Multiple sequence alignment - TraesCS3D01G000300

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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 TraesCS3D01G000300 chr3D 100.000 3212 0 0 1 3212 333518 336729 0.000000e+00 5932
1 TraesCS3D01G000300 chr3D 97.613 2597 50 4 616 3212 468955024 468957608 0.000000e+00 4442
2 TraesCS3D01G000300 chr4D 98.306 2598 42 2 616 3212 491381490 491384086 0.000000e+00 4553
3 TraesCS3D01G000300 chr1D 98.306 2598 41 2 616 3212 316243968 316241373 0.000000e+00 4551
4 TraesCS3D01G000300 chr2D 98.040 2602 44 2 616 3212 130079133 130076534 0.000000e+00 4516
5 TraesCS3D01G000300 chr2D 98.036 2597 50 1 616 3212 617340745 617343340 0.000000e+00 4512
6 TraesCS3D01G000300 chr2D 83.444 151 22 3 1 151 284536560 284536413 1.550000e-28 137
7 TraesCS3D01G000300 chr6D 97.921 2597 49 2 616 3212 420171217 420173808 0.000000e+00 4492
8 TraesCS3D01G000300 chr7D 97.882 2597 44 3 616 3212 531067727 531065142 0.000000e+00 4481
9 TraesCS3D01G000300 chr7D 89.295 2653 196 34 616 3208 503838182 503835558 0.000000e+00 3245
10 TraesCS3D01G000300 chr5D 97.575 2598 56 3 616 3212 78602934 78600343 0.000000e+00 4442
11 TraesCS3D01G000300 chr5D 98.584 2048 26 2 616 2662 555413536 555415581 0.000000e+00 3618
12 TraesCS3D01G000300 chr4A 95.979 2611 78 14 612 3212 731637353 731634760 0.000000e+00 4215
13 TraesCS3D01G000300 chr4A 95.077 2600 86 9 616 3212 478227133 478229693 0.000000e+00 4054
14 TraesCS3D01G000300 chr6B 92.111 2624 157 22 616 3212 630833944 630831344 0.000000e+00 3653
15 TraesCS3D01G000300 chr3A 93.485 614 39 1 1 613 9215481 9214868 0.000000e+00 911
16 TraesCS3D01G000300 chr2A 82.119 151 24 3 1 151 333755616 333755763 3.360000e-25 126


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 TraesCS3D01G000300 chr3D 333518 336729 3211 False 5932 5932 100.000 1 3212 1 chr3D.!!$F1 3211
1 TraesCS3D01G000300 chr3D 468955024 468957608 2584 False 4442 4442 97.613 616 3212 1 chr3D.!!$F2 2596
2 TraesCS3D01G000300 chr4D 491381490 491384086 2596 False 4553 4553 98.306 616 3212 1 chr4D.!!$F1 2596
3 TraesCS3D01G000300 chr1D 316241373 316243968 2595 True 4551 4551 98.306 616 3212 1 chr1D.!!$R1 2596
4 TraesCS3D01G000300 chr2D 130076534 130079133 2599 True 4516 4516 98.040 616 3212 1 chr2D.!!$R1 2596
5 TraesCS3D01G000300 chr2D 617340745 617343340 2595 False 4512 4512 98.036 616 3212 1 chr2D.!!$F1 2596
6 TraesCS3D01G000300 chr6D 420171217 420173808 2591 False 4492 4492 97.921 616 3212 1 chr6D.!!$F1 2596
7 TraesCS3D01G000300 chr7D 531065142 531067727 2585 True 4481 4481 97.882 616 3212 1 chr7D.!!$R2 2596
8 TraesCS3D01G000300 chr7D 503835558 503838182 2624 True 3245 3245 89.295 616 3208 1 chr7D.!!$R1 2592
9 TraesCS3D01G000300 chr5D 78600343 78602934 2591 True 4442 4442 97.575 616 3212 1 chr5D.!!$R1 2596
10 TraesCS3D01G000300 chr5D 555413536 555415581 2045 False 3618 3618 98.584 616 2662 1 chr5D.!!$F1 2046
11 TraesCS3D01G000300 chr4A 731634760 731637353 2593 True 4215 4215 95.979 612 3212 1 chr4A.!!$R1 2600
12 TraesCS3D01G000300 chr4A 478227133 478229693 2560 False 4054 4054 95.077 616 3212 1 chr4A.!!$F1 2596
13 TraesCS3D01G000300 chr6B 630831344 630833944 2600 True 3653 3653 92.111 616 3212 1 chr6B.!!$R1 2596
14 TraesCS3D01G000300 chr3A 9214868 9215481 613 True 911 911 93.485 1 613 1 chr3A.!!$R1 612

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
445 446 0.034059 CCCGCGATGAAGCTAGGAAT 59.966 55.0 8.23 0.00 32.12 3.01 F
540 541 0.108615 CTTGAGGTGCCGAGAACGAT 60.109 55.0 0.00 0.00 42.66 3.73 F
1248 1282 0.308993 GCAAACTCCTGACACTGTGC 59.691 55.0 7.90 1.49 0.00 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1248 1282 2.168728 GCCCACAGAAACTAGGGTCTAG 59.831 54.545 0.0 0.83 43.42 2.43 R
2124 2189 3.533547 GAGCTCAGCAATGACATTCTCT 58.466 45.455 9.4 0.00 0.00 3.10 R
2844 2954 0.832135 AGACGAAGAGGAGGTGCCAA 60.832 55.000 0.0 0.00 40.02 4.52 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
28 29 5.382616 TCTTGGTTTTAGTTTCTCTTCCCC 58.617 41.667 0.00 0.00 0.00 4.81
33 34 4.910458 TTTAGTTTCTCTTCCCCTCCAG 57.090 45.455 0.00 0.00 0.00 3.86
49 50 5.377478 CCCTCCAGTTTCTTCCCATTATAC 58.623 45.833 0.00 0.00 0.00 1.47
122 123 3.687698 ACGAACTGTAAAATAGCGGCAAT 59.312 39.130 1.45 0.00 0.00 3.56
149 150 8.274322 ACACCAACATATTTTGATGATCTCCTA 58.726 33.333 2.87 0.00 29.97 2.94
169 170 2.375014 AACCGGTGGTCCAAATTCTT 57.625 45.000 8.52 0.00 33.12 2.52
197 198 7.256756 TCTTTATAGTCTCGTAGCAACCTAC 57.743 40.000 0.00 0.00 40.44 3.18
206 207 2.618053 GTAGCAACCTACGAGCATTGT 58.382 47.619 0.00 0.00 35.06 2.71
208 209 0.179189 GCAACCTACGAGCATTGTGC 60.179 55.000 0.00 0.00 45.46 4.57
232 233 8.742777 TGCTACTTTTTCTAATGATTCAATGCT 58.257 29.630 0.00 0.00 0.00 3.79
244 245 8.523915 AATGATTCAATGCTAATGGTTACTCA 57.476 30.769 0.00 0.00 0.00 3.41
248 249 6.135290 TCAATGCTAATGGTTACTCAATGC 57.865 37.500 0.00 0.00 0.00 3.56
249 250 5.651576 TCAATGCTAATGGTTACTCAATGCA 59.348 36.000 0.00 0.00 0.00 3.96
263 264 2.070783 CAATGCATTGCTTTGGACCAC 58.929 47.619 25.50 0.00 39.14 4.16
297 298 1.796151 CGATGTCGGCATTGCAGTT 59.204 52.632 2.92 0.00 35.07 3.16
298 299 0.168788 CGATGTCGGCATTGCAGTTT 59.831 50.000 2.92 0.00 35.07 2.66
299 300 1.791555 CGATGTCGGCATTGCAGTTTC 60.792 52.381 2.92 4.96 35.07 2.78
300 301 0.168788 ATGTCGGCATTGCAGTTTCG 59.831 50.000 11.39 4.46 29.54 3.46
301 302 0.882484 TGTCGGCATTGCAGTTTCGA 60.882 50.000 11.39 6.90 0.00 3.71
302 303 0.237235 GTCGGCATTGCAGTTTCGAA 59.763 50.000 11.39 0.00 0.00 3.71
303 304 0.947960 TCGGCATTGCAGTTTCGAAA 59.052 45.000 6.47 6.47 0.00 3.46
304 305 1.539388 TCGGCATTGCAGTTTCGAAAT 59.461 42.857 14.69 0.45 0.00 2.17
305 306 1.913403 CGGCATTGCAGTTTCGAAATC 59.087 47.619 14.69 8.00 0.00 2.17
306 307 2.414559 CGGCATTGCAGTTTCGAAATCT 60.415 45.455 14.69 10.16 0.00 2.40
307 308 3.181511 CGGCATTGCAGTTTCGAAATCTA 60.182 43.478 14.69 4.39 0.00 1.98
308 309 4.496341 CGGCATTGCAGTTTCGAAATCTAT 60.496 41.667 14.69 6.41 0.00 1.98
309 310 4.972440 GGCATTGCAGTTTCGAAATCTATC 59.028 41.667 14.69 0.27 0.00 2.08
310 311 5.220931 GGCATTGCAGTTTCGAAATCTATCT 60.221 40.000 14.69 2.89 0.00 1.98
311 312 5.680229 GCATTGCAGTTTCGAAATCTATCTG 59.320 40.000 14.69 16.01 0.00 2.90
312 313 6.676456 GCATTGCAGTTTCGAAATCTATCTGT 60.676 38.462 14.69 0.00 0.00 3.41
313 314 6.801539 TTGCAGTTTCGAAATCTATCTGTT 57.198 33.333 14.69 0.00 0.00 3.16
314 315 7.899178 TTGCAGTTTCGAAATCTATCTGTTA 57.101 32.000 14.69 7.05 0.00 2.41
315 316 7.290857 TGCAGTTTCGAAATCTATCTGTTAC 57.709 36.000 14.69 4.63 0.00 2.50
316 317 6.871492 TGCAGTTTCGAAATCTATCTGTTACA 59.129 34.615 14.69 6.94 0.00 2.41
317 318 7.549134 TGCAGTTTCGAAATCTATCTGTTACAT 59.451 33.333 14.69 0.00 0.00 2.29
318 319 7.848051 GCAGTTTCGAAATCTATCTGTTACATG 59.152 37.037 14.69 0.00 0.00 3.21
319 320 9.087424 CAGTTTCGAAATCTATCTGTTACATGA 57.913 33.333 14.69 0.00 0.00 3.07
320 321 9.653287 AGTTTCGAAATCTATCTGTTACATGAA 57.347 29.630 14.69 0.00 0.00 2.57
341 342 1.047801 AAAAACTCACCATGCCCACC 58.952 50.000 0.00 0.00 0.00 4.61
342 343 0.105760 AAAACTCACCATGCCCACCA 60.106 50.000 0.00 0.00 0.00 4.17
343 344 0.827507 AAACTCACCATGCCCACCAC 60.828 55.000 0.00 0.00 0.00 4.16
344 345 2.361610 CTCACCATGCCCACCACC 60.362 66.667 0.00 0.00 0.00 4.61
345 346 3.181530 TCACCATGCCCACCACCA 61.182 61.111 0.00 0.00 0.00 4.17
346 347 2.990967 CACCATGCCCACCACCAC 60.991 66.667 0.00 0.00 0.00 4.16
347 348 4.299796 ACCATGCCCACCACCACC 62.300 66.667 0.00 0.00 0.00 4.61
348 349 3.983420 CCATGCCCACCACCACCT 61.983 66.667 0.00 0.00 0.00 4.00
349 350 2.611505 CCATGCCCACCACCACCTA 61.612 63.158 0.00 0.00 0.00 3.08
350 351 1.382240 CATGCCCACCACCACCTAA 59.618 57.895 0.00 0.00 0.00 2.69
351 352 0.680921 CATGCCCACCACCACCTAAG 60.681 60.000 0.00 0.00 0.00 2.18
352 353 0.844661 ATGCCCACCACCACCTAAGA 60.845 55.000 0.00 0.00 0.00 2.10
353 354 1.063070 TGCCCACCACCACCTAAGAA 61.063 55.000 0.00 0.00 0.00 2.52
354 355 0.322546 GCCCACCACCACCTAAGAAG 60.323 60.000 0.00 0.00 0.00 2.85
355 356 1.358152 CCCACCACCACCTAAGAAGA 58.642 55.000 0.00 0.00 0.00 2.87
356 357 1.916181 CCCACCACCACCTAAGAAGAT 59.084 52.381 0.00 0.00 0.00 2.40
357 358 2.092914 CCCACCACCACCTAAGAAGATC 60.093 54.545 0.00 0.00 0.00 2.75
358 359 2.418746 CCACCACCACCTAAGAAGATCG 60.419 54.545 0.00 0.00 0.00 3.69
359 360 1.831736 ACCACCACCTAAGAAGATCGG 59.168 52.381 0.00 0.00 0.00 4.18
360 361 2.108168 CCACCACCTAAGAAGATCGGA 58.892 52.381 0.00 0.00 0.00 4.55
361 362 2.500098 CCACCACCTAAGAAGATCGGAA 59.500 50.000 0.00 0.00 0.00 4.30
362 363 3.055385 CCACCACCTAAGAAGATCGGAAA 60.055 47.826 0.00 0.00 0.00 3.13
363 364 4.564821 CCACCACCTAAGAAGATCGGAAAA 60.565 45.833 0.00 0.00 0.00 2.29
364 365 5.001232 CACCACCTAAGAAGATCGGAAAAA 58.999 41.667 0.00 0.00 0.00 1.94
425 426 9.594478 TTATACATTGTCTTGTAGTGTACATGG 57.406 33.333 0.00 0.00 38.68 3.66
426 427 4.695455 ACATTGTCTTGTAGTGTACATGGC 59.305 41.667 0.00 0.00 38.68 4.40
427 428 3.328382 TGTCTTGTAGTGTACATGGCC 57.672 47.619 0.00 0.00 37.57 5.36
428 429 2.027561 TGTCTTGTAGTGTACATGGCCC 60.028 50.000 0.00 0.00 37.57 5.80
429 430 1.206132 TCTTGTAGTGTACATGGCCCG 59.794 52.381 0.00 0.00 38.68 6.13
430 431 0.391927 TTGTAGTGTACATGGCCCGC 60.392 55.000 0.00 0.00 38.68 6.13
431 432 1.881252 GTAGTGTACATGGCCCGCG 60.881 63.158 0.00 0.00 0.00 6.46
432 433 2.053277 TAGTGTACATGGCCCGCGA 61.053 57.895 8.23 0.00 0.00 5.87
433 434 1.396607 TAGTGTACATGGCCCGCGAT 61.397 55.000 8.23 0.00 0.00 4.58
434 435 2.203001 TGTACATGGCCCGCGATG 60.203 61.111 8.23 5.70 37.99 3.84
435 436 2.108157 GTACATGGCCCGCGATGA 59.892 61.111 17.16 0.32 36.01 2.92
436 437 1.522806 GTACATGGCCCGCGATGAA 60.523 57.895 17.16 0.00 36.01 2.57
437 438 1.227527 TACATGGCCCGCGATGAAG 60.228 57.895 17.16 0.00 36.01 3.02
438 439 3.957535 CATGGCCCGCGATGAAGC 61.958 66.667 8.23 1.61 34.70 3.86
439 440 4.181010 ATGGCCCGCGATGAAGCT 62.181 61.111 8.23 0.00 34.40 3.74
440 441 2.807107 ATGGCCCGCGATGAAGCTA 61.807 57.895 8.23 0.00 34.40 3.32
441 442 2.663188 GGCCCGCGATGAAGCTAG 60.663 66.667 8.23 0.00 34.40 3.42
442 443 2.663188 GCCCGCGATGAAGCTAGG 60.663 66.667 8.23 0.00 34.40 3.02
443 444 3.129300 CCCGCGATGAAGCTAGGA 58.871 61.111 8.23 0.00 32.12 2.94
444 445 1.441729 CCCGCGATGAAGCTAGGAA 59.558 57.895 8.23 0.00 32.12 3.36
445 446 0.034059 CCCGCGATGAAGCTAGGAAT 59.966 55.000 8.23 0.00 32.12 3.01
446 447 1.541233 CCCGCGATGAAGCTAGGAATT 60.541 52.381 8.23 0.00 32.12 2.17
447 448 2.213499 CCGCGATGAAGCTAGGAATTT 58.787 47.619 8.23 0.00 34.40 1.82
448 449 2.221981 CCGCGATGAAGCTAGGAATTTC 59.778 50.000 8.23 0.00 34.40 2.17
449 450 2.221981 CGCGATGAAGCTAGGAATTTCC 59.778 50.000 0.00 7.39 33.74 3.13
450 451 3.206150 GCGATGAAGCTAGGAATTTCCA 58.794 45.455 17.57 3.23 39.61 3.53
451 452 3.817647 GCGATGAAGCTAGGAATTTCCAT 59.182 43.478 17.57 5.57 39.61 3.41
452 453 4.997395 GCGATGAAGCTAGGAATTTCCATA 59.003 41.667 17.57 6.37 39.61 2.74
453 454 5.645497 GCGATGAAGCTAGGAATTTCCATAT 59.355 40.000 17.57 0.00 39.61 1.78
454 455 6.818644 GCGATGAAGCTAGGAATTTCCATATA 59.181 38.462 17.57 0.92 39.61 0.86
455 456 7.497249 GCGATGAAGCTAGGAATTTCCATATAT 59.503 37.037 17.57 0.90 39.61 0.86
456 457 9.388506 CGATGAAGCTAGGAATTTCCATATATT 57.611 33.333 17.57 5.59 39.61 1.28
481 482 4.700268 TTGTCATGCAACATACATGGAC 57.300 40.909 0.00 0.00 44.09 4.02
482 483 3.683802 TGTCATGCAACATACATGGACA 58.316 40.909 0.00 0.00 44.09 4.02
483 484 4.077822 TGTCATGCAACATACATGGACAA 58.922 39.130 0.00 0.00 44.09 3.18
484 485 4.705991 TGTCATGCAACATACATGGACAAT 59.294 37.500 0.00 0.00 44.09 2.71
485 486 5.884792 TGTCATGCAACATACATGGACAATA 59.115 36.000 0.00 0.00 44.09 1.90
486 487 6.038492 TGTCATGCAACATACATGGACAATAG 59.962 38.462 0.00 0.00 44.09 1.73
487 488 5.532032 TCATGCAACATACATGGACAATAGG 59.468 40.000 0.00 0.00 44.09 2.57
488 489 4.854173 TGCAACATACATGGACAATAGGT 58.146 39.130 0.00 0.00 0.00 3.08
489 490 5.995446 TGCAACATACATGGACAATAGGTA 58.005 37.500 0.00 0.00 0.00 3.08
490 491 6.600388 TGCAACATACATGGACAATAGGTAT 58.400 36.000 0.00 0.00 0.00 2.73
491 492 7.059788 TGCAACATACATGGACAATAGGTATT 58.940 34.615 0.00 0.00 0.00 1.89
492 493 7.559533 TGCAACATACATGGACAATAGGTATTT 59.440 33.333 0.00 0.00 0.00 1.40
493 494 7.862372 GCAACATACATGGACAATAGGTATTTG 59.138 37.037 0.00 0.00 0.00 2.32
494 495 8.902806 CAACATACATGGACAATAGGTATTTGT 58.097 33.333 0.00 0.00 0.00 2.83
495 496 9.474313 AACATACATGGACAATAGGTATTTGTT 57.526 29.630 0.00 0.00 0.00 2.83
496 497 8.902806 ACATACATGGACAATAGGTATTTGTTG 58.097 33.333 0.00 0.00 0.00 3.33
497 498 8.902806 CATACATGGACAATAGGTATTTGTTGT 58.097 33.333 0.00 0.00 37.49 3.32
498 499 7.391148 ACATGGACAATAGGTATTTGTTGTC 57.609 36.000 8.20 8.20 45.90 3.18
499 500 6.093495 ACATGGACAATAGGTATTTGTTGTCG 59.907 38.462 9.99 1.61 46.96 4.35
500 501 5.795972 TGGACAATAGGTATTTGTTGTCGA 58.204 37.500 9.99 4.78 46.96 4.20
501 502 6.231951 TGGACAATAGGTATTTGTTGTCGAA 58.768 36.000 9.99 0.75 46.96 3.71
502 503 6.882140 TGGACAATAGGTATTTGTTGTCGAAT 59.118 34.615 9.99 0.00 46.96 3.34
503 504 7.392113 TGGACAATAGGTATTTGTTGTCGAATT 59.608 33.333 9.99 0.00 46.96 2.17
504 505 8.241367 GGACAATAGGTATTTGTTGTCGAATTT 58.759 33.333 9.99 0.00 46.96 1.82
505 506 9.274065 GACAATAGGTATTTGTTGTCGAATTTC 57.726 33.333 0.00 0.00 40.44 2.17
506 507 8.788806 ACAATAGGTATTTGTTGTCGAATTTCA 58.211 29.630 0.00 0.00 29.39 2.69
507 508 9.061610 CAATAGGTATTTGTTGTCGAATTTCAC 57.938 33.333 0.00 0.00 0.00 3.18
508 509 6.877611 AGGTATTTGTTGTCGAATTTCACT 57.122 33.333 0.00 0.00 0.00 3.41
509 510 7.972832 AGGTATTTGTTGTCGAATTTCACTA 57.027 32.000 0.00 0.00 0.00 2.74
510 511 8.029642 AGGTATTTGTTGTCGAATTTCACTAG 57.970 34.615 0.00 0.00 0.00 2.57
511 512 7.876068 AGGTATTTGTTGTCGAATTTCACTAGA 59.124 33.333 0.00 0.00 0.00 2.43
512 513 8.169268 GGTATTTGTTGTCGAATTTCACTAGAG 58.831 37.037 0.00 0.00 0.00 2.43
513 514 7.962964 ATTTGTTGTCGAATTTCACTAGAGA 57.037 32.000 0.00 0.00 0.00 3.10
514 515 7.780008 TTTGTTGTCGAATTTCACTAGAGAA 57.220 32.000 0.00 0.00 0.00 2.87
515 516 7.780008 TTGTTGTCGAATTTCACTAGAGAAA 57.220 32.000 16.22 16.22 41.31 2.52
516 517 7.408132 TGTTGTCGAATTTCACTAGAGAAAG 57.592 36.000 18.27 7.51 40.49 2.62
517 518 6.984474 TGTTGTCGAATTTCACTAGAGAAAGT 59.016 34.615 18.27 16.29 40.49 2.66
518 519 8.139350 TGTTGTCGAATTTCACTAGAGAAAGTA 58.861 33.333 18.27 2.32 40.49 2.24
519 520 9.141400 GTTGTCGAATTTCACTAGAGAAAGTAT 57.859 33.333 18.27 9.03 40.49 2.12
521 522 9.784680 TGTCGAATTTCACTAGAGAAAGTATAC 57.215 33.333 18.27 16.18 40.49 1.47
528 529 8.880991 TTCACTAGAGAAAGTATACTTGAGGT 57.119 34.615 18.70 3.02 36.12 3.85
529 530 8.282455 TCACTAGAGAAAGTATACTTGAGGTG 57.718 38.462 18.70 18.25 36.12 4.00
530 531 6.975772 CACTAGAGAAAGTATACTTGAGGTGC 59.024 42.308 18.70 6.09 36.12 5.01
531 532 5.346181 AGAGAAAGTATACTTGAGGTGCC 57.654 43.478 18.70 4.97 36.12 5.01
532 533 4.113354 GAGAAAGTATACTTGAGGTGCCG 58.887 47.826 18.70 0.00 36.12 5.69
533 534 3.767673 AGAAAGTATACTTGAGGTGCCGA 59.232 43.478 18.70 0.00 36.12 5.54
534 535 3.802948 AAGTATACTTGAGGTGCCGAG 57.197 47.619 17.35 0.00 34.38 4.63
535 536 3.014304 AGTATACTTGAGGTGCCGAGA 57.986 47.619 0.00 0.00 0.00 4.04
536 537 3.362706 AGTATACTTGAGGTGCCGAGAA 58.637 45.455 0.00 0.00 0.00 2.87
537 538 2.674796 ATACTTGAGGTGCCGAGAAC 57.325 50.000 0.00 0.00 0.00 3.01
538 539 0.242825 TACTTGAGGTGCCGAGAACG 59.757 55.000 0.00 0.00 39.43 3.95
539 540 1.289066 CTTGAGGTGCCGAGAACGA 59.711 57.895 0.00 0.00 42.66 3.85
540 541 0.108615 CTTGAGGTGCCGAGAACGAT 60.109 55.000 0.00 0.00 42.66 3.73
541 542 0.320374 TTGAGGTGCCGAGAACGATT 59.680 50.000 0.00 0.00 42.66 3.34
542 543 0.320374 TGAGGTGCCGAGAACGATTT 59.680 50.000 0.00 0.00 42.66 2.17
543 544 1.270625 TGAGGTGCCGAGAACGATTTT 60.271 47.619 0.00 0.00 42.66 1.82
544 545 1.128692 GAGGTGCCGAGAACGATTTTG 59.871 52.381 0.00 0.00 42.66 2.44
545 546 0.872388 GGTGCCGAGAACGATTTTGT 59.128 50.000 0.00 0.00 42.66 2.83
546 547 1.265905 GGTGCCGAGAACGATTTTGTT 59.734 47.619 0.00 0.00 42.66 2.83
547 548 2.307049 GTGCCGAGAACGATTTTGTTG 58.693 47.619 0.00 0.00 42.66 3.33
548 549 1.265635 TGCCGAGAACGATTTTGTTGG 59.734 47.619 0.00 0.00 42.66 3.77
549 550 1.533731 GCCGAGAACGATTTTGTTGGA 59.466 47.619 0.00 0.00 42.66 3.53
550 551 2.031508 GCCGAGAACGATTTTGTTGGAA 60.032 45.455 0.00 0.00 42.66 3.53
551 552 3.365969 GCCGAGAACGATTTTGTTGGAAT 60.366 43.478 0.00 0.00 42.66 3.01
552 553 4.142773 GCCGAGAACGATTTTGTTGGAATA 60.143 41.667 0.00 0.00 42.66 1.75
553 554 5.321516 CCGAGAACGATTTTGTTGGAATAC 58.678 41.667 0.00 0.00 42.66 1.89
554 555 5.013236 CGAGAACGATTTTGTTGGAATACG 58.987 41.667 0.00 0.00 42.66 3.06
555 556 5.164031 CGAGAACGATTTTGTTGGAATACGA 60.164 40.000 0.00 0.00 42.66 3.43
556 557 6.455113 CGAGAACGATTTTGTTGGAATACGAT 60.455 38.462 0.00 0.00 42.66 3.73
557 558 7.253850 CGAGAACGATTTTGTTGGAATACGATA 60.254 37.037 0.00 0.00 42.66 2.92
558 559 7.906160 AGAACGATTTTGTTGGAATACGATAG 58.094 34.615 0.00 0.00 35.12 2.08
559 560 7.762615 AGAACGATTTTGTTGGAATACGATAGA 59.237 33.333 0.00 0.00 33.61 1.98
560 561 7.464830 ACGATTTTGTTGGAATACGATAGAG 57.535 36.000 0.00 0.00 41.38 2.43
561 562 7.262772 ACGATTTTGTTGGAATACGATAGAGA 58.737 34.615 0.00 0.00 41.38 3.10
562 563 7.762615 ACGATTTTGTTGGAATACGATAGAGAA 59.237 33.333 0.00 0.00 41.38 2.87
563 564 8.600625 CGATTTTGTTGGAATACGATAGAGAAA 58.399 33.333 0.00 0.00 41.38 2.52
576 577 7.932120 ACGATAGAGAAATTAATTGAGTCGG 57.068 36.000 0.39 0.00 41.38 4.79
577 578 6.421202 ACGATAGAGAAATTAATTGAGTCGGC 59.579 38.462 0.39 0.00 41.38 5.54
578 579 6.642950 CGATAGAGAAATTAATTGAGTCGGCT 59.357 38.462 0.39 0.00 39.76 5.52
579 580 7.148885 CGATAGAGAAATTAATTGAGTCGGCTC 60.149 40.741 10.89 10.89 39.59 4.70
580 581 5.983540 AGAGAAATTAATTGAGTCGGCTCT 58.016 37.500 19.37 0.00 42.13 4.09
581 582 7.113658 AGAGAAATTAATTGAGTCGGCTCTA 57.886 36.000 19.37 11.64 42.13 2.43
582 583 7.731054 AGAGAAATTAATTGAGTCGGCTCTAT 58.269 34.615 19.37 13.70 42.13 1.98
583 584 8.207545 AGAGAAATTAATTGAGTCGGCTCTATT 58.792 33.333 25.66 25.66 44.81 1.73
584 585 8.147642 AGAAATTAATTGAGTCGGCTCTATTG 57.852 34.615 28.92 0.00 43.42 1.90
585 586 7.987458 AGAAATTAATTGAGTCGGCTCTATTGA 59.013 33.333 28.92 23.54 43.42 2.57
586 587 8.506168 AAATTAATTGAGTCGGCTCTATTGAA 57.494 30.769 28.92 20.37 43.42 2.69
587 588 8.506168 AATTAATTGAGTCGGCTCTATTGAAA 57.494 30.769 28.92 19.57 43.42 2.69
588 589 8.682936 ATTAATTGAGTCGGCTCTATTGAAAT 57.317 30.769 28.92 20.63 43.42 2.17
589 590 8.506168 TTAATTGAGTCGGCTCTATTGAAATT 57.494 30.769 28.92 20.93 43.42 1.82
590 591 7.396540 AATTGAGTCGGCTCTATTGAAATTT 57.603 32.000 22.81 1.11 42.54 1.82
591 592 6.817765 TTGAGTCGGCTCTATTGAAATTTT 57.182 33.333 19.37 0.00 42.13 1.82
592 593 7.915293 TTGAGTCGGCTCTATTGAAATTTTA 57.085 32.000 19.37 0.00 42.13 1.52
593 594 8.506168 TTGAGTCGGCTCTATTGAAATTTTAT 57.494 30.769 19.37 0.00 42.13 1.40
594 595 7.919690 TGAGTCGGCTCTATTGAAATTTTATG 58.080 34.615 19.37 0.00 42.13 1.90
595 596 7.552687 TGAGTCGGCTCTATTGAAATTTTATGT 59.447 33.333 19.37 0.00 42.13 2.29
596 597 7.697691 AGTCGGCTCTATTGAAATTTTATGTG 58.302 34.615 0.00 0.00 0.00 3.21
597 598 7.336931 AGTCGGCTCTATTGAAATTTTATGTGT 59.663 33.333 0.00 0.00 0.00 3.72
598 599 8.609176 GTCGGCTCTATTGAAATTTTATGTGTA 58.391 33.333 0.00 0.00 0.00 2.90
599 600 8.609176 TCGGCTCTATTGAAATTTTATGTGTAC 58.391 33.333 0.00 0.00 0.00 2.90
600 601 8.394877 CGGCTCTATTGAAATTTTATGTGTACA 58.605 33.333 0.00 0.00 0.00 2.90
779 784 0.734253 ACAGCGATTCTGACGTGAGC 60.734 55.000 0.00 0.00 45.72 4.26
789 795 4.681978 ACGTGAGCGGCCCACTTC 62.682 66.667 12.85 0.00 43.45 3.01
1029 1051 1.954146 GCCGAACAGCAACGAGACA 60.954 57.895 0.00 0.00 0.00 3.41
1248 1282 0.308993 GCAAACTCCTGACACTGTGC 59.691 55.000 7.90 1.49 0.00 4.57
1388 1422 4.141711 GGATGTGCTACTGAGGTAATGGAA 60.142 45.833 0.00 0.00 0.00 3.53
2124 2189 8.423906 TCCTTAAAGAAGAGAAGAAGAAGCTA 57.576 34.615 0.00 0.00 34.25 3.32
2547 2647 5.618640 GCTTCATCACAGGTTCAGACAAATC 60.619 44.000 0.00 0.00 0.00 2.17
2640 2741 7.968405 ACACTGAAATTGTTCAAAGACACTTAC 59.032 33.333 0.00 0.00 43.18 2.34
2844 2954 1.127567 TGAGTGGTAGGTGGCAGCTT 61.128 55.000 25.69 5.96 0.00 3.74
3015 3128 1.553690 GCTGCCCACTGTTCCCTCTA 61.554 60.000 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 7.282585 TGATGTATAATGGGAAGAAACTGGAG 58.717 38.462 0.00 0.00 0.00 3.86
49 50 9.956720 AACAAAAGATCTTTCTGTAGTTTGATG 57.043 29.630 20.71 12.61 33.30 3.07
93 94 6.089820 CCGCTATTTTACAGTTCGTGACTAAA 59.910 38.462 0.00 0.00 36.65 1.85
100 101 2.690786 TGCCGCTATTTTACAGTTCGT 58.309 42.857 0.00 0.00 0.00 3.85
122 123 8.274322 AGGAGATCATCAAAATATGTTGGTGTA 58.726 33.333 16.81 6.22 40.02 2.90
149 150 2.375014 AGAATTTGGACCACCGGTTT 57.625 45.000 2.97 0.00 35.25 3.27
169 170 8.910944 AGGTTGCTACGAGACTATAAAGAAATA 58.089 33.333 0.00 0.00 0.00 1.40
206 207 8.742777 AGCATTGAATCATTAGAAAAAGTAGCA 58.257 29.630 0.00 0.00 0.00 3.49
232 233 6.528537 AAGCAATGCATTGAGTAACCATTA 57.471 33.333 37.36 0.00 40.14 1.90
244 245 1.693062 TGTGGTCCAAAGCAATGCATT 59.307 42.857 5.99 5.99 34.02 3.56
248 249 2.624838 AGTCTTGTGGTCCAAAGCAATG 59.375 45.455 0.00 0.00 34.02 2.82
249 250 2.949447 AGTCTTGTGGTCCAAAGCAAT 58.051 42.857 0.00 0.00 34.02 3.56
263 264 4.161333 GACATCGCCATTTGAAAGTCTTG 58.839 43.478 0.00 0.00 0.00 3.02
322 323 1.047801 GGTGGGCATGGTGAGTTTTT 58.952 50.000 0.00 0.00 0.00 1.94
323 324 0.105760 TGGTGGGCATGGTGAGTTTT 60.106 50.000 0.00 0.00 0.00 2.43
324 325 0.827507 GTGGTGGGCATGGTGAGTTT 60.828 55.000 0.00 0.00 0.00 2.66
325 326 1.228552 GTGGTGGGCATGGTGAGTT 60.229 57.895 0.00 0.00 0.00 3.01
326 327 2.436109 GTGGTGGGCATGGTGAGT 59.564 61.111 0.00 0.00 0.00 3.41
327 328 2.361610 GGTGGTGGGCATGGTGAG 60.362 66.667 0.00 0.00 0.00 3.51
328 329 3.181530 TGGTGGTGGGCATGGTGA 61.182 61.111 0.00 0.00 0.00 4.02
329 330 2.990967 GTGGTGGTGGGCATGGTG 60.991 66.667 0.00 0.00 0.00 4.17
330 331 4.299796 GGTGGTGGTGGGCATGGT 62.300 66.667 0.00 0.00 0.00 3.55
331 332 2.148723 TTAGGTGGTGGTGGGCATGG 62.149 60.000 0.00 0.00 0.00 3.66
332 333 0.680921 CTTAGGTGGTGGTGGGCATG 60.681 60.000 0.00 0.00 0.00 4.06
333 334 0.844661 TCTTAGGTGGTGGTGGGCAT 60.845 55.000 0.00 0.00 0.00 4.40
334 335 1.063070 TTCTTAGGTGGTGGTGGGCA 61.063 55.000 0.00 0.00 0.00 5.36
335 336 0.322546 CTTCTTAGGTGGTGGTGGGC 60.323 60.000 0.00 0.00 0.00 5.36
336 337 1.358152 TCTTCTTAGGTGGTGGTGGG 58.642 55.000 0.00 0.00 0.00 4.61
337 338 2.418746 CGATCTTCTTAGGTGGTGGTGG 60.419 54.545 0.00 0.00 0.00 4.61
338 339 2.418746 CCGATCTTCTTAGGTGGTGGTG 60.419 54.545 0.00 0.00 0.00 4.17
339 340 1.831736 CCGATCTTCTTAGGTGGTGGT 59.168 52.381 0.00 0.00 0.00 4.16
340 341 2.108168 TCCGATCTTCTTAGGTGGTGG 58.892 52.381 0.00 0.00 0.00 4.61
341 342 3.887621 TTCCGATCTTCTTAGGTGGTG 57.112 47.619 0.00 0.00 0.00 4.17
342 343 4.903045 TTTTCCGATCTTCTTAGGTGGT 57.097 40.909 0.00 0.00 0.00 4.16
399 400 9.594478 CCATGTACACTACAAGACAATGTATAA 57.406 33.333 0.00 0.00 42.76 0.98
400 401 7.709182 GCCATGTACACTACAAGACAATGTATA 59.291 37.037 0.00 0.00 42.76 1.47
401 402 6.538742 GCCATGTACACTACAAGACAATGTAT 59.461 38.462 0.00 0.00 42.76 2.29
402 403 5.872617 GCCATGTACACTACAAGACAATGTA 59.127 40.000 0.00 0.00 42.76 2.29
403 404 4.695455 GCCATGTACACTACAAGACAATGT 59.305 41.667 0.00 0.00 42.76 2.71
404 405 4.094887 GGCCATGTACACTACAAGACAATG 59.905 45.833 0.00 0.00 42.76 2.82
405 406 4.261801 GGCCATGTACACTACAAGACAAT 58.738 43.478 0.00 0.00 42.76 2.71
406 407 3.558321 GGGCCATGTACACTACAAGACAA 60.558 47.826 4.39 0.00 42.76 3.18
407 408 2.027561 GGGCCATGTACACTACAAGACA 60.028 50.000 4.39 0.00 42.76 3.41
408 409 2.629051 GGGCCATGTACACTACAAGAC 58.371 52.381 4.39 0.00 42.76 3.01
409 410 1.206132 CGGGCCATGTACACTACAAGA 59.794 52.381 4.39 0.00 42.76 3.02
410 411 1.651987 CGGGCCATGTACACTACAAG 58.348 55.000 4.39 0.00 42.76 3.16
411 412 0.391927 GCGGGCCATGTACACTACAA 60.392 55.000 4.39 0.00 42.76 2.41
412 413 1.219664 GCGGGCCATGTACACTACA 59.780 57.895 4.39 0.00 43.80 2.74
413 414 1.881252 CGCGGGCCATGTACACTAC 60.881 63.158 4.39 0.00 0.00 2.73
414 415 1.396607 ATCGCGGGCCATGTACACTA 61.397 55.000 6.13 0.00 0.00 2.74
415 416 2.731571 ATCGCGGGCCATGTACACT 61.732 57.895 6.13 0.00 0.00 3.55
416 417 2.203015 ATCGCGGGCCATGTACAC 60.203 61.111 6.13 0.00 0.00 2.90
417 418 2.203001 CATCGCGGGCCATGTACA 60.203 61.111 6.13 0.00 0.00 2.90
418 419 1.498865 CTTCATCGCGGGCCATGTAC 61.499 60.000 6.13 0.00 0.00 2.90
419 420 1.227527 CTTCATCGCGGGCCATGTA 60.228 57.895 6.13 0.00 0.00 2.29
420 421 2.514592 CTTCATCGCGGGCCATGT 60.515 61.111 6.13 0.00 0.00 3.21
421 422 2.994387 TAGCTTCATCGCGGGCCATG 62.994 60.000 6.13 2.12 34.40 3.66
422 423 2.721971 CTAGCTTCATCGCGGGCCAT 62.722 60.000 6.13 0.00 34.40 4.40
423 424 3.445518 CTAGCTTCATCGCGGGCCA 62.446 63.158 6.13 0.00 34.40 5.36
424 425 2.663188 CTAGCTTCATCGCGGGCC 60.663 66.667 6.13 0.00 34.40 5.80
425 426 2.644555 TTCCTAGCTTCATCGCGGGC 62.645 60.000 6.13 3.51 34.40 6.13
426 427 0.034059 ATTCCTAGCTTCATCGCGGG 59.966 55.000 6.13 0.00 34.40 6.13
427 428 1.871080 AATTCCTAGCTTCATCGCGG 58.129 50.000 6.13 0.00 34.40 6.46
428 429 2.221981 GGAAATTCCTAGCTTCATCGCG 59.778 50.000 4.46 0.00 32.53 5.87
429 430 3.206150 TGGAAATTCCTAGCTTCATCGC 58.794 45.455 13.78 0.00 37.46 4.58
430 431 8.954950 ATATATGGAAATTCCTAGCTTCATCG 57.045 34.615 13.78 0.00 37.46 3.84
460 461 4.077822 TGTCCATGTATGTTGCATGACAA 58.922 39.130 0.00 0.00 44.60 3.18
461 462 3.683802 TGTCCATGTATGTTGCATGACA 58.316 40.909 0.00 0.00 44.60 3.58
462 463 4.700268 TTGTCCATGTATGTTGCATGAC 57.300 40.909 0.00 4.84 44.60 3.06
463 464 5.532032 CCTATTGTCCATGTATGTTGCATGA 59.468 40.000 0.00 0.00 44.60 3.07
464 465 5.300034 ACCTATTGTCCATGTATGTTGCATG 59.700 40.000 0.00 0.00 42.29 4.06
465 466 5.448654 ACCTATTGTCCATGTATGTTGCAT 58.551 37.500 0.00 0.00 0.00 3.96
466 467 4.854173 ACCTATTGTCCATGTATGTTGCA 58.146 39.130 0.00 0.00 0.00 4.08
467 468 7.510549 AATACCTATTGTCCATGTATGTTGC 57.489 36.000 0.00 0.00 0.00 4.17
468 469 8.902806 ACAAATACCTATTGTCCATGTATGTTG 58.097 33.333 0.00 0.00 36.28 3.33
469 470 9.474313 AACAAATACCTATTGTCCATGTATGTT 57.526 29.630 0.00 0.00 39.98 2.71
470 471 8.902806 CAACAAATACCTATTGTCCATGTATGT 58.097 33.333 0.00 0.00 39.98 2.29
471 472 8.902806 ACAACAAATACCTATTGTCCATGTATG 58.097 33.333 0.00 0.00 39.98 2.39
472 473 9.120538 GACAACAAATACCTATTGTCCATGTAT 57.879 33.333 4.92 0.00 43.28 2.29
473 474 7.279090 CGACAACAAATACCTATTGTCCATGTA 59.721 37.037 9.66 0.00 45.25 2.29
474 475 6.093495 CGACAACAAATACCTATTGTCCATGT 59.907 38.462 9.66 0.00 45.25 3.21
475 476 6.315144 TCGACAACAAATACCTATTGTCCATG 59.685 38.462 9.66 0.00 45.25 3.66
476 477 6.411376 TCGACAACAAATACCTATTGTCCAT 58.589 36.000 9.66 0.00 45.25 3.41
477 478 5.795972 TCGACAACAAATACCTATTGTCCA 58.204 37.500 9.66 0.00 45.25 4.02
478 479 6.730960 TTCGACAACAAATACCTATTGTCC 57.269 37.500 9.66 0.00 45.25 4.02
479 480 9.274065 GAAATTCGACAACAAATACCTATTGTC 57.726 33.333 6.00 6.00 44.81 3.18
480 481 8.788806 TGAAATTCGACAACAAATACCTATTGT 58.211 29.630 0.00 0.00 42.56 2.71
481 482 9.061610 GTGAAATTCGACAACAAATACCTATTG 57.938 33.333 0.00 0.00 0.00 1.90
482 483 9.010029 AGTGAAATTCGACAACAAATACCTATT 57.990 29.630 0.00 0.00 0.00 1.73
483 484 8.561738 AGTGAAATTCGACAACAAATACCTAT 57.438 30.769 0.00 0.00 0.00 2.57
484 485 7.972832 AGTGAAATTCGACAACAAATACCTA 57.027 32.000 0.00 0.00 0.00 3.08
485 486 6.877611 AGTGAAATTCGACAACAAATACCT 57.122 33.333 0.00 0.00 0.00 3.08
486 487 8.025243 TCTAGTGAAATTCGACAACAAATACC 57.975 34.615 0.00 0.00 0.00 2.73
487 488 8.922676 TCTCTAGTGAAATTCGACAACAAATAC 58.077 33.333 0.00 0.00 0.00 1.89
488 489 9.483916 TTCTCTAGTGAAATTCGACAACAAATA 57.516 29.630 4.78 0.00 0.00 1.40
489 490 7.962964 TCTCTAGTGAAATTCGACAACAAAT 57.037 32.000 0.00 0.00 0.00 2.32
490 491 7.780008 TTCTCTAGTGAAATTCGACAACAAA 57.220 32.000 4.78 0.00 0.00 2.83
491 492 7.494625 ACTTTCTCTAGTGAAATTCGACAACAA 59.505 33.333 17.75 0.00 35.68 2.83
492 493 6.984474 ACTTTCTCTAGTGAAATTCGACAACA 59.016 34.615 17.75 0.00 35.68 3.33
493 494 7.409465 ACTTTCTCTAGTGAAATTCGACAAC 57.591 36.000 17.75 0.00 35.68 3.32
495 496 9.784680 GTATACTTTCTCTAGTGAAATTCGACA 57.215 33.333 17.75 1.66 35.68 4.35
502 503 9.310449 ACCTCAAGTATACTTTCTCTAGTGAAA 57.690 33.333 15.60 16.78 33.11 2.69
503 504 8.740906 CACCTCAAGTATACTTTCTCTAGTGAA 58.259 37.037 15.60 3.12 33.11 3.18
504 505 7.148052 GCACCTCAAGTATACTTTCTCTAGTGA 60.148 40.741 15.60 7.34 33.11 3.41
505 506 6.975772 GCACCTCAAGTATACTTTCTCTAGTG 59.024 42.308 15.60 16.02 33.11 2.74
506 507 6.097129 GGCACCTCAAGTATACTTTCTCTAGT 59.903 42.308 15.60 5.27 33.11 2.57
507 508 6.508777 GGCACCTCAAGTATACTTTCTCTAG 58.491 44.000 15.60 3.90 33.11 2.43
508 509 5.067413 CGGCACCTCAAGTATACTTTCTCTA 59.933 44.000 15.60 0.00 33.11 2.43
509 510 4.142138 CGGCACCTCAAGTATACTTTCTCT 60.142 45.833 15.60 0.00 33.11 3.10
510 511 4.113354 CGGCACCTCAAGTATACTTTCTC 58.887 47.826 15.60 2.70 33.11 2.87
511 512 3.767673 TCGGCACCTCAAGTATACTTTCT 59.232 43.478 15.60 0.00 33.11 2.52
512 513 4.113354 CTCGGCACCTCAAGTATACTTTC 58.887 47.826 15.60 1.75 33.11 2.62
513 514 3.767673 TCTCGGCACCTCAAGTATACTTT 59.232 43.478 15.60 0.00 33.11 2.66
514 515 3.362706 TCTCGGCACCTCAAGTATACTT 58.637 45.455 12.50 12.50 36.45 2.24
515 516 3.014304 TCTCGGCACCTCAAGTATACT 57.986 47.619 0.00 0.00 0.00 2.12
516 517 3.445857 GTTCTCGGCACCTCAAGTATAC 58.554 50.000 0.00 0.00 0.00 1.47
517 518 2.098607 CGTTCTCGGCACCTCAAGTATA 59.901 50.000 0.00 0.00 0.00 1.47
518 519 1.135083 CGTTCTCGGCACCTCAAGTAT 60.135 52.381 0.00 0.00 0.00 2.12
519 520 0.242825 CGTTCTCGGCACCTCAAGTA 59.757 55.000 0.00 0.00 0.00 2.24
520 521 1.006102 CGTTCTCGGCACCTCAAGT 60.006 57.895 0.00 0.00 0.00 3.16
521 522 0.108615 ATCGTTCTCGGCACCTCAAG 60.109 55.000 0.00 0.00 37.69 3.02
522 523 0.320374 AATCGTTCTCGGCACCTCAA 59.680 50.000 0.00 0.00 37.69 3.02
523 524 0.320374 AAATCGTTCTCGGCACCTCA 59.680 50.000 0.00 0.00 37.69 3.86
524 525 1.128692 CAAAATCGTTCTCGGCACCTC 59.871 52.381 0.00 0.00 37.69 3.85
525 526 1.156736 CAAAATCGTTCTCGGCACCT 58.843 50.000 0.00 0.00 37.69 4.00
526 527 0.872388 ACAAAATCGTTCTCGGCACC 59.128 50.000 0.00 0.00 37.69 5.01
527 528 2.307049 CAACAAAATCGTTCTCGGCAC 58.693 47.619 0.00 0.00 37.69 5.01
528 529 1.265635 CCAACAAAATCGTTCTCGGCA 59.734 47.619 0.00 0.00 37.69 5.69
529 530 1.533731 TCCAACAAAATCGTTCTCGGC 59.466 47.619 0.00 0.00 37.69 5.54
530 531 3.889196 TTCCAACAAAATCGTTCTCGG 57.111 42.857 0.00 0.00 37.69 4.63
531 532 5.013236 CGTATTCCAACAAAATCGTTCTCG 58.987 41.667 0.00 0.00 38.55 4.04
532 533 6.160664 TCGTATTCCAACAAAATCGTTCTC 57.839 37.500 0.00 0.00 0.00 2.87
533 534 6.737254 ATCGTATTCCAACAAAATCGTTCT 57.263 33.333 0.00 0.00 0.00 3.01
534 535 7.902032 TCTATCGTATTCCAACAAAATCGTTC 58.098 34.615 0.00 0.00 0.00 3.95
535 536 7.762615 TCTCTATCGTATTCCAACAAAATCGTT 59.237 33.333 0.00 0.00 0.00 3.85
536 537 7.262772 TCTCTATCGTATTCCAACAAAATCGT 58.737 34.615 0.00 0.00 0.00 3.73
537 538 7.694388 TCTCTATCGTATTCCAACAAAATCG 57.306 36.000 0.00 0.00 0.00 3.34
550 551 9.627395 CCGACTCAATTAATTTCTCTATCGTAT 57.373 33.333 0.00 0.00 0.00 3.06
551 552 7.594015 GCCGACTCAATTAATTTCTCTATCGTA 59.406 37.037 0.00 0.00 0.00 3.43
552 553 6.421202 GCCGACTCAATTAATTTCTCTATCGT 59.579 38.462 0.00 0.00 0.00 3.73
553 554 6.642950 AGCCGACTCAATTAATTTCTCTATCG 59.357 38.462 0.00 3.15 0.00 2.92
554 555 7.870445 AGAGCCGACTCAATTAATTTCTCTATC 59.130 37.037 0.35 0.00 46.09 2.08
555 556 7.731054 AGAGCCGACTCAATTAATTTCTCTAT 58.269 34.615 0.35 0.00 46.09 1.98
556 557 7.113658 AGAGCCGACTCAATTAATTTCTCTA 57.886 36.000 0.35 0.00 46.09 2.43
557 558 5.983540 AGAGCCGACTCAATTAATTTCTCT 58.016 37.500 0.35 0.44 46.09 3.10
558 559 7.954788 ATAGAGCCGACTCAATTAATTTCTC 57.045 36.000 0.35 0.00 46.09 2.87
559 560 7.987458 TCAATAGAGCCGACTCAATTAATTTCT 59.013 33.333 0.35 0.00 46.09 2.52
560 561 8.142994 TCAATAGAGCCGACTCAATTAATTTC 57.857 34.615 0.35 0.00 46.09 2.17
561 562 8.506168 TTCAATAGAGCCGACTCAATTAATTT 57.494 30.769 0.35 0.00 46.09 1.82
562 563 8.506168 TTTCAATAGAGCCGACTCAATTAATT 57.494 30.769 0.35 0.00 46.09 1.40
563 564 8.682936 ATTTCAATAGAGCCGACTCAATTAAT 57.317 30.769 0.35 0.00 46.09 1.40
564 565 8.506168 AATTTCAATAGAGCCGACTCAATTAA 57.494 30.769 0.35 0.00 46.09 1.40
565 566 8.506168 AAATTTCAATAGAGCCGACTCAATTA 57.494 30.769 0.35 0.00 46.09 1.40
566 567 7.396540 AAATTTCAATAGAGCCGACTCAATT 57.603 32.000 0.35 0.00 46.09 2.32
567 568 7.396540 AAAATTTCAATAGAGCCGACTCAAT 57.603 32.000 0.35 0.00 46.09 2.57
568 569 6.817765 AAAATTTCAATAGAGCCGACTCAA 57.182 33.333 0.35 0.00 46.09 3.02
569 570 7.552687 ACATAAAATTTCAATAGAGCCGACTCA 59.447 33.333 0.35 0.00 46.09 3.41
570 571 7.852945 CACATAAAATTTCAATAGAGCCGACTC 59.147 37.037 0.00 0.00 43.82 3.36
571 572 7.336931 ACACATAAAATTTCAATAGAGCCGACT 59.663 33.333 0.00 0.00 0.00 4.18
572 573 7.472543 ACACATAAAATTTCAATAGAGCCGAC 58.527 34.615 0.00 0.00 0.00 4.79
573 574 7.624360 ACACATAAAATTTCAATAGAGCCGA 57.376 32.000 0.00 0.00 0.00 5.54
574 575 8.394877 TGTACACATAAAATTTCAATAGAGCCG 58.605 33.333 0.00 0.00 0.00 5.52
589 590 9.786105 CATGAAAAGCACATATGTACACATAAA 57.214 29.630 8.32 0.00 41.60 1.40
590 591 9.171877 TCATGAAAAGCACATATGTACACATAA 57.828 29.630 8.32 0.00 41.60 1.90
591 592 8.729805 TCATGAAAAGCACATATGTACACATA 57.270 30.769 8.32 4.61 42.38 2.29
592 593 7.337689 ACTCATGAAAAGCACATATGTACACAT 59.662 33.333 8.32 5.38 40.22 3.21
593 594 6.654582 ACTCATGAAAAGCACATATGTACACA 59.345 34.615 8.32 3.33 0.00 3.72
594 595 6.963242 CACTCATGAAAAGCACATATGTACAC 59.037 38.462 8.32 1.29 0.00 2.90
595 596 6.654582 ACACTCATGAAAAGCACATATGTACA 59.345 34.615 8.32 0.00 0.00 2.90
596 597 7.076842 ACACTCATGAAAAGCACATATGTAC 57.923 36.000 8.32 2.44 0.00 2.90
597 598 7.686438 AACACTCATGAAAAGCACATATGTA 57.314 32.000 8.32 0.00 0.00 2.29
598 599 6.579666 AACACTCATGAAAAGCACATATGT 57.420 33.333 1.41 1.41 0.00 2.29
599 600 7.061441 GTCAAACACTCATGAAAAGCACATATG 59.939 37.037 0.00 0.00 0.00 1.78
600 601 7.086376 GTCAAACACTCATGAAAAGCACATAT 58.914 34.615 0.00 0.00 0.00 1.78
601 602 6.039159 TGTCAAACACTCATGAAAAGCACATA 59.961 34.615 0.00 0.00 0.00 2.29
602 603 5.163530 TGTCAAACACTCATGAAAAGCACAT 60.164 36.000 0.00 0.00 0.00 3.21
603 604 4.157472 TGTCAAACACTCATGAAAAGCACA 59.843 37.500 0.00 0.00 0.00 4.57
604 605 4.671377 TGTCAAACACTCATGAAAAGCAC 58.329 39.130 0.00 0.00 0.00 4.40
605 606 4.979943 TGTCAAACACTCATGAAAAGCA 57.020 36.364 0.00 0.00 0.00 3.91
606 607 6.645700 TTTTGTCAAACACTCATGAAAAGC 57.354 33.333 0.00 0.00 0.00 3.51
636 638 0.738762 GGACGCGAACCCCTAAACTC 60.739 60.000 15.93 0.00 0.00 3.01
873 888 1.905512 GGTCGGCCAGGTTATGACT 59.094 57.895 0.00 0.00 34.09 3.41
1029 1051 0.809385 ACTCGTCATCGTCGTCCAAT 59.191 50.000 0.00 0.00 38.33 3.16
1248 1282 2.168728 GCCCACAGAAACTAGGGTCTAG 59.831 54.545 0.00 0.83 43.42 2.43
1388 1422 5.278957 GCTAATCAAATCCACACCAACTTGT 60.279 40.000 0.00 0.00 0.00 3.16
2124 2189 3.533547 GAGCTCAGCAATGACATTCTCT 58.466 45.455 9.40 0.00 0.00 3.10
2458 2535 7.129622 ACAACACACACAAATAAACTACATCG 58.870 34.615 0.00 0.00 0.00 3.84
2547 2647 4.904241 AGATGTCTTCCAAACTTCTCTGG 58.096 43.478 0.00 0.00 0.00 3.86
2640 2741 4.685165 CAGTGAGATTCAGTTCTGTCAGTG 59.315 45.833 0.00 9.76 0.00 3.66
2844 2954 0.832135 AGACGAAGAGGAGGTGCCAA 60.832 55.000 0.00 0.00 40.02 4.52
3005 3118 1.204146 GATGCTGGGTAGAGGGAACA 58.796 55.000 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.