Multiple sequence alignment - TraesCS5B01G143700

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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 TraesCS5B01G143700 chr5B 100.000 2884 0 0 1 2884 271139861 271142744 0.000000e+00 5326.0
1 TraesCS5B01G143700 chr5B 86.547 223 22 8 1097 1314 271110144 271110363 3.710000e-59 239.0
2 TraesCS5B01G143700 chr5A 90.371 2212 94 48 758 2878 321019552 321021735 0.000000e+00 2795.0
3 TraesCS5B01G143700 chr5A 86.496 274 24 10 214 475 297582580 297582308 3.640000e-74 289.0
4 TraesCS5B01G143700 chr5A 87.448 239 10 11 545 764 321013651 321013888 1.030000e-64 257.0
5 TraesCS5B01G143700 chr5A 89.062 192 17 4 1125 1314 321001436 321001625 4.800000e-58 235.0
6 TraesCS5B01G143700 chr5D 91.388 1672 71 32 543 2182 233743036 233741406 0.000000e+00 2222.0
7 TraesCS5B01G143700 chr5D 92.087 733 26 14 2182 2884 233741357 233740627 0.000000e+00 1003.0
8 TraesCS5B01G143700 chr5D 87.215 219 23 5 1098 1314 233748941 233748726 7.980000e-61 244.0
9 TraesCS5B01G143700 chr5D 81.193 218 18 9 1 216 233743309 233743113 1.380000e-33 154.0
10 TraesCS5B01G143700 chr5D 89.130 92 8 1 503 594 233743104 233743015 2.350000e-21 113.0
11 TraesCS5B01G143700 chr6A 89.575 259 16 4 214 468 220375780 220376031 4.640000e-83 318.0
12 TraesCS5B01G143700 chr6A 90.455 220 17 2 256 471 195330982 195330763 1.310000e-73 287.0
13 TraesCS5B01G143700 chr1D 88.764 267 17 8 215 468 49766598 49766332 6.000000e-82 315.0
14 TraesCS5B01G143700 chr1D 86.667 105 12 2 260 364 14937555 14937453 6.530000e-22 115.0
15 TraesCS5B01G143700 chr7D 92.627 217 12 2 256 468 103925358 103925574 2.790000e-80 309.0
16 TraesCS5B01G143700 chr3A 87.405 262 19 7 215 468 623968393 623968648 3.640000e-74 289.0
17 TraesCS5B01G143700 chr2D 89.956 229 16 4 256 477 459305963 459305735 3.640000e-74 289.0
18 TraesCS5B01G143700 chr2D 88.053 226 15 4 256 471 139511736 139511513 1.030000e-64 257.0
19 TraesCS5B01G143700 chr1A 87.072 263 22 9 215 468 49960510 49960251 1.310000e-73 287.0
20 TraesCS5B01G143700 chr2B 90.367 218 15 5 256 468 649073 648857 6.080000e-72 281.0
21 TraesCS5B01G143700 chr2B 86.842 76 2 2 214 281 118819052 118818977 8.570000e-11 78.7
22 TraesCS5B01G143700 chr3D 88.106 227 24 3 256 480 388809670 388809895 1.700000e-67 267.0
23 TraesCS5B01G143700 chr2A 85.641 195 18 3 257 442 756119331 756119524 2.270000e-46 196.0
24 TraesCS5B01G143700 chr3B 80.488 123 15 5 214 328 732141561 732141682 5.120000e-13 86.1


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 TraesCS5B01G143700 chr5B 271139861 271142744 2883 False 5326 5326 100.0000 1 2884 1 chr5B.!!$F2 2883
1 TraesCS5B01G143700 chr5A 321019552 321021735 2183 False 2795 2795 90.3710 758 2878 1 chr5A.!!$F3 2120
2 TraesCS5B01G143700 chr5D 233740627 233743309 2682 True 873 2222 88.4495 1 2884 4 chr5D.!!$R2 2883

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
929 981 0.111061 ATCAAGAGCCAAGCACCACA 59.889 50.0 0.0 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2191 2329 0.031585 GAGGTCACAGTGTGCGTGTA 59.968 55.0 18.8 0.0 35.79 2.9 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
33 34 8.797674 TCTCCCAAAATTATATTCCCTACCTTT 58.202 33.333 0.00 0.00 0.00 3.11
54 55 2.127003 GCACCCGCTTTTACACGC 60.127 61.111 0.00 0.00 34.30 5.34
57 58 0.239879 CACCCGCTTTTACACGCAAT 59.760 50.000 0.00 0.00 0.00 3.56
77 78 5.007332 GCAATACAGAAACTAACATACGGGG 59.993 44.000 0.00 0.00 0.00 5.73
78 79 5.945144 ATACAGAAACTAACATACGGGGT 57.055 39.130 0.00 0.00 0.00 4.95
79 80 3.934068 ACAGAAACTAACATACGGGGTG 58.066 45.455 0.00 0.00 0.00 4.61
80 81 3.325716 ACAGAAACTAACATACGGGGTGT 59.674 43.478 0.00 0.00 0.00 4.16
81 82 3.930848 CAGAAACTAACATACGGGGTGTC 59.069 47.826 0.00 0.00 0.00 3.67
82 83 2.660189 AACTAACATACGGGGTGTCG 57.340 50.000 0.00 0.00 0.00 4.35
83 84 0.174162 ACTAACATACGGGGTGTCGC 59.826 55.000 0.00 0.00 0.00 5.19
90 91 3.113979 CGGGGTGTCGCGTTTACC 61.114 66.667 16.82 16.82 43.13 2.85
92 93 3.113979 GGGTGTCGCGTTTACCCG 61.114 66.667 24.38 0.00 44.13 5.28
93 94 2.049248 GGTGTCGCGTTTACCCGA 60.049 61.111 5.77 0.00 0.00 5.14
94 95 1.664333 GGTGTCGCGTTTACCCGAA 60.664 57.895 5.77 0.00 35.00 4.30
95 96 1.220817 GGTGTCGCGTTTACCCGAAA 61.221 55.000 5.77 0.00 35.00 3.46
96 97 0.162294 GTGTCGCGTTTACCCGAAAG 59.838 55.000 5.77 0.00 35.00 2.62
97 98 0.249405 TGTCGCGTTTACCCGAAAGT 60.249 50.000 5.77 0.00 35.00 2.66
98 99 1.000827 TGTCGCGTTTACCCGAAAGTA 60.001 47.619 5.77 0.00 35.00 2.24
99 100 2.058057 GTCGCGTTTACCCGAAAGTAA 58.942 47.619 5.77 0.00 35.00 2.24
100 101 2.474735 GTCGCGTTTACCCGAAAGTAAA 59.525 45.455 5.77 0.00 39.33 2.01
144 145 2.783832 CAGACGTAGCACACATACATCG 59.216 50.000 0.00 0.00 0.00 3.84
161 162 9.647797 ACATACATCGATTTACTCACTTACAAA 57.352 29.630 0.00 0.00 0.00 2.83
166 167 5.353123 TCGATTTACTCACTTACAAATGGGC 59.647 40.000 0.00 0.00 0.00 5.36
170 171 1.818674 CTCACTTACAAATGGGCCCAC 59.181 52.381 31.51 0.00 0.00 4.61
181 183 4.777854 GGCCCACCAATGACCCCC 62.778 72.222 0.00 0.00 35.26 5.40
188 190 1.157276 CCAATGACCCCCAAACCCA 59.843 57.895 0.00 0.00 0.00 4.51
191 193 0.266152 AATGACCCCCAAACCCAACA 59.734 50.000 0.00 0.00 0.00 3.33
228 230 5.724328 TCTTGTAGAAGACTAGCCACAATG 58.276 41.667 0.00 0.00 32.98 2.82
229 231 4.471904 TGTAGAAGACTAGCCACAATGG 57.528 45.455 0.00 0.00 41.55 3.16
230 232 4.093743 TGTAGAAGACTAGCCACAATGGA 58.906 43.478 0.00 0.00 40.96 3.41
231 233 4.716784 TGTAGAAGACTAGCCACAATGGAT 59.283 41.667 0.00 0.00 40.96 3.41
232 234 5.897250 TGTAGAAGACTAGCCACAATGGATA 59.103 40.000 0.00 0.00 40.96 2.59
242 244 6.747414 AGCCACAATGGATAGTAACATAGA 57.253 37.500 0.00 0.00 40.96 1.98
243 245 6.525629 AGCCACAATGGATAGTAACATAGAC 58.474 40.000 0.00 0.00 40.96 2.59
244 246 6.327626 AGCCACAATGGATAGTAACATAGACT 59.672 38.462 0.00 0.00 40.96 3.24
245 247 7.509318 AGCCACAATGGATAGTAACATAGACTA 59.491 37.037 0.00 0.00 40.96 2.59
246 248 7.815068 GCCACAATGGATAGTAACATAGACTAG 59.185 40.741 0.00 0.00 40.96 2.57
247 249 8.861086 CCACAATGGATAGTAACATAGACTAGT 58.139 37.037 0.00 0.00 40.96 2.57
261 263 8.680039 ACATAGACTAGTAACATGTCTACCTC 57.320 38.462 0.00 0.76 43.32 3.85
262 264 8.496088 ACATAGACTAGTAACATGTCTACCTCT 58.504 37.037 0.00 7.16 43.32 3.69
263 265 9.999660 CATAGACTAGTAACATGTCTACCTCTA 57.000 37.037 0.00 8.76 43.32 2.43
268 270 9.781633 ACTAGTAACATGTCTACCTCTATAGTG 57.218 37.037 0.00 0.00 0.00 2.74
269 271 9.221933 CTAGTAACATGTCTACCTCTATAGTGG 57.778 40.741 17.49 17.49 34.99 4.00
270 272 7.813331 AGTAACATGTCTACCTCTATAGTGGA 58.187 38.462 24.32 9.50 33.21 4.02
271 273 8.280084 AGTAACATGTCTACCTCTATAGTGGAA 58.720 37.037 24.32 8.93 33.21 3.53
272 274 7.973048 AACATGTCTACCTCTATAGTGGAAA 57.027 36.000 24.32 12.38 33.21 3.13
273 275 7.589958 ACATGTCTACCTCTATAGTGGAAAG 57.410 40.000 24.32 19.37 33.21 2.62
274 276 7.126733 ACATGTCTACCTCTATAGTGGAAAGT 58.873 38.462 24.32 7.27 33.21 2.66
275 277 8.280084 ACATGTCTACCTCTATAGTGGAAAGTA 58.720 37.037 24.32 14.54 33.21 2.24
276 278 9.132923 CATGTCTACCTCTATAGTGGAAAGTAA 57.867 37.037 24.32 13.88 33.21 2.24
277 279 8.517062 TGTCTACCTCTATAGTGGAAAGTAAC 57.483 38.462 24.32 15.51 33.21 2.50
278 280 8.111545 TGTCTACCTCTATAGTGGAAAGTAACA 58.888 37.037 24.32 17.23 33.21 2.41
279 281 9.134055 GTCTACCTCTATAGTGGAAAGTAACAT 57.866 37.037 24.32 4.38 33.21 2.71
283 285 9.435570 ACCTCTATAGTGGAAAGTAACATATGT 57.564 33.333 24.32 1.41 33.21 2.29
284 286 9.698309 CCTCTATAGTGGAAAGTAACATATGTG 57.302 37.037 14.57 0.00 0.00 3.21
287 289 9.817809 CTATAGTGGAAAGTAACATATGTGTGT 57.182 33.333 9.63 0.00 38.92 3.72
290 292 8.911918 AGTGGAAAGTAACATATGTGTGTTAA 57.088 30.769 9.63 0.00 43.82 2.01
291 293 8.780249 AGTGGAAAGTAACATATGTGTGTTAAC 58.220 33.333 9.63 0.00 43.82 2.01
292 294 8.561212 GTGGAAAGTAACATATGTGTGTTAACA 58.439 33.333 9.63 3.59 43.82 2.41
293 295 9.290988 TGGAAAGTAACATATGTGTGTTAACAT 57.709 29.630 12.26 0.00 43.82 2.71
294 296 9.554724 GGAAAGTAACATATGTGTGTTAACATG 57.445 33.333 12.26 7.30 43.82 3.21
295 297 8.964420 AAAGTAACATATGTGTGTTAACATGC 57.036 30.769 12.26 8.35 43.82 4.06
296 298 7.680442 AGTAACATATGTGTGTTAACATGCA 57.320 32.000 12.26 13.63 43.82 3.96
297 299 8.105097 AGTAACATATGTGTGTTAACATGCAA 57.895 30.769 12.26 5.85 43.82 4.08
298 300 8.739039 AGTAACATATGTGTGTTAACATGCAAT 58.261 29.630 12.26 6.44 43.82 3.56
299 301 9.995957 GTAACATATGTGTGTTAACATGCAATA 57.004 29.630 12.26 8.32 43.82 1.90
300 302 8.909708 AACATATGTGTGTTAACATGCAATAC 57.090 30.769 12.26 5.55 40.93 1.89
301 303 8.279970 ACATATGTGTGTTAACATGCAATACT 57.720 30.769 12.26 2.25 40.93 2.12
302 304 8.739039 ACATATGTGTGTTAACATGCAATACTT 58.261 29.630 12.26 5.87 40.93 2.24
303 305 9.225201 CATATGTGTGTTAACATGCAATACTTC 57.775 33.333 12.26 0.00 40.93 3.01
304 306 6.625873 TGTGTGTTAACATGCAATACTTCA 57.374 33.333 12.26 0.00 38.92 3.02
305 307 7.213216 TGTGTGTTAACATGCAATACTTCAT 57.787 32.000 12.26 0.00 38.92 2.57
306 308 7.656412 TGTGTGTTAACATGCAATACTTCATT 58.344 30.769 12.26 0.00 38.92 2.57
307 309 8.140628 TGTGTGTTAACATGCAATACTTCATTT 58.859 29.630 12.26 0.00 38.92 2.32
308 310 9.619316 GTGTGTTAACATGCAATACTTCATTTA 57.381 29.630 12.26 0.00 38.92 1.40
315 317 8.469309 ACATGCAATACTTCATTTATTAGGCT 57.531 30.769 0.00 0.00 0.00 4.58
316 318 9.573166 ACATGCAATACTTCATTTATTAGGCTA 57.427 29.630 0.00 0.00 0.00 3.93
335 337 9.588096 TTAGGCTATAGACACATCTTATCTTGA 57.412 33.333 8.68 0.00 36.29 3.02
336 338 8.663209 AGGCTATAGACACATCTTATCTTGAT 57.337 34.615 8.68 0.00 36.29 2.57
337 339 9.760926 AGGCTATAGACACATCTTATCTTGATA 57.239 33.333 8.68 0.00 36.29 2.15
371 373 9.192642 TGTTACTCATAACTAGCTATGTTACCA 57.807 33.333 11.88 3.15 41.24 3.25
372 374 9.460906 GTTACTCATAACTAGCTATGTTACCAC 57.539 37.037 11.88 2.75 38.15 4.16
373 375 7.899648 ACTCATAACTAGCTATGTTACCACT 57.100 36.000 11.88 1.78 33.45 4.00
374 376 8.307582 ACTCATAACTAGCTATGTTACCACTT 57.692 34.615 11.88 1.52 33.45 3.16
375 377 8.759782 ACTCATAACTAGCTATGTTACCACTTT 58.240 33.333 11.88 1.01 33.45 2.66
376 378 9.250624 CTCATAACTAGCTATGTTACCACTTTC 57.749 37.037 11.88 0.00 33.45 2.62
377 379 8.202137 TCATAACTAGCTATGTTACCACTTTCC 58.798 37.037 11.88 0.00 33.45 3.13
378 380 6.622427 AACTAGCTATGTTACCACTTTCCT 57.378 37.500 0.00 0.00 0.00 3.36
379 381 6.223351 ACTAGCTATGTTACCACTTTCCTC 57.777 41.667 0.00 0.00 0.00 3.71
380 382 5.958987 ACTAGCTATGTTACCACTTTCCTCT 59.041 40.000 0.00 0.00 0.00 3.69
381 383 5.346181 AGCTATGTTACCACTTTCCTCTC 57.654 43.478 0.00 0.00 0.00 3.20
382 384 5.026790 AGCTATGTTACCACTTTCCTCTCT 58.973 41.667 0.00 0.00 0.00 3.10
383 385 5.485708 AGCTATGTTACCACTTTCCTCTCTT 59.514 40.000 0.00 0.00 0.00 2.85
384 386 6.013293 AGCTATGTTACCACTTTCCTCTCTTT 60.013 38.462 0.00 0.00 0.00 2.52
385 387 6.314152 GCTATGTTACCACTTTCCTCTCTTTC 59.686 42.308 0.00 0.00 0.00 2.62
386 388 5.888982 TGTTACCACTTTCCTCTCTTTCT 57.111 39.130 0.00 0.00 0.00 2.52
387 389 6.248569 TGTTACCACTTTCCTCTCTTTCTT 57.751 37.500 0.00 0.00 0.00 2.52
388 390 6.289064 TGTTACCACTTTCCTCTCTTTCTTC 58.711 40.000 0.00 0.00 0.00 2.87
389 391 6.126883 TGTTACCACTTTCCTCTCTTTCTTCA 60.127 38.462 0.00 0.00 0.00 3.02
390 392 5.574970 ACCACTTTCCTCTCTTTCTTCAT 57.425 39.130 0.00 0.00 0.00 2.57
391 393 5.946486 ACCACTTTCCTCTCTTTCTTCATT 58.054 37.500 0.00 0.00 0.00 2.57
392 394 6.368805 ACCACTTTCCTCTCTTTCTTCATTT 58.631 36.000 0.00 0.00 0.00 2.32
393 395 7.518188 ACCACTTTCCTCTCTTTCTTCATTTA 58.482 34.615 0.00 0.00 0.00 1.40
394 396 8.166726 ACCACTTTCCTCTCTTTCTTCATTTAT 58.833 33.333 0.00 0.00 0.00 1.40
395 397 9.018582 CCACTTTCCTCTCTTTCTTCATTTATT 57.981 33.333 0.00 0.00 0.00 1.40
443 445 9.815306 ATCTAGATATGTGTGATGTTACTACCT 57.185 33.333 2.53 0.00 0.00 3.08
447 449 9.368416 AGATATGTGTGATGTTACTACCTATGT 57.632 33.333 0.00 0.00 0.00 2.29
448 450 9.982651 GATATGTGTGATGTTACTACCTATGTT 57.017 33.333 0.00 0.00 0.00 2.71
451 453 8.357290 TGTGTGATGTTACTACCTATGTTACT 57.643 34.615 0.00 0.00 0.00 2.24
452 454 8.464404 TGTGTGATGTTACTACCTATGTTACTC 58.536 37.037 0.00 0.00 0.00 2.59
453 455 7.919621 GTGTGATGTTACTACCTATGTTACTCC 59.080 40.741 0.00 0.00 0.00 3.85
454 456 7.069085 TGTGATGTTACTACCTATGTTACTCCC 59.931 40.741 0.00 0.00 0.00 4.30
455 457 7.069085 GTGATGTTACTACCTATGTTACTCCCA 59.931 40.741 0.00 0.00 0.00 4.37
456 458 6.780457 TGTTACTACCTATGTTACTCCCAC 57.220 41.667 0.00 0.00 0.00 4.61
457 459 6.496743 TGTTACTACCTATGTTACTCCCACT 58.503 40.000 0.00 0.00 0.00 4.00
458 460 6.379133 TGTTACTACCTATGTTACTCCCACTG 59.621 42.308 0.00 0.00 0.00 3.66
459 461 4.944177 ACTACCTATGTTACTCCCACTGT 58.056 43.478 0.00 0.00 0.00 3.55
460 462 4.710375 ACTACCTATGTTACTCCCACTGTG 59.290 45.833 0.00 0.00 0.00 3.66
461 463 2.838202 ACCTATGTTACTCCCACTGTGG 59.162 50.000 20.01 20.01 37.25 4.17
482 484 4.122776 GGGTAGTCGAAGTAGATACGTGA 58.877 47.826 0.00 0.00 0.00 4.35
487 489 5.414360 AGTCGAAGTAGATACGTGACACTA 58.586 41.667 0.00 0.00 32.68 2.74
488 490 5.871524 AGTCGAAGTAGATACGTGACACTAA 59.128 40.000 0.00 0.00 32.68 2.24
490 492 7.065563 AGTCGAAGTAGATACGTGACACTAAAT 59.934 37.037 0.00 0.00 32.68 1.40
492 494 8.239314 TCGAAGTAGATACGTGACACTAAATTT 58.761 33.333 0.00 0.00 0.00 1.82
493 495 8.857216 CGAAGTAGATACGTGACACTAAATTTT 58.143 33.333 0.00 0.00 0.00 1.82
520 522 6.899393 AAAAATGGCATTTCACTAGACTGA 57.101 33.333 24.51 0.00 0.00 3.41
521 523 5.886960 AAATGGCATTTCACTAGACTGAC 57.113 39.130 19.39 0.00 0.00 3.51
527 529 6.265196 TGGCATTTCACTAGACTGACAAAAAT 59.735 34.615 0.00 0.00 0.00 1.82
558 560 7.442364 TGTCTGCTGAATAATGGCTTTATACTC 59.558 37.037 6.11 2.87 30.11 2.59
596 627 5.354234 ACAATGGCTTTATACTTTGTCTCCG 59.646 40.000 0.00 0.00 31.78 4.63
602 633 5.353394 TTTATACTTTGTCTCCGCTGGAT 57.647 39.130 0.00 0.00 0.00 3.41
655 693 2.164338 CTTTTGGGCTTTAACGGGCTA 58.836 47.619 0.00 0.00 0.00 3.93
659 697 0.746923 GGGCTTTAACGGGCTAGTGG 60.747 60.000 0.00 0.00 0.00 4.00
660 698 1.374343 GGCTTTAACGGGCTAGTGGC 61.374 60.000 0.00 0.00 40.90 5.01
661 699 0.392595 GCTTTAACGGGCTAGTGGCT 60.393 55.000 0.00 0.00 41.46 4.75
696 734 1.164041 CGCCGGCCTTAAATACTGGG 61.164 60.000 23.46 0.00 0.00 4.45
698 736 1.409101 GCCGGCCTTAAATACTGGGAA 60.409 52.381 18.11 0.00 0.00 3.97
699 737 2.294979 CCGGCCTTAAATACTGGGAAC 58.705 52.381 0.00 0.00 0.00 3.62
700 738 1.937899 CGGCCTTAAATACTGGGAACG 59.062 52.381 0.00 0.00 0.00 3.95
764 805 0.329261 CCATACCCATCCATCCGCAT 59.671 55.000 0.00 0.00 0.00 4.73
777 818 1.079543 CCGCATCCATCCTCGATCC 60.080 63.158 0.00 0.00 0.00 3.36
816 857 4.798682 CCCGCACCCCTCCCTACT 62.799 72.222 0.00 0.00 0.00 2.57
817 858 3.155167 CCGCACCCCTCCCTACTC 61.155 72.222 0.00 0.00 0.00 2.59
818 859 3.155167 CGCACCCCTCCCTACTCC 61.155 72.222 0.00 0.00 0.00 3.85
819 860 3.155167 GCACCCCTCCCTACTCCG 61.155 72.222 0.00 0.00 0.00 4.63
820 861 2.687902 CACCCCTCCCTACTCCGA 59.312 66.667 0.00 0.00 0.00 4.55
821 862 1.455959 CACCCCTCCCTACTCCGAG 60.456 68.421 0.00 0.00 0.00 4.63
899 951 4.090057 GCCTGCACGTTCGCTTCC 62.090 66.667 0.00 0.00 0.00 3.46
929 981 0.111061 ATCAAGAGCCAAGCACCACA 59.889 50.000 0.00 0.00 0.00 4.17
972 1025 1.293963 ATTCATCCATCCATCGCGCG 61.294 55.000 26.76 26.76 0.00 6.86
1020 1073 2.926779 TGCCTGCTGCTCTCTGGT 60.927 61.111 0.00 0.00 42.00 4.00
1023 1076 1.612395 GCCTGCTGCTCTCTGGTAGT 61.612 60.000 0.00 0.00 36.87 2.73
1036 1089 0.542467 TGGTAGTACCAGCGGACCAA 60.542 55.000 18.45 0.00 44.79 3.67
1330 1405 2.741517 CAGGTACGCATCATCACAACAA 59.258 45.455 0.00 0.00 0.00 2.83
1338 1413 4.153986 GCATCATCACAACAACTTCTTCG 58.846 43.478 0.00 0.00 0.00 3.79
1345 1420 2.538449 ACAACAACTTCTTCGCACGTAG 59.462 45.455 0.00 0.00 0.00 3.51
1368 1446 1.666888 CCATCAAACTTTGCGTCTGGC 60.667 52.381 0.00 0.00 43.96 4.85
1455 1538 0.472471 AGTTGCACCGGGAGAAGAAA 59.528 50.000 6.32 0.00 0.00 2.52
1507 1590 2.298955 AGCAGCTCTTCTCCATGCT 58.701 52.632 0.00 0.00 42.18 3.79
1940 2027 4.809426 TCAGTCAAGAGTTTTCGTCCTTTC 59.191 41.667 0.00 0.00 0.00 2.62
1960 2047 2.496070 TCGTTGGATGAATCGGAGAACT 59.504 45.455 0.00 0.00 43.58 3.01
2002 2089 2.224867 CCCCACTTCCTGAAGACATTGT 60.225 50.000 13.58 0.00 40.79 2.71
2027 2114 5.134202 TGTCGAAGAGCTGTTCTTTATCA 57.866 39.130 20.17 9.58 46.12 2.15
2074 2163 6.744082 GTCATTTGTACGGGTTGTAAAATAGC 59.256 38.462 0.00 0.00 34.07 2.97
2075 2164 4.925061 TTGTACGGGTTGTAAAATAGCG 57.075 40.909 0.00 0.00 34.07 4.26
2076 2165 3.260740 TGTACGGGTTGTAAAATAGCGG 58.739 45.455 0.00 0.00 34.07 5.52
2159 2248 6.359087 GCATCAAGTATCATGAAAATCGCTTC 59.641 38.462 0.00 0.00 0.00 3.86
2191 2329 5.066893 TCTGGTCGAGTGCGTAAATATACTT 59.933 40.000 0.00 0.00 38.98 2.24
2239 2377 3.581755 CAATTCCATTTGCAGTGGAGTG 58.418 45.455 18.68 16.82 45.85 3.51
2248 2386 3.228188 TGCAGTGGAGTGGAGAAATTT 57.772 42.857 0.00 0.00 0.00 1.82
2279 2417 4.862641 AGTGGATACCCAAAGCACTAAT 57.137 40.909 0.00 0.00 45.59 1.73
2280 2418 4.526970 AGTGGATACCCAAAGCACTAATG 58.473 43.478 0.00 0.00 45.59 1.90
2284 2431 4.385310 GGATACCCAAAGCACTAATGGAGT 60.385 45.833 4.43 4.00 39.82 3.85
2299 2446 3.237268 TGGAGTAATGGTTGCCTTTGT 57.763 42.857 0.00 0.00 0.00 2.83
2328 2475 3.942601 CGAAGGAGGAGGAGACCC 58.057 66.667 0.00 0.00 0.00 4.46
2382 2529 0.813184 AGCAGGCGAACAATGAATGG 59.187 50.000 0.00 0.00 0.00 3.16
2534 2688 2.175184 CTCACCGCTTGGCAAAGACG 62.175 60.000 4.56 7.82 35.19 4.18
2649 2807 1.813513 CATCCGGTGAGACAAAAGCT 58.186 50.000 0.00 0.00 0.00 3.74
2737 2909 4.647424 TGAAAATGACCAAAGTCCACAC 57.353 40.909 0.00 0.00 42.81 3.82
2867 3039 7.765360 TGCTGAAATTCAATCAATCAAATACCC 59.235 33.333 0.00 0.00 0.00 3.69
2868 3040 7.043192 GCTGAAATTCAATCAATCAAATACCCG 60.043 37.037 0.00 0.00 0.00 5.28
2869 3041 6.756074 TGAAATTCAATCAATCAAATACCCGC 59.244 34.615 0.00 0.00 0.00 6.13
2881 3053 4.163458 TCAAATACCCGCAAAGGATCTACT 59.837 41.667 0.00 0.00 45.00 2.57
2882 3054 3.753294 ATACCCGCAAAGGATCTACTG 57.247 47.619 0.00 0.00 45.00 2.74
2883 3055 1.276622 ACCCGCAAAGGATCTACTGT 58.723 50.000 0.00 0.00 45.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 7.990055 AGGTAGGGAATATAATTTTGGGAGAG 58.010 38.462 0.00 0.00 0.00 3.20
48 49 7.008538 CGTATGTTAGTTTCTGTATTGCGTGTA 59.991 37.037 0.00 0.00 0.00 2.90
54 55 6.036735 CACCCCGTATGTTAGTTTCTGTATTG 59.963 42.308 0.00 0.00 0.00 1.90
57 58 4.527816 ACACCCCGTATGTTAGTTTCTGTA 59.472 41.667 0.00 0.00 0.00 2.74
81 82 2.826371 GTTTACTTTCGGGTAAACGCG 58.174 47.619 3.53 3.53 45.93 6.01
85 86 6.208402 GGTAAATGGGTTTACTTTCGGGTAAA 59.792 38.462 9.96 0.00 45.73 2.01
86 87 5.709631 GGTAAATGGGTTTACTTTCGGGTAA 59.290 40.000 9.96 0.00 45.73 2.85
87 88 5.252547 GGTAAATGGGTTTACTTTCGGGTA 58.747 41.667 9.96 0.00 45.73 3.69
88 89 4.081406 GGTAAATGGGTTTACTTTCGGGT 58.919 43.478 9.96 0.00 45.73 5.28
89 90 3.444742 GGGTAAATGGGTTTACTTTCGGG 59.555 47.826 9.96 0.00 45.73 5.14
90 91 3.127376 CGGGTAAATGGGTTTACTTTCGG 59.873 47.826 9.96 0.00 45.73 4.30
91 92 4.002316 TCGGGTAAATGGGTTTACTTTCG 58.998 43.478 9.96 10.88 45.73 3.46
92 93 5.963176 TTCGGGTAAATGGGTTTACTTTC 57.037 39.130 9.96 2.27 45.73 2.62
93 94 5.834742 ACTTTCGGGTAAATGGGTTTACTTT 59.165 36.000 9.96 0.00 45.73 2.66
94 95 5.387788 ACTTTCGGGTAAATGGGTTTACTT 58.612 37.500 9.96 0.00 45.73 2.24
95 96 4.989277 ACTTTCGGGTAAATGGGTTTACT 58.011 39.130 9.96 0.00 45.73 2.24
96 97 6.092670 GTCTACTTTCGGGTAAATGGGTTTAC 59.907 42.308 3.16 3.16 45.73 2.01
97 98 6.172630 GTCTACTTTCGGGTAAATGGGTTTA 58.827 40.000 0.00 0.00 0.00 2.01
98 99 5.005740 GTCTACTTTCGGGTAAATGGGTTT 58.994 41.667 0.00 0.00 0.00 3.27
99 100 4.566278 GGTCTACTTTCGGGTAAATGGGTT 60.566 45.833 0.00 0.00 0.00 4.11
100 101 3.054875 GGTCTACTTTCGGGTAAATGGGT 60.055 47.826 0.00 0.00 0.00 4.51
101 102 3.538591 GGTCTACTTTCGGGTAAATGGG 58.461 50.000 0.00 0.00 0.00 4.00
102 103 3.054948 TGGGTCTACTTTCGGGTAAATGG 60.055 47.826 0.00 0.00 0.00 3.16
103 104 4.081309 TCTGGGTCTACTTTCGGGTAAATG 60.081 45.833 0.00 0.00 0.00 2.32
104 105 4.081254 GTCTGGGTCTACTTTCGGGTAAAT 60.081 45.833 0.00 0.00 0.00 1.40
111 112 2.477525 GCTACGTCTGGGTCTACTTTCG 60.478 54.545 0.00 0.00 0.00 3.46
144 145 5.163550 GGGCCCATTTGTAAGTGAGTAAATC 60.164 44.000 19.95 0.00 0.00 2.17
161 162 2.364160 GGTCATTGGTGGGCCCAT 59.636 61.111 31.45 9.31 44.74 4.00
166 167 1.157276 TTTGGGGGTCATTGGTGGG 59.843 57.895 0.00 0.00 0.00 4.61
170 171 0.472734 TTGGGTTTGGGGGTCATTGG 60.473 55.000 0.00 0.00 0.00 3.16
173 174 0.471022 GTGTTGGGTTTGGGGGTCAT 60.471 55.000 0.00 0.00 0.00 3.06
174 175 1.075896 GTGTTGGGTTTGGGGGTCA 60.076 57.895 0.00 0.00 0.00 4.02
181 183 3.731089 AGCATTTCATGTGTTGGGTTTG 58.269 40.909 0.00 0.00 0.00 2.93
188 190 7.161404 TCTACAAGACTAGCATTTCATGTGTT 58.839 34.615 0.00 0.00 0.00 3.32
191 193 7.615403 TCTTCTACAAGACTAGCATTTCATGT 58.385 34.615 0.00 0.00 33.38 3.21
208 210 4.093743 TCCATTGTGGCTAGTCTTCTACA 58.906 43.478 0.00 0.00 37.47 2.74
209 211 4.737855 TCCATTGTGGCTAGTCTTCTAC 57.262 45.455 0.00 0.00 37.47 2.59
210 212 6.136857 ACTATCCATTGTGGCTAGTCTTCTA 58.863 40.000 6.67 0.00 43.73 2.10
211 213 4.965532 ACTATCCATTGTGGCTAGTCTTCT 59.034 41.667 6.67 0.00 43.73 2.85
212 214 5.283457 ACTATCCATTGTGGCTAGTCTTC 57.717 43.478 6.67 0.00 43.73 2.87
213 215 6.156256 TGTTACTATCCATTGTGGCTAGTCTT 59.844 38.462 13.92 0.00 43.73 3.01
214 216 5.661312 TGTTACTATCCATTGTGGCTAGTCT 59.339 40.000 13.92 0.00 43.73 3.24
215 217 5.914033 TGTTACTATCCATTGTGGCTAGTC 58.086 41.667 13.92 4.48 43.73 2.59
217 219 7.815068 GTCTATGTTACTATCCATTGTGGCTAG 59.185 40.741 5.55 5.55 40.94 3.42
218 220 7.509318 AGTCTATGTTACTATCCATTGTGGCTA 59.491 37.037 0.00 0.00 37.47 3.93
219 221 6.327626 AGTCTATGTTACTATCCATTGTGGCT 59.672 38.462 0.00 0.00 37.47 4.75
220 222 6.525629 AGTCTATGTTACTATCCATTGTGGC 58.474 40.000 0.00 0.00 37.47 5.01
221 223 8.861086 ACTAGTCTATGTTACTATCCATTGTGG 58.139 37.037 0.00 0.00 39.43 4.17
235 237 9.122779 GAGGTAGACATGTTACTAGTCTATGTT 57.877 37.037 16.14 10.94 44.09 2.71
236 238 8.496088 AGAGGTAGACATGTTACTAGTCTATGT 58.504 37.037 15.39 15.39 44.09 2.29
237 239 8.911918 AGAGGTAGACATGTTACTAGTCTATG 57.088 38.462 16.01 5.55 44.09 2.23
242 244 9.781633 CACTATAGAGGTAGACATGTTACTAGT 57.218 37.037 6.78 0.00 0.00 2.57
243 245 9.221933 CCACTATAGAGGTAGACATGTTACTAG 57.778 40.741 6.78 5.23 0.00 2.57
244 246 8.942033 TCCACTATAGAGGTAGACATGTTACTA 58.058 37.037 14.95 0.00 0.00 1.82
245 247 7.813331 TCCACTATAGAGGTAGACATGTTACT 58.187 38.462 14.95 0.00 0.00 2.24
246 248 8.461249 TTCCACTATAGAGGTAGACATGTTAC 57.539 38.462 14.95 4.83 0.00 2.50
247 249 9.132923 CTTTCCACTATAGAGGTAGACATGTTA 57.867 37.037 14.95 0.00 0.00 2.41
248 250 7.620094 ACTTTCCACTATAGAGGTAGACATGTT 59.380 37.037 14.95 0.00 0.00 2.71
249 251 7.126733 ACTTTCCACTATAGAGGTAGACATGT 58.873 38.462 14.95 0.00 0.00 3.21
250 252 7.589958 ACTTTCCACTATAGAGGTAGACATG 57.410 40.000 14.95 0.00 0.00 3.21
251 253 9.134055 GTTACTTTCCACTATAGAGGTAGACAT 57.866 37.037 14.95 2.13 0.00 3.06
252 254 8.111545 TGTTACTTTCCACTATAGAGGTAGACA 58.888 37.037 14.95 11.46 0.00 3.41
253 255 8.517062 TGTTACTTTCCACTATAGAGGTAGAC 57.483 38.462 14.95 9.62 0.00 2.59
257 259 9.435570 ACATATGTTACTTTCCACTATAGAGGT 57.564 33.333 14.95 0.00 0.00 3.85
258 260 9.698309 CACATATGTTACTTTCCACTATAGAGG 57.302 37.037 5.37 9.79 0.00 3.69
261 263 9.817809 ACACACATATGTTACTTTCCACTATAG 57.182 33.333 5.37 0.00 36.72 1.31
264 266 9.999660 TTAACACACATATGTTACTTTCCACTA 57.000 29.630 5.37 0.00 43.14 2.74
265 267 8.780249 GTTAACACACATATGTTACTTTCCACT 58.220 33.333 5.37 0.00 43.14 4.00
266 268 8.561212 TGTTAACACACATATGTTACTTTCCAC 58.439 33.333 5.37 0.00 43.14 4.02
267 269 8.678593 TGTTAACACACATATGTTACTTTCCA 57.321 30.769 5.37 0.00 43.14 3.53
268 270 9.554724 CATGTTAACACACATATGTTACTTTCC 57.445 33.333 11.22 0.00 43.14 3.13
269 271 9.061610 GCATGTTAACACACATATGTTACTTTC 57.938 33.333 11.22 0.00 43.14 2.62
270 272 8.572185 TGCATGTTAACACACATATGTTACTTT 58.428 29.630 11.22 0.14 43.14 2.66
271 273 8.105097 TGCATGTTAACACACATATGTTACTT 57.895 30.769 11.22 0.02 43.14 2.24
272 274 7.680442 TGCATGTTAACACACATATGTTACT 57.320 32.000 11.22 0.00 43.14 2.24
273 275 8.909708 ATTGCATGTTAACACACATATGTTAC 57.090 30.769 11.22 0.00 43.14 2.50
274 276 9.995957 GTATTGCATGTTAACACACATATGTTA 57.004 29.630 11.22 0.00 42.73 2.41
275 277 8.739039 AGTATTGCATGTTAACACACATATGTT 58.261 29.630 11.22 0.00 44.87 2.71
276 278 8.279970 AGTATTGCATGTTAACACACATATGT 57.720 30.769 11.22 1.41 40.80 2.29
277 279 9.225201 GAAGTATTGCATGTTAACACACATATG 57.775 33.333 11.22 5.35 35.51 1.78
278 280 8.955388 TGAAGTATTGCATGTTAACACACATAT 58.045 29.630 11.22 10.28 35.51 1.78
279 281 8.329203 TGAAGTATTGCATGTTAACACACATA 57.671 30.769 11.22 2.82 35.51 2.29
280 282 7.213216 TGAAGTATTGCATGTTAACACACAT 57.787 32.000 11.22 3.77 37.93 3.21
281 283 6.625873 TGAAGTATTGCATGTTAACACACA 57.374 33.333 11.22 9.33 35.03 3.72
282 284 8.519492 AAATGAAGTATTGCATGTTAACACAC 57.481 30.769 11.22 6.59 35.03 3.82
289 291 8.917088 AGCCTAATAAATGAAGTATTGCATGTT 58.083 29.630 0.00 0.00 0.00 2.71
290 292 8.469309 AGCCTAATAAATGAAGTATTGCATGT 57.531 30.769 0.00 0.00 0.00 3.21
309 311 9.588096 TCAAGATAAGATGTGTCTATAGCCTAA 57.412 33.333 0.00 0.00 33.30 2.69
310 312 9.760926 ATCAAGATAAGATGTGTCTATAGCCTA 57.239 33.333 0.00 0.00 33.30 3.93
311 313 8.663209 ATCAAGATAAGATGTGTCTATAGCCT 57.337 34.615 0.00 0.00 33.30 4.58
345 347 9.192642 TGGTAACATAGCTAGTTATGAGTAACA 57.807 33.333 27.42 22.60 46.17 2.41
365 367 6.289064 TGAAGAAAGAGAGGAAAGTGGTAAC 58.711 40.000 0.00 0.00 0.00 2.50
366 368 6.494666 TGAAGAAAGAGAGGAAAGTGGTAA 57.505 37.500 0.00 0.00 0.00 2.85
367 369 6.688073 ATGAAGAAAGAGAGGAAAGTGGTA 57.312 37.500 0.00 0.00 0.00 3.25
368 370 5.574970 ATGAAGAAAGAGAGGAAAGTGGT 57.425 39.130 0.00 0.00 0.00 4.16
369 371 6.890979 AAATGAAGAAAGAGAGGAAAGTGG 57.109 37.500 0.00 0.00 0.00 4.00
417 419 9.815306 AGGTAGTAACATCACACATATCTAGAT 57.185 33.333 10.73 10.73 0.00 1.98
421 423 9.368416 ACATAGGTAGTAACATCACACATATCT 57.632 33.333 0.00 0.00 0.00 1.98
422 424 9.982651 AACATAGGTAGTAACATCACACATATC 57.017 33.333 0.00 0.00 0.00 1.63
425 427 8.978472 AGTAACATAGGTAGTAACATCACACAT 58.022 33.333 0.00 0.00 0.00 3.21
426 428 8.357290 AGTAACATAGGTAGTAACATCACACA 57.643 34.615 0.00 0.00 0.00 3.72
427 429 7.919621 GGAGTAACATAGGTAGTAACATCACAC 59.080 40.741 0.00 0.00 0.00 3.82
428 430 7.069085 GGGAGTAACATAGGTAGTAACATCACA 59.931 40.741 0.00 0.00 0.00 3.58
429 431 7.069085 TGGGAGTAACATAGGTAGTAACATCAC 59.931 40.741 0.00 0.00 0.00 3.06
430 432 7.069085 GTGGGAGTAACATAGGTAGTAACATCA 59.931 40.741 0.00 0.00 0.00 3.07
431 433 7.287235 AGTGGGAGTAACATAGGTAGTAACATC 59.713 40.741 0.00 0.00 0.00 3.06
432 434 7.069578 CAGTGGGAGTAACATAGGTAGTAACAT 59.930 40.741 0.00 0.00 0.00 2.71
433 435 6.379133 CAGTGGGAGTAACATAGGTAGTAACA 59.621 42.308 0.00 0.00 0.00 2.41
434 436 6.379417 ACAGTGGGAGTAACATAGGTAGTAAC 59.621 42.308 0.00 0.00 0.00 2.50
435 437 6.379133 CACAGTGGGAGTAACATAGGTAGTAA 59.621 42.308 0.00 0.00 0.00 2.24
436 438 5.889853 CACAGTGGGAGTAACATAGGTAGTA 59.110 44.000 0.00 0.00 0.00 1.82
437 439 4.710375 CACAGTGGGAGTAACATAGGTAGT 59.290 45.833 0.00 0.00 0.00 2.73
438 440 4.099573 CCACAGTGGGAGTAACATAGGTAG 59.900 50.000 12.40 0.00 32.67 3.18
439 441 4.028131 CCACAGTGGGAGTAACATAGGTA 58.972 47.826 12.40 0.00 32.67 3.08
440 442 2.838202 CCACAGTGGGAGTAACATAGGT 59.162 50.000 12.40 0.00 32.67 3.08
441 443 3.543680 CCACAGTGGGAGTAACATAGG 57.456 52.381 12.40 0.00 32.67 2.57
453 455 0.966920 ACTTCGACTACCCACAGTGG 59.033 55.000 13.35 13.35 37.25 4.00
454 456 3.079578 TCTACTTCGACTACCCACAGTG 58.920 50.000 0.00 0.00 0.00 3.66
455 457 3.430042 TCTACTTCGACTACCCACAGT 57.570 47.619 0.00 0.00 0.00 3.55
456 458 4.025061 CGTATCTACTTCGACTACCCACAG 60.025 50.000 0.00 0.00 0.00 3.66
457 459 3.873361 CGTATCTACTTCGACTACCCACA 59.127 47.826 0.00 0.00 0.00 4.17
458 460 3.873952 ACGTATCTACTTCGACTACCCAC 59.126 47.826 0.00 0.00 0.00 4.61
459 461 3.873361 CACGTATCTACTTCGACTACCCA 59.127 47.826 0.00 0.00 0.00 4.51
460 462 4.025313 GTCACGTATCTACTTCGACTACCC 60.025 50.000 0.00 0.00 0.00 3.69
461 463 4.568359 TGTCACGTATCTACTTCGACTACC 59.432 45.833 0.00 0.00 0.00 3.18
462 464 5.290643 AGTGTCACGTATCTACTTCGACTAC 59.709 44.000 0.00 0.00 0.00 2.73
467 469 7.966157 AATTTAGTGTCACGTATCTACTTCG 57.034 36.000 0.00 0.00 0.00 3.79
497 499 6.265196 TGTCAGTCTAGTGAAATGCCATTTTT 59.735 34.615 3.82 0.00 31.47 1.94
499 501 5.316167 TGTCAGTCTAGTGAAATGCCATTT 58.684 37.500 1.47 1.47 34.64 2.32
500 502 4.910195 TGTCAGTCTAGTGAAATGCCATT 58.090 39.130 0.00 0.00 0.00 3.16
501 503 4.558226 TGTCAGTCTAGTGAAATGCCAT 57.442 40.909 0.00 0.00 0.00 4.40
502 504 4.350368 TTGTCAGTCTAGTGAAATGCCA 57.650 40.909 0.00 0.00 0.00 4.92
503 505 5.689383 TTTTGTCAGTCTAGTGAAATGCC 57.311 39.130 0.00 0.00 0.00 4.40
504 506 7.115378 CCAATTTTTGTCAGTCTAGTGAAATGC 59.885 37.037 0.00 0.00 0.00 3.56
505 507 7.115378 GCCAATTTTTGTCAGTCTAGTGAAATG 59.885 37.037 0.00 0.00 0.00 2.32
506 508 7.014615 AGCCAATTTTTGTCAGTCTAGTGAAAT 59.985 33.333 0.00 0.00 0.00 2.17
507 509 6.321181 AGCCAATTTTTGTCAGTCTAGTGAAA 59.679 34.615 0.00 0.00 0.00 2.69
508 510 5.827797 AGCCAATTTTTGTCAGTCTAGTGAA 59.172 36.000 0.00 0.00 0.00 3.18
509 511 5.239306 CAGCCAATTTTTGTCAGTCTAGTGA 59.761 40.000 0.00 0.00 0.00 3.41
510 512 5.009010 ACAGCCAATTTTTGTCAGTCTAGTG 59.991 40.000 0.00 0.00 0.00 2.74
511 513 5.133221 ACAGCCAATTTTTGTCAGTCTAGT 58.867 37.500 0.00 0.00 0.00 2.57
512 514 5.471456 AGACAGCCAATTTTTGTCAGTCTAG 59.529 40.000 13.30 0.00 42.75 2.43
513 515 5.239306 CAGACAGCCAATTTTTGTCAGTCTA 59.761 40.000 13.30 0.00 42.75 2.59
514 516 4.037208 CAGACAGCCAATTTTTGTCAGTCT 59.963 41.667 13.30 0.00 42.75 3.24
515 517 4.293415 CAGACAGCCAATTTTTGTCAGTC 58.707 43.478 13.30 0.00 42.75 3.51
516 518 3.491447 GCAGACAGCCAATTTTTGTCAGT 60.491 43.478 13.30 0.00 42.75 3.41
517 519 3.054878 GCAGACAGCCAATTTTTGTCAG 58.945 45.455 13.30 8.34 42.75 3.51
518 520 3.096489 GCAGACAGCCAATTTTTGTCA 57.904 42.857 13.30 0.00 42.75 3.58
564 566 8.519526 CAAAGTATAAAGCCATTGTTCACCTAA 58.480 33.333 0.00 0.00 0.00 2.69
565 567 7.668052 ACAAAGTATAAAGCCATTGTTCACCTA 59.332 33.333 0.00 0.00 0.00 3.08
566 568 6.493458 ACAAAGTATAAAGCCATTGTTCACCT 59.507 34.615 0.00 0.00 0.00 4.00
567 569 6.687604 ACAAAGTATAAAGCCATTGTTCACC 58.312 36.000 0.00 0.00 0.00 4.02
570 572 7.251281 GGAGACAAAGTATAAAGCCATTGTTC 58.749 38.462 0.00 0.00 31.68 3.18
571 573 6.128007 CGGAGACAAAGTATAAAGCCATTGTT 60.128 38.462 0.00 0.00 31.68 2.83
573 575 5.730568 GCGGAGACAAAGTATAAAGCCATTG 60.731 44.000 0.00 0.00 0.00 2.82
596 627 0.249238 CAGTCGCTACTCCATCCAGC 60.249 60.000 0.00 0.00 31.97 4.85
602 633 2.360844 CTCTCTTCAGTCGCTACTCCA 58.639 52.381 0.00 0.00 31.97 3.86
655 693 4.586235 AAGCCCGCAACAGCCACT 62.586 61.111 0.00 0.00 0.00 4.00
659 697 4.283403 TTGCAAGCCCGCAACAGC 62.283 61.111 6.30 0.00 46.61 4.40
678 716 0.181824 TCCCAGTATTTAAGGCCGGC 59.818 55.000 21.18 21.18 0.00 6.13
699 737 2.029288 ATGCTGGACAACGAGTGCG 61.029 57.895 0.00 0.00 42.22 5.34
700 738 1.499056 CATGCTGGACAACGAGTGC 59.501 57.895 0.00 0.00 39.32 4.40
764 805 2.861101 GCGCTGGATCGAGGATGGA 61.861 63.158 6.88 0.00 0.00 3.41
810 851 3.597728 GCGAGGCTCGGAGTAGGG 61.598 72.222 35.03 8.17 40.84 3.53
812 853 3.027292 GAGCGAGGCTCGGAGTAG 58.973 66.667 35.03 9.67 45.85 2.57
820 861 1.153549 GAATGGTTCGAGCGAGGCT 60.154 57.895 0.00 0.00 43.88 4.58
821 862 2.174319 GGAATGGTTCGAGCGAGGC 61.174 63.158 0.00 0.00 0.00 4.70
884 932 3.777925 CGGGAAGCGAACGTGCAG 61.778 66.667 0.00 0.00 37.31 4.41
899 951 0.449388 GCTCTTGATTTGTGGAGCGG 59.551 55.000 0.00 0.00 41.03 5.52
940 992 3.493334 TGGATGAATGGAATGAGATGGC 58.507 45.455 0.00 0.00 0.00 4.40
1020 1073 0.542467 TGGTTGGTCCGCTGGTACTA 60.542 55.000 0.00 0.00 39.52 1.82
1023 1076 3.065306 CTGGTTGGTCCGCTGGTA 58.935 61.111 0.00 0.00 39.52 3.25
1320 1395 3.291585 GTGCGAAGAAGTTGTTGTGATG 58.708 45.455 0.00 0.00 0.00 3.07
1330 1405 0.109226 GGCTCTACGTGCGAAGAAGT 60.109 55.000 0.00 0.00 0.00 3.01
1338 1413 1.726853 AGTTTGATGGCTCTACGTGC 58.273 50.000 0.00 0.00 0.00 5.34
1345 1420 1.537202 AGACGCAAAGTTTGATGGCTC 59.463 47.619 19.82 5.52 0.00 4.70
1368 1446 5.096849 GCAGAGAGTAAGAAGAGTTAACGG 58.903 45.833 0.00 0.00 0.00 4.44
1940 2027 2.604914 CAGTTCTCCGATTCATCCAACG 59.395 50.000 0.00 0.00 0.00 4.10
1985 2072 4.978099 ACATCACAATGTCTTCAGGAAGT 58.022 39.130 8.75 0.00 42.59 3.01
2002 2089 3.667497 AAGAACAGCTCTTCGACATCA 57.333 42.857 0.00 0.00 40.61 3.07
2042 2131 7.279750 ACAACCCGTACAAATGACTAAAAAT 57.720 32.000 0.00 0.00 0.00 1.82
2082 2171 2.422597 CACTTTGAGGCATGACGGTAA 58.577 47.619 0.00 0.00 0.00 2.85
2141 2230 8.987599 TTTTATCGAAGCGATTTTCATGATAC 57.012 30.769 7.67 0.00 44.59 2.24
2146 2235 7.134815 CCAGATTTTATCGAAGCGATTTTCAT 58.865 34.615 7.67 0.00 44.59 2.57
2159 2248 2.216488 CGCACTCGACCAGATTTTATCG 59.784 50.000 0.00 0.00 38.10 2.92
2191 2329 0.031585 GAGGTCACAGTGTGCGTGTA 59.968 55.000 18.80 0.00 35.79 2.90
2239 2377 6.659824 TCCACTAATCCCACTAAATTTCTCC 58.340 40.000 0.00 0.00 0.00 3.71
2248 2386 4.562934 TGGGTATCCACTAATCCCACTA 57.437 45.455 0.00 0.00 42.52 2.74
2279 2417 3.153919 GACAAAGGCAACCATTACTCCA 58.846 45.455 0.00 0.00 37.17 3.86
2280 2418 2.161609 CGACAAAGGCAACCATTACTCC 59.838 50.000 0.00 0.00 37.17 3.85
2284 2431 1.268352 GCACGACAAAGGCAACCATTA 59.732 47.619 0.00 0.00 37.17 1.90
2299 2446 2.125552 CCTTCGGCAGATGCACGA 60.126 61.111 7.19 10.24 44.36 4.35
2328 2475 2.473760 TTGGTTGGAACGTGGCGTG 61.474 57.895 0.00 0.00 39.99 5.34
2356 2503 4.043200 GTTCGCCTGCTGGGTTGC 62.043 66.667 12.06 0.00 37.43 4.17
2382 2529 3.788616 TTTGGCGCAGTTGCTTGCC 62.789 57.895 10.83 13.88 44.44 4.52
2582 2740 4.596212 TGATAGGATGTGCTGATGGAGAAT 59.404 41.667 0.00 0.00 0.00 2.40
2649 2807 0.667993 CTTGTGGCAGCGGAAAGAAA 59.332 50.000 0.00 0.00 0.00 2.52
2688 2846 1.473257 CGCTGTGTGCCTGGTATGTAT 60.473 52.381 0.00 0.00 38.78 2.29
2737 2909 3.497103 TCATCCTGTGCATATTCTGGG 57.503 47.619 0.00 0.00 0.00 4.45
2800 2972 1.646189 GCGGAAGAAAGCTCAGGTAG 58.354 55.000 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.