AutoCloner

Multiple sequence alignment - TraesCS2A01G074200

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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	TraesCS2A01G074200	chr2A	100.000	3513	0	0	1	3513	32553194	32556706	0.000000e+00	6488.0
1	TraesCS2A01G074200	chr2A	86.654	1064	79	28	468	1485	32772452	32773498	0.000000e+00	1120.0
2	TraesCS2A01G074200	chr2A	84.969	958	90	24	1567	2493	32773497	32774431	0.000000e+00	922.0
3	TraesCS2A01G074200	chr2A	79.257	834	133	24	1688	2491	32875912	32876735	2.380000e-151	545.0
4	TraesCS2A01G074200	chr2A	86.071	481	39	13	2027	2491	32857038	32857506	3.150000e-135	492.0
5	TraesCS2A01G074200	chr2A	86.765	340	30	6	2167	2491	32818043	32818382	7.170000e-97	364.0
6	TraesCS2A01G074200	chr2A	79.883	512	85	9	980	1485	32863562	32864061	3.330000e-95	359.0
7	TraesCS2A01G074200	chr2A	81.092	476	56	10	1567	2030	32821096	32821549	2.010000e-92	350.0
8	TraesCS2A01G074200	chr2A	86.012	336	20	12	115	448	32758832	32759142	5.620000e-88	335.0
9	TraesCS2A01G074200	chr2A	86.916	214	28	0	1267	1480	32820871	32821084	1.260000e-59	241.0
10	TraesCS2A01G074200	chr2A	92.308	91	7	0	1479	1569	133985009	133985099	2.850000e-26	130.0
11	TraesCS2A01G074200	chr2A	92.308	91	7	0	1483	1573	686654619	686654529	2.850000e-26	130.0
12	TraesCS2A01G074200	chr2A	96.078	51	1	1	782	832	32553877	32553926	8.080000e-12	82.4
13	TraesCS2A01G074200	chr2A	96.078	51	1	1	684	733	32553975	32554025	8.080000e-12	82.4
14	TraesCS2A01G074200	chr2A	96.078	51	1	1	782	832	32772666	32772715	8.080000e-12	82.4
15	TraesCS2A01G074200	chr2A	92.857	56	4	0	680	735	32772789	32772844	8.080000e-12	82.4
16	TraesCS2A01G074200	chr2A	100.000	38	0	0	436	473	32759156	32759193	1.750000e-08	71.3
17	TraesCS2A01G074200	chr2B	98.434	1022	16	0	2492	3513	46005255	46006276	0.000000e+00	1799.0
18	TraesCS2A01G074200	chr2B	93.665	1026	57	5	2491	3513	752878105	752879125	0.000000e+00	1528.0
19	TraesCS2A01G074200	chr2B	90.441	680	54	4	680	1353	50392403	50393077	0.000000e+00	885.0
20	TraesCS2A01G074200	chr2B	84.238	958	98	30	1567	2493	50401576	50402511	0.000000e+00	883.0
21	TraesCS2A01G074200	chr2B	93.631	471	26	2	115	581	50364658	50365128	0.000000e+00	701.0
22	TraesCS2A01G074200	chr2B	81.655	556	89	8	1944	2491	50524181	50523631	1.920000e-122	449.0
23	TraesCS2A01G074200	chr2B	95.312	256	10	1	577	832	50392203	50392456	4.220000e-109	405.0
24	TraesCS2A01G074200	chr2B	89.655	145	15	0	1341	1485	50401433	50401577	5.990000e-43	185.0
25	TraesCS2A01G074200	chr2B	94.643	56	3	0	680	735	50392502	50392557	1.740000e-13	87.9
26	TraesCS2A01G074200	chr2B	96.078	51	1	1	782	832	50392308	50392357	8.080000e-12	82.4
27	TraesCS2A01G074200	chrUn	98.145	1024	15	3	2492	3513	50428650	50427629	0.000000e+00	1783.0
28	TraesCS2A01G074200	chrUn	97.860	1028	16	4	2491	3513	316447080	316448106	0.000000e+00	1772.0
29	TraesCS2A01G074200	chrUn	93.404	1031	58	8	2491	3513	85702456	85703484	0.000000e+00	1519.0
30	TraesCS2A01G074200	chrUn	100.000	119	0	0	1	119	183179652	183179770	1.640000e-53	220.0
31	TraesCS2A01G074200	chr5A	98.143	1023	17	2	2492	3513	687366705	687367726	0.000000e+00	1783.0
32	TraesCS2A01G074200	chr5A	93.478	92	6	0	1478	1569	617361975	617361884	1.700000e-28	137.0
33	TraesCS2A01G074200	chr4A	98.143	1023	16	2	2492	3513	703441491	703440471	0.000000e+00	1781.0
34	TraesCS2A01G074200	chr4A	97.663	1027	19	3	2492	3513	26414813	26415839	0.000000e+00	1759.0
35	TraesCS2A01G074200	chr4A	100.000	119	0	0	1	119	36531944	36531826	1.640000e-53	220.0
36	TraesCS2A01G074200	chr5B	94.049	1025	53	6	2492	3513	576073634	576074653	0.000000e+00	1548.0
37	TraesCS2A01G074200	chr2D	95.021	723	29	3	115	832	30610658	30611378	0.000000e+00	1129.0
38	TraesCS2A01G074200	chr2D	85.714	952	89	20	1567	2491	30612219	30613150	0.000000e+00	961.0
39	TraesCS2A01G074200	chr2D	90.057	704	57	4	790	1485	30611522	30612220	0.000000e+00	900.0
40	TraesCS2A01G074200	chr2D	74.558	904	164	43	1632	2477	30653698	30654593	5.620000e-88	335.0
41	TraesCS2A01G074200	chr2D	91.270	126	11	0	2366	2491	402929024	402928899	4.660000e-39	172.0
42	TraesCS2A01G074200	chr2D	96.386	83	3	0	980	1062	30618660	30618742	1.700000e-28	137.0
43	TraesCS2A01G074200	chr2D	87.179	117	11	1	680	792	30611325	30611441	2.850000e-26	130.0
44	TraesCS2A01G074200	chr2D	92.308	91	7	0	1482	1572	563959331	563959241	2.850000e-26	130.0
45	TraesCS2A01G074200	chr2D	96.078	51	1	1	782	832	30611230	30611279	8.080000e-12	82.4
46	TraesCS2A01G074200	chr6B	99.213	127	0	1	1	127	719772654	719772529	9.810000e-56	228.0
47	TraesCS2A01G074200	chr6B	100.000	119	0	0	1	119	669998192	669998074	1.640000e-53	220.0
48	TraesCS2A01G074200	chr7B	100.000	119	0	0	1	119	610585918	610585800	1.640000e-53	220.0
49	TraesCS2A01G074200	chr7A	100.000	119	0	0	1	119	39314070	39314188	1.640000e-53	220.0
50	TraesCS2A01G074200	chr7A	100.000	119	0	0	1	119	485182937	485182819	1.640000e-53	220.0
51	TraesCS2A01G074200	chr3A	99.174	121	1	0	1	121	141963124	141963244	5.900000e-53	219.0
52	TraesCS2A01G074200	chr4B	98.333	120	2	0	1	120	657307427	657307308	9.880000e-51	211.0
53	TraesCS2A01G074200	chr4B	96.512	86	3	0	1485	1570	193802769	193802854	3.660000e-30	143.0
54	TraesCS2A01G074200	chr3B	94.253	87	5	0	1483	1569	243091205	243091291	2.200000e-27	134.0
55	TraesCS2A01G074200	chr1B	93.333	90	6	0	1480	1569	8153398	8153309	2.200000e-27	134.0
56	TraesCS2A01G074200	chr6A	93.258	89	6	0	1481	1569	103372569	103372657	7.910000e-27	132.0
57	TraesCS2A01G074200	chr6D	92.308	91	7	0	1479	1569	437959828	437959738	2.850000e-26	130.0

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	TraesCS2A01G074200	chr2A	32553194	32556706	3512	False	2217.600000	6488	97.385333	1	3513	3	chr2A.!!$F5	3512
1	TraesCS2A01G074200	chr2A	32772452	32774431	1979	False	551.700000	1120	90.139500	468	2493	4	chr2A.!!$F7	2025
2	TraesCS2A01G074200	chr2A	32875912	32876735	823	False	545.000000	545	79.257000	1688	2491	1	chr2A.!!$F3	803
3	TraesCS2A01G074200	chr2A	32818043	32821549	3506	False	318.333333	364	84.924333	1267	2491	3	chr2A.!!$F8	1224
4	TraesCS2A01G074200	chr2B	46005255	46006276	1021	False	1799.000000	1799	98.434000	2492	3513	1	chr2B.!!$F1	1021
5	TraesCS2A01G074200	chr2B	752878105	752879125	1020	False	1528.000000	1528	93.665000	2491	3513	1	chr2B.!!$F3	1022
6	TraesCS2A01G074200	chr2B	50401433	50402511	1078	False	534.000000	883	86.946500	1341	2493	2	chr2B.!!$F5	1152
7	TraesCS2A01G074200	chr2B	50523631	50524181	550	True	449.000000	449	81.655000	1944	2491	1	chr2B.!!$R1	547
8	TraesCS2A01G074200	chr2B	50392203	50393077	874	False	365.075000	885	94.118500	577	1353	4	chr2B.!!$F4	776
9	TraesCS2A01G074200	chrUn	50427629	50428650	1021	True	1783.000000	1783	98.145000	2492	3513	1	chrUn.!!$R1	1021
10	TraesCS2A01G074200	chrUn	316447080	316448106	1026	False	1772.000000	1772	97.860000	2491	3513	1	chrUn.!!$F3	1022
11	TraesCS2A01G074200	chrUn	85702456	85703484	1028	False	1519.000000	1519	93.404000	2491	3513	1	chrUn.!!$F1	1022
12	TraesCS2A01G074200	chr5A	687366705	687367726	1021	False	1783.000000	1783	98.143000	2492	3513	1	chr5A.!!$F1	1021
13	TraesCS2A01G074200	chr4A	703440471	703441491	1020	True	1781.000000	1781	98.143000	2492	3513	1	chr4A.!!$R2	1021
14	TraesCS2A01G074200	chr4A	26414813	26415839	1026	False	1759.000000	1759	97.663000	2492	3513	1	chr4A.!!$F1	1021
15	TraesCS2A01G074200	chr5B	576073634	576074653	1019	False	1548.000000	1548	94.049000	2492	3513	1	chr5B.!!$F1	1021
16	TraesCS2A01G074200	chr2D	30610658	30613150	2492	False	640.480000	1129	90.809800	115	2491	5	chr2D.!!$F3	2376
17	TraesCS2A01G074200	chr2D	30653698	30654593	895	False	335.000000	335	74.558000	1632	2477	1	chr2D.!!$F2	845

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
79	80	0.249955	AAAATTCAATGGGCTGGGCG	59.750	50.0	0.00	0.0	0.0	6.13	F
1425	2988	0.105760	AGTCTGGGGAGATCGATGCT	60.106	55.0	0.54	0.0	0.0	3.79	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1793	3376	0.032678	CCCGGCAGTAGACAGCATAG	59.967	60.0	0.00	0.0	0.00	2.23	R
2560	4211	0.032267	GGACCTAGCTGTCGGCATAC	59.968	60.0	6.39	0.0	44.79	2.39	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
44	45	3.021451	CTGTTTTCAGGCCCGAACT	57.979	52.632	0.00	0.00	43.61	3.01
45	46	2.178912	CTGTTTTCAGGCCCGAACTA	57.821	50.000	0.00	0.00	43.61	2.24
46	47	2.076863	CTGTTTTCAGGCCCGAACTAG	58.923	52.381	0.00	0.00	43.61	2.57
47	48	1.695242	TGTTTTCAGGCCCGAACTAGA	59.305	47.619	0.00	0.00	0.00	2.43
50	51	4.163458	TGTTTTCAGGCCCGAACTAGATAT	59.837	41.667	0.00	0.00	0.00	1.63
52	53	6.042781	TGTTTTCAGGCCCGAACTAGATATAT	59.957	38.462	0.00	0.00	0.00	0.86
53	54	7.233962	TGTTTTCAGGCCCGAACTAGATATATA	59.766	37.037	0.00	0.00	0.00	0.86
54	55	7.406031	TTTCAGGCCCGAACTAGATATATAG	57.594	40.000	0.00	2.77	0.00	1.31
56	57	5.886474	TCAGGCCCGAACTAGATATATAGTG	59.114	44.000	10.69	0.00	36.14	2.74
58	59	6.827251	CAGGCCCGAACTAGATATATAGTGTA	59.173	42.308	10.69	0.00	36.14	2.90
59	60	7.502895	CAGGCCCGAACTAGATATATAGTGTAT	59.497	40.741	10.69	0.00	36.14	2.29
61	62	9.347240	GGCCCGAACTAGATATATAGTGTATAA	57.653	37.037	10.69	0.00	36.14	0.98
76	77	6.469782	AGTGTATAAAATTCAATGGGCTGG	57.530	37.500	0.00	0.00	0.00	4.85
77	78	5.363580	AGTGTATAAAATTCAATGGGCTGGG	59.636	40.000	0.00	0.00	0.00	4.45
78	79	3.843893	ATAAAATTCAATGGGCTGGGC	57.156	42.857	0.00	0.00	0.00	5.36
79	80	0.249955	AAAATTCAATGGGCTGGGCG	59.750	50.000	0.00	0.00	0.00	6.13
81	82	4.757355	TTCAATGGGCTGGGCGGG	62.757	66.667	0.00	0.00	0.00	6.13
112	113	2.046507	AGCCTTGCTGAAGCTCCG	60.047	61.111	3.61	0.00	42.66	4.63
113	114	3.808656	GCCTTGCTGAAGCTCCGC	61.809	66.667	3.61	0.00	42.66	5.54
183	184	8.465201	AGTGCAATCTAAGAGGAAATTTTGATC	58.535	33.333	0.00	0.00	0.00	2.92
193	194	6.543831	AGAGGAAATTTTGATCGGAACTATGG	59.456	38.462	0.00	0.00	0.00	2.74
194	195	5.067805	AGGAAATTTTGATCGGAACTATGGC	59.932	40.000	0.00	0.00	0.00	4.40
275	276	2.354510	TGTAGTTGCACACTTTGAGCAC	59.645	45.455	6.82	0.59	43.28	4.40
292	293	3.326747	AGCACGTCTAAACTGAATCCAC	58.673	45.455	0.00	0.00	0.00	4.02
327	328	1.482182	CTGGGATCGATGGAACTGTCA	59.518	52.381	0.54	0.00	0.00	3.58
338	339	5.163913	CGATGGAACTGTCAGTGAATCTTTC	60.164	44.000	6.18	0.00	0.00	2.62
374	375	6.948228	CGATTATCTTTCATTATAACCGTGCG	59.052	38.462	0.00	0.00	0.00	5.34
399	400	7.037438	GGACTGTAATGTCGGAACACTATAAA	58.963	38.462	0.00	0.00	38.48	1.40
401	402	7.039882	ACTGTAATGTCGGAACACTATAAAGG	58.960	38.462	0.00	0.00	38.48	3.11
416	417	8.963725	ACACTATAAAGGCCAGGTAAAAATAAC	58.036	33.333	5.01	0.00	0.00	1.89
444	449	7.685481	TCCTTTGTTTCTAACCAGTATCATCA	58.315	34.615	0.00	0.00	0.00	3.07
590	597	7.810759	CCCGTTTTGTGTTTTATAGCTTTGTAT	59.189	33.333	0.00	0.00	0.00	2.29
591	598	9.828852	CCGTTTTGTGTTTTATAGCTTTGTATA	57.171	29.630	0.00	0.00	0.00	1.47
627	634	2.053747	TAGTGGACCCAAAGACCCAT	57.946	50.000	0.00	0.00	0.00	4.00
673	680	3.458189	AGTGGAGAAGTCTTCAAACACG	58.542	45.455	14.97	0.00	32.30	4.49
913	1226	2.928801	AATAGTCCACACAGCACACA	57.071	45.000	0.00	0.00	0.00	3.72
947	1260	2.330924	ATCTTTGCCCTAGCCGCCTC	62.331	60.000	0.00	0.00	38.69	4.70
955	1268	1.175983	CCTAGCCGCCTCTACTCCAG	61.176	65.000	0.00	0.00	0.00	3.86
956	1269	0.466555	CTAGCCGCCTCTACTCCAGT	60.467	60.000	0.00	0.00	0.00	4.00
1041	1361	2.174319	GGAGGAATTGCTCGCCGAC	61.174	63.158	19.27	2.96	0.00	4.79
1122	1442	2.398554	GGGCATCATCAACGCACGT	61.399	57.895	0.00	0.00	0.00	4.49
1218	1538	2.602267	TTCTTCGCCCGTCCCTCA	60.602	61.111	0.00	0.00	0.00	3.86
1230	1550	4.722700	CCCTCAACAGGCCCCACG	62.723	72.222	0.00	0.00	38.72	4.94
1260	1580	2.120940	TTCGACTACCTGCCCCCA	59.879	61.111	0.00	0.00	0.00	4.96
1261	1581	2.288025	TTCGACTACCTGCCCCCAC	61.288	63.158	0.00	0.00	0.00	4.61
1262	1582	3.000819	CGACTACCTGCCCCCACA	61.001	66.667	0.00	0.00	0.00	4.17
1265	1585	1.541368	ACTACCTGCCCCCACACAT	60.541	57.895	0.00	0.00	0.00	3.21
1266	1586	1.140134	ACTACCTGCCCCCACACATT	61.140	55.000	0.00	0.00	0.00	2.71
1267	1587	0.680921	CTACCTGCCCCCACACATTG	60.681	60.000	0.00	0.00	0.00	2.82
1268	1588	2.148723	TACCTGCCCCCACACATTGG	62.149	60.000	0.00	0.00	46.47	3.16
1293	2856	5.019785	ACTCCCAGTATCGTGGTAAAATC	57.980	43.478	0.00	0.00	35.60	2.17
1302	2865	4.665833	TCGTGGTAAAATCGAGGATCAT	57.334	40.909	0.00	0.00	33.17	2.45
1315	2878	2.035576	GAGGATCATTGCAATGGCCTTC	59.964	50.000	34.73	27.40	39.77	3.46
1410	2973	1.352352	CACCCTTCCATGTCCAAGTCT	59.648	52.381	0.00	0.00	0.00	3.24
1411	2974	1.352352	ACCCTTCCATGTCCAAGTCTG	59.648	52.381	0.00	0.00	0.00	3.51
1412	2975	1.340405	CCCTTCCATGTCCAAGTCTGG	60.340	57.143	0.00	0.00	45.08	3.86
1419	2982	1.573108	TGTCCAAGTCTGGGGAGATC	58.427	55.000	0.00	0.00	43.71	2.75
1425	2988	0.105760	AGTCTGGGGAGATCGATGCT	60.106	55.000	0.54	0.00	0.00	3.79
1433	2996	2.468831	GGAGATCGATGCTGACTTCAC	58.531	52.381	0.54	0.00	0.00	3.18
1450	3013	5.084519	ACTTCACATACCAAGAGTACCTCA	58.915	41.667	0.00	0.00	32.46	3.86
1452	3015	5.854010	TCACATACCAAGAGTACCTCATC	57.146	43.478	0.00	0.00	32.46	2.92
1485	3056	3.752868	CGGTATCACCCCACTATCAGGTA	60.753	52.174	0.00	0.00	33.75	3.08
1486	3057	3.577415	GGTATCACCCCACTATCAGGTAC	59.423	52.174	0.00	0.00	30.98	3.34
1487	3058	3.708236	ATCACCCCACTATCAGGTACT	57.292	47.619	0.00	0.00	43.88	2.73
1488	3059	3.028094	TCACCCCACTATCAGGTACTC	57.972	52.381	0.00	0.00	34.60	2.59
1489	3060	2.040178	CACCCCACTATCAGGTACTCC	58.960	57.143	0.00	0.00	34.60	3.85
1490	3061	1.062352	ACCCCACTATCAGGTACTCCC	60.062	57.143	0.00	0.00	34.60	4.30
1492	3063	2.599677	CCCACTATCAGGTACTCCCTC	58.400	57.143	0.00	0.00	43.86	4.30
1493	3064	2.599677	CCACTATCAGGTACTCCCTCC	58.400	57.143	0.00	0.00	43.86	4.30
1494	3065	2.231529	CACTATCAGGTACTCCCTCCG	58.768	57.143	0.00	0.00	43.86	4.63
1495	3066	1.851653	ACTATCAGGTACTCCCTCCGT	59.148	52.381	0.00	0.00	43.86	4.69
1496	3067	3.051581	ACTATCAGGTACTCCCTCCGTA	58.948	50.000	0.00	0.00	43.86	4.02
1497	3068	3.461085	ACTATCAGGTACTCCCTCCGTAA	59.539	47.826	0.00	0.00	43.86	3.18
1498	3069	2.905415	TCAGGTACTCCCTCCGTAAA	57.095	50.000	0.00	0.00	43.86	2.01
1499	3070	2.450476	TCAGGTACTCCCTCCGTAAAC	58.550	52.381	0.00	0.00	43.86	2.01
1500	3071	2.042162	TCAGGTACTCCCTCCGTAAACT	59.958	50.000	0.00	0.00	43.86	2.66
1501	3072	3.266772	TCAGGTACTCCCTCCGTAAACTA	59.733	47.826	0.00	0.00	43.86	2.24
1502	3073	4.019174	CAGGTACTCCCTCCGTAAACTAA	58.981	47.826	0.00	0.00	43.86	2.24
1503	3074	4.648307	CAGGTACTCCCTCCGTAAACTAAT	59.352	45.833	0.00	0.00	43.86	1.73
1504	3075	5.829924	CAGGTACTCCCTCCGTAAACTAATA	59.170	44.000	0.00	0.00	43.86	0.98
1505	3076	6.492772	CAGGTACTCCCTCCGTAAACTAATAT	59.507	42.308	0.00	0.00	43.86	1.28
1506	3077	7.667219	CAGGTACTCCCTCCGTAAACTAATATA	59.333	40.741	0.00	0.00	43.86	0.86
1507	3078	8.227507	AGGTACTCCCTCCGTAAACTAATATAA	58.772	37.037	0.00	0.00	40.71	0.98
1508	3079	8.518702	GGTACTCCCTCCGTAAACTAATATAAG	58.481	40.741	0.00	0.00	0.00	1.73
1509	3080	9.289782	GTACTCCCTCCGTAAACTAATATAAGA	57.710	37.037	0.00	0.00	0.00	2.10
1510	3081	8.773033	ACTCCCTCCGTAAACTAATATAAGAA	57.227	34.615	0.00	0.00	0.00	2.52
1511	3082	8.637099	ACTCCCTCCGTAAACTAATATAAGAAC	58.363	37.037	0.00	0.00	0.00	3.01
1512	3083	8.537728	TCCCTCCGTAAACTAATATAAGAACA	57.462	34.615	0.00	0.00	0.00	3.18
1513	3084	9.151177	TCCCTCCGTAAACTAATATAAGAACAT	57.849	33.333	0.00	0.00	0.00	2.71
1514	3085	9.774413	CCCTCCGTAAACTAATATAAGAACATT	57.226	33.333	0.00	0.00	0.00	2.71
1588	3159	7.442666	GGGAGTATTTGTGATCTCAAATCCTAC	59.557	40.741	29.43	25.11	43.87	3.18
1590	3161	6.986817	AGTATTTGTGATCTCAAATCCTACGG	59.013	38.462	29.43	0.00	43.87	4.02
1596	3167	3.644966	TCTCAAATCCTACGGGCAAAT	57.355	42.857	0.00	0.00	0.00	2.32
1597	3168	3.278574	TCTCAAATCCTACGGGCAAATG	58.721	45.455	0.00	0.00	0.00	2.32
1607	3178	3.200522	GGCAAATGGAAGCCCGAG	58.799	61.111	0.00	0.00	45.18	4.63
1616	3187	1.667154	GGAAGCCCGAGGATTTTGGC	61.667	60.000	0.00	0.00	44.35	4.52
1626	3197	3.372206	CGAGGATTTTGGCTACAACAGAG	59.628	47.826	0.00	0.00	36.06	3.35
1628	3199	2.819608	GGATTTTGGCTACAACAGAGCA	59.180	45.455	0.00	0.00	41.98	4.26
1644	3215	5.748402	ACAGAGCATTGGATGAATTAGACA	58.252	37.500	0.00	0.00	0.00	3.41
1679	3250	1.355381	TCTGAATGGCCACCATCTGTT	59.645	47.619	8.16	0.00	44.40	3.16
1682	3253	1.895131	GAATGGCCACCATCTGTTTGT	59.105	47.619	8.16	0.00	44.40	2.83
1685	3256	1.290009	GCCACCATCTGTTTGTGCC	59.710	57.895	0.00	0.00	0.00	5.01
1686	3257	1.966762	CCACCATCTGTTTGTGCCC	59.033	57.895	0.00	0.00	0.00	5.36
1706	3277	0.944311	TGCACGTTTTCTCCTCGAGC	60.944	55.000	6.99	0.00	40.34	5.03
1756	3327	1.910722	GAGATGGGAAGGCTGCAGA	59.089	57.895	20.43	0.00	0.00	4.26
1793	3376	1.797537	GCGGCATTTCGACAAGCAC	60.798	57.895	0.88	0.00	0.00	4.40
1861	3445	7.736893	ACTGATTTCATAATGAGGTACCTACC	58.263	38.462	16.29	3.70	46.82	3.18
1878	3463	6.449830	ACCTACCCACTCTCTTTAAACATT	57.550	37.500	0.00	0.00	0.00	2.71
1967	3560	8.200792	TGTTTATTAACAATTTCTTGTGCAGGT	58.799	29.630	0.00	0.00	44.83	4.00
1989	3582	8.019669	CAGGTTCTCTTTGTCAAATGATAAGTG	58.980	37.037	0.00	6.25	0.00	3.16
2026	3619	1.475034	CCGATACATGGTGAACTGGGG	60.475	57.143	0.00	0.00	0.00	4.96
2052	3645	1.272092	CCCAAAGCTCCATCTTGGACA	60.272	52.381	14.49	0.00	42.67	4.02
2056	3649	4.015084	CAAAGCTCCATCTTGGACAATCT	58.985	43.478	0.00	0.00	42.67	2.40
2080	3676	3.740364	AGGGGTCTACCTTGCATCT	57.260	52.632	0.00	0.00	37.69	2.90
2081	3677	2.868964	AGGGGTCTACCTTGCATCTA	57.131	50.000	0.00	0.00	37.69	1.98
2082	3678	3.352611	AGGGGTCTACCTTGCATCTAT	57.647	47.619	0.00	0.00	37.69	1.98
2091	3717	7.067494	GGTCTACCTTGCATCTATTTGTGAAAT	59.933	37.037	0.00	0.00	34.90	2.17
2131	3757	0.677288	TCCTTGACGAATCGTGTGGT	59.323	50.000	14.87	0.00	41.37	4.16
2165	3791	3.253188	GGTCTTGAAGCATAACAGTTGCA	59.747	43.478	0.00	0.00	42.62	4.08
2195	3824	5.656859	CCCATACTGGATTATGATCGTCCTA	59.343	44.000	0.00	0.00	40.96	2.94
2281	3929	7.439356	CACACTGATACGGAAGACATGAAATAT	59.561	37.037	0.00	0.00	0.00	1.28
2290	3938	9.319143	ACGGAAGACATGAAATATCTAAAAGAG	57.681	33.333	0.00	0.00	0.00	2.85
2314	3965	5.615925	AGAAACTACAGTTGAACTCCAGT	57.384	39.130	0.00	0.00	38.44	4.00
2338	3989	5.568620	AGGAAGAGCTAGTGGAAGAAAAA	57.431	39.130	0.00	0.00	0.00	1.94
2368	4019	4.761739	TGGGACTCTCAAAATGACAACATC	59.238	41.667	0.00	0.00	35.50	3.06
2413	4064	3.911661	GCTCATGGCAATGGATACTTC	57.088	47.619	0.00	0.00	41.35	3.01
2498	4149	4.853468	TTGGCCTATCATTTCACTACCA	57.147	40.909	3.32	0.00	0.00	3.25
2739	4390	0.740868	CCGCCGACAACACTCATCAT	60.741	55.000	0.00	0.00	0.00	2.45
2907	4558	2.270205	CGCTGTCCATCTGCCCTT	59.730	61.111	0.00	0.00	37.66	3.95

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
15	16	3.545703	CCTGAAAACAGTAGCCCATAGG	58.454	50.000	0.00	0.00	0.00	2.57
16	17	2.945668	GCCTGAAAACAGTAGCCCATAG	59.054	50.000	0.00	0.00	0.00	2.23
21	22	1.305930	CGGGCCTGAAAACAGTAGCC	61.306	60.000	5.28	0.00	39.73	3.93
22	23	0.321298	TCGGGCCTGAAAACAGTAGC	60.321	55.000	13.31	0.00	0.00	3.58
24	25	1.418637	AGTTCGGGCCTGAAAACAGTA	59.581	47.619	28.65	1.55	0.00	2.74
25	26	0.182775	AGTTCGGGCCTGAAAACAGT	59.817	50.000	28.65	7.06	0.00	3.55
27	28	1.695242	TCTAGTTCGGGCCTGAAAACA	59.305	47.619	28.65	14.93	0.00	2.83
28	29	2.467566	TCTAGTTCGGGCCTGAAAAC	57.532	50.000	28.65	18.04	0.00	2.43
29	30	6.681729	ATATATCTAGTTCGGGCCTGAAAA	57.318	37.500	28.65	18.04	0.00	2.29
32	33	5.886474	CACTATATATCTAGTTCGGGCCTGA	59.114	44.000	11.27	11.27	29.41	3.86
33	34	5.652891	ACACTATATATCTAGTTCGGGCCTG	59.347	44.000	4.71	4.71	29.41	4.85
34	35	5.828871	ACACTATATATCTAGTTCGGGCCT	58.171	41.667	0.84	0.00	29.41	5.19
50	51	9.295825	CCAGCCCATTGAATTTTATACACTATA	57.704	33.333	0.00	0.00	0.00	1.31
52	53	6.549364	CCCAGCCCATTGAATTTTATACACTA	59.451	38.462	0.00	0.00	0.00	2.74
53	54	5.363580	CCCAGCCCATTGAATTTTATACACT	59.636	40.000	0.00	0.00	0.00	3.55
54	55	5.600696	CCCAGCCCATTGAATTTTATACAC	58.399	41.667	0.00	0.00	0.00	2.90
56	57	4.631131	GCCCAGCCCATTGAATTTTATAC	58.369	43.478	0.00	0.00	0.00	1.47
58	59	2.102925	CGCCCAGCCCATTGAATTTTAT	59.897	45.455	0.00	0.00	0.00	1.40
59	60	1.480137	CGCCCAGCCCATTGAATTTTA	59.520	47.619	0.00	0.00	0.00	1.52
61	62	1.616091	CCGCCCAGCCCATTGAATTT	61.616	55.000	0.00	0.00	0.00	1.82
62	63	2.059786	CCGCCCAGCCCATTGAATT	61.060	57.895	0.00	0.00	0.00	2.17
183	184	3.680642	CAACTCATTGCCATAGTTCCG	57.319	47.619	0.00	0.00	31.21	4.30
258	259	0.098728	ACGTGCTCAAAGTGTGCAAC	59.901	50.000	6.56	0.00	46.51	4.17
275	276	3.834610	ACTCGTGGATTCAGTTTAGACG	58.165	45.455	0.00	0.00	0.00	4.18
292	293	2.168496	TCCCAGAAGGTTCAGTACTCG	58.832	52.381	0.00	0.00	36.75	4.18
327	328	6.108687	TCGTCAGCAATATGAAAGATTCACT	58.891	36.000	0.00	0.00	43.48	3.41
367	368	0.389426	GACATTACAGTCCGCACGGT	60.389	55.000	9.23	0.00	34.94	4.83
374	375	3.314541	AGTGTTCCGACATTACAGTCC	57.685	47.619	0.00	0.00	38.23	3.85
399	400	5.589831	AGGAATGTTATTTTTACCTGGCCT	58.410	37.500	3.32	0.00	0.00	5.19
401	402	7.158697	ACAAAGGAATGTTATTTTTACCTGGC	58.841	34.615	0.00	0.00	0.00	4.85
416	417	8.335532	TGATACTGGTTAGAAACAAAGGAATG	57.664	34.615	0.00	0.00	0.00	2.67
444	449	1.990160	TTGCCGAGAAAGGTGGTGGT	61.990	55.000	0.00	0.00	0.00	4.16
590	597	7.715249	GGTCCACTATGAAATTTATGCTGTCTA	59.285	37.037	0.00	0.00	0.00	2.59
591	598	6.543831	GGTCCACTATGAAATTTATGCTGTCT	59.456	38.462	0.00	0.00	0.00	3.41
673	680	9.830975	AATAATATACCAAAAATTCTTGTGGGC	57.169	29.630	0.00	0.00	43.55	5.36
913	1226	4.099419	GGCAAAGATTTTGGGGATACGAAT	59.901	41.667	3.97	0.00	37.60	3.34
947	1260	0.978146	CTGGGTGGGGACTGGAGTAG	60.978	65.000	0.00	0.00	0.00	2.57
955	1268	0.895559	CTGAAAAGCTGGGTGGGGAC	60.896	60.000	0.00	0.00	0.00	4.46
956	1269	1.460255	CTGAAAAGCTGGGTGGGGA	59.540	57.895	0.00	0.00	0.00	4.81
1218	1538	2.670148	GGAGATCGTGGGGCCTGTT	61.670	63.158	0.84	0.00	0.00	3.16
1230	1550	1.104630	AGTCGAACCTTCCGGAGATC	58.895	55.000	3.34	0.00	0.00	2.75
1242	1562	2.288025	TGGGGGCAGGTAGTCGAAC	61.288	63.158	0.00	0.00	0.00	3.95
1268	1588	0.686769	ACCACGATACTGGGAGTCCC	60.687	60.000	22.54	22.54	45.71	4.46
1269	1589	2.062971	TACCACGATACTGGGAGTCC	57.937	55.000	0.00	0.00	35.34	3.85
1270	1590	4.460948	TTTTACCACGATACTGGGAGTC	57.539	45.455	0.00	0.00	35.34	3.36
1284	2847	4.522114	TGCAATGATCCTCGATTTTACCA	58.478	39.130	0.00	0.00	0.00	3.25
1293	2856	0.313043	GGCCATTGCAATGATCCTCG	59.687	55.000	35.47	20.62	38.70	4.63
1302	2865	3.347216	GAGTAAGAGAAGGCCATTGCAA	58.653	45.455	5.01	0.00	40.13	4.08
1410	2973	0.397675	AGTCAGCATCGATCTCCCCA	60.398	55.000	0.00	0.00	0.00	4.96
1411	2974	0.755686	AAGTCAGCATCGATCTCCCC	59.244	55.000	0.00	0.00	0.00	4.81
1412	2975	1.410517	TGAAGTCAGCATCGATCTCCC	59.589	52.381	0.00	0.00	0.00	4.30
1419	2982	2.892374	TGGTATGTGAAGTCAGCATCG	58.108	47.619	0.00	0.00	0.00	3.84
1425	2988	5.084519	AGGTACTCTTGGTATGTGAAGTCA	58.915	41.667	0.00	0.00	32.56	3.41
1450	3013	3.181454	GGTGATACCGTGGGATCAAAGAT	60.181	47.826	15.36	0.00	33.96	2.40
1452	3015	2.561569	GGTGATACCGTGGGATCAAAG	58.438	52.381	15.36	0.00	33.96	2.77
1485	3056	8.637099	GTTCTTATATTAGTTTACGGAGGGAGT	58.363	37.037	0.00	0.00	0.00	3.85
1486	3057	8.636213	TGTTCTTATATTAGTTTACGGAGGGAG	58.364	37.037	0.00	0.00	0.00	4.30
1487	3058	8.537728	TGTTCTTATATTAGTTTACGGAGGGA	57.462	34.615	0.00	0.00	0.00	4.20
1488	3059	9.774413	AATGTTCTTATATTAGTTTACGGAGGG	57.226	33.333	0.00	0.00	0.00	4.30
1549	3120	9.802039	TCACAAATACTCCCTTTGTAAACTAAT	57.198	29.630	1.51	0.00	43.15	1.73
1550	3121	9.802039	ATCACAAATACTCCCTTTGTAAACTAA	57.198	29.630	1.51	0.00	43.15	2.24
1551	3122	9.444600	GATCACAAATACTCCCTTTGTAAACTA	57.555	33.333	1.51	0.00	43.15	2.24
1552	3123	8.164070	AGATCACAAATACTCCCTTTGTAAACT	58.836	33.333	0.00	0.21	43.15	2.66
1553	3124	8.336801	AGATCACAAATACTCCCTTTGTAAAC	57.663	34.615	0.00	0.00	43.15	2.01
1554	3125	8.160765	TGAGATCACAAATACTCCCTTTGTAAA	58.839	33.333	0.00	0.00	43.15	2.01
1555	3126	7.685481	TGAGATCACAAATACTCCCTTTGTAA	58.315	34.615	0.00	0.00	43.15	2.41
1556	3127	7.252612	TGAGATCACAAATACTCCCTTTGTA	57.747	36.000	0.00	0.00	43.15	2.41
1557	3128	6.126863	TGAGATCACAAATACTCCCTTTGT	57.873	37.500	0.00	0.00	45.23	2.83
1558	3129	7.452880	TTTGAGATCACAAATACTCCCTTTG	57.547	36.000	13.45	0.00	39.08	2.77
1559	3130	7.340487	GGATTTGAGATCACAAATACTCCCTTT	59.660	37.037	25.23	7.63	46.18	3.11
1560	3131	6.830838	GGATTTGAGATCACAAATACTCCCTT	59.169	38.462	25.23	8.23	46.18	3.95
1561	3132	6.360618	GGATTTGAGATCACAAATACTCCCT	58.639	40.000	25.23	8.83	46.18	4.20
1562	3133	6.625873	GGATTTGAGATCACAAATACTCCC	57.374	41.667	25.23	19.47	46.18	4.30
1596	3167	0.323360	CCAAAATCCTCGGGCTTCCA	60.323	55.000	0.00	0.00	0.00	3.53
1597	3168	1.667154	GCCAAAATCCTCGGGCTTCC	61.667	60.000	0.00	0.00	43.09	3.46
1607	3178	2.819608	TGCTCTGTTGTAGCCAAAATCC	59.180	45.455	0.00	0.00	39.30	3.01
1616	3187	6.446781	AATTCATCCAATGCTCTGTTGTAG	57.553	37.500	0.00	0.00	0.00	2.74
1626	3197	5.824904	ACAGTGTCTAATTCATCCAATGC	57.175	39.130	0.00	0.00	0.00	3.56
1628	3199	8.274322	TCCATAACAGTGTCTAATTCATCCAAT	58.726	33.333	0.00	0.00	0.00	3.16
1644	3215	5.688807	CCATTCAGATTCCTCCATAACAGT	58.311	41.667	0.00	0.00	0.00	3.55
1682	3253	1.896660	GGAGAAAACGTGCAGGGCA	60.897	57.895	11.67	0.00	35.60	5.36
1685	3256	0.319555	TCGAGGAGAAAACGTGCAGG	60.320	55.000	4.53	4.53	0.00	4.85
1686	3257	1.063806	CTCGAGGAGAAAACGTGCAG	58.936	55.000	3.91	0.00	0.00	4.41
1793	3376	0.032678	CCCGGCAGTAGACAGCATAG	59.967	60.000	0.00	0.00	0.00	2.23
1957	3550	2.945008	TGACAAAGAGAACCTGCACAAG	59.055	45.455	0.00	0.00	0.00	3.16
1967	3560	6.489700	TGGCACTTATCATTTGACAAAGAGAA	59.510	34.615	6.77	6.93	0.00	2.87
1989	3582	4.976224	ATCGGTGGTTTAATTACTTGGC	57.024	40.909	0.00	0.00	0.00	4.52
2052	3645	5.325239	CAAGGTAGACCCCTTTTTCAGATT	58.675	41.667	0.00	0.00	42.24	2.40
2056	3649	2.175931	TGCAAGGTAGACCCCTTTTTCA	59.824	45.455	0.00	0.00	42.24	2.69
2080	3676	6.368791	CCAGAAGACGAGACATTTCACAAATA	59.631	38.462	0.00	0.00	0.00	1.40
2081	3677	5.180117	CCAGAAGACGAGACATTTCACAAAT	59.820	40.000	0.00	0.00	0.00	2.32
2082	3678	4.511454	CCAGAAGACGAGACATTTCACAAA	59.489	41.667	0.00	0.00	0.00	2.83
2091	3717	1.070134	CCCAAACCAGAAGACGAGACA	59.930	52.381	0.00	0.00	0.00	3.41
2131	3757	3.664107	CTTCAAGACCCAATTCGTCTGA	58.336	45.455	5.65	3.94	39.69	3.27
2195	3824	0.712380	AAGACCCATGGGCCAAGAAT	59.288	50.000	31.73	9.42	39.32	2.40
2254	3887	3.119137	TCATGTCTTCCGTATCAGTGTGG	60.119	47.826	0.00	0.00	0.00	4.17
2290	3938	6.049790	ACTGGAGTTCAACTGTAGTTTCTTC	58.950	40.000	0.00	0.00	35.83	2.87
2297	3945	5.723672	TCCTTACTGGAGTTCAACTGTAG	57.276	43.478	0.00	0.00	40.56	2.74
2314	3965	6.681729	TTTTCTTCCACTAGCTCTTCCTTA	57.318	37.500	0.00	0.00	0.00	2.69
2338	3989	6.494491	TGTCATTTTGAGAGTCCCATTCAATT	59.506	34.615	0.00	0.00	31.54	2.32
2339	3990	6.012113	TGTCATTTTGAGAGTCCCATTCAAT	58.988	36.000	0.00	0.00	31.54	2.57
2413	4064	2.371841	TGGATGGAACCCAAGGATATCG	59.628	50.000	0.00	0.00	36.95	2.92
2425	4076	9.566432	AAGACAATCTCTTTATATGGATGGAAC	57.434	33.333	0.00	0.00	35.49	3.62
2560	4211	0.032267	GGACCTAGCTGTCGGCATAC	59.968	60.000	6.39	0.00	44.79	2.39
2739	4390	4.424566	GACGTCGTTAGCCGGCCA	62.425	66.667	26.15	6.66	38.13	5.36
2860	4511	0.389817	GTGACGTGTCAGCTATGCCA	60.390	55.000	2.31	0.00	40.75	4.92

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.