Multiple sequence alignment - TraesCS7D01G362800

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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 TraesCS7D01G362800 chr7D 100.000 3894 0 0 1 3894 466048035 466051928 0.000000e+00 7191.0
1 TraesCS7D01G362800 chr7D 82.486 177 25 6 430 602 69959033 69958859 2.420000e-32 150.0
2 TraesCS7D01G362800 chr7B 97.016 2346 59 4 654 2989 490597892 490600236 0.000000e+00 3934.0
3 TraesCS7D01G362800 chr7B 96.897 838 18 5 3051 3888 490600240 490601069 0.000000e+00 1397.0
4 TraesCS7D01G362800 chr7B 82.906 117 17 2 253 368 12956644 12956530 6.880000e-18 102.0
5 TraesCS7D01G362800 chr7B 92.857 56 1 3 129 183 490597699 490597752 1.160000e-10 78.7
6 TraesCS7D01G362800 chr7A 94.663 1930 82 6 696 2604 533906665 533904736 0.000000e+00 2974.0
7 TraesCS7D01G362800 chr7A 84.483 58 7 2 2339 2396 705679589 705679644 5.440000e-04 56.5
8 TraesCS7D01G362800 chr5D 89.929 566 57 0 1306 1871 527961645 527962210 0.000000e+00 730.0
9 TraesCS7D01G362800 chr5D 90.103 485 42 2 1867 2351 528001625 528002103 3.300000e-175 625.0
10 TraesCS7D01G362800 chr5D 98.438 64 1 0 2990 3053 305184398 305184335 3.180000e-21 113.0
11 TraesCS7D01G362800 chr5D 79.832 119 15 7 251 368 544240123 544240233 1.160000e-10 78.7
12 TraesCS7D01G362800 chr6D 99.231 130 1 0 1 130 265162120 265162249 6.500000e-58 235.0
13 TraesCS7D01G362800 chr6D 99.231 130 1 0 1 130 277632367 277632496 6.500000e-58 235.0
14 TraesCS7D01G362800 chr6D 97.122 139 4 0 1 139 456708439 456708301 6.500000e-58 235.0
15 TraesCS7D01G362800 chr6D 98.438 64 1 0 2990 3053 283156448 283156511 3.180000e-21 113.0
16 TraesCS7D01G362800 chr3D 99.231 130 1 0 1 130 401857848 401857977 6.500000e-58 235.0
17 TraesCS7D01G362800 chr3D 84.699 183 20 6 421 598 263813243 263813422 4.000000e-40 176.0
18 TraesCS7D01G362800 chr3D 85.333 75 4 7 368 436 595764502 595764429 1.940000e-08 71.3
19 TraesCS7D01G362800 chr1D 99.231 130 1 0 1 130 26759877 26760006 6.500000e-58 235.0
20 TraesCS7D01G362800 chr1D 99.231 130 1 0 1 130 76480521 76480650 6.500000e-58 235.0
21 TraesCS7D01G362800 chr1D 99.231 130 1 0 1 130 460224492 460224621 6.500000e-58 235.0
22 TraesCS7D01G362800 chr1D 99.231 130 1 0 1 130 460227007 460227136 6.500000e-58 235.0
23 TraesCS7D01G362800 chr1D 99.231 130 1 0 1 130 460233363 460233492 6.500000e-58 235.0
24 TraesCS7D01G362800 chr5B 85.227 176 20 5 429 601 292166490 292166318 4.000000e-40 176.0
25 TraesCS7D01G362800 chr5B 98.438 64 1 0 2990 3053 130536506 130536569 3.180000e-21 113.0
26 TraesCS7D01G362800 chr5B 98.438 64 1 0 2990 3053 130569528 130569465 3.180000e-21 113.0
27 TraesCS7D01G362800 chr3A 85.714 175 14 10 429 598 269653796 269653628 1.440000e-39 174.0
28 TraesCS7D01G362800 chr2D 100.000 64 0 0 2990 3053 521222042 521222105 6.830000e-23 119.0
29 TraesCS7D01G362800 chr2D 98.438 64 1 0 2990 3053 635068390 635068327 3.180000e-21 113.0
30 TraesCS7D01G362800 chr2D 98.438 64 1 0 2990 3053 644702491 644702554 3.180000e-21 113.0
31 TraesCS7D01G362800 chr2D 81.356 118 19 3 252 368 629508638 629508523 4.140000e-15 93.5
32 TraesCS7D01G362800 chr2D 78.107 169 20 9 423 588 440780073 440779919 1.490000e-14 91.6
33 TraesCS7D01G362800 chrUn 98.438 64 1 0 2990 3053 261513837 261513774 3.180000e-21 113.0
34 TraesCS7D01G362800 chrUn 98.438 64 1 0 2990 3053 462084375 462084312 3.180000e-21 113.0
35 TraesCS7D01G362800 chrUn 86.667 60 6 2 255 312 53926525 53926466 9.030000e-07 65.8
36 TraesCS7D01G362800 chr3B 79.528 127 19 7 254 376 76455873 76455996 2.490000e-12 84.2
37 TraesCS7D01G362800 chr5A 87.143 70 8 1 253 322 472106373 472106305 1.160000e-10 78.7
38 TraesCS7D01G362800 chr5A 87.500 64 7 1 252 314 26152931 26152868 5.400000e-09 73.1
39 TraesCS7D01G362800 chr6B 85.915 71 9 1 252 322 240381585 240381516 1.500000e-09 75.0
40 TraesCS7D01G362800 chr4A 81.481 81 5 5 253 333 580730565 580730635 1.510000e-04 58.4


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 TraesCS7D01G362800 chr7D 466048035 466051928 3893 False 7191.000000 7191 100.000 1 3894 1 chr7D.!!$F1 3893
1 TraesCS7D01G362800 chr7B 490597699 490601069 3370 False 1803.233333 3934 95.590 129 3888 3 chr7B.!!$F1 3759
2 TraesCS7D01G362800 chr7A 533904736 533906665 1929 True 2974.000000 2974 94.663 696 2604 1 chr7A.!!$R1 1908
3 TraesCS7D01G362800 chr5D 527961645 527962210 565 False 730.000000 730 89.929 1306 1871 1 chr5D.!!$F1 565
4 TraesCS7D01G362800 chr1D 460224492 460227136 2644 False 235.000000 235 99.231 1 130 2 chr1D.!!$F4 129

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
254 300 0.037975 GACGAGCCCTAAACACCGAA 60.038 55.0 0.00 0.0 0.0 4.30 F
648 694 0.107831 AACAGTAGCGCTTTGGGTGA 59.892 50.0 18.68 0.0 0.0 4.02 F
649 695 0.324943 ACAGTAGCGCTTTGGGTGAT 59.675 50.0 18.68 0.0 0.0 3.06 F
2181 3947 0.969409 AACTTCCCCTACCTCGACCG 60.969 60.0 0.00 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1677 2370 0.107654 GTGCTCGGCCATAAACTCCT 60.108 55.0 2.24 0.00 0.0 3.69 R
2181 3947 0.529992 CGTCGCCTCCTTTATCACCC 60.530 60.0 0.00 0.00 0.0 4.61 R
2483 4249 2.842188 TAGCGGCGGTAGAGGTGGAA 62.842 60.0 15.64 0.00 0.0 3.53 R
3010 4776 0.539986 ATCGAAATGGTACCAGCCGT 59.460 50.0 21.41 4.91 0.0 5.68 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
162 163 2.134789 AGTGGCCTGGATAAGCAAAG 57.865 50.000 3.32 0.00 0.00 2.77
214 260 3.185246 AGGAGGCGACAAACAGATATG 57.815 47.619 0.00 0.00 0.00 1.78
221 267 5.523916 AGGCGACAAACAGATATGACATAAC 59.476 40.000 0.00 0.00 0.00 1.89
241 287 7.570875 ACATAACTATGTCACGTATAGACGAGC 60.571 40.741 18.05 5.92 46.50 5.03
251 297 3.974912 GTATAGACGAGCCCTAAACACC 58.025 50.000 0.00 0.00 0.00 4.16
252 298 0.813184 TAGACGAGCCCTAAACACCG 59.187 55.000 0.00 0.00 0.00 4.94
253 299 0.896940 AGACGAGCCCTAAACACCGA 60.897 55.000 0.00 0.00 0.00 4.69
254 300 0.037975 GACGAGCCCTAAACACCGAA 60.038 55.000 0.00 0.00 0.00 4.30
255 301 0.393820 ACGAGCCCTAAACACCGAAA 59.606 50.000 0.00 0.00 0.00 3.46
256 302 1.076332 CGAGCCCTAAACACCGAAAG 58.924 55.000 0.00 0.00 0.00 2.62
257 303 1.607251 CGAGCCCTAAACACCGAAAGT 60.607 52.381 0.00 0.00 0.00 2.66
258 304 2.074576 GAGCCCTAAACACCGAAAGTC 58.925 52.381 0.00 0.00 0.00 3.01
259 305 1.162698 GCCCTAAACACCGAAAGTCC 58.837 55.000 0.00 0.00 0.00 3.85
260 306 1.271217 GCCCTAAACACCGAAAGTCCT 60.271 52.381 0.00 0.00 0.00 3.85
261 307 2.027837 GCCCTAAACACCGAAAGTCCTA 60.028 50.000 0.00 0.00 0.00 2.94
262 308 3.370209 GCCCTAAACACCGAAAGTCCTAT 60.370 47.826 0.00 0.00 0.00 2.57
263 309 4.840271 CCCTAAACACCGAAAGTCCTATT 58.160 43.478 0.00 0.00 0.00 1.73
264 310 4.874396 CCCTAAACACCGAAAGTCCTATTC 59.126 45.833 0.00 0.00 0.00 1.75
265 311 5.338137 CCCTAAACACCGAAAGTCCTATTCT 60.338 44.000 0.00 0.00 0.00 2.40
266 312 5.581085 CCTAAACACCGAAAGTCCTATTCTG 59.419 44.000 0.00 0.00 0.00 3.02
267 313 4.884668 AACACCGAAAGTCCTATTCTGA 57.115 40.909 0.00 0.00 0.00 3.27
268 314 5.422214 AACACCGAAAGTCCTATTCTGAT 57.578 39.130 0.00 0.00 0.00 2.90
269 315 5.012328 ACACCGAAAGTCCTATTCTGATC 57.988 43.478 0.00 0.00 0.00 2.92
270 316 4.141914 ACACCGAAAGTCCTATTCTGATCC 60.142 45.833 0.00 0.00 0.00 3.36
271 317 3.388350 ACCGAAAGTCCTATTCTGATCCC 59.612 47.826 0.00 0.00 0.00 3.85
272 318 3.553096 CCGAAAGTCCTATTCTGATCCCG 60.553 52.174 0.00 0.00 0.00 5.14
273 319 3.318275 CGAAAGTCCTATTCTGATCCCGA 59.682 47.826 0.00 0.00 0.00 5.14
274 320 4.557695 CGAAAGTCCTATTCTGATCCCGAG 60.558 50.000 0.00 0.00 0.00 4.63
275 321 2.243810 AGTCCTATTCTGATCCCGAGC 58.756 52.381 0.00 0.00 0.00 5.03
276 322 2.158385 AGTCCTATTCTGATCCCGAGCT 60.158 50.000 0.00 0.00 0.00 4.09
277 323 2.230266 GTCCTATTCTGATCCCGAGCTC 59.770 54.545 2.73 2.73 0.00 4.09
278 324 2.158460 TCCTATTCTGATCCCGAGCTCA 60.158 50.000 15.40 0.00 0.00 4.26
279 325 2.630098 CCTATTCTGATCCCGAGCTCAA 59.370 50.000 15.40 0.00 0.00 3.02
280 326 3.070159 CCTATTCTGATCCCGAGCTCAAA 59.930 47.826 15.40 0.00 0.00 2.69
281 327 3.853355 ATTCTGATCCCGAGCTCAAAT 57.147 42.857 15.40 3.24 0.00 2.32
282 328 4.963318 ATTCTGATCCCGAGCTCAAATA 57.037 40.909 15.40 0.00 0.00 1.40
283 329 4.963318 TTCTGATCCCGAGCTCAAATAT 57.037 40.909 15.40 0.87 0.00 1.28
284 330 6.611613 ATTCTGATCCCGAGCTCAAATATA 57.388 37.500 15.40 0.00 0.00 0.86
285 331 5.392767 TCTGATCCCGAGCTCAAATATAC 57.607 43.478 15.40 0.00 0.00 1.47
286 332 4.220821 TCTGATCCCGAGCTCAAATATACC 59.779 45.833 15.40 0.00 0.00 2.73
287 333 3.260884 TGATCCCGAGCTCAAATATACCC 59.739 47.826 15.40 0.00 0.00 3.69
288 334 2.972348 TCCCGAGCTCAAATATACCCT 58.028 47.619 15.40 0.00 0.00 4.34
289 335 2.632996 TCCCGAGCTCAAATATACCCTG 59.367 50.000 15.40 0.00 0.00 4.45
290 336 2.632996 CCCGAGCTCAAATATACCCTGA 59.367 50.000 15.40 0.00 0.00 3.86
291 337 3.261897 CCCGAGCTCAAATATACCCTGAT 59.738 47.826 15.40 0.00 0.00 2.90
292 338 4.248859 CCGAGCTCAAATATACCCTGATG 58.751 47.826 15.40 0.00 0.00 3.07
293 339 4.021104 CCGAGCTCAAATATACCCTGATGA 60.021 45.833 15.40 0.00 0.00 2.92
294 340 5.511373 CCGAGCTCAAATATACCCTGATGAA 60.511 44.000 15.40 0.00 0.00 2.57
295 341 6.169094 CGAGCTCAAATATACCCTGATGAAT 58.831 40.000 15.40 0.00 0.00 2.57
296 342 7.323420 CGAGCTCAAATATACCCTGATGAATA 58.677 38.462 15.40 0.00 0.00 1.75
297 343 7.490725 CGAGCTCAAATATACCCTGATGAATAG 59.509 40.741 15.40 0.00 0.00 1.73
298 344 8.212259 AGCTCAAATATACCCTGATGAATAGT 57.788 34.615 0.00 0.00 0.00 2.12
299 345 9.326489 AGCTCAAATATACCCTGATGAATAGTA 57.674 33.333 0.00 0.00 0.00 1.82
300 346 9.944376 GCTCAAATATACCCTGATGAATAGTAA 57.056 33.333 0.00 0.00 0.00 2.24
369 415 9.436957 TTTTTGTGGTAAACTTTAAGAAATGCA 57.563 25.926 0.00 0.00 0.00 3.96
370 416 9.606631 TTTTGTGGTAAACTTTAAGAAATGCAT 57.393 25.926 0.00 0.00 0.00 3.96
372 418 9.685828 TTGTGGTAAACTTTAAGAAATGCATAC 57.314 29.630 0.00 0.00 0.00 2.39
373 419 8.851145 TGTGGTAAACTTTAAGAAATGCATACA 58.149 29.630 0.00 0.00 0.00 2.29
374 420 9.685828 GTGGTAAACTTTAAGAAATGCATACAA 57.314 29.630 0.00 0.00 0.00 2.41
449 495 0.378962 TTTTTGCCACGACTTCCACG 59.621 50.000 0.00 0.00 0.00 4.94
450 496 0.462225 TTTTGCCACGACTTCCACGA 60.462 50.000 0.00 0.00 34.70 4.35
451 497 0.462225 TTTGCCACGACTTCCACGAA 60.462 50.000 0.00 0.00 34.70 3.85
452 498 1.155424 TTGCCACGACTTCCACGAAC 61.155 55.000 0.00 0.00 34.70 3.95
453 499 1.593209 GCCACGACTTCCACGAACA 60.593 57.895 0.00 0.00 34.70 3.18
454 500 0.949105 GCCACGACTTCCACGAACAT 60.949 55.000 0.00 0.00 34.70 2.71
455 501 1.068474 CCACGACTTCCACGAACATC 58.932 55.000 0.00 0.00 34.70 3.06
456 502 1.604438 CCACGACTTCCACGAACATCA 60.604 52.381 0.00 0.00 34.70 3.07
457 503 2.337583 CACGACTTCCACGAACATCAT 58.662 47.619 0.00 0.00 34.70 2.45
458 504 2.736721 CACGACTTCCACGAACATCATT 59.263 45.455 0.00 0.00 34.70 2.57
459 505 3.186409 CACGACTTCCACGAACATCATTT 59.814 43.478 0.00 0.00 34.70 2.32
460 506 3.432252 ACGACTTCCACGAACATCATTTC 59.568 43.478 0.00 0.00 34.70 2.17
478 524 3.706802 TTCGTTCTGAAATTGCAAGCA 57.293 38.095 4.94 2.23 32.37 3.91
479 525 3.921119 TCGTTCTGAAATTGCAAGCAT 57.079 38.095 4.94 0.00 0.00 3.79
480 526 5.369685 TTCGTTCTGAAATTGCAAGCATA 57.630 34.783 4.94 0.00 32.37 3.14
481 527 4.722194 TCGTTCTGAAATTGCAAGCATAC 58.278 39.130 4.94 4.22 0.00 2.39
482 528 4.215185 TCGTTCTGAAATTGCAAGCATACA 59.785 37.500 4.94 0.21 0.00 2.29
483 529 4.916831 CGTTCTGAAATTGCAAGCATACAA 59.083 37.500 4.94 0.00 0.00 2.41
484 530 5.401972 CGTTCTGAAATTGCAAGCATACAAA 59.598 36.000 4.94 0.00 0.00 2.83
485 531 6.074409 CGTTCTGAAATTGCAAGCATACAAAA 60.074 34.615 4.94 0.00 0.00 2.44
486 532 6.768029 TCTGAAATTGCAAGCATACAAAAC 57.232 33.333 4.94 0.00 0.00 2.43
487 533 6.279123 TCTGAAATTGCAAGCATACAAAACA 58.721 32.000 4.94 0.00 0.00 2.83
488 534 6.930164 TCTGAAATTGCAAGCATACAAAACAT 59.070 30.769 4.94 0.00 0.00 2.71
489 535 7.441760 TCTGAAATTGCAAGCATACAAAACATT 59.558 29.630 4.94 0.00 0.00 2.71
490 536 7.353497 TGAAATTGCAAGCATACAAAACATTG 58.647 30.769 4.94 0.00 0.00 2.82
491 537 6.864360 AATTGCAAGCATACAAAACATTGT 57.136 29.167 4.94 0.00 38.85 2.71
492 538 6.864360 ATTGCAAGCATACAAAACATTGTT 57.136 29.167 4.94 0.00 36.44 2.83
493 539 7.959689 ATTGCAAGCATACAAAACATTGTTA 57.040 28.000 4.94 0.00 36.44 2.41
494 540 7.776933 TTGCAAGCATACAAAACATTGTTAA 57.223 28.000 1.76 0.00 36.44 2.01
495 541 7.776933 TGCAAGCATACAAAACATTGTTAAA 57.223 28.000 1.76 0.00 36.44 1.52
496 542 7.849496 TGCAAGCATACAAAACATTGTTAAAG 58.151 30.769 1.76 0.00 36.44 1.85
497 543 6.791775 GCAAGCATACAAAACATTGTTAAAGC 59.208 34.615 1.76 2.49 36.44 3.51
498 544 7.307337 GCAAGCATACAAAACATTGTTAAAGCT 60.307 33.333 1.76 4.60 36.44 3.74
499 545 8.550376 CAAGCATACAAAACATTGTTAAAGCTT 58.450 29.630 1.76 9.74 37.09 3.74
500 546 9.757227 AAGCATACAAAACATTGTTAAAGCTTA 57.243 25.926 16.09 0.00 36.06 3.09
501 547 9.927668 AGCATACAAAACATTGTTAAAGCTTAT 57.072 25.926 0.00 0.00 36.44 1.73
506 552 9.593134 ACAAAACATTGTTAAAGCTTATCAACA 57.407 25.926 14.03 14.03 0.00 3.33
569 615 8.815565 TTTATTTTACTATTCATCAGGGTGCA 57.184 30.769 0.00 0.00 0.00 4.57
570 616 8.995027 TTATTTTACTATTCATCAGGGTGCAT 57.005 30.769 0.00 0.00 0.00 3.96
571 617 7.902920 ATTTTACTATTCATCAGGGTGCATT 57.097 32.000 0.00 0.00 0.00 3.56
572 618 7.716799 TTTTACTATTCATCAGGGTGCATTT 57.283 32.000 0.00 0.00 0.00 2.32
573 619 6.698008 TTACTATTCATCAGGGTGCATTTG 57.302 37.500 0.00 0.00 0.00 2.32
574 620 4.858850 ACTATTCATCAGGGTGCATTTGA 58.141 39.130 0.00 0.00 0.00 2.69
575 621 4.885907 ACTATTCATCAGGGTGCATTTGAG 59.114 41.667 0.00 0.00 0.00 3.02
576 622 1.466856 TCATCAGGGTGCATTTGAGC 58.533 50.000 0.00 0.00 0.00 4.26
577 623 1.005097 TCATCAGGGTGCATTTGAGCT 59.995 47.619 0.00 0.00 34.99 4.09
578 624 1.404391 CATCAGGGTGCATTTGAGCTC 59.596 52.381 6.82 6.82 34.99 4.09
579 625 0.401356 TCAGGGTGCATTTGAGCTCA 59.599 50.000 13.74 13.74 34.99 4.26
580 626 0.809385 CAGGGTGCATTTGAGCTCAG 59.191 55.000 17.43 6.81 34.99 3.35
581 627 0.323178 AGGGTGCATTTGAGCTCAGG 60.323 55.000 17.43 11.70 34.99 3.86
582 628 0.322816 GGGTGCATTTGAGCTCAGGA 60.323 55.000 17.43 10.35 34.99 3.86
583 629 1.093159 GGTGCATTTGAGCTCAGGAG 58.907 55.000 17.43 11.33 34.99 3.69
614 660 1.271163 ACGTCCCCTAAACACACCATG 60.271 52.381 0.00 0.00 0.00 3.66
635 681 8.908903 ACCATGTTCTTTTTGACATAAACAGTA 58.091 29.630 0.00 0.00 30.95 2.74
636 682 9.398170 CCATGTTCTTTTTGACATAAACAGTAG 57.602 33.333 0.00 0.00 30.95 2.57
637 683 8.905702 CATGTTCTTTTTGACATAAACAGTAGC 58.094 33.333 0.00 0.00 30.95 3.58
638 684 7.129622 TGTTCTTTTTGACATAAACAGTAGCG 58.870 34.615 0.00 0.00 0.00 4.26
639 685 5.685841 TCTTTTTGACATAAACAGTAGCGC 58.314 37.500 0.00 0.00 0.00 5.92
640 686 5.468746 TCTTTTTGACATAAACAGTAGCGCT 59.531 36.000 17.26 17.26 0.00 5.92
641 687 5.682943 TTTTGACATAAACAGTAGCGCTT 57.317 34.783 18.68 0.00 0.00 4.68
642 688 5.682943 TTTGACATAAACAGTAGCGCTTT 57.317 34.783 18.68 5.74 0.00 3.51
643 689 4.661993 TGACATAAACAGTAGCGCTTTG 57.338 40.909 18.68 17.65 0.00 2.77
644 690 3.435327 TGACATAAACAGTAGCGCTTTGG 59.565 43.478 18.68 7.89 0.00 3.28
645 691 2.747446 ACATAAACAGTAGCGCTTTGGG 59.253 45.455 18.68 5.81 0.00 4.12
646 692 2.554370 TAAACAGTAGCGCTTTGGGT 57.446 45.000 18.68 6.55 0.00 4.51
647 693 0.951558 AAACAGTAGCGCTTTGGGTG 59.048 50.000 18.68 8.92 0.00 4.61
648 694 0.107831 AACAGTAGCGCTTTGGGTGA 59.892 50.000 18.68 0.00 0.00 4.02
649 695 0.324943 ACAGTAGCGCTTTGGGTGAT 59.675 50.000 18.68 0.00 0.00 3.06
650 696 1.271379 ACAGTAGCGCTTTGGGTGATT 60.271 47.619 18.68 0.00 0.00 2.57
651 697 1.131126 CAGTAGCGCTTTGGGTGATTG 59.869 52.381 18.68 0.00 0.00 2.67
652 698 1.003118 AGTAGCGCTTTGGGTGATTGA 59.997 47.619 18.68 0.00 0.00 2.57
656 702 2.299867 AGCGCTTTGGGTGATTGAATTT 59.700 40.909 2.64 0.00 0.00 1.82
684 730 9.926158 CAATCTACAAGATATCATAACTGCTCT 57.074 33.333 5.32 0.00 32.89 4.09
770 1330 3.609853 CCACGATTCTTCCCTTGAATGA 58.390 45.455 0.00 0.00 34.67 2.57
1036 1649 2.893489 TCTCAAGTGTGCAAGCTCTAGA 59.107 45.455 0.00 0.00 0.00 2.43
1093 1707 4.764771 GCAGGGGAATGGCTGCCA 62.765 66.667 25.65 25.65 37.23 4.92
1747 2939 2.363795 TCGGCGTCCCTCTCCATT 60.364 61.111 6.85 0.00 0.00 3.16
2075 3841 3.437795 CCGCCGTGTACCTCGTCT 61.438 66.667 6.77 0.00 0.00 4.18
2080 3846 2.758089 CGTGTACCTCGTCTCCGGG 61.758 68.421 0.00 0.00 33.95 5.73
2181 3947 0.969409 AACTTCCCCTACCTCGACCG 60.969 60.000 0.00 0.00 0.00 4.79
2483 4249 1.001641 GAGGTGAAGCTGGCCATGT 60.002 57.895 5.51 0.00 0.00 3.21
2698 4464 1.307170 ACCGTATACCAGGGGGCAA 60.307 57.895 0.00 0.00 37.90 4.52
2838 4604 2.353704 CGATCACCCTGCAACTTGACTA 60.354 50.000 0.00 0.00 0.00 2.59
2852 4618 8.027189 TGCAACTTGACTATAGTACTGTACTTG 58.973 37.037 24.09 16.53 40.14 3.16
2892 4658 6.955963 GTCGAGCATTAAAGATAACACACTTG 59.044 38.462 0.00 0.00 0.00 3.16
2893 4659 6.871492 TCGAGCATTAAAGATAACACACTTGA 59.129 34.615 0.00 0.00 0.00 3.02
2954 4720 4.309933 CAAAGAATCCCTTGAGGCAAAAC 58.690 43.478 0.00 0.00 34.79 2.43
2964 4730 2.241160 TGAGGCAAAACATGTCAGCAT 58.759 42.857 15.93 10.66 35.54 3.79
2989 4755 4.664139 GCGACAACATGCATCGTGTATATC 60.664 45.833 10.95 0.88 38.13 1.63
2990 4756 4.444056 CGACAACATGCATCGTGTATATCA 59.556 41.667 10.95 0.00 31.86 2.15
2991 4757 5.051106 CGACAACATGCATCGTGTATATCAA 60.051 40.000 10.95 0.00 31.86 2.57
2992 4758 6.509358 CGACAACATGCATCGTGTATATCAAA 60.509 38.462 10.95 0.00 31.86 2.69
2993 4759 7.263100 ACAACATGCATCGTGTATATCAAAT 57.737 32.000 9.54 0.00 31.86 2.32
2994 4760 7.355017 ACAACATGCATCGTGTATATCAAATC 58.645 34.615 9.54 0.00 31.86 2.17
2995 4761 6.486253 ACATGCATCGTGTATATCAAATCC 57.514 37.500 0.00 0.00 31.23 3.01
2996 4762 6.233434 ACATGCATCGTGTATATCAAATCCT 58.767 36.000 0.00 0.00 31.23 3.24
2997 4763 6.712095 ACATGCATCGTGTATATCAAATCCTT 59.288 34.615 0.00 0.00 31.23 3.36
2998 4764 6.785488 TGCATCGTGTATATCAAATCCTTC 57.215 37.500 0.00 0.00 0.00 3.46
2999 4765 6.524734 TGCATCGTGTATATCAAATCCTTCT 58.475 36.000 0.00 0.00 0.00 2.85
3000 4766 7.666623 TGCATCGTGTATATCAAATCCTTCTA 58.333 34.615 0.00 0.00 0.00 2.10
3001 4767 8.314021 TGCATCGTGTATATCAAATCCTTCTAT 58.686 33.333 0.00 0.00 0.00 1.98
3002 4768 9.155975 GCATCGTGTATATCAAATCCTTCTATT 57.844 33.333 0.00 0.00 0.00 1.73
3014 4780 9.485206 TCAAATCCTTCTATTATTAAGTACGGC 57.515 33.333 0.00 0.00 0.00 5.68
3015 4781 9.490379 CAAATCCTTCTATTATTAAGTACGGCT 57.510 33.333 0.00 0.00 0.00 5.52
3016 4782 9.490379 AAATCCTTCTATTATTAAGTACGGCTG 57.510 33.333 0.00 0.00 0.00 4.85
3017 4783 6.989659 TCCTTCTATTATTAAGTACGGCTGG 58.010 40.000 0.00 0.00 0.00 4.85
3018 4784 6.552350 TCCTTCTATTATTAAGTACGGCTGGT 59.448 38.462 0.00 0.00 0.00 4.00
3019 4785 7.725397 TCCTTCTATTATTAAGTACGGCTGGTA 59.275 37.037 0.00 0.00 0.00 3.25
3027 4793 1.283736 GTACGGCTGGTACCATTTCG 58.716 55.000 16.75 20.13 44.72 3.46
3028 4794 1.135024 GTACGGCTGGTACCATTTCGA 60.135 52.381 27.12 14.49 44.72 3.71
3029 4795 0.539986 ACGGCTGGTACCATTTCGAT 59.460 50.000 27.12 14.87 0.00 3.59
3030 4796 0.937304 CGGCTGGTACCATTTCGATG 59.063 55.000 16.75 2.54 0.00 3.84
3031 4797 1.742411 CGGCTGGTACCATTTCGATGT 60.742 52.381 16.75 0.00 0.00 3.06
3032 4798 1.670811 GGCTGGTACCATTTCGATGTG 59.329 52.381 16.75 0.91 0.00 3.21
3033 4799 2.356135 GCTGGTACCATTTCGATGTGT 58.644 47.619 16.75 0.00 0.00 3.72
3034 4800 2.747446 GCTGGTACCATTTCGATGTGTT 59.253 45.455 16.75 0.00 0.00 3.32
3035 4801 3.190535 GCTGGTACCATTTCGATGTGTTT 59.809 43.478 16.75 0.00 0.00 2.83
3036 4802 4.671766 GCTGGTACCATTTCGATGTGTTTC 60.672 45.833 16.75 0.00 0.00 2.78
3037 4803 4.390264 TGGTACCATTTCGATGTGTTTCA 58.610 39.130 11.60 0.00 0.00 2.69
3038 4804 4.822350 TGGTACCATTTCGATGTGTTTCAA 59.178 37.500 11.60 0.00 0.00 2.69
3039 4805 5.475220 TGGTACCATTTCGATGTGTTTCAAT 59.525 36.000 11.60 0.00 0.00 2.57
3040 4806 6.015856 TGGTACCATTTCGATGTGTTTCAATT 60.016 34.615 11.60 0.00 0.00 2.32
3041 4807 6.866248 GGTACCATTTCGATGTGTTTCAATTT 59.134 34.615 7.15 0.00 0.00 1.82
3042 4808 7.383843 GGTACCATTTCGATGTGTTTCAATTTT 59.616 33.333 7.15 0.00 0.00 1.82
3043 4809 7.784633 ACCATTTCGATGTGTTTCAATTTTT 57.215 28.000 0.00 0.00 0.00 1.94
3080 4846 5.616488 AAAGCAAAATCATGATTTGTGGC 57.384 34.783 29.52 28.65 40.57 5.01
3183 4949 3.367646 TGGGCCGACAAATAACCAATA 57.632 42.857 0.00 0.00 0.00 1.90
3193 4959 7.954786 CCGACAAATAACCAATAAAACAAATGC 59.045 33.333 0.00 0.00 0.00 3.56
3202 4968 7.227156 ACCAATAAAACAAATGCAATACCCAA 58.773 30.769 0.00 0.00 0.00 4.12
3391 5157 3.388350 TGAGACGAGATGCTAGACTAGGA 59.612 47.826 11.48 8.94 0.00 2.94
3449 5215 0.467474 TCCGATACGTCATGCCTCCT 60.467 55.000 0.00 0.00 0.00 3.69
3450 5216 0.039074 CCGATACGTCATGCCTCCTC 60.039 60.000 0.00 0.00 0.00 3.71
3451 5217 0.039074 CGATACGTCATGCCTCCTCC 60.039 60.000 0.00 0.00 0.00 4.30
3476 5242 5.043432 ACCAAAAGAATCATTCCTATGGGGA 60.043 40.000 14.32 0.00 43.41 4.81
3492 5258 0.551396 GGGACCAGGAAATTCCCGAT 59.449 55.000 8.66 0.00 39.83 4.18
3587 5353 6.176183 CCAAGATACTCCATCACTTTTCACT 58.824 40.000 0.00 0.00 35.96 3.41
3589 5355 5.181748 AGATACTCCATCACTTTTCACTGC 58.818 41.667 0.00 0.00 35.96 4.40
3643 5409 3.285484 CTGGCCAAGCAGAAGATTGTAT 58.715 45.455 7.01 0.00 39.44 2.29
3655 5421 6.017605 GCAGAAGATTGTATCCATAAGGTGTG 60.018 42.308 0.00 0.00 35.89 3.82
3656 5422 7.050377 CAGAAGATTGTATCCATAAGGTGTGT 58.950 38.462 0.00 0.00 35.89 3.72
3695 5461 5.662211 AAACAGCATTGCAACTCAATTTC 57.338 34.783 11.91 0.00 42.48 2.17
3701 5467 8.306038 ACAGCATTGCAACTCAATTTCTTATAA 58.694 29.630 11.91 0.00 42.48 0.98
3703 5469 7.761249 AGCATTGCAACTCAATTTCTTATAACC 59.239 33.333 11.91 0.00 42.48 2.85
3704 5470 7.761249 GCATTGCAACTCAATTTCTTATAACCT 59.239 33.333 0.00 0.00 42.48 3.50
3705 5471 9.294030 CATTGCAACTCAATTTCTTATAACCTC 57.706 33.333 0.00 0.00 42.48 3.85
3706 5472 8.635765 TTGCAACTCAATTTCTTATAACCTCT 57.364 30.769 0.00 0.00 0.00 3.69
3861 5627 1.554160 CCCATTTTATGCACAAGCCCA 59.446 47.619 0.00 0.00 41.13 5.36
3862 5628 2.027377 CCCATTTTATGCACAAGCCCAA 60.027 45.455 0.00 0.00 41.13 4.12
3888 5654 2.704572 AGATGAACCTGTTAGTGCAGC 58.295 47.619 0.00 0.00 35.28 5.25
3889 5655 1.740025 GATGAACCTGTTAGTGCAGCC 59.260 52.381 0.00 0.00 35.28 4.85
3890 5656 0.250727 TGAACCTGTTAGTGCAGCCC 60.251 55.000 0.00 0.00 35.28 5.19
3891 5657 0.036875 GAACCTGTTAGTGCAGCCCT 59.963 55.000 0.00 0.00 35.28 5.19
3892 5658 0.036875 AACCTGTTAGTGCAGCCCTC 59.963 55.000 0.00 0.00 35.28 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
186 193 3.886505 TGTTTGTCGCCTCCTTGTTTATT 59.113 39.130 0.00 0.00 0.00 1.40
193 200 3.197766 TCATATCTGTTTGTCGCCTCCTT 59.802 43.478 0.00 0.00 0.00 3.36
194 201 2.766263 TCATATCTGTTTGTCGCCTCCT 59.234 45.455 0.00 0.00 0.00 3.69
195 202 2.866762 GTCATATCTGTTTGTCGCCTCC 59.133 50.000 0.00 0.00 0.00 4.30
230 276 3.549625 CGGTGTTTAGGGCTCGTCTATAC 60.550 52.174 0.00 0.00 0.00 1.47
232 278 1.407979 CGGTGTTTAGGGCTCGTCTAT 59.592 52.381 0.00 0.00 0.00 1.98
237 283 1.076332 CTTTCGGTGTTTAGGGCTCG 58.924 55.000 0.00 0.00 0.00 5.03
241 287 2.853235 AGGACTTTCGGTGTTTAGGG 57.147 50.000 0.00 0.00 0.00 3.53
242 288 5.581085 CAGAATAGGACTTTCGGTGTTTAGG 59.419 44.000 0.00 0.00 0.00 2.69
243 289 6.395629 TCAGAATAGGACTTTCGGTGTTTAG 58.604 40.000 0.00 0.00 0.00 1.85
244 290 6.349243 TCAGAATAGGACTTTCGGTGTTTA 57.651 37.500 0.00 0.00 0.00 2.01
245 291 5.223449 TCAGAATAGGACTTTCGGTGTTT 57.777 39.130 0.00 0.00 0.00 2.83
246 292 4.884668 TCAGAATAGGACTTTCGGTGTT 57.115 40.909 0.00 0.00 0.00 3.32
247 293 4.141914 GGATCAGAATAGGACTTTCGGTGT 60.142 45.833 0.00 0.00 0.00 4.16
248 294 4.372656 GGATCAGAATAGGACTTTCGGTG 58.627 47.826 0.00 0.00 0.00 4.94
249 295 3.388350 GGGATCAGAATAGGACTTTCGGT 59.612 47.826 0.00 0.00 0.00 4.69
250 296 3.553096 CGGGATCAGAATAGGACTTTCGG 60.553 52.174 0.00 0.00 0.00 4.30
251 297 3.318275 TCGGGATCAGAATAGGACTTTCG 59.682 47.826 0.00 0.00 0.00 3.46
252 298 4.797933 GCTCGGGATCAGAATAGGACTTTC 60.798 50.000 0.00 0.00 0.00 2.62
253 299 3.070302 GCTCGGGATCAGAATAGGACTTT 59.930 47.826 0.00 0.00 0.00 2.66
254 300 2.630580 GCTCGGGATCAGAATAGGACTT 59.369 50.000 0.00 0.00 0.00 3.01
255 301 2.158385 AGCTCGGGATCAGAATAGGACT 60.158 50.000 0.00 0.00 0.00 3.85
256 302 2.230266 GAGCTCGGGATCAGAATAGGAC 59.770 54.545 0.00 0.00 0.00 3.85
257 303 2.158460 TGAGCTCGGGATCAGAATAGGA 60.158 50.000 0.00 0.00 32.54 2.94
258 304 2.242926 TGAGCTCGGGATCAGAATAGG 58.757 52.381 0.00 0.00 32.54 2.57
259 305 4.327982 TTTGAGCTCGGGATCAGAATAG 57.672 45.455 2.32 0.00 39.13 1.73
260 306 4.963318 ATTTGAGCTCGGGATCAGAATA 57.037 40.909 2.32 0.00 39.13 1.75
261 307 3.853355 ATTTGAGCTCGGGATCAGAAT 57.147 42.857 2.32 4.33 39.13 2.40
262 308 4.963318 ATATTTGAGCTCGGGATCAGAA 57.037 40.909 2.32 1.91 39.13 3.02
263 309 4.220821 GGTATATTTGAGCTCGGGATCAGA 59.779 45.833 2.32 0.00 39.13 3.27
264 310 4.499183 GGTATATTTGAGCTCGGGATCAG 58.501 47.826 2.32 0.00 39.13 2.90
265 311 3.260884 GGGTATATTTGAGCTCGGGATCA 59.739 47.826 0.00 0.00 35.97 2.92
266 312 3.515901 AGGGTATATTTGAGCTCGGGATC 59.484 47.826 9.64 0.00 0.00 3.36
267 313 3.261897 CAGGGTATATTTGAGCTCGGGAT 59.738 47.826 9.64 5.44 0.00 3.85
268 314 2.632996 CAGGGTATATTTGAGCTCGGGA 59.367 50.000 9.64 0.00 0.00 5.14
269 315 2.632996 TCAGGGTATATTTGAGCTCGGG 59.367 50.000 9.64 0.00 0.00 5.14
270 316 4.021104 TCATCAGGGTATATTTGAGCTCGG 60.021 45.833 9.64 0.00 0.00 4.63
271 317 5.139435 TCATCAGGGTATATTTGAGCTCG 57.861 43.478 9.64 0.00 0.00 5.03
272 318 8.317679 ACTATTCATCAGGGTATATTTGAGCTC 58.682 37.037 6.82 6.82 0.00 4.09
273 319 8.212259 ACTATTCATCAGGGTATATTTGAGCT 57.788 34.615 0.00 0.00 0.00 4.09
274 320 9.944376 TTACTATTCATCAGGGTATATTTGAGC 57.056 33.333 0.00 0.00 0.00 4.26
343 389 9.436957 TGCATTTCTTAAAGTTTACCACAAAAA 57.563 25.926 0.00 0.00 0.00 1.94
344 390 9.606631 ATGCATTTCTTAAAGTTTACCACAAAA 57.393 25.926 0.00 0.00 0.00 2.44
346 392 9.685828 GTATGCATTTCTTAAAGTTTACCACAA 57.314 29.630 3.54 0.00 0.00 3.33
347 393 8.851145 TGTATGCATTTCTTAAAGTTTACCACA 58.149 29.630 3.54 0.00 0.00 4.17
348 394 9.685828 TTGTATGCATTTCTTAAAGTTTACCAC 57.314 29.630 3.54 0.00 0.00 4.16
430 476 0.378962 CGTGGAAGTCGTGGCAAAAA 59.621 50.000 0.00 0.00 0.00 1.94
431 477 0.462225 TCGTGGAAGTCGTGGCAAAA 60.462 50.000 0.00 0.00 0.00 2.44
432 478 0.462225 TTCGTGGAAGTCGTGGCAAA 60.462 50.000 0.00 0.00 0.00 3.68
433 479 1.144276 TTCGTGGAAGTCGTGGCAA 59.856 52.632 0.00 0.00 0.00 4.52
434 480 1.593209 GTTCGTGGAAGTCGTGGCA 60.593 57.895 0.00 0.00 0.00 4.92
435 481 0.949105 ATGTTCGTGGAAGTCGTGGC 60.949 55.000 0.00 0.00 0.00 5.01
436 482 1.068474 GATGTTCGTGGAAGTCGTGG 58.932 55.000 0.00 0.00 0.00 4.94
437 483 1.778334 TGATGTTCGTGGAAGTCGTG 58.222 50.000 0.00 0.00 0.00 4.35
438 484 2.743636 ATGATGTTCGTGGAAGTCGT 57.256 45.000 0.00 0.00 0.00 4.34
439 485 3.481951 CGAAATGATGTTCGTGGAAGTCG 60.482 47.826 0.00 0.00 44.20 4.18
440 486 3.991069 CGAAATGATGTTCGTGGAAGTC 58.009 45.455 0.00 0.00 44.20 3.01
458 504 3.706802 TGCTTGCAATTTCAGAACGAA 57.293 38.095 0.00 0.00 0.00 3.85
459 505 3.921119 ATGCTTGCAATTTCAGAACGA 57.079 38.095 0.00 0.00 0.00 3.85
460 506 4.475028 TGTATGCTTGCAATTTCAGAACG 58.525 39.130 0.00 0.00 0.00 3.95
461 507 6.768029 TTTGTATGCTTGCAATTTCAGAAC 57.232 33.333 0.00 2.86 0.00 3.01
462 508 6.760298 TGTTTTGTATGCTTGCAATTTCAGAA 59.240 30.769 0.00 0.00 0.00 3.02
463 509 6.279123 TGTTTTGTATGCTTGCAATTTCAGA 58.721 32.000 0.00 0.00 0.00 3.27
464 510 6.528014 TGTTTTGTATGCTTGCAATTTCAG 57.472 33.333 0.00 0.00 0.00 3.02
465 511 7.012138 ACAATGTTTTGTATGCTTGCAATTTCA 59.988 29.630 0.00 0.00 44.22 2.69
466 512 7.354257 ACAATGTTTTGTATGCTTGCAATTTC 58.646 30.769 0.00 0.00 44.22 2.17
467 513 7.261829 ACAATGTTTTGTATGCTTGCAATTT 57.738 28.000 0.00 0.00 44.22 1.82
468 514 6.864360 ACAATGTTTTGTATGCTTGCAATT 57.136 29.167 0.00 0.00 44.22 2.32
469 515 6.864360 AACAATGTTTTGTATGCTTGCAAT 57.136 29.167 0.00 0.00 45.30 3.56
470 516 7.776933 TTAACAATGTTTTGTATGCTTGCAA 57.223 28.000 3.17 0.00 45.30 4.08
471 517 7.518052 GCTTTAACAATGTTTTGTATGCTTGCA 60.518 33.333 3.17 0.00 45.30 4.08
472 518 6.791775 GCTTTAACAATGTTTTGTATGCTTGC 59.208 34.615 3.17 0.00 45.30 4.01
473 519 8.075593 AGCTTTAACAATGTTTTGTATGCTTG 57.924 30.769 3.17 0.00 45.30 4.01
474 520 8.661352 AAGCTTTAACAATGTTTTGTATGCTT 57.339 26.923 3.17 9.22 45.30 3.91
475 521 9.927668 ATAAGCTTTAACAATGTTTTGTATGCT 57.072 25.926 3.20 3.78 45.30 3.79
543 589 9.249053 TGCACCCTGATGAATAGTAAAATAAAA 57.751 29.630 0.00 0.00 0.00 1.52
544 590 8.815565 TGCACCCTGATGAATAGTAAAATAAA 57.184 30.769 0.00 0.00 0.00 1.40
545 591 8.995027 ATGCACCCTGATGAATAGTAAAATAA 57.005 30.769 0.00 0.00 0.00 1.40
546 592 8.995027 AATGCACCCTGATGAATAGTAAAATA 57.005 30.769 0.00 0.00 0.00 1.40
547 593 7.902920 AATGCACCCTGATGAATAGTAAAAT 57.097 32.000 0.00 0.00 0.00 1.82
548 594 7.395772 TCAAATGCACCCTGATGAATAGTAAAA 59.604 33.333 0.00 0.00 0.00 1.52
549 595 6.889177 TCAAATGCACCCTGATGAATAGTAAA 59.111 34.615 0.00 0.00 0.00 2.01
550 596 6.422333 TCAAATGCACCCTGATGAATAGTAA 58.578 36.000 0.00 0.00 0.00 2.24
551 597 6.000246 TCAAATGCACCCTGATGAATAGTA 58.000 37.500 0.00 0.00 0.00 1.82
552 598 4.858850 TCAAATGCACCCTGATGAATAGT 58.141 39.130 0.00 0.00 0.00 2.12
553 599 4.261489 GCTCAAATGCACCCTGATGAATAG 60.261 45.833 0.00 0.00 0.00 1.73
554 600 3.633525 GCTCAAATGCACCCTGATGAATA 59.366 43.478 0.00 0.00 0.00 1.75
555 601 2.429610 GCTCAAATGCACCCTGATGAAT 59.570 45.455 0.00 0.00 0.00 2.57
556 602 1.820519 GCTCAAATGCACCCTGATGAA 59.179 47.619 0.00 0.00 0.00 2.57
557 603 1.005097 AGCTCAAATGCACCCTGATGA 59.995 47.619 0.00 0.00 34.99 2.92
558 604 1.404391 GAGCTCAAATGCACCCTGATG 59.596 52.381 9.40 0.00 34.99 3.07
559 605 1.005097 TGAGCTCAAATGCACCCTGAT 59.995 47.619 15.67 0.00 34.99 2.90
560 606 0.401356 TGAGCTCAAATGCACCCTGA 59.599 50.000 15.67 0.00 34.99 3.86
561 607 0.809385 CTGAGCTCAAATGCACCCTG 59.191 55.000 18.85 0.00 34.99 4.45
562 608 0.323178 CCTGAGCTCAAATGCACCCT 60.323 55.000 18.85 0.00 34.99 4.34
563 609 0.322816 TCCTGAGCTCAAATGCACCC 60.323 55.000 18.85 0.00 34.99 4.61
564 610 1.093159 CTCCTGAGCTCAAATGCACC 58.907 55.000 18.85 0.00 34.99 5.01
581 627 0.386113 GGGACGTGGAGTATCTGCTC 59.614 60.000 0.00 0.00 33.73 4.26
582 628 1.043673 GGGGACGTGGAGTATCTGCT 61.044 60.000 0.00 0.00 33.73 4.24
583 629 1.043673 AGGGGACGTGGAGTATCTGC 61.044 60.000 0.00 0.00 33.73 4.26
584 630 2.359981 TAGGGGACGTGGAGTATCTG 57.640 55.000 0.00 0.00 33.73 2.90
585 631 3.029570 GTTTAGGGGACGTGGAGTATCT 58.970 50.000 0.00 0.00 33.73 1.98
586 632 2.762327 TGTTTAGGGGACGTGGAGTATC 59.238 50.000 0.00 0.00 0.00 2.24
587 633 2.498885 GTGTTTAGGGGACGTGGAGTAT 59.501 50.000 0.00 0.00 0.00 2.12
588 634 1.895131 GTGTTTAGGGGACGTGGAGTA 59.105 52.381 0.00 0.00 0.00 2.59
589 635 0.683412 GTGTTTAGGGGACGTGGAGT 59.317 55.000 0.00 0.00 0.00 3.85
590 636 0.682852 TGTGTTTAGGGGACGTGGAG 59.317 55.000 0.00 0.00 0.00 3.86
591 637 0.393820 GTGTGTTTAGGGGACGTGGA 59.606 55.000 0.00 0.00 0.00 4.02
592 638 0.604511 GGTGTGTTTAGGGGACGTGG 60.605 60.000 0.00 0.00 0.00 4.94
593 639 0.107081 TGGTGTGTTTAGGGGACGTG 59.893 55.000 0.00 0.00 0.00 4.49
594 640 1.061546 ATGGTGTGTTTAGGGGACGT 58.938 50.000 0.00 0.00 0.00 4.34
595 641 1.271163 ACATGGTGTGTTTAGGGGACG 60.271 52.381 0.00 0.00 38.01 4.79
596 642 2.579410 ACATGGTGTGTTTAGGGGAC 57.421 50.000 0.00 0.00 38.01 4.46
614 660 6.086371 GCGCTACTGTTTATGTCAAAAAGAAC 59.914 38.462 0.00 0.00 0.00 3.01
617 663 5.689819 AGCGCTACTGTTTATGTCAAAAAG 58.310 37.500 8.99 0.00 0.00 2.27
621 667 4.083537 CCAAAGCGCTACTGTTTATGTCAA 60.084 41.667 12.05 0.00 0.00 3.18
622 668 3.435327 CCAAAGCGCTACTGTTTATGTCA 59.565 43.478 12.05 0.00 0.00 3.58
623 669 3.181510 CCCAAAGCGCTACTGTTTATGTC 60.182 47.826 12.05 0.00 0.00 3.06
624 670 2.747446 CCCAAAGCGCTACTGTTTATGT 59.253 45.455 12.05 0.00 0.00 2.29
635 681 1.549203 ATTCAATCACCCAAAGCGCT 58.451 45.000 2.64 2.64 0.00 5.92
636 682 2.368655 AATTCAATCACCCAAAGCGC 57.631 45.000 0.00 0.00 0.00 5.92
637 683 4.305769 TGAAAATTCAATCACCCAAAGCG 58.694 39.130 0.00 0.00 33.55 4.68
690 736 8.027771 TGTTCAACACACGGTAATTTTTAGTTT 58.972 29.630 0.00 0.00 0.00 2.66
748 1307 2.489938 TTCAAGGGAAGAATCGTGGG 57.510 50.000 0.00 0.00 0.00 4.61
770 1330 4.748892 AGATCGATGAAAATGTCACGAGT 58.251 39.130 0.54 0.00 40.54 4.18
859 1469 0.954452 CTGTTTCTGCAAGTGGGGAC 59.046 55.000 0.00 0.00 33.76 4.46
1254 1868 1.843851 TGAAGATGGGGCCGTATTTCT 59.156 47.619 0.00 0.00 0.00 2.52
1399 2086 2.612115 AGGCCCTTCTGGTGGAGG 60.612 66.667 0.00 0.00 36.04 4.30
1677 2370 0.107654 GTGCTCGGCCATAAACTCCT 60.108 55.000 2.24 0.00 0.00 3.69
2053 3819 2.754658 AGGTACACGGCGGAGGAG 60.755 66.667 13.24 0.00 0.00 3.69
2054 3820 2.753043 GAGGTACACGGCGGAGGA 60.753 66.667 13.24 0.00 0.00 3.71
2181 3947 0.529992 CGTCGCCTCCTTTATCACCC 60.530 60.000 0.00 0.00 0.00 4.61
2483 4249 2.842188 TAGCGGCGGTAGAGGTGGAA 62.842 60.000 15.64 0.00 0.00 3.53
2659 4425 2.631062 TGACTACTTCCGAGGAGCAAAA 59.369 45.455 0.00 0.00 37.35 2.44
2698 4464 0.681175 GAACAAAGCTGGGGCAATGT 59.319 50.000 0.00 0.00 39.82 2.71
2810 4576 1.750193 TGCAGGGTGATCGAATTTCC 58.250 50.000 0.00 0.00 0.00 3.13
2852 4618 7.484035 AATGCTCGACCTGTTATAATTTCTC 57.516 36.000 0.00 0.00 0.00 2.87
2964 4730 1.670730 ACGATGCATGTTGTCGCCA 60.671 52.632 2.46 0.00 38.85 5.69
2972 4738 6.233434 AGGATTTGATATACACGATGCATGT 58.767 36.000 2.46 0.00 0.00 3.21
2989 4755 9.490379 AGCCGTACTTAATAATAGAAGGATTTG 57.510 33.333 0.00 0.00 0.00 2.32
2990 4756 9.490379 CAGCCGTACTTAATAATAGAAGGATTT 57.510 33.333 0.00 0.00 0.00 2.17
2991 4757 8.095169 CCAGCCGTACTTAATAATAGAAGGATT 58.905 37.037 0.00 0.00 0.00 3.01
2992 4758 7.234988 ACCAGCCGTACTTAATAATAGAAGGAT 59.765 37.037 0.00 0.00 0.00 3.24
2993 4759 6.552350 ACCAGCCGTACTTAATAATAGAAGGA 59.448 38.462 0.00 0.00 0.00 3.36
2994 4760 6.756221 ACCAGCCGTACTTAATAATAGAAGG 58.244 40.000 0.00 0.00 0.00 3.46
2995 4761 7.811713 GGTACCAGCCGTACTTAATAATAGAAG 59.188 40.741 7.15 0.00 45.76 2.85
2996 4762 7.287466 TGGTACCAGCCGTACTTAATAATAGAA 59.713 37.037 11.60 0.00 45.76 2.10
2997 4763 6.777091 TGGTACCAGCCGTACTTAATAATAGA 59.223 38.462 11.60 0.00 45.76 1.98
2998 4764 6.985117 TGGTACCAGCCGTACTTAATAATAG 58.015 40.000 11.60 0.00 45.76 1.73
2999 4765 6.975196 TGGTACCAGCCGTACTTAATAATA 57.025 37.500 11.60 0.00 45.76 0.98
3000 4766 5.874897 TGGTACCAGCCGTACTTAATAAT 57.125 39.130 11.60 0.00 45.76 1.28
3001 4767 5.874897 ATGGTACCAGCCGTACTTAATAA 57.125 39.130 21.41 0.00 45.76 1.40
3002 4768 5.874897 AATGGTACCAGCCGTACTTAATA 57.125 39.130 21.41 0.00 45.76 0.98
3003 4769 4.765813 AATGGTACCAGCCGTACTTAAT 57.234 40.909 21.41 0.00 45.76 1.40
3004 4770 4.506758 GAAATGGTACCAGCCGTACTTAA 58.493 43.478 21.41 0.00 45.76 1.85
3005 4771 3.429272 CGAAATGGTACCAGCCGTACTTA 60.429 47.826 21.41 0.00 45.76 2.24
3006 4772 2.675889 CGAAATGGTACCAGCCGTACTT 60.676 50.000 21.41 4.71 45.76 2.24
3007 4773 1.134907 CGAAATGGTACCAGCCGTACT 60.135 52.381 21.41 0.00 45.76 2.73
3008 4774 1.135024 TCGAAATGGTACCAGCCGTAC 60.135 52.381 21.41 7.37 45.76 3.67
3009 4775 1.184431 TCGAAATGGTACCAGCCGTA 58.816 50.000 21.41 10.09 0.00 4.02
3010 4776 0.539986 ATCGAAATGGTACCAGCCGT 59.460 50.000 21.41 4.91 0.00 5.68
3011 4777 0.937304 CATCGAAATGGTACCAGCCG 59.063 55.000 21.41 20.94 0.00 5.52
3012 4778 1.670811 CACATCGAAATGGTACCAGCC 59.329 52.381 21.41 10.46 37.19 4.85
3013 4779 2.356135 ACACATCGAAATGGTACCAGC 58.644 47.619 21.41 11.08 37.19 4.85
3014 4780 4.454161 TGAAACACATCGAAATGGTACCAG 59.546 41.667 21.41 6.64 37.19 4.00
3015 4781 4.390264 TGAAACACATCGAAATGGTACCA 58.610 39.130 18.99 18.99 37.19 3.25
3016 4782 5.365403 TTGAAACACATCGAAATGGTACC 57.635 39.130 4.43 4.43 37.19 3.34
3017 4783 7.867445 AAATTGAAACACATCGAAATGGTAC 57.133 32.000 0.00 0.00 37.19 3.34
3018 4784 8.879342 AAAAATTGAAACACATCGAAATGGTA 57.121 26.923 0.00 0.00 37.19 3.25
3019 4785 7.784633 AAAAATTGAAACACATCGAAATGGT 57.215 28.000 0.00 0.00 37.19 3.55
3193 4959 5.969423 AGTGATCTTGCAATTTGGGTATTG 58.031 37.500 0.00 0.00 38.31 1.90
3202 4968 5.549742 TTTTCCCAAGTGATCTTGCAATT 57.450 34.783 0.00 0.00 46.74 2.32
3312 5078 4.442706 CATAAACTCTACATGAACCGCCT 58.557 43.478 0.00 0.00 0.00 5.52
3366 5132 3.202906 AGTCTAGCATCTCGTCTCAGAC 58.797 50.000 0.00 0.00 32.90 3.51
3449 5215 5.893255 CCATAGGAATGATTCTTTTGGTGGA 59.107 40.000 15.34 0.00 34.62 4.02
3450 5216 5.069516 CCCATAGGAATGATTCTTTTGGTGG 59.930 44.000 19.72 12.05 36.56 4.61
3451 5217 5.069516 CCCCATAGGAATGATTCTTTTGGTG 59.930 44.000 19.72 9.47 36.56 4.17
3476 5242 2.780010 AGATGATCGGGAATTTCCTGGT 59.220 45.455 21.54 16.39 43.23 4.00
3492 5258 8.690203 TGGTTTTGTGAAGAAGAATAAGATGA 57.310 30.769 0.00 0.00 0.00 2.92
3587 5353 0.941542 GCAAAGACGTGGTACTTGCA 59.058 50.000 0.00 0.00 0.00 4.08
3589 5355 4.451096 AGTTATGCAAAGACGTGGTACTTG 59.549 41.667 0.00 0.00 0.00 3.16
3643 5409 3.847184 TGGTCCATTACACACCTTATGGA 59.153 43.478 0.81 0.00 43.11 3.41
3655 5421 7.767261 TGCTGTTTTATGTTATGGTCCATTAC 58.233 34.615 10.33 11.95 0.00 1.89
3656 5422 7.946381 TGCTGTTTTATGTTATGGTCCATTA 57.054 32.000 10.33 0.00 0.00 1.90
3695 5461 6.383147 TCCCCTGTTGTCTAAGAGGTTATAAG 59.617 42.308 0.00 0.00 43.91 1.73
3701 5467 2.258109 GTCCCCTGTTGTCTAAGAGGT 58.742 52.381 0.00 0.00 43.91 3.85
3703 5469 2.257207 TGGTCCCCTGTTGTCTAAGAG 58.743 52.381 0.00 0.00 0.00 2.85
3704 5470 2.409064 TGGTCCCCTGTTGTCTAAGA 57.591 50.000 0.00 0.00 0.00 2.10
3705 5471 3.009033 TGATTGGTCCCCTGTTGTCTAAG 59.991 47.826 0.00 0.00 0.00 2.18
3706 5472 2.983192 TGATTGGTCCCCTGTTGTCTAA 59.017 45.455 0.00 0.00 0.00 2.10
3861 5627 5.182001 GCACTAACAGGTTCATCTTGATGTT 59.818 40.000 10.01 0.00 35.28 2.71
3862 5628 4.697352 GCACTAACAGGTTCATCTTGATGT 59.303 41.667 10.01 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.