Multiple sequence alignment - TraesCS3A01G297800

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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 TraesCS3A01G297800 chr3A 100.000 3224 0 0 1 3224 532455012 532451789 0.000000e+00 5954.0
1 TraesCS3A01G297800 chr3D 95.413 3030 89 22 187 3180 418722565 418725580 0.000000e+00 4780.0
2 TraesCS3A01G297800 chr3B 96.988 2689 74 5 189 2872 545061584 545064270 0.000000e+00 4510.0
3 TraesCS3A01G297800 chr3B 85.667 300 33 8 2889 3180 545064315 545064612 1.120000e-79 307.0
4 TraesCS3A01G297800 chr7A 73.029 1598 374 42 292 1858 91647380 91648951 7.980000e-141 510.0
5 TraesCS3A01G297800 chr7A 99.459 185 1 0 4 188 164990458 164990274 1.430000e-88 337.0
6 TraesCS3A01G297800 chr7A 98.925 186 2 0 1 186 66389513 66389698 1.850000e-87 333.0
7 TraesCS3A01G297800 chr5A 99.462 186 1 0 1 186 599162404 599162219 3.980000e-89 339.0
8 TraesCS3A01G297800 chr5A 88.462 52 4 2 2387 2437 432087965 432088015 9.660000e-06 62.1
9 TraesCS3A01G297800 chr5A 89.362 47 5 0 2389 2435 472473806 472473852 3.470000e-05 60.2
10 TraesCS3A01G297800 chr6A 98.936 188 2 0 1 188 7207347 7207534 1.430000e-88 337.0
11 TraesCS3A01G297800 chr6A 95.122 41 2 0 2388 2428 200454399 200454439 7.470000e-07 65.8
12 TraesCS3A01G297800 chr2A 97.938 194 3 1 1 194 158957074 158956882 5.150000e-88 335.0
13 TraesCS3A01G297800 chr2A 80.412 97 9 6 2324 2420 410850398 410850312 7.470000e-07 65.8
14 TraesCS3A01G297800 chr1A 98.936 188 1 1 1 188 113344615 113344429 5.150000e-88 335.0
15 TraesCS3A01G297800 chr1A 98.925 186 2 0 1 186 113334316 113334131 1.850000e-87 333.0
16 TraesCS3A01G297800 chr1A 97.222 36 1 0 2319 2354 9100472 9100507 9.660000e-06 62.1
17 TraesCS3A01G297800 chr7D 98.925 186 2 0 3 188 407445951 407446136 1.850000e-87 333.0
18 TraesCS3A01G297800 chr7D 98.925 186 2 0 1 186 407495549 407495734 1.850000e-87 333.0
19 TraesCS3A01G297800 chr7D 80.000 110 11 6 2320 2428 23356808 23356907 1.600000e-08 71.3
20 TraesCS3A01G297800 chr2B 71.491 691 178 16 1175 1857 132518320 132518999 1.990000e-37 167.0
21 TraesCS3A01G297800 chr2B 82.474 97 7 3 2324 2420 14834323 14834409 3.450000e-10 76.8
22 TraesCS3A01G297800 chr2D 72.519 524 135 7 1269 1789 80834731 80835248 9.260000e-36 161.0
23 TraesCS3A01G297800 chr2D 71.033 687 182 14 1187 1866 80783156 80782480 2.000000e-32 150.0
24 TraesCS3A01G297800 chr2D 93.333 45 2 1 2388 2431 14895328 14895372 7.470000e-07 65.8
25 TraesCS3A01G297800 chr7B 93.023 43 3 0 2323 2365 481311110 481311068 2.690000e-06 63.9
26 TraesCS3A01G297800 chr5D 89.796 49 4 1 2388 2436 411995084 411995131 9.660000e-06 62.1
27 TraesCS3A01G297800 chr1B 97.222 36 1 0 2323 2358 574864915 574864950 9.660000e-06 62.1
28 TraesCS3A01G297800 chr4D 85.965 57 7 1 2388 2443 7759915 7759859 3.470000e-05 60.2
29 TraesCS3A01G297800 chr4D 85.965 57 6 2 2385 2440 398430865 398430920 3.470000e-05 60.2
30 TraesCS3A01G297800 chr1D 97.143 35 1 0 2324 2358 309921679 309921713 3.470000e-05 60.2


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 TraesCS3A01G297800 chr3A 532451789 532455012 3223 True 5954.0 5954 100.0000 1 3224 1 chr3A.!!$R1 3223
1 TraesCS3A01G297800 chr3D 418722565 418725580 3015 False 4780.0 4780 95.4130 187 3180 1 chr3D.!!$F1 2993
2 TraesCS3A01G297800 chr3B 545061584 545064612 3028 False 2408.5 4510 91.3275 189 3180 2 chr3B.!!$F1 2991
3 TraesCS3A01G297800 chr7A 91647380 91648951 1571 False 510.0 510 73.0290 292 1858 1 chr7A.!!$F2 1566

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
88 89 0.108963 ACAATTTGACGAACCGGGGA 59.891 50.0 6.32 0.0 0.0 4.81 F
1019 1026 0.034670 ATGGGAAAGACTGCTCCTGC 60.035 55.0 4.31 0.0 40.2 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2086 2102 1.300620 CGGTTGGTGCGAACTCTGA 60.301 57.895 0.0 0.0 0.00 3.27 R
2879 2903 0.604073 TAACCGAGCCAATGTCGTGA 59.396 50.000 0.0 0.0 35.59 4.35 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
33 34 9.295825 TGTAACATCATTTTAACACTTCATCCT 57.704 29.630 0.00 0.00 0.00 3.24
36 37 8.408043 ACATCATTTTAACACTTCATCCTTGA 57.592 30.769 0.00 0.00 0.00 3.02
37 38 8.517878 ACATCATTTTAACACTTCATCCTTGAG 58.482 33.333 0.00 0.00 32.27 3.02
38 39 8.733458 CATCATTTTAACACTTCATCCTTGAGA 58.267 33.333 0.00 0.00 32.27 3.27
39 40 8.327941 TCATTTTAACACTTCATCCTTGAGAG 57.672 34.615 0.00 0.00 32.27 3.20
40 41 8.156820 TCATTTTAACACTTCATCCTTGAGAGA 58.843 33.333 0.00 0.00 32.27 3.10
41 42 8.786898 CATTTTAACACTTCATCCTTGAGAGAA 58.213 33.333 0.00 0.00 32.27 2.87
42 43 7.730364 TTTAACACTTCATCCTTGAGAGAAC 57.270 36.000 0.00 0.00 32.27 3.01
43 44 4.278975 ACACTTCATCCTTGAGAGAACC 57.721 45.455 0.00 0.00 32.27 3.62
44 45 3.008485 ACACTTCATCCTTGAGAGAACCC 59.992 47.826 0.00 0.00 32.27 4.11
45 46 3.008375 CACTTCATCCTTGAGAGAACCCA 59.992 47.826 0.00 0.00 32.27 4.51
46 47 3.008485 ACTTCATCCTTGAGAGAACCCAC 59.992 47.826 0.00 0.00 32.27 4.61
47 48 2.907892 TCATCCTTGAGAGAACCCACT 58.092 47.619 0.00 0.00 0.00 4.00
48 49 3.251484 TCATCCTTGAGAGAACCCACTT 58.749 45.455 0.00 0.00 0.00 3.16
49 50 3.261897 TCATCCTTGAGAGAACCCACTTC 59.738 47.826 0.00 0.00 0.00 3.01
50 51 1.618837 TCCTTGAGAGAACCCACTTCG 59.381 52.381 0.00 0.00 33.60 3.79
51 52 1.344763 CCTTGAGAGAACCCACTTCGT 59.655 52.381 0.00 0.00 33.60 3.85
52 53 2.561419 CCTTGAGAGAACCCACTTCGTA 59.439 50.000 0.00 0.00 33.60 3.43
53 54 3.195825 CCTTGAGAGAACCCACTTCGTAT 59.804 47.826 0.00 0.00 33.60 3.06
54 55 3.868757 TGAGAGAACCCACTTCGTATG 57.131 47.619 0.00 0.00 33.60 2.39
55 56 2.094182 TGAGAGAACCCACTTCGTATGC 60.094 50.000 0.00 0.00 33.60 3.14
56 57 2.166664 GAGAGAACCCACTTCGTATGCT 59.833 50.000 0.00 0.00 33.60 3.79
57 58 2.166664 AGAGAACCCACTTCGTATGCTC 59.833 50.000 0.00 0.00 33.60 4.26
58 59 2.166664 GAGAACCCACTTCGTATGCTCT 59.833 50.000 0.00 0.00 33.60 4.09
59 60 2.567615 AGAACCCACTTCGTATGCTCTT 59.432 45.455 0.00 0.00 33.60 2.85
60 61 2.386661 ACCCACTTCGTATGCTCTTG 57.613 50.000 0.00 0.00 0.00 3.02
61 62 1.899814 ACCCACTTCGTATGCTCTTGA 59.100 47.619 0.00 0.00 0.00 3.02
62 63 2.501723 ACCCACTTCGTATGCTCTTGAT 59.498 45.455 0.00 0.00 0.00 2.57
63 64 3.126831 CCCACTTCGTATGCTCTTGATC 58.873 50.000 0.00 0.00 0.00 2.92
64 65 3.126831 CCACTTCGTATGCTCTTGATCC 58.873 50.000 0.00 0.00 0.00 3.36
65 66 3.430790 CCACTTCGTATGCTCTTGATCCA 60.431 47.826 0.00 0.00 0.00 3.41
66 67 3.553511 CACTTCGTATGCTCTTGATCCAC 59.446 47.826 0.00 0.00 0.00 4.02
67 68 3.195610 ACTTCGTATGCTCTTGATCCACA 59.804 43.478 0.00 0.00 0.00 4.17
68 69 3.165058 TCGTATGCTCTTGATCCACAC 57.835 47.619 0.00 0.00 0.00 3.82
69 70 2.495669 TCGTATGCTCTTGATCCACACA 59.504 45.455 0.00 0.00 0.00 3.72
70 71 2.604914 CGTATGCTCTTGATCCACACAC 59.395 50.000 0.00 0.00 0.00 3.82
71 72 2.865119 ATGCTCTTGATCCACACACA 57.135 45.000 0.00 0.00 0.00 3.72
72 73 2.636647 TGCTCTTGATCCACACACAA 57.363 45.000 0.00 0.00 0.00 3.33
73 74 3.144657 TGCTCTTGATCCACACACAAT 57.855 42.857 0.00 0.00 0.00 2.71
74 75 3.489355 TGCTCTTGATCCACACACAATT 58.511 40.909 0.00 0.00 0.00 2.32
75 76 3.890756 TGCTCTTGATCCACACACAATTT 59.109 39.130 0.00 0.00 0.00 1.82
76 77 4.232221 GCTCTTGATCCACACACAATTTG 58.768 43.478 0.00 0.00 0.00 2.32
77 78 4.022935 GCTCTTGATCCACACACAATTTGA 60.023 41.667 2.79 0.00 0.00 2.69
78 79 5.437289 TCTTGATCCACACACAATTTGAC 57.563 39.130 2.79 0.00 0.00 3.18
79 80 3.894782 TGATCCACACACAATTTGACG 57.105 42.857 2.79 0.00 0.00 4.35
80 81 3.471680 TGATCCACACACAATTTGACGA 58.528 40.909 2.79 0.00 0.00 4.20
81 82 3.879892 TGATCCACACACAATTTGACGAA 59.120 39.130 2.79 0.00 0.00 3.85
82 83 3.684103 TCCACACACAATTTGACGAAC 57.316 42.857 2.79 0.00 0.00 3.95
83 84 2.356382 TCCACACACAATTTGACGAACC 59.644 45.455 2.79 0.00 0.00 3.62
84 85 2.371432 CACACACAATTTGACGAACCG 58.629 47.619 2.79 0.00 0.00 4.44
85 86 1.332375 ACACACAATTTGACGAACCGG 59.668 47.619 0.00 0.00 0.00 5.28
86 87 0.948678 ACACAATTTGACGAACCGGG 59.051 50.000 6.32 0.00 0.00 5.73
87 88 0.239879 CACAATTTGACGAACCGGGG 59.760 55.000 6.32 0.00 0.00 5.73
88 89 0.108963 ACAATTTGACGAACCGGGGA 59.891 50.000 6.32 0.00 0.00 4.81
89 90 0.519961 CAATTTGACGAACCGGGGAC 59.480 55.000 6.32 0.00 0.00 4.46
104 105 2.115343 GGGACCAACACCTGAGATTC 57.885 55.000 0.00 0.00 0.00 2.52
105 106 1.351017 GGGACCAACACCTGAGATTCA 59.649 52.381 0.00 0.00 0.00 2.57
106 107 2.427506 GGACCAACACCTGAGATTCAC 58.572 52.381 0.00 0.00 0.00 3.18
107 108 2.039084 GGACCAACACCTGAGATTCACT 59.961 50.000 0.00 0.00 0.00 3.41
108 109 3.496870 GGACCAACACCTGAGATTCACTT 60.497 47.826 0.00 0.00 0.00 3.16
109 110 3.480470 ACCAACACCTGAGATTCACTTG 58.520 45.455 0.00 0.00 0.00 3.16
110 111 3.136443 ACCAACACCTGAGATTCACTTGA 59.864 43.478 0.00 0.00 0.00 3.02
111 112 3.499918 CCAACACCTGAGATTCACTTGAC 59.500 47.826 0.00 0.00 0.00 3.18
112 113 4.129380 CAACACCTGAGATTCACTTGACA 58.871 43.478 0.00 0.00 0.00 3.58
113 114 4.422073 ACACCTGAGATTCACTTGACAA 57.578 40.909 0.00 0.00 0.00 3.18
114 115 4.130118 ACACCTGAGATTCACTTGACAAC 58.870 43.478 0.00 0.00 0.00 3.32
115 116 3.499918 CACCTGAGATTCACTTGACAACC 59.500 47.826 0.00 0.00 0.00 3.77
116 117 3.136443 ACCTGAGATTCACTTGACAACCA 59.864 43.478 0.00 0.00 0.00 3.67
117 118 4.202503 ACCTGAGATTCACTTGACAACCAT 60.203 41.667 0.00 0.00 0.00 3.55
118 119 4.763793 CCTGAGATTCACTTGACAACCATT 59.236 41.667 0.00 0.00 0.00 3.16
119 120 5.335426 CCTGAGATTCACTTGACAACCATTG 60.335 44.000 0.00 0.00 0.00 2.82
121 122 5.593909 TGAGATTCACTTGACAACCATTGTT 59.406 36.000 0.00 0.00 45.52 2.83
122 123 6.770303 TGAGATTCACTTGACAACCATTGTTA 59.230 34.615 0.00 0.00 45.52 2.41
123 124 7.041167 TGAGATTCACTTGACAACCATTGTTAG 60.041 37.037 0.00 0.46 45.52 2.34
124 125 6.772716 AGATTCACTTGACAACCATTGTTAGT 59.227 34.615 0.00 1.03 45.52 2.24
125 126 6.371809 TTCACTTGACAACCATTGTTAGTC 57.628 37.500 0.00 0.00 45.52 2.59
126 127 4.819630 TCACTTGACAACCATTGTTAGTCC 59.180 41.667 0.00 0.00 45.52 3.85
127 128 4.023193 CACTTGACAACCATTGTTAGTCCC 60.023 45.833 0.00 0.00 45.52 4.46
128 129 3.149005 TGACAACCATTGTTAGTCCCC 57.851 47.619 0.00 0.00 45.52 4.81
129 130 2.714250 TGACAACCATTGTTAGTCCCCT 59.286 45.455 0.00 0.00 45.52 4.79
130 131 3.911260 TGACAACCATTGTTAGTCCCCTA 59.089 43.478 0.00 0.00 45.52 3.53
131 132 4.259356 GACAACCATTGTTAGTCCCCTAC 58.741 47.826 0.00 0.00 45.52 3.18
132 133 3.653836 ACAACCATTGTTAGTCCCCTACA 59.346 43.478 0.00 0.00 42.22 2.74
133 134 4.291249 ACAACCATTGTTAGTCCCCTACAT 59.709 41.667 0.00 0.00 42.22 2.29
134 135 4.503714 ACCATTGTTAGTCCCCTACATG 57.496 45.455 0.00 0.00 0.00 3.21
135 136 3.850173 ACCATTGTTAGTCCCCTACATGT 59.150 43.478 2.69 2.69 0.00 3.21
136 137 5.034200 ACCATTGTTAGTCCCCTACATGTA 58.966 41.667 5.25 5.25 0.00 2.29
137 138 5.130477 ACCATTGTTAGTCCCCTACATGTAG 59.870 44.000 23.58 23.58 0.00 2.74
138 139 5.365605 CCATTGTTAGTCCCCTACATGTAGA 59.634 44.000 30.41 11.39 35.21 2.59
139 140 6.043243 CCATTGTTAGTCCCCTACATGTAGAT 59.957 42.308 30.41 11.55 35.21 1.98
140 141 7.420214 CCATTGTTAGTCCCCTACATGTAGATT 60.420 40.741 30.41 12.84 35.21 2.40
141 142 7.504926 TTGTTAGTCCCCTACATGTAGATTT 57.495 36.000 30.41 14.82 35.21 2.17
142 143 7.504926 TGTTAGTCCCCTACATGTAGATTTT 57.495 36.000 30.41 15.42 35.21 1.82
143 144 7.562135 TGTTAGTCCCCTACATGTAGATTTTC 58.438 38.462 30.41 16.93 35.21 2.29
144 145 7.181305 TGTTAGTCCCCTACATGTAGATTTTCA 59.819 37.037 30.41 16.24 35.21 2.69
145 146 6.831664 AGTCCCCTACATGTAGATTTTCAT 57.168 37.500 30.41 10.00 35.21 2.57
146 147 7.213178 AGTCCCCTACATGTAGATTTTCATT 57.787 36.000 30.41 8.39 35.21 2.57
147 148 8.331931 AGTCCCCTACATGTAGATTTTCATTA 57.668 34.615 30.41 5.92 35.21 1.90
148 149 8.778059 AGTCCCCTACATGTAGATTTTCATTAA 58.222 33.333 30.41 4.67 35.21 1.40
149 150 8.837389 GTCCCCTACATGTAGATTTTCATTAAC 58.163 37.037 30.41 11.60 35.21 2.01
150 151 8.553153 TCCCCTACATGTAGATTTTCATTAACA 58.447 33.333 30.41 0.00 35.21 2.41
151 152 9.354673 CCCCTACATGTAGATTTTCATTAACAT 57.645 33.333 30.41 0.00 35.21 2.71
173 174 9.985730 AACATCAAAACATAATATAAGGGCATG 57.014 29.630 0.00 0.00 0.00 4.06
174 175 9.365906 ACATCAAAACATAATATAAGGGCATGA 57.634 29.630 0.00 0.00 0.00 3.07
396 400 4.335400 AACAAATGGCACCTTTAACCTG 57.665 40.909 0.00 0.00 0.00 4.00
437 441 1.853963 ACTCCTCTACACTTCCGCAT 58.146 50.000 0.00 0.00 0.00 4.73
455 459 1.867233 CATGTCGCCTAGTGGTTATGC 59.133 52.381 0.00 0.00 35.27 3.14
558 562 5.237344 CGTCACCAGAAACAAGAATTTCTCT 59.763 40.000 0.00 0.00 45.19 3.10
637 641 3.980646 GCAACCATATATTTGCGGTGA 57.019 42.857 6.41 0.00 38.86 4.02
736 740 2.173143 TCTGTGCAATCCCATGATGCTA 59.827 45.455 0.00 0.00 0.00 3.49
747 751 3.314635 CCCATGATGCTAGCTTCTTTGAC 59.685 47.826 25.75 5.24 0.00 3.18
890 897 2.162681 GCCTGCAAGACCATTACTGTT 58.837 47.619 0.00 0.00 34.07 3.16
928 935 3.591023 TCAACAGTTTTCACAGACACGA 58.409 40.909 0.00 0.00 0.00 4.35
968 975 1.462283 CGCAACTGGAGTCATCAACTG 59.538 52.381 0.00 0.00 38.74 3.16
1019 1026 0.034670 ATGGGAAAGACTGCTCCTGC 60.035 55.000 4.31 0.00 40.20 4.85
1140 1147 8.945195 TCATCCTTATTGCTGGAATTATCATT 57.055 30.769 0.00 0.00 35.81 2.57
1172 1179 5.316167 TGCTCGAAGGAAATTGGCATATAT 58.684 37.500 0.00 0.00 0.00 0.86
1347 1354 3.078837 GGAGGTTGCGGTGAAGAAATTA 58.921 45.455 0.00 0.00 0.00 1.40
1387 1394 6.377146 GCAGGGAACAAAGGAATTCATTACTA 59.623 38.462 5.67 0.00 28.79 1.82
1584 1600 2.655090 TCAAAGGAGTTGCATGTGGA 57.345 45.000 0.00 0.00 37.13 4.02
1691 1707 2.184533 TGGGCGACTAGGAGATTTTGA 58.815 47.619 0.00 0.00 0.00 2.69
1802 1818 2.170187 CAGGCAAGCTGTCTCCTCTTAT 59.830 50.000 0.00 0.00 23.66 1.73
1941 1957 4.157289 CAGAAAGGAACAATGGTGGAGATG 59.843 45.833 0.00 0.00 0.00 2.90
1974 1990 0.102120 TCCAAGGCAAGTGCAAAACG 59.898 50.000 5.52 0.00 44.36 3.60
2554 2574 4.837093 ATACAAGTTGCAGCCCTAGTAA 57.163 40.909 1.81 0.00 0.00 2.24
2618 2638 3.830178 TCGATCCTCTTTTAGTGGTGTCA 59.170 43.478 0.00 0.00 31.13 3.58
2755 2779 4.704540 TGGGCTTCATAATTTGTACCTGTG 59.295 41.667 0.00 0.00 0.00 3.66
2782 2806 3.616821 TGTGATCCACGCTAAAATCTTCG 59.383 43.478 0.00 0.00 37.14 3.79
2800 2824 4.335874 TCTTCGTACTCTTCCATAGCACTC 59.664 45.833 0.00 0.00 0.00 3.51
2822 2846 3.242673 CCGGTACTCGTCTTGTAGATGAC 60.243 52.174 0.00 0.00 35.47 3.06
2839 2863 4.887071 AGATGACTTACAGTTGCCAAACAA 59.113 37.500 0.00 0.00 38.88 2.83
2840 2864 5.359576 AGATGACTTACAGTTGCCAAACAAA 59.640 36.000 0.00 0.00 40.82 2.83
2841 2865 4.739195 TGACTTACAGTTGCCAAACAAAC 58.261 39.130 0.00 0.00 40.82 2.93
2842 2866 3.765026 ACTTACAGTTGCCAAACAAACG 58.235 40.909 0.00 0.00 40.82 3.60
2872 2896 5.119279 CACACGGATCTTGCTAACATATAGC 59.881 44.000 0.59 0.59 40.76 2.97
2874 2898 5.928839 CACGGATCTTGCTAACATATAGCTT 59.071 40.000 8.73 0.00 40.95 3.74
2875 2899 6.090088 CACGGATCTTGCTAACATATAGCTTC 59.910 42.308 8.73 1.92 40.95 3.86
2879 2903 8.093927 GGATCTTGCTAACATATAGCTTCTCTT 58.906 37.037 8.73 0.00 40.95 2.85
2882 2906 7.923344 TCTTGCTAACATATAGCTTCTCTTCAC 59.077 37.037 8.73 0.00 40.95 3.18
2885 2909 6.361214 GCTAACATATAGCTTCTCTTCACGAC 59.639 42.308 0.00 0.00 37.56 4.34
2886 2910 5.836821 ACATATAGCTTCTCTTCACGACA 57.163 39.130 0.00 0.00 0.00 4.35
2887 2911 6.398234 ACATATAGCTTCTCTTCACGACAT 57.602 37.500 0.00 0.00 0.00 3.06
2941 2993 0.404040 TCCAGATTGCCCGGAACTTT 59.596 50.000 0.73 0.00 0.00 2.66
3015 3071 0.991920 GGAACTCCCCAACTGGATCA 59.008 55.000 0.00 0.00 37.39 2.92
3060 3116 0.391130 GTCCACATTACAGCGCCTCA 60.391 55.000 2.29 0.00 0.00 3.86
3184 3258 3.066814 CCAGCAGCAGGCCCTTTC 61.067 66.667 0.00 0.00 46.50 2.62
3185 3259 2.282674 CAGCAGCAGGCCCTTTCA 60.283 61.111 0.00 0.00 46.50 2.69
3186 3260 1.904865 CAGCAGCAGGCCCTTTCAA 60.905 57.895 0.00 0.00 46.50 2.69
3187 3261 1.077985 AGCAGCAGGCCCTTTCAAT 59.922 52.632 0.00 0.00 46.50 2.57
3188 3262 0.543646 AGCAGCAGGCCCTTTCAATT 60.544 50.000 0.00 0.00 46.50 2.32
3189 3263 0.322648 GCAGCAGGCCCTTTCAATTT 59.677 50.000 0.00 0.00 36.11 1.82
3190 3264 1.271001 GCAGCAGGCCCTTTCAATTTT 60.271 47.619 0.00 0.00 36.11 1.82
3191 3265 2.419667 CAGCAGGCCCTTTCAATTTTG 58.580 47.619 0.00 0.00 0.00 2.44
3192 3266 2.037511 CAGCAGGCCCTTTCAATTTTGA 59.962 45.455 0.00 0.00 34.92 2.69
3193 3267 2.301009 AGCAGGCCCTTTCAATTTTGAG 59.699 45.455 0.00 0.00 38.61 3.02
3194 3268 2.613725 GCAGGCCCTTTCAATTTTGAGG 60.614 50.000 0.00 0.00 38.61 3.86
3195 3269 1.625315 AGGCCCTTTCAATTTTGAGGC 59.375 47.619 0.00 11.60 42.24 4.70
3196 3270 1.625315 GGCCCTTTCAATTTTGAGGCT 59.375 47.619 16.82 0.00 42.45 4.58
3197 3271 2.354103 GGCCCTTTCAATTTTGAGGCTC 60.354 50.000 16.82 7.79 42.45 4.70
3198 3272 2.354103 GCCCTTTCAATTTTGAGGCTCC 60.354 50.000 12.86 0.00 40.74 4.70
3199 3273 2.899256 CCCTTTCAATTTTGAGGCTCCA 59.101 45.455 12.86 0.00 38.61 3.86
3200 3274 3.056322 CCCTTTCAATTTTGAGGCTCCAG 60.056 47.826 12.86 0.00 38.61 3.86
3201 3275 3.575687 CCTTTCAATTTTGAGGCTCCAGT 59.424 43.478 12.86 0.00 38.61 4.00
3202 3276 4.039609 CCTTTCAATTTTGAGGCTCCAGTT 59.960 41.667 12.86 0.00 38.61 3.16
3203 3277 4.853924 TTCAATTTTGAGGCTCCAGTTC 57.146 40.909 12.86 0.00 38.61 3.01
3204 3278 2.813754 TCAATTTTGAGGCTCCAGTTCG 59.186 45.455 12.86 0.00 32.50 3.95
3205 3279 2.813754 CAATTTTGAGGCTCCAGTTCGA 59.186 45.455 12.86 0.00 0.00 3.71
3206 3280 2.169832 TTTTGAGGCTCCAGTTCGAG 57.830 50.000 12.86 0.00 0.00 4.04
3207 3281 0.321671 TTTGAGGCTCCAGTTCGAGG 59.678 55.000 12.86 0.00 0.00 4.63
3208 3282 1.544825 TTGAGGCTCCAGTTCGAGGG 61.545 60.000 12.86 0.00 0.00 4.30
3209 3283 3.378399 GAGGCTCCAGTTCGAGGGC 62.378 68.421 2.15 0.00 0.00 5.19
3210 3284 4.821589 GGCTCCAGTTCGAGGGCG 62.822 72.222 0.00 0.00 39.35 6.13
3212 3286 3.764466 CTCCAGTTCGAGGGCGCT 61.764 66.667 7.64 1.38 37.46 5.92
3213 3287 3.997064 CTCCAGTTCGAGGGCGCTG 62.997 68.421 8.56 0.52 37.46 5.18
3214 3288 4.069232 CCAGTTCGAGGGCGCTGA 62.069 66.667 8.56 3.25 37.46 4.26
3215 3289 2.185350 CAGTTCGAGGGCGCTGAT 59.815 61.111 8.56 0.00 37.46 2.90
3216 3290 2.169789 CAGTTCGAGGGCGCTGATG 61.170 63.158 8.56 0.00 37.46 3.07
3217 3291 3.567797 GTTCGAGGGCGCTGATGC 61.568 66.667 8.56 0.00 37.46 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 9.295825 AGGATGAAGTGTTAAAATGATGTTACA 57.704 29.630 0.00 0.00 0.00 2.41
10 11 8.859090 TCAAGGATGAAGTGTTAAAATGATGTT 58.141 29.630 0.00 0.00 30.99 2.71
11 12 8.408043 TCAAGGATGAAGTGTTAAAATGATGT 57.592 30.769 0.00 0.00 30.99 3.06
12 13 8.733458 TCTCAAGGATGAAGTGTTAAAATGATG 58.267 33.333 0.00 0.00 34.49 3.07
13 14 8.868522 TCTCAAGGATGAAGTGTTAAAATGAT 57.131 30.769 0.00 0.00 34.49 2.45
14 15 8.156820 TCTCTCAAGGATGAAGTGTTAAAATGA 58.843 33.333 0.00 0.00 34.49 2.57
15 16 8.327941 TCTCTCAAGGATGAAGTGTTAAAATG 57.672 34.615 0.00 0.00 34.49 2.32
16 17 8.787852 GTTCTCTCAAGGATGAAGTGTTAAAAT 58.212 33.333 0.00 0.00 34.49 1.82
17 18 7.228706 GGTTCTCTCAAGGATGAAGTGTTAAAA 59.771 37.037 0.00 0.00 34.49 1.52
18 19 6.710744 GGTTCTCTCAAGGATGAAGTGTTAAA 59.289 38.462 0.00 0.00 34.49 1.52
19 20 6.231211 GGTTCTCTCAAGGATGAAGTGTTAA 58.769 40.000 0.00 0.00 34.49 2.01
20 21 5.280011 GGGTTCTCTCAAGGATGAAGTGTTA 60.280 44.000 0.00 0.00 34.49 2.41
21 22 4.505742 GGGTTCTCTCAAGGATGAAGTGTT 60.506 45.833 0.00 0.00 34.49 3.32
22 23 3.008485 GGGTTCTCTCAAGGATGAAGTGT 59.992 47.826 0.00 0.00 34.49 3.55
23 24 3.008375 TGGGTTCTCTCAAGGATGAAGTG 59.992 47.826 0.00 0.00 34.49 3.16
24 25 3.008485 GTGGGTTCTCTCAAGGATGAAGT 59.992 47.826 0.00 0.00 34.49 3.01
25 26 3.262915 AGTGGGTTCTCTCAAGGATGAAG 59.737 47.826 0.00 0.00 34.49 3.02
26 27 3.251484 AGTGGGTTCTCTCAAGGATGAA 58.749 45.455 0.00 0.00 34.49 2.57
27 28 2.907892 AGTGGGTTCTCTCAAGGATGA 58.092 47.619 0.00 0.00 0.00 2.92
28 29 3.604582 GAAGTGGGTTCTCTCAAGGATG 58.395 50.000 0.00 0.00 31.73 3.51
29 30 2.234908 CGAAGTGGGTTCTCTCAAGGAT 59.765 50.000 0.00 0.00 32.33 3.24
30 31 1.618837 CGAAGTGGGTTCTCTCAAGGA 59.381 52.381 0.00 0.00 32.33 3.36
31 32 1.344763 ACGAAGTGGGTTCTCTCAAGG 59.655 52.381 0.00 0.00 42.51 3.61
32 33 2.821991 ACGAAGTGGGTTCTCTCAAG 57.178 50.000 0.00 0.00 42.51 3.02
33 34 3.616560 GCATACGAAGTGGGTTCTCTCAA 60.617 47.826 0.00 0.00 45.73 3.02
34 35 2.094182 GCATACGAAGTGGGTTCTCTCA 60.094 50.000 0.00 0.00 45.73 3.27
35 36 2.166664 AGCATACGAAGTGGGTTCTCTC 59.833 50.000 0.00 0.00 45.73 3.20
36 37 2.166664 GAGCATACGAAGTGGGTTCTCT 59.833 50.000 0.00 0.00 45.73 3.10
37 38 2.166664 AGAGCATACGAAGTGGGTTCTC 59.833 50.000 0.00 0.00 45.73 2.87
38 39 2.180276 AGAGCATACGAAGTGGGTTCT 58.820 47.619 0.00 0.00 45.73 3.01
39 40 2.673368 CAAGAGCATACGAAGTGGGTTC 59.327 50.000 0.00 0.00 45.73 3.62
40 41 2.301870 TCAAGAGCATACGAAGTGGGTT 59.698 45.455 0.00 0.00 45.73 4.11
41 42 1.899814 TCAAGAGCATACGAAGTGGGT 59.100 47.619 0.00 0.00 45.73 4.51
42 43 2.672961 TCAAGAGCATACGAAGTGGG 57.327 50.000 0.00 0.00 45.73 4.61
43 44 3.126831 GGATCAAGAGCATACGAAGTGG 58.873 50.000 0.00 0.00 45.73 4.00
44 45 3.553511 GTGGATCAAGAGCATACGAAGTG 59.446 47.826 0.00 0.00 45.73 3.16
46 47 3.553511 GTGTGGATCAAGAGCATACGAAG 59.446 47.826 0.00 0.00 0.00 3.79
47 48 3.056179 TGTGTGGATCAAGAGCATACGAA 60.056 43.478 0.00 0.00 0.00 3.85
48 49 2.495669 TGTGTGGATCAAGAGCATACGA 59.504 45.455 0.00 0.00 0.00 3.43
49 50 2.604914 GTGTGTGGATCAAGAGCATACG 59.395 50.000 0.00 0.00 0.00 3.06
50 51 3.599343 TGTGTGTGGATCAAGAGCATAC 58.401 45.455 0.00 0.00 0.00 2.39
51 52 3.979101 TGTGTGTGGATCAAGAGCATA 57.021 42.857 0.00 0.00 0.00 3.14
52 53 2.865119 TGTGTGTGGATCAAGAGCAT 57.135 45.000 0.00 0.00 0.00 3.79
53 54 2.636647 TTGTGTGTGGATCAAGAGCA 57.363 45.000 0.00 0.00 0.00 4.26
54 55 4.022935 TCAAATTGTGTGTGGATCAAGAGC 60.023 41.667 0.00 0.00 0.00 4.09
55 56 5.455392 GTCAAATTGTGTGTGGATCAAGAG 58.545 41.667 0.00 0.00 0.00 2.85
56 57 4.024133 CGTCAAATTGTGTGTGGATCAAGA 60.024 41.667 0.00 0.00 0.00 3.02
57 58 4.024133 TCGTCAAATTGTGTGTGGATCAAG 60.024 41.667 0.00 0.00 0.00 3.02
58 59 3.879892 TCGTCAAATTGTGTGTGGATCAA 59.120 39.130 0.00 0.00 0.00 2.57
59 60 3.471680 TCGTCAAATTGTGTGTGGATCA 58.528 40.909 0.00 0.00 0.00 2.92
60 61 4.219033 GTTCGTCAAATTGTGTGTGGATC 58.781 43.478 0.00 0.00 0.00 3.36
61 62 3.004315 GGTTCGTCAAATTGTGTGTGGAT 59.996 43.478 0.00 0.00 0.00 3.41
62 63 2.356382 GGTTCGTCAAATTGTGTGTGGA 59.644 45.455 0.00 0.00 0.00 4.02
63 64 2.726633 GGTTCGTCAAATTGTGTGTGG 58.273 47.619 0.00 0.00 0.00 4.17
64 65 2.371432 CGGTTCGTCAAATTGTGTGTG 58.629 47.619 0.00 0.00 0.00 3.82
65 66 1.332375 CCGGTTCGTCAAATTGTGTGT 59.668 47.619 0.00 0.00 0.00 3.72
66 67 1.334599 CCCGGTTCGTCAAATTGTGTG 60.335 52.381 0.00 0.00 0.00 3.82
67 68 0.948678 CCCGGTTCGTCAAATTGTGT 59.051 50.000 0.00 0.00 0.00 3.72
68 69 0.239879 CCCCGGTTCGTCAAATTGTG 59.760 55.000 0.00 0.00 0.00 3.33
69 70 0.108963 TCCCCGGTTCGTCAAATTGT 59.891 50.000 0.00 0.00 0.00 2.71
70 71 0.519961 GTCCCCGGTTCGTCAAATTG 59.480 55.000 0.00 0.00 0.00 2.32
71 72 0.607217 GGTCCCCGGTTCGTCAAATT 60.607 55.000 0.00 0.00 0.00 1.82
72 73 1.002990 GGTCCCCGGTTCGTCAAAT 60.003 57.895 0.00 0.00 0.00 2.32
73 74 1.980784 TTGGTCCCCGGTTCGTCAAA 61.981 55.000 0.00 0.00 0.00 2.69
74 75 2.441675 TTGGTCCCCGGTTCGTCAA 61.442 57.895 0.00 0.00 0.00 3.18
75 76 2.843411 TTGGTCCCCGGTTCGTCA 60.843 61.111 0.00 0.00 0.00 4.35
76 77 2.357881 GTTGGTCCCCGGTTCGTC 60.358 66.667 0.00 0.00 0.00 4.20
77 78 3.162858 TGTTGGTCCCCGGTTCGT 61.163 61.111 0.00 0.00 0.00 3.85
78 79 2.667199 GTGTTGGTCCCCGGTTCG 60.667 66.667 0.00 0.00 0.00 3.95
79 80 2.281970 GGTGTTGGTCCCCGGTTC 60.282 66.667 0.00 0.00 0.00 3.62
80 81 2.775219 AGGTGTTGGTCCCCGGTT 60.775 61.111 0.00 0.00 0.00 4.44
81 82 3.566210 CAGGTGTTGGTCCCCGGT 61.566 66.667 0.00 0.00 0.00 5.28
82 83 3.246112 TCAGGTGTTGGTCCCCGG 61.246 66.667 0.00 0.00 0.00 5.73
83 84 1.553690 ATCTCAGGTGTTGGTCCCCG 61.554 60.000 0.00 0.00 0.00 5.73
84 85 0.698818 AATCTCAGGTGTTGGTCCCC 59.301 55.000 0.00 0.00 0.00 4.81
85 86 1.351017 TGAATCTCAGGTGTTGGTCCC 59.649 52.381 0.00 0.00 0.00 4.46
86 87 2.039084 AGTGAATCTCAGGTGTTGGTCC 59.961 50.000 0.00 0.00 0.00 4.46
87 88 3.409026 AGTGAATCTCAGGTGTTGGTC 57.591 47.619 0.00 0.00 0.00 4.02
88 89 3.136443 TCAAGTGAATCTCAGGTGTTGGT 59.864 43.478 0.00 0.00 0.00 3.67
89 90 3.499918 GTCAAGTGAATCTCAGGTGTTGG 59.500 47.826 0.00 0.00 0.00 3.77
90 91 4.129380 TGTCAAGTGAATCTCAGGTGTTG 58.871 43.478 0.00 0.00 0.00 3.33
91 92 4.422073 TGTCAAGTGAATCTCAGGTGTT 57.578 40.909 0.00 0.00 0.00 3.32
92 93 4.130118 GTTGTCAAGTGAATCTCAGGTGT 58.870 43.478 0.00 0.00 0.00 4.16
93 94 3.499918 GGTTGTCAAGTGAATCTCAGGTG 59.500 47.826 0.00 0.00 0.00 4.00
94 95 3.136443 TGGTTGTCAAGTGAATCTCAGGT 59.864 43.478 0.00 0.00 0.00 4.00
95 96 3.743521 TGGTTGTCAAGTGAATCTCAGG 58.256 45.455 0.00 0.00 0.00 3.86
96 97 5.240183 ACAATGGTTGTCAAGTGAATCTCAG 59.760 40.000 0.00 0.00 40.56 3.35
97 98 5.132502 ACAATGGTTGTCAAGTGAATCTCA 58.867 37.500 0.00 0.00 40.56 3.27
98 99 5.695851 ACAATGGTTGTCAAGTGAATCTC 57.304 39.130 0.00 0.00 40.56 2.75
99 100 6.772716 ACTAACAATGGTTGTCAAGTGAATCT 59.227 34.615 0.00 0.00 44.59 2.40
100 101 6.970484 ACTAACAATGGTTGTCAAGTGAATC 58.030 36.000 0.00 0.00 44.59 2.52
101 102 6.016276 GGACTAACAATGGTTGTCAAGTGAAT 60.016 38.462 14.18 0.00 44.59 2.57
102 103 5.298276 GGACTAACAATGGTTGTCAAGTGAA 59.702 40.000 14.18 0.00 44.59 3.18
103 104 4.819630 GGACTAACAATGGTTGTCAAGTGA 59.180 41.667 14.18 0.00 44.59 3.41
104 105 4.023193 GGGACTAACAATGGTTGTCAAGTG 60.023 45.833 14.18 0.00 44.59 3.16
105 106 4.142038 GGGACTAACAATGGTTGTCAAGT 58.858 43.478 14.18 6.22 44.59 3.16
106 107 3.506067 GGGGACTAACAATGGTTGTCAAG 59.494 47.826 14.18 3.38 44.59 3.02
107 108 3.139397 AGGGGACTAACAATGGTTGTCAA 59.861 43.478 14.18 0.00 44.59 3.18
108 109 2.714250 AGGGGACTAACAATGGTTGTCA 59.286 45.455 14.18 0.00 44.59 3.58
109 110 3.434940 AGGGGACTAACAATGGTTGTC 57.565 47.619 4.32 4.32 44.59 3.18
110 111 3.653836 TGTAGGGGACTAACAATGGTTGT 59.346 43.478 0.00 0.00 46.54 3.32
111 112 4.295141 TGTAGGGGACTAACAATGGTTG 57.705 45.455 0.00 0.00 46.54 3.77
112 113 4.291249 ACATGTAGGGGACTAACAATGGTT 59.709 41.667 0.00 0.00 46.54 3.67
113 114 3.850173 ACATGTAGGGGACTAACAATGGT 59.150 43.478 0.00 0.00 46.54 3.55
114 115 4.503714 ACATGTAGGGGACTAACAATGG 57.496 45.455 0.00 0.00 46.54 3.16
115 116 6.479972 TCTACATGTAGGGGACTAACAATG 57.520 41.667 28.33 3.23 46.54 2.82
116 117 7.691993 AATCTACATGTAGGGGACTAACAAT 57.308 36.000 28.33 10.88 46.54 2.71
117 118 7.504926 AAATCTACATGTAGGGGACTAACAA 57.495 36.000 28.33 9.14 46.54 2.83
118 119 7.181305 TGAAAATCTACATGTAGGGGACTAACA 59.819 37.037 28.33 16.52 46.54 2.41
119 120 7.562135 TGAAAATCTACATGTAGGGGACTAAC 58.438 38.462 28.33 14.66 46.54 2.34
120 121 7.743116 TGAAAATCTACATGTAGGGGACTAA 57.257 36.000 28.33 11.16 46.54 2.24
121 122 7.931015 ATGAAAATCTACATGTAGGGGACTA 57.069 36.000 28.33 11.83 43.67 2.59
123 124 8.837389 GTTAATGAAAATCTACATGTAGGGGAC 58.163 37.037 28.33 17.49 34.06 4.46
124 125 8.553153 TGTTAATGAAAATCTACATGTAGGGGA 58.447 33.333 28.33 13.40 34.06 4.81
125 126 8.746052 TGTTAATGAAAATCTACATGTAGGGG 57.254 34.615 28.33 8.48 34.06 4.79
147 148 9.985730 CATGCCCTTATATTATGTTTTGATGTT 57.014 29.630 0.00 0.00 0.00 2.71
148 149 9.365906 TCATGCCCTTATATTATGTTTTGATGT 57.634 29.630 0.00 0.00 0.00 3.06
170 171 4.178540 GACCCATTGAAAGTGCAATCATG 58.821 43.478 0.00 0.00 36.39 3.07
171 172 3.833650 TGACCCATTGAAAGTGCAATCAT 59.166 39.130 0.00 0.00 36.39 2.45
172 173 3.005684 GTGACCCATTGAAAGTGCAATCA 59.994 43.478 0.00 0.00 36.39 2.57
173 174 3.005684 TGTGACCCATTGAAAGTGCAATC 59.994 43.478 0.00 0.00 36.39 2.67
174 175 2.964464 TGTGACCCATTGAAAGTGCAAT 59.036 40.909 0.00 0.00 38.96 3.56
175 176 2.100584 GTGTGACCCATTGAAAGTGCAA 59.899 45.455 0.00 0.00 0.00 4.08
176 177 1.680735 GTGTGACCCATTGAAAGTGCA 59.319 47.619 0.00 0.00 0.00 4.57
177 178 1.000274 GGTGTGACCCATTGAAAGTGC 60.000 52.381 0.00 0.00 30.04 4.40
396 400 2.106511 TGGGTATAGAGCATGGCCTTTC 59.893 50.000 3.32 0.00 0.00 2.62
437 441 0.899019 TGCATAACCACTAGGCGACA 59.101 50.000 0.00 0.00 40.27 4.35
455 459 7.543868 AGACGAAGATGATAGAAAAAGACTGTG 59.456 37.037 0.00 0.00 0.00 3.66
558 562 3.899981 CTGGGCTGGCAACGCACTA 62.900 63.158 3.28 0.00 39.69 2.74
637 641 6.265196 TCACTATTTTCATTGGTGTCAAGCTT 59.735 34.615 0.00 0.00 36.19 3.74
652 656 6.173339 TGATGTCCTGGAACTCACTATTTTC 58.827 40.000 0.00 0.00 0.00 2.29
702 706 3.876274 TGCACAGAGTGGAGACTATTC 57.124 47.619 0.00 0.00 33.64 1.75
736 740 3.065371 CCAGTTTTGTCGTCAAAGAAGCT 59.935 43.478 7.82 3.70 43.17 3.74
747 751 5.666969 TCTTGAACATACCAGTTTTGTCG 57.333 39.130 0.00 0.00 0.00 4.35
890 897 7.904558 ACTGTTGAGAGATCATAGATGGTTA 57.095 36.000 0.00 0.00 0.00 2.85
928 935 2.738643 CGGACGAGAAGCCAATGTATGT 60.739 50.000 0.00 0.00 0.00 2.29
968 975 6.406692 TCCAGCCAAGTATGTAGTATCTTC 57.593 41.667 0.00 0.00 0.00 2.87
1019 1026 1.664016 GCAGCTTGGTTGTGTCAATCG 60.664 52.381 0.00 0.00 0.00 3.34
1140 1147 7.491048 GCCAATTTCCTTCGAGCAAATAAAATA 59.509 33.333 0.00 0.00 0.00 1.40
1172 1179 1.819288 CCCAGTCTTCTTGTAGCTCGA 59.181 52.381 0.00 0.00 0.00 4.04
1277 1284 2.829023 ACACCTTTCCGAATCCTCCTA 58.171 47.619 0.00 0.00 0.00 2.94
1347 1354 3.972133 TCCCTGCTTTGAATCATGTGAT 58.028 40.909 0.00 0.00 36.07 3.06
1387 1394 1.392589 CGGCCCATGCTAACAATCTT 58.607 50.000 0.00 0.00 37.74 2.40
1584 1600 2.836636 TCTCATGGAGGTAGAGCAGT 57.163 50.000 0.00 0.00 0.00 4.40
1691 1707 5.221106 CCATGATCATACGATTTTGCAAGGT 60.221 40.000 8.15 0.00 29.66 3.50
1941 1957 1.691434 CCTTGGAGCCTCTGGTCTATC 59.309 57.143 0.00 0.00 39.02 2.08
1974 1990 1.527844 GACCAGGCATGCCTCATCC 60.528 63.158 36.65 20.69 46.28 3.51
2077 2093 2.030946 GTGCGAACTCTGATAATGGCAC 59.969 50.000 0.00 8.15 42.03 5.01
2086 2102 1.300620 CGGTTGGTGCGAACTCTGA 60.301 57.895 0.00 0.00 0.00 3.27
2159 2175 1.069978 TGAGCTGTGGATTTGACACGA 59.930 47.619 0.00 0.00 41.64 4.35
2508 2528 5.842907 TCCATGAGACCGTAGAACAATATG 58.157 41.667 0.00 0.00 0.00 1.78
2657 2680 7.880195 GCTTCTAAATCTCCCTGATATTGCTAA 59.120 37.037 0.00 0.00 34.45 3.09
2658 2681 7.390027 GCTTCTAAATCTCCCTGATATTGCTA 58.610 38.462 0.00 0.00 34.45 3.49
2659 2682 6.237154 GCTTCTAAATCTCCCTGATATTGCT 58.763 40.000 0.00 0.00 34.45 3.91
2755 2779 2.380084 TTAGCGTGGATCACAAGACC 57.620 50.000 0.00 0.00 33.40 3.85
2782 2806 2.034812 CCGGAGTGCTATGGAAGAGTAC 59.965 54.545 0.00 0.00 0.00 2.73
2800 2824 2.941064 TCATCTACAAGACGAGTACCGG 59.059 50.000 0.00 0.00 43.93 5.28
2822 2846 3.112580 CCGTTTGTTTGGCAACTGTAAG 58.887 45.455 0.00 0.00 36.72 2.34
2839 2863 3.927163 GATCCGTGTGGCGACCGTT 62.927 63.158 0.00 0.00 44.77 4.44
2840 2864 4.430765 GATCCGTGTGGCGACCGT 62.431 66.667 0.00 0.00 44.77 4.83
2841 2865 3.642778 AAGATCCGTGTGGCGACCG 62.643 63.158 0.00 0.00 44.77 4.79
2842 2866 2.100631 CAAGATCCGTGTGGCGACC 61.101 63.158 0.00 0.00 44.77 4.79
2872 2896 2.670414 GAGCCAATGTCGTGAAGAGAAG 59.330 50.000 0.00 0.00 0.00 2.85
2874 2898 1.402852 CGAGCCAATGTCGTGAAGAGA 60.403 52.381 0.00 0.00 32.62 3.10
2875 2899 0.994995 CGAGCCAATGTCGTGAAGAG 59.005 55.000 0.00 0.00 32.62 2.85
2879 2903 0.604073 TAACCGAGCCAATGTCGTGA 59.396 50.000 0.00 0.00 35.59 4.35
2882 2906 2.031683 GGATTTAACCGAGCCAATGTCG 59.968 50.000 0.00 0.00 37.17 4.35
2885 2909 3.016736 ACAGGATTTAACCGAGCCAATG 58.983 45.455 0.00 0.00 34.73 2.82
2886 2910 3.366052 ACAGGATTTAACCGAGCCAAT 57.634 42.857 0.00 0.00 34.73 3.16
2887 2911 2.871096 ACAGGATTTAACCGAGCCAA 57.129 45.000 0.00 0.00 34.73 4.52
2941 2993 4.221924 TCTTCACTGTCCGATCCAATTGTA 59.778 41.667 4.43 0.00 0.00 2.41
3034 3090 0.744414 CTGTAATGTGGACGGGGCAG 60.744 60.000 0.00 0.00 0.00 4.85
3180 3254 4.861102 ACTGGAGCCTCAAAATTGAAAG 57.139 40.909 0.00 0.00 36.64 2.62
3181 3255 4.261572 CGAACTGGAGCCTCAAAATTGAAA 60.262 41.667 0.00 0.00 36.64 2.69
3182 3256 3.253188 CGAACTGGAGCCTCAAAATTGAA 59.747 43.478 0.00 0.00 36.64 2.69
3183 3257 2.813754 CGAACTGGAGCCTCAAAATTGA 59.186 45.455 0.00 0.00 35.57 2.57
3184 3258 2.813754 TCGAACTGGAGCCTCAAAATTG 59.186 45.455 0.00 0.00 0.00 2.32
3185 3259 3.077359 CTCGAACTGGAGCCTCAAAATT 58.923 45.455 0.00 0.00 0.00 1.82
3186 3260 2.616510 CCTCGAACTGGAGCCTCAAAAT 60.617 50.000 0.00 0.00 32.57 1.82
3187 3261 1.270839 CCTCGAACTGGAGCCTCAAAA 60.271 52.381 0.00 0.00 32.57 2.44
3188 3262 0.321671 CCTCGAACTGGAGCCTCAAA 59.678 55.000 0.00 0.00 32.57 2.69
3189 3263 1.544825 CCCTCGAACTGGAGCCTCAA 61.545 60.000 0.00 0.00 32.57 3.02
3190 3264 1.984570 CCCTCGAACTGGAGCCTCA 60.985 63.158 0.00 0.00 32.57 3.86
3191 3265 2.896443 CCCTCGAACTGGAGCCTC 59.104 66.667 0.00 0.00 32.57 4.70
3192 3266 3.394836 GCCCTCGAACTGGAGCCT 61.395 66.667 0.00 0.00 32.57 4.58
3193 3267 4.821589 CGCCCTCGAACTGGAGCC 62.822 72.222 0.00 0.00 38.10 4.70
3195 3269 3.764466 AGCGCCCTCGAACTGGAG 61.764 66.667 2.29 0.00 38.10 3.86
3196 3270 4.069232 CAGCGCCCTCGAACTGGA 62.069 66.667 2.29 0.00 38.10 3.86
3197 3271 3.376935 ATCAGCGCCCTCGAACTGG 62.377 63.158 2.29 0.00 38.10 4.00
3198 3272 2.169789 CATCAGCGCCCTCGAACTG 61.170 63.158 2.29 0.00 38.10 3.16
3199 3273 2.185350 CATCAGCGCCCTCGAACT 59.815 61.111 2.29 0.00 38.10 3.01
3200 3274 3.567797 GCATCAGCGCCCTCGAAC 61.568 66.667 2.29 0.00 38.10 3.95


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.