Multiple sequence alignment - TraesCS6A01G156900

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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 TraesCS6A01G156900 chr6A 100.000 7029 0 0 1 7029 145999677 146006705 0.000000e+00 12981
1 TraesCS6A01G156900 chr6A 80.870 690 64 35 6303 6931 97631231 97630549 1.370000e-131 481
2 TraesCS6A01G156900 chr6A 97.183 71 1 1 195 265 145246495 145246426 1.240000e-22 119
3 TraesCS6A01G156900 chr6D 97.261 4601 101 7 1686 6284 117418931 117414354 0.000000e+00 7775
4 TraesCS6A01G156900 chr6D 92.238 992 43 13 694 1670 117419951 117418979 0.000000e+00 1375
5 TraesCS6A01G156900 chr6D 92.147 191 11 3 6 195 117420479 117420292 4.180000e-67 267
6 TraesCS6A01G156900 chr6D 85.833 120 4 4 207 325 118582128 118582235 1.600000e-21 115
7 TraesCS6A01G156900 chr6B 94.247 2225 91 18 4062 6284 207927244 207929433 0.000000e+00 3365
8 TraesCS6A01G156900 chr6B 94.160 1524 54 9 1883 3379 207924852 207926367 0.000000e+00 2289
9 TraesCS6A01G156900 chr6B 88.416 1364 73 34 330 1670 207923229 207924530 0.000000e+00 1565
10 TraesCS6A01G156900 chr6B 91.421 711 29 17 3378 4056 207926467 207927177 0.000000e+00 946
11 TraesCS6A01G156900 chr6B 94.000 200 4 5 1686 1884 207924578 207924770 5.330000e-76 296
12 TraesCS6A01G156900 chr6B 95.098 102 2 1 97 195 207923125 207923226 2.620000e-34 158
13 TraesCS6A01G156900 chr6B 92.000 100 6 2 1 99 207922898 207922996 9.510000e-29 139
14 TraesCS6A01G156900 chr6B 90.244 82 4 1 195 272 207463433 207463352 3.470000e-18 104
15 TraesCS6A01G156900 chr4A 88.468 633 44 9 6300 6903 30545894 30546526 0.000000e+00 737
16 TraesCS6A01G156900 chr7A 86.761 710 33 20 6282 6931 98895924 98895216 0.000000e+00 734
17 TraesCS6A01G156900 chr7A 94.848 330 14 1 6605 6931 139674947 139675276 4.860000e-141 512
18 TraesCS6A01G156900 chr7A 82.485 491 84 2 5538 6027 672075209 672075698 5.040000e-116 429
19 TraesCS6A01G156900 chr7A 90.596 319 13 6 6276 6578 139674140 139674457 2.360000e-109 407
20 TraesCS6A01G156900 chr7A 83.881 335 37 15 966 1287 672069780 672070110 3.190000e-78 303
21 TraesCS6A01G156900 chr7A 82.938 211 30 4 4768 4975 672074530 672074737 1.200000e-42 185
22 TraesCS6A01G156900 chr7A 95.050 101 5 0 6929 7029 98893798 98893698 7.300000e-35 159
23 TraesCS6A01G156900 chr7A 95.050 101 5 0 6929 7029 504210687 504210587 7.300000e-35 159
24 TraesCS6A01G156900 chr7B 85.531 546 17 18 6282 6765 725814820 725815365 1.350000e-141 514
25 TraesCS6A01G156900 chr7B 80.085 472 94 0 2786 3257 648106671 648107142 1.120000e-92 351
26 TraesCS6A01G156900 chr7B 82.493 337 41 16 966 1287 648103973 648104306 5.370000e-71 279
27 TraesCS6A01G156900 chr7B 82.464 211 31 4 4768 4975 648108653 648108860 5.600000e-41 180
28 TraesCS6A01G156900 chr7B 95.050 101 5 0 6929 7029 147023454 147023354 7.300000e-35 159
29 TraesCS6A01G156900 chr3A 93.215 339 20 2 6599 6934 598939157 598938819 4.900000e-136 496
30 TraesCS6A01G156900 chr3A 91.892 259 13 7 6275 6525 598939669 598939411 8.670000e-94 355
31 TraesCS6A01G156900 chr3A 95.050 101 5 0 6929 7029 749422961 749422861 7.300000e-35 159
32 TraesCS6A01G156900 chr1A 96.029 277 11 0 6655 6931 68380249 68379973 1.080000e-122 451
33 TraesCS6A01G156900 chr1A 95.455 264 8 2 6300 6560 386418685 386418947 1.090000e-112 418
34 TraesCS6A01G156900 chr1A 88.983 354 18 9 6599 6931 386419366 386419719 1.090000e-112 418
35 TraesCS6A01G156900 chr1A 75.682 440 55 23 6504 6930 497237842 497237442 9.370000e-39 172
36 TraesCS6A01G156900 chr7D 89.548 354 23 9 6282 6629 170952727 170953072 3.010000e-118 436
37 TraesCS6A01G156900 chr7D 84.469 367 54 3 4327 4691 580574454 580574819 6.700000e-95 359
38 TraesCS6A01G156900 chr7D 83.013 312 37 13 990 1287 580570286 580570595 1.160000e-67 268
39 TraesCS6A01G156900 chr7D 83.684 190 25 4 4768 4954 580575010 580575196 2.610000e-39 174
40 TraesCS6A01G156900 chr1B 79.794 678 74 39 6291 6931 668500348 668500999 1.080000e-117 435
41 TraesCS6A01G156900 chr1B 90.909 286 17 7 6300 6579 629315868 629316150 6.660000e-100 375
42 TraesCS6A01G156900 chr1B 81.882 425 49 22 6286 6683 688280913 688280490 4.060000e-87 333
43 TraesCS6A01G156900 chr1B 84.911 338 16 11 6615 6931 573856893 573856570 6.850000e-80 309
44 TraesCS6A01G156900 chr1B 95.050 101 5 0 6929 7029 629318258 629318358 7.300000e-35 159
45 TraesCS6A01G156900 chr3B 92.568 296 17 4 6664 6959 161143577 161143867 3.030000e-113 420
46 TraesCS6A01G156900 chr5D 93.182 264 14 2 6300 6560 274782157 274781895 1.110000e-102 385
47 TraesCS6A01G156900 chr5D 94.059 101 6 0 6929 7029 274779906 274779806 3.400000e-33 154
48 TraesCS6A01G156900 chr2B 88.889 324 15 7 6629 6931 620607150 620607473 5.150000e-101 379
49 TraesCS6A01G156900 chr2B 80.127 473 37 29 6300 6720 333059495 333059962 4.120000e-77 300
50 TraesCS6A01G156900 chr2B 95.050 101 5 0 6929 7029 9711640 9711740 7.300000e-35 159
51 TraesCS6A01G156900 chr2B 95.050 101 5 0 6929 7029 620608891 620608991 7.300000e-35 159
52 TraesCS6A01G156900 chr2B 95.050 101 5 0 6929 7029 635527218 635527318 7.300000e-35 159
53 TraesCS6A01G156900 chr3D 92.607 257 16 1 6300 6553 378041549 378041805 4.010000e-97 366
54 TraesCS6A01G156900 chr4D 93.200 250 11 3 6300 6546 469321356 469321602 5.180000e-96 363
55 TraesCS6A01G156900 chr2A 78.435 524 40 30 6300 6761 702164324 702163812 2.500000e-69 274
56 TraesCS6A01G156900 chr5A 88.942 208 15 6 6566 6765 126776000 126776207 4.210000e-62 250
57 TraesCS6A01G156900 chr5B 80.814 344 38 14 6282 6599 286686472 286686131 1.960000e-60 244
58 TraesCS6A01G156900 chr5B 83.270 263 25 12 6279 6526 658175203 658175461 2.550000e-54 224
59 TraesCS6A01G156900 chr1D 82.890 263 27 10 6279 6526 486378054 486377795 3.300000e-53 220
60 TraesCS6A01G156900 chr1D 81.853 259 29 9 6279 6521 75842013 75842269 1.200000e-47 202
61 TraesCS6A01G156900 chr2D 83.929 168 21 4 6552 6714 31015367 31015201 9.440000e-34 156


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 TraesCS6A01G156900 chr6A 145999677 146006705 7028 False 12981.000000 12981 100.000000 1 7029 1 chr6A.!!$F1 7028
1 TraesCS6A01G156900 chr6A 97630549 97631231 682 True 481.000000 481 80.870000 6303 6931 1 chr6A.!!$R1 628
2 TraesCS6A01G156900 chr6D 117414354 117420479 6125 True 3139.000000 7775 93.882000 6 6284 3 chr6D.!!$R1 6278
3 TraesCS6A01G156900 chr6B 207922898 207929433 6535 False 1251.142857 3365 92.763143 1 6284 7 chr6B.!!$F1 6283
4 TraesCS6A01G156900 chr4A 30545894 30546526 632 False 737.000000 737 88.468000 6300 6903 1 chr4A.!!$F1 603
5 TraesCS6A01G156900 chr7A 139674140 139675276 1136 False 459.500000 512 92.722000 6276 6931 2 chr7A.!!$F2 655
6 TraesCS6A01G156900 chr7A 98893698 98895924 2226 True 446.500000 734 90.905500 6282 7029 2 chr7A.!!$R2 747
7 TraesCS6A01G156900 chr7A 672074530 672075698 1168 False 307.000000 429 82.711500 4768 6027 2 chr7A.!!$F3 1259
8 TraesCS6A01G156900 chr7B 725814820 725815365 545 False 514.000000 514 85.531000 6282 6765 1 chr7B.!!$F1 483
9 TraesCS6A01G156900 chr7B 648103973 648108860 4887 False 270.000000 351 81.680667 966 4975 3 chr7B.!!$F2 4009
10 TraesCS6A01G156900 chr3A 598938819 598939669 850 True 425.500000 496 92.553500 6275 6934 2 chr3A.!!$R2 659
11 TraesCS6A01G156900 chr1A 386418685 386419719 1034 False 418.000000 418 92.219000 6300 6931 2 chr1A.!!$F1 631
12 TraesCS6A01G156900 chr7D 580570286 580575196 4910 False 267.000000 359 83.722000 990 4954 3 chr7D.!!$F2 3964
13 TraesCS6A01G156900 chr1B 668500348 668500999 651 False 435.000000 435 79.794000 6291 6931 1 chr1B.!!$F1 640
14 TraesCS6A01G156900 chr1B 629315868 629318358 2490 False 267.000000 375 92.979500 6300 7029 2 chr1B.!!$F2 729
15 TraesCS6A01G156900 chr5D 274779806 274782157 2351 True 269.500000 385 93.620500 6300 7029 2 chr5D.!!$R1 729
16 TraesCS6A01G156900 chr2B 620607150 620608991 1841 False 269.000000 379 91.969500 6629 7029 2 chr2B.!!$F4 400
17 TraesCS6A01G156900 chr2A 702163812 702164324 512 True 274.000000 274 78.435000 6300 6761 1 chr2A.!!$R1 461

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
197 334 0.039527 AAAACTGGACGGAAATGCGC 60.040 50.000 0.00 0.0 0.00 6.09 F
1583 1922 0.037326 TGTTCTAGCTGGCTGTTCCG 60.037 55.000 5.25 0.0 37.80 4.30 F
1929 2502 0.472471 ATGGACCCGACAGTGTTTGT 59.528 50.000 0.00 0.0 44.55 2.83 F
2086 3051 0.815213 TGACTTGTGCTGCCTGTGTC 60.815 55.000 0.00 1.8 0.00 3.67 F
3650 5126 1.929836 GCGTCTATCTGCAAGGAAGTG 59.070 52.381 0.00 0.0 0.00 3.16 F
4558 6243 1.138661 CTGGAGAGGGCTCAGAATGTC 59.861 57.143 0.00 0.0 43.14 3.06 F
5613 7495 0.461339 AAAGCCGACGTAATCCGCAT 60.461 50.000 0.00 0.0 41.42 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1590 1929 0.532862 AAACTCAGCCCACACGACTG 60.533 55.000 0.0 0.00 0.00 3.51 R
2601 3566 3.501349 AGACTGAACTAGAGAGGCAACA 58.499 45.455 0.0 0.00 41.41 3.33 R
3650 5126 3.010420 GCCTCCAATTACTGAACTGGAC 58.990 50.000 0.0 0.00 34.28 4.02 R
4158 5843 7.714377 ACCTGAAAAGAACATAGATAGCATCAG 59.286 37.037 0.0 0.00 0.00 2.90 R
5507 7389 0.394565 ACTTGAGCTTTCGCAGGAGT 59.605 50.000 0.0 0.00 39.10 3.85 R
5795 7677 0.736325 ATTCGGCTGAACGTCTTCCG 60.736 55.000 10.9 10.85 44.03 4.30 R
6936 11234 1.685180 GCCCTCAAATCCACCCCTTAC 60.685 57.143 0.0 0.00 0.00 2.34 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
50 52 4.717233 TGTTTGCTGAGACATGTTGTTT 57.283 36.364 0.00 0.00 0.00 2.83
58 60 6.033341 GCTGAGACATGTTGTTTGTTGTTTA 58.967 36.000 0.00 0.00 0.00 2.01
180 317 1.228552 GCTTCCCTGGCCTGTCAAA 60.229 57.895 3.32 0.00 0.00 2.69
182 319 0.961753 CTTCCCTGGCCTGTCAAAAC 59.038 55.000 3.32 0.00 0.00 2.43
195 332 2.034053 TGTCAAAACTGGACGGAAATGC 59.966 45.455 0.00 0.00 38.10 3.56
196 333 1.265635 TCAAAACTGGACGGAAATGCG 59.734 47.619 0.00 0.00 0.00 4.73
197 334 0.039527 AAAACTGGACGGAAATGCGC 60.040 50.000 0.00 0.00 0.00 6.09
198 335 1.862602 AAACTGGACGGAAATGCGCC 61.863 55.000 4.18 0.00 0.00 6.53
199 336 2.745884 CTGGACGGAAATGCGCCA 60.746 61.111 4.18 9.28 0.00 5.69
200 337 2.281831 TGGACGGAAATGCGCCAA 60.282 55.556 4.18 0.00 0.00 4.52
201 338 2.257286 CTGGACGGAAATGCGCCAAG 62.257 60.000 4.18 0.00 0.00 3.61
202 339 2.038269 GGACGGAAATGCGCCAAGA 61.038 57.895 4.18 0.00 0.00 3.02
203 340 1.376609 GGACGGAAATGCGCCAAGAT 61.377 55.000 4.18 0.00 0.00 2.40
204 341 1.295792 GACGGAAATGCGCCAAGATA 58.704 50.000 4.18 0.00 0.00 1.98
205 342 1.668751 GACGGAAATGCGCCAAGATAA 59.331 47.619 4.18 0.00 0.00 1.75
206 343 1.670811 ACGGAAATGCGCCAAGATAAG 59.329 47.619 4.18 0.00 0.00 1.73
207 344 1.939934 CGGAAATGCGCCAAGATAAGA 59.060 47.619 4.18 0.00 0.00 2.10
208 345 2.354510 CGGAAATGCGCCAAGATAAGAA 59.645 45.455 4.18 0.00 0.00 2.52
209 346 3.181501 CGGAAATGCGCCAAGATAAGAAA 60.182 43.478 4.18 0.00 0.00 2.52
210 347 4.674101 CGGAAATGCGCCAAGATAAGAAAA 60.674 41.667 4.18 0.00 0.00 2.29
211 348 5.167845 GGAAATGCGCCAAGATAAGAAAAA 58.832 37.500 4.18 0.00 0.00 1.94
212 349 5.062183 GGAAATGCGCCAAGATAAGAAAAAC 59.938 40.000 4.18 0.00 0.00 2.43
213 350 5.391312 AATGCGCCAAGATAAGAAAAACT 57.609 34.783 4.18 0.00 0.00 2.66
214 351 4.159377 TGCGCCAAGATAAGAAAAACTG 57.841 40.909 4.18 0.00 0.00 3.16
215 352 3.057596 TGCGCCAAGATAAGAAAAACTGG 60.058 43.478 4.18 0.00 0.00 4.00
216 353 3.501950 CGCCAAGATAAGAAAAACTGGC 58.498 45.455 0.02 0.02 36.65 4.85
217 354 3.057596 CGCCAAGATAAGAAAAACTGGCA 60.058 43.478 10.50 0.00 39.64 4.92
218 355 4.558496 CGCCAAGATAAGAAAAACTGGCAA 60.558 41.667 10.50 0.00 39.64 4.52
219 356 5.296748 GCCAAGATAAGAAAAACTGGCAAA 58.703 37.500 5.34 0.00 39.48 3.68
220 357 5.757808 GCCAAGATAAGAAAAACTGGCAAAA 59.242 36.000 5.34 0.00 39.48 2.44
221 358 6.427853 GCCAAGATAAGAAAAACTGGCAAAAT 59.572 34.615 5.34 0.00 39.48 1.82
222 359 7.602265 GCCAAGATAAGAAAAACTGGCAAAATA 59.398 33.333 5.34 0.00 39.48 1.40
223 360 9.487790 CCAAGATAAGAAAAACTGGCAAAATAA 57.512 29.630 0.00 0.00 0.00 1.40
229 366 8.800370 AAGAAAAACTGGCAAAATAAAAGGAA 57.200 26.923 0.00 0.00 0.00 3.36
230 367 8.208718 AGAAAAACTGGCAAAATAAAAGGAAC 57.791 30.769 0.00 0.00 0.00 3.62
231 368 6.935741 AAAACTGGCAAAATAAAAGGAACC 57.064 33.333 0.00 0.00 0.00 3.62
232 369 5.622346 AACTGGCAAAATAAAAGGAACCA 57.378 34.783 0.00 0.00 0.00 3.67
234 371 5.213891 CTGGCAAAATAAAAGGAACCAGT 57.786 39.130 0.00 0.00 38.87 4.00
235 372 5.208463 TGGCAAAATAAAAGGAACCAGTC 57.792 39.130 0.00 0.00 0.00 3.51
236 373 4.651503 TGGCAAAATAAAAGGAACCAGTCA 59.348 37.500 0.00 0.00 0.00 3.41
237 374 4.988540 GGCAAAATAAAAGGAACCAGTCAC 59.011 41.667 0.00 0.00 0.00 3.67
238 375 5.221441 GGCAAAATAAAAGGAACCAGTCACT 60.221 40.000 0.00 0.00 0.00 3.41
239 376 5.691754 GCAAAATAAAAGGAACCAGTCACTG 59.308 40.000 0.00 0.00 0.00 3.66
249 386 3.201342 CAGTCACTGGACACGAAGG 57.799 57.895 0.00 0.00 46.80 3.46
250 387 0.673985 CAGTCACTGGACACGAAGGA 59.326 55.000 0.00 0.00 46.80 3.36
251 388 1.273606 CAGTCACTGGACACGAAGGAT 59.726 52.381 0.00 0.00 46.80 3.24
252 389 1.273606 AGTCACTGGACACGAAGGATG 59.726 52.381 0.00 0.00 46.80 3.51
253 390 0.608130 TCACTGGACACGAAGGATGG 59.392 55.000 0.00 0.00 0.00 3.51
254 391 0.608130 CACTGGACACGAAGGATGGA 59.392 55.000 0.00 0.00 0.00 3.41
255 392 0.898320 ACTGGACACGAAGGATGGAG 59.102 55.000 0.00 0.00 0.00 3.86
256 393 0.460987 CTGGACACGAAGGATGGAGC 60.461 60.000 0.00 0.00 0.00 4.70
257 394 1.519455 GGACACGAAGGATGGAGCG 60.519 63.158 0.00 0.00 0.00 5.03
258 395 1.511305 GACACGAAGGATGGAGCGA 59.489 57.895 0.00 0.00 0.00 4.93
259 396 0.526524 GACACGAAGGATGGAGCGAG 60.527 60.000 0.00 0.00 0.00 5.03
260 397 1.880340 CACGAAGGATGGAGCGAGC 60.880 63.158 0.00 0.00 0.00 5.03
261 398 2.351244 ACGAAGGATGGAGCGAGCA 61.351 57.895 0.00 0.00 0.00 4.26
262 399 1.591059 CGAAGGATGGAGCGAGCAG 60.591 63.158 0.00 0.00 0.00 4.24
273 410 3.624300 CGAGCAGCTCAATCGCCG 61.624 66.667 22.49 3.02 0.00 6.46
274 411 2.202797 GAGCAGCTCAATCGCCGA 60.203 61.111 18.17 0.00 0.00 5.54
275 412 2.202851 AGCAGCTCAATCGCCGAG 60.203 61.111 0.00 0.00 0.00 4.63
276 413 2.510238 GCAGCTCAATCGCCGAGT 60.510 61.111 0.00 0.00 32.83 4.18
277 414 2.520904 GCAGCTCAATCGCCGAGTC 61.521 63.158 0.00 0.00 32.83 3.36
278 415 1.153765 CAGCTCAATCGCCGAGTCA 60.154 57.895 0.00 0.00 32.83 3.41
279 416 0.529337 CAGCTCAATCGCCGAGTCAT 60.529 55.000 0.00 0.00 32.83 3.06
280 417 0.249238 AGCTCAATCGCCGAGTCATC 60.249 55.000 0.00 0.00 32.83 2.92
281 418 0.249238 GCTCAATCGCCGAGTCATCT 60.249 55.000 0.00 0.00 32.83 2.90
282 419 1.764851 CTCAATCGCCGAGTCATCTC 58.235 55.000 0.00 0.00 37.35 2.75
283 420 0.385751 TCAATCGCCGAGTCATCTCC 59.614 55.000 0.00 0.00 37.40 3.71
284 421 0.103026 CAATCGCCGAGTCATCTCCA 59.897 55.000 0.00 0.00 37.40 3.86
285 422 0.103208 AATCGCCGAGTCATCTCCAC 59.897 55.000 0.00 0.00 37.40 4.02
286 423 2.064723 ATCGCCGAGTCATCTCCACG 62.065 60.000 0.00 0.00 37.40 4.94
287 424 2.761195 CGCCGAGTCATCTCCACGA 61.761 63.158 0.00 0.00 37.56 4.35
288 425 1.511305 GCCGAGTCATCTCCACGAA 59.489 57.895 0.00 0.00 37.40 3.85
289 426 0.526524 GCCGAGTCATCTCCACGAAG 60.527 60.000 0.00 0.00 37.40 3.79
290 427 0.101399 CCGAGTCATCTCCACGAAGG 59.899 60.000 0.00 0.00 37.40 3.46
291 428 1.095600 CGAGTCATCTCCACGAAGGA 58.904 55.000 0.00 0.00 46.75 3.36
298 435 3.805928 TCCACGAAGGATGGTGCT 58.194 55.556 0.00 0.00 43.07 4.40
299 436 1.296392 TCCACGAAGGATGGTGCTG 59.704 57.895 0.00 0.00 43.07 4.41
300 437 2.401766 CCACGAAGGATGGTGCTGC 61.402 63.158 0.00 0.00 41.22 5.25
301 438 1.376424 CACGAAGGATGGTGCTGCT 60.376 57.895 0.00 0.00 0.00 4.24
302 439 1.376424 ACGAAGGATGGTGCTGCTG 60.376 57.895 0.00 0.00 0.00 4.41
303 440 1.376424 CGAAGGATGGTGCTGCTGT 60.376 57.895 0.00 0.00 0.00 4.40
304 441 0.957395 CGAAGGATGGTGCTGCTGTT 60.957 55.000 0.00 0.00 0.00 3.16
305 442 1.251251 GAAGGATGGTGCTGCTGTTT 58.749 50.000 0.00 0.00 0.00 2.83
306 443 1.200948 GAAGGATGGTGCTGCTGTTTC 59.799 52.381 0.00 0.00 0.00 2.78
307 444 0.610232 AGGATGGTGCTGCTGTTTCC 60.610 55.000 0.00 2.84 0.00 3.13
308 445 1.598701 GGATGGTGCTGCTGTTTCCC 61.599 60.000 0.00 0.00 0.00 3.97
309 446 0.895100 GATGGTGCTGCTGTTTCCCA 60.895 55.000 0.00 0.00 0.00 4.37
310 447 0.896940 ATGGTGCTGCTGTTTCCCAG 60.897 55.000 0.00 0.00 44.53 4.45
311 448 1.529244 GGTGCTGCTGTTTCCCAGT 60.529 57.895 0.00 0.00 43.55 4.00
312 449 0.250727 GGTGCTGCTGTTTCCCAGTA 60.251 55.000 0.00 0.00 43.55 2.74
340 477 7.838884 ACTGGTGTTTCTTAGTAATAGGTCTC 58.161 38.462 0.00 0.00 0.00 3.36
418 555 0.886490 GATCCGAATGCAAGGGCGAT 60.886 55.000 0.00 0.00 45.35 4.58
420 557 2.628106 CGAATGCAAGGGCGATCG 59.372 61.111 11.69 11.69 45.35 3.69
421 558 1.882625 CGAATGCAAGGGCGATCGA 60.883 57.895 21.57 0.00 46.96 3.59
422 559 1.643832 GAATGCAAGGGCGATCGAC 59.356 57.895 21.57 18.00 45.35 4.20
423 560 1.776034 GAATGCAAGGGCGATCGACC 61.776 60.000 33.43 33.43 45.79 4.79
424 561 3.757248 ATGCAAGGGCGATCGACCC 62.757 63.158 36.22 32.12 46.93 4.46
461 598 0.176910 AAAAACACACGGGCCAAAGG 59.823 50.000 4.39 0.00 0.00 3.11
549 692 2.032860 ATAGGCCTGACGCAATCGCT 62.033 55.000 17.99 0.00 40.31 4.93
570 713 2.125552 TGCTTCCGGCGAGTGATG 60.126 61.111 9.30 0.42 45.43 3.07
574 717 1.667154 CTTCCGGCGAGTGATGGAGA 61.667 60.000 9.30 0.00 0.00 3.71
595 744 1.800315 GCTCATGCTTTGCAGTGCG 60.800 57.895 11.20 0.00 43.65 5.34
622 771 1.000607 TGTACGCCGCTAGGATTGATC 60.001 52.381 0.00 0.00 41.02 2.92
627 776 1.793258 CCGCTAGGATTGATCTGCAG 58.207 55.000 7.63 7.63 41.02 4.41
654 812 3.041940 CGCCGAAGCCTTCAACGT 61.042 61.111 5.14 0.00 34.57 3.99
749 907 8.497745 AGTCAAACCATATCACAAGGAGATTAT 58.502 33.333 0.00 0.00 0.00 1.28
765 927 7.107542 AGGAGATTATTAACGCCAGTTTAACA 58.892 34.615 0.00 0.00 41.49 2.41
835 997 1.067635 CATTTTCAGAAACGCCCCCAG 60.068 52.381 0.00 0.00 0.00 4.45
846 1008 4.241555 CCCCCAGAATCCTCGCGG 62.242 72.222 6.13 0.00 0.00 6.46
847 1009 3.154473 CCCCAGAATCCTCGCGGA 61.154 66.667 6.13 0.00 45.16 5.54
856 1018 1.519751 ATCCTCGCGGAATCTCGGAG 61.520 60.000 6.13 0.00 44.02 4.63
867 1029 3.775654 CTCGGAGCCACCCCTCAC 61.776 72.222 0.00 0.00 33.47 3.51
918 1080 2.752238 CCTGCTCGGTCGGTCTCT 60.752 66.667 0.00 0.00 0.00 3.10
921 1083 3.519930 GCTCGGTCGGTCTCTCCC 61.520 72.222 0.00 0.00 0.00 4.30
923 1085 4.437587 TCGGTCGGTCTCTCCCCC 62.438 72.222 0.00 0.00 0.00 5.40
1382 1719 1.678970 GCCCCTGCGGTGAATTCTT 60.679 57.895 7.05 0.00 0.00 2.52
1497 1836 2.905085 TGTCGGTTATGGTGGTTAGGAA 59.095 45.455 0.00 0.00 0.00 3.36
1498 1837 3.264947 GTCGGTTATGGTGGTTAGGAAC 58.735 50.000 0.00 0.00 0.00 3.62
1499 1838 3.055602 GTCGGTTATGGTGGTTAGGAACT 60.056 47.826 0.00 0.00 46.37 3.01
1500 1839 3.583966 TCGGTTATGGTGGTTAGGAACTT 59.416 43.478 0.00 0.00 41.75 2.66
1501 1840 4.776837 TCGGTTATGGTGGTTAGGAACTTA 59.223 41.667 0.00 0.00 41.75 2.24
1502 1841 5.105228 TCGGTTATGGTGGTTAGGAACTTAG 60.105 44.000 0.00 0.00 41.75 2.18
1503 1842 5.434408 GGTTATGGTGGTTAGGAACTTAGG 58.566 45.833 0.00 0.00 41.75 2.69
1504 1843 5.190330 GGTTATGGTGGTTAGGAACTTAGGA 59.810 44.000 0.00 0.00 41.75 2.94
1536 1875 2.035961 ACACTCACAACTCGTGCTGTAT 59.964 45.455 0.00 0.00 45.92 2.29
1549 1888 4.093408 TCGTGCTGTATCTGCTTCATTTTC 59.907 41.667 0.00 0.00 0.00 2.29
1583 1922 0.037326 TGTTCTAGCTGGCTGTTCCG 60.037 55.000 5.25 0.00 37.80 4.30
1590 1929 0.659957 GCTGGCTGTTCCGATTGATC 59.340 55.000 0.00 0.00 37.80 2.92
1610 1949 1.045407 AGTCGTGTGGGCTGAGTTTA 58.955 50.000 0.00 0.00 0.00 2.01
1670 2009 4.009675 AGCGTGTTTGATAATCATGTGGT 58.990 39.130 0.00 0.00 0.00 4.16
1673 2012 6.150307 AGCGTGTTTGATAATCATGTGGTAAA 59.850 34.615 0.00 0.00 0.00 2.01
1674 2013 6.468956 GCGTGTTTGATAATCATGTGGTAAAG 59.531 38.462 0.00 0.00 0.00 1.85
1676 2015 8.397906 CGTGTTTGATAATCATGTGGTAAAGAT 58.602 33.333 0.00 0.00 0.00 2.40
1709 2080 6.561519 ATTGTAAAGGTGCAGTCCTAGTAT 57.438 37.500 0.00 0.00 36.74 2.12
1748 2120 6.904463 TTCAAGTAATTTAACTGGTTCCCC 57.096 37.500 0.00 0.00 0.00 4.81
1763 2135 1.153539 TCCCCAACAGGACCATGAAA 58.846 50.000 0.00 0.00 38.24 2.69
1928 2501 1.604604 AATGGACCCGACAGTGTTTG 58.395 50.000 0.00 0.00 0.00 2.93
1929 2502 0.472471 ATGGACCCGACAGTGTTTGT 59.528 50.000 0.00 0.00 44.55 2.83
1933 2506 2.553086 GACCCGACAGTGTTTGTTGTA 58.447 47.619 0.00 0.00 41.05 2.41
2037 3002 1.490490 TCAGCCAAAGTCACAGAAGGT 59.510 47.619 0.00 0.00 0.00 3.50
2086 3051 0.815213 TGACTTGTGCTGCCTGTGTC 60.815 55.000 0.00 1.80 0.00 3.67
2212 3177 3.192001 GCAAAGATGAGATTGTTCAGGCA 59.808 43.478 0.00 0.00 0.00 4.75
2607 3572 7.442666 TCCTATTTGTTTATGGTTTTTGTTGCC 59.557 33.333 0.00 0.00 0.00 4.52
2934 4307 3.036819 AGATCTGCTCAAGTGGATGCTA 58.963 45.455 0.00 0.00 0.00 3.49
3265 4638 8.964476 TCTGAAATACAAAGGTATCTGATTCC 57.036 34.615 5.25 5.25 39.28 3.01
3650 5126 1.929836 GCGTCTATCTGCAAGGAAGTG 59.070 52.381 0.00 0.00 0.00 3.16
4118 5803 2.857186 TCTTGGTTAGCATGCAGTGA 57.143 45.000 21.98 5.05 0.00 3.41
4158 5843 7.575332 AATAACCATTACGTTTTGTGAATGC 57.425 32.000 0.00 0.00 0.00 3.56
4260 5945 6.916360 ACATGGTAAGTTTCATGGTTCATT 57.084 33.333 17.51 0.49 43.49 2.57
4287 5972 2.015726 TGAGGTTGGGTTTGGGGGT 61.016 57.895 0.00 0.00 0.00 4.95
4299 5984 1.198759 TTGGGGGTGTCAGGCTACTC 61.199 60.000 0.00 0.00 0.00 2.59
4317 6002 7.064728 AGGCTACTCGTGTCTAAAATTTTCATC 59.935 37.037 6.72 0.00 0.00 2.92
4318 6003 7.064728 GGCTACTCGTGTCTAAAATTTTCATCT 59.935 37.037 6.72 0.00 0.00 2.90
4435 6120 3.136443 TGTTCTCCATCTCTGTTGTGGTT 59.864 43.478 0.00 0.00 34.61 3.67
4558 6243 1.138661 CTGGAGAGGGCTCAGAATGTC 59.861 57.143 0.00 0.00 43.14 3.06
4648 6333 2.424956 GTTCTCAGGAATGGATGTTGGC 59.575 50.000 0.00 0.00 33.71 4.52
4669 6354 2.271800 GACTTCCTCACATTGGTAGCG 58.728 52.381 0.00 0.00 0.00 4.26
4701 6386 2.768527 TGAGGCAACAAAACATTCCCAA 59.231 40.909 0.00 0.00 41.41 4.12
5342 7224 2.035237 TTGCAAAGGAGGTCGGTCGT 62.035 55.000 0.00 0.00 0.00 4.34
5369 7251 4.039852 TCTCATGTAGTAGTGCAACCACAA 59.960 41.667 0.00 0.00 44.53 3.33
5459 7341 8.017373 CCTAACTGATTTCATGTGTACAACTTG 58.983 37.037 0.00 1.41 35.70 3.16
5462 7344 8.169977 ACTGATTTCATGTGTACAACTTGATT 57.830 30.769 0.00 0.00 41.23 2.57
5463 7345 9.283768 ACTGATTTCATGTGTACAACTTGATTA 57.716 29.630 0.00 0.00 41.23 1.75
5464 7346 9.546909 CTGATTTCATGTGTACAACTTGATTAC 57.453 33.333 0.00 2.61 41.23 1.89
5465 7347 9.283768 TGATTTCATGTGTACAACTTGATTACT 57.716 29.630 0.00 0.00 41.23 2.24
5466 7348 9.760660 GATTTCATGTGTACAACTTGATTACTC 57.239 33.333 0.00 0.00 41.23 2.59
5467 7349 7.667043 TTCATGTGTACAACTTGATTACTCC 57.333 36.000 0.00 0.00 41.23 3.85
5507 7389 1.123077 ATATGAGTTGCCTCCTGCGA 58.877 50.000 0.00 0.00 45.60 5.10
5512 7394 2.604686 TTGCCTCCTGCGACTCCT 60.605 61.111 0.00 0.00 45.60 3.69
5513 7395 2.947532 TTGCCTCCTGCGACTCCTG 61.948 63.158 0.00 0.00 45.60 3.86
5514 7396 4.828925 GCCTCCTGCGACTCCTGC 62.829 72.222 0.00 0.00 0.00 4.85
5515 7397 4.504916 CCTCCTGCGACTCCTGCG 62.505 72.222 0.00 0.00 34.24 5.18
5612 7494 0.671163 AAAAGCCGACGTAATCCGCA 60.671 50.000 0.00 0.00 41.42 5.69
5613 7495 0.461339 AAAGCCGACGTAATCCGCAT 60.461 50.000 0.00 0.00 41.42 4.73
5795 7677 1.078759 CACGGCGATTGACCTCTCAC 61.079 60.000 16.62 0.00 0.00 3.51
5893 7775 1.674057 CGCACTCTTCCCCTTCACT 59.326 57.895 0.00 0.00 0.00 3.41
5897 7779 0.474660 ACTCTTCCCCTTCACTGGCT 60.475 55.000 0.00 0.00 0.00 4.75
5986 7868 2.094078 GCTGCTGCTGAGGAGATATAGG 60.094 54.545 4.75 0.00 40.04 2.57
6036 7918 6.758886 CAGATAACTGTAGAGTGATTCCAACC 59.241 42.308 0.00 0.00 39.11 3.77
6171 8053 9.506018 AAATAGCACATATATACACAGATGCAA 57.494 29.630 0.00 0.00 34.27 4.08
6261 8144 3.369451 CGAGCCTCTTTTACTTGAGAAGC 59.631 47.826 0.00 0.00 32.44 3.86
6319 8210 5.043356 AGAGCCCTCAAACCCCTAAAAATAT 60.043 40.000 0.00 0.00 0.00 1.28
6322 8213 4.899457 CCCTCAAACCCCTAAAAATATCCC 59.101 45.833 0.00 0.00 0.00 3.85
6486 8394 1.747367 CACTCCTCCTCTCTCGCGT 60.747 63.158 5.77 0.00 0.00 6.01
6874 9741 3.528370 CGAATCTCCTCCCGCCGT 61.528 66.667 0.00 0.00 0.00 5.68
6936 11234 0.322008 GGACCTCCTCCAAAGCAGTG 60.322 60.000 0.00 0.00 39.21 3.66
6943 11241 1.614317 CCTCCAAAGCAGTGTAAGGGG 60.614 57.143 0.00 0.00 0.00 4.79
6947 11245 1.145571 AAAGCAGTGTAAGGGGTGGA 58.854 50.000 0.00 0.00 0.00 4.02
6956 11254 0.629058 TAAGGGGTGGATTTGAGGGC 59.371 55.000 0.00 0.00 0.00 5.19
6996 11294 6.094061 TGTTTTTCAACCCTTAAAAGTGTCG 58.906 36.000 0.00 0.00 31.02 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 2.729491 GCAAACAAGGGAACGCGC 60.729 61.111 5.73 0.00 0.00 6.86
50 52 6.983307 CCTTTGGATCACAACAATAAACAACA 59.017 34.615 0.00 0.00 39.19 3.33
58 60 4.503643 CCTTTGCCTTTGGATCACAACAAT 60.504 41.667 0.00 0.00 39.19 2.71
180 317 2.332654 GGCGCATTTCCGTCCAGTT 61.333 57.895 10.83 0.00 0.00 3.16
182 319 2.257286 CTTGGCGCATTTCCGTCCAG 62.257 60.000 10.83 0.00 36.38 3.86
195 332 3.057596 TGCCAGTTTTTCTTATCTTGGCG 60.058 43.478 7.94 0.00 42.27 5.69
196 333 4.519540 TGCCAGTTTTTCTTATCTTGGC 57.480 40.909 5.69 5.69 40.05 4.52
197 334 7.967890 ATTTTGCCAGTTTTTCTTATCTTGG 57.032 32.000 0.00 0.00 0.00 3.61
203 340 9.892130 TTCCTTTTATTTTGCCAGTTTTTCTTA 57.108 25.926 0.00 0.00 0.00 2.10
204 341 8.673711 GTTCCTTTTATTTTGCCAGTTTTTCTT 58.326 29.630 0.00 0.00 0.00 2.52
205 342 7.282224 GGTTCCTTTTATTTTGCCAGTTTTTCT 59.718 33.333 0.00 0.00 0.00 2.52
206 343 7.066404 TGGTTCCTTTTATTTTGCCAGTTTTTC 59.934 33.333 0.00 0.00 0.00 2.29
207 344 6.887002 TGGTTCCTTTTATTTTGCCAGTTTTT 59.113 30.769 0.00 0.00 0.00 1.94
208 345 6.418946 TGGTTCCTTTTATTTTGCCAGTTTT 58.581 32.000 0.00 0.00 0.00 2.43
209 346 5.995446 TGGTTCCTTTTATTTTGCCAGTTT 58.005 33.333 0.00 0.00 0.00 2.66
210 347 5.610398 CTGGTTCCTTTTATTTTGCCAGTT 58.390 37.500 0.00 0.00 37.90 3.16
211 348 5.213891 CTGGTTCCTTTTATTTTGCCAGT 57.786 39.130 0.00 0.00 37.90 4.00
212 349 5.213891 ACTGGTTCCTTTTATTTTGCCAG 57.786 39.130 0.00 0.00 45.43 4.85
213 350 4.651503 TGACTGGTTCCTTTTATTTTGCCA 59.348 37.500 0.00 0.00 0.00 4.92
214 351 4.988540 GTGACTGGTTCCTTTTATTTTGCC 59.011 41.667 0.00 0.00 0.00 4.52
215 352 5.691754 CAGTGACTGGTTCCTTTTATTTTGC 59.308 40.000 4.28 0.00 0.00 3.68
216 353 6.215845 CCAGTGACTGGTTCCTTTTATTTTG 58.784 40.000 23.27 0.00 45.82 2.44
217 354 6.405278 CCAGTGACTGGTTCCTTTTATTTT 57.595 37.500 23.27 0.00 45.82 1.82
231 368 0.673985 TCCTTCGTGTCCAGTGACTG 59.326 55.000 5.42 5.42 42.28 3.51
232 369 1.273606 CATCCTTCGTGTCCAGTGACT 59.726 52.381 0.00 0.00 42.28 3.41
233 370 1.673033 CCATCCTTCGTGTCCAGTGAC 60.673 57.143 0.00 0.00 42.12 3.67
234 371 0.608130 CCATCCTTCGTGTCCAGTGA 59.392 55.000 0.00 0.00 0.00 3.41
235 372 0.608130 TCCATCCTTCGTGTCCAGTG 59.392 55.000 0.00 0.00 0.00 3.66
236 373 0.898320 CTCCATCCTTCGTGTCCAGT 59.102 55.000 0.00 0.00 0.00 4.00
237 374 0.460987 GCTCCATCCTTCGTGTCCAG 60.461 60.000 0.00 0.00 0.00 3.86
238 375 1.596934 GCTCCATCCTTCGTGTCCA 59.403 57.895 0.00 0.00 0.00 4.02
239 376 1.519455 CGCTCCATCCTTCGTGTCC 60.519 63.158 0.00 0.00 0.00 4.02
240 377 0.526524 CTCGCTCCATCCTTCGTGTC 60.527 60.000 0.00 0.00 0.00 3.67
241 378 1.513158 CTCGCTCCATCCTTCGTGT 59.487 57.895 0.00 0.00 0.00 4.49
242 379 1.880340 GCTCGCTCCATCCTTCGTG 60.880 63.158 0.00 0.00 0.00 4.35
243 380 2.290122 CTGCTCGCTCCATCCTTCGT 62.290 60.000 0.00 0.00 0.00 3.85
244 381 1.591059 CTGCTCGCTCCATCCTTCG 60.591 63.158 0.00 0.00 0.00 3.79
245 382 1.886777 GCTGCTCGCTCCATCCTTC 60.887 63.158 0.00 0.00 35.14 3.46
246 383 2.188994 GCTGCTCGCTCCATCCTT 59.811 61.111 0.00 0.00 35.14 3.36
256 393 3.624300 CGGCGATTGAGCTGCTCG 61.624 66.667 23.35 14.10 36.64 5.03
257 394 2.202797 TCGGCGATTGAGCTGCTC 60.203 61.111 22.38 22.38 42.92 4.26
258 395 2.202851 CTCGGCGATTGAGCTGCT 60.203 61.111 11.27 0.00 42.92 4.24
259 396 2.510238 ACTCGGCGATTGAGCTGC 60.510 61.111 11.27 0.00 42.92 5.25
260 397 0.529337 ATGACTCGGCGATTGAGCTG 60.529 55.000 11.27 0.00 44.50 4.24
261 398 0.249238 GATGACTCGGCGATTGAGCT 60.249 55.000 11.27 0.00 36.94 4.09
262 399 0.249238 AGATGACTCGGCGATTGAGC 60.249 55.000 11.27 0.80 36.94 4.26
263 400 1.601663 GGAGATGACTCGGCGATTGAG 60.602 57.143 11.27 0.09 43.44 3.02
264 401 0.385751 GGAGATGACTCGGCGATTGA 59.614 55.000 11.27 0.00 43.44 2.57
265 402 0.103026 TGGAGATGACTCGGCGATTG 59.897 55.000 11.27 1.43 43.44 2.67
266 403 0.103208 GTGGAGATGACTCGGCGATT 59.897 55.000 11.27 4.13 43.44 3.34
267 404 1.736586 GTGGAGATGACTCGGCGAT 59.263 57.895 11.27 0.00 43.44 4.58
268 405 2.761195 CGTGGAGATGACTCGGCGA 61.761 63.158 10.14 10.14 43.44 5.54
269 406 2.266376 TTCGTGGAGATGACTCGGCG 62.266 60.000 0.00 0.00 43.44 6.46
270 407 0.526524 CTTCGTGGAGATGACTCGGC 60.527 60.000 0.00 0.00 43.44 5.54
271 408 0.101399 CCTTCGTGGAGATGACTCGG 59.899 60.000 0.00 0.00 43.44 4.63
272 409 1.095600 TCCTTCGTGGAGATGACTCG 58.904 55.000 0.00 0.00 43.44 4.18
282 419 2.401766 GCAGCACCATCCTTCGTGG 61.402 63.158 0.00 0.00 42.55 4.94
283 420 1.376424 AGCAGCACCATCCTTCGTG 60.376 57.895 0.00 0.00 0.00 4.35
284 421 1.376424 CAGCAGCACCATCCTTCGT 60.376 57.895 0.00 0.00 0.00 3.85
285 422 0.957395 AACAGCAGCACCATCCTTCG 60.957 55.000 0.00 0.00 0.00 3.79
286 423 1.200948 GAAACAGCAGCACCATCCTTC 59.799 52.381 0.00 0.00 0.00 3.46
287 424 1.251251 GAAACAGCAGCACCATCCTT 58.749 50.000 0.00 0.00 0.00 3.36
288 425 0.610232 GGAAACAGCAGCACCATCCT 60.610 55.000 0.00 0.00 0.00 3.24
289 426 1.598701 GGGAAACAGCAGCACCATCC 61.599 60.000 0.00 0.00 0.00 3.51
290 427 0.895100 TGGGAAACAGCAGCACCATC 60.895 55.000 0.00 0.00 0.00 3.51
291 428 0.896940 CTGGGAAACAGCAGCACCAT 60.897 55.000 0.00 0.00 40.97 3.55
292 429 1.529010 CTGGGAAACAGCAGCACCA 60.529 57.895 0.00 0.00 40.97 4.17
293 430 3.359002 CTGGGAAACAGCAGCACC 58.641 61.111 0.00 0.00 40.97 5.01
308 445 5.470047 ACTAAGAAACACCAGTCCTACTG 57.530 43.478 0.00 0.00 45.53 2.74
309 446 7.793948 ATTACTAAGAAACACCAGTCCTACT 57.206 36.000 0.00 0.00 0.00 2.57
310 447 8.196103 CCTATTACTAAGAAACACCAGTCCTAC 58.804 40.741 0.00 0.00 0.00 3.18
311 448 7.897565 ACCTATTACTAAGAAACACCAGTCCTA 59.102 37.037 0.00 0.00 0.00 2.94
312 449 6.729569 ACCTATTACTAAGAAACACCAGTCCT 59.270 38.462 0.00 0.00 0.00 3.85
313 450 6.944096 ACCTATTACTAAGAAACACCAGTCC 58.056 40.000 0.00 0.00 0.00 3.85
314 451 7.838884 AGACCTATTACTAAGAAACACCAGTC 58.161 38.462 0.00 0.00 0.00 3.51
315 452 7.362747 CGAGACCTATTACTAAGAAACACCAGT 60.363 40.741 0.00 0.00 0.00 4.00
316 453 6.973474 CGAGACCTATTACTAAGAAACACCAG 59.027 42.308 0.00 0.00 0.00 4.00
317 454 6.626623 GCGAGACCTATTACTAAGAAACACCA 60.627 42.308 0.00 0.00 0.00 4.17
318 455 5.747675 GCGAGACCTATTACTAAGAAACACC 59.252 44.000 0.00 0.00 0.00 4.16
319 456 5.454877 CGCGAGACCTATTACTAAGAAACAC 59.545 44.000 0.00 0.00 0.00 3.32
320 457 5.355071 TCGCGAGACCTATTACTAAGAAACA 59.645 40.000 3.71 0.00 33.31 2.83
321 458 5.814783 TCGCGAGACCTATTACTAAGAAAC 58.185 41.667 3.71 0.00 33.31 2.78
322 459 6.441093 TTCGCGAGACCTATTACTAAGAAA 57.559 37.500 9.59 0.00 41.84 2.52
323 460 6.441093 TTTCGCGAGACCTATTACTAAGAA 57.559 37.500 9.59 0.00 41.84 2.52
324 461 6.293845 GGATTTCGCGAGACCTATTACTAAGA 60.294 42.308 9.59 0.00 41.84 2.10
325 462 5.857517 GGATTTCGCGAGACCTATTACTAAG 59.142 44.000 9.59 0.00 41.84 2.18
326 463 5.278660 GGGATTTCGCGAGACCTATTACTAA 60.279 44.000 21.09 6.18 41.84 2.24
327 464 4.217118 GGGATTTCGCGAGACCTATTACTA 59.783 45.833 21.09 0.00 41.84 1.82
328 465 3.005578 GGGATTTCGCGAGACCTATTACT 59.994 47.826 21.09 0.00 41.84 2.24
340 477 1.787847 GTGTGTCTGGGATTTCGCG 59.212 57.895 0.00 0.00 0.00 5.87
385 522 0.249447 CGGATCGCTGGTTGCTGATA 60.249 55.000 0.00 0.00 40.11 2.15
404 541 1.643832 GTCGATCGCCCTTGCATTC 59.356 57.895 11.09 0.00 37.32 2.67
447 584 2.983592 GGTCCTTTGGCCCGTGTG 60.984 66.667 0.00 0.00 0.00 3.82
461 598 6.986250 ACTCTTTCAGAAATCCAATTTGGTC 58.014 36.000 14.98 5.94 39.03 4.02
590 733 1.219522 GGCGTACACAAAGTCGCACT 61.220 55.000 10.29 0.00 43.61 4.40
595 744 0.989890 CTAGCGGCGTACACAAAGTC 59.010 55.000 9.37 0.00 0.00 3.01
622 771 1.717937 GGCGTCAAGTATGCTGCAG 59.282 57.895 10.11 10.11 40.23 4.41
627 776 1.348594 GCTTCGGCGTCAAGTATGC 59.651 57.895 6.85 0.00 39.58 3.14
687 845 4.999311 CGATTGGATTATCTCCTTGCATGA 59.001 41.667 0.00 0.00 45.21 3.07
713 871 0.963225 TGGTTTGACTCGATCGTCCA 59.037 50.000 15.94 8.71 32.97 4.02
749 907 2.228925 GGGGTGTTAAACTGGCGTTAA 58.771 47.619 0.00 0.00 31.86 2.01
846 1008 2.034048 GAGGGGTGGCTCCGAGATTC 62.034 65.000 0.00 0.00 37.00 2.52
847 1009 2.041265 AGGGGTGGCTCCGAGATT 59.959 61.111 0.00 0.00 37.00 2.40
856 1018 4.436998 CGAGACGTGAGGGGTGGC 62.437 72.222 0.00 0.00 0.00 5.01
867 1029 1.133598 TGGGTGTAATAGTGCGAGACG 59.866 52.381 0.00 0.00 0.00 4.18
903 1065 2.750637 GGAGAGACCGACCGAGCA 60.751 66.667 0.00 0.00 0.00 4.26
925 1087 0.252761 GGGAATGGCAAAATGTGGGG 59.747 55.000 0.00 0.00 0.00 4.96
927 1089 1.207811 GAGGGGAATGGCAAAATGTGG 59.792 52.381 0.00 0.00 0.00 4.17
928 1090 1.207811 GGAGGGGAATGGCAAAATGTG 59.792 52.381 0.00 0.00 0.00 3.21
929 1091 1.571955 GGAGGGGAATGGCAAAATGT 58.428 50.000 0.00 0.00 0.00 2.71
930 1092 0.461135 CGGAGGGGAATGGCAAAATG 59.539 55.000 0.00 0.00 0.00 2.32
931 1093 0.334676 TCGGAGGGGAATGGCAAAAT 59.665 50.000 0.00 0.00 0.00 1.82
932 1094 0.113385 TTCGGAGGGGAATGGCAAAA 59.887 50.000 0.00 0.00 0.00 2.44
933 1095 0.334676 ATTCGGAGGGGAATGGCAAA 59.665 50.000 0.00 0.00 35.40 3.68
934 1096 0.334676 AATTCGGAGGGGAATGGCAA 59.665 50.000 0.00 0.00 36.77 4.52
936 1098 2.558359 CAATAATTCGGAGGGGAATGGC 59.442 50.000 0.00 0.00 36.77 4.40
1036 1203 2.485582 CTCCATGTCGTCGTCGCT 59.514 61.111 0.00 0.00 36.96 4.93
1233 1427 3.043713 CGGTTCTGCAGCAGCGAA 61.044 61.111 29.62 6.67 46.23 4.70
1290 1484 1.522569 GGGAGGGATCACACGGAAG 59.477 63.158 0.00 0.00 0.00 3.46
1340 1552 1.755783 CCCAGGCCAAATCTCCAGC 60.756 63.158 5.01 0.00 0.00 4.85
1497 1836 2.735134 GTGTTCGTTTCGCATCCTAAGT 59.265 45.455 0.00 0.00 0.00 2.24
1498 1837 2.993899 AGTGTTCGTTTCGCATCCTAAG 59.006 45.455 0.00 0.00 0.00 2.18
1499 1838 2.991190 GAGTGTTCGTTTCGCATCCTAA 59.009 45.455 0.00 0.00 0.00 2.69
1500 1839 2.029739 TGAGTGTTCGTTTCGCATCCTA 60.030 45.455 0.00 0.00 0.00 2.94
1501 1840 1.270094 TGAGTGTTCGTTTCGCATCCT 60.270 47.619 0.00 0.00 0.00 3.24
1502 1841 1.136336 GTGAGTGTTCGTTTCGCATCC 60.136 52.381 0.00 0.00 0.00 3.51
1503 1842 1.525197 TGTGAGTGTTCGTTTCGCATC 59.475 47.619 0.00 0.00 0.00 3.91
1504 1843 1.577468 TGTGAGTGTTCGTTTCGCAT 58.423 45.000 0.00 0.00 0.00 4.73
1536 1875 1.078709 CGAGCCGAAAATGAAGCAGA 58.921 50.000 0.00 0.00 0.00 4.26
1549 1888 3.883744 AACAAGGACAGGCGAGCCG 62.884 63.158 8.63 6.45 41.95 5.52
1583 1922 1.009829 GCCCACACGACTGATCAATC 58.990 55.000 0.00 0.00 0.00 2.67
1590 1929 0.532862 AAACTCAGCCCACACGACTG 60.533 55.000 0.00 0.00 0.00 3.51
1673 2012 7.668052 TGCACCTTTACAATTTAACTGGTATCT 59.332 33.333 0.00 0.00 0.00 1.98
1674 2013 7.822658 TGCACCTTTACAATTTAACTGGTATC 58.177 34.615 0.00 0.00 0.00 2.24
1676 2015 6.773685 ACTGCACCTTTACAATTTAACTGGTA 59.226 34.615 0.00 0.00 0.00 3.25
1680 2019 6.068670 AGGACTGCACCTTTACAATTTAACT 58.931 36.000 0.00 0.00 36.86 2.24
1684 2023 5.631119 ACTAGGACTGCACCTTTACAATTT 58.369 37.500 0.51 0.00 41.00 1.82
1748 2120 2.294233 CAGGTGTTTCATGGTCCTGTTG 59.706 50.000 0.00 0.00 40.25 3.33
1763 2135 4.145365 TGCAAGTTTACAGTACAGGTGT 57.855 40.909 0.00 0.00 0.00 4.16
1917 2490 4.904116 ACAACATACAACAAACACTGTCG 58.096 39.130 0.00 0.00 37.23 4.35
1928 2501 8.443937 GTCTTCTTCCTGAATACAACATACAAC 58.556 37.037 0.00 0.00 33.57 3.32
1929 2502 8.154203 TGTCTTCTTCCTGAATACAACATACAA 58.846 33.333 0.00 0.00 38.34 2.41
1933 2506 7.667219 ACAATGTCTTCTTCCTGAATACAACAT 59.333 33.333 0.00 0.00 42.39 2.71
2037 3002 5.656416 CCTATCCTAAATTGGCCTGACAAAA 59.344 40.000 3.32 0.00 33.48 2.44
2086 3051 6.936900 TCTTTAAGATCCCTTCAACTGAGTTG 59.063 38.462 18.84 18.84 43.99 3.16
2212 3177 3.071874 TCAAAACCAGCATCCTCGATT 57.928 42.857 0.00 0.00 0.00 3.34
2466 3431 5.348724 CGTACATATGGATTCTGTACATGGC 59.651 44.000 7.80 0.00 43.36 4.40
2601 3566 3.501349 AGACTGAACTAGAGAGGCAACA 58.499 45.455 0.00 0.00 41.41 3.33
2607 3572 8.062065 AGGAAAATGTAGACTGAACTAGAGAG 57.938 38.462 0.00 0.00 0.00 3.20
2652 3617 4.752661 TTTATTTACGGTCACAACTGGC 57.247 40.909 0.00 0.00 35.97 4.85
2654 3619 7.067532 TGCTATTTATTTACGGTCACAACTG 57.932 36.000 0.00 0.00 37.81 3.16
3265 4638 7.786178 TGCATGCTAAGTTACCATAAAGTAG 57.214 36.000 20.33 0.00 0.00 2.57
3650 5126 3.010420 GCCTCCAATTACTGAACTGGAC 58.990 50.000 0.00 0.00 34.28 4.02
4158 5843 7.714377 ACCTGAAAAGAACATAGATAGCATCAG 59.286 37.037 0.00 0.00 0.00 2.90
4260 5945 2.030027 ACCCAACCTCAGACAGATGA 57.970 50.000 0.00 0.00 0.00 2.92
4287 5972 2.484742 TAGACACGAGTAGCCTGACA 57.515 50.000 0.00 0.00 0.00 3.58
4435 6120 1.561076 AGAGCACATGGACAGGCAATA 59.439 47.619 0.00 0.00 0.00 1.90
4648 6333 2.271800 GCTACCAATGTGAGGAAGTCG 58.728 52.381 0.00 0.00 0.00 4.18
4669 6354 3.240134 TTGCCTCACCTCCGCAGAC 62.240 63.158 0.00 0.00 33.30 3.51
4701 6386 7.707035 CACTCTACTACGAATAAGCAAAATCCT 59.293 37.037 0.00 0.00 0.00 3.24
5032 6887 6.872920 TCAAAATATTGAATTACCCAGGCAC 58.127 36.000 0.00 0.00 42.47 5.01
5342 7224 6.816640 GTGGTTGCACTACTACATGAGAATTA 59.183 38.462 0.00 0.00 30.69 1.40
5369 7251 8.253113 AGAAGAATCAAAATAATCAAATGCGGT 58.747 29.630 0.00 0.00 0.00 5.68
5429 7311 6.658816 TGTACACATGAAATCAGTTAGGCAAT 59.341 34.615 0.00 0.00 0.00 3.56
5430 7312 6.000840 TGTACACATGAAATCAGTTAGGCAA 58.999 36.000 0.00 0.00 0.00 4.52
5459 7341 8.125448 GCAACATCAAATCAACTAGGAGTAATC 58.875 37.037 0.00 0.00 0.00 1.75
5462 7344 6.711277 AGCAACATCAAATCAACTAGGAGTA 58.289 36.000 0.00 0.00 0.00 2.59
5463 7345 5.564550 AGCAACATCAAATCAACTAGGAGT 58.435 37.500 0.00 0.00 0.00 3.85
5464 7346 6.506500 AAGCAACATCAAATCAACTAGGAG 57.493 37.500 0.00 0.00 0.00 3.69
5465 7347 9.851686 ATATAAGCAACATCAAATCAACTAGGA 57.148 29.630 0.00 0.00 0.00 2.94
5466 7348 9.888878 CATATAAGCAACATCAAATCAACTAGG 57.111 33.333 0.00 0.00 0.00 3.02
5507 7389 0.394565 ACTTGAGCTTTCGCAGGAGT 59.605 50.000 0.00 0.00 39.10 3.85
5508 7390 1.517242 AACTTGAGCTTTCGCAGGAG 58.483 50.000 0.00 0.00 39.10 3.69
5509 7391 2.831685 TAACTTGAGCTTTCGCAGGA 57.168 45.000 0.00 0.00 39.10 3.86
5510 7392 3.436704 TCAATAACTTGAGCTTTCGCAGG 59.563 43.478 0.00 0.00 36.46 4.85
5511 7393 4.668576 TCAATAACTTGAGCTTTCGCAG 57.331 40.909 0.00 0.00 36.46 5.18
5512 7394 5.212194 GTTTCAATAACTTGAGCTTTCGCA 58.788 37.500 0.00 0.00 42.19 5.10
5513 7395 4.617223 GGTTTCAATAACTTGAGCTTTCGC 59.383 41.667 0.00 0.00 42.19 4.70
5514 7396 5.757886 TGGTTTCAATAACTTGAGCTTTCG 58.242 37.500 0.00 0.00 42.19 3.46
5515 7397 7.653311 ACAATGGTTTCAATAACTTGAGCTTTC 59.347 33.333 0.00 0.00 42.19 2.62
5522 7404 7.596248 CAGAAGGACAATGGTTTCAATAACTTG 59.404 37.037 0.00 0.00 0.00 3.16
5612 7494 2.684927 CGCTCCCATCCTTCTGGAAAAT 60.685 50.000 0.00 0.00 46.80 1.82
5613 7495 1.340017 CGCTCCCATCCTTCTGGAAAA 60.340 52.381 0.00 0.00 46.80 2.29
5795 7677 0.736325 ATTCGGCTGAACGTCTTCCG 60.736 55.000 10.90 10.85 44.03 4.30
5897 7779 4.354939 CCACGGCGGCATTTGCAA 62.355 61.111 13.24 0.00 44.36 4.08
5986 7868 0.879090 CGGTGGTAAGCCTTGGTTTC 59.121 55.000 0.00 0.00 35.27 2.78
6036 7918 1.078426 CAGGCGGGTTAGGTTCCAG 60.078 63.158 0.00 0.00 0.00 3.86
6171 8053 7.933033 ACTGGAAATCTTGCATTACAAACAATT 59.067 29.630 0.00 0.00 37.96 2.32
6261 8144 3.928992 TCTCAGCGCTTAATTCTTCACAG 59.071 43.478 7.50 0.00 0.00 3.66
6936 11234 1.685180 GCCCTCAAATCCACCCCTTAC 60.685 57.143 0.00 0.00 0.00 2.34
6943 11241 4.965200 ATACTAGAGCCCTCAAATCCAC 57.035 45.455 0.00 0.00 0.00 4.02
6947 11245 4.464947 GGCAAATACTAGAGCCCTCAAAT 58.535 43.478 0.00 0.00 41.25 2.32
6956 11254 5.710099 TGAAAAACAGGGGCAAATACTAGAG 59.290 40.000 0.00 0.00 0.00 2.43
6996 11294 2.034685 GGGTTGAGAAGTGCCACTTTTC 59.965 50.000 18.46 18.46 38.80 2.29


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

AutoCloner maintained by Alex Coulton.