Multiple sequence alignment - TraesCS3B01G031500

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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 TraesCS3B01G031500 chr3B 100.000 3608 0 0 1 3608 14328207 14331814 0.000000e+00 6663.0
1 TraesCS3B01G031500 chr3B 100.000 32 0 0 3577 3608 821835840 821835871 3.890000e-05 60.2
2 TraesCS3B01G031500 chr3D 93.782 3538 187 14 2 3516 10133527 10137054 0.000000e+00 5284.0
3 TraesCS3B01G031500 chr3D 83.735 498 54 14 3043 3517 196981046 196980553 2.560000e-121 446.0
4 TraesCS3B01G031500 chr5B 86.297 686 69 8 2853 3517 371181326 371182007 0.000000e+00 723.0
5 TraesCS3B01G031500 chr5B 89.855 207 18 3 2835 3041 371186023 371186226 2.760000e-66 263.0
6 TraesCS3B01G031500 chr5B 100.000 28 0 0 3577 3604 6420193 6420166 7.000000e-03 52.8
7 TraesCS3B01G031500 chr5B 100.000 28 0 0 3577 3604 686898821 686898794 7.000000e-03 52.8
8 TraesCS3B01G031500 chr7D 85.776 689 88 9 2834 3517 2838926 2838243 0.000000e+00 721.0
9 TraesCS3B01G031500 chr7D 100.000 28 0 0 3577 3604 457226509 457226482 7.000000e-03 52.8
10 TraesCS3B01G031500 chr1B 81.283 561 80 13 2978 3516 456964390 456963833 7.160000e-117 431.0
11 TraesCS3B01G031500 chr4D 100.000 29 0 0 3577 3605 493842088 493842116 2.000000e-03 54.7
12 TraesCS3B01G031500 chr4A 100.000 29 0 0 3577 3605 706603611 706603583 2.000000e-03 54.7
13 TraesCS3B01G031500 chr7B 100.000 28 0 0 3577 3604 11093255 11093282 7.000000e-03 52.8
14 TraesCS3B01G031500 chr1A 100.000 28 0 0 3577 3604 15355902 15355929 7.000000e-03 52.8


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 TraesCS3B01G031500 chr3B 14328207 14331814 3607 False 6663 6663 100.000 1 3608 1 chr3B.!!$F1 3607
1 TraesCS3B01G031500 chr3D 10133527 10137054 3527 False 5284 5284 93.782 2 3516 1 chr3D.!!$F1 3514
2 TraesCS3B01G031500 chr5B 371181326 371182007 681 False 723 723 86.297 2853 3517 1 chr5B.!!$F1 664
3 TraesCS3B01G031500 chr7D 2838243 2838926 683 True 721 721 85.776 2834 3517 1 chr7D.!!$R1 683
4 TraesCS3B01G031500 chr1B 456963833 456964390 557 True 431 431 81.283 2978 3516 1 chr1B.!!$R1 538

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
40 41 0.036732 TGCAGCCAAGAATTCGGAGT 59.963 50.0 3.75 0.0 0.00 3.85 F
128 129 0.250727 GCAGCAACTTCAGTGGGGTA 60.251 55.0 0.00 0.0 0.00 3.69 F
1925 1926 0.178981 AGCTTTCTTGAGGCAGCCAA 60.179 50.0 15.80 0.0 32.25 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1390 1391 0.106894 GATAACTCCGGGGCTTCCAG 59.893 60.0 0.00 0.0 34.36 3.86 R
2031 2032 0.307760 CCGTCAAACTGTTGCAGGAC 59.692 55.0 0.00 0.0 35.51 3.85 R
3583 3608 0.035820 AATAGCGGCGGACCTTCAAA 60.036 50.0 9.78 0.0 0.00 2.69 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
24 25 0.036952 GCTCAACCTCAGTAGCTGCA 60.037 55.000 4.12 0.00 32.18 4.41
27 28 1.023513 CAACCTCAGTAGCTGCAGCC 61.024 60.000 34.39 20.47 43.38 4.85
29 30 1.297689 CCTCAGTAGCTGCAGCCAA 59.702 57.895 34.39 20.82 43.38 4.52
33 34 1.280133 TCAGTAGCTGCAGCCAAGAAT 59.720 47.619 34.39 17.78 43.38 2.40
34 35 2.089980 CAGTAGCTGCAGCCAAGAATT 58.910 47.619 34.39 17.02 43.38 2.17
35 36 2.097142 CAGTAGCTGCAGCCAAGAATTC 59.903 50.000 34.39 13.10 43.38 2.17
36 37 1.063174 GTAGCTGCAGCCAAGAATTCG 59.937 52.381 34.39 0.00 43.38 3.34
37 38 1.138247 GCTGCAGCCAAGAATTCGG 59.862 57.895 28.76 0.00 34.31 4.30
38 39 1.308069 GCTGCAGCCAAGAATTCGGA 61.308 55.000 28.76 0.00 34.31 4.55
39 40 0.731417 CTGCAGCCAAGAATTCGGAG 59.269 55.000 0.00 0.00 0.00 4.63
40 41 0.036732 TGCAGCCAAGAATTCGGAGT 59.963 50.000 3.75 0.00 0.00 3.85
56 57 2.219325 GAGTGCGAGTGGGAGGTGAG 62.219 65.000 0.00 0.00 0.00 3.51
75 76 3.034635 GAGATCAGCCCCTCTTTGACTA 58.965 50.000 0.00 0.00 0.00 2.59
80 81 1.630878 AGCCCCTCTTTGACTACCTTG 59.369 52.381 0.00 0.00 0.00 3.61
83 84 2.025887 CCCCTCTTTGACTACCTTGCAT 60.026 50.000 0.00 0.00 0.00 3.96
91 92 3.930336 TGACTACCTTGCATCACTTGAG 58.070 45.455 0.00 0.00 0.00 3.02
112 113 4.764172 AGGTATTTAGACTTGAGCTGCAG 58.236 43.478 10.11 10.11 0.00 4.41
128 129 0.250727 GCAGCAACTTCAGTGGGGTA 60.251 55.000 0.00 0.00 0.00 3.69
143 144 2.911552 GGGTACAGATCCCCCAAAAA 57.088 50.000 0.00 0.00 39.08 1.94
183 184 6.108015 AGTCTTCAGCATCTTGATCTTTCTC 58.892 40.000 0.00 0.00 0.00 2.87
184 185 5.005586 GTCTTCAGCATCTTGATCTTTCTCG 59.994 44.000 0.00 0.00 0.00 4.04
203 204 2.341176 GCAAGCTTTGTGGGCAGG 59.659 61.111 0.00 0.00 0.00 4.85
237 238 6.156949 ACAGCTTGGTAATCTCTCCAATCTTA 59.843 38.462 0.00 0.00 41.89 2.10
278 279 6.352516 GGACAATCCTTTGTACTCAGATGAT 58.647 40.000 0.00 0.00 46.01 2.45
341 342 5.513495 CGATATGAGCTCGGTTAATCTTAGC 59.487 44.000 9.64 2.55 32.58 3.09
345 346 3.786635 AGCTCGGTTAATCTTAGCACAG 58.213 45.455 11.24 0.00 35.63 3.66
346 347 3.195825 AGCTCGGTTAATCTTAGCACAGT 59.804 43.478 11.24 0.00 35.63 3.55
396 397 6.324561 AGCTTCCTTCATTGAAAGTTCTTC 57.675 37.500 0.01 0.00 0.00 2.87
487 488 4.929808 GGTGTTGGATATCAGCGGTAATAG 59.070 45.833 4.83 0.00 0.00 1.73
499 500 2.213499 CGGTAATAGCTTTCAGGCTGG 58.787 52.381 15.73 0.00 43.01 4.85
568 569 4.227982 TGATCTCTCCCAATGTGATTTCCA 59.772 41.667 0.00 0.00 0.00 3.53
572 573 2.101917 CTCCCAATGTGATTTCCATGGC 59.898 50.000 6.96 0.00 0.00 4.40
575 576 2.101917 CCAATGTGATTTCCATGGCTCC 59.898 50.000 6.96 0.00 0.00 4.70
731 732 4.422592 ACCACAGGGGATATAGGAGAACTA 59.577 45.833 0.00 0.00 41.15 2.24
842 843 8.877195 TGGTTTAGACCTCTAACTAATTTGACT 58.123 33.333 3.79 0.00 46.66 3.41
913 914 1.692411 GGAGCACTTCCAAAACTGGT 58.308 50.000 0.00 0.00 46.01 4.00
917 918 4.321230 GGAGCACTTCCAAAACTGGTTATG 60.321 45.833 0.00 0.00 46.01 1.90
920 921 4.217550 GCACTTCCAAAACTGGTTATGCTA 59.782 41.667 8.19 0.00 32.41 3.49
1062 1063 3.274288 GGTTCCTTCATTCAGGCTACAG 58.726 50.000 0.00 0.00 33.35 2.74
1105 1106 0.682855 GATTGGACCCGCATTCCCAA 60.683 55.000 0.00 0.00 42.16 4.12
1119 1120 1.679977 CCCAACATGGCTCAGGTGG 60.680 63.158 0.00 2.16 35.79 4.61
1135 1136 2.821969 AGGTGGCAATCTGACATTCAAC 59.178 45.455 0.00 0.00 37.93 3.18
1263 1264 1.425066 ACACTCCCAGCATCCTTTGAA 59.575 47.619 0.00 0.00 0.00 2.69
1270 1271 2.159338 CCAGCATCCTTTGAAACGATGG 60.159 50.000 15.33 1.77 35.09 3.51
1276 1277 2.813754 TCCTTTGAAACGATGGAAGCAG 59.186 45.455 0.00 0.00 0.00 4.24
1277 1278 2.813754 CCTTTGAAACGATGGAAGCAGA 59.186 45.455 0.00 0.00 0.00 4.26
1280 1281 2.964740 TGAAACGATGGAAGCAGAGAG 58.035 47.619 0.00 0.00 0.00 3.20
1294 1295 4.100373 AGCAGAGAGAATGGACCTAAGTT 58.900 43.478 0.00 0.00 0.00 2.66
1295 1296 4.534103 AGCAGAGAGAATGGACCTAAGTTT 59.466 41.667 0.00 0.00 0.00 2.66
1390 1391 1.524482 GGGACACTGCCCTCAGATC 59.476 63.158 0.00 0.00 45.12 2.75
1391 1392 0.980231 GGGACACTGCCCTCAGATCT 60.980 60.000 0.00 0.00 45.12 2.75
1400 1401 1.704007 CCCTCAGATCTGGAAGCCCC 61.704 65.000 22.42 0.00 0.00 5.80
1437 1438 6.985645 TGCTTGCTCTTTACAACAATTCAATT 59.014 30.769 0.00 0.00 0.00 2.32
1489 1490 9.768662 GCAATTATTCATTGGAAATATTGGACT 57.231 29.630 12.57 0.00 42.51 3.85
1523 1524 1.938585 CTGACAGGAGAGGTACCCAA 58.061 55.000 8.74 0.00 0.00 4.12
1556 1557 0.681243 GATCTTGGGGGCTTCACACC 60.681 60.000 0.00 0.00 0.00 4.16
1662 1663 7.312657 TCTTGATCTTGCATACAATCAGTTC 57.687 36.000 0.00 0.00 34.61 3.01
1725 1726 1.634757 TTGCATTGCTACGACTGCGG 61.635 55.000 10.49 0.00 43.17 5.69
1806 1807 1.210155 GGACCTCGCATGCAACAAC 59.790 57.895 19.57 5.60 0.00 3.32
1873 1874 6.132791 TCGCTCGGATTAATGGATATAGTC 57.867 41.667 0.00 0.00 0.00 2.59
1886 1887 7.803487 ATGGATATAGTCATTCACTGGATGA 57.197 36.000 0.00 0.00 36.43 2.92
1925 1926 0.178981 AGCTTTCTTGAGGCAGCCAA 60.179 50.000 15.80 0.00 32.25 4.52
1929 1930 1.737838 TTCTTGAGGCAGCCAATACG 58.262 50.000 15.80 0.00 0.00 3.06
1947 1948 1.271217 ACGGCTAGGGTCAAACTTTCC 60.271 52.381 0.00 0.00 0.00 3.13
1989 1990 4.820173 GTGCTTACTAAGGGACAACAACTT 59.180 41.667 0.00 0.00 0.00 2.66
1999 2000 3.488553 GGGACAACAACTTGAGTTTTCCG 60.489 47.826 0.00 0.00 43.45 4.30
2010 2011 2.218603 GAGTTTTCCGAAGAGTTGCCA 58.781 47.619 0.00 0.00 0.00 4.92
2034 2035 8.950210 CCATACATGGTAAATATTGATCTGTCC 58.050 37.037 0.00 0.00 43.05 4.02
2042 2043 6.446781 AAATATTGATCTGTCCTGCAACAG 57.553 37.500 11.61 11.61 46.54 3.16
2044 2045 2.936919 TGATCTGTCCTGCAACAGTT 57.063 45.000 16.22 9.56 45.57 3.16
2049 2050 1.003545 CTGTCCTGCAACAGTTTGACG 60.004 52.381 9.92 0.00 41.43 4.35
2114 2115 5.113502 AGCTTGAACTTTTCTTGGAATCG 57.886 39.130 0.00 0.00 0.00 3.34
2120 2121 5.466728 TGAACTTTTCTTGGAATCGTCTGAG 59.533 40.000 0.00 0.00 0.00 3.35
2133 2134 0.461961 GTCTGAGTGGGAGGATTCCG 59.538 60.000 0.00 0.00 45.04 4.30
2145 2146 4.202472 GGGAGGATTCCGAAGAATATTGGT 60.202 45.833 0.00 0.00 42.93 3.67
2153 2154 5.667466 TCCGAAGAATATTGGTAACCTCAC 58.333 41.667 0.00 0.00 0.00 3.51
2154 2155 5.424252 TCCGAAGAATATTGGTAACCTCACT 59.576 40.000 0.00 0.00 0.00 3.41
2178 2179 1.144093 CTCGAGTCCCTGGACCTATCT 59.856 57.143 12.66 0.00 45.59 1.98
2188 2189 4.145807 CCTGGACCTATCTCATAACGAGT 58.854 47.826 0.00 0.00 42.88 4.18
2252 2253 1.537202 GAGCCGCTTCAACTTGTCATT 59.463 47.619 0.00 0.00 0.00 2.57
2265 2266 8.099364 TCAACTTGTCATTTAACAATCTCTCC 57.901 34.615 0.00 0.00 38.41 3.71
2279 2280 1.564818 TCTCTCCGGACAGATACCAGT 59.435 52.381 5.17 0.00 0.00 4.00
2290 2291 4.884961 ACAGATACCAGTAGGGAATCAGT 58.115 43.478 0.00 0.00 41.15 3.41
2297 2298 2.026822 CAGTAGGGAATCAGTTGCAGGT 60.027 50.000 0.00 0.00 0.00 4.00
2309 2310 2.512515 GCAGGTGCTCGATGACCC 60.513 66.667 8.94 0.00 38.21 4.46
2311 2312 1.296392 CAGGTGCTCGATGACCCAA 59.704 57.895 8.94 0.00 32.03 4.12
2328 2329 5.044476 TGACCCAACATCCAGTTATATTGGT 60.044 40.000 0.00 0.00 38.74 3.67
2363 2364 0.035915 GGGCCTCCACTCTTGAAGAC 60.036 60.000 0.84 0.00 0.00 3.01
2367 2368 2.224402 GCCTCCACTCTTGAAGACTTGT 60.224 50.000 0.00 0.00 0.00 3.16
2373 2374 4.443457 CCACTCTTGAAGACTTGTTCTCCA 60.443 45.833 0.00 0.00 31.02 3.86
2377 2378 6.830838 ACTCTTGAAGACTTGTTCTCCAAATT 59.169 34.615 0.00 0.00 26.24 1.82
2384 2385 6.564328 AGACTTGTTCTCCAAATTCAACAAC 58.436 36.000 0.00 0.00 34.56 3.32
2387 2388 6.589907 ACTTGTTCTCCAAATTCAACAACAAC 59.410 34.615 0.00 0.00 34.56 3.32
2397 2398 0.958822 CAACAACAACTACCCCAGCC 59.041 55.000 0.00 0.00 0.00 4.85
2399 2400 0.553819 ACAACAACTACCCCAGCCAA 59.446 50.000 0.00 0.00 0.00 4.52
2410 2411 3.909587 CCAGCCAAAGATGATGGGA 57.090 52.632 0.00 0.00 38.44 4.37
2427 2428 2.158914 TGGGAATCATCACGATGGAGTG 60.159 50.000 7.17 0.00 43.11 3.51
2429 2430 2.103094 GGAATCATCACGATGGAGTGGA 59.897 50.000 7.17 0.00 42.10 4.02
2454 2455 3.181465 CGTCCATCTACCTAAGCATGGTT 60.181 47.826 15.47 15.47 38.88 3.67
2505 2506 5.266242 GTCTTCTGTGTCATGTTGTTCAAC 58.734 41.667 8.52 8.52 0.00 3.18
2538 2539 1.445871 ACGCCTATTTCCGTTTCACC 58.554 50.000 0.00 0.00 33.26 4.02
2565 2566 3.535280 ATGTACCACATGATGTGCGTA 57.465 42.857 19.69 18.22 46.51 4.42
2570 2571 6.188859 TGTACCACATGATGTGCGTACATAC 61.189 44.000 32.31 21.47 46.84 2.39
2594 2595 1.228552 TTGCCTGGAACCTCCTTGC 60.229 57.895 0.00 0.00 37.46 4.01
2608 2609 0.253044 CCTTGCGAGGAAGGGATGAA 59.747 55.000 15.76 0.00 46.74 2.57
2611 2612 3.433598 CCTTGCGAGGAAGGGATGAATAA 60.434 47.826 15.76 0.00 46.74 1.40
2631 2632 9.131791 TGAATAATTTTAGATAAGGTGAAGGGC 57.868 33.333 0.00 0.00 0.00 5.19
2632 2633 8.478775 AATAATTTTAGATAAGGTGAAGGGCC 57.521 34.615 0.00 0.00 0.00 5.80
2645 2646 2.223876 TGAAGGGCCGATATACAACGAC 60.224 50.000 0.00 0.00 0.00 4.34
2708 2709 6.523546 CAGTACTTCGAGTGTGTATGTAACTG 59.476 42.308 0.00 4.13 0.00 3.16
2734 2735 0.544223 TCCATTCATACGGGTGGTGG 59.456 55.000 0.00 0.00 33.47 4.61
2805 2806 5.522460 GCTACATAAATAAGGTCTGTTCGCA 59.478 40.000 0.00 0.00 0.00 5.10
2807 2808 5.242434 ACATAAATAAGGTCTGTTCGCACA 58.758 37.500 0.00 0.00 0.00 4.57
2827 2828 6.425504 GCACACTCATGAATAAATACTGAGC 58.574 40.000 0.00 0.00 37.45 4.26
2878 2879 3.809832 GGATGTAAACCGACCTGATGATG 59.190 47.826 0.00 0.00 0.00 3.07
3048 3051 3.050619 CCTACGAGCGCTTAAATGGTAG 58.949 50.000 13.26 15.25 0.00 3.18
3113 3119 2.554142 CGCATCCTCAATCAGCAAGTA 58.446 47.619 0.00 0.00 0.00 2.24
3117 3123 5.545588 GCATCCTCAATCAGCAAGTATCTA 58.454 41.667 0.00 0.00 0.00 1.98
3209 3215 3.581101 TGCTGGTTATCTAGATGGCTCT 58.419 45.455 15.79 0.00 35.39 4.09
3233 3240 0.618981 AGGGACGGAGAAAACCATCC 59.381 55.000 0.00 0.00 41.02 3.51
3266 3273 1.925972 GGGGGAAGTCAGGAAGCCT 60.926 63.158 0.00 0.00 0.00 4.58
3272 3279 2.421619 GAAGTCAGGAAGCCTTCACTG 58.578 52.381 6.80 10.95 35.71 3.66
3329 3336 4.181578 CAAGTTCTGGGGTACGTATTCAG 58.818 47.826 0.00 7.42 0.00 3.02
3365 3372 0.249911 GTGTTGACTCAGGTCGCCTT 60.250 55.000 0.00 0.00 44.83 4.35
3379 3404 2.700773 GCCTTACTTTGGGCAGCCG 61.701 63.158 5.00 0.00 46.84 5.52
3412 3437 2.713895 TTCTTCTCAGTCTCGTGCTG 57.286 50.000 3.51 3.51 35.43 4.41
3447 3472 3.973305 TCAGGATGGCTATGTCCAACATA 59.027 43.478 0.00 0.31 39.96 2.29
3454 3479 6.656632 TGGCTATGTCCAACATAAACAAAA 57.343 33.333 1.82 0.00 40.23 2.44
3467 3492 9.912634 CAACATAAACAAAAGGAATATGTCTGT 57.087 29.630 0.00 0.00 36.47 3.41
3488 3513 6.942005 TCTGTTGCAGATTATTTCTCCAAGAA 59.058 34.615 0.00 0.00 32.71 2.52
3494 3519 6.601217 GCAGATTATTTCTCCAAGAAGAAGGT 59.399 38.462 0.00 0.00 35.37 3.50
3521 3546 3.464207 ATGACATGCATCTGTCGCA 57.536 47.368 14.14 1.01 46.89 5.10
3531 3556 5.871465 TGCATCTGTCGCATAGTTTTAAA 57.129 34.783 0.00 0.00 33.55 1.52
3532 3557 6.435430 TGCATCTGTCGCATAGTTTTAAAT 57.565 33.333 0.00 0.00 33.55 1.40
3533 3558 7.546778 TGCATCTGTCGCATAGTTTTAAATA 57.453 32.000 0.00 0.00 33.55 1.40
3534 3559 7.630026 TGCATCTGTCGCATAGTTTTAAATAG 58.370 34.615 0.00 0.00 33.55 1.73
3535 3560 6.575201 GCATCTGTCGCATAGTTTTAAATAGC 59.425 38.462 0.00 0.00 0.00 2.97
3536 3561 6.598753 TCTGTCGCATAGTTTTAAATAGCC 57.401 37.500 0.00 0.00 0.00 3.93
3537 3562 5.233476 TCTGTCGCATAGTTTTAAATAGCCG 59.767 40.000 0.00 0.00 0.00 5.52
3538 3563 4.271533 TGTCGCATAGTTTTAAATAGCCGG 59.728 41.667 0.00 0.00 0.00 6.13
3539 3564 3.249080 TCGCATAGTTTTAAATAGCCGGC 59.751 43.478 21.89 21.89 0.00 6.13
3540 3565 3.250040 CGCATAGTTTTAAATAGCCGGCT 59.750 43.478 34.85 34.85 0.00 5.52
3541 3566 4.449743 CGCATAGTTTTAAATAGCCGGCTA 59.550 41.667 36.88 36.88 0.00 3.93
3542 3567 5.121768 CGCATAGTTTTAAATAGCCGGCTAT 59.878 40.000 37.79 37.79 40.63 2.97
3543 3568 6.311935 CGCATAGTTTTAAATAGCCGGCTATA 59.688 38.462 41.53 28.18 38.20 1.31
3544 3569 7.148540 CGCATAGTTTTAAATAGCCGGCTATAA 60.149 37.037 41.53 31.52 38.20 0.98
3545 3570 7.961283 GCATAGTTTTAAATAGCCGGCTATAAC 59.039 37.037 41.53 36.86 38.20 1.89
3546 3571 6.872628 AGTTTTAAATAGCCGGCTATAACC 57.127 37.500 41.53 27.04 38.20 2.85
3547 3572 5.766670 AGTTTTAAATAGCCGGCTATAACCC 59.233 40.000 41.53 27.50 38.20 4.11
3548 3573 2.873094 AAATAGCCGGCTATAACCCC 57.127 50.000 41.53 5.55 38.20 4.95
3549 3574 0.611714 AATAGCCGGCTATAACCCCG 59.388 55.000 41.53 0.00 43.97 5.73
3550 3575 1.896122 ATAGCCGGCTATAACCCCGC 61.896 60.000 41.03 5.41 43.05 6.13
3551 3576 3.937447 GCCGGCTATAACCCCGCT 61.937 66.667 22.15 0.00 43.05 5.52
3552 3577 2.576832 GCCGGCTATAACCCCGCTA 61.577 63.158 22.15 0.00 43.05 4.26
3553 3578 2.051941 CCGGCTATAACCCCGCTAA 58.948 57.895 0.00 0.00 43.05 3.09
3554 3579 0.037605 CCGGCTATAACCCCGCTAAG 60.038 60.000 0.00 0.00 43.05 2.18
3555 3580 0.677842 CGGCTATAACCCCGCTAAGT 59.322 55.000 0.00 0.00 37.85 2.24
3556 3581 1.604693 CGGCTATAACCCCGCTAAGTG 60.605 57.143 0.00 0.00 37.85 3.16
3557 3582 1.270678 GGCTATAACCCCGCTAAGTGG 60.271 57.143 0.00 0.00 0.00 4.00
3558 3583 1.415289 GCTATAACCCCGCTAAGTGGT 59.585 52.381 0.00 0.00 0.00 4.16
3559 3584 2.547430 GCTATAACCCCGCTAAGTGGTC 60.547 54.545 0.00 0.00 0.00 4.02
3560 3585 1.875488 ATAACCCCGCTAAGTGGTCT 58.125 50.000 0.00 0.00 0.00 3.85
3561 3586 1.188863 TAACCCCGCTAAGTGGTCTC 58.811 55.000 0.00 0.00 0.00 3.36
3562 3587 0.834687 AACCCCGCTAAGTGGTCTCA 60.835 55.000 0.00 0.00 0.00 3.27
3563 3588 0.617820 ACCCCGCTAAGTGGTCTCAT 60.618 55.000 0.00 0.00 0.00 2.90
3564 3589 0.179073 CCCCGCTAAGTGGTCTCATG 60.179 60.000 0.00 0.00 0.00 3.07
3565 3590 0.811616 CCCGCTAAGTGGTCTCATGC 60.812 60.000 0.00 0.00 0.00 4.06
3566 3591 0.108186 CCGCTAAGTGGTCTCATGCA 60.108 55.000 0.00 0.00 0.00 3.96
3567 3592 1.002366 CGCTAAGTGGTCTCATGCAC 58.998 55.000 0.00 0.00 0.00 4.57
3568 3593 1.672737 CGCTAAGTGGTCTCATGCACA 60.673 52.381 0.00 0.00 0.00 4.57
3569 3594 2.426522 GCTAAGTGGTCTCATGCACAA 58.573 47.619 0.00 0.00 0.00 3.33
3570 3595 2.813754 GCTAAGTGGTCTCATGCACAAA 59.186 45.455 0.00 0.00 0.00 2.83
3571 3596 3.441572 GCTAAGTGGTCTCATGCACAAAT 59.558 43.478 0.00 0.00 0.00 2.32
3572 3597 3.928727 AAGTGGTCTCATGCACAAATG 57.071 42.857 0.00 0.00 0.00 2.32
3573 3598 2.165167 AGTGGTCTCATGCACAAATGG 58.835 47.619 0.00 0.00 0.00 3.16
3574 3599 2.161855 GTGGTCTCATGCACAAATGGA 58.838 47.619 0.00 0.00 0.00 3.41
3575 3600 2.095059 GTGGTCTCATGCACAAATGGAC 60.095 50.000 0.00 0.00 31.94 4.02
3576 3601 2.224843 TGGTCTCATGCACAAATGGACT 60.225 45.455 0.00 0.00 32.67 3.85
3577 3602 3.008923 TGGTCTCATGCACAAATGGACTA 59.991 43.478 0.00 0.00 32.67 2.59
3578 3603 3.624861 GGTCTCATGCACAAATGGACTAG 59.375 47.826 0.00 0.00 32.67 2.57
3579 3604 3.064545 GTCTCATGCACAAATGGACTAGC 59.935 47.826 0.00 0.00 30.96 3.42
3580 3605 3.054875 TCTCATGCACAAATGGACTAGCT 60.055 43.478 0.00 0.00 0.00 3.32
3581 3606 3.011818 TCATGCACAAATGGACTAGCTG 58.988 45.455 0.00 0.00 0.00 4.24
3582 3607 2.857186 TGCACAAATGGACTAGCTGA 57.143 45.000 0.00 0.00 0.00 4.26
3583 3608 3.354948 TGCACAAATGGACTAGCTGAT 57.645 42.857 0.00 0.00 0.00 2.90
3584 3609 3.689347 TGCACAAATGGACTAGCTGATT 58.311 40.909 0.00 0.00 0.00 2.57
3585 3610 4.081406 TGCACAAATGGACTAGCTGATTT 58.919 39.130 0.00 0.00 0.00 2.17
3586 3611 4.082625 TGCACAAATGGACTAGCTGATTTG 60.083 41.667 14.74 14.74 40.24 2.32
3587 3612 4.156556 GCACAAATGGACTAGCTGATTTGA 59.843 41.667 19.90 0.00 37.80 2.69
3588 3613 5.335897 GCACAAATGGACTAGCTGATTTGAA 60.336 40.000 19.90 0.00 37.80 2.69
3589 3614 6.320171 CACAAATGGACTAGCTGATTTGAAG 58.680 40.000 19.90 12.02 37.80 3.02
3590 3615 5.416952 ACAAATGGACTAGCTGATTTGAAGG 59.583 40.000 19.90 3.01 37.80 3.46
3591 3616 4.851639 ATGGACTAGCTGATTTGAAGGT 57.148 40.909 0.00 0.00 0.00 3.50
3592 3617 4.207891 TGGACTAGCTGATTTGAAGGTC 57.792 45.455 0.00 0.00 0.00 3.85
3593 3618 3.055094 TGGACTAGCTGATTTGAAGGTCC 60.055 47.826 0.00 0.00 41.39 4.46
3594 3619 3.190874 GACTAGCTGATTTGAAGGTCCG 58.809 50.000 0.00 0.00 0.00 4.79
3595 3620 1.936547 CTAGCTGATTTGAAGGTCCGC 59.063 52.381 0.00 0.00 0.00 5.54
3596 3621 0.678048 AGCTGATTTGAAGGTCCGCC 60.678 55.000 0.00 0.00 0.00 6.13
3597 3622 1.982073 GCTGATTTGAAGGTCCGCCG 61.982 60.000 0.00 0.00 40.50 6.46
3598 3623 1.982073 CTGATTTGAAGGTCCGCCGC 61.982 60.000 0.00 0.00 40.50 6.53
3599 3624 1.745489 GATTTGAAGGTCCGCCGCT 60.745 57.895 0.00 0.00 40.50 5.52
3600 3625 0.461339 GATTTGAAGGTCCGCCGCTA 60.461 55.000 0.00 0.00 40.50 4.26
3601 3626 0.180406 ATTTGAAGGTCCGCCGCTAT 59.820 50.000 0.00 0.00 40.50 2.97
3602 3627 0.035820 TTTGAAGGTCCGCCGCTATT 60.036 50.000 0.00 0.00 40.50 1.73
3603 3628 0.035820 TTGAAGGTCCGCCGCTATTT 60.036 50.000 0.00 0.00 40.50 1.40
3604 3629 0.825410 TGAAGGTCCGCCGCTATTTA 59.175 50.000 0.00 0.00 40.50 1.40
3605 3630 1.202486 TGAAGGTCCGCCGCTATTTAG 60.202 52.381 0.00 0.00 40.50 1.85
3606 3631 0.532196 AAGGTCCGCCGCTATTTAGC 60.532 55.000 0.00 0.00 45.62 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.233431 AGCTACTGAGGTTGAGCTTGAG 59.767 50.000 0.00 0.00 42.59 3.02
5 6 0.036952 TGCAGCTACTGAGGTTGAGC 60.037 55.000 0.00 0.00 32.44 4.26
18 19 1.310933 CCGAATTCTTGGCTGCAGCT 61.311 55.000 35.82 16.47 41.70 4.24
24 25 1.021390 CGCACTCCGAATTCTTGGCT 61.021 55.000 3.52 0.00 40.02 4.75
27 28 1.391485 CACTCGCACTCCGAATTCTTG 59.609 52.381 3.52 0.00 46.81 3.02
29 30 0.108615 CCACTCGCACTCCGAATTCT 60.109 55.000 3.52 0.00 46.81 2.40
33 34 2.599281 TCCCACTCGCACTCCGAA 60.599 61.111 0.00 0.00 46.81 4.30
34 35 3.062466 CTCCCACTCGCACTCCGA 61.062 66.667 0.00 0.00 45.15 4.55
35 36 4.135153 CCTCCCACTCGCACTCCG 62.135 72.222 0.00 0.00 38.61 4.63
36 37 2.997897 ACCTCCCACTCGCACTCC 60.998 66.667 0.00 0.00 0.00 3.85
37 38 2.219325 CTCACCTCCCACTCGCACTC 62.219 65.000 0.00 0.00 0.00 3.51
38 39 2.203640 TCACCTCCCACTCGCACT 60.204 61.111 0.00 0.00 0.00 4.40
39 40 1.608717 ATCTCACCTCCCACTCGCAC 61.609 60.000 0.00 0.00 0.00 5.34
40 41 1.305297 ATCTCACCTCCCACTCGCA 60.305 57.895 0.00 0.00 0.00 5.10
56 57 2.158885 GGTAGTCAAAGAGGGGCTGATC 60.159 54.545 0.00 0.00 0.00 2.92
75 76 4.307032 AATACCTCAAGTGATGCAAGGT 57.693 40.909 8.91 8.91 0.00 3.50
80 81 6.818644 TCAAGTCTAAATACCTCAAGTGATGC 59.181 38.462 0.00 0.00 0.00 3.91
83 84 6.211584 AGCTCAAGTCTAAATACCTCAAGTGA 59.788 38.462 0.00 0.00 0.00 3.41
91 92 3.311048 GCTGCAGCTCAAGTCTAAATACC 59.689 47.826 31.33 0.00 38.21 2.73
112 113 1.071699 TCTGTACCCCACTGAAGTTGC 59.928 52.381 0.00 0.00 32.68 4.17
142 143 8.138074 GCTGAAGACTTTTAAGAGAACCAATTT 58.862 33.333 0.00 0.00 0.00 1.82
143 144 7.285401 TGCTGAAGACTTTTAAGAGAACCAATT 59.715 33.333 0.00 0.00 0.00 2.32
144 145 6.772716 TGCTGAAGACTTTTAAGAGAACCAAT 59.227 34.615 0.00 0.00 0.00 3.16
148 149 7.665561 AGATGCTGAAGACTTTTAAGAGAAC 57.334 36.000 0.00 0.00 0.00 3.01
183 184 2.355009 GCCCACAAAGCTTGCACG 60.355 61.111 0.00 0.00 0.00 5.34
184 185 1.300388 CTGCCCACAAAGCTTGCAC 60.300 57.895 0.00 0.00 0.00 4.57
237 238 5.661056 TTGTCCGAGACACTGAGAAATAT 57.339 39.130 6.27 0.00 42.60 1.28
278 279 4.877823 GTGAGATGTGATAACCATGCAAGA 59.122 41.667 0.00 0.00 0.00 3.02
341 342 1.271325 TGCACCCAATCCACTACTGTG 60.271 52.381 0.00 0.00 43.45 3.66
345 346 0.740737 GCATGCACCCAATCCACTAC 59.259 55.000 14.21 0.00 0.00 2.73
346 347 0.330941 TGCATGCACCCAATCCACTA 59.669 50.000 18.46 0.00 0.00 2.74
396 397 3.653344 TGAGATCACTGTCTTCCAAACG 58.347 45.455 0.00 0.00 0.00 3.60
487 488 3.500558 GAGAAAATCCAGCCTGAAAGC 57.499 47.619 0.00 0.00 0.00 3.51
568 569 3.675348 TTTCATCAGGAATGGAGCCAT 57.325 42.857 0.00 0.00 38.46 4.40
572 573 4.174704 TCCCATTTCATCAGGAATGGAG 57.825 45.455 15.48 7.21 36.82 3.86
575 576 6.774170 TCATACTTCCCATTTCATCAGGAATG 59.226 38.462 0.00 0.00 37.74 2.67
731 732 2.765122 CATTTTGGCAACCGTTCCATT 58.235 42.857 0.00 0.00 31.54 3.16
765 766 3.056393 TCCGAGAAATCCAACACGTACAT 60.056 43.478 0.00 0.00 0.00 2.29
774 775 3.546724 TGTTGTTGTCCGAGAAATCCAA 58.453 40.909 0.00 0.00 0.00 3.53
917 918 9.757227 ACTAGTTGATTAGAATGAAGATGTAGC 57.243 33.333 0.00 0.00 0.00 3.58
920 921 9.388506 CCAACTAGTTGATTAGAATGAAGATGT 57.611 33.333 32.50 0.00 42.93 3.06
972 973 4.103311 AGTTCTTGTAAACTTCTCAGCCCT 59.897 41.667 0.00 0.00 36.02 5.19
1105 1106 0.682209 GATTGCCACCTGAGCCATGT 60.682 55.000 0.00 0.00 0.00 3.21
1119 1120 5.798934 GTCAATGAGTTGAATGTCAGATTGC 59.201 40.000 0.00 0.00 45.38 3.56
1135 1136 4.447054 GGACGCATTAGAGATGTCAATGAG 59.553 45.833 14.76 13.84 36.10 2.90
1263 1264 3.529533 CATTCTCTCTGCTTCCATCGTT 58.470 45.455 0.00 0.00 0.00 3.85
1270 1271 4.161377 ACTTAGGTCCATTCTCTCTGCTTC 59.839 45.833 0.00 0.00 0.00 3.86
1294 1295 9.049050 TGGGACTGTACCAGTAAATCTATTAAA 57.951 33.333 7.92 0.00 45.44 1.52
1295 1296 8.612486 TGGGACTGTACCAGTAAATCTATTAA 57.388 34.615 7.92 0.00 45.44 1.40
1312 1313 3.790089 CCTAGGAAACTTTGGGACTGT 57.210 47.619 1.05 0.00 43.67 3.55
1390 1391 0.106894 GATAACTCCGGGGCTTCCAG 59.893 60.000 0.00 0.00 34.36 3.86
1391 1392 0.326238 AGATAACTCCGGGGCTTCCA 60.326 55.000 0.00 0.00 34.36 3.53
1400 1401 1.929836 GAGCAAGCACAGATAACTCCG 59.070 52.381 0.00 0.00 0.00 4.63
1437 1438 3.270027 CGAAGATGGTATGTTGCCAGAA 58.730 45.455 0.00 0.00 39.65 3.02
1485 1486 6.291377 TGTCAGCATATTTCCTGATAAGTCC 58.709 40.000 0.00 0.00 39.95 3.85
1489 1490 6.327365 TCTCCTGTCAGCATATTTCCTGATAA 59.673 38.462 0.00 0.00 39.95 1.75
1523 1524 0.924823 AAGATCTCCCTGCTGGCAAT 59.075 50.000 3.63 0.00 0.00 3.56
1605 1606 6.436843 TCTTTTGACCTTTGAAGAACTGAC 57.563 37.500 0.00 0.00 0.00 3.51
1681 1682 6.012858 AGGGATGTCATGTTTTCTACTAACCA 60.013 38.462 0.00 0.00 0.00 3.67
1806 1807 6.100424 AGGATTCAGGTATACCTCCAGAAAAG 59.900 42.308 22.09 8.28 46.65 2.27
1925 1926 3.370209 GGAAAGTTTGACCCTAGCCGTAT 60.370 47.826 0.00 0.00 0.00 3.06
1929 1930 2.881111 AGGAAAGTTTGACCCTAGCC 57.119 50.000 0.00 0.00 0.00 3.93
1947 1948 3.787476 GCACGGACAAAGTTGTTGTGTAG 60.787 47.826 21.43 6.95 43.60 2.74
1989 1990 2.218603 GGCAACTCTTCGGAAAACTCA 58.781 47.619 0.00 0.00 0.00 3.41
2010 2011 9.730705 CAGGACAGATCAATATTTACCATGTAT 57.269 33.333 0.00 0.00 0.00 2.29
2031 2032 0.307760 CCGTCAAACTGTTGCAGGAC 59.692 55.000 0.00 0.00 35.51 3.85
2034 2035 0.588252 CTCCCGTCAAACTGTTGCAG 59.412 55.000 0.00 0.00 37.52 4.41
2061 2062 6.824553 AGCAATCAGAGCACTAAATCTATCA 58.175 36.000 0.00 0.00 0.00 2.15
2064 2065 7.105588 TCAAAGCAATCAGAGCACTAAATCTA 58.894 34.615 0.00 0.00 0.00 1.98
2065 2066 5.942236 TCAAAGCAATCAGAGCACTAAATCT 59.058 36.000 0.00 0.00 0.00 2.40
2067 2068 6.579666 TTCAAAGCAATCAGAGCACTAAAT 57.420 33.333 0.00 0.00 0.00 1.40
2068 2069 6.389830 TTTCAAAGCAATCAGAGCACTAAA 57.610 33.333 0.00 0.00 0.00 1.85
2114 2115 0.461961 CGGAATCCTCCCACTCAGAC 59.538 60.000 0.00 0.00 38.71 3.51
2120 2121 4.625607 ATATTCTTCGGAATCCTCCCAC 57.374 45.455 0.00 0.00 42.93 4.61
2133 2134 5.880332 TGCAGTGAGGTTACCAATATTCTTC 59.120 40.000 3.51 0.00 0.00 2.87
2145 2146 1.540267 GACTCGAGTGCAGTGAGGTTA 59.460 52.381 25.58 0.00 34.03 2.85
2153 2154 1.979155 TCCAGGGACTCGAGTGCAG 60.979 63.158 33.73 25.30 38.19 4.41
2154 2155 2.117423 TCCAGGGACTCGAGTGCA 59.883 61.111 33.73 14.44 38.19 4.57
2178 2179 5.462530 TTTCTCCAGACAACTCGTTATGA 57.537 39.130 0.00 0.00 0.00 2.15
2188 2189 4.655963 CTTGAAGGGATTTCTCCAGACAA 58.344 43.478 0.00 0.00 44.08 3.18
2252 2253 5.068723 GGTATCTGTCCGGAGAGATTGTTAA 59.931 44.000 39.60 23.91 41.12 2.01
2265 2266 2.359981 TCCCTACTGGTATCTGTCCG 57.640 55.000 0.00 0.00 34.77 4.79
2279 2280 1.340017 GCACCTGCAACTGATTCCCTA 60.340 52.381 0.00 0.00 41.59 3.53
2290 2291 1.375908 GGTCATCGAGCACCTGCAA 60.376 57.895 8.09 0.00 45.16 4.08
2297 2298 0.107703 GGATGTTGGGTCATCGAGCA 60.108 55.000 0.00 0.00 43.39 4.26
2309 2310 9.734620 CAATGTTACCAATATAACTGGATGTTG 57.265 33.333 10.45 5.36 39.55 3.33
2311 2312 8.058847 ACCAATGTTACCAATATAACTGGATGT 58.941 33.333 10.45 0.00 35.45 3.06
2328 2329 4.020543 GAGGCCCACATAAACCAATGTTA 58.979 43.478 0.00 0.00 38.01 2.41
2363 2364 6.813152 AGTTGTTGTTGAATTTGGAGAACAAG 59.187 34.615 10.32 0.00 40.82 3.16
2367 2368 6.183360 GGGTAGTTGTTGTTGAATTTGGAGAA 60.183 38.462 0.00 0.00 0.00 2.87
2373 2374 4.202212 GCTGGGGTAGTTGTTGTTGAATTT 60.202 41.667 0.00 0.00 0.00 1.82
2377 2378 1.477923 GGCTGGGGTAGTTGTTGTTGA 60.478 52.381 0.00 0.00 0.00 3.18
2384 2385 2.094675 CATCTTTGGCTGGGGTAGTTG 58.905 52.381 0.00 0.00 0.00 3.16
2387 2388 2.579873 CATCATCTTTGGCTGGGGTAG 58.420 52.381 0.00 0.00 0.00 3.18
2410 2411 3.033909 TCTCCACTCCATCGTGATGATT 58.966 45.455 11.35 0.00 41.20 2.57
2419 2420 2.579878 TGGACGTCTCCACTCCATC 58.420 57.895 16.46 0.00 42.15 3.51
2427 2428 2.293955 GCTTAGGTAGATGGACGTCTCC 59.706 54.545 16.46 0.00 37.04 3.71
2429 2430 3.014304 TGCTTAGGTAGATGGACGTCT 57.986 47.619 16.46 0.00 0.00 4.18
2445 2446 1.485895 ACAAAGCCAACAACCATGCTT 59.514 42.857 0.00 0.00 45.40 3.91
2454 2455 1.452145 GGCCGAAGACAAAGCCAACA 61.452 55.000 0.00 0.00 45.07 3.33
2505 2506 5.398603 AATAGGCGTATCTCCATCTCTTG 57.601 43.478 0.00 0.00 0.00 3.02
2565 2566 3.258123 GGTTCCAGGCAACAATTGTATGT 59.742 43.478 12.39 0.00 41.41 2.29
2570 2571 1.273327 GGAGGTTCCAGGCAACAATTG 59.727 52.381 3.24 3.24 36.28 2.32
2575 2576 1.527433 GCAAGGAGGTTCCAGGCAAC 61.527 60.000 0.00 0.00 39.61 4.17
2594 2595 8.854614 ATCTAAAATTATTCATCCCTTCCTCG 57.145 34.615 0.00 0.00 0.00 4.63
2608 2609 6.715264 CGGCCCTTCACCTTATCTAAAATTAT 59.285 38.462 0.00 0.00 0.00 1.28
2611 2612 4.165372 TCGGCCCTTCACCTTATCTAAAAT 59.835 41.667 0.00 0.00 0.00 1.82
2621 2622 2.097110 TGTATATCGGCCCTTCACCT 57.903 50.000 0.00 0.00 0.00 4.00
2622 2623 2.490991 GTTGTATATCGGCCCTTCACC 58.509 52.381 0.00 0.00 0.00 4.02
2631 2632 3.003068 AGGAGAACGTCGTTGTATATCGG 59.997 47.826 16.75 0.00 0.00 4.18
2632 2633 4.206698 AGGAGAACGTCGTTGTATATCG 57.793 45.455 16.75 0.00 0.00 2.92
2645 2646 0.531532 CCCAGCTGCATAGGAGAACG 60.532 60.000 8.66 0.00 0.00 3.95
2708 2709 2.146342 CCCGTATGAATGGAGATGCAC 58.854 52.381 0.00 0.00 33.01 4.57
2805 2806 7.334090 ACAGCTCAGTATTTATTCATGAGTGT 58.666 34.615 0.13 0.00 39.63 3.55
2807 2808 7.655328 GCTACAGCTCAGTATTTATTCATGAGT 59.345 37.037 0.00 0.00 39.63 3.41
2827 2828 9.760660 GACAAATTTGTATTCTTACAGCTACAG 57.239 33.333 23.33 0.00 42.43 2.74
2849 2850 3.008594 AGGTCGGTTTACATCCATGACAA 59.991 43.478 0.00 0.00 0.00 3.18
2850 2851 2.569853 AGGTCGGTTTACATCCATGACA 59.430 45.455 0.00 0.00 0.00 3.58
2878 2879 1.971481 AACCACCACCGAACCTTTAC 58.029 50.000 0.00 0.00 0.00 2.01
3048 3051 1.956629 TACGGGCTAACAGGCTCTGC 61.957 60.000 2.50 0.00 41.09 4.26
3113 3119 4.569943 TCTCGCTTGTGAGCTTTTTAGAT 58.430 39.130 6.34 0.00 46.96 1.98
3117 3123 4.202050 ACAATTCTCGCTTGTGAGCTTTTT 60.202 37.500 6.34 0.00 46.96 1.94
3131 3137 1.428448 TCCGCAAGACACAATTCTCG 58.572 50.000 0.00 0.00 43.02 4.04
3158 3164 0.456628 CATGAATTGGCGGCATGACA 59.543 50.000 14.32 13.37 41.35 3.58
3209 3215 1.346722 GGTTTTCTCCGTCCCTGAAGA 59.653 52.381 0.00 0.00 0.00 2.87
3296 3303 3.503748 CCCCAGAACTTGTTGATCTTGAC 59.496 47.826 0.00 0.00 0.00 3.18
3329 3336 1.700186 ACACTTCCTTGGAGAGGGAAC 59.300 52.381 7.68 0.00 46.31 3.62
3365 3372 2.047655 CGACGGCTGCCCAAAGTA 60.048 61.111 14.12 0.00 0.00 2.24
3447 3472 6.815089 TGCAACAGACATATTCCTTTTGTTT 58.185 32.000 0.00 0.00 0.00 2.83
3454 3479 8.757982 AAATAATCTGCAACAGACATATTCCT 57.242 30.769 13.54 2.85 43.63 3.36
3516 3541 4.769215 CCGGCTATTTAAAACTATGCGAC 58.231 43.478 0.00 0.00 0.00 5.19
3517 3542 3.249080 GCCGGCTATTTAAAACTATGCGA 59.751 43.478 22.15 0.00 0.00 5.10
3518 3543 3.250040 AGCCGGCTATTTAAAACTATGCG 59.750 43.478 31.86 0.00 0.00 4.73
3519 3544 4.830826 AGCCGGCTATTTAAAACTATGC 57.169 40.909 31.86 0.00 0.00 3.14
3520 3545 8.448615 GGTTATAGCCGGCTATTTAAAACTATG 58.551 37.037 44.65 0.00 39.65 2.23
3521 3546 7.609146 GGGTTATAGCCGGCTATTTAAAACTAT 59.391 37.037 44.65 26.21 39.65 2.12
3522 3547 6.936335 GGGTTATAGCCGGCTATTTAAAACTA 59.064 38.462 44.65 26.55 39.65 2.24
3523 3548 5.766670 GGGTTATAGCCGGCTATTTAAAACT 59.233 40.000 44.65 26.62 39.65 2.66
3524 3549 5.048504 GGGGTTATAGCCGGCTATTTAAAAC 60.049 44.000 44.65 38.01 39.65 2.43
3525 3550 5.072055 GGGGTTATAGCCGGCTATTTAAAA 58.928 41.667 44.65 32.18 39.65 1.52
3526 3551 4.654915 GGGGTTATAGCCGGCTATTTAAA 58.345 43.478 44.65 32.50 39.65 1.52
3527 3552 3.306919 CGGGGTTATAGCCGGCTATTTAA 60.307 47.826 44.65 33.14 39.65 1.52
3528 3553 2.234414 CGGGGTTATAGCCGGCTATTTA 59.766 50.000 44.65 31.98 39.65 1.40
3529 3554 1.002773 CGGGGTTATAGCCGGCTATTT 59.997 52.381 44.65 30.05 39.65 1.40
3530 3555 0.611714 CGGGGTTATAGCCGGCTATT 59.388 55.000 44.65 30.54 39.65 1.73
3531 3556 2.283824 CGGGGTTATAGCCGGCTAT 58.716 57.895 42.09 42.09 41.58 2.97
3532 3557 3.781760 CGGGGTTATAGCCGGCTA 58.218 61.111 36.88 36.88 36.39 3.93
3535 3560 0.037605 CTTAGCGGGGTTATAGCCGG 60.038 60.000 0.00 0.00 36.39 6.13
3536 3561 0.677842 ACTTAGCGGGGTTATAGCCG 59.322 55.000 0.00 0.00 36.39 5.52
3537 3562 1.270678 CCACTTAGCGGGGTTATAGCC 60.271 57.143 0.00 0.00 34.31 3.93
3538 3563 1.415289 ACCACTTAGCGGGGTTATAGC 59.585 52.381 0.00 0.00 0.00 2.97
3539 3564 2.963782 AGACCACTTAGCGGGGTTATAG 59.036 50.000 0.00 0.00 34.39 1.31
3540 3565 2.961062 GAGACCACTTAGCGGGGTTATA 59.039 50.000 0.00 0.00 34.39 0.98
3541 3566 1.761198 GAGACCACTTAGCGGGGTTAT 59.239 52.381 0.00 0.00 34.39 1.89
3542 3567 1.188863 GAGACCACTTAGCGGGGTTA 58.811 55.000 0.00 0.00 34.39 2.85
3543 3568 0.834687 TGAGACCACTTAGCGGGGTT 60.835 55.000 0.00 0.00 34.39 4.11
3544 3569 0.617820 ATGAGACCACTTAGCGGGGT 60.618 55.000 0.00 0.00 37.70 4.95
3545 3570 0.179073 CATGAGACCACTTAGCGGGG 60.179 60.000 0.00 0.00 0.00 5.73
3546 3571 0.811616 GCATGAGACCACTTAGCGGG 60.812 60.000 0.00 0.00 0.00 6.13
3547 3572 0.108186 TGCATGAGACCACTTAGCGG 60.108 55.000 0.00 0.00 0.00 5.52
3548 3573 1.002366 GTGCATGAGACCACTTAGCG 58.998 55.000 0.00 0.00 0.00 4.26
3549 3574 2.099141 TGTGCATGAGACCACTTAGC 57.901 50.000 0.00 0.00 33.26 3.09
3550 3575 4.142534 CCATTTGTGCATGAGACCACTTAG 60.143 45.833 0.00 0.00 33.26 2.18
3551 3576 3.758023 CCATTTGTGCATGAGACCACTTA 59.242 43.478 0.00 0.00 33.26 2.24
3552 3577 2.559668 CCATTTGTGCATGAGACCACTT 59.440 45.455 0.00 0.00 33.26 3.16
3553 3578 2.165167 CCATTTGTGCATGAGACCACT 58.835 47.619 0.00 0.00 33.26 4.00
3554 3579 2.095059 GTCCATTTGTGCATGAGACCAC 60.095 50.000 0.00 0.00 0.00 4.16
3555 3580 2.161855 GTCCATTTGTGCATGAGACCA 58.838 47.619 0.00 0.00 0.00 4.02
3556 3581 2.440409 AGTCCATTTGTGCATGAGACC 58.560 47.619 0.00 0.00 30.52 3.85
3557 3582 3.064545 GCTAGTCCATTTGTGCATGAGAC 59.935 47.826 0.00 0.00 0.00 3.36
3558 3583 3.054875 AGCTAGTCCATTTGTGCATGAGA 60.055 43.478 0.00 0.00 0.00 3.27
3559 3584 3.064958 CAGCTAGTCCATTTGTGCATGAG 59.935 47.826 0.00 0.00 0.00 2.90
3560 3585 3.011818 CAGCTAGTCCATTTGTGCATGA 58.988 45.455 0.00 0.00 0.00 3.07
3561 3586 3.011818 TCAGCTAGTCCATTTGTGCATG 58.988 45.455 0.00 0.00 0.00 4.06
3562 3587 3.354948 TCAGCTAGTCCATTTGTGCAT 57.645 42.857 0.00 0.00 0.00 3.96
3563 3588 2.857186 TCAGCTAGTCCATTTGTGCA 57.143 45.000 0.00 0.00 0.00 4.57
3564 3589 4.156556 TCAAATCAGCTAGTCCATTTGTGC 59.843 41.667 15.87 0.00 37.46 4.57
3565 3590 5.885230 TCAAATCAGCTAGTCCATTTGTG 57.115 39.130 15.87 1.40 37.46 3.33
3566 3591 5.416952 CCTTCAAATCAGCTAGTCCATTTGT 59.583 40.000 15.87 0.00 37.46 2.83
3567 3592 5.416952 ACCTTCAAATCAGCTAGTCCATTTG 59.583 40.000 12.58 12.58 37.51 2.32
3568 3593 5.574188 ACCTTCAAATCAGCTAGTCCATTT 58.426 37.500 0.00 0.00 0.00 2.32
3569 3594 5.184892 ACCTTCAAATCAGCTAGTCCATT 57.815 39.130 0.00 0.00 0.00 3.16
3570 3595 4.384647 GGACCTTCAAATCAGCTAGTCCAT 60.385 45.833 0.00 0.00 41.73 3.41
3571 3596 3.055094 GGACCTTCAAATCAGCTAGTCCA 60.055 47.826 0.00 0.00 41.73 4.02
3572 3597 3.536570 GGACCTTCAAATCAGCTAGTCC 58.463 50.000 0.00 0.00 36.12 3.85
3573 3598 3.190874 CGGACCTTCAAATCAGCTAGTC 58.809 50.000 0.00 0.00 0.00 2.59
3574 3599 2.678190 GCGGACCTTCAAATCAGCTAGT 60.678 50.000 0.00 0.00 33.80 2.57
3575 3600 1.936547 GCGGACCTTCAAATCAGCTAG 59.063 52.381 0.00 0.00 33.80 3.42
3576 3601 1.406887 GGCGGACCTTCAAATCAGCTA 60.407 52.381 0.00 0.00 36.44 3.32
3577 3602 0.678048 GGCGGACCTTCAAATCAGCT 60.678 55.000 0.00 0.00 36.44 4.24
3578 3603 1.803289 GGCGGACCTTCAAATCAGC 59.197 57.895 0.00 0.00 35.57 4.26
3579 3604 1.982073 GCGGCGGACCTTCAAATCAG 61.982 60.000 9.78 0.00 0.00 2.90
3580 3605 2.038269 GCGGCGGACCTTCAAATCA 61.038 57.895 9.78 0.00 0.00 2.57
3581 3606 0.461339 TAGCGGCGGACCTTCAAATC 60.461 55.000 9.78 0.00 0.00 2.17
3582 3607 0.180406 ATAGCGGCGGACCTTCAAAT 59.820 50.000 9.78 0.00 0.00 2.32
3583 3608 0.035820 AATAGCGGCGGACCTTCAAA 60.036 50.000 9.78 0.00 0.00 2.69
3584 3609 0.035820 AAATAGCGGCGGACCTTCAA 60.036 50.000 9.78 0.00 0.00 2.69
3585 3610 0.825410 TAAATAGCGGCGGACCTTCA 59.175 50.000 9.78 0.00 0.00 3.02
3586 3611 1.499049 CTAAATAGCGGCGGACCTTC 58.501 55.000 9.78 0.00 0.00 3.46
3587 3612 0.532196 GCTAAATAGCGGCGGACCTT 60.532 55.000 9.78 0.00 39.82 3.50
3588 3613 1.069258 GCTAAATAGCGGCGGACCT 59.931 57.895 9.78 0.00 39.82 3.85
3589 3614 3.638971 GCTAAATAGCGGCGGACC 58.361 61.111 9.78 0.00 39.82 4.46


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

AutoCloner maintained by Alex Coulton.