Multiple sequence alignment - TraesCS7B01G080800

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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 TraesCS7B01G080800 chr7B 100.000 2688 0 0 1 2688 91207030 91209717 0.000000e+00 4964
1 TraesCS7B01G080800 chr7B 93.220 236 14 2 2047 2282 693406685 693406918 1.980000e-91 346
2 TraesCS7B01G080800 chr7D 94.833 658 24 7 1398 2046 129795973 129796629 0.000000e+00 1018
3 TraesCS7B01G080800 chr7D 86.364 792 48 26 460 1198 129794988 129795772 0.000000e+00 809
4 TraesCS7B01G080800 chr7D 87.069 348 34 7 2045 2387 597565820 597565479 1.510000e-102 383
5 TraesCS7B01G080800 chr7A 82.045 1242 117 57 1 1170 128910238 128911445 0.000000e+00 961
6 TraesCS7B01G080800 chr7A 88.802 643 64 8 2047 2688 112282803 112283438 0.000000e+00 782
7 TraesCS7B01G080800 chr7A 86.983 653 52 16 2047 2688 20694154 20694784 0.000000e+00 704
8 TraesCS7B01G080800 chr7A 88.764 534 20 16 1400 1933 128912020 128912513 3.800000e-173 617
9 TraesCS7B01G080800 chr5A 90.062 644 55 7 2047 2688 33128129 33128765 0.000000e+00 826
10 TraesCS7B01G080800 chr5A 89.752 644 60 5 2047 2688 47663392 47664031 0.000000e+00 819
11 TraesCS7B01G080800 chr5B 93.143 525 36 0 2047 2571 479722578 479722054 0.000000e+00 771
12 TraesCS7B01G080800 chr4A 86.335 644 51 9 2047 2688 12602190 12601582 0.000000e+00 667
13 TraesCS7B01G080800 chr4A 91.093 247 22 0 2047 2293 615193349 615193103 4.290000e-88 335
14 TraesCS7B01G080800 chr2D 89.524 525 34 11 2047 2571 467064556 467064053 0.000000e+00 645
15 TraesCS7B01G080800 chr2D 93.644 236 15 0 2047 2282 317597936 317597701 1.180000e-93 353
16 TraesCS7B01G080800 chr3D 94.286 140 8 0 2326 2465 89054032 89053893 5.830000e-52 215
17 TraesCS7B01G080800 chr3B 91.241 137 12 0 2326 2462 814580759 814580895 1.270000e-43 187


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 TraesCS7B01G080800 chr7B 91207030 91209717 2687 False 4964.0 4964 100.0000 1 2688 1 chr7B.!!$F1 2687
1 TraesCS7B01G080800 chr7D 129794988 129796629 1641 False 913.5 1018 90.5985 460 2046 2 chr7D.!!$F1 1586
2 TraesCS7B01G080800 chr7A 128910238 128912513 2275 False 789.0 961 85.4045 1 1933 2 chr7A.!!$F3 1932
3 TraesCS7B01G080800 chr7A 112282803 112283438 635 False 782.0 782 88.8020 2047 2688 1 chr7A.!!$F2 641
4 TraesCS7B01G080800 chr7A 20694154 20694784 630 False 704.0 704 86.9830 2047 2688 1 chr7A.!!$F1 641
5 TraesCS7B01G080800 chr5A 33128129 33128765 636 False 826.0 826 90.0620 2047 2688 1 chr5A.!!$F1 641
6 TraesCS7B01G080800 chr5A 47663392 47664031 639 False 819.0 819 89.7520 2047 2688 1 chr5A.!!$F2 641
7 TraesCS7B01G080800 chr5B 479722054 479722578 524 True 771.0 771 93.1430 2047 2571 1 chr5B.!!$R1 524
8 TraesCS7B01G080800 chr4A 12601582 12602190 608 True 667.0 667 86.3350 2047 2688 1 chr4A.!!$R1 641
9 TraesCS7B01G080800 chr2D 467064053 467064556 503 True 645.0 645 89.5240 2047 2571 1 chr2D.!!$R2 524

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
372 387 0.031010 CCCTAACCCTGGCCTCTACT 60.031 60.0 3.32 0.0 0.00 2.57 F
440 460 0.035739 GGGACACCTCCGTAGCAAAA 59.964 55.0 0.00 0.0 37.46 2.44 F
1160 1271 0.037232 CCCTTCTTCCAGGACGACAC 60.037 60.0 0.00 0.0 35.71 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1307 1421 0.038251 TGTCAGTTAGTGCGCCTGAG 60.038 55.000 12.71 0.00 35.99 3.35 R
1309 1423 1.069906 GTTTGTCAGTTAGTGCGCCTG 60.070 52.381 4.18 4.34 0.00 4.85 R
2066 2566 1.271934 CAAACGATGCCCCAAATGTGA 59.728 47.619 0.00 0.00 0.00 3.58 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
44 45 3.430862 GCGCCATCTTGACCGCAA 61.431 61.111 0.00 0.00 45.21 4.85
51 52 1.943046 CATCTTGACCGCAAGCTGACT 60.943 52.381 4.04 0.00 46.16 3.41
56 57 1.067565 TGACCGCAAGCTGACTCTTAG 60.068 52.381 0.00 0.00 0.00 2.18
57 58 0.969894 ACCGCAAGCTGACTCTTAGT 59.030 50.000 0.00 0.00 0.00 2.24
58 59 1.067495 ACCGCAAGCTGACTCTTAGTC 60.067 52.381 0.01 0.01 45.26 2.59
59 60 1.634702 CGCAAGCTGACTCTTAGTCC 58.365 55.000 4.69 0.00 44.44 3.85
60 61 1.203523 CGCAAGCTGACTCTTAGTCCT 59.796 52.381 4.69 0.00 44.44 3.85
61 62 2.353208 CGCAAGCTGACTCTTAGTCCTT 60.353 50.000 4.69 0.00 44.44 3.36
62 63 3.119459 CGCAAGCTGACTCTTAGTCCTTA 60.119 47.826 4.69 0.00 44.44 2.69
63 64 4.177783 GCAAGCTGACTCTTAGTCCTTAC 58.822 47.826 4.69 0.00 44.44 2.34
64 65 4.416620 CAAGCTGACTCTTAGTCCTTACG 58.583 47.826 4.69 0.00 44.44 3.18
65 66 3.688235 AGCTGACTCTTAGTCCTTACGT 58.312 45.455 4.69 0.00 44.44 3.57
66 67 3.440872 AGCTGACTCTTAGTCCTTACGTG 59.559 47.826 0.00 0.00 44.44 4.49
67 68 3.760537 CTGACTCTTAGTCCTTACGTGC 58.239 50.000 0.00 0.00 44.44 5.34
74 75 0.317479 AGTCCTTACGTGCAGTGGTC 59.683 55.000 0.00 0.00 0.00 4.02
81 82 2.243957 CGTGCAGTGGTCGCAAAGA 61.244 57.895 0.00 0.00 41.97 2.52
84 85 0.880278 TGCAGTGGTCGCAAAGAGAC 60.880 55.000 0.00 0.00 36.17 3.36
146 147 2.585876 AAAAACACCCCGCAACACT 58.414 47.368 0.00 0.00 0.00 3.55
148 149 1.720694 AAAACACCCCGCAACACTCG 61.721 55.000 0.00 0.00 0.00 4.18
157 172 2.352030 CCCGCAACACTCGAGTTAGTTA 60.352 50.000 17.26 0.00 0.00 2.24
161 176 5.107220 CCGCAACACTCGAGTTAGTTAATTT 60.107 40.000 17.26 0.00 0.00 1.82
162 177 5.783654 CGCAACACTCGAGTTAGTTAATTTG 59.216 40.000 17.26 7.71 0.00 2.32
164 179 6.655062 CAACACTCGAGTTAGTTAATTTGCA 58.345 36.000 17.26 0.00 0.00 4.08
183 198 2.319136 AACCACACGTTGAGCACTTA 57.681 45.000 0.00 0.00 31.79 2.24
189 204 1.714460 CACGTTGAGCACTTACTCGAC 59.286 52.381 2.42 2.42 44.48 4.20
192 207 0.312729 TTGAGCACTTACTCGACGCA 59.687 50.000 0.00 0.00 39.68 5.24
193 208 0.109735 TGAGCACTTACTCGACGCAG 60.110 55.000 0.00 0.00 39.68 5.18
230 245 2.385013 TCATGAAGCACGCATGTACT 57.615 45.000 11.53 0.00 42.77 2.73
231 246 3.518634 TCATGAAGCACGCATGTACTA 57.481 42.857 11.53 0.00 42.77 1.82
233 248 3.865164 TCATGAAGCACGCATGTACTAAG 59.135 43.478 11.53 0.00 42.77 2.18
234 249 1.999735 TGAAGCACGCATGTACTAAGC 59.000 47.619 0.00 0.00 0.00 3.09
235 250 1.999735 GAAGCACGCATGTACTAAGCA 59.000 47.619 0.00 0.00 0.00 3.91
236 251 1.359848 AGCACGCATGTACTAAGCAC 58.640 50.000 0.00 0.00 0.00 4.40
237 252 1.066858 AGCACGCATGTACTAAGCACT 60.067 47.619 0.00 0.00 0.00 4.40
238 253 2.165641 AGCACGCATGTACTAAGCACTA 59.834 45.455 0.00 0.00 0.00 2.74
242 257 5.520632 CACGCATGTACTAAGCACTATAGT 58.479 41.667 0.00 0.00 37.39 2.12
245 260 5.795939 CGCATGTACTAAGCACTATAGTAGC 59.204 44.000 4.74 11.50 36.73 3.58
246 261 6.094061 GCATGTACTAAGCACTATAGTAGCC 58.906 44.000 18.00 6.51 36.73 3.93
247 262 6.294564 GCATGTACTAAGCACTATAGTAGCCA 60.295 42.308 18.00 11.24 36.73 4.75
248 263 6.879276 TGTACTAAGCACTATAGTAGCCAG 57.121 41.667 18.00 17.10 36.73 4.85
249 264 5.768662 TGTACTAAGCACTATAGTAGCCAGG 59.231 44.000 18.00 12.59 36.73 4.45
250 265 4.805744 ACTAAGCACTATAGTAGCCAGGT 58.194 43.478 18.00 13.02 31.96 4.00
251 266 4.585162 ACTAAGCACTATAGTAGCCAGGTG 59.415 45.833 18.00 10.29 31.96 4.00
252 267 3.033659 AGCACTATAGTAGCCAGGTGT 57.966 47.619 18.00 2.78 0.00 4.16
253 268 4.180377 AGCACTATAGTAGCCAGGTGTA 57.820 45.455 18.00 0.00 0.00 2.90
254 269 3.890147 AGCACTATAGTAGCCAGGTGTAC 59.110 47.826 18.00 0.00 0.00 2.90
259 274 6.771749 CACTATAGTAGCCAGGTGTACTTAGT 59.228 42.308 4.74 11.49 31.79 2.24
261 276 2.496470 AGTAGCCAGGTGTACTTAGTGC 59.504 50.000 0.00 0.00 0.00 4.40
262 277 0.613777 AGCCAGGTGTACTTAGTGCC 59.386 55.000 0.00 0.00 0.00 5.01
264 279 1.065418 GCCAGGTGTACTTAGTGCCAT 60.065 52.381 0.00 0.00 0.00 4.40
265 280 2.169769 GCCAGGTGTACTTAGTGCCATA 59.830 50.000 0.00 0.00 0.00 2.74
267 282 3.451178 CCAGGTGTACTTAGTGCCATAGT 59.549 47.826 0.00 0.00 0.00 2.12
268 283 4.647853 CCAGGTGTACTTAGTGCCATAGTA 59.352 45.833 0.00 0.00 0.00 1.82
269 284 5.304614 CCAGGTGTACTTAGTGCCATAGTAT 59.695 44.000 0.00 0.00 0.00 2.12
270 285 6.492429 CCAGGTGTACTTAGTGCCATAGTATA 59.508 42.308 0.00 0.00 0.00 1.47
271 286 7.178628 CCAGGTGTACTTAGTGCCATAGTATAT 59.821 40.741 0.00 0.00 0.00 0.86
272 287 8.244802 CAGGTGTACTTAGTGCCATAGTATATC 58.755 40.741 0.00 0.00 0.00 1.63
273 288 8.171400 AGGTGTACTTAGTGCCATAGTATATCT 58.829 37.037 0.00 0.00 0.00 1.98
274 289 9.458727 GGTGTACTTAGTGCCATAGTATATCTA 57.541 37.037 0.00 0.00 0.00 1.98
291 306 9.751542 AGTATATCTACTAATGTGCTGTCAAAC 57.248 33.333 0.00 0.00 36.40 2.93
294 309 6.785488 TCTACTAATGTGCTGTCAAACAAG 57.215 37.500 0.00 0.00 0.00 3.16
297 312 3.738830 AATGTGCTGTCAAACAAGCAT 57.261 38.095 0.11 0.00 35.73 3.79
298 313 2.495409 TGTGCTGTCAAACAAGCATG 57.505 45.000 0.11 0.00 35.73 4.06
299 314 1.750206 TGTGCTGTCAAACAAGCATGT 59.250 42.857 0.11 0.00 43.14 3.21
301 316 3.243035 TGTGCTGTCAAACAAGCATGTAC 60.243 43.478 0.00 0.00 39.40 2.90
303 318 2.032030 GCTGTCAAACAAGCATGTACGT 60.032 45.455 0.00 0.00 39.40 3.57
304 319 3.185594 GCTGTCAAACAAGCATGTACGTA 59.814 43.478 0.00 0.00 39.40 3.57
305 320 4.698276 CTGTCAAACAAGCATGTACGTAC 58.302 43.478 18.90 18.90 39.40 3.67
306 321 3.182772 TGTCAAACAAGCATGTACGTACG 59.817 43.478 20.18 15.01 39.40 3.67
307 322 2.732500 TCAAACAAGCATGTACGTACGG 59.267 45.455 21.06 15.57 39.40 4.02
308 323 2.443887 AACAAGCATGTACGTACGGT 57.556 45.000 21.06 10.03 39.40 4.83
309 324 3.574284 AACAAGCATGTACGTACGGTA 57.426 42.857 21.06 6.84 39.40 4.02
330 345 1.533129 CGTAGATCGACCAATCACGCA 60.533 52.381 0.00 0.00 42.86 5.24
334 349 0.802222 ATCGACCAATCACGCACTCG 60.802 55.000 0.00 0.00 42.43 4.18
358 373 1.399744 ATCATCTCGCGCCACCCTAA 61.400 55.000 0.00 0.00 0.00 2.69
360 375 3.090219 ATCTCGCGCCACCCTAACC 62.090 63.158 0.00 0.00 0.00 2.85
361 376 4.832608 CTCGCGCCACCCTAACCC 62.833 72.222 0.00 0.00 0.00 4.11
364 379 4.796495 GCGCCACCCTAACCCTGG 62.796 72.222 0.00 0.00 0.00 4.45
366 381 4.442454 GCCACCCTAACCCTGGCC 62.442 72.222 0.00 0.00 44.15 5.36
367 382 2.614013 CCACCCTAACCCTGGCCT 60.614 66.667 3.32 0.00 0.00 5.19
369 384 1.616628 CACCCTAACCCTGGCCTCT 60.617 63.158 3.32 0.00 0.00 3.69
370 385 0.326238 CACCCTAACCCTGGCCTCTA 60.326 60.000 3.32 0.00 0.00 2.43
371 386 0.326332 ACCCTAACCCTGGCCTCTAC 60.326 60.000 3.32 0.00 0.00 2.59
372 387 0.031010 CCCTAACCCTGGCCTCTACT 60.031 60.000 3.32 0.00 0.00 2.57
373 388 1.123928 CCTAACCCTGGCCTCTACTG 58.876 60.000 3.32 0.00 0.00 2.74
374 389 0.466124 CTAACCCTGGCCTCTACTGC 59.534 60.000 3.32 0.00 0.00 4.40
376 391 1.557269 AACCCTGGCCTCTACTGCAG 61.557 60.000 13.48 13.48 0.00 4.41
377 392 1.992277 CCCTGGCCTCTACTGCAGT 60.992 63.158 25.12 25.12 0.00 4.40
385 400 2.805099 GCCTCTACTGCAGTAATCATGC 59.195 50.000 25.95 19.04 44.11 4.06
389 404 2.512692 ACTGCAGTAATCATGCCCAA 57.487 45.000 20.16 0.00 43.18 4.12
390 405 2.094675 ACTGCAGTAATCATGCCCAAC 58.905 47.619 20.16 0.00 43.18 3.77
411 431 1.525442 CCCCTAATCCACCACCGTC 59.475 63.158 0.00 0.00 0.00 4.79
412 432 0.981277 CCCCTAATCCACCACCGTCT 60.981 60.000 0.00 0.00 0.00 4.18
413 433 0.178068 CCCTAATCCACCACCGTCTG 59.822 60.000 0.00 0.00 0.00 3.51
414 434 0.462047 CCTAATCCACCACCGTCTGC 60.462 60.000 0.00 0.00 0.00 4.26
416 436 0.036765 TAATCCACCACCGTCTGCAC 60.037 55.000 0.00 0.00 0.00 4.57
419 439 2.972505 CACCACCGTCTGCACCAC 60.973 66.667 0.00 0.00 0.00 4.16
420 440 3.475494 ACCACCGTCTGCACCACA 61.475 61.111 0.00 0.00 0.00 4.17
428 448 2.281761 CTGCACCACAGGGACACC 60.282 66.667 0.00 0.00 43.19 4.16
430 450 2.032681 GCACCACAGGGACACCTC 59.967 66.667 0.00 0.00 46.95 3.85
431 451 2.750350 CACCACAGGGACACCTCC 59.250 66.667 0.00 0.00 46.95 4.30
432 452 2.923035 ACCACAGGGACACCTCCG 60.923 66.667 0.00 0.00 46.95 4.63
433 453 2.923035 CCACAGGGACACCTCCGT 60.923 66.667 0.00 0.00 46.95 4.69
434 454 1.608336 CCACAGGGACACCTCCGTA 60.608 63.158 0.00 0.00 46.95 4.02
435 455 1.605058 CCACAGGGACACCTCCGTAG 61.605 65.000 0.00 0.00 46.95 3.51
436 456 1.982938 ACAGGGACACCTCCGTAGC 60.983 63.158 0.00 0.00 46.95 3.58
437 457 1.982395 CAGGGACACCTCCGTAGCA 60.982 63.158 0.00 0.00 46.95 3.49
439 459 0.834687 AGGGACACCTCCGTAGCAAA 60.835 55.000 0.00 0.00 46.95 3.68
440 460 0.035739 GGGACACCTCCGTAGCAAAA 59.964 55.000 0.00 0.00 37.46 2.44
442 462 0.788391 GACACCTCCGTAGCAAAACG 59.212 55.000 0.00 0.00 42.49 3.60
443 463 0.390124 ACACCTCCGTAGCAAAACGA 59.610 50.000 7.71 0.00 45.68 3.85
450 492 2.162208 TCCGTAGCAAAACGACGTAGAT 59.838 45.455 0.00 0.00 44.80 1.98
469 516 5.432680 AGATGTGACCAGAGATGACAATT 57.567 39.130 0.00 0.00 0.00 2.32
486 533 5.183713 TGACAATTCATCATCAAAGTGGACC 59.816 40.000 0.00 0.00 0.00 4.46
508 555 4.045104 CGTGGCTAAGCTAGATGTTACTG 58.955 47.826 0.00 0.00 0.00 2.74
510 557 3.706594 TGGCTAAGCTAGATGTTACTGCT 59.293 43.478 0.00 0.00 35.30 4.24
511 558 4.054671 GGCTAAGCTAGATGTTACTGCTG 58.945 47.826 0.00 0.00 33.96 4.41
526 579 2.425592 CTGAGTTCCACACGGCCA 59.574 61.111 2.24 0.00 0.00 5.36
527 580 1.669115 CTGAGTTCCACACGGCCAG 60.669 63.158 2.24 0.00 0.00 4.85
660 713 2.123988 TAAGTGCAACGCCCGCTTTG 62.124 55.000 1.79 1.79 45.86 2.77
670 728 1.375396 CCCGCTTTGATCGTGTGGA 60.375 57.895 11.86 0.00 33.56 4.02
676 734 2.766313 CTTTGATCGTGTGGACCAGAA 58.234 47.619 0.00 0.00 0.00 3.02
679 737 2.489971 TGATCGTGTGGACCAGAAAAC 58.510 47.619 0.00 0.00 0.00 2.43
720 786 3.252215 CGCATCCAGTTTTTCACAGGTTA 59.748 43.478 0.00 0.00 33.60 2.85
735 801 2.947652 CAGGTTATGTCAAGCTGATGGG 59.052 50.000 9.94 0.00 45.67 4.00
752 818 3.003763 GACTTCTCGGCCCCTGGT 61.004 66.667 0.00 0.00 0.00 4.00
766 832 3.223661 CTGGTGCAGGAGTCAACTC 57.776 57.895 1.37 1.37 42.14 3.01
874 940 5.785940 GTCACTCCTCCCTATTTATACCCAT 59.214 44.000 0.00 0.00 0.00 4.00
882 948 3.701040 CCTATTTATACCCATGCCATGCC 59.299 47.826 0.00 0.00 0.00 4.40
883 949 2.763736 TTTATACCCATGCCATGCCA 57.236 45.000 0.00 0.00 0.00 4.92
884 950 2.997070 TTATACCCATGCCATGCCAT 57.003 45.000 0.00 0.00 0.00 4.40
885 951 2.219080 TATACCCATGCCATGCCATG 57.781 50.000 9.68 9.68 41.71 3.66
886 952 1.189524 ATACCCATGCCATGCCATGC 61.190 55.000 11.13 0.00 40.92 4.06
887 953 3.936203 CCCATGCCATGCCATGCC 61.936 66.667 11.13 0.00 40.92 4.40
888 954 3.157949 CCATGCCATGCCATGCCA 61.158 61.111 11.13 0.00 40.92 4.92
889 955 2.515979 CCATGCCATGCCATGCCAT 61.516 57.895 11.13 0.00 40.92 4.40
890 956 1.301637 CATGCCATGCCATGCCATG 60.302 57.895 13.50 13.50 41.71 3.66
891 957 1.764454 ATGCCATGCCATGCCATGT 60.764 52.632 14.98 0.00 40.72 3.21
981 1080 2.047274 GCAGGTGCGGTGCTCTAA 60.047 61.111 0.00 0.00 37.96 2.10
1014 1113 1.002274 AGAGATGGAGGCGAGGGTT 59.998 57.895 0.00 0.00 0.00 4.11
1160 1271 0.037232 CCCTTCTTCCAGGACGACAC 60.037 60.000 0.00 0.00 35.71 3.67
1164 1275 0.471211 TCTTCCAGGACGACACCCTT 60.471 55.000 0.00 0.00 0.00 3.95
1171 1282 0.037605 GGACGACACCCTTGGTACAG 60.038 60.000 0.00 0.00 42.39 2.74
1173 1284 0.677842 ACGACACCCTTGGTACAGAC 59.322 55.000 0.00 0.00 42.39 3.51
1174 1285 0.677288 CGACACCCTTGGTACAGACA 59.323 55.000 0.00 0.00 42.39 3.41
1175 1286 1.604693 CGACACCCTTGGTACAGACAC 60.605 57.143 0.00 0.00 42.39 3.67
1177 1288 1.841277 ACACCCTTGGTACAGACACAA 59.159 47.619 0.00 0.00 42.39 3.33
1178 1289 2.441750 ACACCCTTGGTACAGACACAAT 59.558 45.455 0.00 0.00 42.39 2.71
1188 1301 6.920817 TGGTACAGACACAATTACTACTCTG 58.079 40.000 0.00 0.00 32.94 3.35
1198 1311 2.306341 TACTACTCTGCTCGCGTACT 57.694 50.000 5.77 0.00 0.00 2.73
1200 1313 1.130749 ACTACTCTGCTCGCGTACTTG 59.869 52.381 5.77 0.00 0.00 3.16
1201 1314 0.179171 TACTCTGCTCGCGTACTTGC 60.179 55.000 5.77 4.97 0.00 4.01
1202 1315 1.153939 CTCTGCTCGCGTACTTGCT 60.154 57.895 5.77 0.00 0.00 3.91
1203 1316 0.734253 CTCTGCTCGCGTACTTGCTT 60.734 55.000 5.77 0.00 0.00 3.91
1206 1319 0.511221 TGCTCGCGTACTTGCTTTTC 59.489 50.000 5.77 0.00 0.00 2.29
1207 1320 0.790814 GCTCGCGTACTTGCTTTTCT 59.209 50.000 5.77 0.00 0.00 2.52
1208 1321 1.201823 GCTCGCGTACTTGCTTTTCTC 60.202 52.381 5.77 0.00 0.00 2.87
1209 1322 2.329379 CTCGCGTACTTGCTTTTCTCT 58.671 47.619 5.77 0.00 0.00 3.10
1210 1323 2.058798 TCGCGTACTTGCTTTTCTCTG 58.941 47.619 5.77 0.00 0.00 3.35
1211 1324 2.058798 CGCGTACTTGCTTTTCTCTGA 58.941 47.619 0.00 0.00 0.00 3.27
1212 1325 2.668457 CGCGTACTTGCTTTTCTCTGAT 59.332 45.455 0.00 0.00 0.00 2.90
1213 1326 3.482598 CGCGTACTTGCTTTTCTCTGATG 60.483 47.826 0.00 0.00 0.00 3.07
1214 1327 3.679980 GCGTACTTGCTTTTCTCTGATGA 59.320 43.478 0.00 0.00 0.00 2.92
1218 1331 6.312426 CGTACTTGCTTTTCTCTGATGATCTT 59.688 38.462 0.00 0.00 0.00 2.40
1219 1332 7.489435 CGTACTTGCTTTTCTCTGATGATCTTA 59.511 37.037 0.00 0.00 0.00 2.10
1239 1352 5.189145 TCTTAGTTCAGTATTGGTTCCCTCC 59.811 44.000 0.00 0.00 0.00 4.30
1240 1353 2.576648 AGTTCAGTATTGGTTCCCTCCC 59.423 50.000 0.00 0.00 0.00 4.30
1241 1354 2.576648 GTTCAGTATTGGTTCCCTCCCT 59.423 50.000 0.00 0.00 0.00 4.20
1242 1355 2.478292 TCAGTATTGGTTCCCTCCCTC 58.522 52.381 0.00 0.00 0.00 4.30
1244 1357 2.171448 CAGTATTGGTTCCCTCCCTCTG 59.829 54.545 0.00 0.00 0.00 3.35
1246 1359 1.290134 ATTGGTTCCCTCCCTCTGTC 58.710 55.000 0.00 0.00 0.00 3.51
1247 1360 0.104672 TTGGTTCCCTCCCTCTGTCA 60.105 55.000 0.00 0.00 0.00 3.58
1278 1391 6.524101 AATGTGTTTTTCTACACTTGTGGT 57.476 33.333 5.72 0.00 46.67 4.16
1284 1398 7.597369 GTGTTTTTCTACACTTGTGGTCTTTTT 59.403 33.333 5.72 0.00 43.92 1.94
1299 1413 6.412943 GTGGTCTTTTTAAACACTTTACGCTC 59.587 38.462 0.00 0.00 0.00 5.03
1300 1414 5.911280 GGTCTTTTTAAACACTTTACGCTCC 59.089 40.000 0.00 0.00 0.00 4.70
1301 1415 5.911280 GTCTTTTTAAACACTTTACGCTCCC 59.089 40.000 0.00 0.00 0.00 4.30
1302 1416 5.824097 TCTTTTTAAACACTTTACGCTCCCT 59.176 36.000 0.00 0.00 0.00 4.20
1304 1418 4.612264 TTAAACACTTTACGCTCCCTCT 57.388 40.909 0.00 0.00 0.00 3.69
1305 1419 5.726980 TTAAACACTTTACGCTCCCTCTA 57.273 39.130 0.00 0.00 0.00 2.43
1307 1421 3.589495 ACACTTTACGCTCCCTCTAAC 57.411 47.619 0.00 0.00 0.00 2.34
1309 1423 3.193056 ACACTTTACGCTCCCTCTAACTC 59.807 47.826 0.00 0.00 0.00 3.01
1310 1424 3.192844 CACTTTACGCTCCCTCTAACTCA 59.807 47.826 0.00 0.00 0.00 3.41
1312 1426 2.054232 TACGCTCCCTCTAACTCAGG 57.946 55.000 0.00 0.00 0.00 3.86
1313 1427 1.324005 ACGCTCCCTCTAACTCAGGC 61.324 60.000 0.00 0.00 0.00 4.85
1314 1428 1.439644 GCTCCCTCTAACTCAGGCG 59.560 63.158 0.00 0.00 0.00 5.52
1315 1429 1.439644 CTCCCTCTAACTCAGGCGC 59.560 63.158 0.00 0.00 0.00 6.53
1316 1430 1.304962 TCCCTCTAACTCAGGCGCA 60.305 57.895 10.83 0.00 0.00 6.09
1317 1431 1.153549 CCCTCTAACTCAGGCGCAC 60.154 63.158 10.83 0.00 0.00 5.34
1318 1432 1.608717 CCCTCTAACTCAGGCGCACT 61.609 60.000 10.83 0.02 0.00 4.40
1319 1433 1.103803 CCTCTAACTCAGGCGCACTA 58.896 55.000 10.83 0.00 0.00 2.74
1323 1437 2.094700 TCTAACTCAGGCGCACTAACTG 60.095 50.000 10.83 7.04 0.00 3.16
1326 1440 0.038251 CTCAGGCGCACTAACTGACA 60.038 55.000 10.83 0.00 36.41 3.58
1331 1445 2.036733 AGGCGCACTAACTGACAAACTA 59.963 45.455 10.83 0.00 0.00 2.24
1332 1446 3.000727 GGCGCACTAACTGACAAACTAT 58.999 45.455 10.83 0.00 0.00 2.12
1336 1450 6.183360 GGCGCACTAACTGACAAACTATAAAT 60.183 38.462 10.83 0.00 0.00 1.40
1339 1453 9.901724 CGCACTAACTGACAAACTATAAATAAG 57.098 33.333 0.00 0.00 0.00 1.73
1363 1481 3.923017 AAACTAACTGCAACATCAGGC 57.077 42.857 0.00 0.00 38.36 4.85
1368 1486 4.697352 ACTAACTGCAACATCAGGCTTTAG 59.303 41.667 0.00 0.00 38.36 1.85
1375 1493 4.919754 GCAACATCAGGCTTTAGAAAACAG 59.080 41.667 0.00 0.00 0.00 3.16
1395 1520 4.100529 CAGCAAAGTTGTTCACTGAACTG 58.899 43.478 20.18 12.00 42.39 3.16
1401 1893 1.953559 TGTTCACTGAACTGGAGTGC 58.046 50.000 20.18 0.00 42.39 4.40
1418 1910 2.998279 GCTTGGATGCTGGGTGTGC 61.998 63.158 0.00 0.00 0.00 4.57
1419 1911 1.604308 CTTGGATGCTGGGTGTGCA 60.604 57.895 0.00 0.00 44.95 4.57
1788 2284 5.625656 CGCCTTCTTCTTCCTATTCTGTCTT 60.626 44.000 0.00 0.00 0.00 3.01
1789 2285 5.584251 GCCTTCTTCTTCCTATTCTGTCTTG 59.416 44.000 0.00 0.00 0.00 3.02
1809 2305 8.243426 TGTCTTGAATCATTTGTTATACTTGCC 58.757 33.333 0.00 0.00 0.00 4.52
1940 2439 1.705154 CGCGCGTGTGTTGCTATAA 59.295 52.632 24.19 0.00 0.00 0.98
1948 2447 5.395195 CGCGTGTGTTGCTATAAATTAATGG 59.605 40.000 0.00 0.00 0.00 3.16
1950 2449 6.632834 GCGTGTGTTGCTATAAATTAATGGAG 59.367 38.462 0.00 0.00 0.00 3.86
2036 2536 2.578480 CCCTAAAAAGGCCCTCTCTTCT 59.422 50.000 0.00 0.00 0.00 2.85
2130 2633 2.370281 TTTTGCAAAACTCACCGCAA 57.630 40.000 20.46 0.00 42.29 4.85
2182 2685 3.967332 AAGGTGATTTGGCTCATTTGG 57.033 42.857 0.00 0.00 0.00 3.28
2190 2693 4.751767 TTTGGCTCATTTGGTCACTTTT 57.248 36.364 0.00 0.00 0.00 2.27
2225 2728 4.187694 CCAGATTGTAAGGAGCTGACTTC 58.812 47.826 0.00 0.00 0.00 3.01
2319 2840 2.031012 CTTGGTGCTCGCTGTCCA 59.969 61.111 0.00 0.00 0.00 4.02
2320 2841 1.376424 CTTGGTGCTCGCTGTCCAT 60.376 57.895 0.00 0.00 0.00 3.41
2353 2874 2.419198 GACCTCATCGGCGCAGAT 59.581 61.111 17.67 17.67 35.61 2.90
2366 2887 2.986306 GCAGATGGCCACACAGTGC 61.986 63.158 8.16 9.36 36.11 4.40
2399 2920 2.034376 AGAGCTCCTCGACGGTGT 59.966 61.111 10.93 0.00 35.36 4.16
2596 3122 2.537560 GCTTGTGCTCGTGCTGTGT 61.538 57.895 11.19 0.00 40.48 3.72
2679 3207 2.754867 CGGCTAGGGAAAGAGAGAGGAT 60.755 54.545 0.00 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 3.252484 GAATTCGTCGCCGACCGG 61.252 66.667 12.26 0.00 44.13 5.28
44 45 3.440872 CACGTAAGGACTAAGAGTCAGCT 59.559 47.826 8.77 0.00 46.79 4.24
51 52 2.230508 CCACTGCACGTAAGGACTAAGA 59.769 50.000 0.00 0.00 46.39 2.10
56 57 1.007336 CGACCACTGCACGTAAGGAC 61.007 60.000 0.00 0.00 46.39 3.85
57 58 1.287815 CGACCACTGCACGTAAGGA 59.712 57.895 0.00 0.00 46.39 3.36
58 59 2.380410 GCGACCACTGCACGTAAGG 61.380 63.158 0.00 0.00 46.39 2.69
59 60 1.218875 TTGCGACCACTGCACGTAAG 61.219 55.000 0.00 0.00 43.10 2.34
60 61 0.810426 TTTGCGACCACTGCACGTAA 60.810 50.000 0.00 0.00 43.10 3.18
61 62 1.218875 CTTTGCGACCACTGCACGTA 61.219 55.000 0.00 0.00 43.10 3.57
62 63 2.512745 TTTGCGACCACTGCACGT 60.513 55.556 0.00 0.00 43.10 4.49
63 64 2.162921 CTCTTTGCGACCACTGCACG 62.163 60.000 0.00 0.00 43.10 5.34
64 65 0.880278 TCTCTTTGCGACCACTGCAC 60.880 55.000 0.00 0.00 43.10 4.57
65 66 0.880278 GTCTCTTTGCGACCACTGCA 60.880 55.000 0.00 0.00 41.38 4.41
66 67 1.862806 GTCTCTTTGCGACCACTGC 59.137 57.895 0.00 0.00 0.00 4.40
74 75 1.219522 AAACGACGGGTCTCTTTGCG 61.220 55.000 0.00 0.00 0.00 4.85
128 129 0.458260 GAGTGTTGCGGGGTGTTTTT 59.542 50.000 0.00 0.00 0.00 1.94
130 131 2.184167 CGAGTGTTGCGGGGTGTTT 61.184 57.895 0.00 0.00 0.00 2.83
132 133 3.515316 CTCGAGTGTTGCGGGGTGT 62.515 63.158 3.62 0.00 0.00 4.16
133 134 2.738521 CTCGAGTGTTGCGGGGTG 60.739 66.667 3.62 0.00 0.00 4.61
134 135 1.466025 TAACTCGAGTGTTGCGGGGT 61.466 55.000 20.85 1.97 32.46 4.95
135 136 0.736325 CTAACTCGAGTGTTGCGGGG 60.736 60.000 20.85 0.00 32.46 5.73
138 139 5.511088 AATTAACTAACTCGAGTGTTGCG 57.489 39.130 24.10 12.68 0.00 4.85
139 140 5.564127 GCAAATTAACTAACTCGAGTGTTGC 59.436 40.000 24.10 20.14 31.97 4.17
140 141 6.655062 TGCAAATTAACTAACTCGAGTGTTG 58.345 36.000 24.10 17.32 0.00 3.33
141 142 6.854496 TGCAAATTAACTAACTCGAGTGTT 57.146 33.333 20.85 20.87 0.00 3.32
142 143 6.293244 GGTTGCAAATTAACTAACTCGAGTGT 60.293 38.462 20.85 11.02 0.00 3.55
143 144 6.077838 GGTTGCAAATTAACTAACTCGAGTG 58.922 40.000 20.85 10.28 0.00 3.51
145 146 6.077838 GTGGTTGCAAATTAACTAACTCGAG 58.922 40.000 11.84 11.84 0.00 4.04
146 147 5.527951 TGTGGTTGCAAATTAACTAACTCGA 59.472 36.000 0.00 0.00 0.00 4.04
148 149 5.623673 CGTGTGGTTGCAAATTAACTAACTC 59.376 40.000 0.00 0.00 0.00 3.01
164 179 1.937899 GTAAGTGCTCAACGTGTGGTT 59.062 47.619 0.00 0.00 40.22 3.67
183 198 2.256764 CTGAGTGCTGCGTCGAGT 59.743 61.111 0.00 0.00 0.00 4.18
189 204 2.783275 GTCATGCTGAGTGCTGCG 59.217 61.111 0.00 0.00 43.37 5.18
192 207 2.569072 ATCGCGTCATGCTGAGTGCT 62.569 55.000 5.77 0.00 43.27 4.40
193 208 2.087095 GATCGCGTCATGCTGAGTGC 62.087 60.000 5.77 0.00 43.27 4.40
213 228 2.609459 GCTTAGTACATGCGTGCTTCAT 59.391 45.455 5.64 0.00 39.08 2.57
230 245 4.543689 ACACCTGGCTACTATAGTGCTTA 58.456 43.478 15.90 9.20 0.00 3.09
231 246 3.375699 ACACCTGGCTACTATAGTGCTT 58.624 45.455 15.90 0.00 0.00 3.91
233 248 3.890147 AGTACACCTGGCTACTATAGTGC 59.110 47.826 15.90 15.38 0.00 4.40
234 249 6.771749 ACTAAGTACACCTGGCTACTATAGTG 59.228 42.308 15.90 6.78 0.00 2.74
235 250 6.771749 CACTAAGTACACCTGGCTACTATAGT 59.228 42.308 10.87 10.87 0.00 2.12
236 251 6.294065 GCACTAAGTACACCTGGCTACTATAG 60.294 46.154 0.00 0.00 0.00 1.31
237 252 5.533903 GCACTAAGTACACCTGGCTACTATA 59.466 44.000 5.35 1.81 0.00 1.31
238 253 4.341520 GCACTAAGTACACCTGGCTACTAT 59.658 45.833 5.35 0.96 0.00 2.12
242 257 1.829222 GGCACTAAGTACACCTGGCTA 59.171 52.381 0.00 0.00 0.00 3.93
245 260 3.451178 ACTATGGCACTAAGTACACCTGG 59.549 47.826 0.00 0.00 0.00 4.45
246 261 4.737855 ACTATGGCACTAAGTACACCTG 57.262 45.455 0.00 0.00 0.00 4.00
247 262 8.171400 AGATATACTATGGCACTAAGTACACCT 58.829 37.037 7.99 4.11 31.36 4.00
248 263 8.350852 AGATATACTATGGCACTAAGTACACC 57.649 38.462 7.99 2.42 31.36 4.16
259 274 8.470002 CAGCACATTAGTAGATATACTATGGCA 58.530 37.037 8.02 0.00 33.10 4.92
265 280 9.751542 GTTTGACAGCACATTAGTAGATATACT 57.248 33.333 5.20 5.20 0.00 2.12
268 283 9.102757 CTTGTTTGACAGCACATTAGTAGATAT 57.897 33.333 0.00 0.00 0.00 1.63
269 284 7.064609 GCTTGTTTGACAGCACATTAGTAGATA 59.935 37.037 0.00 0.00 0.00 1.98
270 285 6.128172 GCTTGTTTGACAGCACATTAGTAGAT 60.128 38.462 0.00 0.00 0.00 1.98
271 286 5.179368 GCTTGTTTGACAGCACATTAGTAGA 59.821 40.000 0.00 0.00 0.00 2.59
272 287 5.049474 TGCTTGTTTGACAGCACATTAGTAG 60.049 40.000 0.00 0.00 31.03 2.57
273 288 4.819088 TGCTTGTTTGACAGCACATTAGTA 59.181 37.500 0.00 0.00 31.03 1.82
274 289 3.631686 TGCTTGTTTGACAGCACATTAGT 59.368 39.130 0.00 0.00 31.03 2.24
278 293 2.363038 ACATGCTTGTTTGACAGCACAT 59.637 40.909 0.00 0.00 35.96 3.21
280 295 2.497107 ACATGCTTGTTTGACAGCAC 57.503 45.000 0.00 0.00 35.96 4.40
291 306 1.841944 CGTACCGTACGTACATGCTTG 59.158 52.381 24.50 7.69 46.67 4.01
303 318 2.595124 TGGTCGATCTACGTACCGTA 57.405 50.000 0.00 0.00 41.54 4.02
304 319 1.737838 TTGGTCGATCTACGTACCGT 58.262 50.000 0.00 0.00 44.35 4.83
305 320 2.288729 TGATTGGTCGATCTACGTACCG 59.711 50.000 0.00 0.00 41.46 4.02
306 321 3.625938 GTGATTGGTCGATCTACGTACC 58.374 50.000 0.00 0.00 43.13 3.34
307 322 3.286576 CGTGATTGGTCGATCTACGTAC 58.713 50.000 0.00 0.00 43.13 3.67
308 323 2.286595 GCGTGATTGGTCGATCTACGTA 60.287 50.000 13.63 0.00 43.13 3.57
309 324 1.533338 GCGTGATTGGTCGATCTACGT 60.533 52.381 13.63 0.00 43.13 3.57
310 325 1.121240 GCGTGATTGGTCGATCTACG 58.879 55.000 0.00 4.25 44.09 3.51
311 326 1.852895 GTGCGTGATTGGTCGATCTAC 59.147 52.381 0.00 0.00 0.00 2.59
312 327 1.749063 AGTGCGTGATTGGTCGATCTA 59.251 47.619 0.00 0.00 0.00 1.98
313 328 0.532573 AGTGCGTGATTGGTCGATCT 59.467 50.000 0.00 0.00 0.00 2.75
315 330 0.802222 CGAGTGCGTGATTGGTCGAT 60.802 55.000 0.00 0.00 0.00 3.59
316 331 1.443702 CGAGTGCGTGATTGGTCGA 60.444 57.895 0.00 0.00 0.00 4.20
317 332 3.071459 GCGAGTGCGTGATTGGTCG 62.071 63.158 0.00 0.00 40.36 4.79
334 349 0.233332 GTGGCGCGAGATGATTAAGC 59.767 55.000 12.10 0.00 0.00 3.09
358 373 1.992277 CTGCAGTAGAGGCCAGGGT 60.992 63.158 5.01 0.00 0.00 4.34
360 375 1.195115 TTACTGCAGTAGAGGCCAGG 58.805 55.000 24.79 0.00 0.00 4.45
361 376 2.432146 TGATTACTGCAGTAGAGGCCAG 59.568 50.000 24.79 0.00 0.00 4.85
362 377 2.466846 TGATTACTGCAGTAGAGGCCA 58.533 47.619 24.79 16.13 0.00 5.36
363 378 3.397482 CATGATTACTGCAGTAGAGGCC 58.603 50.000 24.79 14.09 0.00 5.19
364 379 2.805099 GCATGATTACTGCAGTAGAGGC 59.195 50.000 24.79 20.70 39.46 4.70
366 381 3.181462 TGGGCATGATTACTGCAGTAGAG 60.181 47.826 24.79 15.18 41.47 2.43
367 382 2.771372 TGGGCATGATTACTGCAGTAGA 59.229 45.455 24.79 16.64 41.47 2.59
369 384 3.278574 GTTGGGCATGATTACTGCAGTA 58.721 45.455 22.67 22.67 41.47 2.74
370 385 2.094675 GTTGGGCATGATTACTGCAGT 58.905 47.619 25.12 25.12 41.47 4.40
371 386 1.064505 CGTTGGGCATGATTACTGCAG 59.935 52.381 13.48 13.48 41.47 4.41
372 387 1.093972 CGTTGGGCATGATTACTGCA 58.906 50.000 0.00 0.00 41.47 4.41
373 388 0.248621 GCGTTGGGCATGATTACTGC 60.249 55.000 0.00 0.00 42.87 4.40
374 389 0.381801 GGCGTTGGGCATGATTACTG 59.618 55.000 0.00 0.00 46.16 2.74
376 391 1.733526 GGGCGTTGGGCATGATTAC 59.266 57.895 0.00 0.00 46.16 1.89
377 392 1.454847 GGGGCGTTGGGCATGATTA 60.455 57.895 0.00 0.00 46.16 1.75
385 400 2.194868 GGATTAGGGGGCGTTGGG 59.805 66.667 0.00 0.00 0.00 4.12
389 404 2.285818 TGGTGGATTAGGGGGCGT 60.286 61.111 0.00 0.00 0.00 5.68
390 405 2.192175 GTGGTGGATTAGGGGGCG 59.808 66.667 0.00 0.00 0.00 6.13
411 431 2.281761 GGTGTCCCTGTGGTGCAG 60.282 66.667 0.00 0.00 44.63 4.41
412 432 2.772191 AGGTGTCCCTGTGGTGCA 60.772 61.111 0.00 0.00 40.58 4.57
413 433 2.032681 GAGGTGTCCCTGTGGTGC 59.967 66.667 0.00 0.00 42.86 5.01
414 434 2.750350 GGAGGTGTCCCTGTGGTG 59.250 66.667 0.00 0.00 42.86 4.17
416 436 1.605058 CTACGGAGGTGTCCCTGTGG 61.605 65.000 0.00 0.00 42.86 4.17
419 439 1.541310 TTGCTACGGAGGTGTCCCTG 61.541 60.000 0.00 0.00 42.86 4.45
420 440 0.834687 TTTGCTACGGAGGTGTCCCT 60.835 55.000 0.00 0.00 46.66 4.20
422 442 1.154197 GTTTTGCTACGGAGGTGTCC 58.846 55.000 0.00 0.00 39.88 4.02
423 443 0.788391 CGTTTTGCTACGGAGGTGTC 59.212 55.000 0.00 0.00 37.86 3.67
425 445 0.788391 GTCGTTTTGCTACGGAGGTG 59.212 55.000 0.00 0.00 41.67 4.00
426 446 0.665369 CGTCGTTTTGCTACGGAGGT 60.665 55.000 0.00 0.00 41.67 3.85
428 448 1.909532 CTACGTCGTTTTGCTACGGAG 59.090 52.381 1.78 0.00 40.14 4.63
429 449 1.535028 TCTACGTCGTTTTGCTACGGA 59.465 47.619 1.78 0.00 40.08 4.69
430 450 1.967762 TCTACGTCGTTTTGCTACGG 58.032 50.000 1.78 0.00 40.08 4.02
431 451 2.912967 ACATCTACGTCGTTTTGCTACG 59.087 45.455 1.78 0.00 41.31 3.51
432 452 3.916172 TCACATCTACGTCGTTTTGCTAC 59.084 43.478 1.78 0.00 0.00 3.58
433 453 3.916172 GTCACATCTACGTCGTTTTGCTA 59.084 43.478 1.78 0.00 0.00 3.49
434 454 2.729882 GTCACATCTACGTCGTTTTGCT 59.270 45.455 1.78 0.00 0.00 3.91
435 455 2.159881 GGTCACATCTACGTCGTTTTGC 60.160 50.000 1.78 0.00 0.00 3.68
436 456 3.054166 TGGTCACATCTACGTCGTTTTG 58.946 45.455 1.78 1.74 0.00 2.44
437 457 3.005050 TCTGGTCACATCTACGTCGTTTT 59.995 43.478 1.78 0.00 0.00 2.43
439 459 2.156917 TCTGGTCACATCTACGTCGTT 58.843 47.619 1.78 0.00 0.00 3.85
440 460 1.738350 CTCTGGTCACATCTACGTCGT 59.262 52.381 2.21 2.21 0.00 4.34
442 462 3.628032 TCATCTCTGGTCACATCTACGTC 59.372 47.826 0.00 0.00 0.00 4.34
443 463 3.378742 GTCATCTCTGGTCACATCTACGT 59.621 47.826 0.00 0.00 0.00 3.57
450 492 4.622260 TGAATTGTCATCTCTGGTCACA 57.378 40.909 0.00 0.00 0.00 3.58
469 516 2.615240 CCACGGTCCACTTTGATGATGA 60.615 50.000 0.00 0.00 0.00 2.92
473 520 0.606401 AGCCACGGTCCACTTTGATG 60.606 55.000 0.00 0.00 0.00 3.07
486 533 4.045104 CAGTAACATCTAGCTTAGCCACG 58.955 47.826 0.00 0.00 0.00 4.94
508 555 3.050275 GGCCGTGTGGAACTCAGC 61.050 66.667 0.00 0.00 38.04 4.26
510 557 2.425592 CTGGCCGTGTGGAACTCA 59.574 61.111 0.00 0.00 38.04 3.41
511 558 2.358737 CCTGGCCGTGTGGAACTC 60.359 66.667 0.00 0.00 38.04 3.01
526 579 3.570212 GTGGACACCACTGGCCCT 61.570 66.667 12.88 0.00 46.90 5.19
565 618 2.432628 GCGAGCGTGCTTAGTGGT 60.433 61.111 0.00 0.00 0.00 4.16
641 694 1.894756 AAAGCGGGCGTTGCACTTA 60.895 52.632 0.00 0.00 33.85 2.24
660 713 2.767505 AGTTTTCTGGTCCACACGATC 58.232 47.619 0.00 0.00 0.00 3.69
670 728 4.277423 CGGGTCATTGTTTAGTTTTCTGGT 59.723 41.667 0.00 0.00 0.00 4.00
676 734 4.212636 CGTTCTCGGGTCATTGTTTAGTTT 59.787 41.667 0.00 0.00 0.00 2.66
679 737 2.093783 GCGTTCTCGGGTCATTGTTTAG 59.906 50.000 0.00 0.00 37.56 1.85
720 786 2.575279 AGAAGTCCCATCAGCTTGACAT 59.425 45.455 0.00 0.00 0.00 3.06
735 801 3.003763 ACCAGGGGCCGAGAAGTC 61.004 66.667 0.00 0.00 0.00 3.01
752 818 2.049156 CGCGAGTTGACTCCTGCA 60.049 61.111 0.00 0.00 39.79 4.41
814 880 2.661866 GTTGCGTCGGAGTGCAGT 60.662 61.111 0.00 0.00 40.39 4.40
853 919 4.536489 GCATGGGTATAAATAGGGAGGAGT 59.464 45.833 0.00 0.00 0.00 3.85
882 948 1.953686 TGATGAGCATGACATGGCATG 59.046 47.619 33.31 33.31 46.48 4.06
883 949 1.954382 GTGATGAGCATGACATGGCAT 59.046 47.619 8.71 8.71 0.00 4.40
884 950 1.340211 TGTGATGAGCATGACATGGCA 60.340 47.619 17.03 2.18 30.13 4.92
885 951 1.385528 TGTGATGAGCATGACATGGC 58.614 50.000 17.03 9.27 30.13 4.40
886 952 3.428452 GGTTTGTGATGAGCATGACATGG 60.428 47.826 17.03 0.00 35.01 3.66
887 953 3.191791 TGGTTTGTGATGAGCATGACATG 59.808 43.478 11.27 11.27 35.01 3.21
888 954 3.423749 TGGTTTGTGATGAGCATGACAT 58.576 40.909 3.69 0.61 35.01 3.06
889 955 2.815503 CTGGTTTGTGATGAGCATGACA 59.184 45.455 0.00 0.00 33.21 3.58
890 956 2.163010 CCTGGTTTGTGATGAGCATGAC 59.837 50.000 0.00 0.00 0.00 3.06
891 957 2.439409 CCTGGTTTGTGATGAGCATGA 58.561 47.619 0.00 0.00 0.00 3.07
981 1080 3.244353 CCATCTCTCAACCACAGACAAGT 60.244 47.826 0.00 0.00 0.00 3.16
1160 1271 4.906618 AGTAATTGTGTCTGTACCAAGGG 58.093 43.478 0.00 0.00 0.00 3.95
1164 1275 6.571731 GCAGAGTAGTAATTGTGTCTGTACCA 60.572 42.308 0.00 0.00 35.02 3.25
1171 1282 3.548268 GCGAGCAGAGTAGTAATTGTGTC 59.452 47.826 0.00 0.00 0.00 3.67
1173 1284 2.531912 CGCGAGCAGAGTAGTAATTGTG 59.468 50.000 0.00 0.00 0.00 3.33
1174 1285 2.163815 ACGCGAGCAGAGTAGTAATTGT 59.836 45.455 15.93 0.00 0.00 2.71
1175 1286 2.798680 ACGCGAGCAGAGTAGTAATTG 58.201 47.619 15.93 0.00 0.00 2.32
1177 1288 3.204526 AGTACGCGAGCAGAGTAGTAAT 58.795 45.455 15.93 0.00 37.08 1.89
1178 1289 2.625737 AGTACGCGAGCAGAGTAGTAA 58.374 47.619 15.93 0.00 37.08 2.24
1188 1301 0.790814 AGAAAAGCAAGTACGCGAGC 59.209 50.000 15.93 8.68 36.85 5.03
1198 1311 7.879677 TGAACTAAGATCATCAGAGAAAAGCAA 59.120 33.333 0.00 0.00 0.00 3.91
1200 1313 7.548780 ACTGAACTAAGATCATCAGAGAAAAGC 59.451 37.037 15.03 0.00 41.38 3.51
1206 1319 8.420222 ACCAATACTGAACTAAGATCATCAGAG 58.580 37.037 15.03 0.00 41.38 3.35
1207 1320 8.311395 ACCAATACTGAACTAAGATCATCAGA 57.689 34.615 15.03 4.53 41.38 3.27
1208 1321 8.954950 AACCAATACTGAACTAAGATCATCAG 57.045 34.615 0.00 3.49 43.79 2.90
1209 1322 7.987458 GGAACCAATACTGAACTAAGATCATCA 59.013 37.037 0.00 0.00 0.00 3.07
1210 1323 8.371770 GGAACCAATACTGAACTAAGATCATC 57.628 38.462 0.00 0.00 0.00 2.92
1260 1373 9.628746 TTAAAAAGACCACAAGTGTAGAAAAAC 57.371 29.630 0.00 0.00 0.00 2.43
1266 1379 7.758495 AGTGTTTAAAAAGACCACAAGTGTAG 58.242 34.615 8.17 0.00 33.06 2.74
1267 1380 7.690952 AGTGTTTAAAAAGACCACAAGTGTA 57.309 32.000 8.17 0.00 33.06 2.90
1272 1385 6.527372 GCGTAAAGTGTTTAAAAAGACCACAA 59.473 34.615 8.17 0.00 33.06 3.33
1273 1386 6.028987 GCGTAAAGTGTTTAAAAAGACCACA 58.971 36.000 8.17 0.00 33.06 4.17
1275 1388 6.439675 AGCGTAAAGTGTTTAAAAAGACCA 57.560 33.333 0.00 0.00 33.06 4.02
1276 1389 5.911280 GGAGCGTAAAGTGTTTAAAAAGACC 59.089 40.000 0.00 0.00 33.06 3.85
1278 1391 5.824097 AGGGAGCGTAAAGTGTTTAAAAAGA 59.176 36.000 0.00 0.00 0.00 2.52
1284 1398 5.244626 AGTTAGAGGGAGCGTAAAGTGTTTA 59.755 40.000 0.00 0.00 0.00 2.01
1299 1413 1.153549 GTGCGCCTGAGTTAGAGGG 60.154 63.158 4.18 0.00 0.00 4.30
1300 1414 1.103803 TAGTGCGCCTGAGTTAGAGG 58.896 55.000 4.18 0.00 0.00 3.69
1301 1415 2.164624 AGTTAGTGCGCCTGAGTTAGAG 59.835 50.000 4.18 0.00 0.00 2.43
1302 1416 2.094700 CAGTTAGTGCGCCTGAGTTAGA 60.095 50.000 4.18 0.00 0.00 2.10
1304 1418 1.890489 TCAGTTAGTGCGCCTGAGTTA 59.110 47.619 4.18 0.00 31.84 2.24
1305 1419 0.679505 TCAGTTAGTGCGCCTGAGTT 59.320 50.000 4.18 0.00 31.84 3.01
1307 1421 0.038251 TGTCAGTTAGTGCGCCTGAG 60.038 55.000 12.71 0.00 35.99 3.35
1309 1423 1.069906 GTTTGTCAGTTAGTGCGCCTG 60.070 52.381 4.18 4.34 0.00 4.85
1310 1424 1.202651 AGTTTGTCAGTTAGTGCGCCT 60.203 47.619 4.18 3.99 0.00 5.52
1312 1426 5.773239 TTATAGTTTGTCAGTTAGTGCGC 57.227 39.130 0.00 0.00 0.00 6.09
1313 1427 9.901724 CTTATTTATAGTTTGTCAGTTAGTGCG 57.098 33.333 0.00 0.00 0.00 5.34
1346 1460 4.937620 TCTAAAGCCTGATGTTGCAGTTAG 59.062 41.667 0.00 0.00 34.06 2.34
1347 1461 4.905429 TCTAAAGCCTGATGTTGCAGTTA 58.095 39.130 0.00 0.00 34.06 2.24
1361 1479 5.109210 ACAACTTTGCTGTTTTCTAAAGCC 58.891 37.500 0.00 0.00 36.05 4.35
1363 1481 7.542130 AGTGAACAACTTTGCTGTTTTCTAAAG 59.458 33.333 0.00 0.00 37.14 1.85
1368 1486 5.160641 TCAGTGAACAACTTTGCTGTTTTC 58.839 37.500 0.00 0.00 36.83 2.29
1375 1493 3.128589 TCCAGTTCAGTGAACAACTTTGC 59.871 43.478 32.02 8.08 44.11 3.68
1395 1520 1.751927 CCCAGCATCCAAGCACTCC 60.752 63.158 0.00 0.00 36.85 3.85
1401 1893 1.604308 TGCACACCCAGCATCCAAG 60.604 57.895 0.00 0.00 37.02 3.61
1418 1910 1.124297 GTCGTACGTGAACACTGCATG 59.876 52.381 16.05 0.00 0.00 4.06
1419 1911 1.415374 GTCGTACGTGAACACTGCAT 58.585 50.000 16.05 0.00 0.00 3.96
1719 2215 2.815211 CTGTGGACGCCATGGACG 60.815 66.667 18.40 20.56 35.28 4.79
1788 2284 5.356751 AGCGGCAAGTATAACAAATGATTCA 59.643 36.000 1.45 0.00 0.00 2.57
1789 2285 5.821204 AGCGGCAAGTATAACAAATGATTC 58.179 37.500 1.45 0.00 0.00 2.52
1809 2305 6.183359 GCAACAATTGTGATAACTTACAAGCG 60.183 38.462 12.82 0.00 39.83 4.68
1940 2439 8.857098 CATTTCTCATCACATCCTCCATTAATT 58.143 33.333 0.00 0.00 0.00 1.40
1948 2447 4.102210 TCCCTCATTTCTCATCACATCCTC 59.898 45.833 0.00 0.00 0.00 3.71
1950 2449 4.133078 GTCCCTCATTTCTCATCACATCC 58.867 47.826 0.00 0.00 0.00 3.51
1990 2489 5.601662 AGAAAAGAGAGATCGACACAACAA 58.398 37.500 0.00 0.00 0.00 2.83
2066 2566 1.271934 CAAACGATGCCCCAAATGTGA 59.728 47.619 0.00 0.00 0.00 3.58
2130 2633 6.617529 GCGATTTGCAAAATGTTTACCGAATT 60.618 34.615 17.19 0.00 45.45 2.17
2162 2665 3.242011 ACCAAATGAGCCAAATCACCTT 58.758 40.909 0.00 0.00 30.46 3.50
2190 2693 2.174639 ACAATCTGGTCCCACTTGTCAA 59.825 45.455 4.46 0.00 0.00 3.18
2225 2728 5.295787 AGGGTGTGTATGTAAATGTTATGCG 59.704 40.000 0.00 0.00 0.00 4.73
2353 2874 3.480679 CTCCTGCACTGTGTGGCCA 62.481 63.158 0.00 0.00 33.64 5.36
2358 2879 2.520536 GGGACCTCCTGCACTGTGT 61.521 63.158 9.86 0.00 35.95 3.72
2663 3189 2.360209 CCTCCATCCTCTCTCTTTCCCT 60.360 54.545 0.00 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.