Multiple sequence alignment - TraesCS2B01G218700

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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 TraesCS2B01G218700 chr2B 100.000 3807 0 0 1 3807 207601444 207597638 0.000000e+00 7031.0
1 TraesCS2B01G218700 chr2B 81.886 1336 233 8 1369 2701 207482275 207483604 0.000000e+00 1118.0
2 TraesCS2B01G218700 chr2B 80.118 1358 257 11 1369 2721 207471408 207472757 0.000000e+00 1000.0
3 TraesCS2B01G218700 chr2A 93.315 3665 141 47 175 3760 154412752 154416391 0.000000e+00 5315.0
4 TraesCS2B01G218700 chr2A 81.777 1339 235 8 1369 2704 154422566 154421234 0.000000e+00 1112.0
5 TraesCS2B01G218700 chr2A 91.549 71 0 2 3743 3807 154416408 154416478 4.050000e-15 93.5
6 TraesCS2B01G218700 chr2D 95.638 2384 67 18 783 3139 147968863 147966490 0.000000e+00 3792.0
7 TraesCS2B01G218700 chr2D 95.597 636 16 5 3177 3807 147966487 147965859 0.000000e+00 1009.0
8 TraesCS2B01G218700 chr2D 91.586 309 10 4 490 785 147971177 147970872 2.740000e-111 412.0
9 TraesCS2B01G218700 chr2D 96.528 144 4 1 259 402 147971318 147971176 1.770000e-58 237.0
10 TraesCS2B01G218700 chr2D 95.652 46 2 0 175 220 147971372 147971327 1.470000e-09 75.0
11 TraesCS2B01G218700 chr4B 73.751 1341 308 33 1380 2689 532582604 532581277 1.590000e-133 486.0
12 TraesCS2B01G218700 chr4D 73.602 1341 310 28 1380 2689 434030834 434029507 3.440000e-130 475.0
13 TraesCS2B01G218700 chr4A 73.472 1342 310 30 1380 2689 35477812 35476485 7.450000e-127 464.0
14 TraesCS2B01G218700 chr5D 72.424 1291 294 47 1367 2632 497493010 497491757 4.680000e-94 355.0
15 TraesCS2B01G218700 chr5D 85.057 174 26 0 1 174 425798041 425798214 1.090000e-40 178.0
16 TraesCS2B01G218700 chr6B 95.376 173 8 0 3 175 658982637 658982465 3.750000e-70 276.0


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 TraesCS2B01G218700 chr2B 207597638 207601444 3806 True 7031.00 7031 100.0000 1 3807 1 chr2B.!!$R1 3806
1 TraesCS2B01G218700 chr2B 207482275 207483604 1329 False 1118.00 1118 81.8860 1369 2701 1 chr2B.!!$F2 1332
2 TraesCS2B01G218700 chr2B 207471408 207472757 1349 False 1000.00 1000 80.1180 1369 2721 1 chr2B.!!$F1 1352
3 TraesCS2B01G218700 chr2A 154412752 154416478 3726 False 2704.25 5315 92.4320 175 3807 2 chr2A.!!$F1 3632
4 TraesCS2B01G218700 chr2A 154421234 154422566 1332 True 1112.00 1112 81.7770 1369 2704 1 chr2A.!!$R1 1335
5 TraesCS2B01G218700 chr2D 147965859 147971372 5513 True 1105.00 3792 95.0002 175 3807 5 chr2D.!!$R1 3632
6 TraesCS2B01G218700 chr4B 532581277 532582604 1327 True 486.00 486 73.7510 1380 2689 1 chr4B.!!$R1 1309
7 TraesCS2B01G218700 chr4D 434029507 434030834 1327 True 475.00 475 73.6020 1380 2689 1 chr4D.!!$R1 1309
8 TraesCS2B01G218700 chr4A 35476485 35477812 1327 True 464.00 464 73.4720 1380 2689 1 chr4A.!!$R1 1309
9 TraesCS2B01G218700 chr5D 497491757 497493010 1253 True 355.00 355 72.4240 1367 2632 1 chr5D.!!$R1 1265

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
107 108 0.035458 CGGCTCCAGGTTGAACTCTT 59.965 55.0 0.00 0.00 0.00 2.85 F
443 483 0.037160 TGCATGCATGAGTGGTGAGT 59.963 50.0 30.64 0.00 0.00 3.41 F
457 497 0.038159 GTGAGTGGCGCTACAAGTCT 60.038 55.0 26.36 4.25 0.00 3.24 F
488 528 0.038310 CCTTTCGAGGGAGGCCTTTT 59.962 55.0 6.77 0.00 0.00 2.27 F
1352 3537 0.963962 CTTTGCATGGGCTGAACACT 59.036 50.0 0.00 0.00 41.91 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1012 3185 1.003233 GGGGAGGGACGCATTTATAGG 59.997 57.143 0.00 0.00 0.00 2.57 R
2114 4317 0.036388 TGGAAGAAGTGGATGCCGAC 60.036 55.000 0.00 0.00 0.00 4.79 R
2323 4526 1.133325 ACTAGGGAGACGATCATGCCT 60.133 52.381 7.61 7.61 0.00 4.75 R
2693 4922 1.219124 GCGAGCTCATGTCCTCCAA 59.781 57.895 15.40 0.00 0.00 3.53 R
3111 5353 0.108945 AACGCCACGGAAGTAGCTAC 60.109 55.000 16.43 16.43 46.74 3.58 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
20 21 2.648059 CCCTCCTGATCAACATGTTCC 58.352 52.381 8.48 1.72 0.00 3.62
21 22 2.240667 CCCTCCTGATCAACATGTTCCT 59.759 50.000 8.48 0.00 0.00 3.36
22 23 3.276857 CCTCCTGATCAACATGTTCCTG 58.723 50.000 8.48 0.00 0.00 3.86
23 24 3.054875 CCTCCTGATCAACATGTTCCTGA 60.055 47.826 8.48 4.47 0.00 3.86
24 25 4.384978 CCTCCTGATCAACATGTTCCTGAT 60.385 45.833 8.48 9.72 32.49 2.90
25 26 5.183530 TCCTGATCAACATGTTCCTGATT 57.816 39.130 8.48 0.00 29.97 2.57
26 27 5.573219 TCCTGATCAACATGTTCCTGATTT 58.427 37.500 8.48 0.00 29.97 2.17
27 28 5.649395 TCCTGATCAACATGTTCCTGATTTC 59.351 40.000 8.48 0.72 29.97 2.17
28 29 5.163581 CCTGATCAACATGTTCCTGATTTCC 60.164 44.000 8.48 0.00 29.97 3.13
29 30 5.323581 TGATCAACATGTTCCTGATTTCCA 58.676 37.500 8.48 1.88 29.97 3.53
30 31 5.183713 TGATCAACATGTTCCTGATTTCCAC 59.816 40.000 8.48 0.00 29.97 4.02
31 32 3.826157 TCAACATGTTCCTGATTTCCACC 59.174 43.478 8.48 0.00 0.00 4.61
32 33 2.436417 ACATGTTCCTGATTTCCACCG 58.564 47.619 0.00 0.00 0.00 4.94
33 34 2.039746 ACATGTTCCTGATTTCCACCGA 59.960 45.455 0.00 0.00 0.00 4.69
34 35 2.940994 TGTTCCTGATTTCCACCGAA 57.059 45.000 0.00 0.00 0.00 4.30
35 36 2.500229 TGTTCCTGATTTCCACCGAAC 58.500 47.619 0.00 0.00 33.07 3.95
36 37 1.463444 GTTCCTGATTTCCACCGAACG 59.537 52.381 0.00 0.00 0.00 3.95
37 38 0.970640 TCCTGATTTCCACCGAACGA 59.029 50.000 0.00 0.00 0.00 3.85
38 39 1.076332 CCTGATTTCCACCGAACGAC 58.924 55.000 0.00 0.00 0.00 4.34
39 40 1.606994 CCTGATTTCCACCGAACGACA 60.607 52.381 0.00 0.00 0.00 4.35
40 41 1.726791 CTGATTTCCACCGAACGACAG 59.273 52.381 0.00 0.00 0.00 3.51
41 42 1.341852 TGATTTCCACCGAACGACAGA 59.658 47.619 0.00 0.00 0.00 3.41
42 43 1.993370 GATTTCCACCGAACGACAGAG 59.007 52.381 0.00 0.00 0.00 3.35
43 44 0.748450 TTTCCACCGAACGACAGAGT 59.252 50.000 0.00 0.00 0.00 3.24
44 45 1.608055 TTCCACCGAACGACAGAGTA 58.392 50.000 0.00 0.00 0.00 2.59
45 46 0.877071 TCCACCGAACGACAGAGTAC 59.123 55.000 0.00 0.00 0.00 2.73
46 47 0.109412 CCACCGAACGACAGAGTACC 60.109 60.000 0.00 0.00 0.00 3.34
47 48 0.594602 CACCGAACGACAGAGTACCA 59.405 55.000 0.00 0.00 0.00 3.25
48 49 1.001048 CACCGAACGACAGAGTACCAA 60.001 52.381 0.00 0.00 0.00 3.67
49 50 1.682854 ACCGAACGACAGAGTACCAAA 59.317 47.619 0.00 0.00 0.00 3.28
50 51 2.101249 ACCGAACGACAGAGTACCAAAA 59.899 45.455 0.00 0.00 0.00 2.44
51 52 3.125316 CCGAACGACAGAGTACCAAAAA 58.875 45.455 0.00 0.00 0.00 1.94
70 71 3.351794 AAATCCTCCGGAAAGAACTCC 57.648 47.619 5.23 0.00 34.34 3.85
71 72 1.205055 ATCCTCCGGAAAGAACTCCC 58.795 55.000 5.23 0.00 34.34 4.30
72 73 0.116541 TCCTCCGGAAAGAACTCCCT 59.883 55.000 5.23 0.00 31.03 4.20
73 74 1.360162 TCCTCCGGAAAGAACTCCCTA 59.640 52.381 5.23 0.00 31.03 3.53
74 75 2.185387 CCTCCGGAAAGAACTCCCTAA 58.815 52.381 5.23 0.00 31.03 2.69
75 76 2.772515 CCTCCGGAAAGAACTCCCTAAT 59.227 50.000 5.23 0.00 31.03 1.73
76 77 3.181464 CCTCCGGAAAGAACTCCCTAATC 60.181 52.174 5.23 0.00 31.03 1.75
77 78 2.429610 TCCGGAAAGAACTCCCTAATCG 59.570 50.000 0.00 0.00 31.03 3.34
78 79 2.429610 CCGGAAAGAACTCCCTAATCGA 59.570 50.000 0.00 0.00 31.03 3.59
79 80 3.445857 CGGAAAGAACTCCCTAATCGAC 58.554 50.000 0.00 0.00 31.03 4.20
80 81 3.119245 CGGAAAGAACTCCCTAATCGACA 60.119 47.826 0.00 0.00 31.03 4.35
81 82 4.441634 CGGAAAGAACTCCCTAATCGACAT 60.442 45.833 0.00 0.00 31.03 3.06
82 83 4.811557 GGAAAGAACTCCCTAATCGACATG 59.188 45.833 0.00 0.00 0.00 3.21
83 84 5.420409 GAAAGAACTCCCTAATCGACATGT 58.580 41.667 0.00 0.00 0.00 3.21
84 85 4.657436 AGAACTCCCTAATCGACATGTC 57.343 45.455 16.21 16.21 0.00 3.06
85 86 3.385111 AGAACTCCCTAATCGACATGTCC 59.615 47.826 20.03 2.90 0.00 4.02
86 87 2.747177 ACTCCCTAATCGACATGTCCA 58.253 47.619 20.03 8.09 0.00 4.02
87 88 2.695666 ACTCCCTAATCGACATGTCCAG 59.304 50.000 20.03 11.41 0.00 3.86
88 89 1.412710 TCCCTAATCGACATGTCCAGC 59.587 52.381 20.03 0.00 0.00 4.85
89 90 1.491670 CCTAATCGACATGTCCAGCG 58.508 55.000 20.03 9.25 0.00 5.18
90 91 1.491670 CTAATCGACATGTCCAGCGG 58.508 55.000 20.03 5.83 0.00 5.52
91 92 0.529773 TAATCGACATGTCCAGCGGC 60.530 55.000 20.03 0.00 0.00 6.53
92 93 2.244117 AATCGACATGTCCAGCGGCT 62.244 55.000 20.03 0.00 0.00 5.52
93 94 2.635229 ATCGACATGTCCAGCGGCTC 62.635 60.000 20.03 0.00 0.00 4.70
94 95 2.512515 GACATGTCCAGCGGCTCC 60.513 66.667 15.31 0.00 0.00 4.70
95 96 3.315142 GACATGTCCAGCGGCTCCA 62.315 63.158 15.31 0.00 0.00 3.86
96 97 2.513204 CATGTCCAGCGGCTCCAG 60.513 66.667 0.00 0.00 0.00 3.86
97 98 3.790437 ATGTCCAGCGGCTCCAGG 61.790 66.667 0.00 0.00 0.00 4.45
99 100 4.021925 GTCCAGCGGCTCCAGGTT 62.022 66.667 0.00 0.00 0.00 3.50
100 101 4.020617 TCCAGCGGCTCCAGGTTG 62.021 66.667 0.00 0.00 0.00 3.77
101 102 4.020617 CCAGCGGCTCCAGGTTGA 62.021 66.667 0.00 0.00 0.00 3.18
102 103 2.032528 CAGCGGCTCCAGGTTGAA 59.967 61.111 0.00 0.00 0.00 2.69
103 104 2.032681 AGCGGCTCCAGGTTGAAC 59.967 61.111 0.00 0.00 0.00 3.18
104 105 2.032681 GCGGCTCCAGGTTGAACT 59.967 61.111 0.00 0.00 0.00 3.01
105 106 2.035442 GCGGCTCCAGGTTGAACTC 61.035 63.158 0.00 0.00 0.00 3.01
106 107 1.674057 CGGCTCCAGGTTGAACTCT 59.326 57.895 0.00 0.00 0.00 3.24
107 108 0.035458 CGGCTCCAGGTTGAACTCTT 59.965 55.000 0.00 0.00 0.00 2.85
108 109 1.528129 GGCTCCAGGTTGAACTCTTG 58.472 55.000 0.00 0.00 0.00 3.02
109 110 0.877743 GCTCCAGGTTGAACTCTTGC 59.122 55.000 0.00 0.00 0.00 4.01
110 111 1.815408 GCTCCAGGTTGAACTCTTGCA 60.815 52.381 0.00 0.00 0.00 4.08
111 112 1.876156 CTCCAGGTTGAACTCTTGCAC 59.124 52.381 0.00 0.00 0.00 4.57
112 113 1.211703 TCCAGGTTGAACTCTTGCACA 59.788 47.619 0.00 0.00 0.00 4.57
113 114 2.023673 CCAGGTTGAACTCTTGCACAA 58.976 47.619 0.00 0.00 0.00 3.33
114 115 2.624838 CCAGGTTGAACTCTTGCACAAT 59.375 45.455 0.00 0.00 0.00 2.71
115 116 3.551454 CCAGGTTGAACTCTTGCACAATG 60.551 47.826 0.00 0.00 0.00 2.82
116 117 2.624838 AGGTTGAACTCTTGCACAATGG 59.375 45.455 0.00 0.00 0.00 3.16
117 118 2.397549 GTTGAACTCTTGCACAATGGC 58.602 47.619 0.00 0.00 0.00 4.40
118 119 0.592637 TGAACTCTTGCACAATGGCG 59.407 50.000 0.00 0.00 36.28 5.69
119 120 0.109597 GAACTCTTGCACAATGGCGG 60.110 55.000 0.00 0.00 36.28 6.13
120 121 2.146073 AACTCTTGCACAATGGCGGC 62.146 55.000 0.00 0.00 36.28 6.53
121 122 2.596923 TCTTGCACAATGGCGGCA 60.597 55.556 16.34 16.34 36.28 5.69
122 123 2.126228 CTTGCACAATGGCGGCAG 60.126 61.111 19.29 7.31 38.97 4.85
123 124 4.360964 TTGCACAATGGCGGCAGC 62.361 61.111 19.29 15.83 38.97 5.25
148 149 2.799371 GCAAGATCTGCCTGCTGC 59.201 61.111 10.09 5.00 46.13 5.25
149 150 2.772691 GCAAGATCTGCCTGCTGCC 61.773 63.158 10.09 0.00 46.13 4.85
150 151 1.077644 CAAGATCTGCCTGCTGCCT 60.078 57.895 0.00 0.00 40.16 4.75
151 152 1.096386 CAAGATCTGCCTGCTGCCTC 61.096 60.000 0.00 0.00 40.16 4.70
152 153 1.559965 AAGATCTGCCTGCTGCCTCA 61.560 55.000 0.00 0.00 40.16 3.86
153 154 1.148723 GATCTGCCTGCTGCCTCAT 59.851 57.895 0.00 0.00 40.16 2.90
154 155 1.152943 ATCTGCCTGCTGCCTCATG 60.153 57.895 0.00 0.00 40.16 3.07
155 156 3.518998 CTGCCTGCTGCCTCATGC 61.519 66.667 0.00 0.00 40.16 4.06
158 159 2.361992 CCTGCTGCCTCATGCCAA 60.362 61.111 0.00 0.00 40.16 4.52
159 160 2.707849 CCTGCTGCCTCATGCCAAC 61.708 63.158 0.00 0.00 40.16 3.77
160 161 2.677524 TGCTGCCTCATGCCAACC 60.678 61.111 0.00 0.00 40.16 3.77
161 162 2.677524 GCTGCCTCATGCCAACCA 60.678 61.111 0.00 0.00 40.16 3.67
162 163 2.998279 GCTGCCTCATGCCAACCAC 61.998 63.158 0.00 0.00 40.16 4.16
163 164 2.283101 TGCCTCATGCCAACCACC 60.283 61.111 0.00 0.00 40.16 4.61
164 165 3.443045 GCCTCATGCCAACCACCG 61.443 66.667 0.00 0.00 0.00 4.94
165 166 2.350895 CCTCATGCCAACCACCGA 59.649 61.111 0.00 0.00 0.00 4.69
166 167 1.746615 CCTCATGCCAACCACCGAG 60.747 63.158 0.00 0.00 0.00 4.63
167 168 1.296392 CTCATGCCAACCACCGAGA 59.704 57.895 0.00 0.00 31.18 4.04
168 169 1.003839 TCATGCCAACCACCGAGAC 60.004 57.895 0.00 0.00 0.00 3.36
169 170 2.040544 CATGCCAACCACCGAGACC 61.041 63.158 0.00 0.00 0.00 3.85
170 171 2.525124 ATGCCAACCACCGAGACCA 61.525 57.895 0.00 0.00 0.00 4.02
171 172 2.668550 GCCAACCACCGAGACCAC 60.669 66.667 0.00 0.00 0.00 4.16
172 173 2.032071 CCAACCACCGAGACCACC 59.968 66.667 0.00 0.00 0.00 4.61
173 174 2.813726 CCAACCACCGAGACCACCA 61.814 63.158 0.00 0.00 0.00 4.17
174 175 1.374947 CAACCACCGAGACCACCAT 59.625 57.895 0.00 0.00 0.00 3.55
175 176 0.611200 CAACCACCGAGACCACCATA 59.389 55.000 0.00 0.00 0.00 2.74
176 177 1.002659 CAACCACCGAGACCACCATAA 59.997 52.381 0.00 0.00 0.00 1.90
177 178 1.354101 ACCACCGAGACCACCATAAA 58.646 50.000 0.00 0.00 0.00 1.40
178 179 1.002773 ACCACCGAGACCACCATAAAC 59.997 52.381 0.00 0.00 0.00 2.01
179 180 1.002659 CCACCGAGACCACCATAAACA 59.997 52.381 0.00 0.00 0.00 2.83
180 181 2.355716 CCACCGAGACCACCATAAACAT 60.356 50.000 0.00 0.00 0.00 2.71
181 182 3.118555 CCACCGAGACCACCATAAACATA 60.119 47.826 0.00 0.00 0.00 2.29
182 183 4.119862 CACCGAGACCACCATAAACATAG 58.880 47.826 0.00 0.00 0.00 2.23
183 184 3.773119 ACCGAGACCACCATAAACATAGT 59.227 43.478 0.00 0.00 0.00 2.12
225 226 4.585581 TGCCAGATGGATTATTGTGATTGG 59.414 41.667 2.18 0.00 37.39 3.16
248 249 4.301662 AAGGAGGAAGGGGCCCCA 62.302 66.667 42.48 0.00 38.92 4.96
291 331 4.395625 TCGGTGTGATAGAGGGTAGTATG 58.604 47.826 0.00 0.00 0.00 2.39
324 364 6.176975 TCGAGCAAACATAAGTACATTTGG 57.823 37.500 0.00 0.00 33.55 3.28
396 436 6.204688 ACATGTCTAATGCTCGAAACTCAAAA 59.795 34.615 0.00 0.00 0.00 2.44
398 438 5.179368 TGTCTAATGCTCGAAACTCAAAAGG 59.821 40.000 0.00 0.00 0.00 3.11
399 439 5.408604 GTCTAATGCTCGAAACTCAAAAGGA 59.591 40.000 0.00 0.00 0.00 3.36
400 440 4.489679 AATGCTCGAAACTCAAAAGGAC 57.510 40.909 0.00 0.00 0.00 3.85
401 441 2.912771 TGCTCGAAACTCAAAAGGACA 58.087 42.857 0.00 0.00 0.00 4.02
402 442 2.872245 TGCTCGAAACTCAAAAGGACAG 59.128 45.455 0.00 0.00 0.00 3.51
403 443 2.349912 GCTCGAAACTCAAAAGGACAGC 60.350 50.000 0.00 0.00 0.00 4.40
404 444 2.872245 CTCGAAACTCAAAAGGACAGCA 59.128 45.455 0.00 0.00 0.00 4.41
405 445 3.275143 TCGAAACTCAAAAGGACAGCAA 58.725 40.909 0.00 0.00 0.00 3.91
406 446 3.882888 TCGAAACTCAAAAGGACAGCAAT 59.117 39.130 0.00 0.00 0.00 3.56
407 447 5.060506 TCGAAACTCAAAAGGACAGCAATA 58.939 37.500 0.00 0.00 0.00 1.90
408 448 5.049680 TCGAAACTCAAAAGGACAGCAATAC 60.050 40.000 0.00 0.00 0.00 1.89
409 449 5.049405 CGAAACTCAAAAGGACAGCAATACT 60.049 40.000 0.00 0.00 0.00 2.12
429 469 2.733517 TGCGTATGAAATGCATGCATG 58.266 42.857 32.79 22.70 45.29 4.06
441 481 3.581163 ATGCATGCATGAGTGGTGA 57.419 47.368 31.74 0.21 35.03 4.02
442 482 1.389555 ATGCATGCATGAGTGGTGAG 58.610 50.000 31.74 0.20 35.03 3.51
443 483 0.037160 TGCATGCATGAGTGGTGAGT 59.963 50.000 30.64 0.00 0.00 3.41
444 484 0.450583 GCATGCATGAGTGGTGAGTG 59.549 55.000 30.64 0.46 0.00 3.51
445 485 1.092348 CATGCATGAGTGGTGAGTGG 58.908 55.000 22.59 0.00 0.00 4.00
446 486 0.679002 ATGCATGAGTGGTGAGTGGC 60.679 55.000 0.00 0.00 0.00 5.01
447 487 2.393768 GCATGAGTGGTGAGTGGCG 61.394 63.158 0.00 0.00 0.00 5.69
448 488 2.046892 ATGAGTGGTGAGTGGCGC 60.047 61.111 0.00 0.00 0.00 6.53
449 489 2.587247 ATGAGTGGTGAGTGGCGCT 61.587 57.895 7.64 0.00 0.00 5.92
450 490 1.257750 ATGAGTGGTGAGTGGCGCTA 61.258 55.000 7.64 0.00 0.00 4.26
451 491 1.446272 GAGTGGTGAGTGGCGCTAC 60.446 63.158 17.10 17.10 38.61 3.58
452 492 2.154798 GAGTGGTGAGTGGCGCTACA 62.155 60.000 26.36 4.15 40.53 2.74
453 493 1.301401 GTGGTGAGTGGCGCTACAA 60.301 57.895 26.36 10.96 38.26 2.41
454 494 1.005037 TGGTGAGTGGCGCTACAAG 60.005 57.895 26.36 0.00 0.00 3.16
455 495 1.004918 GGTGAGTGGCGCTACAAGT 60.005 57.895 26.36 5.10 0.00 3.16
456 496 1.014564 GGTGAGTGGCGCTACAAGTC 61.015 60.000 26.36 15.05 0.00 3.01
457 497 0.038159 GTGAGTGGCGCTACAAGTCT 60.038 55.000 26.36 4.25 0.00 3.24
458 498 0.679505 TGAGTGGCGCTACAAGTCTT 59.320 50.000 26.36 3.42 0.00 3.01
459 499 1.070134 TGAGTGGCGCTACAAGTCTTT 59.930 47.619 26.36 2.59 0.00 2.52
460 500 1.461127 GAGTGGCGCTACAAGTCTTTG 59.539 52.381 26.36 0.00 40.24 2.77
462 502 2.036733 AGTGGCGCTACAAGTCTTTGTA 59.963 45.455 26.36 0.80 45.45 2.41
463 503 2.157085 GTGGCGCTACAAGTCTTTGTAC 59.843 50.000 19.95 0.00 45.45 2.90
464 504 1.389106 GGCGCTACAAGTCTTTGTACG 59.611 52.381 7.64 13.14 45.45 3.67
465 505 1.389106 GCGCTACAAGTCTTTGTACGG 59.611 52.381 0.00 6.59 45.45 4.02
466 506 2.669364 CGCTACAAGTCTTTGTACGGT 58.331 47.619 11.19 0.00 45.45 4.83
467 507 3.054878 CGCTACAAGTCTTTGTACGGTT 58.945 45.455 11.19 0.00 45.45 4.44
468 508 3.120782 CGCTACAAGTCTTTGTACGGTTC 59.879 47.826 11.19 0.00 45.45 3.62
469 509 3.431233 GCTACAAGTCTTTGTACGGTTCC 59.569 47.826 0.00 0.00 45.45 3.62
470 510 2.842457 ACAAGTCTTTGTACGGTTCCC 58.158 47.619 0.00 0.00 45.45 3.97
471 511 2.436911 ACAAGTCTTTGTACGGTTCCCT 59.563 45.455 0.00 0.00 45.45 4.20
472 512 3.118149 ACAAGTCTTTGTACGGTTCCCTT 60.118 43.478 0.00 0.00 45.45 3.95
473 513 3.851458 AGTCTTTGTACGGTTCCCTTT 57.149 42.857 0.00 0.00 0.00 3.11
474 514 3.736720 AGTCTTTGTACGGTTCCCTTTC 58.263 45.455 0.00 0.00 0.00 2.62
475 515 2.477754 GTCTTTGTACGGTTCCCTTTCG 59.522 50.000 0.00 0.00 0.00 3.46
476 516 2.364970 TCTTTGTACGGTTCCCTTTCGA 59.635 45.455 0.00 0.00 0.00 3.71
477 517 2.443887 TTGTACGGTTCCCTTTCGAG 57.556 50.000 0.00 0.00 0.00 4.04
478 518 0.604578 TGTACGGTTCCCTTTCGAGG 59.395 55.000 0.00 0.00 0.00 4.63
486 526 3.404773 CCTTTCGAGGGAGGCCTT 58.595 61.111 6.77 0.00 0.00 4.35
487 527 1.685820 CCTTTCGAGGGAGGCCTTT 59.314 57.895 6.77 0.00 0.00 3.11
488 528 0.038310 CCTTTCGAGGGAGGCCTTTT 59.962 55.000 6.77 0.00 0.00 2.27
526 656 2.360191 TCCAAAGGGGATGCTGCC 59.640 61.111 0.00 0.00 42.15 4.85
602 732 6.406624 GGGTTGAGAAAATCATGCAGATTGAT 60.407 38.462 10.78 4.17 46.09 2.57
856 3015 1.609555 GAGGAGATAGCTACACCACCG 59.390 57.143 0.00 0.00 0.00 4.94
858 3017 1.400737 GAGATAGCTACACCACCGGT 58.599 55.000 0.00 0.00 35.62 5.28
1257 3430 1.075896 GACCTCCATCCTCCTCGGT 60.076 63.158 0.00 0.00 0.00 4.69
1314 3498 4.335400 TTCGCTGGATCTGTTGCATATA 57.665 40.909 0.00 0.00 0.00 0.86
1315 3499 3.653344 TCGCTGGATCTGTTGCATATAC 58.347 45.455 0.00 0.00 0.00 1.47
1328 3513 7.011389 TCTGTTGCATATACTAGTACGTACGTT 59.989 37.037 27.92 12.33 0.00 3.99
1348 3533 1.667151 GTGCTTTGCATGGGCTGAA 59.333 52.632 0.00 0.00 41.91 3.02
1352 3537 0.963962 CTTTGCATGGGCTGAACACT 59.036 50.000 0.00 0.00 41.91 3.55
1741 3926 2.749621 GTTCATCAACTTCGGCATCCTT 59.250 45.455 0.00 0.00 0.00 3.36
2114 4317 1.300465 CACATCCTCATCGCGGGAG 60.300 63.158 18.06 18.06 34.89 4.30
2602 4831 1.303561 GCTGTCCAAGGCCATGACA 60.304 57.895 10.18 14.86 37.45 3.58
2721 4950 3.482783 GAGCTCGCTGTTCGGCAC 61.483 66.667 0.00 0.00 37.01 5.01
3079 5321 2.202824 CAATCGCCGCCGGACTAA 60.203 61.111 7.68 0.00 34.56 2.24
3111 5353 2.434428 AGAGTGTAGAGGTGTACCGTG 58.566 52.381 0.00 0.00 42.08 4.94
3137 5379 0.878523 CTTCCGTGGCGTTTGTCTCA 60.879 55.000 0.00 0.00 0.00 3.27
3140 5382 0.999406 CCGTGGCGTTTGTCTCATAG 59.001 55.000 0.00 0.00 0.00 2.23
3262 5504 5.694458 GCCACGGAAAATGTGTAAGAAAAAT 59.306 36.000 0.00 0.00 35.56 1.82
3358 5607 8.703336 CATATATTCATGTGTCCTCGTTACAAG 58.297 37.037 0.00 0.00 0.00 3.16
3416 5665 0.462047 ATCGGCTTGATCACGGGAAC 60.462 55.000 0.00 0.00 28.49 3.62
3471 5720 0.976641 CAGCTGGTCCTGGTCTTGTA 59.023 55.000 5.57 0.00 0.00 2.41
3545 5798 2.816958 CAGGCCTAGTGTGCAGCG 60.817 66.667 3.98 0.00 0.00 5.18
3566 5819 7.276658 GCAGCGCAGTGATTATAGTAGATTATT 59.723 37.037 11.47 0.00 0.00 1.40
3624 5877 3.181524 GCATGTGCAACGATAACTTACGT 60.182 43.478 0.00 0.00 42.39 3.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.240667 AGGAACATGTTGATCAGGAGGG 59.759 50.000 17.58 0.00 0.00 4.30
1 2 3.054875 TCAGGAACATGTTGATCAGGAGG 60.055 47.826 17.58 0.00 0.00 4.30
2 3 4.212143 TCAGGAACATGTTGATCAGGAG 57.788 45.455 17.58 0.00 0.00 3.69
3 4 4.849813 ATCAGGAACATGTTGATCAGGA 57.150 40.909 17.58 5.23 0.00 3.86
5 6 5.416639 TGGAAATCAGGAACATGTTGATCAG 59.583 40.000 17.58 2.79 31.50 2.90
6 7 5.183713 GTGGAAATCAGGAACATGTTGATCA 59.816 40.000 17.58 5.42 31.50 2.92
7 8 5.393461 GGTGGAAATCAGGAACATGTTGATC 60.393 44.000 17.58 0.96 31.50 2.92
8 9 4.463891 GGTGGAAATCAGGAACATGTTGAT 59.536 41.667 17.58 10.78 33.18 2.57
9 10 3.826157 GGTGGAAATCAGGAACATGTTGA 59.174 43.478 17.58 8.63 0.00 3.18
10 11 3.366273 CGGTGGAAATCAGGAACATGTTG 60.366 47.826 17.58 2.23 0.00 3.33
11 12 2.819608 CGGTGGAAATCAGGAACATGTT 59.180 45.455 11.78 11.78 0.00 2.71
12 13 2.039746 TCGGTGGAAATCAGGAACATGT 59.960 45.455 0.00 0.00 0.00 3.21
13 14 2.710377 TCGGTGGAAATCAGGAACATG 58.290 47.619 0.00 0.00 0.00 3.21
14 15 3.081804 GTTCGGTGGAAATCAGGAACAT 58.918 45.455 0.00 0.00 38.67 2.71
15 16 2.500229 GTTCGGTGGAAATCAGGAACA 58.500 47.619 0.00 0.00 38.67 3.18
16 17 1.463444 CGTTCGGTGGAAATCAGGAAC 59.537 52.381 0.00 0.00 36.99 3.62
17 18 1.345089 TCGTTCGGTGGAAATCAGGAA 59.655 47.619 0.00 0.00 33.05 3.36
18 19 0.970640 TCGTTCGGTGGAAATCAGGA 59.029 50.000 0.00 0.00 33.05 3.86
19 20 1.076332 GTCGTTCGGTGGAAATCAGG 58.924 55.000 0.00 0.00 33.05 3.86
20 21 1.726791 CTGTCGTTCGGTGGAAATCAG 59.273 52.381 0.00 0.00 33.05 2.90
21 22 1.341852 TCTGTCGTTCGGTGGAAATCA 59.658 47.619 0.00 0.00 33.05 2.57
22 23 1.993370 CTCTGTCGTTCGGTGGAAATC 59.007 52.381 0.00 0.00 33.05 2.17
23 24 1.343465 ACTCTGTCGTTCGGTGGAAAT 59.657 47.619 0.00 0.00 33.05 2.17
24 25 0.748450 ACTCTGTCGTTCGGTGGAAA 59.252 50.000 0.00 0.00 33.05 3.13
25 26 1.267806 GTACTCTGTCGTTCGGTGGAA 59.732 52.381 0.00 0.00 0.00 3.53
26 27 0.877071 GTACTCTGTCGTTCGGTGGA 59.123 55.000 0.00 0.00 0.00 4.02
27 28 0.109412 GGTACTCTGTCGTTCGGTGG 60.109 60.000 0.00 0.00 0.00 4.61
28 29 0.594602 TGGTACTCTGTCGTTCGGTG 59.405 55.000 0.00 0.00 0.00 4.94
29 30 1.321474 TTGGTACTCTGTCGTTCGGT 58.679 50.000 0.00 0.00 0.00 4.69
30 31 2.427232 TTTGGTACTCTGTCGTTCGG 57.573 50.000 0.00 0.00 0.00 4.30
55 56 3.491104 CGATTAGGGAGTTCTTTCCGGAG 60.491 52.174 3.34 0.00 38.17 4.63
56 57 2.429610 CGATTAGGGAGTTCTTTCCGGA 59.570 50.000 0.00 0.00 38.17 5.14
57 58 2.429610 TCGATTAGGGAGTTCTTTCCGG 59.570 50.000 0.00 0.00 38.17 5.14
58 59 3.119245 TGTCGATTAGGGAGTTCTTTCCG 60.119 47.826 0.00 0.00 38.17 4.30
59 60 4.467198 TGTCGATTAGGGAGTTCTTTCC 57.533 45.455 0.00 0.00 36.46 3.13
60 61 5.420409 ACATGTCGATTAGGGAGTTCTTTC 58.580 41.667 0.00 0.00 0.00 2.62
61 62 5.420409 GACATGTCGATTAGGGAGTTCTTT 58.580 41.667 10.69 0.00 0.00 2.52
62 63 4.141914 GGACATGTCGATTAGGGAGTTCTT 60.142 45.833 19.33 0.00 0.00 2.52
63 64 3.385111 GGACATGTCGATTAGGGAGTTCT 59.615 47.826 19.33 0.00 0.00 3.01
64 65 3.132289 TGGACATGTCGATTAGGGAGTTC 59.868 47.826 19.33 1.69 0.00 3.01
65 66 3.104512 TGGACATGTCGATTAGGGAGTT 58.895 45.455 19.33 0.00 0.00 3.01
66 67 2.695666 CTGGACATGTCGATTAGGGAGT 59.304 50.000 19.33 0.00 0.00 3.85
67 68 2.546795 GCTGGACATGTCGATTAGGGAG 60.547 54.545 19.33 3.46 0.00 4.30
68 69 1.412710 GCTGGACATGTCGATTAGGGA 59.587 52.381 19.33 0.00 0.00 4.20
69 70 1.869754 CGCTGGACATGTCGATTAGGG 60.870 57.143 19.33 16.89 0.00 3.53
70 71 1.491670 CGCTGGACATGTCGATTAGG 58.508 55.000 19.33 5.22 0.00 2.69
71 72 1.491670 CCGCTGGACATGTCGATTAG 58.508 55.000 19.33 14.70 0.00 1.73
72 73 0.529773 GCCGCTGGACATGTCGATTA 60.530 55.000 19.33 5.32 0.00 1.75
73 74 1.815421 GCCGCTGGACATGTCGATT 60.815 57.895 19.33 0.00 0.00 3.34
74 75 2.202932 GCCGCTGGACATGTCGAT 60.203 61.111 19.33 0.00 0.00 3.59
75 76 3.356639 GAGCCGCTGGACATGTCGA 62.357 63.158 19.33 14.89 0.00 4.20
76 77 2.887568 GAGCCGCTGGACATGTCG 60.888 66.667 19.33 8.65 0.00 4.35
77 78 2.512515 GGAGCCGCTGGACATGTC 60.513 66.667 17.91 17.91 0.00 3.06
78 79 3.320879 CTGGAGCCGCTGGACATGT 62.321 63.158 0.00 0.00 0.00 3.21
79 80 2.513204 CTGGAGCCGCTGGACATG 60.513 66.667 0.00 0.00 0.00 3.21
80 81 3.790437 CCTGGAGCCGCTGGACAT 61.790 66.667 0.00 0.00 0.00 3.06
82 83 4.021925 AACCTGGAGCCGCTGGAC 62.022 66.667 0.00 0.00 0.00 4.02
83 84 4.020617 CAACCTGGAGCCGCTGGA 62.021 66.667 0.00 0.00 0.00 3.86
84 85 3.551496 TTCAACCTGGAGCCGCTGG 62.551 63.158 0.00 0.00 0.00 4.85
85 86 2.032528 TTCAACCTGGAGCCGCTG 59.967 61.111 0.00 0.00 0.00 5.18
86 87 2.032681 GTTCAACCTGGAGCCGCT 59.967 61.111 0.00 0.00 0.00 5.52
87 88 2.032681 AGTTCAACCTGGAGCCGC 59.967 61.111 0.00 0.00 0.00 6.53
88 89 0.035458 AAGAGTTCAACCTGGAGCCG 59.965 55.000 0.00 0.00 0.00 5.52
89 90 1.528129 CAAGAGTTCAACCTGGAGCC 58.472 55.000 0.00 0.00 0.00 4.70
90 91 0.877743 GCAAGAGTTCAACCTGGAGC 59.122 55.000 0.00 0.00 0.00 4.70
91 92 1.876156 GTGCAAGAGTTCAACCTGGAG 59.124 52.381 0.00 0.00 0.00 3.86
92 93 1.211703 TGTGCAAGAGTTCAACCTGGA 59.788 47.619 0.00 0.00 0.00 3.86
93 94 1.679139 TGTGCAAGAGTTCAACCTGG 58.321 50.000 0.00 0.00 0.00 4.45
94 95 3.551454 CCATTGTGCAAGAGTTCAACCTG 60.551 47.826 0.00 0.00 0.00 4.00
95 96 2.624838 CCATTGTGCAAGAGTTCAACCT 59.375 45.455 0.00 0.00 0.00 3.50
96 97 2.863704 GCCATTGTGCAAGAGTTCAACC 60.864 50.000 0.00 0.00 0.00 3.77
97 98 2.397549 GCCATTGTGCAAGAGTTCAAC 58.602 47.619 0.00 0.00 0.00 3.18
98 99 1.001487 CGCCATTGTGCAAGAGTTCAA 60.001 47.619 0.00 0.00 0.00 2.69
99 100 0.592637 CGCCATTGTGCAAGAGTTCA 59.407 50.000 0.00 0.00 0.00 3.18
100 101 0.109597 CCGCCATTGTGCAAGAGTTC 60.110 55.000 0.00 0.00 0.00 3.01
101 102 1.959085 CCGCCATTGTGCAAGAGTT 59.041 52.632 0.00 0.00 0.00 3.01
102 103 2.629656 GCCGCCATTGTGCAAGAGT 61.630 57.895 0.00 0.00 0.00 3.24
103 104 2.180017 GCCGCCATTGTGCAAGAG 59.820 61.111 0.00 0.00 0.00 2.85
104 105 2.596923 TGCCGCCATTGTGCAAGA 60.597 55.556 0.00 0.00 30.85 3.02
105 106 2.126228 CTGCCGCCATTGTGCAAG 60.126 61.111 0.00 0.00 34.06 4.01
106 107 4.360964 GCTGCCGCCATTGTGCAA 62.361 61.111 0.00 0.00 34.06 4.08
147 148 3.443045 CGGTGGTTGGCATGAGGC 61.443 66.667 0.00 0.00 43.74 4.70
148 149 1.746615 CTCGGTGGTTGGCATGAGG 60.747 63.158 0.00 0.00 0.00 3.86
149 150 1.021390 GTCTCGGTGGTTGGCATGAG 61.021 60.000 0.00 0.00 0.00 2.90
150 151 1.003839 GTCTCGGTGGTTGGCATGA 60.004 57.895 0.00 0.00 0.00 3.07
151 152 2.040544 GGTCTCGGTGGTTGGCATG 61.041 63.158 0.00 0.00 0.00 4.06
152 153 2.351276 GGTCTCGGTGGTTGGCAT 59.649 61.111 0.00 0.00 0.00 4.40
153 154 3.164977 TGGTCTCGGTGGTTGGCA 61.165 61.111 0.00 0.00 0.00 4.92
154 155 2.668550 GTGGTCTCGGTGGTTGGC 60.669 66.667 0.00 0.00 0.00 4.52
155 156 2.032071 GGTGGTCTCGGTGGTTGG 59.968 66.667 0.00 0.00 0.00 3.77
156 157 0.611200 TATGGTGGTCTCGGTGGTTG 59.389 55.000 0.00 0.00 0.00 3.77
157 158 1.354101 TTATGGTGGTCTCGGTGGTT 58.646 50.000 0.00 0.00 0.00 3.67
158 159 1.002773 GTTTATGGTGGTCTCGGTGGT 59.997 52.381 0.00 0.00 0.00 4.16
159 160 1.002659 TGTTTATGGTGGTCTCGGTGG 59.997 52.381 0.00 0.00 0.00 4.61
160 161 2.465860 TGTTTATGGTGGTCTCGGTG 57.534 50.000 0.00 0.00 0.00 4.94
161 162 3.773119 ACTATGTTTATGGTGGTCTCGGT 59.227 43.478 0.00 0.00 0.00 4.69
162 163 4.402056 ACTATGTTTATGGTGGTCTCGG 57.598 45.455 0.00 0.00 0.00 4.63
163 164 5.751990 GGTAACTATGTTTATGGTGGTCTCG 59.248 44.000 0.00 0.00 0.00 4.04
182 183 3.122445 GCAGTGTACGTAAAGCAGGTAAC 59.878 47.826 0.00 0.00 29.68 2.50
183 184 3.319755 GCAGTGTACGTAAAGCAGGTAA 58.680 45.455 0.00 0.00 29.68 2.85
225 226 0.544223 GCCCCTTCCTCCTTCTTCTC 59.456 60.000 0.00 0.00 0.00 2.87
248 249 2.176247 AGGATTACGATCAGGTGGGT 57.824 50.000 0.00 0.00 33.77 4.51
302 342 4.793216 GCCAAATGTACTTATGTTTGCTCG 59.207 41.667 0.00 0.00 31.87 5.03
403 443 7.276256 ATGCATGCATTTCATACGCAGTATTG 61.276 38.462 27.46 0.00 41.74 1.90
404 444 5.278610 ATGCATGCATTTCATACGCAGTATT 60.279 36.000 27.46 0.00 41.74 1.89
405 445 4.216902 ATGCATGCATTTCATACGCAGTAT 59.783 37.500 27.46 0.00 43.93 2.12
406 446 3.565063 ATGCATGCATTTCATACGCAGTA 59.435 39.130 27.46 0.00 39.78 2.74
407 447 2.359848 ATGCATGCATTTCATACGCAGT 59.640 40.909 27.46 1.07 37.47 4.40
408 448 2.478547 TGCATGCATTTCATACGCAG 57.521 45.000 18.46 0.00 39.39 5.18
409 449 2.733517 CATGCATGCATTTCATACGCA 58.266 42.857 30.32 7.91 38.12 5.24
423 463 1.340697 ACTCACCACTCATGCATGCAT 60.341 47.619 27.46 27.46 37.08 3.96
424 464 0.037160 ACTCACCACTCATGCATGCA 59.963 50.000 25.04 25.04 0.00 3.96
425 465 0.450583 CACTCACCACTCATGCATGC 59.549 55.000 22.25 11.82 0.00 4.06
426 466 1.092348 CCACTCACCACTCATGCATG 58.908 55.000 21.07 21.07 0.00 4.06
427 467 0.679002 GCCACTCACCACTCATGCAT 60.679 55.000 0.00 0.00 0.00 3.96
428 468 1.302752 GCCACTCACCACTCATGCA 60.303 57.895 0.00 0.00 0.00 3.96
429 469 2.393768 CGCCACTCACCACTCATGC 61.394 63.158 0.00 0.00 0.00 4.06
430 470 2.393768 GCGCCACTCACCACTCATG 61.394 63.158 0.00 0.00 0.00 3.07
431 471 1.257750 TAGCGCCACTCACCACTCAT 61.258 55.000 2.29 0.00 0.00 2.90
432 472 1.906333 TAGCGCCACTCACCACTCA 60.906 57.895 2.29 0.00 0.00 3.41
433 473 1.446272 GTAGCGCCACTCACCACTC 60.446 63.158 2.29 0.00 0.00 3.51
434 474 1.754380 TTGTAGCGCCACTCACCACT 61.754 55.000 7.64 0.00 0.00 4.00
435 475 1.291877 CTTGTAGCGCCACTCACCAC 61.292 60.000 7.64 0.00 0.00 4.16
436 476 1.005037 CTTGTAGCGCCACTCACCA 60.005 57.895 7.64 0.00 0.00 4.17
437 477 1.004918 ACTTGTAGCGCCACTCACC 60.005 57.895 7.64 0.00 0.00 4.02
438 478 0.038159 AGACTTGTAGCGCCACTCAC 60.038 55.000 7.64 0.00 0.00 3.51
439 479 0.679505 AAGACTTGTAGCGCCACTCA 59.320 50.000 7.64 0.00 0.00 3.41
440 480 1.461127 CAAAGACTTGTAGCGCCACTC 59.539 52.381 7.64 0.00 0.00 3.51
441 481 1.202651 ACAAAGACTTGTAGCGCCACT 60.203 47.619 7.64 0.00 44.14 4.00
442 482 1.226746 ACAAAGACTTGTAGCGCCAC 58.773 50.000 2.29 0.00 44.14 5.01
443 483 2.409975 GTACAAAGACTTGTAGCGCCA 58.590 47.619 2.29 0.00 46.28 5.69
444 484 1.389106 CGTACAAAGACTTGTAGCGCC 59.611 52.381 2.29 0.00 46.28 6.53
445 485 1.389106 CCGTACAAAGACTTGTAGCGC 59.611 52.381 0.00 0.00 46.28 5.92
446 486 2.669364 ACCGTACAAAGACTTGTAGCG 58.331 47.619 0.00 5.79 46.28 4.26
447 487 3.431233 GGAACCGTACAAAGACTTGTAGC 59.569 47.826 0.00 0.00 46.28 3.58
448 488 3.992427 GGGAACCGTACAAAGACTTGTAG 59.008 47.826 0.00 0.00 43.41 2.74
449 489 3.993920 GGGAACCGTACAAAGACTTGTA 58.006 45.455 0.00 0.00 41.30 2.41
450 490 2.842457 GGGAACCGTACAAAGACTTGT 58.158 47.619 0.00 0.00 44.17 3.16
469 509 0.038310 AAAAGGCCTCCCTCGAAAGG 59.962 55.000 5.23 4.23 41.90 3.11
470 510 1.271379 TGAAAAGGCCTCCCTCGAAAG 60.271 52.381 5.23 0.00 41.90 2.62
471 511 0.768622 TGAAAAGGCCTCCCTCGAAA 59.231 50.000 5.23 0.00 41.90 3.46
472 512 0.036306 GTGAAAAGGCCTCCCTCGAA 59.964 55.000 5.23 0.00 41.90 3.71
473 513 1.677552 GTGAAAAGGCCTCCCTCGA 59.322 57.895 5.23 0.00 41.90 4.04
474 514 1.377333 GGTGAAAAGGCCTCCCTCG 60.377 63.158 5.23 0.00 41.90 4.63
475 515 0.405973 AAGGTGAAAAGGCCTCCCTC 59.594 55.000 5.23 3.43 41.90 4.30
476 516 0.405973 GAAGGTGAAAAGGCCTCCCT 59.594 55.000 5.23 3.70 45.77 4.20
477 517 0.405973 AGAAGGTGAAAAGGCCTCCC 59.594 55.000 5.23 1.01 33.24 4.30
478 518 3.653835 ATAGAAGGTGAAAAGGCCTCC 57.346 47.619 5.23 1.44 33.24 4.30
479 519 3.696548 CCAATAGAAGGTGAAAAGGCCTC 59.303 47.826 5.23 0.00 33.24 4.70
480 520 3.333680 TCCAATAGAAGGTGAAAAGGCCT 59.666 43.478 0.00 0.00 36.51 5.19
481 521 3.444034 GTCCAATAGAAGGTGAAAAGGCC 59.556 47.826 0.00 0.00 0.00 5.19
482 522 3.444034 GGTCCAATAGAAGGTGAAAAGGC 59.556 47.826 0.00 0.00 0.00 4.35
483 523 4.017126 GGGTCCAATAGAAGGTGAAAAGG 58.983 47.826 0.00 0.00 0.00 3.11
484 524 4.923415 AGGGTCCAATAGAAGGTGAAAAG 58.077 43.478 0.00 0.00 0.00 2.27
485 525 6.457159 TTAGGGTCCAATAGAAGGTGAAAA 57.543 37.500 0.00 0.00 0.00 2.29
486 526 6.353602 GGATTAGGGTCCAATAGAAGGTGAAA 60.354 42.308 0.00 0.00 38.20 2.69
487 527 5.132144 GGATTAGGGTCCAATAGAAGGTGAA 59.868 44.000 0.00 0.00 38.20 3.18
488 528 4.658901 GGATTAGGGTCCAATAGAAGGTGA 59.341 45.833 0.00 0.00 38.20 4.02
526 656 4.159857 GTGCTTTCTCACTAGAGTACGTG 58.840 47.826 0.00 0.00 42.66 4.49
581 711 7.399245 TTCATCAATCTGCATGATTTTCTCA 57.601 32.000 0.00 0.00 43.00 3.27
592 722 3.139584 AGGGGATCATTCATCAATCTGCA 59.860 43.478 0.00 0.00 32.33 4.41
602 732 4.921991 AGAATGGGATTAGGGGATCATTCA 59.078 41.667 13.83 0.00 41.41 2.57
653 796 3.682155 GCTGCATCATCTCTTTCCTGACT 60.682 47.826 0.00 0.00 0.00 3.41
696 839 2.224066 GGTTATCACCAGATCACCTCCG 60.224 54.545 0.00 0.00 42.66 4.63
856 3015 4.671766 GCCGTTGAATAATCAGTTGTCACC 60.672 45.833 0.00 0.00 36.78 4.02
858 3017 4.068599 TGCCGTTGAATAATCAGTTGTCA 58.931 39.130 0.00 0.00 36.78 3.58
859 3018 4.403453 GTGCCGTTGAATAATCAGTTGTC 58.597 43.478 0.00 0.00 36.78 3.18
860 3019 3.120338 CGTGCCGTTGAATAATCAGTTGT 60.120 43.478 0.00 0.00 36.78 3.32
861 3020 3.124466 TCGTGCCGTTGAATAATCAGTTG 59.876 43.478 0.00 0.00 36.78 3.16
862 3021 3.331150 TCGTGCCGTTGAATAATCAGTT 58.669 40.909 0.00 0.00 36.78 3.16
863 3022 2.967362 TCGTGCCGTTGAATAATCAGT 58.033 42.857 0.00 0.00 36.78 3.41
1012 3185 1.003233 GGGGAGGGACGCATTTATAGG 59.997 57.143 0.00 0.00 0.00 2.57
1314 3498 2.069273 AGCACGAACGTACGTACTAGT 58.931 47.619 23.12 15.61 44.76 2.57
1315 3499 2.795121 AGCACGAACGTACGTACTAG 57.205 50.000 23.12 14.97 44.76 2.57
1328 3513 2.282391 AGCCCATGCAAAGCACGA 60.282 55.556 8.45 0.00 43.04 4.35
1348 3533 1.476488 GCAGACCCAAACAAACAGTGT 59.524 47.619 0.00 0.00 44.64 3.55
1352 3537 1.748493 GTCTGCAGACCCAAACAAACA 59.252 47.619 32.55 0.00 39.07 2.83
1393 3578 2.101582 GTCCTTCTGGATGTACAGCGAT 59.898 50.000 4.81 0.00 45.29 4.58
1741 3926 3.315470 CGAAGTTGGAGACATATCCGAGA 59.685 47.826 0.00 0.00 42.77 4.04
1906 4091 4.164843 AGTCTTGGCAAGAACAACCTTA 57.835 40.909 30.06 3.37 39.67 2.69
2114 4317 0.036388 TGGAAGAAGTGGATGCCGAC 60.036 55.000 0.00 0.00 0.00 4.79
2152 4355 2.566529 CTGTAGAGCACGACGGCA 59.433 61.111 10.28 0.00 35.83 5.69
2323 4526 1.133325 ACTAGGGAGACGATCATGCCT 60.133 52.381 7.61 7.61 0.00 4.75
2693 4922 1.219124 GCGAGCTCATGTCCTCCAA 59.781 57.895 15.40 0.00 0.00 3.53
2721 4950 4.980903 GCTTGTGCGTTGCCGTGG 62.981 66.667 0.00 0.00 36.15 4.94
2763 4992 3.310860 TTCTTCTCCTTCCCGGCGC 62.311 63.158 0.00 0.00 0.00 6.53
2876 5105 2.760650 ACTTCGTCATCTATGTGGCAGA 59.239 45.455 0.00 0.00 0.00 4.26
3062 5300 1.812093 TTTAGTCCGGCGGCGATTG 60.812 57.895 34.49 16.70 0.00 2.67
3079 5321 7.104939 CACCTCTACACTCTACTACAGTAGTT 58.895 42.308 18.56 2.22 46.08 2.24
3094 5336 2.159462 GCTACACGGTACACCTCTACAC 60.159 54.545 0.00 0.00 0.00 2.90
3111 5353 0.108945 AACGCCACGGAAGTAGCTAC 60.109 55.000 16.43 16.43 46.74 3.58
3137 5379 2.280389 CCCATGCAGCGCGACTAT 60.280 61.111 12.10 0.00 0.00 2.12
3273 5515 7.088905 CGTACTCCAAGTCTTTACAATACACT 58.911 38.462 0.00 0.00 0.00 3.55
3358 5607 2.112815 GTGGCCAACCGCTACCATC 61.113 63.158 7.24 0.00 42.88 3.51
3416 5665 6.500684 TCTTTCAAGATTTCAAGATTCCGG 57.499 37.500 0.00 0.00 0.00 5.14


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

AutoCloner maintained by Alex Coulton.