Multiple sequence alignment - TraesCS2A01G209100

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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 TraesCS2A01G209100 chr2A 100.000 9359 0 0 1 9359 192513065 192503707 0.000000e+00 17283.0
1 TraesCS2A01G209100 chr2A 94.853 136 7 0 7180 7315 321155659 321155524 7.360000e-51 213.0
2 TraesCS2A01G209100 chr2A 90.164 61 4 2 1 60 763366756 763366815 2.800000e-10 78.7
3 TraesCS2A01G209100 chr2D 97.219 6904 132 24 306 7181 177865564 177858693 0.000000e+00 11631.0
4 TraesCS2A01G209100 chr2D 97.637 1989 30 8 7305 9281 177858694 177856711 0.000000e+00 3397.0
5 TraesCS2A01G209100 chr2D 94.643 56 3 0 9285 9340 595549524 595549469 4.660000e-13 87.9
6 TraesCS2A01G209100 chr2B 95.374 6918 233 38 314 7180 234640914 234634033 0.000000e+00 10922.0
7 TraesCS2A01G209100 chr2B 94.127 1805 50 27 7308 9099 234634030 234632269 0.000000e+00 2695.0
8 TraesCS2A01G209100 chr3A 94.043 470 14 5 511 972 589604047 589603584 0.000000e+00 701.0
9 TraesCS2A01G209100 chr3A 94.815 405 12 3 576 972 589603561 589603158 2.870000e-174 623.0
10 TraesCS2A01G209100 chr3A 93.612 407 12 4 513 911 589602847 589602447 6.260000e-166 595.0
11 TraesCS2A01G209100 chr3A 86.456 443 33 15 71 509 589606149 589605730 2.380000e-125 460.0
12 TraesCS2A01G209100 chr3A 95.000 60 3 0 1 60 172971278 172971219 2.780000e-15 95.3
13 TraesCS2A01G209100 chr6D 88.945 199 18 4 2638 2833 53269873 53269676 9.390000e-60 243.0
14 TraesCS2A01G209100 chr6D 94.643 56 3 0 9285 9340 433638067 433638122 4.660000e-13 87.9
15 TraesCS2A01G209100 chr5D 88.945 199 18 4 2638 2833 440489643 440489446 9.390000e-60 243.0
16 TraesCS2A01G209100 chr5D 94.643 56 3 0 9285 9340 240855430 240855375 4.660000e-13 87.9
17 TraesCS2A01G209100 chr5D 94.643 56 3 0 9285 9340 368736348 368736293 4.660000e-13 87.9
18 TraesCS2A01G209100 chr5D 94.643 56 3 0 9285 9340 368740374 368740319 4.660000e-13 87.9
19 TraesCS2A01G209100 chr5D 90.000 60 5 1 8 66 343098868 343098809 1.010000e-09 76.8
20 TraesCS2A01G209100 chr3D 97.656 128 2 1 7179 7306 166094720 166094846 1.580000e-52 219.0
21 TraesCS2A01G209100 chr3D 88.136 59 5 2 2 60 24871978 24872034 1.690000e-07 69.4
22 TraesCS2A01G209100 chr5B 96.212 132 5 0 7175 7306 96879074 96878943 5.690000e-52 217.0
23 TraesCS2A01G209100 chr4A 94.815 135 7 0 7180 7314 722866898 722866764 2.650000e-50 211.0
24 TraesCS2A01G209100 chr4A 90.000 70 7 0 1 70 37008548 37008479 3.600000e-14 91.6
25 TraesCS2A01G209100 chr7B 93.525 139 9 0 7177 7315 219565278 219565140 3.430000e-49 207.0
26 TraesCS2A01G209100 chr7B 87.952 166 15 4 7143 7306 720120552 720120714 3.450000e-44 191.0
27 TraesCS2A01G209100 chr7B 89.041 73 7 1 1 73 336193034 336192963 1.290000e-13 89.8
28 TraesCS2A01G209100 chr6B 91.333 150 11 2 7157 7306 191197986 191198133 4.430000e-48 204.0
29 TraesCS2A01G209100 chr3B 90.196 153 13 2 7160 7310 20356543 20356695 2.060000e-46 198.0
30 TraesCS2A01G209100 chr3B 89.375 160 13 2 7148 7306 544781580 544781424 2.060000e-46 198.0
31 TraesCS2A01G209100 chr6A 94.915 59 3 0 2 60 68625664 68625722 1.000000e-14 93.5
32 TraesCS2A01G209100 chr6A 92.308 52 4 0 2776 2827 305369801 305369750 3.620000e-09 75.0
33 TraesCS2A01G209100 chr4D 94.643 56 3 0 9285 9340 20431112 20431057 4.660000e-13 87.9
34 TraesCS2A01G209100 chr4D 94.643 56 3 0 9285 9340 473839638 473839693 4.660000e-13 87.9
35 TraesCS2A01G209100 chr4D 94.643 56 3 0 9285 9340 473843668 473843723 4.660000e-13 87.9
36 TraesCS2A01G209100 chr1D 94.643 56 3 0 9285 9340 382212915 382212970 4.660000e-13 87.9
37 TraesCS2A01G209100 chr1B 88.889 72 7 1 1 72 395987272 395987202 4.660000e-13 87.9
38 TraesCS2A01G209100 chr1B 83.333 72 10 2 4 73 633139910 633139981 2.180000e-06 65.8


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 TraesCS2A01G209100 chr2A 192503707 192513065 9358 True 17283.00 17283 100.0000 1 9359 1 chr2A.!!$R1 9358
1 TraesCS2A01G209100 chr2D 177856711 177865564 8853 True 7514.00 11631 97.4280 306 9281 2 chr2D.!!$R2 8975
2 TraesCS2A01G209100 chr2B 234632269 234640914 8645 True 6808.50 10922 94.7505 314 9099 2 chr2B.!!$R1 8785
3 TraesCS2A01G209100 chr3A 589602447 589606149 3702 True 594.75 701 92.2315 71 972 4 chr3A.!!$R2 901

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
172 174 0.034960 TTTTGAATGGCCGGATCCGA 60.035 50.000 35.42 16.50 42.83 4.55 F
176 178 1.099689 GAATGGCCGGATCCGAAAAA 58.900 50.000 35.42 17.44 42.83 1.94 F
415 419 1.202794 GGCGGCTAGTAGAGTCCTAGT 60.203 57.143 0.00 0.00 35.40 2.57 F
416 420 2.038295 GGCGGCTAGTAGAGTCCTAGTA 59.962 54.545 0.00 0.00 35.40 1.82 F
2402 4545 2.126882 AGGTTGCACCATCTATGCCTA 58.873 47.619 7.86 0.00 41.95 3.93 F
2562 4732 1.035385 CAGCAGCAGCATCATTCCCA 61.035 55.000 3.17 0.00 45.49 4.37 F
2632 4802 1.065401 CAGCAACAGCAAACGAGGAAA 59.935 47.619 0.00 0.00 0.00 3.13 F
4604 7237 1.005097 TCAGCTTCTGTGGATGCCAAT 59.995 47.619 0.00 0.00 41.66 3.16 F
5123 7756 0.181114 TTGAGCCGGATGATTGGGAG 59.819 55.000 5.05 0.00 0.00 4.30 F
7195 9830 0.033796 ACATACTCCCTCCGTCCGAA 60.034 55.000 0.00 0.00 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1544 3674 1.031571 GCAATCCGGGTGAATCTGCA 61.032 55.000 0.00 0.0 31.15 4.41 R
1735 3865 2.001872 CAGCACATGTTAGTCATCGCA 58.998 47.619 0.00 0.0 35.59 5.10 R
2402 4545 3.610911 GCTGTTTTAGAGCTGGTGGTAT 58.389 45.455 0.00 0.0 33.37 2.73 R
2483 4629 2.503061 CTGCTGGGACGAGGGATG 59.497 66.667 0.00 0.0 0.00 3.51 R
4048 6681 2.158475 TGATGTCAAGCCTGAACCCTTT 60.158 45.455 0.00 0.0 31.88 3.11 R
4604 7237 2.306805 AGAATTGGCCTCAGACACATCA 59.693 45.455 3.32 0.0 0.00 3.07 R
4880 7513 0.322975 TTCTCCCAGCTGCAGACTTC 59.677 55.000 20.43 0.0 0.00 3.01 R
6023 8656 2.369860 TGCTTCAGCTTCCTCTCTTTCA 59.630 45.455 0.00 0.0 42.66 2.69 R
7283 9918 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.0 44.66 2.12 R
9318 11969 0.040204 CTGTTTGGGCAAGGGGAGAT 59.960 55.000 0.00 0.0 0.00 2.75 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
35 36 9.598517 AAGTTTGTAAAGCTTGAATTTGATCAA 57.401 25.926 3.38 3.38 45.94 2.57
36 37 9.598517 AGTTTGTAAAGCTTGAATTTGATCAAA 57.401 25.926 22.52 22.52 38.75 2.69
39 40 9.598517 TTGTAAAGCTTGAATTTGATCAAAACT 57.401 25.926 23.91 14.39 38.75 2.66
80 81 6.496338 AAATCAAAGGAAGTATGTCCGAAC 57.504 37.500 0.00 0.00 43.03 3.95
87 88 9.158233 CAAAGGAAGTATGTCCGAACTTTAATA 57.842 33.333 0.00 0.00 43.03 0.98
158 160 9.944663 GTTTGAAATATATGCGGATAGTTTTGA 57.055 29.630 2.29 0.00 0.00 2.69
162 164 9.559958 GAAATATATGCGGATAGTTTTGAATGG 57.440 33.333 2.29 0.00 0.00 3.16
167 169 2.650322 GGATAGTTTTGAATGGCCGGA 58.350 47.619 5.05 0.00 0.00 5.14
171 173 0.100503 GTTTTGAATGGCCGGATCCG 59.899 55.000 27.65 27.65 39.44 4.18
172 174 0.034960 TTTTGAATGGCCGGATCCGA 60.035 50.000 35.42 16.50 42.83 4.55
173 175 0.034960 TTTGAATGGCCGGATCCGAA 60.035 50.000 35.42 20.00 42.83 4.30
175 177 0.034960 TGAATGGCCGGATCCGAAAA 60.035 50.000 35.42 19.27 42.83 2.29
176 178 1.099689 GAATGGCCGGATCCGAAAAA 58.900 50.000 35.42 17.44 42.83 1.94
415 419 1.202794 GGCGGCTAGTAGAGTCCTAGT 60.203 57.143 0.00 0.00 35.40 2.57
416 420 2.038295 GGCGGCTAGTAGAGTCCTAGTA 59.962 54.545 0.00 0.00 35.40 1.82
417 421 3.328505 GCGGCTAGTAGAGTCCTAGTAG 58.671 54.545 0.00 9.03 45.41 2.57
484 488 3.556423 CCATCCAATCGCATCTGATCTGA 60.556 47.826 4.63 4.63 0.00 3.27
526 2211 3.945640 AGGGTCTCTCTCTCTCCTAAC 57.054 52.381 0.00 0.00 0.00 2.34
537 2222 5.516984 TCTCTCTCCTAACCGGAACTAAAT 58.483 41.667 9.46 0.00 42.53 1.40
538 2223 5.593502 TCTCTCTCCTAACCGGAACTAAATC 59.406 44.000 9.46 0.00 42.53 2.17
539 2224 5.266788 TCTCTCCTAACCGGAACTAAATCA 58.733 41.667 9.46 0.00 42.53 2.57
540 2225 5.718130 TCTCTCCTAACCGGAACTAAATCAA 59.282 40.000 9.46 0.00 42.53 2.57
541 2226 6.211986 TCTCTCCTAACCGGAACTAAATCAAA 59.788 38.462 9.46 0.00 42.53 2.69
1544 3674 3.945981 TTGCATGCATGTTCTCAATGT 57.054 38.095 26.79 0.00 0.00 2.71
1853 3991 4.782019 TCTGCTGTTTTGTTTGTGTTCT 57.218 36.364 0.00 0.00 0.00 3.01
1854 3992 5.132897 TCTGCTGTTTTGTTTGTGTTCTT 57.867 34.783 0.00 0.00 0.00 2.52
1855 3993 5.537188 TCTGCTGTTTTGTTTGTGTTCTTT 58.463 33.333 0.00 0.00 0.00 2.52
1971 4109 4.643784 CCTATCTTTTCCAGCTTGCATCTT 59.356 41.667 0.00 0.00 0.00 2.40
2402 4545 2.126882 AGGTTGCACCATCTATGCCTA 58.873 47.619 7.86 0.00 41.95 3.93
2490 4636 3.210528 GCAGCAGCAGCATCCCTC 61.211 66.667 4.63 0.00 45.49 4.30
2491 4637 2.895865 CAGCAGCAGCATCCCTCG 60.896 66.667 3.17 0.00 45.49 4.63
2492 4638 3.397439 AGCAGCAGCATCCCTCGT 61.397 61.111 3.17 0.00 45.49 4.18
2493 4639 2.894387 GCAGCAGCATCCCTCGTC 60.894 66.667 0.00 0.00 41.58 4.20
2494 4640 2.202987 CAGCAGCATCCCTCGTCC 60.203 66.667 0.00 0.00 0.00 4.79
2495 4641 3.474570 AGCAGCATCCCTCGTCCC 61.475 66.667 0.00 0.00 0.00 4.46
2496 4642 3.785859 GCAGCATCCCTCGTCCCA 61.786 66.667 0.00 0.00 0.00 4.37
2497 4643 2.503061 CAGCATCCCTCGTCCCAG 59.497 66.667 0.00 0.00 0.00 4.45
2498 4644 3.474570 AGCATCCCTCGTCCCAGC 61.475 66.667 0.00 0.00 0.00 4.85
2499 4645 3.785859 GCATCCCTCGTCCCAGCA 61.786 66.667 0.00 0.00 0.00 4.41
2500 4646 2.503061 CATCCCTCGTCCCAGCAG 59.497 66.667 0.00 0.00 0.00 4.24
2501 4647 3.474570 ATCCCTCGTCCCAGCAGC 61.475 66.667 0.00 0.00 0.00 5.25
2503 4649 4.463879 CCCTCGTCCCAGCAGCAG 62.464 72.222 0.00 0.00 0.00 4.24
2538 4684 2.195139 GCAGCAGCATCATCCCCT 59.805 61.111 0.00 0.00 41.58 4.79
2544 4714 4.881440 GCATCATCCCCTGCCGCA 62.881 66.667 0.00 0.00 32.15 5.69
2558 4728 2.771639 CCGCAGCAGCAGCATCATT 61.772 57.895 10.77 0.00 45.49 2.57
2561 4731 1.734137 CAGCAGCAGCATCATTCCC 59.266 57.895 3.17 0.00 45.49 3.97
2562 4732 1.035385 CAGCAGCAGCATCATTCCCA 61.035 55.000 3.17 0.00 45.49 4.37
2568 4738 2.829914 GCATCATTCCCAGCCGCA 60.830 61.111 0.00 0.00 0.00 5.69
2632 4802 1.065401 CAGCAACAGCAAACGAGGAAA 59.935 47.619 0.00 0.00 0.00 3.13
2972 5175 3.718434 TGCTCATACAATCCCTCCTCAAT 59.282 43.478 0.00 0.00 0.00 2.57
3097 5300 6.803154 AATACTAACAAAGAAGTGGTGCTC 57.197 37.500 0.00 0.00 0.00 4.26
3123 5326 2.092914 GGCCTTCACCTAATGTAGCAGT 60.093 50.000 0.00 0.00 0.00 4.40
3124 5327 2.939103 GCCTTCACCTAATGTAGCAGTG 59.061 50.000 0.00 0.00 0.00 3.66
3277 5480 3.279434 CAGGTTTAGTTATCCTGCCACC 58.721 50.000 0.00 0.00 41.46 4.61
3528 5731 9.226606 ACATCGACAAAAGGATAATGAAGTTAA 57.773 29.630 0.00 0.00 0.00 2.01
3646 5849 1.450312 CGTGGAGAAGCATCCCACC 60.450 63.158 18.07 7.08 40.75 4.61
3773 5976 9.822727 AAAAGAAAGAATCCCTTCCAATAACTA 57.177 29.630 0.00 0.00 33.02 2.24
3846 6049 1.749286 GCCACAACAACCACAGGTACT 60.749 52.381 0.00 0.00 43.88 2.73
3849 6052 3.541632 CACAACAACCACAGGTACTCTT 58.458 45.455 0.00 0.00 34.60 2.85
4033 6666 5.482908 ACAAAGAGCTTCGATAGTGAACAT 58.517 37.500 0.00 0.00 37.40 2.71
4043 6676 7.517417 GCTTCGATAGTGAACATGTGGATTTAG 60.517 40.741 0.00 0.00 37.40 1.85
4048 6681 4.009675 GTGAACATGTGGATTTAGCCAGA 58.990 43.478 0.00 0.00 38.95 3.86
4080 6713 2.159421 GCTTGACATCAGCAACATCTGG 60.159 50.000 0.00 0.00 34.91 3.86
4240 6873 1.930908 GCTGCTGATGTTCCTGCCAC 61.931 60.000 0.00 0.00 0.00 5.01
4276 6909 1.446907 AAATTGTCCTCTGCGAGCAG 58.553 50.000 18.20 18.20 44.86 4.24
4383 7016 7.259882 TGAATCTGGTGATGTCAAAATTATGC 58.740 34.615 0.00 0.00 32.44 3.14
4478 7111 3.019564 GCCTGGTAATTCAGATGCAACT 58.980 45.455 0.00 0.00 36.93 3.16
4604 7237 1.005097 TCAGCTTCTGTGGATGCCAAT 59.995 47.619 0.00 0.00 41.66 3.16
4880 7513 1.078759 CTGCAGAGCTTACCCGAACG 61.079 60.000 8.42 0.00 0.00 3.95
5090 7723 3.313750 GCGATGTGCGAGGATGAC 58.686 61.111 0.00 0.00 44.57 3.06
5123 7756 0.181114 TTGAGCCGGATGATTGGGAG 59.819 55.000 5.05 0.00 0.00 4.30
5154 7787 3.055530 AGACATGTCTACTCCAAAGCTGG 60.056 47.826 26.87 0.00 40.26 4.85
5193 7826 1.160137 CCAGGCTAGTGCAGTTCAAC 58.840 55.000 0.00 0.00 41.91 3.18
5296 7929 1.067295 AGTCTTCCTGTTGGCATCCA 58.933 50.000 0.00 0.00 0.00 3.41
5515 8148 2.010582 TTGACAAACGGCCCAGCAAC 62.011 55.000 0.00 0.00 0.00 4.17
5879 8512 7.809331 GTGATTTCACAGATATTTGACAAAGCA 59.191 33.333 6.77 4.77 45.75 3.91
6023 8656 1.981495 CAAGAGGAGTTTGAGAGGGGT 59.019 52.381 0.00 0.00 0.00 4.95
6032 8665 3.326297 AGTTTGAGAGGGGTGAAAGAGAG 59.674 47.826 0.00 0.00 0.00 3.20
7186 9821 9.802039 TTATTTTCTTTGTAACACATACTCCCT 57.198 29.630 0.00 0.00 35.42 4.20
7187 9822 7.739498 TTTTCTTTGTAACACATACTCCCTC 57.261 36.000 0.00 0.00 35.42 4.30
7188 9823 5.416271 TCTTTGTAACACATACTCCCTCC 57.584 43.478 0.00 0.00 35.42 4.30
7189 9824 3.880047 TTGTAACACATACTCCCTCCG 57.120 47.619 0.00 0.00 35.42 4.63
7190 9825 2.811410 TGTAACACATACTCCCTCCGT 58.189 47.619 0.00 0.00 35.42 4.69
7191 9826 2.756760 TGTAACACATACTCCCTCCGTC 59.243 50.000 0.00 0.00 35.42 4.79
7192 9827 1.192428 AACACATACTCCCTCCGTCC 58.808 55.000 0.00 0.00 0.00 4.79
7193 9828 1.035932 ACACATACTCCCTCCGTCCG 61.036 60.000 0.00 0.00 0.00 4.79
7194 9829 0.750546 CACATACTCCCTCCGTCCGA 60.751 60.000 0.00 0.00 0.00 4.55
7195 9830 0.033796 ACATACTCCCTCCGTCCGAA 60.034 55.000 0.00 0.00 0.00 4.30
7196 9831 1.108776 CATACTCCCTCCGTCCGAAA 58.891 55.000 0.00 0.00 0.00 3.46
7197 9832 1.479323 CATACTCCCTCCGTCCGAAAA 59.521 52.381 0.00 0.00 0.00 2.29
7198 9833 1.856629 TACTCCCTCCGTCCGAAAAT 58.143 50.000 0.00 0.00 0.00 1.82
7199 9834 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
7200 9835 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
7201 9836 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
7202 9837 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
7203 9838 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
7204 9839 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
7205 9840 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
7206 9841 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
7207 9842 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
7208 9843 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
7209 9844 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
7210 9845 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
7211 9846 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
7212 9847 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
7213 9848 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
7214 9849 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
7215 9850 8.020819 GTCCGAAAATACTTGTCATCAAAATGA 58.979 33.333 0.00 0.00 39.63 2.57
7216 9851 8.572185 TCCGAAAATACTTGTCATCAAAATGAA 58.428 29.630 0.00 0.00 43.42 2.57
7217 9852 9.357652 CCGAAAATACTTGTCATCAAAATGAAT 57.642 29.630 0.00 0.00 43.42 2.57
7225 9860 9.492973 ACTTGTCATCAAAATGAATAAAAAGGG 57.507 29.630 0.00 0.00 43.42 3.95
7226 9861 9.709495 CTTGTCATCAAAATGAATAAAAAGGGA 57.291 29.630 0.00 0.00 43.42 4.20
7228 9863 9.656040 TGTCATCAAAATGAATAAAAAGGGATG 57.344 29.630 0.00 0.00 43.42 3.51
7229 9864 9.657419 GTCATCAAAATGAATAAAAAGGGATGT 57.343 29.630 0.00 0.00 43.42 3.06
7271 9906 9.096823 ACGTATAGATACATCCCCTTTTATTCA 57.903 33.333 0.00 0.00 32.87 2.57
7277 9912 9.713684 AGATACATCCCCTTTTATTCATTTTGA 57.286 29.630 0.00 0.00 0.00 2.69
7296 9931 9.594038 CATTTTGATAATAAGTATTTCCGGACG 57.406 33.333 1.83 0.00 0.00 4.79
7297 9932 7.718272 TTTGATAATAAGTATTTCCGGACGG 57.282 36.000 1.83 3.96 0.00 4.79
7298 9933 6.653526 TGATAATAAGTATTTCCGGACGGA 57.346 37.500 1.83 9.76 43.52 4.69
7299 9934 6.684686 TGATAATAAGTATTTCCGGACGGAG 58.315 40.000 13.64 0.00 46.06 4.63
7300 9935 4.332428 AATAAGTATTTCCGGACGGAGG 57.668 45.455 13.64 0.00 46.06 4.30
7301 9936 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
7302 9937 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
7303 9938 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
7304 9939 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
7305 9940 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
7350 9985 4.579340 TCGGCAACTGGTAATTTGTTGTAA 59.421 37.500 0.00 0.00 41.93 2.41
7416 10051 5.195185 AGACTCTTAGTACTTCCTACCAGC 58.805 45.833 0.00 0.00 0.00 4.85
7439 10074 1.350193 TTCTCGCGTCTCTGCAAATC 58.650 50.000 5.77 0.00 34.15 2.17
7936 10572 7.039784 GGTGGATATAATTTATTGAGCAAGCCA 60.040 37.037 0.00 0.00 0.00 4.75
7965 10601 1.286553 TGTGGGGTGAGTTCCTTTGTT 59.713 47.619 0.00 0.00 0.00 2.83
8217 10854 0.249615 GCATCGCAGCTGATGTCCTA 60.250 55.000 20.43 0.00 45.98 2.94
8280 10917 1.734655 TCTTGAAGGAGGCCAAGACT 58.265 50.000 5.01 0.00 42.48 3.24
8702 11347 7.009179 TGTGAAGTGAAGAAGATGTATTCCT 57.991 36.000 0.00 0.00 0.00 3.36
8904 11549 0.036388 GGTTCGACTTGATGCCTCCA 60.036 55.000 0.00 0.00 0.00 3.86
9053 11698 9.269453 GTATCGTTTTATTTACTTATCTGGGCT 57.731 33.333 0.00 0.00 0.00 5.19
9061 11706 5.707242 TTACTTATCTGGGCTATCGTCTG 57.293 43.478 0.00 0.00 0.00 3.51
9065 11710 2.447408 TCTGGGCTATCGTCTGGTTA 57.553 50.000 0.00 0.00 0.00 2.85
9116 11761 3.778954 ACTGTCCCCTCTTTTCTCTTG 57.221 47.619 0.00 0.00 0.00 3.02
9263 11914 8.511604 ACCCATTGTTGTTCTATCAATCTTAG 57.488 34.615 0.00 0.00 30.74 2.18
9265 11916 8.616076 CCCATTGTTGTTCTATCAATCTTAGAC 58.384 37.037 0.00 0.00 30.74 2.59
9273 11924 9.554395 TGTTCTATCAATCTTAGACAACAAACA 57.446 29.630 0.00 0.00 0.00 2.83
9276 11927 9.942850 TCTATCAATCTTAGACAACAAACATGA 57.057 29.630 0.00 0.00 0.00 3.07
9281 11932 8.729756 CAATCTTAGACAACAAACATGACCATA 58.270 33.333 0.00 0.00 0.00 2.74
9282 11933 9.466497 AATCTTAGACAACAAACATGACCATAT 57.534 29.630 0.00 0.00 0.00 1.78
9284 11935 9.599866 TCTTAGACAACAAACATGACCATATAG 57.400 33.333 0.00 0.00 0.00 1.31
9285 11936 9.383519 CTTAGACAACAAACATGACCATATAGT 57.616 33.333 0.00 0.00 0.00 2.12
9286 11937 9.733556 TTAGACAACAAACATGACCATATAGTT 57.266 29.630 0.00 0.00 0.00 2.24
9287 11938 8.044060 AGACAACAAACATGACCATATAGTTG 57.956 34.615 0.00 0.00 39.57 3.16
9288 11939 7.121168 AGACAACAAACATGACCATATAGTTGG 59.879 37.037 0.00 0.00 42.82 3.77
9289 11940 6.945435 ACAACAAACATGACCATATAGTTGGA 59.055 34.615 0.00 0.00 39.25 3.53
9290 11941 7.450014 ACAACAAACATGACCATATAGTTGGAA 59.550 33.333 0.00 0.00 39.25 3.53
9291 11942 8.469200 CAACAAACATGACCATATAGTTGGAAT 58.531 33.333 0.00 0.00 39.25 3.01
9292 11943 8.593945 ACAAACATGACCATATAGTTGGAATT 57.406 30.769 0.00 0.00 39.25 2.17
9293 11944 9.693739 ACAAACATGACCATATAGTTGGAATTA 57.306 29.630 0.00 0.00 39.25 1.40
9319 11970 9.752228 AATTACAATTTGCAATTAGGGGAAAAT 57.248 25.926 0.00 0.00 0.00 1.82
9320 11971 8.785329 TTACAATTTGCAATTAGGGGAAAATC 57.215 30.769 0.00 0.00 0.00 2.17
9321 11972 7.019656 ACAATTTGCAATTAGGGGAAAATCT 57.980 32.000 0.00 0.00 0.00 2.40
9322 11973 7.105588 ACAATTTGCAATTAGGGGAAAATCTC 58.894 34.615 0.00 0.00 0.00 2.75
9323 11974 5.675684 TTTGCAATTAGGGGAAAATCTCC 57.324 39.130 0.00 0.00 44.54 3.71
9331 11982 2.901975 GGAAAATCTCCCCTTGCCC 58.098 57.895 0.00 0.00 38.44 5.36
9332 11983 0.041090 GGAAAATCTCCCCTTGCCCA 59.959 55.000 0.00 0.00 38.44 5.36
9333 11984 1.552254 GGAAAATCTCCCCTTGCCCAA 60.552 52.381 0.00 0.00 38.44 4.12
9334 11985 2.256306 GAAAATCTCCCCTTGCCCAAA 58.744 47.619 0.00 0.00 0.00 3.28
9335 11986 1.644509 AAATCTCCCCTTGCCCAAAC 58.355 50.000 0.00 0.00 0.00 2.93
9336 11987 0.486879 AATCTCCCCTTGCCCAAACA 59.513 50.000 0.00 0.00 0.00 2.83
9337 11988 0.040204 ATCTCCCCTTGCCCAAACAG 59.960 55.000 0.00 0.00 0.00 3.16
9338 11989 1.153756 CTCCCCTTGCCCAAACAGT 59.846 57.895 0.00 0.00 0.00 3.55
9339 11990 0.895559 CTCCCCTTGCCCAAACAGTC 60.896 60.000 0.00 0.00 0.00 3.51
9340 11991 1.153756 CCCCTTGCCCAAACAGTCT 59.846 57.895 0.00 0.00 0.00 3.24
9341 11992 0.895559 CCCCTTGCCCAAACAGTCTC 60.896 60.000 0.00 0.00 0.00 3.36
9342 11993 0.895559 CCCTTGCCCAAACAGTCTCC 60.896 60.000 0.00 0.00 0.00 3.71
9343 11994 0.895559 CCTTGCCCAAACAGTCTCCC 60.896 60.000 0.00 0.00 0.00 4.30
9344 11995 0.111253 CTTGCCCAAACAGTCTCCCT 59.889 55.000 0.00 0.00 0.00 4.20
9345 11996 0.555769 TTGCCCAAACAGTCTCCCTT 59.444 50.000 0.00 0.00 0.00 3.95
9346 11997 0.178992 TGCCCAAACAGTCTCCCTTG 60.179 55.000 0.00 0.00 0.00 3.61
9347 11998 0.110486 GCCCAAACAGTCTCCCTTGA 59.890 55.000 0.00 0.00 0.00 3.02
9348 11999 1.272147 GCCCAAACAGTCTCCCTTGAT 60.272 52.381 0.00 0.00 0.00 2.57
9349 12000 2.716217 CCCAAACAGTCTCCCTTGATC 58.284 52.381 0.00 0.00 0.00 2.92
9350 12001 2.307098 CCCAAACAGTCTCCCTTGATCT 59.693 50.000 0.00 0.00 0.00 2.75
9351 12002 3.604582 CCAAACAGTCTCCCTTGATCTC 58.395 50.000 0.00 0.00 0.00 2.75
9352 12003 3.262915 CCAAACAGTCTCCCTTGATCTCT 59.737 47.826 0.00 0.00 0.00 3.10
9353 12004 4.263243 CCAAACAGTCTCCCTTGATCTCTT 60.263 45.833 0.00 0.00 0.00 2.85
9354 12005 4.550076 AACAGTCTCCCTTGATCTCTTG 57.450 45.455 0.00 0.00 0.00 3.02
9355 12006 2.836981 ACAGTCTCCCTTGATCTCTTGG 59.163 50.000 0.00 0.00 0.00 3.61
9356 12007 3.102972 CAGTCTCCCTTGATCTCTTGGA 58.897 50.000 0.00 0.00 0.00 3.53
9357 12008 3.517100 CAGTCTCCCTTGATCTCTTGGAA 59.483 47.826 0.00 0.00 0.00 3.53
9358 12009 3.774216 AGTCTCCCTTGATCTCTTGGAAG 59.226 47.826 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 7.810766 TCAAGCTTTACAAACTTTGACAAAG 57.189 32.000 23.41 23.41 44.10 2.77
2 3 8.770438 ATTCAAGCTTTACAAACTTTGACAAA 57.230 26.923 8.55 0.00 0.00 2.83
3 4 8.770438 AATTCAAGCTTTACAAACTTTGACAA 57.230 26.923 8.55 0.00 0.00 3.18
4 5 8.655092 CAAATTCAAGCTTTACAAACTTTGACA 58.345 29.630 8.55 0.00 0.00 3.58
5 6 8.868916 TCAAATTCAAGCTTTACAAACTTTGAC 58.131 29.630 8.55 0.00 0.00 3.18
6 7 8.994429 TCAAATTCAAGCTTTACAAACTTTGA 57.006 26.923 8.55 3.47 0.00 2.69
7 8 9.853921 GATCAAATTCAAGCTTTACAAACTTTG 57.146 29.630 0.00 0.00 0.00 2.77
8 9 9.598517 TGATCAAATTCAAGCTTTACAAACTTT 57.401 25.926 0.00 0.00 0.00 2.66
9 10 9.598517 TTGATCAAATTCAAGCTTTACAAACTT 57.401 25.926 5.45 0.00 32.07 2.66
10 11 9.598517 TTTGATCAAATTCAAGCTTTACAAACT 57.401 25.926 16.91 0.00 36.97 2.66
13 14 9.598517 AGTTTTGATCAAATTCAAGCTTTACAA 57.401 25.926 21.10 0.00 36.97 2.41
44 45 9.077885 ACTTCCTTTGATTTTATTTACTCTGCA 57.922 29.630 0.00 0.00 0.00 4.41
52 53 9.238368 TCGGACATACTTCCTTTGATTTTATTT 57.762 29.630 0.00 0.00 32.88 1.40
53 54 8.801882 TCGGACATACTTCCTTTGATTTTATT 57.198 30.769 0.00 0.00 32.88 1.40
54 55 8.674607 GTTCGGACATACTTCCTTTGATTTTAT 58.325 33.333 0.00 0.00 32.88 1.40
55 56 7.881232 AGTTCGGACATACTTCCTTTGATTTTA 59.119 33.333 0.00 0.00 32.88 1.52
56 57 6.715264 AGTTCGGACATACTTCCTTTGATTTT 59.285 34.615 0.00 0.00 32.88 1.82
57 58 6.238648 AGTTCGGACATACTTCCTTTGATTT 58.761 36.000 0.00 0.00 32.88 2.17
58 59 5.805728 AGTTCGGACATACTTCCTTTGATT 58.194 37.500 0.00 0.00 32.88 2.57
59 60 5.422214 AGTTCGGACATACTTCCTTTGAT 57.578 39.130 0.00 0.00 32.88 2.57
60 61 4.884668 AGTTCGGACATACTTCCTTTGA 57.115 40.909 0.00 0.00 32.88 2.69
61 62 5.941948 AAAGTTCGGACATACTTCCTTTG 57.058 39.130 0.00 0.00 33.66 2.77
62 63 9.729281 TTATTAAAGTTCGGACATACTTCCTTT 57.271 29.630 0.00 0.00 33.66 3.11
63 64 9.729281 TTTATTAAAGTTCGGACATACTTCCTT 57.271 29.630 0.00 0.00 33.66 3.36
64 65 9.901172 ATTTATTAAAGTTCGGACATACTTCCT 57.099 29.630 0.00 0.00 33.66 3.36
68 69 8.823818 CGGAATTTATTAAAGTTCGGACATACT 58.176 33.333 8.97 0.00 34.09 2.12
69 70 8.606602 ACGGAATTTATTAAAGTTCGGACATAC 58.393 33.333 18.38 0.00 41.42 2.39
87 88 8.924691 CAAATTGTATCAAACATGACGGAATTT 58.075 29.630 0.00 0.00 38.10 1.82
92 93 6.611381 AGACAAATTGTATCAAACATGACGG 58.389 36.000 0.00 0.00 38.10 4.79
127 128 8.999431 ACTATCCGCATATATTTCAAACGAATT 58.001 29.630 0.00 0.00 0.00 2.17
130 131 7.956420 AACTATCCGCATATATTTCAAACGA 57.044 32.000 0.00 0.00 0.00 3.85
143 145 2.362077 GGCCATTCAAAACTATCCGCAT 59.638 45.455 0.00 0.00 0.00 4.73
149 151 3.222603 GGATCCGGCCATTCAAAACTAT 58.777 45.455 2.24 0.00 0.00 2.12
150 152 2.650322 GGATCCGGCCATTCAAAACTA 58.350 47.619 2.24 0.00 0.00 2.24
158 160 3.274601 TTTTTCGGATCCGGCCATT 57.725 47.368 32.79 0.00 40.25 3.16
227 229 1.247567 AAGGGCATCTCCAACGTTTG 58.752 50.000 0.00 0.00 36.21 2.93
230 232 5.818678 TTATATAAGGGCATCTCCAACGT 57.181 39.130 0.00 0.00 36.21 3.99
231 233 8.964476 ATAATTATATAAGGGCATCTCCAACG 57.036 34.615 0.00 0.00 36.21 4.10
269 273 8.974060 AAAGCATTTAACTATATTTCCCTCGA 57.026 30.769 0.00 0.00 35.86 4.04
302 306 9.204337 TGCTCCTTATGGTTACTTTGTACTATA 57.796 33.333 0.00 0.00 34.23 1.31
303 307 7.985752 GTGCTCCTTATGGTTACTTTGTACTAT 59.014 37.037 0.00 0.00 34.23 2.12
304 308 7.325694 GTGCTCCTTATGGTTACTTTGTACTA 58.674 38.462 0.00 0.00 34.23 1.82
312 316 2.159085 GCTCGTGCTCCTTATGGTTACT 60.159 50.000 1.41 0.00 36.03 2.24
415 419 3.838271 CGCTCGCCTTGGCCTCTA 61.838 66.667 3.32 0.00 0.00 2.43
452 456 1.728490 GATTGGATGGCTGGCGTTCC 61.728 60.000 13.86 13.86 0.00 3.62
484 488 2.584391 GCGGTCAGGTCAAGGAGGT 61.584 63.158 0.00 0.00 0.00 3.85
1386 3516 2.437180 CAGGCGCATTCTGAGGCA 60.437 61.111 10.83 0.00 44.69 4.75
1544 3674 1.031571 GCAATCCGGGTGAATCTGCA 61.032 55.000 0.00 0.00 31.15 4.41
1734 3864 2.610833 CAGCACATGTTAGTCATCGCAT 59.389 45.455 0.00 0.00 35.59 4.73
1735 3865 2.001872 CAGCACATGTTAGTCATCGCA 58.998 47.619 0.00 0.00 35.59 5.10
1793 3923 7.055667 ACATGTCTACTATCCGAACAATGAT 57.944 36.000 0.00 0.00 0.00 2.45
1971 4109 7.416664 CCAGAAACTGAAGAAATTTGAACCTCA 60.417 37.037 0.00 0.00 32.44 3.86
2336 4479 4.832248 AGAGCATGGAAAGATAACGTGAA 58.168 39.130 0.00 0.00 0.00 3.18
2402 4545 3.610911 GCTGTTTTAGAGCTGGTGGTAT 58.389 45.455 0.00 0.00 33.37 2.73
2483 4629 2.503061 CTGCTGGGACGAGGGATG 59.497 66.667 0.00 0.00 0.00 3.51
2484 4630 3.474570 GCTGCTGGGACGAGGGAT 61.475 66.667 0.00 0.00 0.00 3.85
2486 4632 4.463879 CTGCTGCTGGGACGAGGG 62.464 72.222 0.00 0.00 0.00 4.30
2488 4634 3.677284 ATGCTGCTGCTGGGACGAG 62.677 63.158 17.00 0.00 40.48 4.18
2489 4635 3.670637 GATGCTGCTGCTGGGACGA 62.671 63.158 17.00 0.00 40.48 4.20
2490 4636 3.200593 GATGCTGCTGCTGGGACG 61.201 66.667 17.00 0.00 40.48 4.79
2491 4637 1.445716 GATGATGCTGCTGCTGGGAC 61.446 60.000 17.00 4.52 40.48 4.46
2492 4638 1.153025 GATGATGCTGCTGCTGGGA 60.153 57.895 17.00 0.00 40.48 4.37
2493 4639 2.194212 GGATGATGCTGCTGCTGGG 61.194 63.158 17.00 0.00 40.48 4.45
2494 4640 2.194212 GGGATGATGCTGCTGCTGG 61.194 63.158 17.00 0.00 40.48 4.85
2495 4641 2.194212 GGGGATGATGCTGCTGCTG 61.194 63.158 17.00 0.77 40.48 4.41
2496 4642 2.195139 GGGGATGATGCTGCTGCT 59.805 61.111 17.00 2.26 40.48 4.24
2497 4643 2.194212 CAGGGGATGATGCTGCTGC 61.194 63.158 8.89 8.89 40.20 5.25
2498 4644 2.194212 GCAGGGGATGATGCTGCTG 61.194 63.158 0.00 0.00 39.38 4.41
2499 4645 2.195139 GCAGGGGATGATGCTGCT 59.805 61.111 0.00 0.00 39.38 4.24
2500 4646 2.910994 GGCAGGGGATGATGCTGC 60.911 66.667 0.00 0.00 42.19 5.25
2501 4647 2.593725 CGGCAGGGGATGATGCTG 60.594 66.667 0.00 0.00 42.19 4.41
2502 4648 4.575973 GCGGCAGGGGATGATGCT 62.576 66.667 0.00 0.00 42.19 3.79
2503 4649 4.881440 TGCGGCAGGGGATGATGC 62.881 66.667 0.00 0.00 41.80 3.91
2544 4714 0.752009 CTGGGAATGATGCTGCTGCT 60.752 55.000 17.00 2.26 40.48 4.24
2554 4724 3.982316 CTGCTGCGGCTGGGAATGA 62.982 63.158 20.27 0.00 39.59 2.57
2568 4738 3.671411 GCTGTTGCTGCTGCTGCT 61.671 61.111 27.67 0.00 40.48 4.24
2972 5175 5.704515 CCATGTTCAAATTAACATTGCCCAA 59.295 36.000 4.20 0.00 45.54 4.12
3097 5300 3.400599 ATTAGGTGAAGGCCGCCCG 62.401 63.158 5.55 0.00 46.65 6.13
3124 5327 2.253452 CTGACTTGCTGCGGTTGC 59.747 61.111 0.00 0.00 43.20 4.17
3277 5480 2.827322 TGGAATTGATTGACCAGCTTGG 59.173 45.455 1.16 1.16 45.02 3.61
3528 5731 3.627395 TCGAAACCATAGCACCAGAAT 57.373 42.857 0.00 0.00 0.00 2.40
3829 6032 3.926058 AAGAGTACCTGTGGTTGTTGT 57.074 42.857 0.00 0.00 37.09 3.32
3846 6049 6.070995 TGCTAGGAATAGGAAACGAGAAAAGA 60.071 38.462 0.00 0.00 0.00 2.52
3849 6052 5.187186 AGTGCTAGGAATAGGAAACGAGAAA 59.813 40.000 0.00 0.00 0.00 2.52
4033 6666 2.378547 ACCCTTTCTGGCTAAATCCACA 59.621 45.455 0.00 0.00 31.74 4.17
4048 6681 2.158475 TGATGTCAAGCCTGAACCCTTT 60.158 45.455 0.00 0.00 31.88 3.11
4174 6807 7.912056 AATCGAAAAGAGAGACAATTCATCA 57.088 32.000 0.00 0.00 0.00 3.07
4185 6818 7.746929 AGCATGTTAGAAAATCGAAAAGAGAG 58.253 34.615 0.00 0.00 0.00 3.20
4240 6873 4.100529 CAATTTTGCAGAGCTGATTACCG 58.899 43.478 0.85 0.00 0.00 4.02
4383 7016 6.037500 TGCGATTCATTTTCAGTAGAATCAGG 59.962 38.462 12.68 1.41 43.96 3.86
4478 7111 2.920524 TGCGGGTCAGTTACAAAAGAA 58.079 42.857 0.00 0.00 0.00 2.52
4604 7237 2.306805 AGAATTGGCCTCAGACACATCA 59.693 45.455 3.32 0.00 0.00 3.07
4880 7513 0.322975 TTCTCCCAGCTGCAGACTTC 59.677 55.000 20.43 0.00 0.00 3.01
5123 7756 2.208431 GTAGACATGTCTGCTGCATCC 58.792 52.381 33.76 10.60 40.71 3.51
5154 7787 2.806818 GGTTTCCAGAGTCCGAACTTTC 59.193 50.000 0.00 0.00 35.28 2.62
5193 7826 5.211174 TCAGTCATATCAGAATCTGGCAG 57.789 43.478 8.58 8.58 31.51 4.85
5296 7929 4.515944 GCGTACTAGTGACAGTATCCATCT 59.484 45.833 5.39 0.00 33.71 2.90
5879 8512 5.139727 TCACAGAAAGTTGGTTCCATCAAT 58.860 37.500 3.26 0.00 0.00 2.57
6023 8656 2.369860 TGCTTCAGCTTCCTCTCTTTCA 59.630 45.455 0.00 0.00 42.66 2.69
6032 8665 3.181506 CCGTTTTATCTGCTTCAGCTTCC 60.182 47.826 0.00 0.00 42.66 3.46
6746 9379 4.654262 CCTCTTAAAGACATACCCCTAGCA 59.346 45.833 0.00 0.00 0.00 3.49
7181 9816 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
7182 9817 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
7183 9818 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
7184 9819 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
7185 9820 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
7186 9821 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
7187 9822 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
7188 9823 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
7189 9824 8.020819 TCATTTTGATGACAAGTATTTTCGGAC 58.979 33.333 0.00 0.00 37.32 4.79
7190 9825 8.105097 TCATTTTGATGACAAGTATTTTCGGA 57.895 30.769 0.00 0.00 37.32 4.55
7191 9826 8.741101 TTCATTTTGATGACAAGTATTTTCGG 57.259 30.769 0.00 0.00 37.32 4.30
7199 9834 9.492973 CCCTTTTTATTCATTTTGATGACAAGT 57.507 29.630 0.00 0.00 37.32 3.16
7200 9835 9.709495 TCCCTTTTTATTCATTTTGATGACAAG 57.291 29.630 0.00 0.00 37.32 3.16
7202 9837 9.656040 CATCCCTTTTTATTCATTTTGATGACA 57.344 29.630 0.00 0.00 0.00 3.58
7203 9838 9.657419 ACATCCCTTTTTATTCATTTTGATGAC 57.343 29.630 0.00 0.00 32.39 3.06
7245 9880 9.096823 TGAATAAAAGGGGATGTATCTATACGT 57.903 33.333 0.00 0.00 36.06 3.57
7251 9886 9.713684 TCAAAATGAATAAAAGGGGATGTATCT 57.286 29.630 0.00 0.00 0.00 1.98
7270 9905 9.594038 CGTCCGGAAATACTTATTATCAAAATG 57.406 33.333 5.23 0.00 0.00 2.32
7271 9906 8.780249 CCGTCCGGAAATACTTATTATCAAAAT 58.220 33.333 5.23 0.00 37.50 1.82
7272 9907 7.986320 TCCGTCCGGAAATACTTATTATCAAAA 59.014 33.333 5.23 0.00 42.05 2.44
7273 9908 7.499292 TCCGTCCGGAAATACTTATTATCAAA 58.501 34.615 5.23 0.00 42.05 2.69
7274 9909 7.053316 TCCGTCCGGAAATACTTATTATCAA 57.947 36.000 5.23 0.00 42.05 2.57
7275 9910 6.294899 CCTCCGTCCGGAAATACTTATTATCA 60.295 42.308 5.23 0.00 44.66 2.15
7276 9911 6.098017 CCTCCGTCCGGAAATACTTATTATC 58.902 44.000 5.23 0.00 44.66 1.75
7277 9912 5.046807 CCCTCCGTCCGGAAATACTTATTAT 60.047 44.000 5.23 0.00 44.66 1.28
7278 9913 4.281688 CCCTCCGTCCGGAAATACTTATTA 59.718 45.833 5.23 0.00 44.66 0.98
7279 9914 3.070590 CCCTCCGTCCGGAAATACTTATT 59.929 47.826 5.23 0.00 44.66 1.40
7280 9915 2.631545 CCCTCCGTCCGGAAATACTTAT 59.368 50.000 5.23 0.00 44.66 1.73
7281 9916 2.034124 CCCTCCGTCCGGAAATACTTA 58.966 52.381 5.23 0.00 44.66 2.24
7282 9917 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
7283 9918 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
7284 9919 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
7285 9920 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
7286 9921 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
7287 9922 0.682209 CTACTCCCTCCGTCCGGAAA 60.682 60.000 5.23 0.00 44.66 3.13
7288 9923 1.077212 CTACTCCCTCCGTCCGGAA 60.077 63.158 5.23 0.00 44.66 4.30
7289 9924 1.351080 ATCTACTCCCTCCGTCCGGA 61.351 60.000 0.00 0.00 42.90 5.14
7290 9925 1.150992 ATCTACTCCCTCCGTCCGG 59.849 63.158 0.00 0.00 0.00 5.14
7291 9926 0.179026 TCATCTACTCCCTCCGTCCG 60.179 60.000 0.00 0.00 0.00 4.79
7292 9927 2.296073 ATCATCTACTCCCTCCGTCC 57.704 55.000 0.00 0.00 0.00 4.79
7293 9928 7.122948 ACATTATTATCATCTACTCCCTCCGTC 59.877 40.741 0.00 0.00 0.00 4.79
7294 9929 6.954684 ACATTATTATCATCTACTCCCTCCGT 59.045 38.462 0.00 0.00 0.00 4.69
7295 9930 7.261325 CACATTATTATCATCTACTCCCTCCG 58.739 42.308 0.00 0.00 0.00 4.63
7296 9931 7.044798 GCACATTATTATCATCTACTCCCTCC 58.955 42.308 0.00 0.00 0.00 4.30
7297 9932 7.846066 AGCACATTATTATCATCTACTCCCTC 58.154 38.462 0.00 0.00 0.00 4.30
7298 9933 7.805083 AGCACATTATTATCATCTACTCCCT 57.195 36.000 0.00 0.00 0.00 4.20
7299 9934 8.754080 AGTAGCACATTATTATCATCTACTCCC 58.246 37.037 0.00 0.00 32.54 4.30
7305 9940 7.923344 GCCGATAGTAGCACATTATTATCATCT 59.077 37.037 0.00 0.00 0.00 2.90
7350 9985 2.692557 CCTAGTCTCACAGCAGCAGTAT 59.307 50.000 0.00 0.00 0.00 2.12
7416 10051 0.109551 TGCAGAGACGCGAGAAAGAG 60.110 55.000 15.93 0.00 33.35 2.85
7703 10339 4.762765 ACATAATGGAAACTTGGCACGTTA 59.237 37.500 9.95 0.00 0.00 3.18
7936 10572 0.037303 CTCACCCCACAATGAGCTGT 59.963 55.000 0.00 0.00 36.22 4.40
7947 10583 1.850345 AGAACAAAGGAACTCACCCCA 59.150 47.619 0.00 0.00 38.49 4.96
7965 10601 1.134640 GCATCAATGGGCAATGCAAGA 60.135 47.619 7.79 0.00 44.07 3.02
8217 10854 2.227036 CCACTCCAAGACTGCCCCT 61.227 63.158 0.00 0.00 0.00 4.79
8576 11215 1.607467 GGTGGCTGGGTGCAAAGAT 60.607 57.895 0.00 0.00 45.15 2.40
8702 11347 8.867097 ACCACTAACAAGTCTCAATAGTAGAAA 58.133 33.333 0.00 0.00 0.00 2.52
8710 11355 4.706842 ACCACCACTAACAAGTCTCAAT 57.293 40.909 0.00 0.00 0.00 2.57
9053 11698 0.384309 CGCAGCCTAACCAGACGATA 59.616 55.000 0.00 0.00 0.00 2.92
9054 11699 1.141881 CGCAGCCTAACCAGACGAT 59.858 57.895 0.00 0.00 0.00 3.73
9103 11748 5.762218 TGAGAAGAAAGCAAGAGAAAAGAGG 59.238 40.000 0.00 0.00 0.00 3.69
9116 11761 3.189910 TGCATCACATGTGAGAAGAAAGC 59.810 43.478 30.63 22.91 43.61 3.51
9165 11816 9.502091 AAGTTCTTATGTGTCTTTTATAGTGCA 57.498 29.630 0.00 0.00 0.00 4.57
9173 11824 6.263168 CACTCCCAAGTTCTTATGTGTCTTTT 59.737 38.462 0.00 0.00 31.71 2.27
9254 11905 6.770303 TGGTCATGTTTGTTGTCTAAGATTGA 59.230 34.615 0.00 0.00 0.00 2.57
9263 11914 7.120579 TCCAACTATATGGTCATGTTTGTTGTC 59.879 37.037 16.28 0.00 41.46 3.18
9265 11916 7.389803 TCCAACTATATGGTCATGTTTGTTG 57.610 36.000 13.48 13.48 41.46 3.33
9267 11918 8.593945 AATTCCAACTATATGGTCATGTTTGT 57.406 30.769 0.00 0.00 41.46 2.83
9293 11944 9.752228 ATTTTCCCCTAATTGCAAATTGTAATT 57.248 25.926 21.82 21.82 43.35 1.40
9294 11945 9.394767 GATTTTCCCCTAATTGCAAATTGTAAT 57.605 29.630 1.71 3.46 34.13 1.89
9295 11946 8.601546 AGATTTTCCCCTAATTGCAAATTGTAA 58.398 29.630 1.71 0.00 0.00 2.41
9296 11947 8.144862 AGATTTTCCCCTAATTGCAAATTGTA 57.855 30.769 1.71 0.00 0.00 2.41
9297 11948 7.019656 AGATTTTCCCCTAATTGCAAATTGT 57.980 32.000 1.71 0.00 0.00 2.71
9298 11949 6.539826 GGAGATTTTCCCCTAATTGCAAATTG 59.460 38.462 1.71 0.00 40.37 2.32
9299 11950 6.653020 GGAGATTTTCCCCTAATTGCAAATT 58.347 36.000 1.71 1.18 40.37 1.82
9300 11951 6.239217 GGAGATTTTCCCCTAATTGCAAAT 57.761 37.500 1.71 0.00 40.37 2.32
9301 11952 5.675684 GGAGATTTTCCCCTAATTGCAAA 57.324 39.130 1.71 0.00 40.37 3.68
9313 11964 0.041090 TGGGCAAGGGGAGATTTTCC 59.959 55.000 0.00 0.00 46.00 3.13
9314 11965 1.937191 TTGGGCAAGGGGAGATTTTC 58.063 50.000 0.00 0.00 0.00 2.29
9315 11966 1.977854 GTTTGGGCAAGGGGAGATTTT 59.022 47.619 0.00 0.00 0.00 1.82
9316 11967 1.132881 TGTTTGGGCAAGGGGAGATTT 60.133 47.619 0.00 0.00 0.00 2.17
9317 11968 0.486879 TGTTTGGGCAAGGGGAGATT 59.513 50.000 0.00 0.00 0.00 2.40
9318 11969 0.040204 CTGTTTGGGCAAGGGGAGAT 59.960 55.000 0.00 0.00 0.00 2.75
9319 11970 1.360393 ACTGTTTGGGCAAGGGGAGA 61.360 55.000 0.00 0.00 0.00 3.71
9320 11971 0.895559 GACTGTTTGGGCAAGGGGAG 60.896 60.000 0.00 0.00 0.00 4.30
9321 11972 1.152830 GACTGTTTGGGCAAGGGGA 59.847 57.895 0.00 0.00 0.00 4.81
9322 11973 0.895559 GAGACTGTTTGGGCAAGGGG 60.896 60.000 0.00 0.00 0.00 4.79
9323 11974 0.895559 GGAGACTGTTTGGGCAAGGG 60.896 60.000 0.00 0.00 0.00 3.95
9324 11975 0.895559 GGGAGACTGTTTGGGCAAGG 60.896 60.000 0.00 0.00 0.00 3.61
9325 11976 0.111253 AGGGAGACTGTTTGGGCAAG 59.889 55.000 0.00 0.00 0.00 4.01
9326 11977 0.555769 AAGGGAGACTGTTTGGGCAA 59.444 50.000 0.00 0.00 0.00 4.52
9327 11978 0.178992 CAAGGGAGACTGTTTGGGCA 60.179 55.000 0.00 0.00 0.00 5.36
9328 11979 0.110486 TCAAGGGAGACTGTTTGGGC 59.890 55.000 0.00 0.00 0.00 5.36
9329 11980 2.307098 AGATCAAGGGAGACTGTTTGGG 59.693 50.000 0.00 0.00 0.00 4.12
9330 11981 3.262915 AGAGATCAAGGGAGACTGTTTGG 59.737 47.826 0.00 0.00 0.00 3.28
9331 11982 4.550076 AGAGATCAAGGGAGACTGTTTG 57.450 45.455 0.00 0.00 0.00 2.93
9332 11983 4.263243 CCAAGAGATCAAGGGAGACTGTTT 60.263 45.833 0.00 0.00 0.00 2.83
9333 11984 3.262915 CCAAGAGATCAAGGGAGACTGTT 59.737 47.826 0.00 0.00 0.00 3.16
9334 11985 2.836981 CCAAGAGATCAAGGGAGACTGT 59.163 50.000 0.00 0.00 0.00 3.55
9335 11986 3.102972 TCCAAGAGATCAAGGGAGACTG 58.897 50.000 0.00 0.00 0.00 3.51
9336 11987 3.481559 TCCAAGAGATCAAGGGAGACT 57.518 47.619 0.00 0.00 0.00 3.24
9337 11988 4.135747 CTTCCAAGAGATCAAGGGAGAC 57.864 50.000 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.