Multiple sequence alignment - TraesCS1B01G258900

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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 TraesCS1B01G258900 chr1B 100.000 3283 0 0 958 4240 456261664 456258382 0.000000e+00 6063.0
1 TraesCS1B01G258900 chr1B 100.000 654 0 0 1 654 456262621 456261968 0.000000e+00 1208.0
2 TraesCS1B01G258900 chr1B 97.872 94 2 0 1 94 449126943 449127036 3.390000e-36 163.0
3 TraesCS1B01G258900 chr1B 77.922 154 27 6 1388 1536 600919635 600919786 5.840000e-14 89.8
4 TraesCS1B01G258900 chr1D 93.799 2548 116 27 958 3480 340656127 340653597 0.000000e+00 3792.0
5 TraesCS1B01G258900 chr1D 92.174 460 27 7 2937 3389 46663006 46662549 3.570000e-180 641.0
6 TraesCS1B01G258900 chr1D 88.914 451 19 12 210 654 340657011 340656586 1.040000e-145 527.0
7 TraesCS1B01G258900 chr1D 87.339 466 36 15 3480 3944 340653282 340652839 2.920000e-141 512.0
8 TraesCS1B01G258900 chr1D 96.212 264 9 1 3978 4240 340652841 340652578 8.420000e-117 431.0
9 TraesCS1B01G258900 chr1A 93.407 2366 111 25 958 3287 440438171 440435815 0.000000e+00 3463.0
10 TraesCS1B01G258900 chr1A 91.290 597 37 9 3351 3936 440435686 440435094 0.000000e+00 800.0
11 TraesCS1B01G258900 chr1A 90.069 433 19 10 205 633 440439188 440438776 1.340000e-149 540.0
12 TraesCS1B01G258900 chr1A 92.776 263 19 0 3978 4240 440435088 440434826 8.600000e-102 381.0
13 TraesCS1B01G258900 chr1A 79.237 236 40 7 1862 2091 67825765 67825533 5.680000e-34 156.0
14 TraesCS1B01G258900 chr6D 93.261 460 22 4 2937 3389 413801603 413801146 0.000000e+00 669.0
15 TraesCS1B01G258900 chr3D 92.174 460 27 5 2937 3389 141583235 141582778 3.570000e-180 641.0
16 TraesCS1B01G258900 chr4D 91.957 460 28 5 2937 3389 108879545 108880002 1.660000e-178 636.0
17 TraesCS1B01G258900 chr4D 95.699 93 4 0 89 181 40339121 40339029 2.640000e-32 150.0
18 TraesCS1B01G258900 chr4D 90.323 93 9 0 89 181 40339771 40339863 5.760000e-24 122.0
19 TraesCS1B01G258900 chr5A 91.613 465 27 6 2935 3389 554992228 554991766 2.150000e-177 632.0
20 TraesCS1B01G258900 chr5A 90.968 465 30 6 2935 3389 555016703 555016241 2.170000e-172 616.0
21 TraesCS1B01G258900 chr5A 90.753 465 31 6 2935 3389 555027896 555027434 1.010000e-170 610.0
22 TraesCS1B01G258900 chr5B 98.936 94 1 0 1 94 710358109 710358202 7.290000e-38 169.0
23 TraesCS1B01G258900 chr5B 97.872 94 2 0 1 94 56851277 56851184 3.390000e-36 163.0
24 TraesCS1B01G258900 chr3B 97.872 94 2 0 1 94 116939818 116939725 3.390000e-36 163.0
25 TraesCS1B01G258900 chr3B 97.872 94 2 0 1 94 582468918 582468825 3.390000e-36 163.0
26 TraesCS1B01G258900 chr3B 97.872 94 2 0 1 94 809037095 809037002 3.390000e-36 163.0
27 TraesCS1B01G258900 chr3B 89.247 93 10 0 89 181 812654332 812654240 2.680000e-22 117.0
28 TraesCS1B01G258900 chr2B 97.872 94 2 0 1 94 5711077 5710984 3.390000e-36 163.0
29 TraesCS1B01G258900 chr2B 97.872 94 2 0 1 94 472911389 472911482 3.390000e-36 163.0
30 TraesCS1B01G258900 chr2B 89.691 97 9 1 85 181 8372116 8372211 5.760000e-24 122.0
31 TraesCS1B01G258900 chrUn 96.809 94 3 0 1 94 264394305 264394212 1.580000e-34 158.0
32 TraesCS1B01G258900 chrUn 89.691 97 9 1 85 181 255483207 255483302 5.760000e-24 122.0
33 TraesCS1B01G258900 chrUn 89.691 97 9 1 85 181 365674752 365674657 5.760000e-24 122.0
34 TraesCS1B01G258900 chr7B 93.407 91 6 0 89 179 310252460 310252550 7.390000e-28 135.0
35 TraesCS1B01G258900 chr2A 92.473 93 7 0 89 181 211095130 211095038 2.660000e-27 134.0
36 TraesCS1B01G258900 chr5D 89.362 94 8 2 89 181 352817075 352816983 2.680000e-22 117.0


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 TraesCS1B01G258900 chr1B 456258382 456262621 4239 True 3635.5 6063 100.0000 1 4240 2 chr1B.!!$R1 4239
1 TraesCS1B01G258900 chr1D 340652578 340657011 4433 True 1315.5 3792 91.5660 210 4240 4 chr1D.!!$R2 4030
2 TraesCS1B01G258900 chr1A 440434826 440439188 4362 True 1296.0 3463 91.8855 205 4240 4 chr1A.!!$R2 4035

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
203 204 0.104855 TGGGCTCGAATTCGGATCTG 59.895 55.0 26.47 13.01 40.29 2.90 F
1548 2237 0.466555 TTTGGTGGGAAAGGTCGTGG 60.467 55.0 0.00 0.00 0.00 4.94 F
1909 2615 0.250901 GCAGTGTCCCAACTCCATGT 60.251 55.0 0.00 0.00 0.00 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1569 2259 0.032130 GGTCAGACAACGAGCAGACA 59.968 55.0 2.17 0.0 0.00 3.41 R
2988 3706 0.108585 GTGTCCCTTGGCTCTGTCAA 59.891 55.0 0.00 0.0 0.00 3.18 R
3738 4870 0.108041 GCATGCCTTTGTTCCATGGG 60.108 55.0 13.02 0.0 37.43 4.00 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
29 30 8.107399 TCAATCTATTCATCTTCAATCATGGC 57.893 34.615 0.00 0.00 0.00 4.40
30 31 7.722285 TCAATCTATTCATCTTCAATCATGGCA 59.278 33.333 0.00 0.00 0.00 4.92
31 32 7.689446 ATCTATTCATCTTCAATCATGGCAG 57.311 36.000 0.00 0.00 0.00 4.85
32 33 6.598503 TCTATTCATCTTCAATCATGGCAGT 58.401 36.000 0.00 0.00 0.00 4.40
33 34 7.738847 TCTATTCATCTTCAATCATGGCAGTA 58.261 34.615 0.00 0.00 0.00 2.74
34 35 8.380867 TCTATTCATCTTCAATCATGGCAGTAT 58.619 33.333 0.00 0.00 0.00 2.12
35 36 9.662947 CTATTCATCTTCAATCATGGCAGTATA 57.337 33.333 0.00 0.00 0.00 1.47
36 37 8.929260 ATTCATCTTCAATCATGGCAGTATAA 57.071 30.769 0.00 0.00 0.00 0.98
37 38 7.734924 TCATCTTCAATCATGGCAGTATAAC 57.265 36.000 0.00 0.00 0.00 1.89
38 39 6.424812 TCATCTTCAATCATGGCAGTATAACG 59.575 38.462 0.00 0.00 0.00 3.18
39 40 5.912892 TCTTCAATCATGGCAGTATAACGA 58.087 37.500 0.00 0.00 0.00 3.85
40 41 6.345298 TCTTCAATCATGGCAGTATAACGAA 58.655 36.000 0.00 0.00 0.00 3.85
41 42 6.992123 TCTTCAATCATGGCAGTATAACGAAT 59.008 34.615 0.00 0.00 0.00 3.34
42 43 8.147704 TCTTCAATCATGGCAGTATAACGAATA 58.852 33.333 0.00 0.00 0.00 1.75
43 44 7.652300 TCAATCATGGCAGTATAACGAATAC 57.348 36.000 0.00 0.00 40.80 1.89
44 45 6.649141 TCAATCATGGCAGTATAACGAATACC 59.351 38.462 0.00 0.00 41.33 2.73
45 46 5.538849 TCATGGCAGTATAACGAATACCA 57.461 39.130 0.00 0.00 41.33 3.25
46 47 5.538118 TCATGGCAGTATAACGAATACCAG 58.462 41.667 0.00 4.62 41.33 4.00
47 48 5.303333 TCATGGCAGTATAACGAATACCAGA 59.697 40.000 0.00 0.00 41.33 3.86
48 49 5.601583 TGGCAGTATAACGAATACCAGAA 57.398 39.130 8.43 0.00 41.33 3.02
49 50 5.979993 TGGCAGTATAACGAATACCAGAAA 58.020 37.500 8.43 0.00 41.33 2.52
50 51 6.588204 TGGCAGTATAACGAATACCAGAAAT 58.412 36.000 8.43 0.00 41.33 2.17
51 52 7.728148 TGGCAGTATAACGAATACCAGAAATA 58.272 34.615 8.43 0.00 41.33 1.40
52 53 8.205512 TGGCAGTATAACGAATACCAGAAATAA 58.794 33.333 8.43 0.00 41.33 1.40
53 54 9.048446 GGCAGTATAACGAATACCAGAAATAAA 57.952 33.333 8.43 0.00 41.33 1.40
76 77 7.787725 AAAATTACATCCAGATTCGTAGACC 57.212 36.000 0.00 0.00 34.32 3.85
77 78 6.479972 AATTACATCCAGATTCGTAGACCA 57.520 37.500 0.00 0.00 34.32 4.02
78 79 3.802948 ACATCCAGATTCGTAGACCAC 57.197 47.619 0.00 0.00 34.32 4.16
79 80 2.431057 ACATCCAGATTCGTAGACCACC 59.569 50.000 0.00 0.00 34.32 4.61
80 81 2.526888 TCCAGATTCGTAGACCACCT 57.473 50.000 0.00 0.00 34.32 4.00
81 82 3.657398 TCCAGATTCGTAGACCACCTA 57.343 47.619 0.00 0.00 34.32 3.08
82 83 3.552875 TCCAGATTCGTAGACCACCTAG 58.447 50.000 0.00 0.00 34.32 3.02
83 84 2.034812 CCAGATTCGTAGACCACCTAGC 59.965 54.545 0.00 0.00 34.32 3.42
84 85 1.948145 AGATTCGTAGACCACCTAGCG 59.052 52.381 0.00 0.00 34.32 4.26
85 86 1.945394 GATTCGTAGACCACCTAGCGA 59.055 52.381 0.00 0.00 34.32 4.93
86 87 1.089920 TTCGTAGACCACCTAGCGAC 58.910 55.000 0.00 0.00 34.32 5.19
87 88 1.086067 TCGTAGACCACCTAGCGACG 61.086 60.000 0.00 0.00 31.20 5.12
88 89 1.726265 GTAGACCACCTAGCGACGG 59.274 63.158 0.00 0.00 0.00 4.79
89 90 2.117156 TAGACCACCTAGCGACGGC 61.117 63.158 0.00 0.00 40.37 5.68
100 101 1.495951 GCGACGGCTACACAAAAGG 59.504 57.895 0.00 0.00 35.83 3.11
101 102 1.908066 GCGACGGCTACACAAAAGGG 61.908 60.000 0.00 0.00 35.83 3.95
102 103 0.601841 CGACGGCTACACAAAAGGGT 60.602 55.000 0.00 0.00 0.00 4.34
103 104 1.154197 GACGGCTACACAAAAGGGTC 58.846 55.000 0.00 0.00 0.00 4.46
104 105 0.470766 ACGGCTACACAAAAGGGTCA 59.529 50.000 0.00 0.00 0.00 4.02
105 106 1.156736 CGGCTACACAAAAGGGTCAG 58.843 55.000 0.00 0.00 0.00 3.51
106 107 0.881796 GGCTACACAAAAGGGTCAGC 59.118 55.000 0.00 0.00 0.00 4.26
107 108 0.881796 GCTACACAAAAGGGTCAGCC 59.118 55.000 0.00 0.00 0.00 4.85
108 109 1.156736 CTACACAAAAGGGTCAGCCG 58.843 55.000 0.00 0.00 34.97 5.52
109 110 0.250553 TACACAAAAGGGTCAGCCGG 60.251 55.000 0.00 0.00 34.97 6.13
110 111 1.228124 CACAAAAGGGTCAGCCGGA 60.228 57.895 5.05 0.00 34.97 5.14
111 112 0.609131 CACAAAAGGGTCAGCCGGAT 60.609 55.000 5.05 0.00 34.97 4.18
112 113 0.609131 ACAAAAGGGTCAGCCGGATG 60.609 55.000 15.12 15.12 34.97 3.51
113 114 0.322456 CAAAAGGGTCAGCCGGATGA 60.322 55.000 20.59 20.59 34.97 2.92
114 115 0.404040 AAAAGGGTCAGCCGGATGAA 59.596 50.000 26.48 5.79 34.97 2.57
115 116 0.404040 AAAGGGTCAGCCGGATGAAA 59.596 50.000 26.48 0.00 34.97 2.69
116 117 0.625849 AAGGGTCAGCCGGATGAAAT 59.374 50.000 26.48 10.51 34.97 2.17
117 118 0.625849 AGGGTCAGCCGGATGAAATT 59.374 50.000 26.48 9.71 34.97 1.82
118 119 1.005924 AGGGTCAGCCGGATGAAATTT 59.994 47.619 26.48 7.73 34.97 1.82
119 120 1.824852 GGGTCAGCCGGATGAAATTTT 59.175 47.619 26.48 0.00 34.97 1.82
120 121 2.233676 GGGTCAGCCGGATGAAATTTTT 59.766 45.455 26.48 0.00 34.97 1.94
141 142 6.624710 TTTTCGTCAACAGTTCATTTTGTG 57.375 33.333 0.00 0.00 0.00 3.33
142 143 5.553290 TTCGTCAACAGTTCATTTTGTGA 57.447 34.783 0.00 0.00 34.25 3.58
143 144 5.553290 TCGTCAACAGTTCATTTTGTGAA 57.447 34.783 0.00 0.00 44.36 3.18
169 170 6.639671 TTTTTCGTTCACAGGTCAAATTTG 57.360 33.333 12.15 12.15 0.00 2.32
170 171 4.974368 TTCGTTCACAGGTCAAATTTGT 57.026 36.364 17.47 0.00 0.00 2.83
171 172 4.974368 TCGTTCACAGGTCAAATTTGTT 57.026 36.364 17.47 2.85 0.00 2.83
172 173 4.667262 TCGTTCACAGGTCAAATTTGTTG 58.333 39.130 17.47 15.53 0.00 3.33
173 174 4.156922 TCGTTCACAGGTCAAATTTGTTGT 59.843 37.500 17.47 16.08 0.00 3.32
174 175 4.862018 CGTTCACAGGTCAAATTTGTTGTT 59.138 37.500 17.47 0.49 0.00 2.83
175 176 5.347364 CGTTCACAGGTCAAATTTGTTGTTT 59.653 36.000 17.47 0.00 0.00 2.83
176 177 6.128688 CGTTCACAGGTCAAATTTGTTGTTTT 60.129 34.615 17.47 0.00 0.00 2.43
177 178 7.570324 CGTTCACAGGTCAAATTTGTTGTTTTT 60.570 33.333 17.47 0.00 0.00 1.94
178 179 7.126726 TCACAGGTCAAATTTGTTGTTTTTG 57.873 32.000 17.47 9.93 0.00 2.44
179 180 5.794448 CACAGGTCAAATTTGTTGTTTTTGC 59.206 36.000 17.47 0.00 31.88 3.68
180 181 5.106357 ACAGGTCAAATTTGTTGTTTTTGCC 60.106 36.000 17.47 7.45 31.88 4.52
181 182 4.397730 AGGTCAAATTTGTTGTTTTTGCCC 59.602 37.500 17.47 4.31 32.12 5.36
182 183 4.439426 GGTCAAATTTGTTGTTTTTGCCCC 60.439 41.667 17.47 0.00 31.88 5.80
183 184 4.156739 GTCAAATTTGTTGTTTTTGCCCCA 59.843 37.500 17.47 0.00 31.88 4.96
184 185 4.952335 TCAAATTTGTTGTTTTTGCCCCAT 59.048 33.333 17.47 0.00 31.88 4.00
185 186 4.915158 AATTTGTTGTTTTTGCCCCATG 57.085 36.364 0.00 0.00 0.00 3.66
186 187 2.338577 TTGTTGTTTTTGCCCCATGG 57.661 45.000 4.14 4.14 0.00 3.66
196 197 4.164258 CCCCATGGGCTCGAATTC 57.836 61.111 26.87 0.00 35.35 2.17
197 198 1.893808 CCCCATGGGCTCGAATTCG 60.894 63.158 26.87 21.78 35.35 3.34
198 199 1.893808 CCCATGGGCTCGAATTCGG 60.894 63.158 26.47 17.90 40.29 4.30
199 200 1.146041 CCATGGGCTCGAATTCGGA 59.854 57.895 26.47 12.90 40.29 4.55
200 201 0.250467 CCATGGGCTCGAATTCGGAT 60.250 55.000 26.47 9.19 40.29 4.18
201 202 1.151668 CATGGGCTCGAATTCGGATC 58.848 55.000 26.47 15.31 40.29 3.36
202 203 1.051812 ATGGGCTCGAATTCGGATCT 58.948 50.000 26.47 5.51 40.29 2.75
203 204 0.104855 TGGGCTCGAATTCGGATCTG 59.895 55.000 26.47 13.01 40.29 2.90
284 285 1.134491 GGGTACGGACTAGCATGCTTT 60.134 52.381 28.02 13.76 0.00 3.51
287 288 4.377897 GGTACGGACTAGCATGCTTTTAT 58.622 43.478 28.02 9.02 0.00 1.40
314 316 3.263425 GGGAAAGAGAAGATGTACCACCA 59.737 47.826 0.00 0.00 0.00 4.17
315 317 4.254492 GGAAAGAGAAGATGTACCACCAC 58.746 47.826 0.00 0.00 0.00 4.16
316 318 3.983044 AAGAGAAGATGTACCACCACC 57.017 47.619 0.00 0.00 0.00 4.61
344 346 1.079612 CCTGTCCCGGTCCGTTTAC 60.080 63.158 11.06 5.77 0.00 2.01
345 347 1.538687 CCTGTCCCGGTCCGTTTACT 61.539 60.000 11.06 0.00 0.00 2.24
346 348 1.176527 CTGTCCCGGTCCGTTTACTA 58.823 55.000 11.06 0.00 0.00 1.82
412 415 2.509336 CTAGTCGCCGTTGCCAGG 60.509 66.667 0.00 0.00 0.00 4.45
433 436 1.078848 CAGCTCCTTCCTTCCACCG 60.079 63.158 0.00 0.00 0.00 4.94
434 437 2.436824 GCTCCTTCCTTCCACCGC 60.437 66.667 0.00 0.00 0.00 5.68
435 438 2.125512 CTCCTTCCTTCCACCGCG 60.126 66.667 0.00 0.00 0.00 6.46
436 439 4.388499 TCCTTCCTTCCACCGCGC 62.388 66.667 0.00 0.00 0.00 6.86
438 441 4.697756 CTTCCTTCCACCGCGCCA 62.698 66.667 0.00 0.00 0.00 5.69
439 442 4.257654 TTCCTTCCACCGCGCCAA 62.258 61.111 0.00 0.00 0.00 4.52
490 493 3.122727 AAAAACCCACCTCGCCGGA 62.123 57.895 5.05 0.00 36.31 5.14
618 627 4.863925 GGCTCAGCCTCGCTCGTC 62.864 72.222 9.09 0.00 46.69 4.20
1207 1885 2.680352 ACCGACGGCAGGTCAGAT 60.680 61.111 15.39 0.00 46.42 2.90
1291 1971 1.550524 TGCCTACTTGCTGACCTGTAG 59.449 52.381 0.00 0.00 34.02 2.74
1300 1980 2.308690 GCTGACCTGTAGTAGTAGGGG 58.691 57.143 5.60 0.00 38.42 4.79
1307 1987 4.909695 ACCTGTAGTAGTAGGGGTTTGTTT 59.090 41.667 5.60 0.00 38.42 2.83
1312 1992 5.494390 AGTAGTAGGGGTTTGTTTACCTG 57.506 43.478 0.00 0.00 38.30 4.00
1365 2054 6.590234 AACTCTTGTTGGAATTTGGATACC 57.410 37.500 0.00 0.00 34.71 2.73
1376 2065 6.496565 TGGAATTTGGATACCACAAACTTGAT 59.503 34.615 0.00 0.00 40.25 2.57
1423 2112 2.357569 GGACTGCTCCATCCTTCCAAAT 60.358 50.000 0.00 0.00 36.42 2.32
1493 2182 2.837591 TGCAGCTCCACCATAGAGTTTA 59.162 45.455 0.00 0.00 33.69 2.01
1502 2191 6.195700 TCCACCATAGAGTTTAGCTTCTAGT 58.804 40.000 0.00 0.00 0.00 2.57
1524 2213 0.679002 GCTCCAGCTTCAGGAATGCA 60.679 55.000 0.00 0.00 38.21 3.96
1548 2237 0.466555 TTTGGTGGGAAAGGTCGTGG 60.467 55.000 0.00 0.00 0.00 4.94
1549 2238 1.346479 TTGGTGGGAAAGGTCGTGGA 61.346 55.000 0.00 0.00 0.00 4.02
1565 2255 2.203437 GACCAGGTTTTGCGGGGT 60.203 61.111 0.00 0.00 33.78 4.95
1569 2259 4.218686 AGGTTTTGCGGGGTGGCT 62.219 61.111 0.00 0.00 0.00 4.75
1582 2272 1.595382 GTGGCTGTCTGCTCGTTGT 60.595 57.895 1.44 0.00 42.39 3.32
1811 2517 2.965831 TGGAGGAGAATGAAGGGATACG 59.034 50.000 0.00 0.00 37.60 3.06
1821 2527 1.617357 GAAGGGATACGCGGATAAGGT 59.383 52.381 12.47 0.00 37.60 3.50
1827 2533 2.877089 TACGCGGATAAGGTGGGGGT 62.877 60.000 12.47 0.00 0.00 4.95
1828 2534 2.192175 GCGGATAAGGTGGGGGTG 59.808 66.667 0.00 0.00 0.00 4.61
1829 2535 2.192175 CGGATAAGGTGGGGGTGC 59.808 66.667 0.00 0.00 0.00 5.01
1830 2536 2.192175 GGATAAGGTGGGGGTGCG 59.808 66.667 0.00 0.00 0.00 5.34
1885 2591 6.293698 AGAAACAAACCGTTATCCACTTACT 58.706 36.000 0.00 0.00 36.59 2.24
1909 2615 0.250901 GCAGTGTCCCAACTCCATGT 60.251 55.000 0.00 0.00 0.00 3.21
1960 2666 2.416162 CCTCCTGAAGAGCTACACGAAC 60.416 54.545 0.00 0.00 41.74 3.95
1972 2678 2.582728 ACACGAACAACACGGAGTTA 57.417 45.000 0.00 0.00 41.61 2.24
1984 2690 2.047830 ACGGAGTTATCCCCCAGATTC 58.952 52.381 0.00 0.00 37.78 2.52
1985 2691 2.047061 CGGAGTTATCCCCCAGATTCA 58.953 52.381 0.00 0.00 43.39 2.57
1987 2693 3.118038 CGGAGTTATCCCCCAGATTCAAA 60.118 47.826 0.00 0.00 43.39 2.69
2007 2716 2.199652 TTTTTGCGGAGTGGGGCAG 61.200 57.895 0.00 0.00 40.75 4.85
2008 2717 2.920076 TTTTTGCGGAGTGGGGCAGT 62.920 55.000 0.00 0.00 40.75 4.40
2009 2718 4.641645 TTGCGGAGTGGGGCAGTG 62.642 66.667 0.00 0.00 40.75 3.66
2028 2737 1.844289 TGGAGCTACCCCGTTTGGT 60.844 57.895 0.00 0.00 42.62 3.67
2047 2756 2.758423 GGTTTGTGGTTTTGAGAGTGGT 59.242 45.455 0.00 0.00 0.00 4.16
2108 2819 6.539173 TCTTAATCTTTGCAGTGAAGGGTAA 58.461 36.000 0.00 0.00 0.00 2.85
2203 2915 5.556915 TGGAGTTACAGGATTGTTCGATTT 58.443 37.500 0.00 0.00 38.76 2.17
2209 2921 7.606456 AGTTACAGGATTGTTCGATTTGTGTAT 59.394 33.333 0.00 0.00 38.76 2.29
2210 2922 6.817765 ACAGGATTGTTCGATTTGTGTATT 57.182 33.333 0.00 0.00 32.28 1.89
2223 2935 8.879759 TCGATTTGTGTATTCTAAATCTGAACC 58.120 33.333 0.00 0.00 38.20 3.62
2251 2963 4.793201 CCTCTAAAGGGAGGGGTTATTTG 58.207 47.826 2.84 0.00 46.63 2.32
2259 2971 8.513139 AAAGGGAGGGGTTATTTGAAATTTAA 57.487 30.769 0.00 0.00 0.00 1.52
2260 2972 7.733773 AGGGAGGGGTTATTTGAAATTTAAG 57.266 36.000 0.00 0.00 0.00 1.85
2262 2974 8.129001 AGGGAGGGGTTATTTGAAATTTAAGAT 58.871 33.333 0.00 0.00 0.00 2.40
2263 2975 8.204160 GGGAGGGGTTATTTGAAATTTAAGATG 58.796 37.037 0.00 0.00 0.00 2.90
2300 3015 1.271163 CGGGGTTTGTACATCACCTGT 60.271 52.381 19.35 0.00 42.13 4.00
2380 3097 5.880332 GTGTGGGTACATGACATATTGACTT 59.120 40.000 0.00 0.00 39.39 3.01
2431 3148 7.073342 ACTAGGTGAAATTGTATCTTTTCGC 57.927 36.000 0.00 0.00 40.11 4.70
2597 3315 7.516198 AGACTGCAATTTTTCTTCAGTGTAT 57.484 32.000 0.00 0.00 38.03 2.29
2675 3393 2.509916 CAGCCCTCTGGATCTGGC 59.490 66.667 0.00 0.00 44.35 4.85
2793 3511 4.079958 AGGAAGGTGGTCAAACAGTAAACT 60.080 41.667 0.00 0.00 0.00 2.66
2897 3615 3.563808 GGATTAATGGTGTGCGCTATGAA 59.436 43.478 9.73 0.00 0.00 2.57
2978 3696 1.069668 GATGGCATGGGGAAAGAATGC 59.930 52.381 3.81 0.00 44.75 3.56
2988 3706 2.945668 GGGAAAGAATGCGTTATCTGCT 59.054 45.455 0.00 0.00 0.00 4.24
3042 3760 5.069516 CCTTGCAGGCATTTGGTAAGATAAT 59.930 40.000 0.00 0.00 0.00 1.28
3044 3762 6.147864 TGCAGGCATTTGGTAAGATAATTC 57.852 37.500 0.00 0.00 0.00 2.17
3228 3951 8.152023 ACTAATGGAGATCAAAGTTAGGAGTT 57.848 34.615 0.00 0.00 0.00 3.01
3277 4000 1.337703 TGGTTGTTGCTGCATTCTGTC 59.662 47.619 1.84 0.00 0.00 3.51
3287 4010 4.023279 TGCTGCATTCTGTCGTTTATTGTT 60.023 37.500 0.00 0.00 0.00 2.83
3342 4065 5.534654 AGTGCATAGTTATGTTGTTGGTTGT 59.465 36.000 0.00 0.00 36.11 3.32
3587 4709 6.827727 TCTGGCTAAGTTTCTCCCAATATAC 58.172 40.000 0.00 0.00 0.00 1.47
3679 4809 2.562298 CCTGGTTAATTGTGTGGTGCAT 59.438 45.455 0.00 0.00 0.00 3.96
3681 4811 3.225940 TGGTTAATTGTGTGGTGCATCA 58.774 40.909 0.00 0.00 0.00 3.07
3682 4812 3.831333 TGGTTAATTGTGTGGTGCATCAT 59.169 39.130 1.27 0.00 0.00 2.45
3683 4813 4.082300 TGGTTAATTGTGTGGTGCATCATC 60.082 41.667 1.27 0.00 0.00 2.92
3687 4817 3.579335 TTGTGTGGTGCATCATCATTG 57.421 42.857 1.27 0.00 0.00 2.82
3689 4819 2.229302 TGTGTGGTGCATCATCATTGTG 59.771 45.455 1.27 0.00 0.00 3.33
3690 4820 1.819903 TGTGGTGCATCATCATTGTGG 59.180 47.619 1.27 0.00 0.00 4.17
3691 4821 2.093890 GTGGTGCATCATCATTGTGGA 58.906 47.619 1.27 0.00 0.00 4.02
3725 4857 3.674997 CATACTGCAACCCAAGTGTACT 58.325 45.455 0.00 0.00 0.00 2.73
3733 4865 4.502604 GCAACCCAAGTGTACTCTGTTCTA 60.503 45.833 0.00 0.00 0.00 2.10
3738 4870 6.015603 ACCCAAGTGTACTCTGTTCTAGTTAC 60.016 42.308 0.00 0.00 0.00 2.50
3773 4905 1.081892 ATGCTTCGCTGCTTAGTGTG 58.918 50.000 0.00 0.00 0.00 3.82
3777 4909 0.966179 TTCGCTGCTTAGTGTGAGGA 59.034 50.000 0.00 0.00 0.00 3.71
3878 5010 9.473007 TCATTTTATATGGGACTTGATTTGACA 57.527 29.630 0.00 0.00 0.00 3.58
3884 5016 3.820467 TGGGACTTGATTTGACACATCAC 59.180 43.478 3.74 0.00 33.38 3.06
3899 5031 3.302434 CACATCACTTTTGCGATGAATGC 59.698 43.478 6.40 0.00 40.40 3.56
3916 5048 7.172190 CGATGAATGCCAACTTAGTAGATGATT 59.828 37.037 0.00 0.00 0.00 2.57
3939 5071 7.956420 TTATACACATTTAAGTAGATGCGGG 57.044 36.000 0.00 0.00 0.00 6.13
3940 5072 4.216411 ACACATTTAAGTAGATGCGGGT 57.784 40.909 0.00 0.00 0.00 5.28
3941 5073 5.347620 ACACATTTAAGTAGATGCGGGTA 57.652 39.130 0.00 0.00 0.00 3.69
3942 5074 5.925509 ACACATTTAAGTAGATGCGGGTAT 58.074 37.500 0.00 0.00 0.00 2.73
3943 5075 6.354130 ACACATTTAAGTAGATGCGGGTATT 58.646 36.000 0.00 0.00 0.00 1.89
3944 5076 6.260050 ACACATTTAAGTAGATGCGGGTATTG 59.740 38.462 0.00 0.00 0.00 1.90
3945 5077 5.763204 ACATTTAAGTAGATGCGGGTATTGG 59.237 40.000 0.00 0.00 0.00 3.16
3946 5078 2.930826 AAGTAGATGCGGGTATTGGG 57.069 50.000 0.00 0.00 0.00 4.12
3947 5079 1.056660 AGTAGATGCGGGTATTGGGG 58.943 55.000 0.00 0.00 0.00 4.96
3948 5080 0.036306 GTAGATGCGGGTATTGGGGG 59.964 60.000 0.00 0.00 0.00 5.40
3949 5081 0.400815 TAGATGCGGGTATTGGGGGT 60.401 55.000 0.00 0.00 0.00 4.95
3950 5082 1.528309 GATGCGGGTATTGGGGGTG 60.528 63.158 0.00 0.00 0.00 4.61
3951 5083 2.279037 GATGCGGGTATTGGGGGTGT 62.279 60.000 0.00 0.00 0.00 4.16
3952 5084 1.869824 ATGCGGGTATTGGGGGTGTT 61.870 55.000 0.00 0.00 0.00 3.32
3953 5085 1.206135 TGCGGGTATTGGGGGTGTTA 61.206 55.000 0.00 0.00 0.00 2.41
3954 5086 0.184211 GCGGGTATTGGGGGTGTTAT 59.816 55.000 0.00 0.00 0.00 1.89
3955 5087 1.975660 CGGGTATTGGGGGTGTTATG 58.024 55.000 0.00 0.00 0.00 1.90
3956 5088 1.699730 GGGTATTGGGGGTGTTATGC 58.300 55.000 0.00 0.00 0.00 3.14
3957 5089 1.063567 GGGTATTGGGGGTGTTATGCA 60.064 52.381 0.00 0.00 0.00 3.96
3958 5090 2.425683 GGGTATTGGGGGTGTTATGCAT 60.426 50.000 3.79 3.79 0.00 3.96
3959 5091 3.304829 GGTATTGGGGGTGTTATGCATT 58.695 45.455 3.54 0.00 0.00 3.56
3960 5092 3.320826 GGTATTGGGGGTGTTATGCATTC 59.679 47.826 3.54 0.00 0.00 2.67
3961 5093 2.917713 TTGGGGGTGTTATGCATTCT 57.082 45.000 3.54 0.00 0.00 2.40
3962 5094 2.142356 TGGGGGTGTTATGCATTCTG 57.858 50.000 3.54 0.00 0.00 3.02
3963 5095 0.746659 GGGGGTGTTATGCATTCTGC 59.253 55.000 3.54 0.00 45.29 4.26
3981 5113 9.173939 GCATTCTGCAATTACATGAATAGTTAC 57.826 33.333 0.00 0.00 44.26 2.50
4093 5226 7.770897 GCTATGAATTTAGAGACTCCTTTCCAA 59.229 37.037 0.00 0.00 0.00 3.53
4134 5267 9.658799 CATGAAAGACCTAATTCTTTACTCAGA 57.341 33.333 0.00 0.00 44.27 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 8.573885 GCCATGATTGAAGATGAATAGATTGAA 58.426 33.333 0.00 0.00 0.00 2.69
4 5 7.722285 TGCCATGATTGAAGATGAATAGATTGA 59.278 33.333 0.00 0.00 0.00 2.57
5 6 7.882179 TGCCATGATTGAAGATGAATAGATTG 58.118 34.615 0.00 0.00 0.00 2.67
6 7 7.724506 ACTGCCATGATTGAAGATGAATAGATT 59.275 33.333 0.00 0.00 0.00 2.40
7 8 7.232188 ACTGCCATGATTGAAGATGAATAGAT 58.768 34.615 0.00 0.00 0.00 1.98
8 9 6.598503 ACTGCCATGATTGAAGATGAATAGA 58.401 36.000 0.00 0.00 0.00 1.98
9 10 6.879276 ACTGCCATGATTGAAGATGAATAG 57.121 37.500 0.00 0.00 0.00 1.73
11 12 8.790718 GTTATACTGCCATGATTGAAGATGAAT 58.209 33.333 0.00 0.00 0.00 2.57
12 13 7.041848 CGTTATACTGCCATGATTGAAGATGAA 60.042 37.037 0.00 0.00 0.00 2.57
13 14 6.424812 CGTTATACTGCCATGATTGAAGATGA 59.575 38.462 0.00 0.00 0.00 2.92
14 15 6.424812 TCGTTATACTGCCATGATTGAAGATG 59.575 38.462 0.00 0.00 0.00 2.90
15 16 6.524734 TCGTTATACTGCCATGATTGAAGAT 58.475 36.000 0.00 0.00 0.00 2.40
16 17 5.912892 TCGTTATACTGCCATGATTGAAGA 58.087 37.500 0.00 0.00 0.00 2.87
17 18 6.603237 TTCGTTATACTGCCATGATTGAAG 57.397 37.500 0.00 0.00 0.00 3.02
18 19 7.172532 GGTATTCGTTATACTGCCATGATTGAA 59.827 37.037 0.00 0.00 39.30 2.69
19 20 6.649141 GGTATTCGTTATACTGCCATGATTGA 59.351 38.462 0.00 0.00 39.30 2.57
20 21 6.426633 TGGTATTCGTTATACTGCCATGATTG 59.573 38.462 0.00 0.00 39.30 2.67
21 22 6.530120 TGGTATTCGTTATACTGCCATGATT 58.470 36.000 0.00 0.00 39.30 2.57
22 23 6.014584 TCTGGTATTCGTTATACTGCCATGAT 60.015 38.462 0.00 0.00 39.30 2.45
23 24 5.303333 TCTGGTATTCGTTATACTGCCATGA 59.697 40.000 0.00 0.00 39.30 3.07
24 25 5.538118 TCTGGTATTCGTTATACTGCCATG 58.462 41.667 9.26 0.00 39.30 3.66
25 26 5.801531 TCTGGTATTCGTTATACTGCCAT 57.198 39.130 9.26 0.00 39.30 4.40
26 27 5.601583 TTCTGGTATTCGTTATACTGCCA 57.398 39.130 9.26 0.00 39.30 4.92
27 28 8.597662 TTATTTCTGGTATTCGTTATACTGCC 57.402 34.615 9.26 0.00 39.30 4.85
50 51 9.321562 GGTCTACGAATCTGGATGTAATTTTTA 57.678 33.333 0.00 0.00 0.00 1.52
51 52 7.827236 TGGTCTACGAATCTGGATGTAATTTTT 59.173 33.333 0.00 0.00 0.00 1.94
52 53 7.280205 GTGGTCTACGAATCTGGATGTAATTTT 59.720 37.037 0.00 0.00 0.00 1.82
53 54 6.761714 GTGGTCTACGAATCTGGATGTAATTT 59.238 38.462 0.00 0.00 0.00 1.82
54 55 6.281405 GTGGTCTACGAATCTGGATGTAATT 58.719 40.000 0.00 0.00 0.00 1.40
55 56 5.221461 GGTGGTCTACGAATCTGGATGTAAT 60.221 44.000 0.00 0.00 0.00 1.89
56 57 4.098960 GGTGGTCTACGAATCTGGATGTAA 59.901 45.833 0.00 0.00 0.00 2.41
57 58 3.635373 GGTGGTCTACGAATCTGGATGTA 59.365 47.826 0.00 0.00 0.00 2.29
58 59 2.431057 GGTGGTCTACGAATCTGGATGT 59.569 50.000 0.00 0.00 0.00 3.06
59 60 2.695666 AGGTGGTCTACGAATCTGGATG 59.304 50.000 0.00 0.00 0.00 3.51
60 61 3.033659 AGGTGGTCTACGAATCTGGAT 57.966 47.619 0.00 0.00 0.00 3.41
61 62 2.526888 AGGTGGTCTACGAATCTGGA 57.473 50.000 0.00 0.00 0.00 3.86
62 63 2.034812 GCTAGGTGGTCTACGAATCTGG 59.965 54.545 0.00 0.00 0.00 3.86
63 64 2.287069 CGCTAGGTGGTCTACGAATCTG 60.287 54.545 0.00 0.00 0.00 2.90
64 65 1.948145 CGCTAGGTGGTCTACGAATCT 59.052 52.381 0.00 0.00 0.00 2.40
65 66 1.945394 TCGCTAGGTGGTCTACGAATC 59.055 52.381 0.00 0.00 32.69 2.52
66 67 1.674962 GTCGCTAGGTGGTCTACGAAT 59.325 52.381 0.00 0.00 35.22 3.34
67 68 1.089920 GTCGCTAGGTGGTCTACGAA 58.910 55.000 0.00 0.00 35.22 3.85
68 69 1.086067 CGTCGCTAGGTGGTCTACGA 61.086 60.000 0.00 0.00 32.96 3.43
69 70 1.351012 CGTCGCTAGGTGGTCTACG 59.649 63.158 0.00 0.00 0.00 3.51
70 71 1.726265 CCGTCGCTAGGTGGTCTAC 59.274 63.158 0.00 0.00 0.00 2.59
71 72 2.117156 GCCGTCGCTAGGTGGTCTA 61.117 63.158 0.00 0.00 0.00 2.59
72 73 2.547640 TAGCCGTCGCTAGGTGGTCT 62.548 60.000 0.00 0.00 46.08 3.85
73 74 2.117156 TAGCCGTCGCTAGGTGGTC 61.117 63.158 0.00 0.00 46.08 4.02
74 75 2.044650 TAGCCGTCGCTAGGTGGT 60.045 61.111 0.00 0.00 46.08 4.16
80 81 1.670674 CCTTTTGTGTAGCCGTCGCTA 60.671 52.381 0.00 0.00 46.08 4.26
82 83 1.495951 CCTTTTGTGTAGCCGTCGC 59.504 57.895 0.00 0.00 0.00 5.19
83 84 0.601841 ACCCTTTTGTGTAGCCGTCG 60.602 55.000 0.00 0.00 0.00 5.12
84 85 1.154197 GACCCTTTTGTGTAGCCGTC 58.846 55.000 0.00 0.00 0.00 4.79
85 86 0.470766 TGACCCTTTTGTGTAGCCGT 59.529 50.000 0.00 0.00 0.00 5.68
86 87 1.156736 CTGACCCTTTTGTGTAGCCG 58.843 55.000 0.00 0.00 0.00 5.52
87 88 0.881796 GCTGACCCTTTTGTGTAGCC 59.118 55.000 0.00 0.00 0.00 3.93
88 89 0.881796 GGCTGACCCTTTTGTGTAGC 59.118 55.000 0.00 0.00 0.00 3.58
89 90 1.156736 CGGCTGACCCTTTTGTGTAG 58.843 55.000 0.00 0.00 0.00 2.74
90 91 0.250553 CCGGCTGACCCTTTTGTGTA 60.251 55.000 0.00 0.00 0.00 2.90
91 92 1.528309 CCGGCTGACCCTTTTGTGT 60.528 57.895 0.00 0.00 0.00 3.72
92 93 0.609131 ATCCGGCTGACCCTTTTGTG 60.609 55.000 0.00 0.00 0.00 3.33
93 94 0.609131 CATCCGGCTGACCCTTTTGT 60.609 55.000 0.00 0.00 0.00 2.83
94 95 0.322456 TCATCCGGCTGACCCTTTTG 60.322 55.000 3.28 0.00 0.00 2.44
95 96 0.404040 TTCATCCGGCTGACCCTTTT 59.596 50.000 7.67 0.00 0.00 2.27
96 97 0.404040 TTTCATCCGGCTGACCCTTT 59.596 50.000 7.67 0.00 0.00 3.11
97 98 0.625849 ATTTCATCCGGCTGACCCTT 59.374 50.000 7.67 0.00 0.00 3.95
98 99 0.625849 AATTTCATCCGGCTGACCCT 59.374 50.000 7.67 0.00 0.00 4.34
99 100 1.474330 AAATTTCATCCGGCTGACCC 58.526 50.000 7.67 0.00 0.00 4.46
100 101 3.592898 AAAAATTTCATCCGGCTGACC 57.407 42.857 7.67 0.00 0.00 4.02
117 118 6.863645 TCACAAAATGAACTGTTGACGAAAAA 59.136 30.769 0.00 0.00 33.02 1.94
118 119 6.382608 TCACAAAATGAACTGTTGACGAAAA 58.617 32.000 0.00 0.00 33.02 2.29
119 120 5.944013 TCACAAAATGAACTGTTGACGAAA 58.056 33.333 0.00 0.00 33.02 3.46
120 121 5.553290 TCACAAAATGAACTGTTGACGAA 57.447 34.783 0.00 0.00 33.02 3.85
121 122 5.553290 TTCACAAAATGAACTGTTGACGA 57.447 34.783 0.00 0.00 42.62 4.20
146 147 6.159988 ACAAATTTGACCTGTGAACGAAAAA 58.840 32.000 24.64 0.00 0.00 1.94
147 148 5.715070 ACAAATTTGACCTGTGAACGAAAA 58.285 33.333 24.64 0.00 0.00 2.29
148 149 5.317733 ACAAATTTGACCTGTGAACGAAA 57.682 34.783 24.64 0.00 0.00 3.46
149 150 4.974368 ACAAATTTGACCTGTGAACGAA 57.026 36.364 24.64 0.00 0.00 3.85
150 151 4.156922 ACAACAAATTTGACCTGTGAACGA 59.843 37.500 24.64 0.00 0.00 3.85
151 152 4.420168 ACAACAAATTTGACCTGTGAACG 58.580 39.130 24.64 3.16 0.00 3.95
152 153 6.720012 AAACAACAAATTTGACCTGTGAAC 57.280 33.333 24.64 0.00 0.00 3.18
153 154 7.579726 CAAAAACAACAAATTTGACCTGTGAA 58.420 30.769 24.64 0.00 36.41 3.18
154 155 6.348050 GCAAAAACAACAAATTTGACCTGTGA 60.348 34.615 24.64 0.00 36.41 3.58
155 156 5.794448 GCAAAAACAACAAATTTGACCTGTG 59.206 36.000 24.64 14.65 36.41 3.66
156 157 5.106357 GGCAAAAACAACAAATTTGACCTGT 60.106 36.000 24.64 18.89 36.32 4.00
157 158 5.331098 GGCAAAAACAACAAATTTGACCTG 58.669 37.500 24.64 18.32 36.32 4.00
158 159 5.559427 GGCAAAAACAACAAATTTGACCT 57.441 34.783 24.64 5.84 36.32 3.85
160 161 4.156739 TGGGGCAAAAACAACAAATTTGAC 59.843 37.500 24.64 0.00 40.55 3.18
161 162 4.335416 TGGGGCAAAAACAACAAATTTGA 58.665 34.783 24.64 0.00 36.41 2.69
162 163 4.708726 TGGGGCAAAAACAACAAATTTG 57.291 36.364 16.67 16.67 37.17 2.32
163 164 4.099113 CCATGGGGCAAAAACAACAAATTT 59.901 37.500 2.85 0.00 0.00 1.82
164 165 3.635836 CCATGGGGCAAAAACAACAAATT 59.364 39.130 2.85 0.00 0.00 1.82
165 166 3.220940 CCATGGGGCAAAAACAACAAAT 58.779 40.909 2.85 0.00 0.00 2.32
166 167 2.648059 CCATGGGGCAAAAACAACAAA 58.352 42.857 2.85 0.00 0.00 2.83
167 168 1.133976 CCCATGGGGCAAAAACAACAA 60.134 47.619 24.53 0.00 35.35 2.83
168 169 0.471617 CCCATGGGGCAAAAACAACA 59.528 50.000 24.53 0.00 35.35 3.33
169 170 3.320823 CCCATGGGGCAAAAACAAC 57.679 52.632 24.53 0.00 35.35 3.32
179 180 1.893808 CGAATTCGAGCCCATGGGG 60.894 63.158 32.23 15.94 43.84 4.96
180 181 1.893808 CCGAATTCGAGCCCATGGG 60.894 63.158 28.76 27.87 43.02 4.00
181 182 0.250467 ATCCGAATTCGAGCCCATGG 60.250 55.000 28.76 4.14 43.02 3.66
182 183 1.151668 GATCCGAATTCGAGCCCATG 58.848 55.000 28.76 10.33 43.02 3.66
183 184 1.051812 AGATCCGAATTCGAGCCCAT 58.948 50.000 28.76 11.79 43.02 4.00
184 185 0.104855 CAGATCCGAATTCGAGCCCA 59.895 55.000 28.76 7.55 43.02 5.36
185 186 0.105039 ACAGATCCGAATTCGAGCCC 59.895 55.000 28.76 14.00 43.02 5.19
186 187 1.941325 AACAGATCCGAATTCGAGCC 58.059 50.000 28.76 15.67 43.02 4.70
187 188 3.061139 CGTTAACAGATCCGAATTCGAGC 60.061 47.826 28.76 16.71 43.02 5.03
188 189 4.204573 GTCGTTAACAGATCCGAATTCGAG 59.795 45.833 28.76 18.02 43.02 4.04
189 190 4.100529 GTCGTTAACAGATCCGAATTCGA 58.899 43.478 28.76 14.98 43.02 3.71
190 191 3.855379 TGTCGTTAACAGATCCGAATTCG 59.145 43.478 20.92 20.92 34.56 3.34
202 203 1.558741 AACGCGTTCTGTCGTTAACA 58.441 45.000 20.79 0.00 45.61 2.41
203 204 2.543646 GAAACGCGTTCTGTCGTTAAC 58.456 47.619 26.77 0.00 46.56 2.01
284 285 7.614192 GGTACATCTTCTCTTTCCCCAAAATAA 59.386 37.037 0.00 0.00 0.00 1.40
287 288 5.163034 TGGTACATCTTCTCTTTCCCCAAAA 60.163 40.000 0.00 0.00 0.00 2.44
314 316 3.637273 GACAGGAAGGGTGCGGGT 61.637 66.667 0.00 0.00 0.00 5.28
315 317 4.410400 GGACAGGAAGGGTGCGGG 62.410 72.222 0.00 0.00 0.00 6.13
316 318 4.410400 GGGACAGGAAGGGTGCGG 62.410 72.222 0.00 0.00 0.00 5.69
328 330 1.477700 CATAGTAAACGGACCGGGACA 59.522 52.381 20.00 4.61 0.00 4.02
344 346 2.954868 GTCACCGTCGGCGCATAG 60.955 66.667 12.28 0.00 36.67 2.23
345 347 3.284133 TTGTCACCGTCGGCGCATA 62.284 57.895 12.28 0.00 36.67 3.14
346 348 4.673298 TTGTCACCGTCGGCGCAT 62.673 61.111 12.28 0.00 36.67 4.73
412 415 0.035915 GTGGAAGGAAGGAGCTGTCC 60.036 60.000 0.00 0.00 44.33 4.02
475 478 2.627839 TTTTTCCGGCGAGGTGGGTT 62.628 55.000 9.30 0.00 41.99 4.11
476 479 3.122727 TTTTTCCGGCGAGGTGGGT 62.123 57.895 9.30 0.00 41.99 4.51
478 481 1.574702 GACTTTTTCCGGCGAGGTGG 61.575 60.000 9.30 0.00 41.99 4.61
488 491 3.676093 AGGACTCCGATTGACTTTTTCC 58.324 45.455 0.00 0.00 0.00 3.13
490 493 4.570930 GAGAGGACTCCGATTGACTTTTT 58.429 43.478 0.00 0.00 37.19 1.94
614 623 2.271497 GGAGGAGGAGGACGACGA 59.729 66.667 0.00 0.00 0.00 4.20
615 624 2.829458 GGGAGGAGGAGGACGACG 60.829 72.222 0.00 0.00 0.00 5.12
616 625 2.829458 CGGGAGGAGGAGGACGAC 60.829 72.222 0.00 0.00 0.00 4.34
617 626 4.816984 GCGGGAGGAGGAGGACGA 62.817 72.222 0.00 0.00 0.00 4.20
618 627 4.824515 AGCGGGAGGAGGAGGACG 62.825 72.222 0.00 0.00 0.00 4.79
619 628 2.835895 GAGCGGGAGGAGGAGGAC 60.836 72.222 0.00 0.00 0.00 3.85
1207 1885 0.601046 CTCAGCGTTGGAGACAGCAA 60.601 55.000 0.00 0.00 42.42 3.91
1291 1971 4.566278 CCCAGGTAAACAAACCCCTACTAC 60.566 50.000 0.00 0.00 40.71 2.73
1323 2003 7.793927 AGAGTTTAGCCTAAAATATGTGCTC 57.206 36.000 0.00 0.24 33.63 4.26
1365 2054 6.492007 AGCTTCACATAGATCAAGTTTGTG 57.508 37.500 0.00 1.65 39.16 3.33
1376 2065 4.026744 ACAGGCTCTAAGCTTCACATAGA 58.973 43.478 0.00 0.00 41.99 1.98
1423 2112 0.843309 TTTGGTGGAGTGGAGCTGAA 59.157 50.000 0.00 0.00 0.00 3.02
1454 2143 0.764890 CAACTCCTGGGTGGAACTGA 59.235 55.000 0.00 0.00 45.63 3.41
1517 2206 3.749226 TCCCACCAAAATTTTGCATTCC 58.251 40.909 22.90 0.00 36.86 3.01
1524 2213 3.452990 ACGACCTTTCCCACCAAAATTTT 59.547 39.130 0.00 0.00 0.00 1.82
1548 2237 2.203437 ACCCCGCAAAACCTGGTC 60.203 61.111 0.00 0.00 0.00 4.02
1549 2238 2.520741 CACCCCGCAAAACCTGGT 60.521 61.111 0.00 0.00 0.00 4.00
1569 2259 0.032130 GGTCAGACAACGAGCAGACA 59.968 55.000 2.17 0.00 0.00 3.41
1575 2265 2.022129 GGCACGGTCAGACAACGAG 61.022 63.158 2.17 0.00 0.00 4.18
1778 2484 1.272490 TCTCCTCCACATCACGAACAC 59.728 52.381 0.00 0.00 0.00 3.32
1811 2517 2.192175 CACCCCCACCTTATCCGC 59.808 66.667 0.00 0.00 0.00 5.54
1830 2536 4.973055 TACCCCACACGCACGCAC 62.973 66.667 0.00 0.00 0.00 5.34
1857 2563 6.270064 AGTGGATAACGGTTTGTTTCTTTTG 58.730 36.000 0.00 0.00 42.09 2.44
1885 2591 0.685097 GAGTTGGGACACTGCCACTA 59.315 55.000 0.00 0.00 37.69 2.74
1909 2615 5.888982 AAAACTCTAGTTTCAGGAGTCCA 57.111 39.130 12.86 0.00 46.47 4.02
1960 2666 0.616371 TGGGGGATAACTCCGTGTTG 59.384 55.000 1.94 0.00 43.11 3.33
2004 2713 2.269241 GGGGTAGCTCCACACTGC 59.731 66.667 0.00 0.00 39.94 4.40
2007 2716 0.953960 CAAACGGGGTAGCTCCACAC 60.954 60.000 0.00 0.00 40.26 3.82
2008 2717 1.373435 CAAACGGGGTAGCTCCACA 59.627 57.895 0.00 0.00 40.26 4.17
2009 2718 1.376812 CCAAACGGGGTAGCTCCAC 60.377 63.158 0.00 0.00 38.11 4.02
2028 2737 2.165437 GCACCACTCTCAAAACCACAAA 59.835 45.455 0.00 0.00 0.00 2.83
2047 2756 3.430374 GCTCTACTCCGTAAATTCCAGCA 60.430 47.826 0.00 0.00 0.00 4.41
2108 2819 9.512588 AGTCACTAATTCATGAGATTGAAAAGT 57.487 29.630 11.20 6.00 38.98 2.66
2157 2868 8.937835 TCCATCATTTCTAATCTATCCTTCACA 58.062 33.333 0.00 0.00 0.00 3.58
2177 2888 4.221924 TCGAACAATCCTGTAACTCCATCA 59.778 41.667 0.00 0.00 33.45 3.07
2203 2915 7.118680 GGTTTCGGTTCAGATTTAGAATACACA 59.881 37.037 0.00 0.00 0.00 3.72
2209 2921 5.012768 AGAGGGTTTCGGTTCAGATTTAGAA 59.987 40.000 0.00 0.00 0.00 2.10
2210 2922 4.530946 AGAGGGTTTCGGTTCAGATTTAGA 59.469 41.667 0.00 0.00 0.00 2.10
2259 2971 6.816140 CCCCGCATACAAAAATTTAAACATCT 59.184 34.615 0.00 0.00 0.00 2.90
2260 2972 6.592220 ACCCCGCATACAAAAATTTAAACATC 59.408 34.615 0.00 0.00 0.00 3.06
2262 2974 5.855045 ACCCCGCATACAAAAATTTAAACA 58.145 33.333 0.00 0.00 0.00 2.83
2263 2975 6.788684 AACCCCGCATACAAAAATTTAAAC 57.211 33.333 0.00 0.00 0.00 2.01
2270 2985 3.635373 TGTACAAACCCCGCATACAAAAA 59.365 39.130 0.00 0.00 0.00 1.94
2272 2987 2.860009 TGTACAAACCCCGCATACAAA 58.140 42.857 0.00 0.00 0.00 2.83
2357 3074 5.692115 AGTCAATATGTCATGTACCCACA 57.308 39.130 0.00 0.00 39.52 4.17
2597 3315 0.836606 TTGGTGTCTGCAAGTCTGGA 59.163 50.000 0.00 0.00 33.76 3.86
2675 3393 6.039493 CCAGAGAAAAGAATCCCAGATCAATG 59.961 42.308 0.00 0.00 0.00 2.82
2793 3511 1.240256 GTAATTTGTGCCCGTGTGGA 58.760 50.000 0.00 0.00 37.49 4.02
2897 3615 9.699410 TTGACAATCCCATATATTTCTTTCAGT 57.301 29.630 0.00 0.00 0.00 3.41
2988 3706 0.108585 GTGTCCCTTGGCTCTGTCAA 59.891 55.000 0.00 0.00 0.00 3.18
3042 3760 7.715249 AGCAAAAGAACTACAGACTACAATGAA 59.285 33.333 0.00 0.00 0.00 2.57
3044 3762 7.426929 AGCAAAAGAACTACAGACTACAATG 57.573 36.000 0.00 0.00 0.00 2.82
3052 3770 6.582636 TCTGAGAAAGCAAAAGAACTACAGA 58.417 36.000 0.00 0.00 0.00 3.41
3056 3774 7.386299 GTGAGATCTGAGAAAGCAAAAGAACTA 59.614 37.037 0.00 0.00 0.00 2.24
3110 3833 5.872617 GCACATACACTGTACAACATAGGAA 59.127 40.000 0.00 0.00 35.91 3.36
3228 3951 4.039730 GCATAGTCTTCCTTATGGCTCAGA 59.960 45.833 0.00 0.00 0.00 3.27
3300 4023 9.282247 CTATGCACTTTGAAAACTGATATTGTC 57.718 33.333 0.00 0.00 0.00 3.18
3312 4035 7.651304 CCAACAACATAACTATGCACTTTGAAA 59.349 33.333 0.00 0.00 37.19 2.69
3364 4171 9.725019 ACATAGTTCAAGTGTCAAAATGATAGA 57.275 29.630 0.00 0.00 0.00 1.98
3456 4263 3.065648 TGTTACAAAACTTTGACGAGGGC 59.934 43.478 9.12 0.00 40.55 5.19
3620 4742 4.783242 ACTGTGCTTTAATTTACGTGCTG 58.217 39.130 0.00 0.00 0.00 4.41
3626 4748 7.210718 ACCCAGTAACTGTGCTTTAATTTAC 57.789 36.000 0.00 0.00 0.00 2.01
3679 4809 5.473162 CCACTTACAAACTCCACAATGATGA 59.527 40.000 0.00 0.00 0.00 2.92
3681 4811 4.218417 GCCACTTACAAACTCCACAATGAT 59.782 41.667 0.00 0.00 0.00 2.45
3682 4812 3.568007 GCCACTTACAAACTCCACAATGA 59.432 43.478 0.00 0.00 0.00 2.57
3683 4813 3.317711 TGCCACTTACAAACTCCACAATG 59.682 43.478 0.00 0.00 0.00 2.82
3687 4817 4.154195 CAGTATGCCACTTACAAACTCCAC 59.846 45.833 0.00 0.00 34.26 4.02
3689 4819 4.946784 CAGTATGCCACTTACAAACTCC 57.053 45.455 0.00 0.00 34.26 3.85
3725 4857 4.841813 TGTTCCATGGGTAACTAGAACAGA 59.158 41.667 13.02 0.00 0.00 3.41
3733 4865 2.158385 TGCCTTTGTTCCATGGGTAACT 60.158 45.455 13.02 0.00 0.00 2.24
3738 4870 0.108041 GCATGCCTTTGTTCCATGGG 60.108 55.000 13.02 0.00 37.43 4.00
3757 4889 1.067565 TCCTCACACTAAGCAGCGAAG 60.068 52.381 0.00 0.00 0.00 3.79
3773 4905 1.276622 TTAACCTCAGCAGGGTCCTC 58.723 55.000 0.00 0.00 45.53 3.71
3777 4909 1.004745 CCACATTAACCTCAGCAGGGT 59.995 52.381 0.00 0.00 45.53 4.34
3864 4996 5.695851 AAGTGATGTGTCAAATCAAGTCC 57.304 39.130 7.29 0.00 35.87 3.85
3878 5010 3.504863 GCATTCATCGCAAAAGTGATGT 58.495 40.909 15.94 0.00 42.05 3.06
3884 5016 2.950433 AGTTGGCATTCATCGCAAAAG 58.050 42.857 0.00 0.00 0.00 2.27
3916 5048 7.058023 ACCCGCATCTACTTAAATGTGTATA 57.942 36.000 0.00 0.00 32.71 1.47
3926 5058 2.635915 CCCCAATACCCGCATCTACTTA 59.364 50.000 0.00 0.00 0.00 2.24
3928 5060 1.056660 CCCCAATACCCGCATCTACT 58.943 55.000 0.00 0.00 0.00 2.57
3930 5062 0.400815 ACCCCCAATACCCGCATCTA 60.401 55.000 0.00 0.00 0.00 1.98
3931 5063 1.696314 ACCCCCAATACCCGCATCT 60.696 57.895 0.00 0.00 0.00 2.90
3932 5064 1.528309 CACCCCCAATACCCGCATC 60.528 63.158 0.00 0.00 0.00 3.91
3933 5065 1.869824 AACACCCCCAATACCCGCAT 61.870 55.000 0.00 0.00 0.00 4.73
3934 5066 1.206135 TAACACCCCCAATACCCGCA 61.206 55.000 0.00 0.00 0.00 5.69
3935 5067 0.184211 ATAACACCCCCAATACCCGC 59.816 55.000 0.00 0.00 0.00 6.13
3936 5068 1.975660 CATAACACCCCCAATACCCG 58.024 55.000 0.00 0.00 0.00 5.28
3939 5071 4.037923 CAGAATGCATAACACCCCCAATAC 59.962 45.833 0.00 0.00 0.00 1.89
3940 5072 4.214310 CAGAATGCATAACACCCCCAATA 58.786 43.478 0.00 0.00 0.00 1.90
3941 5073 3.033184 CAGAATGCATAACACCCCCAAT 58.967 45.455 0.00 0.00 0.00 3.16
3942 5074 2.455557 CAGAATGCATAACACCCCCAA 58.544 47.619 0.00 0.00 0.00 4.12
3943 5075 2.142356 CAGAATGCATAACACCCCCA 57.858 50.000 0.00 0.00 0.00 4.96
3995 5128 6.074648 AGACATCCCACCTAATTTGTTGAAA 58.925 36.000 0.00 0.00 0.00 2.69
4026 5159 3.810743 GCAATGGTGGGTCTGTAAGTTCT 60.811 47.826 0.00 0.00 33.76 3.01
4093 5226 4.832266 TCTTTCATGCATTTGTACCCACTT 59.168 37.500 0.00 0.00 0.00 3.16
4134 5267 4.976224 AAAGGTGAGCAAAAACTTACGT 57.024 36.364 0.00 0.00 0.00 3.57
4206 5339 3.040147 TCGAGTTCAGATCCACCAAAC 57.960 47.619 0.00 0.00 0.00 2.93


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

AutoCloner maintained by Alex Coulton.