Multiple sequence alignment - TraesCS4A01G111500

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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 TraesCS4A01G111500 chr4A 100.000 5646 0 0 1 5646 136610606 136616251 0.000000e+00 10427.0
1 TraesCS4A01G111500 chr4D 92.524 5578 231 77 1 5509 336848273 336842813 0.000000e+00 7819.0
2 TraesCS4A01G111500 chr4D 97.727 88 1 1 5554 5641 336842719 336842633 3.520000e-32 150.0
3 TraesCS4A01G111500 chr4B 92.829 5313 210 76 1 5250 415129287 415124083 0.000000e+00 7542.0
4 TraesCS4A01G111500 chr4B 91.860 86 2 1 5248 5333 415124058 415123978 1.290000e-21 115.0
5 TraesCS4A01G111500 chr3D 94.286 35 2 0 1727 1761 104731574 104731540 3.000000e-03 54.7


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 TraesCS4A01G111500 chr4A 136610606 136616251 5645 False 10427.0 10427 100.0000 1 5646 1 chr4A.!!$F1 5645
1 TraesCS4A01G111500 chr4D 336842633 336848273 5640 True 3984.5 7819 95.1255 1 5641 2 chr4D.!!$R1 5640
2 TraesCS4A01G111500 chr4B 415123978 415129287 5309 True 3828.5 7542 92.3445 1 5333 2 chr4B.!!$R1 5332

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
243 255 0.178973 TCTGACCGGTGAGTTCCAGA 60.179 55.000 21.00 17.89 0.00 3.86 F
340 352 1.131693 ACACGTTATCGATGAGTGCGA 59.868 47.619 21.47 0.00 42.48 5.10 F
1695 1716 1.421485 CTTGAGGCGCGACACAATC 59.579 57.895 24.95 8.77 0.00 2.67 F
3428 3491 1.115467 AGAAGGCTGCTATGCGTAGT 58.885 50.000 14.37 0.00 0.00 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1755 1776 3.012518 CCACAAGTCATTGGTCTCATCC 58.987 50.000 0.00 0.00 40.97 3.51 R
2337 2361 1.503542 CAACTCTGCGCATTCCCAC 59.496 57.895 12.24 0.00 0.00 4.61 R
3593 3656 0.378962 CGTCAAGGCTAGAGTCTCCG 59.621 60.000 0.00 0.00 0.00 4.63 R
4951 5047 0.176910 GAGCCCCTAGTCTTGCTGAC 59.823 60.000 0.00 2.86 45.67 3.51 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
23 25 1.693606 CATTTGGGGTCCAGCACTTTT 59.306 47.619 0.00 0.00 33.81 2.27
37 39 3.580458 AGCACTTTTCTAGCTGAGAGGAA 59.420 43.478 0.00 0.00 37.20 3.36
53 56 2.025589 GGAAACAATCCTCCGACTCC 57.974 55.000 0.00 0.00 45.56 3.85
67 70 1.000607 CGACTCCTTCTTTGACCGACA 60.001 52.381 0.00 0.00 0.00 4.35
69 72 3.665190 GACTCCTTCTTTGACCGACAAT 58.335 45.455 0.00 0.00 38.36 2.71
76 79 5.220416 CCTTCTTTGACCGACAATATTCGAC 60.220 44.000 0.00 0.00 41.78 4.20
100 104 1.056660 ATTGGTGTTGTCGAGGGAGT 58.943 50.000 0.00 0.00 0.00 3.85
111 115 2.619646 GTCGAGGGAGTCTTATGAGGTC 59.380 54.545 0.00 0.00 0.00 3.85
121 126 3.964031 GTCTTATGAGGTCATGTCTCCCT 59.036 47.826 13.40 6.16 37.15 4.20
123 128 1.407936 ATGAGGTCATGTCTCCCTCG 58.592 55.000 13.40 0.00 46.36 4.63
133 138 5.242838 GTCATGTCTCCCTCGAATCTATCTT 59.757 44.000 0.00 0.00 0.00 2.40
137 142 5.644206 TGTCTCCCTCGAATCTATCTTATCG 59.356 44.000 0.00 0.00 36.67 2.92
170 175 3.146847 GTCTTCCATCCTTTTTCACCGT 58.853 45.455 0.00 0.00 0.00 4.83
173 178 3.053831 TCCATCCTTTTTCACCGTCTC 57.946 47.619 0.00 0.00 0.00 3.36
220 229 6.292488 CCAGAGCATTGTTGTCAACATTTTTC 60.292 38.462 18.83 13.76 41.79 2.29
239 251 1.079750 GGCTCTGACCGGTGAGTTC 60.080 63.158 21.00 12.97 33.22 3.01
243 255 0.178973 TCTGACCGGTGAGTTCCAGA 60.179 55.000 21.00 17.89 0.00 3.86
254 266 2.581216 AGTTCCAGACTCCTACGTCA 57.419 50.000 0.00 0.00 36.38 4.35
260 272 3.576982 TCCAGACTCCTACGTCAACAATT 59.423 43.478 0.00 0.00 36.38 2.32
261 273 4.039973 TCCAGACTCCTACGTCAACAATTT 59.960 41.667 0.00 0.00 36.38 1.82
293 305 1.519408 CGATGGTGTTTCGGAGGTTT 58.481 50.000 0.00 0.00 33.05 3.27
298 310 2.967201 TGGTGTTTCGGAGGTTTAGAGA 59.033 45.455 0.00 0.00 0.00 3.10
302 314 3.581332 TGTTTCGGAGGTTTAGAGATGGT 59.419 43.478 0.00 0.00 0.00 3.55
327 339 1.335810 AGCTTCACTCACGACACGTTA 59.664 47.619 0.00 0.00 38.32 3.18
331 343 1.799994 TCACTCACGACACGTTATCGA 59.200 47.619 22.20 3.66 42.25 3.59
339 351 1.513178 GACACGTTATCGATGAGTGCG 59.487 52.381 21.47 11.64 40.62 5.34
340 352 1.131693 ACACGTTATCGATGAGTGCGA 59.868 47.619 21.47 0.00 42.48 5.10
343 355 2.286477 ACGTTATCGATGAGTGCGAGAG 60.286 50.000 8.54 0.00 41.49 3.20
357 369 1.989430 CGAGAGCAGGAAGAAGACAC 58.011 55.000 0.00 0.00 0.00 3.67
368 380 4.995487 AGGAAGAAGACACCGTTAATTCAC 59.005 41.667 0.00 0.00 0.00 3.18
369 381 4.995487 GGAAGAAGACACCGTTAATTCACT 59.005 41.667 0.00 0.00 0.00 3.41
372 384 7.172019 GGAAGAAGACACCGTTAATTCACTAAA 59.828 37.037 0.00 0.00 0.00 1.85
378 390 6.293698 ACACCGTTAATTCACTAAAGAAGGT 58.706 36.000 0.00 0.00 0.00 3.50
383 395 7.075741 CGTTAATTCACTAAAGAAGGTTGTGG 58.924 38.462 0.00 0.00 0.00 4.17
385 397 6.884280 AATTCACTAAAGAAGGTTGTGGAG 57.116 37.500 0.00 0.00 0.00 3.86
398 410 5.265989 AGGTTGTGGAGTTTCAGGTTTTTA 58.734 37.500 0.00 0.00 0.00 1.52
400 412 7.064229 AGGTTGTGGAGTTTCAGGTTTTTATA 58.936 34.615 0.00 0.00 0.00 0.98
402 414 7.812669 GGTTGTGGAGTTTCAGGTTTTTATATG 59.187 37.037 0.00 0.00 0.00 1.78
435 448 6.455647 TGTAGGGCTGATCGACTTTAATATG 58.544 40.000 0.00 0.00 0.00 1.78
450 463 8.845413 ACTTTAATATGCATTTTTGCCTTTCA 57.155 26.923 3.54 0.00 0.00 2.69
451 464 9.282569 ACTTTAATATGCATTTTTGCCTTTCAA 57.717 25.926 3.54 0.00 0.00 2.69
487 500 5.231265 ACTGTCTTTCGAAAGGAAACAAC 57.769 39.130 31.82 22.78 39.67 3.32
652 669 4.377635 CGGAGAAAAATTAAACGCGAAGGA 60.378 41.667 15.93 0.00 0.00 3.36
653 670 5.637809 GGAGAAAAATTAAACGCGAAGGAT 58.362 37.500 15.93 0.00 0.00 3.24
655 672 5.637809 AGAAAAATTAAACGCGAAGGATCC 58.362 37.500 15.93 2.48 0.00 3.36
657 674 5.379732 AAAATTAAACGCGAAGGATCCAA 57.620 34.783 15.93 0.00 0.00 3.53
701 722 4.631740 TGGTGACAGCGGGAGGGA 62.632 66.667 0.00 0.00 35.01 4.20
716 737 2.037527 GGAGACCCACCCGACTCT 59.962 66.667 0.00 0.00 0.00 3.24
955 976 4.891727 ACATGATCGCCGCCGTCC 62.892 66.667 0.00 0.00 35.54 4.79
1695 1716 1.421485 CTTGAGGCGCGACACAATC 59.579 57.895 24.95 8.77 0.00 2.67
1740 1761 1.974265 TCGATGAGAGCGAGGAAGAT 58.026 50.000 0.00 0.00 33.33 2.40
1741 1762 1.606189 TCGATGAGAGCGAGGAAGATG 59.394 52.381 0.00 0.00 33.33 2.90
1742 1763 1.606189 CGATGAGAGCGAGGAAGATGA 59.394 52.381 0.00 0.00 0.00 2.92
1743 1764 2.228582 CGATGAGAGCGAGGAAGATGAT 59.771 50.000 0.00 0.00 0.00 2.45
1744 1765 3.577667 GATGAGAGCGAGGAAGATGATG 58.422 50.000 0.00 0.00 0.00 3.07
1745 1766 2.659428 TGAGAGCGAGGAAGATGATGA 58.341 47.619 0.00 0.00 0.00 2.92
1746 1767 3.229293 TGAGAGCGAGGAAGATGATGAT 58.771 45.455 0.00 0.00 0.00 2.45
1747 1768 3.005578 TGAGAGCGAGGAAGATGATGATG 59.994 47.826 0.00 0.00 0.00 3.07
1748 1769 3.229293 AGAGCGAGGAAGATGATGATGA 58.771 45.455 0.00 0.00 0.00 2.92
1749 1770 3.833650 AGAGCGAGGAAGATGATGATGAT 59.166 43.478 0.00 0.00 0.00 2.45
1755 1776 5.865013 CGAGGAAGATGATGATGATGAAGAG 59.135 44.000 0.00 0.00 0.00 2.85
2448 2472 1.985116 GGAGTGGTTCGAGGAGGCT 60.985 63.158 0.00 0.00 0.00 4.58
2592 2616 2.431260 TACCAAGAACGCGCCGTC 60.431 61.111 5.73 0.51 39.99 4.79
2683 2707 2.277591 TACAAGTACCGTGCCGCCT 61.278 57.895 0.00 0.00 0.00 5.52
3206 3233 9.757227 AAGTTTATGCTGTCTAGATCTTCATAC 57.243 33.333 0.00 0.00 0.00 2.39
3209 3236 4.809193 TGCTGTCTAGATCTTCATACCCT 58.191 43.478 0.00 0.00 0.00 4.34
3211 3238 5.770663 TGCTGTCTAGATCTTCATACCCTAC 59.229 44.000 0.00 0.00 0.00 3.18
3287 3315 6.539324 TCACAAAAACGACAACAGTTTCTAG 58.461 36.000 0.00 0.00 40.49 2.43
3288 3316 6.369340 TCACAAAAACGACAACAGTTTCTAGA 59.631 34.615 0.00 0.00 40.49 2.43
3289 3317 7.065324 TCACAAAAACGACAACAGTTTCTAGAT 59.935 33.333 0.00 0.00 40.49 1.98
3290 3318 7.373441 CACAAAAACGACAACAGTTTCTAGATC 59.627 37.037 0.00 0.00 40.49 2.75
3291 3319 7.280205 ACAAAAACGACAACAGTTTCTAGATCT 59.720 33.333 0.00 0.00 40.49 2.75
3292 3320 7.787725 AAAACGACAACAGTTTCTAGATCTT 57.212 32.000 0.00 0.00 40.49 2.40
3293 3321 7.409465 AAACGACAACAGTTTCTAGATCTTC 57.591 36.000 0.00 0.00 37.23 2.87
3349 3412 5.978814 TCTGCCTATCTTGGAGTAGTTTTC 58.021 41.667 0.00 0.00 0.00 2.29
3401 3464 2.512692 TCCACATGCATTGTAGGCTT 57.487 45.000 0.00 0.00 36.57 4.35
3428 3491 1.115467 AGAAGGCTGCTATGCGTAGT 58.885 50.000 14.37 0.00 0.00 2.73
3455 3518 4.088638 CGATTAGCACGGAATAGTTCGATG 59.911 45.833 0.00 0.00 0.00 3.84
3464 3527 3.248602 GGAATAGTTCGATGCATGACCAC 59.751 47.826 2.46 0.00 0.00 4.16
3479 3542 5.508153 GCATGACCACGAGAGACTTGTATAT 60.508 44.000 0.00 0.00 0.00 0.86
3503 3566 5.833667 TGAAGGATGGATCTTATACGACACT 59.166 40.000 0.00 0.00 0.00 3.55
3572 3635 5.295292 TCTCCAAAGATCATTCGAAGCATTC 59.705 40.000 3.35 0.00 43.09 2.67
3593 3656 5.283457 TCTTCCTAAAGGCTTATGCTCTC 57.717 43.478 0.00 0.00 39.59 3.20
3707 3770 4.210331 GGCAAGTAAGAACCATCCATCAT 58.790 43.478 0.00 0.00 0.00 2.45
3724 3787 4.277672 CCATCATCGCTTCTCATTTTCCAT 59.722 41.667 0.00 0.00 0.00 3.41
3755 3818 6.690098 GTGTTCATCATTTGTGCTAATAGCTG 59.310 38.462 13.88 3.09 42.97 4.24
3756 3819 6.375174 TGTTCATCATTTGTGCTAATAGCTGT 59.625 34.615 13.88 0.00 42.97 4.40
3757 3820 7.094248 TGTTCATCATTTGTGCTAATAGCTGTT 60.094 33.333 13.88 0.04 42.97 3.16
3803 3866 6.160992 ACAATATGGGGAGCATATATGTGGAT 59.839 38.462 14.14 0.00 0.00 3.41
4034 4097 3.018598 AGTGATCTCAATATGGCGACG 57.981 47.619 0.00 0.00 0.00 5.12
4093 4156 1.670406 CAGCTGGTGAGTCCACTGC 60.670 63.158 5.57 5.31 41.93 4.40
4142 4215 4.464951 TGAATCTTCTTGATGGCTTTGCAT 59.535 37.500 0.00 0.00 35.21 3.96
4177 4250 4.591202 CACAAACTTTACAGCAGTGTCAG 58.409 43.478 0.00 0.00 38.19 3.51
4188 4261 1.401552 GCAGTGTCAGCTTTCAACACA 59.598 47.619 16.41 0.00 44.46 3.72
4240 4313 9.462174 TTGCATTCTGTTAAGTTTAGAACAATG 57.538 29.630 0.00 0.00 35.24 2.82
4258 4331 2.455674 TGCGCGGAATTCATAGCTAT 57.544 45.000 8.83 0.00 0.00 2.97
4259 4332 2.337583 TGCGCGGAATTCATAGCTATC 58.662 47.619 8.83 0.00 0.00 2.08
4260 4333 1.661112 GCGCGGAATTCATAGCTATCC 59.339 52.381 8.83 1.47 0.00 2.59
4261 4334 2.930887 GCGCGGAATTCATAGCTATCCA 60.931 50.000 8.83 0.00 0.00 3.41
4262 4335 3.525537 CGCGGAATTCATAGCTATCCAT 58.474 45.455 2.34 0.00 0.00 3.41
4263 4336 3.308053 CGCGGAATTCATAGCTATCCATG 59.692 47.826 2.34 0.00 0.00 3.66
4264 4337 4.256920 GCGGAATTCATAGCTATCCATGT 58.743 43.478 2.34 0.00 0.00 3.21
4265 4338 5.419542 GCGGAATTCATAGCTATCCATGTA 58.580 41.667 2.34 0.00 0.00 2.29
4276 4349 9.950496 CATAGCTATCCATGTATCTTAAGGTTT 57.050 33.333 2.34 0.00 0.00 3.27
4384 4463 6.218019 TGAAGAGTTTTTCAATGGCTTGATG 58.782 36.000 1.23 0.00 40.95 3.07
4385 4464 6.040729 TGAAGAGTTTTTCAATGGCTTGATGA 59.959 34.615 1.23 0.00 40.95 2.92
4386 4465 6.600882 AGAGTTTTTCAATGGCTTGATGAT 57.399 33.333 1.23 0.00 40.95 2.45
4397 4476 4.746729 TGGCTTGATGATAACATGTTTGC 58.253 39.130 17.78 9.72 36.82 3.68
4423 4503 0.613260 CCCCAGTTCTGATGGACGAA 59.387 55.000 1.00 0.00 40.51 3.85
4456 4536 3.532155 GCGATCGGGGAGCTGACT 61.532 66.667 18.30 0.00 0.00 3.41
4459 4539 1.739049 GATCGGGGAGCTGACTCAG 59.261 63.158 1.21 1.21 45.42 3.35
4519 4599 4.821589 GCGGCCTTCCAGGACTCG 62.822 72.222 0.00 0.00 42.96 4.18
4616 4696 1.981495 AGCTCTACAACAAGGCTTCCT 59.019 47.619 0.00 0.00 33.87 3.36
4628 4708 3.092851 GCTTCCTCCAAGGCTGATC 57.907 57.895 0.00 0.00 34.61 2.92
4629 4709 0.254178 GCTTCCTCCAAGGCTGATCA 59.746 55.000 0.00 0.00 34.61 2.92
4630 4710 1.133853 GCTTCCTCCAAGGCTGATCAT 60.134 52.381 0.00 0.00 34.61 2.45
4647 4727 2.591923 TCATCAATCCGAGAGCTAGCT 58.408 47.619 19.45 19.45 0.00 3.32
4648 4728 2.295629 TCATCAATCCGAGAGCTAGCTG 59.704 50.000 24.99 7.83 0.00 4.24
4649 4729 1.035923 TCAATCCGAGAGCTAGCTGG 58.964 55.000 24.99 17.70 0.00 4.85
4650 4730 0.033228 CAATCCGAGAGCTAGCTGGG 59.967 60.000 24.99 19.70 35.33 4.45
4651 4731 0.397816 AATCCGAGAGCTAGCTGGGT 60.398 55.000 24.99 11.16 35.51 4.51
4652 4732 0.825840 ATCCGAGAGCTAGCTGGGTC 60.826 60.000 24.99 20.43 35.51 4.46
4653 4733 1.454847 CCGAGAGCTAGCTGGGTCT 60.455 63.158 29.09 29.09 45.20 3.85
4654 4734 0.179015 CCGAGAGCTAGCTGGGTCTA 60.179 60.000 28.81 0.00 43.01 2.59
4655 4735 1.546773 CCGAGAGCTAGCTGGGTCTAT 60.547 57.143 28.81 11.07 43.01 1.98
4656 4736 1.810151 CGAGAGCTAGCTGGGTCTATC 59.190 57.143 28.81 17.76 43.01 2.08
4657 4737 2.167662 GAGAGCTAGCTGGGTCTATCC 58.832 57.143 28.81 14.92 43.01 2.59
4658 4738 1.786441 AGAGCTAGCTGGGTCTATCCT 59.214 52.381 27.87 6.46 41.48 3.24
4659 4739 1.892474 GAGCTAGCTGGGTCTATCCTG 59.108 57.143 24.99 0.00 36.25 3.86
4662 4742 2.280457 GCTGGGTCTATCCTGCGC 60.280 66.667 0.00 0.00 40.85 6.09
4663 4743 2.028190 CTGGGTCTATCCTGCGCG 59.972 66.667 0.00 0.00 36.25 6.86
4722 4808 0.541764 AAGCGATTTTGGCCCTTCCA 60.542 50.000 0.00 0.00 44.85 3.53
4737 4823 2.224621 CCTTCCACAGCAAGGAGAGAAA 60.225 50.000 0.00 0.00 42.94 2.52
4742 4828 3.571401 CCACAGCAAGGAGAGAAAAATGT 59.429 43.478 0.00 0.00 0.00 2.71
4789 4880 1.202268 GGACGGACCGATGAGTGTAAG 60.202 57.143 23.38 0.00 0.00 2.34
4791 4882 0.866061 CGGACCGATGAGTGTAAGCG 60.866 60.000 8.64 0.00 0.00 4.68
4876 4967 2.641815 AGGTTGATGAGAGAGCTTGGTT 59.358 45.455 0.00 0.00 0.00 3.67
4877 4968 2.746362 GGTTGATGAGAGAGCTTGGTTG 59.254 50.000 0.00 0.00 0.00 3.77
4878 4969 2.105006 TGATGAGAGAGCTTGGTTGC 57.895 50.000 0.00 0.00 0.00 4.17
4919 5010 1.339610 AGCAAAGCGTGTAAATGGCAA 59.660 42.857 0.00 0.00 0.00 4.52
4920 5011 2.131183 GCAAAGCGTGTAAATGGCAAA 58.869 42.857 0.00 0.00 0.00 3.68
4921 5012 2.541762 GCAAAGCGTGTAAATGGCAAAA 59.458 40.909 0.00 0.00 0.00 2.44
4922 5013 3.186205 GCAAAGCGTGTAAATGGCAAAAT 59.814 39.130 0.00 0.00 0.00 1.82
4923 5014 4.700332 CAAAGCGTGTAAATGGCAAAATG 58.300 39.130 0.00 0.00 0.00 2.32
4924 5015 2.958213 AGCGTGTAAATGGCAAAATGG 58.042 42.857 0.00 0.00 0.00 3.16
4925 5016 1.393196 GCGTGTAAATGGCAAAATGGC 59.607 47.619 0.00 0.00 44.03 4.40
4962 5058 4.698780 TGTACTGTATACGTCAGCAAGACT 59.301 41.667 0.00 0.00 45.32 3.24
4980 5077 0.264955 CTAGGGGCTCCAGGGAACTA 59.735 60.000 4.79 0.00 40.21 2.24
4981 5078 0.949582 TAGGGGCTCCAGGGAACTAT 59.050 55.000 4.79 0.00 40.21 2.12
5009 5106 5.413833 GGTCTGATGAGAGCTGAATGAAAAA 59.586 40.000 3.96 0.00 42.50 1.94
5035 5132 2.281070 AGGGCTGCGACACAACAG 60.281 61.111 0.00 0.00 36.96 3.16
5055 5162 0.106015 AACAGAACAGGCTGCCCTTT 60.106 50.000 16.57 8.71 40.33 3.11
5093 5200 0.679002 GGCAGGCTCATGCTTTCTCA 60.679 55.000 6.48 0.00 45.75 3.27
5107 5214 5.388654 TGCTTTCTCATTCTTTTTCCTCCT 58.611 37.500 0.00 0.00 0.00 3.69
5211 5321 1.073199 CTTTTCCACGACCCAGCCT 59.927 57.895 0.00 0.00 0.00 4.58
5238 5356 1.034838 TTGCTTGGTTGGTTGTCGCT 61.035 50.000 0.00 0.00 0.00 4.93
5294 5439 1.767759 CCACCCATCTGTTCCATTCC 58.232 55.000 0.00 0.00 0.00 3.01
5295 5440 1.005805 CCACCCATCTGTTCCATTCCA 59.994 52.381 0.00 0.00 0.00 3.53
5296 5441 2.358510 CCACCCATCTGTTCCATTCCAT 60.359 50.000 0.00 0.00 0.00 3.41
5297 5442 3.368248 CACCCATCTGTTCCATTCCATT 58.632 45.455 0.00 0.00 0.00 3.16
5298 5443 3.382546 CACCCATCTGTTCCATTCCATTC 59.617 47.826 0.00 0.00 0.00 2.67
5339 5484 4.263727 TGGCTTTTCTTATTCTGCTACCCA 60.264 41.667 0.00 0.00 0.00 4.51
5340 5485 4.336713 GGCTTTTCTTATTCTGCTACCCAG 59.663 45.833 0.00 0.00 43.17 4.45
5384 5529 3.742369 TCGTCTTCATAAAAACCACGACC 59.258 43.478 0.00 0.00 30.28 4.79
5389 5534 5.765677 TCTTCATAAAAACCACGACCATCAA 59.234 36.000 0.00 0.00 0.00 2.57
5401 5546 3.243068 ACGACCATCAACTGTTTTTGCTC 60.243 43.478 0.00 0.00 0.00 4.26
5406 5551 4.687483 CCATCAACTGTTTTTGCTCCATTC 59.313 41.667 0.00 0.00 0.00 2.67
5412 5557 4.279420 ACTGTTTTTGCTCCATTCCTTCTC 59.721 41.667 0.00 0.00 0.00 2.87
5423 5568 6.631314 GCTCCATTCCTTCTCTTCTCAACATA 60.631 42.308 0.00 0.00 0.00 2.29
5432 5577 8.449397 CCTTCTCTTCTCAACATATTTGTCAAG 58.551 37.037 0.00 0.00 34.06 3.02
5442 5587 9.809096 TCAACATATTTGTCAAGCTTGTTTTTA 57.191 25.926 25.19 12.41 34.06 1.52
5505 5691 4.342359 TGGGTAGAGACTACTCCTTTGTC 58.658 47.826 6.38 0.00 43.53 3.18
5516 5702 5.711976 ACTACTCCTTTGTCATTGATTTGGG 59.288 40.000 0.00 0.00 0.00 4.12
5521 5707 0.897401 TGTCATTGATTTGGGCCGCA 60.897 50.000 0.00 0.00 0.00 5.69
5523 5709 0.246086 TCATTGATTTGGGCCGCAAC 59.754 50.000 6.19 0.00 0.00 4.17
5524 5710 0.037512 CATTGATTTGGGCCGCAACA 60.038 50.000 6.19 0.79 0.00 3.33
5525 5711 0.683973 ATTGATTTGGGCCGCAACAA 59.316 45.000 6.19 8.65 0.00 2.83
5526 5712 0.683973 TTGATTTGGGCCGCAACAAT 59.316 45.000 6.19 0.00 0.00 2.71
5527 5713 0.246086 TGATTTGGGCCGCAACAATC 59.754 50.000 6.19 8.34 0.00 2.67
5528 5714 0.460109 GATTTGGGCCGCAACAATCC 60.460 55.000 6.19 0.00 0.00 3.01
5529 5715 2.224495 ATTTGGGCCGCAACAATCCG 62.224 55.000 6.19 0.00 0.00 4.18
5530 5716 4.652131 TGGGCCGCAACAATCCGT 62.652 61.111 0.00 0.00 0.00 4.69
5531 5717 3.810896 GGGCCGCAACAATCCGTC 61.811 66.667 0.00 0.00 0.00 4.79
5532 5718 3.053291 GGCCGCAACAATCCGTCA 61.053 61.111 0.00 0.00 0.00 4.35
5533 5719 2.622011 GGCCGCAACAATCCGTCAA 61.622 57.895 0.00 0.00 0.00 3.18
5534 5720 1.506262 GCCGCAACAATCCGTCAAT 59.494 52.632 0.00 0.00 0.00 2.57
5535 5721 0.523335 GCCGCAACAATCCGTCAATC 60.523 55.000 0.00 0.00 0.00 2.67
5536 5722 0.098728 CCGCAACAATCCGTCAATCC 59.901 55.000 0.00 0.00 0.00 3.01
5537 5723 0.098728 CGCAACAATCCGTCAATCCC 59.901 55.000 0.00 0.00 0.00 3.85
5538 5724 0.098728 GCAACAATCCGTCAATCCCG 59.901 55.000 0.00 0.00 0.00 5.14
5539 5725 1.448985 CAACAATCCGTCAATCCCGT 58.551 50.000 0.00 0.00 0.00 5.28
5540 5726 2.623535 CAACAATCCGTCAATCCCGTA 58.376 47.619 0.00 0.00 0.00 4.02
5541 5727 3.004171 CAACAATCCGTCAATCCCGTAA 58.996 45.455 0.00 0.00 0.00 3.18
5542 5728 3.337694 ACAATCCGTCAATCCCGTAAA 57.662 42.857 0.00 0.00 0.00 2.01
5543 5729 3.677190 ACAATCCGTCAATCCCGTAAAA 58.323 40.909 0.00 0.00 0.00 1.52
5544 5730 4.266714 ACAATCCGTCAATCCCGTAAAAT 58.733 39.130 0.00 0.00 0.00 1.82
5545 5731 4.703093 ACAATCCGTCAATCCCGTAAAATT 59.297 37.500 0.00 0.00 0.00 1.82
5546 5732 5.184287 ACAATCCGTCAATCCCGTAAAATTT 59.816 36.000 0.00 0.00 0.00 1.82
5547 5733 4.688511 TCCGTCAATCCCGTAAAATTTG 57.311 40.909 0.00 0.00 0.00 2.32
5548 5734 3.119779 TCCGTCAATCCCGTAAAATTTGC 60.120 43.478 0.00 0.00 0.00 3.68
5641 5856 3.363844 GAGTCGCCACTCTCCAGGC 62.364 68.421 3.99 0.00 45.20 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 9 1.351017 CTAGAAAAGTGCTGGACCCCA 59.649 52.381 0.00 0.00 0.00 4.96
16 18 3.601443 TCCTCTCAGCTAGAAAAGTGC 57.399 47.619 0.00 0.00 32.46 4.40
23 25 4.744795 GGATTGTTTCCTCTCAGCTAGA 57.255 45.455 0.00 0.00 41.78 2.43
37 39 2.541466 AGAAGGAGTCGGAGGATTGTT 58.459 47.619 0.00 0.00 0.00 2.83
46 49 0.601558 TCGGTCAAAGAAGGAGTCGG 59.398 55.000 0.00 0.00 0.00 4.79
53 56 5.220416 GGTCGAATATTGTCGGTCAAAGAAG 60.220 44.000 0.00 0.00 41.43 2.85
93 97 3.964031 ACATGACCTCATAAGACTCCCTC 59.036 47.826 0.00 0.00 34.26 4.30
100 104 4.271807 AGGGAGACATGACCTCATAAGA 57.728 45.455 17.13 0.00 34.26 2.10
111 115 5.720371 AAGATAGATTCGAGGGAGACATG 57.280 43.478 0.00 0.00 0.00 3.21
121 126 6.415573 TCCAGATCCGATAAGATAGATTCGA 58.584 40.000 0.00 0.00 33.59 3.71
123 128 7.639113 ACTCCAGATCCGATAAGATAGATTC 57.361 40.000 0.00 0.00 0.00 2.52
133 138 3.637229 GGAAGACAACTCCAGATCCGATA 59.363 47.826 0.00 0.00 0.00 2.92
137 142 3.432890 GGATGGAAGACAACTCCAGATCC 60.433 52.174 0.00 0.00 36.92 3.36
182 191 5.296780 ACAATGCTCTGGAAACATATAACCG 59.703 40.000 0.00 0.00 41.51 4.44
239 251 3.594603 ATTGTTGACGTAGGAGTCTGG 57.405 47.619 0.00 0.00 41.47 3.86
261 273 1.339610 CACCATCGCAACTGGGAAAAA 59.660 47.619 0.17 0.00 40.44 1.94
293 305 2.950309 GTGAAGCTCGGTACCATCTCTA 59.050 50.000 13.54 0.00 0.00 2.43
327 339 0.030504 CTGCTCTCGCACTCATCGAT 59.969 55.000 0.00 0.00 42.25 3.59
331 343 0.175302 CTTCCTGCTCTCGCACTCAT 59.825 55.000 0.00 0.00 42.25 2.90
339 351 1.403514 CGGTGTCTTCTTCCTGCTCTC 60.404 57.143 0.00 0.00 0.00 3.20
340 352 0.605589 CGGTGTCTTCTTCCTGCTCT 59.394 55.000 0.00 0.00 0.00 4.09
343 355 2.450609 TAACGGTGTCTTCTTCCTGC 57.549 50.000 0.00 0.00 0.00 4.85
344 356 4.994852 TGAATTAACGGTGTCTTCTTCCTG 59.005 41.667 0.00 0.00 0.00 3.86
347 359 7.647907 TTAGTGAATTAACGGTGTCTTCTTC 57.352 36.000 0.00 0.00 0.00 2.87
349 361 7.439381 TCTTTAGTGAATTAACGGTGTCTTCT 58.561 34.615 0.00 0.00 0.00 2.85
353 365 6.426025 ACCTTCTTTAGTGAATTAACGGTGTC 59.574 38.462 0.00 0.00 0.00 3.67
354 366 6.293698 ACCTTCTTTAGTGAATTAACGGTGT 58.706 36.000 0.00 0.00 0.00 4.16
355 367 6.796705 ACCTTCTTTAGTGAATTAACGGTG 57.203 37.500 0.00 0.00 0.00 4.94
356 368 6.769341 ACAACCTTCTTTAGTGAATTAACGGT 59.231 34.615 0.00 0.00 0.00 4.83
357 369 7.075741 CACAACCTTCTTTAGTGAATTAACGG 58.924 38.462 0.00 0.00 32.14 4.44
368 380 5.239525 CCTGAAACTCCACAACCTTCTTTAG 59.760 44.000 0.00 0.00 0.00 1.85
369 381 5.130350 CCTGAAACTCCACAACCTTCTTTA 58.870 41.667 0.00 0.00 0.00 1.85
372 384 2.509964 ACCTGAAACTCCACAACCTTCT 59.490 45.455 0.00 0.00 0.00 2.85
378 390 8.698973 TCATATAAAAACCTGAAACTCCACAA 57.301 30.769 0.00 0.00 0.00 3.33
383 395 7.706607 GGCCATTCATATAAAAACCTGAAACTC 59.293 37.037 0.00 0.00 31.92 3.01
385 397 7.555965 AGGCCATTCATATAAAAACCTGAAAC 58.444 34.615 5.01 0.00 31.92 2.78
421 434 7.491682 AGGCAAAAATGCATATTAAAGTCGAT 58.508 30.769 0.00 0.00 36.33 3.59
602 617 4.560136 TGCTTTGCTTGAAATGTTCGTA 57.440 36.364 0.00 0.00 0.00 3.43
652 669 2.676076 GCTGCACGAACAAAATTGGAT 58.324 42.857 0.00 0.00 0.00 3.41
653 670 2.132740 GCTGCACGAACAAAATTGGA 57.867 45.000 0.00 0.00 0.00 3.53
698 719 3.075641 GAGTCGGGTGGGTCTCCC 61.076 72.222 0.00 0.00 45.71 4.30
699 720 2.037527 AGAGTCGGGTGGGTCTCC 59.962 66.667 0.00 0.00 0.00 3.71
701 722 2.361357 CGAGAGTCGGGTGGGTCT 60.361 66.667 0.00 0.00 36.00 3.85
1740 1761 5.011840 GGTCTCATCCTCTTCATCATCATCA 59.988 44.000 0.00 0.00 0.00 3.07
1741 1762 5.011840 TGGTCTCATCCTCTTCATCATCATC 59.988 44.000 0.00 0.00 0.00 2.92
1742 1763 4.906060 TGGTCTCATCCTCTTCATCATCAT 59.094 41.667 0.00 0.00 0.00 2.45
1743 1764 4.292643 TGGTCTCATCCTCTTCATCATCA 58.707 43.478 0.00 0.00 0.00 3.07
1744 1765 4.952071 TGGTCTCATCCTCTTCATCATC 57.048 45.455 0.00 0.00 0.00 2.92
1745 1766 5.368816 TCATTGGTCTCATCCTCTTCATCAT 59.631 40.000 0.00 0.00 0.00 2.45
1746 1767 4.718276 TCATTGGTCTCATCCTCTTCATCA 59.282 41.667 0.00 0.00 0.00 3.07
1747 1768 5.055812 GTCATTGGTCTCATCCTCTTCATC 58.944 45.833 0.00 0.00 0.00 2.92
1748 1769 4.720773 AGTCATTGGTCTCATCCTCTTCAT 59.279 41.667 0.00 0.00 0.00 2.57
1749 1770 4.099633 AGTCATTGGTCTCATCCTCTTCA 58.900 43.478 0.00 0.00 0.00 3.02
1755 1776 3.012518 CCACAAGTCATTGGTCTCATCC 58.987 50.000 0.00 0.00 40.97 3.51
2337 2361 1.503542 CAACTCTGCGCATTCCCAC 59.496 57.895 12.24 0.00 0.00 4.61
2448 2472 4.015406 ACATGGCCTTCCGCGACA 62.015 61.111 8.23 0.00 38.94 4.35
2487 2511 3.022287 CACTTGAACTTGGCGCGT 58.978 55.556 8.43 0.00 0.00 6.01
2592 2616 0.970937 TCTCCTTCCCCACGCAGTAG 60.971 60.000 0.00 0.00 41.61 2.57
2683 2707 0.473694 TTGTCCTCCTCCAGCAAGGA 60.474 55.000 2.92 2.92 46.75 3.36
3206 3233 9.391006 TCTTATGTGTAAAATAAAGCAGTAGGG 57.609 33.333 0.00 0.00 0.00 3.53
3209 3236 9.443323 TGCTCTTATGTGTAAAATAAAGCAGTA 57.557 29.630 0.00 0.00 36.32 2.74
3211 3238 7.912250 CCTGCTCTTATGTGTAAAATAAAGCAG 59.088 37.037 19.67 19.67 45.42 4.24
3308 3336 4.928615 GGCAGATACTACTCGTATACTCGT 59.071 45.833 0.56 0.57 38.90 4.18
3310 3338 8.199449 AGATAGGCAGATACTACTCGTATACTC 58.801 40.741 0.56 0.00 38.90 2.59
3311 3339 8.081517 AGATAGGCAGATACTACTCGTATACT 57.918 38.462 0.56 0.00 38.90 2.12
3312 3340 8.605746 CAAGATAGGCAGATACTACTCGTATAC 58.394 40.741 0.00 0.00 38.90 1.47
3313 3341 7.769507 CCAAGATAGGCAGATACTACTCGTATA 59.230 40.741 0.00 0.00 38.90 1.47
3314 3342 6.600032 CCAAGATAGGCAGATACTACTCGTAT 59.400 42.308 0.00 0.00 41.46 3.06
3315 3343 5.938710 CCAAGATAGGCAGATACTACTCGTA 59.061 44.000 0.00 0.00 0.00 3.43
3316 3344 4.762765 CCAAGATAGGCAGATACTACTCGT 59.237 45.833 0.00 0.00 0.00 4.18
3317 3345 5.004448 TCCAAGATAGGCAGATACTACTCG 58.996 45.833 0.00 0.00 0.00 4.18
3318 3346 6.007703 ACTCCAAGATAGGCAGATACTACTC 58.992 44.000 0.00 0.00 0.00 2.59
3319 3347 5.959512 ACTCCAAGATAGGCAGATACTACT 58.040 41.667 0.00 0.00 0.00 2.57
3320 3348 6.943718 ACTACTCCAAGATAGGCAGATACTAC 59.056 42.308 0.00 0.00 0.00 2.73
3321 3349 7.092748 ACTACTCCAAGATAGGCAGATACTA 57.907 40.000 0.00 0.00 0.00 1.82
3322 3350 5.959512 ACTACTCCAAGATAGGCAGATACT 58.040 41.667 0.00 0.00 0.00 2.12
3323 3351 6.658188 AACTACTCCAAGATAGGCAGATAC 57.342 41.667 0.00 0.00 0.00 2.24
3374 3437 4.669206 ACAATGCATGTGGAAAACAGAA 57.331 36.364 0.00 0.00 43.64 3.02
3380 3443 2.806434 AGCCTACAATGCATGTGGAAA 58.194 42.857 0.00 0.00 42.76 3.13
3401 3464 3.879295 GCATAGCAGCCTTCTGACAATTA 59.121 43.478 0.00 0.00 42.95 1.40
3455 3518 1.337260 ACAAGTCTCTCGTGGTCATGC 60.337 52.381 0.00 0.00 0.00 4.06
3464 3527 6.207614 TCCATCCTTCATATACAAGTCTCTCG 59.792 42.308 0.00 0.00 0.00 4.04
3479 3542 5.833667 AGTGTCGTATAAGATCCATCCTTCA 59.166 40.000 0.00 0.00 0.00 3.02
3503 3566 2.896854 GCTTCATCGCGATGCCCA 60.897 61.111 37.84 24.48 38.54 5.36
3572 3635 4.054671 CGAGAGCATAAGCCTTTAGGAAG 58.945 47.826 0.00 0.00 43.56 3.46
3593 3656 0.378962 CGTCAAGGCTAGAGTCTCCG 59.621 60.000 0.00 0.00 0.00 4.63
3707 3770 3.673902 TGTCATGGAAAATGAGAAGCGA 58.326 40.909 0.00 0.00 0.00 4.93
3724 3787 4.338964 AGCACAAATGATGAACACTTGTCA 59.661 37.500 0.00 0.00 43.93 3.58
3755 3818 2.134789 ATGCCTGGAGGATGTCAAAC 57.865 50.000 0.00 0.00 37.39 2.93
3756 3819 2.575735 TGTATGCCTGGAGGATGTCAAA 59.424 45.455 0.00 0.00 37.39 2.69
3757 3820 2.195727 TGTATGCCTGGAGGATGTCAA 58.804 47.619 0.00 0.00 37.39 3.18
3803 3866 1.820519 GCCTCATCCAGCAAATCACAA 59.179 47.619 0.00 0.00 0.00 3.33
4093 4156 2.292569 GCCAGCCATCATATGTTCAGTG 59.707 50.000 1.90 0.00 0.00 3.66
4142 4215 9.891828 CTGTAAAGTTTGTGCACATTAGAATAA 57.108 29.630 22.39 7.10 0.00 1.40
4177 4250 6.343226 TGTTTAGCATTTTGTGTTGAAAGC 57.657 33.333 0.00 0.00 0.00 3.51
4240 4313 1.661112 GGATAGCTATGAATTCCGCGC 59.339 52.381 11.94 0.00 0.00 6.86
4265 4338 9.401058 CTCCAGACATTAATGAAACCTTAAGAT 57.599 33.333 22.16 0.00 0.00 2.40
4276 4349 6.546034 TCACTATCGTCTCCAGACATTAATGA 59.454 38.462 22.16 0.00 44.99 2.57
4341 4420 6.451393 TCTTCAGACTTTAGCTCTGAACTTC 58.549 40.000 10.40 0.00 45.64 3.01
4343 4422 5.538433 ACTCTTCAGACTTTAGCTCTGAACT 59.462 40.000 10.40 0.00 45.64 3.01
4344 4423 5.778862 ACTCTTCAGACTTTAGCTCTGAAC 58.221 41.667 10.40 0.00 45.64 3.18
4384 4463 4.202050 GGGGATCACAGCAAACATGTTATC 60.202 45.833 12.39 8.93 32.79 1.75
4385 4464 3.701040 GGGGATCACAGCAAACATGTTAT 59.299 43.478 12.39 0.00 0.00 1.89
4386 4465 3.088532 GGGGATCACAGCAAACATGTTA 58.911 45.455 12.39 0.00 0.00 2.41
4397 4476 2.421107 CCATCAGAACTGGGGATCACAG 60.421 54.545 13.32 13.32 41.64 3.66
4423 4503 0.836400 TCGCCTCCTCCTCCTTGTTT 60.836 55.000 0.00 0.00 0.00 2.83
4456 4536 1.968017 CTTGAAAGCCAGCGCCTGA 60.968 57.895 2.29 0.00 32.44 3.86
4577 4657 2.047844 CAGGGTGTCTCCGTGCTG 60.048 66.667 0.98 0.00 43.61 4.41
4616 4696 2.486013 CGGATTGATGATCAGCCTTGGA 60.486 50.000 8.78 0.00 36.43 3.53
4627 4707 2.295629 CAGCTAGCTCTCGGATTGATGA 59.704 50.000 16.15 0.00 0.00 2.92
4628 4708 2.609984 CCAGCTAGCTCTCGGATTGATG 60.610 54.545 16.15 0.00 0.00 3.07
4629 4709 1.617850 CCAGCTAGCTCTCGGATTGAT 59.382 52.381 16.15 0.00 0.00 2.57
4630 4710 1.035923 CCAGCTAGCTCTCGGATTGA 58.964 55.000 16.15 0.00 0.00 2.57
4647 4727 2.758327 ACGCGCAGGATAGACCCA 60.758 61.111 5.73 0.00 40.05 4.51
4648 4728 2.279517 CACGCGCAGGATAGACCC 60.280 66.667 5.73 0.00 40.05 4.46
4649 4729 2.962253 GCACGCGCAGGATAGACC 60.962 66.667 5.73 0.00 38.36 3.85
4650 4730 3.323136 CGCACGCGCAGGATAGAC 61.323 66.667 5.73 0.00 38.40 2.59
4651 4731 3.514362 TCGCACGCGCAGGATAGA 61.514 61.111 5.73 0.00 38.40 1.98
4652 4732 3.323136 GTCGCACGCGCAGGATAG 61.323 66.667 5.73 0.00 38.40 2.08
4653 4733 4.865761 GGTCGCACGCGCAGGATA 62.866 66.667 5.73 0.00 38.40 2.59
4662 4742 3.179265 GACGATGGTGGTCGCACG 61.179 66.667 0.00 0.00 45.12 5.34
4705 4785 3.693411 TGGAAGGGCCAAAATCGC 58.307 55.556 6.18 0.00 45.87 4.58
4722 4808 5.869579 TCTACATTTTTCTCTCCTTGCTGT 58.130 37.500 0.00 0.00 0.00 4.40
4737 4823 1.144057 CCCGCCTCGCTCTACATTT 59.856 57.895 0.00 0.00 0.00 2.32
4742 4828 4.815108 TCTGCCCGCCTCGCTCTA 62.815 66.667 0.00 0.00 0.00 2.43
4782 4873 2.933495 TCGTATGCTTCGCTTACACT 57.067 45.000 10.97 0.00 38.52 3.55
4801 4892 2.486504 CTCGCCGTTGCATTGCAT 59.513 55.556 12.95 0.00 38.76 3.96
4802 4893 3.736100 CCTCGCCGTTGCATTGCA 61.736 61.111 7.38 7.38 37.32 4.08
4804 4895 4.817063 CGCCTCGCCGTTGCATTG 62.817 66.667 0.00 0.00 37.32 2.82
4876 4967 8.572185 TGCTATTCTTACATTTTTGTTACAGCA 58.428 29.630 0.00 0.00 0.00 4.41
4877 4968 8.964420 TGCTATTCTTACATTTTTGTTACAGC 57.036 30.769 0.00 0.00 0.00 4.40
4920 5011 7.148086 ACAGTACATACGAAAAATGATGCCATT 60.148 33.333 0.00 0.00 44.38 3.16
4921 5012 6.318648 ACAGTACATACGAAAAATGATGCCAT 59.681 34.615 0.00 0.00 33.66 4.40
4922 5013 5.645929 ACAGTACATACGAAAAATGATGCCA 59.354 36.000 0.00 0.00 0.00 4.92
4923 5014 6.119144 ACAGTACATACGAAAAATGATGCC 57.881 37.500 0.00 0.00 0.00 4.40
4924 5015 9.793245 GTATACAGTACATACGAAAAATGATGC 57.207 33.333 0.00 0.00 0.00 3.91
4951 5047 0.176910 GAGCCCCTAGTCTTGCTGAC 59.823 60.000 0.00 2.86 45.67 3.51
4962 5058 0.949582 ATAGTTCCCTGGAGCCCCTA 59.050 55.000 0.00 0.00 0.00 3.53
4980 5077 2.836372 TCAGCTCTCATCAGACCAACAT 59.164 45.455 0.00 0.00 0.00 2.71
4981 5078 2.250924 TCAGCTCTCATCAGACCAACA 58.749 47.619 0.00 0.00 0.00 3.33
5009 5106 1.610673 TCGCAGCCCTCTTCCTCTT 60.611 57.895 0.00 0.00 0.00 2.85
5035 5132 0.538287 AAGGGCAGCCTGTTCTGTTC 60.538 55.000 12.43 0.00 36.49 3.18
5055 5162 0.462581 CTTGCCGGCTGCTCTGATTA 60.463 55.000 29.70 0.00 42.00 1.75
5078 5185 4.715527 AAAGAATGAGAAAGCATGAGCC 57.284 40.909 0.00 0.00 43.56 4.70
5211 5321 4.762765 ACAACCAACCAAGCAAATCGTATA 59.237 37.500 0.00 0.00 0.00 1.47
5294 5439 5.278660 CCAGAAAACTGTCTCTTTGGGAATG 60.279 44.000 0.00 0.00 0.00 2.67
5295 5440 4.829492 CCAGAAAACTGTCTCTTTGGGAAT 59.171 41.667 0.00 0.00 0.00 3.01
5296 5441 4.207165 CCAGAAAACTGTCTCTTTGGGAA 58.793 43.478 0.00 0.00 0.00 3.97
5297 5442 3.820557 CCAGAAAACTGTCTCTTTGGGA 58.179 45.455 0.00 0.00 0.00 4.37
5298 5443 2.294512 GCCAGAAAACTGTCTCTTTGGG 59.705 50.000 0.00 0.00 0.00 4.12
5384 5529 4.687483 GGAATGGAGCAAAAACAGTTGATG 59.313 41.667 0.00 0.00 0.00 3.07
5389 5534 4.218312 AGAAGGAATGGAGCAAAAACAGT 58.782 39.130 0.00 0.00 0.00 3.55
5401 5546 8.404000 CAAATATGTTGAGAAGAGAAGGAATGG 58.596 37.037 0.00 0.00 0.00 3.16
5406 5551 7.912056 TGACAAATATGTTGAGAAGAGAAGG 57.088 36.000 5.11 0.00 40.74 3.46
5412 5557 7.365741 ACAAGCTTGACAAATATGTTGAGAAG 58.634 34.615 32.50 0.00 40.74 2.85
5423 5568 6.756542 GTGGAGTAAAAACAAGCTTGACAAAT 59.243 34.615 32.50 15.73 0.00 2.32
5432 5577 6.037830 TGACTTACAGTGGAGTAAAAACAAGC 59.962 38.462 0.00 0.00 33.89 4.01
5442 5587 5.012046 TGTGATTGATGACTTACAGTGGAGT 59.988 40.000 0.00 0.00 0.00 3.85
5505 5691 0.037512 TGTTGCGGCCCAAATCAATG 60.038 50.000 8.06 0.00 34.68 2.82
5516 5702 0.523335 GATTGACGGATTGTTGCGGC 60.523 55.000 0.00 0.00 46.34 6.53
5521 5707 3.337694 TTACGGGATTGACGGATTGTT 57.662 42.857 0.00 0.00 35.23 2.83
5523 5709 4.893424 ATTTTACGGGATTGACGGATTG 57.107 40.909 0.00 0.00 35.23 2.67
5524 5710 5.646606 CAAATTTTACGGGATTGACGGATT 58.353 37.500 0.00 0.00 35.23 3.01
5525 5711 4.439563 GCAAATTTTACGGGATTGACGGAT 60.440 41.667 0.00 0.00 35.23 4.18
5526 5712 3.119779 GCAAATTTTACGGGATTGACGGA 60.120 43.478 0.00 0.00 35.23 4.69
5527 5713 3.175929 GCAAATTTTACGGGATTGACGG 58.824 45.455 0.00 0.00 35.23 4.79
5528 5714 3.175929 GGCAAATTTTACGGGATTGACG 58.824 45.455 0.00 0.00 37.36 4.35
5529 5715 3.517602 GGGCAAATTTTACGGGATTGAC 58.482 45.455 0.00 0.00 0.00 3.18
5530 5716 2.164624 CGGGCAAATTTTACGGGATTGA 59.835 45.455 0.00 0.00 0.00 2.57
5531 5717 2.535331 CGGGCAAATTTTACGGGATTG 58.465 47.619 0.00 0.00 0.00 2.67
5532 5718 1.134936 GCGGGCAAATTTTACGGGATT 60.135 47.619 7.69 0.00 0.00 3.01
5533 5719 0.458260 GCGGGCAAATTTTACGGGAT 59.542 50.000 7.69 0.00 0.00 3.85
5534 5720 0.894184 TGCGGGCAAATTTTACGGGA 60.894 50.000 7.69 0.00 0.00 5.14
5535 5721 0.038159 TTGCGGGCAAATTTTACGGG 60.038 50.000 3.16 0.00 32.44 5.28
5536 5722 1.784525 TTTGCGGGCAAATTTTACGG 58.215 45.000 14.35 1.54 40.51 4.02
5537 5723 2.797719 AGTTTTGCGGGCAAATTTTACG 59.202 40.909 18.43 0.00 44.14 3.18
5538 5724 4.055360 AGAGTTTTGCGGGCAAATTTTAC 58.945 39.130 18.43 13.50 44.14 2.01
5539 5725 4.329462 AGAGTTTTGCGGGCAAATTTTA 57.671 36.364 18.43 2.19 44.14 1.52
5540 5726 3.192541 AGAGTTTTGCGGGCAAATTTT 57.807 38.095 18.43 8.13 44.14 1.82
5541 5727 2.908688 AGAGTTTTGCGGGCAAATTT 57.091 40.000 18.43 10.38 44.14 1.82
5542 5728 2.871633 CAAAGAGTTTTGCGGGCAAATT 59.128 40.909 18.43 10.70 44.14 1.82
5543 5729 2.482864 CAAAGAGTTTTGCGGGCAAAT 58.517 42.857 18.43 5.85 44.14 2.32
5544 5730 1.472376 CCAAAGAGTTTTGCGGGCAAA 60.472 47.619 14.35 14.35 41.87 3.68
5545 5731 0.103937 CCAAAGAGTTTTGCGGGCAA 59.896 50.000 1.21 1.21 41.87 4.52
5546 5732 1.739049 CCAAAGAGTTTTGCGGGCA 59.261 52.632 0.00 0.00 41.87 5.36
5547 5733 1.006220 CCCAAAGAGTTTTGCGGGC 60.006 57.895 0.00 0.00 41.87 6.13
5548 5734 1.006220 GCCCAAAGAGTTTTGCGGG 60.006 57.895 0.00 0.00 41.87 6.13
5584 5799 3.118592 CGGGCCTAAATCACTCTTCTTCT 60.119 47.826 0.84 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.