Multiple sequence alignment - TraesCS6A01G268700

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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 TraesCS6A01G268700 chr6A 100.000 8749 0 0 1 8749 495434326 495425578 0.000000e+00 16157.0
1 TraesCS6A01G268700 chr6A 94.899 843 23 5 7921 8749 596549400 596550236 0.000000e+00 1301.0
2 TraesCS6A01G268700 chr6A 94.253 174 6 3 4822 4991 457379539 457379366 6.740000e-66 263.0
3 TraesCS6A01G268700 chr6A 92.035 113 6 2 7814 7925 91886124 91886014 1.180000e-33 156.0
4 TraesCS6A01G268700 chr6D 95.452 4178 108 23 318 4451 348275726 348279865 0.000000e+00 6588.0
5 TraesCS6A01G268700 chr6D 95.341 3327 104 15 4513 7816 348279983 348283281 0.000000e+00 5238.0
6 TraesCS6A01G268700 chr6D 97.368 38 1 0 4478 4515 348279865 348279902 2.040000e-06 65.8
7 TraesCS6A01G268700 chr6D 100.000 30 0 0 4992 5021 348280249 348280278 1.000000e-03 56.5
8 TraesCS6A01G268700 chr6B 93.972 3766 157 31 1 3742 531531020 531527301 0.000000e+00 5633.0
9 TraesCS6A01G268700 chr6B 95.200 2500 77 15 5345 7816 531525513 531523029 0.000000e+00 3912.0
10 TraesCS6A01G268700 chr6B 90.859 1619 92 15 3739 5346 531527179 531525606 0.000000e+00 2119.0
11 TraesCS6A01G268700 chr6B 92.593 108 6 1 7814 7921 169224538 169224643 4.230000e-33 154.0
12 TraesCS6A01G268700 chr6B 100.000 30 0 0 4992 5021 531526161 531526132 1.000000e-03 56.5
13 TraesCS6A01G268700 chr5B 96.204 843 13 3 7921 8749 390705189 390706026 0.000000e+00 1362.0
14 TraesCS6A01G268700 chr5B 94.253 174 6 2 4822 4992 574956616 574956444 6.740000e-66 263.0
15 TraesCS6A01G268700 chr5A 95.709 839 20 3 7921 8749 475250153 475250985 0.000000e+00 1336.0
16 TraesCS6A01G268700 chr5A 95.232 839 29 3 7921 8749 6669830 6670667 0.000000e+00 1317.0
17 TraesCS6A01G268700 chr5A 94.887 841 25 5 7919 8749 505615453 505616285 0.000000e+00 1299.0
18 TraesCS6A01G268700 chr1A 95.590 839 27 2 7921 8749 565043139 565043977 0.000000e+00 1336.0
19 TraesCS6A01G268700 chr1A 95.119 840 25 3 7920 8749 532794632 532793799 0.000000e+00 1310.0
20 TraesCS6A01G268700 chr1A 95.119 840 24 4 7921 8749 107941814 107940981 0.000000e+00 1308.0
21 TraesCS6A01G268700 chr1A 94.293 841 33 4 7921 8749 29795326 29794489 0.000000e+00 1273.0
22 TraesCS6A01G268700 chr1A 93.519 108 5 1 7814 7921 256211865 256211970 9.090000e-35 159.0
23 TraesCS6A01G268700 chr1A 92.593 108 6 1 7814 7921 516041661 516041766 4.230000e-33 154.0
24 TraesCS6A01G268700 chr3A 95.600 841 19 5 7921 8749 204868814 204869648 0.000000e+00 1332.0
25 TraesCS6A01G268700 chr3A 94.700 849 31 5 7911 8749 708828292 708829136 0.000000e+00 1306.0
26 TraesCS6A01G268700 chr3A 94.272 838 39 2 7920 8749 742418775 742417939 0.000000e+00 1273.0
27 TraesCS6A01G268700 chr3A 93.333 840 34 4 7919 8749 32178128 32178954 0.000000e+00 1221.0
28 TraesCS6A01G268700 chr4A 95.585 838 22 2 7921 8749 448532634 448533465 0.000000e+00 1328.0
29 TraesCS6A01G268700 chr7A 94.656 842 33 3 7918 8749 365457423 365458262 0.000000e+00 1295.0
30 TraesCS6A01G268700 chr7A 93.678 174 8 1 4822 4992 83785005 83784832 3.130000e-64 257.0
31 TraesCS6A01G268700 chr7A 96.117 103 2 1 7819 7921 218195789 218195689 5.430000e-37 167.0
32 TraesCS6A01G268700 chr1D 94.649 841 33 3 7919 8749 460863785 460862947 0.000000e+00 1293.0
33 TraesCS6A01G268700 chr4D 90.996 833 60 11 7923 8747 344817661 344816836 0.000000e+00 1109.0
34 TraesCS6A01G268700 chr4D 92.614 176 10 1 4816 4988 482703448 482703623 5.240000e-62 250.0
35 TraesCS6A01G268700 chr3D 93.182 176 9 1 4816 4988 422517617 422517792 1.130000e-63 255.0
36 TraesCS6A01G268700 chr3D 92.697 178 8 4 4822 4996 422517816 422517991 1.460000e-62 252.0
37 TraesCS6A01G268700 chr3D 92.614 176 9 2 4822 4993 376923808 376923633 5.240000e-62 250.0
38 TraesCS6A01G268700 chr2A 91.964 112 6 2 7814 7924 510433482 510433591 4.230000e-33 154.0
39 TraesCS6A01G268700 chr2A 89.744 117 10 1 7805 7921 418825243 418825129 1.970000e-31 148.0
40 TraesCS6A01G268700 chr1B 91.892 111 7 2 7811 7921 329950972 329951080 4.230000e-33 154.0
41 TraesCS6A01G268700 chr2D 91.150 113 7 2 7813 7924 67702558 67702668 5.470000e-32 150.0


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 TraesCS6A01G268700 chr6A 495425578 495434326 8748 True 16157.000 16157 100.00000 1 8749 1 chr6A.!!$R3 8748
1 TraesCS6A01G268700 chr6A 596549400 596550236 836 False 1301.000 1301 94.89900 7921 8749 1 chr6A.!!$F1 828
2 TraesCS6A01G268700 chr6D 348275726 348283281 7555 False 2987.075 6588 97.04025 318 7816 4 chr6D.!!$F1 7498
3 TraesCS6A01G268700 chr6B 531523029 531531020 7991 True 2930.125 5633 95.00775 1 7816 4 chr6B.!!$R1 7815
4 TraesCS6A01G268700 chr5B 390705189 390706026 837 False 1362.000 1362 96.20400 7921 8749 1 chr5B.!!$F1 828
5 TraesCS6A01G268700 chr5A 475250153 475250985 832 False 1336.000 1336 95.70900 7921 8749 1 chr5A.!!$F2 828
6 TraesCS6A01G268700 chr5A 6669830 6670667 837 False 1317.000 1317 95.23200 7921 8749 1 chr5A.!!$F1 828
7 TraesCS6A01G268700 chr5A 505615453 505616285 832 False 1299.000 1299 94.88700 7919 8749 1 chr5A.!!$F3 830
8 TraesCS6A01G268700 chr1A 565043139 565043977 838 False 1336.000 1336 95.59000 7921 8749 1 chr1A.!!$F3 828
9 TraesCS6A01G268700 chr1A 532793799 532794632 833 True 1310.000 1310 95.11900 7920 8749 1 chr1A.!!$R3 829
10 TraesCS6A01G268700 chr1A 107940981 107941814 833 True 1308.000 1308 95.11900 7921 8749 1 chr1A.!!$R2 828
11 TraesCS6A01G268700 chr1A 29794489 29795326 837 True 1273.000 1273 94.29300 7921 8749 1 chr1A.!!$R1 828
12 TraesCS6A01G268700 chr3A 204868814 204869648 834 False 1332.000 1332 95.60000 7921 8749 1 chr3A.!!$F2 828
13 TraesCS6A01G268700 chr3A 708828292 708829136 844 False 1306.000 1306 94.70000 7911 8749 1 chr3A.!!$F3 838
14 TraesCS6A01G268700 chr3A 742417939 742418775 836 True 1273.000 1273 94.27200 7920 8749 1 chr3A.!!$R1 829
15 TraesCS6A01G268700 chr3A 32178128 32178954 826 False 1221.000 1221 93.33300 7919 8749 1 chr3A.!!$F1 830
16 TraesCS6A01G268700 chr4A 448532634 448533465 831 False 1328.000 1328 95.58500 7921 8749 1 chr4A.!!$F1 828
17 TraesCS6A01G268700 chr7A 365457423 365458262 839 False 1295.000 1295 94.65600 7918 8749 1 chr7A.!!$F1 831
18 TraesCS6A01G268700 chr1D 460862947 460863785 838 True 1293.000 1293 94.64900 7919 8749 1 chr1D.!!$R1 830
19 TraesCS6A01G268700 chr4D 344816836 344817661 825 True 1109.000 1109 90.99600 7923 8747 1 chr4D.!!$R1 824

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
170 171 0.039035 TGGTGCGGCCCTTTTTATCT 59.961 50.000 0.00 0.00 36.04 1.98 F
264 266 0.325016 GAGGGGTAAGAAGGGTCCGA 60.325 60.000 0.00 0.00 0.00 4.55 F
1222 1255 0.584396 CGCCAGCGTGTAAGTTTTCA 59.416 50.000 3.35 0.00 34.35 2.69 F
1449 1487 0.680061 AAGTTTCGTTCGAGGAGCCT 59.320 50.000 0.00 0.00 0.00 4.58 F
2084 2138 0.911184 GTTGTTGCACGTTCAAACCG 59.089 50.000 1.20 0.00 0.00 4.44 F
2606 2666 4.541973 ATCTTTTGTTCTTTCCCCATGC 57.458 40.909 0.00 0.00 0.00 4.06 F
3994 4182 1.867865 GGCAGACTATTCTAAAGCGGC 59.132 52.381 0.00 0.00 0.00 6.53 F
4919 5198 0.248289 GTAGGGAAAGGCTGCGTACA 59.752 55.000 0.00 0.00 36.89 2.90 F
5087 5369 0.036577 CCAACTGAGAGCTCACCCTG 60.037 60.000 17.77 10.71 35.46 4.45 F
5092 5374 0.251787 TGAGAGCTCACCCTGCAGTA 60.252 55.000 17.77 0.00 34.14 2.74 F
5385 5763 0.545309 CTCCCCTTCTCTCCACCACA 60.545 60.000 0.00 0.00 0.00 4.17 F
6781 7186 1.472480 CCGCAAATCACCAGGTTAAGG 59.528 52.381 0.00 0.00 0.00 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1634 1672 0.179076 ATGATGCAACTGCCGATCGA 60.179 50.000 18.66 0.00 41.18 3.59 R
1886 1937 1.405526 CGCCTAGGCTCTAGCAAAACA 60.406 52.381 30.55 0.00 44.36 2.83 R
2590 2645 2.238521 GAGTGCATGGGGAAAGAACAA 58.761 47.619 0.00 0.00 0.00 2.83 R
3164 3225 4.961730 ACTGATAAGATTCTCTGAGGTGCT 59.038 41.667 4.59 0.00 0.00 4.40 R
3677 3738 1.263217 CGTACTTTGCAAAAGCTCCGT 59.737 47.619 13.84 8.86 0.00 4.69 R
4258 4448 0.110295 TCTAGCCACAAGCCAAAGCA 59.890 50.000 0.00 0.00 45.47 3.91 R
5077 5359 0.987294 ACATTACTGCAGGGTGAGCT 59.013 50.000 19.93 0.00 0.00 4.09 R
6549 6954 0.400213 GGTGGTCAGTGGAACCATCA 59.600 55.000 8.96 0.00 37.80 3.07 R
7008 7413 0.033601 ACACAACCTTTGCAGGGACA 60.034 50.000 13.63 0.00 46.01 4.02 R
7053 7458 1.045350 CAGCAGCTAGAGGTGGCCTA 61.045 60.000 3.32 0.00 43.24 3.93 R
7377 7782 1.305887 CCCCCTTAGTGGAGGTCGT 60.306 63.158 0.00 0.00 38.35 4.34 R
8135 8573 0.322546 ATTTCCTGACGAAGGCCCAC 60.323 55.000 0.00 0.00 46.92 4.61 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
45 46 2.696504 GGGAGGGGAAGGGAAGGG 60.697 72.222 0.00 0.00 0.00 3.95
53 54 2.283676 AAGGGAAGGGTCGCGAGA 60.284 61.111 10.24 0.00 41.49 4.04
90 91 2.482664 GCTTGATCCGATGCTTGAGAGA 60.483 50.000 0.00 0.00 0.00 3.10
104 105 2.324860 TGAGAGACAACGCAACATACG 58.675 47.619 0.00 0.00 0.00 3.06
109 110 0.665068 ACAACGCAACATACGCTCGA 60.665 50.000 0.00 0.00 0.00 4.04
122 123 3.069980 GCTCGAGATGTGACCGGCT 62.070 63.158 18.75 0.00 0.00 5.52
132 133 4.506255 GACCGGCTGGGGGAATGG 62.506 72.222 18.00 0.00 41.60 3.16
152 153 2.258591 CCAGTCGACCGGTGTCTG 59.741 66.667 14.63 16.89 39.47 3.51
170 171 0.039035 TGGTGCGGCCCTTTTTATCT 59.961 50.000 0.00 0.00 36.04 1.98
183 184 6.007703 CCCTTTTTATCTGAACCCTGTGTAA 58.992 40.000 0.00 0.00 0.00 2.41
197 198 1.219646 GTGTAAGTTTTCGACCGGCA 58.780 50.000 0.00 0.00 0.00 5.69
203 204 0.651031 GTTTTCGACCGGCATCTAGC 59.349 55.000 0.00 0.00 44.65 3.42
216 217 3.166657 GCATCTAGCGCAGTTCTTTTTG 58.833 45.455 11.47 0.00 0.00 2.44
219 220 2.806244 TCTAGCGCAGTTCTTTTTGTCC 59.194 45.455 11.47 0.00 0.00 4.02
223 224 2.604614 GCGCAGTTCTTTTTGTCCGAAT 60.605 45.455 0.30 0.00 0.00 3.34
239 240 3.007635 CCGAATCCTGTGTAGGTTTTCC 58.992 50.000 0.00 0.00 44.88 3.13
241 242 2.109425 ATCCTGTGTAGGTTTTCCGC 57.891 50.000 0.00 0.00 44.88 5.54
243 244 1.156736 CCTGTGTAGGTTTTCCGCTG 58.843 55.000 0.00 0.00 46.35 5.18
245 246 2.069273 CTGTGTAGGTTTTCCGCTGAG 58.931 52.381 0.00 0.00 46.35 3.35
256 258 2.591915 CCGCTGAGAGGGGTAAGAA 58.408 57.895 0.00 0.00 42.78 2.52
264 266 0.325016 GAGGGGTAAGAAGGGTCCGA 60.325 60.000 0.00 0.00 0.00 4.55
274 276 2.103263 AGAAGGGTCCGATTGTAGATGC 59.897 50.000 0.00 0.00 0.00 3.91
280 282 4.192317 GGTCCGATTGTAGATGCTCTTTT 58.808 43.478 0.00 0.00 0.00 2.27
281 283 5.357257 GGTCCGATTGTAGATGCTCTTTTA 58.643 41.667 0.00 0.00 0.00 1.52
341 343 1.651987 GTGTACCACCGATCCATGTG 58.348 55.000 0.00 0.00 0.00 3.21
356 358 0.768622 ATGTGGAAGTGGAAACCCGA 59.231 50.000 0.00 0.00 0.00 5.14
419 421 2.346365 GACCCTTCGCGGTTCCTT 59.654 61.111 6.13 0.00 35.79 3.36
427 429 2.815647 GCGGTTCCTTCTCAGGCG 60.816 66.667 0.00 0.00 40.58 5.52
428 430 2.815647 CGGTTCCTTCTCAGGCGC 60.816 66.667 0.00 0.00 40.58 6.53
429 431 2.815647 GGTTCCTTCTCAGGCGCG 60.816 66.667 0.00 0.00 40.58 6.86
430 432 2.815647 GTTCCTTCTCAGGCGCGG 60.816 66.667 8.83 0.00 40.58 6.46
431 433 4.760047 TTCCTTCTCAGGCGCGGC 62.760 66.667 27.06 27.06 40.58 6.53
738 762 0.996762 GGAGGAGAGGAGAGGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
748 781 1.820481 GAGGGAGGACGAGGACGAG 60.820 68.421 0.00 0.00 42.66 4.18
1132 1165 2.605299 GCAGGATCCTGGGCCAAT 59.395 61.111 36.92 0.00 43.77 3.16
1222 1255 0.584396 CGCCAGCGTGTAAGTTTTCA 59.416 50.000 3.35 0.00 34.35 2.69
1403 1441 3.128242 GTCCATGAAATCAGCCAGTTGAG 59.872 47.826 0.00 0.00 0.00 3.02
1419 1457 5.112686 CAGTTGAGTCCTAAATCCTGCTAC 58.887 45.833 0.00 0.00 0.00 3.58
1449 1487 0.680061 AAGTTTCGTTCGAGGAGCCT 59.320 50.000 0.00 0.00 0.00 4.58
1500 1538 6.183360 ACCAGGAAATCTTATTTTCATGCTCG 60.183 38.462 0.00 0.00 42.84 5.03
1529 1567 2.536928 GCTCGCTACCAGTTTATTTGCG 60.537 50.000 0.00 0.00 42.70 4.85
1681 1720 2.711311 CGTCTGATGCGGCATTGG 59.289 61.111 17.78 12.58 0.00 3.16
1811 1854 3.022557 AGTGCCAGGCATCAATTGTAT 57.977 42.857 19.75 0.00 41.91 2.29
1850 1893 3.433615 GTGTTCTTCTGACTAAAGCGCAT 59.566 43.478 11.47 0.00 0.00 4.73
1886 1937 1.012486 GCGCACGTTAAGCACTAGGT 61.012 55.000 0.30 0.00 0.00 3.08
2084 2138 0.911184 GTTGTTGCACGTTCAAACCG 59.089 50.000 1.20 0.00 0.00 4.44
2606 2666 4.541973 ATCTTTTGTTCTTTCCCCATGC 57.458 40.909 0.00 0.00 0.00 4.06
2635 2695 8.617809 TCAACTAGTGTAAATTTGTCTTTCCAC 58.382 33.333 0.00 0.00 0.00 4.02
3164 3225 5.784177 AGATAAACTTTTCAGAGTCGCAGA 58.216 37.500 0.00 0.00 0.00 4.26
3462 3523 5.221661 CCACCTATCGGGCTAAAAGAAGTAT 60.222 44.000 0.00 0.00 39.10 2.12
3465 3526 7.545965 CACCTATCGGGCTAAAAGAAGTATATG 59.454 40.741 0.00 0.00 39.10 1.78
3677 3738 7.332926 GCTCAGAAAGTGAAACAGAAGATGATA 59.667 37.037 0.00 0.00 41.43 2.15
3797 3983 7.319646 TGGTAACAGATAATTTTTGCATCACC 58.680 34.615 0.00 0.00 46.17 4.02
3874 4060 9.092876 TCAAATTTGACAAAGGAAAACATGTAC 57.907 29.630 16.91 0.00 31.01 2.90
3885 4071 4.215613 GGAAAACATGTACTTCTCACACCC 59.784 45.833 16.19 0.66 0.00 4.61
3906 4093 2.416547 CCAACTATTTCCTGACTGCACG 59.583 50.000 0.00 0.00 0.00 5.34
3928 4116 4.515944 CGTACCCACCTGAACAATAAAACA 59.484 41.667 0.00 0.00 0.00 2.83
3994 4182 1.867865 GGCAGACTATTCTAAAGCGGC 59.132 52.381 0.00 0.00 0.00 6.53
4000 4188 5.525378 CAGACTATTCTAAAGCGGCTTTGAT 59.475 40.000 32.22 24.15 35.21 2.57
4099 4287 8.216423 ACTGCATAATGGATTTAGTCAGAGAAT 58.784 33.333 0.00 0.00 32.12 2.40
4142 4330 9.429359 CTAATATCATCCTCCTTGTTATGTCAC 57.571 37.037 0.00 0.00 0.00 3.67
4257 4447 4.199432 ACAAATGTTTGGTTTGTGCAGA 57.801 36.364 9.98 0.00 45.27 4.26
4258 4448 4.768583 ACAAATGTTTGGTTTGTGCAGAT 58.231 34.783 9.98 0.00 45.27 2.90
4259 4449 4.571580 ACAAATGTTTGGTTTGTGCAGATG 59.428 37.500 9.98 0.00 45.27 2.90
4260 4450 2.222007 TGTTTGGTTTGTGCAGATGC 57.778 45.000 0.00 0.00 42.50 3.91
4261 4451 1.755959 TGTTTGGTTTGTGCAGATGCT 59.244 42.857 6.35 0.00 42.66 3.79
4262 4452 2.168106 TGTTTGGTTTGTGCAGATGCTT 59.832 40.909 6.35 0.00 42.66 3.91
4263 4453 3.197265 GTTTGGTTTGTGCAGATGCTTT 58.803 40.909 6.35 0.00 42.66 3.51
4264 4454 2.512485 TGGTTTGTGCAGATGCTTTG 57.488 45.000 6.35 0.00 42.66 2.77
4265 4455 1.068895 TGGTTTGTGCAGATGCTTTGG 59.931 47.619 6.35 0.00 42.66 3.28
4266 4456 1.142474 GTTTGTGCAGATGCTTTGGC 58.858 50.000 6.35 0.00 42.66 4.52
4267 4457 1.042229 TTTGTGCAGATGCTTTGGCT 58.958 45.000 6.35 0.00 42.66 4.75
4268 4458 1.042229 TTGTGCAGATGCTTTGGCTT 58.958 45.000 6.35 0.00 42.66 4.35
4269 4459 0.315886 TGTGCAGATGCTTTGGCTTG 59.684 50.000 6.35 0.00 42.66 4.01
4270 4460 0.316204 GTGCAGATGCTTTGGCTTGT 59.684 50.000 6.35 0.00 42.66 3.16
4271 4461 0.315886 TGCAGATGCTTTGGCTTGTG 59.684 50.000 6.35 0.00 42.66 3.33
4284 4474 1.135286 GGCTTGTGGCTAGAACATTGC 60.135 52.381 0.00 5.16 41.46 3.56
4286 4476 2.415090 GCTTGTGGCTAGAACATTGCTG 60.415 50.000 0.00 0.00 38.06 4.41
4379 4570 5.385198 AGAGGGTAATTTTTGCACTTCTGA 58.615 37.500 0.00 0.00 0.00 3.27
4405 4598 5.163290 TGTGATCCACCTAAATACCGCATAA 60.163 40.000 0.00 0.00 32.73 1.90
4464 4657 3.713826 TCATGAAGTGTAGGGGTTTCC 57.286 47.619 0.00 0.00 0.00 3.13
4470 4663 6.147437 TGAAGTGTAGGGGTTTCCATTTAT 57.853 37.500 0.00 0.00 38.24 1.40
4550 4826 0.390209 GTTGGACAACATGCCCATGC 60.390 55.000 10.13 0.00 42.39 4.06
4558 4834 0.837260 ACATGCCCATGCCCAAAACT 60.837 50.000 8.11 0.00 42.39 2.66
4616 4892 5.625251 TGACTCGTGACTAATTACTCGTTC 58.375 41.667 0.00 0.00 0.00 3.95
4648 4924 5.163581 GGCATGTCAACAATAAATCAGAGCT 60.164 40.000 0.00 0.00 0.00 4.09
4699 4975 5.945784 AGACAAGCATGCTATGTTAAAAGGA 59.054 36.000 23.00 0.00 0.00 3.36
4871 5148 1.676968 CCATGAGGTCACGGGTTCA 59.323 57.895 0.00 0.00 0.00 3.18
4919 5198 0.248289 GTAGGGAAAGGCTGCGTACA 59.752 55.000 0.00 0.00 36.89 2.90
4935 5214 2.152016 GTACAGAAGACCCAAAGTGGC 58.848 52.381 0.00 0.00 35.79 5.01
5077 5359 0.898320 GCACCTCTAGCCAACTGAGA 59.102 55.000 0.00 0.00 0.00 3.27
5078 5360 1.134848 GCACCTCTAGCCAACTGAGAG 60.135 57.143 0.00 0.00 37.13 3.20
5079 5361 1.134848 CACCTCTAGCCAACTGAGAGC 60.135 57.143 0.00 0.00 36.23 4.09
5080 5362 1.272985 ACCTCTAGCCAACTGAGAGCT 60.273 52.381 0.00 0.00 40.66 4.09
5081 5363 1.408702 CCTCTAGCCAACTGAGAGCTC 59.591 57.143 5.27 5.27 38.06 4.09
5082 5364 2.098614 CTCTAGCCAACTGAGAGCTCA 58.901 52.381 17.77 0.00 38.06 4.26
5083 5365 1.821753 TCTAGCCAACTGAGAGCTCAC 59.178 52.381 17.77 10.80 38.06 3.51
5084 5366 0.898320 TAGCCAACTGAGAGCTCACC 59.102 55.000 17.77 7.86 38.06 4.02
5085 5367 1.376553 GCCAACTGAGAGCTCACCC 60.377 63.158 17.77 5.16 35.46 4.61
5086 5368 1.835927 GCCAACTGAGAGCTCACCCT 61.836 60.000 17.77 0.00 35.46 4.34
5087 5369 0.036577 CCAACTGAGAGCTCACCCTG 60.037 60.000 17.77 10.71 35.46 4.45
5088 5370 0.673022 CAACTGAGAGCTCACCCTGC 60.673 60.000 17.77 0.00 35.46 4.85
5089 5371 1.123861 AACTGAGAGCTCACCCTGCA 61.124 55.000 17.77 3.13 35.46 4.41
5090 5372 1.218585 CTGAGAGCTCACCCTGCAG 59.781 63.158 17.77 6.78 35.46 4.41
5091 5373 1.534959 TGAGAGCTCACCCTGCAGT 60.535 57.895 17.77 0.00 34.14 4.40
5092 5374 0.251787 TGAGAGCTCACCCTGCAGTA 60.252 55.000 17.77 0.00 34.14 2.74
5093 5375 0.898320 GAGAGCTCACCCTGCAGTAA 59.102 55.000 17.77 0.00 0.00 2.24
5094 5376 1.484240 GAGAGCTCACCCTGCAGTAAT 59.516 52.381 17.77 0.00 0.00 1.89
5114 5396 9.337396 CAGTAATGTTTGGTTAGCCATTAGATA 57.663 33.333 0.00 0.00 45.56 1.98
5134 5416 6.987386 AGATAACTTGATCGGATGGTTAGAG 58.013 40.000 0.00 0.00 0.00 2.43
5199 5481 2.847327 AGGATGAGTCACCTTGTGTG 57.153 50.000 0.00 0.00 46.88 3.82
5200 5482 2.050144 AGGATGAGTCACCTTGTGTGT 58.950 47.619 0.00 0.00 45.61 3.72
5201 5483 2.146342 GGATGAGTCACCTTGTGTGTG 58.854 52.381 0.00 0.00 45.61 3.82
5202 5484 2.485479 GGATGAGTCACCTTGTGTGTGT 60.485 50.000 0.00 0.00 45.61 3.72
5203 5485 2.022764 TGAGTCACCTTGTGTGTGTG 57.977 50.000 0.00 0.00 45.61 3.82
5277 5559 5.581126 TCCTGTCAAACATGGAATATTGC 57.419 39.130 0.00 0.00 0.00 3.56
5278 5560 5.015515 TCCTGTCAAACATGGAATATTGCA 58.984 37.500 12.37 12.37 0.00 4.08
5279 5561 5.657745 TCCTGTCAAACATGGAATATTGCAT 59.342 36.000 15.98 15.98 40.00 3.96
5281 5563 6.256975 CCTGTCAAACATGGAATATTGCATTG 59.743 38.462 18.75 15.43 37.10 2.82
5282 5564 6.699366 TGTCAAACATGGAATATTGCATTGT 58.301 32.000 18.75 16.30 37.10 2.71
5385 5763 0.545309 CTCCCCTTCTCTCCACCACA 60.545 60.000 0.00 0.00 0.00 4.17
5402 5780 5.007528 CCACCACAATTTCAAAACACCATTC 59.992 40.000 0.00 0.00 0.00 2.67
5473 5853 6.127196 TGCCACCTTAATTTTGAGAAACAAGT 60.127 34.615 0.00 0.00 39.77 3.16
5490 5870 6.959639 AACAAGTGAACTAATGATGGTTGT 57.040 33.333 0.00 0.00 29.37 3.32
5584 5968 9.360093 ACTAGACAGAAAGATTTCGATAACTTG 57.640 33.333 0.00 0.00 41.92 3.16
5587 5971 7.389053 AGACAGAAAGATTTCGATAACTTGCTT 59.611 33.333 4.00 0.00 41.92 3.91
5663 6047 5.584649 CCTTCATTATTACTGCGGTTCAGAA 59.415 40.000 1.99 0.00 45.72 3.02
5874 6276 5.995897 TGATGATGATGATGACAATGAGGTC 59.004 40.000 0.00 0.00 38.29 3.85
5936 6338 2.544721 AGAGGATGGTTCTTCTGAGCA 58.455 47.619 0.00 0.00 36.97 4.26
6182 6584 5.847304 TGATGAAACAGATCTATTCGAGGG 58.153 41.667 13.03 0.00 0.00 4.30
6314 6719 5.256474 TGATTCTTCCAAGATTTCTCCACC 58.744 41.667 0.00 0.00 34.49 4.61
6549 6954 8.531146 CACCCTATCCAAATTGAAATACTTGTT 58.469 33.333 0.00 0.00 0.00 2.83
6621 7026 1.673665 CACAGGAGCTCCAACTGCC 60.674 63.158 33.90 6.37 38.89 4.85
6626 7031 3.557903 GAGCTCCAACTGCCTGGCA 62.558 63.158 21.96 21.96 36.32 4.92
6781 7186 1.472480 CCGCAAATCACCAGGTTAAGG 59.528 52.381 0.00 0.00 0.00 2.69
6782 7187 1.472480 CGCAAATCACCAGGTTAAGGG 59.528 52.381 0.00 0.00 0.00 3.95
6783 7188 2.525368 GCAAATCACCAGGTTAAGGGT 58.475 47.619 0.00 0.00 38.10 4.34
6807 7212 8.462016 GGTGATAAGAAAAGCATGTCAAATAGT 58.538 33.333 0.00 0.00 0.00 2.12
6920 7325 2.356432 CCACTGGAAGAAGGCATCATGA 60.356 50.000 0.00 0.00 37.43 3.07
7008 7413 3.758554 GAGCAATTCCACCAGTTACATGT 59.241 43.478 2.69 2.69 0.00 3.21
7053 7458 2.789409 GGATACTGGAAGCAGTTGGT 57.211 50.000 0.00 0.00 37.60 3.67
7106 7511 1.656587 ATGGTTAGTCCTGAGGCACA 58.343 50.000 0.00 0.00 37.07 4.57
7377 7782 0.179234 TCGGACAACAGTTCAGCCAA 59.821 50.000 0.00 0.00 0.00 4.52
7677 8085 0.963962 GAGAACTACACCGGTCACCA 59.036 55.000 2.59 0.00 0.00 4.17
7678 8086 1.342174 GAGAACTACACCGGTCACCAA 59.658 52.381 2.59 0.00 0.00 3.67
7693 8101 5.410132 CGGTCACCAAATGATGTTAACAGTA 59.590 40.000 14.65 5.77 40.28 2.74
7694 8102 6.072948 CGGTCACCAAATGATGTTAACAGTAA 60.073 38.462 14.65 2.41 40.28 2.24
7695 8103 7.361713 CGGTCACCAAATGATGTTAACAGTAAT 60.362 37.037 14.65 4.70 40.28 1.89
7696 8104 8.303876 GGTCACCAAATGATGTTAACAGTAATT 58.696 33.333 14.65 10.24 40.28 1.40
7714 8124 8.548721 ACAGTAATTTTCTCTGTGAAGTTTACG 58.451 33.333 14.20 12.62 40.29 3.18
7730 8140 6.833342 AGTTTACGTGAATACTCGTGTTTT 57.167 33.333 0.00 0.00 44.05 2.43
7735 8145 4.131714 CGTGAATACTCGTGTTTTGTTCG 58.868 43.478 0.00 0.00 0.00 3.95
7741 8151 4.703899 ACTCGTGTTTTGTTCGTGTATC 57.296 40.909 0.00 0.00 31.41 2.24
7768 8180 3.935203 CTGATCGGTACATTTCAAGCTGT 59.065 43.478 0.00 0.00 0.00 4.40
7769 8181 3.684305 TGATCGGTACATTTCAAGCTGTG 59.316 43.478 0.00 0.00 0.00 3.66
7818 8231 8.719478 CAACATCTGTTGTTTCAATCTACTTC 57.281 34.615 13.64 0.00 46.51 3.01
7819 8232 7.440523 ACATCTGTTGTTTCAATCTACTTCC 57.559 36.000 0.00 0.00 33.74 3.46
7820 8233 7.227156 ACATCTGTTGTTTCAATCTACTTCCT 58.773 34.615 0.00 0.00 33.74 3.36
7821 8234 7.389053 ACATCTGTTGTTTCAATCTACTTCCTC 59.611 37.037 0.00 0.00 33.74 3.71
7822 8235 6.231211 TCTGTTGTTTCAATCTACTTCCTCC 58.769 40.000 0.00 0.00 0.00 4.30
7823 8236 4.994852 TGTTGTTTCAATCTACTTCCTCCG 59.005 41.667 0.00 0.00 0.00 4.63
7824 8237 4.884668 TGTTTCAATCTACTTCCTCCGT 57.115 40.909 0.00 0.00 0.00 4.69
7825 8238 5.223449 TGTTTCAATCTACTTCCTCCGTT 57.777 39.130 0.00 0.00 0.00 4.44
7826 8239 5.235516 TGTTTCAATCTACTTCCTCCGTTC 58.764 41.667 0.00 0.00 0.00 3.95
7827 8240 4.467198 TTCAATCTACTTCCTCCGTTCC 57.533 45.455 0.00 0.00 0.00 3.62
7828 8241 2.426024 TCAATCTACTTCCTCCGTTCCG 59.574 50.000 0.00 0.00 0.00 4.30
7829 8242 2.426024 CAATCTACTTCCTCCGTTCCGA 59.574 50.000 0.00 0.00 0.00 4.55
7830 8243 2.205022 TCTACTTCCTCCGTTCCGAA 57.795 50.000 0.00 0.00 0.00 4.30
7831 8244 2.731572 TCTACTTCCTCCGTTCCGAAT 58.268 47.619 0.00 0.00 0.00 3.34
7832 8245 3.094572 TCTACTTCCTCCGTTCCGAATT 58.905 45.455 0.00 0.00 0.00 2.17
7833 8246 4.272489 TCTACTTCCTCCGTTCCGAATTA 58.728 43.478 0.00 0.00 0.00 1.40
7834 8247 3.242549 ACTTCCTCCGTTCCGAATTAC 57.757 47.619 0.00 0.00 0.00 1.89
7835 8248 2.830321 ACTTCCTCCGTTCCGAATTACT 59.170 45.455 0.00 0.00 0.00 2.24
7836 8249 3.260128 ACTTCCTCCGTTCCGAATTACTT 59.740 43.478 0.00 0.00 0.00 2.24
7837 8250 3.241067 TCCTCCGTTCCGAATTACTTG 57.759 47.619 0.00 0.00 0.00 3.16
7838 8251 2.564062 TCCTCCGTTCCGAATTACTTGT 59.436 45.455 0.00 0.00 0.00 3.16
7839 8252 3.007182 TCCTCCGTTCCGAATTACTTGTT 59.993 43.478 0.00 0.00 0.00 2.83
7840 8253 3.124636 CCTCCGTTCCGAATTACTTGTTG 59.875 47.826 0.00 0.00 0.00 3.33
7841 8254 2.481185 TCCGTTCCGAATTACTTGTTGC 59.519 45.455 0.00 0.00 0.00 4.17
7842 8255 2.224549 CCGTTCCGAATTACTTGTTGCA 59.775 45.455 0.00 0.00 0.00 4.08
7843 8256 3.479006 CGTTCCGAATTACTTGTTGCAG 58.521 45.455 0.00 0.00 0.00 4.41
7844 8257 3.666902 CGTTCCGAATTACTTGTTGCAGG 60.667 47.826 0.00 0.00 0.00 4.85
7845 8258 3.134574 TCCGAATTACTTGTTGCAGGT 57.865 42.857 0.00 0.00 0.00 4.00
7846 8259 4.274602 TCCGAATTACTTGTTGCAGGTA 57.725 40.909 0.00 0.00 0.00 3.08
7847 8260 4.839121 TCCGAATTACTTGTTGCAGGTAT 58.161 39.130 0.00 0.00 0.00 2.73
7848 8261 4.634004 TCCGAATTACTTGTTGCAGGTATG 59.366 41.667 0.00 0.00 0.00 2.39
7849 8262 4.201910 CCGAATTACTTGTTGCAGGTATGG 60.202 45.833 0.00 0.00 0.00 2.74
7850 8263 4.634004 CGAATTACTTGTTGCAGGTATGGA 59.366 41.667 0.00 0.00 0.00 3.41
7851 8264 5.296780 CGAATTACTTGTTGCAGGTATGGAT 59.703 40.000 0.00 0.00 0.00 3.41
7852 8265 6.183360 CGAATTACTTGTTGCAGGTATGGATT 60.183 38.462 0.00 0.00 0.00 3.01
7853 8266 7.480760 AATTACTTGTTGCAGGTATGGATTT 57.519 32.000 0.00 0.00 0.00 2.17
7854 8267 8.588290 AATTACTTGTTGCAGGTATGGATTTA 57.412 30.769 0.00 0.00 0.00 1.40
7855 8268 8.766994 ATTACTTGTTGCAGGTATGGATTTAT 57.233 30.769 0.00 0.00 0.00 1.40
7856 8269 6.699575 ACTTGTTGCAGGTATGGATTTATC 57.300 37.500 0.00 0.00 0.00 1.75
7857 8270 6.426587 ACTTGTTGCAGGTATGGATTTATCT 58.573 36.000 0.00 0.00 0.00 1.98
7858 8271 7.573710 ACTTGTTGCAGGTATGGATTTATCTA 58.426 34.615 0.00 0.00 0.00 1.98
7859 8272 7.716998 ACTTGTTGCAGGTATGGATTTATCTAG 59.283 37.037 0.00 0.00 0.00 2.43
7860 8273 7.373617 TGTTGCAGGTATGGATTTATCTAGA 57.626 36.000 0.00 0.00 0.00 2.43
7861 8274 7.977818 TGTTGCAGGTATGGATTTATCTAGAT 58.022 34.615 10.73 10.73 0.00 1.98
7862 8275 7.879677 TGTTGCAGGTATGGATTTATCTAGATG 59.120 37.037 15.79 0.00 0.00 2.90
7863 8276 7.559335 TGCAGGTATGGATTTATCTAGATGT 57.441 36.000 15.79 1.25 0.00 3.06
7864 8277 8.664669 TGCAGGTATGGATTTATCTAGATGTA 57.335 34.615 15.79 3.39 0.00 2.29
7865 8278 9.271921 TGCAGGTATGGATTTATCTAGATGTAT 57.728 33.333 15.79 8.15 0.00 2.29
7912 8325 9.695526 TTTTTCTGTGATGAGTAATTTGGAATG 57.304 29.630 0.00 0.00 0.00 2.67
7913 8326 7.395190 TTCTGTGATGAGTAATTTGGAATGG 57.605 36.000 0.00 0.00 0.00 3.16
7914 8327 6.720309 TCTGTGATGAGTAATTTGGAATGGA 58.280 36.000 0.00 0.00 0.00 3.41
7915 8328 6.825213 TCTGTGATGAGTAATTTGGAATGGAG 59.175 38.462 0.00 0.00 0.00 3.86
7916 8329 5.887598 TGTGATGAGTAATTTGGAATGGAGG 59.112 40.000 0.00 0.00 0.00 4.30
7953 8367 3.763897 GGCAACTTGTATTTCCATGAGGT 59.236 43.478 0.00 0.00 35.89 3.85
8089 8524 2.509548 CCCCTCAAACTCATGGTGGATA 59.490 50.000 0.00 0.00 0.00 2.59
8135 8573 2.105006 AGCCATGTTGTGCTCTAGTG 57.895 50.000 0.00 0.00 30.33 2.74
8419 8866 1.740296 CGGCACTCGAACGGGAAAT 60.740 57.895 0.00 0.00 42.43 2.17
8629 9077 6.547880 ACACGAAGGAGATGACTATAGTGAAT 59.452 38.462 10.90 3.68 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 1.091771 CCCCTCACATCATCGCACAC 61.092 60.000 0.00 0.00 0.00 3.82
30 31 2.368011 CGACCCTTCCCTTCCCCTC 61.368 68.421 0.00 0.00 0.00 4.30
34 35 3.372554 CTCGCGACCCTTCCCTTCC 62.373 68.421 3.71 0.00 0.00 3.46
36 37 1.889530 CTTCTCGCGACCCTTCCCTT 61.890 60.000 3.71 0.00 0.00 3.95
42 43 2.042843 ATCCCTTCTCGCGACCCT 60.043 61.111 3.71 0.00 0.00 4.34
45 46 1.281899 CTTTGATCCCTTCTCGCGAC 58.718 55.000 3.71 0.00 0.00 5.19
53 54 2.043953 GCCCCGCTTTGATCCCTT 60.044 61.111 0.00 0.00 0.00 3.95
80 81 0.937304 GTTGCGTTGTCTCTCAAGCA 59.063 50.000 0.00 0.00 37.90 3.91
90 91 0.665068 TCGAGCGTATGTTGCGTTGT 60.665 50.000 0.00 0.00 37.44 3.32
104 105 2.583593 GCCGGTCACATCTCGAGC 60.584 66.667 7.81 0.00 0.00 5.03
109 110 3.402681 CCCCAGCCGGTCACATCT 61.403 66.667 1.90 0.00 0.00 2.90
146 147 4.643387 AAGGGCCGCACCAGACAC 62.643 66.667 0.00 0.00 42.05 3.67
147 148 2.920076 AAAAAGGGCCGCACCAGACA 62.920 55.000 0.00 0.00 42.05 3.41
148 149 0.891904 TAAAAAGGGCCGCACCAGAC 60.892 55.000 0.00 0.00 42.05 3.51
152 153 0.455815 CAGATAAAAAGGGCCGCACC 59.544 55.000 0.00 0.00 37.93 5.01
157 158 2.760650 CAGGGTTCAGATAAAAAGGGCC 59.239 50.000 0.00 0.00 0.00 5.80
170 171 3.872771 GTCGAAAACTTACACAGGGTTCA 59.127 43.478 0.00 0.00 0.00 3.18
183 184 1.739371 GCTAGATGCCGGTCGAAAACT 60.739 52.381 1.90 0.00 35.15 2.66
197 198 3.437049 GGACAAAAAGAACTGCGCTAGAT 59.563 43.478 9.73 0.00 0.00 1.98
203 204 2.748461 TTCGGACAAAAAGAACTGCG 57.252 45.000 0.00 0.00 0.00 5.18
206 207 4.275936 CACAGGATTCGGACAAAAAGAACT 59.724 41.667 0.00 0.00 0.00 3.01
209 210 3.815809 ACACAGGATTCGGACAAAAAGA 58.184 40.909 0.00 0.00 0.00 2.52
216 217 3.329929 AAACCTACACAGGATTCGGAC 57.670 47.619 0.00 0.00 45.91 4.79
219 220 2.671396 CGGAAAACCTACACAGGATTCG 59.329 50.000 0.00 0.00 45.91 3.34
223 224 1.053424 AGCGGAAAACCTACACAGGA 58.947 50.000 0.00 0.00 45.91 3.86
239 240 0.461961 CCTTCTTACCCCTCTCAGCG 59.538 60.000 0.00 0.00 0.00 5.18
241 242 2.112190 GACCCTTCTTACCCCTCTCAG 58.888 57.143 0.00 0.00 0.00 3.35
243 244 1.498264 GGACCCTTCTTACCCCTCTC 58.502 60.000 0.00 0.00 0.00 3.20
245 246 0.325016 TCGGACCCTTCTTACCCCTC 60.325 60.000 0.00 0.00 0.00 4.30
250 251 4.996788 TCTACAATCGGACCCTTCTTAC 57.003 45.455 0.00 0.00 0.00 2.34
251 252 4.202223 GCATCTACAATCGGACCCTTCTTA 60.202 45.833 0.00 0.00 0.00 2.10
253 254 2.103263 GCATCTACAATCGGACCCTTCT 59.897 50.000 0.00 0.00 0.00 2.85
256 258 1.689273 GAGCATCTACAATCGGACCCT 59.311 52.381 0.00 0.00 0.00 4.34
297 299 7.127686 CGTACGTTAAGACAGGAACAATTTTT 58.872 34.615 7.22 0.00 0.00 1.94
298 300 6.258507 ACGTACGTTAAGACAGGAACAATTTT 59.741 34.615 16.72 0.00 0.00 1.82
299 301 5.754890 ACGTACGTTAAGACAGGAACAATTT 59.245 36.000 16.72 0.00 0.00 1.82
300 302 5.176223 CACGTACGTTAAGACAGGAACAATT 59.824 40.000 20.23 0.00 0.00 2.32
308 310 4.145876 TGGTACACGTACGTTAAGACAG 57.854 45.455 20.23 8.19 36.94 3.51
341 343 2.223876 GGTTTTTCGGGTTTCCACTTCC 60.224 50.000 0.00 0.00 0.00 3.46
342 344 2.427812 TGGTTTTTCGGGTTTCCACTTC 59.572 45.455 0.00 0.00 0.00 3.01
343 345 2.166870 GTGGTTTTTCGGGTTTCCACTT 59.833 45.455 0.00 0.00 41.14 3.16
344 346 1.752498 GTGGTTTTTCGGGTTTCCACT 59.248 47.619 0.00 0.00 41.14 4.00
345 347 1.477295 TGTGGTTTTTCGGGTTTCCAC 59.523 47.619 0.00 0.00 43.58 4.02
346 348 1.751924 CTGTGGTTTTTCGGGTTTCCA 59.248 47.619 0.00 0.00 0.00 3.53
356 358 2.317230 CGTCTCGCCTGTGGTTTTT 58.683 52.632 0.00 0.00 0.00 1.94
738 762 2.272797 CCTCCTCCTCGTCCTCGT 59.727 66.667 0.00 0.00 38.33 4.18
748 781 4.423209 ACTCCTGGGGCCTCCTCC 62.423 72.222 0.00 0.00 36.20 4.30
1220 1253 2.071778 AGCAAAAAGGCAGGAGTTGA 57.928 45.000 0.00 0.00 35.83 3.18
1222 1255 2.101415 GACAAGCAAAAAGGCAGGAGTT 59.899 45.455 0.00 0.00 35.83 3.01
1403 1441 4.081087 TGGAGTTGTAGCAGGATTTAGGAC 60.081 45.833 0.00 0.00 0.00 3.85
1419 1457 4.025229 TCGAACGAAACTTCATTGGAGTTG 60.025 41.667 11.12 2.70 0.00 3.16
1461 1499 3.879844 TGGTACAACCAGAGGCGT 58.120 55.556 0.00 0.00 44.79 5.68
1487 1525 4.908736 GCTTAACAGCGAGCATGAAAATA 58.091 39.130 0.00 0.00 38.73 1.40
1529 1567 3.904571 TCTCAAAATGCATGCACAGAAC 58.095 40.909 25.37 0.00 0.00 3.01
1634 1672 0.179076 ATGATGCAACTGCCGATCGA 60.179 50.000 18.66 0.00 41.18 3.59
1793 1836 2.737544 ACATACAATTGATGCCTGGCA 58.262 42.857 25.65 25.65 44.86 4.92
1803 1846 2.923020 GCGCTGGGAAAACATACAATTG 59.077 45.455 3.24 3.24 0.00 2.32
1811 1854 1.454847 ACAAGGCGCTGGGAAAACA 60.455 52.632 7.64 0.00 0.00 2.83
1850 1893 3.917380 GTGCGCATAATTGTGTTTAAGCA 59.083 39.130 15.91 5.88 35.72 3.91
1886 1937 1.405526 CGCCTAGGCTCTAGCAAAACA 60.406 52.381 30.55 0.00 44.36 2.83
1985 2039 8.228206 AGATATATACCAGTGTCTCTCTTCCAA 58.772 37.037 0.00 0.00 0.00 3.53
2528 2583 5.175859 CCAGCGAAATAGAACAGGAAACTA 58.824 41.667 0.00 0.00 40.21 2.24
2588 2643 3.037549 AGTGCATGGGGAAAGAACAAAA 58.962 40.909 0.00 0.00 0.00 2.44
2590 2645 2.238521 GAGTGCATGGGGAAAGAACAA 58.761 47.619 0.00 0.00 0.00 2.83
2635 2695 8.777413 TGTCATAACTCAGAAACTTTGAAGATG 58.223 33.333 0.00 0.00 0.00 2.90
3164 3225 4.961730 ACTGATAAGATTCTCTGAGGTGCT 59.038 41.667 4.59 0.00 0.00 4.40
3677 3738 1.263217 CGTACTTTGCAAAAGCTCCGT 59.737 47.619 13.84 8.86 0.00 4.69
3874 4060 4.010349 GGAAATAGTTGGGGTGTGAGAAG 58.990 47.826 0.00 0.00 0.00 2.85
3885 4071 2.416547 CGTGCAGTCAGGAAATAGTTGG 59.583 50.000 0.00 0.00 0.00 3.77
3906 4093 5.048294 CCTGTTTTATTGTTCAGGTGGGTAC 60.048 44.000 0.00 0.00 41.51 3.34
3928 4116 8.408043 TGAAAGTTGATGATTACATTTGTCCT 57.592 30.769 0.00 0.00 36.82 3.85
3958 4146 3.054655 GTCTGCCAGGGACATTTTACCTA 60.055 47.826 0.00 0.00 34.23 3.08
3968 4156 4.698575 CTTTAGAATAGTCTGCCAGGGAC 58.301 47.826 2.23 0.00 35.12 4.46
3969 4157 3.134804 GCTTTAGAATAGTCTGCCAGGGA 59.865 47.826 2.23 0.00 35.12 4.20
4000 4188 4.661222 TGCCTAGAACCACATTGAAATGA 58.339 39.130 9.94 0.00 39.67 2.57
4157 4345 2.034558 GCTGTTAGCTGCACCTTTTGAA 59.965 45.455 1.02 0.00 38.45 2.69
4254 4444 0.389426 GCCACAAGCCAAAGCATCTG 60.389 55.000 0.00 0.00 43.56 2.90
4255 4445 0.541296 AGCCACAAGCCAAAGCATCT 60.541 50.000 0.00 0.00 45.47 2.90
4256 4446 1.133790 CTAGCCACAAGCCAAAGCATC 59.866 52.381 0.00 0.00 45.47 3.91
4257 4447 1.180029 CTAGCCACAAGCCAAAGCAT 58.820 50.000 0.00 0.00 45.47 3.79
4258 4448 0.110295 TCTAGCCACAAGCCAAAGCA 59.890 50.000 0.00 0.00 45.47 3.91
4259 4449 1.068264 GTTCTAGCCACAAGCCAAAGC 60.068 52.381 0.00 0.00 45.47 3.51
4260 4450 2.229792 TGTTCTAGCCACAAGCCAAAG 58.770 47.619 0.00 0.00 45.47 2.77
4261 4451 2.356665 TGTTCTAGCCACAAGCCAAA 57.643 45.000 0.00 0.00 45.47 3.28
4262 4452 2.557924 CAATGTTCTAGCCACAAGCCAA 59.442 45.455 0.00 0.00 45.47 4.52
4263 4453 2.161855 CAATGTTCTAGCCACAAGCCA 58.838 47.619 0.00 0.00 45.47 4.75
4264 4454 1.135286 GCAATGTTCTAGCCACAAGCC 60.135 52.381 9.61 0.00 45.47 4.35
4265 4455 1.815003 AGCAATGTTCTAGCCACAAGC 59.185 47.619 11.51 11.51 44.25 4.01
4266 4456 2.816087 ACAGCAATGTTCTAGCCACAAG 59.184 45.455 0.00 0.00 0.00 3.16
4267 4457 2.813754 GACAGCAATGTTCTAGCCACAA 59.186 45.455 0.00 0.00 0.00 3.33
4268 4458 2.038952 AGACAGCAATGTTCTAGCCACA 59.961 45.455 0.00 0.00 0.00 4.17
4269 4459 2.704572 AGACAGCAATGTTCTAGCCAC 58.295 47.619 0.00 0.00 0.00 5.01
4270 4460 4.551702 TTAGACAGCAATGTTCTAGCCA 57.448 40.909 0.00 0.00 0.00 4.75
4271 4461 5.007136 GTGATTAGACAGCAATGTTCTAGCC 59.993 44.000 0.00 0.00 0.00 3.93
4379 4570 3.431766 GCGGTATTTAGGTGGATCACAGT 60.432 47.826 0.00 0.00 35.86 3.55
4405 4598 2.897969 GGACATATACAGGTGGGTCGAT 59.102 50.000 0.00 0.00 0.00 3.59
4546 4822 7.041635 TCATACATATGAAGTTTTGGGCATG 57.958 36.000 10.38 0.00 39.58 4.06
4550 4826 6.985117 CCCATCATACATATGAAGTTTTGGG 58.015 40.000 17.30 17.30 44.80 4.12
4558 4834 4.999469 ACTGCCCCATCATACATATGAA 57.001 40.909 10.38 0.00 44.96 2.57
4616 4892 0.964860 TGTTGACATGCCCCATTCGG 60.965 55.000 0.00 0.00 0.00 4.30
4648 4924 9.108284 CATGTAATCACATTCTACCATACAACA 57.892 33.333 0.00 0.00 42.98 3.33
4741 5018 3.411446 CAAAGGTGCTACTGTCCATTGA 58.589 45.455 0.00 0.00 33.52 2.57
4751 5028 8.789762 TCTAACTAAAAATTCCAAAGGTGCTAC 58.210 33.333 0.00 0.00 0.00 3.58
4871 5148 1.439543 AGAGGCTGTTTCCAGGACTT 58.560 50.000 0.00 0.00 39.22 3.01
4919 5198 1.073199 CGGCCACTTTGGGTCTTCT 59.927 57.895 2.24 0.00 38.19 2.85
4978 5260 2.239400 AGTTTCTTAACAAGGGCAGCC 58.761 47.619 1.26 1.26 36.70 4.85
5077 5359 0.987294 ACATTACTGCAGGGTGAGCT 59.013 50.000 19.93 0.00 0.00 4.09
5078 5360 1.826385 AACATTACTGCAGGGTGAGC 58.174 50.000 19.93 0.00 0.00 4.26
5079 5361 2.489329 CCAAACATTACTGCAGGGTGAG 59.511 50.000 19.93 6.29 0.00 3.51
5080 5362 2.158534 ACCAAACATTACTGCAGGGTGA 60.159 45.455 19.93 0.55 0.00 4.02
5081 5363 2.238521 ACCAAACATTACTGCAGGGTG 58.761 47.619 19.93 15.27 0.00 4.61
5082 5364 2.675658 ACCAAACATTACTGCAGGGT 57.324 45.000 19.93 9.94 0.00 4.34
5083 5365 3.119495 GCTAACCAAACATTACTGCAGGG 60.119 47.826 19.93 9.25 0.00 4.45
5084 5366 3.119495 GGCTAACCAAACATTACTGCAGG 60.119 47.826 19.93 1.96 35.26 4.85
5085 5367 3.505680 TGGCTAACCAAACATTACTGCAG 59.494 43.478 13.48 13.48 45.37 4.41
5086 5368 3.491342 TGGCTAACCAAACATTACTGCA 58.509 40.909 0.00 0.00 45.37 4.41
5114 5396 5.878406 ATCTCTAACCATCCGATCAAGTT 57.122 39.130 0.00 0.00 0.00 2.66
5163 5445 6.088016 TCATCCTTGTGAATTTGAAACCTG 57.912 37.500 0.00 0.00 0.00 4.00
5166 5448 6.638468 GTGACTCATCCTTGTGAATTTGAAAC 59.362 38.462 0.00 0.00 0.00 2.78
5199 5481 5.419542 TGTCATATAAGAGCTTGGTCACAC 58.580 41.667 2.64 0.00 0.00 3.82
5200 5482 5.675684 TGTCATATAAGAGCTTGGTCACA 57.324 39.130 2.64 0.00 0.00 3.58
5201 5483 5.874810 TGTTGTCATATAAGAGCTTGGTCAC 59.125 40.000 2.64 0.00 0.00 3.67
5202 5484 6.048732 TGTTGTCATATAAGAGCTTGGTCA 57.951 37.500 2.64 0.00 0.00 4.02
5203 5485 6.985188 TTGTTGTCATATAAGAGCTTGGTC 57.015 37.500 0.00 0.00 0.00 4.02
5277 5559 4.997565 ACTTGTTCTTGAACCACACAATG 58.002 39.130 10.51 0.00 0.00 2.82
5278 5560 4.949856 AGACTTGTTCTTGAACCACACAAT 59.050 37.500 10.51 0.00 0.00 2.71
5279 5561 4.155826 CAGACTTGTTCTTGAACCACACAA 59.844 41.667 10.51 0.00 28.96 3.33
5281 5563 3.065371 CCAGACTTGTTCTTGAACCACAC 59.935 47.826 10.51 1.77 28.96 3.82
5282 5564 3.278574 CCAGACTTGTTCTTGAACCACA 58.721 45.455 10.51 0.00 28.96 4.17
5385 5763 6.245890 TGAAGGGAATGGTGTTTTGAAATT 57.754 33.333 0.00 0.00 0.00 1.82
5402 5780 1.002087 AGTAACGGTGAAGCTGAAGGG 59.998 52.381 0.00 0.00 0.00 3.95
5697 6081 6.809869 AGGAAAAATTCAAAACTCCACAGAG 58.190 36.000 0.00 0.00 46.36 3.35
6126 6528 3.563479 GGGGCTCCTCTTTGATTTGGTTA 60.563 47.826 0.00 0.00 0.00 2.85
6182 6584 2.674380 CCTCAGGGTGGCTTGTGC 60.674 66.667 0.00 0.00 38.76 4.57
6314 6719 9.868277 GAAATATCTGATCTGTATCCCAGTTAG 57.132 37.037 0.00 0.00 42.19 2.34
6549 6954 0.400213 GGTGGTCAGTGGAACCATCA 59.600 55.000 8.96 0.00 37.80 3.07
6621 7026 1.147824 CCTCCTGCCTGTATGCCAG 59.852 63.158 0.00 0.00 41.15 4.85
6626 7031 2.216148 GCTGTCCTCCTGCCTGTAT 58.784 57.895 0.00 0.00 32.24 2.29
6718 7123 3.754965 CTGGTTTCATTTCCCAGTCTGA 58.245 45.455 0.00 0.00 40.72 3.27
6781 7186 8.462016 ACTATTTGACATGCTTTTCTTATCACC 58.538 33.333 0.00 0.00 0.00 4.02
6788 7193 9.507329 TCTTCTTACTATTTGACATGCTTTTCT 57.493 29.630 0.00 0.00 0.00 2.52
6789 7194 9.766277 CTCTTCTTACTATTTGACATGCTTTTC 57.234 33.333 0.00 0.00 0.00 2.29
6807 7212 2.365617 GGATGCCGATGACCTCTTCTTA 59.634 50.000 0.00 0.00 0.00 2.10
6920 7325 1.035139 CTTTGCTTGAGTGCCACCTT 58.965 50.000 0.00 0.00 0.00 3.50
7008 7413 0.033601 ACACAACCTTTGCAGGGACA 60.034 50.000 13.63 0.00 46.01 4.02
7053 7458 1.045350 CAGCAGCTAGAGGTGGCCTA 61.045 60.000 3.32 0.00 43.24 3.93
7106 7511 6.069440 TCCTGTTGATTCCTATGTTGGATCTT 60.069 38.462 0.00 0.00 35.83 2.40
7377 7782 1.305887 CCCCCTTAGTGGAGGTCGT 60.306 63.158 0.00 0.00 38.35 4.34
7693 8101 7.548196 TCACGTAAACTTCACAGAGAAAATT 57.452 32.000 0.00 0.00 35.40 1.82
7694 8102 7.548196 TTCACGTAAACTTCACAGAGAAAAT 57.452 32.000 0.00 0.00 35.40 1.82
7695 8103 6.971527 TTCACGTAAACTTCACAGAGAAAA 57.028 33.333 0.00 0.00 35.40 2.29
7696 8104 7.924412 AGTATTCACGTAAACTTCACAGAGAAA 59.076 33.333 0.00 0.00 35.40 2.52
7699 8107 6.032565 CGAGTATTCACGTAAACTTCACAGAG 59.967 42.308 0.00 0.00 0.00 3.35
7703 8111 5.400485 ACACGAGTATTCACGTAAACTTCAC 59.600 40.000 0.00 0.00 38.65 3.18
7714 8124 4.896238 CACGAACAAAACACGAGTATTCAC 59.104 41.667 0.00 0.00 0.00 3.18
7741 8151 4.123497 TGAAATGTACCGATCAGAGTGG 57.877 45.455 0.00 0.00 0.00 4.00
7768 8180 5.596845 GGTTTGATAAAGAGCAAAACACCA 58.403 37.500 0.00 0.00 45.91 4.17
7823 8236 3.252458 ACCTGCAACAAGTAATTCGGAAC 59.748 43.478 0.00 0.00 0.00 3.62
7824 8237 3.482436 ACCTGCAACAAGTAATTCGGAA 58.518 40.909 0.00 0.00 0.00 4.30
7825 8238 3.134574 ACCTGCAACAAGTAATTCGGA 57.865 42.857 0.00 0.00 0.00 4.55
7826 8239 4.201910 CCATACCTGCAACAAGTAATTCGG 60.202 45.833 0.00 0.00 0.00 4.30
7827 8240 4.634004 TCCATACCTGCAACAAGTAATTCG 59.366 41.667 0.00 0.00 0.00 3.34
7828 8241 6.699575 ATCCATACCTGCAACAAGTAATTC 57.300 37.500 0.00 0.00 0.00 2.17
7829 8242 7.480760 AAATCCATACCTGCAACAAGTAATT 57.519 32.000 0.00 0.00 0.00 1.40
7830 8243 8.766994 ATAAATCCATACCTGCAACAAGTAAT 57.233 30.769 0.00 0.00 0.00 1.89
7831 8244 8.052748 AGATAAATCCATACCTGCAACAAGTAA 58.947 33.333 0.00 0.00 0.00 2.24
7832 8245 7.573710 AGATAAATCCATACCTGCAACAAGTA 58.426 34.615 0.00 0.00 0.00 2.24
7833 8246 6.426587 AGATAAATCCATACCTGCAACAAGT 58.573 36.000 0.00 0.00 0.00 3.16
7834 8247 6.949352 AGATAAATCCATACCTGCAACAAG 57.051 37.500 0.00 0.00 0.00 3.16
7835 8248 7.801104 TCTAGATAAATCCATACCTGCAACAA 58.199 34.615 0.00 0.00 0.00 2.83
7836 8249 7.373617 TCTAGATAAATCCATACCTGCAACA 57.626 36.000 0.00 0.00 0.00 3.33
7837 8250 7.880195 ACATCTAGATAAATCCATACCTGCAAC 59.120 37.037 4.54 0.00 0.00 4.17
7838 8251 7.977818 ACATCTAGATAAATCCATACCTGCAA 58.022 34.615 4.54 0.00 0.00 4.08
7839 8252 7.559335 ACATCTAGATAAATCCATACCTGCA 57.441 36.000 4.54 0.00 0.00 4.41
7886 8299 9.695526 CATTCCAAATTACTCATCACAGAAAAA 57.304 29.630 0.00 0.00 0.00 1.94
7887 8300 8.306038 CCATTCCAAATTACTCATCACAGAAAA 58.694 33.333 0.00 0.00 0.00 2.29
7888 8301 7.669304 TCCATTCCAAATTACTCATCACAGAAA 59.331 33.333 0.00 0.00 0.00 2.52
7889 8302 7.174413 TCCATTCCAAATTACTCATCACAGAA 58.826 34.615 0.00 0.00 0.00 3.02
7890 8303 6.720309 TCCATTCCAAATTACTCATCACAGA 58.280 36.000 0.00 0.00 0.00 3.41
7891 8304 6.039047 CCTCCATTCCAAATTACTCATCACAG 59.961 42.308 0.00 0.00 0.00 3.66
7892 8305 5.887598 CCTCCATTCCAAATTACTCATCACA 59.112 40.000 0.00 0.00 0.00 3.58
7893 8306 5.300286 CCCTCCATTCCAAATTACTCATCAC 59.700 44.000 0.00 0.00 0.00 3.06
7894 8307 5.193527 TCCCTCCATTCCAAATTACTCATCA 59.806 40.000 0.00 0.00 0.00 3.07
7895 8308 5.694995 TCCCTCCATTCCAAATTACTCATC 58.305 41.667 0.00 0.00 0.00 2.92
7896 8309 5.194537 ACTCCCTCCATTCCAAATTACTCAT 59.805 40.000 0.00 0.00 0.00 2.90
7897 8310 4.540099 ACTCCCTCCATTCCAAATTACTCA 59.460 41.667 0.00 0.00 0.00 3.41
7898 8311 4.884164 CACTCCCTCCATTCCAAATTACTC 59.116 45.833 0.00 0.00 0.00 2.59
7899 8312 4.292306 ACACTCCCTCCATTCCAAATTACT 59.708 41.667 0.00 0.00 0.00 2.24
7900 8313 4.600062 ACACTCCCTCCATTCCAAATTAC 58.400 43.478 0.00 0.00 0.00 1.89
7901 8314 4.946160 ACACTCCCTCCATTCCAAATTA 57.054 40.909 0.00 0.00 0.00 1.40
7902 8315 3.833559 ACACTCCCTCCATTCCAAATT 57.166 42.857 0.00 0.00 0.00 1.82
7903 8316 3.833559 AACACTCCCTCCATTCCAAAT 57.166 42.857 0.00 0.00 0.00 2.32
7904 8317 3.913799 TCTAACACTCCCTCCATTCCAAA 59.086 43.478 0.00 0.00 0.00 3.28
7905 8318 3.526899 TCTAACACTCCCTCCATTCCAA 58.473 45.455 0.00 0.00 0.00 3.53
7906 8319 3.199442 TCTAACACTCCCTCCATTCCA 57.801 47.619 0.00 0.00 0.00 3.53
7907 8320 4.569719 TTTCTAACACTCCCTCCATTCC 57.430 45.455 0.00 0.00 0.00 3.01
7908 8321 6.292150 CCTATTTCTAACACTCCCTCCATTC 58.708 44.000 0.00 0.00 0.00 2.67
7909 8322 5.398012 GCCTATTTCTAACACTCCCTCCATT 60.398 44.000 0.00 0.00 0.00 3.16
7910 8323 4.103311 GCCTATTTCTAACACTCCCTCCAT 59.897 45.833 0.00 0.00 0.00 3.41
7911 8324 3.454812 GCCTATTTCTAACACTCCCTCCA 59.545 47.826 0.00 0.00 0.00 3.86
7912 8325 3.454812 TGCCTATTTCTAACACTCCCTCC 59.545 47.826 0.00 0.00 0.00 4.30
7913 8326 4.755266 TGCCTATTTCTAACACTCCCTC 57.245 45.455 0.00 0.00 0.00 4.30
7914 8327 4.536489 AGTTGCCTATTTCTAACACTCCCT 59.464 41.667 0.00 0.00 0.00 4.20
7915 8328 4.844884 AGTTGCCTATTTCTAACACTCCC 58.155 43.478 0.00 0.00 0.00 4.30
7916 8329 5.705905 ACAAGTTGCCTATTTCTAACACTCC 59.294 40.000 1.81 0.00 0.00 3.85
8060 8487 4.569653 CCATGAGTTTGAGGGGGATGTTAA 60.570 45.833 0.00 0.00 0.00 2.01
8066 8493 0.698238 CACCATGAGTTTGAGGGGGA 59.302 55.000 0.00 0.00 0.00 4.81
8089 8524 4.843728 TCTCTCCAAACTCAGTGTTGTTT 58.156 39.130 9.86 9.86 39.13 2.83
8135 8573 0.322546 ATTTCCTGACGAAGGCCCAC 60.323 55.000 0.00 0.00 46.92 4.61
8419 8866 4.438200 GGAAGACGAAGAAACAACTTGCAA 60.438 41.667 0.00 0.00 0.00 4.08
8594 9042 2.681848 TCTCCTTCGTGTTCTCCGATAC 59.318 50.000 0.00 0.00 33.81 2.24
8629 9077 0.611896 TGTCTCTGCTCCCACATCGA 60.612 55.000 0.00 0.00 0.00 3.59


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

AutoCloner maintained by Alex Coulton.