Multiple sequence alignment - TraesCS1D01G143300

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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 TraesCS1D01G143300 chr1D 100.000 2888 0 0 1 2888 199019414 199022301 0.000000e+00 5334.0
1 TraesCS1D01G143300 chr1D 84.783 92 13 1 365 455 488546781 488546690 1.100000e-14 91.6
2 TraesCS1D01G143300 chr1B 91.989 1860 121 18 557 2410 278934547 278936384 0.000000e+00 2584.0
3 TraesCS1D01G143300 chr1B 92.469 239 12 1 1 233 278932336 278932574 1.280000e-88 337.0
4 TraesCS1D01G143300 chr1B 77.249 189 19 12 288 452 308616439 308616627 3.960000e-14 89.8
5 TraesCS1D01G143300 chr1A 91.265 1866 116 23 638 2491 249774029 249775859 0.000000e+00 2499.0
6 TraesCS1D01G143300 chr1A 81.068 412 38 21 2495 2885 249775963 249776355 2.810000e-75 292.0
7 TraesCS1D01G143300 chr1A 86.420 243 17 7 4 244 249773262 249773490 4.780000e-63 252.0
8 TraesCS1D01G143300 chr1A 91.489 47 3 1 314 360 9654637 9654682 2.400000e-06 63.9
9 TraesCS1D01G143300 chr4A 81.362 1615 252 28 796 2391 617288845 617290429 0.000000e+00 1269.0
10 TraesCS1D01G143300 chr4A 81.115 1615 257 27 796 2391 617348914 617350499 0.000000e+00 1249.0
11 TraesCS1D01G143300 chr4A 82.531 1351 206 16 796 2132 617360200 617361534 0.000000e+00 1160.0
12 TraesCS1D01G143300 chr4A 88.636 88 9 1 367 453 658346525 658346438 3.940000e-19 106.0
13 TraesCS1D01G143300 chr5B 80.113 1775 270 52 638 2376 702552955 702551228 0.000000e+00 1245.0
14 TraesCS1D01G143300 chr5B 83.455 1366 188 23 796 2142 702479546 702478200 0.000000e+00 1236.0
15 TraesCS1D01G143300 chr5B 89.773 88 6 3 367 452 655021777 655021691 3.040000e-20 110.0
16 TraesCS1D01G143300 chr5B 88.462 78 9 0 288 365 128561306 128561383 8.520000e-16 95.3
17 TraesCS1D01G143300 chr5D 83.790 1314 181 19 796 2089 550301207 550299906 0.000000e+00 1218.0
18 TraesCS1D01G143300 chr5D 83.706 1209 175 15 796 1996 550402695 550401501 0.000000e+00 1122.0
19 TraesCS1D01G143300 chr5D 86.239 109 12 2 638 743 550402943 550402835 6.540000e-22 115.0
20 TraesCS1D01G143300 chr4B 90.217 92 8 1 365 455 592701562 592701471 5.060000e-23 119.0
21 TraesCS1D01G143300 chr7B 93.056 72 5 0 365 436 638739450 638739379 3.940000e-19 106.0
22 TraesCS1D01G143300 chr6B 78.421 190 17 12 288 453 169602319 169602508 5.090000e-18 102.0
23 TraesCS1D01G143300 chr6B 87.179 78 10 0 288 365 298290309 298290386 3.960000e-14 89.8
24 TraesCS1D01G143300 chr6B 85.882 85 11 1 286 370 638375480 638375563 3.960000e-14 89.8
25 TraesCS1D01G143300 chr2B 78.421 190 17 13 288 453 524034208 524034019 5.090000e-18 102.0
26 TraesCS1D01G143300 chr2B 87.356 87 10 1 368 453 789508557 789508643 6.590000e-17 99.0
27 TraesCS1D01G143300 chr2B 77.487 191 18 13 291 456 16906400 16906210 1.100000e-14 91.6
28 TraesCS1D01G143300 chr2B 87.143 70 8 1 288 356 712054204 712054273 8.580000e-11 78.7
29 TraesCS1D01G143300 chr3D 86.667 90 10 1 366 455 168853222 168853135 6.590000e-17 99.0
30 TraesCS1D01G143300 chr2A 89.744 78 7 1 362 439 96089000 96088924 6.590000e-17 99.0
31 TraesCS1D01G143300 chr2D 85.915 71 8 2 291 360 637736810 637736879 1.110000e-09 75.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G143300 chr1D 199019414 199022301 2887 False 5334.000000 5334 100.0000 1 2888 1 chr1D.!!$F1 2887
1 TraesCS1D01G143300 chr1B 278932336 278936384 4048 False 1460.500000 2584 92.2290 1 2410 2 chr1B.!!$F2 2409
2 TraesCS1D01G143300 chr1A 249773262 249776355 3093 False 1014.333333 2499 86.2510 4 2885 3 chr1A.!!$F2 2881
3 TraesCS1D01G143300 chr4A 617288845 617290429 1584 False 1269.000000 1269 81.3620 796 2391 1 chr4A.!!$F1 1595
4 TraesCS1D01G143300 chr4A 617348914 617350499 1585 False 1249.000000 1249 81.1150 796 2391 1 chr4A.!!$F2 1595
5 TraesCS1D01G143300 chr4A 617360200 617361534 1334 False 1160.000000 1160 82.5310 796 2132 1 chr4A.!!$F3 1336
6 TraesCS1D01G143300 chr5B 702551228 702552955 1727 True 1245.000000 1245 80.1130 638 2376 1 chr5B.!!$R3 1738
7 TraesCS1D01G143300 chr5B 702478200 702479546 1346 True 1236.000000 1236 83.4550 796 2142 1 chr5B.!!$R2 1346
8 TraesCS1D01G143300 chr5D 550299906 550301207 1301 True 1218.000000 1218 83.7900 796 2089 1 chr5D.!!$R1 1293
9 TraesCS1D01G143300 chr5D 550401501 550402943 1442 True 618.500000 1122 84.9725 638 1996 2 chr5D.!!$R2 1358

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
209 219 0.107456 AAGTCCACACACTCTGCCTG 59.893 55.0 0.0 0.0 0.00 4.85 F
801 3051 0.467384 ATGCTGTCTGCGGCTAGATT 59.533 50.0 0.0 0.0 46.77 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1735 4009 0.603065 GTACTACCGGTTTGTCCCGT 59.397 55.0 15.04 1.61 46.66 5.28 R
2798 5204 0.039180 TAGTGGCGTCTCTCCCAGAA 59.961 55.0 0.00 0.00 30.72 3.02 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
27 28 4.320494 GGTCAGCTTGGACAGTGTAATTTG 60.320 45.833 0.00 0.00 39.59 2.32
115 122 2.634193 AAAGTTGTGGACACCGGGGG 62.634 60.000 9.50 0.00 0.00 5.40
209 219 0.107456 AAGTCCACACACTCTGCCTG 59.893 55.000 0.00 0.00 0.00 4.85
233 243 6.127647 TGGTACGTCGTTTACCAGAAGATTAT 60.128 38.462 14.63 0.00 43.39 1.28
245 1839 5.364157 ACCAGAAGATTATCTTAACTCGGCT 59.636 40.000 7.52 0.00 36.73 5.52
248 1842 7.040340 CCAGAAGATTATCTTAACTCGGCTAGA 60.040 40.741 7.52 0.00 36.73 2.43
255 1849 3.128938 TCTTAACTCGGCTAGAAGACAGC 59.871 47.826 0.00 0.00 38.35 4.40
263 1857 4.456222 TCGGCTAGAAGACAGCAGATATAC 59.544 45.833 0.00 0.00 38.13 1.47
264 1858 4.457603 CGGCTAGAAGACAGCAGATATACT 59.542 45.833 0.00 0.00 40.95 2.12
265 1859 5.644206 CGGCTAGAAGACAGCAGATATACTA 59.356 44.000 0.00 0.00 40.95 1.82
266 1860 6.317642 CGGCTAGAAGACAGCAGATATACTAT 59.682 42.308 0.00 0.00 40.95 2.12
267 1861 7.466725 CGGCTAGAAGACAGCAGATATACTATC 60.467 44.444 0.00 0.00 40.95 2.08
268 1862 7.556275 GGCTAGAAGACAGCAGATATACTATCT 59.444 40.741 0.00 0.00 40.95 1.98
269 1863 8.612619 GCTAGAAGACAGCAGATATACTATCTC 58.387 40.741 0.00 0.00 38.93 2.75
270 1864 7.938140 AGAAGACAGCAGATATACTATCTCC 57.062 40.000 0.00 0.00 0.00 3.71
271 1865 6.597672 AGAAGACAGCAGATATACTATCTCCG 59.402 42.308 0.00 0.00 0.00 4.63
272 1866 5.811190 AGACAGCAGATATACTATCTCCGT 58.189 41.667 0.00 0.00 0.00 4.69
273 1867 6.948589 AGACAGCAGATATACTATCTCCGTA 58.051 40.000 0.00 0.00 0.00 4.02
274 1868 6.819649 AGACAGCAGATATACTATCTCCGTAC 59.180 42.308 0.00 0.00 0.00 3.67
275 1869 6.713276 ACAGCAGATATACTATCTCCGTACT 58.287 40.000 0.00 0.00 0.00 2.73
276 1870 6.596106 ACAGCAGATATACTATCTCCGTACTG 59.404 42.308 0.00 0.00 0.00 2.74
277 1871 6.596106 CAGCAGATATACTATCTCCGTACTGT 59.404 42.308 0.00 0.00 0.00 3.55
278 1872 7.119992 CAGCAGATATACTATCTCCGTACTGTT 59.880 40.741 0.00 0.00 0.00 3.16
279 1873 7.666388 AGCAGATATACTATCTCCGTACTGTTT 59.334 37.037 0.00 0.00 0.00 2.83
280 1874 8.298140 GCAGATATACTATCTCCGTACTGTTTT 58.702 37.037 0.00 0.00 0.00 2.43
286 1880 9.804977 ATACTATCTCCGTACTGTTTTATAGGT 57.195 33.333 0.00 0.00 0.00 3.08
287 1881 8.530804 ACTATCTCCGTACTGTTTTATAGGTT 57.469 34.615 0.00 0.00 0.00 3.50
288 1882 9.632638 ACTATCTCCGTACTGTTTTATAGGTTA 57.367 33.333 0.00 0.00 0.00 2.85
290 1884 7.944729 TCTCCGTACTGTTTTATAGGTTAGT 57.055 36.000 0.00 0.00 0.00 2.24
291 1885 8.353423 TCTCCGTACTGTTTTATAGGTTAGTT 57.647 34.615 0.00 0.00 0.00 2.24
292 1886 8.806146 TCTCCGTACTGTTTTATAGGTTAGTTT 58.194 33.333 0.00 0.00 0.00 2.66
293 1887 8.761575 TCCGTACTGTTTTATAGGTTAGTTTG 57.238 34.615 0.00 0.00 0.00 2.93
294 1888 8.367156 TCCGTACTGTTTTATAGGTTAGTTTGT 58.633 33.333 0.00 0.00 0.00 2.83
295 1889 8.437742 CCGTACTGTTTTATAGGTTAGTTTGTG 58.562 37.037 0.00 0.00 0.00 3.33
296 1890 8.981647 CGTACTGTTTTATAGGTTAGTTTGTGT 58.018 33.333 0.00 0.00 0.00 3.72
298 1892 8.080083 ACTGTTTTATAGGTTAGTTTGTGTCG 57.920 34.615 0.00 0.00 0.00 4.35
299 1893 7.927629 ACTGTTTTATAGGTTAGTTTGTGTCGA 59.072 33.333 0.00 0.00 0.00 4.20
300 1894 8.659925 TGTTTTATAGGTTAGTTTGTGTCGAA 57.340 30.769 0.00 0.00 0.00 3.71
301 1895 9.275398 TGTTTTATAGGTTAGTTTGTGTCGAAT 57.725 29.630 0.00 0.00 0.00 3.34
342 1936 8.532977 AACTAACAAAATGTTAATGCATGTCC 57.467 30.769 0.00 0.00 41.70 4.02
343 1937 7.665690 ACTAACAAAATGTTAATGCATGTCCA 58.334 30.769 0.00 0.00 41.70 4.02
344 1938 8.313292 ACTAACAAAATGTTAATGCATGTCCAT 58.687 29.630 0.00 0.00 41.70 3.41
345 1939 9.800433 CTAACAAAATGTTAATGCATGTCCATA 57.200 29.630 0.00 0.00 41.70 2.74
347 1941 9.499479 AACAAAATGTTAATGCATGTCCATAAA 57.501 25.926 0.00 0.00 39.09 1.40
348 1942 9.499479 ACAAAATGTTAATGCATGTCCATAAAA 57.501 25.926 0.00 0.00 0.00 1.52
396 1990 9.550406 AATTTTCTGTGACATGAATGAACATTT 57.450 25.926 0.00 0.00 31.35 2.32
397 1991 8.945481 TTTTCTGTGACATGAATGAACATTTT 57.055 26.923 0.00 0.00 31.35 1.82
398 1992 7.933728 TTCTGTGACATGAATGAACATTTTG 57.066 32.000 0.00 5.89 31.35 2.44
399 1993 7.041635 TCTGTGACATGAATGAACATTTTGT 57.958 32.000 0.00 13.05 33.24 2.83
400 1994 7.490840 TCTGTGACATGAATGAACATTTTGTT 58.509 30.769 0.00 0.00 44.37 2.83
401 1995 8.628280 TCTGTGACATGAATGAACATTTTGTTA 58.372 29.630 0.00 9.73 41.28 2.41
402 1996 8.800231 TGTGACATGAATGAACATTTTGTTAG 57.200 30.769 0.00 2.48 41.28 2.34
403 1997 8.412456 TGTGACATGAATGAACATTTTGTTAGT 58.588 29.630 0.00 4.69 41.28 2.24
404 1998 9.248291 GTGACATGAATGAACATTTTGTTAGTT 57.752 29.630 0.00 0.00 41.28 2.24
405 1999 9.814899 TGACATGAATGAACATTTTGTTAGTTT 57.185 25.926 0.00 0.00 41.28 2.66
440 2034 8.686397 TCAAAATTTGACATGAAATACGATGG 57.314 30.769 4.03 0.00 34.08 3.51
441 2035 8.303156 TCAAAATTTGACATGAAATACGATGGT 58.697 29.630 4.03 0.00 34.08 3.55
442 2036 9.566530 CAAAATTTGACATGAAATACGATGGTA 57.433 29.630 0.00 0.00 0.00 3.25
443 2037 9.567848 AAAATTTGACATGAAATACGATGGTAC 57.432 29.630 0.00 0.00 0.00 3.34
444 2038 6.671614 TTTGACATGAAATACGATGGTACC 57.328 37.500 4.43 4.43 0.00 3.34
445 2039 5.346181 TGACATGAAATACGATGGTACCA 57.654 39.130 18.99 18.99 0.00 3.25
446 2040 5.735766 TGACATGAAATACGATGGTACCAA 58.264 37.500 20.76 1.79 0.00 3.67
447 2041 6.353323 TGACATGAAATACGATGGTACCAAT 58.647 36.000 20.76 10.26 0.00 3.16
448 2042 7.501844 TGACATGAAATACGATGGTACCAATA 58.498 34.615 20.76 12.23 0.00 1.90
449 2043 7.988028 TGACATGAAATACGATGGTACCAATAA 59.012 33.333 20.76 5.34 0.00 1.40
450 2044 8.740123 ACATGAAATACGATGGTACCAATAAA 57.260 30.769 20.76 5.74 0.00 1.40
451 2045 8.617809 ACATGAAATACGATGGTACCAATAAAC 58.382 33.333 20.76 7.42 0.00 2.01
452 2046 7.556733 TGAAATACGATGGTACCAATAAACC 57.443 36.000 20.76 5.25 36.24 3.27
464 2058 4.941713 ACCAATAAACCAGATAGCCCAAA 58.058 39.130 0.00 0.00 0.00 3.28
473 2067 4.263905 ACCAGATAGCCCAAAGATGAAACA 60.264 41.667 0.00 0.00 0.00 2.83
532 2126 3.427425 CGCCCGAATTGCACCGAA 61.427 61.111 4.17 0.00 0.00 4.30
540 2134 3.119849 CCGAATTGCACCGAAGAAGATTT 60.120 43.478 4.17 0.00 0.00 2.17
596 2457 3.639538 GCACTGGTAATACACGATCGAT 58.360 45.455 24.34 11.98 0.00 3.59
597 2458 3.425525 GCACTGGTAATACACGATCGATG 59.574 47.826 24.34 17.90 0.00 3.84
598 2459 3.425525 CACTGGTAATACACGATCGATGC 59.574 47.826 24.34 5.73 0.00 3.91
599 2460 3.067601 ACTGGTAATACACGATCGATGCA 59.932 43.478 24.34 7.57 0.00 3.96
611 2474 5.458779 CACGATCGATGCATGTAAGAGTAAA 59.541 40.000 24.34 0.00 0.00 2.01
620 2483 8.969260 ATGCATGTAAGAGTAAAATGATCTCA 57.031 30.769 0.00 0.00 0.00 3.27
633 2498 9.674824 GTAAAATGATCTCAGGCATTCATTAAG 57.325 33.333 0.00 0.00 37.72 1.85
772 2947 6.558771 TGATCTGCATCAATAAATTACCGG 57.441 37.500 0.00 0.00 35.99 5.28
792 3042 1.081892 CTGGTGTACATGCTGTCTGC 58.918 55.000 0.00 0.00 43.25 4.26
794 3044 1.361668 GGTGTACATGCTGTCTGCGG 61.362 60.000 0.00 0.00 46.63 5.69
801 3051 0.467384 ATGCTGTCTGCGGCTAGATT 59.533 50.000 0.00 0.00 46.77 2.40
824 3076 9.687210 GATTGATATATACACAGTCAACGGTAA 57.313 33.333 0.00 0.00 32.30 2.85
874 3128 5.989477 TCTCATCGAATAACCCACTGAATT 58.011 37.500 0.00 0.00 0.00 2.17
895 3154 2.169789 CAACCAGGAGCGCTCGATG 61.170 63.158 29.81 27.67 0.00 3.84
902 3161 4.271816 AGCGCTCGATGGCCGTAG 62.272 66.667 2.64 0.00 39.75 3.51
944 3209 4.966805 GGCCCCAGCACTATATATACCTAA 59.033 45.833 0.00 0.00 42.56 2.69
947 3212 5.365895 CCCCAGCACTATATATACCTAACCC 59.634 48.000 0.00 0.00 0.00 4.11
949 3214 6.615726 CCCAGCACTATATATACCTAACCCAT 59.384 42.308 0.00 0.00 0.00 4.00
950 3215 7.127339 CCCAGCACTATATATACCTAACCCATT 59.873 40.741 0.00 0.00 0.00 3.16
952 3217 8.204836 CAGCACTATATATACCTAACCCATTCC 58.795 40.741 0.00 0.00 0.00 3.01
1363 3637 0.827925 CTCCGCATCAGCCCCTAGTA 60.828 60.000 0.00 0.00 37.52 1.82
1431 3705 4.408821 GGCGGTGCAGATGGGTCA 62.409 66.667 0.00 0.00 0.00 4.02
1724 3998 2.448582 TTGGAGTTGGGTCTGGCGT 61.449 57.895 0.00 0.00 0.00 5.68
1735 4009 4.641645 CTGGCGTTGGGTCTGGCA 62.642 66.667 0.00 0.00 36.67 4.92
1851 4125 3.892104 AACCGGTAGCGGTGGAGGA 62.892 63.158 37.12 0.00 42.06 3.71
1872 4146 1.766059 TGGATCCGGATCTGGTGGG 60.766 63.158 36.72 1.09 37.92 4.61
1884 4158 3.735097 GGTGGGGGCGGTTACCAT 61.735 66.667 1.13 0.00 36.54 3.55
1893 4167 3.952967 GGGGCGGTTACCATTAAATTACA 59.047 43.478 1.13 0.00 0.00 2.41
1895 4169 4.641541 GGGCGGTTACCATTAAATTACACT 59.358 41.667 1.13 0.00 0.00 3.55
1918 4193 1.893137 TCTTGAGCAAGCTAGAACCGA 59.107 47.619 5.37 0.00 38.28 4.69
2006 4282 1.916181 ACGAAAGGGATGATCCTTGGT 59.084 47.619 11.87 3.48 45.67 3.67
2063 4341 1.751924 CTTTAGCTCCTACTGCCGTCT 59.248 52.381 0.00 0.00 0.00 4.18
2069 4347 2.485124 GCTCCTACTGCCGTCTAGACTA 60.485 54.545 20.34 5.11 0.00 2.59
2170 4453 8.539544 CACCTTATCCCTTTATTTTGTTTCCAT 58.460 33.333 0.00 0.00 0.00 3.41
2191 4482 8.789881 TCCATTGTCTTTTTACACATTTTACG 57.210 30.769 0.00 0.00 0.00 3.18
2209 4500 2.277084 ACGTGTTCAGGTGTGTTTCTC 58.723 47.619 0.00 0.00 0.00 2.87
2283 4580 8.340618 TCTTCAGTTTTTAGAGCTATGCAATT 57.659 30.769 0.00 0.00 0.00 2.32
2286 4583 9.762933 TTCAGTTTTTAGAGCTATGCAATTTTT 57.237 25.926 0.00 0.00 0.00 1.94
2410 4707 1.603802 AGGTCGAGCAAATTGTGTGTG 59.396 47.619 18.15 0.00 0.00 3.82
2411 4708 1.333619 GGTCGAGCAAATTGTGTGTGT 59.666 47.619 10.30 0.00 0.00 3.72
2412 4709 2.546368 GGTCGAGCAAATTGTGTGTGTA 59.454 45.455 10.30 0.00 0.00 2.90
2413 4710 3.363970 GGTCGAGCAAATTGTGTGTGTAG 60.364 47.826 10.30 0.00 0.00 2.74
2414 4711 2.805671 TCGAGCAAATTGTGTGTGTAGG 59.194 45.455 0.00 0.00 0.00 3.18
2415 4712 2.805671 CGAGCAAATTGTGTGTGTAGGA 59.194 45.455 0.00 0.00 0.00 2.94
2416 4713 3.436704 CGAGCAAATTGTGTGTGTAGGAT 59.563 43.478 0.00 0.00 0.00 3.24
2417 4714 4.629634 CGAGCAAATTGTGTGTGTAGGATA 59.370 41.667 0.00 0.00 0.00 2.59
2418 4715 5.220472 CGAGCAAATTGTGTGTGTAGGATAG 60.220 44.000 0.00 0.00 0.00 2.08
2419 4716 5.804639 AGCAAATTGTGTGTGTAGGATAGA 58.195 37.500 0.00 0.00 0.00 1.98
2420 4717 5.643777 AGCAAATTGTGTGTGTAGGATAGAC 59.356 40.000 0.00 0.00 35.05 2.59
2431 4728 3.445805 TGTAGGATAGACGACATGCAACA 59.554 43.478 0.00 0.00 0.00 3.33
2432 4729 3.170791 AGGATAGACGACATGCAACAG 57.829 47.619 0.00 0.00 0.00 3.16
2433 4730 2.159043 AGGATAGACGACATGCAACAGG 60.159 50.000 0.00 0.00 0.00 4.00
2434 4731 2.418746 GGATAGACGACATGCAACAGGT 60.419 50.000 0.00 0.00 0.00 4.00
2435 4732 2.363788 TAGACGACATGCAACAGGTC 57.636 50.000 2.45 2.45 41.03 3.85
2436 4733 0.681733 AGACGACATGCAACAGGTCT 59.318 50.000 10.23 7.72 42.06 3.85
2437 4734 0.792640 GACGACATGCAACAGGTCTG 59.207 55.000 10.23 6.72 42.06 3.51
2491 4788 1.654220 GGTTGTGACGCATGCAGTT 59.346 52.632 19.57 0.00 0.00 3.16
2492 4789 0.385974 GGTTGTGACGCATGCAGTTC 60.386 55.000 19.57 11.05 0.00 3.01
2502 4899 2.607526 CGCATGCAGTTCCATGTCAAAA 60.608 45.455 19.57 0.00 43.46 2.44
2516 4913 4.508461 TGTCAAAAGATGGATGTGCAAG 57.492 40.909 0.00 0.00 0.00 4.01
2528 4925 1.317613 TGTGCAAGTGACCCATGTTC 58.682 50.000 0.00 0.00 0.00 3.18
2534 4931 4.646945 TGCAAGTGACCCATGTTCTTTTAA 59.353 37.500 0.00 0.00 0.00 1.52
2542 4939 6.095720 TGACCCATGTTCTTTTAAACGAACTT 59.904 34.615 27.72 21.91 40.04 2.66
2560 4957 2.940410 ACTTGTACCCACAAAAGACGTG 59.060 45.455 0.00 0.00 43.92 4.49
2621 5018 8.746530 TGTTACTATCAAGGAAACTATCTTCGT 58.253 33.333 0.00 0.00 42.68 3.85
2630 5027 9.893305 CAAGGAAACTATCTTCGTAAAAACAAT 57.107 29.630 0.00 0.00 42.68 2.71
2674 5074 6.415573 AGGGTTGTTGATTCTTGAGTATACC 58.584 40.000 0.00 0.00 0.00 2.73
2696 5096 7.423844 ACCATGACAGATCTACATTAACTCA 57.576 36.000 10.59 0.00 0.00 3.41
2745 5145 7.607607 AGATTTACATGACACATACAAGCAAGA 59.392 33.333 0.00 0.00 0.00 3.02
2746 5146 7.503521 TTTACATGACACATACAAGCAAGAA 57.496 32.000 0.00 0.00 0.00 2.52
2747 5147 7.503521 TTACATGACACATACAAGCAAGAAA 57.496 32.000 0.00 0.00 0.00 2.52
2748 5148 6.005583 ACATGACACATACAAGCAAGAAAG 57.994 37.500 0.00 0.00 0.00 2.62
2750 5150 5.673337 TGACACATACAAGCAAGAAAGAC 57.327 39.130 0.00 0.00 0.00 3.01
2751 5151 4.515191 TGACACATACAAGCAAGAAAGACC 59.485 41.667 0.00 0.00 0.00 3.85
2752 5152 4.460263 ACACATACAAGCAAGAAAGACCA 58.540 39.130 0.00 0.00 0.00 4.02
2753 5153 4.275936 ACACATACAAGCAAGAAAGACCAC 59.724 41.667 0.00 0.00 0.00 4.16
2754 5154 3.821033 ACATACAAGCAAGAAAGACCACC 59.179 43.478 0.00 0.00 0.00 4.61
2761 5167 1.726192 AAGAAAGACCACCCCACCCC 61.726 60.000 0.00 0.00 0.00 4.95
2762 5168 2.037677 AAAGACCACCCCACCCCT 60.038 61.111 0.00 0.00 0.00 4.79
2785 5191 6.102897 TCCAAGAAAGAAAACCACAAAACA 57.897 33.333 0.00 0.00 0.00 2.83
2789 5195 7.094848 CCAAGAAAGAAAACCACAAAACAACAT 60.095 33.333 0.00 0.00 0.00 2.71
2790 5196 7.363205 AGAAAGAAAACCACAAAACAACATG 57.637 32.000 0.00 0.00 0.00 3.21
2792 5198 7.823799 AGAAAGAAAACCACAAAACAACATGAT 59.176 29.630 0.00 0.00 0.00 2.45
2793 5199 6.907206 AGAAAACCACAAAACAACATGATG 57.093 33.333 0.00 0.00 0.00 3.07
2795 5201 6.757947 AGAAAACCACAAAACAACATGATGAG 59.242 34.615 10.29 0.00 0.00 2.90
2796 5202 4.589216 ACCACAAAACAACATGATGAGG 57.411 40.909 10.29 4.36 0.00 3.86
2797 5203 4.214310 ACCACAAAACAACATGATGAGGA 58.786 39.130 10.29 0.00 0.00 3.71
2798 5204 4.834496 ACCACAAAACAACATGATGAGGAT 59.166 37.500 10.29 0.00 0.00 3.24
2799 5205 5.305128 ACCACAAAACAACATGATGAGGATT 59.695 36.000 10.29 0.00 0.00 3.01
2801 5207 6.294899 CCACAAAACAACATGATGAGGATTCT 60.295 38.462 10.29 0.00 0.00 2.40
2802 5208 6.584942 CACAAAACAACATGATGAGGATTCTG 59.415 38.462 10.29 0.00 0.00 3.02
2805 5211 3.524789 ACAACATGATGAGGATTCTGGGA 59.475 43.478 10.29 0.00 0.00 4.37
2806 5212 4.135306 CAACATGATGAGGATTCTGGGAG 58.865 47.826 0.00 0.00 0.00 4.30
2807 5213 3.662078 ACATGATGAGGATTCTGGGAGA 58.338 45.455 0.00 0.00 0.00 3.71
2808 5214 3.647113 ACATGATGAGGATTCTGGGAGAG 59.353 47.826 0.00 0.00 0.00 3.20
2809 5215 3.695357 TGATGAGGATTCTGGGAGAGA 57.305 47.619 0.00 0.00 0.00 3.10
2810 5216 3.303938 TGATGAGGATTCTGGGAGAGAC 58.696 50.000 0.00 0.00 0.00 3.36
2811 5217 1.769026 TGAGGATTCTGGGAGAGACG 58.231 55.000 0.00 0.00 0.00 4.18
2812 5218 0.387565 GAGGATTCTGGGAGAGACGC 59.612 60.000 0.00 0.00 0.00 5.19
2813 5219 1.045911 AGGATTCTGGGAGAGACGCC 61.046 60.000 0.00 0.00 0.00 5.68
2814 5220 1.330655 GGATTCTGGGAGAGACGCCA 61.331 60.000 0.00 0.00 0.00 5.69
2815 5221 0.179097 GATTCTGGGAGAGACGCCAC 60.179 60.000 0.00 0.00 0.00 5.01
2816 5222 0.616111 ATTCTGGGAGAGACGCCACT 60.616 55.000 0.00 0.00 0.00 4.00
2817 5223 0.039180 TTCTGGGAGAGACGCCACTA 59.961 55.000 0.00 0.00 0.00 2.74
2818 5224 0.394488 TCTGGGAGAGACGCCACTAG 60.394 60.000 0.00 0.00 0.00 2.57
2858 5272 6.276847 AGAGAGACCGCTATGAAAACTTATG 58.723 40.000 0.00 0.00 0.00 1.90
2860 5274 5.812642 AGAGACCGCTATGAAAACTTATGTG 59.187 40.000 0.00 0.00 0.00 3.21
2879 5293 1.547820 TGGCAAGCAAGTGTTTCACAA 59.452 42.857 2.80 0.00 36.74 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.717032 ACACTGTCCAAGCTGACCTA 58.283 50.000 2.02 0.00 34.25 3.08
27 28 1.297745 GAGAGACGTCGATCGGTGC 60.298 63.158 16.41 5.27 44.69 5.01
51 52 1.787155 GTGATAGTAATGGCGACGCAG 59.213 52.381 23.09 0.00 0.00 5.18
115 122 1.416050 CGACCTAGGGTTTAACGCGC 61.416 60.000 14.81 0.00 35.25 6.86
209 219 3.559238 TCTTCTGGTAAACGACGTACC 57.441 47.619 12.16 12.16 41.32 3.34
233 243 3.128938 GCTGTCTTCTAGCCGAGTTAAGA 59.871 47.826 0.00 0.00 35.15 2.10
245 1839 7.766738 CGGAGATAGTATATCTGCTGTCTTCTA 59.233 40.741 14.01 0.00 36.07 2.10
248 1842 6.242396 ACGGAGATAGTATATCTGCTGTCTT 58.758 40.000 12.58 0.00 36.07 3.01
264 1858 9.632638 ACTAACCTATAAAACAGTACGGAGATA 57.367 33.333 0.00 0.00 0.00 1.98
265 1859 8.530804 ACTAACCTATAAAACAGTACGGAGAT 57.469 34.615 0.00 0.00 0.00 2.75
266 1860 7.944729 ACTAACCTATAAAACAGTACGGAGA 57.055 36.000 0.00 0.00 0.00 3.71
267 1861 8.866956 CAAACTAACCTATAAAACAGTACGGAG 58.133 37.037 0.00 0.00 0.00 4.63
268 1862 8.367156 ACAAACTAACCTATAAAACAGTACGGA 58.633 33.333 0.00 0.00 0.00 4.69
269 1863 8.437742 CACAAACTAACCTATAAAACAGTACGG 58.562 37.037 0.00 0.00 0.00 4.02
270 1864 8.981647 ACACAAACTAACCTATAAAACAGTACG 58.018 33.333 0.00 0.00 0.00 3.67
272 1866 9.195411 CGACACAAACTAACCTATAAAACAGTA 57.805 33.333 0.00 0.00 0.00 2.74
273 1867 7.927629 TCGACACAAACTAACCTATAAAACAGT 59.072 33.333 0.00 0.00 0.00 3.55
274 1868 8.301730 TCGACACAAACTAACCTATAAAACAG 57.698 34.615 0.00 0.00 0.00 3.16
275 1869 8.659925 TTCGACACAAACTAACCTATAAAACA 57.340 30.769 0.00 0.00 0.00 2.83
316 1910 9.632807 GGACATGCATTAACATTTTGTTAGTTA 57.367 29.630 0.00 0.00 42.93 2.24
317 1911 8.147058 TGGACATGCATTAACATTTTGTTAGTT 58.853 29.630 0.00 0.00 42.93 2.24
318 1912 7.665690 TGGACATGCATTAACATTTTGTTAGT 58.334 30.769 0.00 0.00 42.93 2.24
319 1913 8.706492 ATGGACATGCATTAACATTTTGTTAG 57.294 30.769 0.00 0.00 42.93 2.34
321 1915 9.499479 TTTATGGACATGCATTAACATTTTGTT 57.501 25.926 10.84 0.00 43.88 2.83
322 1916 9.499479 TTTTATGGACATGCATTAACATTTTGT 57.501 25.926 10.84 0.00 0.00 2.83
370 1964 9.550406 AAATGTTCATTCATGTCACAGAAAATT 57.450 25.926 0.00 0.00 0.00 1.82
371 1965 9.550406 AAAATGTTCATTCATGTCACAGAAAAT 57.450 25.926 0.00 0.00 0.00 1.82
372 1966 8.819015 CAAAATGTTCATTCATGTCACAGAAAA 58.181 29.630 0.00 0.00 0.00 2.29
373 1967 7.980662 ACAAAATGTTCATTCATGTCACAGAAA 59.019 29.630 9.52 0.00 0.00 2.52
374 1968 7.490840 ACAAAATGTTCATTCATGTCACAGAA 58.509 30.769 9.52 0.00 0.00 3.02
375 1969 7.041635 ACAAAATGTTCATTCATGTCACAGA 57.958 32.000 9.52 0.00 0.00 3.41
376 1970 7.703298 AACAAAATGTTCATTCATGTCACAG 57.297 32.000 13.34 0.00 35.27 3.66
377 1971 8.412456 ACTAACAAAATGTTCATTCATGTCACA 58.588 29.630 13.34 0.00 40.22 3.58
378 1972 8.801715 ACTAACAAAATGTTCATTCATGTCAC 57.198 30.769 13.34 0.00 40.22 3.67
379 1973 9.814899 AAACTAACAAAATGTTCATTCATGTCA 57.185 25.926 13.34 3.71 40.22 3.58
414 2008 9.304731 CCATCGTATTTCATGTCAAATTTTGAT 57.695 29.630 14.54 0.00 42.47 2.57
415 2009 8.303156 ACCATCGTATTTCATGTCAAATTTTGA 58.697 29.630 7.74 7.74 37.33 2.69
416 2010 8.464770 ACCATCGTATTTCATGTCAAATTTTG 57.535 30.769 2.59 2.59 0.00 2.44
417 2011 9.567848 GTACCATCGTATTTCATGTCAAATTTT 57.432 29.630 0.00 0.00 0.00 1.82
418 2012 8.188139 GGTACCATCGTATTTCATGTCAAATTT 58.812 33.333 7.15 0.00 0.00 1.82
419 2013 7.338196 TGGTACCATCGTATTTCATGTCAAATT 59.662 33.333 11.60 0.00 0.00 1.82
420 2014 6.826231 TGGTACCATCGTATTTCATGTCAAAT 59.174 34.615 11.60 0.00 0.00 2.32
421 2015 6.174049 TGGTACCATCGTATTTCATGTCAAA 58.826 36.000 11.60 0.00 0.00 2.69
422 2016 5.735766 TGGTACCATCGTATTTCATGTCAA 58.264 37.500 11.60 0.00 0.00 3.18
423 2017 5.346181 TGGTACCATCGTATTTCATGTCA 57.654 39.130 11.60 0.00 0.00 3.58
424 2018 6.861065 ATTGGTACCATCGTATTTCATGTC 57.139 37.500 17.17 0.00 0.00 3.06
425 2019 8.617809 GTTTATTGGTACCATCGTATTTCATGT 58.382 33.333 17.17 0.00 0.00 3.21
426 2020 8.073768 GGTTTATTGGTACCATCGTATTTCATG 58.926 37.037 17.17 0.00 34.48 3.07
427 2021 7.776030 TGGTTTATTGGTACCATCGTATTTCAT 59.224 33.333 17.17 5.27 39.44 2.57
428 2022 7.110810 TGGTTTATTGGTACCATCGTATTTCA 58.889 34.615 17.17 5.43 39.44 2.69
429 2023 7.496591 TCTGGTTTATTGGTACCATCGTATTTC 59.503 37.037 17.17 2.84 43.15 2.17
430 2024 7.340256 TCTGGTTTATTGGTACCATCGTATTT 58.660 34.615 17.17 0.00 43.15 1.40
431 2025 6.891388 TCTGGTTTATTGGTACCATCGTATT 58.109 36.000 17.17 0.00 43.15 1.89
432 2026 6.488769 TCTGGTTTATTGGTACCATCGTAT 57.511 37.500 17.17 8.80 43.15 3.06
433 2027 5.936187 TCTGGTTTATTGGTACCATCGTA 57.064 39.130 17.17 6.75 43.15 3.43
434 2028 4.829872 TCTGGTTTATTGGTACCATCGT 57.170 40.909 17.17 7.79 43.15 3.73
435 2029 5.408604 GCTATCTGGTTTATTGGTACCATCG 59.591 44.000 17.17 0.00 43.15 3.84
436 2030 5.705905 GGCTATCTGGTTTATTGGTACCATC 59.294 44.000 17.17 4.39 43.15 3.51
437 2031 5.457633 GGGCTATCTGGTTTATTGGTACCAT 60.458 44.000 17.17 8.68 43.15 3.55
438 2032 4.141344 GGGCTATCTGGTTTATTGGTACCA 60.141 45.833 11.60 11.60 41.97 3.25
439 2033 4.141344 TGGGCTATCTGGTTTATTGGTACC 60.141 45.833 4.43 4.43 34.93 3.34
440 2034 5.043737 TGGGCTATCTGGTTTATTGGTAC 57.956 43.478 0.00 0.00 0.00 3.34
441 2035 5.718801 TTGGGCTATCTGGTTTATTGGTA 57.281 39.130 0.00 0.00 0.00 3.25
442 2036 4.601406 TTGGGCTATCTGGTTTATTGGT 57.399 40.909 0.00 0.00 0.00 3.67
443 2037 5.200483 TCTTTGGGCTATCTGGTTTATTGG 58.800 41.667 0.00 0.00 0.00 3.16
444 2038 6.547141 TCATCTTTGGGCTATCTGGTTTATTG 59.453 38.462 0.00 0.00 0.00 1.90
445 2039 6.672593 TCATCTTTGGGCTATCTGGTTTATT 58.327 36.000 0.00 0.00 0.00 1.40
446 2040 6.266131 TCATCTTTGGGCTATCTGGTTTAT 57.734 37.500 0.00 0.00 0.00 1.40
447 2041 5.708736 TCATCTTTGGGCTATCTGGTTTA 57.291 39.130 0.00 0.00 0.00 2.01
448 2042 4.591321 TCATCTTTGGGCTATCTGGTTT 57.409 40.909 0.00 0.00 0.00 3.27
449 2043 4.591321 TTCATCTTTGGGCTATCTGGTT 57.409 40.909 0.00 0.00 0.00 3.67
450 2044 4.263905 TGTTTCATCTTTGGGCTATCTGGT 60.264 41.667 0.00 0.00 0.00 4.00
451 2045 4.272489 TGTTTCATCTTTGGGCTATCTGG 58.728 43.478 0.00 0.00 0.00 3.86
452 2046 4.201990 GCTGTTTCATCTTTGGGCTATCTG 60.202 45.833 0.00 0.00 0.00 2.90
453 2047 3.950395 GCTGTTTCATCTTTGGGCTATCT 59.050 43.478 0.00 0.00 0.00 1.98
454 2048 3.242870 CGCTGTTTCATCTTTGGGCTATC 60.243 47.826 0.00 0.00 0.00 2.08
455 2049 2.684881 CGCTGTTTCATCTTTGGGCTAT 59.315 45.455 0.00 0.00 0.00 2.97
456 2050 2.083774 CGCTGTTTCATCTTTGGGCTA 58.916 47.619 0.00 0.00 0.00 3.93
457 2051 0.883833 CGCTGTTTCATCTTTGGGCT 59.116 50.000 0.00 0.00 0.00 5.19
458 2052 0.733909 GCGCTGTTTCATCTTTGGGC 60.734 55.000 0.00 0.00 0.00 5.36
459 2053 0.883833 AGCGCTGTTTCATCTTTGGG 59.116 50.000 10.39 0.00 0.00 4.12
464 2058 1.649664 CTGCTAGCGCTGTTTCATCT 58.350 50.000 22.90 0.00 36.97 2.90
499 2093 2.323580 GCGCATGATCCAGCTAGCC 61.324 63.158 12.13 0.00 0.00 3.93
500 2094 2.323580 GGCGCATGATCCAGCTAGC 61.324 63.158 10.83 6.62 0.00 3.42
501 2095 1.670406 GGGCGCATGATCCAGCTAG 60.670 63.158 10.83 0.00 0.00 3.42
502 2096 2.427320 GGGCGCATGATCCAGCTA 59.573 61.111 10.83 0.00 0.00 3.32
503 2097 4.923942 CGGGCGCATGATCCAGCT 62.924 66.667 10.83 0.00 0.00 4.24
507 2101 1.283793 CAATTCGGGCGCATGATCC 59.716 57.895 10.83 0.00 0.00 3.36
512 2106 3.825611 GGTGCAATTCGGGCGCAT 61.826 61.111 10.83 0.00 43.32 4.73
532 2126 5.743117 ACATGCTAGCTCTTCAAATCTTCT 58.257 37.500 17.23 0.00 0.00 2.85
540 2134 5.239744 GCTACTACTACATGCTAGCTCTTCA 59.760 44.000 17.23 0.00 0.00 3.02
579 2440 3.719173 TGCATCGATCGTGTATTACCA 57.281 42.857 15.94 2.81 0.00 3.25
583 2444 5.528870 TCTTACATGCATCGATCGTGTATT 58.471 37.500 15.94 10.33 36.26 1.89
596 2457 7.496920 CCTGAGATCATTTTACTCTTACATGCA 59.503 37.037 0.00 0.00 0.00 3.96
597 2458 7.519649 GCCTGAGATCATTTTACTCTTACATGC 60.520 40.741 0.00 0.00 0.00 4.06
598 2459 7.496920 TGCCTGAGATCATTTTACTCTTACATG 59.503 37.037 0.00 0.00 0.00 3.21
599 2460 7.568349 TGCCTGAGATCATTTTACTCTTACAT 58.432 34.615 0.00 0.00 0.00 2.29
611 2474 5.831525 TGCTTAATGAATGCCTGAGATCATT 59.168 36.000 0.00 5.34 43.08 2.57
620 2483 6.290294 AGTTGATTTGCTTAATGAATGCCT 57.710 33.333 0.00 0.00 0.00 4.75
633 2498 3.183237 AGAACGCGTAAGTTGATTTGC 57.817 42.857 14.46 0.00 41.68 3.68
792 3042 7.762382 TGACTGTGTATATATCAATCTAGCCG 58.238 38.462 0.00 0.00 0.00 5.52
794 3044 9.066939 CGTTGACTGTGTATATATCAATCTAGC 57.933 37.037 0.00 0.00 32.30 3.42
824 3076 7.016072 AGCTTTCTATAATCAGAGTGGCAGTAT 59.984 37.037 0.00 0.00 0.00 2.12
848 3100 3.557595 CAGTGGGTTATTCGATGAGAAGC 59.442 47.826 0.00 0.00 42.92 3.86
874 3128 2.343758 GAGCGCTCCTGGTTGTGA 59.656 61.111 27.22 0.00 0.00 3.58
895 3154 0.535797 GGGTGCTATATCCTACGGCC 59.464 60.000 0.00 0.00 0.00 6.13
944 3209 1.202330 CTGAGCAGAGAGGAATGGGT 58.798 55.000 0.00 0.00 0.00 4.51
947 3212 1.654317 GTGCTGAGCAGAGAGGAATG 58.346 55.000 7.71 0.00 40.08 2.67
949 3214 1.548357 GGGTGCTGAGCAGAGAGGAA 61.548 60.000 7.71 0.00 40.08 3.36
950 3215 1.986757 GGGTGCTGAGCAGAGAGGA 60.987 63.158 7.71 0.00 40.08 3.71
952 3217 0.673022 GTTGGGTGCTGAGCAGAGAG 60.673 60.000 7.71 0.00 40.08 3.20
1151 3425 1.307343 CCTCCACCCCATCCACTCT 60.307 63.158 0.00 0.00 0.00 3.24
1605 3879 3.721370 ATCATTGCCGGCCTGTCCC 62.721 63.158 26.77 0.00 0.00 4.46
1620 3894 0.842030 AGCCCCCAGAAGTGTCATCA 60.842 55.000 0.00 0.00 0.00 3.07
1724 3998 3.948719 GTCCCGTGCCAGACCCAA 61.949 66.667 0.00 0.00 0.00 4.12
1735 4009 0.603065 GTACTACCGGTTTGTCCCGT 59.397 55.000 15.04 1.61 46.66 5.28
1851 4125 0.833287 CACCAGATCCGGATCCACTT 59.167 55.000 35.53 18.32 38.58 3.16
1872 4146 4.641541 AGTGTAATTTAATGGTAACCGCCC 59.358 41.667 0.00 0.00 0.00 6.13
1884 4158 8.413229 AGCTTGCTCAAGAAAAGTGTAATTTAA 58.587 29.630 13.33 0.00 40.79 1.52
1893 4167 4.517075 GGTTCTAGCTTGCTCAAGAAAAGT 59.483 41.667 13.33 0.00 40.79 2.66
1895 4169 3.498397 CGGTTCTAGCTTGCTCAAGAAAA 59.502 43.478 13.33 0.00 40.79 2.29
1961 4236 1.522668 CCATGTCTCCTTTCACGCAA 58.477 50.000 0.00 0.00 0.00 4.85
1967 4243 1.133790 GTGCATGCCATGTCTCCTTTC 59.866 52.381 16.68 0.00 0.00 2.62
2003 4279 7.764443 GTGCTATTTATTTCTCTAGTGACACCA 59.236 37.037 0.84 0.00 0.00 4.17
2006 4282 9.587772 GAAGTGCTATTTATTTCTCTAGTGACA 57.412 33.333 0.00 0.00 0.00 3.58
2114 4396 6.293845 GGCCATTCAGATAGAAATTGCTACAG 60.294 42.308 0.00 0.00 40.22 2.74
2170 4453 8.967552 AACACGTAAAATGTGTAAAAAGACAA 57.032 26.923 5.40 0.00 46.74 3.18
2191 4482 2.277084 ACGAGAAACACACCTGAACAC 58.723 47.619 0.00 0.00 0.00 3.32
2222 4516 6.169557 TGTGGGTATGGACAAGATACATAC 57.830 41.667 0.00 0.00 43.74 2.39
2223 4517 6.816616 TTGTGGGTATGGACAAGATACATA 57.183 37.500 0.00 0.00 0.00 2.29
2224 4518 5.708736 TTGTGGGTATGGACAAGATACAT 57.291 39.130 0.00 0.00 0.00 2.29
2261 4558 9.195411 CAAAAATTGCATAGCTCTAAAAACTGA 57.805 29.630 0.00 0.00 0.00 3.41
2378 4675 4.537135 TGCTCGACCTTCTATCTTGTTT 57.463 40.909 0.00 0.00 0.00 2.83
2380 4677 4.537135 TTTGCTCGACCTTCTATCTTGT 57.463 40.909 0.00 0.00 0.00 3.16
2410 4707 4.041740 TGTTGCATGTCGTCTATCCTAC 57.958 45.455 0.00 0.00 0.00 3.18
2411 4708 3.068165 CCTGTTGCATGTCGTCTATCCTA 59.932 47.826 0.00 0.00 0.00 2.94
2412 4709 2.159043 CCTGTTGCATGTCGTCTATCCT 60.159 50.000 0.00 0.00 0.00 3.24
2413 4710 2.205074 CCTGTTGCATGTCGTCTATCC 58.795 52.381 0.00 0.00 0.00 2.59
2414 4711 2.860735 GACCTGTTGCATGTCGTCTATC 59.139 50.000 0.00 0.00 0.00 2.08
2415 4712 2.497675 AGACCTGTTGCATGTCGTCTAT 59.502 45.455 5.50 0.00 34.92 1.98
2416 4713 1.893137 AGACCTGTTGCATGTCGTCTA 59.107 47.619 5.50 0.00 34.92 2.59
2417 4714 0.681733 AGACCTGTTGCATGTCGTCT 59.318 50.000 0.00 0.00 34.92 4.18
2418 4715 0.792640 CAGACCTGTTGCATGTCGTC 59.207 55.000 0.00 0.00 34.92 4.20
2419 4716 1.230635 GCAGACCTGTTGCATGTCGT 61.231 55.000 0.00 0.00 41.17 4.34
2420 4717 1.229975 TGCAGACCTGTTGCATGTCG 61.230 55.000 0.00 0.00 45.89 4.35
2433 4730 8.210868 TGTAACACACATATGCAACTGCAGAC 62.211 42.308 23.35 9.97 45.61 3.51
2434 4731 6.258666 TGTAACACACATATGCAACTGCAGA 61.259 40.000 23.35 5.97 46.91 4.26
2435 4732 4.083377 TGTAACACACATATGCAACTGCAG 60.083 41.667 13.48 13.48 43.08 4.41
2436 4733 3.817647 TGTAACACACATATGCAACTGCA 59.182 39.130 6.88 6.88 43.63 4.41
2437 4734 4.418013 TGTAACACACATATGCAACTGC 57.582 40.909 1.58 0.00 35.07 4.40
2491 4788 3.444742 GCACATCCATCTTTTGACATGGA 59.555 43.478 3.17 3.17 45.97 3.41
2492 4789 3.193903 TGCACATCCATCTTTTGACATGG 59.806 43.478 0.00 0.00 35.58 3.66
2502 4899 1.340405 GGGTCACTTGCACATCCATCT 60.340 52.381 0.00 0.00 0.00 2.90
2516 4913 5.427036 TCGTTTAAAAGAACATGGGTCAC 57.573 39.130 1.03 0.00 0.00 3.67
2528 4925 6.121613 TGTGGGTACAAGTTCGTTTAAAAG 57.878 37.500 0.00 0.00 32.88 2.27
2534 4931 4.095334 GTCTTTTGTGGGTACAAGTTCGTT 59.905 41.667 0.00 0.00 46.63 3.85
2542 4939 1.134340 AGCACGTCTTTTGTGGGTACA 60.134 47.619 0.00 0.00 37.80 2.90
2595 4992 8.746530 ACGAAGATAGTTTCCTTGATAGTAACA 58.253 33.333 0.00 0.00 0.00 2.41
2603 5000 8.665643 TGTTTTTACGAAGATAGTTTCCTTGA 57.334 30.769 0.00 0.00 0.00 3.02
2631 5028 8.548877 ACAACCCTAGTAATGTTTCACAGATAT 58.451 33.333 0.00 0.00 0.00 1.63
2637 5034 6.870971 TCAACAACCCTAGTAATGTTTCAC 57.129 37.500 2.55 0.00 33.97 3.18
2723 5123 7.443879 TCTTTCTTGCTTGTATGTGTCATGTAA 59.556 33.333 0.00 0.00 0.00 2.41
2728 5128 4.515191 GGTCTTTCTTGCTTGTATGTGTCA 59.485 41.667 0.00 0.00 0.00 3.58
2729 5129 4.515191 TGGTCTTTCTTGCTTGTATGTGTC 59.485 41.667 0.00 0.00 0.00 3.67
2731 5131 4.320494 GGTGGTCTTTCTTGCTTGTATGTG 60.320 45.833 0.00 0.00 0.00 3.21
2745 5145 2.037677 AGGGGTGGGGTGGTCTTT 60.038 61.111 0.00 0.00 0.00 2.52
2746 5146 2.531942 GAGGGGTGGGGTGGTCTT 60.532 66.667 0.00 0.00 0.00 3.01
2747 5147 4.677151 GGAGGGGTGGGGTGGTCT 62.677 72.222 0.00 0.00 0.00 3.85
2748 5148 4.995058 TGGAGGGGTGGGGTGGTC 62.995 72.222 0.00 0.00 0.00 4.02
2750 5150 3.661648 CTTGGAGGGGTGGGGTGG 61.662 72.222 0.00 0.00 0.00 4.61
2751 5151 1.725169 TTTCTTGGAGGGGTGGGGTG 61.725 60.000 0.00 0.00 0.00 4.61
2752 5152 1.388217 TTTCTTGGAGGGGTGGGGT 60.388 57.895 0.00 0.00 0.00 4.95
2753 5153 1.140134 TCTTTCTTGGAGGGGTGGGG 61.140 60.000 0.00 0.00 0.00 4.96
2754 5154 0.777446 TTCTTTCTTGGAGGGGTGGG 59.223 55.000 0.00 0.00 0.00 4.61
2761 5167 6.162777 TGTTTTGTGGTTTTCTTTCTTGGAG 58.837 36.000 0.00 0.00 0.00 3.86
2762 5168 6.102897 TGTTTTGTGGTTTTCTTTCTTGGA 57.897 33.333 0.00 0.00 0.00 3.53
2785 5191 4.042884 TCTCCCAGAATCCTCATCATGTT 58.957 43.478 0.00 0.00 0.00 2.71
2789 5195 3.303938 GTCTCTCCCAGAATCCTCATCA 58.696 50.000 0.00 0.00 30.72 3.07
2790 5196 2.295909 CGTCTCTCCCAGAATCCTCATC 59.704 54.545 0.00 0.00 30.72 2.92
2792 5198 1.769026 CGTCTCTCCCAGAATCCTCA 58.231 55.000 0.00 0.00 30.72 3.86
2793 5199 0.387565 GCGTCTCTCCCAGAATCCTC 59.612 60.000 0.00 0.00 30.72 3.71
2795 5201 1.330655 TGGCGTCTCTCCCAGAATCC 61.331 60.000 0.00 0.00 30.72 3.01
2796 5202 0.179097 GTGGCGTCTCTCCCAGAATC 60.179 60.000 0.00 0.00 30.72 2.52
2797 5203 0.616111 AGTGGCGTCTCTCCCAGAAT 60.616 55.000 0.00 0.00 30.72 2.40
2798 5204 0.039180 TAGTGGCGTCTCTCCCAGAA 59.961 55.000 0.00 0.00 30.72 3.02
2799 5205 0.394488 CTAGTGGCGTCTCTCCCAGA 60.394 60.000 0.00 0.00 0.00 3.86
2801 5207 0.965866 CACTAGTGGCGTCTCTCCCA 60.966 60.000 15.49 0.00 0.00 4.37
2802 5208 0.966370 ACACTAGTGGCGTCTCTCCC 60.966 60.000 26.12 0.00 34.19 4.30
2805 5211 1.179174 TGCACACTAGTGGCGTCTCT 61.179 55.000 26.12 0.73 45.98 3.10
2806 5212 1.009389 GTGCACACTAGTGGCGTCTC 61.009 60.000 26.12 13.51 45.98 3.36
2807 5213 1.006102 GTGCACACTAGTGGCGTCT 60.006 57.895 26.12 2.28 45.98 4.18
2808 5214 2.027625 GGTGCACACTAGTGGCGTC 61.028 63.158 26.12 19.60 45.98 5.19
2809 5215 2.030562 GGTGCACACTAGTGGCGT 59.969 61.111 26.12 3.08 45.98 5.68
2810 5216 2.742372 GGGTGCACACTAGTGGCG 60.742 66.667 26.12 17.39 45.98 5.69
2811 5217 2.742372 CGGGTGCACACTAGTGGC 60.742 66.667 26.12 23.88 45.98 5.01
2812 5218 2.047274 CCGGGTGCACACTAGTGG 60.047 66.667 26.12 15.85 45.98 4.00
2814 5220 2.283529 CCTCCGGGTGCACACTAGT 61.284 63.158 18.70 0.00 0.00 2.57
2815 5221 2.579201 CCTCCGGGTGCACACTAG 59.421 66.667 18.70 14.02 0.00 2.57
2816 5222 3.000819 CCCTCCGGGTGCACACTA 61.001 66.667 18.70 4.02 38.25 2.74
2817 5223 4.954118 TCCCTCCGGGTGCACACT 62.954 66.667 18.70 0.00 44.74 3.55
2818 5224 4.394712 CTCCCTCCGGGTGCACAC 62.395 72.222 20.43 15.50 44.74 3.82
2842 5248 4.614555 TGCCACATAAGTTTTCATAGCG 57.385 40.909 0.00 0.00 0.00 4.26
2858 5272 1.135141 TGTGAAACACTTGCTTGCCAC 60.135 47.619 0.00 0.00 45.67 5.01


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

AutoCloner maintained by Alex Coulton.