40
685	699	0.250793	ATGGTGCACGGGATTTCGTA	59.749	50.000	11.45	0.00	41.86	3.43
692	706	1.555533	TGTACAATATGGTGCACGGGA	59.444	47.619	11.45	0.00	0.00	5.14
747	761	4.261741	GGTTACTTCGGCTCCATTATCGTA	60.262	45.833	0.00	0.00	0.00	3.43
804	818	1.104577	TGGCCACGGAAACCTTGAAC	61.105	55.000	0.00	0.00	0.00	3.18
930	944	1.831580	GAAGCAGACTCTTTGGCCAT	58.168	50.000	6.09	0.00	0.00	4.40
1017	1031	1.607251	CCCGACGATAATTGGGTAGGC	60.607	57.143	0.00	0.00	38.41	3.93
1228	1242	8.192110	CGCTCTCTTCCTAAACTTCTTTACTAT	58.808	37.037	0.00	0.00	0.00	2.12
1449	1463	3.827302	GGTATCCTAGATCTTTCGAGGCA	59.173	47.826	0.00	0.00	42.71	4.75
1827	1843	6.530887	CACCGTGCAAATGAATGATTGAAATA	59.469	34.615	0.00	0.00	0.00	1.40
1906	1922	2.090719	AGAATCGGGGGTAGAGGATGAA	60.091	50.000	0.00	0.00	0.00	2.57
1950	1966	6.633500	TCCTTTTTGTGAATGTTCTTCGAT	57.367	33.333	0.00	0.00	0.00	3.59
1998	2014	4.178540	GGTAGTAAAACATAGCGCTGTCA	58.821	43.478	22.90	0.00	0.00	3.58
2004	2020	5.447279	CCTTGCTTGGTAGTAAAACATAGCG	60.447	44.000	0.00	0.00	32.86	4.26
2041	2057	0.250513	CCCCTTCTCTTCTTGTCCCG	59.749	60.000	0.00	0.00	0.00	5.14
2104	2121	2.457366	AGAGAATCGTTCGGTTGCTT	57.543	45.000	0.00	0.00	42.67	3.91
2332	2349	3.025262	GTCCTTCTCCGTAGAACATCCT	58.975	50.000	0.00	0.00	36.80	3.24
2526	2543	4.518970	AGTTTCACCGTGCATAACTCAAAT	59.481	37.500	0.00	0.00	0.00	2.32
2572	2589	0.250553	CGCTAGTCGAGGAGGAGGAT	60.251	60.000	0.98	0.00	41.67	3.24
2603	2620	2.810164	GTACCCCAAAATGCCCTAACA	58.190	47.619	0.00	0.00	0.00	2.41
2690	2730	2.479275	GCATCATCACATGAGTCGATGG	59.521	50.000	18.37	7.97	43.53	3.51
2883	2925	7.320399	TCCATCTAAACAATGATATACGCGAT	58.680	34.615	15.93	4.50	0.00	4.58
2928	2970	7.514591	CGAAAATTGCGATACAAGTCTCGAATA	60.515	37.037	11.46	0.00	42.87	1.75
2947	2989	5.746245	GTCTCTCGTCATCATCTCGAAAATT	59.254	40.000	0.00	0.00	33.32	1.82
3174	3217	2.477825	CTACTGACAATGCTGCGCTAT	58.522	47.619	9.73	0.00	0.00	2.97
3181	3224	1.078759	GACGCGCTACTGACAATGCT	61.079	55.000	5.73	0.00	0.00	3.79
3232	3275	4.821935	CTCTTTGGGAAAGGGCGT	57.178	55.556	0.00	0.00	39.01	5.68
3281	3324	2.995574	AGTAGCGCCGGTTGTCCT	60.996	61.111	2.29	0.00	0.00	3.85
3371	3414	2.917205	ACTAGGGAAAAGCCTACCAGT	58.083	47.619	0.00	0.00	36.66	4.00
3404	3447	6.037172	CCTCGATAATGGTAAAACAAGTCCAG	59.963	42.308	0.00	0.00	33.33	3.86
3405	3448	5.878116	CCTCGATAATGGTAAAACAAGTCCA	59.122	40.000	0.00	0.00	0.00	4.02
3406	3449	6.110707	TCCTCGATAATGGTAAAACAAGTCC	58.889	40.000	0.00	0.00	0.00	3.85
3407	3450	7.280205	ACATCCTCGATAATGGTAAAACAAGTC	59.720	37.037	10.78	0.00	0.00	3.01
3408	3451	7.110155	ACATCCTCGATAATGGTAAAACAAGT	58.890	34.615	10.78	0.00	0.00	3.16
3409	3452	7.495934	AGACATCCTCGATAATGGTAAAACAAG	59.504	37.037	10.78	0.00	0.00	3.16
3410	3453	7.335627	AGACATCCTCGATAATGGTAAAACAA	58.664	34.615	10.78	0.00	0.00	2.83
3411	3454	6.884832	AGACATCCTCGATAATGGTAAAACA	58.115	36.000	10.78	0.00	0.00	2.83
3412	3455	7.280205	ACAAGACATCCTCGATAATGGTAAAAC	59.720	37.037	10.78	0.00	0.00	2.43
3413	3456	7.335627	ACAAGACATCCTCGATAATGGTAAAA	58.664	34.615	10.78	0.00	0.00	1.52
3414	3457	6.884832	ACAAGACATCCTCGATAATGGTAAA	58.115	36.000	10.78	0.00	0.00	2.01
3415	3458	6.479972	ACAAGACATCCTCGATAATGGTAA	57.520	37.500	10.78	0.00	0.00	2.85
3416	3459	7.431249	GTTACAAGACATCCTCGATAATGGTA	58.569	38.462	10.78	2.64	0.00	3.25
3417	3460	6.281405	GTTACAAGACATCCTCGATAATGGT	58.719	40.000	10.78	3.37	0.00	3.55
3418	3461	5.696724	GGTTACAAGACATCCTCGATAATGG	59.303	44.000	10.78	0.00	0.00	3.16
3419	3462	5.402568	CGGTTACAAGACATCCTCGATAATG	59.597	44.000	5.80	5.80	0.00	1.90
3420	3463	5.509163	CCGGTTACAAGACATCCTCGATAAT	60.509	44.000	0.00	0.00	0.00	1.28
3421	3464	4.202080	CCGGTTACAAGACATCCTCGATAA	60.202	45.833	0.00	0.00	0.00	1.75
3422	3465	3.317149	CCGGTTACAAGACATCCTCGATA	59.683	47.826	0.00	0.00	0.00	2.92
3423	3466	2.100916	CCGGTTACAAGACATCCTCGAT	59.899	50.000	0.00	0.00	0.00	3.59
3424	3467	1.475280	CCGGTTACAAGACATCCTCGA	59.525	52.381	0.00	0.00	0.00	4.04
3425	3468	1.470979	CCCGGTTACAAGACATCCTCG	60.471	57.143	0.00	0.00	0.00	4.63
3426	3469	1.829222	TCCCGGTTACAAGACATCCTC	59.171	52.381	0.00	0.00	0.00	3.71
3427	3470	1.946984	TCCCGGTTACAAGACATCCT	58.053	50.000	0.00	0.00	0.00	3.24
3428	3471	3.203716	GAATCCCGGTTACAAGACATCC	58.796	50.000	0.00	0.00	0.00	3.51
3429	3472	3.203716	GGAATCCCGGTTACAAGACATC	58.796	50.000	0.00	0.00	0.00	3.06
3430	3473	3.277142	GGAATCCCGGTTACAAGACAT	57.723	47.619	0.00	0.00	0.00	3.06
3431	3474	2.773993	GGAATCCCGGTTACAAGACA	57.226	50.000	0.00	0.00	0.00	3.41
3443	3486	1.319541	TCGATCAGACTCGGAATCCC	58.680	55.000	0.00	0.00	39.13	3.85
3444	3487	3.651803	ATTCGATCAGACTCGGAATCC	57.348	47.619	0.00	0.00	39.13	3.01
3445	3488	4.363999	ACAATTCGATCAGACTCGGAATC	58.636	43.478	0.00	0.00	39.13	2.52
3446	3489	4.098654	AGACAATTCGATCAGACTCGGAAT	59.901	41.667	0.00	0.00	39.13	3.01
3447	3490	3.444034	AGACAATTCGATCAGACTCGGAA	59.556	43.478	0.00	0.00	39.13	4.30
3448	3491	3.017442	AGACAATTCGATCAGACTCGGA	58.983	45.455	0.00	0.00	39.13	4.55
3449	3492	3.428746	AGACAATTCGATCAGACTCGG	57.571	47.619	0.00	0.00	39.13	4.63
3450	3493	3.549471	CCAAGACAATTCGATCAGACTCG	59.451	47.826	0.00	0.00	39.99	4.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.