Multiple sequence alignment - TraesCS4A01G212300

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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 TraesCS4A01G212300 chr4A 100.000 4103 0 0 1 4103 507958947 507963049 0.000000e+00 7577.0
1 TraesCS4A01G212300 chr4A 90.741 54 5 0 467 520 625108145 625108198 5.690000e-09 73.1
2 TraesCS4A01G212300 chr4B 90.245 2778 160 28 609 3333 109788256 109790975 0.000000e+00 3526.0
3 TraesCS4A01G212300 chr4B 91.089 101 7 2 245 344 342857167 342857068 7.150000e-28 135.0
4 TraesCS4A01G212300 chr4D 92.478 1675 86 13 330 1983 78368578 78366923 0.000000e+00 2359.0
5 TraesCS4A01G212300 chr4D 90.111 900 44 14 1912 2773 78366915 78366023 0.000000e+00 1127.0
6 TraesCS4A01G212300 chr4D 92.110 583 40 5 2754 3333 78365762 78365183 0.000000e+00 817.0
7 TraesCS4A01G212300 chr4D 92.179 179 13 1 1 179 78368847 78368670 6.810000e-63 252.0
8 TraesCS4A01G212300 chr4D 93.407 91 4 2 251 340 501331778 501331689 2.570000e-27 134.0
9 TraesCS4A01G212300 chr4D 88.421 95 10 1 161 254 78368666 78368572 3.350000e-21 113.0
10 TraesCS4A01G212300 chr6D 94.611 668 32 4 3438 4103 211712468 211713133 0.000000e+00 1031.0
11 TraesCS4A01G212300 chr6D 88.991 109 12 0 1078 1186 33253267 33253159 7.150000e-28 135.0
12 TraesCS4A01G212300 chr6D 85.385 130 19 0 1057 1186 33305551 33305422 7.150000e-28 135.0
13 TraesCS4A01G212300 chr6D 80.925 173 28 4 2101 2272 24450141 24449973 9.250000e-27 132.0
14 TraesCS4A01G212300 chr6D 80.571 175 27 4 2101 2273 24881069 24881238 1.200000e-25 128.0
15 TraesCS4A01G212300 chr6D 79.762 168 25 5 2105 2269 24670293 24670132 3.350000e-21 113.0
16 TraesCS4A01G212300 chr6D 91.935 62 5 0 459 520 461540164 461540225 2.030000e-13 87.9
17 TraesCS4A01G212300 chr3A 94.946 653 29 2 3454 4103 480160748 480160097 0.000000e+00 1020.0
18 TraesCS4A01G212300 chr3A 94.487 653 31 3 3454 4103 309612227 309611577 0.000000e+00 1002.0
19 TraesCS4A01G212300 chr3A 94.316 651 35 2 3453 4103 193484065 193483417 0.000000e+00 996.0
20 TraesCS4A01G212300 chr2A 94.923 650 31 1 3454 4103 637911726 637912373 0.000000e+00 1016.0
21 TraesCS4A01G212300 chr2A 94.624 651 34 1 3453 4103 11720360 11721009 0.000000e+00 1007.0
22 TraesCS4A01G212300 chr2A 92.391 92 5 2 253 343 672113356 672113266 3.330000e-26 130.0
23 TraesCS4A01G212300 chr1A 94.462 650 34 2 3454 4103 517940426 517941073 0.000000e+00 1000.0
24 TraesCS4A01G212300 chr1A 90.722 97 7 2 253 348 571275539 571275444 1.200000e-25 128.0
25 TraesCS4A01G212300 chr5A 94.343 654 32 3 3454 4103 631749866 631750518 0.000000e+00 998.0
26 TraesCS4A01G212300 chr7A 94.207 656 33 2 3451 4103 267382177 267382830 0.000000e+00 996.0
27 TraesCS4A01G212300 chr2B 92.632 95 5 2 250 342 709839414 709839320 7.150000e-28 135.0
28 TraesCS4A01G212300 chr2B 92.308 91 6 1 250 339 696361648 696361738 1.200000e-25 128.0
29 TraesCS4A01G212300 chr2B 89.873 79 7 1 445 523 798537488 798537565 2.610000e-17 100.0
30 TraesCS4A01G212300 chr6B 80.925 173 28 4 2101 2272 39676173 39676005 9.250000e-27 132.0
31 TraesCS4A01G212300 chr6B 91.398 93 6 2 253 344 480382697 480382606 4.310000e-25 126.0
32 TraesCS4A01G212300 chr6B 79.070 172 27 5 2101 2269 40590559 40590724 4.340000e-20 110.0
33 TraesCS4A01G212300 chr3D 92.308 91 6 1 252 341 435299689 435299779 1.200000e-25 128.0
34 TraesCS4A01G212300 chr6A 80.000 170 29 4 2101 2269 23427367 23427532 2.000000e-23 121.0
35 TraesCS4A01G212300 chr5B 91.011 89 6 2 250 336 625957444 625957532 7.200000e-23 119.0
36 TraesCS4A01G212300 chr2D 89.412 85 9 0 442 526 579903834 579903750 1.560000e-19 108.0


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 TraesCS4A01G212300 chr4A 507958947 507963049 4102 False 7577.0 7577 100.0000 1 4103 1 chr4A.!!$F1 4102
1 TraesCS4A01G212300 chr4B 109788256 109790975 2719 False 3526.0 3526 90.2450 609 3333 1 chr4B.!!$F1 2724
2 TraesCS4A01G212300 chr4D 78365183 78368847 3664 True 933.6 2359 91.0598 1 3333 5 chr4D.!!$R2 3332
3 TraesCS4A01G212300 chr6D 211712468 211713133 665 False 1031.0 1031 94.6110 3438 4103 1 chr6D.!!$F2 665
4 TraesCS4A01G212300 chr3A 480160097 480160748 651 True 1020.0 1020 94.9460 3454 4103 1 chr3A.!!$R3 649
5 TraesCS4A01G212300 chr3A 309611577 309612227 650 True 1002.0 1002 94.4870 3454 4103 1 chr3A.!!$R2 649
6 TraesCS4A01G212300 chr3A 193483417 193484065 648 True 996.0 996 94.3160 3453 4103 1 chr3A.!!$R1 650
7 TraesCS4A01G212300 chr2A 637911726 637912373 647 False 1016.0 1016 94.9230 3454 4103 1 chr2A.!!$F2 649
8 TraesCS4A01G212300 chr2A 11720360 11721009 649 False 1007.0 1007 94.6240 3453 4103 1 chr2A.!!$F1 650
9 TraesCS4A01G212300 chr1A 517940426 517941073 647 False 1000.0 1000 94.4620 3454 4103 1 chr1A.!!$F1 649
10 TraesCS4A01G212300 chr5A 631749866 631750518 652 False 998.0 998 94.3430 3454 4103 1 chr5A.!!$F1 649
11 TraesCS4A01G212300 chr7A 267382177 267382830 653 False 996.0 996 94.2070 3451 4103 1 chr7A.!!$F1 652

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
949 978 0.032815 TTCCGTGATCGTGTCTTGCA 59.967 50.0 0.0 0.0 35.01 4.08 F
961 990 0.600255 GTCTTGCACAGCTGTACGGT 60.600 55.0 21.2 0.0 0.00 4.83 F
2203 2326 0.253044 ATGAATACTGGTGCGTGCCT 59.747 50.0 0.0 0.0 0.00 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1812 1856 1.476085 AGAAGCACCGAGTCATGAGAG 59.524 52.381 0.0 0.0 0.0 3.20 R
2554 2677 1.821216 AATGTAGAAAGCGTGGGGTG 58.179 50.000 0.0 0.0 0.0 4.61 R
3347 3785 0.035056 AAATCAGTCAAGGGAGGGCG 60.035 55.000 0.0 0.0 0.0 6.13 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
37 38 7.878127 CCCACAGGTAATCTAAAGGTACATATG 59.122 40.741 0.00 0.00 0.00 1.78
103 104 0.690762 ACGCCCAAGGTCATAACTGT 59.309 50.000 0.00 0.00 0.00 3.55
133 134 4.571984 TCTGTTCAATGCTAATGTGATCCG 59.428 41.667 0.00 0.00 0.00 4.18
134 135 4.260985 TGTTCAATGCTAATGTGATCCGT 58.739 39.130 0.00 0.00 0.00 4.69
224 247 7.783090 TGATTTCAACTATCTTGAGATGCTC 57.217 36.000 3.79 0.00 36.05 4.26
229 253 6.673106 TCAACTATCTTGAGATGCTCGATAC 58.327 40.000 3.79 0.00 36.05 2.24
236 260 4.944619 TGAGATGCTCGATACCAAGAAT 57.055 40.909 0.00 0.00 32.35 2.40
237 261 5.282055 TGAGATGCTCGATACCAAGAATT 57.718 39.130 0.00 0.00 32.35 2.17
241 265 3.937814 TGCTCGATACCAAGAATTGTGT 58.062 40.909 0.00 0.00 46.99 3.72
252 276 5.982890 CAAGAATTGTGTCCTTGGGTTAT 57.017 39.130 0.00 0.00 42.34 1.89
254 278 6.852664 CAAGAATTGTGTCCTTGGGTTATAC 58.147 40.000 0.00 0.00 42.34 1.47
255 279 6.388619 AGAATTGTGTCCTTGGGTTATACT 57.611 37.500 0.00 0.00 0.00 2.12
256 280 6.790319 AGAATTGTGTCCTTGGGTTATACTT 58.210 36.000 0.00 0.00 0.00 2.24
257 281 6.884836 AGAATTGTGTCCTTGGGTTATACTTC 59.115 38.462 0.00 0.00 0.00 3.01
258 282 4.563140 TGTGTCCTTGGGTTATACTTCC 57.437 45.455 0.00 0.00 0.00 3.46
259 283 4.172807 TGTGTCCTTGGGTTATACTTCCT 58.827 43.478 0.00 0.00 0.00 3.36
260 284 4.224370 TGTGTCCTTGGGTTATACTTCCTC 59.776 45.833 0.00 0.00 0.00 3.71
261 285 3.778629 TGTCCTTGGGTTATACTTCCTCC 59.221 47.826 0.00 0.00 0.00 4.30
262 286 3.036091 TCCTTGGGTTATACTTCCTCCG 58.964 50.000 0.00 0.00 0.00 4.63
263 287 2.770232 CCTTGGGTTATACTTCCTCCGT 59.230 50.000 0.00 0.00 0.00 4.69
264 288 3.181468 CCTTGGGTTATACTTCCTCCGTC 60.181 52.174 0.00 0.00 0.00 4.79
265 289 2.391678 TGGGTTATACTTCCTCCGTCC 58.608 52.381 0.00 0.00 0.00 4.79
266 290 1.690893 GGGTTATACTTCCTCCGTCCC 59.309 57.143 0.00 0.00 0.00 4.46
267 291 2.391678 GGTTATACTTCCTCCGTCCCA 58.608 52.381 0.00 0.00 0.00 4.37
268 292 2.970640 GGTTATACTTCCTCCGTCCCAT 59.029 50.000 0.00 0.00 0.00 4.00
269 293 4.154942 GGTTATACTTCCTCCGTCCCATA 58.845 47.826 0.00 0.00 0.00 2.74
270 294 4.590222 GGTTATACTTCCTCCGTCCCATAA 59.410 45.833 0.00 0.00 0.00 1.90
271 295 5.247792 GGTTATACTTCCTCCGTCCCATAAT 59.752 44.000 0.00 0.00 0.00 1.28
272 296 6.438425 GGTTATACTTCCTCCGTCCCATAATA 59.562 42.308 0.00 0.00 0.00 0.98
273 297 7.125356 GGTTATACTTCCTCCGTCCCATAATAT 59.875 40.741 0.00 0.00 0.00 1.28
274 298 9.193806 GTTATACTTCCTCCGTCCCATAATATA 57.806 37.037 0.00 0.00 0.00 0.86
275 299 9.772605 TTATACTTCCTCCGTCCCATAATATAA 57.227 33.333 0.00 0.00 0.00 0.98
276 300 6.607004 ACTTCCTCCGTCCCATAATATAAG 57.393 41.667 0.00 0.00 0.00 1.73
277 301 6.320518 ACTTCCTCCGTCCCATAATATAAGA 58.679 40.000 0.00 0.00 0.00 2.10
278 302 6.785963 ACTTCCTCCGTCCCATAATATAAGAA 59.214 38.462 0.00 0.00 0.00 2.52
279 303 6.600882 TCCTCCGTCCCATAATATAAGAAC 57.399 41.667 0.00 0.00 0.00 3.01
280 304 5.184479 TCCTCCGTCCCATAATATAAGAACG 59.816 44.000 0.00 0.00 0.00 3.95
281 305 5.047519 CCTCCGTCCCATAATATAAGAACGT 60.048 44.000 0.00 0.00 0.00 3.99
282 306 6.409524 TCCGTCCCATAATATAAGAACGTT 57.590 37.500 0.00 0.00 0.00 3.99
283 307 6.819284 TCCGTCCCATAATATAAGAACGTTT 58.181 36.000 0.46 0.00 0.00 3.60
284 308 7.274447 TCCGTCCCATAATATAAGAACGTTTT 58.726 34.615 0.46 0.00 0.00 2.43
285 309 7.769970 TCCGTCCCATAATATAAGAACGTTTTT 59.230 33.333 9.22 9.22 0.00 1.94
286 310 7.853929 CCGTCCCATAATATAAGAACGTTTTTG 59.146 37.037 13.87 0.00 0.00 2.44
287 311 8.605746 CGTCCCATAATATAAGAACGTTTTTGA 58.394 33.333 13.87 2.81 0.00 2.69
288 312 9.712359 GTCCCATAATATAAGAACGTTTTTGAC 57.288 33.333 13.87 5.89 0.00 3.18
289 313 9.451002 TCCCATAATATAAGAACGTTTTTGACA 57.549 29.630 13.87 0.01 0.00 3.58
290 314 9.498307 CCCATAATATAAGAACGTTTTTGACAC 57.502 33.333 13.87 0.00 0.00 3.67
294 318 8.776680 AATATAAGAACGTTTTTGACACACAC 57.223 30.769 13.87 0.00 0.00 3.82
295 319 4.759516 AAGAACGTTTTTGACACACACT 57.240 36.364 0.46 0.00 0.00 3.55
296 320 5.866335 AAGAACGTTTTTGACACACACTA 57.134 34.783 0.46 0.00 0.00 2.74
297 321 5.464965 AGAACGTTTTTGACACACACTAG 57.535 39.130 0.46 0.00 0.00 2.57
298 322 4.933400 AGAACGTTTTTGACACACACTAGT 59.067 37.500 0.46 0.00 0.00 2.57
329 353 9.763465 AAAACGTTTTTATATTATGTGACGGAG 57.237 29.630 20.26 0.00 33.95 4.63
330 354 7.473027 ACGTTTTTATATTATGTGACGGAGG 57.527 36.000 0.00 0.00 33.95 4.30
331 355 7.043565 ACGTTTTTATATTATGTGACGGAGGT 58.956 34.615 0.00 0.00 33.95 3.85
332 356 8.196771 ACGTTTTTATATTATGTGACGGAGGTA 58.803 33.333 0.00 0.00 33.95 3.08
367 391 4.617959 TGTTTCAGTCACTTACTCTTCCG 58.382 43.478 0.00 0.00 35.76 4.30
368 392 4.340097 TGTTTCAGTCACTTACTCTTCCGA 59.660 41.667 0.00 0.00 35.76 4.55
381 405 9.333724 ACTTACTCTTCCGATAGAAAACAAAAA 57.666 29.630 0.00 0.00 32.88 1.94
503 528 9.250624 ACAAAATTAAGAGTGATAGCGTATCTC 57.749 33.333 6.58 0.00 36.17 2.75
531 556 4.512571 GTGCAGCAAAATGTGATCCTTTTT 59.487 37.500 0.00 0.00 32.35 1.94
572 597 7.276953 AGCGATTGTTGGATTTAAATTTTCG 57.723 32.000 1.43 5.39 0.00 3.46
576 601 7.327275 CGATTGTTGGATTTAAATTTTCGGTGA 59.673 33.333 1.43 0.00 0.00 4.02
594 619 6.050432 TCGGTGATAGGTAAAATGCGTATTT 58.950 36.000 5.58 5.58 38.11 1.40
595 620 6.539464 TCGGTGATAGGTAAAATGCGTATTTT 59.461 34.615 24.30 24.30 45.71 1.82
658 683 1.470494 GCAAACCAAGCTAGCTTCTCC 59.530 52.381 27.08 8.82 33.42 3.71
678 703 0.457851 CTCGAAGGTCCTGCGAATCT 59.542 55.000 22.60 0.00 41.34 2.40
738 763 4.899239 GGTCTCCATGGCGCTCGG 62.899 72.222 6.96 5.57 0.00 4.63
801 826 1.866059 TACGTTGAGCATCGCGTCG 60.866 57.895 5.77 0.00 43.70 5.12
908 933 0.463474 GCTTCCTGCATCTGTCTCCC 60.463 60.000 0.00 0.00 42.31 4.30
946 975 1.359848 GCATTCCGTGATCGTGTCTT 58.640 50.000 0.00 0.00 35.01 3.01
947 976 1.061131 GCATTCCGTGATCGTGTCTTG 59.939 52.381 0.00 0.00 35.01 3.02
948 977 1.061131 CATTCCGTGATCGTGTCTTGC 59.939 52.381 0.00 0.00 35.01 4.01
949 978 0.032815 TTCCGTGATCGTGTCTTGCA 59.967 50.000 0.00 0.00 35.01 4.08
950 979 0.666274 TCCGTGATCGTGTCTTGCAC 60.666 55.000 0.00 0.00 44.36 4.57
961 990 0.600255 GTCTTGCACAGCTGTACGGT 60.600 55.000 21.20 0.00 0.00 4.83
1007 1036 1.413767 CTGTTCGACGGAATGCCTCG 61.414 60.000 5.48 5.48 36.67 4.63
1092 1121 2.163390 CGATCTCCTGCAGCACGTG 61.163 63.158 12.28 12.28 0.00 4.49
1169 1198 2.897350 CGGCCTCTGGAAATCCGC 60.897 66.667 0.00 0.00 39.43 5.54
1171 1200 2.272146 GCCTCTGGAAATCCGCCA 59.728 61.111 0.00 0.00 39.43 5.69
1197 1226 2.125147 CGCATCACCGGTGTCCAT 60.125 61.111 32.74 17.52 0.00 3.41
1338 1382 2.420642 CTCTGGATCCGGCACATTATG 58.579 52.381 16.48 0.00 0.00 1.90
1401 1445 5.163824 GGACGGCTATGGTGTTTACTTTTAC 60.164 44.000 0.00 0.00 0.00 2.01
1432 1476 0.814812 GCCTCTTGCCTCTCAGCATC 60.815 60.000 0.00 0.00 43.64 3.91
1467 1511 3.821033 AGCTCATTGACACAGGGTTAAAC 59.179 43.478 0.00 0.00 0.00 2.01
1476 1520 2.223377 CACAGGGTTAAACGACAGCTTC 59.777 50.000 0.00 0.00 0.00 3.86
1479 1523 2.074576 GGGTTAAACGACAGCTTCCTC 58.925 52.381 0.00 0.00 0.00 3.71
1512 1556 1.112113 GTCCGGTGCTGGAAGATCTA 58.888 55.000 0.00 0.00 40.44 1.98
1547 1591 2.341257 CTGTTTCGTCCATGTCAGGAG 58.659 52.381 0.00 0.00 38.64 3.69
1581 1625 1.004277 TCTCTAAAACGCCTGGCCATT 59.996 47.619 14.12 4.96 0.00 3.16
1623 1667 2.473984 GCATGCCCGTACTCGTATTTAC 59.526 50.000 6.36 0.00 35.01 2.01
1683 1727 3.223661 CAGGACTCCTGTGCTTGAC 57.776 57.895 16.18 0.00 45.82 3.18
1725 1769 5.449041 GGCTGCATTCGTCAGATTTATCAAA 60.449 40.000 0.50 0.00 33.54 2.69
1773 1817 1.541588 GACTCTTGGGATTGCCACAAC 59.458 52.381 0.00 0.00 35.15 3.32
1812 1856 5.404946 TGTTACGATCTACAGGCTGTTAAC 58.595 41.667 27.24 23.92 0.00 2.01
1910 1955 8.968969 GGTATGTATGTTTTAACCCCATTTACA 58.031 33.333 0.00 0.00 0.00 2.41
1956 2001 8.650490 TCTGTTGCAATATCTATGACCATCTAA 58.350 33.333 0.59 0.00 0.00 2.10
2025 2147 4.497507 GCTTTTACATTATTCCCCACGCTC 60.498 45.833 0.00 0.00 0.00 5.03
2038 2160 2.228582 CCCACGCTCAAAACAATCATCA 59.771 45.455 0.00 0.00 0.00 3.07
2047 2169 7.699391 CGCTCAAAACAATCATCATGTAATCTT 59.301 33.333 0.00 0.00 0.00 2.40
2173 2296 7.825761 TGCCCTACATTTAGTAAGTTAAAGACC 59.174 37.037 0.00 0.00 30.92 3.85
2203 2326 0.253044 ATGAATACTGGTGCGTGCCT 59.747 50.000 0.00 0.00 0.00 4.75
2226 2349 1.004918 ACTTCCGCGCACTAGCTTT 60.005 52.632 8.75 0.00 39.10 3.51
2269 2392 5.657826 TTCTGGAGATTCTCACTCTTCAG 57.342 43.478 15.36 11.35 44.55 3.02
2329 2452 7.595130 GGGAATTCTTTAACTTGCACTGTAAAG 59.405 37.037 5.23 12.74 0.00 1.85
2367 2490 8.737168 TTATCTGATCGGTTTTGATTCAATCT 57.263 30.769 0.42 0.00 0.00 2.40
2430 2553 3.003480 GAGGTTACAATGCAGTGGAGAC 58.997 50.000 19.57 12.82 0.00 3.36
2452 2575 4.708421 ACCTCAGCTGCAATATCAAAACAT 59.292 37.500 9.47 0.00 0.00 2.71
2494 2617 1.278238 GTAACTCGGTTGATGCGGAG 58.722 55.000 0.00 0.00 40.33 4.63
2554 2677 8.594881 ACATATGTAAGCTAACTATCAACAGC 57.405 34.615 6.56 0.00 0.00 4.40
2555 2678 8.204160 ACATATGTAAGCTAACTATCAACAGCA 58.796 33.333 6.56 0.00 36.47 4.41
2556 2679 6.910536 ATGTAAGCTAACTATCAACAGCAC 57.089 37.500 0.00 0.00 36.47 4.40
2557 2680 5.175859 TGTAAGCTAACTATCAACAGCACC 58.824 41.667 0.00 0.00 36.47 5.01
2562 2685 0.036388 ACTATCAACAGCACCCCACG 60.036 55.000 0.00 0.00 0.00 4.94
2594 2717 4.405116 TTCTGCAGTTTGCCTTCATTTT 57.595 36.364 14.67 0.00 44.23 1.82
2595 2718 3.719924 TCTGCAGTTTGCCTTCATTTTG 58.280 40.909 14.67 0.00 44.23 2.44
2596 2719 3.384146 TCTGCAGTTTGCCTTCATTTTGA 59.616 39.130 14.67 0.00 44.23 2.69
2597 2720 4.121317 CTGCAGTTTGCCTTCATTTTGAA 58.879 39.130 5.25 0.00 44.23 2.69
2709 2865 7.033530 TGTTTGGAAGTGTTAACTACAATGG 57.966 36.000 7.22 0.00 38.80 3.16
2756 2912 0.035534 TGGTAGCACGGCATGTTGAT 60.036 50.000 0.00 0.00 0.00 2.57
2776 2932 6.507958 TGATTTTGTTGAACAGTTCTGACA 57.492 33.333 14.51 14.84 0.00 3.58
2819 3255 7.704472 CCAGTTGCAATTCAGTTTGTTTACTTA 59.296 33.333 0.59 0.00 0.00 2.24
2823 3259 8.586570 TGCAATTCAGTTTGTTTACTTATTGG 57.413 30.769 0.00 0.00 32.98 3.16
2950 3386 2.219458 CACTGGATGCCATTGCTAGAG 58.781 52.381 0.00 0.00 38.71 2.43
2968 3404 7.513371 GCTAGAGAGCTAATCCTAACAGTTA 57.487 40.000 0.00 0.00 45.98 2.24
3000 3436 6.419484 TCTCAACTCTAACCAGATGTTGAA 57.581 37.500 14.64 8.10 42.16 2.69
3002 3438 6.706270 TCTCAACTCTAACCAGATGTTGAAAC 59.294 38.462 14.64 0.00 42.16 2.78
3088 3524 2.225091 ACTGAATCTTGTGGCCCATTGA 60.225 45.455 0.00 0.33 0.00 2.57
3140 3578 2.113139 AAGTGACACCCCCGCAAG 59.887 61.111 0.84 0.00 0.00 4.01
3158 3596 3.563390 GCAAGCTTCTCATCCTTCCATAC 59.437 47.826 0.00 0.00 0.00 2.39
3159 3597 4.774124 CAAGCTTCTCATCCTTCCATACA 58.226 43.478 0.00 0.00 0.00 2.29
3164 3602 6.100279 AGCTTCTCATCCTTCCATACATGTAA 59.900 38.462 10.14 0.00 0.00 2.41
3172 3610 7.027874 TCCTTCCATACATGTAAAGGTTTCT 57.972 36.000 24.46 1.10 38.72 2.52
3184 3622 6.320518 TGTAAAGGTTTCTAGGGAGAGAAGA 58.679 40.000 0.00 0.00 36.80 2.87
3277 3715 1.156736 CGAGGATGCGACCTTTTGTT 58.843 50.000 3.08 0.00 40.73 2.83
3296 3734 3.004210 TGTTGGACATTCATGTTGGTTCG 59.996 43.478 0.00 0.00 41.95 3.95
3301 3739 2.736721 ACATTCATGTTGGTTCGACTCG 59.263 45.455 0.00 0.00 37.90 4.18
3324 3762 5.389935 CGGTGAAGCAGCTTAGAAAAAGTAG 60.390 44.000 7.92 0.00 0.00 2.57
3328 3766 6.202954 TGAAGCAGCTTAGAAAAAGTAGTGAC 59.797 38.462 7.92 0.00 0.00 3.67
3333 3771 7.117812 GCAGCTTAGAAAAAGTAGTGACATGTA 59.882 37.037 0.00 0.00 0.00 2.29
3334 3772 8.436200 CAGCTTAGAAAAAGTAGTGACATGTAC 58.564 37.037 0.00 0.00 0.00 2.90
3335 3773 8.368668 AGCTTAGAAAAAGTAGTGACATGTACT 58.631 33.333 0.00 5.80 0.00 2.73
3336 3774 9.635520 GCTTAGAAAAAGTAGTGACATGTACTA 57.364 33.333 0.00 4.80 0.00 1.82
3359 3797 3.443145 TTTTTAATCGCCCTCCCTTGA 57.557 42.857 0.00 0.00 0.00 3.02
3360 3798 2.413310 TTTAATCGCCCTCCCTTGAC 57.587 50.000 0.00 0.00 0.00 3.18
3361 3799 1.580059 TTAATCGCCCTCCCTTGACT 58.420 50.000 0.00 0.00 0.00 3.41
3362 3800 0.830648 TAATCGCCCTCCCTTGACTG 59.169 55.000 0.00 0.00 0.00 3.51
3363 3801 0.909610 AATCGCCCTCCCTTGACTGA 60.910 55.000 0.00 0.00 0.00 3.41
3364 3802 0.692419 ATCGCCCTCCCTTGACTGAT 60.692 55.000 0.00 0.00 0.00 2.90
3365 3803 0.909610 TCGCCCTCCCTTGACTGATT 60.910 55.000 0.00 0.00 0.00 2.57
3366 3804 0.035056 CGCCCTCCCTTGACTGATTT 60.035 55.000 0.00 0.00 0.00 2.17
3367 3805 1.209504 CGCCCTCCCTTGACTGATTTA 59.790 52.381 0.00 0.00 0.00 1.40
3368 3806 2.158755 CGCCCTCCCTTGACTGATTTAT 60.159 50.000 0.00 0.00 0.00 1.40
3369 3807 3.481453 GCCCTCCCTTGACTGATTTATC 58.519 50.000 0.00 0.00 0.00 1.75
3370 3808 3.137360 GCCCTCCCTTGACTGATTTATCT 59.863 47.826 0.00 0.00 0.00 1.98
3371 3809 4.745172 GCCCTCCCTTGACTGATTTATCTC 60.745 50.000 0.00 0.00 0.00 2.75
3372 3810 4.502259 CCCTCCCTTGACTGATTTATCTCG 60.502 50.000 0.00 0.00 0.00 4.04
3373 3811 4.054671 CTCCCTTGACTGATTTATCTCGC 58.945 47.826 0.00 0.00 0.00 5.03
3374 3812 3.706594 TCCCTTGACTGATTTATCTCGCT 59.293 43.478 0.00 0.00 0.00 4.93
3375 3813 3.806521 CCCTTGACTGATTTATCTCGCTG 59.193 47.826 0.00 0.00 0.00 5.18
3376 3814 4.442052 CCCTTGACTGATTTATCTCGCTGA 60.442 45.833 0.00 0.00 0.00 4.26
3377 3815 5.111989 CCTTGACTGATTTATCTCGCTGAA 58.888 41.667 0.00 0.00 0.00 3.02
3378 3816 5.233902 CCTTGACTGATTTATCTCGCTGAAG 59.766 44.000 0.00 0.00 0.00 3.02
3379 3817 5.582689 TGACTGATTTATCTCGCTGAAGA 57.417 39.130 0.00 0.00 0.00 2.87
3380 3818 6.154203 TGACTGATTTATCTCGCTGAAGAT 57.846 37.500 0.00 0.00 39.35 2.40
3381 3819 5.981915 TGACTGATTTATCTCGCTGAAGATG 59.018 40.000 4.02 0.00 36.66 2.90
3382 3820 5.911752 ACTGATTTATCTCGCTGAAGATGT 58.088 37.500 4.02 0.00 36.66 3.06
3383 3821 7.043961 ACTGATTTATCTCGCTGAAGATGTA 57.956 36.000 4.02 0.00 36.66 2.29
3384 3822 7.665690 ACTGATTTATCTCGCTGAAGATGTAT 58.334 34.615 4.02 0.00 36.66 2.29
3385 3823 8.147058 ACTGATTTATCTCGCTGAAGATGTATT 58.853 33.333 4.02 0.00 36.66 1.89
3386 3824 8.893219 TGATTTATCTCGCTGAAGATGTATTT 57.107 30.769 4.02 0.00 36.66 1.40
3387 3825 9.330063 TGATTTATCTCGCTGAAGATGTATTTT 57.670 29.630 4.02 0.00 36.66 1.82
3388 3826 9.591404 GATTTATCTCGCTGAAGATGTATTTTG 57.409 33.333 4.02 0.00 36.66 2.44
3389 3827 8.716646 TTTATCTCGCTGAAGATGTATTTTGA 57.283 30.769 4.02 0.00 36.66 2.69
3390 3828 6.595772 ATCTCGCTGAAGATGTATTTTGAC 57.404 37.500 0.00 0.00 34.68 3.18
3391 3829 5.724328 TCTCGCTGAAGATGTATTTTGACT 58.276 37.500 0.00 0.00 0.00 3.41
3392 3830 6.166279 TCTCGCTGAAGATGTATTTTGACTT 58.834 36.000 0.00 0.00 0.00 3.01
3393 3831 6.311445 TCTCGCTGAAGATGTATTTTGACTTC 59.689 38.462 0.00 0.00 37.87 3.01
3394 3832 6.166279 TCGCTGAAGATGTATTTTGACTTCT 58.834 36.000 0.00 0.00 38.10 2.85
3395 3833 6.091305 TCGCTGAAGATGTATTTTGACTTCTG 59.909 38.462 0.00 0.00 38.10 3.02
3396 3834 6.128445 CGCTGAAGATGTATTTTGACTTCTGT 60.128 38.462 0.00 0.00 38.14 3.41
3397 3835 7.571983 CGCTGAAGATGTATTTTGACTTCTGTT 60.572 37.037 0.00 0.00 38.14 3.16
3398 3836 7.536622 GCTGAAGATGTATTTTGACTTCTGTTG 59.463 37.037 0.00 0.00 38.14 3.33
3399 3837 8.450578 TGAAGATGTATTTTGACTTCTGTTGT 57.549 30.769 0.00 0.00 38.10 3.32
3400 3838 8.902806 TGAAGATGTATTTTGACTTCTGTTGTT 58.097 29.630 0.00 0.00 38.10 2.83
3401 3839 9.173939 GAAGATGTATTTTGACTTCTGTTGTTG 57.826 33.333 0.00 0.00 34.88 3.33
3402 3840 8.225603 AGATGTATTTTGACTTCTGTTGTTGT 57.774 30.769 0.00 0.00 33.76 3.32
3403 3841 9.337396 AGATGTATTTTGACTTCTGTTGTTGTA 57.663 29.630 0.00 0.00 33.76 2.41
3411 3849 9.729023 TTTGACTTCTGTTGTTGTATTAATGTG 57.271 29.630 0.00 0.00 0.00 3.21
3412 3850 8.445275 TGACTTCTGTTGTTGTATTAATGTGT 57.555 30.769 0.00 0.00 0.00 3.72
3413 3851 8.556194 TGACTTCTGTTGTTGTATTAATGTGTC 58.444 33.333 0.00 0.00 0.00 3.67
3414 3852 7.572759 ACTTCTGTTGTTGTATTAATGTGTCG 58.427 34.615 0.00 0.00 0.00 4.35
3415 3853 6.474819 TCTGTTGTTGTATTAATGTGTCGG 57.525 37.500 0.00 0.00 0.00 4.79
3416 3854 6.224584 TCTGTTGTTGTATTAATGTGTCGGA 58.775 36.000 0.00 0.00 0.00 4.55
3417 3855 6.706716 TCTGTTGTTGTATTAATGTGTCGGAA 59.293 34.615 0.00 0.00 0.00 4.30
3418 3856 6.660722 TGTTGTTGTATTAATGTGTCGGAAC 58.339 36.000 0.00 0.00 0.00 3.62
3419 3857 5.866335 TGTTGTATTAATGTGTCGGAACC 57.134 39.130 0.00 0.00 0.00 3.62
3420 3858 5.553123 TGTTGTATTAATGTGTCGGAACCT 58.447 37.500 0.00 0.00 0.00 3.50
3421 3859 5.998981 TGTTGTATTAATGTGTCGGAACCTT 59.001 36.000 0.00 0.00 0.00 3.50
3422 3860 6.072948 TGTTGTATTAATGTGTCGGAACCTTG 60.073 38.462 0.00 0.00 0.00 3.61
3423 3861 4.393680 TGTATTAATGTGTCGGAACCTTGC 59.606 41.667 0.00 0.00 0.00 4.01
3424 3862 1.434555 TAATGTGTCGGAACCTTGCG 58.565 50.000 0.00 0.00 43.70 4.85
3425 3863 1.852067 AATGTGTCGGAACCTTGCGC 61.852 55.000 0.00 0.00 41.99 6.09
3426 3864 3.723348 GTGTCGGAACCTTGCGCC 61.723 66.667 4.18 0.00 41.99 6.53
3427 3865 4.243008 TGTCGGAACCTTGCGCCA 62.243 61.111 4.18 0.00 41.99 5.69
3428 3866 2.746277 GTCGGAACCTTGCGCCAT 60.746 61.111 4.18 0.00 41.99 4.40
3429 3867 1.448893 GTCGGAACCTTGCGCCATA 60.449 57.895 4.18 0.00 41.99 2.74
3430 3868 0.814010 GTCGGAACCTTGCGCCATAT 60.814 55.000 4.18 0.00 41.99 1.78
3431 3869 0.531974 TCGGAACCTTGCGCCATATC 60.532 55.000 4.18 0.00 41.99 1.63
3432 3870 0.532862 CGGAACCTTGCGCCATATCT 60.533 55.000 4.18 0.00 34.72 1.98
3433 3871 1.230324 GGAACCTTGCGCCATATCTC 58.770 55.000 4.18 0.00 0.00 2.75
3434 3872 1.475034 GGAACCTTGCGCCATATCTCA 60.475 52.381 4.18 0.00 0.00 3.27
3435 3873 2.498167 GAACCTTGCGCCATATCTCAT 58.502 47.619 4.18 0.00 0.00 2.90
3436 3874 3.557054 GGAACCTTGCGCCATATCTCATA 60.557 47.826 4.18 0.00 0.00 2.15
3437 3875 3.045601 ACCTTGCGCCATATCTCATAC 57.954 47.619 4.18 0.00 0.00 2.39
3438 3876 2.634940 ACCTTGCGCCATATCTCATACT 59.365 45.455 4.18 0.00 0.00 2.12
3439 3877 3.257393 CCTTGCGCCATATCTCATACTC 58.743 50.000 4.18 0.00 0.00 2.59
3440 3878 2.636768 TGCGCCATATCTCATACTCG 57.363 50.000 4.18 0.00 0.00 4.18
3441 3879 1.272781 GCGCCATATCTCATACTCGC 58.727 55.000 0.00 0.00 34.61 5.03
3442 3880 1.135257 GCGCCATATCTCATACTCGCT 60.135 52.381 0.00 0.00 38.48 4.93
3451 3889 0.106868 TCATACTCGCTCCTTCCCGA 60.107 55.000 0.00 0.00 0.00 5.14
3471 3909 3.565307 GAATAAGGATGGCAATGGGTCA 58.435 45.455 0.00 0.00 34.17 4.02
3486 3924 0.906775 GGTCAGGTTTGGATCGGGTA 59.093 55.000 0.00 0.00 0.00 3.69
3488 3926 1.134491 GTCAGGTTTGGATCGGGTAGG 60.134 57.143 0.00 0.00 0.00 3.18
3605 4044 4.927267 TGGATATCCATACCCATTGGAC 57.073 45.455 20.98 0.00 45.71 4.02
3699 4138 0.178998 CATGGCAGGCTAGGCTTCAT 60.179 55.000 17.59 18.99 34.73 2.57
3728 4167 7.001674 TGGTAAATCAACATCCACTAACAACT 58.998 34.615 0.00 0.00 0.00 3.16
3813 4256 0.912486 AGAGGGGTGTTGGAGTATGC 59.088 55.000 0.00 0.00 0.00 3.14
3816 4259 2.706190 GAGGGGTGTTGGAGTATGCTAT 59.294 50.000 0.00 0.00 0.00 2.97
3831 4274 6.032039 AGTATGCTATGGAGGGGATTGAATA 58.968 40.000 0.00 0.00 0.00 1.75
3940 4384 2.822637 CGTGGGGCAGGGATAGCAT 61.823 63.158 0.00 0.00 0.00 3.79
4028 4473 3.451902 CCATGCCCTATCCACAAACAATT 59.548 43.478 0.00 0.00 0.00 2.32
4087 4532 5.560724 CATATCCAAACCCTATCCATTCGT 58.439 41.667 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.850568 ACCTTTAGATTACCTGTGGGGG 59.149 50.000 0.00 0.00 40.03 5.40
10 11 4.472108 TGTACCTTTAGATTACCTGTGGGG 59.528 45.833 0.00 0.00 41.89 4.96
27 28 7.495934 GTGTTTCTGTAATCTGCATATGTACCT 59.504 37.037 4.29 0.00 0.00 3.08
72 73 2.422127 CCTTGGGCGTAAGTAACCATTG 59.578 50.000 0.00 0.00 37.53 2.82
74 75 1.631898 ACCTTGGGCGTAAGTAACCAT 59.368 47.619 0.00 0.00 37.53 3.55
76 77 1.002315 TGACCTTGGGCGTAAGTAACC 59.998 52.381 0.00 0.00 41.68 2.85
171 172 6.500684 TGCAAAGAAGACAGGATAATTCAC 57.499 37.500 0.00 0.00 0.00 3.18
179 180 2.574006 ATGCTGCAAAGAAGACAGGA 57.426 45.000 6.36 0.00 36.16 3.86
180 181 3.005050 TCAAATGCTGCAAAGAAGACAGG 59.995 43.478 6.36 0.00 31.94 4.00
181 182 4.233123 TCAAATGCTGCAAAGAAGACAG 57.767 40.909 6.36 0.00 34.48 3.51
224 247 5.221891 CAAGGACACAATTCTTGGTATCG 57.778 43.478 0.00 0.00 35.53 2.92
236 260 4.600111 AGGAAGTATAACCCAAGGACACAA 59.400 41.667 0.00 0.00 0.00 3.33
237 261 4.172807 AGGAAGTATAACCCAAGGACACA 58.827 43.478 0.00 0.00 0.00 3.72
241 265 3.036091 CGGAGGAAGTATAACCCAAGGA 58.964 50.000 0.00 0.00 0.00 3.36
251 275 8.120538 TCTTATATTATGGGACGGAGGAAGTAT 58.879 37.037 0.00 0.00 0.00 2.12
252 276 7.472741 TCTTATATTATGGGACGGAGGAAGTA 58.527 38.462 0.00 0.00 0.00 2.24
253 277 6.320518 TCTTATATTATGGGACGGAGGAAGT 58.679 40.000 0.00 0.00 0.00 3.01
254 278 6.852420 TCTTATATTATGGGACGGAGGAAG 57.148 41.667 0.00 0.00 0.00 3.46
255 279 6.294899 CGTTCTTATATTATGGGACGGAGGAA 60.295 42.308 0.00 0.00 0.00 3.36
256 280 5.184479 CGTTCTTATATTATGGGACGGAGGA 59.816 44.000 0.00 0.00 0.00 3.71
257 281 5.047519 ACGTTCTTATATTATGGGACGGAGG 60.048 44.000 13.18 0.00 0.00 4.30
258 282 6.022163 ACGTTCTTATATTATGGGACGGAG 57.978 41.667 13.18 0.00 0.00 4.63
259 283 6.409524 AACGTTCTTATATTATGGGACGGA 57.590 37.500 0.00 0.00 0.00 4.69
260 284 7.486802 AAAACGTTCTTATATTATGGGACGG 57.513 36.000 0.00 1.76 0.00 4.79
261 285 8.605746 TCAAAAACGTTCTTATATTATGGGACG 58.394 33.333 0.00 9.33 0.00 4.79
262 286 9.712359 GTCAAAAACGTTCTTATATTATGGGAC 57.288 33.333 0.00 0.00 0.00 4.46
263 287 9.451002 TGTCAAAAACGTTCTTATATTATGGGA 57.549 29.630 0.00 0.00 0.00 4.37
264 288 9.498307 GTGTCAAAAACGTTCTTATATTATGGG 57.502 33.333 0.00 0.00 0.00 4.00
268 292 9.866936 GTGTGTGTCAAAAACGTTCTTATATTA 57.133 29.630 0.00 0.00 0.00 0.98
269 293 8.617809 AGTGTGTGTCAAAAACGTTCTTATATT 58.382 29.630 0.00 0.00 0.00 1.28
270 294 8.149973 AGTGTGTGTCAAAAACGTTCTTATAT 57.850 30.769 0.00 0.00 0.00 0.86
271 295 7.542534 AGTGTGTGTCAAAAACGTTCTTATA 57.457 32.000 0.00 0.00 0.00 0.98
272 296 6.431198 AGTGTGTGTCAAAAACGTTCTTAT 57.569 33.333 0.00 0.00 0.00 1.73
273 297 5.866335 AGTGTGTGTCAAAAACGTTCTTA 57.134 34.783 0.00 0.00 0.00 2.10
274 298 4.759516 AGTGTGTGTCAAAAACGTTCTT 57.240 36.364 0.00 0.00 0.00 2.52
275 299 4.933400 ACTAGTGTGTGTCAAAAACGTTCT 59.067 37.500 0.00 0.00 0.00 3.01
276 300 5.019498 CACTAGTGTGTGTCAAAAACGTTC 58.981 41.667 15.06 0.00 39.24 3.95
277 301 4.965062 CACTAGTGTGTGTCAAAAACGTT 58.035 39.130 15.06 0.00 39.24 3.99
278 302 4.593597 CACTAGTGTGTGTCAAAAACGT 57.406 40.909 15.06 0.00 39.24 3.99
287 311 7.861872 AAAAACGTTTTTAACACTAGTGTGTGT 59.138 29.630 31.82 15.86 44.97 3.72
288 312 8.218256 AAAAACGTTTTTAACACTAGTGTGTG 57.782 30.769 31.82 14.87 44.97 3.82
303 327 9.763465 CTCCGTCACATAATATAAAAACGTTTT 57.237 29.630 20.26 20.26 0.00 2.43
304 328 8.392612 CCTCCGTCACATAATATAAAAACGTTT 58.607 33.333 7.96 7.96 0.00 3.60
305 329 7.550196 ACCTCCGTCACATAATATAAAAACGTT 59.450 33.333 0.00 0.00 0.00 3.99
306 330 7.043565 ACCTCCGTCACATAATATAAAAACGT 58.956 34.615 0.00 0.00 0.00 3.99
307 331 7.473027 ACCTCCGTCACATAATATAAAAACG 57.527 36.000 0.00 0.00 0.00 3.60
308 332 9.538508 ACTACCTCCGTCACATAATATAAAAAC 57.461 33.333 0.00 0.00 0.00 2.43
311 335 8.517878 GCTACTACCTCCGTCACATAATATAAA 58.482 37.037 0.00 0.00 0.00 1.40
312 336 7.666804 TGCTACTACCTCCGTCACATAATATAA 59.333 37.037 0.00 0.00 0.00 0.98
313 337 7.170277 TGCTACTACCTCCGTCACATAATATA 58.830 38.462 0.00 0.00 0.00 0.86
314 338 6.008331 TGCTACTACCTCCGTCACATAATAT 58.992 40.000 0.00 0.00 0.00 1.28
315 339 5.379187 TGCTACTACCTCCGTCACATAATA 58.621 41.667 0.00 0.00 0.00 0.98
316 340 4.212716 TGCTACTACCTCCGTCACATAAT 58.787 43.478 0.00 0.00 0.00 1.28
317 341 3.623703 TGCTACTACCTCCGTCACATAA 58.376 45.455 0.00 0.00 0.00 1.90
318 342 3.286329 TGCTACTACCTCCGTCACATA 57.714 47.619 0.00 0.00 0.00 2.29
319 343 2.139323 TGCTACTACCTCCGTCACAT 57.861 50.000 0.00 0.00 0.00 3.21
320 344 2.139323 ATGCTACTACCTCCGTCACA 57.861 50.000 0.00 0.00 0.00 3.58
321 345 3.521947 AAATGCTACTACCTCCGTCAC 57.478 47.619 0.00 0.00 0.00 3.67
322 346 4.546829 AAAAATGCTACTACCTCCGTCA 57.453 40.909 0.00 0.00 0.00 4.35
344 368 5.047847 CGGAAGAGTAAGTGACTGAAACAA 58.952 41.667 0.00 0.00 39.06 2.83
389 413 8.248117 GCATTTGCTTCTGATTAATTTGAGTT 57.752 30.769 0.00 0.00 38.21 3.01
478 503 8.420945 CGAGATACGCTATCACTCTTAATTTTG 58.579 37.037 7.46 0.00 37.65 2.44
485 510 3.251245 CACCGAGATACGCTATCACTCTT 59.749 47.826 7.46 0.00 41.07 2.85
496 521 1.878522 GCTGCACCACCGAGATACG 60.879 63.158 0.00 0.00 42.18 3.06
503 528 0.940519 CACATTTTGCTGCACCACCG 60.941 55.000 0.00 0.00 0.00 4.94
531 556 8.803397 ACAATCGCTATACATATACACTAGGA 57.197 34.615 0.00 0.00 0.00 2.94
594 619 4.510571 GGATTAAAAGGAGGCGAGTGTAA 58.489 43.478 0.00 0.00 0.00 2.41
595 620 3.118519 GGGATTAAAAGGAGGCGAGTGTA 60.119 47.826 0.00 0.00 0.00 2.90
658 683 0.528684 GATTCGCAGGACCTTCGAGG 60.529 60.000 15.77 0.00 42.49 4.63
678 703 4.933483 GCGTTTGCGACATGGAAA 57.067 50.000 0.00 0.00 41.33 3.13
691 716 2.224523 TGAGGAGTTGGAGAAATGCGTT 60.225 45.455 0.00 0.00 0.00 4.84
738 763 2.110226 GTCGCTACTGATACGAGCAAC 58.890 52.381 0.00 0.00 36.34 4.17
801 826 1.146358 GGCAACTGATACGAGCGACC 61.146 60.000 0.00 0.00 0.00 4.79
890 915 0.179936 GGGGAGACAGATGCAGGAAG 59.820 60.000 0.00 0.00 0.00 3.46
898 923 0.915364 GGCAAAGAGGGGAGACAGAT 59.085 55.000 0.00 0.00 0.00 2.90
908 933 3.365265 GGCGTGGTGGCAAAGAGG 61.365 66.667 0.00 0.00 44.08 3.69
946 975 1.145156 ACAACCGTACAGCTGTGCA 59.855 52.632 30.39 10.50 0.00 4.57
947 976 1.569493 CACAACCGTACAGCTGTGC 59.431 57.895 29.57 26.38 33.41 4.57
948 977 1.569493 GCACAACCGTACAGCTGTG 59.431 57.895 29.57 15.20 41.68 3.66
949 978 1.597027 GGCACAACCGTACAGCTGT 60.597 57.895 25.12 25.12 0.00 4.40
950 979 3.253955 GGCACAACCGTACAGCTG 58.746 61.111 13.48 13.48 0.00 4.24
982 1011 2.107041 ATTCCGTCGAACAGGTGGCA 62.107 55.000 0.00 0.00 0.00 4.92
1052 1081 3.044305 GTAGGGCGCCGATGATGC 61.044 66.667 22.54 4.09 0.00 3.91
1193 1222 1.313091 CGTCACCTCCGACTCATGGA 61.313 60.000 0.00 0.00 33.54 3.41
1197 1226 3.371063 GGCGTCACCTCCGACTCA 61.371 66.667 0.00 0.00 33.54 3.41
1257 1301 2.202492 AGCTCGCACGTGTCGATC 60.202 61.111 26.76 23.57 35.25 3.69
1269 1313 4.421479 ACGGCGAACCTGAGCTCG 62.421 66.667 16.62 3.88 38.11 5.03
1401 1445 1.714794 CAAGAGGCAGGTTGTCTACG 58.285 55.000 0.00 0.00 28.93 3.51
1432 1476 1.317613 ATGAGCTCTAGCCTCGTCAG 58.682 55.000 16.19 0.00 43.38 3.51
1467 1511 1.201965 GCAAAATCGAGGAAGCTGTCG 60.202 52.381 6.99 6.99 37.54 4.35
1476 1520 1.982073 GACAGCCGGCAAAATCGAGG 61.982 60.000 31.54 8.28 0.00 4.63
1479 1523 2.485122 GGACAGCCGGCAAAATCG 59.515 61.111 31.54 11.71 0.00 3.34
1499 1543 6.983906 TGATGATTACTAGATCTTCCAGCA 57.016 37.500 0.00 0.00 32.25 4.41
1512 1556 4.943705 ACGAAACAGCCATTGATGATTACT 59.056 37.500 0.00 0.00 0.00 2.24
1547 1591 6.183360 GCGTTTTAGAGACTTTGAAGAGATCC 60.183 42.308 0.00 0.00 0.00 3.36
1623 1667 2.135933 AGAGAAACGAAACTTGGAGCG 58.864 47.619 0.00 0.00 0.00 5.03
1650 1694 1.185618 TCCTGTCCCAGTTGTCCTCG 61.186 60.000 0.00 0.00 0.00 4.63
1683 1727 1.133253 CTTCAACGACGGCATGCTG 59.867 57.895 25.08 25.08 0.00 4.41
1725 1769 3.864789 AAACACCTGTCCACAGATTCT 57.135 42.857 8.36 0.00 46.59 2.40
1773 1817 2.240493 AACAACCTTGACAGTCCTCG 57.760 50.000 0.00 0.00 0.00 4.63
1812 1856 1.476085 AGAAGCACCGAGTCATGAGAG 59.524 52.381 0.00 0.00 0.00 3.20
1910 1955 9.383519 CAACAGATATATAATAGGACCGCAAAT 57.616 33.333 0.00 0.00 0.00 2.32
1963 2008 9.897744 TTGCATTGTTTATGACTTTCTAAGAAG 57.102 29.630 0.00 0.00 36.26 2.85
1972 2094 4.281688 AGCTGGTTGCATTGTTTATGACTT 59.718 37.500 0.00 0.00 45.94 3.01
2075 2197 5.700832 AGAGAACAAATTAATCGTCACTGCA 59.299 36.000 0.00 0.00 0.00 4.41
2173 2296 6.546395 GCACCAGTATTCATTGAGTAACAAG 58.454 40.000 0.00 0.00 42.02 3.16
2203 2326 2.523184 CTAGTGCGCGGAAGTCGTCA 62.523 60.000 8.83 0.00 41.72 4.35
2214 2337 4.600012 TCAAGAATAAAAGCTAGTGCGC 57.400 40.909 0.00 0.00 45.42 6.09
2226 2349 7.040478 CCAGAAATGGTGAGTGTTCAAGAATAA 60.040 37.037 0.00 0.00 34.49 1.40
2315 2438 4.073293 AGTGTAGCTTTACAGTGCAAGT 57.927 40.909 0.00 0.00 32.79 3.16
2329 2452 8.215926 ACCGATCAGATAATAGATAGTGTAGC 57.784 38.462 0.00 0.00 0.00 3.58
2430 2553 4.707030 TGTTTTGATATTGCAGCTGAGG 57.293 40.909 20.43 0.00 0.00 3.86
2452 2575 4.330944 TTTGACTTCGACTGCCTTAAGA 57.669 40.909 3.36 0.00 0.00 2.10
2554 2677 1.821216 AATGTAGAAAGCGTGGGGTG 58.179 50.000 0.00 0.00 0.00 4.61
2555 2678 2.039879 AGAAATGTAGAAAGCGTGGGGT 59.960 45.455 0.00 0.00 0.00 4.95
2556 2679 2.420022 CAGAAATGTAGAAAGCGTGGGG 59.580 50.000 0.00 0.00 0.00 4.96
2557 2680 2.159517 GCAGAAATGTAGAAAGCGTGGG 60.160 50.000 0.00 0.00 0.00 4.61
2562 2685 4.383948 GCAAACTGCAGAAATGTAGAAAGC 59.616 41.667 23.35 4.26 44.26 3.51
2594 2717 9.364653 ACTCTTTCTACTAAACTAGGAACTTCA 57.635 33.333 0.00 0.00 41.75 3.02
2595 2718 9.628746 CACTCTTTCTACTAAACTAGGAACTTC 57.371 37.037 0.00 0.00 41.75 3.01
2596 2719 9.364653 TCACTCTTTCTACTAAACTAGGAACTT 57.635 33.333 0.00 0.00 41.75 2.66
2597 2720 8.937207 TCACTCTTTCTACTAAACTAGGAACT 57.063 34.615 0.00 0.00 46.37 3.01
2617 2763 9.817809 TTCTCATTACTGGTATAACATTCACTC 57.182 33.333 0.00 0.00 0.00 3.51
2709 2865 5.117592 GTGCAGTGCATTTCAATCTAAACAC 59.882 40.000 22.87 0.00 41.91 3.32
2756 2912 7.655328 ACAAAATGTCAGAACTGTTCAACAAAA 59.345 29.630 23.47 8.89 33.35 2.44
2776 2932 4.322057 ACTGGAATAGGAGCCACAAAAT 57.678 40.909 0.00 0.00 0.00 1.82
2819 3255 7.093377 ACCATAATGTTGACATTGTAAGCCAAT 60.093 33.333 17.28 0.42 45.34 3.16
2823 3259 7.088589 AGACCATAATGTTGACATTGTAAGC 57.911 36.000 17.28 6.29 45.34 3.09
2933 3369 2.924757 CTCTCTAGCAATGGCATCCA 57.075 50.000 0.00 0.00 44.61 3.41
2950 3386 9.601217 TCTTGATTTAACTGTTAGGATTAGCTC 57.399 33.333 0.00 0.00 0.00 4.09
2968 3404 7.911651 TCTGGTTAGAGTTGAGATCTTGATTT 58.088 34.615 0.00 0.00 0.00 2.17
3000 3436 7.699566 TCTAATTACTCAAAAGTTTGCACGTT 58.300 30.769 0.00 0.00 38.05 3.99
3002 3438 8.728088 AATCTAATTACTCAAAAGTTTGCACG 57.272 30.769 0.00 0.00 38.05 5.34
3125 3561 4.643387 AGCTTGCGGGGGTGTCAC 62.643 66.667 0.00 0.00 0.00 3.67
3140 3578 4.712476 ACATGTATGGAAGGATGAGAAGC 58.288 43.478 0.00 0.00 0.00 3.86
3158 3596 6.546428 TCTCTCCCTAGAAACCTTTACATG 57.454 41.667 0.00 0.00 0.00 3.21
3159 3597 6.960542 TCTTCTCTCCCTAGAAACCTTTACAT 59.039 38.462 0.00 0.00 35.14 2.29
3164 3602 4.098155 GGTCTTCTCTCCCTAGAAACCTT 58.902 47.826 0.00 0.00 35.73 3.50
3172 3610 1.362932 AGCCAAGGTCTTCTCTCCCTA 59.637 52.381 0.00 0.00 0.00 3.53
3184 3622 2.684927 GCCATATGTCTTCAGCCAAGGT 60.685 50.000 1.24 0.00 32.22 3.50
3277 3715 2.811431 GTCGAACCAACATGAATGTCCA 59.189 45.455 0.00 0.00 40.80 4.02
3296 3734 1.202582 TCTAAGCTGCTTCACCGAGTC 59.797 52.381 19.62 0.00 0.00 3.36
3301 3739 4.837896 ACTTTTTCTAAGCTGCTTCACC 57.162 40.909 19.62 0.00 0.00 4.02
3339 3777 3.086282 GTCAAGGGAGGGCGATTAAAAA 58.914 45.455 0.00 0.00 0.00 1.94
3340 3778 2.307686 AGTCAAGGGAGGGCGATTAAAA 59.692 45.455 0.00 0.00 0.00 1.52
3341 3779 1.913419 AGTCAAGGGAGGGCGATTAAA 59.087 47.619 0.00 0.00 0.00 1.52
3342 3780 1.209504 CAGTCAAGGGAGGGCGATTAA 59.790 52.381 0.00 0.00 0.00 1.40
3343 3781 0.830648 CAGTCAAGGGAGGGCGATTA 59.169 55.000 0.00 0.00 0.00 1.75
3344 3782 0.909610 TCAGTCAAGGGAGGGCGATT 60.910 55.000 0.00 0.00 0.00 3.34
3345 3783 0.692419 ATCAGTCAAGGGAGGGCGAT 60.692 55.000 0.00 0.00 0.00 4.58
3346 3784 0.909610 AATCAGTCAAGGGAGGGCGA 60.910 55.000 0.00 0.00 0.00 5.54
3347 3785 0.035056 AAATCAGTCAAGGGAGGGCG 60.035 55.000 0.00 0.00 0.00 6.13
3348 3786 3.137360 AGATAAATCAGTCAAGGGAGGGC 59.863 47.826 0.00 0.00 0.00 5.19
3349 3787 4.502259 CGAGATAAATCAGTCAAGGGAGGG 60.502 50.000 0.00 0.00 0.00 4.30
3350 3788 4.626042 CGAGATAAATCAGTCAAGGGAGG 58.374 47.826 0.00 0.00 0.00 4.30
3351 3789 4.054671 GCGAGATAAATCAGTCAAGGGAG 58.945 47.826 0.00 0.00 0.00 4.30
3352 3790 3.706594 AGCGAGATAAATCAGTCAAGGGA 59.293 43.478 0.00 0.00 0.00 4.20
3353 3791 3.806521 CAGCGAGATAAATCAGTCAAGGG 59.193 47.826 0.00 0.00 0.00 3.95
3354 3792 4.686972 TCAGCGAGATAAATCAGTCAAGG 58.313 43.478 0.00 0.00 0.00 3.61
3355 3793 6.038985 TCTTCAGCGAGATAAATCAGTCAAG 58.961 40.000 0.00 0.00 0.00 3.02
3356 3794 5.965922 TCTTCAGCGAGATAAATCAGTCAA 58.034 37.500 0.00 0.00 0.00 3.18
3357 3795 5.582689 TCTTCAGCGAGATAAATCAGTCA 57.417 39.130 0.00 0.00 0.00 3.41
3358 3796 5.982516 ACATCTTCAGCGAGATAAATCAGTC 59.017 40.000 0.00 0.00 34.68 3.51
3359 3797 5.911752 ACATCTTCAGCGAGATAAATCAGT 58.088 37.500 0.00 0.00 34.68 3.41
3360 3798 8.531622 AATACATCTTCAGCGAGATAAATCAG 57.468 34.615 0.00 0.00 34.68 2.90
3361 3799 8.893219 AAATACATCTTCAGCGAGATAAATCA 57.107 30.769 0.00 0.00 34.68 2.57
3362 3800 9.591404 CAAAATACATCTTCAGCGAGATAAATC 57.409 33.333 0.00 0.00 34.68 2.17
3363 3801 9.330063 TCAAAATACATCTTCAGCGAGATAAAT 57.670 29.630 0.00 0.00 34.68 1.40
3364 3802 8.604035 GTCAAAATACATCTTCAGCGAGATAAA 58.396 33.333 0.00 0.00 34.68 1.40
3365 3803 7.981789 AGTCAAAATACATCTTCAGCGAGATAA 59.018 33.333 0.00 0.00 34.68 1.75
3366 3804 7.492524 AGTCAAAATACATCTTCAGCGAGATA 58.507 34.615 0.00 0.00 34.68 1.98
3367 3805 6.344500 AGTCAAAATACATCTTCAGCGAGAT 58.656 36.000 0.00 0.00 36.84 2.75
3368 3806 5.724328 AGTCAAAATACATCTTCAGCGAGA 58.276 37.500 0.00 0.00 0.00 4.04
3369 3807 6.312426 AGAAGTCAAAATACATCTTCAGCGAG 59.688 38.462 0.00 0.00 37.53 5.03
3370 3808 6.091305 CAGAAGTCAAAATACATCTTCAGCGA 59.909 38.462 0.00 0.00 37.53 4.93
3371 3809 6.128445 ACAGAAGTCAAAATACATCTTCAGCG 60.128 38.462 0.00 0.00 37.53 5.18
3372 3810 7.138692 ACAGAAGTCAAAATACATCTTCAGC 57.861 36.000 0.00 0.00 37.53 4.26
3373 3811 8.562892 ACAACAGAAGTCAAAATACATCTTCAG 58.437 33.333 0.00 0.00 37.53 3.02
3374 3812 8.450578 ACAACAGAAGTCAAAATACATCTTCA 57.549 30.769 0.00 0.00 37.53 3.02
3375 3813 9.173939 CAACAACAGAAGTCAAAATACATCTTC 57.826 33.333 0.00 0.00 35.98 2.87
3376 3814 8.686334 ACAACAACAGAAGTCAAAATACATCTT 58.314 29.630 0.00 0.00 0.00 2.40
3377 3815 8.225603 ACAACAACAGAAGTCAAAATACATCT 57.774 30.769 0.00 0.00 0.00 2.90
3385 3823 9.729023 CACATTAATACAACAACAGAAGTCAAA 57.271 29.630 0.00 0.00 0.00 2.69
3386 3824 8.898761 ACACATTAATACAACAACAGAAGTCAA 58.101 29.630 0.00 0.00 0.00 3.18
3387 3825 8.445275 ACACATTAATACAACAACAGAAGTCA 57.555 30.769 0.00 0.00 0.00 3.41
3388 3826 7.740346 CGACACATTAATACAACAACAGAAGTC 59.260 37.037 0.00 0.00 0.00 3.01
3389 3827 7.307751 CCGACACATTAATACAACAACAGAAGT 60.308 37.037 0.00 0.00 0.00 3.01
3390 3828 7.015289 CCGACACATTAATACAACAACAGAAG 58.985 38.462 0.00 0.00 0.00 2.85
3391 3829 6.706716 TCCGACACATTAATACAACAACAGAA 59.293 34.615 0.00 0.00 0.00 3.02
3392 3830 6.224584 TCCGACACATTAATACAACAACAGA 58.775 36.000 0.00 0.00 0.00 3.41
3393 3831 6.474819 TCCGACACATTAATACAACAACAG 57.525 37.500 0.00 0.00 0.00 3.16
3394 3832 6.293516 GGTTCCGACACATTAATACAACAACA 60.294 38.462 0.00 0.00 0.00 3.33
3395 3833 6.072893 AGGTTCCGACACATTAATACAACAAC 60.073 38.462 0.00 0.00 0.00 3.32
3396 3834 5.998981 AGGTTCCGACACATTAATACAACAA 59.001 36.000 0.00 0.00 0.00 2.83
3397 3835 5.553123 AGGTTCCGACACATTAATACAACA 58.447 37.500 0.00 0.00 0.00 3.33
3398 3836 6.311723 CAAGGTTCCGACACATTAATACAAC 58.688 40.000 0.00 0.00 0.00 3.32
3399 3837 5.106475 GCAAGGTTCCGACACATTAATACAA 60.106 40.000 0.00 0.00 0.00 2.41
3400 3838 4.393680 GCAAGGTTCCGACACATTAATACA 59.606 41.667 0.00 0.00 0.00 2.29
3401 3839 4.493545 CGCAAGGTTCCGACACATTAATAC 60.494 45.833 0.00 0.00 0.00 1.89
3402 3840 3.619483 CGCAAGGTTCCGACACATTAATA 59.381 43.478 0.00 0.00 0.00 0.98
3403 3841 2.418628 CGCAAGGTTCCGACACATTAAT 59.581 45.455 0.00 0.00 0.00 1.40
3404 3842 1.801771 CGCAAGGTTCCGACACATTAA 59.198 47.619 0.00 0.00 0.00 1.40
3405 3843 1.434555 CGCAAGGTTCCGACACATTA 58.565 50.000 0.00 0.00 0.00 1.90
3406 3844 1.852067 GCGCAAGGTTCCGACACATT 61.852 55.000 0.30 0.00 38.28 2.71
3407 3845 2.325082 GCGCAAGGTTCCGACACAT 61.325 57.895 0.30 0.00 38.28 3.21
3408 3846 2.970324 GCGCAAGGTTCCGACACA 60.970 61.111 0.30 0.00 38.28 3.72
3409 3847 3.723348 GGCGCAAGGTTCCGACAC 61.723 66.667 10.83 0.00 38.28 3.67
3410 3848 4.243008 TGGCGCAAGGTTCCGACA 62.243 61.111 10.83 0.00 40.70 4.35
3411 3849 0.814010 ATATGGCGCAAGGTTCCGAC 60.814 55.000 10.83 0.00 38.28 4.79
3412 3850 0.531974 GATATGGCGCAAGGTTCCGA 60.532 55.000 10.83 0.00 38.28 4.55
3413 3851 0.532862 AGATATGGCGCAAGGTTCCG 60.533 55.000 10.83 0.00 38.28 4.30
3414 3852 1.230324 GAGATATGGCGCAAGGTTCC 58.770 55.000 10.83 0.00 38.28 3.62
3415 3853 1.953559 TGAGATATGGCGCAAGGTTC 58.046 50.000 10.83 0.00 38.28 3.62
3416 3854 2.645838 ATGAGATATGGCGCAAGGTT 57.354 45.000 10.83 0.00 38.28 3.50
3417 3855 2.634940 AGTATGAGATATGGCGCAAGGT 59.365 45.455 10.83 0.00 38.28 3.50
3418 3856 3.257393 GAGTATGAGATATGGCGCAAGG 58.743 50.000 10.83 0.00 38.28 3.61
3419 3857 2.919859 CGAGTATGAGATATGGCGCAAG 59.080 50.000 10.83 0.00 43.44 4.01
3420 3858 2.926586 GCGAGTATGAGATATGGCGCAA 60.927 50.000 10.83 0.00 42.41 4.85
3421 3859 1.402852 GCGAGTATGAGATATGGCGCA 60.403 52.381 10.83 0.00 42.41 6.09
3422 3860 1.135257 AGCGAGTATGAGATATGGCGC 60.135 52.381 0.00 0.00 43.09 6.53
3423 3861 2.478709 GGAGCGAGTATGAGATATGGCG 60.479 54.545 0.00 0.00 0.00 5.69
3424 3862 2.757868 AGGAGCGAGTATGAGATATGGC 59.242 50.000 0.00 0.00 0.00 4.40
3425 3863 4.142271 GGAAGGAGCGAGTATGAGATATGG 60.142 50.000 0.00 0.00 0.00 2.74
3426 3864 4.142271 GGGAAGGAGCGAGTATGAGATATG 60.142 50.000 0.00 0.00 0.00 1.78
3427 3865 4.020543 GGGAAGGAGCGAGTATGAGATAT 58.979 47.826 0.00 0.00 0.00 1.63
3428 3866 3.422796 GGGAAGGAGCGAGTATGAGATA 58.577 50.000 0.00 0.00 0.00 1.98
3429 3867 2.243810 GGGAAGGAGCGAGTATGAGAT 58.756 52.381 0.00 0.00 0.00 2.75
3430 3868 1.693627 GGGAAGGAGCGAGTATGAGA 58.306 55.000 0.00 0.00 0.00 3.27
3431 3869 0.312416 CGGGAAGGAGCGAGTATGAG 59.688 60.000 0.00 0.00 0.00 2.90
3432 3870 0.106868 TCGGGAAGGAGCGAGTATGA 60.107 55.000 0.00 0.00 0.00 2.15
3433 3871 0.744874 TTCGGGAAGGAGCGAGTATG 59.255 55.000 0.00 0.00 0.00 2.39
3434 3872 1.705873 ATTCGGGAAGGAGCGAGTAT 58.294 50.000 0.00 0.00 0.00 2.12
3435 3873 2.353357 TATTCGGGAAGGAGCGAGTA 57.647 50.000 0.00 0.00 0.00 2.59
3436 3874 1.409427 CTTATTCGGGAAGGAGCGAGT 59.591 52.381 0.00 0.00 0.00 4.18
3437 3875 1.269831 CCTTATTCGGGAAGGAGCGAG 60.270 57.143 5.30 0.00 45.52 5.03
3438 3876 0.750850 CCTTATTCGGGAAGGAGCGA 59.249 55.000 5.30 0.00 45.52 4.93
3439 3877 0.750850 TCCTTATTCGGGAAGGAGCG 59.249 55.000 8.88 0.00 46.08 5.03
3451 3889 3.569491 CTGACCCATTGCCATCCTTATT 58.431 45.455 0.00 0.00 0.00 1.40
3471 3909 1.201424 GTCCTACCCGATCCAAACCT 58.799 55.000 0.00 0.00 0.00 3.50
3605 4044 1.069823 CTCGAGAGGACCCAATGGATG 59.930 57.143 6.58 0.00 34.81 3.51
3699 4138 9.521841 TGTTAGTGGATGTTGATTTACCATAAA 57.478 29.630 0.00 0.00 33.19 1.40
3813 4256 7.025520 AGTTGATATTCAATCCCCTCCATAG 57.974 40.000 0.00 0.00 38.79 2.23
3816 4259 6.840090 TTAGTTGATATTCAATCCCCTCCA 57.160 37.500 0.00 0.00 38.79 3.86
3905 4349 2.564771 CACGCTCATATGTCCCACAAT 58.435 47.619 1.90 0.00 0.00 2.71
3921 4365 4.937431 GCTATCCCTGCCCCACGC 62.937 72.222 0.00 0.00 38.31 5.34
4048 4493 3.953612 GGATATGCTTTTGTGTCCATGGA 59.046 43.478 11.44 11.44 0.00 3.41


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

AutoCloner maintained by Alex Coulton.