Multiple sequence alignment - TraesCS2D01G582400

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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 TraesCS2D01G582400 chr2D 100.000 4394 0 0 1 4394 643229039 643233432 0.000000e+00 8115.0
1 TraesCS2D01G582400 chr2D 79.221 154 31 1 1972 2124 384251473 384251320 6.010000e-19 106.0
2 TraesCS2D01G582400 chr2D 84.259 108 13 2 1585 1690 384251823 384251718 7.770000e-18 102.0
3 TraesCS2D01G582400 chr2A 93.922 2139 69 10 1561 3657 768121068 768123187 0.000000e+00 3173.0
4 TraesCS2D01G582400 chr2A 95.658 737 27 4 3660 4394 239384597 239385330 0.000000e+00 1179.0
5 TraesCS2D01G582400 chr2A 86.124 1045 50 32 508 1545 768120066 768121022 0.000000e+00 1038.0
6 TraesCS2D01G582400 chr2A 86.057 459 28 14 66 516 768112155 768112585 1.110000e-125 460.0
7 TraesCS2D01G582400 chr2A 85.616 146 13 6 79 218 768119723 768119866 3.540000e-31 147.0
8 TraesCS2D01G582400 chr2A 85.185 108 12 2 1585 1690 519530586 519530481 1.670000e-19 108.0
9 TraesCS2D01G582400 chr2A 79.333 150 31 0 1972 2121 519530236 519530087 6.010000e-19 106.0
10 TraesCS2D01G582400 chrUn 95.206 1481 55 4 2181 3658 31713816 31715283 0.000000e+00 2327.0
11 TraesCS2D01G582400 chrUn 86.146 1256 65 49 473 1701 31712034 31713207 0.000000e+00 1254.0
12 TraesCS2D01G582400 chrUn 95.444 439 14 2 1746 2182 31713358 31713792 0.000000e+00 695.0
13 TraesCS2D01G582400 chrUn 89.000 100 7 2 80 175 31711694 31711793 2.150000e-23 121.0
14 TraesCS2D01G582400 chr1D 99.592 735 3 0 3660 4394 485585413 485586147 0.000000e+00 1341.0
15 TraesCS2D01G582400 chr1A 95.946 740 24 5 3657 4394 347352536 347353271 0.000000e+00 1195.0
16 TraesCS2D01G582400 chr1A 91.452 737 52 10 3660 4394 11468536 11467809 0.000000e+00 1002.0
17 TraesCS2D01G582400 chr1A 80.769 208 25 9 982 1189 350392335 350392527 9.850000e-32 148.0
18 TraesCS2D01G582400 chr7A 96.065 737 22 7 3660 4394 719457687 719458418 0.000000e+00 1194.0
19 TraesCS2D01G582400 chr7A 95.929 737 24 5 3660 4394 719459666 719458934 0.000000e+00 1190.0
20 TraesCS2D01G582400 chr7A 95.528 738 25 7 3660 4394 112250646 112249914 0.000000e+00 1173.0
21 TraesCS2D01G582400 chr5D 92.925 735 43 6 3660 4392 184289911 184289184 0.000000e+00 1061.0
22 TraesCS2D01G582400 chr6B 89.439 748 61 9 3660 4394 462641402 462642144 0.000000e+00 928.0
23 TraesCS2D01G582400 chr6B 81.250 208 24 9 982 1189 673815198 673815390 2.120000e-33 154.0
24 TraesCS2D01G582400 chr6B 80.769 208 25 8 982 1189 673800165 673800357 9.850000e-32 148.0
25 TraesCS2D01G582400 chr2B 78.395 162 32 3 1972 2131 454343560 454343400 7.770000e-18 102.0
26 TraesCS2D01G582400 chr2B 83.333 108 14 2 1585 1690 454343907 454343802 3.620000e-16 97.1


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 TraesCS2D01G582400 chr2D 643229039 643233432 4393 False 8115.000000 8115 100.000 1 4394 1 chr2D.!!$F1 4393
1 TraesCS2D01G582400 chr2A 768119723 768123187 3464 False 1452.666667 3173 88.554 79 3657 3 chr2A.!!$F3 3578
2 TraesCS2D01G582400 chr2A 239384597 239385330 733 False 1179.000000 1179 95.658 3660 4394 1 chr2A.!!$F1 734
3 TraesCS2D01G582400 chrUn 31711694 31715283 3589 False 1099.250000 2327 91.449 80 3658 4 chrUn.!!$F1 3578
4 TraesCS2D01G582400 chr1D 485585413 485586147 734 False 1341.000000 1341 99.592 3660 4394 1 chr1D.!!$F1 734
5 TraesCS2D01G582400 chr1A 347352536 347353271 735 False 1195.000000 1195 95.946 3657 4394 1 chr1A.!!$F1 737
6 TraesCS2D01G582400 chr1A 11467809 11468536 727 True 1002.000000 1002 91.452 3660 4394 1 chr1A.!!$R1 734
7 TraesCS2D01G582400 chr7A 719457687 719458418 731 False 1194.000000 1194 96.065 3660 4394 1 chr7A.!!$F1 734
8 TraesCS2D01G582400 chr7A 719458934 719459666 732 True 1190.000000 1190 95.929 3660 4394 1 chr7A.!!$R2 734
9 TraesCS2D01G582400 chr7A 112249914 112250646 732 True 1173.000000 1173 95.528 3660 4394 1 chr7A.!!$R1 734
10 TraesCS2D01G582400 chr5D 184289184 184289911 727 True 1061.000000 1061 92.925 3660 4392 1 chr5D.!!$R1 732
11 TraesCS2D01G582400 chr6B 462641402 462642144 742 False 928.000000 928 89.439 3660 4394 1 chr6B.!!$F1 734

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
264 278 0.029567 AGGAACACGCTCGATCGATC 59.970 55.0 19.78 15.68 0.00 3.69 F
785 879 0.249657 CTCTCCTATTCCTGGCACGC 60.250 60.0 0.00 0.00 0.00 5.34 F
1740 2005 0.169672 ATCCAACGTACGTCTCACCG 59.830 55.0 23.05 6.19 0.00 4.94 F
2639 2955 0.733566 CAAATGTGGGTGCGCACATC 60.734 55.0 38.60 29.22 40.71 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1331 1426 0.040067 ACCGTACGTCACCTTTCGTC 60.040 55.0 15.21 0.0 40.70 4.20 R
1885 2154 0.179205 CGGTGTACTCCTCGACGAAC 60.179 60.0 11.98 0.0 0.00 3.95 R
2784 3100 0.313672 GTGACGAAGCCAATGCCAAA 59.686 50.0 0.00 0.0 38.69 3.28 R
3658 3974 0.323451 AAAATCTCAAGACCGGCCCC 60.323 55.0 0.00 0.0 0.00 5.80 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
21 22 3.799137 GCATTGTGCAGGAACAAAATG 57.201 42.857 0.00 3.55 44.70 2.32
22 23 2.481185 GCATTGTGCAGGAACAAAATGG 59.519 45.455 8.95 0.00 42.94 3.16
23 24 3.803021 GCATTGTGCAGGAACAAAATGGA 60.803 43.478 8.95 0.00 42.94 3.41
24 25 3.731652 TTGTGCAGGAACAAAATGGAG 57.268 42.857 0.00 0.00 37.12 3.86
25 26 2.665165 TGTGCAGGAACAAAATGGAGT 58.335 42.857 0.00 0.00 0.00 3.85
26 27 3.826524 TGTGCAGGAACAAAATGGAGTA 58.173 40.909 0.00 0.00 0.00 2.59
27 28 3.820467 TGTGCAGGAACAAAATGGAGTAG 59.180 43.478 0.00 0.00 0.00 2.57
28 29 3.191371 GTGCAGGAACAAAATGGAGTAGG 59.809 47.826 0.00 0.00 0.00 3.18
29 30 2.755103 GCAGGAACAAAATGGAGTAGGG 59.245 50.000 0.00 0.00 0.00 3.53
30 31 3.356290 CAGGAACAAAATGGAGTAGGGG 58.644 50.000 0.00 0.00 0.00 4.79
31 32 2.100197 GGAACAAAATGGAGTAGGGGC 58.900 52.381 0.00 0.00 0.00 5.80
32 33 2.100197 GAACAAAATGGAGTAGGGGCC 58.900 52.381 0.00 0.00 0.00 5.80
33 34 1.080638 ACAAAATGGAGTAGGGGCCA 58.919 50.000 4.39 0.00 38.78 5.36
34 35 1.645919 ACAAAATGGAGTAGGGGCCAT 59.354 47.619 4.39 0.00 46.49 4.40
35 36 2.856231 ACAAAATGGAGTAGGGGCCATA 59.144 45.455 4.39 0.00 43.85 2.74
36 37 3.222603 CAAAATGGAGTAGGGGCCATAC 58.777 50.000 20.25 20.25 43.85 2.39
37 38 1.446016 AATGGAGTAGGGGCCATACC 58.554 55.000 23.67 15.03 43.85 2.73
38 39 0.836400 ATGGAGTAGGGGCCATACCG 60.836 60.000 23.67 0.00 42.86 4.02
39 40 2.214920 GGAGTAGGGGCCATACCGG 61.215 68.421 23.67 0.00 40.62 5.28
40 41 2.122547 AGTAGGGGCCATACCGGG 60.123 66.667 23.67 0.00 40.62 5.73
41 42 3.246880 GTAGGGGCCATACCGGGG 61.247 72.222 17.33 0.00 40.62 5.73
42 43 4.585216 TAGGGGCCATACCGGGGG 62.585 72.222 6.32 5.42 40.62 5.40
56 57 4.822734 GGGGGTCAAGCTAGGGTA 57.177 61.111 0.00 0.00 0.00 3.69
57 58 3.259336 GGGGGTCAAGCTAGGGTAT 57.741 57.895 0.00 0.00 0.00 2.73
58 59 2.410790 GGGGGTCAAGCTAGGGTATA 57.589 55.000 0.00 0.00 0.00 1.47
59 60 2.258109 GGGGGTCAAGCTAGGGTATAG 58.742 57.143 0.00 0.00 0.00 1.31
60 61 2.158204 GGGGGTCAAGCTAGGGTATAGA 60.158 54.545 0.00 0.00 0.00 1.98
61 62 3.584294 GGGGTCAAGCTAGGGTATAGAA 58.416 50.000 0.00 0.00 0.00 2.10
62 63 3.324268 GGGGTCAAGCTAGGGTATAGAAC 59.676 52.174 0.00 0.00 0.00 3.01
63 64 3.005578 GGGTCAAGCTAGGGTATAGAACG 59.994 52.174 0.00 0.00 0.00 3.95
64 65 3.635836 GGTCAAGCTAGGGTATAGAACGT 59.364 47.826 0.00 0.00 0.00 3.99
65 66 4.499357 GGTCAAGCTAGGGTATAGAACGTG 60.499 50.000 0.00 0.00 0.00 4.49
66 67 3.635373 TCAAGCTAGGGTATAGAACGTGG 59.365 47.826 0.00 0.00 0.00 4.94
67 68 3.309600 AGCTAGGGTATAGAACGTGGT 57.690 47.619 0.00 0.00 0.00 4.16
68 69 2.957006 AGCTAGGGTATAGAACGTGGTG 59.043 50.000 0.00 0.00 0.00 4.17
69 70 2.545322 GCTAGGGTATAGAACGTGGTGC 60.545 54.545 0.00 0.00 0.00 5.01
70 71 1.563924 AGGGTATAGAACGTGGTGCA 58.436 50.000 0.00 0.00 0.00 4.57
71 72 2.116238 AGGGTATAGAACGTGGTGCAT 58.884 47.619 0.00 0.00 0.00 3.96
72 73 2.102588 AGGGTATAGAACGTGGTGCATC 59.897 50.000 0.00 0.00 0.00 3.91
73 74 2.124903 GGTATAGAACGTGGTGCATCG 58.875 52.381 0.00 0.00 0.00 3.84
74 75 2.223641 GGTATAGAACGTGGTGCATCGA 60.224 50.000 13.90 0.00 0.00 3.59
75 76 2.890808 ATAGAACGTGGTGCATCGAT 57.109 45.000 13.90 0.00 0.00 3.59
76 77 2.665649 TAGAACGTGGTGCATCGATT 57.334 45.000 13.90 0.00 0.00 3.34
77 78 1.808411 AGAACGTGGTGCATCGATTT 58.192 45.000 13.90 0.00 0.00 2.17
82 83 1.464023 CGTGGTGCATCGATTTGTGTC 60.464 52.381 0.00 0.00 0.00 3.67
96 97 0.800012 TGTGTCGATCGATCACGTGA 59.200 50.000 28.77 22.48 40.69 4.35
115 126 4.340263 GTGAACGTGTTTCTTGTTCCTTC 58.660 43.478 0.00 0.00 40.92 3.46
183 194 9.453572 CATGCACAAAGGTATATATAGGAACAT 57.546 33.333 0.00 0.00 0.00 2.71
199 210 6.910259 AGGAACATAAAGAAAGATAGGGGT 57.090 37.500 0.00 0.00 0.00 4.95
205 219 7.475299 ACATAAAGAAAGATAGGGGTTTGGAA 58.525 34.615 0.00 0.00 0.00 3.53
218 232 0.730265 TTTGGAATGGATACGTGCGC 59.270 50.000 0.00 0.00 42.51 6.09
220 234 0.391793 TGGAATGGATACGTGCGCAA 60.392 50.000 14.00 0.00 42.51 4.85
222 236 1.131504 GGAATGGATACGTGCGCAAAA 59.868 47.619 14.00 0.00 42.51 2.44
223 237 2.440501 GAATGGATACGTGCGCAAAAG 58.559 47.619 14.00 9.72 42.51 2.27
224 238 0.732571 ATGGATACGTGCGCAAAAGG 59.267 50.000 14.00 4.33 42.51 3.11
225 239 1.302383 TGGATACGTGCGCAAAAGGG 61.302 55.000 14.00 1.40 42.51 3.95
226 240 1.303091 GGATACGTGCGCAAAAGGGT 61.303 55.000 14.00 8.12 0.00 4.34
227 241 0.096454 GATACGTGCGCAAAAGGGTC 59.904 55.000 14.00 2.01 0.00 4.46
228 242 1.632046 ATACGTGCGCAAAAGGGTCG 61.632 55.000 14.00 12.77 0.00 4.79
229 243 2.974935 TACGTGCGCAAAAGGGTCGT 62.975 55.000 20.94 20.94 0.00 4.34
230 244 2.051345 GTGCGCAAAAGGGTCGTG 60.051 61.111 14.00 0.00 0.00 4.35
231 245 3.959975 TGCGCAAAAGGGTCGTGC 61.960 61.111 8.16 0.00 36.70 5.34
232 246 3.959975 GCGCAAAAGGGTCGTGCA 61.960 61.111 0.30 0.00 38.19 4.57
233 247 2.051345 CGCAAAAGGGTCGTGCAC 60.051 61.111 6.82 6.82 38.19 4.57
234 248 2.829206 CGCAAAAGGGTCGTGCACA 61.829 57.895 18.64 0.81 38.19 4.57
235 249 1.435515 GCAAAAGGGTCGTGCACAA 59.564 52.632 18.64 0.00 38.19 3.33
236 250 0.179124 GCAAAAGGGTCGTGCACAAA 60.179 50.000 18.64 0.46 38.19 2.83
237 251 1.737363 GCAAAAGGGTCGTGCACAAAA 60.737 47.619 18.64 0.00 38.19 2.44
238 252 2.192624 CAAAAGGGTCGTGCACAAAAG 58.807 47.619 18.64 0.00 0.00 2.27
239 253 0.744281 AAAGGGTCGTGCACAAAAGG 59.256 50.000 18.64 0.00 0.00 3.11
240 254 0.395173 AAGGGTCGTGCACAAAAGGT 60.395 50.000 18.64 0.00 0.00 3.50
241 255 0.470766 AGGGTCGTGCACAAAAGGTA 59.529 50.000 18.64 0.00 0.00 3.08
242 256 1.073284 AGGGTCGTGCACAAAAGGTAT 59.927 47.619 18.64 0.00 0.00 2.73
243 257 2.303600 AGGGTCGTGCACAAAAGGTATA 59.696 45.455 18.64 0.00 0.00 1.47
244 258 2.417586 GGGTCGTGCACAAAAGGTATAC 59.582 50.000 18.64 0.00 0.00 1.47
245 259 3.068560 GGTCGTGCACAAAAGGTATACA 58.931 45.455 18.64 0.00 0.00 2.29
246 260 3.124636 GGTCGTGCACAAAAGGTATACAG 59.875 47.826 18.64 0.00 0.00 2.74
247 261 3.124636 GTCGTGCACAAAAGGTATACAGG 59.875 47.826 18.64 0.00 0.00 4.00
248 262 3.007074 TCGTGCACAAAAGGTATACAGGA 59.993 43.478 18.64 0.00 0.00 3.86
249 263 3.749088 CGTGCACAAAAGGTATACAGGAA 59.251 43.478 18.64 0.00 0.00 3.36
250 264 4.378046 CGTGCACAAAAGGTATACAGGAAC 60.378 45.833 18.64 0.00 0.00 3.62
251 265 4.517453 GTGCACAAAAGGTATACAGGAACA 59.483 41.667 13.17 0.00 0.00 3.18
252 266 4.517453 TGCACAAAAGGTATACAGGAACAC 59.483 41.667 5.01 0.00 0.00 3.32
253 267 4.378046 GCACAAAAGGTATACAGGAACACG 60.378 45.833 5.01 0.00 0.00 4.49
254 268 3.749609 ACAAAAGGTATACAGGAACACGC 59.250 43.478 5.01 0.00 0.00 5.34
255 269 3.975168 AAAGGTATACAGGAACACGCT 57.025 42.857 5.01 0.00 0.00 5.07
256 270 3.521947 AAGGTATACAGGAACACGCTC 57.478 47.619 5.01 0.00 0.00 5.03
257 271 1.404391 AGGTATACAGGAACACGCTCG 59.596 52.381 5.01 0.00 0.00 5.03
258 272 1.402968 GGTATACAGGAACACGCTCGA 59.597 52.381 5.01 0.00 0.00 4.04
259 273 2.034305 GGTATACAGGAACACGCTCGAT 59.966 50.000 5.01 0.00 0.00 3.59
260 274 2.493713 ATACAGGAACACGCTCGATC 57.506 50.000 0.00 0.00 0.00 3.69
261 275 0.098200 TACAGGAACACGCTCGATCG 59.902 55.000 9.36 9.36 0.00 3.69
262 276 1.136774 CAGGAACACGCTCGATCGA 59.863 57.895 18.32 18.32 0.00 3.59
263 277 0.248661 CAGGAACACGCTCGATCGAT 60.249 55.000 19.78 1.60 0.00 3.59
264 278 0.029567 AGGAACACGCTCGATCGATC 59.970 55.000 19.78 15.68 0.00 3.69
292 330 1.448540 CTGACCGATGTGGACCTGC 60.449 63.158 0.00 0.00 42.00 4.85
327 367 4.771903 TCACTCACTGGCTCTACTACTAG 58.228 47.826 0.00 0.00 0.00 2.57
328 368 4.225492 TCACTCACTGGCTCTACTACTAGT 59.775 45.833 0.00 0.00 0.00 2.57
329 369 5.424573 TCACTCACTGGCTCTACTACTAGTA 59.575 44.000 1.89 1.89 0.00 1.82
331 371 5.426185 ACTCACTGGCTCTACTACTAGTAGT 59.574 44.000 32.39 32.39 46.31 2.73
332 372 6.610830 ACTCACTGGCTCTACTACTAGTAGTA 59.389 42.308 31.39 31.39 46.31 1.82
333 373 6.815089 TCACTGGCTCTACTACTAGTAGTAC 58.185 44.000 30.50 22.82 46.31 2.73
334 374 5.990996 CACTGGCTCTACTACTAGTAGTACC 59.009 48.000 30.50 28.37 46.31 3.34
335 375 5.207110 TGGCTCTACTACTAGTAGTACCG 57.793 47.826 30.50 24.57 46.31 4.02
336 376 4.651503 TGGCTCTACTACTAGTAGTACCGT 59.348 45.833 30.50 15.50 46.31 4.83
352 392 5.611374 AGTACCGTACCGTGTGTATAGTAT 58.389 41.667 5.02 0.00 0.00 2.12
353 393 6.755206 AGTACCGTACCGTGTGTATAGTATA 58.245 40.000 5.02 0.00 0.00 1.47
354 394 6.868864 AGTACCGTACCGTGTGTATAGTATAG 59.131 42.308 5.02 0.00 0.00 1.31
355 395 5.611374 ACCGTACCGTGTGTATAGTATAGT 58.389 41.667 0.00 0.00 0.00 2.12
356 396 5.696724 ACCGTACCGTGTGTATAGTATAGTC 59.303 44.000 0.00 0.00 0.00 2.59
357 397 5.164051 CCGTACCGTGTGTATAGTATAGTCG 60.164 48.000 0.00 0.00 0.00 4.18
358 398 5.402568 CGTACCGTGTGTATAGTATAGTCGT 59.597 44.000 0.00 0.00 0.00 4.34
359 399 6.581166 CGTACCGTGTGTATAGTATAGTCGTA 59.419 42.308 0.00 0.00 0.00 3.43
360 400 6.771188 ACCGTGTGTATAGTATAGTCGTAC 57.229 41.667 0.00 0.00 0.00 3.67
388 444 7.281549 ACGTGGAATAAATAAATAAAGCGAGGT 59.718 33.333 0.00 0.00 0.00 3.85
420 480 3.952811 GTCGCAAAAGGACGAGCT 58.047 55.556 0.00 0.00 39.30 4.09
421 481 1.782181 GTCGCAAAAGGACGAGCTC 59.218 57.895 2.73 2.73 39.30 4.09
422 482 1.733041 TCGCAAAAGGACGAGCTCG 60.733 57.895 33.45 33.45 46.33 5.03
423 483 2.476499 GCAAAAGGACGAGCTCGC 59.524 61.111 34.83 25.65 44.43 5.03
424 484 3.028366 GCAAAAGGACGAGCTCGCC 62.028 63.158 34.83 32.12 44.43 5.54
425 485 2.047179 AAAAGGACGAGCTCGCCC 60.047 61.111 34.83 33.15 42.45 6.13
426 486 3.934391 AAAAGGACGAGCTCGCCCG 62.934 63.158 34.83 13.78 46.79 6.13
455 515 4.937431 GGCAGGTATCCGGCAGCC 62.937 72.222 0.00 0.00 46.17 4.85
456 516 4.175337 GCAGGTATCCGGCAGCCA 62.175 66.667 13.30 0.00 43.90 4.75
457 517 2.109799 CAGGTATCCGGCAGCCAG 59.890 66.667 13.30 0.00 0.00 4.85
458 518 3.866582 AGGTATCCGGCAGCCAGC 61.867 66.667 13.30 0.79 44.65 4.85
479 546 4.741239 TGGTGGCCTCCCTCCCTC 62.741 72.222 21.06 0.00 42.88 4.30
592 668 2.721425 TTTTCTTTGGTCCCGTGTCT 57.279 45.000 0.00 0.00 0.00 3.41
620 696 4.087892 CCTCTCCCTGCCGGTGTG 62.088 72.222 1.90 0.00 0.00 3.82
621 697 4.087892 CTCTCCCTGCCGGTGTGG 62.088 72.222 1.90 2.64 42.50 4.17
624 700 4.263572 TCCCTGCCGGTGTGGTTG 62.264 66.667 1.90 0.00 41.21 3.77
652 729 3.899981 ATGCCGGCGCTTCTCACAA 62.900 57.895 23.90 0.00 35.36 3.33
714 800 2.434884 CACGTACCAGCCAGCCAG 60.435 66.667 0.00 0.00 0.00 4.85
715 801 4.394712 ACGTACCAGCCAGCCAGC 62.395 66.667 0.00 0.00 0.00 4.85
717 803 4.033776 GTACCAGCCAGCCAGCCA 62.034 66.667 0.00 0.00 0.00 4.75
718 804 3.720601 TACCAGCCAGCCAGCCAG 61.721 66.667 0.00 0.00 0.00 4.85
767 857 1.750399 CAACATAAGCTGCCGGCCT 60.750 57.895 26.77 12.40 43.05 5.19
778 868 1.839296 GCCGGCCTCTCCTATTCCT 60.839 63.158 18.11 0.00 0.00 3.36
785 879 0.249657 CTCTCCTATTCCTGGCACGC 60.250 60.000 0.00 0.00 0.00 5.34
851 945 4.101790 CGCCCGCGCACATTCTTT 62.102 61.111 8.75 0.00 34.03 2.52
928 1022 1.306226 CCTCCCTCCCTCTCCGTTT 60.306 63.158 0.00 0.00 0.00 3.60
929 1023 1.331399 CCTCCCTCCCTCTCCGTTTC 61.331 65.000 0.00 0.00 0.00 2.78
930 1024 0.324830 CTCCCTCCCTCTCCGTTTCT 60.325 60.000 0.00 0.00 0.00 2.52
931 1025 0.324460 TCCCTCCCTCTCCGTTTCTC 60.324 60.000 0.00 0.00 0.00 2.87
932 1026 0.324830 CCCTCCCTCTCCGTTTCTCT 60.325 60.000 0.00 0.00 0.00 3.10
933 1027 1.107945 CCTCCCTCTCCGTTTCTCTC 58.892 60.000 0.00 0.00 0.00 3.20
934 1028 1.341581 CCTCCCTCTCCGTTTCTCTCT 60.342 57.143 0.00 0.00 0.00 3.10
935 1029 2.021457 CTCCCTCTCCGTTTCTCTCTC 58.979 57.143 0.00 0.00 0.00 3.20
936 1030 1.636519 TCCCTCTCCGTTTCTCTCTCT 59.363 52.381 0.00 0.00 0.00 3.10
937 1031 2.021457 CCCTCTCCGTTTCTCTCTCTC 58.979 57.143 0.00 0.00 0.00 3.20
938 1032 2.356741 CCCTCTCCGTTTCTCTCTCTCT 60.357 54.545 0.00 0.00 0.00 3.10
960 1054 5.429762 TCTCTCTCTCTCTCTCTTTCCATCT 59.570 44.000 0.00 0.00 0.00 2.90
1058 1152 4.787280 CGGCACCCTCCTCCTCCT 62.787 72.222 0.00 0.00 0.00 3.69
1059 1153 2.766229 GGCACCCTCCTCCTCCTC 60.766 72.222 0.00 0.00 0.00 3.71
1060 1154 3.151022 GCACCCTCCTCCTCCTCG 61.151 72.222 0.00 0.00 0.00 4.63
1072 1166 1.215382 CTCCTCGTGATTGTCGCCA 59.785 57.895 0.00 0.00 0.00 5.69
1268 1362 2.254350 GCGCGTTTCCTTGGTTCC 59.746 61.111 8.43 0.00 0.00 3.62
1311 1406 2.642254 TTCCGCTGGTCCCACGTAG 61.642 63.158 0.00 0.00 0.00 3.51
1312 1407 4.143333 CCGCTGGTCCCACGTAGG 62.143 72.222 0.00 0.00 37.03 3.18
1313 1408 3.379445 CGCTGGTCCCACGTAGGT 61.379 66.667 0.00 0.00 34.66 3.08
1314 1409 2.048023 CGCTGGTCCCACGTAGGTA 61.048 63.158 0.00 0.00 34.66 3.08
1315 1410 1.514553 GCTGGTCCCACGTAGGTAC 59.485 63.158 0.00 0.00 34.66 3.34
1333 1428 2.677671 GTACGTAACGTGCGCGAC 59.322 61.111 28.73 14.21 41.39 5.19
1342 1437 3.033764 GTGCGCGACGAAAGGTGA 61.034 61.111 12.10 0.00 0.00 4.02
1343 1438 3.033764 TGCGCGACGAAAGGTGAC 61.034 61.111 12.10 0.00 0.00 3.67
1344 1439 4.117372 GCGCGACGAAAGGTGACG 62.117 66.667 12.10 0.00 0.00 4.35
1345 1440 2.728383 CGCGACGAAAGGTGACGT 60.728 61.111 0.00 0.00 45.32 4.34
1346 1441 1.440850 CGCGACGAAAGGTGACGTA 60.441 57.895 0.00 0.00 42.74 3.57
1347 1442 1.659262 CGCGACGAAAGGTGACGTAC 61.659 60.000 0.00 0.00 42.74 3.67
1348 1443 1.659262 GCGACGAAAGGTGACGTACG 61.659 60.000 15.01 15.01 42.74 3.67
1503 1598 1.218316 CGACCAGCTCAAGGTACCC 59.782 63.158 8.74 0.00 40.09 3.69
1517 1612 2.950781 GGTACCCACCTACCTACCTAC 58.049 57.143 0.00 0.00 42.11 3.18
1518 1613 2.244769 GGTACCCACCTACCTACCTACA 59.755 54.545 0.00 0.00 42.11 2.74
1519 1614 2.539432 ACCCACCTACCTACCTACAC 57.461 55.000 0.00 0.00 0.00 2.90
1520 1615 1.007600 ACCCACCTACCTACCTACACC 59.992 57.143 0.00 0.00 0.00 4.16
1521 1616 1.290130 CCCACCTACCTACCTACACCT 59.710 57.143 0.00 0.00 0.00 4.00
1522 1617 2.385803 CCACCTACCTACCTACACCTG 58.614 57.143 0.00 0.00 0.00 4.00
1545 1643 7.094291 CCTGCTTCTTCTCTTTGAATGAATTCT 60.094 37.037 7.05 0.00 37.67 2.40
1546 1644 7.591165 TGCTTCTTCTCTTTGAATGAATTCTG 58.409 34.615 7.05 0.00 37.67 3.02
1547 1645 7.230108 TGCTTCTTCTCTTTGAATGAATTCTGT 59.770 33.333 7.05 0.00 37.67 3.41
1548 1646 8.081025 GCTTCTTCTCTTTGAATGAATTCTGTT 58.919 33.333 7.05 1.75 37.67 3.16
1582 1719 1.745115 AACGTGGACGATGCATGGG 60.745 57.895 13.62 3.25 43.02 4.00
1730 1995 2.024655 ACCCTACCTCTCATCCAACGTA 60.025 50.000 0.00 0.00 0.00 3.57
1731 1996 2.361438 CCCTACCTCTCATCCAACGTAC 59.639 54.545 0.00 0.00 0.00 3.67
1732 1997 2.033049 CCTACCTCTCATCCAACGTACG 59.967 54.545 15.01 15.01 0.00 3.67
1733 1998 1.542492 ACCTCTCATCCAACGTACGT 58.458 50.000 16.72 16.72 0.00 3.57
1734 1999 1.471684 ACCTCTCATCCAACGTACGTC 59.528 52.381 23.05 0.00 0.00 4.34
1735 2000 1.743958 CCTCTCATCCAACGTACGTCT 59.256 52.381 23.05 9.27 0.00 4.18
1736 2001 2.223294 CCTCTCATCCAACGTACGTCTC 60.223 54.545 23.05 0.00 0.00 3.36
1737 2002 2.418976 CTCTCATCCAACGTACGTCTCA 59.581 50.000 23.05 8.48 0.00 3.27
1738 2003 2.161012 TCTCATCCAACGTACGTCTCAC 59.839 50.000 23.05 0.00 0.00 3.51
1739 2004 1.200716 TCATCCAACGTACGTCTCACC 59.799 52.381 23.05 0.00 0.00 4.02
1740 2005 0.169672 ATCCAACGTACGTCTCACCG 59.830 55.000 23.05 6.19 0.00 4.94
1741 2006 1.443194 CCAACGTACGTCTCACCGG 60.443 63.158 23.05 11.36 0.00 5.28
1779 2048 1.802314 CCATGCACGCACGTACGTA 60.802 57.895 22.34 4.43 46.34 3.57
1780 2049 1.339134 CATGCACGCACGTACGTAC 59.661 57.895 22.34 15.19 46.34 3.67
1797 2066 2.154798 TACGTGCCGCTTCTGCTTCT 62.155 55.000 0.00 0.00 36.97 2.85
1798 2067 2.734673 CGTGCCGCTTCTGCTTCTC 61.735 63.158 0.00 0.00 36.97 2.87
1799 2068 2.046892 TGCCGCTTCTGCTTCTCC 60.047 61.111 0.00 0.00 36.97 3.71
1800 2069 2.046892 GCCGCTTCTGCTTCTCCA 60.047 61.111 0.00 0.00 36.97 3.86
2152 2423 5.960113 TCCTTCTTCTTCTTCTCGAATCTG 58.040 41.667 0.00 0.00 0.00 2.90
2572 2885 1.139734 CGACAGCATCGCCTACTGT 59.860 57.895 0.00 0.00 45.52 3.55
2639 2955 0.733566 CAAATGTGGGTGCGCACATC 60.734 55.000 38.60 29.22 40.71 3.06
2709 3025 3.364441 GGAACATGCGCACTGCCA 61.364 61.111 14.90 0.00 45.60 4.92
2784 3100 0.461961 CTTCCTCCTCGCCGAAATCT 59.538 55.000 0.00 0.00 0.00 2.40
2883 3199 3.289062 TCGTGGTCTTCGTCGGCA 61.289 61.111 0.00 0.00 0.00 5.69
2962 3278 1.986882 AGCTTTGTCACCTTCCTTGG 58.013 50.000 0.00 0.00 0.00 3.61
2975 3291 1.000896 CCTTGGCCCCGTCTTCATT 60.001 57.895 0.00 0.00 0.00 2.57
3060 3376 2.337583 CCGTCATCGTCACTGTTGAAT 58.662 47.619 0.00 0.00 31.90 2.57
3138 3454 5.540337 TGAACTCAATCCAGAGAGTACAACT 59.460 40.000 0.00 0.00 43.88 3.16
3159 3475 0.251297 CAGATGAAGGGGCAACACCA 60.251 55.000 0.00 0.00 46.76 4.17
3196 3512 4.289672 ACAGTACTCCAAATCAAGGGATGT 59.710 41.667 0.00 0.00 32.92 3.06
3199 3515 2.292267 CTCCAAATCAAGGGATGTCGG 58.708 52.381 0.00 0.00 32.92 4.79
3442 3758 2.418746 GGTGAACGACTGTGCTGGATAT 60.419 50.000 0.00 0.00 0.00 1.63
3466 3782 1.606668 GCCGACCTCAGATCTGTAGAG 59.393 57.143 21.92 12.19 0.00 2.43
3510 3826 1.139989 CAATGGCGGCGTATAGTCAG 58.860 55.000 9.37 0.00 0.00 3.51
3601 3917 3.629398 AGCCATGCACAAATAGTTAGAGC 59.371 43.478 0.00 0.00 0.00 4.09
3658 3974 4.556233 TCAGAGATGTGTAAACTGAACCG 58.444 43.478 0.00 0.00 35.20 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.481185 CCATTTTGTTCCTGCACAATGC 59.519 45.455 0.00 0.00 45.29 3.56
2 3 3.991773 CTCCATTTTGTTCCTGCACAATG 59.008 43.478 0.00 0.00 36.54 2.82
3 4 3.642848 ACTCCATTTTGTTCCTGCACAAT 59.357 39.130 0.00 0.00 36.54 2.71
4 5 3.030291 ACTCCATTTTGTTCCTGCACAA 58.970 40.909 0.00 0.00 34.76 3.33
5 6 2.665165 ACTCCATTTTGTTCCTGCACA 58.335 42.857 0.00 0.00 0.00 4.57
6 7 3.191371 CCTACTCCATTTTGTTCCTGCAC 59.809 47.826 0.00 0.00 0.00 4.57
7 8 3.420893 CCTACTCCATTTTGTTCCTGCA 58.579 45.455 0.00 0.00 0.00 4.41
8 9 2.755103 CCCTACTCCATTTTGTTCCTGC 59.245 50.000 0.00 0.00 0.00 4.85
9 10 3.356290 CCCCTACTCCATTTTGTTCCTG 58.644 50.000 0.00 0.00 0.00 3.86
10 11 2.291605 GCCCCTACTCCATTTTGTTCCT 60.292 50.000 0.00 0.00 0.00 3.36
11 12 2.100197 GCCCCTACTCCATTTTGTTCC 58.900 52.381 0.00 0.00 0.00 3.62
12 13 2.100197 GGCCCCTACTCCATTTTGTTC 58.900 52.381 0.00 0.00 0.00 3.18
13 14 1.431243 TGGCCCCTACTCCATTTTGTT 59.569 47.619 0.00 0.00 0.00 2.83
14 15 1.080638 TGGCCCCTACTCCATTTTGT 58.919 50.000 0.00 0.00 0.00 2.83
15 16 2.459555 ATGGCCCCTACTCCATTTTG 57.540 50.000 0.00 0.00 39.95 2.44
16 17 2.177016 GGTATGGCCCCTACTCCATTTT 59.823 50.000 0.00 0.00 42.62 1.82
17 18 1.780919 GGTATGGCCCCTACTCCATTT 59.219 52.381 0.00 0.00 42.62 2.32
18 19 1.446016 GGTATGGCCCCTACTCCATT 58.554 55.000 0.00 0.00 42.62 3.16
19 20 0.836400 CGGTATGGCCCCTACTCCAT 60.836 60.000 0.00 0.00 44.62 3.41
20 21 1.458777 CGGTATGGCCCCTACTCCA 60.459 63.158 0.00 0.00 36.70 3.86
21 22 2.214920 CCGGTATGGCCCCTACTCC 61.215 68.421 0.00 0.00 0.00 3.85
22 23 2.214920 CCCGGTATGGCCCCTACTC 61.215 68.421 0.00 0.00 35.87 2.59
23 24 2.122547 CCCGGTATGGCCCCTACT 60.123 66.667 0.00 0.00 35.87 2.57
24 25 3.246880 CCCCGGTATGGCCCCTAC 61.247 72.222 0.00 1.64 35.87 3.18
25 26 4.585216 CCCCCGGTATGGCCCCTA 62.585 72.222 0.00 0.00 35.87 3.53
39 40 2.158204 TCTATACCCTAGCTTGACCCCC 60.158 54.545 0.00 0.00 0.00 5.40
40 41 3.255634 TCTATACCCTAGCTTGACCCC 57.744 52.381 0.00 0.00 0.00 4.95
41 42 3.005578 CGTTCTATACCCTAGCTTGACCC 59.994 52.174 0.00 0.00 0.00 4.46
42 43 3.635836 ACGTTCTATACCCTAGCTTGACC 59.364 47.826 0.00 0.00 0.00 4.02
43 44 4.499357 CCACGTTCTATACCCTAGCTTGAC 60.499 50.000 0.00 0.00 0.00 3.18
44 45 3.635373 CCACGTTCTATACCCTAGCTTGA 59.365 47.826 0.00 0.00 0.00 3.02
45 46 3.383825 ACCACGTTCTATACCCTAGCTTG 59.616 47.826 0.00 0.00 0.00 4.01
46 47 3.383825 CACCACGTTCTATACCCTAGCTT 59.616 47.826 0.00 0.00 0.00 3.74
47 48 2.957006 CACCACGTTCTATACCCTAGCT 59.043 50.000 0.00 0.00 0.00 3.32
48 49 2.545322 GCACCACGTTCTATACCCTAGC 60.545 54.545 0.00 0.00 0.00 3.42
49 50 2.691526 TGCACCACGTTCTATACCCTAG 59.308 50.000 0.00 0.00 0.00 3.02
50 51 2.737544 TGCACCACGTTCTATACCCTA 58.262 47.619 0.00 0.00 0.00 3.53
51 52 1.563924 TGCACCACGTTCTATACCCT 58.436 50.000 0.00 0.00 0.00 4.34
52 53 2.480845 GATGCACCACGTTCTATACCC 58.519 52.381 0.00 0.00 0.00 3.69
53 54 2.124903 CGATGCACCACGTTCTATACC 58.875 52.381 0.00 0.00 0.00 2.73
54 55 3.074504 TCGATGCACCACGTTCTATAC 57.925 47.619 9.03 0.00 0.00 1.47
55 56 4.316205 AATCGATGCACCACGTTCTATA 57.684 40.909 0.00 0.00 0.00 1.31
56 57 2.890808 ATCGATGCACCACGTTCTAT 57.109 45.000 0.00 0.00 0.00 1.98
57 58 2.665649 AATCGATGCACCACGTTCTA 57.334 45.000 0.00 0.00 0.00 2.10
58 59 1.464608 CAAATCGATGCACCACGTTCT 59.535 47.619 0.00 0.00 0.00 3.01
59 60 1.196808 ACAAATCGATGCACCACGTTC 59.803 47.619 0.00 0.00 0.00 3.95
60 61 1.069296 CACAAATCGATGCACCACGTT 60.069 47.619 0.00 0.03 0.00 3.99
61 62 0.516877 CACAAATCGATGCACCACGT 59.483 50.000 0.00 0.00 0.00 4.49
62 63 0.516877 ACACAAATCGATGCACCACG 59.483 50.000 0.00 0.00 0.00 4.94
63 64 1.464023 CGACACAAATCGATGCACCAC 60.464 52.381 0.00 0.00 45.13 4.16
64 65 0.795698 CGACACAAATCGATGCACCA 59.204 50.000 0.00 0.00 45.13 4.17
65 66 1.075542 TCGACACAAATCGATGCACC 58.924 50.000 0.00 0.00 45.84 5.01
72 73 2.098353 CGTGATCGATCGACACAAATCG 60.098 50.000 31.23 23.61 44.66 3.34
73 74 2.852413 ACGTGATCGATCGACACAAATC 59.148 45.455 31.23 21.74 40.62 2.17
74 75 2.598637 CACGTGATCGATCGACACAAAT 59.401 45.455 31.23 21.17 40.62 2.32
75 76 1.982913 CACGTGATCGATCGACACAAA 59.017 47.619 31.23 13.98 40.62 2.83
76 77 1.198178 TCACGTGATCGATCGACACAA 59.802 47.619 31.23 21.07 40.62 3.33
77 78 0.800012 TCACGTGATCGATCGACACA 59.200 50.000 31.23 25.82 40.62 3.72
96 97 3.264104 TCGAAGGAACAAGAAACACGTT 58.736 40.909 0.00 0.00 0.00 3.99
100 105 4.131649 TGTCTCGAAGGAACAAGAAACA 57.868 40.909 0.00 0.00 0.00 2.83
108 113 1.986378 CGTGTCATGTCTCGAAGGAAC 59.014 52.381 8.41 0.00 0.00 3.62
183 194 6.895204 CCATTCCAAACCCCTATCTTTCTTTA 59.105 38.462 0.00 0.00 0.00 1.85
194 205 1.920351 ACGTATCCATTCCAAACCCCT 59.080 47.619 0.00 0.00 0.00 4.79
197 208 1.063469 CGCACGTATCCATTCCAAACC 59.937 52.381 0.00 0.00 0.00 3.27
199 210 0.730265 GCGCACGTATCCATTCCAAA 59.270 50.000 0.30 0.00 0.00 3.28
205 219 0.732571 CCTTTTGCGCACGTATCCAT 59.267 50.000 11.12 0.00 0.00 3.41
218 232 2.192624 CTTTTGTGCACGACCCTTTTG 58.807 47.619 13.13 0.00 0.00 2.44
220 234 0.744281 CCTTTTGTGCACGACCCTTT 59.256 50.000 13.13 0.00 0.00 3.11
222 236 0.470766 TACCTTTTGTGCACGACCCT 59.529 50.000 13.13 0.00 0.00 4.34
223 237 1.530323 ATACCTTTTGTGCACGACCC 58.470 50.000 13.13 0.00 0.00 4.46
224 238 3.068560 TGTATACCTTTTGTGCACGACC 58.931 45.455 13.13 0.00 0.00 4.79
225 239 3.124636 CCTGTATACCTTTTGTGCACGAC 59.875 47.826 13.13 0.00 0.00 4.34
226 240 3.007074 TCCTGTATACCTTTTGTGCACGA 59.993 43.478 13.13 7.71 0.00 4.35
227 241 3.331150 TCCTGTATACCTTTTGTGCACG 58.669 45.455 13.13 0.00 0.00 5.34
228 242 4.517453 TGTTCCTGTATACCTTTTGTGCAC 59.483 41.667 10.75 10.75 0.00 4.57
229 243 4.517453 GTGTTCCTGTATACCTTTTGTGCA 59.483 41.667 0.00 0.00 0.00 4.57
230 244 4.378046 CGTGTTCCTGTATACCTTTTGTGC 60.378 45.833 0.00 0.00 0.00 4.57
231 245 4.378046 GCGTGTTCCTGTATACCTTTTGTG 60.378 45.833 0.00 0.00 0.00 3.33
232 246 3.749609 GCGTGTTCCTGTATACCTTTTGT 59.250 43.478 0.00 0.00 0.00 2.83
233 247 4.000988 AGCGTGTTCCTGTATACCTTTTG 58.999 43.478 0.00 0.00 0.00 2.44
234 248 4.251268 GAGCGTGTTCCTGTATACCTTTT 58.749 43.478 0.00 0.00 0.00 2.27
235 249 3.675228 CGAGCGTGTTCCTGTATACCTTT 60.675 47.826 0.00 0.00 0.00 3.11
236 250 2.159282 CGAGCGTGTTCCTGTATACCTT 60.159 50.000 0.00 0.00 0.00 3.50
237 251 1.404391 CGAGCGTGTTCCTGTATACCT 59.596 52.381 0.00 0.00 0.00 3.08
238 252 1.402968 TCGAGCGTGTTCCTGTATACC 59.597 52.381 0.00 0.00 0.00 2.73
239 253 2.838386 TCGAGCGTGTTCCTGTATAC 57.162 50.000 0.00 0.00 0.00 1.47
240 254 2.032290 CGATCGAGCGTGTTCCTGTATA 60.032 50.000 16.15 0.00 0.00 1.47
241 255 1.268589 CGATCGAGCGTGTTCCTGTAT 60.269 52.381 16.15 0.00 0.00 2.29
242 256 0.098200 CGATCGAGCGTGTTCCTGTA 59.902 55.000 16.15 0.00 0.00 2.74
243 257 1.154016 CGATCGAGCGTGTTCCTGT 60.154 57.895 16.15 0.00 0.00 4.00
244 258 0.248661 ATCGATCGAGCGTGTTCCTG 60.249 55.000 23.61 0.00 0.00 3.86
245 259 0.029567 GATCGATCGAGCGTGTTCCT 59.970 55.000 23.61 2.57 0.00 3.36
246 260 2.496718 GATCGATCGAGCGTGTTCC 58.503 57.895 23.61 5.19 0.00 3.62
257 271 1.676529 TCAGTGACCCTTCGATCGATC 59.323 52.381 20.18 15.68 0.00 3.69
258 272 1.405821 GTCAGTGACCCTTCGATCGAT 59.594 52.381 20.18 3.14 0.00 3.59
259 273 0.809385 GTCAGTGACCCTTCGATCGA 59.191 55.000 15.15 15.15 0.00 3.59
260 274 0.179134 GGTCAGTGACCCTTCGATCG 60.179 60.000 29.13 9.36 46.19 3.69
261 275 3.742983 GGTCAGTGACCCTTCGATC 57.257 57.895 29.13 3.66 46.19 3.69
270 284 0.389948 GGTCCACATCGGTCAGTGAC 60.390 60.000 15.24 15.24 37.97 3.67
271 285 0.541998 AGGTCCACATCGGTCAGTGA 60.542 55.000 0.00 0.00 37.97 3.41
272 286 0.390340 CAGGTCCACATCGGTCAGTG 60.390 60.000 0.00 0.00 35.57 3.66
273 287 1.975327 CAGGTCCACATCGGTCAGT 59.025 57.895 0.00 0.00 35.57 3.41
274 288 1.448540 GCAGGTCCACATCGGTCAG 60.449 63.158 0.00 0.00 35.57 3.51
275 289 1.763546 TTGCAGGTCCACATCGGTCA 61.764 55.000 0.00 0.00 35.57 4.02
335 375 6.771188 ACGACTATACTATACACACGGTAC 57.229 41.667 0.00 0.00 34.07 3.34
336 376 7.658261 AGTACGACTATACTATACACACGGTA 58.342 38.462 0.00 0.00 33.50 4.02
360 400 9.793245 CTCGCTTTATTTATTTATTCCACGTAG 57.207 33.333 0.00 0.00 0.00 3.51
388 444 1.809869 CGACGCATCCTTCTCCTCA 59.190 57.895 0.00 0.00 0.00 3.86
438 498 4.937431 GGCTGCCGGATACCTGCC 62.937 72.222 5.05 8.98 38.58 4.85
439 499 4.175337 TGGCTGCCGGATACCTGC 62.175 66.667 14.98 2.38 34.31 4.85
440 500 2.109799 CTGGCTGCCGGATACCTG 59.890 66.667 23.22 2.20 29.82 4.00
441 501 3.866582 GCTGGCTGCCGGATACCT 61.867 66.667 31.08 0.00 35.15 3.08
443 503 4.221422 TCGCTGGCTGCCGGATAC 62.221 66.667 31.08 12.36 38.78 2.24
444 504 3.916544 CTCGCTGGCTGCCGGATA 61.917 66.667 31.08 15.93 38.78 2.59
455 515 4.767255 GGAGGCCACCACTCGCTG 62.767 72.222 15.24 0.00 35.82 5.18
458 518 3.775654 GAGGGAGGCCACCACTCG 61.776 72.222 21.72 0.00 35.82 4.18
459 519 3.403558 GGAGGGAGGCCACCACTC 61.404 72.222 21.72 21.62 0.00 3.51
462 522 4.741239 GAGGGAGGGAGGCCACCA 62.741 72.222 21.72 0.00 0.00 4.17
494 561 3.493303 GGTGGCTCCCCCTCATCC 61.493 72.222 0.00 0.00 0.00 3.51
592 668 2.043852 GGAGAGGGAGAGCGACCA 60.044 66.667 0.00 0.00 0.00 4.02
644 721 4.556233 CTCATGGTACGAAGTTGTGAGAA 58.444 43.478 0.00 0.00 37.78 2.87
647 724 2.611971 GCCTCATGGTACGAAGTTGTGA 60.612 50.000 0.00 0.00 45.11 3.58
714 800 3.670377 GTTCACCGGTTGGCTGGC 61.670 66.667 2.97 0.00 45.10 4.85
715 801 2.983592 GGTTCACCGGTTGGCTGG 60.984 66.667 2.97 0.00 46.63 4.85
767 857 1.686325 GGCGTGCCAGGAATAGGAGA 61.686 60.000 5.89 0.00 35.81 3.71
928 1022 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
929 1023 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
930 1024 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
931 1025 5.867903 AAGAGAGAGAGAGAGAGAGAGAG 57.132 47.826 0.00 0.00 0.00 3.20
932 1026 5.129485 GGAAAGAGAGAGAGAGAGAGAGAGA 59.871 48.000 0.00 0.00 0.00 3.10
933 1027 5.104776 TGGAAAGAGAGAGAGAGAGAGAGAG 60.105 48.000 0.00 0.00 0.00 3.20
934 1028 4.782691 TGGAAAGAGAGAGAGAGAGAGAGA 59.217 45.833 0.00 0.00 0.00 3.10
935 1029 5.102953 TGGAAAGAGAGAGAGAGAGAGAG 57.897 47.826 0.00 0.00 0.00 3.20
936 1030 5.429762 AGATGGAAAGAGAGAGAGAGAGAGA 59.570 44.000 0.00 0.00 0.00 3.10
937 1031 5.530171 CAGATGGAAAGAGAGAGAGAGAGAG 59.470 48.000 0.00 0.00 0.00 3.20
938 1032 5.439721 CAGATGGAAAGAGAGAGAGAGAGA 58.560 45.833 0.00 0.00 0.00 3.10
979 1073 3.052620 TTCGCTAGCTCGCTCGCTT 62.053 57.895 13.93 0.00 41.30 4.68
980 1074 3.509757 TTCGCTAGCTCGCTCGCT 61.510 61.111 13.93 2.17 43.83 4.93
981 1075 3.316278 GTTCGCTAGCTCGCTCGC 61.316 66.667 13.93 5.44 0.00 5.03
982 1076 2.703425 ATCGTTCGCTAGCTCGCTCG 62.703 60.000 13.93 10.11 0.00 5.03
1046 1140 0.397816 AATCACGAGGAGGAGGAGGG 60.398 60.000 0.00 0.00 0.00 4.30
1053 1147 1.519455 GGCGACAATCACGAGGAGG 60.519 63.158 0.00 0.00 0.00 4.30
1054 1148 1.215382 TGGCGACAATCACGAGGAG 59.785 57.895 0.00 0.00 37.44 3.69
1268 1362 2.280708 CGCGGAACCTACATTTACGAAG 59.719 50.000 0.00 0.00 0.00 3.79
1316 1411 2.677671 GTCGCGCACGTTACGTAC 59.322 61.111 10.89 3.62 38.32 3.67
1317 1412 2.864699 CGTCGCGCACGTTACGTA 60.865 61.111 10.89 0.00 44.07 3.57
1330 1425 1.061799 CCGTACGTCACCTTTCGTCG 61.062 60.000 15.21 0.00 40.70 5.12
1331 1426 0.040067 ACCGTACGTCACCTTTCGTC 60.040 55.000 15.21 0.00 40.70 4.20
1332 1427 0.318107 CACCGTACGTCACCTTTCGT 60.318 55.000 15.21 0.00 42.82 3.85
1333 1428 1.611592 GCACCGTACGTCACCTTTCG 61.612 60.000 15.21 0.00 0.00 3.46
1334 1429 1.611592 CGCACCGTACGTCACCTTTC 61.612 60.000 15.21 0.00 0.00 2.62
1335 1430 1.662446 CGCACCGTACGTCACCTTT 60.662 57.895 15.21 0.00 0.00 3.11
1336 1431 2.049802 CGCACCGTACGTCACCTT 60.050 61.111 15.21 0.00 0.00 3.50
1337 1432 2.848858 AACGCACCGTACGTCACCT 61.849 57.895 15.21 0.00 44.30 4.00
1338 1433 2.355009 AACGCACCGTACGTCACC 60.355 61.111 15.21 0.00 44.30 4.02
1339 1434 2.841389 CAACGCACCGTACGTCAC 59.159 61.111 15.21 1.49 44.30 3.67
1340 1435 3.031457 GCAACGCACCGTACGTCA 61.031 61.111 15.21 0.00 44.30 4.35
1341 1436 2.995450 CTGCAACGCACCGTACGTC 61.995 63.158 15.21 1.99 44.30 4.34
1343 1438 3.773630 CCTGCAACGCACCGTACG 61.774 66.667 8.69 8.69 39.99 3.67
1344 1439 3.419759 CCCTGCAACGCACCGTAC 61.420 66.667 0.00 0.00 39.99 3.67
1503 1598 1.755380 GCAGGTGTAGGTAGGTAGGTG 59.245 57.143 0.00 0.00 0.00 4.00
1514 1609 4.887748 TCAAAGAGAAGAAGCAGGTGTAG 58.112 43.478 0.00 0.00 0.00 2.74
1515 1610 4.955811 TCAAAGAGAAGAAGCAGGTGTA 57.044 40.909 0.00 0.00 0.00 2.90
1516 1611 3.845781 TCAAAGAGAAGAAGCAGGTGT 57.154 42.857 0.00 0.00 0.00 4.16
1517 1612 4.758674 TCATTCAAAGAGAAGAAGCAGGTG 59.241 41.667 0.00 0.00 40.15 4.00
1518 1613 4.978099 TCATTCAAAGAGAAGAAGCAGGT 58.022 39.130 0.00 0.00 40.15 4.00
1519 1614 5.954296 TTCATTCAAAGAGAAGAAGCAGG 57.046 39.130 0.00 0.00 40.15 4.85
1520 1615 7.751348 CAGAATTCATTCAAAGAGAAGAAGCAG 59.249 37.037 8.44 0.00 40.15 4.24
1521 1616 7.230108 ACAGAATTCATTCAAAGAGAAGAAGCA 59.770 33.333 8.44 0.00 40.15 3.91
1522 1617 7.592051 ACAGAATTCATTCAAAGAGAAGAAGC 58.408 34.615 8.44 0.00 40.15 3.86
1546 1644 3.128068 ACGTTGAGACCTTTTTGTGGAAC 59.872 43.478 0.00 0.00 37.35 3.62
1547 1645 3.127895 CACGTTGAGACCTTTTTGTGGAA 59.872 43.478 0.00 0.00 0.00 3.53
1548 1646 2.680841 CACGTTGAGACCTTTTTGTGGA 59.319 45.455 0.00 0.00 0.00 4.02
1582 1719 3.414700 CCTCACGCCGTTCTGCAC 61.415 66.667 0.00 0.00 0.00 4.57
1734 1999 2.383245 ATTAGATGGCGGCCGGTGAG 62.383 60.000 29.38 0.00 0.00 3.51
1735 2000 2.377628 GATTAGATGGCGGCCGGTGA 62.378 60.000 29.38 0.00 0.00 4.02
1736 2001 1.961277 GATTAGATGGCGGCCGGTG 60.961 63.158 29.38 0.00 0.00 4.94
1737 2002 0.830444 TAGATTAGATGGCGGCCGGT 60.830 55.000 29.38 5.36 0.00 5.28
1738 2003 0.320374 TTAGATTAGATGGCGGCCGG 59.680 55.000 29.38 8.95 0.00 6.13
1739 2004 2.271800 GATTAGATTAGATGGCGGCCG 58.728 52.381 24.05 24.05 0.00 6.13
1740 2005 3.003480 GTGATTAGATTAGATGGCGGCC 58.997 50.000 13.32 13.32 0.00 6.13
1741 2006 3.003480 GGTGATTAGATTAGATGGCGGC 58.997 50.000 0.00 0.00 0.00 6.53
1885 2154 0.179205 CGGTGTACTCCTCGACGAAC 60.179 60.000 11.98 0.00 0.00 3.95
2152 2423 0.247460 TGATCCATGGCGATCGATCC 59.753 55.000 21.57 12.28 41.39 3.36
2448 2757 3.796717 CAGCATCACAATGACAATGCATC 59.203 43.478 16.55 0.00 45.39 3.91
2456 2765 2.486951 GCCATCAGCATCACAATGAC 57.513 50.000 0.00 0.00 42.97 3.06
2572 2885 4.280174 GCTTAGACGTGGATGGATACCTTA 59.720 45.833 0.00 0.00 0.00 2.69
2619 2935 1.825622 TGTGCGCACCCACATTTGA 60.826 52.632 35.72 12.75 40.55 2.69
2639 2955 9.745880 ACATATGTTAGTCGGTACAAGATTAAG 57.254 33.333 1.41 0.00 0.00 1.85
2709 3025 1.890894 CGAGGACAGGGTTGACGAT 59.109 57.895 0.00 0.00 0.00 3.73
2784 3100 0.313672 GTGACGAAGCCAATGCCAAA 59.686 50.000 0.00 0.00 38.69 3.28
2883 3199 5.596836 TGAAAGAAAACAAGGACAATGCT 57.403 34.783 0.00 0.00 0.00 3.79
2962 3278 3.140814 GGGCAATGAAGACGGGGC 61.141 66.667 0.00 0.00 0.00 5.80
2991 3307 1.227002 GAGGGTCGAAGGCTTAGCG 60.227 63.158 0.00 0.00 0.00 4.26
3060 3376 5.839063 TGGAGACTTCTTCTTTGGAGACTTA 59.161 40.000 0.00 0.00 33.22 2.24
3138 3454 1.004277 GGTGTTGCCCCTTCATCTGTA 59.996 52.381 0.00 0.00 0.00 2.74
3159 3475 3.714391 AGTACTGTTCGAAGACGCTTTT 58.286 40.909 0.00 0.00 39.58 2.27
3420 3736 1.961277 CCAGCACAGTCGTTCACCC 60.961 63.158 0.00 0.00 0.00 4.61
3442 3758 1.039785 CAGATCTGAGGTCGGCTCCA 61.040 60.000 18.34 0.00 0.00 3.86
3510 3826 7.378181 TGGAAAAGATTGAAAAACTATCAGCC 58.622 34.615 0.00 0.00 34.22 4.85
3658 3974 0.323451 AAAATCTCAAGACCGGCCCC 60.323 55.000 0.00 0.00 0.00 5.80


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

AutoCloner maintained by Alex Coulton.