Multiple sequence alignment - TraesCS5D01G189400

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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 TraesCS5D01G189400 chr5D 100.000 5127 0 0 1 5127 291874667 291879793 0.000000e+00 9468.0
1 TraesCS5D01G189400 chr5D 83.784 74 11 1 694 767 421088562 421088634 9.210000e-08 69.4
2 TraesCS5D01G189400 chr5A 97.798 1953 29 6 1425 3363 384187488 384189440 0.000000e+00 3356.0
3 TraesCS5D01G189400 chr5A 95.166 1593 58 9 3544 5127 384189749 384191331 0.000000e+00 2497.0
4 TraesCS5D01G189400 chr5A 87.029 1434 114 39 1 1427 384185876 384187244 0.000000e+00 1552.0
5 TraesCS5D01G189400 chr5A 80.702 114 15 3 416 522 526894686 526894799 1.180000e-11 82.4
6 TraesCS5D01G189400 chr5A 83.784 74 11 1 694 767 693387273 693387201 9.210000e-08 69.4
7 TraesCS5D01G189400 chr5A 100.000 36 0 0 3396 3431 384189449 384189484 3.310000e-07 67.6
8 TraesCS5D01G189400 chr5B 92.699 1397 57 21 1457 2811 332427413 332428806 0.000000e+00 1973.0
9 TraesCS5D01G189400 chr5B 88.502 1635 113 37 3517 5127 332429290 332430873 0.000000e+00 1908.0
10 TraesCS5D01G189400 chr5B 90.734 518 36 8 913 1428 332426611 332427118 0.000000e+00 680.0
11 TraesCS5D01G189400 chr5B 81.923 520 42 15 2842 3337 332428803 332429294 4.810000e-105 392.0
12 TraesCS5D01G189400 chr3B 87.349 166 20 1 2216 2381 57283624 57283460 6.780000e-44 189.0
13 TraesCS5D01G189400 chr3B 87.349 166 20 1 2216 2381 57350137 57349973 6.780000e-44 189.0
14 TraesCS5D01G189400 chr3B 79.070 129 20 4 407 529 240514615 240514488 1.180000e-11 82.4
15 TraesCS5D01G189400 chr6A 85.294 170 24 1 2216 2385 259899681 259899513 1.900000e-39 174.0
16 TraesCS5D01G189400 chr6A 84.118 170 26 1 2216 2385 261284600 261284432 4.110000e-36 163.0
17 TraesCS5D01G189400 chr6A 85.135 74 10 1 694 767 605784923 605784851 1.980000e-09 75.0
18 TraesCS5D01G189400 chr7A 83.051 177 21 5 2216 2385 577672081 577671907 8.890000e-33 152.0
19 TraesCS5D01G189400 chr7A 82.486 177 23 4 2216 2385 577496232 577496407 1.150000e-31 148.0
20 TraesCS5D01G189400 chr7A 77.249 189 29 11 567 744 674312934 674313119 1.170000e-16 99.0
21 TraesCS5D01G189400 chr3D 80.702 171 23 7 411 574 403240337 403240504 1.940000e-24 124.0
22 TraesCS5D01G189400 chr2D 81.034 174 18 12 469 629 136034332 136034503 1.940000e-24 124.0
23 TraesCS5D01G189400 chr2D 88.333 60 7 0 710 769 577141847 577141906 7.120000e-09 73.1
24 TraesCS5D01G189400 chr4A 73.643 387 62 27 407 763 556232363 556232739 4.200000e-21 113.0
25 TraesCS5D01G189400 chr4A 86.207 58 8 0 710 767 612003224 612003281 4.290000e-06 63.9
26 TraesCS5D01G189400 chr1A 78.453 181 29 9 455 629 405818238 405818414 5.430000e-20 110.0
27 TraesCS5D01G189400 chr1A 78.571 126 21 6 710 832 580965088 580964966 1.530000e-10 78.7
28 TraesCS5D01G189400 chr2B 77.976 168 16 18 415 575 381853783 381853936 9.150000e-13 86.1
29 TraesCS5D01G189400 chr2A 87.097 62 8 0 706 767 546341036 546340975 2.560000e-08 71.3
30 TraesCS5D01G189400 chr1B 90.566 53 5 0 471 523 653819616 653819564 2.560000e-08 71.3


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 TraesCS5D01G189400 chr5D 291874667 291879793 5126 False 9468.00 9468 100.00000 1 5127 1 chr5D.!!$F1 5126
1 TraesCS5D01G189400 chr5A 384185876 384191331 5455 False 1868.15 3356 94.99825 1 5127 4 chr5A.!!$F2 5126
2 TraesCS5D01G189400 chr5B 332426611 332430873 4262 False 1238.25 1973 88.46450 913 5127 4 chr5B.!!$F1 4214

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
879 900 0.321653 AAGGTGGGAGTGATCGTTGC 60.322 55.000 0.00 0.0 0.0 4.17 F
1078 1101 0.179134 GCCACTAGACGACGATGCTT 60.179 55.000 0.00 0.0 0.0 3.91 F
2405 2747 2.041701 AGGCTTGCCTTGAATTGTTGT 58.958 42.857 8.56 0.0 0.0 3.32 F
3362 3731 0.167689 GCGCCTTCTCAGCTTTCTTG 59.832 55.000 0.00 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2000 2322 1.904287 TGCGGCAACCAGAAAAGTAT 58.096 45.000 0.00 0.0 0.00 2.12 R
2579 2928 2.704572 GTGATGTCTCTGGGGAAACAG 58.295 52.381 0.00 0.0 39.84 3.16 R
3452 3821 0.764890 GGGGGATGCATGCTGTACTA 59.235 55.000 20.33 0.0 0.00 1.82 R
4796 5337 1.727062 AAACATGTGCCATTCCCCAA 58.273 45.000 0.00 0.0 0.00 4.12 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
18 19 2.974148 CGTCAAGCTGCTGCCACA 60.974 61.111 12.44 0.00 40.80 4.17
24 25 1.111116 AAGCTGCTGCCACATGTTGT 61.111 50.000 12.44 0.00 40.80 3.32
38 39 0.814457 TGTTGTGTGTTGGGTGCTTC 59.186 50.000 0.00 0.00 0.00 3.86
44 45 0.954452 GTGTTGGGTGCTTCCTCAAG 59.046 55.000 0.00 0.00 36.25 3.02
46 47 1.425066 TGTTGGGTGCTTCCTCAAGAT 59.575 47.619 0.00 0.00 36.25 2.40
47 48 2.158475 TGTTGGGTGCTTCCTCAAGATT 60.158 45.455 0.00 0.00 36.25 2.40
48 49 2.893489 GTTGGGTGCTTCCTCAAGATTT 59.107 45.455 0.00 0.00 36.25 2.17
49 50 3.243359 TGGGTGCTTCCTCAAGATTTT 57.757 42.857 0.00 0.00 36.25 1.82
77 78 8.859517 TTTTTAGGTGTTTTCGGTTTTAGATG 57.140 30.769 0.00 0.00 0.00 2.90
81 82 6.869695 AGGTGTTTTCGGTTTTAGATGTTTT 58.130 32.000 0.00 0.00 0.00 2.43
82 83 7.998580 AGGTGTTTTCGGTTTTAGATGTTTTA 58.001 30.769 0.00 0.00 0.00 1.52
83 84 7.916977 AGGTGTTTTCGGTTTTAGATGTTTTAC 59.083 33.333 0.00 0.00 0.00 2.01
90 94 7.354257 TCGGTTTTAGATGTTTTACTTTTCGG 58.646 34.615 0.00 0.00 0.00 4.30
114 118 2.158579 TCCGCCTGGTTTTTCTTAGGTT 60.159 45.455 0.00 0.00 36.30 3.50
121 125 5.596772 CCTGGTTTTTCTTAGGTTTTGGAGA 59.403 40.000 0.00 0.00 0.00 3.71
122 126 6.097696 CCTGGTTTTTCTTAGGTTTTGGAGAA 59.902 38.462 0.00 0.00 0.00 2.87
199 203 2.005451 CGATTGTGCCTCTCTCAAAGG 58.995 52.381 0.00 0.00 36.95 3.11
200 204 2.363683 GATTGTGCCTCTCTCAAAGGG 58.636 52.381 0.00 0.00 34.26 3.95
201 205 1.434188 TTGTGCCTCTCTCAAAGGGA 58.566 50.000 0.00 0.00 34.26 4.20
202 206 1.434188 TGTGCCTCTCTCAAAGGGAA 58.566 50.000 0.00 0.00 35.86 3.97
203 207 1.774254 TGTGCCTCTCTCAAAGGGAAA 59.226 47.619 0.00 0.00 35.86 3.13
204 208 2.174639 TGTGCCTCTCTCAAAGGGAAAA 59.825 45.455 0.00 0.00 35.86 2.29
205 209 3.222603 GTGCCTCTCTCAAAGGGAAAAA 58.777 45.455 0.00 0.00 35.86 1.94
234 238 2.386661 TTTCTTCCACGAGAGGCATC 57.613 50.000 0.00 0.00 0.00 3.91
247 251 2.064762 GAGGCATCGATTTGATCCTCG 58.935 52.381 0.00 3.74 39.46 4.63
291 295 2.634940 TGAGAAGCAAAGTAGTGCCTCT 59.365 45.455 0.00 0.00 45.81 3.69
294 298 1.257743 AGCAAAGTAGTGCCTCTCGA 58.742 50.000 0.00 0.00 46.14 4.04
303 307 4.991687 AGTAGTGCCTCTCGAAAAGAAAAG 59.008 41.667 0.00 0.00 32.23 2.27
304 308 4.073293 AGTGCCTCTCGAAAAGAAAAGA 57.927 40.909 0.00 0.00 32.23 2.52
312 316 7.196331 CCTCTCGAAAAGAAAAGAAATGTGTT 58.804 34.615 0.00 0.00 32.23 3.32
345 349 6.817184 TCCATTAGAGGCACATAGTTACTTC 58.183 40.000 0.00 0.00 0.00 3.01
352 356 3.119245 GGCACATAGTTACTTCCACGAGA 60.119 47.826 0.00 0.00 0.00 4.04
353 357 4.491676 GCACATAGTTACTTCCACGAGAA 58.508 43.478 0.00 0.00 0.00 2.87
362 366 3.193157 CTTCCACGAGAAGCACAATTG 57.807 47.619 3.24 3.24 45.38 2.32
363 367 2.254546 TCCACGAGAAGCACAATTGT 57.745 45.000 4.92 4.92 0.00 2.71
364 368 3.607775 CTTCCACGAGAAGCACAATTGTG 60.608 47.826 30.20 30.20 45.38 3.33
407 411 5.428496 TTTACTTCACGAGAGAGACGAAA 57.572 39.130 0.00 0.00 34.70 3.46
438 457 1.927895 CTTCCGCGAGAAGCATAACT 58.072 50.000 19.55 0.00 45.38 2.24
441 460 3.733988 CTTCCGCGAGAAGCATAACTGTA 60.734 47.826 19.55 0.00 45.38 2.74
448 467 4.800993 CGAGAAGCATAACTGTACCTCTTG 59.199 45.833 0.00 0.00 0.00 3.02
455 474 5.123979 GCATAACTGTACCTCTTGGAAAAGG 59.876 44.000 0.00 0.00 38.70 3.11
498 518 6.260936 CCACGAGAGGCACATATTTATTTCTT 59.739 38.462 0.00 0.00 0.00 2.52
510 530 5.649782 ATTTATTTCTTGTGGAGGCACAG 57.350 39.130 0.00 0.00 36.35 3.66
515 535 2.507484 TCTTGTGGAGGCACAGATTTG 58.493 47.619 0.00 0.00 36.35 2.32
521 541 1.538047 GAGGCACAGATTTGCTTCCA 58.462 50.000 0.00 0.00 41.54 3.53
591 611 3.476552 TCTTTCACGAGAGGCATTGTTT 58.523 40.909 0.00 0.00 0.00 2.83
594 614 3.126001 TCACGAGAGGCATTGTTTCTT 57.874 42.857 0.00 0.00 0.00 2.52
595 615 4.265904 TCACGAGAGGCATTGTTTCTTA 57.734 40.909 0.00 0.00 0.00 2.10
602 622 4.018050 AGAGGCATTGTTTCTTATGGAGGT 60.018 41.667 0.00 0.00 0.00 3.85
604 624 6.018433 AGGCATTGTTTCTTATGGAGGTAT 57.982 37.500 0.00 0.00 0.00 2.73
617 637 7.444183 TCTTATGGAGGTATAAATTTGCTTCCG 59.556 37.037 0.00 0.00 30.82 4.30
642 662 4.712122 AAAGCACAACTTTTCGGAAAGA 57.288 36.364 23.08 0.00 46.73 2.52
761 782 2.804697 TCGTCACGAGAAATCCAACA 57.195 45.000 0.00 0.00 0.00 3.33
780 801 4.605640 ACAGTGAAAATGGTTTGGGATG 57.394 40.909 0.00 0.00 35.33 3.51
785 806 4.749598 GTGAAAATGGTTTGGGATGTGAAC 59.250 41.667 0.00 0.00 0.00 3.18
865 886 5.541845 TCTTTGTGAGTGTATGAGAAGGTG 58.458 41.667 0.00 0.00 0.00 4.00
879 900 0.321653 AAGGTGGGAGTGATCGTTGC 60.322 55.000 0.00 0.00 0.00 4.17
928 951 4.177026 TGCGCTCAGAGAGATTCTTAAAC 58.823 43.478 9.73 0.00 32.41 2.01
978 1001 4.067896 CCCAAAGGTCCATCAATATCTCG 58.932 47.826 0.00 0.00 0.00 4.04
1073 1096 3.807538 GCCGCCACTAGACGACGA 61.808 66.667 0.00 0.00 0.00 4.20
1075 1098 1.298413 CCGCCACTAGACGACGATG 60.298 63.158 0.00 0.00 0.00 3.84
1076 1099 1.939785 CGCCACTAGACGACGATGC 60.940 63.158 0.00 0.00 0.00 3.91
1077 1100 1.433879 GCCACTAGACGACGATGCT 59.566 57.895 0.00 0.00 0.00 3.79
1078 1101 0.179134 GCCACTAGACGACGATGCTT 60.179 55.000 0.00 0.00 0.00 3.91
1385 1408 7.275560 GGGATTTCATGTTGTACAAAGCATTAC 59.724 37.037 10.51 0.00 0.00 1.89
1490 1798 2.536365 GCGTGCTGCAGTATTACTACA 58.464 47.619 16.64 0.00 45.45 2.74
1509 1823 2.158559 CATGGTGAAATGGTGTCGGAA 58.841 47.619 0.00 0.00 0.00 4.30
1523 1837 5.360144 TGGTGTCGGAAAATTTCAAGGTTTA 59.640 36.000 8.09 0.00 0.00 2.01
1524 1838 5.918576 GGTGTCGGAAAATTTCAAGGTTTAG 59.081 40.000 8.09 0.00 0.00 1.85
1773 2095 5.467735 AGGTTCTTCAAATGAAAAATGCAGC 59.532 36.000 0.00 0.00 33.07 5.25
1885 2207 7.110155 AGGAAGTCGGAATAAAATCTTTGCTA 58.890 34.615 0.00 0.00 0.00 3.49
2000 2322 4.775780 AGCTACCACTACCACAAGTAATCA 59.224 41.667 0.00 0.00 0.00 2.57
2155 2484 3.804036 TGGTAATAGATGGGCAACTTCG 58.196 45.455 0.00 0.00 0.00 3.79
2230 2571 5.259632 AGCTCTGTTCATCAAGCCTTTTAT 58.740 37.500 0.00 0.00 33.76 1.40
2405 2747 2.041701 AGGCTTGCCTTGAATTGTTGT 58.958 42.857 8.56 0.00 0.00 3.32
2579 2928 6.855836 TGATGGCTGTATTTGAACTTCATTC 58.144 36.000 0.00 0.00 37.88 2.67
2686 3035 1.753649 GTGATCTCAGCTGCTGGAGTA 59.246 52.381 27.79 13.96 31.51 2.59
2837 3186 6.375174 TGCAGTATCACTTCTATTGCATGTTT 59.625 34.615 0.00 0.00 37.04 2.83
2838 3187 6.690098 GCAGTATCACTTCTATTGCATGTTTG 59.310 38.462 0.00 0.00 33.46 2.93
3362 3731 0.167689 GCGCCTTCTCAGCTTTCTTG 59.832 55.000 0.00 0.00 0.00 3.02
3363 3732 1.517242 CGCCTTCTCAGCTTTCTTGT 58.483 50.000 0.00 0.00 0.00 3.16
3364 3733 1.462670 CGCCTTCTCAGCTTTCTTGTC 59.537 52.381 0.00 0.00 0.00 3.18
3365 3734 2.498167 GCCTTCTCAGCTTTCTTGTCA 58.502 47.619 0.00 0.00 0.00 3.58
3366 3735 3.080319 GCCTTCTCAGCTTTCTTGTCAT 58.920 45.455 0.00 0.00 0.00 3.06
3367 3736 4.256920 GCCTTCTCAGCTTTCTTGTCATA 58.743 43.478 0.00 0.00 0.00 2.15
3368 3737 4.880696 GCCTTCTCAGCTTTCTTGTCATAT 59.119 41.667 0.00 0.00 0.00 1.78
3369 3738 6.051717 GCCTTCTCAGCTTTCTTGTCATATA 58.948 40.000 0.00 0.00 0.00 0.86
3370 3739 6.540189 GCCTTCTCAGCTTTCTTGTCATATAA 59.460 38.462 0.00 0.00 0.00 0.98
3371 3740 7.254727 GCCTTCTCAGCTTTCTTGTCATATAAG 60.255 40.741 0.00 0.00 0.00 1.73
3372 3741 7.984050 CCTTCTCAGCTTTCTTGTCATATAAGA 59.016 37.037 0.00 0.00 32.64 2.10
3373 3742 9.376075 CTTCTCAGCTTTCTTGTCATATAAGAA 57.624 33.333 0.00 0.00 41.11 2.52
3374 3743 9.725019 TTCTCAGCTTTCTTGTCATATAAGAAA 57.275 29.630 10.18 10.18 46.29 2.52
3375 3744 9.896645 TCTCAGCTTTCTTGTCATATAAGAAAT 57.103 29.630 10.78 0.00 46.84 2.17
3376 3745 9.932699 CTCAGCTTTCTTGTCATATAAGAAATG 57.067 33.333 10.78 8.46 46.84 2.32
3377 3746 9.671279 TCAGCTTTCTTGTCATATAAGAAATGA 57.329 29.630 10.78 10.05 46.84 2.57
3378 3747 9.713740 CAGCTTTCTTGTCATATAAGAAATGAC 57.286 33.333 10.78 8.84 46.84 3.06
3394 3763 5.649395 AGAAATGACACATTTCGATCCATGT 59.351 36.000 22.59 7.92 41.49 3.21
3432 3801 7.827819 TCAACATTAGTAATGACTCTTTCGG 57.172 36.000 26.08 7.25 41.46 4.30
3433 3802 7.383687 TCAACATTAGTAATGACTCTTTCGGT 58.616 34.615 26.08 0.36 41.46 4.69
3434 3803 8.525316 TCAACATTAGTAATGACTCTTTCGGTA 58.475 33.333 26.08 0.00 41.46 4.02
3435 3804 9.146984 CAACATTAGTAATGACTCTTTCGGTAA 57.853 33.333 26.08 0.00 41.46 2.85
3436 3805 8.928270 ACATTAGTAATGACTCTTTCGGTAAG 57.072 34.615 26.08 0.00 41.46 2.34
3437 3806 8.746530 ACATTAGTAATGACTCTTTCGGTAAGA 58.253 33.333 26.08 0.00 41.46 2.10
3469 3838 6.633500 TTTTAATAGTACAGCATGCATCCC 57.367 37.500 21.98 4.86 42.53 3.85
3470 3839 2.867109 ATAGTACAGCATGCATCCCC 57.133 50.000 21.98 3.32 42.53 4.81
3471 3840 0.764890 TAGTACAGCATGCATCCCCC 59.235 55.000 21.98 2.17 42.53 5.40
3500 3869 2.269562 CCAAATGGGTACGCGGGA 59.730 61.111 12.47 0.00 0.00 5.14
3501 3870 1.377463 CCAAATGGGTACGCGGGAA 60.377 57.895 12.47 0.00 0.00 3.97
3502 3871 1.373590 CCAAATGGGTACGCGGGAAG 61.374 60.000 12.47 0.00 0.00 3.46
3503 3872 1.747745 AAATGGGTACGCGGGAAGC 60.748 57.895 12.47 4.92 43.95 3.86
3504 3873 3.692370 AATGGGTACGCGGGAAGCC 62.692 63.158 12.47 15.10 44.76 4.35
3506 3875 4.171103 GGGTACGCGGGAAGCCAT 62.171 66.667 12.47 0.00 44.76 4.40
3507 3876 2.895372 GGTACGCGGGAAGCCATG 60.895 66.667 12.47 0.00 44.76 3.66
3508 3877 2.895372 GTACGCGGGAAGCCATGG 60.895 66.667 12.47 7.63 44.76 3.66
3509 3878 4.169696 TACGCGGGAAGCCATGGG 62.170 66.667 15.13 0.00 44.76 4.00
3813 4335 4.248058 CGTGAAACCCGTCCTATAAAACT 58.752 43.478 0.00 0.00 0.00 2.66
3837 4359 1.831736 GAACTAGGGCTGCTACTTGGA 59.168 52.381 0.00 0.00 0.00 3.53
3993 4515 0.986527 TCTGCCCATTGCTCTCAAGA 59.013 50.000 0.00 0.00 42.00 3.02
4071 4593 5.741388 ATGCTTGATAATGTCCGAACTTC 57.259 39.130 0.00 0.00 0.00 3.01
4085 4607 7.113437 TGTCCGAACTTCCAATAATTTATCCA 58.887 34.615 0.00 0.00 0.00 3.41
4111 4633 5.792188 TGTCTGGGGATCATATGAATATGGT 59.208 40.000 9.99 3.39 40.35 3.55
4258 4781 1.876156 CAGTCTCAACAGGCAGTTTCC 59.124 52.381 0.00 0.00 38.74 3.13
4342 4876 8.361889 TGAGATAAAATCGACCAATATACGGAA 58.638 33.333 0.00 0.00 0.00 4.30
4352 4886 7.866898 TCGACCAATATACGGAAATTCGAATTA 59.133 33.333 22.99 8.21 0.00 1.40
4415 4951 2.688446 TGAAGATACTGACCGCACCTAG 59.312 50.000 0.00 0.00 0.00 3.02
4419 4955 0.038599 TACTGACCGCACCTAGTCCA 59.961 55.000 0.00 0.00 31.76 4.02
4423 4959 1.064240 TGACCGCACCTAGTCCATCTA 60.064 52.381 0.00 0.00 31.76 1.98
4468 5004 4.564821 GCCAGGTAGTTAATTGACCAGTGA 60.565 45.833 0.00 0.00 35.56 3.41
4490 5026 8.299570 AGTGATTGATAAGCAGGTGTTAAAAAG 58.700 33.333 0.00 0.00 0.00 2.27
4491 5027 8.082242 GTGATTGATAAGCAGGTGTTAAAAAGT 58.918 33.333 0.00 0.00 0.00 2.66
4493 5029 7.575414 TTGATAAGCAGGTGTTAAAAAGTGA 57.425 32.000 0.00 0.00 0.00 3.41
4494 5030 7.759489 TGATAAGCAGGTGTTAAAAAGTGAT 57.241 32.000 0.00 0.00 0.00 3.06
4495 5031 8.177119 TGATAAGCAGGTGTTAAAAAGTGATT 57.823 30.769 0.00 0.00 0.00 2.57
4498 5034 7.538303 AAGCAGGTGTTAAAAAGTGATTTTG 57.462 32.000 0.00 0.00 41.29 2.44
4509 5045 6.667007 AAAAGTGATTTTGCTGTTCTTTGG 57.333 33.333 0.00 0.00 0.00 3.28
4529 5065 6.924913 TTGGATCAGGGAGATTACTATGAG 57.075 41.667 0.00 0.00 37.00 2.90
4669 5205 8.988064 TGTTAACTCTGTCTCATTCAACTATC 57.012 34.615 7.22 0.00 0.00 2.08
4696 5236 4.161565 AGAACATACAAGATAGCCGACCAA 59.838 41.667 0.00 0.00 0.00 3.67
4698 5238 2.973694 TACAAGATAGCCGACCAACC 57.026 50.000 0.00 0.00 0.00 3.77
4723 5263 6.942576 CCAGAGAAGGGAAATAAGAACTGAAA 59.057 38.462 0.00 0.00 0.00 2.69
4796 5337 5.186198 GTGAGGGCATAAGTTGAAGTACAT 58.814 41.667 0.00 0.00 0.00 2.29
4797 5338 5.648092 GTGAGGGCATAAGTTGAAGTACATT 59.352 40.000 0.00 0.00 0.00 2.71
4806 5347 4.344104 AGTTGAAGTACATTGGGGAATGG 58.656 43.478 0.00 0.00 34.56 3.16
4830 5371 3.888323 ACATGTTTACATTGGCAGACACA 59.112 39.130 0.00 0.00 33.61 3.72
4839 5380 4.588528 ACATTGGCAGACACATAAAAAGGT 59.411 37.500 0.00 0.00 0.00 3.50
4893 5434 5.189180 GTTCTCAACCCATTAGCTTCAGAT 58.811 41.667 0.00 0.00 0.00 2.90
4959 5500 6.073222 CCCAGTTGTACTGTTTCAATCTACAC 60.073 42.308 6.13 0.00 44.50 2.90
4968 5509 6.072508 ACTGTTTCAATCTACACGATGCAATT 60.073 34.615 0.00 0.00 31.20 2.32
4989 5530 7.698130 GCAATTAGTCATACCATCAGTCAAAAC 59.302 37.037 0.00 0.00 0.00 2.43
5015 5556 1.356124 ATCACCAAGTGTGCCTCTCT 58.644 50.000 0.00 0.00 45.03 3.10
5016 5557 1.131638 TCACCAAGTGTGCCTCTCTT 58.868 50.000 0.00 0.00 45.03 2.85
5038 5580 6.376299 TCTTTGATTCATTCAGGAACATGGAG 59.624 38.462 0.00 0.00 35.27 3.86
5039 5581 5.183530 TGATTCATTCAGGAACATGGAGT 57.816 39.130 0.00 0.00 0.00 3.85
5042 5584 6.156775 TGATTCATTCAGGAACATGGAGTAGA 59.843 38.462 0.00 0.00 0.00 2.59
5043 5585 5.344743 TCATTCAGGAACATGGAGTAGAC 57.655 43.478 0.00 0.00 0.00 2.59
5044 5586 4.777366 TCATTCAGGAACATGGAGTAGACA 59.223 41.667 0.00 0.00 0.00 3.41
5045 5587 5.248248 TCATTCAGGAACATGGAGTAGACAA 59.752 40.000 0.00 0.00 0.00 3.18
5046 5588 5.762179 TTCAGGAACATGGAGTAGACAAT 57.238 39.130 0.00 0.00 0.00 2.71
5050 5596 7.861629 TCAGGAACATGGAGTAGACAATAAAT 58.138 34.615 0.00 0.00 0.00 1.40
5061 5607 9.197694 GGAGTAGACAATAAATAGTATGTGCAG 57.802 37.037 0.00 0.00 0.00 4.41
5106 5652 6.860023 CCTTTGCATTTTCAACACAAACAAAA 59.140 30.769 0.00 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.111116 ACAACATGTGGCAGCAGCTT 61.111 50.000 0.00 0.00 41.70 3.74
18 19 1.408702 GAAGCACCCAACACACAACAT 59.591 47.619 0.00 0.00 0.00 2.71
24 25 0.257328 TTGAGGAAGCACCCAACACA 59.743 50.000 0.00 0.00 40.05 3.72
90 94 2.882927 AAGAAAAACCAGGCGGAAAC 57.117 45.000 2.43 0.00 35.59 2.78
94 98 1.905637 ACCTAAGAAAAACCAGGCGG 58.094 50.000 0.00 0.00 38.77 6.13
96 100 4.100344 TCCAAAACCTAAGAAAAACCAGGC 59.900 41.667 0.00 0.00 0.00 4.85
98 102 6.709018 TCTCCAAAACCTAAGAAAAACCAG 57.291 37.500 0.00 0.00 0.00 4.00
150 154 9.437045 CTTCTCGCAAAAGCAAAATTTATTTTT 57.563 25.926 0.00 0.00 37.86 1.94
151 155 7.587392 GCTTCTCGCAAAAGCAAAATTTATTTT 59.413 29.630 9.19 0.00 46.63 1.82
152 156 7.071414 GCTTCTCGCAAAAGCAAAATTTATTT 58.929 30.769 9.19 0.00 46.63 1.40
153 157 6.593072 GCTTCTCGCAAAAGCAAAATTTATT 58.407 32.000 9.19 0.00 46.63 1.40
154 158 6.156932 GCTTCTCGCAAAAGCAAAATTTAT 57.843 33.333 9.19 0.00 46.63 1.40
155 159 5.574815 GCTTCTCGCAAAAGCAAAATTTA 57.425 34.783 9.19 0.00 46.63 1.40
156 160 4.457433 GCTTCTCGCAAAAGCAAAATTT 57.543 36.364 9.19 0.00 46.63 1.82
182 186 1.434188 TCCCTTTGAGAGAGGCACAA 58.566 50.000 0.00 0.00 32.74 3.33
184 188 2.568623 TTTCCCTTTGAGAGAGGCAC 57.431 50.000 0.00 0.00 32.74 5.01
205 209 2.743126 TCGTGGAAGAAAAACGTGTGTT 59.257 40.909 0.00 0.00 40.98 3.32
206 210 2.348660 TCGTGGAAGAAAAACGTGTGT 58.651 42.857 0.00 0.00 38.43 3.72
207 211 2.605818 TCTCGTGGAAGAAAAACGTGTG 59.394 45.455 0.00 0.00 38.43 3.82
208 212 2.864343 CTCTCGTGGAAGAAAAACGTGT 59.136 45.455 0.00 0.00 38.43 4.49
209 213 2.221055 CCTCTCGTGGAAGAAAAACGTG 59.779 50.000 0.00 0.00 38.43 4.49
210 214 2.480845 CCTCTCGTGGAAGAAAAACGT 58.519 47.619 0.00 0.00 38.43 3.99
211 215 1.194772 GCCTCTCGTGGAAGAAAAACG 59.805 52.381 0.00 0.00 38.64 3.60
212 216 2.218603 TGCCTCTCGTGGAAGAAAAAC 58.781 47.619 0.00 0.00 0.00 2.43
213 217 2.631160 TGCCTCTCGTGGAAGAAAAA 57.369 45.000 0.00 0.00 0.00 1.94
214 218 2.699954 GATGCCTCTCGTGGAAGAAAA 58.300 47.619 0.00 0.00 0.00 2.29
215 219 1.404181 CGATGCCTCTCGTGGAAGAAA 60.404 52.381 0.00 0.00 34.00 2.52
224 228 2.064762 GGATCAAATCGATGCCTCTCG 58.935 52.381 0.00 0.00 36.50 4.04
234 238 2.159240 TGTCTCCACGAGGATCAAATCG 60.159 50.000 0.78 11.32 44.70 3.34
263 267 6.293955 GGCACTACTTTGCTTCTCATGTAAAA 60.294 38.462 0.00 0.00 42.56 1.52
264 268 5.181245 GGCACTACTTTGCTTCTCATGTAAA 59.819 40.000 0.00 0.00 42.56 2.01
267 271 3.077359 GGCACTACTTTGCTTCTCATGT 58.923 45.455 0.00 0.00 42.56 3.21
268 272 3.341823 AGGCACTACTTTGCTTCTCATG 58.658 45.455 0.00 0.00 42.56 3.07
269 273 3.604582 GAGGCACTACTTTGCTTCTCAT 58.395 45.455 0.36 0.00 43.46 2.90
270 274 3.045601 GAGGCACTACTTTGCTTCTCA 57.954 47.619 0.36 0.00 43.46 3.27
312 316 3.258123 GTGCCTCTAATGGAAGCCAAAAA 59.742 43.478 0.00 0.00 36.95 1.94
325 329 5.393787 CGTGGAAGTAACTATGTGCCTCTAA 60.394 44.000 0.00 0.00 0.00 2.10
326 330 4.097437 CGTGGAAGTAACTATGTGCCTCTA 59.903 45.833 0.00 0.00 0.00 2.43
345 349 2.320805 CACAATTGTGCTTCTCGTGG 57.679 50.000 24.69 0.00 39.39 4.94
383 387 5.428496 TCGTCTCTCTCGTGAAGTAAAAA 57.572 39.130 0.00 0.00 0.00 1.94
384 388 5.428496 TTCGTCTCTCTCGTGAAGTAAAA 57.572 39.130 0.00 0.00 0.00 1.52
385 389 5.008415 ACTTTCGTCTCTCTCGTGAAGTAAA 59.992 40.000 0.00 0.00 35.75 2.01
386 390 4.514441 ACTTTCGTCTCTCTCGTGAAGTAA 59.486 41.667 0.00 0.00 35.75 2.24
387 391 4.063689 ACTTTCGTCTCTCTCGTGAAGTA 58.936 43.478 0.00 0.00 35.75 2.24
388 392 2.879646 ACTTTCGTCTCTCTCGTGAAGT 59.120 45.455 0.00 0.00 34.25 3.01
389 393 3.546002 ACTTTCGTCTCTCTCGTGAAG 57.454 47.619 0.00 0.00 0.00 3.02
390 394 3.811497 TGTACTTTCGTCTCTCTCGTGAA 59.189 43.478 0.00 0.00 0.00 3.18
391 395 3.396560 TGTACTTTCGTCTCTCTCGTGA 58.603 45.455 0.00 0.00 0.00 4.35
394 398 6.517597 CAAATTTGTACTTTCGTCTCTCTCG 58.482 40.000 10.15 0.00 0.00 4.04
462 481 3.071479 GCCTCTCGTGGAAAAATACACA 58.929 45.455 0.00 0.00 37.45 3.72
463 482 3.071479 TGCCTCTCGTGGAAAAATACAC 58.929 45.455 0.00 0.00 0.00 2.90
464 483 3.071479 GTGCCTCTCGTGGAAAAATACA 58.929 45.455 0.00 0.00 0.00 2.29
465 484 3.071479 TGTGCCTCTCGTGGAAAAATAC 58.929 45.455 0.00 0.00 0.00 1.89
466 485 3.410631 TGTGCCTCTCGTGGAAAAATA 57.589 42.857 0.00 0.00 0.00 1.40
467 486 2.270352 TGTGCCTCTCGTGGAAAAAT 57.730 45.000 0.00 0.00 0.00 1.82
521 541 5.127194 TGAGAGGCACAATTATACTTCTCGT 59.873 40.000 0.00 0.00 0.00 4.18
580 600 4.273318 ACCTCCATAAGAAACAATGCCTC 58.727 43.478 0.00 0.00 0.00 4.70
582 602 7.817418 TTATACCTCCATAAGAAACAATGCC 57.183 36.000 0.00 0.00 0.00 4.40
591 611 7.444183 CGGAAGCAAATTTATACCTCCATAAGA 59.556 37.037 0.00 0.00 0.00 2.10
745 766 3.744238 TCACTGTTGGATTTCTCGTGA 57.256 42.857 0.00 0.00 0.00 4.35
757 778 4.399004 TCCCAAACCATTTTCACTGTTG 57.601 40.909 0.00 0.00 0.00 3.33
761 782 4.222336 TCACATCCCAAACCATTTTCACT 58.778 39.130 0.00 0.00 0.00 3.41
865 886 0.804989 CCTTTGCAACGATCACTCCC 59.195 55.000 4.19 0.00 0.00 4.30
928 951 1.008995 CCACGTGACCGGCTTTTTG 60.009 57.895 19.30 0.00 38.78 2.44
978 1001 0.878086 GCAGCTCTAGGCCGAATGAC 60.878 60.000 0.00 0.00 43.05 3.06
1053 1076 3.057548 TCGTCTAGTGGCGGCGAA 61.058 61.111 12.98 0.00 0.00 4.70
1073 1096 2.017049 GTAACAAGCGGGATGAAGCAT 58.983 47.619 0.00 0.00 35.48 3.79
1075 1098 0.733150 GGTAACAAGCGGGATGAAGC 59.267 55.000 0.00 0.00 0.00 3.86
1076 1099 2.280628 GAGGTAACAAGCGGGATGAAG 58.719 52.381 0.00 0.00 41.41 3.02
1077 1100 1.065709 GGAGGTAACAAGCGGGATGAA 60.066 52.381 0.00 0.00 41.41 2.57
1078 1101 0.539986 GGAGGTAACAAGCGGGATGA 59.460 55.000 0.00 0.00 41.41 2.92
1284 1307 8.295288 CAGAGATTAGCAAGAAAAACATGAGTT 58.705 33.333 0.00 0.00 40.40 3.01
1294 1317 5.294306 CCATAACGCAGAGATTAGCAAGAAA 59.706 40.000 0.00 0.00 0.00 2.52
1408 1431 8.641498 ACCATTATTCTCAAACTTCACATTCT 57.359 30.769 0.00 0.00 0.00 2.40
1413 1436 8.978539 GGAAAAACCATTATTCTCAAACTTCAC 58.021 33.333 0.00 0.00 38.79 3.18
1467 1775 0.373716 GTAATACTGCAGCACGCCAC 59.626 55.000 15.27 0.64 41.33 5.01
1490 1798 2.577606 TTCCGACACCATTTCACCAT 57.422 45.000 0.00 0.00 0.00 3.55
1523 1837 5.338953 GCTAGTCCCAACCATAAAAGGTACT 60.339 44.000 0.00 0.00 42.25 2.73
1524 1838 4.880120 GCTAGTCCCAACCATAAAAGGTAC 59.120 45.833 0.00 0.00 42.25 3.34
2000 2322 1.904287 TGCGGCAACCAGAAAAGTAT 58.096 45.000 0.00 0.00 0.00 2.12
2405 2747 6.301486 CCATGAGATCAATACCAGATTGGAA 58.699 40.000 1.40 0.00 40.96 3.53
2579 2928 2.704572 GTGATGTCTCTGGGGAAACAG 58.295 52.381 0.00 0.00 39.84 3.16
2686 3035 2.711547 ACTTCCTCTTACAAGGTTGGCT 59.288 45.455 0.00 0.00 37.69 4.75
3022 3371 7.642586 GGTGGCGATTTAATAGTACAAATTGAC 59.357 37.037 0.00 5.54 35.08 3.18
3105 3454 5.884232 AGGGAAAACGAAAGGGTTATGTATC 59.116 40.000 0.00 0.00 0.00 2.24
3149 3498 2.736347 AGTAGGCGGTCATCAGTAGTT 58.264 47.619 0.00 0.00 0.00 2.24
3364 3733 9.817365 GGATCGAAATGTGTCATTTCTTATATG 57.183 33.333 23.45 12.79 36.24 1.78
3365 3734 9.559732 TGGATCGAAATGTGTCATTTCTTATAT 57.440 29.630 23.45 15.24 36.24 0.86
3366 3735 8.956533 TGGATCGAAATGTGTCATTTCTTATA 57.043 30.769 23.45 12.51 36.24 0.98
3367 3736 7.864108 TGGATCGAAATGTGTCATTTCTTAT 57.136 32.000 23.45 18.53 36.24 1.73
3368 3737 7.336679 ACATGGATCGAAATGTGTCATTTCTTA 59.663 33.333 23.45 15.89 35.71 2.10
3369 3738 6.151648 ACATGGATCGAAATGTGTCATTTCTT 59.848 34.615 23.45 15.30 35.71 2.52
3370 3739 5.649395 ACATGGATCGAAATGTGTCATTTCT 59.351 36.000 23.45 12.38 35.71 2.52
3371 3740 5.883661 ACATGGATCGAAATGTGTCATTTC 58.116 37.500 19.14 19.14 35.71 2.17
3372 3741 5.902613 ACATGGATCGAAATGTGTCATTT 57.097 34.783 10.03 7.32 35.71 2.32
3373 3742 5.415389 TGAACATGGATCGAAATGTGTCATT 59.585 36.000 11.20 0.00 37.11 2.57
3374 3743 4.943093 TGAACATGGATCGAAATGTGTCAT 59.057 37.500 11.20 0.00 37.11 3.06
3375 3744 4.322567 TGAACATGGATCGAAATGTGTCA 58.677 39.130 11.20 12.61 37.11 3.58
3376 3745 4.201851 CCTGAACATGGATCGAAATGTGTC 60.202 45.833 11.20 10.92 37.11 3.67
3377 3746 3.691118 CCTGAACATGGATCGAAATGTGT 59.309 43.478 11.20 2.58 37.11 3.72
3378 3747 3.940852 TCCTGAACATGGATCGAAATGTG 59.059 43.478 11.20 2.02 37.11 3.21
3379 3748 3.941483 GTCCTGAACATGGATCGAAATGT 59.059 43.478 0.00 6.06 38.66 2.71
3380 3749 3.940852 TGTCCTGAACATGGATCGAAATG 59.059 43.478 0.00 0.00 35.87 2.32
3381 3750 4.220693 TGTCCTGAACATGGATCGAAAT 57.779 40.909 0.00 0.00 35.87 2.17
3382 3751 3.694043 TGTCCTGAACATGGATCGAAA 57.306 42.857 0.00 0.00 35.87 3.46
3383 3752 3.694043 TTGTCCTGAACATGGATCGAA 57.306 42.857 0.00 0.00 37.82 3.71
3384 3753 3.694043 TTTGTCCTGAACATGGATCGA 57.306 42.857 0.00 0.00 37.82 3.59
3385 3754 4.764679 TTTTTGTCCTGAACATGGATCG 57.235 40.909 0.00 0.00 37.82 3.69
3445 3814 6.040391 GGGGATGCATGCTGTACTATTAAAAA 59.960 38.462 20.33 0.00 0.00 1.94
3446 3815 5.534654 GGGGATGCATGCTGTACTATTAAAA 59.465 40.000 20.33 0.00 0.00 1.52
3447 3816 5.070001 GGGGATGCATGCTGTACTATTAAA 58.930 41.667 20.33 0.00 0.00 1.52
3448 3817 4.506625 GGGGGATGCATGCTGTACTATTAA 60.507 45.833 20.33 0.00 0.00 1.40
3449 3818 3.009033 GGGGGATGCATGCTGTACTATTA 59.991 47.826 20.33 0.00 0.00 0.98
3450 3819 2.224867 GGGGGATGCATGCTGTACTATT 60.225 50.000 20.33 0.00 0.00 1.73
3451 3820 1.352352 GGGGGATGCATGCTGTACTAT 59.648 52.381 20.33 1.92 0.00 2.12
3452 3821 0.764890 GGGGGATGCATGCTGTACTA 59.235 55.000 20.33 0.00 0.00 1.82
3453 3822 1.533711 GGGGGATGCATGCTGTACT 59.466 57.895 20.33 0.00 0.00 2.73
3454 3823 4.164258 GGGGGATGCATGCTGTAC 57.836 61.111 20.33 8.30 0.00 2.90
3483 3852 1.373590 CTTCCCGCGTACCCATTTGG 61.374 60.000 4.92 0.00 41.37 3.28
3484 3853 1.988834 GCTTCCCGCGTACCCATTTG 61.989 60.000 4.92 0.00 0.00 2.32
3485 3854 1.747745 GCTTCCCGCGTACCCATTT 60.748 57.895 4.92 0.00 0.00 2.32
3486 3855 2.124860 GCTTCCCGCGTACCCATT 60.125 61.111 4.92 0.00 0.00 3.16
3487 3856 4.171103 GGCTTCCCGCGTACCCAT 62.171 66.667 4.92 0.00 40.44 4.00
3489 3858 4.171103 ATGGCTTCCCGCGTACCC 62.171 66.667 4.92 0.00 40.44 3.69
3490 3859 2.895372 CATGGCTTCCCGCGTACC 60.895 66.667 4.92 0.00 40.44 3.34
3491 3860 2.895372 CCATGGCTTCCCGCGTAC 60.895 66.667 4.92 0.00 40.44 3.67
3492 3861 4.169696 CCCATGGCTTCCCGCGTA 62.170 66.667 6.09 0.00 40.44 4.42
3500 3869 9.988250 TATGTATTACATTGGTGCCCATGGCTT 62.988 40.741 14.23 0.00 43.56 4.35
3501 3870 7.934335 ATGTATTACATTGGTGCCCATGGCT 62.934 44.000 6.09 0.00 42.22 4.75
3502 3871 5.776452 ATGTATTACATTGGTGCCCATGGC 61.776 45.833 6.09 2.35 42.12 4.40
3503 3872 3.295093 TGTATTACATTGGTGCCCATGG 58.705 45.455 4.14 4.14 31.53 3.66
3504 3873 6.839124 ATATGTATTACATTGGTGCCCATG 57.161 37.500 14.23 1.27 39.88 3.66
3505 3874 7.854166 AAATATGTATTACATTGGTGCCCAT 57.146 32.000 14.23 0.00 39.88 4.00
3506 3875 7.667575 AAAATATGTATTACATTGGTGCCCA 57.332 32.000 14.23 0.00 39.88 5.36
3507 3876 8.421002 AGAAAAATATGTATTACATTGGTGCCC 58.579 33.333 14.23 1.04 39.88 5.36
3508 3877 9.816354 AAGAAAAATATGTATTACATTGGTGCC 57.184 29.630 14.23 2.30 39.88 5.01
3519 3888 9.700831 AGCCAAGTAGGAAGAAAAATATGTATT 57.299 29.630 0.00 0.00 41.22 1.89
3520 3889 9.125026 CAGCCAAGTAGGAAGAAAAATATGTAT 57.875 33.333 0.00 0.00 41.22 2.29
3813 4335 4.072131 CAAGTAGCAGCCCTAGTTCAAAA 58.928 43.478 0.00 0.00 37.54 2.44
4085 4607 7.036352 ACCATATTCATATGATCCCCAGACAAT 60.036 37.037 6.17 0.00 42.05 2.71
4111 4633 5.659525 TGCTAGTATGCTAGAAACTGGGTTA 59.340 40.000 20.68 0.00 45.77 2.85
4342 4876 3.120108 TCCCCCAGAGGTAATTCGAATT 58.880 45.455 25.48 25.48 0.00 2.17
4352 4886 2.047830 GTCGATTATTCCCCCAGAGGT 58.952 52.381 0.00 0.00 0.00 3.85
4392 4928 3.296854 AGGTGCGGTCAGTATCTTCATA 58.703 45.455 0.00 0.00 0.00 2.15
4415 4951 1.834263 AGTCCCTGCAGTTAGATGGAC 59.166 52.381 22.77 22.77 42.00 4.02
4419 4955 1.853963 ACGAGTCCCTGCAGTTAGAT 58.146 50.000 13.81 0.00 0.00 1.98
4423 4959 2.052782 AAAAACGAGTCCCTGCAGTT 57.947 45.000 13.81 0.00 0.00 3.16
4468 5004 8.177119 TCACTTTTTAACACCTGCTTATCAAT 57.823 30.769 0.00 0.00 0.00 2.57
4490 5026 5.531634 TGATCCAAAGAACAGCAAAATCAC 58.468 37.500 0.00 0.00 0.00 3.06
4491 5027 5.279106 CCTGATCCAAAGAACAGCAAAATCA 60.279 40.000 0.00 0.00 40.60 2.57
4493 5029 4.020839 CCCTGATCCAAAGAACAGCAAAAT 60.021 41.667 0.00 0.00 40.60 1.82
4494 5030 3.321682 CCCTGATCCAAAGAACAGCAAAA 59.678 43.478 0.00 0.00 40.60 2.44
4495 5031 2.892852 CCCTGATCCAAAGAACAGCAAA 59.107 45.455 0.00 0.00 40.60 3.68
4498 5034 2.026822 TCTCCCTGATCCAAAGAACAGC 60.027 50.000 0.00 0.00 40.60 4.40
4509 5045 5.991933 TGCTCATAGTAATCTCCCTGATC 57.008 43.478 0.00 0.00 33.57 2.92
4631 5167 9.520515 AGACAGAGTTAACATTTTTCCATGTAT 57.479 29.630 8.61 0.00 36.30 2.29
4651 5187 5.420104 TCTGCTGATAGTTGAATGAGACAGA 59.580 40.000 0.00 0.00 0.00 3.41
4669 5205 3.492383 CGGCTATCTTGTATGTTCTGCTG 59.508 47.826 0.00 0.00 0.00 4.41
4698 5238 6.054860 TCAGTTCTTATTTCCCTTCTCTGG 57.945 41.667 0.00 0.00 0.00 3.86
4770 5311 4.012374 ACTTCAACTTATGCCCTCACATG 58.988 43.478 0.00 0.00 0.00 3.21
4796 5337 1.727062 AAACATGTGCCATTCCCCAA 58.273 45.000 0.00 0.00 0.00 4.12
4797 5338 2.175202 GTAAACATGTGCCATTCCCCA 58.825 47.619 0.00 0.00 0.00 4.96
4806 5347 3.244976 GTCTGCCAATGTAAACATGTGC 58.755 45.455 0.00 9.13 36.56 4.57
4819 5360 3.572255 GGACCTTTTTATGTGTCTGCCAA 59.428 43.478 0.00 0.00 0.00 4.52
4822 5363 5.009610 TCAAAGGACCTTTTTATGTGTCTGC 59.990 40.000 17.16 0.00 30.60 4.26
4830 5371 8.706322 AGTATGTTGTCAAAGGACCTTTTTAT 57.294 30.769 17.16 7.85 43.65 1.40
4839 5380 2.695359 GGCGAGTATGTTGTCAAAGGA 58.305 47.619 0.00 0.00 0.00 3.36
4893 5434 4.826733 TGGCAGAGCAGAAAATTGAACTTA 59.173 37.500 0.00 0.00 0.00 2.24
4959 5500 5.698089 ACTGATGGTATGACTAATTGCATCG 59.302 40.000 0.00 0.00 0.00 3.84
4968 5509 6.873605 CACAGTTTTGACTGATGGTATGACTA 59.126 38.462 13.02 0.00 39.99 2.59
5015 5556 6.012113 ACTCCATGTTCCTGAATGAATCAAA 58.988 36.000 0.00 0.00 37.67 2.69
5016 5557 5.573219 ACTCCATGTTCCTGAATGAATCAA 58.427 37.500 0.00 0.00 37.67 2.57
5050 5596 7.611770 ACAGAAGTTGATAACTGCACATACTA 58.388 34.615 2.76 0.00 41.91 1.82
5061 5607 7.750903 GCAAAGGTATGAACAGAAGTTGATAAC 59.249 37.037 0.00 0.00 40.48 1.89
5106 5652 3.589951 ATGGAGGCATGCTACAAAGAT 57.410 42.857 18.92 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.