Multiple sequence alignment - TraesCS4D01G181500

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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 TraesCS4D01G181500 chr4D 100.000 3142 0 0 803 3944 317203049 317199908 0.000000e+00 5803.0
1 TraesCS4D01G181500 chr4D 100.000 538 0 0 1 538 317203851 317203314 0.000000e+00 994.0
2 TraesCS4D01G181500 chr4B 96.900 3032 86 8 917 3944 394389017 394385990 0.000000e+00 5072.0
3 TraesCS4D01G181500 chr4B 83.707 491 48 12 6 481 394389482 394389009 6.050000e-118 435.0
4 TraesCS4D01G181500 chr4A 96.787 3050 65 11 917 3938 157557552 157560596 0.000000e+00 5059.0
5 TraesCS4D01G181500 chr4A 82.447 188 26 6 154 338 704759146 704759329 1.470000e-34 158.0
6 TraesCS4D01G181500 chr4A 96.552 58 2 0 481 538 666932745 666932688 3.240000e-16 97.1
7 TraesCS4D01G181500 chr5A 89.000 100 3 4 817 916 338387508 338387599 2.490000e-22 117.0
8 TraesCS4D01G181500 chr1B 82.143 140 21 3 215 353 488417783 488417647 2.490000e-22 117.0
9 TraesCS4D01G181500 chr7D 87.736 106 4 7 812 916 154207305 154207208 8.960000e-22 115.0
10 TraesCS4D01G181500 chr7D 96.226 53 2 0 486 538 70185105 70185157 1.950000e-13 87.9
11 TraesCS4D01G181500 chr1A 87.736 106 4 2 812 916 29215238 29215335 8.960000e-22 115.0
12 TraesCS4D01G181500 chr1A 85.981 107 6 2 812 917 54021954 54021856 5.390000e-19 106.0
13 TraesCS4D01G181500 chr1A 96.491 57 2 0 482 538 531881878 531881934 1.170000e-15 95.3
14 TraesCS4D01G181500 chr2B 85.981 107 6 5 812 917 53045671 53045769 5.390000e-19 106.0
15 TraesCS4D01G181500 chr2B 96.491 57 2 0 482 538 53045589 53045645 1.170000e-15 95.3
16 TraesCS4D01G181500 chr7A 90.789 76 6 1 812 886 621908616 621908541 2.510000e-17 100.0
17 TraesCS4D01G181500 chr2A 87.912 91 3 1 827 917 624950846 624950928 2.510000e-17 100.0
18 TraesCS4D01G181500 chr2A 94.737 57 3 0 482 538 624950750 624950806 5.430000e-14 89.8
19 TraesCS4D01G181500 chr6B 96.610 59 2 0 480 538 40492645 40492703 9.020000e-17 99.0
20 TraesCS4D01G181500 chr6B 93.750 64 3 1 476 538 618131155 618131092 1.170000e-15 95.3
21 TraesCS4D01G181500 chr7B 96.491 57 2 0 482 538 508656851 508656907 1.170000e-15 95.3
22 TraesCS4D01G181500 chr3A 96.491 57 2 0 482 538 660056132 660056188 1.170000e-15 95.3


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 TraesCS4D01G181500 chr4D 317199908 317203851 3943 True 3398.5 5803 100.0000 1 3944 2 chr4D.!!$R1 3943
1 TraesCS4D01G181500 chr4B 394385990 394389482 3492 True 2753.5 5072 90.3035 6 3944 2 chr4B.!!$R1 3938
2 TraesCS4D01G181500 chr4A 157557552 157560596 3044 False 5059.0 5059 96.7870 917 3938 1 chr4A.!!$F1 3021

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
864 879 0.040499 AAACCACCACAACACCCTGT 59.960 50.0 0.0 0.0 0.0 4.00 F
886 901 0.253347 ACCCCTCATCCCTGTGACAT 60.253 55.0 0.0 0.0 0.0 3.06 F
2446 2462 0.234884 GAACGGCCTTGTGACGAAAG 59.765 55.0 0.0 0.0 0.0 2.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2294 2310 3.100671 AGGCTAGTCCCAAGTACAAGAG 58.899 50.000 0.00 0.0 34.51 2.85 R
2601 2617 4.445453 TGCATCCATAGTGTCTGATGTTC 58.555 43.478 0.00 0.0 37.51 3.18 R
3303 3321 0.464554 TTGCACCATGGTTCACGACA 60.465 50.000 17.34 0.0 0.00 4.35 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
34 35 6.314400 GGAGTAGATAGCTAGTTCGAATCGAT 59.686 42.308 6.06 0.00 35.23 3.59
35 36 7.148373 GGAGTAGATAGCTAGTTCGAATCGATT 60.148 40.741 11.20 11.20 35.23 3.34
36 37 7.745015 AGTAGATAGCTAGTTCGAATCGATTC 58.255 38.462 25.18 25.18 35.23 2.52
99 100 2.233922 ACGACAACTCCTGGATCGATTT 59.766 45.455 20.69 0.00 36.64 2.17
104 105 1.212616 CTCCTGGATCGATTTGACGC 58.787 55.000 0.00 0.00 0.00 5.19
155 156 2.113433 TCCTAGACGCTGGCGACTC 61.113 63.158 21.77 9.51 42.55 3.36
171 172 0.322187 ACTCCGTATTTGGCCGCTTT 60.322 50.000 0.00 0.00 0.00 3.51
175 176 0.455972 CGTATTTGGCCGCTTTGTGG 60.456 55.000 0.00 0.00 36.10 4.17
177 178 0.540830 TATTTGGCCGCTTTGTGGGT 60.541 50.000 0.00 0.00 33.18 4.51
196 197 2.202756 GTCTGCCGGCTTCGTAGG 60.203 66.667 29.70 8.77 0.00 3.18
207 208 1.268845 GCTTCGTAGGAGTGAGCTAGC 60.269 57.143 6.62 6.62 0.00 3.42
212 213 2.225491 CGTAGGAGTGAGCTAGCTGATC 59.775 54.545 24.99 16.13 0.00 2.92
217 218 2.627221 GAGTGAGCTAGCTGATCATGGA 59.373 50.000 24.99 0.00 43.41 3.41
225 226 1.884464 CTGATCATGGACACGGGCG 60.884 63.158 0.00 0.00 0.00 6.13
227 228 1.592669 GATCATGGACACGGGCGAG 60.593 63.158 0.00 0.00 0.00 5.03
231 232 1.982395 ATGGACACGGGCGAGAGAA 60.982 57.895 0.00 0.00 0.00 2.87
233 234 1.446272 GGACACGGGCGAGAGAAAG 60.446 63.158 0.00 0.00 0.00 2.62
244 245 2.659279 GCGAGAGAAAGAAGAAGACGTG 59.341 50.000 0.00 0.00 0.00 4.49
247 248 4.481463 GAGAGAAAGAAGAAGACGTGAGG 58.519 47.826 0.00 0.00 0.00 3.86
253 254 6.768381 AGAAAGAAGAAGACGTGAGGAAAAAT 59.232 34.615 0.00 0.00 0.00 1.82
258 262 8.899771 AGAAGAAGACGTGAGGAAAAATAAAAA 58.100 29.630 0.00 0.00 0.00 1.94
310 321 2.967615 GGTCTATTCGGCCGCAGC 60.968 66.667 23.51 12.55 38.76 5.25
319 330 2.744709 GGCCGCAGCTTAAACCGA 60.745 61.111 0.00 0.00 39.73 4.69
325 336 2.602878 CGCAGCTTAAACCGACTCTTA 58.397 47.619 0.00 0.00 0.00 2.10
326 337 2.599082 CGCAGCTTAAACCGACTCTTAG 59.401 50.000 0.00 0.00 0.00 2.18
337 348 4.436332 ACCGACTCTTAGAACACGTTTTT 58.564 39.130 0.00 0.00 0.00 1.94
338 349 5.591099 ACCGACTCTTAGAACACGTTTTTA 58.409 37.500 0.00 0.00 0.00 1.52
347 358 3.866910 AGAACACGTTTTTAGCGAACTGA 59.133 39.130 0.00 0.00 0.00 3.41
348 359 4.330620 AGAACACGTTTTTAGCGAACTGAA 59.669 37.500 0.00 0.00 0.00 3.02
349 360 4.603231 ACACGTTTTTAGCGAACTGAAA 57.397 36.364 0.00 0.00 30.17 2.69
350 361 4.972201 ACACGTTTTTAGCGAACTGAAAA 58.028 34.783 0.00 0.00 38.60 2.29
354 365 4.619437 TTTTTAGCGAACTGAAAACCGT 57.381 36.364 0.00 0.00 36.70 4.83
355 366 5.731599 TTTTTAGCGAACTGAAAACCGTA 57.268 34.783 0.00 0.00 36.70 4.02
356 367 4.977741 TTTAGCGAACTGAAAACCGTAG 57.022 40.909 0.00 0.00 0.00 3.51
357 368 5.277442 TTTTTAGCGAACTGAAAACCGTAGG 60.277 40.000 0.00 0.00 39.38 3.18
371 382 0.238817 CGTAGGTCCGCTAGAGATGC 59.761 60.000 0.00 0.00 0.00 3.91
416 428 1.364901 CTGTTTGGTTGGGCTGCAG 59.635 57.895 10.11 10.11 0.00 4.41
435 447 2.094675 AGAGTGCAGCAACACAAACTT 58.905 42.857 11.18 0.00 43.23 2.66
436 448 2.159338 AGAGTGCAGCAACACAAACTTG 60.159 45.455 11.18 0.00 43.23 3.16
440 452 3.431572 GTGCAGCAACACAAACTTGAAAA 59.568 39.130 0.00 0.00 40.40 2.29
441 453 4.434593 GTGCAGCAACACAAACTTGAAAAG 60.435 41.667 0.00 0.00 44.44 2.27
442 454 6.580569 GTGCAGCAACACAAACTTGAAAAGA 61.581 40.000 0.00 0.00 42.84 2.52
443 455 8.291012 GTGCAGCAACACAAACTTGAAAAGAG 62.291 42.308 0.00 0.00 42.84 2.85
457 472 3.119316 TGAAAAGAGAAAAAGCGTGCCAA 60.119 39.130 0.00 0.00 0.00 4.52
481 496 4.511826 AGAGGAAACAATCGACTGACAAAC 59.488 41.667 0.00 0.00 0.00 2.93
482 497 4.196193 AGGAAACAATCGACTGACAAACA 58.804 39.130 0.00 0.00 0.00 2.83
483 498 4.638421 AGGAAACAATCGACTGACAAACAA 59.362 37.500 0.00 0.00 0.00 2.83
484 499 5.124776 AGGAAACAATCGACTGACAAACAAA 59.875 36.000 0.00 0.00 0.00 2.83
485 500 5.802956 GGAAACAATCGACTGACAAACAAAA 59.197 36.000 0.00 0.00 0.00 2.44
486 501 6.309251 GGAAACAATCGACTGACAAACAAAAA 59.691 34.615 0.00 0.00 0.00 1.94
487 502 7.010091 GGAAACAATCGACTGACAAACAAAAAT 59.990 33.333 0.00 0.00 0.00 1.82
488 503 6.810888 ACAATCGACTGACAAACAAAAATG 57.189 33.333 0.00 0.00 0.00 2.32
489 504 5.231991 ACAATCGACTGACAAACAAAAATGC 59.768 36.000 0.00 0.00 0.00 3.56
490 505 4.630894 TCGACTGACAAACAAAAATGCT 57.369 36.364 0.00 0.00 0.00 3.79
491 506 5.743026 TCGACTGACAAACAAAAATGCTA 57.257 34.783 0.00 0.00 0.00 3.49
492 507 5.747565 TCGACTGACAAACAAAAATGCTAG 58.252 37.500 0.00 0.00 0.00 3.42
493 508 5.525745 TCGACTGACAAACAAAAATGCTAGA 59.474 36.000 0.00 0.00 0.00 2.43
494 509 6.037720 TCGACTGACAAACAAAAATGCTAGAA 59.962 34.615 0.00 0.00 0.00 2.10
495 510 6.358030 CGACTGACAAACAAAAATGCTAGAAG 59.642 38.462 0.00 0.00 0.00 2.85
496 511 7.100458 ACTGACAAACAAAAATGCTAGAAGT 57.900 32.000 0.00 0.00 0.00 3.01
497 512 8.220755 ACTGACAAACAAAAATGCTAGAAGTA 57.779 30.769 0.00 0.00 0.00 2.24
498 513 8.129211 ACTGACAAACAAAAATGCTAGAAGTAC 58.871 33.333 0.00 0.00 0.00 2.73
499 514 7.990917 TGACAAACAAAAATGCTAGAAGTACA 58.009 30.769 0.00 0.00 0.00 2.90
500 515 8.128582 TGACAAACAAAAATGCTAGAAGTACAG 58.871 33.333 0.00 0.00 0.00 2.74
501 516 7.425606 ACAAACAAAAATGCTAGAAGTACAGG 58.574 34.615 0.00 0.00 0.00 4.00
502 517 5.629079 ACAAAAATGCTAGAAGTACAGGC 57.371 39.130 0.00 0.00 0.00 4.85
503 518 5.316987 ACAAAAATGCTAGAAGTACAGGCT 58.683 37.500 0.00 0.00 0.00 4.58
504 519 5.770162 ACAAAAATGCTAGAAGTACAGGCTT 59.230 36.000 0.00 0.00 0.00 4.35
505 520 6.265422 ACAAAAATGCTAGAAGTACAGGCTTT 59.735 34.615 0.00 0.00 0.00 3.51
506 521 6.901081 AAAATGCTAGAAGTACAGGCTTTT 57.099 33.333 0.00 0.61 33.76 2.27
507 522 7.996098 AAAATGCTAGAAGTACAGGCTTTTA 57.004 32.000 0.00 0.00 32.66 1.52
508 523 6.986904 AATGCTAGAAGTACAGGCTTTTAC 57.013 37.500 0.00 0.00 0.00 2.01
509 524 5.477607 TGCTAGAAGTACAGGCTTTTACA 57.522 39.130 0.00 0.00 0.00 2.41
510 525 5.479306 TGCTAGAAGTACAGGCTTTTACAG 58.521 41.667 0.00 0.00 0.00 2.74
511 526 4.870991 GCTAGAAGTACAGGCTTTTACAGG 59.129 45.833 0.00 0.00 0.00 4.00
512 527 4.976540 AGAAGTACAGGCTTTTACAGGT 57.023 40.909 0.00 0.00 0.00 4.00
513 528 5.306114 AGAAGTACAGGCTTTTACAGGTT 57.694 39.130 0.00 0.00 0.00 3.50
514 529 5.691896 AGAAGTACAGGCTTTTACAGGTTT 58.308 37.500 0.00 0.00 0.00 3.27
515 530 5.763698 AGAAGTACAGGCTTTTACAGGTTTC 59.236 40.000 0.00 1.95 0.00 2.78
516 531 5.306114 AGTACAGGCTTTTACAGGTTTCT 57.694 39.130 0.00 0.00 0.00 2.52
517 532 6.429521 AGTACAGGCTTTTACAGGTTTCTA 57.570 37.500 0.00 0.00 0.00 2.10
518 533 6.228995 AGTACAGGCTTTTACAGGTTTCTAC 58.771 40.000 0.00 0.00 0.00 2.59
519 534 5.043737 ACAGGCTTTTACAGGTTTCTACA 57.956 39.130 0.00 0.00 0.00 2.74
520 535 5.063880 ACAGGCTTTTACAGGTTTCTACAG 58.936 41.667 0.00 0.00 0.00 2.74
521 536 4.455877 CAGGCTTTTACAGGTTTCTACAGG 59.544 45.833 0.00 0.00 0.00 4.00
522 537 3.190744 GGCTTTTACAGGTTTCTACAGGC 59.809 47.826 0.00 0.00 0.00 4.85
523 538 4.072839 GCTTTTACAGGTTTCTACAGGCT 58.927 43.478 0.00 0.00 0.00 4.58
524 539 4.154375 GCTTTTACAGGTTTCTACAGGCTC 59.846 45.833 0.00 0.00 0.00 4.70
525 540 3.975168 TTACAGGTTTCTACAGGCTCC 57.025 47.619 0.00 0.00 0.00 4.70
526 541 2.031495 ACAGGTTTCTACAGGCTCCT 57.969 50.000 0.00 0.00 0.00 3.69
527 542 2.339769 ACAGGTTTCTACAGGCTCCTT 58.660 47.619 0.00 0.00 0.00 3.36
528 543 2.711547 ACAGGTTTCTACAGGCTCCTTT 59.288 45.455 0.00 0.00 0.00 3.11
529 544 3.244596 ACAGGTTTCTACAGGCTCCTTTC 60.245 47.826 0.00 0.00 0.00 2.62
530 545 2.979678 AGGTTTCTACAGGCTCCTTTCA 59.020 45.455 0.00 0.00 0.00 2.69
531 546 3.394606 AGGTTTCTACAGGCTCCTTTCAA 59.605 43.478 0.00 0.00 0.00 2.69
532 547 4.141251 AGGTTTCTACAGGCTCCTTTCAAA 60.141 41.667 0.00 0.00 0.00 2.69
533 548 4.023107 GGTTTCTACAGGCTCCTTTCAAAC 60.023 45.833 0.00 0.00 0.00 2.93
534 549 4.706842 TTCTACAGGCTCCTTTCAAACT 57.293 40.909 0.00 0.00 0.00 2.66
535 550 4.706842 TCTACAGGCTCCTTTCAAACTT 57.293 40.909 0.00 0.00 0.00 2.66
536 551 5.048846 TCTACAGGCTCCTTTCAAACTTT 57.951 39.130 0.00 0.00 0.00 2.66
537 552 5.063880 TCTACAGGCTCCTTTCAAACTTTC 58.936 41.667 0.00 0.00 0.00 2.62
830 845 2.761324 GGATGGGCCCTACCTCTAC 58.239 63.158 25.70 5.04 39.10 2.59
831 846 0.191314 GGATGGGCCCTACCTCTACT 59.809 60.000 25.70 0.00 39.10 2.57
832 847 1.432024 GGATGGGCCCTACCTCTACTA 59.568 57.143 25.70 0.00 39.10 1.82
833 848 2.158204 GGATGGGCCCTACCTCTACTAA 60.158 54.545 25.70 0.00 39.10 2.24
834 849 3.504343 GGATGGGCCCTACCTCTACTAAT 60.504 52.174 25.70 2.31 39.10 1.73
835 850 2.972348 TGGGCCCTACCTCTACTAATG 58.028 52.381 25.70 0.00 39.10 1.90
836 851 2.520980 TGGGCCCTACCTCTACTAATGA 59.479 50.000 25.70 0.00 39.10 2.57
837 852 2.898612 GGGCCCTACCTCTACTAATGAC 59.101 54.545 17.04 0.00 39.10 3.06
838 853 2.898612 GGCCCTACCTCTACTAATGACC 59.101 54.545 0.00 0.00 34.51 4.02
839 854 3.573695 GCCCTACCTCTACTAATGACCA 58.426 50.000 0.00 0.00 0.00 4.02
840 855 3.965347 GCCCTACCTCTACTAATGACCAA 59.035 47.826 0.00 0.00 0.00 3.67
841 856 4.593634 GCCCTACCTCTACTAATGACCAAT 59.406 45.833 0.00 0.00 0.00 3.16
842 857 5.071923 GCCCTACCTCTACTAATGACCAATT 59.928 44.000 0.00 0.00 0.00 2.32
843 858 6.269307 GCCCTACCTCTACTAATGACCAATTA 59.731 42.308 0.00 0.00 0.00 1.40
844 859 7.202066 GCCCTACCTCTACTAATGACCAATTAA 60.202 40.741 0.00 0.00 30.24 1.40
845 860 8.711170 CCCTACCTCTACTAATGACCAATTAAA 58.289 37.037 0.00 0.00 30.24 1.52
849 864 9.239551 ACCTCTACTAATGACCAATTAAAAACC 57.760 33.333 0.00 0.00 30.24 3.27
850 865 9.238368 CCTCTACTAATGACCAATTAAAAACCA 57.762 33.333 0.00 0.00 30.24 3.67
852 867 9.016438 TCTACTAATGACCAATTAAAAACCACC 57.984 33.333 0.00 0.00 30.24 4.61
853 868 7.604657 ACTAATGACCAATTAAAAACCACCA 57.395 32.000 0.00 0.00 30.24 4.17
854 869 7.438564 ACTAATGACCAATTAAAAACCACCAC 58.561 34.615 0.00 0.00 30.24 4.16
855 870 5.878406 ATGACCAATTAAAAACCACCACA 57.122 34.783 0.00 0.00 0.00 4.17
856 871 5.677319 TGACCAATTAAAAACCACCACAA 57.323 34.783 0.00 0.00 0.00 3.33
857 872 5.420409 TGACCAATTAAAAACCACCACAAC 58.580 37.500 0.00 0.00 0.00 3.32
858 873 5.046591 TGACCAATTAAAAACCACCACAACA 60.047 36.000 0.00 0.00 0.00 3.33
859 874 5.179533 ACCAATTAAAAACCACCACAACAC 58.820 37.500 0.00 0.00 0.00 3.32
860 875 4.572795 CCAATTAAAAACCACCACAACACC 59.427 41.667 0.00 0.00 0.00 4.16
861 876 3.889520 TTAAAAACCACCACAACACCC 57.110 42.857 0.00 0.00 0.00 4.61
862 877 1.945580 AAAAACCACCACAACACCCT 58.054 45.000 0.00 0.00 0.00 4.34
863 878 1.190643 AAAACCACCACAACACCCTG 58.809 50.000 0.00 0.00 0.00 4.45
864 879 0.040499 AAACCACCACAACACCCTGT 59.960 50.000 0.00 0.00 0.00 4.00
865 880 0.920438 AACCACCACAACACCCTGTA 59.080 50.000 0.00 0.00 0.00 2.74
866 881 0.920438 ACCACCACAACACCCTGTAA 59.080 50.000 0.00 0.00 0.00 2.41
867 882 1.285373 ACCACCACAACACCCTGTAAA 59.715 47.619 0.00 0.00 0.00 2.01
868 883 1.679153 CCACCACAACACCCTGTAAAC 59.321 52.381 0.00 0.00 0.00 2.01
869 884 1.679153 CACCACAACACCCTGTAAACC 59.321 52.381 0.00 0.00 0.00 3.27
870 885 1.324383 CCACAACACCCTGTAAACCC 58.676 55.000 0.00 0.00 0.00 4.11
871 886 1.324383 CACAACACCCTGTAAACCCC 58.676 55.000 0.00 0.00 0.00 4.95
872 887 1.133606 CACAACACCCTGTAAACCCCT 60.134 52.381 0.00 0.00 0.00 4.79
873 888 1.144298 ACAACACCCTGTAAACCCCTC 59.856 52.381 0.00 0.00 0.00 4.30
874 889 1.144093 CAACACCCTGTAAACCCCTCA 59.856 52.381 0.00 0.00 0.00 3.86
875 890 1.755200 ACACCCTGTAAACCCCTCAT 58.245 50.000 0.00 0.00 0.00 2.90
876 891 1.633945 ACACCCTGTAAACCCCTCATC 59.366 52.381 0.00 0.00 0.00 2.92
877 892 1.064685 CACCCTGTAAACCCCTCATCC 60.065 57.143 0.00 0.00 0.00 3.51
878 893 0.551396 CCCTGTAAACCCCTCATCCC 59.449 60.000 0.00 0.00 0.00 3.85
879 894 1.596496 CCTGTAAACCCCTCATCCCT 58.404 55.000 0.00 0.00 0.00 4.20
880 895 1.212935 CCTGTAAACCCCTCATCCCTG 59.787 57.143 0.00 0.00 0.00 4.45
881 896 1.916181 CTGTAAACCCCTCATCCCTGT 59.084 52.381 0.00 0.00 0.00 4.00
882 897 1.633432 TGTAAACCCCTCATCCCTGTG 59.367 52.381 0.00 0.00 0.00 3.66
883 898 1.913419 GTAAACCCCTCATCCCTGTGA 59.087 52.381 0.00 0.00 0.00 3.58
884 899 0.698818 AAACCCCTCATCCCTGTGAC 59.301 55.000 0.00 0.00 0.00 3.67
885 900 0.475632 AACCCCTCATCCCTGTGACA 60.476 55.000 0.00 0.00 0.00 3.58
886 901 0.253347 ACCCCTCATCCCTGTGACAT 60.253 55.000 0.00 0.00 0.00 3.06
887 902 0.471617 CCCCTCATCCCTGTGACATC 59.528 60.000 0.00 0.00 0.00 3.06
888 903 0.471617 CCCTCATCCCTGTGACATCC 59.528 60.000 0.00 0.00 0.00 3.51
889 904 1.504912 CCTCATCCCTGTGACATCCT 58.495 55.000 0.00 0.00 0.00 3.24
890 905 2.682594 CCTCATCCCTGTGACATCCTA 58.317 52.381 0.00 0.00 0.00 2.94
891 906 3.041211 CCTCATCCCTGTGACATCCTAA 58.959 50.000 0.00 0.00 0.00 2.69
892 907 3.181461 CCTCATCCCTGTGACATCCTAAC 60.181 52.174 0.00 0.00 0.00 2.34
893 908 3.449918 TCATCCCTGTGACATCCTAACA 58.550 45.455 0.00 0.00 0.00 2.41
894 909 4.040047 TCATCCCTGTGACATCCTAACAT 58.960 43.478 0.00 0.00 0.00 2.71
895 910 4.101585 TCATCCCTGTGACATCCTAACATC 59.898 45.833 0.00 0.00 0.00 3.06
896 911 2.771943 TCCCTGTGACATCCTAACATCC 59.228 50.000 0.00 0.00 0.00 3.51
897 912 2.774234 CCCTGTGACATCCTAACATCCT 59.226 50.000 0.00 0.00 0.00 3.24
898 913 3.432749 CCCTGTGACATCCTAACATCCTG 60.433 52.174 0.00 0.00 0.00 3.86
899 914 3.198635 CCTGTGACATCCTAACATCCTGT 59.801 47.826 0.00 0.00 0.00 4.00
900 915 4.405680 CCTGTGACATCCTAACATCCTGTA 59.594 45.833 0.00 0.00 0.00 2.74
901 916 5.339008 TGTGACATCCTAACATCCTGTAC 57.661 43.478 0.00 0.00 0.00 2.90
902 917 4.142249 TGTGACATCCTAACATCCTGTACG 60.142 45.833 0.00 0.00 0.00 3.67
903 918 4.021229 TGACATCCTAACATCCTGTACGT 58.979 43.478 0.00 0.00 0.00 3.57
904 919 4.142249 TGACATCCTAACATCCTGTACGTG 60.142 45.833 0.00 0.00 0.00 4.49
905 920 3.767673 ACATCCTAACATCCTGTACGTGT 59.232 43.478 0.00 0.00 0.00 4.49
906 921 4.951715 ACATCCTAACATCCTGTACGTGTA 59.048 41.667 0.00 0.00 0.00 2.90
907 922 5.067413 ACATCCTAACATCCTGTACGTGTAG 59.933 44.000 0.00 0.00 0.00 2.74
908 923 3.379372 TCCTAACATCCTGTACGTGTAGC 59.621 47.826 0.00 0.00 0.00 3.58
909 924 3.129813 CCTAACATCCTGTACGTGTAGCA 59.870 47.826 0.00 0.00 0.00 3.49
910 925 3.671008 AACATCCTGTACGTGTAGCAA 57.329 42.857 0.00 0.00 0.00 3.91
911 926 3.671008 ACATCCTGTACGTGTAGCAAA 57.329 42.857 0.00 0.00 0.00 3.68
912 927 3.585862 ACATCCTGTACGTGTAGCAAAG 58.414 45.455 0.00 0.00 0.00 2.77
913 928 2.074547 TCCTGTACGTGTAGCAAAGC 57.925 50.000 0.00 0.00 0.00 3.51
914 929 1.616865 TCCTGTACGTGTAGCAAAGCT 59.383 47.619 0.00 0.00 43.41 3.74
915 930 1.993370 CCTGTACGTGTAGCAAAGCTC 59.007 52.381 0.00 0.00 40.44 4.09
940 955 3.121611 TGACAAATACCGTACGCGAAAAG 59.878 43.478 15.93 2.22 41.33 2.27
941 956 2.412770 ACAAATACCGTACGCGAAAAGG 59.587 45.455 15.93 14.80 41.33 3.11
1557 1573 2.182842 GCATGCTGGGGATGTCGAC 61.183 63.158 11.37 9.11 0.00 4.20
2294 2310 6.843069 AAGGCAAAACAAATGTTACATCAC 57.157 33.333 0.00 0.00 37.25 3.06
2446 2462 0.234884 GAACGGCCTTGTGACGAAAG 59.765 55.000 0.00 0.00 0.00 2.62
2520 2536 9.667107 AATGAGATAACTTTCATCGGAGTTTTA 57.333 29.630 0.00 0.00 37.32 1.52
2601 2617 1.136085 CACAAGTACCGAATTGTGCCG 60.136 52.381 11.40 0.00 46.79 5.69
2921 2937 5.885912 TCCCAAAAGTTTCAGGATATAGTGC 59.114 40.000 8.27 0.00 0.00 4.40
2980 2997 7.543359 TGATCCACCTCAAATGAAAATCTTT 57.457 32.000 0.00 0.00 0.00 2.52
3024 3041 5.530171 CCTTACAAGGTCATGAATGGATCTG 59.470 44.000 0.00 0.00 41.41 2.90
3044 3061 5.720202 TCTGTACTTATCTGCGATTTGTGT 58.280 37.500 0.00 0.00 0.00 3.72
3162 3179 6.096141 ACATGGCATCAACGACCAAATTATTA 59.904 34.615 0.00 0.00 36.94 0.98
3205 3222 2.155279 GTCAGGCAGAACTTCCTTTCC 58.845 52.381 0.00 0.00 0.00 3.13
3220 3237 8.183104 ACTTCCTTTCCTTCCTTATTTCTTTG 57.817 34.615 0.00 0.00 0.00 2.77
3227 3244 8.821686 TTCCTTCCTTATTTCTTTGCATGATA 57.178 30.769 0.00 0.00 0.00 2.15
3262 3280 3.435671 GGAATACTGAACAGGGAACAACG 59.564 47.826 6.76 0.00 0.00 4.10
3271 3289 2.175811 GGAACAACGCACGCCATC 59.824 61.111 0.00 0.00 0.00 3.51
3292 3310 6.376018 CCATCGTCAGGGTTTCCTTATTTTTA 59.624 38.462 0.00 0.00 42.67 1.52
3433 3451 5.930837 TGGAAAAAGAAAGGAAGAGCAAA 57.069 34.783 0.00 0.00 0.00 3.68
3510 3528 9.863845 TCTTTTATCGTCTGAACAACATGTATA 57.136 29.630 0.00 0.00 0.00 1.47
3653 3672 8.726650 TTCAGAATTGTTACGAAAATGTGATG 57.273 30.769 0.00 0.00 0.00 3.07
3743 3763 5.977821 AGGAAGGGAGGTAGAATAAAAGG 57.022 43.478 0.00 0.00 0.00 3.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.258457 AGCTATCTACTCCAGGAGTTGT 57.742 45.455 27.73 16.77 40.28 3.32
1 2 5.381757 ACTAGCTATCTACTCCAGGAGTTG 58.618 45.833 27.73 24.36 40.28 3.16
2 3 5.656549 ACTAGCTATCTACTCCAGGAGTT 57.343 43.478 27.73 12.38 40.28 3.01
3 4 5.627135 GAACTAGCTATCTACTCCAGGAGT 58.373 45.833 25.92 25.92 45.54 3.85
4 5 4.693566 CGAACTAGCTATCTACTCCAGGAG 59.306 50.000 15.72 15.72 35.52 3.69
34 35 0.962489 GCTAGCTAGCTCCCATCGAA 59.038 55.000 33.71 0.00 45.62 3.71
35 36 2.647356 GCTAGCTAGCTCCCATCGA 58.353 57.895 33.71 0.00 45.62 3.59
73 74 1.608055 TCCAGGAGTTGTCGTCGTAA 58.392 50.000 0.00 0.00 0.00 3.18
79 80 2.586258 AATCGATCCAGGAGTTGTCG 57.414 50.000 0.00 4.06 0.00 4.35
146 147 1.429148 GCCAAATACGGAGTCGCCAG 61.429 60.000 0.00 0.00 43.93 4.85
147 148 1.448893 GCCAAATACGGAGTCGCCA 60.449 57.895 0.00 0.00 43.93 5.69
155 156 0.455972 CACAAAGCGGCCAAATACGG 60.456 55.000 2.24 0.00 0.00 4.02
171 172 4.947147 GCCGGCAGACAACCCACA 62.947 66.667 24.80 0.00 0.00 4.17
175 176 2.775032 TACGAAGCCGGCAGACAACC 62.775 60.000 31.54 7.87 40.78 3.77
177 178 1.080093 CTACGAAGCCGGCAGACAA 60.080 57.895 31.54 10.05 40.78 3.18
196 197 2.627221 TCCATGATCAGCTAGCTCACTC 59.373 50.000 16.15 12.10 0.00 3.51
207 208 1.884464 CGCCCGTGTCCATGATCAG 60.884 63.158 0.09 0.00 0.00 2.90
212 213 2.202797 CTCTCGCCCGTGTCCATG 60.203 66.667 0.00 0.00 0.00 3.66
217 218 0.038159 CTTCTTTCTCTCGCCCGTGT 60.038 55.000 0.00 0.00 0.00 4.49
225 226 4.216687 TCCTCACGTCTTCTTCTTTCTCTC 59.783 45.833 0.00 0.00 0.00 3.20
227 228 4.506886 TCCTCACGTCTTCTTCTTTCTC 57.493 45.455 0.00 0.00 0.00 2.87
231 232 8.446599 TTTATTTTTCCTCACGTCTTCTTCTT 57.553 30.769 0.00 0.00 0.00 2.52
233 234 8.955002 GTTTTTATTTTTCCTCACGTCTTCTTC 58.045 33.333 0.00 0.00 0.00 2.87
279 283 6.750501 GCCGAATAGACCCTTCAAATTTAAAC 59.249 38.462 0.00 0.00 0.00 2.01
283 287 3.699538 GGCCGAATAGACCCTTCAAATTT 59.300 43.478 0.00 0.00 0.00 1.82
289 293 1.594564 GCGGCCGAATAGACCCTTC 60.595 63.158 33.48 1.41 0.00 3.46
292 296 2.280186 CTGCGGCCGAATAGACCC 60.280 66.667 33.48 9.04 0.00 4.46
298 302 1.654023 GGTTTAAGCTGCGGCCGAAT 61.654 55.000 33.48 6.01 39.73 3.34
299 303 2.329614 GGTTTAAGCTGCGGCCGAA 61.330 57.895 33.48 20.72 39.73 4.30
310 321 5.218139 ACGTGTTCTAAGAGTCGGTTTAAG 58.782 41.667 0.00 0.00 0.00 1.85
319 330 5.284079 TCGCTAAAAACGTGTTCTAAGAGT 58.716 37.500 0.00 0.00 0.00 3.24
325 336 3.866910 TCAGTTCGCTAAAAACGTGTTCT 59.133 39.130 0.00 0.00 0.00 3.01
326 337 4.186241 TCAGTTCGCTAAAAACGTGTTC 57.814 40.909 0.00 0.00 0.00 3.18
337 348 2.297033 ACCTACGGTTTTCAGTTCGCTA 59.703 45.455 0.00 0.00 27.29 4.26
338 349 1.069668 ACCTACGGTTTTCAGTTCGCT 59.930 47.619 0.00 0.00 27.29 4.93
347 358 1.475682 CTCTAGCGGACCTACGGTTTT 59.524 52.381 0.00 0.00 42.53 2.43
348 359 1.101331 CTCTAGCGGACCTACGGTTT 58.899 55.000 0.00 0.00 42.53 3.27
349 360 0.254178 TCTCTAGCGGACCTACGGTT 59.746 55.000 0.00 0.00 42.53 4.44
351 362 0.875728 CATCTCTAGCGGACCTACGG 59.124 60.000 0.00 0.00 0.00 4.02
352 363 0.238817 GCATCTCTAGCGGACCTACG 59.761 60.000 0.00 0.00 0.00 3.51
353 364 1.268352 CAGCATCTCTAGCGGACCTAC 59.732 57.143 0.00 0.00 37.01 3.18
354 365 1.133761 ACAGCATCTCTAGCGGACCTA 60.134 52.381 0.00 0.00 37.01 3.08
355 366 0.396417 ACAGCATCTCTAGCGGACCT 60.396 55.000 0.00 0.00 37.01 3.85
356 367 0.031449 GACAGCATCTCTAGCGGACC 59.969 60.000 0.00 0.00 37.01 4.46
357 368 0.741326 TGACAGCATCTCTAGCGGAC 59.259 55.000 0.00 0.00 37.01 4.79
358 369 0.741326 GTGACAGCATCTCTAGCGGA 59.259 55.000 0.00 0.00 37.01 5.54
359 370 0.593518 CGTGACAGCATCTCTAGCGG 60.594 60.000 0.00 0.00 37.01 5.52
360 371 1.205485 GCGTGACAGCATCTCTAGCG 61.205 60.000 0.00 0.00 37.01 4.26
389 400 0.954452 CAACCAAACAGGACTGCTCC 59.046 55.000 0.00 0.00 41.22 4.70
399 410 1.076412 TCTGCAGCCCAACCAAACA 60.076 52.632 9.47 0.00 0.00 2.83
416 428 2.159393 TCAAGTTTGTGTTGCTGCACTC 60.159 45.455 0.00 0.00 39.89 3.51
435 447 2.425312 TGGCACGCTTTTTCTCTTTTCA 59.575 40.909 0.00 0.00 0.00 2.69
436 448 3.078594 TGGCACGCTTTTTCTCTTTTC 57.921 42.857 0.00 0.00 0.00 2.29
440 452 2.291741 CTCTTTGGCACGCTTTTTCTCT 59.708 45.455 0.00 0.00 0.00 3.10
441 453 2.605580 CCTCTTTGGCACGCTTTTTCTC 60.606 50.000 0.00 0.00 0.00 2.87
442 454 1.338020 CCTCTTTGGCACGCTTTTTCT 59.662 47.619 0.00 0.00 0.00 2.52
443 455 1.336755 TCCTCTTTGGCACGCTTTTTC 59.663 47.619 0.00 0.00 35.26 2.29
444 456 1.398692 TCCTCTTTGGCACGCTTTTT 58.601 45.000 0.00 0.00 35.26 1.94
446 458 1.067060 GTTTCCTCTTTGGCACGCTTT 59.933 47.619 0.00 0.00 35.26 3.51
447 459 0.668535 GTTTCCTCTTTGGCACGCTT 59.331 50.000 0.00 0.00 35.26 4.68
452 467 2.552315 GTCGATTGTTTCCTCTTTGGCA 59.448 45.455 0.00 0.00 35.26 4.92
457 472 4.336889 TGTCAGTCGATTGTTTCCTCTT 57.663 40.909 7.87 0.00 0.00 2.85
481 496 5.886960 AGCCTGTACTTCTAGCATTTTTG 57.113 39.130 0.00 0.00 0.00 2.44
482 497 6.901081 AAAGCCTGTACTTCTAGCATTTTT 57.099 33.333 0.00 0.00 0.00 1.94
483 498 6.901081 AAAAGCCTGTACTTCTAGCATTTT 57.099 33.333 0.00 0.00 0.00 1.82
484 499 6.940298 TGTAAAAGCCTGTACTTCTAGCATTT 59.060 34.615 0.00 0.00 0.00 2.32
485 500 6.472887 TGTAAAAGCCTGTACTTCTAGCATT 58.527 36.000 0.00 0.00 0.00 3.56
486 501 6.049955 TGTAAAAGCCTGTACTTCTAGCAT 57.950 37.500 0.00 0.00 0.00 3.79
487 502 5.477607 TGTAAAAGCCTGTACTTCTAGCA 57.522 39.130 0.00 0.00 0.00 3.49
488 503 4.870991 CCTGTAAAAGCCTGTACTTCTAGC 59.129 45.833 0.00 0.00 0.00 3.42
489 504 6.038997 ACCTGTAAAAGCCTGTACTTCTAG 57.961 41.667 0.00 0.00 0.00 2.43
490 505 6.429521 AACCTGTAAAAGCCTGTACTTCTA 57.570 37.500 0.00 0.00 0.00 2.10
491 506 4.976540 ACCTGTAAAAGCCTGTACTTCT 57.023 40.909 0.00 0.00 0.00 2.85
492 507 5.763698 AGAAACCTGTAAAAGCCTGTACTTC 59.236 40.000 0.00 0.00 0.00 3.01
493 508 5.691896 AGAAACCTGTAAAAGCCTGTACTT 58.308 37.500 0.00 0.00 0.00 2.24
494 509 5.306114 AGAAACCTGTAAAAGCCTGTACT 57.694 39.130 0.00 0.00 0.00 2.73
495 510 5.993441 TGTAGAAACCTGTAAAAGCCTGTAC 59.007 40.000 0.00 0.00 0.00 2.90
496 511 6.177310 TGTAGAAACCTGTAAAAGCCTGTA 57.823 37.500 0.00 0.00 0.00 2.74
497 512 5.043737 TGTAGAAACCTGTAAAAGCCTGT 57.956 39.130 0.00 0.00 0.00 4.00
498 513 4.455877 CCTGTAGAAACCTGTAAAAGCCTG 59.544 45.833 0.00 0.00 0.00 4.85
499 514 4.652822 CCTGTAGAAACCTGTAAAAGCCT 58.347 43.478 0.00 0.00 0.00 4.58
500 515 3.190744 GCCTGTAGAAACCTGTAAAAGCC 59.809 47.826 0.00 0.00 0.00 4.35
501 516 4.072839 AGCCTGTAGAAACCTGTAAAAGC 58.927 43.478 0.00 0.00 0.00 3.51
502 517 4.695928 GGAGCCTGTAGAAACCTGTAAAAG 59.304 45.833 0.00 0.00 0.00 2.27
503 518 4.349930 AGGAGCCTGTAGAAACCTGTAAAA 59.650 41.667 0.00 0.00 0.00 1.52
504 519 3.908103 AGGAGCCTGTAGAAACCTGTAAA 59.092 43.478 0.00 0.00 0.00 2.01
505 520 3.517612 AGGAGCCTGTAGAAACCTGTAA 58.482 45.455 0.00 0.00 0.00 2.41
506 521 3.185880 AGGAGCCTGTAGAAACCTGTA 57.814 47.619 0.00 0.00 0.00 2.74
507 522 2.031495 AGGAGCCTGTAGAAACCTGT 57.969 50.000 0.00 0.00 0.00 4.00
508 523 3.244561 TGAAAGGAGCCTGTAGAAACCTG 60.245 47.826 0.00 0.00 0.00 4.00
509 524 2.979678 TGAAAGGAGCCTGTAGAAACCT 59.020 45.455 0.00 0.00 0.00 3.50
510 525 3.418684 TGAAAGGAGCCTGTAGAAACC 57.581 47.619 0.00 0.00 0.00 3.27
511 526 4.822350 AGTTTGAAAGGAGCCTGTAGAAAC 59.178 41.667 6.00 6.00 0.00 2.78
512 527 5.048846 AGTTTGAAAGGAGCCTGTAGAAA 57.951 39.130 0.00 0.00 0.00 2.52
513 528 4.706842 AGTTTGAAAGGAGCCTGTAGAA 57.293 40.909 0.00 0.00 0.00 2.10
514 529 4.706842 AAGTTTGAAAGGAGCCTGTAGA 57.293 40.909 0.00 0.00 0.00 2.59
515 530 5.363979 GAAAGTTTGAAAGGAGCCTGTAG 57.636 43.478 0.00 0.00 0.00 2.74
812 827 0.191314 AGTAGAGGTAGGGCCCATCC 59.809 60.000 27.56 24.75 38.26 3.51
813 828 2.994957 TAGTAGAGGTAGGGCCCATC 57.005 55.000 27.56 16.33 38.26 3.51
814 829 3.144125 TCATTAGTAGAGGTAGGGCCCAT 59.856 47.826 27.56 12.06 38.26 4.00
815 830 2.520980 TCATTAGTAGAGGTAGGGCCCA 59.479 50.000 27.56 7.27 38.26 5.36
816 831 2.898612 GTCATTAGTAGAGGTAGGGCCC 59.101 54.545 16.46 16.46 38.26 5.80
817 832 2.898612 GGTCATTAGTAGAGGTAGGGCC 59.101 54.545 0.00 0.00 37.58 5.80
818 833 3.573695 TGGTCATTAGTAGAGGTAGGGC 58.426 50.000 0.00 0.00 0.00 5.19
819 834 6.749036 AATTGGTCATTAGTAGAGGTAGGG 57.251 41.667 0.00 0.00 0.00 3.53
823 838 9.239551 GGTTTTTAATTGGTCATTAGTAGAGGT 57.760 33.333 0.00 0.00 0.00 3.85
824 839 9.238368 TGGTTTTTAATTGGTCATTAGTAGAGG 57.762 33.333 0.00 0.00 0.00 3.69
826 841 9.016438 GGTGGTTTTTAATTGGTCATTAGTAGA 57.984 33.333 0.00 0.00 0.00 2.59
827 842 8.798402 TGGTGGTTTTTAATTGGTCATTAGTAG 58.202 33.333 0.00 0.00 0.00 2.57
828 843 8.578151 GTGGTGGTTTTTAATTGGTCATTAGTA 58.422 33.333 0.00 0.00 0.00 1.82
829 844 7.070074 TGTGGTGGTTTTTAATTGGTCATTAGT 59.930 33.333 0.00 0.00 0.00 2.24
830 845 7.437748 TGTGGTGGTTTTTAATTGGTCATTAG 58.562 34.615 0.00 0.00 0.00 1.73
831 846 7.361457 TGTGGTGGTTTTTAATTGGTCATTA 57.639 32.000 0.00 0.00 0.00 1.90
832 847 6.240549 TGTGGTGGTTTTTAATTGGTCATT 57.759 33.333 0.00 0.00 0.00 2.57
833 848 5.878406 TGTGGTGGTTTTTAATTGGTCAT 57.122 34.783 0.00 0.00 0.00 3.06
834 849 5.046591 TGTTGTGGTGGTTTTTAATTGGTCA 60.047 36.000 0.00 0.00 0.00 4.02
835 850 5.292345 GTGTTGTGGTGGTTTTTAATTGGTC 59.708 40.000 0.00 0.00 0.00 4.02
836 851 5.179533 GTGTTGTGGTGGTTTTTAATTGGT 58.820 37.500 0.00 0.00 0.00 3.67
837 852 4.572795 GGTGTTGTGGTGGTTTTTAATTGG 59.427 41.667 0.00 0.00 0.00 3.16
838 853 4.572795 GGGTGTTGTGGTGGTTTTTAATTG 59.427 41.667 0.00 0.00 0.00 2.32
839 854 4.471747 AGGGTGTTGTGGTGGTTTTTAATT 59.528 37.500 0.00 0.00 0.00 1.40
840 855 4.034410 AGGGTGTTGTGGTGGTTTTTAAT 58.966 39.130 0.00 0.00 0.00 1.40
841 856 3.195825 CAGGGTGTTGTGGTGGTTTTTAA 59.804 43.478 0.00 0.00 0.00 1.52
842 857 2.761208 CAGGGTGTTGTGGTGGTTTTTA 59.239 45.455 0.00 0.00 0.00 1.52
843 858 1.552792 CAGGGTGTTGTGGTGGTTTTT 59.447 47.619 0.00 0.00 0.00 1.94
844 859 1.190643 CAGGGTGTTGTGGTGGTTTT 58.809 50.000 0.00 0.00 0.00 2.43
845 860 0.040499 ACAGGGTGTTGTGGTGGTTT 59.960 50.000 0.00 0.00 0.00 3.27
846 861 0.920438 TACAGGGTGTTGTGGTGGTT 59.080 50.000 0.00 0.00 32.56 3.67
847 862 0.920438 TTACAGGGTGTTGTGGTGGT 59.080 50.000 0.00 0.00 32.56 4.16
848 863 1.679153 GTTTACAGGGTGTTGTGGTGG 59.321 52.381 0.00 0.00 32.56 4.61
849 864 1.679153 GGTTTACAGGGTGTTGTGGTG 59.321 52.381 0.00 0.00 32.56 4.17
850 865 1.410507 GGGTTTACAGGGTGTTGTGGT 60.411 52.381 0.00 0.00 32.56 4.16
851 866 1.324383 GGGTTTACAGGGTGTTGTGG 58.676 55.000 0.00 0.00 32.56 4.17
852 867 1.133606 AGGGGTTTACAGGGTGTTGTG 60.134 52.381 0.00 0.00 32.56 3.33
853 868 1.144298 GAGGGGTTTACAGGGTGTTGT 59.856 52.381 0.00 0.00 35.09 3.32
854 869 1.144093 TGAGGGGTTTACAGGGTGTTG 59.856 52.381 0.00 0.00 0.00 3.33
855 870 1.525175 TGAGGGGTTTACAGGGTGTT 58.475 50.000 0.00 0.00 0.00 3.32
856 871 1.633945 GATGAGGGGTTTACAGGGTGT 59.366 52.381 0.00 0.00 0.00 4.16
857 872 1.064685 GGATGAGGGGTTTACAGGGTG 60.065 57.143 0.00 0.00 0.00 4.61
858 873 1.296002 GGATGAGGGGTTTACAGGGT 58.704 55.000 0.00 0.00 0.00 4.34
859 874 0.551396 GGGATGAGGGGTTTACAGGG 59.449 60.000 0.00 0.00 0.00 4.45
860 875 1.212935 CAGGGATGAGGGGTTTACAGG 59.787 57.143 0.00 0.00 0.00 4.00
861 876 1.916181 ACAGGGATGAGGGGTTTACAG 59.084 52.381 0.00 0.00 0.00 2.74
862 877 1.633432 CACAGGGATGAGGGGTTTACA 59.367 52.381 0.00 0.00 0.00 2.41
863 878 1.913419 TCACAGGGATGAGGGGTTTAC 59.087 52.381 0.00 0.00 0.00 2.01
864 879 1.913419 GTCACAGGGATGAGGGGTTTA 59.087 52.381 0.00 0.00 0.00 2.01
865 880 0.698818 GTCACAGGGATGAGGGGTTT 59.301 55.000 0.00 0.00 0.00 3.27
866 881 0.475632 TGTCACAGGGATGAGGGGTT 60.476 55.000 0.00 0.00 0.00 4.11
867 882 0.253347 ATGTCACAGGGATGAGGGGT 60.253 55.000 0.00 0.00 0.00 4.95
868 883 0.471617 GATGTCACAGGGATGAGGGG 59.528 60.000 0.00 0.00 0.00 4.79
869 884 0.471617 GGATGTCACAGGGATGAGGG 59.528 60.000 0.00 0.00 0.00 4.30
870 885 1.504912 AGGATGTCACAGGGATGAGG 58.495 55.000 0.00 0.00 0.00 3.86
871 886 3.452264 TGTTAGGATGTCACAGGGATGAG 59.548 47.826 0.00 0.00 0.00 2.90
872 887 3.449918 TGTTAGGATGTCACAGGGATGA 58.550 45.455 0.00 0.00 0.00 2.92
873 888 3.912496 TGTTAGGATGTCACAGGGATG 57.088 47.619 0.00 0.00 0.00 3.51
874 889 3.392616 GGATGTTAGGATGTCACAGGGAT 59.607 47.826 0.00 0.00 0.00 3.85
875 890 2.771943 GGATGTTAGGATGTCACAGGGA 59.228 50.000 0.00 0.00 0.00 4.20
876 891 2.774234 AGGATGTTAGGATGTCACAGGG 59.226 50.000 0.00 0.00 0.00 4.45
877 892 3.801698 CAGGATGTTAGGATGTCACAGG 58.198 50.000 0.00 0.00 0.00 4.00
889 904 8.459621 AGCTTTGCTACACGTACAGGATGTTA 62.460 42.308 0.00 0.00 42.80 2.41
890 905 7.756778 AGCTTTGCTACACGTACAGGATGTT 62.757 44.000 0.00 0.00 42.80 2.71
891 906 6.362100 AGCTTTGCTACACGTACAGGATGT 62.362 45.833 0.00 0.00 46.30 3.06
892 907 2.348666 GCTTTGCTACACGTACAGGATG 59.651 50.000 0.00 0.00 46.00 3.51
893 908 2.233922 AGCTTTGCTACACGTACAGGAT 59.766 45.455 0.00 0.00 36.99 3.24
894 909 1.616865 AGCTTTGCTACACGTACAGGA 59.383 47.619 0.00 0.00 36.99 3.86
895 910 1.993370 GAGCTTTGCTACACGTACAGG 59.007 52.381 0.00 0.00 39.88 4.00
896 911 2.408704 GTGAGCTTTGCTACACGTACAG 59.591 50.000 0.00 0.00 39.88 2.74
897 912 2.035449 AGTGAGCTTTGCTACACGTACA 59.965 45.455 12.61 0.00 39.88 2.90
898 913 2.408704 CAGTGAGCTTTGCTACACGTAC 59.591 50.000 12.61 0.00 39.88 3.67
899 914 2.295070 TCAGTGAGCTTTGCTACACGTA 59.705 45.455 12.61 6.21 39.88 3.57
900 915 1.068588 TCAGTGAGCTTTGCTACACGT 59.931 47.619 12.61 0.00 39.88 4.49
901 916 1.457303 GTCAGTGAGCTTTGCTACACG 59.543 52.381 0.00 9.68 39.88 4.49
902 917 2.483876 TGTCAGTGAGCTTTGCTACAC 58.516 47.619 0.00 11.37 39.88 2.90
903 918 2.908688 TGTCAGTGAGCTTTGCTACA 57.091 45.000 0.00 0.00 39.88 2.74
904 919 4.756084 ATTTGTCAGTGAGCTTTGCTAC 57.244 40.909 0.00 0.00 39.88 3.58
905 920 4.695455 GGTATTTGTCAGTGAGCTTTGCTA 59.305 41.667 0.00 0.00 39.88 3.49
906 921 3.503748 GGTATTTGTCAGTGAGCTTTGCT 59.496 43.478 0.00 0.00 43.88 3.91
907 922 3.667960 CGGTATTTGTCAGTGAGCTTTGC 60.668 47.826 0.00 0.00 0.00 3.68
908 923 3.498397 ACGGTATTTGTCAGTGAGCTTTG 59.502 43.478 0.00 0.00 0.00 2.77
909 924 3.740115 ACGGTATTTGTCAGTGAGCTTT 58.260 40.909 0.00 0.00 0.00 3.51
910 925 3.402628 ACGGTATTTGTCAGTGAGCTT 57.597 42.857 0.00 0.00 0.00 3.74
911 926 3.672511 CGTACGGTATTTGTCAGTGAGCT 60.673 47.826 7.57 0.00 0.00 4.09
912 927 2.597305 CGTACGGTATTTGTCAGTGAGC 59.403 50.000 7.57 0.00 0.00 4.26
913 928 2.597305 GCGTACGGTATTTGTCAGTGAG 59.403 50.000 18.39 0.00 0.00 3.51
914 929 2.598589 GCGTACGGTATTTGTCAGTGA 58.401 47.619 18.39 0.00 0.00 3.41
915 930 1.319374 CGCGTACGGTATTTGTCAGTG 59.681 52.381 18.39 0.00 34.97 3.66
1557 1573 4.596585 AACACCCCAACCGCCTGG 62.597 66.667 0.00 0.00 42.84 4.45
1588 1604 4.170062 CGCTGTGGCATTCCGCTG 62.170 66.667 0.00 0.00 43.26 5.18
2294 2310 3.100671 AGGCTAGTCCCAAGTACAAGAG 58.899 50.000 0.00 0.00 34.51 2.85
2601 2617 4.445453 TGCATCCATAGTGTCTGATGTTC 58.555 43.478 0.00 0.00 37.51 3.18
2921 2937 5.611796 TCAAGAATGAGACATTTCAACGG 57.388 39.130 0.00 0.00 0.00 4.44
2947 2963 2.540383 TGAGGTGGATCAACTGCTAGT 58.460 47.619 0.00 0.00 28.17 2.57
2980 2997 4.362677 AGGCTTCAACTTGGACCTATCTA 58.637 43.478 0.00 0.00 0.00 1.98
3024 3041 6.955963 CAGAAACACAAATCGCAGATAAGTAC 59.044 38.462 0.00 0.00 45.12 2.73
3044 3061 6.455647 ACACACGATGATAGAAAGTCAGAAA 58.544 36.000 0.00 0.00 0.00 2.52
3162 3179 9.416284 TGACCTCTGGTAAAAGTTTAAAAGATT 57.584 29.630 0.00 0.00 35.25 2.40
3182 3199 0.980423 AGGAAGTTCTGCCTGACCTC 59.020 55.000 2.25 0.00 32.06 3.85
3205 3222 9.688592 GGATTATCATGCAAAGAAATAAGGAAG 57.311 33.333 0.00 0.00 0.00 3.46
3220 3237 4.851843 TCCAGATGGATGGATTATCATGC 58.148 43.478 0.00 0.00 44.56 4.06
3271 3289 9.483916 AAAATTAAAAATAAGGAAACCCTGACG 57.516 29.630 0.00 0.00 33.44 4.35
3303 3321 0.464554 TTGCACCATGGTTCACGACA 60.465 50.000 17.34 0.00 0.00 4.35
3433 3451 6.661740 TTCCACCCCATAGTTAATTTACCT 57.338 37.500 0.00 0.00 0.00 3.08
3475 3493 9.268268 TGTTCAGACGATAAAAGAATTACAAGT 57.732 29.630 0.00 0.00 0.00 3.16
3510 3528 7.440255 CCACAAATCTTTTTCTGAGCATTTCTT 59.560 33.333 0.00 0.00 0.00 2.52
3511 3529 6.927381 CCACAAATCTTTTTCTGAGCATTTCT 59.073 34.615 0.00 0.00 0.00 2.52
3553 3572 8.456221 AGGAATTAGCCTAGATATAGCCTTTT 57.544 34.615 0.00 0.00 36.22 2.27
3617 3636 7.390440 TCGTAACAATTCTGAAGATGGTGAAAT 59.610 33.333 6.75 0.00 0.00 2.17
3618 3637 6.708502 TCGTAACAATTCTGAAGATGGTGAAA 59.291 34.615 6.75 0.00 0.00 2.69
3704 3724 9.632638 CTCCCTTCCTAATCAAATATTTCTTGA 57.367 33.333 0.00 0.00 37.22 3.02
3743 3763 5.057149 CACTAGAACCTGCATACCCAATAC 58.943 45.833 0.00 0.00 0.00 1.89


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

AutoCloner maintained by Alex Coulton.