Multiple sequence alignment - TraesCS1D01G356800

Loading Multiple Alignment...

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 TraesCS1D01G356800 chr1D 100.000 2948 0 0 1 2948 441035744 441032797 0.000000e+00 5445
1 TraesCS1D01G356800 chr1D 77.820 266 36 12 2683 2948 441008190 441007948 3.060000e-30 143
2 TraesCS1D01G356800 chr1A 94.024 2209 70 25 668 2847 537069703 537071878 0.000000e+00 3291
3 TraesCS1D01G356800 chr1B 91.491 2327 129 30 667 2948 598703320 598701018 0.000000e+00 3136
4 TraesCS1D01G356800 chr1B 84.953 319 38 7 1 318 598703627 598703318 6.130000e-82 315
5 TraesCS1D01G356800 chr1B 95.455 66 3 0 2682 2747 598689948 598689883 4.020000e-19 106
6 TraesCS1D01G356800 chr3A 88.628 853 82 7 1097 1949 515828947 515828110 0.000000e+00 1024
7 TraesCS1D01G356800 chr3A 86.905 252 26 6 317 562 303149331 303149081 2.890000e-70 276
8 TraesCS1D01G356800 chr3D 88.318 856 85 7 1094 1949 395667255 395666415 0.000000e+00 1013
9 TraesCS1D01G356800 chr3B 88.173 854 86 7 1097 1950 520611580 520610742 0.000000e+00 1003
10 TraesCS1D01G356800 chr2D 89.558 249 19 4 320 562 194452347 194452100 2.850000e-80 309
11 TraesCS1D01G356800 chr5A 88.095 252 23 3 317 562 123979525 123979775 2.870000e-75 292
12 TraesCS1D01G356800 chr5A 86.000 250 29 5 318 562 601168896 601169144 2.250000e-66 263
13 TraesCS1D01G356800 chr6A 87.302 252 25 3 317 562 350839685 350839435 6.220000e-72 281
14 TraesCS1D01G356800 chr5B 86.508 252 27 6 317 562 496093526 496093776 1.350000e-68 270
15 TraesCS1D01G356800 chr5B 85.771 253 29 6 317 562 351571581 351571329 8.100000e-66 261
16 TraesCS1D01G356800 chr2B 86.508 252 27 7 317 562 470786055 470786305 1.350000e-68 270
17 TraesCS1D01G356800 chr4B 86.290 248 27 7 320 562 546236110 546235865 2.250000e-66 263


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 TraesCS1D01G356800 chr1D 441032797 441035744 2947 True 5445.0 5445 100.000 1 2948 1 chr1D.!!$R2 2947
1 TraesCS1D01G356800 chr1A 537069703 537071878 2175 False 3291.0 3291 94.024 668 2847 1 chr1A.!!$F1 2179
2 TraesCS1D01G356800 chr1B 598701018 598703627 2609 True 1725.5 3136 88.222 1 2948 2 chr1B.!!$R2 2947
3 TraesCS1D01G356800 chr3A 515828110 515828947 837 True 1024.0 1024 88.628 1097 1949 1 chr3A.!!$R2 852
4 TraesCS1D01G356800 chr3D 395666415 395667255 840 True 1013.0 1013 88.318 1094 1949 1 chr3D.!!$R1 855
5 TraesCS1D01G356800 chr3B 520610742 520611580 838 True 1003.0 1003 88.173 1097 1950 1 chr3B.!!$R1 853

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
592 594 0.032813 AAGCTAATGGGCATGCCACT 60.033 50.0 36.56 22.16 37.98 4.00 F
595 597 0.106569 CTAATGGGCATGCCACTCCA 60.107 55.0 36.56 25.30 37.98 3.86 F
714 716 0.316854 GTCGCCGGAGAAGATCGTAC 60.317 60.0 10.32 0.00 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1866 1896 0.824595 TGTCCTCGTCCTTGTCGGAA 60.825 55.000 0.00 0.0 45.32 4.30 R
1921 1951 1.228769 TGTAGTCGGACCACTGCCT 60.229 57.895 8.14 0.0 0.00 4.75 R
2625 2680 1.196766 AGCATGTGGGAGCTCAGTGA 61.197 55.000 17.19 0.0 36.00 3.41 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 3.902218 CATCTAAAAGGATGGGAAGCCA 58.098 45.455 0.00 0.00 39.33 4.75
63 64 5.750067 GCCATAAATGTTGAATGCACTTAGG 59.250 40.000 0.00 0.00 0.00 2.69
71 72 1.745653 GAATGCACTTAGGCTTGGGAC 59.254 52.381 0.00 0.00 34.04 4.46
74 75 0.107654 GCACTTAGGCTTGGGACGAT 60.108 55.000 0.00 0.00 0.00 3.73
118 119 3.157932 TCACCAAAACGCCAAAGAAAG 57.842 42.857 0.00 0.00 0.00 2.62
143 144 6.593770 GGGATTATACCAACAAAGGCAAAAAG 59.406 38.462 0.00 0.00 0.00 2.27
183 185 1.690893 ACAGACTCATCGGATCCATGG 59.309 52.381 13.41 4.97 0.00 3.66
187 189 1.417890 ACTCATCGGATCCATGGGAAC 59.582 52.381 23.11 3.56 34.34 3.62
196 198 0.617935 TCCATGGGAACGAATCTGCA 59.382 50.000 13.02 0.00 0.00 4.41
198 200 1.402968 CCATGGGAACGAATCTGCAAG 59.597 52.381 2.85 0.00 0.00 4.01
203 205 2.359900 GGAACGAATCTGCAAGGACAT 58.640 47.619 0.00 0.00 0.00 3.06
210 212 4.201851 CGAATCTGCAAGGACATAAACCTG 60.202 45.833 0.00 0.00 37.85 4.00
216 218 3.826729 GCAAGGACATAAACCTGAAACCT 59.173 43.478 0.00 0.00 37.85 3.50
221 223 4.321230 GGACATAAACCTGAAACCTGCAAG 60.321 45.833 0.00 0.00 0.00 4.01
240 242 1.420138 AGGTCGGACACACCAAATCTT 59.580 47.619 10.76 0.00 38.90 2.40
241 243 2.635915 AGGTCGGACACACCAAATCTTA 59.364 45.455 10.76 0.00 38.90 2.10
243 245 3.816523 GGTCGGACACACCAAATCTTAAA 59.183 43.478 10.76 0.00 38.90 1.52
244 246 4.276431 GGTCGGACACACCAAATCTTAAAA 59.724 41.667 10.76 0.00 38.90 1.52
261 263 2.159179 AAAAACACAAGCTCCCTGGT 57.841 45.000 0.00 0.00 0.00 4.00
276 278 0.240945 CTGGTTTCATGACAACGCCC 59.759 55.000 0.00 0.00 0.00 6.13
278 280 1.231958 GGTTTCATGACAACGCCCGA 61.232 55.000 0.00 0.00 0.00 5.14
279 281 0.802494 GTTTCATGACAACGCCCGAT 59.198 50.000 0.00 0.00 0.00 4.18
280 282 0.801872 TTTCATGACAACGCCCGATG 59.198 50.000 0.00 0.00 0.00 3.84
281 283 0.036858 TTCATGACAACGCCCGATGA 60.037 50.000 0.00 0.00 0.00 2.92
282 284 0.460109 TCATGACAACGCCCGATGAG 60.460 55.000 4.95 0.00 0.00 2.90
283 285 0.460109 CATGACAACGCCCGATGAGA 60.460 55.000 4.95 0.00 0.00 3.27
292 294 2.264480 CCGATGAGACACCGCCAA 59.736 61.111 0.00 0.00 0.00 4.52
293 295 2.100631 CCGATGAGACACCGCCAAC 61.101 63.158 0.00 0.00 0.00 3.77
311 313 2.163818 ACGCGGTTGAAGAATCAGAA 57.836 45.000 12.47 0.00 36.78 3.02
313 315 2.673368 ACGCGGTTGAAGAATCAGAATC 59.327 45.455 12.47 0.00 36.78 2.52
318 320 4.702131 CGGTTGAAGAATCAGAATCCCTTT 59.298 41.667 0.00 0.00 36.78 3.11
319 321 5.880332 CGGTTGAAGAATCAGAATCCCTTTA 59.120 40.000 0.00 0.00 36.78 1.85
320 322 6.037610 CGGTTGAAGAATCAGAATCCCTTTAG 59.962 42.308 0.00 0.00 36.78 1.85
321 323 6.319911 GGTTGAAGAATCAGAATCCCTTTAGG 59.680 42.308 0.00 0.00 36.78 2.69
322 324 6.319911 GTTGAAGAATCAGAATCCCTTTAGGG 59.680 42.308 8.63 8.63 46.25 3.53
323 325 7.085481 TTGAAGAATCAGAATCCCTTTAGGGC 61.085 42.308 10.12 0.00 45.30 5.19
324 326 9.182561 TTGAAGAATCAGAATCCCTTTAGGGCT 62.183 40.741 10.12 0.00 45.30 5.19
335 337 3.968265 CCTTTAGGGCTCCTTTGATTCA 58.032 45.455 0.00 0.00 34.61 2.57
336 338 4.344104 CCTTTAGGGCTCCTTTGATTCAA 58.656 43.478 0.00 0.00 34.61 2.69
337 339 4.772100 CCTTTAGGGCTCCTTTGATTCAAA 59.228 41.667 11.19 11.19 34.61 2.69
350 352 7.975866 CTTTGATTCAAAGGAATTCCATACG 57.024 36.000 26.22 11.45 44.75 3.06
351 353 7.695480 TTTGATTCAAAGGAATTCCATACGA 57.305 32.000 26.22 13.51 43.69 3.43
352 354 7.880160 TTGATTCAAAGGAATTCCATACGAT 57.120 32.000 26.22 13.66 43.69 3.73
353 355 7.880160 TGATTCAAAGGAATTCCATACGATT 57.120 32.000 26.22 12.36 43.69 3.34
354 356 8.292444 TGATTCAAAGGAATTCCATACGATTT 57.708 30.769 26.22 13.43 43.69 2.17
355 357 8.748412 TGATTCAAAGGAATTCCATACGATTTT 58.252 29.630 26.22 12.74 43.69 1.82
356 358 9.586435 GATTCAAAGGAATTCCATACGATTTTT 57.414 29.630 26.22 12.04 43.69 1.94
357 359 8.755696 TTCAAAGGAATTCCATACGATTTTTG 57.244 30.769 26.22 21.64 38.89 2.44
358 360 8.116651 TCAAAGGAATTCCATACGATTTTTGA 57.883 30.769 26.22 23.26 38.89 2.69
359 361 8.580720 TCAAAGGAATTCCATACGATTTTTGAA 58.419 29.630 26.22 11.55 38.89 2.69
360 362 8.863049 CAAAGGAATTCCATACGATTTTTGAAG 58.137 33.333 26.22 1.74 38.89 3.02
361 363 7.100458 AGGAATTCCATACGATTTTTGAAGG 57.900 36.000 26.22 0.00 38.89 3.46
362 364 6.889722 AGGAATTCCATACGATTTTTGAAGGA 59.110 34.615 26.22 0.00 38.89 3.36
363 365 7.561356 AGGAATTCCATACGATTTTTGAAGGAT 59.439 33.333 26.22 0.00 38.89 3.24
364 366 8.197439 GGAATTCCATACGATTTTTGAAGGATT 58.803 33.333 20.04 0.00 35.64 3.01
367 369 9.627123 ATTCCATACGATTTTTGAAGGATTAGA 57.373 29.630 0.00 0.00 0.00 2.10
368 370 9.456147 TTCCATACGATTTTTGAAGGATTAGAA 57.544 29.630 0.00 0.00 0.00 2.10
369 371 9.627123 TCCATACGATTTTTGAAGGATTAGAAT 57.373 29.630 0.00 0.00 0.00 2.40
370 372 9.884465 CCATACGATTTTTGAAGGATTAGAATC 57.116 33.333 0.00 0.00 34.66 2.52
398 400 7.492352 AGTATATTTTTCCTACATTGGTCGC 57.508 36.000 0.00 0.00 0.00 5.19
399 401 7.280356 AGTATATTTTTCCTACATTGGTCGCT 58.720 34.615 0.00 0.00 0.00 4.93
400 402 7.773690 AGTATATTTTTCCTACATTGGTCGCTT 59.226 33.333 0.00 0.00 0.00 4.68
401 403 4.497473 TTTTTCCTACATTGGTCGCTTG 57.503 40.909 0.00 0.00 0.00 4.01
402 404 3.410631 TTTCCTACATTGGTCGCTTGA 57.589 42.857 0.00 0.00 0.00 3.02
403 405 3.627395 TTCCTACATTGGTCGCTTGAT 57.373 42.857 0.00 0.00 0.00 2.57
404 406 3.627395 TCCTACATTGGTCGCTTGATT 57.373 42.857 0.00 0.00 0.00 2.57
405 407 3.531538 TCCTACATTGGTCGCTTGATTC 58.468 45.455 0.00 0.00 0.00 2.52
406 408 3.055458 TCCTACATTGGTCGCTTGATTCA 60.055 43.478 0.00 0.00 0.00 2.57
407 409 3.879295 CCTACATTGGTCGCTTGATTCAT 59.121 43.478 0.00 0.00 0.00 2.57
408 410 5.056480 CCTACATTGGTCGCTTGATTCATA 58.944 41.667 0.00 0.00 0.00 2.15
409 411 5.702670 CCTACATTGGTCGCTTGATTCATAT 59.297 40.000 0.00 0.00 0.00 1.78
410 412 5.428496 ACATTGGTCGCTTGATTCATATG 57.572 39.130 0.00 0.00 0.00 1.78
411 413 5.125356 ACATTGGTCGCTTGATTCATATGA 58.875 37.500 0.00 0.00 0.00 2.15
412 414 5.766670 ACATTGGTCGCTTGATTCATATGAT 59.233 36.000 6.17 0.00 0.00 2.45
413 415 6.263842 ACATTGGTCGCTTGATTCATATGATT 59.736 34.615 6.17 2.68 0.00 2.57
414 416 5.678132 TGGTCGCTTGATTCATATGATTG 57.322 39.130 6.17 0.00 0.00 2.67
415 417 5.367302 TGGTCGCTTGATTCATATGATTGA 58.633 37.500 6.17 0.00 0.00 2.57
416 418 5.821995 TGGTCGCTTGATTCATATGATTGAA 59.178 36.000 6.17 2.89 39.77 2.69
417 419 6.487668 TGGTCGCTTGATTCATATGATTGAAT 59.512 34.615 6.17 0.00 46.39 2.57
455 457 9.913310 TTTTTATATGGAATCATGTGTACTGGA 57.087 29.630 0.00 0.00 34.96 3.86
459 461 6.949352 ATGGAATCATGTGTACTGGATTTC 57.051 37.500 0.00 0.00 30.60 2.17
460 462 5.814481 TGGAATCATGTGTACTGGATTTCA 58.186 37.500 0.00 0.94 33.89 2.69
461 463 6.425735 TGGAATCATGTGTACTGGATTTCAT 58.574 36.000 0.00 0.00 31.91 2.57
462 464 6.891361 TGGAATCATGTGTACTGGATTTCATT 59.109 34.615 0.00 0.00 31.91 2.57
463 465 7.148035 TGGAATCATGTGTACTGGATTTCATTG 60.148 37.037 0.00 0.00 31.91 2.82
464 466 6.704289 ATCATGTGTACTGGATTTCATTGG 57.296 37.500 0.00 0.00 0.00 3.16
465 467 5.814481 TCATGTGTACTGGATTTCATTGGA 58.186 37.500 0.00 0.00 0.00 3.53
466 468 6.244654 TCATGTGTACTGGATTTCATTGGAA 58.755 36.000 0.00 0.00 0.00 3.53
467 469 6.718912 TCATGTGTACTGGATTTCATTGGAAA 59.281 34.615 0.00 0.00 46.36 3.13
478 480 4.314522 TTCATTGGAAATCTAGCACCCA 57.685 40.909 0.00 0.00 0.00 4.51
479 481 3.620488 TCATTGGAAATCTAGCACCCAC 58.380 45.455 0.00 0.00 0.00 4.61
480 482 3.266772 TCATTGGAAATCTAGCACCCACT 59.733 43.478 0.00 0.00 0.00 4.00
481 483 3.350219 TTGGAAATCTAGCACCCACTC 57.650 47.619 0.00 0.00 0.00 3.51
482 484 1.559682 TGGAAATCTAGCACCCACTCC 59.440 52.381 0.00 0.00 0.00 3.85
483 485 1.559682 GGAAATCTAGCACCCACTCCA 59.440 52.381 0.00 0.00 0.00 3.86
484 486 2.026262 GGAAATCTAGCACCCACTCCAA 60.026 50.000 0.00 0.00 0.00 3.53
485 487 2.789409 AATCTAGCACCCACTCCAAC 57.211 50.000 0.00 0.00 0.00 3.77
486 488 0.912486 ATCTAGCACCCACTCCAACC 59.088 55.000 0.00 0.00 0.00 3.77
487 489 0.178903 TCTAGCACCCACTCCAACCT 60.179 55.000 0.00 0.00 0.00 3.50
488 490 0.250513 CTAGCACCCACTCCAACCTC 59.749 60.000 0.00 0.00 0.00 3.85
489 491 0.178903 TAGCACCCACTCCAACCTCT 60.179 55.000 0.00 0.00 0.00 3.69
490 492 1.302832 GCACCCACTCCAACCTCTG 60.303 63.158 0.00 0.00 0.00 3.35
491 493 2.056906 GCACCCACTCCAACCTCTGT 62.057 60.000 0.00 0.00 0.00 3.41
492 494 0.474184 CACCCACTCCAACCTCTGTT 59.526 55.000 0.00 0.00 34.14 3.16
493 495 1.133792 CACCCACTCCAACCTCTGTTT 60.134 52.381 0.00 0.00 30.42 2.83
494 496 1.569072 ACCCACTCCAACCTCTGTTTT 59.431 47.619 0.00 0.00 30.42 2.43
495 497 2.230660 CCCACTCCAACCTCTGTTTTC 58.769 52.381 0.00 0.00 30.42 2.29
496 498 2.422803 CCCACTCCAACCTCTGTTTTCA 60.423 50.000 0.00 0.00 30.42 2.69
497 499 2.618709 CCACTCCAACCTCTGTTTTCAC 59.381 50.000 0.00 0.00 30.42 3.18
498 500 3.545703 CACTCCAACCTCTGTTTTCACT 58.454 45.455 0.00 0.00 30.42 3.41
499 501 3.947834 CACTCCAACCTCTGTTTTCACTT 59.052 43.478 0.00 0.00 30.42 3.16
500 502 4.399303 CACTCCAACCTCTGTTTTCACTTT 59.601 41.667 0.00 0.00 30.42 2.66
501 503 4.640647 ACTCCAACCTCTGTTTTCACTTTC 59.359 41.667 0.00 0.00 30.42 2.62
502 504 4.855340 TCCAACCTCTGTTTTCACTTTCT 58.145 39.130 0.00 0.00 30.42 2.52
503 505 5.261216 TCCAACCTCTGTTTTCACTTTCTT 58.739 37.500 0.00 0.00 30.42 2.52
504 506 5.714806 TCCAACCTCTGTTTTCACTTTCTTT 59.285 36.000 0.00 0.00 30.42 2.52
505 507 5.807011 CCAACCTCTGTTTTCACTTTCTTTG 59.193 40.000 0.00 0.00 30.42 2.77
506 508 6.389906 CAACCTCTGTTTTCACTTTCTTTGT 58.610 36.000 0.00 0.00 30.42 2.83
507 509 6.590234 ACCTCTGTTTTCACTTTCTTTGTT 57.410 33.333 0.00 0.00 0.00 2.83
508 510 6.993079 ACCTCTGTTTTCACTTTCTTTGTTT 58.007 32.000 0.00 0.00 0.00 2.83
509 511 7.441836 ACCTCTGTTTTCACTTTCTTTGTTTT 58.558 30.769 0.00 0.00 0.00 2.43
510 512 7.931407 ACCTCTGTTTTCACTTTCTTTGTTTTT 59.069 29.630 0.00 0.00 0.00 1.94
534 536 8.641499 TTTGACATCAAACACTTTGTTAATCC 57.359 30.769 2.89 0.00 40.14 3.01
535 537 7.581213 TGACATCAAACACTTTGTTAATCCT 57.419 32.000 0.00 0.00 40.14 3.24
536 538 8.684386 TGACATCAAACACTTTGTTAATCCTA 57.316 30.769 0.00 0.00 40.14 2.94
537 539 9.295825 TGACATCAAACACTTTGTTAATCCTAT 57.704 29.630 0.00 0.00 40.14 2.57
538 540 9.559958 GACATCAAACACTTTGTTAATCCTATG 57.440 33.333 0.00 0.00 40.14 2.23
539 541 9.295825 ACATCAAACACTTTGTTAATCCTATGA 57.704 29.630 0.00 0.00 40.14 2.15
540 542 9.778993 CATCAAACACTTTGTTAATCCTATGAG 57.221 33.333 0.00 0.00 40.14 2.90
541 543 9.739276 ATCAAACACTTTGTTAATCCTATGAGA 57.261 29.630 0.00 0.00 40.14 3.27
542 544 9.739276 TCAAACACTTTGTTAATCCTATGAGAT 57.261 29.630 0.00 0.00 40.14 2.75
552 554 9.077885 TGTTAATCCTATGAGATTTAAATGGGC 57.922 33.333 5.17 0.00 37.62 5.36
553 555 9.077885 GTTAATCCTATGAGATTTAAATGGGCA 57.922 33.333 5.17 1.32 37.62 5.36
554 556 9.827198 TTAATCCTATGAGATTTAAATGGGCAT 57.173 29.630 5.17 8.48 37.62 4.40
555 557 7.713734 ATCCTATGAGATTTAAATGGGCATG 57.286 36.000 5.17 0.00 0.00 4.06
556 558 5.477984 TCCTATGAGATTTAAATGGGCATGC 59.522 40.000 9.90 9.90 0.00 4.06
557 559 4.612264 ATGAGATTTAAATGGGCATGCC 57.388 40.909 29.47 29.47 0.00 4.40
558 560 3.372897 TGAGATTTAAATGGGCATGCCA 58.627 40.909 36.56 23.14 37.98 4.92
559 561 3.132646 TGAGATTTAAATGGGCATGCCAC 59.867 43.478 36.56 25.50 37.98 5.01
560 562 3.377573 AGATTTAAATGGGCATGCCACT 58.622 40.909 36.56 20.94 37.98 4.00
561 563 3.385755 AGATTTAAATGGGCATGCCACTC 59.614 43.478 36.56 20.78 37.98 3.51
562 564 2.530460 TTAAATGGGCATGCCACTCT 57.470 45.000 36.56 20.41 37.98 3.24
563 565 2.530460 TAAATGGGCATGCCACTCTT 57.470 45.000 36.56 24.11 37.98 2.85
564 566 1.648116 AAATGGGCATGCCACTCTTT 58.352 45.000 36.56 24.35 37.98 2.52
565 567 1.648116 AATGGGCATGCCACTCTTTT 58.352 45.000 36.56 17.16 37.98 2.27
566 568 1.648116 ATGGGCATGCCACTCTTTTT 58.352 45.000 36.56 9.78 37.98 1.94
588 590 2.965572 TTTGAAGCTAATGGGCATGC 57.034 45.000 9.90 9.90 34.17 4.06
589 591 1.113788 TTGAAGCTAATGGGCATGCC 58.886 50.000 29.47 29.47 34.17 4.40
590 592 0.033306 TGAAGCTAATGGGCATGCCA 60.033 50.000 36.56 23.14 37.98 4.92
591 593 0.386838 GAAGCTAATGGGCATGCCAC 59.613 55.000 36.56 25.50 37.98 5.01
592 594 0.032813 AAGCTAATGGGCATGCCACT 60.033 50.000 36.56 22.16 37.98 4.00
593 595 0.466922 AGCTAATGGGCATGCCACTC 60.467 55.000 36.56 20.78 37.98 3.51
594 596 1.458639 GCTAATGGGCATGCCACTCC 61.459 60.000 36.56 20.41 37.98 3.85
595 597 0.106569 CTAATGGGCATGCCACTCCA 60.107 55.000 36.56 25.30 37.98 3.86
596 598 0.334335 TAATGGGCATGCCACTCCAA 59.666 50.000 36.56 14.67 37.98 3.53
597 599 0.325860 AATGGGCATGCCACTCCAAT 60.326 50.000 36.56 16.54 37.98 3.16
598 600 0.757935 ATGGGCATGCCACTCCAATC 60.758 55.000 36.56 17.81 37.98 2.67
599 601 2.129785 GGGCATGCCACTCCAATCC 61.130 63.158 36.56 13.39 37.98 3.01
600 602 2.484062 GGCATGCCACTCCAATCCG 61.484 63.158 32.08 0.00 35.81 4.18
601 603 1.750399 GCATGCCACTCCAATCCGT 60.750 57.895 6.36 0.00 0.00 4.69
602 604 1.315257 GCATGCCACTCCAATCCGTT 61.315 55.000 6.36 0.00 0.00 4.44
603 605 2.016604 GCATGCCACTCCAATCCGTTA 61.017 52.381 6.36 0.00 0.00 3.18
604 606 2.575532 CATGCCACTCCAATCCGTTAT 58.424 47.619 0.00 0.00 0.00 1.89
605 607 2.799126 TGCCACTCCAATCCGTTATT 57.201 45.000 0.00 0.00 0.00 1.40
606 608 3.080300 TGCCACTCCAATCCGTTATTT 57.920 42.857 0.00 0.00 0.00 1.40
607 609 3.426615 TGCCACTCCAATCCGTTATTTT 58.573 40.909 0.00 0.00 0.00 1.82
608 610 3.829601 TGCCACTCCAATCCGTTATTTTT 59.170 39.130 0.00 0.00 0.00 1.94
609 611 4.082463 TGCCACTCCAATCCGTTATTTTTC 60.082 41.667 0.00 0.00 0.00 2.29
610 612 4.676986 GCCACTCCAATCCGTTATTTTTCC 60.677 45.833 0.00 0.00 0.00 3.13
611 613 4.705023 CCACTCCAATCCGTTATTTTTCCT 59.295 41.667 0.00 0.00 0.00 3.36
612 614 5.883673 CCACTCCAATCCGTTATTTTTCCTA 59.116 40.000 0.00 0.00 0.00 2.94
613 615 6.546034 CCACTCCAATCCGTTATTTTTCCTAT 59.454 38.462 0.00 0.00 0.00 2.57
614 616 7.255139 CCACTCCAATCCGTTATTTTTCCTATC 60.255 40.741 0.00 0.00 0.00 2.08
615 617 6.771267 ACTCCAATCCGTTATTTTTCCTATCC 59.229 38.462 0.00 0.00 0.00 2.59
616 618 6.906848 TCCAATCCGTTATTTTTCCTATCCT 58.093 36.000 0.00 0.00 0.00 3.24
617 619 6.770785 TCCAATCCGTTATTTTTCCTATCCTG 59.229 38.462 0.00 0.00 0.00 3.86
618 620 6.546034 CCAATCCGTTATTTTTCCTATCCTGT 59.454 38.462 0.00 0.00 0.00 4.00
619 621 7.417612 CAATCCGTTATTTTTCCTATCCTGTG 58.582 38.462 0.00 0.00 0.00 3.66
620 622 6.057321 TCCGTTATTTTTCCTATCCTGTGT 57.943 37.500 0.00 0.00 0.00 3.72
621 623 6.478129 TCCGTTATTTTTCCTATCCTGTGTT 58.522 36.000 0.00 0.00 0.00 3.32
622 624 6.943718 TCCGTTATTTTTCCTATCCTGTGTTT 59.056 34.615 0.00 0.00 0.00 2.83
623 625 7.449086 TCCGTTATTTTTCCTATCCTGTGTTTT 59.551 33.333 0.00 0.00 0.00 2.43
624 626 8.085909 CCGTTATTTTTCCTATCCTGTGTTTTT 58.914 33.333 0.00 0.00 0.00 1.94
632 634 8.575649 TTCCTATCCTGTGTTTTTAAGAATCC 57.424 34.615 0.00 0.00 0.00 3.01
633 635 7.928873 TCCTATCCTGTGTTTTTAAGAATCCT 58.071 34.615 0.00 0.00 0.00 3.24
634 636 9.053472 TCCTATCCTGTGTTTTTAAGAATCCTA 57.947 33.333 0.00 0.00 0.00 2.94
635 637 9.110502 CCTATCCTGTGTTTTTAAGAATCCTAC 57.889 37.037 0.00 0.00 0.00 3.18
636 638 7.611213 ATCCTGTGTTTTTAAGAATCCTACG 57.389 36.000 0.00 0.00 0.00 3.51
637 639 6.761312 TCCTGTGTTTTTAAGAATCCTACGA 58.239 36.000 0.00 0.00 0.00 3.43
638 640 7.218614 TCCTGTGTTTTTAAGAATCCTACGAA 58.781 34.615 0.00 0.00 0.00 3.85
639 641 7.881232 TCCTGTGTTTTTAAGAATCCTACGAAT 59.119 33.333 0.00 0.00 0.00 3.34
640 642 8.175716 CCTGTGTTTTTAAGAATCCTACGAATC 58.824 37.037 0.00 0.00 0.00 2.52
641 643 8.610248 TGTGTTTTTAAGAATCCTACGAATCA 57.390 30.769 0.00 0.00 0.00 2.57
642 644 9.058174 TGTGTTTTTAAGAATCCTACGAATCAA 57.942 29.630 0.00 0.00 0.00 2.57
643 645 9.887406 GTGTTTTTAAGAATCCTACGAATCAAA 57.113 29.630 0.00 0.00 0.00 2.69
649 651 9.884636 TTAAGAATCCTACGAATCAAAGAATCA 57.115 29.630 0.00 0.00 0.00 2.57
650 652 8.792830 AAGAATCCTACGAATCAAAGAATCAA 57.207 30.769 0.00 0.00 0.00 2.57
651 653 8.792830 AGAATCCTACGAATCAAAGAATCAAA 57.207 30.769 0.00 0.00 0.00 2.69
652 654 8.887717 AGAATCCTACGAATCAAAGAATCAAAG 58.112 33.333 0.00 0.00 0.00 2.77
653 655 8.792830 AATCCTACGAATCAAAGAATCAAAGA 57.207 30.769 0.00 0.00 0.00 2.52
654 656 8.792830 ATCCTACGAATCAAAGAATCAAAGAA 57.207 30.769 0.00 0.00 0.00 2.52
655 657 8.792830 TCCTACGAATCAAAGAATCAAAGAAT 57.207 30.769 0.00 0.00 0.00 2.40
656 658 8.883731 TCCTACGAATCAAAGAATCAAAGAATC 58.116 33.333 0.00 0.00 0.00 2.52
657 659 8.668353 CCTACGAATCAAAGAATCAAAGAATCA 58.332 33.333 0.00 0.00 0.00 2.57
660 662 9.403110 ACGAATCAAAGAATCAAAGAATCAAAG 57.597 29.630 0.00 0.00 0.00 2.77
661 663 9.616634 CGAATCAAAGAATCAAAGAATCAAAGA 57.383 29.630 0.00 0.00 0.00 2.52
665 667 8.790718 TCAAAGAATCAAAGAATCAAAGAGAGG 58.209 33.333 0.00 0.00 0.00 3.69
666 668 6.756299 AGAATCAAAGAATCAAAGAGAGGC 57.244 37.500 0.00 0.00 0.00 4.70
697 699 2.032377 TCGCATCCTTTGTGAAAACGTC 60.032 45.455 0.00 0.00 41.79 4.34
702 704 0.656205 CTTTGTGAAAACGTCGCCGG 60.656 55.000 0.00 0.00 38.78 6.13
703 705 1.088340 TTTGTGAAAACGTCGCCGGA 61.088 50.000 5.05 0.00 38.78 5.14
707 709 0.942410 TGAAAACGTCGCCGGAGAAG 60.942 55.000 18.72 18.72 38.78 2.85
708 710 0.665369 GAAAACGTCGCCGGAGAAGA 60.665 55.000 26.10 6.69 38.78 2.87
714 716 0.316854 GTCGCCGGAGAAGATCGTAC 60.317 60.000 10.32 0.00 0.00 3.67
778 789 2.377628 AAAAGTCTCCGACGGCTGCA 62.378 55.000 9.66 0.00 37.67 4.41
789 800 2.514824 GGCTGCACTCCGAATCCC 60.515 66.667 0.50 0.00 0.00 3.85
862 877 2.116556 TTTTTCGGGGCCCCACTC 59.883 61.111 40.06 14.14 35.37 3.51
949 973 2.038762 AACCCTCACCCACCCACT 60.039 61.111 0.00 0.00 0.00 4.00
951 975 3.706373 CCCTCACCCACCCACTCG 61.706 72.222 0.00 0.00 0.00 4.18
1866 1896 2.446802 GGAGGGAGGAAGGGCGAT 60.447 66.667 0.00 0.00 0.00 4.58
1921 1951 4.141413 CCATGGATCACACCTCCTTCATAA 60.141 45.833 5.56 0.00 33.69 1.90
2143 2181 8.730680 TGATAGCAGATGATTGATGAATGAATG 58.269 33.333 0.00 0.00 0.00 2.67
2182 2221 6.072397 TGGTGGATTTGGTTGTACTTTAATCG 60.072 38.462 0.00 0.00 0.00 3.34
2277 2316 5.810074 TCACATGATTATAGTGTGTGAACCG 59.190 40.000 0.00 0.00 44.19 4.44
2302 2350 6.882610 TGATGATGCCACATACTAAATTCC 57.117 37.500 0.00 0.00 0.00 3.01
2376 2426 9.039870 CAAATGAACTGTATTAGAGCTCTTAGG 57.960 37.037 23.84 9.10 0.00 2.69
2603 2658 6.911250 TCATCTCTTTGTAGTTGTAGGACA 57.089 37.500 0.00 0.00 0.00 4.02
2604 2659 7.482169 TCATCTCTTTGTAGTTGTAGGACAT 57.518 36.000 0.00 0.00 0.00 3.06
2605 2660 8.589701 TCATCTCTTTGTAGTTGTAGGACATA 57.410 34.615 0.00 0.00 0.00 2.29
2606 2661 9.201989 TCATCTCTTTGTAGTTGTAGGACATAT 57.798 33.333 0.00 0.00 0.00 1.78
2607 2662 9.254133 CATCTCTTTGTAGTTGTAGGACATATG 57.746 37.037 0.00 0.00 0.00 1.78
2608 2663 7.782049 TCTCTTTGTAGTTGTAGGACATATGG 58.218 38.462 7.80 0.00 0.00 2.74
2609 2664 6.346096 TCTTTGTAGTTGTAGGACATATGGC 58.654 40.000 7.80 3.17 0.00 4.40
2610 2665 5.950544 TTGTAGTTGTAGGACATATGGCT 57.049 39.130 8.85 0.00 0.00 4.75
2613 2668 4.142609 AGTTGTAGGACATATGGCTGTG 57.857 45.455 8.85 0.00 0.00 3.66
2616 2671 3.103742 TGTAGGACATATGGCTGTGTGA 58.896 45.455 8.85 0.00 0.00 3.58
2645 2700 1.025113 CACTGAGCTCCCACATGCTG 61.025 60.000 12.15 0.00 39.91 4.41
2648 2703 1.140452 CTGAGCTCCCACATGCTGTAT 59.860 52.381 12.15 0.00 39.91 2.29
2649 2704 2.366590 CTGAGCTCCCACATGCTGTATA 59.633 50.000 12.15 0.00 39.91 1.47
2725 2782 1.588674 AACAATGTCGCCTTCGTTGA 58.411 45.000 8.63 0.00 36.19 3.18
2747 2804 5.104776 TGAATGGGTCAATGAAGACTAGGAG 60.105 44.000 0.00 0.00 38.57 3.69
2749 2806 3.769844 TGGGTCAATGAAGACTAGGAGAC 59.230 47.826 0.00 0.00 38.57 3.36
2750 2807 3.769844 GGGTCAATGAAGACTAGGAGACA 59.230 47.826 0.00 0.00 38.57 3.41
2752 2809 5.280011 GGGTCAATGAAGACTAGGAGACAAA 60.280 44.000 0.00 0.00 38.57 2.83
2753 2810 6.231211 GGTCAATGAAGACTAGGAGACAAAA 58.769 40.000 0.00 0.00 38.57 2.44
2754 2811 6.710744 GGTCAATGAAGACTAGGAGACAAAAA 59.289 38.462 0.00 0.00 38.57 1.94
2755 2812 7.308049 GGTCAATGAAGACTAGGAGACAAAAAC 60.308 40.741 0.00 0.00 38.57 2.43
2756 2813 7.226720 GTCAATGAAGACTAGGAGACAAAAACA 59.773 37.037 0.00 0.00 35.65 2.83
2757 2814 7.226720 TCAATGAAGACTAGGAGACAAAAACAC 59.773 37.037 0.00 0.00 0.00 3.32
2758 2815 6.235231 TGAAGACTAGGAGACAAAAACACT 57.765 37.500 0.00 0.00 0.00 3.55
2770 2827 9.581099 GGAGACAAAAACACTTATTTTCTGAAA 57.419 29.630 0.00 0.00 31.35 2.69
2802 2860 1.237285 TTGCCTTCTGAAGCTTCCGC 61.237 55.000 23.42 16.02 0.00 5.54
2813 2871 2.035442 GCTTCCGCCTGACTGTTCC 61.035 63.158 0.00 0.00 0.00 3.62
2836 2894 4.910746 AGTCATCGAGTCAACAAATTCG 57.089 40.909 0.00 0.00 34.56 3.34
2837 2895 4.556233 AGTCATCGAGTCAACAAATTCGA 58.444 39.130 0.00 0.00 44.88 3.71
2863 2921 3.699538 TCTTTCGAGCTAAGAGCACCATA 59.300 43.478 0.64 0.00 45.56 2.74
2864 2922 3.438297 TTCGAGCTAAGAGCACCATAC 57.562 47.619 0.64 0.00 45.56 2.39
2868 2926 4.023107 TCGAGCTAAGAGCACCATACATAC 60.023 45.833 0.64 0.00 45.56 2.39
2886 2944 3.314331 AGTGACGTGCTGGGAGGG 61.314 66.667 0.00 0.00 0.00 4.30
2901 2959 1.636003 GGAGGGGTTCCTGTTCATTCT 59.364 52.381 0.00 0.00 45.05 2.40
2903 2961 2.305927 GAGGGGTTCCTGTTCATTCTCA 59.694 50.000 0.00 0.00 45.05 3.27
2917 2975 4.582869 TCATTCTCACTTCACAATGGAGG 58.417 43.478 0.00 0.00 0.00 4.30
2920 2978 2.082231 CTCACTTCACAATGGAGGCAG 58.918 52.381 0.00 0.00 0.00 4.85
2925 2983 2.885135 TCACAATGGAGGCAGTCATT 57.115 45.000 0.00 0.00 34.31 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 4.567959 GTGCATTCAACATTTATGGCTTCC 59.432 41.667 0.00 0.00 0.00 3.46
42 43 6.780457 AGCCTAAGTGCATTCAACATTTAT 57.220 33.333 0.00 0.00 0.00 1.40
63 64 2.952978 TCTTCTAGAGATCGTCCCAAGC 59.047 50.000 0.00 0.00 0.00 4.01
71 72 7.547370 ACATCTTTTGGTTTCTTCTAGAGATCG 59.453 37.037 0.00 0.00 33.49 3.69
74 75 8.210946 TGAACATCTTTTGGTTTCTTCTAGAGA 58.789 33.333 0.00 0.00 0.00 3.10
118 119 5.669164 TTTGCCTTTGTTGGTATAATCCC 57.331 39.130 0.00 0.00 0.00 3.85
150 151 4.689612 TGAGTCTGTGTTAGCCTCTTTT 57.310 40.909 0.00 0.00 32.65 2.27
152 153 3.119316 CGATGAGTCTGTGTTAGCCTCTT 60.119 47.826 0.00 0.00 32.65 2.85
153 154 2.425312 CGATGAGTCTGTGTTAGCCTCT 59.575 50.000 0.00 0.00 32.65 3.69
154 155 2.480416 CCGATGAGTCTGTGTTAGCCTC 60.480 54.545 0.00 0.00 32.07 4.70
155 156 1.478510 CCGATGAGTCTGTGTTAGCCT 59.521 52.381 0.00 0.00 0.00 4.58
156 157 1.476891 TCCGATGAGTCTGTGTTAGCC 59.523 52.381 0.00 0.00 0.00 3.93
157 158 2.941453 TCCGATGAGTCTGTGTTAGC 57.059 50.000 0.00 0.00 0.00 3.09
159 160 3.361786 TGGATCCGATGAGTCTGTGTTA 58.638 45.455 7.39 0.00 0.00 2.41
165 166 1.133041 TCCCATGGATCCGATGAGTCT 60.133 52.381 15.22 0.00 0.00 3.24
183 185 1.808411 TGTCCTTGCAGATTCGTTCC 58.192 50.000 0.00 0.00 0.00 3.62
187 189 3.941483 AGGTTTATGTCCTTGCAGATTCG 59.059 43.478 0.00 0.00 30.18 3.34
196 198 3.826729 GCAGGTTTCAGGTTTATGTCCTT 59.173 43.478 0.00 0.00 32.37 3.36
198 200 3.153919 TGCAGGTTTCAGGTTTATGTCC 58.846 45.455 0.00 0.00 0.00 4.02
216 218 2.110213 GGTGTGTCCGACCTTGCA 59.890 61.111 0.00 0.00 0.00 4.08
221 223 1.892209 AAGATTTGGTGTGTCCGACC 58.108 50.000 0.00 0.00 39.52 4.79
243 245 2.159179 AACCAGGGAGCTTGTGTTTT 57.841 45.000 0.00 0.00 0.00 2.43
244 246 2.031870 GAAACCAGGGAGCTTGTGTTT 58.968 47.619 0.00 0.00 0.00 2.83
252 254 1.541588 GTTGTCATGAAACCAGGGAGC 59.458 52.381 0.00 0.00 0.00 4.70
256 258 0.240945 GGCGTTGTCATGAAACCAGG 59.759 55.000 0.00 0.00 0.00 4.45
259 261 1.209127 CGGGCGTTGTCATGAAACC 59.791 57.895 0.00 0.00 0.00 3.27
261 263 0.801872 CATCGGGCGTTGTCATGAAA 59.198 50.000 0.00 0.00 0.00 2.69
276 278 2.444624 CGTTGGCGGTGTCTCATCG 61.445 63.158 0.00 0.00 41.32 3.84
278 280 2.742372 GCGTTGGCGGTGTCTCAT 60.742 61.111 0.00 0.00 38.78 2.90
292 294 2.163818 TTCTGATTCTTCAACCGCGT 57.836 45.000 4.92 0.00 0.00 6.01
293 295 2.030946 GGATTCTGATTCTTCAACCGCG 59.969 50.000 0.00 0.00 0.00 6.46
296 298 6.319911 CCTAAAGGGATTCTGATTCTTCAACC 59.680 42.308 0.21 0.00 37.23 3.77
327 329 7.695480 TCGTATGGAATTCCTTTGAATCAAA 57.305 32.000 24.73 8.25 40.34 2.69
328 330 7.880160 ATCGTATGGAATTCCTTTGAATCAA 57.120 32.000 24.73 1.85 40.34 2.57
329 331 7.880160 AATCGTATGGAATTCCTTTGAATCA 57.120 32.000 24.73 2.61 40.34 2.57
330 332 9.586435 AAAAATCGTATGGAATTCCTTTGAATC 57.414 29.630 24.73 7.86 40.34 2.52
331 333 9.369904 CAAAAATCGTATGGAATTCCTTTGAAT 57.630 29.630 24.73 12.14 43.08 2.57
332 334 8.580720 TCAAAAATCGTATGGAATTCCTTTGAA 58.419 29.630 24.73 4.93 36.82 2.69
333 335 8.116651 TCAAAAATCGTATGGAATTCCTTTGA 57.883 30.769 24.73 22.68 36.82 2.69
334 336 8.755696 TTCAAAAATCGTATGGAATTCCTTTG 57.244 30.769 24.73 21.07 36.82 2.77
335 337 8.034804 CCTTCAAAAATCGTATGGAATTCCTTT 58.965 33.333 24.73 12.83 36.82 3.11
336 338 7.396055 TCCTTCAAAAATCGTATGGAATTCCTT 59.604 33.333 24.73 20.40 36.82 3.36
337 339 6.889722 TCCTTCAAAAATCGTATGGAATTCCT 59.110 34.615 24.73 12.90 36.82 3.36
338 340 7.095695 TCCTTCAAAAATCGTATGGAATTCC 57.904 36.000 18.17 18.17 0.00 3.01
341 343 9.627123 TCTAATCCTTCAAAAATCGTATGGAAT 57.373 29.630 0.00 0.00 0.00 3.01
342 344 9.456147 TTCTAATCCTTCAAAAATCGTATGGAA 57.544 29.630 0.00 0.00 0.00 3.53
343 345 9.627123 ATTCTAATCCTTCAAAAATCGTATGGA 57.373 29.630 0.00 0.00 0.00 3.41
344 346 9.884465 GATTCTAATCCTTCAAAAATCGTATGG 57.116 33.333 0.00 0.00 0.00 2.74
372 374 9.048446 GCGACCAATGTAGGAAAAATATACTAA 57.952 33.333 0.00 0.00 0.00 2.24
373 375 8.426489 AGCGACCAATGTAGGAAAAATATACTA 58.574 33.333 0.00 0.00 0.00 1.82
374 376 7.280356 AGCGACCAATGTAGGAAAAATATACT 58.720 34.615 0.00 0.00 0.00 2.12
375 377 7.492352 AGCGACCAATGTAGGAAAAATATAC 57.508 36.000 0.00 0.00 0.00 1.47
376 378 7.771361 TCAAGCGACCAATGTAGGAAAAATATA 59.229 33.333 0.00 0.00 0.00 0.86
377 379 6.601613 TCAAGCGACCAATGTAGGAAAAATAT 59.398 34.615 0.00 0.00 0.00 1.28
378 380 5.941058 TCAAGCGACCAATGTAGGAAAAATA 59.059 36.000 0.00 0.00 0.00 1.40
379 381 4.764823 TCAAGCGACCAATGTAGGAAAAAT 59.235 37.500 0.00 0.00 0.00 1.82
380 382 4.138290 TCAAGCGACCAATGTAGGAAAAA 58.862 39.130 0.00 0.00 0.00 1.94
381 383 3.745799 TCAAGCGACCAATGTAGGAAAA 58.254 40.909 0.00 0.00 0.00 2.29
382 384 3.410631 TCAAGCGACCAATGTAGGAAA 57.589 42.857 0.00 0.00 0.00 3.13
383 385 3.627395 ATCAAGCGACCAATGTAGGAA 57.373 42.857 0.00 0.00 0.00 3.36
384 386 3.055458 TGAATCAAGCGACCAATGTAGGA 60.055 43.478 0.00 0.00 0.00 2.94
385 387 3.270027 TGAATCAAGCGACCAATGTAGG 58.730 45.455 0.00 0.00 0.00 3.18
386 388 6.424812 TCATATGAATCAAGCGACCAATGTAG 59.575 38.462 1.98 0.00 0.00 2.74
387 389 6.287525 TCATATGAATCAAGCGACCAATGTA 58.712 36.000 1.98 0.00 0.00 2.29
388 390 5.125356 TCATATGAATCAAGCGACCAATGT 58.875 37.500 1.98 0.00 0.00 2.71
389 391 5.678132 TCATATGAATCAAGCGACCAATG 57.322 39.130 1.98 0.00 0.00 2.82
390 392 6.487668 TCAATCATATGAATCAAGCGACCAAT 59.512 34.615 9.99 0.00 0.00 3.16
391 393 5.821995 TCAATCATATGAATCAAGCGACCAA 59.178 36.000 9.99 0.00 0.00 3.67
392 394 5.367302 TCAATCATATGAATCAAGCGACCA 58.633 37.500 9.99 0.00 0.00 4.02
393 395 5.929697 TCAATCATATGAATCAAGCGACC 57.070 39.130 9.99 0.00 0.00 4.79
429 431 9.913310 TCCAGTACACATGATTCCATATAAAAA 57.087 29.630 0.00 0.00 0.00 1.94
433 435 9.725019 GAAATCCAGTACACATGATTCCATATA 57.275 33.333 0.00 0.00 0.00 0.86
434 436 8.219868 TGAAATCCAGTACACATGATTCCATAT 58.780 33.333 0.00 0.00 0.00 1.78
435 437 7.572814 TGAAATCCAGTACACATGATTCCATA 58.427 34.615 0.00 0.00 0.00 2.74
436 438 6.425735 TGAAATCCAGTACACATGATTCCAT 58.574 36.000 0.00 0.00 0.00 3.41
437 439 5.814481 TGAAATCCAGTACACATGATTCCA 58.186 37.500 0.00 0.00 0.00 3.53
438 440 6.949352 ATGAAATCCAGTACACATGATTCC 57.051 37.500 0.00 0.00 0.00 3.01
439 441 7.067372 TCCAATGAAATCCAGTACACATGATTC 59.933 37.037 0.00 0.00 0.00 2.52
440 442 6.891361 TCCAATGAAATCCAGTACACATGATT 59.109 34.615 0.00 0.00 0.00 2.57
441 443 6.425735 TCCAATGAAATCCAGTACACATGAT 58.574 36.000 0.00 0.00 0.00 2.45
442 444 5.814481 TCCAATGAAATCCAGTACACATGA 58.186 37.500 0.00 0.00 0.00 3.07
443 445 6.513806 TTCCAATGAAATCCAGTACACATG 57.486 37.500 0.00 0.00 0.00 3.21
444 446 7.722949 ATTTCCAATGAAATCCAGTACACAT 57.277 32.000 0.00 0.00 45.87 3.21
456 458 4.462483 GTGGGTGCTAGATTTCCAATGAAA 59.538 41.667 0.00 0.00 44.22 2.69
457 459 4.016444 GTGGGTGCTAGATTTCCAATGAA 58.984 43.478 0.00 0.00 0.00 2.57
458 460 3.266772 AGTGGGTGCTAGATTTCCAATGA 59.733 43.478 0.00 0.00 0.00 2.57
459 461 3.624777 AGTGGGTGCTAGATTTCCAATG 58.375 45.455 0.00 0.00 0.00 2.82
460 462 3.372025 GGAGTGGGTGCTAGATTTCCAAT 60.372 47.826 0.00 0.00 0.00 3.16
461 463 2.026262 GGAGTGGGTGCTAGATTTCCAA 60.026 50.000 0.00 0.00 0.00 3.53
462 464 1.559682 GGAGTGGGTGCTAGATTTCCA 59.440 52.381 0.00 0.00 0.00 3.53
463 465 1.559682 TGGAGTGGGTGCTAGATTTCC 59.440 52.381 0.00 0.00 0.00 3.13
464 466 3.010420 GTTGGAGTGGGTGCTAGATTTC 58.990 50.000 0.00 0.00 0.00 2.17
465 467 2.290960 GGTTGGAGTGGGTGCTAGATTT 60.291 50.000 0.00 0.00 0.00 2.17
466 468 1.282157 GGTTGGAGTGGGTGCTAGATT 59.718 52.381 0.00 0.00 0.00 2.40
467 469 0.912486 GGTTGGAGTGGGTGCTAGAT 59.088 55.000 0.00 0.00 0.00 1.98
468 470 0.178903 AGGTTGGAGTGGGTGCTAGA 60.179 55.000 0.00 0.00 0.00 2.43
469 471 0.250513 GAGGTTGGAGTGGGTGCTAG 59.749 60.000 0.00 0.00 0.00 3.42
470 472 0.178903 AGAGGTTGGAGTGGGTGCTA 60.179 55.000 0.00 0.00 0.00 3.49
471 473 1.462238 AGAGGTTGGAGTGGGTGCT 60.462 57.895 0.00 0.00 0.00 4.40
472 474 1.302832 CAGAGGTTGGAGTGGGTGC 60.303 63.158 0.00 0.00 0.00 5.01
473 475 0.474184 AACAGAGGTTGGAGTGGGTG 59.526 55.000 0.00 0.00 35.46 4.61
474 476 1.222567 AAACAGAGGTTGGAGTGGGT 58.777 50.000 0.00 0.00 37.30 4.51
475 477 2.230660 GAAAACAGAGGTTGGAGTGGG 58.769 52.381 0.00 0.00 37.30 4.61
476 478 2.618709 GTGAAAACAGAGGTTGGAGTGG 59.381 50.000 0.00 0.00 37.30 4.00
477 479 3.545703 AGTGAAAACAGAGGTTGGAGTG 58.454 45.455 0.00 0.00 37.30 3.51
478 480 3.933861 AGTGAAAACAGAGGTTGGAGT 57.066 42.857 0.00 0.00 37.30 3.85
479 481 4.884164 AGAAAGTGAAAACAGAGGTTGGAG 59.116 41.667 0.00 0.00 37.30 3.86
480 482 4.855340 AGAAAGTGAAAACAGAGGTTGGA 58.145 39.130 0.00 0.00 37.30 3.53
481 483 5.582689 AAGAAAGTGAAAACAGAGGTTGG 57.417 39.130 0.00 0.00 37.30 3.77
482 484 6.389906 ACAAAGAAAGTGAAAACAGAGGTTG 58.610 36.000 0.00 0.00 37.30 3.77
483 485 6.590234 ACAAAGAAAGTGAAAACAGAGGTT 57.410 33.333 0.00 0.00 39.43 3.50
484 486 6.590234 AACAAAGAAAGTGAAAACAGAGGT 57.410 33.333 0.00 0.00 0.00 3.85
485 487 7.889589 AAAACAAAGAAAGTGAAAACAGAGG 57.110 32.000 0.00 0.00 0.00 3.69
508 510 9.092876 GGATTAACAAAGTGTTTGATGTCAAAA 57.907 29.630 9.55 0.00 46.08 2.44
509 511 8.474025 AGGATTAACAAAGTGTTTGATGTCAAA 58.526 29.630 6.40 4.16 43.26 2.69
510 512 8.006298 AGGATTAACAAAGTGTTTGATGTCAA 57.994 30.769 6.40 0.00 43.26 3.18
511 513 7.581213 AGGATTAACAAAGTGTTTGATGTCA 57.419 32.000 6.40 0.00 43.26 3.58
512 514 9.559958 CATAGGATTAACAAAGTGTTTGATGTC 57.440 33.333 6.40 0.00 43.26 3.06
513 515 9.295825 TCATAGGATTAACAAAGTGTTTGATGT 57.704 29.630 6.40 0.00 43.26 3.06
514 516 9.778993 CTCATAGGATTAACAAAGTGTTTGATG 57.221 33.333 6.40 0.00 43.26 3.07
515 517 9.739276 TCTCATAGGATTAACAAAGTGTTTGAT 57.261 29.630 6.40 0.00 43.26 2.57
516 518 9.739276 ATCTCATAGGATTAACAAAGTGTTTGA 57.261 29.630 6.40 0.00 43.26 2.69
526 528 9.077885 GCCCATTTAAATCTCATAGGATTAACA 57.922 33.333 0.00 0.00 35.19 2.41
527 529 9.077885 TGCCCATTTAAATCTCATAGGATTAAC 57.922 33.333 0.00 0.00 35.19 2.01
528 530 9.827198 ATGCCCATTTAAATCTCATAGGATTAA 57.173 29.630 0.00 0.00 35.19 1.40
529 531 9.246670 CATGCCCATTTAAATCTCATAGGATTA 57.753 33.333 0.00 0.00 35.19 1.75
530 532 7.310237 GCATGCCCATTTAAATCTCATAGGATT 60.310 37.037 6.36 0.00 37.51 3.01
531 533 6.154021 GCATGCCCATTTAAATCTCATAGGAT 59.846 38.462 6.36 0.00 0.00 3.24
532 534 5.477984 GCATGCCCATTTAAATCTCATAGGA 59.522 40.000 6.36 0.00 0.00 2.94
533 535 5.337009 GGCATGCCCATTTAAATCTCATAGG 60.337 44.000 27.24 0.00 0.00 2.57
534 536 5.244402 TGGCATGCCCATTTAAATCTCATAG 59.756 40.000 33.44 0.41 39.18 2.23
535 537 5.146298 TGGCATGCCCATTTAAATCTCATA 58.854 37.500 33.44 6.19 39.18 2.15
536 538 3.968649 TGGCATGCCCATTTAAATCTCAT 59.031 39.130 33.44 0.00 39.18 2.90
537 539 3.372897 TGGCATGCCCATTTAAATCTCA 58.627 40.909 33.44 7.40 39.18 3.27
548 550 3.146218 AAAAAGAGTGGCATGCCCA 57.854 47.368 33.44 18.73 42.79 5.36
567 569 3.598299 GCATGCCCATTAGCTTCAAAAA 58.402 40.909 6.36 0.00 0.00 1.94
568 570 2.093553 GGCATGCCCATTAGCTTCAAAA 60.094 45.455 27.24 0.00 0.00 2.44
569 571 1.481772 GGCATGCCCATTAGCTTCAAA 59.518 47.619 27.24 0.00 0.00 2.69
570 572 1.113788 GGCATGCCCATTAGCTTCAA 58.886 50.000 27.24 0.00 0.00 2.69
571 573 0.033306 TGGCATGCCCATTAGCTTCA 60.033 50.000 33.44 8.21 39.18 3.02
572 574 2.811307 TGGCATGCCCATTAGCTTC 58.189 52.632 33.44 5.25 39.18 3.86
580 582 1.380246 GATTGGAGTGGCATGCCCA 60.380 57.895 33.44 20.96 42.79 5.36
581 583 2.129785 GGATTGGAGTGGCATGCCC 61.130 63.158 33.44 23.56 34.56 5.36
582 584 2.484062 CGGATTGGAGTGGCATGCC 61.484 63.158 30.54 30.54 0.00 4.40
583 585 1.315257 AACGGATTGGAGTGGCATGC 61.315 55.000 9.90 9.90 0.00 4.06
584 586 2.036958 TAACGGATTGGAGTGGCATG 57.963 50.000 0.00 0.00 0.00 4.06
585 587 3.297134 AATAACGGATTGGAGTGGCAT 57.703 42.857 0.00 0.00 0.00 4.40
586 588 2.799126 AATAACGGATTGGAGTGGCA 57.201 45.000 0.00 0.00 0.00 4.92
587 589 4.421058 GAAAAATAACGGATTGGAGTGGC 58.579 43.478 0.00 0.00 0.00 5.01
588 590 4.705023 AGGAAAAATAACGGATTGGAGTGG 59.295 41.667 0.00 0.00 0.00 4.00
589 591 5.897377 AGGAAAAATAACGGATTGGAGTG 57.103 39.130 0.00 0.00 0.00 3.51
590 592 6.771267 GGATAGGAAAAATAACGGATTGGAGT 59.229 38.462 0.00 0.00 0.00 3.85
591 593 6.998673 AGGATAGGAAAAATAACGGATTGGAG 59.001 38.462 0.00 0.00 0.00 3.86
592 594 6.770785 CAGGATAGGAAAAATAACGGATTGGA 59.229 38.462 0.00 0.00 0.00 3.53
593 595 6.546034 ACAGGATAGGAAAAATAACGGATTGG 59.454 38.462 0.00 0.00 0.00 3.16
594 596 7.067008 ACACAGGATAGGAAAAATAACGGATTG 59.933 37.037 0.00 0.00 0.00 2.67
595 597 7.116736 ACACAGGATAGGAAAAATAACGGATT 58.883 34.615 0.00 0.00 0.00 3.01
596 598 6.659824 ACACAGGATAGGAAAAATAACGGAT 58.340 36.000 0.00 0.00 0.00 4.18
597 599 6.057321 ACACAGGATAGGAAAAATAACGGA 57.943 37.500 0.00 0.00 0.00 4.69
598 600 6.753107 AACACAGGATAGGAAAAATAACGG 57.247 37.500 0.00 0.00 0.00 4.44
606 608 9.020731 GGATTCTTAAAAACACAGGATAGGAAA 57.979 33.333 0.00 0.00 0.00 3.13
607 609 8.390921 AGGATTCTTAAAAACACAGGATAGGAA 58.609 33.333 0.00 0.00 0.00 3.36
608 610 7.928873 AGGATTCTTAAAAACACAGGATAGGA 58.071 34.615 0.00 0.00 0.00 2.94
609 611 9.110502 GTAGGATTCTTAAAAACACAGGATAGG 57.889 37.037 0.00 0.00 0.00 2.57
610 612 8.818057 CGTAGGATTCTTAAAAACACAGGATAG 58.182 37.037 0.00 0.00 0.00 2.08
611 613 8.533657 TCGTAGGATTCTTAAAAACACAGGATA 58.466 33.333 0.00 0.00 0.00 2.59
612 614 7.391620 TCGTAGGATTCTTAAAAACACAGGAT 58.608 34.615 0.00 0.00 0.00 3.24
613 615 6.761312 TCGTAGGATTCTTAAAAACACAGGA 58.239 36.000 0.00 0.00 0.00 3.86
614 616 7.429636 TTCGTAGGATTCTTAAAAACACAGG 57.570 36.000 0.00 0.00 0.00 4.00
615 617 8.717821 TGATTCGTAGGATTCTTAAAAACACAG 58.282 33.333 8.35 0.00 0.00 3.66
616 618 8.610248 TGATTCGTAGGATTCTTAAAAACACA 57.390 30.769 8.35 0.00 0.00 3.72
617 619 9.887406 TTTGATTCGTAGGATTCTTAAAAACAC 57.113 29.630 8.35 0.00 0.00 3.32
623 625 9.884636 TGATTCTTTGATTCGTAGGATTCTTAA 57.115 29.630 8.35 3.52 0.00 1.85
624 626 9.884636 TTGATTCTTTGATTCGTAGGATTCTTA 57.115 29.630 8.35 0.00 0.00 2.10
625 627 8.792830 TTGATTCTTTGATTCGTAGGATTCTT 57.207 30.769 8.35 0.00 0.00 2.52
626 628 8.792830 TTTGATTCTTTGATTCGTAGGATTCT 57.207 30.769 8.35 0.00 0.00 2.40
627 629 8.883731 TCTTTGATTCTTTGATTCGTAGGATTC 58.116 33.333 1.32 1.32 0.00 2.52
628 630 8.792830 TCTTTGATTCTTTGATTCGTAGGATT 57.207 30.769 0.00 0.00 0.00 3.01
629 631 8.792830 TTCTTTGATTCTTTGATTCGTAGGAT 57.207 30.769 0.00 0.00 0.00 3.24
630 632 8.792830 ATTCTTTGATTCTTTGATTCGTAGGA 57.207 30.769 0.00 0.00 0.00 2.94
631 633 8.668353 TGATTCTTTGATTCTTTGATTCGTAGG 58.332 33.333 0.00 0.00 0.00 3.18
634 636 9.403110 CTTTGATTCTTTGATTCTTTGATTCGT 57.597 29.630 0.00 0.00 0.00 3.85
635 637 9.616634 TCTTTGATTCTTTGATTCTTTGATTCG 57.383 29.630 0.00 0.00 0.00 3.34
639 641 8.790718 CCTCTCTTTGATTCTTTGATTCTTTGA 58.209 33.333 0.00 0.00 0.00 2.69
640 642 7.541437 GCCTCTCTTTGATTCTTTGATTCTTTG 59.459 37.037 0.00 0.00 0.00 2.77
641 643 7.450944 AGCCTCTCTTTGATTCTTTGATTCTTT 59.549 33.333 0.00 0.00 0.00 2.52
642 644 6.947158 AGCCTCTCTTTGATTCTTTGATTCTT 59.053 34.615 0.00 0.00 0.00 2.52
643 645 6.483405 AGCCTCTCTTTGATTCTTTGATTCT 58.517 36.000 0.00 0.00 0.00 2.40
644 646 6.756299 AGCCTCTCTTTGATTCTTTGATTC 57.244 37.500 0.00 0.00 0.00 2.52
645 647 8.820153 ATAAGCCTCTCTTTGATTCTTTGATT 57.180 30.769 0.00 0.00 36.25 2.57
646 648 8.820153 AATAAGCCTCTCTTTGATTCTTTGAT 57.180 30.769 0.00 0.00 36.25 2.57
647 649 8.105829 AGAATAAGCCTCTCTTTGATTCTTTGA 58.894 33.333 0.00 0.00 37.03 2.69
648 650 8.278729 AGAATAAGCCTCTCTTTGATTCTTTG 57.721 34.615 0.00 0.00 37.03 2.77
649 651 8.105829 TGAGAATAAGCCTCTCTTTGATTCTTT 58.894 33.333 1.88 0.00 38.91 2.52
650 652 7.628234 TGAGAATAAGCCTCTCTTTGATTCTT 58.372 34.615 1.88 0.00 38.91 2.52
651 653 7.192852 TGAGAATAAGCCTCTCTTTGATTCT 57.807 36.000 0.00 0.00 40.32 2.40
652 654 7.095691 CGATGAGAATAAGCCTCTCTTTGATTC 60.096 40.741 1.88 0.00 40.10 2.52
653 655 6.705381 CGATGAGAATAAGCCTCTCTTTGATT 59.295 38.462 1.88 0.00 40.10 2.57
654 656 6.222389 CGATGAGAATAAGCCTCTCTTTGAT 58.778 40.000 1.88 0.00 40.10 2.57
655 657 5.595885 CGATGAGAATAAGCCTCTCTTTGA 58.404 41.667 1.88 0.00 40.10 2.69
656 658 4.210955 GCGATGAGAATAAGCCTCTCTTTG 59.789 45.833 1.88 1.24 40.10 2.77
657 659 4.141846 TGCGATGAGAATAAGCCTCTCTTT 60.142 41.667 1.88 0.00 40.10 2.52
658 660 3.386078 TGCGATGAGAATAAGCCTCTCTT 59.614 43.478 1.88 0.00 40.10 2.85
659 661 2.961741 TGCGATGAGAATAAGCCTCTCT 59.038 45.455 1.88 0.00 40.10 3.10
660 662 3.377346 TGCGATGAGAATAAGCCTCTC 57.623 47.619 0.00 0.00 39.89 3.20
661 663 3.306641 GGATGCGATGAGAATAAGCCTCT 60.307 47.826 0.00 0.00 0.00 3.69
662 664 2.999355 GGATGCGATGAGAATAAGCCTC 59.001 50.000 0.00 0.00 0.00 4.70
663 665 2.636893 AGGATGCGATGAGAATAAGCCT 59.363 45.455 0.00 0.00 0.00 4.58
664 666 3.051081 AGGATGCGATGAGAATAAGCC 57.949 47.619 0.00 0.00 0.00 4.35
665 667 4.274459 ACAAAGGATGCGATGAGAATAAGC 59.726 41.667 0.00 0.00 0.00 3.09
666 668 5.525012 TCACAAAGGATGCGATGAGAATAAG 59.475 40.000 0.00 0.00 0.00 1.73
697 699 0.099968 TTGTACGATCTTCTCCGGCG 59.900 55.000 0.00 0.00 0.00 6.46
702 704 4.027295 CAGCGTGATTTGTACGATCTTCTC 60.027 45.833 1.32 1.23 43.82 2.87
703 705 3.859961 CAGCGTGATTTGTACGATCTTCT 59.140 43.478 1.32 3.16 43.82 2.85
707 709 2.921121 TGTCAGCGTGATTTGTACGATC 59.079 45.455 1.32 2.90 43.82 3.69
708 710 2.923655 CTGTCAGCGTGATTTGTACGAT 59.076 45.455 1.32 0.00 43.82 3.73
714 716 0.451628 CGTGCTGTCAGCGTGATTTG 60.452 55.000 19.68 0.98 46.26 2.32
749 760 2.436542 TCGGAGACTTTTTCTGGTTCCA 59.563 45.455 0.00 0.00 33.22 3.53
778 789 1.710816 GAGGAGATGGGATTCGGAGT 58.289 55.000 0.00 0.00 0.00 3.85
789 800 0.807667 CCTTTGGCGACGAGGAGATG 60.808 60.000 4.52 0.00 38.24 2.90
934 954 3.706373 CGAGTGGGTGGGTGAGGG 61.706 72.222 0.00 0.00 0.00 4.30
949 973 2.891941 GATGGATTGCTGGTGGGCGA 62.892 60.000 0.00 0.00 34.52 5.54
951 975 2.129785 GGATGGATTGCTGGTGGGC 61.130 63.158 0.00 0.00 0.00 5.36
1734 1764 1.252215 TGACGTTGCCGAGGATGGTA 61.252 55.000 0.00 0.00 37.88 3.25
1866 1896 0.824595 TGTCCTCGTCCTTGTCGGAA 60.825 55.000 0.00 0.00 45.32 4.30
1921 1951 1.228769 TGTAGTCGGACCACTGCCT 60.229 57.895 8.14 0.00 0.00 4.75
2039 2070 2.821969 AGTTGATGTTCATCCACAAGCC 59.178 45.455 15.78 0.00 0.00 4.35
2182 2221 7.009540 CAGAAAAGCATGATTAATCCGGAAAAC 59.990 37.037 9.01 0.00 0.00 2.43
2267 2306 2.009051 GCATCATCATCGGTTCACACA 58.991 47.619 0.00 0.00 0.00 3.72
2277 2316 7.175467 TGGAATTTAGTATGTGGCATCATCATC 59.825 37.037 5.95 1.03 0.00 2.92
2302 2350 4.330250 AGTGGGATCTGAAAACATGTCTG 58.670 43.478 0.00 0.00 0.00 3.51
2384 2434 3.689649 CCCGTTCCAGAACTTAAGAATGG 59.310 47.826 10.09 13.25 42.57 3.16
2616 2671 3.245016 TGGGAGCTCAGTGATTGTGAAAT 60.245 43.478 17.19 0.00 0.00 2.17
2625 2680 1.196766 AGCATGTGGGAGCTCAGTGA 61.197 55.000 17.19 0.00 36.00 3.41
2628 2683 4.220413 CAGCATGTGGGAGCTCAG 57.780 61.111 17.19 0.00 39.50 3.35
2725 2782 5.032846 TCTCCTAGTCTTCATTGACCCATT 58.967 41.667 0.00 0.00 37.66 3.16
2782 2839 1.457346 CGGAAGCTTCAGAAGGCAAT 58.543 50.000 27.02 0.00 0.00 3.56
2802 2860 2.029020 TCGATGACTTGGAACAGTCAGG 60.029 50.000 9.28 4.54 44.67 3.86
2813 2871 5.075448 CGAATTTGTTGACTCGATGACTTG 58.925 41.667 0.00 0.00 33.13 3.16
2836 2894 4.090786 GTGCTCTTAGCTCGAAAGACTTTC 59.909 45.833 16.58 16.58 42.97 2.62
2837 2895 3.991121 GTGCTCTTAGCTCGAAAGACTTT 59.009 43.478 0.00 0.00 42.97 2.66
2852 2910 4.678044 CGTCACTGTATGTATGGTGCTCTT 60.678 45.833 0.00 0.00 0.00 2.85
2863 2921 0.037326 CCCAGCACGTCACTGTATGT 60.037 55.000 12.75 0.00 33.09 2.29
2864 2922 0.246360 TCCCAGCACGTCACTGTATG 59.754 55.000 12.75 3.34 33.09 2.39
2868 2926 2.047844 CCTCCCAGCACGTCACTG 60.048 66.667 7.93 7.93 34.82 3.66
2886 2944 4.214332 GTGAAGTGAGAATGAACAGGAACC 59.786 45.833 0.00 0.00 0.00 3.62
2901 2959 1.421268 ACTGCCTCCATTGTGAAGTGA 59.579 47.619 0.00 0.00 0.00 3.41
2903 2961 1.421268 TGACTGCCTCCATTGTGAAGT 59.579 47.619 0.00 0.00 0.00 3.01
2920 2978 1.880027 ACCAAGAACCGCAGAAATGAC 59.120 47.619 0.00 0.00 0.00 3.06
2925 2983 1.347707 AGATCACCAAGAACCGCAGAA 59.652 47.619 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.