Multiple sequence alignment - TraesCS2B01G472000

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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 TraesCS2B01G472000 chr2B 100.000 4689 0 0 1 4689 668385026 668380338 0.000000e+00 8660.0
1 TraesCS2B01G472000 chr2B 95.588 68 1 2 1308 1375 779049941 779050006 1.780000e-19 108.0
2 TraesCS2B01G472000 chr2B 89.706 68 2 3 1918 1981 38218221 38218287 1.080000e-11 82.4
3 TraesCS2B01G472000 chr2A 93.928 2355 122 18 1845 4190 699876033 699873691 0.000000e+00 3537.0
4 TraesCS2B01G472000 chr2A 92.050 478 35 2 1372 1849 699876534 699876060 0.000000e+00 669.0
5 TraesCS2B01G472000 chr2A 91.667 408 23 5 909 1312 699876936 699876536 5.300000e-154 555.0
6 TraesCS2B01G472000 chr2A 90.135 223 10 6 658 869 699877607 699877386 3.570000e-71 279.0
7 TraesCS2B01G472000 chr2A 87.179 234 24 5 4158 4389 699873692 699873463 1.290000e-65 261.0
8 TraesCS2B01G472000 chr2A 80.392 306 40 10 288 586 699877928 699877636 1.020000e-51 215.0
9 TraesCS2B01G472000 chr2A 82.791 215 7 14 4477 4689 699871198 699871012 1.040000e-36 165.0
10 TraesCS2B01G472000 chr2D 94.101 2170 109 16 1978 4138 559319326 559317167 0.000000e+00 3280.0
11 TraesCS2B01G472000 chr2D 91.736 1077 55 15 246 1312 559320966 559319914 0.000000e+00 1465.0
12 TraesCS2B01G472000 chr2D 89.319 543 27 15 4159 4689 559317096 559316573 0.000000e+00 652.0
13 TraesCS2B01G472000 chr2D 89.583 480 40 5 1372 1849 559319912 559319441 6.710000e-168 601.0
14 TraesCS2B01G472000 chr2D 92.742 248 11 4 2 245 216233410 216233166 7.470000e-93 351.0
15 TraesCS2B01G472000 chr2D 94.737 76 3 1 598 672 87812045 87811970 2.960000e-22 117.0
16 TraesCS2B01G472000 chr2D 88.372 86 7 3 588 671 192300990 192301074 2.990000e-17 100.0
17 TraesCS2B01G472000 chr3D 91.935 248 14 4 2 245 114900188 114900433 4.490000e-90 342.0
18 TraesCS2B01G472000 chr3D 91.870 246 14 4 4 245 114897593 114897836 5.810000e-89 339.0
19 TraesCS2B01G472000 chr3D 88.889 90 8 2 583 670 398269052 398268963 4.960000e-20 110.0
20 TraesCS2B01G472000 chr3D 93.333 60 3 1 1924 1982 591618642 591618701 2.320000e-13 87.9
21 TraesCS2B01G472000 chr6D 91.935 248 13 5 2 245 185176739 185176495 1.620000e-89 340.0
22 TraesCS2B01G472000 chr6D 91.532 248 15 4 3 245 401597790 401598036 2.090000e-88 337.0
23 TraesCS2B01G472000 chr6D 86.813 91 10 2 581 669 2965667 2965577 2.990000e-17 100.0
24 TraesCS2B01G472000 chr5D 91.566 249 15 4 2 245 17267097 17267344 5.810000e-89 339.0
25 TraesCS2B01G472000 chr5D 91.532 248 15 4 2 245 91982197 91981952 2.090000e-88 337.0
26 TraesCS2B01G472000 chr5D 84.444 90 10 4 582 668 42040504 42040592 8.360000e-13 86.1
27 TraesCS2B01G472000 chr5D 92.188 64 0 3 1925 1983 461211553 461211490 8.360000e-13 86.1
28 TraesCS2B01G472000 chr7D 91.566 249 14 5 2 245 431744040 431744286 2.090000e-88 337.0
29 TraesCS2B01G472000 chr4D 91.532 248 15 4 2 245 221058205 221057960 2.090000e-88 337.0
30 TraesCS2B01G472000 chr7B 93.671 79 3 2 1300 1376 472334305 472334383 2.960000e-22 117.0
31 TraesCS2B01G472000 chr7B 92.405 79 4 2 1300 1376 472399788 472399866 1.380000e-20 111.0
32 TraesCS2B01G472000 chr1D 90.805 87 6 2 583 668 377800830 377800745 1.070000e-21 115.0
33 TraesCS2B01G472000 chr1D 94.203 69 2 2 1306 1372 247902436 247902504 2.310000e-18 104.0
34 TraesCS2B01G472000 chr1A 94.667 75 2 2 1303 1376 540148830 540148903 1.070000e-21 115.0
35 TraesCS2B01G472000 chr4B 98.438 64 1 0 1310 1373 10507534 10507471 3.830000e-21 113.0
36 TraesCS2B01G472000 chr5A 95.652 69 1 2 1306 1372 507895374 507895442 4.960000e-20 110.0
37 TraesCS2B01G472000 chr3B 95.652 69 1 2 1306 1372 801555559 801555627 4.960000e-20 110.0
38 TraesCS2B01G472000 chr3B 89.535 86 5 4 588 670 50534584 50534668 6.420000e-19 106.0
39 TraesCS2B01G472000 chr3B 88.406 69 5 2 1923 1991 373884172 373884237 3.890000e-11 80.5
40 TraesCS2B01G472000 chr7A 94.203 69 2 2 1308 1376 713130317 713130251 2.310000e-18 104.0
41 TraesCS2B01G472000 chr7A 86.813 91 10 2 583 671 640541943 640541853 2.990000e-17 100.0
42 TraesCS2B01G472000 chr4A 89.286 84 6 2 583 665 624289978 624289897 8.300000e-18 102.0
43 TraesCS2B01G472000 chr6B 85.227 88 11 2 579 665 678330103 678330017 6.460000e-14 89.8
44 TraesCS2B01G472000 chr6B 94.737 57 1 2 1918 1973 713960619 713960564 2.320000e-13 87.9
45 TraesCS2B01G472000 chr1B 92.063 63 3 2 1920 1981 411211865 411211926 2.320000e-13 87.9
46 TraesCS2B01G472000 chr1B 92.063 63 3 1 1919 1981 579608060 579608120 2.320000e-13 87.9
47 TraesCS2B01G472000 chr1B 81.651 109 14 6 564 668 550460492 550460386 8.360000e-13 86.1
48 TraesCS2B01G472000 chrUn 88.235 68 6 2 1924 1991 88110428 88110493 3.890000e-11 80.5


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 TraesCS2B01G472000 chr2B 668380338 668385026 4688 True 8660.000000 8660 100.00000 1 4689 1 chr2B.!!$R1 4688
1 TraesCS2B01G472000 chr2A 699871012 699877928 6916 True 811.571429 3537 88.30600 288 4689 7 chr2A.!!$R1 4401
2 TraesCS2B01G472000 chr2D 559316573 559320966 4393 True 1499.500000 3280 91.18475 246 4689 4 chr2D.!!$R3 4443
3 TraesCS2B01G472000 chr3D 114897593 114900433 2840 False 340.500000 342 91.90250 2 245 2 chr3D.!!$F2 243

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
979 4011 2.839098 CCCGGCCTTATCCTGCAT 59.161 61.111 0.00 0.0 0.00 3.96 F
1220 4253 0.250513 AAACTCGCCCAGCTAGAAGG 59.749 55.000 0.00 0.0 0.00 3.46 F
2490 5565 0.331278 TTGTCTTGGGCATCCGGAAT 59.669 50.000 9.01 0.0 35.24 3.01 F
3466 6545 0.451383 TAATCGCATGCAACAGTGGC 59.549 50.000 19.57 0.0 0.00 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2308 5383 2.082231 AGCTGCAATTAGAGCACACTG 58.918 47.619 1.02 0.00 37.02 3.66 R
2984 6062 2.229792 CCACTGTTAAGCTTGCTTCCA 58.770 47.619 9.86 8.87 0.00 3.53 R
3557 6636 0.169230 ATCGCTAGATCGTGATCGCC 59.831 55.000 0.00 0.00 42.48 5.54 R
4607 9929 0.456653 AAACGCCGCAATCAGCAATC 60.457 50.000 0.00 0.00 46.13 2.67 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
33 34 8.522830 TCAATTTTCTTCAGTCTGTTTGTCTTT 58.477 29.630 0.00 0.00 0.00 2.52
34 35 9.787532 CAATTTTCTTCAGTCTGTTTGTCTTTA 57.212 29.630 0.00 0.00 0.00 1.85
37 38 8.964476 TTTCTTCAGTCTGTTTGTCTTTATCT 57.036 30.769 0.00 0.00 0.00 1.98
40 41 7.987458 TCTTCAGTCTGTTTGTCTTTATCTTGT 59.013 33.333 0.00 0.00 0.00 3.16
73 74 4.530710 TTATGCTTTCTGTACTCCGTGT 57.469 40.909 0.00 0.00 0.00 4.49
90 91 4.973051 TCCGTGTTTGTTTTCATTTCATCG 59.027 37.500 0.00 0.00 0.00 3.84
110 111 6.542005 TCATCGTGATAACCATGCTTATGTTT 59.458 34.615 0.00 0.00 0.00 2.83
170 2768 6.698380 AGTAGTTCTTCGCTTAGGAATTTCA 58.302 36.000 0.00 0.00 0.00 2.69
171 2769 5.864628 AGTTCTTCGCTTAGGAATTTCAC 57.135 39.130 0.00 0.00 0.00 3.18
173 2771 3.606687 TCTTCGCTTAGGAATTTCACCC 58.393 45.455 0.00 0.00 0.00 4.61
174 2772 3.263425 TCTTCGCTTAGGAATTTCACCCT 59.737 43.478 0.00 0.00 36.60 4.34
175 2773 2.985896 TCGCTTAGGAATTTCACCCTG 58.014 47.619 0.00 0.00 34.11 4.45
216 2818 7.823745 ATTCATAAAAATCGCCTATTCACCT 57.176 32.000 0.00 0.00 0.00 4.00
217 2819 7.639113 TTCATAAAAATCGCCTATTCACCTT 57.361 32.000 0.00 0.00 0.00 3.50
236 2838 5.768662 CACCTTCCCTCTAGTCGATATAACA 59.231 44.000 0.00 0.00 0.00 2.41
245 2847 7.644551 CCTCTAGTCGATATAACACACTTTCAC 59.355 40.741 0.00 0.00 0.00 3.18
246 2848 8.047413 TCTAGTCGATATAACACACTTTCACA 57.953 34.615 0.00 0.00 0.00 3.58
247 2849 8.683615 TCTAGTCGATATAACACACTTTCACAT 58.316 33.333 0.00 0.00 0.00 3.21
248 2850 9.946165 CTAGTCGATATAACACACTTTCACATA 57.054 33.333 0.00 0.00 0.00 2.29
249 2851 8.858003 AGTCGATATAACACACTTTCACATAG 57.142 34.615 0.00 0.00 0.00 2.23
250 2852 7.921214 AGTCGATATAACACACTTTCACATAGG 59.079 37.037 0.00 0.00 0.00 2.57
257 2859 5.570320 ACACACTTTCACATAGGGCTAATT 58.430 37.500 0.00 0.00 0.00 1.40
329 2931 6.906659 AGTAGCAAAATCAATGACTTGACTG 58.093 36.000 10.14 0.00 43.92 3.51
489 3097 6.344572 TCACATCAATCTGTTTATGCGTAC 57.655 37.500 0.00 0.00 0.00 3.67
491 3099 6.538381 TCACATCAATCTGTTTATGCGTACAT 59.462 34.615 0.00 0.00 40.49 2.29
508 3117 4.680708 CGTACATCAAACCAGATAGCACCT 60.681 45.833 0.00 0.00 0.00 4.00
516 3125 7.118723 TCAAACCAGATAGCACCTTTCAATAT 58.881 34.615 0.00 0.00 0.00 1.28
518 3127 7.573968 AACCAGATAGCACCTTTCAATATTC 57.426 36.000 0.00 0.00 0.00 1.75
662 3275 7.090953 GTCTTATATTATGAGACGGAGGGAG 57.909 44.000 11.50 0.00 36.39 4.30
663 3276 6.660094 GTCTTATATTATGAGACGGAGGGAGT 59.340 42.308 11.50 0.00 36.39 3.85
817 3438 3.669036 AAAACAACGCACGCACGCA 62.669 52.632 0.00 0.00 36.19 5.24
818 3439 4.879686 AACAACGCACGCACGCAC 62.880 61.111 0.00 0.00 36.19 5.34
832 3454 3.660111 GCACGCCGCTTTCCTTGT 61.660 61.111 0.00 0.00 37.77 3.16
939 3971 3.309193 CGATCCCATCCCTCTCTACCATA 60.309 52.174 0.00 0.00 0.00 2.74
978 4010 4.189580 GCCCGGCCTTATCCTGCA 62.190 66.667 0.00 0.00 0.00 4.41
979 4011 2.839098 CCCGGCCTTATCCTGCAT 59.161 61.111 0.00 0.00 0.00 3.96
1002 4034 2.464459 GCCGTCCTTGGAAGCGATG 61.464 63.158 1.92 0.00 0.00 3.84
1003 4035 1.815421 CCGTCCTTGGAAGCGATGG 60.815 63.158 1.92 0.00 0.00 3.51
1004 4036 2.464459 CGTCCTTGGAAGCGATGGC 61.464 63.158 0.00 0.00 40.37 4.40
1127 4159 0.712979 TCCTCCTCCTCTCACCACAT 59.287 55.000 0.00 0.00 0.00 3.21
1160 4192 3.599730 TGCAGTTCGTCTGAATCTGAT 57.400 42.857 12.77 0.00 46.27 2.90
1167 4199 2.431782 TCGTCTGAATCTGATGCCATGA 59.568 45.455 0.00 0.00 0.00 3.07
1168 4200 2.801111 CGTCTGAATCTGATGCCATGAG 59.199 50.000 0.00 0.00 0.00 2.90
1169 4201 2.548904 GTCTGAATCTGATGCCATGAGC 59.451 50.000 0.00 0.00 44.14 4.26
1207 4240 5.154932 AGATCACGTGACTTCTTAAACTCG 58.845 41.667 22.71 0.00 0.00 4.18
1220 4253 0.250513 AAACTCGCCCAGCTAGAAGG 59.749 55.000 0.00 0.00 0.00 3.46
1228 4261 2.183679 CCCAGCTAGAAGGTTGAGTCT 58.816 52.381 0.00 0.00 0.00 3.24
1254 4290 8.687242 TCTGATTTCGTAGTGTTGATAGATTCT 58.313 33.333 0.00 0.00 0.00 2.40
1305 4341 4.446889 GCATGTCTAGGAGATCCCCAATTT 60.447 45.833 0.00 0.00 36.42 1.82
1306 4342 5.312079 CATGTCTAGGAGATCCCCAATTTC 58.688 45.833 0.00 0.00 36.42 2.17
1307 4343 4.635473 TGTCTAGGAGATCCCCAATTTCT 58.365 43.478 0.00 0.00 36.42 2.52
1308 4344 4.410228 TGTCTAGGAGATCCCCAATTTCTG 59.590 45.833 0.00 0.00 36.42 3.02
1309 4345 4.410555 GTCTAGGAGATCCCCAATTTCTGT 59.589 45.833 0.00 0.00 36.42 3.41
1310 4346 5.602978 GTCTAGGAGATCCCCAATTTCTGTA 59.397 44.000 0.00 0.00 36.42 2.74
1312 4348 4.375313 AGGAGATCCCCAATTTCTGTACT 58.625 43.478 0.00 0.00 36.42 2.73
1313 4349 5.538877 AGGAGATCCCCAATTTCTGTACTA 58.461 41.667 0.00 0.00 36.42 1.82
1314 4350 5.367060 AGGAGATCCCCAATTTCTGTACTAC 59.633 44.000 0.00 0.00 36.42 2.73
1315 4351 5.367060 GGAGATCCCCAATTTCTGTACTACT 59.633 44.000 0.00 0.00 0.00 2.57
1316 4352 6.463190 GGAGATCCCCAATTTCTGTACTACTC 60.463 46.154 0.00 0.00 0.00 2.59
1317 4353 5.367060 AGATCCCCAATTTCTGTACTACTCC 59.633 44.000 0.00 0.00 0.00 3.85
1318 4354 3.778629 TCCCCAATTTCTGTACTACTCCC 59.221 47.826 0.00 0.00 0.00 4.30
1319 4355 3.780850 CCCCAATTTCTGTACTACTCCCT 59.219 47.826 0.00 0.00 0.00 4.20
1320 4356 4.141688 CCCCAATTTCTGTACTACTCCCTC 60.142 50.000 0.00 0.00 0.00 4.30
1321 4357 4.141688 CCCAATTTCTGTACTACTCCCTCC 60.142 50.000 0.00 0.00 0.00 4.30
1322 4358 4.441634 CCAATTTCTGTACTACTCCCTCCG 60.442 50.000 0.00 0.00 0.00 4.63
1323 4359 3.446442 TTTCTGTACTACTCCCTCCGT 57.554 47.619 0.00 0.00 0.00 4.69
1324 4360 3.446442 TTCTGTACTACTCCCTCCGTT 57.554 47.619 0.00 0.00 0.00 4.44
1325 4361 2.996631 TCTGTACTACTCCCTCCGTTC 58.003 52.381 0.00 0.00 0.00 3.95
1326 4362 2.022934 CTGTACTACTCCCTCCGTTCC 58.977 57.143 0.00 0.00 0.00 3.62
1327 4363 1.355381 TGTACTACTCCCTCCGTTCCA 59.645 52.381 0.00 0.00 0.00 3.53
1328 4364 2.225091 TGTACTACTCCCTCCGTTCCAA 60.225 50.000 0.00 0.00 0.00 3.53
1329 4365 2.019807 ACTACTCCCTCCGTTCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
1330 4366 2.332117 ACTACTCCCTCCGTTCCAAAA 58.668 47.619 0.00 0.00 0.00 2.44
1331 4367 2.910977 ACTACTCCCTCCGTTCCAAAAT 59.089 45.455 0.00 0.00 0.00 1.82
1332 4368 4.098894 ACTACTCCCTCCGTTCCAAAATA 58.901 43.478 0.00 0.00 0.00 1.40
1333 4369 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
1334 4370 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
1335 4371 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
1336 4372 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
1337 4373 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
1338 4374 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
1339 4375 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
1340 4376 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
1341 4377 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
1342 4378 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
1343 4379 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
1344 4380 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
1345 4381 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
1346 4382 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
1347 4383 7.535258 CGTTCCAAAATAGATGACTCAACTTTG 59.465 37.037 0.00 0.00 0.00 2.77
1348 4384 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
1349 4385 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
1350 4386 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
1351 4387 9.003658 CCAAAATAGATGACTCAACTTTGTACT 57.996 33.333 0.00 0.00 0.00 2.73
1358 4394 9.003658 AGATGACTCAACTTTGTACTATTTTGG 57.996 33.333 0.00 0.00 0.00 3.28
1359 4395 8.918202 ATGACTCAACTTTGTACTATTTTGGA 57.082 30.769 0.00 0.00 0.00 3.53
1360 4396 8.740123 TGACTCAACTTTGTACTATTTTGGAA 57.260 30.769 0.00 0.00 0.00 3.53
1361 4397 8.617809 TGACTCAACTTTGTACTATTTTGGAAC 58.382 33.333 0.00 0.00 0.00 3.62
1362 4398 7.636326 ACTCAACTTTGTACTATTTTGGAACG 58.364 34.615 0.00 0.00 0.00 3.95
1363 4399 6.961576 TCAACTTTGTACTATTTTGGAACGG 58.038 36.000 0.00 0.00 0.00 4.44
1364 4400 6.766944 TCAACTTTGTACTATTTTGGAACGGA 59.233 34.615 0.00 0.00 0.00 4.69
1365 4401 6.796705 ACTTTGTACTATTTTGGAACGGAG 57.203 37.500 0.00 0.00 0.00 4.63
1366 4402 5.704053 ACTTTGTACTATTTTGGAACGGAGG 59.296 40.000 0.00 0.00 0.00 4.30
1367 4403 4.210724 TGTACTATTTTGGAACGGAGGG 57.789 45.455 0.00 0.00 0.00 4.30
1368 4404 3.839490 TGTACTATTTTGGAACGGAGGGA 59.161 43.478 0.00 0.00 0.00 4.20
1369 4405 3.629142 ACTATTTTGGAACGGAGGGAG 57.371 47.619 0.00 0.00 0.00 4.30
1370 4406 2.910977 ACTATTTTGGAACGGAGGGAGT 59.089 45.455 0.00 0.00 0.00 3.85
1379 4415 2.431954 ACGGAGGGAGTAGATTCGAA 57.568 50.000 0.00 0.00 0.00 3.71
1383 4419 3.440872 CGGAGGGAGTAGATTCGAATAGG 59.559 52.174 11.38 0.00 0.00 2.57
1392 4428 2.505819 AGATTCGAATAGGCTGGTGGTT 59.494 45.455 11.38 0.00 0.00 3.67
1403 4439 1.476110 GCTGGTGGTTGTTCAGGTGTA 60.476 52.381 0.00 0.00 0.00 2.90
1413 4449 5.811100 GGTTGTTCAGGTGTAGTATAAGAGC 59.189 44.000 0.00 0.00 0.00 4.09
1415 4451 5.962433 TGTTCAGGTGTAGTATAAGAGCAC 58.038 41.667 0.00 0.00 0.00 4.40
1454 4491 6.442952 TCCTTTTCATACGAATTGGTGTTTG 58.557 36.000 3.01 0.00 0.00 2.93
1484 4521 7.757173 TGATAGCTTATAATTAGCTTGCTCGAG 59.243 37.037 8.45 8.45 46.42 4.04
1487 4524 5.347364 GCTTATAATTAGCTTGCTCGAGGAG 59.653 44.000 15.58 6.79 35.74 3.69
1488 4525 2.611225 AATTAGCTTGCTCGAGGAGG 57.389 50.000 15.58 13.65 0.00 4.30
1499 4536 1.038130 TCGAGGAGGCTAGGAGCAAC 61.038 60.000 0.21 0.00 44.75 4.17
1504 4541 1.137282 GGAGGCTAGGAGCAACTACAC 59.863 57.143 0.21 0.00 44.75 2.90
1539 4576 2.223537 TCGCACGTCAGCAATATGAT 57.776 45.000 0.00 0.00 0.00 2.45
1618 4655 7.609760 TGAACAATGTATGATAACACCTGTC 57.390 36.000 0.00 0.00 31.10 3.51
1673 4710 4.808364 GGTGCTGAGAGATTGATAGTTGAC 59.192 45.833 0.00 0.00 0.00 3.18
1712 4749 0.752743 CCCATGGGCACGATGTTCAT 60.753 55.000 20.41 0.00 43.15 2.57
1859 4927 7.148188 CCATATCTGAGTTGCAAGTATTTGTGT 60.148 37.037 6.80 0.00 36.65 3.72
1936 5011 4.087907 GTCCCATACATAGTACTCCCTCC 58.912 52.174 0.00 0.00 0.00 4.30
1951 5026 8.858094 AGTACTCCCTCCGTAAAGAAATATAAG 58.142 37.037 0.00 0.00 0.00 1.73
1952 5027 7.909485 ACTCCCTCCGTAAAGAAATATAAGA 57.091 36.000 0.00 0.00 0.00 2.10
1953 5028 7.953752 ACTCCCTCCGTAAAGAAATATAAGAG 58.046 38.462 0.00 0.00 0.00 2.85
1955 5030 6.325545 TCCCTCCGTAAAGAAATATAAGAGCA 59.674 38.462 0.00 0.00 0.00 4.26
1956 5031 7.016268 TCCCTCCGTAAAGAAATATAAGAGCAT 59.984 37.037 0.00 0.00 0.00 3.79
2046 5121 7.716799 TTTTGGTAAGGAATGCTTATGATGT 57.283 32.000 0.00 0.00 0.00 3.06
2207 5282 0.884704 CTGCGTGCTACTTTGGTGGT 60.885 55.000 0.00 0.00 0.00 4.16
2257 5332 5.063204 CAGGTTTCTGTTGTGATTCCACTA 58.937 41.667 0.00 0.00 38.80 2.74
2490 5565 0.331278 TTGTCTTGGGCATCCGGAAT 59.669 50.000 9.01 0.00 35.24 3.01
2559 5634 6.328672 AGAGATCTACTGGCATCCTAATTGTT 59.671 38.462 0.00 0.00 0.00 2.83
2626 5701 7.952671 TGATTCTAGTCAACAGTAAGTTCACT 58.047 34.615 0.00 0.00 44.28 3.41
2653 5728 2.837498 ACTTTTGCCAGGACATTTTGC 58.163 42.857 0.00 0.00 0.00 3.68
2654 5729 2.170187 ACTTTTGCCAGGACATTTTGCA 59.830 40.909 0.00 0.00 0.00 4.08
2787 5862 7.033791 TGTGACTCATTTAGGTTCTATTCGTC 58.966 38.462 0.00 0.00 0.00 4.20
2826 5903 7.997482 ACAATAGCTGTCTCTCTCGTATTTTA 58.003 34.615 0.00 0.00 29.87 1.52
2843 5921 6.532657 CGTATTTTATCCTCGTTTGGTGTAGT 59.467 38.462 0.00 0.00 0.00 2.73
2979 6057 0.729116 CTAAGCAACCTGGTGATGCG 59.271 55.000 15.72 1.22 44.60 4.73
2984 6062 3.557903 AACCTGGTGATGCGCTGCT 62.558 57.895 9.73 0.00 0.00 4.24
3021 6099 2.765699 AGTGGCAGGTGATGTTTGTTTT 59.234 40.909 0.00 0.00 0.00 2.43
3022 6100 3.957497 AGTGGCAGGTGATGTTTGTTTTA 59.043 39.130 0.00 0.00 0.00 1.52
3023 6101 4.588528 AGTGGCAGGTGATGTTTGTTTTAT 59.411 37.500 0.00 0.00 0.00 1.40
3024 6102 5.070313 AGTGGCAGGTGATGTTTGTTTTATT 59.930 36.000 0.00 0.00 0.00 1.40
3038 6116 8.495260 TGTTTGTTTTATTTGTTATTTCCCCCT 58.505 29.630 0.00 0.00 0.00 4.79
3108 6187 3.632145 CAGAATATTAACCACTGGCCACC 59.368 47.826 0.00 0.00 0.00 4.61
3229 6308 9.313118 GAAGGTGTTTCTGAACATGTTAAATTT 57.687 29.630 11.95 0.00 46.63 1.82
3248 6327 9.734620 TTAAATTTGTGACATCTTGTTCTTCAG 57.265 29.630 0.00 0.00 0.00 3.02
3310 6389 6.127952 TGTTGTACACTCCAAAGGTAAACAAC 60.128 38.462 0.00 7.39 39.37 3.32
3377 6456 7.946655 TTATTCTAATTCAGCCTACATGTCG 57.053 36.000 0.00 0.00 0.00 4.35
3378 6457 5.339008 TTCTAATTCAGCCTACATGTCGT 57.661 39.130 0.00 0.00 0.00 4.34
3466 6545 0.451383 TAATCGCATGCAACAGTGGC 59.549 50.000 19.57 0.00 0.00 5.01
3526 6605 2.368192 TGCGATCCCTCCCCCATT 60.368 61.111 0.00 0.00 0.00 3.16
3545 6624 4.396790 CCATTGAATTTTCCAAAGCCATGG 59.603 41.667 7.63 7.63 42.12 3.66
3557 6636 1.331214 AGCCATGGTGAAGTTTGTGG 58.669 50.000 14.67 0.00 0.00 4.17
3575 6654 1.574925 GGCGATCACGATCTAGCGA 59.425 57.895 5.55 0.00 42.66 4.93
3696 6775 3.705579 CAGAGGATGGAGTGATCTGAGTT 59.294 47.826 0.00 0.00 39.80 3.01
3751 6830 6.653020 TGAGTAGCACATTAACATCATCCTT 58.347 36.000 0.00 0.00 0.00 3.36
3838 6920 1.002257 TTGCATGGTGATGGCGACT 60.002 52.632 0.00 0.00 0.00 4.18
3842 6924 1.167851 CATGGTGATGGCGACTTTGT 58.832 50.000 0.00 0.00 0.00 2.83
3852 6934 2.353269 TGGCGACTTTGTATTATTGGCG 59.647 45.455 0.00 0.00 0.00 5.69
3853 6935 2.610374 GGCGACTTTGTATTATTGGCGA 59.390 45.455 0.00 0.00 0.00 5.54
3854 6936 3.545426 GGCGACTTTGTATTATTGGCGAC 60.545 47.826 0.00 0.00 0.00 5.19
3907 6990 1.067565 TCTCTCGGATATTCATGCGGC 60.068 52.381 0.00 0.00 45.16 6.53
4047 7131 4.608269 TGTGCCAATTATTTCCTGATGGA 58.392 39.130 0.00 0.00 41.36 3.41
4105 7189 2.027561 TCCAACCACCGTATTTCTCCAG 60.028 50.000 0.00 0.00 0.00 3.86
4108 7192 0.909623 CCACCGTATTTCTCCAGGGT 59.090 55.000 0.00 0.00 33.29 4.34
4114 7198 2.354704 CGTATTTCTCCAGGGTTCTGCA 60.355 50.000 0.00 0.00 39.61 4.41
4123 7209 1.078426 GGGTTCTGCAGCCATACGT 60.078 57.895 9.47 0.00 43.39 3.57
4138 7224 4.151512 GCCATACGTTTTTGGGAAATGTTG 59.848 41.667 12.18 2.16 33.40 3.33
4148 7254 1.405933 GGGAAATGTTGGCCTGAATGC 60.406 52.381 3.32 0.00 0.00 3.56
4150 7256 1.202114 GAAATGTTGGCCTGAATGCGA 59.798 47.619 3.32 0.00 0.00 5.10
4197 7334 1.401761 AATGCTGTGTGCTGAACCAA 58.598 45.000 0.00 0.00 43.37 3.67
4213 7350 8.637986 TGCTGAACCAAAAAGTTAAACTATGAT 58.362 29.630 0.00 0.00 0.00 2.45
4249 7386 3.254657 AGGAGAAACTCTCGAGTGTGAAG 59.745 47.826 19.97 8.61 44.28 3.02
4265 7402 5.041287 GTGTGAAGAAGCAAAGTAAAACCC 58.959 41.667 0.00 0.00 0.00 4.11
4277 7415 2.304761 AGTAAAACCCCTCGATCTGCAA 59.695 45.455 0.00 0.00 0.00 4.08
4294 7437 0.725784 CAATGTCAACGCGGTTCTGC 60.726 55.000 12.47 0.00 0.00 4.26
4334 7477 4.143740 CTCAGAGGGAACTGGGCT 57.856 61.111 0.00 0.00 44.43 5.19
4378 7521 0.251033 AAACCCCAAAGTCTACGGCC 60.251 55.000 0.00 0.00 0.00 6.13
4395 7538 3.950395 ACGGCCCGGAGTATATATTACTC 59.050 47.826 8.57 12.79 42.28 2.59
4415 7558 4.710375 ACTCCGTACTATGTGAATTCCTGT 59.290 41.667 2.27 0.00 0.00 4.00
4442 7589 3.057596 CACCAGCGAACAATACCAAATGT 60.058 43.478 0.00 0.00 0.00 2.71
4453 7610 5.470098 ACAATACCAAATGTCTGACAGTGTC 59.530 40.000 16.68 16.68 0.00 3.67
4456 7613 4.067896 ACCAAATGTCTGACAGTGTCATC 58.932 43.478 25.65 20.34 41.94 2.92
4555 9877 2.480224 TATCGGATTCGTCAACGGAC 57.520 50.000 2.31 0.00 40.77 4.79
4568 9890 0.036294 AACGGACCTTAGCAGCTTCC 60.036 55.000 0.00 0.00 0.00 3.46
4607 9929 3.162735 CAGCTGTGCTACGTGCTG 58.837 61.111 5.25 8.65 43.37 4.41
4608 9930 1.373371 CAGCTGTGCTACGTGCTGA 60.373 57.895 15.96 0.82 44.90 4.26
4609 9931 0.738762 CAGCTGTGCTACGTGCTGAT 60.739 55.000 15.96 1.67 44.90 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.050377 ACAGACTGAAGAAAATTGAACTGAGA 58.950 34.615 10.08 0.00 0.00 3.27
1 2 7.256756 ACAGACTGAAGAAAATTGAACTGAG 57.743 36.000 10.08 0.00 0.00 3.35
3 4 7.756722 ACAAACAGACTGAAGAAAATTGAACTG 59.243 33.333 10.08 0.00 0.00 3.16
4 5 7.830739 ACAAACAGACTGAAGAAAATTGAACT 58.169 30.769 10.08 0.00 0.00 3.01
5 6 7.970614 AGACAAACAGACTGAAGAAAATTGAAC 59.029 33.333 10.08 3.87 0.00 3.18
6 7 8.055279 AGACAAACAGACTGAAGAAAATTGAA 57.945 30.769 10.08 0.00 0.00 2.69
7 8 7.630242 AGACAAACAGACTGAAGAAAATTGA 57.370 32.000 10.08 0.00 0.00 2.57
8 9 8.693542 AAAGACAAACAGACTGAAGAAAATTG 57.306 30.769 10.08 5.28 0.00 2.32
11 12 9.396022 AGATAAAGACAAACAGACTGAAGAAAA 57.604 29.630 10.08 0.00 0.00 2.29
37 38 9.409312 CAGAAAGCATAAACACATGATAAACAA 57.591 29.630 0.00 0.00 0.00 2.83
46 47 5.351465 CGGAGTACAGAAAGCATAAACACAT 59.649 40.000 0.00 0.00 0.00 3.21
55 56 2.869801 CAAACACGGAGTACAGAAAGCA 59.130 45.455 0.00 0.00 41.61 3.91
73 74 8.138074 TGGTTATCACGATGAAATGAAAACAAA 58.862 29.630 0.00 0.00 0.00 2.83
90 91 9.801873 ATAACAAAACATAAGCATGGTTATCAC 57.198 29.630 23.82 0.00 41.34 3.06
110 111 7.744087 AAGTACTCAGATGCAAACATAACAA 57.256 32.000 0.00 0.00 36.35 2.83
190 2792 8.695456 AGGTGAATAGGCGATTTTTATGAATTT 58.305 29.630 0.00 0.00 0.00 1.82
216 2818 6.363065 AGTGTGTTATATCGACTAGAGGGAA 58.637 40.000 0.00 0.00 0.00 3.97
217 2819 5.938279 AGTGTGTTATATCGACTAGAGGGA 58.062 41.667 0.00 0.00 0.00 4.20
236 2838 5.105756 GCAAATTAGCCCTATGTGAAAGTGT 60.106 40.000 0.00 0.00 0.00 3.55
245 2847 2.808543 GTCCGAGCAAATTAGCCCTATG 59.191 50.000 0.00 0.00 34.23 2.23
246 2848 2.224548 GGTCCGAGCAAATTAGCCCTAT 60.225 50.000 0.00 0.00 34.23 2.57
247 2849 1.140252 GGTCCGAGCAAATTAGCCCTA 59.860 52.381 0.00 0.00 34.23 3.53
248 2850 0.107165 GGTCCGAGCAAATTAGCCCT 60.107 55.000 0.00 0.00 34.23 5.19
249 2851 0.393808 TGGTCCGAGCAAATTAGCCC 60.394 55.000 0.00 0.00 34.23 5.19
250 2852 1.459450 TTGGTCCGAGCAAATTAGCC 58.541 50.000 10.56 0.00 32.03 3.93
329 2931 1.291906 CGGGGCATTTTGGTTGGAC 59.708 57.895 0.00 0.00 0.00 4.02
477 3085 4.998033 TCTGGTTTGATGTACGCATAAACA 59.002 37.500 13.27 8.13 35.07 2.83
489 3097 4.701651 TGAAAGGTGCTATCTGGTTTGATG 59.298 41.667 0.00 0.00 0.00 3.07
491 3099 4.365514 TGAAAGGTGCTATCTGGTTTGA 57.634 40.909 0.00 0.00 0.00 2.69
508 3117 5.878116 ACTTTCGACGGATGGAATATTGAAA 59.122 36.000 0.00 0.00 0.00 2.69
644 3257 7.850935 AAAATACTCCCTCCGTCTCATAATA 57.149 36.000 0.00 0.00 0.00 0.98
651 3264 4.382793 GCTGTAAAAATACTCCCTCCGTCT 60.383 45.833 0.00 0.00 0.00 4.18
654 3267 3.621715 GTGCTGTAAAAATACTCCCTCCG 59.378 47.826 0.00 0.00 0.00 4.63
656 3269 4.585879 TGGTGCTGTAAAAATACTCCCTC 58.414 43.478 0.00 0.00 0.00 4.30
657 3270 4.650972 TGGTGCTGTAAAAATACTCCCT 57.349 40.909 0.00 0.00 0.00 4.20
658 3271 4.947388 TGATGGTGCTGTAAAAATACTCCC 59.053 41.667 0.00 0.00 0.00 4.30
659 3272 6.322491 GTTGATGGTGCTGTAAAAATACTCC 58.678 40.000 0.00 0.00 0.00 3.85
660 3273 6.151144 AGGTTGATGGTGCTGTAAAAATACTC 59.849 38.462 0.00 0.00 0.00 2.59
661 3274 6.010219 AGGTTGATGGTGCTGTAAAAATACT 58.990 36.000 0.00 0.00 0.00 2.12
662 3275 6.267496 AGGTTGATGGTGCTGTAAAAATAC 57.733 37.500 0.00 0.00 0.00 1.89
663 3276 6.909550 AAGGTTGATGGTGCTGTAAAAATA 57.090 33.333 0.00 0.00 0.00 1.40
817 3438 2.668550 GGACAAGGAAAGCGGCGT 60.669 61.111 9.37 0.00 0.00 5.68
818 3439 3.431725 GGGACAAGGAAAGCGGCG 61.432 66.667 0.51 0.51 0.00 6.46
819 3440 3.431725 CGGGACAAGGAAAGCGGC 61.432 66.667 0.00 0.00 0.00 6.53
894 3516 4.715130 TGGAGGGTCGACAGGGGG 62.715 72.222 18.91 0.00 0.00 5.40
899 3521 2.203640 AGCTGTGGAGGGTCGACA 60.204 61.111 18.91 0.00 34.03 4.35
900 3522 2.574399 GAGCTGTGGAGGGTCGAC 59.426 66.667 7.13 7.13 0.00 4.20
904 3526 2.060980 GGATCGAGCTGTGGAGGGT 61.061 63.158 0.00 0.00 0.00 4.34
956 3988 3.868985 GATAAGGCCGGGCGGGAA 61.869 66.667 23.81 9.74 38.47 3.97
965 3997 1.968540 GGCGATGCAGGATAAGGCC 60.969 63.158 0.00 0.00 0.00 5.19
1108 4140 0.712979 ATGTGGTGAGAGGAGGAGGA 59.287 55.000 0.00 0.00 0.00 3.71
1167 4199 0.847373 TCTACTCGATCCTCCCAGCT 59.153 55.000 0.00 0.00 0.00 4.24
1168 4200 1.816224 GATCTACTCGATCCTCCCAGC 59.184 57.143 0.00 0.00 42.24 4.85
1169 4201 2.817258 GTGATCTACTCGATCCTCCCAG 59.183 54.545 0.00 0.00 46.52 4.45
1207 4240 0.615850 ACTCAACCTTCTAGCTGGGC 59.384 55.000 0.00 0.00 0.00 5.36
1220 4253 5.462405 ACACTACGAAATCAGAGACTCAAC 58.538 41.667 5.02 0.00 0.00 3.18
1228 4261 8.687242 AGAATCTATCAACACTACGAAATCAGA 58.313 33.333 0.00 0.00 0.00 3.27
1254 4290 2.748798 GCTCAGTGATACCGTCCTCCTA 60.749 54.545 0.00 0.00 0.00 2.94
1305 4341 2.356535 GGAACGGAGGGAGTAGTACAGA 60.357 54.545 2.52 0.00 0.00 3.41
1306 4342 2.022934 GGAACGGAGGGAGTAGTACAG 58.977 57.143 2.52 0.00 0.00 2.74
1307 4343 1.355381 TGGAACGGAGGGAGTAGTACA 59.645 52.381 2.52 0.00 0.00 2.90
1308 4344 2.134789 TGGAACGGAGGGAGTAGTAC 57.865 55.000 0.00 0.00 0.00 2.73
1309 4345 2.905415 TTGGAACGGAGGGAGTAGTA 57.095 50.000 0.00 0.00 0.00 1.82
1310 4346 2.019807 TTTGGAACGGAGGGAGTAGT 57.980 50.000 0.00 0.00 0.00 2.73
1312 4348 4.355549 TCTATTTTGGAACGGAGGGAGTA 58.644 43.478 0.00 0.00 0.00 2.59
1313 4349 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
1314 4350 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
1315 4351 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
1316 4352 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
1317 4353 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
1318 4354 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
1319 4355 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
1320 4356 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
1321 4357 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
1322 4358 8.352942 ACAAAGTTGAGTCATCTATTTTGGAAC 58.647 33.333 14.35 0.00 40.00 3.62
1323 4359 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
1324 4360 8.999431 GTACAAAGTTGAGTCATCTATTTTGGA 58.001 33.333 14.35 6.88 40.00 3.53
1325 4361 9.003658 AGTACAAAGTTGAGTCATCTATTTTGG 57.996 33.333 14.35 0.00 40.00 3.28
1332 4368 9.003658 CCAAAATAGTACAAAGTTGAGTCATCT 57.996 33.333 0.00 0.00 0.00 2.90
1333 4369 8.999431 TCCAAAATAGTACAAAGTTGAGTCATC 58.001 33.333 0.00 0.00 0.00 2.92
1334 4370 8.918202 TCCAAAATAGTACAAAGTTGAGTCAT 57.082 30.769 0.00 0.00 0.00 3.06
1335 4371 8.617809 GTTCCAAAATAGTACAAAGTTGAGTCA 58.382 33.333 0.00 0.00 0.00 3.41
1336 4372 7.797123 CGTTCCAAAATAGTACAAAGTTGAGTC 59.203 37.037 0.00 0.00 0.00 3.36
1337 4373 7.255001 CCGTTCCAAAATAGTACAAAGTTGAGT 60.255 37.037 0.00 0.00 0.00 3.41
1338 4374 7.041644 TCCGTTCCAAAATAGTACAAAGTTGAG 60.042 37.037 0.00 0.00 0.00 3.02
1339 4375 6.766944 TCCGTTCCAAAATAGTACAAAGTTGA 59.233 34.615 0.00 0.00 0.00 3.18
1340 4376 6.961576 TCCGTTCCAAAATAGTACAAAGTTG 58.038 36.000 0.00 0.00 0.00 3.16
1341 4377 6.206048 CCTCCGTTCCAAAATAGTACAAAGTT 59.794 38.462 0.00 0.00 0.00 2.66
1342 4378 5.704053 CCTCCGTTCCAAAATAGTACAAAGT 59.296 40.000 0.00 0.00 0.00 2.66
1343 4379 5.123344 CCCTCCGTTCCAAAATAGTACAAAG 59.877 44.000 0.00 0.00 0.00 2.77
1344 4380 5.005094 CCCTCCGTTCCAAAATAGTACAAA 58.995 41.667 0.00 0.00 0.00 2.83
1345 4381 4.286549 TCCCTCCGTTCCAAAATAGTACAA 59.713 41.667 0.00 0.00 0.00 2.41
1346 4382 3.839490 TCCCTCCGTTCCAAAATAGTACA 59.161 43.478 0.00 0.00 0.00 2.90
1347 4383 4.081254 ACTCCCTCCGTTCCAAAATAGTAC 60.081 45.833 0.00 0.00 0.00 2.73
1348 4384 4.098894 ACTCCCTCCGTTCCAAAATAGTA 58.901 43.478 0.00 0.00 0.00 1.82
1349 4385 2.910977 ACTCCCTCCGTTCCAAAATAGT 59.089 45.455 0.00 0.00 0.00 2.12
1350 4386 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
1351 4387 4.355549 TCTACTCCCTCCGTTCCAAAATA 58.644 43.478 0.00 0.00 0.00 1.40
1352 4388 3.178865 TCTACTCCCTCCGTTCCAAAAT 58.821 45.455 0.00 0.00 0.00 1.82
1353 4389 2.612000 TCTACTCCCTCCGTTCCAAAA 58.388 47.619 0.00 0.00 0.00 2.44
1354 4390 2.314071 TCTACTCCCTCCGTTCCAAA 57.686 50.000 0.00 0.00 0.00 3.28
1355 4391 2.544844 ATCTACTCCCTCCGTTCCAA 57.455 50.000 0.00 0.00 0.00 3.53
1356 4392 2.385803 GAATCTACTCCCTCCGTTCCA 58.614 52.381 0.00 0.00 0.00 3.53
1357 4393 1.337387 CGAATCTACTCCCTCCGTTCC 59.663 57.143 0.00 0.00 0.00 3.62
1358 4394 2.295885 TCGAATCTACTCCCTCCGTTC 58.704 52.381 0.00 0.00 0.00 3.95
1359 4395 2.431954 TCGAATCTACTCCCTCCGTT 57.568 50.000 0.00 0.00 0.00 4.44
1360 4396 2.431954 TTCGAATCTACTCCCTCCGT 57.568 50.000 0.00 0.00 0.00 4.69
1361 4397 3.440872 CCTATTCGAATCTACTCCCTCCG 59.559 52.174 15.25 0.00 0.00 4.63
1362 4398 3.193903 GCCTATTCGAATCTACTCCCTCC 59.806 52.174 15.25 0.00 0.00 4.30
1363 4399 4.082463 CAGCCTATTCGAATCTACTCCCTC 60.082 50.000 15.25 0.00 0.00 4.30
1364 4400 3.829601 CAGCCTATTCGAATCTACTCCCT 59.170 47.826 15.25 0.21 0.00 4.20
1365 4401 3.056465 CCAGCCTATTCGAATCTACTCCC 60.056 52.174 15.25 0.00 0.00 4.30
1366 4402 3.574826 ACCAGCCTATTCGAATCTACTCC 59.425 47.826 15.25 0.00 0.00 3.85
1367 4403 4.551388 CACCAGCCTATTCGAATCTACTC 58.449 47.826 15.25 1.12 0.00 2.59
1368 4404 3.322254 CCACCAGCCTATTCGAATCTACT 59.678 47.826 15.25 7.38 0.00 2.57
1369 4405 3.069729 ACCACCAGCCTATTCGAATCTAC 59.930 47.826 15.25 5.04 0.00 2.59
1370 4406 3.305720 ACCACCAGCCTATTCGAATCTA 58.694 45.455 15.25 0.00 0.00 1.98
1379 4415 1.004745 CCTGAACAACCACCAGCCTAT 59.995 52.381 0.00 0.00 0.00 2.57
1383 4419 0.751643 ACACCTGAACAACCACCAGC 60.752 55.000 0.00 0.00 0.00 4.85
1392 4428 5.392703 CGTGCTCTTATACTACACCTGAACA 60.393 44.000 0.00 0.00 0.00 3.18
1403 4439 3.802948 CACTTCCCGTGCTCTTATACT 57.197 47.619 0.00 0.00 36.72 2.12
1413 4449 0.310854 GGAAAACAGCACTTCCCGTG 59.689 55.000 0.00 0.00 46.58 4.94
1415 4451 1.318576 AAGGAAAACAGCACTTCCCG 58.681 50.000 0.00 0.00 41.86 5.14
1424 4460 7.114811 CACCAATTCGTATGAAAAGGAAAACAG 59.885 37.037 19.86 4.79 37.71 3.16
1427 4463 7.045126 ACACCAATTCGTATGAAAAGGAAAA 57.955 32.000 19.86 0.00 37.71 2.29
1478 4515 2.561037 GCTCCTAGCCTCCTCGAGC 61.561 68.421 6.99 0.00 36.82 5.03
1484 4521 1.137282 GTGTAGTTGCTCCTAGCCTCC 59.863 57.143 0.00 0.00 41.51 4.30
1487 4524 0.815734 TCGTGTAGTTGCTCCTAGCC 59.184 55.000 0.00 0.00 41.51 3.93
1488 4525 1.473278 AGTCGTGTAGTTGCTCCTAGC 59.527 52.381 0.00 0.00 42.82 3.42
1499 4536 1.611977 TCCCACACTGAAGTCGTGTAG 59.388 52.381 8.05 3.17 43.26 2.74
1504 4541 1.078759 GCGATCCCACACTGAAGTCG 61.079 60.000 0.00 0.00 0.00 4.18
1539 4576 7.929245 TCTGTACATGCTTTGTAACTGAAAGTA 59.071 33.333 0.00 0.00 43.27 2.24
1628 4665 7.305474 CACCACCTACATCAAAAGTGTTATTC 58.695 38.462 0.00 0.00 0.00 1.75
1631 4668 4.517453 GCACCACCTACATCAAAAGTGTTA 59.483 41.667 0.00 0.00 0.00 2.41
1673 4710 4.824166 GCAAGCTGACATGCCGCG 62.824 66.667 0.00 0.00 34.44 6.46
1712 4749 3.950395 TGTCATGGTGTGATGTGAAAACA 59.050 39.130 0.00 0.00 39.48 2.83
2024 5099 6.095300 CACACATCATAAGCATTCCTTACCAA 59.905 38.462 0.00 0.00 38.77 3.67
2032 5107 8.830580 ACTTGTATACACACATCATAAGCATTC 58.169 33.333 4.68 0.00 33.30 2.67
2046 5121 9.787435 AGAAGTCCAATAAAACTTGTATACACA 57.213 29.630 4.68 0.00 35.90 3.72
2207 5282 5.715439 ACCAATATGACATCAAAGGAGGA 57.285 39.130 0.00 0.00 0.00 3.71
2257 5332 7.451566 ACCTTTGATGATGCCTTTAGTTTAAGT 59.548 33.333 0.00 0.00 0.00 2.24
2308 5383 2.082231 AGCTGCAATTAGAGCACACTG 58.918 47.619 1.02 0.00 37.02 3.66
2647 5722 4.639310 CCTCTAGCATGAAGACTGCAAAAT 59.361 41.667 0.00 0.00 42.15 1.82
2653 5728 4.037327 TCGATTCCTCTAGCATGAAGACTG 59.963 45.833 0.00 0.00 0.00 3.51
2654 5729 4.211125 TCGATTCCTCTAGCATGAAGACT 58.789 43.478 0.00 0.00 0.00 3.24
2787 5862 9.988815 AGACAGCTATTGTATACTAAAATCTGG 57.011 33.333 4.17 0.00 41.05 3.86
2826 5903 3.864921 GCTTCACTACACCAAACGAGGAT 60.865 47.826 0.00 0.00 0.00 3.24
2984 6062 2.229792 CCACTGTTAAGCTTGCTTCCA 58.770 47.619 9.86 8.87 0.00 3.53
3022 6100 8.885346 TGTGAATAAAAGGGGGAAATAACAAAT 58.115 29.630 0.00 0.00 0.00 2.32
3023 6101 8.263854 TGTGAATAAAAGGGGGAAATAACAAA 57.736 30.769 0.00 0.00 0.00 2.83
3024 6102 7.038658 CCTGTGAATAAAAGGGGGAAATAACAA 60.039 37.037 0.00 0.00 0.00 2.83
3108 6187 6.144854 TCAGCATGAGAAATGAAAGAAAACG 58.855 36.000 0.00 0.00 42.56 3.60
3229 6308 3.811497 CAGCTGAAGAACAAGATGTCACA 59.189 43.478 8.42 0.00 0.00 3.58
3248 6327 2.545946 ACAGAAGCTCGTTTCTTTCAGC 59.454 45.455 0.00 0.00 35.28 4.26
3466 6545 0.884704 CCACTGTTTCCACTGGACCG 60.885 60.000 0.00 0.00 28.83 4.79
3526 6605 3.645212 TCACCATGGCTTTGGAAAATTCA 59.355 39.130 13.04 0.00 39.25 2.57
3545 6624 1.069227 GTGATCGCCCACAAACTTCAC 60.069 52.381 0.00 0.00 37.04 3.18
3557 6636 0.169230 ATCGCTAGATCGTGATCGCC 59.831 55.000 0.00 0.00 42.48 5.54
3575 6654 1.454479 CTTGCTTGCCCATCCGGAT 60.454 57.895 12.38 12.38 0.00 4.18
3691 6770 2.338620 CTGCCGACACCGAACTCA 59.661 61.111 0.00 0.00 38.22 3.41
3838 6920 6.597672 AGTTCATCAGTCGCCAATAATACAAA 59.402 34.615 0.00 0.00 0.00 2.83
3842 6924 5.912892 TCAGTTCATCAGTCGCCAATAATA 58.087 37.500 0.00 0.00 0.00 0.98
3852 6934 5.288232 CGACAGAGAAATCAGTTCATCAGTC 59.712 44.000 0.00 0.00 38.86 3.51
3853 6935 5.047731 TCGACAGAGAAATCAGTTCATCAGT 60.048 40.000 0.00 0.00 38.86 3.41
3854 6936 5.405797 TCGACAGAGAAATCAGTTCATCAG 58.594 41.667 0.00 0.00 38.86 2.90
3907 6990 6.405842 GGTCAAACCCTTATTTATGAGCTTGG 60.406 42.308 0.00 0.00 33.73 3.61
3942 7025 1.344438 AGAACTGATGCCGACTGTTCA 59.656 47.619 18.53 0.00 43.49 3.18
4047 7131 2.560981 CACCGAATTAACAAAAGGGGCT 59.439 45.455 0.00 0.00 0.00 5.19
4105 7189 0.676782 AACGTATGGCTGCAGAACCC 60.677 55.000 20.43 10.15 0.00 4.11
4108 7192 2.030363 CCAAAAACGTATGGCTGCAGAA 60.030 45.455 20.43 4.69 0.00 3.02
4114 7198 3.576550 ACATTTCCCAAAAACGTATGGCT 59.423 39.130 8.94 0.00 35.28 4.75
4123 7209 2.774234 TCAGGCCAACATTTCCCAAAAA 59.226 40.909 5.01 0.00 0.00 1.94
4138 7224 1.701704 CTTGTTTTCGCATTCAGGCC 58.298 50.000 0.00 0.00 0.00 5.19
4148 7254 4.797471 TGGATCAGATTTGCTTGTTTTCG 58.203 39.130 0.00 0.00 0.00 3.46
4150 7256 5.069516 ACACTGGATCAGATTTGCTTGTTTT 59.930 36.000 1.59 0.00 35.18 2.43
4161 7267 4.398358 CAGCATTTTGACACTGGATCAGAT 59.602 41.667 1.59 0.00 35.18 2.90
4162 7268 3.754850 CAGCATTTTGACACTGGATCAGA 59.245 43.478 1.59 0.00 35.18 3.27
4197 7334 8.706322 AAGACACCCATCATAGTTTAACTTTT 57.294 30.769 1.94 0.00 0.00 2.27
4213 7350 0.404426 TCTCCTCGAGAAGACACCCA 59.596 55.000 15.71 0.00 35.59 4.51
4249 7386 3.143728 TCGAGGGGTTTTACTTTGCTTC 58.856 45.455 0.00 0.00 0.00 3.86
4265 7402 1.325640 CGTTGACATTGCAGATCGAGG 59.674 52.381 0.00 0.00 0.00 4.63
4277 7415 2.325082 GGCAGAACCGCGTTGACAT 61.325 57.895 4.92 0.00 0.00 3.06
4333 7476 4.338118 TCCTACAGTTTTTGACCTTGCAAG 59.662 41.667 19.93 19.93 0.00 4.01
4334 7477 4.274147 TCCTACAGTTTTTGACCTTGCAA 58.726 39.130 0.00 0.00 0.00 4.08
4362 7505 2.271173 GGGCCGTAGACTTTGGGG 59.729 66.667 0.00 0.00 0.00 4.96
4395 7538 6.570692 AGTTACAGGAATTCACATAGTACGG 58.429 40.000 7.93 0.00 0.00 4.02
4415 7558 3.007074 TGGTATTGTTCGCTGGTGAGTTA 59.993 43.478 0.00 0.00 0.00 2.24
4442 7589 8.575649 TTTACTATACTGATGACACTGTCAGA 57.424 34.615 16.80 5.89 46.04 3.27
4511 9833 2.157834 AACAAATGTACGCGTCCTCA 57.842 45.000 18.63 14.70 0.00 3.86
4555 9877 2.996249 TCATCAGGAAGCTGCTAAGG 57.004 50.000 0.90 0.00 0.00 2.69
4604 9926 1.588139 GCCGCAATCAGCAATCAGC 60.588 57.895 0.00 0.00 46.13 4.26
4605 9927 1.298116 CGCCGCAATCAGCAATCAG 60.298 57.895 0.00 0.00 46.13 2.90
4606 9928 1.585267 AACGCCGCAATCAGCAATCA 61.585 50.000 0.00 0.00 46.13 2.57
4607 9929 0.456653 AAACGCCGCAATCAGCAATC 60.457 50.000 0.00 0.00 46.13 2.67
4608 9930 0.456653 GAAACGCCGCAATCAGCAAT 60.457 50.000 0.00 0.00 46.13 3.56
4609 9931 1.081509 GAAACGCCGCAATCAGCAA 60.082 52.632 0.00 0.00 46.13 3.91
4646 9968 2.360726 GGTTTGACCGCCCCGATT 60.361 61.111 0.00 0.00 0.00 3.34


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

AutoCloner maintained by Alex Coulton.