Multiple sequence alignment - TraesCS1B01G427700

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 TraesCS1B01G427700 chr1B 100.000 4600 0 0 1 4600 653044617 653049216 0.000000e+00 8495
1 TraesCS1B01G427700 chr1B 97.183 142 4 0 987 1128 684903791 684903650 1.650000e-59 241
2 TraesCS1B01G427700 chr1D 90.940 3201 202 45 1437 4598 470410427 470413578 0.000000e+00 4224
3 TraesCS1B01G427700 chr1D 88.668 653 22 22 751 1363 470409788 470410428 0.000000e+00 749
4 TraesCS1B01G427700 chr1D 93.350 406 25 2 4079 4483 392820970 392820566 2.370000e-167 599
5 TraesCS1B01G427700 chr1A 91.930 1648 107 9 2218 3854 564086118 564087750 0.000000e+00 2283
6 TraesCS1B01G427700 chr1A 91.938 645 42 5 1 644 564083023 564083658 0.000000e+00 894
7 TraesCS1B01G427700 chr1A 83.316 965 94 26 1220 2162 564085197 564086116 0.000000e+00 828
8 TraesCS1B01G427700 chr1A 92.378 328 21 2 3853 4176 564087813 564088140 9.010000e-127 464
9 TraesCS1B01G427700 chr1A 86.226 363 27 13 760 1119 564084518 564084860 5.620000e-99 372
10 TraesCS1B01G427700 chr5D 91.972 573 40 5 3916 4483 503906110 503906681 0.000000e+00 798
11 TraesCS1B01G427700 chr5D 93.103 406 26 2 4079 4483 74862182 74861778 1.100000e-165 593
12 TraesCS1B01G427700 chr5D 78.284 571 90 20 2903 3458 428436067 428436618 2.050000e-88 337
13 TraesCS1B01G427700 chr2D 93.350 406 25 2 4079 4483 380986799 380986395 2.370000e-167 599
14 TraesCS1B01G427700 chr2D 93.103 406 26 2 4079 4483 393343500 393343096 1.100000e-165 593
15 TraesCS1B01G427700 chr3D 93.103 406 26 2 4079 4483 525208776 525208372 1.100000e-165 593
16 TraesCS1B01G427700 chr6D 92.857 406 27 2 4079 4483 25071997 25071593 5.130000e-164 588
17 TraesCS1B01G427700 chr6D 92.857 406 27 2 4079 4483 40663293 40662889 5.130000e-164 588
18 TraesCS1B01G427700 chr6A 93.578 218 8 4 973 1189 409919862 409920074 2.060000e-83 320
19 TraesCS1B01G427700 chr7A 96.335 191 6 1 987 1177 646921700 646921511 3.460000e-81 313
20 TraesCS1B01G427700 chr7A 95.812 191 7 1 987 1177 641530206 641530017 1.610000e-79 307
21 TraesCS1B01G427700 chr3A 93.627 204 10 3 987 1189 19078006 19077805 7.480000e-78 302
22 TraesCS1B01G427700 chr5A 94.839 155 7 1 1036 1189 579649931 579649777 1.650000e-59 241
23 TraesCS1B01G427700 chr5A 90.476 84 6 2 4495 4577 564599472 564599390 4.870000e-20 110
24 TraesCS1B01G427700 chr4A 94.231 156 5 3 973 1128 66162377 66162528 7.690000e-58 235


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 TraesCS1B01G427700 chr1B 653044617 653049216 4599 False 8495.0 8495 100.0000 1 4600 1 chr1B.!!$F1 4599
1 TraesCS1B01G427700 chr1D 470409788 470413578 3790 False 2486.5 4224 89.8040 751 4598 2 chr1D.!!$F1 3847
2 TraesCS1B01G427700 chr1A 564083023 564088140 5117 False 968.2 2283 89.1576 1 4176 5 chr1A.!!$F1 4175
3 TraesCS1B01G427700 chr5D 503906110 503906681 571 False 798.0 798 91.9720 3916 4483 1 chr5D.!!$F2 567
4 TraesCS1B01G427700 chr5D 428436067 428436618 551 False 337.0 337 78.2840 2903 3458 1 chr5D.!!$F1 555

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
746 1473 0.037882 CATCTGTCCGTGCAGTCACT 60.038 55.0 0.00 0.0 40.99 3.41 F
748 1475 0.596577 TCTGTCCGTGCAGTCACTAC 59.403 55.0 0.00 0.0 40.99 2.73 F
749 1476 0.598562 CTGTCCGTGCAGTCACTACT 59.401 55.0 0.00 0.0 40.99 2.57 F
1369 2388 1.153353 TCGTGCAAATCGAGGTTTCC 58.847 50.0 0.00 0.0 33.38 3.13 F
2366 3406 0.383590 TACTCTCTGCGCAGATCAGC 59.616 55.0 38.11 0.0 36.76 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2013 3053 0.370273 CGCTGTATGCTGGTTTCGTC 59.630 55.000 0.0 0.0 40.11 4.20 R
2081 3121 0.546747 TGTTGGTGAGGGGTAGGAGG 60.547 60.000 0.0 0.0 0.00 4.30 R
2103 3143 0.603065 GCTGTAGGTTTGCCCTTTGG 59.397 55.000 0.0 0.0 42.73 3.28 R
2452 3492 1.493022 TGTAGTGGACTGGGCAAAACT 59.507 47.619 0.0 0.0 0.00 2.66 R
3911 5044 0.396811 CCACGAGTCTGTTCCCCTTT 59.603 55.000 0.0 0.0 0.00 3.11 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
29 30 8.728337 TGGAAGACTCTTGATGATATTGAAAG 57.272 34.615 0.00 0.00 0.00 2.62
104 105 3.969117 CTGCACAAGCTGAAACTAACA 57.031 42.857 0.00 0.00 41.71 2.41
111 112 4.757149 ACAAGCTGAAACTAACATCTGACC 59.243 41.667 0.00 0.00 0.00 4.02
112 113 3.944087 AGCTGAAACTAACATCTGACCC 58.056 45.455 0.00 0.00 0.00 4.46
153 154 7.393515 AGAAATTCGCCTAAATAAGTGAAACCT 59.606 33.333 0.00 0.00 37.80 3.50
154 155 8.570068 AAATTCGCCTAAATAAGTGAAACCTA 57.430 30.769 0.00 0.00 37.80 3.08
155 156 8.747538 AATTCGCCTAAATAAGTGAAACCTAT 57.252 30.769 0.00 0.00 37.80 2.57
156 157 9.841295 AATTCGCCTAAATAAGTGAAACCTATA 57.159 29.630 0.00 0.00 37.80 1.31
230 231 3.425359 CGTTCTGCTGCTAAATCAACCTG 60.425 47.826 0.00 0.00 0.00 4.00
232 233 1.747355 CTGCTGCTAAATCAACCTGGG 59.253 52.381 0.00 0.00 0.00 4.45
233 234 0.457443 GCTGCTAAATCAACCTGGGC 59.543 55.000 0.00 0.00 0.00 5.36
234 235 1.838112 CTGCTAAATCAACCTGGGCA 58.162 50.000 0.00 0.00 0.00 5.36
272 273 3.127425 AGGTTGAGTTGTAAGAGCCAC 57.873 47.619 0.00 0.00 0.00 5.01
284 285 0.837691 AGAGCCACATGAGACACCCA 60.838 55.000 0.00 0.00 0.00 4.51
305 307 5.429130 CCACCTGAAAAATAGGTAGAGGAC 58.571 45.833 0.00 0.00 46.55 3.85
311 313 7.442666 CCTGAAAAATAGGTAGAGGACTAATGC 59.557 40.741 0.00 0.00 0.00 3.56
321 323 1.202698 AGGACTAATGCTTGGATCGCC 60.203 52.381 0.00 0.00 0.00 5.54
361 363 2.959421 AGGAGGAAGAGATTGGAGGT 57.041 50.000 0.00 0.00 0.00 3.85
364 366 2.192263 GAGGAAGAGATTGGAGGTGGT 58.808 52.381 0.00 0.00 0.00 4.16
385 387 1.117749 TGAGGATGGAGATGAGGGCG 61.118 60.000 0.00 0.00 0.00 6.13
406 408 1.422024 TCGAGGGAGGAAGAGATCGAT 59.578 52.381 0.00 0.00 34.57 3.59
419 421 5.004361 AGAGATCGATATGAAAGGAGGGA 57.996 43.478 0.00 0.00 0.00 4.20
421 423 5.841237 AGAGATCGATATGAAAGGAGGGAAA 59.159 40.000 0.00 0.00 0.00 3.13
448 450 3.323979 TGTCGATTATTCTAGGAAGGGGC 59.676 47.826 0.00 0.00 0.00 5.80
471 473 3.244911 ACAAGTTCCCATCACACCCTTAG 60.245 47.826 0.00 0.00 0.00 2.18
477 479 3.118038 TCCCATCACACCCTTAGCATAAC 60.118 47.826 0.00 0.00 0.00 1.89
510 512 3.932545 TTGCGGCAAATGACTTGTATT 57.067 38.095 13.93 0.00 37.36 1.89
513 515 4.006989 TGCGGCAAATGACTTGTATTACT 58.993 39.130 0.00 0.00 37.36 2.24
517 519 5.121611 CGGCAAATGACTTGTATTACTCACA 59.878 40.000 0.00 0.00 37.36 3.58
521 523 7.852945 GCAAATGACTTGTATTACTCACATAGC 59.147 37.037 0.00 0.00 37.36 2.97
524 526 4.945246 ACTTGTATTACTCACATAGCCGG 58.055 43.478 0.00 0.00 0.00 6.13
525 527 4.202223 ACTTGTATTACTCACATAGCCGGG 60.202 45.833 2.18 0.00 0.00 5.73
540 542 3.507411 AGCCGGGCTATACTCAGAATTA 58.493 45.455 22.47 0.00 36.99 1.40
541 543 3.511934 AGCCGGGCTATACTCAGAATTAG 59.488 47.826 22.47 0.00 36.99 1.73
561 563 7.701539 ATTAGCAAGTTTGACAATACCATCA 57.298 32.000 0.00 0.00 0.00 3.07
566 568 5.505181 AGTTTGACAATACCATCAGGACT 57.495 39.130 0.00 0.00 38.69 3.85
604 606 3.631227 GGCAGTACGTCCACTAGTTCTAT 59.369 47.826 0.00 0.00 0.00 1.98
607 609 5.008811 GCAGTACGTCCACTAGTTCTATCAT 59.991 44.000 0.00 0.00 0.00 2.45
609 611 7.094720 GCAGTACGTCCACTAGTTCTATCATAT 60.095 40.741 0.00 0.00 0.00 1.78
610 612 9.433153 CAGTACGTCCACTAGTTCTATCATATA 57.567 37.037 0.00 0.00 0.00 0.86
706 1433 2.093128 AGAACAGTTTTCCAGTCGGTGT 60.093 45.455 0.00 0.00 0.00 4.16
710 1437 2.878406 CAGTTTTCCAGTCGGTGTGAAT 59.122 45.455 0.00 0.00 0.00 2.57
715 1442 1.621317 TCCAGTCGGTGTGAATTAGCA 59.379 47.619 0.00 0.00 0.00 3.49
717 1444 2.002586 CAGTCGGTGTGAATTAGCAGG 58.997 52.381 0.00 0.00 0.00 4.85
718 1445 1.623811 AGTCGGTGTGAATTAGCAGGT 59.376 47.619 0.00 0.00 0.00 4.00
736 1463 0.882042 GTATGGGCTGCATCTGTCCG 60.882 60.000 0.50 0.00 29.45 4.79
739 1466 3.503363 GGCTGCATCTGTCCGTGC 61.503 66.667 0.50 0.00 41.61 5.34
742 1469 2.743060 TGCATCTGTCCGTGCAGT 59.257 55.556 0.00 0.00 45.60 4.40
743 1470 1.374631 TGCATCTGTCCGTGCAGTC 60.375 57.895 0.00 0.00 45.60 3.51
745 1472 1.630244 GCATCTGTCCGTGCAGTCAC 61.630 60.000 0.00 0.00 40.94 3.67
746 1473 0.037882 CATCTGTCCGTGCAGTCACT 60.038 55.000 0.00 0.00 40.99 3.41
748 1475 0.596577 TCTGTCCGTGCAGTCACTAC 59.403 55.000 0.00 0.00 40.99 2.73
749 1476 0.598562 CTGTCCGTGCAGTCACTACT 59.401 55.000 0.00 0.00 40.99 2.57
760 1487 1.683917 AGTCACTACTGATCCATCCGC 59.316 52.381 0.00 0.00 33.57 5.54
850 1604 2.291043 AAGCGGATCCACGTCCCTT 61.291 57.895 13.41 1.14 34.67 3.95
851 1605 2.511600 GCGGATCCACGTCCCTTG 60.512 66.667 13.41 0.00 34.67 3.61
993 1757 3.950254 CCGATCTCCGTCCGTCCG 61.950 72.222 0.00 0.00 36.31 4.79
1074 1841 2.766229 GCCCACTCCTCCTCCTCC 60.766 72.222 0.00 0.00 0.00 4.30
1137 1904 2.728435 CCCCGCCCAGTACCAGTAC 61.728 68.421 0.00 0.00 36.35 2.73
1140 1907 2.186125 GCCCAGTACCAGTACGGC 59.814 66.667 10.00 10.00 40.80 5.68
1298 2307 4.354162 GGCCGCCCCAGGTACAAA 62.354 66.667 0.00 0.00 0.00 2.83
1299 2308 3.060000 GCCGCCCCAGGTACAAAC 61.060 66.667 0.00 0.00 0.00 2.93
1300 2309 2.432563 CCGCCCCAGGTACAAACA 59.567 61.111 0.00 0.00 0.00 2.83
1301 2310 1.228306 CCGCCCCAGGTACAAACAA 60.228 57.895 0.00 0.00 0.00 2.83
1306 2315 2.821625 GCCCCAGGTACAAACAATTCCT 60.822 50.000 0.00 0.00 0.00 3.36
1308 2317 2.747446 CCCAGGTACAAACAATTCCTCG 59.253 50.000 0.00 0.00 0.00 4.63
1312 2321 4.634004 CAGGTACAAACAATTCCTCGCATA 59.366 41.667 0.00 0.00 0.00 3.14
1327 2346 3.717707 TCGCATACTCTTGCTTACCATC 58.282 45.455 0.00 0.00 40.54 3.51
1341 2360 3.903208 CCATCTTTGGTCGGGGATT 57.097 52.632 0.00 0.00 38.30 3.01
1369 2388 1.153353 TCGTGCAAATCGAGGTTTCC 58.847 50.000 0.00 0.00 33.38 3.13
1381 2400 2.725641 GTTTCCGTGGGGCACAAC 59.274 61.111 0.00 0.00 33.40 3.32
1396 2415 1.221466 ACAACGCCGTGTCAGTGATG 61.221 55.000 0.00 0.00 0.00 3.07
1397 2416 2.317609 AACGCCGTGTCAGTGATGC 61.318 57.895 0.00 0.00 0.00 3.91
1398 2417 3.490759 CGCCGTGTCAGTGATGCC 61.491 66.667 0.00 0.00 0.00 4.40
1399 2418 3.127533 GCCGTGTCAGTGATGCCC 61.128 66.667 0.00 0.00 0.00 5.36
1400 2419 2.815211 CCGTGTCAGTGATGCCCG 60.815 66.667 0.00 0.00 0.00 6.13
1401 2420 2.261361 CGTGTCAGTGATGCCCGA 59.739 61.111 0.00 0.00 0.00 5.14
1423 2445 1.945387 ATGATGCACATCTCACGGTC 58.055 50.000 11.66 0.00 38.60 4.79
1431 2453 2.276116 ATCTCACGGTCGCCTGTGT 61.276 57.895 5.18 0.00 37.38 3.72
1432 2454 2.492449 ATCTCACGGTCGCCTGTGTG 62.492 60.000 5.18 3.08 37.38 3.82
1435 2457 4.314440 ACGGTCGCCTGTGTGCAT 62.314 61.111 0.00 0.00 0.00 3.96
1491 2514 1.677576 GCGCATGATCCAAATTCCAGA 59.322 47.619 0.30 0.00 0.00 3.86
1496 2519 4.643784 GCATGATCCAAATTCCAGAACTCT 59.356 41.667 0.00 0.00 0.00 3.24
1498 2521 5.768980 TGATCCAAATTCCAGAACTCTCT 57.231 39.130 0.00 0.00 0.00 3.10
1503 2526 7.277174 TCCAAATTCCAGAACTCTCTTTTTC 57.723 36.000 0.00 0.00 0.00 2.29
1504 2527 7.062957 TCCAAATTCCAGAACTCTCTTTTTCT 58.937 34.615 0.00 0.00 32.02 2.52
1505 2528 7.229506 TCCAAATTCCAGAACTCTCTTTTTCTC 59.770 37.037 0.00 0.00 29.23 2.87
1506 2529 7.366513 CAAATTCCAGAACTCTCTTTTTCTCC 58.633 38.462 0.00 0.00 29.23 3.71
1508 2531 3.328050 TCCAGAACTCTCTTTTTCTCCCC 59.672 47.826 0.00 0.00 29.23 4.81
1509 2532 3.330267 CAGAACTCTCTTTTTCTCCCCG 58.670 50.000 0.00 0.00 29.23 5.73
1511 2534 1.353091 ACTCTCTTTTTCTCCCCGCT 58.647 50.000 0.00 0.00 0.00 5.52
1516 2543 3.326880 TCTCTTTTTCTCCCCGCTTAGTT 59.673 43.478 0.00 0.00 0.00 2.24
1542 2569 8.779303 TCAGCGAAAAATTCTAGTTGTAAATGA 58.221 29.630 0.00 0.00 0.00 2.57
1555 2582 7.158099 AGTTGTAAATGAACCCTATGCTTTC 57.842 36.000 0.00 0.00 0.00 2.62
1559 2586 1.737838 TGAACCCTATGCTTTCGCTG 58.262 50.000 0.00 0.00 36.97 5.18
1566 2600 3.181475 CCCTATGCTTTCGCTGAACTAGA 60.181 47.826 0.00 0.00 36.97 2.43
1567 2601 4.433615 CCTATGCTTTCGCTGAACTAGAA 58.566 43.478 0.00 0.00 36.97 2.10
1568 2602 4.870426 CCTATGCTTTCGCTGAACTAGAAA 59.130 41.667 0.00 0.00 36.97 2.52
1572 2606 5.689819 TGCTTTCGCTGAACTAGAAAAATC 58.310 37.500 0.00 0.00 34.07 2.17
1577 2611 4.566759 TCGCTGAACTAGAAAAATCCATCG 59.433 41.667 0.00 0.00 0.00 3.84
1597 2631 3.381590 TCGACTCACCACATGGATTCTAG 59.618 47.826 4.53 0.00 38.94 2.43
1605 2639 4.227300 ACCACATGGATTCTAGGCTAAACA 59.773 41.667 4.53 0.00 38.94 2.83
1638 2672 9.268268 TGTTGTTTAAACTGGAACACTAGATAG 57.732 33.333 18.72 0.00 35.66 2.08
1693 2732 5.590259 AGTCTTGATTAGTATTTGCGGCAAT 59.410 36.000 17.19 9.27 0.00 3.56
1694 2733 5.682862 GTCTTGATTAGTATTTGCGGCAATG 59.317 40.000 17.19 0.00 0.00 2.82
1727 2766 4.976731 CGGATCGTTACATCGAAGAGAATT 59.023 41.667 0.00 0.00 43.63 2.17
1728 2767 5.108217 CGGATCGTTACATCGAAGAGAATTG 60.108 44.000 0.00 0.00 43.63 2.32
1737 2776 2.038426 TCGAAGAGAATTGTTGGGAGCA 59.962 45.455 0.00 0.00 0.00 4.26
1739 2778 3.064545 CGAAGAGAATTGTTGGGAGCATC 59.935 47.826 0.00 0.00 0.00 3.91
1742 2781 5.441718 AGAGAATTGTTGGGAGCATCTAA 57.558 39.130 0.00 0.00 33.73 2.10
1749 2788 5.692115 TGTTGGGAGCATCTAAAGACATA 57.308 39.130 0.00 0.00 33.73 2.29
1750 2789 6.252599 TGTTGGGAGCATCTAAAGACATAT 57.747 37.500 0.00 0.00 33.73 1.78
1751 2790 7.373617 TGTTGGGAGCATCTAAAGACATATA 57.626 36.000 0.00 0.00 33.73 0.86
1752 2791 7.977818 TGTTGGGAGCATCTAAAGACATATAT 58.022 34.615 0.00 0.00 33.73 0.86
1753 2792 9.100197 TGTTGGGAGCATCTAAAGACATATATA 57.900 33.333 0.00 0.00 33.73 0.86
1754 2793 9.944376 GTTGGGAGCATCTAAAGACATATATAA 57.056 33.333 0.00 0.00 33.73 0.98
1822 2861 9.830975 AAATATAATGTTTGGAAGGTTATTGCC 57.169 29.630 0.00 0.00 0.00 4.52
1823 2862 6.865834 ATAATGTTTGGAAGGTTATTGCCA 57.134 33.333 0.00 0.00 0.00 4.92
1831 2870 6.073447 TGGAAGGTTATTGCCATTCTTCTA 57.927 37.500 0.00 0.00 33.33 2.10
1834 2873 7.001073 GGAAGGTTATTGCCATTCTTCTATCT 58.999 38.462 0.00 0.00 33.33 1.98
1857 2896 6.038382 TCTGTCACCTTATACTTCTAGAAGCG 59.962 42.308 28.64 10.90 41.99 4.68
1872 2911 9.202273 CTTCTAGAAGCGAGCAAGATAAATAAT 57.798 33.333 19.23 0.00 0.00 1.28
1876 2915 7.643579 AGAAGCGAGCAAGATAAATAATTTCC 58.356 34.615 0.00 0.00 0.00 3.13
1903 2942 5.063204 CCTATTTCGCATCAATTACTGGGA 58.937 41.667 3.05 3.05 33.14 4.37
2013 3053 6.418101 TCCTGGTTCCATCTTTCATAGAAAG 58.582 40.000 12.12 12.12 36.22 2.62
2023 3063 7.413438 CCATCTTTCATAGAAAGACGAAACCAG 60.413 40.741 20.65 7.01 38.88 4.00
2054 3094 4.452455 CGTCAGCTTTTAAGGTTCACAGAT 59.548 41.667 0.00 0.00 33.87 2.90
2078 3118 3.057033 AGCTAAGCTCACAAATGCAAAGG 60.057 43.478 0.00 0.00 30.62 3.11
2103 3143 1.375523 CTACCCCTCACCAACACGC 60.376 63.158 0.00 0.00 0.00 5.34
2163 3203 4.202461 ACAGCAAGAACAGAAATACTCCCA 60.202 41.667 0.00 0.00 0.00 4.37
2164 3204 4.946157 CAGCAAGAACAGAAATACTCCCAT 59.054 41.667 0.00 0.00 0.00 4.00
2165 3205 5.065731 CAGCAAGAACAGAAATACTCCCATC 59.934 44.000 0.00 0.00 0.00 3.51
2166 3206 5.045286 AGCAAGAACAGAAATACTCCCATCT 60.045 40.000 0.00 0.00 0.00 2.90
2167 3207 6.156949 AGCAAGAACAGAAATACTCCCATCTA 59.843 38.462 0.00 0.00 0.00 1.98
2168 3208 6.823689 GCAAGAACAGAAATACTCCCATCTAA 59.176 38.462 0.00 0.00 0.00 2.10
2169 3209 7.011857 GCAAGAACAGAAATACTCCCATCTAAG 59.988 40.741 0.00 0.00 0.00 2.18
2170 3210 7.130681 AGAACAGAAATACTCCCATCTAAGG 57.869 40.000 0.00 0.00 0.00 2.69
2210 3250 4.284746 CACTTCTTCAAAGAGGGGACTACT 59.715 45.833 6.80 0.00 44.43 2.57
2211 3251 4.908481 ACTTCTTCAAAGAGGGGACTACTT 59.092 41.667 6.80 0.00 44.43 2.24
2213 3253 5.485209 TCTTCAAAGAGGGGACTACTTTC 57.515 43.478 0.00 0.00 44.43 2.62
2251 3291 2.376518 ACACCCTGAACACATGGATTCT 59.623 45.455 11.24 0.00 0.00 2.40
2255 3295 4.474651 ACCCTGAACACATGGATTCTATCA 59.525 41.667 11.24 0.00 0.00 2.15
2259 3299 6.053632 TGAACACATGGATTCTATCACTGT 57.946 37.500 11.24 0.00 0.00 3.55
2366 3406 0.383590 TACTCTCTGCGCAGATCAGC 59.616 55.000 38.11 0.00 36.76 4.26
2452 3492 3.778265 CCCCCAAGAATTTCCTTGAGAA 58.222 45.455 8.15 0.00 44.66 2.87
2471 3511 2.271944 AGTTTTGCCCAGTCCACTAC 57.728 50.000 0.00 0.00 0.00 2.73
2495 3535 1.640670 ACCCACTATCAAATGCCCAGT 59.359 47.619 0.00 0.00 0.00 4.00
2723 3764 7.066163 TGCATTCAGAAAACAGGTGATATACTG 59.934 37.037 0.00 0.00 40.48 2.74
2725 3766 9.599866 CATTCAGAAAACAGGTGATATACTGTA 57.400 33.333 7.40 0.00 46.49 2.74
2771 3812 5.131142 AGTGAATATACTCCAGAGGTTTGGG 59.869 44.000 0.00 0.00 38.81 4.12
3093 4135 3.210227 CATTCCGTGGTATATTGGTGCA 58.790 45.455 0.00 0.00 0.00 4.57
3108 4150 3.216800 TGGTGCATTCATCCTAATCTGC 58.783 45.455 0.00 0.00 0.00 4.26
3188 4230 8.380099 TGTAAGTTACCTTTCTGATACAACCAT 58.620 33.333 10.51 0.00 31.89 3.55
3248 4295 5.437060 TGAGACTTAGTTTTATGGCCCATC 58.563 41.667 0.00 0.00 0.00 3.51
3262 4309 0.890683 CCCATCCAACCAGCTTTGTC 59.109 55.000 0.00 0.00 0.00 3.18
3272 4319 5.240623 CCAACCAGCTTTGTCACATTAACTA 59.759 40.000 0.00 0.00 0.00 2.24
3330 4390 9.058174 TGCTGCTTACACTTACAGTTAATTTTA 57.942 29.630 0.00 0.00 32.65 1.52
3365 4425 6.265422 GCTCCAGTTAAAATATTGGTATGCCT 59.735 38.462 0.16 0.00 35.27 4.75
3478 4544 5.416271 ACGACCTATAACCTGTCACAATT 57.584 39.130 0.00 0.00 0.00 2.32
3483 4549 8.335356 CGACCTATAACCTGTCACAATTAATTG 58.665 37.037 23.60 23.60 43.26 2.32
3515 4581 3.942130 ACTTGGGCTAACTTTGCATTC 57.058 42.857 0.00 0.00 0.00 2.67
3521 4587 4.021544 TGGGCTAACTTTGCATTCGAATTT 60.022 37.500 8.21 1.74 0.00 1.82
3593 4659 4.448060 GGAGTAACAAAAGGAACAGACTCG 59.552 45.833 0.00 0.00 34.27 4.18
3886 5019 9.121517 GTTGAAATTTGATGTATCACTCAACAG 57.878 33.333 20.04 0.00 39.33 3.16
3911 5044 2.127651 ACCCCTCCTTGGAGTAACAA 57.872 50.000 14.77 0.00 38.35 2.83
3914 5047 3.181433 ACCCCTCCTTGGAGTAACAAAAG 60.181 47.826 14.77 0.00 38.35 2.27
3966 5099 1.885887 TCTTGGCAGTGGTTATGTTGC 59.114 47.619 0.00 0.00 35.87 4.17
3985 5118 5.182950 TGTTGCTGAATATAAGTGGTGGTTG 59.817 40.000 0.00 0.00 0.00 3.77
4003 5136 1.522668 TGTTTCAGTTCCTGCATCGG 58.477 50.000 0.00 0.00 0.00 4.18
4008 5141 3.499737 GTTCCTGCATCGGCCGTG 61.500 66.667 27.15 22.51 40.13 4.94
4037 5170 7.445945 GTCCTCTTGTGCCTATATTTGATACT 58.554 38.462 0.00 0.00 0.00 2.12
4046 5179 9.003658 GTGCCTATATTTGATACTTACTGCATT 57.996 33.333 0.00 0.00 0.00 3.56
4063 5196 0.178984 ATTGATGATGCGATGCCCCA 60.179 50.000 0.00 0.00 0.00 4.96
4065 5198 0.691904 TGATGATGCGATGCCCCATA 59.308 50.000 0.00 0.00 0.00 2.74
4207 5344 9.799106 CCCCAAAGTAGATTCATATTGTATCTT 57.201 33.333 2.60 0.00 36.23 2.40
4264 5401 6.460781 ACTATGCGATATTTACCATCCGAAA 58.539 36.000 0.00 0.00 0.00 3.46
4276 5413 5.277857 ACCATCCGAAACAGAACCTATAG 57.722 43.478 0.00 0.00 0.00 1.31
4316 5453 6.017440 TGTTAGTTTATGTTCCAGCTTGACAC 60.017 38.462 0.00 0.00 0.00 3.67
4326 5463 3.128589 TCCAGCTTGACACTTTGTTTGTC 59.871 43.478 0.00 0.00 43.22 3.18
4357 5494 7.469456 GCAGTGATGTTGTTAGTTTAAAGGGAA 60.469 37.037 0.00 0.00 0.00 3.97
4360 5497 7.860872 GTGATGTTGTTAGTTTAAAGGGAACAG 59.139 37.037 8.62 0.00 32.05 3.16
4361 5498 7.776030 TGATGTTGTTAGTTTAAAGGGAACAGA 59.224 33.333 8.62 3.21 32.05 3.41
4364 5501 7.281549 TGTTGTTAGTTTAAAGGGAACAGACTC 59.718 37.037 8.62 4.50 32.05 3.36
4424 5561 3.228188 TGTTTGGCATGAAGAACCTCT 57.772 42.857 0.00 0.00 0.00 3.69
4493 5630 2.322355 AGAGACGAATGAGGGCATTG 57.678 50.000 0.00 0.00 44.47 2.82
4540 5690 5.838529 AGTTTTATGTTTTAAGTTGCCGCT 58.161 33.333 0.00 0.00 0.00 5.52
4544 5694 0.040781 GTTTTAAGTTGCCGCTGCGA 60.041 50.000 25.45 0.32 41.78 5.10
4554 5704 2.705826 CGCTGCGATTTCTCTGCC 59.294 61.111 18.66 0.00 0.00 4.85
4555 5705 2.817423 CGCTGCGATTTCTCTGCCC 61.817 63.158 18.66 0.00 0.00 5.36
4575 5725 2.158755 CCCCCATCTCTATGTTGTGGTC 60.159 54.545 0.00 0.00 0.00 4.02
4590 5740 7.899178 TGTTGTGGTCATGTTTATAGTAGTG 57.101 36.000 0.00 0.00 0.00 2.74
4598 5748 7.148639 GGTCATGTTTATAGTAGTGTGTGTGTG 60.149 40.741 0.00 0.00 0.00 3.82
4599 5749 7.384115 GTCATGTTTATAGTAGTGTGTGTGTGT 59.616 37.037 0.00 0.00 0.00 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 1.202222 CGTTGGCCTCATTGATGAAGC 60.202 52.381 3.32 6.11 42.15 3.86
44 45 2.261671 CCGGTCCAGAGACGTTGG 59.738 66.667 0.00 0.00 44.54 3.77
47 48 3.681835 GCACCGGTCCAGAGACGT 61.682 66.667 2.59 0.00 44.54 4.34
104 105 4.977739 TCCTCAAATCTTATGGGGTCAGAT 59.022 41.667 0.00 0.00 39.58 2.90
111 112 6.514048 GCGAATTTCTCCTCAAATCTTATGGG 60.514 42.308 0.00 0.00 0.00 4.00
112 113 6.433766 GCGAATTTCTCCTCAAATCTTATGG 58.566 40.000 0.00 0.00 0.00 2.74
153 154 9.513906 CCACCACATGTTCAATGGTTATATATA 57.486 33.333 0.00 0.00 44.51 0.86
154 155 7.451255 CCCACCACATGTTCAATGGTTATATAT 59.549 37.037 0.00 0.00 44.51 0.86
155 156 6.775142 CCCACCACATGTTCAATGGTTATATA 59.225 38.462 0.00 0.00 44.51 0.86
156 157 5.598005 CCCACCACATGTTCAATGGTTATAT 59.402 40.000 0.00 0.00 44.51 0.86
208 209 2.744202 AGGTTGATTTAGCAGCAGAACG 59.256 45.455 0.00 0.00 0.00 3.95
230 231 6.101997 CCTTCTGTTATTTTGATCTTTGCCC 58.898 40.000 0.00 0.00 0.00 5.36
232 233 7.867403 TCAACCTTCTGTTATTTTGATCTTTGC 59.133 33.333 0.00 0.00 34.69 3.68
233 234 9.403110 CTCAACCTTCTGTTATTTTGATCTTTG 57.597 33.333 0.00 0.00 34.69 2.77
234 235 9.136323 ACTCAACCTTCTGTTATTTTGATCTTT 57.864 29.630 0.00 0.00 34.69 2.52
272 273 2.566833 TTTCAGGTGGGTGTCTCATG 57.433 50.000 0.00 0.00 0.00 3.07
321 323 7.173907 CCTCCTAATACTTGTGCCATCTATTTG 59.826 40.741 0.00 0.00 0.00 2.32
348 350 2.304180 CTCACACCACCTCCAATCTCTT 59.696 50.000 0.00 0.00 0.00 2.85
361 363 2.113807 CTCATCTCCATCCTCACACCA 58.886 52.381 0.00 0.00 0.00 4.17
364 366 1.798626 CCCTCATCTCCATCCTCACA 58.201 55.000 0.00 0.00 0.00 3.58
385 387 0.948678 CGATCTCTTCCTCCCTCGAC 59.051 60.000 0.00 0.00 0.00 4.20
406 408 5.261216 GACACCATTTTCCCTCCTTTCATA 58.739 41.667 0.00 0.00 0.00 2.15
419 421 7.499232 CCTTCCTAGAATAATCGACACCATTTT 59.501 37.037 0.00 0.00 0.00 1.82
421 423 6.464465 CCCTTCCTAGAATAATCGACACCATT 60.464 42.308 0.00 0.00 0.00 3.16
448 450 1.202927 AGGGTGTGATGGGAACTTGTG 60.203 52.381 0.00 0.00 0.00 3.33
496 498 8.338259 GGCTATGTGAGTAATACAAGTCATTTG 58.662 37.037 0.00 0.00 42.68 2.32
510 512 3.833729 TAGCCCGGCTATGTGAGTA 57.166 52.632 15.59 0.00 40.44 2.59
521 523 3.258372 TGCTAATTCTGAGTATAGCCCGG 59.742 47.826 0.00 0.00 39.96 5.73
524 526 7.495934 TCAAACTTGCTAATTCTGAGTATAGCC 59.504 37.037 12.72 1.37 39.96 3.93
525 527 8.331742 GTCAAACTTGCTAATTCTGAGTATAGC 58.668 37.037 9.93 9.93 40.84 2.97
529 531 8.621532 ATTGTCAAACTTGCTAATTCTGAGTA 57.378 30.769 0.00 0.00 0.00 2.59
540 542 4.460382 CCTGATGGTATTGTCAAACTTGCT 59.540 41.667 0.00 0.00 0.00 3.91
541 543 4.458989 TCCTGATGGTATTGTCAAACTTGC 59.541 41.667 0.00 0.00 34.23 4.01
561 563 1.003696 GTTTGGCTTGGCTCTAGTCCT 59.996 52.381 5.62 0.00 0.00 3.85
566 568 4.713946 CCGTTTGGCTTGGCTCTA 57.286 55.556 0.00 0.00 0.00 2.43
681 1311 4.100498 ACCGACTGGAAAACTGTTCTTCTA 59.900 41.667 0.00 0.00 39.21 2.10
686 1316 2.031683 CACACCGACTGGAAAACTGTTC 59.968 50.000 0.00 0.00 39.21 3.18
697 1327 2.002586 CCTGCTAATTCACACCGACTG 58.997 52.381 0.00 0.00 0.00 3.51
700 1330 3.431626 CCATACCTGCTAATTCACACCGA 60.432 47.826 0.00 0.00 0.00 4.69
701 1331 2.872245 CCATACCTGCTAATTCACACCG 59.128 50.000 0.00 0.00 0.00 4.94
706 1433 3.213206 CAGCCCATACCTGCTAATTCA 57.787 47.619 0.00 0.00 35.69 2.57
715 1442 0.471617 GACAGATGCAGCCCATACCT 59.528 55.000 0.00 0.00 33.29 3.08
717 1444 0.882042 CGGACAGATGCAGCCCATAC 60.882 60.000 0.00 0.00 33.29 2.39
718 1445 1.337384 ACGGACAGATGCAGCCCATA 61.337 55.000 0.00 0.00 33.29 2.74
742 1469 1.040646 GGCGGATGGATCAGTAGTGA 58.959 55.000 1.95 1.95 37.02 3.41
743 1470 0.034059 GGGCGGATGGATCAGTAGTG 59.966 60.000 0.00 0.00 0.00 2.74
745 1472 0.319728 CTGGGCGGATGGATCAGTAG 59.680 60.000 0.00 0.00 0.00 2.57
746 1473 1.121407 CCTGGGCGGATGGATCAGTA 61.121 60.000 0.00 0.00 33.16 2.74
748 1475 2.429058 CCTGGGCGGATGGATCAG 59.571 66.667 0.00 0.00 33.16 2.90
749 1476 3.877450 GCCTGGGCGGATGGATCA 61.877 66.667 0.00 0.00 33.16 2.92
750 1477 4.650377 GGCCTGGGCGGATGGATC 62.650 72.222 3.84 0.00 43.06 3.36
759 1486 3.670377 GTTGTTGACGGCCTGGGC 61.670 66.667 10.75 10.75 41.06 5.36
783 1533 2.900337 GCGGGCCGGTAGAATTGG 60.900 66.667 29.48 0.00 0.00 3.16
803 1553 1.148273 TGGACTGACTGGTGGTTGC 59.852 57.895 0.00 0.00 0.00 4.17
993 1757 4.530857 CCGGCTCCCATGGTCGAC 62.531 72.222 11.73 7.13 0.00 4.20
1052 1816 2.367512 AGGAGGAGTGGGCCATCC 60.368 66.667 20.82 20.82 35.71 3.51
1298 2307 2.939103 GCAAGAGTATGCGAGGAATTGT 59.061 45.455 0.00 0.00 36.45 2.71
1299 2308 3.599046 GCAAGAGTATGCGAGGAATTG 57.401 47.619 0.00 0.00 36.45 2.32
1308 2317 5.220931 CCAAAGATGGTAAGCAAGAGTATGC 60.221 44.000 0.00 0.00 43.15 3.14
1327 2346 0.462047 CCTCGAATCCCCGACCAAAG 60.462 60.000 0.00 0.00 34.56 2.77
1381 2400 3.490759 GGCATCACTGACACGGCG 61.491 66.667 4.80 4.80 0.00 6.46
1388 2407 1.122227 TCATCATCGGGCATCACTGA 58.878 50.000 0.00 0.00 0.00 3.41
1396 2415 2.637521 ATGTGCATCATCATCGGGC 58.362 52.632 0.00 0.00 29.76 6.13
1423 2445 0.741927 TCTGATCATGCACACAGGCG 60.742 55.000 0.00 0.00 36.28 5.52
1431 2453 5.742063 AGACTTCTGAATTCTGATCATGCA 58.258 37.500 14.89 0.00 0.00 3.96
1432 2454 6.509837 CGAAGACTTCTGAATTCTGATCATGC 60.510 42.308 14.89 4.98 0.00 4.06
1435 2457 6.272822 TCGAAGACTTCTGAATTCTGATCA 57.727 37.500 14.89 0.00 0.00 2.92
1491 2514 1.700186 AGCGGGGAGAAAAAGAGAGTT 59.300 47.619 0.00 0.00 0.00 3.01
1496 2519 3.071892 TGAACTAAGCGGGGAGAAAAAGA 59.928 43.478 0.00 0.00 0.00 2.52
1498 2521 3.408634 CTGAACTAAGCGGGGAGAAAAA 58.591 45.455 0.00 0.00 0.00 1.94
1503 2526 4.522971 GCTGAACTAAGCGGGGAG 57.477 61.111 0.00 0.00 32.56 4.30
1509 2532 6.832804 ACTAGAATTTTTCGCTGAACTAAGC 58.167 36.000 0.00 0.00 39.94 3.09
1511 2534 8.149973 ACAACTAGAATTTTTCGCTGAACTAA 57.850 30.769 0.00 0.00 34.02 2.24
1516 2543 8.779303 TCATTTACAACTAGAATTTTTCGCTGA 58.221 29.630 0.00 0.00 34.02 4.26
1555 2582 4.566759 TCGATGGATTTTTCTAGTTCAGCG 59.433 41.667 0.00 0.00 34.52 5.18
1559 2586 6.036191 GGTGAGTCGATGGATTTTTCTAGTTC 59.964 42.308 0.00 0.00 0.00 3.01
1566 2600 3.750371 TGTGGTGAGTCGATGGATTTTT 58.250 40.909 0.00 0.00 0.00 1.94
1567 2601 3.417069 TGTGGTGAGTCGATGGATTTT 57.583 42.857 0.00 0.00 0.00 1.82
1568 2602 3.273434 CATGTGGTGAGTCGATGGATTT 58.727 45.455 0.00 0.00 0.00 2.17
1572 2606 0.536724 TCCATGTGGTGAGTCGATGG 59.463 55.000 0.00 0.00 35.79 3.51
1577 2611 3.742640 GCCTAGAATCCATGTGGTGAGTC 60.743 52.174 0.00 0.00 36.34 3.36
1605 2639 5.043737 TCCAGTTTAAACAACAGTAGCCT 57.956 39.130 20.06 0.00 0.00 4.58
1638 2672 6.403309 GCCTAAAGGAGCAAACACTACATAAC 60.403 42.308 0.00 0.00 37.39 1.89
1646 2680 3.818773 TGTTAGCCTAAAGGAGCAAACAC 59.181 43.478 0.00 0.00 37.39 3.32
1650 2684 4.041691 AGACTTGTTAGCCTAAAGGAGCAA 59.958 41.667 0.00 0.00 37.39 3.91
1693 2732 3.264159 CGATCCGCTGCGCAATCA 61.264 61.111 24.97 0.00 0.00 2.57
1694 2733 1.487452 TAACGATCCGCTGCGCAATC 61.487 55.000 18.00 18.87 0.00 2.67
1701 2740 1.781429 CTTCGATGTAACGATCCGCTG 59.219 52.381 0.00 0.00 41.82 5.18
1709 2748 5.445939 CCCAACAATTCTCTTCGATGTAACG 60.446 44.000 0.00 0.00 0.00 3.18
1727 2766 4.574674 ATGTCTTTAGATGCTCCCAACA 57.425 40.909 0.00 0.00 0.00 3.33
1728 2767 9.944376 TTATATATGTCTTTAGATGCTCCCAAC 57.056 33.333 0.00 0.00 0.00 3.77
1831 2870 7.255312 CGCTTCTAGAAGTATAAGGTGACAGAT 60.255 40.741 28.72 0.00 40.45 2.90
1834 2873 5.884232 TCGCTTCTAGAAGTATAAGGTGACA 59.116 40.000 28.72 2.27 40.45 3.58
1855 2894 5.985781 TCGGAAATTATTTATCTTGCTCGC 58.014 37.500 0.00 0.00 0.00 5.03
1857 2896 8.329203 AGGATCGGAAATTATTTATCTTGCTC 57.671 34.615 0.00 0.00 0.00 4.26
1872 2911 4.066646 TGATGCGAAATAGGATCGGAAA 57.933 40.909 0.00 0.00 43.73 3.13
1876 2915 6.401474 CCAGTAATTGATGCGAAATAGGATCG 60.401 42.308 0.00 0.00 41.12 3.69
1908 2947 3.838317 TGTGTGAGTCTAGGCACCTATTT 59.162 43.478 0.00 0.00 34.19 1.40
2013 3053 0.370273 CGCTGTATGCTGGTTTCGTC 59.630 55.000 0.00 0.00 40.11 4.20
2037 3077 7.625185 GCTTAGCTCATCTGTGAACCTTAAAAG 60.625 40.741 0.00 0.00 33.05 2.27
2078 3118 2.368011 GGTGAGGGGTAGGAGGTGC 61.368 68.421 0.00 0.00 0.00 5.01
2081 3121 0.546747 TGTTGGTGAGGGGTAGGAGG 60.547 60.000 0.00 0.00 0.00 4.30
2103 3143 0.603065 GCTGTAGGTTTGCCCTTTGG 59.397 55.000 0.00 0.00 42.73 3.28
2119 3159 4.764823 TGTAAGGTCCTTTGGTAATTGCTG 59.235 41.667 10.04 0.00 0.00 4.41
2163 3203 5.113446 TCTGGTCTCGTTACTCCTTAGAT 57.887 43.478 0.00 0.00 0.00 1.98
2164 3204 4.564782 TCTGGTCTCGTTACTCCTTAGA 57.435 45.455 0.00 0.00 0.00 2.10
2165 3205 4.882427 TGATCTGGTCTCGTTACTCCTTAG 59.118 45.833 0.00 0.00 0.00 2.18
2166 3206 4.639310 GTGATCTGGTCTCGTTACTCCTTA 59.361 45.833 0.00 0.00 0.00 2.69
2167 3207 3.444388 GTGATCTGGTCTCGTTACTCCTT 59.556 47.826 0.00 0.00 0.00 3.36
2168 3208 3.018149 GTGATCTGGTCTCGTTACTCCT 58.982 50.000 0.00 0.00 0.00 3.69
2169 3209 3.018149 AGTGATCTGGTCTCGTTACTCC 58.982 50.000 0.00 0.00 0.00 3.85
2170 3210 4.396790 AGAAGTGATCTGGTCTCGTTACTC 59.603 45.833 0.00 0.00 36.88 2.59
2175 3215 3.157881 TGAAGAAGTGATCTGGTCTCGT 58.842 45.455 0.00 0.00 38.79 4.18
2251 3291 4.346709 TGAAGAACCTTGGACACAGTGATA 59.653 41.667 7.81 0.00 0.00 2.15
2255 3295 3.136443 TGATGAAGAACCTTGGACACAGT 59.864 43.478 0.00 0.00 0.00 3.55
2259 3299 2.711009 ACCTGATGAAGAACCTTGGACA 59.289 45.455 0.00 0.00 0.00 4.02
2442 3482 2.958355 CTGGGCAAAACTTCTCAAGGAA 59.042 45.455 0.00 0.00 0.00 3.36
2452 3492 1.493022 TGTAGTGGACTGGGCAAAACT 59.507 47.619 0.00 0.00 0.00 2.66
2471 3511 4.214310 TGGGCATTTGATAGTGGGTTATG 58.786 43.478 0.00 0.00 0.00 1.90
2557 3598 3.541996 TTCTTCTGCAGTTCTGTGTGA 57.458 42.857 14.67 0.00 0.00 3.58
2746 3787 6.284459 CCAAACCTCTGGAGTATATTCACTC 58.716 44.000 0.00 0.00 43.55 3.51
2755 3796 2.829023 CCTACCCAAACCTCTGGAGTA 58.171 52.381 0.00 0.00 38.96 2.59
2771 3812 5.375283 AGGATTTAGGAAAAGAGGCCTAC 57.625 43.478 4.42 0.00 36.53 3.18
3093 4135 2.289072 CCGGACGCAGATTAGGATGAAT 60.289 50.000 0.00 0.00 0.00 2.57
3248 4295 4.037923 AGTTAATGTGACAAAGCTGGTTGG 59.962 41.667 3.31 0.00 32.50 3.77
3293 4343 4.466370 AGTGTAAGCAGCACCTGAGTATAA 59.534 41.667 0.00 0.00 37.56 0.98
3330 4390 3.788227 TTAACTGGAGCCATCACAAGT 57.212 42.857 0.00 0.00 0.00 3.16
3365 4425 6.629128 TGTTGAAAGAGCTTTTGTCAATTCA 58.371 32.000 13.59 8.32 32.11 2.57
3410 4476 6.813152 ACCATGTTACTTGCAATTGCTAAATC 59.187 34.615 29.37 15.89 42.66 2.17
3515 4581 4.769657 TGCGATGCAGCAAATTCG 57.230 50.000 11.76 11.76 45.06 3.34
3521 4587 1.283487 CTGTTTGTGCGATGCAGCA 59.717 52.632 1.53 0.00 45.96 4.41
3886 5019 2.491675 CTCCAAGGAGGGGTAACAAC 57.508 55.000 8.28 0.00 38.51 3.32
3911 5044 0.396811 CCACGAGTCTGTTCCCCTTT 59.603 55.000 0.00 0.00 0.00 3.11
3914 5047 1.004918 CACCACGAGTCTGTTCCCC 60.005 63.158 0.00 0.00 0.00 4.81
3966 5099 7.174946 ACTGAAACAACCACCACTTATATTCAG 59.825 37.037 0.00 0.00 43.33 3.02
4008 5141 1.972660 ATAGGCACAAGAGGACGGCC 61.973 60.000 0.00 0.00 44.92 6.13
4011 5144 4.693283 TCAAATATAGGCACAAGAGGACG 58.307 43.478 0.00 0.00 0.00 4.79
4046 5179 0.691904 TATGGGGCATCGCATCATCA 59.308 50.000 0.00 0.00 44.04 3.07
4059 5192 5.242795 AGAAACCCGAAATATCTATGGGG 57.757 43.478 0.07 4.94 44.47 4.96
4065 5198 9.901172 ATTACAAAGTAGAAACCCGAAATATCT 57.099 29.630 0.00 0.00 0.00 1.98
4207 5344 9.842775 ATGATAATGAGAAATGAGACTTGCTTA 57.157 29.630 0.00 0.00 0.00 3.09
4239 5376 6.762702 TCGGATGGTAAATATCGCATAGTA 57.237 37.500 0.00 0.00 0.00 1.82
4240 5377 5.654603 TCGGATGGTAAATATCGCATAGT 57.345 39.130 0.00 0.00 0.00 2.12
4241 5378 6.367695 TGTTTCGGATGGTAAATATCGCATAG 59.632 38.462 0.00 0.00 0.00 2.23
4244 5381 4.443621 TGTTTCGGATGGTAAATATCGCA 58.556 39.130 0.00 0.00 0.00 5.10
4247 5384 6.766467 AGGTTCTGTTTCGGATGGTAAATATC 59.234 38.462 0.00 0.00 0.00 1.63
4256 5393 4.508124 GCACTATAGGTTCTGTTTCGGATG 59.492 45.833 4.43 0.00 0.00 3.51
4257 5394 4.443034 GGCACTATAGGTTCTGTTTCGGAT 60.443 45.833 4.43 0.00 0.00 4.18
4264 5401 2.546899 TGTGGGCACTATAGGTTCTGT 58.453 47.619 4.43 0.00 0.00 3.41
4276 5413 4.519540 ACTAACAAATTGATGTGGGCAC 57.480 40.909 0.00 0.00 32.81 5.01
4316 5453 4.014847 TCACTGCTTTCGACAAACAAAG 57.985 40.909 0.00 0.00 33.45 2.77
4326 5463 4.732285 ACTAACAACATCACTGCTTTCG 57.268 40.909 0.00 0.00 0.00 3.46
4357 5494 1.196766 TCATGGGCAGCAGAGTCTGT 61.197 55.000 21.06 5.77 36.49 3.41
4360 5497 1.674962 GATTTCATGGGCAGCAGAGTC 59.325 52.381 0.00 0.00 0.00 3.36
4361 5498 1.284198 AGATTTCATGGGCAGCAGAGT 59.716 47.619 0.00 0.00 0.00 3.24
4364 5501 1.471119 ACAGATTTCATGGGCAGCAG 58.529 50.000 0.00 0.00 0.00 4.24
4436 5573 9.755064 CTACTTTTTATTGTTACTCGAATGGTG 57.245 33.333 0.00 0.00 0.00 4.17
4540 5690 2.272146 GGGGGCAGAGAAATCGCA 59.728 61.111 0.00 0.00 0.00 5.10
4554 5704 2.645838 CCACAACATAGAGATGGGGG 57.354 55.000 0.00 0.00 39.78 5.40
4575 5725 7.652300 ACACACACACACTACTATAAACATG 57.348 36.000 0.00 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.