Multiple sequence alignment - TraesCS1A01G223100

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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 TraesCS1A01G223100 chr1A 100.000 5246 0 0 1 5246 392786949 392781704 0.000000e+00 9688.0
1 TraesCS1A01G223100 chr1A 88.679 53 5 1 3501 3553 7183445 7183394 4.390000e-06 63.9
2 TraesCS1A01G223100 chr1D 88.908 2885 176 53 1961 4751 313214489 313211655 0.000000e+00 3422.0
3 TraesCS1A01G223100 chr1D 95.978 1964 65 5 1 1957 313216484 313214528 0.000000e+00 3177.0
4 TraesCS1A01G223100 chr1D 85.015 327 19 15 4941 5246 313211369 313211052 6.600000e-79 305.0
5 TraesCS1A01G223100 chr1D 89.583 192 17 1 4757 4945 313211608 313211417 1.890000e-59 241.0
6 TraesCS1A01G223100 chr1B 95.929 1965 66 7 1 1957 423593421 423591463 0.000000e+00 3173.0
7 TraesCS1A01G223100 chr1B 88.386 2299 136 54 2471 4693 423590759 423588516 0.000000e+00 2645.0
8 TraesCS1A01G223100 chr1B 92.549 510 24 5 1961 2467 423591424 423590926 0.000000e+00 719.0
9 TraesCS1A01G223100 chr1B 83.789 475 70 6 3759 4232 587495734 587496202 1.340000e-120 444.0
10 TraesCS1A01G223100 chr1B 87.556 225 13 7 4941 5150 423588190 423587966 4.060000e-61 246.0
11 TraesCS1A01G223100 chr1B 91.160 181 9 3 4757 4930 423588432 423588252 6.790000e-59 239.0
12 TraesCS1A01G223100 chr1B 100.000 37 0 0 4715 4751 423588516 423588480 9.430000e-08 69.4
13 TraesCS1A01G223100 chr6D 82.326 1737 235 41 201 1907 16196719 16195025 0.000000e+00 1441.0
14 TraesCS1A01G223100 chr6D 81.157 605 93 14 3638 4238 16380513 16381100 2.860000e-127 466.0
15 TraesCS1A01G223100 chr6D 82.745 510 64 10 3737 4241 16191293 16190803 2.900000e-117 433.0
16 TraesCS1A01G223100 chr6D 100.000 30 0 0 1928 1957 438882349 438882378 7.340000e-04 56.5
17 TraesCS1A01G223100 chr6A 81.876 1727 236 45 204 1907 16460734 16459062 0.000000e+00 1384.0
18 TraesCS1A01G223100 chr6A 82.857 490 70 10 3759 4247 16712913 16712437 1.350000e-115 427.0
19 TraesCS1A01G223100 chr6B 84.430 1368 177 25 581 1923 27944703 27943347 0.000000e+00 1314.0
20 TraesCS1A01G223100 chr6B 81.112 1726 235 51 201 1895 28002497 28004162 0.000000e+00 1297.0
21 TraesCS1A01G223100 chr6B 83.469 490 67 11 3759 4247 28945080 28944604 1.340000e-120 444.0
22 TraesCS1A01G223100 chr6B 82.653 490 69 7 3759 4238 59301499 59301016 2.260000e-113 420.0
23 TraesCS1A01G223100 chr6B 84.043 376 51 6 3874 4247 29048037 29047669 2.320000e-93 353.0
24 TraesCS1A01G223100 chr6B 86.316 285 38 1 910 1194 27996256 27996539 5.100000e-80 309.0
25 TraesCS1A01G223100 chr6B 82.421 347 40 11 574 903 27995840 27996182 3.090000e-72 283.0
26 TraesCS1A01G223100 chr6B 80.481 374 53 15 2629 2990 28005280 28005645 8.660000e-68 268.0
27 TraesCS1A01G223100 chr6B 88.000 50 6 0 3557 3606 20707244 20707293 5.670000e-05 60.2
28 TraesCS1A01G223100 chr2B 82.270 1568 200 35 201 1737 46602134 46600614 0.000000e+00 1284.0
29 TraesCS1A01G223100 chr2B 87.940 199 24 0 2792 2990 46596230 46596032 8.780000e-58 235.0
30 TraesCS1A01G223100 chr3A 89.000 100 8 1 3503 3599 195460680 195460581 2.570000e-23 121.0
31 TraesCS1A01G223100 chr2D 85.714 105 13 2 3493 3597 577324456 577324558 5.550000e-20 110.0
32 TraesCS1A01G223100 chr2A 84.615 91 14 0 3501 3591 680084121 680084211 2.010000e-14 91.6
33 TraesCS1A01G223100 chr2A 90.769 65 2 4 3490 3552 180978885 180978947 3.370000e-12 84.2
34 TraesCS1A01G223100 chr7D 83.673 98 5 5 3503 3600 151326444 151326530 1.210000e-11 82.4
35 TraesCS1A01G223100 chr7D 92.500 40 3 0 3561 3600 569401916 569401877 2.040000e-04 58.4
36 TraesCS1A01G223100 chr5A 81.188 101 16 3 3495 3595 617257331 617257234 1.570000e-10 78.7
37 TraesCS1A01G223100 chr5B 89.362 47 5 0 3502 3548 45388524 45388570 5.670000e-05 60.2


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 TraesCS1A01G223100 chr1A 392781704 392786949 5245 True 9688.00 9688 100.000000 1 5246 1 chr1A.!!$R2 5245
1 TraesCS1A01G223100 chr1D 313211052 313216484 5432 True 1786.25 3422 89.871000 1 5246 4 chr1D.!!$R1 5245
2 TraesCS1A01G223100 chr1B 423587966 423593421 5455 True 1181.90 3173 92.596667 1 5150 6 chr1B.!!$R1 5149
3 TraesCS1A01G223100 chr6D 16190803 16196719 5916 True 937.00 1441 82.535500 201 4241 2 chr6D.!!$R1 4040
4 TraesCS1A01G223100 chr6D 16380513 16381100 587 False 466.00 466 81.157000 3638 4238 1 chr6D.!!$F1 600
5 TraesCS1A01G223100 chr6A 16459062 16460734 1672 True 1384.00 1384 81.876000 204 1907 1 chr6A.!!$R1 1703
6 TraesCS1A01G223100 chr6B 27943347 27944703 1356 True 1314.00 1314 84.430000 581 1923 1 chr6B.!!$R1 1342
7 TraesCS1A01G223100 chr6B 28002497 28005645 3148 False 782.50 1297 80.796500 201 2990 2 chr6B.!!$F3 2789
8 TraesCS1A01G223100 chr6B 27995840 27996539 699 False 296.00 309 84.368500 574 1194 2 chr6B.!!$F2 620
9 TraesCS1A01G223100 chr2B 46600614 46602134 1520 True 1284.00 1284 82.270000 201 1737 1 chr2B.!!$R2 1536

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
462 472 0.105401 ACAAAACCCCCAAATCCCGT 60.105 50.000 0.00 0.00 0.00 5.28 F
559 575 1.435515 GACTTTGTTGTTGGCGCCA 59.564 52.632 29.03 29.03 0.00 5.69 F
1740 1886 2.161410 TGATGTTGCGCATGGTAACTTC 59.839 45.455 12.75 14.05 42.12 3.01 F
2420 5531 1.065491 TGCATTACCGCTGGATTGTCT 60.065 47.619 1.50 0.00 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1778 1930 0.109458 CTTGACATGCGTGCATTGCT 60.109 50.000 10.49 0.0 33.90 3.91 R
2394 5505 2.722094 TCCAGCGGTAATGCAGAAAAT 58.278 42.857 0.00 0.0 37.31 1.82 R
3287 6754 1.228737 CCCTTCCCCGCCAGAAAAA 60.229 57.895 0.00 0.0 0.00 1.94 R
4400 7891 0.106894 AGCTTCTTATACTGCCCCGC 59.893 55.000 0.00 0.0 0.00 6.13 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
17 18 4.007457 ACGCGTGCCCTAGTTAGA 57.993 55.556 12.93 0.00 0.00 2.10
22 23 2.350580 CGCGTGCCCTAGTTAGATAGTC 60.351 54.545 0.00 0.00 0.00 2.59
211 215 1.285962 CCCACACTTCTCCCATGGATT 59.714 52.381 15.22 0.00 31.69 3.01
264 274 1.075226 AGGCGGAGGAGGAAGCATA 60.075 57.895 0.00 0.00 0.00 3.14
425 435 2.819595 CGGCACCATGTCCTTCCG 60.820 66.667 0.00 0.00 0.00 4.30
462 472 0.105401 ACAAAACCCCCAAATCCCGT 60.105 50.000 0.00 0.00 0.00 5.28
477 487 3.076278 CGTACCCCCGCACCCTAA 61.076 66.667 0.00 0.00 0.00 2.69
519 535 4.463879 CCCCCTGCTGCGACTGAG 62.464 72.222 0.00 0.00 0.00 3.35
520 536 3.385384 CCCCTGCTGCGACTGAGA 61.385 66.667 0.00 0.00 0.00 3.27
521 537 2.125753 CCCTGCTGCGACTGAGAC 60.126 66.667 0.00 0.00 0.00 3.36
522 538 2.644212 CCCTGCTGCGACTGAGACT 61.644 63.158 0.00 0.00 0.00 3.24
549 565 3.712881 GAGCCGCGCGACTTTGTT 61.713 61.111 34.63 12.34 0.00 2.83
550 566 3.911155 GAGCCGCGCGACTTTGTTG 62.911 63.158 34.63 13.18 0.00 3.33
551 567 4.307908 GCCGCGCGACTTTGTTGT 62.308 61.111 34.63 0.00 0.00 3.32
559 575 1.435515 GACTTTGTTGTTGGCGCCA 59.564 52.632 29.03 29.03 0.00 5.69
838 895 6.757010 TGTCAGTTTACTCTCTTGTTCAGTTC 59.243 38.462 0.00 0.00 0.00 3.01
982 1115 3.365364 GCGAAGGGTTGAGTTCATCTTTG 60.365 47.826 0.00 0.00 0.00 2.77
1245 1378 2.362120 GCTGCAGCTGGGTCCATT 60.362 61.111 31.33 0.00 38.21 3.16
1474 1614 7.149307 GGCTCTAAGAGTTCAGTATAACATCC 58.851 42.308 0.00 0.00 31.39 3.51
1622 1768 3.341318 AGATGGGTCTGATCCTGATGA 57.659 47.619 8.69 0.00 32.13 2.92
1623 1769 3.241156 AGATGGGTCTGATCCTGATGAG 58.759 50.000 8.69 0.00 32.13 2.90
1740 1886 2.161410 TGATGTTGCGCATGGTAACTTC 59.839 45.455 12.75 14.05 42.12 3.01
1801 1954 2.385013 ATGCACGCATGTCAAGTCTA 57.615 45.000 3.17 0.00 35.03 2.59
1882 2035 5.980116 ACATGTTATTCTAGCTTCTAGTGCG 59.020 40.000 0.00 0.00 35.28 5.34
1907 2060 7.388224 CGGTAGCTATGTCATAAGAGAGACTAA 59.612 40.741 0.00 0.00 35.81 2.24
1959 2122 8.667076 AAATAAGTGTCGTGGTTTTAGTTACT 57.333 30.769 0.00 0.00 0.00 2.24
2013 4769 6.436738 TTGTGTTAACAGGTTATACCCTCA 57.563 37.500 8.98 0.00 39.75 3.86
2067 4830 8.197592 TGGTAATTTTCAGTTACTGAGGTAGA 57.802 34.615 14.99 0.00 41.75 2.59
2214 4991 3.383761 CATGGAGTTTGTGGCTTTGTTC 58.616 45.455 0.00 0.00 0.00 3.18
2218 4995 3.130340 GGAGTTTGTGGCTTTGTTCTTCA 59.870 43.478 0.00 0.00 0.00 3.02
2229 5006 9.423061 GTGGCTTTGTTCTTCACAATAAATAAT 57.577 29.630 0.00 0.00 45.17 1.28
2394 5505 7.201741 CGAGTATCTTCCAGTGAGAAATACTGA 60.202 40.741 19.24 7.57 46.52 3.41
2409 5520 7.697691 AGAAATACTGATTTTCTGCATTACCG 58.302 34.615 8.17 0.00 40.86 4.02
2420 5531 1.065491 TGCATTACCGCTGGATTGTCT 60.065 47.619 1.50 0.00 0.00 3.41
2430 5542 4.291783 CGCTGGATTGTCTAGTAAGCTAC 58.708 47.826 0.00 0.00 0.00 3.58
2438 5550 7.229707 GGATTGTCTAGTAAGCTACTCTCATGA 59.770 40.741 0.00 0.00 40.14 3.07
2503 5778 7.703328 AGAACAACTCATTACGTGTCAAATTT 58.297 30.769 0.00 0.00 0.00 1.82
2510 5810 8.188139 ACTCATTACGTGTCAAATTTTCAACTT 58.812 29.630 0.00 0.00 0.00 2.66
2528 5828 5.065988 TCAACTTAGACAAAACTGCACTTCC 59.934 40.000 0.00 0.00 0.00 3.46
2554 5854 6.464222 TCTTTCTTTCGTACAGATGGTGATT 58.536 36.000 0.00 0.00 0.00 2.57
2785 6222 8.380099 TGTGACTGGACCAAATATTTACTAGTT 58.620 33.333 0.00 0.00 0.00 2.24
2850 6287 5.930837 AGGACCTTCACTCTTATCTCAAG 57.069 43.478 0.00 0.00 0.00 3.02
2890 6327 1.076841 TCCCTGGGATTGCATGTTCAA 59.923 47.619 12.53 0.00 0.00 2.69
2984 6421 4.552166 ATTGTTGTCAACTCTTGTTCGG 57.448 40.909 16.45 0.00 36.33 4.30
3014 6451 3.067106 TCAAGCAGTAAAGCTGTAGTGC 58.933 45.455 29.32 29.32 45.89 4.40
3060 6505 8.805175 CATCATGGAGTACTTCTCATCTTATCT 58.195 37.037 2.07 0.00 44.40 1.98
3113 6558 6.817765 TTTGTCTTGGCTCTACTTTAATGG 57.182 37.500 0.00 0.00 0.00 3.16
3137 6582 2.314549 TCCCTTTTGTGGGCTGGATTAT 59.685 45.455 0.00 0.00 46.67 1.28
3145 6590 4.348486 TGTGGGCTGGATTATTTTGCTTA 58.652 39.130 0.00 0.00 0.00 3.09
3147 6592 3.384467 TGGGCTGGATTATTTTGCTTAGC 59.616 43.478 0.00 0.00 0.00 3.09
3148 6593 3.638627 GGGCTGGATTATTTTGCTTAGCT 59.361 43.478 5.60 0.00 0.00 3.32
3180 6634 8.230486 CAGCATCTAGTGTAAACAAGGTTAAAG 58.770 37.037 0.00 0.00 0.00 1.85
3200 6654 1.562672 AATGGTGTCCCTAGGCGCTT 61.563 55.000 7.64 0.52 0.00 4.68
3268 6735 1.878953 CAGTGGTTGGTGGTGTAGAC 58.121 55.000 0.00 0.00 0.00 2.59
3272 6739 1.370064 GTTGGTGGTGTAGACGGCT 59.630 57.895 0.00 0.00 0.00 5.52
3287 6754 1.739338 CGGCTAGCCAGGAATCGACT 61.739 60.000 32.47 0.00 35.37 4.18
3304 6771 0.539669 ACTTTTTCTGGCGGGGAAGG 60.540 55.000 0.00 0.00 0.00 3.46
3352 6819 8.885494 TGTTACTTGCAAGAAAATTGCTATTT 57.115 26.923 32.50 7.97 45.13 1.40
3418 6885 5.590259 ACTTCAAATTTATACGGATGCAGCT 59.410 36.000 0.22 0.00 0.00 4.24
3448 6918 3.382865 TGAGTGCAAACCATTAACAGCAA 59.617 39.130 0.00 0.00 33.37 3.91
3474 6944 9.784531 AGGTTGTATCTATGGATGTTATTTCAG 57.215 33.333 1.10 0.00 33.71 3.02
3511 6982 6.207614 GCATGGAAAAATATCTTACTCCCTCC 59.792 42.308 0.00 0.00 0.00 4.30
3529 7000 7.236847 ACTCCCTCCGATCCATATTAATTGTTA 59.763 37.037 0.00 0.00 0.00 2.41
3573 7053 2.092211 CGAAGTTGTACTAAAGCTGCGG 59.908 50.000 0.00 0.00 0.00 5.69
3590 7070 2.223688 TGCGGCAATTAATTTGGATCGG 60.224 45.455 0.00 0.00 35.75 4.18
3596 7076 5.299279 GGCAATTAATTTGGATCGGAGAGAA 59.701 40.000 0.00 0.00 36.25 2.87
3723 7206 3.912496 AAAGCCCCTATTTCATTTGCC 57.088 42.857 0.00 0.00 0.00 4.52
3724 7207 2.548464 AGCCCCTATTTCATTTGCCA 57.452 45.000 0.00 0.00 0.00 4.92
3730 7213 4.435425 CCCTATTTCATTTGCCACACATG 58.565 43.478 0.00 0.00 0.00 3.21
3779 7262 4.999950 GGATGTAGCACCTTGAGGATTATG 59.000 45.833 3.59 0.00 38.94 1.90
3793 7276 1.840141 GATTATGCACGCGTCTTTTGC 59.160 47.619 9.86 10.75 36.76 3.68
3801 7284 1.134694 GCGTCTTTTGCGGGTGATC 59.865 57.895 0.00 0.00 0.00 2.92
3872 7355 1.741401 CTCGCATGGAGGAAACGCA 60.741 57.895 0.00 0.00 39.22 5.24
3957 7443 3.697619 TCTGCATCATCATCAGGGATC 57.302 47.619 0.00 0.00 0.00 3.36
4016 7502 0.618458 TATCTGCCGCCAAGGAAGTT 59.382 50.000 0.00 0.00 46.52 2.66
4102 7588 3.362986 CGGACATGCTGATTATTACGTGC 60.363 47.826 0.00 0.00 0.00 5.34
4194 7680 2.364002 GAGGAGACTTGCCTGGATAGAC 59.636 54.545 0.00 0.00 44.43 2.59
4200 7686 2.016393 TTGCCTGGATAGACGAGCGG 62.016 60.000 0.00 0.00 0.00 5.52
4251 7737 8.831550 CAGAATCCACCTATTAGCTAAGTTTTC 58.168 37.037 12.54 7.51 0.00 2.29
4252 7738 8.773216 AGAATCCACCTATTAGCTAAGTTTTCT 58.227 33.333 12.54 9.26 0.00 2.52
4253 7739 9.397280 GAATCCACCTATTAGCTAAGTTTTCTT 57.603 33.333 12.54 0.00 43.24 2.52
4254 7740 9.755122 AATCCACCTATTAGCTAAGTTTTCTTT 57.245 29.630 12.54 0.00 40.91 2.52
4255 7741 9.755122 ATCCACCTATTAGCTAAGTTTTCTTTT 57.245 29.630 12.54 0.00 40.91 2.27
4256 7742 9.582648 TCCACCTATTAGCTAAGTTTTCTTTTT 57.417 29.630 12.54 0.00 40.91 1.94
4257 7743 9.841880 CCACCTATTAGCTAAGTTTTCTTTTTC 57.158 33.333 12.54 0.00 40.91 2.29
4290 7781 7.597288 TCTACCTAGTTAAGCTAATGATGCA 57.403 36.000 0.00 0.00 0.00 3.96
4297 7788 7.636150 AGTTAAGCTAATGATGCATGAAAGT 57.364 32.000 2.46 0.00 0.00 2.66
4334 7825 4.301628 GAGCAAAAGGAAAGGACATGTTG 58.698 43.478 0.00 0.00 0.00 3.33
4335 7826 3.706086 AGCAAAAGGAAAGGACATGTTGT 59.294 39.130 0.00 0.00 0.00 3.32
4336 7827 4.162131 AGCAAAAGGAAAGGACATGTTGTT 59.838 37.500 0.00 0.00 0.00 2.83
4341 7832 5.262588 AGGAAAGGACATGTTGTTTTCAC 57.737 39.130 21.66 15.07 31.90 3.18
4353 7844 3.143807 TGTTTTCACGCTGAAGGTTTG 57.856 42.857 1.72 0.00 37.70 2.93
4367 7858 6.516527 GCTGAAGGTTTGATGGATTGTTGTAA 60.517 38.462 0.00 0.00 0.00 2.41
4368 7859 7.537596 TGAAGGTTTGATGGATTGTTGTAAT 57.462 32.000 0.00 0.00 0.00 1.89
4369 7860 7.377398 TGAAGGTTTGATGGATTGTTGTAATG 58.623 34.615 0.00 0.00 0.00 1.90
4372 7863 5.868801 GGTTTGATGGATTGTTGTAATGTGG 59.131 40.000 0.00 0.00 0.00 4.17
4373 7864 6.454795 GTTTGATGGATTGTTGTAATGTGGT 58.545 36.000 0.00 0.00 0.00 4.16
4374 7865 5.641783 TGATGGATTGTTGTAATGTGGTG 57.358 39.130 0.00 0.00 0.00 4.17
4376 7867 5.415389 TGATGGATTGTTGTAATGTGGTGAG 59.585 40.000 0.00 0.00 0.00 3.51
4377 7868 4.724399 TGGATTGTTGTAATGTGGTGAGT 58.276 39.130 0.00 0.00 0.00 3.41
4379 7870 4.759693 GGATTGTTGTAATGTGGTGAGTCA 59.240 41.667 0.00 0.00 0.00 3.41
4380 7871 5.106555 GGATTGTTGTAATGTGGTGAGTCAG 60.107 44.000 0.00 0.00 0.00 3.51
4381 7872 4.415881 TGTTGTAATGTGGTGAGTCAGT 57.584 40.909 0.00 0.00 0.00 3.41
4382 7873 5.538849 TGTTGTAATGTGGTGAGTCAGTA 57.461 39.130 0.00 0.00 0.00 2.74
4383 7874 6.109156 TGTTGTAATGTGGTGAGTCAGTAT 57.891 37.500 0.00 0.00 0.00 2.12
4384 7875 7.234661 TGTTGTAATGTGGTGAGTCAGTATA 57.765 36.000 0.00 0.00 0.00 1.47
4385 7876 7.672240 TGTTGTAATGTGGTGAGTCAGTATAA 58.328 34.615 0.00 0.00 0.00 0.98
4387 7878 7.712204 TGTAATGTGGTGAGTCAGTATAAGA 57.288 36.000 0.00 0.00 0.00 2.10
4388 7879 8.129496 TGTAATGTGGTGAGTCAGTATAAGAA 57.871 34.615 0.00 0.00 0.00 2.52
4389 7880 8.251026 TGTAATGTGGTGAGTCAGTATAAGAAG 58.749 37.037 0.00 0.00 0.00 2.85
4390 7881 5.073311 TGTGGTGAGTCAGTATAAGAAGC 57.927 43.478 0.00 0.00 0.00 3.86
4392 7883 5.246203 TGTGGTGAGTCAGTATAAGAAGCTT 59.754 40.000 0.00 0.00 0.00 3.74
4393 7884 6.166982 GTGGTGAGTCAGTATAAGAAGCTTT 58.833 40.000 0.00 0.00 0.00 3.51
4394 7885 6.651225 GTGGTGAGTCAGTATAAGAAGCTTTT 59.349 38.462 0.00 0.00 0.00 2.27
4395 7886 7.173390 GTGGTGAGTCAGTATAAGAAGCTTTTT 59.827 37.037 7.46 7.46 0.00 1.94
4448 7939 6.282930 TCTTTCCTTTTCTTTTGGCAATCAG 58.717 36.000 0.00 0.20 0.00 2.90
4489 7980 7.278135 AGCTCATACATGTAACACATCAATCT 58.722 34.615 10.14 0.00 36.53 2.40
4490 7981 7.772292 AGCTCATACATGTAACACATCAATCTT 59.228 33.333 10.14 0.00 36.53 2.40
4491 7982 8.066595 GCTCATACATGTAACACATCAATCTTC 58.933 37.037 10.14 0.00 36.53 2.87
4494 7985 8.886719 CATACATGTAACACATCAATCTTCAGT 58.113 33.333 10.14 0.00 36.53 3.41
4495 7986 7.369803 ACATGTAACACATCAATCTTCAGTC 57.630 36.000 0.00 0.00 36.53 3.51
4510 8027 5.342433 TCTTCAGTCAATTTTGCACACAAG 58.658 37.500 0.00 0.00 37.04 3.16
4513 8030 3.552699 CAGTCAATTTTGCACACAAGTGG 59.447 43.478 5.08 0.00 45.98 4.00
4522 8039 2.183478 CACACAAGTGGGCATACAGA 57.817 50.000 5.08 0.00 42.13 3.41
4569 8086 8.990163 AAGATGACTTAAAGGAGTTAAAACCA 57.010 30.769 0.00 0.00 34.28 3.67
4570 8087 9.588096 AAGATGACTTAAAGGAGTTAAAACCAT 57.412 29.630 0.00 0.00 34.28 3.55
4586 8117 3.963428 ACCATGTCTAAACTCGAAGCT 57.037 42.857 0.00 0.00 0.00 3.74
4598 8129 5.344743 AACTCGAAGCTCCATAATCTCAA 57.655 39.130 0.00 0.00 0.00 3.02
4619 8150 1.361271 CTGCATTGCGGCCTATTGG 59.639 57.895 4.19 0.00 0.00 3.16
4696 8228 1.312815 AGTGTTTCAGCTGTCAAGGC 58.687 50.000 14.67 4.24 0.00 4.35
4698 8230 1.405105 GTGTTTCAGCTGTCAAGGCAA 59.595 47.619 14.67 0.00 0.00 4.52
4702 8234 1.817357 TCAGCTGTCAAGGCAATCAG 58.183 50.000 14.67 0.00 0.00 2.90
4751 8283 2.136026 AGAAAGAACTCCCCACCTGTT 58.864 47.619 0.00 0.00 0.00 3.16
4752 8284 2.158608 AGAAAGAACTCCCCACCTGTTG 60.159 50.000 0.00 0.00 0.00 3.33
4753 8285 1.518367 AAGAACTCCCCACCTGTTGA 58.482 50.000 0.00 0.00 0.00 3.18
4755 8287 0.765510 GAACTCCCCACCTGTTGACT 59.234 55.000 0.00 0.00 0.00 3.41
4769 8343 1.136305 GTTGACTAGTAGGCCGCATCA 59.864 52.381 0.00 0.00 0.00 3.07
4796 8374 3.067684 ACCTTGATAAAACCAGGACGG 57.932 47.619 0.00 0.00 42.50 4.79
4837 8415 5.163733 CCTTGCAGAAAGTGTTTTTGCAAAT 60.164 36.000 22.84 0.00 42.54 2.32
4867 8448 3.316308 GGACCACAATGGCATAGATTGAC 59.684 47.826 0.00 0.00 42.67 3.18
4917 8498 1.129998 CAACTGCGCTTTCTCATCAGG 59.870 52.381 9.73 0.00 0.00 3.86
4930 8511 1.417517 TCATCAGGCAGCAACCGATAT 59.582 47.619 0.00 0.00 33.69 1.63
4932 8513 0.179048 TCAGGCAGCAACCGATATGG 60.179 55.000 0.00 0.00 46.41 2.74
4934 8515 2.555547 GGCAGCAACCGATATGGCC 61.556 63.158 0.00 0.00 43.94 5.36
4941 8522 3.146066 GCAACCGATATGGCCATCTTAA 58.854 45.455 24.80 4.57 43.94 1.85
4945 8526 2.993899 CCGATATGGCCATCTTAACGAC 59.006 50.000 24.80 5.06 0.00 4.34
4947 8528 4.307432 CGATATGGCCATCTTAACGACTT 58.693 43.478 24.80 0.00 0.00 3.01
4948 8529 4.750098 CGATATGGCCATCTTAACGACTTT 59.250 41.667 24.80 0.00 0.00 2.66
4949 8530 5.107453 CGATATGGCCATCTTAACGACTTTC 60.107 44.000 24.80 0.00 0.00 2.62
4950 8531 2.343101 TGGCCATCTTAACGACTTTCG 58.657 47.619 0.00 0.00 46.93 3.46
4985 8618 6.475504 TCCAGAATTTCATAAGCTTCAGTCA 58.524 36.000 0.00 0.00 0.00 3.41
4993 8635 1.131638 AAGCTTCAGTCAGTGGGTCA 58.868 50.000 0.00 0.00 0.00 4.02
5015 8657 3.210232 AGATCCTCGTTCCATCTACGA 57.790 47.619 0.00 0.00 44.88 3.43
5023 8665 3.133542 TCGTTCCATCTACGACCTCTCTA 59.866 47.826 0.00 0.00 42.51 2.43
5024 8666 3.875727 CGTTCCATCTACGACCTCTCTAA 59.124 47.826 0.00 0.00 41.33 2.10
5025 8667 4.260702 CGTTCCATCTACGACCTCTCTAAC 60.261 50.000 0.00 0.00 41.33 2.34
5026 8668 4.498894 TCCATCTACGACCTCTCTAACA 57.501 45.455 0.00 0.00 0.00 2.41
5027 8669 4.452825 TCCATCTACGACCTCTCTAACAG 58.547 47.826 0.00 0.00 0.00 3.16
5053 8700 0.904865 AGCGGGTGATCTTGGAGTCA 60.905 55.000 0.00 0.00 0.00 3.41
5068 8715 2.606519 TCACTCTCCCAACCCCCG 60.607 66.667 0.00 0.00 0.00 5.73
5144 8800 6.154877 TGCATAAATTCCATCAATTGTGTCCT 59.845 34.615 5.13 0.00 34.69 3.85
5181 8840 4.202609 CCCTATCCAATGGAAGGTGCTTAT 60.203 45.833 20.99 1.73 34.34 1.73
5184 8843 6.825721 CCTATCCAATGGAAGGTGCTTATATC 59.174 42.308 5.89 0.00 34.34 1.63
5187 8846 5.369404 TCCAATGGAAGGTGCTTATATCTCA 59.631 40.000 0.00 0.00 0.00 3.27
5229 8888 6.581171 AAAGGGTCTTCACAATCAGATTTC 57.419 37.500 0.00 0.00 0.00 2.17
5233 8892 4.398247 GTCTTCACAATCAGATTTCGTGC 58.602 43.478 8.23 0.00 0.00 5.34
5240 8899 4.889409 ACAATCAGATTTCGTGCCCATTAT 59.111 37.500 0.00 0.00 0.00 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
190 194 0.178876 TCCATGGGAGAAGTGTGGGA 60.179 55.000 13.02 0.00 0.00 4.37
297 307 0.521291 CGTCGTCGGGGTTGTACTTA 59.479 55.000 0.00 0.00 0.00 2.24
298 308 1.286880 CGTCGTCGGGGTTGTACTT 59.713 57.895 0.00 0.00 0.00 2.24
353 363 2.920912 GGGTGGAGGTGTGGACGA 60.921 66.667 0.00 0.00 0.00 4.20
425 435 1.674322 TTGGCTTGGCTAACTCGGC 60.674 57.895 0.00 0.00 0.00 5.54
462 472 2.688299 GGTTAGGGTGCGGGGGTA 60.688 66.667 0.00 0.00 0.00 3.69
477 487 1.072459 AGTGGGGTAAGGGGTTGGT 60.072 57.895 0.00 0.00 0.00 3.67
519 535 1.137825 CGGCTCCTCGAAGTCAGTC 59.862 63.158 0.00 0.00 0.00 3.51
520 536 2.995872 GCGGCTCCTCGAAGTCAGT 61.996 63.158 0.00 0.00 0.00 3.41
521 537 2.202676 GCGGCTCCTCGAAGTCAG 60.203 66.667 0.00 0.00 0.00 3.51
522 538 4.116328 CGCGGCTCCTCGAAGTCA 62.116 66.667 0.00 0.00 0.00 3.41
549 565 3.604667 CAAGCCTTGGCGCCAACA 61.605 61.111 37.30 19.77 0.00 3.33
550 566 4.362476 CCAAGCCTTGGCGCCAAC 62.362 66.667 37.30 27.62 45.17 3.77
687 706 0.621571 AGATAGTTCCAGCCAGGCCA 60.622 55.000 8.22 0.00 37.29 5.36
767 799 3.695606 GCACAGCCTCGTCCTCCA 61.696 66.667 0.00 0.00 0.00 3.86
782 826 1.000618 CAGAGCACTTCAGTCTCTGCA 59.999 52.381 16.65 0.00 40.16 4.41
838 895 4.264253 TGCTCTGGTCTTTCAATGGTATG 58.736 43.478 0.00 0.00 0.00 2.39
934 1067 4.043200 GCGTGGCAAGGCTTCACC 62.043 66.667 12.01 10.38 39.61 4.02
935 1068 2.844451 TTGCGTGGCAAGGCTTCAC 61.844 57.895 7.39 8.59 43.99 3.18
982 1115 1.002366 ATCGTTCTCAATGAGCGCAC 58.998 50.000 11.47 3.13 46.58 5.34
1245 1378 2.419673 CTGCAATCCTATTCGTTGTGCA 59.580 45.455 0.00 0.00 38.13 4.57
1300 1433 5.233225 CAGAGACAACTCATTCAAGTAGCA 58.767 41.667 0.00 0.00 44.79 3.49
1474 1614 2.040813 CCTCCCATATCCCTTGACCATG 59.959 54.545 0.00 0.00 0.00 3.66
1567 1712 3.008485 GTCTCACAAATCTCCTGAAGGGT 59.992 47.826 0.00 0.00 36.25 4.34
1622 1768 5.456763 GGCCTCATAGATGGTGGTAAATTCT 60.457 44.000 0.00 0.00 0.00 2.40
1623 1769 4.762251 GGCCTCATAGATGGTGGTAAATTC 59.238 45.833 0.00 0.00 0.00 2.17
1740 1886 4.186159 GGATTGAAGCAAATGGTCATTGG 58.814 43.478 0.00 0.00 0.00 3.16
1778 1930 0.109458 CTTGACATGCGTGCATTGCT 60.109 50.000 10.49 0.00 33.90 3.91
1785 1938 3.525537 AGGATTAGACTTGACATGCGTG 58.474 45.455 3.82 3.82 0.00 5.34
1882 2035 8.624367 TTAGTCTCTCTTATGACATAGCTACC 57.376 38.462 0.00 0.00 35.81 3.18
1919 2077 7.816031 CGACACTTATTTTAACAGAGGGAGTAA 59.184 37.037 0.00 0.00 0.00 2.24
1957 2120 4.140663 AGGCTACCATAATACTCCCTCAGT 60.141 45.833 0.00 0.00 39.41 3.41
1958 2121 4.421131 AGGCTACCATAATACTCCCTCAG 58.579 47.826 0.00 0.00 0.00 3.35
1959 2122 4.487282 AGGCTACCATAATACTCCCTCA 57.513 45.455 0.00 0.00 0.00 3.86
2013 4769 3.757270 AGACTAGCGGCTCTACACATAT 58.243 45.455 5.39 0.00 0.00 1.78
2169 4944 7.589395 TGCATACATCAACGTATTGTTTTTCT 58.411 30.769 3.67 0.00 39.29 2.52
2176 4951 5.237127 ACTCCATGCATACATCAACGTATTG 59.763 40.000 0.00 0.00 32.87 1.90
2234 5011 7.103641 GTGGAAGTACAGATCCAAGAAATGTA 58.896 38.462 14.39 0.00 46.78 2.29
2242 5019 4.974645 AAGTGTGGAAGTACAGATCCAA 57.025 40.909 14.39 5.40 46.78 3.53
2251 5028 7.147880 GGAGCTCTCTATTTAAGTGTGGAAGTA 60.148 40.741 14.64 0.00 0.00 2.24
2365 5476 3.687125 TCTCACTGGAAGATACTCGTGT 58.313 45.455 0.00 0.00 37.43 4.49
2394 5505 2.722094 TCCAGCGGTAATGCAGAAAAT 58.278 42.857 0.00 0.00 37.31 1.82
2409 5520 5.300792 AGAGTAGCTTACTAGACAATCCAGC 59.699 44.000 0.00 0.00 39.59 4.85
2420 5531 9.069082 GTAAGGAATCATGAGAGTAGCTTACTA 57.931 37.037 0.09 0.00 39.59 1.82
2430 5542 6.875726 TCTGTTTGTGTAAGGAATCATGAGAG 59.124 38.462 0.09 0.00 0.00 3.20
2438 5550 6.708054 CAGAACTCTCTGTTTGTGTAAGGAAT 59.292 38.462 0.00 0.00 43.64 3.01
2469 5581 2.902705 TGAGTTGTTCTACAGCCGTT 57.097 45.000 0.00 0.00 28.84 4.44
2503 5778 6.404293 GGAAGTGCAGTTTTGTCTAAGTTGAA 60.404 38.462 8.48 0.00 0.00 2.69
2510 5810 4.973168 AGATGGAAGTGCAGTTTTGTCTA 58.027 39.130 8.48 0.00 0.00 2.59
2528 5828 5.869344 TCACCATCTGTACGAAAGAAAGATG 59.131 40.000 9.17 9.17 41.22 2.90
2554 5854 4.993028 ACAATGCTAAAGGGAAGTTACCA 58.007 39.130 6.96 0.00 0.00 3.25
2670 6092 9.121517 GATTTGTGAACTTATGAGAACAACATG 57.878 33.333 0.00 0.00 30.18 3.21
2671 6093 8.849168 TGATTTGTGAACTTATGAGAACAACAT 58.151 29.630 0.00 0.00 30.18 2.71
2672 6094 8.128582 GTGATTTGTGAACTTATGAGAACAACA 58.871 33.333 0.00 0.00 30.18 3.33
2673 6095 7.321271 CGTGATTTGTGAACTTATGAGAACAAC 59.679 37.037 0.00 0.00 30.18 3.32
2727 6163 6.088824 CCAGACAAGAATGCATTCAGTAAAC 58.911 40.000 34.59 21.40 39.23 2.01
2730 6167 3.691118 GCCAGACAAGAATGCATTCAGTA 59.309 43.478 34.59 0.00 39.23 2.74
2809 6246 7.787028 AGGTCCTTTGAATAGTCTGTAGAATC 58.213 38.462 0.00 0.00 0.00 2.52
2850 6287 7.029563 CAGGGAAAACAATATCTTTGCAGTAC 58.970 38.462 0.00 0.00 0.00 2.73
3060 6505 3.242867 ACAGTGAGGATTTGAGGAGTCA 58.757 45.455 0.00 0.00 0.00 3.41
3147 6592 8.479313 TTGTTTACACTAGATGCTGATAACAG 57.521 34.615 0.00 0.00 45.91 3.16
3148 6593 7.549134 CCTTGTTTACACTAGATGCTGATAACA 59.451 37.037 0.00 0.00 0.00 2.41
3180 6634 1.523938 GCGCCTAGGGACACCATTC 60.524 63.158 11.72 0.00 40.13 2.67
3183 6637 2.606519 AAGCGCCTAGGGACACCA 60.607 61.111 11.72 0.00 40.13 4.17
3268 6735 1.300233 GTCGATTCCTGGCTAGCCG 60.300 63.158 28.28 21.44 39.42 5.52
3272 6739 4.253685 CAGAAAAAGTCGATTCCTGGCTA 58.746 43.478 0.00 0.00 0.00 3.93
3287 6754 1.228737 CCCTTCCCCGCCAGAAAAA 60.229 57.895 0.00 0.00 0.00 1.94
3304 6771 1.411651 GCTCCCTCCCTGGTATGTCC 61.412 65.000 0.00 0.00 0.00 4.02
3418 6885 3.011566 TGGTTTGCACTCAAGAGGAAA 57.988 42.857 1.73 0.00 33.12 3.13
3448 6918 9.784531 CTGAAATAACATCCATAGATACAACCT 57.215 33.333 0.00 0.00 0.00 3.50
3473 6943 9.729281 ATATTTTTCCATGCTGATTTTGTTTCT 57.271 25.926 0.00 0.00 0.00 2.52
3474 6944 9.977762 GATATTTTTCCATGCTGATTTTGTTTC 57.022 29.630 0.00 0.00 0.00 2.78
3553 7033 2.159693 GCCGCAGCTTTAGTACAACTTC 60.160 50.000 0.00 0.00 35.50 3.01
3573 7053 6.377327 TTCTCTCCGATCCAAATTAATTGC 57.623 37.500 0.39 0.00 37.73 3.56
3793 7276 1.086696 AAATCAACAGCGATCACCCG 58.913 50.000 0.00 0.00 0.00 5.28
3801 7284 3.763097 TTAGCCATCAAATCAACAGCG 57.237 42.857 0.00 0.00 0.00 5.18
3872 7355 3.417069 TCATCACTCCATTCGTGGTTT 57.583 42.857 0.00 0.00 33.31 3.27
3934 7417 4.448720 TCCCTGATGATGATGCAGAAAT 57.551 40.909 0.00 0.00 0.00 2.17
3957 7443 3.129287 CCATTTCCGACTTGATCCTTTGG 59.871 47.826 0.00 0.00 0.00 3.28
4016 7502 4.778213 AGGTAGCCATTTGATCTAAGCA 57.222 40.909 0.00 0.00 0.00 3.91
4102 7588 3.103738 GCTTTGCAAATGAGCGTATCAG 58.896 45.455 13.23 0.00 42.53 2.90
4194 7680 1.663074 GCTTCTGCCTATCCGCTCG 60.663 63.158 0.00 0.00 0.00 5.03
4200 7686 1.878734 GCATCCAAGCTTCTGCCTATC 59.121 52.381 12.15 0.00 40.80 2.08
4254 7740 9.227777 GCTTAACTAGGTAGATGGAAAAAGAAA 57.772 33.333 0.00 0.00 0.00 2.52
4255 7741 8.603304 AGCTTAACTAGGTAGATGGAAAAAGAA 58.397 33.333 0.00 0.00 31.41 2.52
4256 7742 8.147244 AGCTTAACTAGGTAGATGGAAAAAGA 57.853 34.615 0.00 0.00 31.41 2.52
4257 7743 9.886132 TTAGCTTAACTAGGTAGATGGAAAAAG 57.114 33.333 0.00 0.00 38.05 2.27
4264 7755 8.090831 TGCATCATTAGCTTAACTAGGTAGATG 58.909 37.037 0.00 6.59 39.78 2.90
4290 7781 6.114221 TCGAAAAAGAAACACGACTTTCAT 57.886 33.333 10.70 0.00 35.66 2.57
4297 7788 4.343811 TTTGCTCGAAAAAGAAACACGA 57.656 36.364 0.00 0.00 0.00 4.35
4334 7825 3.414549 TCAAACCTTCAGCGTGAAAAC 57.585 42.857 2.82 0.00 35.73 2.43
4335 7826 3.243367 CCATCAAACCTTCAGCGTGAAAA 60.243 43.478 2.82 0.00 35.73 2.29
4336 7827 2.293122 CCATCAAACCTTCAGCGTGAAA 59.707 45.455 2.82 0.00 35.73 2.69
4341 7832 2.489329 ACAATCCATCAAACCTTCAGCG 59.511 45.455 0.00 0.00 0.00 5.18
4353 7844 5.415701 ACTCACCACATTACAACAATCCATC 59.584 40.000 0.00 0.00 0.00 3.51
4367 7858 5.423610 AGCTTCTTATACTGACTCACCACAT 59.576 40.000 0.00 0.00 0.00 3.21
4368 7859 4.772624 AGCTTCTTATACTGACTCACCACA 59.227 41.667 0.00 0.00 0.00 4.17
4369 7860 5.331876 AGCTTCTTATACTGACTCACCAC 57.668 43.478 0.00 0.00 0.00 4.16
4395 7886 3.074675 TCTTATACTGCCCCGCAAAAA 57.925 42.857 0.00 0.00 38.41 1.94
4396 7887 2.791347 TCTTATACTGCCCCGCAAAA 57.209 45.000 0.00 0.00 38.41 2.44
4397 7888 2.639065 CTTCTTATACTGCCCCGCAAA 58.361 47.619 0.00 0.00 38.41 3.68
4398 7889 1.745827 GCTTCTTATACTGCCCCGCAA 60.746 52.381 0.00 0.00 38.41 4.85
4399 7890 0.179056 GCTTCTTATACTGCCCCGCA 60.179 55.000 0.00 0.00 36.92 5.69
4400 7891 0.106894 AGCTTCTTATACTGCCCCGC 59.893 55.000 0.00 0.00 0.00 6.13
4401 7892 2.622064 AAGCTTCTTATACTGCCCCG 57.378 50.000 0.00 0.00 0.00 5.73
4402 7893 5.037383 AGTAAAGCTTCTTATACTGCCCC 57.963 43.478 0.00 0.00 0.00 5.80
4403 7894 5.919755 AGAGTAAAGCTTCTTATACTGCCC 58.080 41.667 12.22 0.69 0.00 5.36
4404 7895 7.011576 GGAAAGAGTAAAGCTTCTTATACTGCC 59.988 40.741 12.22 5.95 0.00 4.85
4405 7896 7.766738 AGGAAAGAGTAAAGCTTCTTATACTGC 59.233 37.037 12.22 5.69 0.00 4.40
4478 7969 6.643770 GCAAAATTGACTGAAGATTGATGTGT 59.356 34.615 0.00 0.00 0.00 3.72
4479 7970 6.643360 TGCAAAATTGACTGAAGATTGATGTG 59.357 34.615 0.00 0.00 0.00 3.21
4481 7972 6.643360 TGTGCAAAATTGACTGAAGATTGATG 59.357 34.615 0.00 0.00 0.00 3.07
4482 7973 6.643770 GTGTGCAAAATTGACTGAAGATTGAT 59.356 34.615 0.00 0.00 0.00 2.57
4483 7974 5.978919 GTGTGCAAAATTGACTGAAGATTGA 59.021 36.000 0.00 0.00 0.00 2.57
4484 7975 5.749588 TGTGTGCAAAATTGACTGAAGATTG 59.250 36.000 0.00 0.00 0.00 2.67
4485 7976 5.904941 TGTGTGCAAAATTGACTGAAGATT 58.095 33.333 0.00 0.00 0.00 2.40
4486 7977 5.518848 TGTGTGCAAAATTGACTGAAGAT 57.481 34.783 0.00 0.00 0.00 2.40
4487 7978 4.979943 TGTGTGCAAAATTGACTGAAGA 57.020 36.364 0.00 0.00 0.00 2.87
4489 7980 4.863689 CACTTGTGTGCAAAATTGACTGAA 59.136 37.500 0.00 0.00 37.38 3.02
4490 7981 4.422840 CACTTGTGTGCAAAATTGACTGA 58.577 39.130 0.00 0.00 37.38 3.41
4491 7982 3.552699 CCACTTGTGTGCAAAATTGACTG 59.447 43.478 0.00 0.00 42.54 3.51
4494 7985 2.741228 GCCCACTTGTGTGCAAAATTGA 60.741 45.455 3.49 0.00 42.54 2.57
4495 7986 1.598601 GCCCACTTGTGTGCAAAATTG 59.401 47.619 3.49 0.00 42.54 2.32
4510 8027 4.455606 AGAAGCTAATTCTGTATGCCCAC 58.544 43.478 0.00 0.00 46.80 4.61
4545 8062 9.014297 CATGGTTTTAACTCCTTTAAGTCATCT 57.986 33.333 0.00 0.00 31.11 2.90
4546 8063 8.793592 ACATGGTTTTAACTCCTTTAAGTCATC 58.206 33.333 0.00 0.00 31.11 2.92
4548 8065 7.996644 AGACATGGTTTTAACTCCTTTAAGTCA 59.003 33.333 0.00 0.00 31.11 3.41
4549 8066 8.392372 AGACATGGTTTTAACTCCTTTAAGTC 57.608 34.615 0.00 0.00 31.11 3.01
4550 8067 9.856162 TTAGACATGGTTTTAACTCCTTTAAGT 57.144 29.630 0.00 0.00 31.11 2.24
4553 8070 9.856162 AGTTTAGACATGGTTTTAACTCCTTTA 57.144 29.630 0.00 0.00 0.00 1.85
4569 8086 4.744795 ATGGAGCTTCGAGTTTAGACAT 57.255 40.909 0.00 0.00 0.00 3.06
4570 8087 5.654603 TTATGGAGCTTCGAGTTTAGACA 57.345 39.130 0.00 0.00 0.00 3.41
4577 8094 5.112686 GTTTGAGATTATGGAGCTTCGAGT 58.887 41.667 0.00 0.00 0.00 4.18
4578 8095 4.509600 GGTTTGAGATTATGGAGCTTCGAG 59.490 45.833 0.00 0.00 0.00 4.04
4586 8117 4.098349 GCAATGCAGGTTTGAGATTATGGA 59.902 41.667 0.00 0.00 0.00 3.41
4598 8129 0.684153 AATAGGCCGCAATGCAGGTT 60.684 50.000 5.91 3.75 0.00 3.50
4619 8150 3.192633 GTGGTTTTGGTGGATATGTGGAC 59.807 47.826 0.00 0.00 0.00 4.02
4696 8228 6.929606 TCAGAGATATGAAGATGTGCTGATTG 59.070 38.462 0.00 0.00 0.00 2.67
4698 8230 6.667558 TCAGAGATATGAAGATGTGCTGAT 57.332 37.500 0.00 0.00 0.00 2.90
4702 8234 4.629092 TGCTCAGAGATATGAAGATGTGC 58.371 43.478 0.00 0.00 0.00 4.57
4706 8238 4.561938 GCAGCTGCTCAGAGATATGAAGAT 60.562 45.833 31.33 0.00 38.21 2.40
4708 8240 3.061322 GCAGCTGCTCAGAGATATGAAG 58.939 50.000 31.33 0.00 38.21 3.02
4751 8283 1.136305 GTTGATGCGGCCTACTAGTCA 59.864 52.381 0.00 0.00 0.00 3.41
4752 8284 1.136305 TGTTGATGCGGCCTACTAGTC 59.864 52.381 0.00 0.00 0.00 2.59
4753 8285 1.191535 TGTTGATGCGGCCTACTAGT 58.808 50.000 0.00 0.00 0.00 2.57
4755 8287 4.124238 GTTAATGTTGATGCGGCCTACTA 58.876 43.478 0.00 0.00 0.00 1.82
4769 8343 7.308951 CGTCCTGGTTTTATCAAGGTTAATGTT 60.309 37.037 0.00 0.00 0.00 2.71
4796 8374 0.621862 AGGGTGAAGGGGAGACATCC 60.622 60.000 0.00 0.00 45.85 3.51
4867 8448 1.239968 GGAGGGACACTGCAGCAAAG 61.240 60.000 15.27 3.95 37.51 2.77
4917 8498 1.174712 ATGGCCATATCGGTTGCTGC 61.175 55.000 19.18 0.00 36.97 5.25
4930 8511 2.028839 TCGAAAGTCGTTAAGATGGCCA 60.029 45.455 8.56 8.56 41.35 5.36
4932 8513 3.924686 TCTTCGAAAGTCGTTAAGATGGC 59.075 43.478 0.00 0.00 41.35 4.40
4934 8515 5.399858 TCCTCTTCGAAAGTCGTTAAGATG 58.600 41.667 0.00 0.00 41.35 2.90
4941 8522 3.640592 GAAGTTCCTCTTCGAAAGTCGT 58.359 45.455 0.00 0.00 42.26 4.34
4985 8618 1.645710 ACGAGGATCTTTGACCCACT 58.354 50.000 0.00 0.00 0.00 4.00
4993 8635 3.952323 TCGTAGATGGAACGAGGATCTTT 59.048 43.478 0.00 0.00 43.90 2.52
5023 8665 2.526873 ACCCGCTCCACCTCTGTT 60.527 61.111 0.00 0.00 0.00 3.16
5024 8666 3.314331 CACCCGCTCCACCTCTGT 61.314 66.667 0.00 0.00 0.00 3.41
5025 8667 2.303549 GATCACCCGCTCCACCTCTG 62.304 65.000 0.00 0.00 0.00 3.35
5026 8668 2.039624 ATCACCCGCTCCACCTCT 59.960 61.111 0.00 0.00 0.00 3.69
5027 8669 1.617947 AAGATCACCCGCTCCACCTC 61.618 60.000 0.00 0.00 0.00 3.85
5053 8700 4.265507 ACCGGGGGTTGGGAGAGT 62.266 66.667 6.32 0.00 27.29 3.24
5068 8715 1.028330 TTAGCAGCAGCATCAGCACC 61.028 55.000 3.17 0.00 45.49 5.01
5072 8722 4.142447 ACAAAATCTTAGCAGCAGCATCAG 60.142 41.667 3.17 0.00 45.49 2.90
5075 8725 3.675228 GCACAAAATCTTAGCAGCAGCAT 60.675 43.478 3.17 0.00 45.49 3.79
5157 8813 1.215423 GCACCTTCCATTGGATAGGGT 59.785 52.381 25.17 20.69 35.67 4.34


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

AutoCloner maintained by Alex Coulton.