Multiple sequence alignment - TraesCS3D01G142400

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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 TraesCS3D01G142400 chr3D 100.000 2552 0 0 1 2552 104294319 104291768 0.000000e+00 4713.0
1 TraesCS3D01G142400 chr3B 91.322 2201 98 35 84 2239 155420094 155417942 0.000000e+00 2920.0
2 TraesCS3D01G142400 chr3B 100.000 35 0 0 2518 2552 155415275 155415241 5.890000e-07 65.8
3 TraesCS3D01G142400 chr3A 82.944 1284 123 51 752 1987 551762158 551763393 0.000000e+00 1070.0
4 TraesCS3D01G142400 chr3A 83.279 305 27 9 430 722 551761550 551761842 2.520000e-65 259.0
5 TraesCS3D01G142400 chr3A 97.222 36 0 1 2518 2552 15563900 15563935 2.740000e-05 60.2
6 TraesCS3D01G142400 chr1D 76.033 242 43 13 1277 1515 140055609 140055380 7.460000e-21 111.0
7 TraesCS3D01G142400 chr1B 85.714 98 14 0 1277 1374 198486613 198486710 1.250000e-18 104.0
8 TraesCS3D01G142400 chr1A 84.694 98 15 0 1277 1374 150860902 150860999 5.810000e-17 99.0
9 TraesCS3D01G142400 chr7A 89.333 75 7 1 2445 2518 111853194 111853120 2.700000e-15 93.5
10 TraesCS3D01G142400 chr7A 100.000 32 0 0 2521 2552 411541875 411541844 2.740000e-05 60.2
11 TraesCS3D01G142400 chr7B 100.000 32 0 0 2521 2552 705729778 705729809 2.740000e-05 60.2
12 TraesCS3D01G142400 chr6B 100.000 32 0 0 2521 2552 213304299 213304268 2.740000e-05 60.2
13 TraesCS3D01G142400 chr5D 100.000 32 0 0 2521 2552 482164431 482164400 2.740000e-05 60.2
14 TraesCS3D01G142400 chr5B 100.000 32 0 0 2521 2552 488214392 488214423 2.740000e-05 60.2
15 TraesCS3D01G142400 chr4A 100.000 32 0 0 2521 2552 80248816 80248847 2.740000e-05 60.2
16 TraesCS3D01G142400 chr2D 100.000 32 0 0 2521 2552 37922996 37923027 2.740000e-05 60.2


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G142400 chr3D 104291768 104294319 2551 True 4713.0 4713 100.0000 1 2552 1 chr3D.!!$R1 2551
1 TraesCS3D01G142400 chr3B 155415241 155420094 4853 True 1492.9 2920 95.6610 84 2552 2 chr3B.!!$R1 2468
2 TraesCS3D01G142400 chr3A 551761550 551763393 1843 False 664.5 1070 83.1115 430 1987 2 chr3A.!!$F2 1557

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
317 323 1.081041 TCGCACGCGATAACACAGT 60.081 52.632 15.93 0.0 44.01 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2252 2648 0.036875 GGGAGGGGCGATTCATTAGG 59.963 60.0 0.0 0.0 0.0 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
21 22 3.827008 TCTTATGCACTAAGGCCTCTG 57.173 47.619 5.23 4.25 37.91 3.35
22 23 3.107601 TCTTATGCACTAAGGCCTCTGT 58.892 45.455 5.23 5.03 37.91 3.41
23 24 3.519510 TCTTATGCACTAAGGCCTCTGTT 59.480 43.478 5.23 0.00 37.91 3.16
24 25 2.887151 ATGCACTAAGGCCTCTGTTT 57.113 45.000 5.23 0.00 0.00 2.83
25 26 2.656947 TGCACTAAGGCCTCTGTTTT 57.343 45.000 5.23 0.00 0.00 2.43
26 27 2.504367 TGCACTAAGGCCTCTGTTTTC 58.496 47.619 5.23 0.70 0.00 2.29
27 28 2.158682 TGCACTAAGGCCTCTGTTTTCA 60.159 45.455 5.23 3.32 0.00 2.69
28 29 9.219657 CTTATGCACTAAGGCCTCTGTTTTCAG 62.220 44.444 5.23 0.00 39.88 3.02
29 30 3.744660 CACTAAGGCCTCTGTTTTCAGT 58.255 45.455 5.23 0.00 46.98 3.41
30 31 4.802918 GCACTAAGGCCTCTGTTTTCAGTA 60.803 45.833 5.23 0.00 46.98 2.74
31 32 5.491982 CACTAAGGCCTCTGTTTTCAGTAT 58.508 41.667 5.23 0.00 46.98 2.12
32 33 5.940470 CACTAAGGCCTCTGTTTTCAGTATT 59.060 40.000 5.23 0.00 46.98 1.89
33 34 6.431234 CACTAAGGCCTCTGTTTTCAGTATTT 59.569 38.462 5.23 0.00 46.98 1.40
34 35 7.004691 ACTAAGGCCTCTGTTTTCAGTATTTT 58.995 34.615 5.23 0.00 46.98 1.82
35 36 6.731292 AAGGCCTCTGTTTTCAGTATTTTT 57.269 33.333 5.23 0.00 46.98 1.94
36 37 6.089249 AGGCCTCTGTTTTCAGTATTTTTG 57.911 37.500 0.00 0.00 46.98 2.44
37 38 5.598417 AGGCCTCTGTTTTCAGTATTTTTGT 59.402 36.000 0.00 0.00 46.98 2.83
38 39 5.920840 GGCCTCTGTTTTCAGTATTTTTGTC 59.079 40.000 0.00 0.00 46.98 3.18
39 40 6.239036 GGCCTCTGTTTTCAGTATTTTTGTCT 60.239 38.462 0.00 0.00 46.98 3.41
40 41 7.040686 GGCCTCTGTTTTCAGTATTTTTGTCTA 60.041 37.037 0.00 0.00 46.98 2.59
41 42 8.017946 GCCTCTGTTTTCAGTATTTTTGTCTAG 58.982 37.037 0.00 0.00 46.98 2.43
42 43 8.017946 CCTCTGTTTTCAGTATTTTTGTCTAGC 58.982 37.037 0.00 0.00 46.98 3.42
43 44 8.677148 TCTGTTTTCAGTATTTTTGTCTAGCT 57.323 30.769 0.00 0.00 46.98 3.32
44 45 8.774586 TCTGTTTTCAGTATTTTTGTCTAGCTC 58.225 33.333 0.00 0.00 46.98 4.09
45 46 8.445275 TGTTTTCAGTATTTTTGTCTAGCTCA 57.555 30.769 0.00 0.00 0.00 4.26
46 47 9.066892 TGTTTTCAGTATTTTTGTCTAGCTCAT 57.933 29.630 0.00 0.00 0.00 2.90
47 48 9.548208 GTTTTCAGTATTTTTGTCTAGCTCATC 57.452 33.333 0.00 0.00 0.00 2.92
48 49 9.507329 TTTTCAGTATTTTTGTCTAGCTCATCT 57.493 29.630 0.00 0.00 0.00 2.90
49 50 8.484641 TTCAGTATTTTTGTCTAGCTCATCTG 57.515 34.615 0.00 0.00 0.00 2.90
50 51 7.615403 TCAGTATTTTTGTCTAGCTCATCTGT 58.385 34.615 0.00 0.00 0.00 3.41
51 52 8.749354 TCAGTATTTTTGTCTAGCTCATCTGTA 58.251 33.333 0.00 0.00 0.00 2.74
52 53 9.371136 CAGTATTTTTGTCTAGCTCATCTGTAA 57.629 33.333 0.00 0.00 0.00 2.41
53 54 9.372369 AGTATTTTTGTCTAGCTCATCTGTAAC 57.628 33.333 0.00 0.00 0.00 2.50
54 55 9.151471 GTATTTTTGTCTAGCTCATCTGTAACA 57.849 33.333 0.00 0.00 0.00 2.41
55 56 7.421530 TTTTTGTCTAGCTCATCTGTAACAC 57.578 36.000 0.00 0.00 0.00 3.32
56 57 5.722021 TTGTCTAGCTCATCTGTAACACA 57.278 39.130 0.00 0.00 0.00 3.72
57 58 5.921962 TGTCTAGCTCATCTGTAACACAT 57.078 39.130 0.00 0.00 0.00 3.21
58 59 5.654497 TGTCTAGCTCATCTGTAACACATG 58.346 41.667 0.00 0.00 0.00 3.21
59 60 5.418840 TGTCTAGCTCATCTGTAACACATGA 59.581 40.000 0.00 0.00 0.00 3.07
60 61 6.071391 TGTCTAGCTCATCTGTAACACATGAA 60.071 38.462 0.00 0.00 0.00 2.57
61 62 6.254589 GTCTAGCTCATCTGTAACACATGAAC 59.745 42.308 0.00 0.00 0.00 3.18
62 63 3.928992 AGCTCATCTGTAACACATGAACG 59.071 43.478 0.00 0.00 0.00 3.95
63 64 3.926527 GCTCATCTGTAACACATGAACGA 59.073 43.478 0.00 0.00 0.00 3.85
64 65 4.032217 GCTCATCTGTAACACATGAACGAG 59.968 45.833 0.00 0.00 0.00 4.18
65 66 4.494484 TCATCTGTAACACATGAACGAGG 58.506 43.478 0.00 0.00 0.00 4.63
66 67 4.219725 TCATCTGTAACACATGAACGAGGA 59.780 41.667 0.00 0.00 0.00 3.71
67 68 4.174411 TCTGTAACACATGAACGAGGAG 57.826 45.455 0.00 0.00 0.00 3.69
68 69 2.668457 CTGTAACACATGAACGAGGAGC 59.332 50.000 0.00 0.00 0.00 4.70
69 70 2.299013 TGTAACACATGAACGAGGAGCT 59.701 45.455 0.00 0.00 0.00 4.09
70 71 3.508402 TGTAACACATGAACGAGGAGCTA 59.492 43.478 0.00 0.00 0.00 3.32
71 72 3.678056 AACACATGAACGAGGAGCTAA 57.322 42.857 0.00 0.00 0.00 3.09
72 73 3.895232 ACACATGAACGAGGAGCTAAT 57.105 42.857 0.00 0.00 0.00 1.73
73 74 4.207891 ACACATGAACGAGGAGCTAATT 57.792 40.909 0.00 0.00 0.00 1.40
74 75 4.579869 ACACATGAACGAGGAGCTAATTT 58.420 39.130 0.00 0.00 0.00 1.82
75 76 5.730550 ACACATGAACGAGGAGCTAATTTA 58.269 37.500 0.00 0.00 0.00 1.40
76 77 6.170506 ACACATGAACGAGGAGCTAATTTAA 58.829 36.000 0.00 0.00 0.00 1.52
77 78 6.823689 ACACATGAACGAGGAGCTAATTTAAT 59.176 34.615 0.00 0.00 0.00 1.40
78 79 7.336931 ACACATGAACGAGGAGCTAATTTAATT 59.663 33.333 0.00 0.00 0.00 1.40
79 80 7.641411 CACATGAACGAGGAGCTAATTTAATTG 59.359 37.037 0.00 0.00 0.00 2.32
80 81 6.677781 TGAACGAGGAGCTAATTTAATTGG 57.322 37.500 0.00 0.00 0.00 3.16
81 82 6.411376 TGAACGAGGAGCTAATTTAATTGGA 58.589 36.000 5.23 0.00 0.00 3.53
82 83 6.538742 TGAACGAGGAGCTAATTTAATTGGAG 59.461 38.462 5.23 0.00 0.00 3.86
125 127 9.643693 CTAACTTGCAAAAACCATATCAGAATT 57.356 29.630 0.00 0.00 0.00 2.17
126 128 8.538409 AACTTGCAAAAACCATATCAGAATTC 57.462 30.769 0.00 0.00 0.00 2.17
130 132 8.481974 TGCAAAAACCATATCAGAATTCATTG 57.518 30.769 8.44 0.00 0.00 2.82
165 167 7.615365 TCCATAATCTTAAAGATGTGTGCCTTT 59.385 33.333 0.00 0.00 34.65 3.11
197 199 4.039245 TCATTGGTTCTCGCCCTCTAATAG 59.961 45.833 0.00 0.00 0.00 1.73
198 200 2.317040 TGGTTCTCGCCCTCTAATAGG 58.683 52.381 0.00 0.00 46.09 2.57
242 244 7.120579 TGTTTATGCAGATATCTTTTGTCCGTT 59.879 33.333 1.33 0.00 0.00 4.44
244 246 3.689161 TGCAGATATCTTTTGTCCGTTGG 59.311 43.478 1.33 0.00 0.00 3.77
256 258 1.301874 CCGTTGGAAAGTACGGGCA 60.302 57.895 5.80 0.00 41.55 5.36
267 269 5.292834 GGAAAGTACGGGCAATTTACTAGTC 59.707 44.000 0.00 0.00 0.00 2.59
271 273 4.755266 ACGGGCAATTTACTAGTCTCAT 57.245 40.909 0.00 0.00 0.00 2.90
275 279 7.280356 ACGGGCAATTTACTAGTCTCATAAAT 58.720 34.615 0.00 0.00 31.39 1.40
277 281 9.268268 CGGGCAATTTACTAGTCTCATAAATAA 57.732 33.333 0.00 0.00 30.24 1.40
301 307 1.205655 TCATCTCTGTCAAAGCCCTCG 59.794 52.381 0.00 0.00 0.00 4.63
317 323 1.081041 TCGCACGCGATAACACAGT 60.081 52.632 15.93 0.00 44.01 3.55
339 345 5.586243 AGTTAGTGGTGAATTTGATGATCCG 59.414 40.000 0.00 0.00 0.00 4.18
364 370 3.135414 GTGCATTTAATTCTCGCAGCA 57.865 42.857 0.00 0.00 32.31 4.41
365 371 2.848302 GTGCATTTAATTCTCGCAGCAC 59.152 45.455 0.00 0.00 43.27 4.40
388 394 5.538813 ACTTGTTCACAGTCCACTCTGTATA 59.461 40.000 0.00 0.00 45.37 1.47
392 398 7.450074 TGTTCACAGTCCACTCTGTATATTTT 58.550 34.615 0.00 0.00 45.37 1.82
419 428 8.405531 CCAAACAAAGTATTGATACTGGTATGG 58.594 37.037 4.52 6.63 42.47 2.74
420 429 8.956426 CAAACAAAGTATTGATACTGGTATGGT 58.044 33.333 4.52 0.00 42.47 3.55
421 430 8.732746 AACAAAGTATTGATACTGGTATGGTC 57.267 34.615 4.52 0.00 42.47 4.02
423 432 7.769044 ACAAAGTATTGATACTGGTATGGTCAC 59.231 37.037 4.52 0.00 42.47 3.67
424 433 6.420913 AGTATTGATACTGGTATGGTCACC 57.579 41.667 2.96 0.00 41.77 4.02
432 441 2.677836 CTGGTATGGTCACCAATGAACG 59.322 50.000 0.00 0.00 46.50 3.95
442 459 6.108015 GGTCACCAATGAACGGTAAAGTATA 58.892 40.000 0.00 0.00 36.31 1.47
443 460 6.764560 GGTCACCAATGAACGGTAAAGTATAT 59.235 38.462 0.00 0.00 36.31 0.86
451 468 6.973843 TGAACGGTAAAGTATATATCGTGCT 58.026 36.000 0.00 0.00 39.04 4.40
502 519 2.040544 GGGACGGTGCACCAATCAG 61.041 63.158 34.16 20.18 35.14 2.90
629 657 9.174166 GACCACCAACTGTCAAAAATATACTAT 57.826 33.333 0.00 0.00 0.00 2.12
749 786 6.325919 CTGATTCCAGGACTCTACATCTAC 57.674 45.833 8.24 0.00 36.77 2.59
888 1206 9.767684 CGTTTCTTGAACTGCAATATATAAACA 57.232 29.630 0.00 0.00 35.59 2.83
968 1304 1.425412 GGTTCGTGTGCATACGTTCT 58.575 50.000 30.87 0.00 44.06 3.01
1150 1486 2.738521 GCTTCTTCTCCGCGCACA 60.739 61.111 8.75 0.00 0.00 4.57
1300 1639 3.768922 GCGAGGAGCTGCTGGAGT 61.769 66.667 21.20 0.00 44.04 3.85
1392 1731 3.827898 CTCCGCGTCCTGGACCTC 61.828 72.222 20.68 11.75 0.00 3.85
1570 1909 1.308069 GGCAGTAGGTGTCGTCGGTA 61.308 60.000 0.00 0.00 0.00 4.02
1747 2135 9.174166 GTACCCTTTTCTTAGATGCTAATTTCA 57.826 33.333 0.00 0.00 0.00 2.69
1797 2185 2.233355 CACTTGTCAAATTACAGCGCG 58.767 47.619 0.00 0.00 0.00 6.86
1823 2211 7.576236 CATAATAAAAATCGAGCGAGTTGGAT 58.424 34.615 6.34 1.04 32.53 3.41
1824 2212 5.659048 ATAAAAATCGAGCGAGTTGGATC 57.341 39.130 6.34 0.00 32.53 3.36
1826 2214 2.215907 AATCGAGCGAGTTGGATCAG 57.784 50.000 0.00 0.00 0.00 2.90
1835 2223 1.002069 AGTTGGATCAGAATGGGGCA 58.998 50.000 0.00 0.00 36.16 5.36
1847 2235 6.539173 TCAGAATGGGGCATAAATAACGTAT 58.461 36.000 0.00 0.00 36.16 3.06
1890 2281 1.597937 GCTCTGATATTTTTGGCGCGG 60.598 52.381 8.83 0.00 0.00 6.46
1893 2284 3.734463 TCTGATATTTTTGGCGCGGATA 58.266 40.909 8.83 0.00 0.00 2.59
1983 2378 1.177895 TTCAATGCGGCACATGGTGT 61.178 50.000 4.03 0.00 39.60 4.16
2024 2419 7.167468 ACTGCAAGATTCGTTCAATAAACAAAC 59.833 33.333 0.00 0.00 35.81 2.93
2064 2459 7.042335 AGTAAAAAGTCTACGATGGAGATTGG 58.958 38.462 0.00 0.00 0.00 3.16
2076 2471 2.505407 TGGAGATTGGGACGATCAACAT 59.495 45.455 0.00 0.00 0.00 2.71
2116 2511 5.220873 GGAAATCCTTTTAGCAGGAATCGAC 60.221 44.000 0.00 0.00 46.50 4.20
2176 2572 7.390440 ACAGTAAGTATGAGCAAAAATGCTACA 59.610 33.333 2.89 4.66 46.36 2.74
2188 2584 2.990066 ATGCTACACCTACAGGCTTC 57.010 50.000 0.00 0.00 39.32 3.86
2215 2611 2.829720 ACAAACTCTACATACGGGCTGA 59.170 45.455 0.00 0.00 0.00 4.26
2238 2634 6.431543 TGATTTGTACTCTTTTAATTGGCCGA 59.568 34.615 0.00 0.00 0.00 5.54
2239 2635 6.636562 TTTGTACTCTTTTAATTGGCCGAA 57.363 33.333 0.00 0.00 0.00 4.30
2240 2636 6.827586 TTGTACTCTTTTAATTGGCCGAAT 57.172 33.333 0.00 0.00 0.00 3.34
2241 2637 6.827586 TGTACTCTTTTAATTGGCCGAATT 57.172 33.333 14.78 14.78 37.96 2.17
2242 2638 7.925043 TGTACTCTTTTAATTGGCCGAATTA 57.075 32.000 13.23 13.23 35.74 1.40
2243 2639 7.981142 TGTACTCTTTTAATTGGCCGAATTAG 58.019 34.615 15.41 10.68 37.72 1.73
2244 2640 5.891451 ACTCTTTTAATTGGCCGAATTAGC 58.109 37.500 15.41 0.00 37.72 3.09
2245 2641 5.652452 ACTCTTTTAATTGGCCGAATTAGCT 59.348 36.000 15.41 0.00 37.72 3.32
2246 2642 6.826741 ACTCTTTTAATTGGCCGAATTAGCTA 59.173 34.615 15.41 0.00 37.72 3.32
2247 2643 7.023197 TCTTTTAATTGGCCGAATTAGCTAC 57.977 36.000 15.41 0.00 37.72 3.58
2248 2644 5.761165 TTTAATTGGCCGAATTAGCTACC 57.239 39.130 15.41 0.00 37.72 3.18
2249 2645 2.271944 ATTGGCCGAATTAGCTACCC 57.728 50.000 0.00 0.00 0.00 3.69
2250 2646 0.913205 TTGGCCGAATTAGCTACCCA 59.087 50.000 0.00 0.00 0.00 4.51
2251 2647 1.136828 TGGCCGAATTAGCTACCCAT 58.863 50.000 0.00 0.00 0.00 4.00
2252 2648 1.071699 TGGCCGAATTAGCTACCCATC 59.928 52.381 0.00 0.00 0.00 3.51
2253 2649 1.610886 GGCCGAATTAGCTACCCATCC 60.611 57.143 0.00 0.00 0.00 3.51
2254 2650 1.348036 GCCGAATTAGCTACCCATCCT 59.652 52.381 0.00 0.00 0.00 3.24
2255 2651 2.565834 GCCGAATTAGCTACCCATCCTA 59.434 50.000 0.00 0.00 0.00 2.94
2256 2652 3.007614 GCCGAATTAGCTACCCATCCTAA 59.992 47.826 0.00 0.00 0.00 2.69
2257 2653 4.323562 GCCGAATTAGCTACCCATCCTAAT 60.324 45.833 0.00 0.00 34.25 1.73
2258 2654 5.178797 CCGAATTAGCTACCCATCCTAATG 58.821 45.833 0.00 0.00 33.40 1.90
2259 2655 5.046591 CCGAATTAGCTACCCATCCTAATGA 60.047 44.000 0.00 0.00 33.40 2.57
2260 2656 6.464222 CGAATTAGCTACCCATCCTAATGAA 58.536 40.000 0.00 0.00 33.40 2.57
2261 2657 7.106239 CGAATTAGCTACCCATCCTAATGAAT 58.894 38.462 0.00 0.00 33.40 2.57
2262 2658 7.278868 CGAATTAGCTACCCATCCTAATGAATC 59.721 40.741 0.00 0.00 33.40 2.52
2263 2659 4.543590 AGCTACCCATCCTAATGAATCG 57.456 45.455 0.00 0.00 34.61 3.34
2264 2660 3.003480 GCTACCCATCCTAATGAATCGC 58.997 50.000 0.00 0.00 34.61 4.58
2265 2661 2.568623 ACCCATCCTAATGAATCGCC 57.431 50.000 0.00 0.00 34.61 5.54
2266 2662 1.073923 ACCCATCCTAATGAATCGCCC 59.926 52.381 0.00 0.00 34.61 6.13
2267 2663 1.614317 CCCATCCTAATGAATCGCCCC 60.614 57.143 0.00 0.00 34.61 5.80
2268 2664 1.352352 CCATCCTAATGAATCGCCCCT 59.648 52.381 0.00 0.00 34.61 4.79
2269 2665 2.616510 CCATCCTAATGAATCGCCCCTC 60.617 54.545 0.00 0.00 34.61 4.30
2270 2666 1.056660 TCCTAATGAATCGCCCCTCC 58.943 55.000 0.00 0.00 0.00 4.30
2271 2667 0.036875 CCTAATGAATCGCCCCTCCC 59.963 60.000 0.00 0.00 0.00 4.30
2272 2668 0.764890 CTAATGAATCGCCCCTCCCA 59.235 55.000 0.00 0.00 0.00 4.37
2273 2669 0.764890 TAATGAATCGCCCCTCCCAG 59.235 55.000 0.00 0.00 0.00 4.45
2274 2670 1.999634 AATGAATCGCCCCTCCCAGG 62.000 60.000 0.00 0.00 34.30 4.45
2296 2692 2.190048 GGGGCGCCCATTTACGTA 59.810 61.111 44.46 0.00 44.65 3.57
2297 2693 1.451747 GGGGCGCCCATTTACGTAA 60.452 57.895 44.46 3.29 44.65 3.18
2298 2694 1.031029 GGGGCGCCCATTTACGTAAA 61.031 55.000 44.46 22.12 44.65 2.01
2299 2695 0.810016 GGGCGCCCATTTACGTAAAA 59.190 50.000 40.73 8.50 35.81 1.52
2300 2696 1.467883 GGGCGCCCATTTACGTAAAAC 60.468 52.381 40.73 7.27 35.81 2.43
2301 2697 1.467883 GGCGCCCATTTACGTAAAACC 60.468 52.381 23.49 14.04 0.00 3.27
2302 2698 1.467883 GCGCCCATTTACGTAAAACCC 60.468 52.381 23.49 11.69 0.00 4.11
2303 2699 1.132834 CGCCCATTTACGTAAAACCCC 59.867 52.381 23.49 12.00 0.00 4.95
2304 2700 1.477700 GCCCATTTACGTAAAACCCCC 59.522 52.381 23.49 8.63 0.00 5.40
2305 2701 1.744522 CCCATTTACGTAAAACCCCCG 59.255 52.381 23.49 8.81 0.00 5.73
2306 2702 2.435422 CCATTTACGTAAAACCCCCGT 58.565 47.619 23.49 3.65 38.53 5.28
2307 2703 3.604582 CCATTTACGTAAAACCCCCGTA 58.395 45.455 23.49 0.00 36.12 4.02
2308 2704 3.622612 CCATTTACGTAAAACCCCCGTAG 59.377 47.826 23.49 6.41 38.20 3.51
2321 2717 3.558411 CGTAGGCGCTTGCTGCTC 61.558 66.667 7.64 0.00 40.11 4.26
2322 2718 2.434884 GTAGGCGCTTGCTGCTCA 60.435 61.111 7.64 0.00 40.11 4.26
2328 2724 0.522076 GCGCTTGCTGCTCAACATAC 60.522 55.000 0.00 0.00 40.11 2.39
2336 2732 2.675348 GCTGCTCAACATACTGACCTTC 59.325 50.000 0.00 0.00 0.00 3.46
2373 2769 7.914465 CAGTCTAATTCTTTGACTGCCTTATC 58.086 38.462 15.06 0.00 46.95 1.75
2431 2827 6.814146 AGTTTGTAGTCATTTAGTAGCTGAGC 59.186 38.462 0.00 0.00 0.00 4.26
2439 2835 9.454859 AGTCATTTAGTAGCTGAGCTTAAATTT 57.545 29.630 14.14 3.75 40.44 1.82
2451 2858 9.410556 GCTGAGCTTAAATTTCTTTTCAATACA 57.589 29.630 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.107601 ACAGAGGCCTTAGTGCATAAGA 58.892 45.455 6.77 0.00 43.17 2.10
4 5 4.261801 GAAAACAGAGGCCTTAGTGCATA 58.738 43.478 6.77 0.00 0.00 3.14
5 6 2.887151 AAACAGAGGCCTTAGTGCAT 57.113 45.000 6.77 0.00 0.00 3.96
6 7 2.158682 TGAAAACAGAGGCCTTAGTGCA 60.159 45.455 6.77 5.87 0.00 4.57
7 8 2.485814 CTGAAAACAGAGGCCTTAGTGC 59.514 50.000 6.77 3.30 0.00 4.40
8 9 3.744660 ACTGAAAACAGAGGCCTTAGTG 58.255 45.455 6.77 8.03 0.00 2.74
9 10 5.763876 ATACTGAAAACAGAGGCCTTAGT 57.236 39.130 6.77 5.86 0.00 2.24
10 11 7.454260 AAAATACTGAAAACAGAGGCCTTAG 57.546 36.000 6.77 5.07 0.00 2.18
11 12 7.286775 ACAAAAATACTGAAAACAGAGGCCTTA 59.713 33.333 6.77 0.00 0.00 2.69
12 13 6.098266 ACAAAAATACTGAAAACAGAGGCCTT 59.902 34.615 6.77 0.00 0.00 4.35
13 14 5.598417 ACAAAAATACTGAAAACAGAGGCCT 59.402 36.000 3.86 3.86 0.00 5.19
14 15 5.842907 ACAAAAATACTGAAAACAGAGGCC 58.157 37.500 0.00 0.00 0.00 5.19
15 16 6.739112 AGACAAAAATACTGAAAACAGAGGC 58.261 36.000 0.00 0.00 0.00 4.70
16 17 8.017946 GCTAGACAAAAATACTGAAAACAGAGG 58.982 37.037 0.00 0.00 0.00 3.69
17 18 8.778358 AGCTAGACAAAAATACTGAAAACAGAG 58.222 33.333 0.00 0.00 0.00 3.35
18 19 8.677148 AGCTAGACAAAAATACTGAAAACAGA 57.323 30.769 0.00 0.00 0.00 3.41
19 20 8.559536 TGAGCTAGACAAAAATACTGAAAACAG 58.440 33.333 0.00 0.00 0.00 3.16
20 21 8.445275 TGAGCTAGACAAAAATACTGAAAACA 57.555 30.769 0.00 0.00 0.00 2.83
21 22 9.548208 GATGAGCTAGACAAAAATACTGAAAAC 57.452 33.333 0.00 0.00 0.00 2.43
22 23 9.507329 AGATGAGCTAGACAAAAATACTGAAAA 57.493 29.630 0.00 0.00 0.00 2.29
23 24 8.939929 CAGATGAGCTAGACAAAAATACTGAAA 58.060 33.333 0.00 0.00 0.00 2.69
24 25 8.097038 ACAGATGAGCTAGACAAAAATACTGAA 58.903 33.333 0.00 0.00 0.00 3.02
25 26 7.615403 ACAGATGAGCTAGACAAAAATACTGA 58.385 34.615 0.00 0.00 0.00 3.41
26 27 7.840342 ACAGATGAGCTAGACAAAAATACTG 57.160 36.000 0.00 0.00 0.00 2.74
27 28 9.372369 GTTACAGATGAGCTAGACAAAAATACT 57.628 33.333 0.00 0.00 0.00 2.12
28 29 9.151471 TGTTACAGATGAGCTAGACAAAAATAC 57.849 33.333 0.00 0.00 0.00 1.89
29 30 9.151471 GTGTTACAGATGAGCTAGACAAAAATA 57.849 33.333 0.00 0.00 0.00 1.40
30 31 7.661437 TGTGTTACAGATGAGCTAGACAAAAAT 59.339 33.333 0.00 0.00 0.00 1.82
31 32 6.989759 TGTGTTACAGATGAGCTAGACAAAAA 59.010 34.615 0.00 0.00 0.00 1.94
32 33 6.521162 TGTGTTACAGATGAGCTAGACAAAA 58.479 36.000 0.00 0.00 0.00 2.44
33 34 6.096673 TGTGTTACAGATGAGCTAGACAAA 57.903 37.500 0.00 0.00 0.00 2.83
34 35 5.722021 TGTGTTACAGATGAGCTAGACAA 57.278 39.130 0.00 0.00 0.00 3.18
35 36 5.418840 TCATGTGTTACAGATGAGCTAGACA 59.581 40.000 19.16 0.00 38.83 3.41
36 37 5.895928 TCATGTGTTACAGATGAGCTAGAC 58.104 41.667 19.16 0.00 38.83 2.59
37 38 6.333416 GTTCATGTGTTACAGATGAGCTAGA 58.667 40.000 24.28 9.94 43.24 2.43
38 39 5.230936 CGTTCATGTGTTACAGATGAGCTAG 59.769 44.000 26.81 14.90 43.24 3.42
39 40 5.102313 CGTTCATGTGTTACAGATGAGCTA 58.898 41.667 26.81 12.53 43.24 3.32
40 41 3.928992 CGTTCATGTGTTACAGATGAGCT 59.071 43.478 26.81 0.00 43.24 4.09
41 42 3.926527 TCGTTCATGTGTTACAGATGAGC 59.073 43.478 22.62 22.62 43.24 4.26
42 43 4.564372 CCTCGTTCATGTGTTACAGATGAG 59.436 45.833 21.33 13.33 43.24 2.90
43 44 4.219725 TCCTCGTTCATGTGTTACAGATGA 59.780 41.667 19.16 19.16 41.31 2.92
44 45 4.494484 TCCTCGTTCATGTGTTACAGATG 58.506 43.478 15.20 15.20 36.62 2.90
45 46 4.748892 CTCCTCGTTCATGTGTTACAGAT 58.251 43.478 0.00 0.00 0.00 2.90
46 47 3.614150 GCTCCTCGTTCATGTGTTACAGA 60.614 47.826 0.00 0.00 0.00 3.41
47 48 2.668457 GCTCCTCGTTCATGTGTTACAG 59.332 50.000 0.00 0.00 0.00 2.74
48 49 2.299013 AGCTCCTCGTTCATGTGTTACA 59.701 45.455 0.00 0.00 0.00 2.41
49 50 2.960819 AGCTCCTCGTTCATGTGTTAC 58.039 47.619 0.00 0.00 0.00 2.50
50 51 4.794278 TTAGCTCCTCGTTCATGTGTTA 57.206 40.909 0.00 0.00 0.00 2.41
51 52 3.678056 TTAGCTCCTCGTTCATGTGTT 57.322 42.857 0.00 0.00 0.00 3.32
52 53 3.895232 ATTAGCTCCTCGTTCATGTGT 57.105 42.857 0.00 0.00 0.00 3.72
53 54 6.662414 TTAAATTAGCTCCTCGTTCATGTG 57.338 37.500 0.00 0.00 0.00 3.21
54 55 7.201732 CCAATTAAATTAGCTCCTCGTTCATGT 60.202 37.037 0.00 0.00 0.00 3.21
55 56 7.012327 TCCAATTAAATTAGCTCCTCGTTCATG 59.988 37.037 0.00 0.00 0.00 3.07
56 57 7.054124 TCCAATTAAATTAGCTCCTCGTTCAT 58.946 34.615 0.00 0.00 0.00 2.57
57 58 6.411376 TCCAATTAAATTAGCTCCTCGTTCA 58.589 36.000 0.00 0.00 0.00 3.18
58 59 6.017852 CCTCCAATTAAATTAGCTCCTCGTTC 60.018 42.308 0.00 0.00 0.00 3.95
59 60 5.823045 CCTCCAATTAAATTAGCTCCTCGTT 59.177 40.000 0.00 0.00 0.00 3.85
60 61 5.104485 ACCTCCAATTAAATTAGCTCCTCGT 60.104 40.000 0.00 0.00 0.00 4.18
61 62 5.368989 ACCTCCAATTAAATTAGCTCCTCG 58.631 41.667 0.00 0.00 0.00 4.63
62 63 5.765677 GGACCTCCAATTAAATTAGCTCCTC 59.234 44.000 0.00 0.00 35.64 3.71
63 64 5.193728 TGGACCTCCAATTAAATTAGCTCCT 59.806 40.000 0.00 0.00 44.35 3.69
64 65 5.445964 TGGACCTCCAATTAAATTAGCTCC 58.554 41.667 0.00 0.00 44.35 4.70
78 79 9.225682 AGTTAGAAATATATCTTTGGACCTCCA 57.774 33.333 0.00 0.00 45.94 3.86
81 82 9.343539 GCAAGTTAGAAATATATCTTTGGACCT 57.656 33.333 0.00 0.00 0.00 3.85
82 83 9.120538 TGCAAGTTAGAAATATATCTTTGGACC 57.879 33.333 0.00 0.00 0.00 4.46
98 99 7.994425 TCTGATATGGTTTTTGCAAGTTAGA 57.006 32.000 0.00 0.00 0.00 2.10
140 142 6.949352 AGGCACACATCTTTAAGATTATGG 57.051 37.500 16.00 5.16 31.32 2.74
165 167 5.355910 GGGCGAGAACCAATGAAGTAAAATA 59.644 40.000 0.00 0.00 0.00 1.40
170 172 1.906574 AGGGCGAGAACCAATGAAGTA 59.093 47.619 0.00 0.00 0.00 2.24
174 176 1.860641 TAGAGGGCGAGAACCAATGA 58.139 50.000 0.00 0.00 0.00 2.57
213 215 9.807649 GGACAAAAGATATCTGCATAAACAAAT 57.192 29.630 5.86 0.00 0.00 2.32
214 216 7.967854 CGGACAAAAGATATCTGCATAAACAAA 59.032 33.333 5.86 0.00 0.00 2.83
215 217 7.120579 ACGGACAAAAGATATCTGCATAAACAA 59.879 33.333 5.86 0.00 0.00 2.83
216 218 6.597672 ACGGACAAAAGATATCTGCATAAACA 59.402 34.615 5.86 0.00 0.00 2.83
217 219 7.016361 ACGGACAAAAGATATCTGCATAAAC 57.984 36.000 5.86 0.00 0.00 2.01
218 220 7.415095 CCAACGGACAAAAGATATCTGCATAAA 60.415 37.037 5.86 0.00 0.00 1.40
219 221 6.038161 CCAACGGACAAAAGATATCTGCATAA 59.962 38.462 5.86 0.00 0.00 1.90
220 222 5.527214 CCAACGGACAAAAGATATCTGCATA 59.473 40.000 5.86 0.00 0.00 3.14
221 223 4.336433 CCAACGGACAAAAGATATCTGCAT 59.664 41.667 5.86 0.00 0.00 3.96
222 224 3.689161 CCAACGGACAAAAGATATCTGCA 59.311 43.478 5.86 0.00 0.00 4.41
223 225 3.938963 TCCAACGGACAAAAGATATCTGC 59.061 43.478 5.86 0.00 0.00 4.26
224 226 6.149474 ACTTTCCAACGGACAAAAGATATCTG 59.851 38.462 5.86 0.00 33.85 2.90
225 227 6.238648 ACTTTCCAACGGACAAAAGATATCT 58.761 36.000 0.00 0.00 33.85 1.98
226 228 6.496338 ACTTTCCAACGGACAAAAGATATC 57.504 37.500 0.00 0.00 33.85 1.63
227 229 6.091713 CGTACTTTCCAACGGACAAAAGATAT 59.908 38.462 8.86 0.00 35.51 1.63
228 230 5.406175 CGTACTTTCCAACGGACAAAAGATA 59.594 40.000 8.86 0.00 35.51 1.98
229 231 4.212636 CGTACTTTCCAACGGACAAAAGAT 59.787 41.667 8.86 0.00 35.51 2.40
230 232 3.556775 CGTACTTTCCAACGGACAAAAGA 59.443 43.478 8.86 0.00 35.51 2.52
231 233 3.868835 CGTACTTTCCAACGGACAAAAG 58.131 45.455 0.00 0.00 35.51 2.27
242 244 4.023726 AGTAAATTGCCCGTACTTTCCA 57.976 40.909 0.00 0.00 0.00 3.53
244 246 6.104665 AGACTAGTAAATTGCCCGTACTTTC 58.895 40.000 0.00 0.00 30.81 2.62
271 273 9.113838 GGCTTTGACAGAGATGAGATTTATTTA 57.886 33.333 0.00 0.00 0.00 1.40
275 279 5.190528 AGGGCTTTGACAGAGATGAGATTTA 59.809 40.000 0.00 0.00 0.00 1.40
277 281 3.522750 AGGGCTTTGACAGAGATGAGATT 59.477 43.478 0.00 0.00 0.00 2.40
301 307 1.990563 ACTAACTGTGTTATCGCGTGC 59.009 47.619 5.77 0.00 0.00 5.34
313 319 6.375455 GGATCATCAAATTCACCACTAACTGT 59.625 38.462 0.00 0.00 0.00 3.55
317 323 5.739959 TCGGATCATCAAATTCACCACTAA 58.260 37.500 0.00 0.00 0.00 2.24
323 329 5.335127 CACCTTTCGGATCATCAAATTCAC 58.665 41.667 0.00 0.00 0.00 3.18
339 345 4.732784 TGCGAGAATTAAATGCACCTTTC 58.267 39.130 0.00 0.00 0.00 2.62
347 353 4.726416 ACAAGTGCTGCGAGAATTAAATG 58.274 39.130 0.00 0.00 0.00 2.32
351 357 3.186409 GTGAACAAGTGCTGCGAGAATTA 59.814 43.478 0.00 0.00 0.00 1.40
364 370 3.185246 CAGAGTGGACTGTGAACAAGT 57.815 47.619 0.00 0.00 39.36 3.16
388 394 9.927668 CCAGTATCAATACTTTGTTTGGAAAAT 57.072 29.630 0.00 0.00 41.44 1.82
392 398 9.173021 CATACCAGTATCAATACTTTGTTTGGA 57.827 33.333 9.56 0.00 41.44 3.53
419 428 7.781548 ATATACTTTACCGTTCATTGGTGAC 57.218 36.000 0.00 0.00 40.73 3.67
420 429 9.701098 GATATATACTTTACCGTTCATTGGTGA 57.299 33.333 0.00 0.00 40.73 4.02
421 430 8.644619 CGATATATACTTTACCGTTCATTGGTG 58.355 37.037 0.00 0.00 40.73 4.17
423 432 8.644619 CACGATATATACTTTACCGTTCATTGG 58.355 37.037 0.00 0.00 0.00 3.16
424 433 8.160342 GCACGATATATACTTTACCGTTCATTG 58.840 37.037 0.00 0.00 0.00 2.82
427 436 6.973843 AGCACGATATATACTTTACCGTTCA 58.026 36.000 0.00 0.00 0.00 3.18
428 437 7.270793 CAGAGCACGATATATACTTTACCGTTC 59.729 40.741 0.00 0.00 0.00 3.95
430 439 6.609533 CAGAGCACGATATATACTTTACCGT 58.390 40.000 0.00 0.00 0.00 4.83
431 440 5.512082 GCAGAGCACGATATATACTTTACCG 59.488 44.000 0.00 0.00 0.00 4.02
432 441 6.622549 AGCAGAGCACGATATATACTTTACC 58.377 40.000 0.00 0.00 0.00 2.85
442 459 1.000385 GCAGAGAGCAGAGCACGATAT 60.000 52.381 0.00 0.00 44.79 1.63
443 460 0.383590 GCAGAGAGCAGAGCACGATA 59.616 55.000 0.00 0.00 44.79 2.92
629 657 7.094634 CGGTGGTCTTAACAAGTAGAAGTAGTA 60.095 40.741 0.00 0.00 0.00 1.82
630 658 6.294397 CGGTGGTCTTAACAAGTAGAAGTAGT 60.294 42.308 0.00 0.00 0.00 2.73
631 659 6.091437 CGGTGGTCTTAACAAGTAGAAGTAG 58.909 44.000 0.00 0.00 0.00 2.57
632 660 5.047802 CCGGTGGTCTTAACAAGTAGAAGTA 60.048 44.000 0.00 0.00 0.00 2.24
633 661 4.262335 CCGGTGGTCTTAACAAGTAGAAGT 60.262 45.833 0.00 0.00 0.00 3.01
634 662 4.243270 CCGGTGGTCTTAACAAGTAGAAG 58.757 47.826 0.00 0.00 0.00 2.85
638 666 1.002315 GGCCGGTGGTCTTAACAAGTA 59.998 52.381 1.90 0.00 0.00 2.24
749 786 6.916440 TGAGTGGATCTGTGAATCATTTTTG 58.084 36.000 0.00 0.00 0.00 2.44
888 1206 5.116882 CGATTAAGCTGGCTAGGTTAGTTT 58.883 41.667 19.17 10.32 44.84 2.66
944 1280 0.730155 GTATGCACACGAACCGACGA 60.730 55.000 0.00 0.00 37.03 4.20
945 1281 1.700029 GTATGCACACGAACCGACG 59.300 57.895 0.00 0.00 39.31 5.12
946 1282 1.005294 ACGTATGCACACGAACCGAC 61.005 55.000 26.40 0.00 44.69 4.79
947 1283 0.318869 AACGTATGCACACGAACCGA 60.319 50.000 26.40 0.00 44.69 4.69
948 1284 0.092351 GAACGTATGCACACGAACCG 59.908 55.000 26.40 0.00 44.69 4.44
949 1285 1.126113 CAGAACGTATGCACACGAACC 59.874 52.381 26.40 12.08 44.69 3.62
950 1286 1.790623 ACAGAACGTATGCACACGAAC 59.209 47.619 26.40 16.56 44.69 3.95
951 1287 2.143008 ACAGAACGTATGCACACGAA 57.857 45.000 26.40 0.00 44.69 3.85
968 1304 1.061411 CGCCGATCGACGACTTACA 59.939 57.895 19.48 0.00 45.77 2.41
1150 1486 2.872388 CGATGCCCGGCAGGTAGAT 61.872 63.158 18.96 0.00 43.65 1.98
1206 1545 4.514577 AGCCGGCCATCTTCGTCG 62.515 66.667 26.15 0.00 0.00 5.12
1417 1756 2.158959 CGAACGCCCACGAGATCAC 61.159 63.158 0.00 0.00 43.93 3.06
1641 1990 2.831685 TCTAAGCACCACACGTCAAT 57.168 45.000 0.00 0.00 0.00 2.57
1704 2054 7.981102 AAGGGTACAGAAATTAAGAACTCAC 57.019 36.000 0.00 0.00 0.00 3.51
1747 2135 7.500227 CCATCTCTGTTACACATCAACCATAAT 59.500 37.037 0.00 0.00 0.00 1.28
1752 2140 4.832248 TCCATCTCTGTTACACATCAACC 58.168 43.478 0.00 0.00 0.00 3.77
1765 2153 3.949842 TGACAAGTGTCTCCATCTCTG 57.050 47.619 12.43 0.00 44.99 3.35
1797 2185 5.621228 CCAACTCGCTCGATTTTTATTATGC 59.379 40.000 0.00 0.00 0.00 3.14
1823 2211 4.787551 ACGTTATTTATGCCCCATTCTGA 58.212 39.130 0.00 0.00 0.00 3.27
1824 2212 6.817765 ATACGTTATTTATGCCCCATTCTG 57.182 37.500 0.00 0.00 0.00 3.02
1826 2214 6.977213 ACAATACGTTATTTATGCCCCATTC 58.023 36.000 0.00 0.00 0.00 2.67
1835 2223 7.170998 GTGCCTAGCTGACAATACGTTATTTAT 59.829 37.037 0.00 0.00 0.00 1.40
1847 2235 1.676916 GCTCATGTGCCTAGCTGACAA 60.677 52.381 8.59 0.00 33.40 3.18
1890 2281 0.912528 GTCAACGGCGAACTCGTATC 59.087 55.000 16.62 0.00 40.18 2.24
1893 2284 0.599204 AATGTCAACGGCGAACTCGT 60.599 50.000 16.62 0.00 43.14 4.18
1901 2292 0.240945 CCCTTGTCAATGTCAACGGC 59.759 55.000 0.00 0.00 0.00 5.68
1903 2294 0.240945 GGCCCTTGTCAATGTCAACG 59.759 55.000 0.00 0.00 0.00 4.10
1920 2311 1.215647 CTGTGGACCACTACTCGGC 59.784 63.158 24.81 0.00 35.11 5.54
1983 2378 4.461431 TCTTGCAGTCTACTCCGTATTTCA 59.539 41.667 0.00 0.00 0.00 2.69
1988 2383 3.064958 CGAATCTTGCAGTCTACTCCGTA 59.935 47.826 0.00 0.00 0.00 4.02
1989 2384 2.159366 CGAATCTTGCAGTCTACTCCGT 60.159 50.000 0.00 0.00 0.00 4.69
1990 2385 2.159366 ACGAATCTTGCAGTCTACTCCG 60.159 50.000 0.00 0.00 0.00 4.63
1991 2386 3.512033 ACGAATCTTGCAGTCTACTCC 57.488 47.619 0.00 0.00 0.00 3.85
1992 2387 4.486090 TGAACGAATCTTGCAGTCTACTC 58.514 43.478 0.00 0.00 0.00 2.59
1993 2388 4.521130 TGAACGAATCTTGCAGTCTACT 57.479 40.909 0.00 0.00 0.00 2.57
1994 2389 5.786401 ATTGAACGAATCTTGCAGTCTAC 57.214 39.130 0.00 0.00 0.00 2.59
1999 2394 7.167302 TGTTTGTTTATTGAACGAATCTTGCAG 59.833 33.333 0.00 0.00 42.20 4.41
2029 2424 6.071728 TCGTAGACTTTTTACTTCGAGGGATT 60.072 38.462 0.00 0.00 32.84 3.01
2030 2425 5.416952 TCGTAGACTTTTTACTTCGAGGGAT 59.583 40.000 0.00 0.00 32.84 3.85
2116 2511 4.453136 TCTGACGGGACTTTTTAAATTCCG 59.547 41.667 5.62 5.62 38.29 4.30
2188 2584 5.589192 CCCGTATGTAGAGTTTGTAAGGAG 58.411 45.833 0.00 0.00 0.00 3.69
2215 2611 6.827586 TCGGCCAATTAAAAGAGTACAAAT 57.172 33.333 2.24 0.00 0.00 2.32
2238 2634 7.106239 CGATTCATTAGGATGGGTAGCTAATT 58.894 38.462 0.00 0.00 33.93 1.40
2239 2635 6.644347 CGATTCATTAGGATGGGTAGCTAAT 58.356 40.000 0.00 0.00 33.93 1.73
2240 2636 5.568825 GCGATTCATTAGGATGGGTAGCTAA 60.569 44.000 0.00 0.00 33.93 3.09
2241 2637 4.081642 GCGATTCATTAGGATGGGTAGCTA 60.082 45.833 0.00 0.00 33.93 3.32
2242 2638 3.307059 GCGATTCATTAGGATGGGTAGCT 60.307 47.826 0.00 0.00 33.93 3.32
2243 2639 3.003480 GCGATTCATTAGGATGGGTAGC 58.997 50.000 0.00 0.00 33.93 3.58
2244 2640 3.600388 GGCGATTCATTAGGATGGGTAG 58.400 50.000 0.00 0.00 33.93 3.18
2245 2641 2.304761 GGGCGATTCATTAGGATGGGTA 59.695 50.000 0.00 0.00 33.93 3.69
2246 2642 1.073923 GGGCGATTCATTAGGATGGGT 59.926 52.381 0.00 0.00 33.93 4.51
2247 2643 1.614317 GGGGCGATTCATTAGGATGGG 60.614 57.143 0.00 0.00 33.93 4.00
2248 2644 1.352352 AGGGGCGATTCATTAGGATGG 59.648 52.381 0.00 0.00 33.93 3.51
2249 2645 2.616510 GGAGGGGCGATTCATTAGGATG 60.617 54.545 0.00 0.00 34.46 3.51
2250 2646 1.630878 GGAGGGGCGATTCATTAGGAT 59.369 52.381 0.00 0.00 0.00 3.24
2251 2647 1.056660 GGAGGGGCGATTCATTAGGA 58.943 55.000 0.00 0.00 0.00 2.94
2252 2648 0.036875 GGGAGGGGCGATTCATTAGG 59.963 60.000 0.00 0.00 0.00 2.69
2253 2649 0.764890 TGGGAGGGGCGATTCATTAG 59.235 55.000 0.00 0.00 0.00 1.73
2254 2650 0.764890 CTGGGAGGGGCGATTCATTA 59.235 55.000 0.00 0.00 0.00 1.90
2255 2651 1.533711 CTGGGAGGGGCGATTCATT 59.466 57.895 0.00 0.00 0.00 2.57
2256 2652 2.455565 CCTGGGAGGGGCGATTCAT 61.456 63.158 0.00 0.00 0.00 2.57
2257 2653 3.089874 CCTGGGAGGGGCGATTCA 61.090 66.667 0.00 0.00 0.00 2.57
2279 2675 1.031029 TTTACGTAAATGGGCGCCCC 61.031 55.000 41.75 24.99 45.71 5.80
2280 2676 0.810016 TTTTACGTAAATGGGCGCCC 59.190 50.000 39.40 39.40 0.00 6.13
2281 2677 1.467883 GGTTTTACGTAAATGGGCGCC 60.468 52.381 21.18 21.18 0.00 6.53
2282 2678 1.467883 GGGTTTTACGTAAATGGGCGC 60.468 52.381 20.72 14.72 0.00 6.53
2283 2679 1.132834 GGGGTTTTACGTAAATGGGCG 59.867 52.381 20.72 0.00 0.00 6.13
2284 2680 1.477700 GGGGGTTTTACGTAAATGGGC 59.522 52.381 20.72 11.41 0.00 5.36
2285 2681 1.744522 CGGGGGTTTTACGTAAATGGG 59.255 52.381 20.72 4.97 0.00 4.00
2286 2682 2.435422 ACGGGGGTTTTACGTAAATGG 58.565 47.619 20.72 9.46 39.30 3.16
2287 2683 3.622612 CCTACGGGGGTTTTACGTAAATG 59.377 47.826 20.72 9.62 41.77 2.32
2288 2684 3.872696 CCTACGGGGGTTTTACGTAAAT 58.127 45.455 20.72 7.36 41.77 1.40
2289 2685 2.614229 GCCTACGGGGGTTTTACGTAAA 60.614 50.000 16.59 16.59 41.77 2.01
2290 2686 1.066502 GCCTACGGGGGTTTTACGTAA 60.067 52.381 3.29 3.29 41.77 3.18
2291 2687 0.534873 GCCTACGGGGGTTTTACGTA 59.465 55.000 0.00 0.00 41.53 3.57
2292 2688 1.296392 GCCTACGGGGGTTTTACGT 59.704 57.895 0.00 0.00 43.88 3.57
2293 2689 1.810853 CGCCTACGGGGGTTTTACG 60.811 63.158 0.00 0.00 40.23 3.18
2294 2690 2.108514 GCGCCTACGGGGGTTTTAC 61.109 63.158 0.00 0.00 45.92 2.01
2295 2691 2.268600 GCGCCTACGGGGGTTTTA 59.731 61.111 0.00 0.00 45.92 1.52
2296 2692 3.643554 AGCGCCTACGGGGGTTTT 61.644 61.111 2.29 0.00 43.69 2.43
2310 2706 3.500404 TCAGTATGTTGAGCAGCAAGCG 61.500 50.000 0.00 0.00 43.39 4.68
2311 2707 2.079158 TCAGTATGTTGAGCAGCAAGC 58.921 47.619 0.00 0.00 40.09 4.01
2312 2708 2.417933 GGTCAGTATGTTGAGCAGCAAG 59.582 50.000 0.00 0.00 43.30 4.01
2313 2709 2.038952 AGGTCAGTATGTTGAGCAGCAA 59.961 45.455 11.46 0.00 45.55 3.91
2314 2710 1.625315 AGGTCAGTATGTTGAGCAGCA 59.375 47.619 11.46 0.00 45.55 4.41
2315 2711 2.393271 AGGTCAGTATGTTGAGCAGC 57.607 50.000 11.46 0.00 45.55 5.25
2316 2712 3.265791 GGAAGGTCAGTATGTTGAGCAG 58.734 50.000 11.46 0.00 45.55 4.24
2317 2713 2.637382 TGGAAGGTCAGTATGTTGAGCA 59.363 45.455 11.46 0.00 45.55 4.26
2318 2714 3.265791 CTGGAAGGTCAGTATGTTGAGC 58.734 50.000 3.16 3.16 43.95 4.26
2319 2715 4.543590 ACTGGAAGGTCAGTATGTTGAG 57.456 45.455 0.00 0.00 45.18 3.02
2320 2716 4.974645 AACTGGAAGGTCAGTATGTTGA 57.025 40.909 0.00 0.00 46.17 3.18
2321 2717 5.586243 CCATAACTGGAAGGTCAGTATGTTG 59.414 44.000 0.00 0.00 46.17 3.33
2322 2718 5.250774 ACCATAACTGGAAGGTCAGTATGTT 59.749 40.000 0.00 0.00 46.17 2.71
2354 2750 6.944862 AGACAAGATAAGGCAGTCAAAGAATT 59.055 34.615 0.00 0.00 0.00 2.17
2389 2785 9.924650 ACTACAAACTGATCGATTTAAACTAGT 57.075 29.630 0.00 0.00 0.00 2.57
2402 2798 8.812329 CAGCTACTAAATGACTACAAACTGATC 58.188 37.037 0.00 0.00 0.00 2.92
2413 2809 9.454859 AAATTTAAGCTCAGCTACTAAATGACT 57.545 29.630 14.49 0.65 38.25 3.41
2505 2913 7.536964 CACTCATCTATAGAACTACATGCGAAG 59.463 40.741 6.52 0.00 0.00 3.79
2508 2916 6.580416 CACACTCATCTATAGAACTACATGCG 59.420 42.308 6.52 0.00 0.00 4.73


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

AutoCloner maintained by Alex Coulton.