Multiple sequence alignment - TraesCS5B01G044000

Loading Multiple Alignment...

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 TraesCS5B01G044000 chr5B 100.000 4036 0 0 1 4036 48982073 48978038 0.000000e+00 7454.0
1 TraesCS5B01G044000 chr5B 84.165 1263 172 18 1030 2274 51062315 51061063 0.000000e+00 1199.0
2 TraesCS5B01G044000 chr5B 84.003 1269 163 27 1030 2272 50530078 50531332 0.000000e+00 1182.0
3 TraesCS5B01G044000 chr5B 82.064 1221 183 21 1075 2271 48931308 48930100 0.000000e+00 1009.0
4 TraesCS5B01G044000 chr5B 80.531 1243 168 42 1045 2255 50226654 50227854 0.000000e+00 887.0
5 TraesCS5B01G044000 chr5B 83.824 340 46 6 179 517 62207748 62208079 8.420000e-82 315.0
6 TraesCS5B01G044000 chr5B 90.909 66 6 0 534 599 62220680 62220745 5.560000e-14 89.8
7 TraesCS5B01G044000 chr5D 92.911 1721 79 23 746 2449 46847918 46846224 0.000000e+00 2462.0
8 TraesCS5B01G044000 chr5D 93.972 1128 33 11 2463 3581 46846042 46844941 0.000000e+00 1674.0
9 TraesCS5B01G044000 chr5D 83.608 1275 177 20 1030 2282 48315081 48313817 0.000000e+00 1168.0
10 TraesCS5B01G044000 chr5D 81.507 1168 186 18 1128 2271 46732711 46731550 0.000000e+00 933.0
11 TraesCS5B01G044000 chr5D 80.800 1250 175 35 1045 2271 47280644 47281851 0.000000e+00 918.0
12 TraesCS5B01G044000 chr5D 92.358 458 31 4 3581 4036 46844896 46844441 0.000000e+00 649.0
13 TraesCS5B01G044000 chr5D 85.629 501 56 6 33 532 46849177 46848692 2.780000e-141 512.0
14 TraesCS5B01G044000 chr5D 78.399 787 140 23 1502 2282 47088337 47087575 6.060000e-133 484.0
15 TraesCS5B01G044000 chr5D 85.714 329 44 3 1532 1857 48032294 48032622 1.070000e-90 344.0
16 TraesCS5B01G044000 chr5D 82.741 394 50 9 1904 2282 47916510 47916900 6.460000e-88 335.0
17 TraesCS5B01G044000 chr5D 74.774 773 123 43 2575 3290 46607785 46608542 8.540000e-72 281.0
18 TraesCS5B01G044000 chr5D 72.553 991 214 40 1319 2271 48657025 48657995 1.850000e-68 270.0
19 TraesCS5B01G044000 chr5D 88.688 221 24 1 1531 1751 47915958 47916177 6.650000e-68 268.0
20 TraesCS5B01G044000 chr5D 78.490 437 67 13 1851 2272 48033612 48034036 1.110000e-65 261.0
21 TraesCS5B01G044000 chr5D 89.241 158 15 2 598 755 216062875 216063030 3.180000e-46 196.0
22 TraesCS5B01G044000 chr5D 88.535 157 16 2 602 758 76972625 76972471 5.330000e-44 189.0
23 TraesCS5B01G044000 chr5D 88.591 149 16 1 601 749 442957896 442957749 3.200000e-41 180.0
24 TraesCS5B01G044000 chr5D 85.057 174 24 2 1304 1476 47915775 47915947 4.150000e-40 176.0
25 TraesCS5B01G044000 chr5D 100.000 30 0 0 2368 2397 48034155 48034184 5.640000e-04 56.5
26 TraesCS5B01G044000 chr5A 95.399 1065 43 3 1391 2449 37780630 37779566 0.000000e+00 1690.0
27 TraesCS5B01G044000 chr5A 90.989 1143 53 16 2463 3581 37779384 37778268 0.000000e+00 1495.0
28 TraesCS5B01G044000 chr5A 82.548 1146 155 19 1163 2282 38055685 38054559 0.000000e+00 966.0
29 TraesCS5B01G044000 chr5A 93.987 449 24 3 3590 4036 37778215 37777768 0.000000e+00 676.0
30 TraesCS5B01G044000 chr5A 93.674 411 23 3 3628 4036 536782453 536782862 2.670000e-171 612.0
31 TraesCS5B01G044000 chr5A 73.119 997 210 38 1310 2268 38118868 38119844 1.820000e-78 303.0
32 TraesCS5B01G044000 chr5A 89.796 147 13 2 605 751 465123386 465123530 1.920000e-43 187.0
33 TraesCS5B01G044000 chr5A 97.959 98 2 0 955 1052 37780723 37780626 1.930000e-38 171.0
34 TraesCS5B01G044000 chr3A 91.485 458 33 6 3581 4036 290190612 290190159 3.420000e-175 625.0
35 TraesCS5B01G044000 chr3A 87.912 91 3 1 3491 3581 290190739 290190657 2.570000e-17 100.0
36 TraesCS5B01G044000 chr3A 86.813 91 4 1 3491 3581 91891461 91891543 1.190000e-15 95.3
37 TraesCS5B01G044000 chr1A 94.161 411 20 4 3628 4036 73429557 73429149 1.230000e-174 623.0
38 TraesCS5B01G044000 chr4A 94.132 409 21 3 3628 4034 292635699 292635292 1.590000e-173 619.0
39 TraesCS5B01G044000 chr4A 93.571 420 20 6 3619 4036 529088902 529088488 1.590000e-173 619.0
40 TraesCS5B01G044000 chr6A 93.674 411 23 3 3628 4036 508366364 508365955 2.670000e-171 612.0
41 TraesCS5B01G044000 chr6A 93.643 409 22 4 3628 4034 57851911 57852317 3.450000e-170 608.0
42 TraesCS5B01G044000 chr6A 87.912 91 3 1 3491 3581 473293164 473293246 2.570000e-17 100.0
43 TraesCS5B01G044000 chr1B 89.404 151 14 2 602 751 434646764 434646615 5.330000e-44 189.0
44 TraesCS5B01G044000 chrUn 88.387 155 16 2 602 756 97328439 97328287 6.890000e-43 185.0
45 TraesCS5B01G044000 chr2B 88.667 150 16 1 602 751 46413715 46413863 8.910000e-42 182.0
46 TraesCS5B01G044000 chr2B 88.079 151 16 2 601 751 38017361 38017213 1.150000e-40 178.0
47 TraesCS5B01G044000 chr3B 86.503 163 18 3 596 758 698121176 698121018 4.150000e-40 176.0


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 TraesCS5B01G044000 chr5B 48978038 48982073 4035 True 7454.000000 7454 100.000000 1 4036 1 chr5B.!!$R2 4035
1 TraesCS5B01G044000 chr5B 51061063 51062315 1252 True 1199.000000 1199 84.165000 1030 2274 1 chr5B.!!$R3 1244
2 TraesCS5B01G044000 chr5B 50530078 50531332 1254 False 1182.000000 1182 84.003000 1030 2272 1 chr5B.!!$F2 1242
3 TraesCS5B01G044000 chr5B 48930100 48931308 1208 True 1009.000000 1009 82.064000 1075 2271 1 chr5B.!!$R1 1196
4 TraesCS5B01G044000 chr5B 50226654 50227854 1200 False 887.000000 887 80.531000 1045 2255 1 chr5B.!!$F1 1210
5 TraesCS5B01G044000 chr5D 46844441 46849177 4736 True 1324.250000 2462 91.217500 33 4036 4 chr5D.!!$R6 4003
6 TraesCS5B01G044000 chr5D 48313817 48315081 1264 True 1168.000000 1168 83.608000 1030 2282 1 chr5D.!!$R3 1252
7 TraesCS5B01G044000 chr5D 46731550 46732711 1161 True 933.000000 933 81.507000 1128 2271 1 chr5D.!!$R1 1143
8 TraesCS5B01G044000 chr5D 47280644 47281851 1207 False 918.000000 918 80.800000 1045 2271 1 chr5D.!!$F2 1226
9 TraesCS5B01G044000 chr5D 47087575 47088337 762 True 484.000000 484 78.399000 1502 2282 1 chr5D.!!$R2 780
10 TraesCS5B01G044000 chr5D 46607785 46608542 757 False 281.000000 281 74.774000 2575 3290 1 chr5D.!!$F1 715
11 TraesCS5B01G044000 chr5D 48657025 48657995 970 False 270.000000 270 72.553000 1319 2271 1 chr5D.!!$F3 952
12 TraesCS5B01G044000 chr5D 47915775 47916900 1125 False 259.666667 335 85.495333 1304 2282 3 chr5D.!!$F5 978
13 TraesCS5B01G044000 chr5D 48032294 48034184 1890 False 220.500000 344 88.068000 1532 2397 3 chr5D.!!$F6 865
14 TraesCS5B01G044000 chr5A 37777768 37780723 2955 True 1008.000000 1690 94.583500 955 4036 4 chr5A.!!$R2 3081
15 TraesCS5B01G044000 chr5A 38054559 38055685 1126 True 966.000000 966 82.548000 1163 2282 1 chr5A.!!$R1 1119
16 TraesCS5B01G044000 chr5A 38118868 38119844 976 False 303.000000 303 73.119000 1310 2268 1 chr5A.!!$F1 958
17 TraesCS5B01G044000 chr3A 290190159 290190739 580 True 362.500000 625 89.698500 3491 4036 2 chr3A.!!$R1 545

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
849 1556 0.030638 TTTGCTTTTGTCAGGCTCGC 59.969 50.0 0.00 0.0 0.00 5.03 F
904 1611 0.409876 TGCCAGGAGTCTACAGGAGT 59.590 55.0 0.00 0.0 0.00 3.85 F
2258 4317 0.040204 CTTCCACCCTGGCTTGGATT 59.960 55.0 14.16 0.0 41.65 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2021 4046 1.536180 TGGTGCTCCAGCTTCCAAA 59.464 52.632 2.64 0.0 40.46 3.28 R
2421 4524 2.038426 CCTCACCACCATCTACAACACA 59.962 50.000 0.00 0.0 0.00 3.72 R
3406 5759 2.027653 GCAGCCCCTCCATCTATTAGTC 60.028 54.545 0.00 0.0 0.00 2.59 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
22 23 5.372343 AAATCAGAAAACCAAAAAGGCCT 57.628 34.783 0.00 0.00 43.14 5.19
23 24 3.817709 TCAGAAAACCAAAAAGGCCTG 57.182 42.857 5.69 0.00 43.14 4.85
24 25 2.433970 TCAGAAAACCAAAAAGGCCTGG 59.566 45.455 5.69 6.62 43.14 4.45
25 26 2.433970 CAGAAAACCAAAAAGGCCTGGA 59.566 45.455 15.38 0.00 43.14 3.86
26 27 3.111484 AGAAAACCAAAAAGGCCTGGAA 58.889 40.909 15.38 0.00 43.14 3.53
27 28 3.716353 AGAAAACCAAAAAGGCCTGGAAT 59.284 39.130 15.38 1.41 43.14 3.01
28 29 4.165950 AGAAAACCAAAAAGGCCTGGAATT 59.834 37.500 15.38 9.10 43.14 2.17
29 30 5.368230 AGAAAACCAAAAAGGCCTGGAATTA 59.632 36.000 15.38 0.00 43.14 1.40
30 31 5.638530 AAACCAAAAAGGCCTGGAATTAA 57.361 34.783 15.38 0.00 43.14 1.40
31 32 4.890158 ACCAAAAAGGCCTGGAATTAAG 57.110 40.909 15.38 0.00 43.14 1.85
75 76 9.638176 AAAGTTGCCTGAAGATATAAGATCAAT 57.362 29.630 0.00 0.00 0.00 2.57
88 89 8.985315 ATATAAGATCAATGAAACAGAGCCAA 57.015 30.769 0.00 0.00 0.00 4.52
91 92 6.600882 AGATCAATGAAACAGAGCCAAAAT 57.399 33.333 0.00 0.00 0.00 1.82
96 97 6.041409 TCAATGAAACAGAGCCAAAATGGTAA 59.959 34.615 0.00 0.00 40.46 2.85
99 100 5.596361 TGAAACAGAGCCAAAATGGTAAGAA 59.404 36.000 0.00 0.00 40.46 2.52
108 109 5.234116 GCCAAAATGGTAAGAACACAAAGTG 59.766 40.000 0.00 0.00 40.46 3.16
133 134 5.948842 AGGTAACCAAATGTGTAAAGGACT 58.051 37.500 0.00 0.00 37.17 3.85
144 145 5.804639 TGTGTAAAGGACTAGTGCATCAAT 58.195 37.500 17.34 0.41 0.00 2.57
145 146 5.874810 TGTGTAAAGGACTAGTGCATCAATC 59.125 40.000 17.34 3.79 0.00 2.67
153 154 6.150307 AGGACTAGTGCATCAATCGTAGATAG 59.850 42.308 17.34 0.00 45.12 2.08
158 159 5.184096 AGTGCATCAATCGTAGATAGTAGGG 59.816 44.000 0.00 0.00 45.12 3.53
182 183 7.365117 GGGAGGAAGTATGACATAGGGAATATG 60.365 44.444 0.00 0.00 45.86 1.78
199 200 8.426489 AGGGAATATGTATAAGCGTGAAAACTA 58.574 33.333 0.00 0.00 0.00 2.24
221 222 9.908747 AACTATGACAACATACTAGTCTAGTCT 57.091 33.333 15.94 3.92 40.14 3.24
231 232 9.969001 ACATACTAGTCTAGTCTTTCTTCTTCT 57.031 33.333 15.94 0.00 40.14 2.85
244 245 0.984230 TTCTTCTTCGATGCCCCTGT 59.016 50.000 0.00 0.00 0.00 4.00
247 248 2.819984 TTCTTCGATGCCCCTGTGCC 62.820 60.000 0.00 0.00 0.00 5.01
257 258 1.296392 CCCTGTGCCATCGTCTTGA 59.704 57.895 0.00 0.00 0.00 3.02
278 279 2.594592 GGACGCTTGCCAGTGGTT 60.595 61.111 11.74 0.00 34.49 3.67
279 280 2.639286 GACGCTTGCCAGTGGTTG 59.361 61.111 11.74 2.46 34.49 3.77
286 287 2.028484 GCCAGTGGTTGTCGTCGA 59.972 61.111 11.74 0.00 0.00 4.20
298 299 4.517703 CGTCGACTCCGTCCTCGC 62.518 72.222 14.70 0.00 37.05 5.03
313 314 0.393132 CTCGCCCTTTTCCTTCTCCC 60.393 60.000 0.00 0.00 0.00 4.30
314 315 1.378646 CGCCCTTTTCCTTCTCCCC 60.379 63.158 0.00 0.00 0.00 4.81
315 316 1.000486 GCCCTTTTCCTTCTCCCCC 60.000 63.158 0.00 0.00 0.00 5.40
316 317 1.510431 GCCCTTTTCCTTCTCCCCCT 61.510 60.000 0.00 0.00 0.00 4.79
317 318 0.626382 CCCTTTTCCTTCTCCCCCTC 59.374 60.000 0.00 0.00 0.00 4.30
318 319 0.626382 CCTTTTCCTTCTCCCCCTCC 59.374 60.000 0.00 0.00 0.00 4.30
319 320 1.675007 CTTTTCCTTCTCCCCCTCCT 58.325 55.000 0.00 0.00 0.00 3.69
320 321 1.562008 CTTTTCCTTCTCCCCCTCCTC 59.438 57.143 0.00 0.00 0.00 3.71
321 322 0.253207 TTTCCTTCTCCCCCTCCTCC 60.253 60.000 0.00 0.00 0.00 4.30
322 323 1.162951 TTCCTTCTCCCCCTCCTCCT 61.163 60.000 0.00 0.00 0.00 3.69
323 324 1.074850 CCTTCTCCCCCTCCTCCTC 60.075 68.421 0.00 0.00 0.00 3.71
324 325 1.074850 CTTCTCCCCCTCCTCCTCC 60.075 68.421 0.00 0.00 0.00 4.30
330 331 2.328589 CCCCTCCTCCTCCTCCTCA 61.329 68.421 0.00 0.00 0.00 3.86
365 366 4.081406 TCTTCATCATGGTTCTTTGGGTG 58.919 43.478 0.00 0.00 0.00 4.61
368 369 1.909700 TCATGGTTCTTTGGGTGCTC 58.090 50.000 0.00 0.00 0.00 4.26
375 376 3.264845 TTTGGGTGCTCCTCCCCC 61.265 66.667 4.53 0.00 44.00 5.40
392 393 2.344203 CCGACTCGGGCTCTGACTT 61.344 63.158 9.85 0.00 44.15 3.01
393 394 1.030488 CCGACTCGGGCTCTGACTTA 61.030 60.000 9.85 0.00 44.15 2.24
395 396 1.465794 GACTCGGGCTCTGACTTAGT 58.534 55.000 0.00 0.00 0.00 2.24
401 402 1.478916 GGGCTCTGACTTAGTGGTCTC 59.521 57.143 0.00 0.00 37.16 3.36
416 418 2.830370 CTCCGATGGGGCTTTGGC 60.830 66.667 0.00 0.00 34.94 4.52
430 432 2.883888 GCTTTGGCCCTTCCATGAACTA 60.884 50.000 0.00 0.00 46.04 2.24
433 435 2.274542 TGGCCCTTCCATGAACTAGAA 58.725 47.619 0.00 0.00 40.72 2.10
468 470 2.435938 GCGAGGGCGGTTTGATGA 60.436 61.111 0.00 0.00 38.16 2.92
473 475 0.532115 AGGGCGGTTTGATGAATTGC 59.468 50.000 0.00 0.00 0.00 3.56
478 480 1.795162 CGGTTTGATGAATTGCGAGCC 60.795 52.381 0.00 0.00 0.00 4.70
485 487 0.392327 TGAATTGCGAGCCCGATGAA 60.392 50.000 0.00 0.00 38.22 2.57
492 494 0.319383 CGAGCCCGATGAATCCTCAG 60.319 60.000 0.00 0.00 38.22 3.35
499 501 3.369892 CCCGATGAATCCTCAGTTGAAGT 60.370 47.826 0.00 0.00 34.23 3.01
502 504 4.931601 CGATGAATCCTCAGTTGAAGTGAA 59.068 41.667 4.07 0.00 34.23 3.18
505 507 5.059161 TGAATCCTCAGTTGAAGTGAACAG 58.941 41.667 4.07 0.00 0.00 3.16
507 509 4.963318 TCCTCAGTTGAAGTGAACAGAT 57.037 40.909 4.07 0.00 0.00 2.90
510 512 4.214971 CCTCAGTTGAAGTGAACAGATTGG 59.785 45.833 4.07 0.00 0.00 3.16
512 514 4.816385 TCAGTTGAAGTGAACAGATTGGTC 59.184 41.667 0.00 0.00 33.88 4.02
517 519 3.753294 AGTGAACAGATTGGTCGTCTT 57.247 42.857 0.00 0.00 36.73 3.01
521 523 3.069586 TGAACAGATTGGTCGTCTTGTCT 59.930 43.478 0.00 0.00 36.73 3.41
525 527 1.390463 GATTGGTCGTCTTGTCTTCGC 59.610 52.381 0.00 0.00 0.00 4.70
532 534 1.016653 GTCTTGTCTTCGCTGGAGGC 61.017 60.000 0.00 0.00 37.64 4.70
533 535 1.188219 TCTTGTCTTCGCTGGAGGCT 61.188 55.000 0.00 0.00 39.13 4.58
548 1254 2.508526 GAGGCTTCCAACAACTGATGT 58.491 47.619 0.00 0.00 46.82 3.06
554 1260 4.555511 GCTTCCAACAACTGATGTCACTTC 60.556 45.833 0.00 0.00 42.99 3.01
556 1262 4.522114 TCCAACAACTGATGTCACTTCAA 58.478 39.130 0.00 0.00 42.99 2.69
557 1263 4.335315 TCCAACAACTGATGTCACTTCAAC 59.665 41.667 0.00 0.00 42.99 3.18
581 1288 1.635487 TGGGAGGCTTGCAGTCTATTT 59.365 47.619 0.00 0.00 24.78 1.40
607 1314 5.527951 TCAAATTTGAAATTGGTGAGGACG 58.472 37.500 18.45 0.00 33.55 4.79
608 1315 4.519540 AATTTGAAATTGGTGAGGACGG 57.480 40.909 1.78 0.00 0.00 4.79
609 1316 1.904287 TTGAAATTGGTGAGGACGGG 58.096 50.000 0.00 0.00 0.00 5.28
610 1317 0.037590 TGAAATTGGTGAGGACGGGG 59.962 55.000 0.00 0.00 0.00 5.73
611 1318 1.304134 AAATTGGTGAGGACGGGGC 60.304 57.895 0.00 0.00 0.00 5.80
612 1319 3.622060 AATTGGTGAGGACGGGGCG 62.622 63.158 0.00 0.00 0.00 6.13
626 1333 4.814294 GGCGTCGATCCGTTGGCT 62.814 66.667 0.00 0.00 0.00 4.75
627 1334 3.554692 GCGTCGATCCGTTGGCTG 61.555 66.667 0.00 0.00 0.00 4.85
628 1335 2.885644 CGTCGATCCGTTGGCTGG 60.886 66.667 0.00 0.00 0.00 4.85
629 1336 2.511600 GTCGATCCGTTGGCTGGG 60.512 66.667 0.00 0.00 0.00 4.45
630 1337 4.467084 TCGATCCGTTGGCTGGGC 62.467 66.667 0.00 0.00 0.00 5.36
631 1338 4.776322 CGATCCGTTGGCTGGGCA 62.776 66.667 0.00 0.00 0.00 5.36
632 1339 2.825836 GATCCGTTGGCTGGGCAG 60.826 66.667 0.00 0.00 0.00 4.85
651 1358 1.901085 CTGGGGTAGCTGTCAGTCC 59.099 63.158 0.00 2.43 0.00 3.85
652 1359 0.904865 CTGGGGTAGCTGTCAGTCCA 60.905 60.000 0.00 2.07 0.00 4.02
653 1360 1.192146 TGGGGTAGCTGTCAGTCCAC 61.192 60.000 0.00 4.20 0.00 4.02
654 1361 0.905337 GGGGTAGCTGTCAGTCCACT 60.905 60.000 0.00 0.00 0.00 4.00
655 1362 0.533032 GGGTAGCTGTCAGTCCACTC 59.467 60.000 0.00 0.00 0.00 3.51
656 1363 1.257743 GGTAGCTGTCAGTCCACTCA 58.742 55.000 0.00 0.00 0.00 3.41
657 1364 1.618837 GGTAGCTGTCAGTCCACTCAA 59.381 52.381 0.00 0.00 0.00 3.02
658 1365 2.353208 GGTAGCTGTCAGTCCACTCAAG 60.353 54.545 0.00 0.00 0.00 3.02
659 1366 1.418334 AGCTGTCAGTCCACTCAAGT 58.582 50.000 0.93 0.00 0.00 3.16
660 1367 1.765314 AGCTGTCAGTCCACTCAAGTT 59.235 47.619 0.93 0.00 0.00 2.66
661 1368 2.139118 GCTGTCAGTCCACTCAAGTTC 58.861 52.381 0.93 0.00 0.00 3.01
662 1369 2.398498 CTGTCAGTCCACTCAAGTTCG 58.602 52.381 0.00 0.00 0.00 3.95
663 1370 2.028876 TGTCAGTCCACTCAAGTTCGA 58.971 47.619 0.00 0.00 0.00 3.71
664 1371 2.034685 TGTCAGTCCACTCAAGTTCGAG 59.965 50.000 0.00 0.00 39.05 4.04
665 1372 1.000163 TCAGTCCACTCAAGTTCGAGC 60.000 52.381 0.00 0.00 36.42 5.03
666 1373 0.318762 AGTCCACTCAAGTTCGAGCC 59.681 55.000 0.00 0.00 36.42 4.70
667 1374 0.670854 GTCCACTCAAGTTCGAGCCC 60.671 60.000 0.00 0.00 36.42 5.19
668 1375 1.376037 CCACTCAAGTTCGAGCCCC 60.376 63.158 0.00 0.00 36.42 5.80
669 1376 1.738099 CACTCAAGTTCGAGCCCCG 60.738 63.158 0.00 0.00 36.42 5.73
670 1377 2.125512 CTCAAGTTCGAGCCCCGG 60.126 66.667 0.00 0.00 39.14 5.73
671 1378 4.388499 TCAAGTTCGAGCCCCGGC 62.388 66.667 0.00 0.00 42.33 6.13
696 1403 2.356313 CGCGGTGCTCACAGAGTT 60.356 61.111 0.00 0.00 31.39 3.01
697 1404 1.956170 CGCGGTGCTCACAGAGTTT 60.956 57.895 0.00 0.00 31.39 2.66
698 1405 1.862806 GCGGTGCTCACAGAGTTTC 59.137 57.895 4.40 0.00 31.39 2.78
699 1406 0.601311 GCGGTGCTCACAGAGTTTCT 60.601 55.000 4.40 0.00 31.39 2.52
700 1407 1.423395 CGGTGCTCACAGAGTTTCTC 58.577 55.000 2.21 0.00 31.39 2.87
701 1408 1.802069 GGTGCTCACAGAGTTTCTCC 58.198 55.000 2.21 0.00 31.39 3.71
702 1409 1.346068 GGTGCTCACAGAGTTTCTCCT 59.654 52.381 2.21 0.00 31.39 3.69
703 1410 2.563179 GGTGCTCACAGAGTTTCTCCTA 59.437 50.000 2.21 0.00 31.39 2.94
704 1411 3.196685 GGTGCTCACAGAGTTTCTCCTAT 59.803 47.826 2.21 0.00 31.39 2.57
705 1412 4.402793 GGTGCTCACAGAGTTTCTCCTATA 59.597 45.833 2.21 0.00 31.39 1.31
706 1413 5.105310 GGTGCTCACAGAGTTTCTCCTATAA 60.105 44.000 2.21 0.00 31.39 0.98
707 1414 6.398918 GTGCTCACAGAGTTTCTCCTATAAA 58.601 40.000 0.00 0.00 31.39 1.40
708 1415 6.874134 GTGCTCACAGAGTTTCTCCTATAAAA 59.126 38.462 0.00 0.00 31.39 1.52
709 1416 7.387948 GTGCTCACAGAGTTTCTCCTATAAAAA 59.612 37.037 0.00 0.00 31.39 1.94
729 1436 4.954933 TGCCAACGAGGGATTAGC 57.045 55.556 0.00 0.00 38.09 3.09
730 1437 1.223487 TGCCAACGAGGGATTAGCC 59.777 57.895 0.00 0.00 38.09 3.93
740 1447 3.207452 GGATTAGCCCTTGGGTTGG 57.793 57.895 7.61 0.00 34.28 3.77
741 1448 0.335019 GGATTAGCCCTTGGGTTGGT 59.665 55.000 7.61 0.00 34.28 3.67
742 1449 1.685180 GGATTAGCCCTTGGGTTGGTC 60.685 57.143 7.61 4.38 34.28 4.02
743 1450 1.285078 GATTAGCCCTTGGGTTGGTCT 59.715 52.381 7.61 0.00 34.28 3.85
744 1451 0.696501 TTAGCCCTTGGGTTGGTCTC 59.303 55.000 7.61 0.00 34.28 3.36
745 1452 0.474854 TAGCCCTTGGGTTGGTCTCA 60.475 55.000 7.61 0.00 34.28 3.27
751 1458 3.006859 CCCTTGGGTTGGTCTCATTTTTC 59.993 47.826 0.00 0.00 0.00 2.29
754 1461 5.163311 CCTTGGGTTGGTCTCATTTTTCTTT 60.163 40.000 0.00 0.00 0.00 2.52
802 1509 1.600023 AAGGTTCAAATTCGGTCGCA 58.400 45.000 0.00 0.00 0.00 5.10
848 1555 2.033299 TCTTTTGCTTTTGTCAGGCTCG 59.967 45.455 0.00 0.00 0.00 5.03
849 1556 0.030638 TTTGCTTTTGTCAGGCTCGC 59.969 50.000 0.00 0.00 0.00 5.03
850 1557 0.819259 TTGCTTTTGTCAGGCTCGCT 60.819 50.000 0.00 0.00 0.00 4.93
851 1558 1.208614 GCTTTTGTCAGGCTCGCTG 59.791 57.895 0.00 0.00 0.00 5.18
852 1559 1.871772 CTTTTGTCAGGCTCGCTGG 59.128 57.895 0.00 0.00 0.00 4.85
853 1560 2.192608 CTTTTGTCAGGCTCGCTGGC 62.193 60.000 0.00 0.00 42.15 4.85
904 1611 0.409876 TGCCAGGAGTCTACAGGAGT 59.590 55.000 0.00 0.00 0.00 3.85
908 1615 3.547746 CCAGGAGTCTACAGGAGTCTAC 58.452 54.545 0.00 0.00 42.44 2.59
910 1617 4.567958 CCAGGAGTCTACAGGAGTCTACAA 60.568 50.000 0.00 0.00 42.44 2.41
911 1618 4.638421 CAGGAGTCTACAGGAGTCTACAAG 59.362 50.000 0.00 0.00 42.44 3.16
912 1619 4.536888 AGGAGTCTACAGGAGTCTACAAGA 59.463 45.833 0.00 0.00 42.44 3.02
913 1620 4.879545 GGAGTCTACAGGAGTCTACAAGAG 59.120 50.000 0.00 0.00 42.44 2.85
926 1633 4.809193 TCTACAAGAGACTAGCCCATCAT 58.191 43.478 0.00 0.00 0.00 2.45
982 1693 4.477975 CTGCGAGGACCGACGGAC 62.478 72.222 23.38 15.26 41.76 4.79
1308 2046 1.262640 ACGGCGTCCTCCAATACCTT 61.263 55.000 6.77 0.00 0.00 3.50
1317 2055 2.271940 CCAATACCTTGGCGGCAAA 58.728 52.632 25.45 11.54 45.28 3.68
1656 2412 1.978580 TCTGAGGAAGGGAAGTGGAAC 59.021 52.381 0.00 0.00 0.00 3.62
2185 4235 3.058016 CGTGGACATGCATAATGGGAATC 60.058 47.826 0.00 0.00 40.94 2.52
2258 4317 0.040204 CTTCCACCCTGGCTTGGATT 59.960 55.000 14.16 0.00 41.65 3.01
2341 4425 3.691118 GGTGCATTGCTTCAGATGTTCTA 59.309 43.478 10.49 0.00 0.00 2.10
2357 4441 2.436173 GTTCTATGCTAGCTTGGGGAGT 59.564 50.000 17.23 0.00 0.00 3.85
2449 4552 4.474651 TGTAGATGGTGGTGAGGAATTGAT 59.525 41.667 0.00 0.00 0.00 2.57
2450 4553 3.894759 AGATGGTGGTGAGGAATTGATG 58.105 45.455 0.00 0.00 0.00 3.07
2451 4554 3.524789 AGATGGTGGTGAGGAATTGATGA 59.475 43.478 0.00 0.00 0.00 2.92
2452 4555 3.805066 TGGTGGTGAGGAATTGATGAA 57.195 42.857 0.00 0.00 0.00 2.57
2453 4556 4.320546 TGGTGGTGAGGAATTGATGAAT 57.679 40.909 0.00 0.00 0.00 2.57
2455 4558 5.085920 TGGTGGTGAGGAATTGATGAATTT 58.914 37.500 0.00 0.00 31.58 1.82
2456 4559 5.543405 TGGTGGTGAGGAATTGATGAATTTT 59.457 36.000 0.00 0.00 31.58 1.82
2459 4562 6.366877 GTGGTGAGGAATTGATGAATTTTGTG 59.633 38.462 0.00 0.00 31.58 3.33
2461 4564 7.038870 TGGTGAGGAATTGATGAATTTTGTGAT 60.039 33.333 0.00 0.00 31.58 3.06
2462 4565 7.820872 GGTGAGGAATTGATGAATTTTGTGATT 59.179 33.333 0.00 0.00 31.58 2.57
2463 4566 8.653338 GTGAGGAATTGATGAATTTTGTGATTG 58.347 33.333 0.00 0.00 31.58 2.67
2464 4567 7.820386 TGAGGAATTGATGAATTTTGTGATTGG 59.180 33.333 0.00 0.00 31.58 3.16
2465 4568 7.682628 AGGAATTGATGAATTTTGTGATTGGT 58.317 30.769 0.00 0.00 31.58 3.67
2466 4569 8.814931 AGGAATTGATGAATTTTGTGATTGGTA 58.185 29.630 0.00 0.00 31.58 3.25
2676 4949 9.900264 GTTTCTGTGAATTTTGAATTTACACAC 57.100 29.630 6.84 0.00 34.08 3.82
2709 4983 8.607459 GTTCTACATGTTATTTCCACATCTCTG 58.393 37.037 2.30 0.00 32.25 3.35
2731 5031 7.156000 TCTGTATGTCGTTTTCAGTTAATGGA 58.844 34.615 0.00 0.00 0.00 3.41
2765 5079 6.947733 TCTTGTTTATTCAACTGATCACCCAT 59.052 34.615 0.00 0.00 36.21 4.00
2936 5267 8.470040 TTGTTCCGAGTTAACATAGATTGTAC 57.530 34.615 8.61 0.00 37.68 2.90
2937 5268 7.833786 TGTTCCGAGTTAACATAGATTGTACT 58.166 34.615 8.61 0.00 37.68 2.73
2938 5269 8.959548 TGTTCCGAGTTAACATAGATTGTACTA 58.040 33.333 8.61 0.00 37.68 1.82
2939 5270 9.793252 GTTCCGAGTTAACATAGATTGTACTAA 57.207 33.333 8.61 0.00 37.68 2.24
3140 5493 3.090210 AGTCATCCATTGGCATTGTCA 57.910 42.857 8.42 0.00 29.99 3.58
3141 5494 3.021695 AGTCATCCATTGGCATTGTCAG 58.978 45.455 8.42 0.00 29.99 3.51
3142 5495 2.756760 GTCATCCATTGGCATTGTCAGT 59.243 45.455 8.42 0.00 0.00 3.41
3242 5595 7.331791 ACTGTTGAGAAGTCTAAAACTGAAGT 58.668 34.615 14.75 6.31 38.58 3.01
3336 5689 6.687081 TGGTGTTTATTCCATTATTCGTCC 57.313 37.500 0.00 0.00 0.00 4.79
3349 5702 6.095440 CCATTATTCGTCCTTCTTTTCCATGT 59.905 38.462 0.00 0.00 0.00 3.21
3350 5703 7.362920 CCATTATTCGTCCTTCTTTTCCATGTT 60.363 37.037 0.00 0.00 0.00 2.71
3351 5704 4.829064 TTCGTCCTTCTTTTCCATGTTG 57.171 40.909 0.00 0.00 0.00 3.33
3352 5705 3.146066 TCGTCCTTCTTTTCCATGTTGG 58.854 45.455 0.00 0.00 39.43 3.77
3353 5706 2.351738 CGTCCTTCTTTTCCATGTTGGC 60.352 50.000 0.00 0.00 37.47 4.52
3354 5707 2.893489 GTCCTTCTTTTCCATGTTGGCT 59.107 45.455 0.00 0.00 37.47 4.75
3355 5708 3.321968 GTCCTTCTTTTCCATGTTGGCTT 59.678 43.478 0.00 0.00 37.47 4.35
3356 5709 3.321682 TCCTTCTTTTCCATGTTGGCTTG 59.678 43.478 0.00 0.00 37.47 4.01
3424 5777 1.909986 GGGACTAATAGATGGAGGGGC 59.090 57.143 0.00 0.00 0.00 5.80
3461 5814 1.202770 AGAAGCTGGCGGTAGTTTGTT 60.203 47.619 0.00 0.00 0.00 2.83
3477 5830 5.351458 AGTTTGTTGAACTCTCATTTTGGC 58.649 37.500 0.00 0.00 45.40 4.52
3502 5856 8.968242 GCGAAATCTGGAATATTTTGGATTTAC 58.032 33.333 16.22 11.43 34.78 2.01
3520 5874 8.375506 TGGATTTACTGTAGTTTCTTGATGAGT 58.624 33.333 0.00 0.00 0.00 3.41
3521 5875 9.220767 GGATTTACTGTAGTTTCTTGATGAGTT 57.779 33.333 0.00 0.00 0.00 3.01
3524 5878 9.485206 TTTACTGTAGTTTCTTGATGAGTTACC 57.515 33.333 0.00 0.00 0.00 2.85
3525 5879 7.062749 ACTGTAGTTTCTTGATGAGTTACCA 57.937 36.000 0.00 0.00 0.00 3.25
3526 5880 7.506114 ACTGTAGTTTCTTGATGAGTTACCAA 58.494 34.615 0.00 0.00 0.00 3.67
3527 5881 7.441458 ACTGTAGTTTCTTGATGAGTTACCAAC 59.559 37.037 0.00 0.00 0.00 3.77
3581 5935 4.825085 GTTGGTTCAACAGTCCATTAGGAA 59.175 41.667 5.97 0.00 43.68 3.36
3583 5937 6.183360 GTTGGTTCAACAGTCCATTAGGAAAA 60.183 38.462 5.97 0.00 43.68 2.29
3584 5938 8.158141 GTTGGTTCAACAGTCCATTAGGAAAAC 61.158 40.741 5.97 0.00 43.68 2.43
3612 6010 5.342806 TGAATGAAGTTACTTGCAAGACG 57.657 39.130 32.50 8.13 0.00 4.18
3627 6025 4.877823 TGCAAGACGATATGCTCATCTTTT 59.122 37.500 11.13 0.00 42.97 2.27
3643 6041 8.008279 GCTCATCTTTTTCTTTTCAAATTCAGC 58.992 33.333 0.00 0.00 0.00 4.26
3687 6086 6.991938 TCTTTTTGTAGGAAAACATGGATGG 58.008 36.000 0.00 0.00 0.00 3.51
3763 6162 6.983307 TGAATTGATGAATGTTTCAACGGTTT 59.017 30.769 0.00 0.00 43.95 3.27
3771 6170 8.167605 TGAATGTTTCAACGGTTTAGGATTTA 57.832 30.769 0.00 0.00 36.59 1.40
3797 6196 5.021033 TGACAAATGCATGTTTTTCACCT 57.979 34.783 0.00 0.00 32.57 4.00
3817 6216 4.520492 ACCTCCTTTATTGCTTGACAACAG 59.480 41.667 0.00 0.00 42.27 3.16
3927 6327 5.457140 TCAACGCACAACAATCCTTTTATC 58.543 37.500 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.125356 CAGGCCTTTTTGGTTTTCTGATTT 58.875 37.500 0.00 0.00 38.35 2.17
1 2 4.444733 CCAGGCCTTTTTGGTTTTCTGATT 60.445 41.667 0.00 0.00 38.35 2.57
2 3 3.071457 CCAGGCCTTTTTGGTTTTCTGAT 59.929 43.478 0.00 0.00 38.35 2.90
3 4 2.433970 CCAGGCCTTTTTGGTTTTCTGA 59.566 45.455 0.00 0.00 38.35 3.27
4 5 2.433970 TCCAGGCCTTTTTGGTTTTCTG 59.566 45.455 0.00 0.00 38.35 3.02
5 6 2.758130 TCCAGGCCTTTTTGGTTTTCT 58.242 42.857 0.00 0.00 38.35 2.52
6 7 3.552132 TTCCAGGCCTTTTTGGTTTTC 57.448 42.857 0.00 0.00 38.35 2.29
7 8 4.518278 AATTCCAGGCCTTTTTGGTTTT 57.482 36.364 0.00 0.00 38.35 2.43
8 9 5.368230 TCTTAATTCCAGGCCTTTTTGGTTT 59.632 36.000 0.00 3.86 38.35 3.27
9 10 4.904853 TCTTAATTCCAGGCCTTTTTGGTT 59.095 37.500 0.00 0.00 38.35 3.67
10 11 4.488770 TCTTAATTCCAGGCCTTTTTGGT 58.511 39.130 0.00 0.00 38.35 3.67
11 12 5.187576 TGATCTTAATTCCAGGCCTTTTTGG 59.812 40.000 0.00 1.27 39.35 3.28
12 13 6.101997 GTGATCTTAATTCCAGGCCTTTTTG 58.898 40.000 0.00 0.00 0.00 2.44
13 14 5.779771 TGTGATCTTAATTCCAGGCCTTTTT 59.220 36.000 0.00 0.00 0.00 1.94
14 15 5.332743 TGTGATCTTAATTCCAGGCCTTTT 58.667 37.500 0.00 0.00 0.00 2.27
15 16 4.934356 TGTGATCTTAATTCCAGGCCTTT 58.066 39.130 0.00 0.00 0.00 3.11
16 17 4.591321 TGTGATCTTAATTCCAGGCCTT 57.409 40.909 0.00 0.00 0.00 4.35
17 18 4.803329 ATGTGATCTTAATTCCAGGCCT 57.197 40.909 0.00 0.00 0.00 5.19
18 19 8.814038 ATATAATGTGATCTTAATTCCAGGCC 57.186 34.615 0.00 0.00 0.00 5.19
19 20 9.678260 AGATATAATGTGATCTTAATTCCAGGC 57.322 33.333 0.00 0.00 0.00 4.85
53 54 9.631257 TTTCATTGATCTTATATCTTCAGGCAA 57.369 29.630 0.00 0.00 0.00 4.52
75 76 5.136828 TCTTACCATTTTGGCTCTGTTTCA 58.863 37.500 0.00 0.00 42.67 2.69
88 89 6.831868 ACCTACACTTTGTGTTCTTACCATTT 59.168 34.615 8.67 0.00 45.08 2.32
91 92 5.362105 ACCTACACTTTGTGTTCTTACCA 57.638 39.130 8.67 0.00 45.08 3.25
96 97 5.362105 TGGTTACCTACACTTTGTGTTCT 57.638 39.130 8.67 0.00 45.08 3.01
108 109 6.938596 AGTCCTTTACACATTTGGTTACCTAC 59.061 38.462 2.07 0.00 0.00 3.18
133 134 6.374613 CCCTACTATCTACGATTGATGCACTA 59.625 42.308 0.00 0.00 0.00 2.74
144 145 6.499699 TCATACTTCCTCCCTACTATCTACGA 59.500 42.308 0.00 0.00 0.00 3.43
145 146 6.594937 GTCATACTTCCTCCCTACTATCTACG 59.405 46.154 0.00 0.00 0.00 3.51
153 154 4.773149 CCCTATGTCATACTTCCTCCCTAC 59.227 50.000 0.00 0.00 0.00 3.18
158 159 8.140112 ACATATTCCCTATGTCATACTTCCTC 57.860 38.462 0.00 0.00 45.99 3.71
182 183 7.735500 TGTTGTCATAGTTTTCACGCTTATAC 58.264 34.615 0.00 0.00 0.00 1.47
183 184 7.892778 TGTTGTCATAGTTTTCACGCTTATA 57.107 32.000 0.00 0.00 0.00 0.98
199 200 9.469097 AGAAAGACTAGACTAGTATGTTGTCAT 57.531 33.333 15.18 7.18 39.59 3.06
201 202 9.777575 GAAGAAAGACTAGACTAGTATGTTGTC 57.222 37.037 15.18 8.31 39.59 3.18
221 222 2.305927 AGGGGCATCGAAGAAGAAGAAA 59.694 45.455 0.00 0.00 43.58 2.52
224 225 1.065854 ACAGGGGCATCGAAGAAGAAG 60.066 52.381 0.00 0.00 43.58 2.85
230 231 2.825836 GGCACAGGGGCATCGAAG 60.826 66.667 0.00 0.00 42.77 3.79
244 245 1.066858 GTCCTCTTCAAGACGATGGCA 60.067 52.381 0.00 0.00 0.00 4.92
257 258 1.302033 CACTGGCAAGCGTCCTCTT 60.302 57.895 0.00 0.00 0.00 2.85
298 299 0.626382 GAGGGGGAGAAGGAAAAGGG 59.374 60.000 0.00 0.00 0.00 3.95
313 314 0.178935 GATGAGGAGGAGGAGGAGGG 60.179 65.000 0.00 0.00 0.00 4.30
314 315 0.560193 TGATGAGGAGGAGGAGGAGG 59.440 60.000 0.00 0.00 0.00 4.30
315 316 1.703411 GTGATGAGGAGGAGGAGGAG 58.297 60.000 0.00 0.00 0.00 3.69
316 317 0.263172 GGTGATGAGGAGGAGGAGGA 59.737 60.000 0.00 0.00 0.00 3.71
317 318 1.112315 CGGTGATGAGGAGGAGGAGG 61.112 65.000 0.00 0.00 0.00 4.30
318 319 0.396417 ACGGTGATGAGGAGGAGGAG 60.396 60.000 0.00 0.00 0.00 3.69
319 320 0.395862 GACGGTGATGAGGAGGAGGA 60.396 60.000 0.00 0.00 0.00 3.71
320 321 1.729470 CGACGGTGATGAGGAGGAGG 61.729 65.000 0.00 0.00 0.00 4.30
321 322 1.032657 ACGACGGTGATGAGGAGGAG 61.033 60.000 0.00 0.00 0.00 3.69
322 323 1.001269 ACGACGGTGATGAGGAGGA 60.001 57.895 0.00 0.00 0.00 3.71
323 324 1.433879 GACGACGGTGATGAGGAGG 59.566 63.158 0.00 0.00 0.00 4.30
324 325 1.062685 CGACGACGGTGATGAGGAG 59.937 63.158 0.00 0.00 35.72 3.69
330 331 0.809385 ATGAAGACGACGACGGTGAT 59.191 50.000 12.58 0.00 44.46 3.06
375 376 0.378962 CTAAGTCAGAGCCCGAGTCG 59.621 60.000 5.29 5.29 0.00 4.18
379 380 0.251653 ACCACTAAGTCAGAGCCCGA 60.252 55.000 0.00 0.00 0.00 5.14
388 389 1.409427 CCCATCGGAGACCACTAAGTC 59.591 57.143 0.00 0.00 42.51 3.01
392 393 1.760875 GCCCCATCGGAGACCACTA 60.761 63.158 0.00 0.00 42.51 2.74
393 394 3.083997 GCCCCATCGGAGACCACT 61.084 66.667 0.00 0.00 42.51 4.00
395 396 1.923395 AAAGCCCCATCGGAGACCA 60.923 57.895 0.00 0.00 42.51 4.02
416 418 6.374333 TCGAATTTTTCTAGTTCATGGAAGGG 59.626 38.462 0.00 0.00 29.12 3.95
423 425 5.581085 CCGACCTCGAATTTTTCTAGTTCAT 59.419 40.000 0.00 0.00 43.02 2.57
430 432 1.949079 GCCCCGACCTCGAATTTTTCT 60.949 52.381 0.00 0.00 43.02 2.52
433 435 1.743995 CGCCCCGACCTCGAATTTT 60.744 57.895 0.00 0.00 43.02 1.82
461 463 0.451383 CGGGCTCGCAATTCATCAAA 59.549 50.000 0.00 0.00 0.00 2.69
462 464 0.392327 TCGGGCTCGCAATTCATCAA 60.392 50.000 0.00 0.00 36.13 2.57
468 470 0.947244 GATTCATCGGGCTCGCAATT 59.053 50.000 0.00 0.00 36.13 2.32
473 475 0.319383 CTGAGGATTCATCGGGCTCG 60.319 60.000 0.00 0.00 31.68 5.03
478 480 3.620374 CACTTCAACTGAGGATTCATCGG 59.380 47.826 5.63 5.63 31.68 4.18
485 487 4.963318 TCTGTTCACTTCAACTGAGGAT 57.037 40.909 0.00 0.00 32.32 3.24
492 494 3.560068 ACGACCAATCTGTTCACTTCAAC 59.440 43.478 0.00 0.00 0.00 3.18
499 501 3.069586 AGACAAGACGACCAATCTGTTCA 59.930 43.478 0.00 0.00 0.00 3.18
502 504 3.654414 GAAGACAAGACGACCAATCTGT 58.346 45.455 0.00 0.00 0.00 3.41
505 507 1.390463 GCGAAGACAAGACGACCAATC 59.610 52.381 0.00 0.00 0.00 2.67
507 509 0.387929 AGCGAAGACAAGACGACCAA 59.612 50.000 0.00 0.00 0.00 3.67
510 512 0.039437 TCCAGCGAAGACAAGACGAC 60.039 55.000 0.00 0.00 0.00 4.34
512 514 0.734253 CCTCCAGCGAAGACAAGACG 60.734 60.000 0.00 0.00 0.00 4.18
532 534 4.576053 TGAAGTGACATCAGTTGTTGGAAG 59.424 41.667 6.69 0.00 39.43 3.46
533 535 4.522114 TGAAGTGACATCAGTTGTTGGAA 58.478 39.130 6.69 0.00 39.43 3.53
537 539 5.895636 TTGTTGAAGTGACATCAGTTGTT 57.104 34.783 6.69 0.00 39.43 2.83
548 1254 2.158475 AGCCTCCCATTTGTTGAAGTGA 60.158 45.455 0.00 0.00 0.00 3.41
554 1260 0.680618 TGCAAGCCTCCCATTTGTTG 59.319 50.000 0.00 0.00 0.00 3.33
556 1262 0.178953 ACTGCAAGCCTCCCATTTGT 60.179 50.000 0.00 0.00 37.60 2.83
557 1263 0.529378 GACTGCAAGCCTCCCATTTG 59.471 55.000 0.00 0.00 37.60 2.32
591 1298 0.037590 CCCCGTCCTCACCAATTTCA 59.962 55.000 0.00 0.00 0.00 2.69
609 1316 4.814294 AGCCAACGGATCGACGCC 62.814 66.667 0.00 0.00 37.37 5.68
610 1317 3.554692 CAGCCAACGGATCGACGC 61.555 66.667 0.00 0.00 37.37 5.19
611 1318 2.885644 CCAGCCAACGGATCGACG 60.886 66.667 0.00 0.00 40.31 5.12
612 1319 2.511600 CCCAGCCAACGGATCGAC 60.512 66.667 0.00 0.00 0.00 4.20
613 1320 4.467084 GCCCAGCCAACGGATCGA 62.467 66.667 0.00 0.00 0.00 3.59
614 1321 4.776322 TGCCCAGCCAACGGATCG 62.776 66.667 0.00 0.00 0.00 3.69
615 1322 2.825836 CTGCCCAGCCAACGGATC 60.826 66.667 0.00 0.00 0.00 3.36
633 1340 0.904865 TGGACTGACAGCTACCCCAG 60.905 60.000 1.25 0.00 0.00 4.45
634 1341 1.157513 TGGACTGACAGCTACCCCA 59.842 57.895 1.25 0.00 0.00 4.96
635 1342 0.905337 AGTGGACTGACAGCTACCCC 60.905 60.000 1.25 0.00 0.00 4.95
636 1343 0.533032 GAGTGGACTGACAGCTACCC 59.467 60.000 1.25 0.00 0.00 3.69
637 1344 1.257743 TGAGTGGACTGACAGCTACC 58.742 55.000 1.25 4.77 0.00 3.18
638 1345 2.297597 ACTTGAGTGGACTGACAGCTAC 59.702 50.000 1.25 3.99 0.00 3.58
639 1346 2.598565 ACTTGAGTGGACTGACAGCTA 58.401 47.619 1.25 0.00 0.00 3.32
640 1347 1.418334 ACTTGAGTGGACTGACAGCT 58.582 50.000 1.25 0.00 0.00 4.24
641 1348 2.139118 GAACTTGAGTGGACTGACAGC 58.861 52.381 1.25 0.00 0.00 4.40
642 1349 2.034685 TCGAACTTGAGTGGACTGACAG 59.965 50.000 0.00 0.00 0.00 3.51
643 1350 2.028876 TCGAACTTGAGTGGACTGACA 58.971 47.619 0.00 0.00 0.00 3.58
644 1351 2.667137 CTCGAACTTGAGTGGACTGAC 58.333 52.381 0.00 0.00 0.00 3.51
645 1352 1.000163 GCTCGAACTTGAGTGGACTGA 60.000 52.381 0.00 0.00 38.28 3.41
646 1353 1.423395 GCTCGAACTTGAGTGGACTG 58.577 55.000 0.00 0.00 38.28 3.51
647 1354 0.318762 GGCTCGAACTTGAGTGGACT 59.681 55.000 0.00 0.00 38.28 3.85
648 1355 0.670854 GGGCTCGAACTTGAGTGGAC 60.671 60.000 0.00 0.00 38.28 4.02
649 1356 1.671742 GGGCTCGAACTTGAGTGGA 59.328 57.895 0.00 0.00 38.28 4.02
650 1357 1.376037 GGGGCTCGAACTTGAGTGG 60.376 63.158 0.00 0.00 38.28 4.00
651 1358 1.738099 CGGGGCTCGAACTTGAGTG 60.738 63.158 0.00 0.00 42.43 3.51
652 1359 2.657237 CGGGGCTCGAACTTGAGT 59.343 61.111 0.00 0.00 42.43 3.41
653 1360 2.125512 CCGGGGCTCGAACTTGAG 60.126 66.667 9.18 0.00 42.43 3.02
654 1361 4.388499 GCCGGGGCTCGAACTTGA 62.388 66.667 9.18 0.00 42.43 3.02
679 1386 1.891060 GAAACTCTGTGAGCACCGCG 61.891 60.000 0.00 0.00 32.04 6.46
680 1387 0.601311 AGAAACTCTGTGAGCACCGC 60.601 55.000 0.00 0.00 32.04 5.68
681 1388 1.423395 GAGAAACTCTGTGAGCACCG 58.577 55.000 0.00 0.00 32.04 4.94
682 1389 1.346068 AGGAGAAACTCTGTGAGCACC 59.654 52.381 0.00 0.00 32.04 5.01
683 1390 2.829741 AGGAGAAACTCTGTGAGCAC 57.170 50.000 0.00 0.00 32.04 4.40
684 1391 6.605471 TTTATAGGAGAAACTCTGTGAGCA 57.395 37.500 0.00 0.00 32.04 4.26
685 1392 7.907214 TTTTTATAGGAGAAACTCTGTGAGC 57.093 36.000 0.00 0.00 32.04 4.26
707 1414 3.119137 GCTAATCCCTCGTTGGCATTTTT 60.119 43.478 0.00 0.00 33.80 1.94
708 1415 2.427095 GCTAATCCCTCGTTGGCATTTT 59.573 45.455 0.00 0.00 33.80 1.82
709 1416 2.024414 GCTAATCCCTCGTTGGCATTT 58.976 47.619 0.00 0.00 33.80 2.32
710 1417 1.680338 GCTAATCCCTCGTTGGCATT 58.320 50.000 0.00 0.00 33.80 3.56
711 1418 0.179018 GGCTAATCCCTCGTTGGCAT 60.179 55.000 0.00 0.00 35.09 4.40
712 1419 1.223487 GGCTAATCCCTCGTTGGCA 59.777 57.895 0.00 0.00 35.09 4.92
713 1420 4.142780 GGCTAATCCCTCGTTGGC 57.857 61.111 0.00 0.00 32.96 4.52
722 1429 0.335019 ACCAACCCAAGGGCTAATCC 59.665 55.000 4.70 0.00 39.32 3.01
723 1430 1.285078 AGACCAACCCAAGGGCTAATC 59.715 52.381 4.70 0.00 44.68 1.75
724 1431 1.382914 AGACCAACCCAAGGGCTAAT 58.617 50.000 4.70 0.00 44.68 1.73
725 1432 2.877150 AGACCAACCCAAGGGCTAA 58.123 52.632 4.70 0.00 44.68 3.09
726 1433 4.681624 AGACCAACCCAAGGGCTA 57.318 55.556 4.70 0.00 44.68 3.93
728 1435 0.251787 AATGAGACCAACCCAAGGGC 60.252 55.000 4.70 0.00 39.32 5.19
729 1436 2.309136 AAATGAGACCAACCCAAGGG 57.691 50.000 2.91 2.91 42.03 3.95
730 1437 3.897505 AGAAAAATGAGACCAACCCAAGG 59.102 43.478 0.00 0.00 0.00 3.61
731 1438 5.535753 AAGAAAAATGAGACCAACCCAAG 57.464 39.130 0.00 0.00 0.00 3.61
732 1439 5.948742 AAAGAAAAATGAGACCAACCCAA 57.051 34.783 0.00 0.00 0.00 4.12
733 1440 7.425224 TTTAAAGAAAAATGAGACCAACCCA 57.575 32.000 0.00 0.00 0.00 4.51
734 1441 8.902540 AATTTAAAGAAAAATGAGACCAACCC 57.097 30.769 0.00 0.00 0.00 4.11
772 1479 5.924254 CGAATTTGAACCTTTTAAACCCTCC 59.076 40.000 0.00 0.00 0.00 4.30
785 1492 0.872388 ACTGCGACCGAATTTGAACC 59.128 50.000 0.00 0.00 0.00 3.62
840 1547 3.767806 CTGAGCCAGCGAGCCTGA 61.768 66.667 0.00 0.00 44.64 3.86
852 1559 4.767255 CCACGGGTCTGCCTGAGC 62.767 72.222 0.00 0.00 43.97 4.26
853 1560 3.314331 ACCACGGGTCTGCCTGAG 61.314 66.667 0.00 0.00 43.97 3.35
904 1611 4.251103 TGATGGGCTAGTCTCTTGTAGA 57.749 45.455 0.00 0.00 0.00 2.59
908 1615 3.388308 CGAATGATGGGCTAGTCTCTTG 58.612 50.000 0.00 0.00 0.00 3.02
910 1617 1.967066 CCGAATGATGGGCTAGTCTCT 59.033 52.381 0.00 0.00 0.00 3.10
911 1618 1.689273 ACCGAATGATGGGCTAGTCTC 59.311 52.381 0.00 0.00 0.00 3.36
912 1619 1.689273 GACCGAATGATGGGCTAGTCT 59.311 52.381 0.00 0.00 0.00 3.24
913 1620 1.270358 GGACCGAATGATGGGCTAGTC 60.270 57.143 0.00 0.00 33.80 2.59
917 1624 0.394352 GTTGGACCGAATGATGGGCT 60.394 55.000 0.00 0.00 33.80 5.19
941 1648 2.280389 AGAGCGTGGTGTGCTGTG 60.280 61.111 0.00 0.00 44.18 3.66
942 1649 2.280389 CAGAGCGTGGTGTGCTGT 60.280 61.111 0.00 0.00 44.18 4.40
943 1650 3.720193 GCAGAGCGTGGTGTGCTG 61.720 66.667 13.16 0.00 44.18 4.41
979 1690 4.295199 GTTGGGGTGGTGGGGTCC 62.295 72.222 0.00 0.00 0.00 4.46
980 1691 4.653888 CGTTGGGGTGGTGGGGTC 62.654 72.222 0.00 0.00 0.00 4.46
1224 1959 2.196997 CTGGGGCGAAGATGTGGGAA 62.197 60.000 0.00 0.00 0.00 3.97
1308 2046 4.243008 TGGACGACTTTGCCGCCA 62.243 61.111 0.00 0.00 33.35 5.69
1317 2055 1.309499 CGAAGAGGAGCTGGACGACT 61.309 60.000 0.00 0.00 0.00 4.18
1797 2557 2.018544 CTCGACGAAGCGGATCTCT 58.981 57.895 0.00 0.00 0.00 3.10
1845 2605 3.712881 GCTTCGTCCACACGTGCC 61.713 66.667 17.22 0.00 46.76 5.01
2021 4046 1.536180 TGGTGCTCCAGCTTCCAAA 59.464 52.632 2.64 0.00 40.46 3.28
2022 4047 3.249805 TGGTGCTCCAGCTTCCAA 58.750 55.556 2.64 0.25 40.46 3.53
2185 4235 2.124570 CGGACAGCCCCCAATCAG 60.125 66.667 0.00 0.00 0.00 2.90
2293 4352 5.518487 ACAAATGCAAAACTGAAACGTAAGG 59.482 36.000 0.00 0.00 46.39 2.69
2341 4425 4.526438 AAAATACTCCCCAAGCTAGCAT 57.474 40.909 18.83 0.65 0.00 3.79
2421 4524 2.038426 CCTCACCACCATCTACAACACA 59.962 50.000 0.00 0.00 0.00 3.72
2452 4555 9.829507 TCAGAAAAATGTTACCAATCACAAAAT 57.170 25.926 0.00 0.00 0.00 1.82
2453 4556 9.658799 TTCAGAAAAATGTTACCAATCACAAAA 57.341 25.926 0.00 0.00 0.00 2.44
2455 4558 7.437862 GCTTCAGAAAAATGTTACCAATCACAA 59.562 33.333 0.00 0.00 0.00 3.33
2456 4559 6.922957 GCTTCAGAAAAATGTTACCAATCACA 59.077 34.615 0.00 0.00 0.00 3.58
2459 4562 6.587608 CAGGCTTCAGAAAAATGTTACCAATC 59.412 38.462 0.00 0.00 0.00 2.67
2461 4564 5.596361 TCAGGCTTCAGAAAAATGTTACCAA 59.404 36.000 0.00 0.00 0.00 3.67
2462 4565 5.136828 TCAGGCTTCAGAAAAATGTTACCA 58.863 37.500 0.00 0.00 0.00 3.25
2463 4566 5.705609 TCAGGCTTCAGAAAAATGTTACC 57.294 39.130 0.00 0.00 0.00 2.85
2464 4567 7.867403 TGATTTCAGGCTTCAGAAAAATGTTAC 59.133 33.333 3.03 0.00 37.30 2.50
2465 4568 7.950512 TGATTTCAGGCTTCAGAAAAATGTTA 58.049 30.769 3.03 0.00 37.30 2.41
2466 4569 6.819284 TGATTTCAGGCTTCAGAAAAATGTT 58.181 32.000 3.03 0.00 37.30 2.71
2531 4801 6.450545 TGTTTGTGACACAAGATTTGAACAA 58.549 32.000 19.74 0.00 39.53 2.83
2636 4906 3.834231 CACAGAAACCAAAGGGGATGATT 59.166 43.478 0.00 0.00 41.15 2.57
2709 4983 7.748847 ACATCCATTAACTGAAAACGACATAC 58.251 34.615 0.00 0.00 0.00 2.39
2731 5031 9.337396 TCAGTTGAATAAACAAGAGTACAACAT 57.663 29.630 0.00 0.00 41.61 2.71
2765 5079 8.334263 ACAAAAATTCTTTTCAAGCCAAAAGA 57.666 26.923 10.36 10.36 46.18 2.52
2784 5098 5.436175 TGACACTGATCAGAGGAACAAAAA 58.564 37.500 29.27 0.31 0.00 1.94
2824 5145 3.944015 AGTATCAAGAATTCAGCACAGCC 59.056 43.478 8.44 0.00 0.00 4.85
2859 5187 4.755266 ATAAGAAATGTACCAGCGGACT 57.245 40.909 1.50 0.00 0.00 3.85
2869 5197 8.991243 ACTACGTGTTGCTTATAAGAAATGTA 57.009 30.769 16.85 13.80 0.00 2.29
2938 5269 9.965902 AAGATACAGGAACTTGAATAACAGATT 57.034 29.630 0.00 0.00 34.60 2.40
2939 5270 9.388506 CAAGATACAGGAACTTGAATAACAGAT 57.611 33.333 0.00 0.00 42.12 2.90
3140 5493 3.008330 ACGATGCGTCTTGAGTACTACT 58.992 45.455 4.05 0.00 33.69 2.57
3141 5494 3.099362 CACGATGCGTCTTGAGTACTAC 58.901 50.000 6.57 0.00 38.32 2.73
3142 5495 2.477357 GCACGATGCGTCTTGAGTACTA 60.477 50.000 16.05 0.00 38.32 1.82
3282 5635 9.733556 ACATCTGGACAACATGTTTACTTATAA 57.266 29.630 8.77 0.00 0.00 0.98
3333 5686 2.893489 AGCCAACATGGAAAAGAAGGAC 59.107 45.455 0.00 0.00 40.96 3.85
3334 5687 3.243359 AGCCAACATGGAAAAGAAGGA 57.757 42.857 0.00 0.00 40.96 3.36
3335 5688 3.070015 ACAAGCCAACATGGAAAAGAAGG 59.930 43.478 0.00 0.00 40.96 3.46
3336 5689 4.326504 ACAAGCCAACATGGAAAAGAAG 57.673 40.909 0.00 0.00 40.96 2.85
3349 5702 3.953612 AGATGTTTGACTCAACAAGCCAA 59.046 39.130 0.00 0.00 31.71 4.52
3350 5703 3.554934 AGATGTTTGACTCAACAAGCCA 58.445 40.909 0.00 0.00 31.71 4.75
3351 5704 3.817647 AGAGATGTTTGACTCAACAAGCC 59.182 43.478 0.00 0.00 35.83 4.35
3352 5705 6.545504 TTAGAGATGTTTGACTCAACAAGC 57.454 37.500 0.00 0.00 35.83 4.01
3354 5707 9.725019 ACATATTAGAGATGTTTGACTCAACAA 57.275 29.630 0.00 0.00 33.70 2.83
3355 5708 9.725019 AACATATTAGAGATGTTTGACTCAACA 57.275 29.630 0.00 0.00 43.38 3.33
3406 5759 2.027653 GCAGCCCCTCCATCTATTAGTC 60.028 54.545 0.00 0.00 0.00 2.59
3424 5777 7.264221 CCAGCTTCTATCCTAATATAGTGCAG 58.736 42.308 0.00 0.00 35.05 4.41
3461 5814 4.761739 AGATTTCGCCAAAATGAGAGTTCA 59.238 37.500 0.00 0.00 37.70 3.18
3502 5856 7.657761 AGTTGGTAACTCATCAAGAAACTACAG 59.342 37.037 0.00 0.00 37.02 2.74
3520 5874 7.230849 TCTAAACGAGATGGTAAGTTGGTAA 57.769 36.000 0.00 0.00 0.00 2.85
3521 5875 6.127535 CCTCTAAACGAGATGGTAAGTTGGTA 60.128 42.308 0.00 0.00 42.62 3.25
3522 5876 5.337330 CCTCTAAACGAGATGGTAAGTTGGT 60.337 44.000 0.00 0.00 42.62 3.67
3523 5877 5.109903 CCTCTAAACGAGATGGTAAGTTGG 58.890 45.833 0.00 0.00 42.62 3.77
3524 5878 5.105473 TCCCTCTAAACGAGATGGTAAGTTG 60.105 44.000 0.00 0.00 42.62 3.16
3525 5879 5.021458 TCCCTCTAAACGAGATGGTAAGTT 58.979 41.667 0.00 0.00 42.62 2.66
3526 5880 4.607239 TCCCTCTAAACGAGATGGTAAGT 58.393 43.478 0.00 0.00 42.62 2.24
3527 5881 5.593679 TTCCCTCTAAACGAGATGGTAAG 57.406 43.478 0.00 0.00 42.62 2.34
3581 5935 6.366877 GCAAGTAACTTCATTCATGCATGTTT 59.633 34.615 25.43 11.92 33.00 2.83
3583 5937 5.047872 TGCAAGTAACTTCATTCATGCATGT 60.048 36.000 25.43 5.20 37.61 3.21
3584 5938 5.404096 TGCAAGTAACTTCATTCATGCATG 58.596 37.500 21.07 21.07 37.61 4.06
3585 5939 5.648178 TGCAAGTAACTTCATTCATGCAT 57.352 34.783 0.00 0.00 37.61 3.96
3592 5990 7.677276 GCATATCGTCTTGCAAGTAACTTCATT 60.677 37.037 25.19 5.65 38.72 2.57
3627 6025 8.997323 TGTTTCTTTTGCTGAATTTGAAAAGAA 58.003 25.926 12.27 12.27 45.71 2.52
3652 6050 9.912634 TTTTCCTACAAAAAGATGAGCTTTATG 57.087 29.630 0.00 0.00 45.85 1.90
3687 6086 9.455847 GTCTACAAGCATTTAAAATCATGGATC 57.544 33.333 0.00 0.00 0.00 3.36
3763 6162 8.467963 ACATGCATTTGTCATGATAAATCCTA 57.532 30.769 23.06 14.43 42.84 2.94
3771 6170 6.148150 GGTGAAAAACATGCATTTGTCATGAT 59.852 34.615 8.52 6.84 42.84 2.45
3797 6196 3.888323 TGCTGTTGTCAAGCAATAAAGGA 59.112 39.130 0.00 0.00 39.55 3.36
3817 6216 2.358957 TGTTGTGCTGGTGATCTATGC 58.641 47.619 0.00 0.00 0.00 3.14
3927 6327 7.041303 TCACACTATACCAAGTCTATAGAAGCG 60.041 40.741 3.40 0.00 31.23 4.68
3987 6387 5.395768 GGACTTATCTTGAAGAGCTAGCCAA 60.396 44.000 12.13 7.53 0.00 4.52


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

AutoCloner maintained by Alex Coulton.