Multiple sequence alignment - TraesCS2A01G351100

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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 TraesCS2A01G351100 chr2A 100.000 4702 0 0 1 4702 591089750 591094451 0.000000e+00 8684
1 TraesCS2A01G351100 chr2A 95.245 715 34 0 3988 4702 697196034 697195320 0.000000e+00 1133
2 TraesCS2A01G351100 chr6B 95.972 2408 92 4 1427 3833 177082439 177080036 0.000000e+00 3904
3 TraesCS2A01G351100 chr6B 94.474 2425 119 10 352 2767 154307889 154310307 0.000000e+00 3722
4 TraesCS2A01G351100 chr6B 94.715 2138 102 8 1845 3979 483463653 483465782 0.000000e+00 3312
5 TraesCS2A01G351100 chr6B 88.242 876 93 8 352 1223 483462153 483463022 0.000000e+00 1038
6 TraesCS2A01G351100 chr4B 95.849 2409 96 3 1427 3834 569526700 569529105 0.000000e+00 3892
7 TraesCS2A01G351100 chr4B 84.494 316 27 6 1950 2252 224186899 224187205 4.600000e-75 292
8 TraesCS2A01G351100 chr4B 96.250 80 3 0 1869 1948 521705987 521706066 1.060000e-26 132
9 TraesCS2A01G351100 chr5B 94.451 2415 119 11 352 2758 566408983 566406576 0.000000e+00 3703
10 TraesCS2A01G351100 chr5B 93.818 1666 86 9 2325 3987 41798412 41796761 0.000000e+00 2490
11 TraesCS2A01G351100 chr2B 93.979 2425 130 11 352 2767 247551202 247553619 0.000000e+00 3655
12 TraesCS2A01G351100 chr2B 93.897 2425 129 15 352 2767 281534351 281531937 0.000000e+00 3640
13 TraesCS2A01G351100 chr2B 93.377 2431 130 15 351 2767 269878571 269880984 0.000000e+00 3568
14 TraesCS2A01G351100 chr2B 93.434 2056 124 9 1845 3896 686782000 686784048 0.000000e+00 3038
15 TraesCS2A01G351100 chr3B 93.416 2430 140 15 348 2767 738242394 738244813 0.000000e+00 3583
16 TraesCS2A01G351100 chr4A 96.802 1970 58 3 351 2317 552228280 552226313 0.000000e+00 3284
17 TraesCS2A01G351100 chr4A 93.825 1992 116 6 1845 3833 465121476 465123463 0.000000e+00 2990
18 TraesCS2A01G351100 chr4A 96.517 1665 55 3 2317 3979 552223077 552221414 0.000000e+00 2750
19 TraesCS2A01G351100 chr4A 94.545 715 39 0 3988 4702 583260668 583261382 0.000000e+00 1105
20 TraesCS2A01G351100 chr4A 95.775 355 10 3 1 351 583260317 583260670 6.830000e-158 568
21 TraesCS2A01G351100 chr3A 94.447 2017 106 5 1845 3859 664910845 664912857 0.000000e+00 3099
22 TraesCS2A01G351100 chr3A 94.685 715 38 0 3988 4702 617188138 617188852 0.000000e+00 1110
23 TraesCS2A01G351100 chr4D 95.846 1613 63 4 2371 3979 45248080 45249692 0.000000e+00 2604
24 TraesCS2A01G351100 chr4D 94.545 715 39 0 3988 4702 482575343 482576057 0.000000e+00 1105
25 TraesCS2A01G351100 chr4D 95.211 355 12 3 1 351 466979261 466978908 1.480000e-154 556
26 TraesCS2A01G351100 chr4D 95.211 355 12 3 1 351 482574992 482575345 1.480000e-154 556
27 TraesCS2A01G351100 chr4D 95.211 355 12 3 1 351 490785892 490785539 1.480000e-154 556
28 TraesCS2A01G351100 chr1B 95.769 1607 64 3 2229 3833 27643281 27644885 0.000000e+00 2588
29 TraesCS2A01G351100 chr1B 96.932 717 21 1 1427 2142 27642566 27643282 0.000000e+00 1201
30 TraesCS2A01G351100 chr1B 89.120 818 80 6 411 1223 87136566 87137379 0.000000e+00 1009
31 TraesCS2A01G351100 chr1B 91.770 243 16 4 3740 3979 87146722 87146963 7.540000e-88 335
32 TraesCS2A01G351100 chr7A 96.084 715 28 0 3988 4702 500047512 500046798 0.000000e+00 1166
33 TraesCS2A01G351100 chr7A 95.670 716 30 1 3988 4702 536438175 536437460 0.000000e+00 1149
34 TraesCS2A01G351100 chr7A 95.524 715 32 0 3988 4702 93361009 93360295 0.000000e+00 1144
35 TraesCS2A01G351100 chr7A 97.443 352 5 3 1 351 536438521 536438173 8.710000e-167 597
36 TraesCS2A01G351100 chr1D 94.825 715 37 0 3988 4702 100592996 100592282 0.000000e+00 1116
37 TraesCS2A01G351100 chr1D 95.775 355 10 3 1 351 366325628 366325981 6.830000e-158 568
38 TraesCS2A01G351100 chr1A 94.685 715 38 0 3988 4702 446474203 446473489 0.000000e+00 1110
39 TraesCS2A01G351100 chr5D 91.753 582 33 5 1269 1849 338653028 338653595 0.000000e+00 795
40 TraesCS2A01G351100 chr3D 95.763 354 11 3 1 351 582447866 582447514 6.830000e-158 568
41 TraesCS2A01G351100 chr3D 94.030 201 12 0 351 551 374813222 374813022 5.910000e-79 305
42 TraesCS2A01G351100 chr3D 92.391 184 11 3 3804 3987 596824015 596823835 4.670000e-65 259
43 TraesCS2A01G351100 chr2D 95.763 354 11 3 1 351 33413140 33413492 6.830000e-158 568
44 TraesCS2A01G351100 chrUn 95.198 354 13 3 1 351 97552975 97552623 1.480000e-154 556
45 TraesCS2A01G351100 chr7D 88.943 407 34 6 1849 2252 418731591 418731193 4.230000e-135 492
46 TraesCS2A01G351100 chr7D 84.830 323 23 7 1950 2258 334884484 334884794 7.650000e-78 302
47 TraesCS2A01G351100 chr7D 90.367 218 18 3 3764 3979 561631861 561631645 2.770000e-72 283
48 TraesCS2A01G351100 chr5A 94.500 200 11 0 352 551 8132326 8132127 4.570000e-80 309


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 TraesCS2A01G351100 chr2A 591089750 591094451 4701 False 8684.0 8684 100.0000 1 4702 1 chr2A.!!$F1 4701
1 TraesCS2A01G351100 chr2A 697195320 697196034 714 True 1133.0 1133 95.2450 3988 4702 1 chr2A.!!$R1 714
2 TraesCS2A01G351100 chr6B 177080036 177082439 2403 True 3904.0 3904 95.9720 1427 3833 1 chr6B.!!$R1 2406
3 TraesCS2A01G351100 chr6B 154307889 154310307 2418 False 3722.0 3722 94.4740 352 2767 1 chr6B.!!$F1 2415
4 TraesCS2A01G351100 chr6B 483462153 483465782 3629 False 2175.0 3312 91.4785 352 3979 2 chr6B.!!$F2 3627
5 TraesCS2A01G351100 chr4B 569526700 569529105 2405 False 3892.0 3892 95.8490 1427 3834 1 chr4B.!!$F3 2407
6 TraesCS2A01G351100 chr5B 566406576 566408983 2407 True 3703.0 3703 94.4510 352 2758 1 chr5B.!!$R2 2406
7 TraesCS2A01G351100 chr5B 41796761 41798412 1651 True 2490.0 2490 93.8180 2325 3987 1 chr5B.!!$R1 1662
8 TraesCS2A01G351100 chr2B 247551202 247553619 2417 False 3655.0 3655 93.9790 352 2767 1 chr2B.!!$F1 2415
9 TraesCS2A01G351100 chr2B 281531937 281534351 2414 True 3640.0 3640 93.8970 352 2767 1 chr2B.!!$R1 2415
10 TraesCS2A01G351100 chr2B 269878571 269880984 2413 False 3568.0 3568 93.3770 351 2767 1 chr2B.!!$F2 2416
11 TraesCS2A01G351100 chr2B 686782000 686784048 2048 False 3038.0 3038 93.4340 1845 3896 1 chr2B.!!$F3 2051
12 TraesCS2A01G351100 chr3B 738242394 738244813 2419 False 3583.0 3583 93.4160 348 2767 1 chr3B.!!$F1 2419
13 TraesCS2A01G351100 chr4A 552221414 552228280 6866 True 3017.0 3284 96.6595 351 3979 2 chr4A.!!$R1 3628
14 TraesCS2A01G351100 chr4A 465121476 465123463 1987 False 2990.0 2990 93.8250 1845 3833 1 chr4A.!!$F1 1988
15 TraesCS2A01G351100 chr4A 583260317 583261382 1065 False 836.5 1105 95.1600 1 4702 2 chr4A.!!$F2 4701
16 TraesCS2A01G351100 chr3A 664910845 664912857 2012 False 3099.0 3099 94.4470 1845 3859 1 chr3A.!!$F2 2014
17 TraesCS2A01G351100 chr3A 617188138 617188852 714 False 1110.0 1110 94.6850 3988 4702 1 chr3A.!!$F1 714
18 TraesCS2A01G351100 chr4D 45248080 45249692 1612 False 2604.0 2604 95.8460 2371 3979 1 chr4D.!!$F1 1608
19 TraesCS2A01G351100 chr4D 482574992 482576057 1065 False 830.5 1105 94.8780 1 4702 2 chr4D.!!$F2 4701
20 TraesCS2A01G351100 chr1B 27642566 27644885 2319 False 1894.5 2588 96.3505 1427 3833 2 chr1B.!!$F3 2406
21 TraesCS2A01G351100 chr1B 87136566 87137379 813 False 1009.0 1009 89.1200 411 1223 1 chr1B.!!$F1 812
22 TraesCS2A01G351100 chr7A 500046798 500047512 714 True 1166.0 1166 96.0840 3988 4702 1 chr7A.!!$R2 714
23 TraesCS2A01G351100 chr7A 93360295 93361009 714 True 1144.0 1144 95.5240 3988 4702 1 chr7A.!!$R1 714
24 TraesCS2A01G351100 chr7A 536437460 536438521 1061 True 873.0 1149 96.5565 1 4702 2 chr7A.!!$R3 4701
25 TraesCS2A01G351100 chr1D 100592282 100592996 714 True 1116.0 1116 94.8250 3988 4702 1 chr1D.!!$R1 714
26 TraesCS2A01G351100 chr1A 446473489 446474203 714 True 1110.0 1110 94.6850 3988 4702 1 chr1A.!!$R1 714
27 TraesCS2A01G351100 chr5D 338653028 338653595 567 False 795.0 795 91.7530 1269 1849 1 chr5D.!!$F1 580

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
314 317 0.034960 GGCTCAAGTTTCTCTCCCCC 60.035 60.0 0.00 0.00 0.0 5.40 F
925 978 0.105194 TCCCCTCGATTCATGCCCTA 60.105 55.0 0.00 0.00 0.0 3.53 F
1363 1420 0.108585 ACGTGCAGATTGGTGGTCTT 59.891 50.0 0.00 0.00 0.0 3.01 F
1509 1568 0.111639 AATAACGGCAAGGGTGGTGT 59.888 50.0 0.00 0.00 0.0 4.16 F
3021 6789 0.107643 TTGCAGGATCCAACGTGTCA 59.892 50.0 15.82 3.43 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1395 1452 3.007290 TGCAAGTAGAATCTGACTGCACT 59.993 43.478 9.79 0.00 30.23 4.40 R
2843 6611 3.181451 TGTTTGTGTCTCTCAGCCTCATT 60.181 43.478 0.00 0.00 0.00 2.57 R
3021 6789 1.827969 CTACTCACAGCCAGCCTTAGT 59.172 52.381 0.00 0.00 0.00 2.24 R
3417 7187 1.481772 TGGATGATCATCTGTGCGACA 59.518 47.619 29.85 17.25 37.92 4.35 R
4369 8145 1.067142 ACACGTGACTGCGTATTCCAT 60.067 47.619 25.01 0.00 43.83 3.41 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
46 49 5.747675 CACATTGAAAGCACATACAACACAA 59.252 36.000 0.00 0.00 0.00 3.33
71 74 5.236911 CGTACTATATTCGAGGCCTCTATCC 59.763 48.000 29.73 4.60 0.00 2.59
103 106 5.258051 AGTCCTCGAGTATTCTCACTCTTT 58.742 41.667 12.31 0.00 42.36 2.52
212 215 0.388134 TCGCCTGAAGACAGTAACGC 60.388 55.000 0.00 0.00 42.05 4.84
213 216 0.388649 CGCCTGAAGACAGTAACGCT 60.389 55.000 0.00 0.00 42.05 5.07
226 229 5.560966 CAGTAACGCTGGGAAAAATATGT 57.439 39.130 0.00 0.00 41.42 2.29
227 230 6.671614 CAGTAACGCTGGGAAAAATATGTA 57.328 37.500 0.00 0.00 41.42 2.29
228 231 6.483687 CAGTAACGCTGGGAAAAATATGTAC 58.516 40.000 0.00 0.00 41.42 2.90
229 232 6.092944 CAGTAACGCTGGGAAAAATATGTACA 59.907 38.462 0.00 0.00 41.42 2.90
230 233 4.957759 ACGCTGGGAAAAATATGTACAC 57.042 40.909 0.00 0.00 0.00 2.90
231 234 4.585879 ACGCTGGGAAAAATATGTACACT 58.414 39.130 0.00 0.00 0.00 3.55
232 235 4.394920 ACGCTGGGAAAAATATGTACACTG 59.605 41.667 0.00 0.00 0.00 3.66
233 236 4.672409 GCTGGGAAAAATATGTACACTGC 58.328 43.478 0.00 0.00 0.00 4.40
234 237 4.157656 GCTGGGAAAAATATGTACACTGCA 59.842 41.667 0.00 0.00 0.00 4.41
235 238 5.336372 GCTGGGAAAAATATGTACACTGCAA 60.336 40.000 0.00 0.00 0.00 4.08
236 239 6.019779 TGGGAAAAATATGTACACTGCAAC 57.980 37.500 0.00 0.00 0.00 4.17
237 240 5.536538 TGGGAAAAATATGTACACTGCAACA 59.463 36.000 0.00 0.00 0.00 3.33
238 241 6.040955 TGGGAAAAATATGTACACTGCAACAA 59.959 34.615 0.00 0.00 0.00 2.83
239 242 6.926272 GGGAAAAATATGTACACTGCAACAAA 59.074 34.615 0.00 0.00 0.00 2.83
240 243 7.439655 GGGAAAAATATGTACACTGCAACAAAA 59.560 33.333 0.00 0.00 0.00 2.44
241 244 8.821894 GGAAAAATATGTACACTGCAACAAAAA 58.178 29.630 0.00 0.00 0.00 1.94
242 245 9.631639 GAAAAATATGTACACTGCAACAAAAAC 57.368 29.630 0.00 0.00 0.00 2.43
243 246 8.709386 AAAATATGTACACTGCAACAAAAACA 57.291 26.923 0.00 0.00 0.00 2.83
244 247 8.885494 AAATATGTACACTGCAACAAAAACAT 57.115 26.923 0.00 0.00 0.00 2.71
245 248 8.885494 AATATGTACACTGCAACAAAAACATT 57.115 26.923 0.00 0.00 0.00 2.71
246 249 6.586868 ATGTACACTGCAACAAAAACATTG 57.413 33.333 0.00 0.00 0.00 2.82
247 250 5.714047 TGTACACTGCAACAAAAACATTGA 58.286 33.333 0.00 0.00 0.00 2.57
248 251 6.159293 TGTACACTGCAACAAAAACATTGAA 58.841 32.000 0.00 0.00 0.00 2.69
249 252 6.815641 TGTACACTGCAACAAAAACATTGAAT 59.184 30.769 0.00 0.00 0.00 2.57
250 253 6.740411 ACACTGCAACAAAAACATTGAATT 57.260 29.167 0.00 0.00 0.00 2.17
251 254 7.143514 ACACTGCAACAAAAACATTGAATTT 57.856 28.000 0.00 0.00 0.00 1.82
252 255 7.022384 ACACTGCAACAAAAACATTGAATTTG 58.978 30.769 13.51 13.51 39.38 2.32
253 256 6.021311 CACTGCAACAAAAACATTGAATTTGC 60.021 34.615 14.44 2.49 37.52 3.68
254 257 5.946298 TGCAACAAAAACATTGAATTTGCA 58.054 29.167 6.98 6.98 44.23 4.08
255 258 6.384224 TGCAACAAAAACATTGAATTTGCAA 58.616 28.000 8.27 0.00 43.66 4.08
256 259 6.864685 TGCAACAAAAACATTGAATTTGCAAA 59.135 26.923 15.44 15.44 43.66 3.68
257 260 7.061905 TGCAACAAAAACATTGAATTTGCAAAG 59.938 29.630 18.19 5.20 43.66 2.77
258 261 7.062022 GCAACAAAAACATTGAATTTGCAAAGT 59.938 29.630 18.19 15.58 38.36 2.66
259 262 8.913656 CAACAAAAACATTGAATTTGCAAAGTT 58.086 25.926 18.19 11.64 40.23 2.66
260 263 8.672214 ACAAAAACATTGAATTTGCAAAGTTC 57.328 26.923 18.19 18.78 42.21 3.01
261 264 8.513774 ACAAAAACATTGAATTTGCAAAGTTCT 58.486 25.926 18.19 1.87 42.34 3.01
262 265 9.344309 CAAAAACATTGAATTTGCAAAGTTCTT 57.656 25.926 18.19 6.74 42.34 2.52
263 266 9.911138 AAAAACATTGAATTTGCAAAGTTCTTT 57.089 22.222 18.19 6.35 42.34 2.52
264 267 8.898983 AAACATTGAATTTGCAAAGTTCTTTG 57.101 26.923 18.19 17.65 42.34 2.77
265 268 7.614124 ACATTGAATTTGCAAAGTTCTTTGT 57.386 28.000 18.19 19.78 42.34 2.83
266 269 8.042944 ACATTGAATTTGCAAAGTTCTTTGTT 57.957 26.923 18.19 4.06 42.34 2.83
267 270 8.177013 ACATTGAATTTGCAAAGTTCTTTGTTC 58.823 29.630 18.19 13.30 42.34 3.18
268 271 6.329838 TGAATTTGCAAAGTTCTTTGTTCG 57.670 33.333 18.19 2.64 42.34 3.95
269 272 5.290643 TGAATTTGCAAAGTTCTTTGTTCGG 59.709 36.000 18.19 2.34 42.34 4.30
270 273 4.442375 TTTGCAAAGTTCTTTGTTCGGA 57.558 36.364 21.20 6.20 34.56 4.55
271 274 4.442375 TTGCAAAGTTCTTTGTTCGGAA 57.558 36.364 21.20 5.53 34.56 4.30
272 275 4.442375 TGCAAAGTTCTTTGTTCGGAAA 57.558 36.364 21.20 2.80 34.56 3.13
273 276 4.420168 TGCAAAGTTCTTTGTTCGGAAAG 58.580 39.130 21.20 0.00 34.56 2.62
274 277 3.242944 GCAAAGTTCTTTGTTCGGAAAGC 59.757 43.478 21.20 5.35 33.63 3.51
275 278 4.420168 CAAAGTTCTTTGTTCGGAAAGCA 58.580 39.130 14.77 0.00 33.63 3.91
276 279 4.712122 AAGTTCTTTGTTCGGAAAGCAA 57.288 36.364 0.00 0.00 33.63 3.91
277 280 4.712122 AGTTCTTTGTTCGGAAAGCAAA 57.288 36.364 6.41 6.41 33.63 3.68
278 281 4.672409 AGTTCTTTGTTCGGAAAGCAAAG 58.328 39.130 19.78 19.78 46.01 2.77
279 282 3.708563 TCTTTGTTCGGAAAGCAAAGG 57.291 42.857 22.91 11.86 45.22 3.11
280 283 3.283751 TCTTTGTTCGGAAAGCAAAGGA 58.716 40.909 22.91 13.24 45.22 3.36
281 284 3.315191 TCTTTGTTCGGAAAGCAAAGGAG 59.685 43.478 22.91 8.48 45.22 3.69
282 285 2.341846 TGTTCGGAAAGCAAAGGAGT 57.658 45.000 0.00 0.00 0.00 3.85
283 286 2.650322 TGTTCGGAAAGCAAAGGAGTT 58.350 42.857 0.00 0.00 0.00 3.01
284 287 3.811083 TGTTCGGAAAGCAAAGGAGTTA 58.189 40.909 0.00 0.00 0.00 2.24
285 288 3.813166 TGTTCGGAAAGCAAAGGAGTTAG 59.187 43.478 0.00 0.00 0.00 2.34
286 289 4.062991 GTTCGGAAAGCAAAGGAGTTAGA 58.937 43.478 0.00 0.00 0.00 2.10
287 290 3.926616 TCGGAAAGCAAAGGAGTTAGAG 58.073 45.455 0.00 0.00 0.00 2.43
288 291 3.576982 TCGGAAAGCAAAGGAGTTAGAGA 59.423 43.478 0.00 0.00 0.00 3.10
289 292 3.680458 CGGAAAGCAAAGGAGTTAGAGAC 59.320 47.826 0.00 0.00 0.00 3.36
290 293 4.561734 CGGAAAGCAAAGGAGTTAGAGACT 60.562 45.833 0.00 0.00 42.70 3.24
291 294 5.336531 CGGAAAGCAAAGGAGTTAGAGACTA 60.337 44.000 0.00 0.00 39.19 2.59
292 295 6.628398 CGGAAAGCAAAGGAGTTAGAGACTAT 60.628 42.308 0.00 0.00 39.19 2.12
293 296 6.536941 GGAAAGCAAAGGAGTTAGAGACTATG 59.463 42.308 0.00 0.00 39.19 2.23
294 297 6.859112 AAGCAAAGGAGTTAGAGACTATGA 57.141 37.500 0.00 0.00 39.19 2.15
295 298 6.463995 AGCAAAGGAGTTAGAGACTATGAG 57.536 41.667 0.00 0.00 39.19 2.90
296 299 5.362430 AGCAAAGGAGTTAGAGACTATGAGG 59.638 44.000 0.00 0.00 39.19 3.86
297 300 5.596845 CAAAGGAGTTAGAGACTATGAGGC 58.403 45.833 0.00 0.00 39.19 4.70
298 301 4.806952 AGGAGTTAGAGACTATGAGGCT 57.193 45.455 0.00 0.00 39.19 4.58
308 311 5.337578 AGACTATGAGGCTCAAGTTTCTC 57.662 43.478 22.84 12.86 0.00 2.87
309 312 5.022787 AGACTATGAGGCTCAAGTTTCTCT 58.977 41.667 22.84 14.59 0.00 3.10
310 313 5.127031 AGACTATGAGGCTCAAGTTTCTCTC 59.873 44.000 22.84 11.96 0.00 3.20
311 314 3.625649 ATGAGGCTCAAGTTTCTCTCC 57.374 47.619 22.84 0.00 0.00 3.71
312 315 1.625818 TGAGGCTCAAGTTTCTCTCCC 59.374 52.381 16.28 0.00 0.00 4.30
313 316 0.988063 AGGCTCAAGTTTCTCTCCCC 59.012 55.000 0.00 0.00 0.00 4.81
314 317 0.034960 GGCTCAAGTTTCTCTCCCCC 60.035 60.000 0.00 0.00 0.00 5.40
315 318 0.693049 GCTCAAGTTTCTCTCCCCCA 59.307 55.000 0.00 0.00 0.00 4.96
316 319 1.339535 GCTCAAGTTTCTCTCCCCCAG 60.340 57.143 0.00 0.00 0.00 4.45
317 320 2.260822 CTCAAGTTTCTCTCCCCCAGA 58.739 52.381 0.00 0.00 0.00 3.86
318 321 1.978580 TCAAGTTTCTCTCCCCCAGAC 59.021 52.381 0.00 0.00 0.00 3.51
319 322 1.699634 CAAGTTTCTCTCCCCCAGACA 59.300 52.381 0.00 0.00 0.00 3.41
320 323 2.106511 CAAGTTTCTCTCCCCCAGACAA 59.893 50.000 0.00 0.00 0.00 3.18
321 324 1.700186 AGTTTCTCTCCCCCAGACAAC 59.300 52.381 0.00 0.00 0.00 3.32
322 325 1.420138 GTTTCTCTCCCCCAGACAACA 59.580 52.381 0.00 0.00 0.00 3.33
323 326 2.040412 GTTTCTCTCCCCCAGACAACAT 59.960 50.000 0.00 0.00 0.00 2.71
324 327 1.573108 TCTCTCCCCCAGACAACATC 58.427 55.000 0.00 0.00 0.00 3.06
325 328 1.203300 TCTCTCCCCCAGACAACATCA 60.203 52.381 0.00 0.00 0.00 3.07
326 329 0.984230 TCTCCCCCAGACAACATCAC 59.016 55.000 0.00 0.00 0.00 3.06
327 330 0.987294 CTCCCCCAGACAACATCACT 59.013 55.000 0.00 0.00 0.00 3.41
328 331 0.692476 TCCCCCAGACAACATCACTG 59.308 55.000 0.00 0.00 0.00 3.66
329 332 0.692476 CCCCCAGACAACATCACTGA 59.308 55.000 0.00 0.00 34.07 3.41
330 333 1.073763 CCCCCAGACAACATCACTGAA 59.926 52.381 0.00 0.00 34.07 3.02
331 334 2.430465 CCCCAGACAACATCACTGAAG 58.570 52.381 0.00 0.00 34.07 3.02
332 335 2.430465 CCCAGACAACATCACTGAAGG 58.570 52.381 0.00 0.00 34.07 3.46
333 336 2.038952 CCCAGACAACATCACTGAAGGA 59.961 50.000 0.00 0.00 34.07 3.36
334 337 3.307975 CCCAGACAACATCACTGAAGGAT 60.308 47.826 0.00 0.00 34.07 3.24
335 338 4.330250 CCAGACAACATCACTGAAGGATT 58.670 43.478 0.00 0.00 34.07 3.01
336 339 4.763793 CCAGACAACATCACTGAAGGATTT 59.236 41.667 0.00 0.00 34.07 2.17
337 340 5.242393 CCAGACAACATCACTGAAGGATTTT 59.758 40.000 0.00 0.00 34.07 1.82
338 341 6.430925 CCAGACAACATCACTGAAGGATTTTA 59.569 38.462 0.00 0.00 34.07 1.52
339 342 7.121759 CCAGACAACATCACTGAAGGATTTTAT 59.878 37.037 0.00 0.00 34.07 1.40
340 343 7.966753 CAGACAACATCACTGAAGGATTTTATG 59.033 37.037 0.00 0.00 34.07 1.90
341 344 7.884877 AGACAACATCACTGAAGGATTTTATGA 59.115 33.333 0.00 0.00 0.00 2.15
342 345 8.408043 ACAACATCACTGAAGGATTTTATGAA 57.592 30.769 0.00 0.00 0.00 2.57
343 346 8.299570 ACAACATCACTGAAGGATTTTATGAAC 58.700 33.333 0.00 0.00 0.00 3.18
344 347 8.298854 CAACATCACTGAAGGATTTTATGAACA 58.701 33.333 0.00 0.00 0.00 3.18
345 348 8.585471 ACATCACTGAAGGATTTTATGAACAT 57.415 30.769 0.00 0.00 0.00 2.71
346 349 9.028284 ACATCACTGAAGGATTTTATGAACATT 57.972 29.630 0.00 0.00 0.00 2.71
366 369 9.668497 GAACATTAAGACACTACTAGGGAAAAT 57.332 33.333 0.00 0.00 0.00 1.82
448 494 2.320745 AGCGAGGGGTATAAAAACCG 57.679 50.000 0.00 0.00 40.73 4.44
524 570 1.224436 TGATCTCCAATGATGCCCCA 58.776 50.000 0.00 0.00 0.00 4.96
585 631 6.140786 CGCGCTAGTAATAGAAACATAGTCA 58.859 40.000 5.56 0.00 0.00 3.41
701 751 2.025636 TTTTCTCCTCTTCCTCCCGT 57.974 50.000 0.00 0.00 0.00 5.28
872 925 4.137872 CCGCGGCTAGGGTTTCGA 62.138 66.667 14.67 0.00 0.00 3.71
892 945 4.329545 GCCTCCAACTCCGGTGCA 62.330 66.667 0.00 0.00 0.00 4.57
925 978 0.105194 TCCCCTCGATTCATGCCCTA 60.105 55.000 0.00 0.00 0.00 3.53
933 986 2.093764 CGATTCATGCCCTATCCTCTCC 60.094 54.545 0.00 0.00 0.00 3.71
976 1030 3.244249 CCCCCTCACCTATTTCTTCGATC 60.244 52.174 0.00 0.00 0.00 3.69
1083 1137 2.224159 GCTGGACCAAGGACCTCCA 61.224 63.158 8.97 0.00 38.89 3.86
1363 1420 0.108585 ACGTGCAGATTGGTGGTCTT 59.891 50.000 0.00 0.00 0.00 3.01
1395 1452 6.095160 TGCAACAGATGTTATTGTGCATATCA 59.905 34.615 5.42 0.00 36.32 2.15
1399 1456 6.140786 CAGATGTTATTGTGCATATCAGTGC 58.859 40.000 0.00 0.00 45.25 4.40
1509 1568 0.111639 AATAACGGCAAGGGTGGTGT 59.888 50.000 0.00 0.00 0.00 4.16
2724 6492 1.207089 TGAACCATACAGGCGAGGAAG 59.793 52.381 0.00 0.00 43.14 3.46
2758 6526 1.129058 AACTCCTCCGTCCAAGTTGT 58.871 50.000 1.45 0.00 31.05 3.32
2760 6528 0.393077 CTCCTCCGTCCAAGTTGTGT 59.607 55.000 1.45 0.00 0.00 3.72
3021 6789 0.107643 TTGCAGGATCCAACGTGTCA 59.892 50.000 15.82 3.43 0.00 3.58
3046 6814 0.108424 GCTGGCTGTGAGTAGAGTGG 60.108 60.000 0.00 0.00 0.00 4.00
3047 6815 0.108424 CTGGCTGTGAGTAGAGTGGC 60.108 60.000 0.00 0.00 0.00 5.01
3119 6887 4.341487 TGGAACAACTAGCTAGTGCTCTA 58.659 43.478 26.70 17.09 42.77 2.43
3185 6954 7.296628 AGTCTCTGTAGTTTCAACTCTGAAT 57.703 36.000 0.00 0.00 41.22 2.57
3248 7017 6.151480 TGTCACTATTGATTCATGTGCATGTT 59.849 34.615 11.38 1.95 35.75 2.71
3256 7025 7.451501 TGATTCATGTGCATGTTCTAGAAAA 57.548 32.000 6.78 1.30 39.72 2.29
3316 7085 7.201794 GCTAACTAACAAGTTTTCACTTTCCCT 60.202 37.037 0.00 0.00 40.66 4.20
3339 7108 1.754234 GGGCGCAGGGTTGATTGAT 60.754 57.895 10.83 0.00 0.00 2.57
3417 7187 4.353437 GTGAAGACCGGCGACCGT 62.353 66.667 9.30 0.00 46.80 4.83
3446 7216 6.531923 CACAGATGATCATCCAGGTAATCTT 58.468 40.000 28.23 6.52 38.58 2.40
3452 7222 2.766263 TCATCCAGGTAATCTTGACGCT 59.234 45.455 0.00 0.00 0.00 5.07
3491 7261 0.531974 GACCTTGACGCCACAGTTCA 60.532 55.000 0.00 0.00 0.00 3.18
3543 7314 8.664992 TCTGAGTCTTGGTAGATACATCTAGAT 58.335 37.037 0.00 0.00 39.87 1.98
3751 7524 3.076621 TGGAAGCAACTGCATCTAACTG 58.923 45.455 4.22 0.00 45.16 3.16
3759 7532 7.308435 AGCAACTGCATCTAACTGTTATTTTC 58.692 34.615 4.22 0.00 45.16 2.29
3928 7703 6.437793 CCCATGCTACTACTACCTATTAGCTT 59.562 42.308 0.00 0.00 35.54 3.74
4011 7786 1.607467 GGTGCTTCACTGGGGCAAT 60.607 57.895 0.00 0.00 37.73 3.56
4144 7919 2.751259 CCATTGACCTGTGGATGTTGAG 59.249 50.000 0.00 0.00 37.72 3.02
4239 8014 4.346709 TCCATTGTCTGTAAGGTTGTCAGA 59.653 41.667 0.00 0.00 36.12 3.27
4276 8052 0.662619 TTCAGCCGTGAAGCAACTTG 59.337 50.000 0.00 0.00 37.79 3.16
4357 8133 3.002791 CCTTTTGTGAATAGAGCGAGCA 58.997 45.455 0.00 0.00 0.00 4.26
4369 8145 7.926018 TGAATAGAGCGAGCAACTAAAATCATA 59.074 33.333 0.00 0.00 0.00 2.15
4441 8217 7.813852 ACTCGTTAGCTGAAGTATTTTACAG 57.186 36.000 0.00 0.00 0.00 2.74
4451 8227 7.241042 TGAAGTATTTTACAGTACAGAGGCT 57.759 36.000 0.00 0.00 0.00 4.58
4593 8369 7.604164 AGAACATAGTGTCTTGTAGAAACATGG 59.396 37.037 0.00 0.00 34.87 3.66
4619 8395 3.625313 TGTTGTTTCTGCAAATCGAGACA 59.375 39.130 0.00 0.00 0.00 3.41
4684 8460 4.698575 GTCACCATCCATCTTCTTCTACC 58.301 47.826 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 6.484977 TGTTGTATGTGCTTTCAATGTGTCTA 59.515 34.615 0.00 0.00 0.00 2.59
46 49 4.018484 AGAGGCCTCGAATATAGTACGT 57.982 45.455 26.95 1.42 34.09 3.57
71 74 1.558233 ACTCGAGGACTACAAAGGGG 58.442 55.000 18.41 0.00 0.00 4.79
103 106 5.624159 CATACTCCTCCCTGAAAATGCATA 58.376 41.667 0.00 0.00 0.00 3.14
212 215 5.895636 TGCAGTGTACATATTTTTCCCAG 57.104 39.130 0.00 0.00 0.00 4.45
213 216 5.536538 TGTTGCAGTGTACATATTTTTCCCA 59.463 36.000 0.00 0.00 0.00 4.37
214 217 6.019779 TGTTGCAGTGTACATATTTTTCCC 57.980 37.500 0.00 0.00 0.00 3.97
215 218 7.938563 TTTGTTGCAGTGTACATATTTTTCC 57.061 32.000 0.00 0.00 0.00 3.13
216 219 9.631639 GTTTTTGTTGCAGTGTACATATTTTTC 57.368 29.630 0.00 0.00 0.00 2.29
217 220 9.155975 TGTTTTTGTTGCAGTGTACATATTTTT 57.844 25.926 0.00 0.00 0.00 1.94
218 221 8.709386 TGTTTTTGTTGCAGTGTACATATTTT 57.291 26.923 0.00 0.00 0.00 1.82
219 222 8.885494 ATGTTTTTGTTGCAGTGTACATATTT 57.115 26.923 0.00 0.00 0.00 1.40
220 223 8.763356 CAATGTTTTTGTTGCAGTGTACATATT 58.237 29.630 0.00 0.00 0.00 1.28
221 224 8.140628 TCAATGTTTTTGTTGCAGTGTACATAT 58.859 29.630 0.00 0.00 31.29 1.78
222 225 7.484140 TCAATGTTTTTGTTGCAGTGTACATA 58.516 30.769 0.00 0.00 31.29 2.29
223 226 6.336566 TCAATGTTTTTGTTGCAGTGTACAT 58.663 32.000 0.00 0.00 31.29 2.29
224 227 5.714047 TCAATGTTTTTGTTGCAGTGTACA 58.286 33.333 0.00 0.00 31.29 2.90
225 228 6.639671 TTCAATGTTTTTGTTGCAGTGTAC 57.360 33.333 0.00 0.00 31.29 2.90
226 229 7.840342 AATTCAATGTTTTTGTTGCAGTGTA 57.160 28.000 0.00 0.00 31.29 2.90
227 230 6.740411 AATTCAATGTTTTTGTTGCAGTGT 57.260 29.167 0.00 0.00 31.29 3.55
228 231 6.021311 GCAAATTCAATGTTTTTGTTGCAGTG 60.021 34.615 0.00 0.00 39.82 3.66
229 232 6.028987 GCAAATTCAATGTTTTTGTTGCAGT 58.971 32.000 0.00 0.00 39.82 4.40
230 233 6.028368 TGCAAATTCAATGTTTTTGTTGCAG 58.972 32.000 3.78 0.00 43.60 4.41
231 234 5.946298 TGCAAATTCAATGTTTTTGTTGCA 58.054 29.167 3.78 3.78 45.55 4.08
232 235 6.866179 TTGCAAATTCAATGTTTTTGTTGC 57.134 29.167 0.00 0.00 40.33 4.17
233 236 8.450385 ACTTTGCAAATTCAATGTTTTTGTTG 57.550 26.923 13.23 0.00 32.57 3.33
234 237 9.127006 GAACTTTGCAAATTCAATGTTTTTGTT 57.873 25.926 13.23 8.20 41.40 2.83
235 238 8.513774 AGAACTTTGCAAATTCAATGTTTTTGT 58.486 25.926 23.86 10.10 41.40 2.83
236 239 8.898983 AGAACTTTGCAAATTCAATGTTTTTG 57.101 26.923 23.86 9.62 41.40 2.44
237 240 9.911138 AAAGAACTTTGCAAATTCAATGTTTTT 57.089 22.222 23.86 16.95 41.40 1.94
238 241 9.344309 CAAAGAACTTTGCAAATTCAATGTTTT 57.656 25.926 23.86 16.56 42.66 2.43
239 242 8.898983 CAAAGAACTTTGCAAATTCAATGTTT 57.101 26.923 23.86 16.78 42.66 2.83
254 257 4.712122 TGCTTTCCGAACAAAGAACTTT 57.288 36.364 5.85 0.00 35.67 2.66
255 258 4.712122 TTGCTTTCCGAACAAAGAACTT 57.288 36.364 5.85 0.00 35.67 2.66
256 259 4.712122 TTTGCTTTCCGAACAAAGAACT 57.288 36.364 5.85 0.00 35.67 3.01
260 263 3.066760 ACTCCTTTGCTTTCCGAACAAAG 59.933 43.478 13.56 13.56 46.25 2.77
261 264 3.020984 ACTCCTTTGCTTTCCGAACAAA 58.979 40.909 0.00 0.00 0.00 2.83
262 265 2.650322 ACTCCTTTGCTTTCCGAACAA 58.350 42.857 0.00 0.00 0.00 2.83
263 266 2.341846 ACTCCTTTGCTTTCCGAACA 57.658 45.000 0.00 0.00 0.00 3.18
264 267 4.062991 TCTAACTCCTTTGCTTTCCGAAC 58.937 43.478 0.00 0.00 0.00 3.95
265 268 4.039973 TCTCTAACTCCTTTGCTTTCCGAA 59.960 41.667 0.00 0.00 0.00 4.30
266 269 3.576982 TCTCTAACTCCTTTGCTTTCCGA 59.423 43.478 0.00 0.00 0.00 4.55
267 270 3.680458 GTCTCTAACTCCTTTGCTTTCCG 59.320 47.826 0.00 0.00 0.00 4.30
268 271 4.900684 AGTCTCTAACTCCTTTGCTTTCC 58.099 43.478 0.00 0.00 30.02 3.13
269 272 7.324178 TCATAGTCTCTAACTCCTTTGCTTTC 58.676 38.462 0.00 0.00 39.55 2.62
270 273 7.246171 TCATAGTCTCTAACTCCTTTGCTTT 57.754 36.000 0.00 0.00 39.55 3.51
271 274 6.127196 CCTCATAGTCTCTAACTCCTTTGCTT 60.127 42.308 0.00 0.00 39.55 3.91
272 275 5.362430 CCTCATAGTCTCTAACTCCTTTGCT 59.638 44.000 0.00 0.00 39.55 3.91
273 276 5.596845 CCTCATAGTCTCTAACTCCTTTGC 58.403 45.833 0.00 0.00 39.55 3.68
274 277 5.362430 AGCCTCATAGTCTCTAACTCCTTTG 59.638 44.000 0.00 0.00 39.55 2.77
275 278 5.524535 AGCCTCATAGTCTCTAACTCCTTT 58.475 41.667 0.00 0.00 39.55 3.11
276 279 5.137412 AGCCTCATAGTCTCTAACTCCTT 57.863 43.478 0.00 0.00 39.55 3.36
277 280 4.167113 TGAGCCTCATAGTCTCTAACTCCT 59.833 45.833 0.00 0.00 39.55 3.69
278 281 4.465886 TGAGCCTCATAGTCTCTAACTCC 58.534 47.826 0.00 0.00 39.55 3.85
279 282 5.592688 ACTTGAGCCTCATAGTCTCTAACTC 59.407 44.000 0.00 0.00 39.55 3.01
280 283 5.515106 ACTTGAGCCTCATAGTCTCTAACT 58.485 41.667 0.00 0.00 42.33 2.24
281 284 5.845391 ACTTGAGCCTCATAGTCTCTAAC 57.155 43.478 0.00 0.00 0.00 2.34
282 285 6.665680 AGAAACTTGAGCCTCATAGTCTCTAA 59.334 38.462 9.63 0.00 0.00 2.10
283 286 6.191315 AGAAACTTGAGCCTCATAGTCTCTA 58.809 40.000 9.63 0.00 0.00 2.43
284 287 5.022787 AGAAACTTGAGCCTCATAGTCTCT 58.977 41.667 0.00 1.54 0.00 3.10
285 288 5.127031 AGAGAAACTTGAGCCTCATAGTCTC 59.873 44.000 13.30 13.30 0.00 3.36
286 289 5.022787 AGAGAAACTTGAGCCTCATAGTCT 58.977 41.667 0.00 0.00 0.00 3.24
287 290 5.337578 AGAGAAACTTGAGCCTCATAGTC 57.662 43.478 0.00 0.00 0.00 2.59
288 291 4.161377 GGAGAGAAACTTGAGCCTCATAGT 59.839 45.833 0.00 0.00 0.00 2.12
289 292 4.442753 GGGAGAGAAACTTGAGCCTCATAG 60.443 50.000 0.00 0.00 0.00 2.23
290 293 3.452627 GGGAGAGAAACTTGAGCCTCATA 59.547 47.826 0.00 0.00 0.00 2.15
291 294 2.238395 GGGAGAGAAACTTGAGCCTCAT 59.762 50.000 0.00 0.00 0.00 2.90
292 295 1.625818 GGGAGAGAAACTTGAGCCTCA 59.374 52.381 0.00 0.00 0.00 3.86
293 296 1.065782 GGGGAGAGAAACTTGAGCCTC 60.066 57.143 0.00 0.00 0.00 4.70
294 297 0.988063 GGGGAGAGAAACTTGAGCCT 59.012 55.000 0.00 0.00 0.00 4.58
295 298 0.034960 GGGGGAGAGAAACTTGAGCC 60.035 60.000 0.00 0.00 0.00 4.70
296 299 0.693049 TGGGGGAGAGAAACTTGAGC 59.307 55.000 0.00 0.00 0.00 4.26
297 300 2.027653 GTCTGGGGGAGAGAAACTTGAG 60.028 54.545 0.00 0.00 0.00 3.02
298 301 1.978580 GTCTGGGGGAGAGAAACTTGA 59.021 52.381 0.00 0.00 0.00 3.02
299 302 1.699634 TGTCTGGGGGAGAGAAACTTG 59.300 52.381 0.00 0.00 0.00 3.16
300 303 2.106684 GTTGTCTGGGGGAGAGAAACTT 59.893 50.000 0.00 0.00 35.80 2.66
301 304 1.700186 GTTGTCTGGGGGAGAGAAACT 59.300 52.381 0.00 0.00 35.80 2.66
302 305 1.420138 TGTTGTCTGGGGGAGAGAAAC 59.580 52.381 0.00 0.00 35.80 2.78
303 306 1.814429 TGTTGTCTGGGGGAGAGAAA 58.186 50.000 0.00 0.00 35.80 2.52
304 307 1.909302 GATGTTGTCTGGGGGAGAGAA 59.091 52.381 0.00 0.00 31.60 2.87
305 308 1.203300 TGATGTTGTCTGGGGGAGAGA 60.203 52.381 0.00 0.00 0.00 3.10
306 309 1.065854 GTGATGTTGTCTGGGGGAGAG 60.066 57.143 0.00 0.00 0.00 3.20
307 310 0.984230 GTGATGTTGTCTGGGGGAGA 59.016 55.000 0.00 0.00 0.00 3.71
308 311 0.987294 AGTGATGTTGTCTGGGGGAG 59.013 55.000 0.00 0.00 0.00 4.30
309 312 0.692476 CAGTGATGTTGTCTGGGGGA 59.308 55.000 0.00 0.00 0.00 4.81
310 313 0.692476 TCAGTGATGTTGTCTGGGGG 59.308 55.000 0.00 0.00 0.00 5.40
311 314 2.430465 CTTCAGTGATGTTGTCTGGGG 58.570 52.381 0.00 0.00 0.00 4.96
312 315 2.038952 TCCTTCAGTGATGTTGTCTGGG 59.961 50.000 0.00 0.00 0.00 4.45
313 316 3.407424 TCCTTCAGTGATGTTGTCTGG 57.593 47.619 0.00 0.00 0.00 3.86
314 317 5.954296 AAATCCTTCAGTGATGTTGTCTG 57.046 39.130 0.00 0.00 0.00 3.51
315 318 7.884877 TCATAAAATCCTTCAGTGATGTTGTCT 59.115 33.333 0.00 0.00 0.00 3.41
316 319 8.044060 TCATAAAATCCTTCAGTGATGTTGTC 57.956 34.615 0.00 0.00 0.00 3.18
317 320 8.299570 GTTCATAAAATCCTTCAGTGATGTTGT 58.700 33.333 0.00 0.00 0.00 3.32
318 321 8.298854 TGTTCATAAAATCCTTCAGTGATGTTG 58.701 33.333 0.00 0.00 0.00 3.33
319 322 8.408043 TGTTCATAAAATCCTTCAGTGATGTT 57.592 30.769 0.00 0.00 0.00 2.71
320 323 8.585471 ATGTTCATAAAATCCTTCAGTGATGT 57.415 30.769 0.00 0.00 0.00 3.06
336 339 9.483489 TCCCTAGTAGTGTCTTAATGTTCATAA 57.517 33.333 0.00 0.00 0.00 1.90
337 340 9.483489 TTCCCTAGTAGTGTCTTAATGTTCATA 57.517 33.333 0.00 0.00 0.00 2.15
338 341 7.973048 TCCCTAGTAGTGTCTTAATGTTCAT 57.027 36.000 0.00 0.00 0.00 2.57
339 342 7.786046 TTCCCTAGTAGTGTCTTAATGTTCA 57.214 36.000 0.00 0.00 0.00 3.18
340 343 9.668497 ATTTTCCCTAGTAGTGTCTTAATGTTC 57.332 33.333 0.00 0.00 0.00 3.18
341 344 9.668497 GATTTTCCCTAGTAGTGTCTTAATGTT 57.332 33.333 0.00 0.00 0.00 2.71
342 345 9.047947 AGATTTTCCCTAGTAGTGTCTTAATGT 57.952 33.333 0.00 0.00 0.00 2.71
343 346 9.892130 AAGATTTTCCCTAGTAGTGTCTTAATG 57.108 33.333 0.00 0.00 0.00 1.90
347 350 7.988028 GCATAAGATTTTCCCTAGTAGTGTCTT 59.012 37.037 0.00 0.00 0.00 3.01
348 351 7.125811 TGCATAAGATTTTCCCTAGTAGTGTCT 59.874 37.037 0.00 0.00 0.00 3.41
349 352 7.224949 GTGCATAAGATTTTCCCTAGTAGTGTC 59.775 40.741 0.00 0.00 0.00 3.67
366 369 8.531982 ACTACTGATAAACTTCTGTGCATAAGA 58.468 33.333 11.89 5.82 0.00 2.10
372 375 4.201628 CGCACTACTGATAAACTTCTGTGC 60.202 45.833 0.00 0.00 43.00 4.57
524 570 4.017808 CGCTACTACTATGGCCTATTCCT 58.982 47.826 3.32 0.00 0.00 3.36
585 631 1.359848 CTTTTCGTGACCAGCGCTAT 58.640 50.000 10.99 0.00 0.00 2.97
872 925 2.526873 ACCGGAGTTGGAGGCAGT 60.527 61.111 9.46 0.00 0.00 4.40
892 945 1.456705 GGGGAGAGGAGATCGCACT 60.457 63.158 0.00 0.00 30.68 4.40
925 978 4.037222 GAGAAGAAAGAAGGGGAGAGGAT 58.963 47.826 0.00 0.00 0.00 3.24
933 986 4.080807 GGGTTAGGAGAGAAGAAAGAAGGG 60.081 50.000 0.00 0.00 0.00 3.95
1083 1137 2.503356 CCAAGCTAGGATCTGTTGAGGT 59.497 50.000 0.00 0.00 0.00 3.85
1363 1420 6.696583 CACAATAACATCTGTTGCAAAGTCAA 59.303 34.615 0.00 0.00 38.90 3.18
1395 1452 3.007290 TGCAAGTAGAATCTGACTGCACT 59.993 43.478 9.79 0.00 30.23 4.40
1399 1456 4.391216 CCTTGTGCAAGTAGAATCTGACTG 59.609 45.833 10.56 0.00 36.72 3.51
1509 1568 8.245195 TGCAGGATGTAACACATATCTACTTA 57.755 34.615 0.00 0.00 39.27 2.24
2724 6492 4.043200 GTTGTTGCGCCTGGGAGC 62.043 66.667 4.18 8.37 41.27 4.70
2843 6611 3.181451 TGTTTGTGTCTCTCAGCCTCATT 60.181 43.478 0.00 0.00 0.00 2.57
3021 6789 1.827969 CTACTCACAGCCAGCCTTAGT 59.172 52.381 0.00 0.00 0.00 2.24
3046 6814 5.773575 TGATTCGTATCCTCTATGAGTTGC 58.226 41.667 0.00 0.00 0.00 4.17
3047 6815 9.729023 GATATGATTCGTATCCTCTATGAGTTG 57.271 37.037 12.96 0.00 0.00 3.16
3316 7085 1.920734 ATCAACCCTGCGCCCATGTA 61.921 55.000 4.18 0.00 0.00 2.29
3417 7187 1.481772 TGGATGATCATCTGTGCGACA 59.518 47.619 29.85 17.25 37.92 4.35
3491 7261 3.542602 ACAGGTGGACCTCCCCCT 61.543 66.667 9.04 0.00 46.65 4.79
3543 7314 5.308497 TCCATCAACCTAAACAGACCACTTA 59.692 40.000 0.00 0.00 0.00 2.24
3787 7561 1.308998 AGCGAGTTGTTGTTTCCCAG 58.691 50.000 0.00 0.00 0.00 4.45
3928 7703 2.869358 CGCTACTAGTATCGCGCTAA 57.131 50.000 19.57 0.00 39.11 3.09
4002 7777 2.439507 TCTAGAAGCCTTATTGCCCCAG 59.560 50.000 0.00 0.00 0.00 4.45
4011 7786 1.400846 CGAGCACGTCTAGAAGCCTTA 59.599 52.381 5.51 0.00 34.56 2.69
4045 7820 6.101150 TCCAAGTTCATATGCCTACAATACCT 59.899 38.462 0.00 0.00 0.00 3.08
4198 7973 6.092259 ACAATGGATAAAGTACAAGCTCGAAC 59.908 38.462 0.00 0.00 0.00 3.95
4239 8014 5.812127 GGCTGAAGATCACAAAAACAAGTTT 59.188 36.000 0.00 0.00 0.00 2.66
4357 8133 8.677148 ACTGCGTATTCCATATGATTTTAGTT 57.323 30.769 3.65 0.00 0.00 2.24
4369 8145 1.067142 ACACGTGACTGCGTATTCCAT 60.067 47.619 25.01 0.00 43.83 3.41
4441 8217 2.815647 GCACGCCAGCCTCTGTAC 60.816 66.667 0.00 0.00 0.00 2.90
4451 8227 2.214216 AGGTACAAGAGGCACGCCA 61.214 57.895 11.35 0.00 38.92 5.69
4619 8395 2.325082 GCGGTTCCACGACAAGCAT 61.325 57.895 0.00 0.00 35.47 3.79


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

AutoCloner maintained by Alex Coulton.