Multiple sequence alignment - TraesCS5D01G303500

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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 TraesCS5D01G303500 chr5D 100.000 5047 0 0 1 5047 399149158 399154204 0.000000e+00 9321.0
1 TraesCS5D01G303500 chr5A 89.408 2719 176 51 2142 4807 504774079 504776738 0.000000e+00 3323.0
2 TraesCS5D01G303500 chr5A 90.271 812 37 15 1523 2325 504773288 504774066 0.000000e+00 1024.0
3 TraesCS5D01G303500 chr5A 87.479 583 43 13 964 1520 504772674 504773252 0.000000e+00 645.0
4 TraesCS5D01G303500 chr5A 81.250 400 42 23 484 873 504769441 504769817 4.940000e-75 292.0
5 TraesCS5D01G303500 chr5A 81.356 118 5 5 865 965 504772532 504772649 4.190000e-11 80.5
6 TraesCS5D01G303500 chr5B 93.894 1605 78 8 3293 4894 479327124 479328711 0.000000e+00 2403.0
7 TraesCS5D01G303500 chr5B 95.945 1159 39 5 2142 3294 479325810 479326966 0.000000e+00 1873.0
8 TraesCS5D01G303500 chr5B 87.923 828 37 25 1 775 479323204 479324021 0.000000e+00 917.0
9 TraesCS5D01G303500 chr5B 95.045 444 11 7 1889 2325 479325358 479325797 0.000000e+00 688.0
10 TraesCS5D01G303500 chr5B 86.837 509 35 18 964 1453 479324301 479324796 1.600000e-149 540.0
11 TraesCS5D01G303500 chr5B 87.812 361 21 7 1532 1889 479324981 479325321 7.870000e-108 401.0
12 TraesCS5D01G303500 chr5B 88.325 197 7 6 595 775 711878755 711878559 6.580000e-54 222.0
13 TraesCS5D01G303500 chr5B 91.781 146 9 2 766 910 479324046 479324189 3.080000e-47 200.0
14 TraesCS5D01G303500 chr5B 81.707 164 18 10 804 967 711878488 711878337 5.300000e-25 126.0
15 TraesCS5D01G303500 chr5B 76.875 160 31 4 4829 4988 586848652 586848499 9.000000e-13 86.1
16 TraesCS5D01G303500 chr5B 97.222 36 1 0 4598 4633 469292143 469292178 1.520000e-05 62.1
17 TraesCS5D01G303500 chr5B 100.000 29 0 0 964 992 711878309 711878281 3.000000e-03 54.7
18 TraesCS5D01G303500 chr1D 95.833 264 11 0 3486 3749 110387740 110388003 1.300000e-115 427.0
19 TraesCS5D01G303500 chr1D 89.933 298 19 9 1057 1351 91563940 91564229 1.720000e-99 374.0
20 TraesCS5D01G303500 chr3B 88.580 324 28 3 1518 1840 170130843 170131158 7.930000e-103 385.0
21 TraesCS5D01G303500 chr7B 100.000 33 0 0 4602 4634 166965297 166965329 1.520000e-05 62.1
22 TraesCS5D01G303500 chr1B 100.000 31 0 0 4602 4632 654091080 654091050 1.960000e-04 58.4
23 TraesCS5D01G303500 chr6D 96.875 32 1 0 4603 4634 438821058 438821027 3.000000e-03 54.7


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 TraesCS5D01G303500 chr5D 399149158 399154204 5046 False 9321.000000 9321 100.000000 1 5047 1 chr5D.!!$F1 5046
1 TraesCS5D01G303500 chr5A 504769441 504776738 7297 False 1072.900000 3323 85.952800 484 4807 5 chr5A.!!$F1 4323
2 TraesCS5D01G303500 chr5B 479323204 479328711 5507 False 1003.142857 2403 91.319571 1 4894 7 chr5B.!!$F2 4893

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
38 39 0.038021 TGAATTAGTGCTGGCTGCCA 59.962 50.000 21.96 21.96 42.00 4.92 F
1350 4246 0.322546 GCCCATCCACCTTCTCGTTT 60.323 55.000 0.00 0.00 0.00 3.60 F
1489 4481 0.963355 TGGGAATTTAGTGGGCGCAC 60.963 55.000 25.22 25.22 0.00 5.34 F
1669 4695 1.133598 TCCACCTCGCACAGTAATACG 59.866 52.381 0.00 0.00 0.00 3.06 F
3082 6574 1.135460 GCCAACAGAATGCTGAGCTTC 60.135 52.381 8.02 7.23 45.17 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1469 4461 0.033601 TGCGCCCACTAAATTCCCAT 60.034 50.000 4.18 0.0 0.00 4.00 R
3200 6692 1.906574 GGAGACAAGTACATGGACCCA 59.093 52.381 3.84 0.0 0.00 4.51 R
3205 6697 3.961480 TGTGAGGAGACAAGTACATGG 57.039 47.619 2.78 0.0 0.00 3.66 R
3534 7187 2.051334 TCACCACACCAACCTGAAAG 57.949 50.000 0.00 0.0 0.00 2.62 R
4939 8614 0.111639 TACTTGGGTCCCACAAAGGC 59.888 55.000 11.24 0.0 35.39 4.35 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
24 25 2.755103 GGCTTTTCCGATCCAGTGAATT 59.245 45.455 0.00 0.00 0.00 2.17
25 26 3.945285 GGCTTTTCCGATCCAGTGAATTA 59.055 43.478 0.00 0.00 0.00 1.40
38 39 0.038021 TGAATTAGTGCTGGCTGCCA 59.962 50.000 21.96 21.96 42.00 4.92
129 130 4.628074 CGGAGGGTTATTATAGTGGTGTG 58.372 47.826 0.00 0.00 0.00 3.82
162 163 5.185249 TGCAACGATAGGTTAGAGAGACTTT 59.815 40.000 0.00 0.00 36.49 2.66
212 213 4.035675 GCATTTGCAGGACTAGTTATGACC 59.964 45.833 11.34 1.42 41.59 4.02
217 219 2.966516 CAGGACTAGTTATGACCTCCCC 59.033 54.545 0.00 0.00 0.00 4.81
238 240 3.507622 CCTGTGTTTCTTGGGAGATTTCC 59.492 47.826 0.00 0.00 43.23 3.13
242 244 5.301805 TGTGTTTCTTGGGAGATTTCCTTTC 59.698 40.000 1.74 0.00 43.49 2.62
245 247 6.611236 TGTTTCTTGGGAGATTTCCTTTCTTT 59.389 34.615 1.74 0.00 43.49 2.52
246 248 7.782644 TGTTTCTTGGGAGATTTCCTTTCTTTA 59.217 33.333 1.74 0.00 43.49 1.85
252 274 6.490040 TGGGAGATTTCCTTTCTTTACTGTTG 59.510 38.462 1.74 0.00 43.49 3.33
260 282 8.433421 TTCCTTTCTTTACTGTTGTAGAAGTG 57.567 34.615 0.00 0.00 0.00 3.16
263 285 7.201696 CCTTTCTTTACTGTTGTAGAAGTGCAA 60.202 37.037 0.00 0.00 0.00 4.08
267 289 8.682710 TCTTTACTGTTGTAGAAGTGCAAAAAT 58.317 29.630 0.00 0.00 29.18 1.82
268 290 8.627487 TTTACTGTTGTAGAAGTGCAAAAATG 57.373 30.769 0.00 0.00 29.18 2.32
270 292 6.265577 ACTGTTGTAGAAGTGCAAAAATGTC 58.734 36.000 0.00 0.00 29.18 3.06
272 294 6.862209 TGTTGTAGAAGTGCAAAAATGTCTT 58.138 32.000 0.00 0.00 29.18 3.01
273 295 6.972328 TGTTGTAGAAGTGCAAAAATGTCTTC 59.028 34.615 0.00 0.00 35.98 2.87
274 296 5.747565 TGTAGAAGTGCAAAAATGTCTTCG 58.252 37.500 0.00 0.00 39.28 3.79
275 297 4.900635 AGAAGTGCAAAAATGTCTTCGT 57.099 36.364 0.00 0.00 39.28 3.85
276 298 6.480651 TGTAGAAGTGCAAAAATGTCTTCGTA 59.519 34.615 0.00 0.00 39.28 3.43
277 299 6.560253 AGAAGTGCAAAAATGTCTTCGTAT 57.440 33.333 0.00 0.00 39.28 3.06
278 300 6.373779 AGAAGTGCAAAAATGTCTTCGTATG 58.626 36.000 0.00 0.00 39.28 2.39
280 302 6.795098 AGTGCAAAAATGTCTTCGTATGTA 57.205 33.333 0.00 0.00 0.00 2.29
281 303 6.599437 AGTGCAAAAATGTCTTCGTATGTAC 58.401 36.000 0.00 0.00 0.00 2.90
290 312 7.747155 ATGTCTTCGTATGTACTAGCTACAT 57.253 36.000 16.81 16.81 46.21 2.29
324 346 5.653769 AGTAGCTCGTACAATGGGTTTAGTA 59.346 40.000 0.00 0.00 33.55 1.82
346 368 1.985473 ACACACCATTGTCATGTGCT 58.015 45.000 10.99 0.46 46.19 4.40
365 387 3.077359 GCTGTTACCTGCACTTTGAGAT 58.923 45.455 0.00 0.00 35.75 2.75
375 397 4.847198 TGCACTTTGAGATGATGTGGTAT 58.153 39.130 0.00 0.00 0.00 2.73
384 406 8.492673 TTGAGATGATGTGGTATTTGAACTAC 57.507 34.615 0.00 0.00 0.00 2.73
511 549 1.198397 GAACAGTCGCGTGTTCGTG 59.802 57.895 21.85 8.25 45.09 4.35
514 552 1.733041 CAGTCGCGTGTTCGTGGAT 60.733 57.895 5.77 0.00 45.94 3.41
541 584 4.517815 CGTTGGCATGGCATGGGC 62.518 66.667 27.48 19.83 40.13 5.36
642 686 2.505982 CCGATCCGTCCCTTGCAT 59.494 61.111 0.00 0.00 0.00 3.96
645 704 1.441729 GATCCGTCCCTTGCATCGA 59.558 57.895 0.00 0.00 0.00 3.59
727 786 4.504916 CTCGGGCCTCTCACGCTG 62.505 72.222 0.84 0.00 0.00 5.18
733 792 4.135153 CCTCTCACGCTGACCGGG 62.135 72.222 6.32 0.00 43.23 5.73
781 840 4.564116 CGGCGCACGGGTAGGTAG 62.564 72.222 10.83 0.00 39.42 3.18
783 842 4.886121 GCGCACGGGTAGGTAGCC 62.886 72.222 0.30 0.00 40.38 3.93
791 850 2.528041 GGGTAGGTAGCCGAATCAAG 57.472 55.000 0.00 0.00 33.75 3.02
792 851 1.540580 GGGTAGGTAGCCGAATCAAGC 60.541 57.143 0.00 0.00 33.75 4.01
793 852 1.540580 GGTAGGTAGCCGAATCAAGCC 60.541 57.143 0.00 0.00 0.00 4.35
794 853 0.756903 TAGGTAGCCGAATCAAGCCC 59.243 55.000 0.00 0.00 0.00 5.19
795 854 1.526225 GGTAGCCGAATCAAGCCCC 60.526 63.158 0.00 0.00 0.00 5.80
796 855 1.526225 GTAGCCGAATCAAGCCCCC 60.526 63.158 0.00 0.00 0.00 5.40
810 909 4.785453 CCCCGGCTGCTCCTGTTC 62.785 72.222 0.00 0.00 0.00 3.18
839 938 1.966451 CAAACCTTCCGCTTCCGCT 60.966 57.895 0.00 0.00 0.00 5.52
840 939 1.228154 AAACCTTCCGCTTCCGCTT 60.228 52.632 0.00 0.00 0.00 4.68
908 3749 2.427812 CCGGTCCTTTTCTACTCCTCTC 59.572 54.545 0.00 0.00 0.00 3.20
1331 4223 0.822164 ACTCATTAACTCCCCCGACG 59.178 55.000 0.00 0.00 0.00 5.12
1336 4232 3.988050 TAACTCCCCCGACGCCCAT 62.988 63.158 0.00 0.00 0.00 4.00
1343 4239 4.096003 CCGACGCCCATCCACCTT 62.096 66.667 0.00 0.00 0.00 3.50
1345 4241 2.990479 GACGCCCATCCACCTTCT 59.010 61.111 0.00 0.00 0.00 2.85
1348 4244 2.990479 GCCCATCCACCTTCTCGT 59.010 61.111 0.00 0.00 0.00 4.18
1349 4245 1.299976 GCCCATCCACCTTCTCGTT 59.700 57.895 0.00 0.00 0.00 3.85
1350 4246 0.322546 GCCCATCCACCTTCTCGTTT 60.323 55.000 0.00 0.00 0.00 3.60
1351 4247 1.453155 CCCATCCACCTTCTCGTTTG 58.547 55.000 0.00 0.00 0.00 2.93
1352 4248 1.271379 CCCATCCACCTTCTCGTTTGT 60.271 52.381 0.00 0.00 0.00 2.83
1354 4250 2.884639 CCATCCACCTTCTCGTTTGTTT 59.115 45.455 0.00 0.00 0.00 2.83
1374 4278 1.483827 TGCTCGATTTGATCTGCTCCT 59.516 47.619 0.00 0.00 0.00 3.69
1403 4312 3.494336 CTGCGTGCTACTGCTGCC 61.494 66.667 0.00 0.00 39.36 4.85
1454 4363 1.210478 TGATGCTGGTTCCCTTCTAGC 59.790 52.381 0.00 0.00 39.32 3.42
1464 4456 1.028905 CCCTTCTAGCGACTCCAGAG 58.971 60.000 0.00 0.00 0.00 3.35
1469 4461 3.283259 TCTAGCGACTCCAGAGATTCA 57.717 47.619 0.70 0.00 0.00 2.57
1489 4481 0.963355 TGGGAATTTAGTGGGCGCAC 60.963 55.000 25.22 25.22 0.00 5.34
1490 4482 0.963355 GGGAATTTAGTGGGCGCACA 60.963 55.000 32.29 9.15 0.00 4.57
1492 4484 1.165270 GAATTTAGTGGGCGCACAGT 58.835 50.000 32.29 25.57 0.00 3.55
1504 4496 2.032178 GGCGCACAGTTTTCATAGGATC 59.968 50.000 10.83 0.00 0.00 3.36
1577 4603 3.940852 GGGATTGGACAAATTGAAATGGC 59.059 43.478 0.00 0.00 0.00 4.40
1669 4695 1.133598 TCCACCTCGCACAGTAATACG 59.866 52.381 0.00 0.00 0.00 3.06
1704 4733 6.043411 GTCTAGTTGTTCTTGCATAGTAGGG 58.957 44.000 0.00 0.00 0.00 3.53
1705 4734 4.910458 AGTTGTTCTTGCATAGTAGGGT 57.090 40.909 0.00 0.00 0.00 4.34
1706 4735 5.242795 AGTTGTTCTTGCATAGTAGGGTT 57.757 39.130 0.00 0.00 0.00 4.11
1707 4736 5.003804 AGTTGTTCTTGCATAGTAGGGTTG 58.996 41.667 0.00 0.00 0.00 3.77
1728 4757 3.621268 TGTTCACTGTTGTCCTCGAAAAG 59.379 43.478 0.00 0.00 0.00 2.27
1735 4764 3.625764 TGTTGTCCTCGAAAAGAACCAAG 59.374 43.478 4.82 0.00 0.00 3.61
1736 4765 3.553828 TGTCCTCGAAAAGAACCAAGT 57.446 42.857 0.00 0.00 0.00 3.16
1737 4766 4.675976 TGTCCTCGAAAAGAACCAAGTA 57.324 40.909 0.00 0.00 0.00 2.24
1738 4767 4.628074 TGTCCTCGAAAAGAACCAAGTAG 58.372 43.478 0.00 0.00 0.00 2.57
1817 4847 3.117888 TGAAGAAGACCTGACCTGCTTTT 60.118 43.478 0.00 0.00 29.87 2.27
1914 4981 9.035607 CACTAGATTGACCATACTTGTGATTAC 57.964 37.037 0.00 0.00 37.94 1.89
1916 4983 9.770097 CTAGATTGACCATACTTGTGATTACAT 57.230 33.333 0.00 0.00 36.53 2.29
1918 4985 9.770097 AGATTGACCATACTTGTGATTACATAG 57.230 33.333 0.00 0.00 36.53 2.23
2002 5071 4.640771 AGATTGGAAGGTTACTTGAGCA 57.359 40.909 0.00 0.00 36.97 4.26
2045 5114 7.184022 ACTTTCAGGGTTTGGTAGATAAGGTAT 59.816 37.037 0.00 0.00 0.00 2.73
2102 5173 4.491676 TCAAGTTATGCGTCCTAGACAAC 58.508 43.478 0.00 0.00 32.09 3.32
2288 5752 9.569167 GCCTCTGGTTTTAAATCTACAAAATAC 57.431 33.333 0.00 0.00 0.00 1.89
2515 5979 3.753294 TTAGCCTATCTTAGCCAGTGC 57.247 47.619 0.00 0.00 37.95 4.40
2650 6115 5.721960 AGACCTCTTAAGCTAGACATTCCAA 59.278 40.000 0.00 0.00 0.00 3.53
2809 6275 6.761714 AGGTGGAATAATTAACTTACTGCTCG 59.238 38.462 0.00 0.00 0.00 5.03
2826 6292 6.326375 ACTGCTCGTAGTCTTTTGATAAGAG 58.674 40.000 0.00 0.00 0.00 2.85
2868 6334 3.429085 GTGTTAAGCTGGCGATGAATTG 58.571 45.455 0.00 0.00 0.00 2.32
2879 6345 3.111098 GCGATGAATTGCTTGGATTCAC 58.889 45.455 2.02 0.00 43.87 3.18
2884 6350 5.787953 TGAATTGCTTGGATTCACTGAAA 57.212 34.783 0.00 0.00 38.29 2.69
3082 6574 1.135460 GCCAACAGAATGCTGAGCTTC 60.135 52.381 8.02 7.23 45.17 3.86
3128 6620 1.323412 ATTACAAACGCCCACTTGCA 58.677 45.000 0.00 0.00 0.00 4.08
3134 6626 3.244044 ACAAACGCCCACTTGCAATTAAT 60.244 39.130 0.00 0.00 0.00 1.40
3205 6697 5.070685 AGTTCCAAGTCTGTATTTTGGGTC 58.929 41.667 2.96 0.00 41.31 4.46
3298 6951 7.051623 TGTACCATGCCTTACCTATTAGTTTG 58.948 38.462 0.00 0.00 0.00 2.93
3390 7043 8.732746 TTCAGCTACTAAAAGTTTTGAGTCTT 57.267 30.769 11.18 0.00 33.86 3.01
3391 7044 9.826574 TTCAGCTACTAAAAGTTTTGAGTCTTA 57.173 29.630 11.18 0.00 33.86 2.10
3505 7158 6.657541 TCAAATACAGAAATTACCAGGTGGAC 59.342 38.462 0.76 0.00 38.94 4.02
3523 7176 5.639931 GGTGGACTAAAGAGAAGTGATCAAC 59.360 44.000 0.00 0.00 0.00 3.18
3531 7184 7.588143 AAAGAGAAGTGATCAACGATTACTG 57.412 36.000 0.00 0.00 37.80 2.74
3534 7187 7.251994 AGAGAAGTGATCAACGATTACTGTAC 58.748 38.462 0.00 0.00 37.80 2.90
3688 7341 5.758790 AGCATCTATCTGTCCAGCATATT 57.241 39.130 0.00 0.00 0.00 1.28
3828 7487 6.449635 TCATCATAACAACCTTTATGCACC 57.550 37.500 0.00 0.00 38.73 5.01
3882 7543 5.581126 TCTTGCAATTCAACTCAACACTT 57.419 34.783 0.00 0.00 0.00 3.16
4066 7727 1.598701 GGGGGACATCACAGCTTTGC 61.599 60.000 0.00 0.00 0.00 3.68
4351 8014 3.698029 TGTTTTCTCTTGCAGCACTTC 57.302 42.857 0.00 0.00 0.00 3.01
4384 8047 1.774110 AGGCAACACCACATTGACAA 58.226 45.000 0.00 0.00 43.14 3.18
4577 8240 8.856103 TCATTTAGGTTCCTTAAAGGTTTTGAG 58.144 33.333 0.00 0.00 36.53 3.02
4597 8261 9.599866 TTTTGAGTAATCACATGAATCGTCTAT 57.400 29.630 0.00 0.00 0.00 1.98
4619 8283 1.276622 ACTTAGGGCATCTCCAACGT 58.723 50.000 0.00 0.00 36.21 3.99
4633 8297 1.196808 CCAACGTTGACCCTCAAATCG 59.803 52.381 29.35 4.16 38.22 3.34
4638 8302 2.711542 GTTGACCCTCAAATCGGACAT 58.288 47.619 0.00 0.00 38.22 3.06
4645 8309 2.477825 CTCAAATCGGACATCGCATCT 58.522 47.619 0.00 0.00 39.05 2.90
4661 8336 2.104967 CATCTGGCCATCCAACATGTT 58.895 47.619 5.51 4.92 42.91 2.71
4677 8352 6.074569 CCAACATGTTTGGTTACATTTCGAAC 60.075 38.462 8.77 0.00 36.64 3.95
4684 8359 5.037015 TGGTTACATTTCGAACGGAATTG 57.963 39.130 0.00 0.00 40.29 2.32
4687 8362 6.072397 TGGTTACATTTCGAACGGAATTGAAT 60.072 34.615 0.00 0.00 37.93 2.57
4828 8503 5.749462 ACTTAGTCTAAATGATTGCTGGCT 58.251 37.500 0.00 0.00 0.00 4.75
4834 8509 0.689745 AATGATTGCTGGCTGGCCAT 60.690 50.000 15.04 0.00 46.15 4.40
4870 8545 3.628646 ATTCCGCCTCCGCAAAGCT 62.629 57.895 0.00 0.00 34.03 3.74
4876 8551 2.564975 CTCCGCAAAGCTGGCAAG 59.435 61.111 10.80 4.11 0.00 4.01
4886 8561 2.359850 CTGGCAAGCGGCTAACCA 60.360 61.111 19.32 19.32 44.01 3.67
4897 8572 3.686622 GCTAACCAGCCGATGATGA 57.313 52.632 0.00 0.00 42.37 2.92
4898 8573 1.953559 GCTAACCAGCCGATGATGAA 58.046 50.000 0.00 0.00 42.37 2.57
4899 8574 1.869767 GCTAACCAGCCGATGATGAAG 59.130 52.381 0.00 0.00 42.37 3.02
4900 8575 2.483714 GCTAACCAGCCGATGATGAAGA 60.484 50.000 0.00 0.00 42.37 2.87
4901 8576 2.787473 AACCAGCCGATGATGAAGAA 57.213 45.000 0.00 0.00 0.00 2.52
4902 8577 2.787473 ACCAGCCGATGATGAAGAAA 57.213 45.000 0.00 0.00 0.00 2.52
4903 8578 2.359900 ACCAGCCGATGATGAAGAAAC 58.640 47.619 0.00 0.00 0.00 2.78
4904 8579 2.026822 ACCAGCCGATGATGAAGAAACT 60.027 45.455 0.00 0.00 0.00 2.66
4905 8580 2.353889 CCAGCCGATGATGAAGAAACTG 59.646 50.000 0.00 0.00 0.00 3.16
4906 8581 2.012673 AGCCGATGATGAAGAAACTGC 58.987 47.619 0.00 0.00 0.00 4.40
4907 8582 1.064654 GCCGATGATGAAGAAACTGCC 59.935 52.381 0.00 0.00 0.00 4.85
4908 8583 2.358957 CCGATGATGAAGAAACTGCCA 58.641 47.619 0.00 0.00 0.00 4.92
4909 8584 2.749076 CCGATGATGAAGAAACTGCCAA 59.251 45.455 0.00 0.00 0.00 4.52
4910 8585 3.181503 CCGATGATGAAGAAACTGCCAAG 60.182 47.826 0.00 0.00 0.00 3.61
4911 8586 3.730061 CGATGATGAAGAAACTGCCAAGC 60.730 47.826 0.00 0.00 0.00 4.01
4912 8587 1.888512 TGATGAAGAAACTGCCAAGCC 59.111 47.619 0.00 0.00 0.00 4.35
4913 8588 2.165998 GATGAAGAAACTGCCAAGCCT 58.834 47.619 0.00 0.00 0.00 4.58
4914 8589 2.949177 TGAAGAAACTGCCAAGCCTA 57.051 45.000 0.00 0.00 0.00 3.93
4915 8590 2.783135 TGAAGAAACTGCCAAGCCTAG 58.217 47.619 0.00 0.00 0.00 3.02
4916 8591 1.470494 GAAGAAACTGCCAAGCCTAGC 59.530 52.381 0.00 0.00 0.00 3.42
4917 8592 0.695347 AGAAACTGCCAAGCCTAGCT 59.305 50.000 0.00 0.00 42.56 3.32
4919 8594 1.470494 GAAACTGCCAAGCCTAGCTTC 59.530 52.381 0.00 0.00 46.77 3.86
4920 8595 0.401738 AACTGCCAAGCCTAGCTTCA 59.598 50.000 0.00 0.00 46.77 3.02
4921 8596 0.401738 ACTGCCAAGCCTAGCTTCAA 59.598 50.000 0.00 0.00 46.77 2.69
4922 8597 0.807496 CTGCCAAGCCTAGCTTCAAC 59.193 55.000 0.00 0.00 46.77 3.18
4923 8598 0.955428 TGCCAAGCCTAGCTTCAACG 60.955 55.000 0.00 0.00 46.77 4.10
4924 8599 1.648467 GCCAAGCCTAGCTTCAACGG 61.648 60.000 0.00 0.00 46.77 4.44
4925 8600 1.026718 CCAAGCCTAGCTTCAACGGG 61.027 60.000 0.00 0.00 46.77 5.28
4926 8601 0.036388 CAAGCCTAGCTTCAACGGGA 60.036 55.000 0.00 0.00 46.77 5.14
4927 8602 0.912486 AAGCCTAGCTTCAACGGGAT 59.088 50.000 0.00 0.00 46.77 3.85
4928 8603 0.179000 AGCCTAGCTTCAACGGGATG 59.821 55.000 0.00 0.00 33.89 3.51
4929 8604 0.815615 GCCTAGCTTCAACGGGATGG 60.816 60.000 0.00 0.00 0.00 3.51
4930 8605 0.179045 CCTAGCTTCAACGGGATGGG 60.179 60.000 0.00 0.00 0.00 4.00
4931 8606 0.179045 CTAGCTTCAACGGGATGGGG 60.179 60.000 0.00 0.00 0.00 4.96
4932 8607 0.619255 TAGCTTCAACGGGATGGGGA 60.619 55.000 0.00 0.00 0.00 4.81
4933 8608 1.452108 GCTTCAACGGGATGGGGAG 60.452 63.158 0.00 0.00 0.00 4.30
4934 8609 1.991230 CTTCAACGGGATGGGGAGT 59.009 57.895 0.00 0.00 0.00 3.85
4935 8610 0.392998 CTTCAACGGGATGGGGAGTG 60.393 60.000 0.00 0.00 0.00 3.51
4936 8611 1.847798 TTCAACGGGATGGGGAGTGG 61.848 60.000 0.00 0.00 0.00 4.00
4937 8612 2.204090 AACGGGATGGGGAGTGGT 60.204 61.111 0.00 0.00 0.00 4.16
4938 8613 2.602676 AACGGGATGGGGAGTGGTG 61.603 63.158 0.00 0.00 0.00 4.17
4939 8614 3.797353 CGGGATGGGGAGTGGTGG 61.797 72.222 0.00 0.00 0.00 4.61
4940 8615 4.129148 GGGATGGGGAGTGGTGGC 62.129 72.222 0.00 0.00 0.00 5.01
4941 8616 4.129148 GGATGGGGAGTGGTGGCC 62.129 72.222 0.00 0.00 0.00 5.36
4942 8617 3.017581 GATGGGGAGTGGTGGCCT 61.018 66.667 3.32 0.00 0.00 5.19
4943 8618 2.535317 ATGGGGAGTGGTGGCCTT 60.535 61.111 3.32 0.00 0.00 4.35
4944 8619 2.155197 GATGGGGAGTGGTGGCCTTT 62.155 60.000 3.32 0.00 0.00 3.11
4945 8620 2.283173 GGGGAGTGGTGGCCTTTG 60.283 66.667 3.32 0.00 0.00 2.77
4946 8621 2.520968 GGGAGTGGTGGCCTTTGT 59.479 61.111 3.32 0.00 0.00 2.83
4947 8622 1.903404 GGGAGTGGTGGCCTTTGTG 60.903 63.158 3.32 0.00 0.00 3.33
4948 8623 1.903404 GGAGTGGTGGCCTTTGTGG 60.903 63.158 3.32 0.00 39.35 4.17
4949 8624 1.903404 GAGTGGTGGCCTTTGTGGG 60.903 63.158 3.32 0.00 36.00 4.61
4950 8625 2.197324 GTGGTGGCCTTTGTGGGA 59.803 61.111 3.32 0.00 36.00 4.37
4951 8626 2.197324 TGGTGGCCTTTGTGGGAC 59.803 61.111 3.32 0.00 36.00 4.46
4952 8627 2.600470 GGTGGCCTTTGTGGGACC 60.600 66.667 3.32 0.00 36.00 4.46
4953 8628 2.600470 GTGGCCTTTGTGGGACCC 60.600 66.667 2.45 2.45 36.00 4.46
4954 8629 3.106609 TGGCCTTTGTGGGACCCA 61.107 61.111 9.95 9.95 36.00 4.51
4955 8630 2.200092 GGCCTTTGTGGGACCCAA 59.800 61.111 16.98 2.74 34.18 4.12
4956 8631 1.908299 GGCCTTTGTGGGACCCAAG 60.908 63.158 16.98 9.45 34.18 3.61
4957 8632 1.152546 GCCTTTGTGGGACCCAAGT 60.153 57.895 16.98 0.00 34.18 3.16
4958 8633 0.111639 GCCTTTGTGGGACCCAAGTA 59.888 55.000 16.98 1.49 34.18 2.24
4959 8634 1.272480 GCCTTTGTGGGACCCAAGTAT 60.272 52.381 16.98 0.00 34.18 2.12
4960 8635 2.723273 CCTTTGTGGGACCCAAGTATC 58.277 52.381 16.98 2.44 34.18 2.24
4961 8636 2.356135 CTTTGTGGGACCCAAGTATCG 58.644 52.381 16.98 0.00 34.18 2.92
4962 8637 0.616371 TTGTGGGACCCAAGTATCGG 59.384 55.000 16.98 0.00 34.18 4.18
4963 8638 1.153229 GTGGGACCCAAGTATCGGC 60.153 63.158 16.98 0.00 34.18 5.54
4964 8639 2.108362 GGGACCCAAGTATCGGCG 59.892 66.667 5.33 0.00 0.00 6.46
4965 8640 2.108362 GGACCCAAGTATCGGCGG 59.892 66.667 7.21 0.00 0.00 6.13
4966 8641 2.588034 GACCCAAGTATCGGCGGC 60.588 66.667 7.21 0.00 0.00 6.53
4967 8642 4.171103 ACCCAAGTATCGGCGGCC 62.171 66.667 9.54 9.54 0.00 6.13
4968 8643 3.861797 CCCAAGTATCGGCGGCCT 61.862 66.667 18.34 1.06 0.00 5.19
4969 8644 2.280186 CCAAGTATCGGCGGCCTC 60.280 66.667 18.34 4.95 0.00 4.70
4970 8645 2.280186 CAAGTATCGGCGGCCTCC 60.280 66.667 18.34 0.01 0.00 4.30
4971 8646 3.547513 AAGTATCGGCGGCCTCCC 61.548 66.667 18.34 2.33 0.00 4.30
4972 8647 4.853142 AGTATCGGCGGCCTCCCA 62.853 66.667 18.34 0.00 0.00 4.37
4973 8648 3.626924 GTATCGGCGGCCTCCCAT 61.627 66.667 18.34 0.66 0.00 4.00
4974 8649 3.625897 TATCGGCGGCCTCCCATG 61.626 66.667 18.34 0.00 0.00 3.66
4979 8654 3.550431 GCGGCCTCCCATGCTCTA 61.550 66.667 0.00 0.00 0.00 2.43
4980 8655 2.423446 CGGCCTCCCATGCTCTAC 59.577 66.667 0.00 0.00 0.00 2.59
4981 8656 2.136878 CGGCCTCCCATGCTCTACT 61.137 63.158 0.00 0.00 0.00 2.57
4982 8657 1.751563 GGCCTCCCATGCTCTACTC 59.248 63.158 0.00 0.00 0.00 2.59
4983 8658 0.762461 GGCCTCCCATGCTCTACTCT 60.762 60.000 0.00 0.00 0.00 3.24
4984 8659 1.127343 GCCTCCCATGCTCTACTCTT 58.873 55.000 0.00 0.00 0.00 2.85
4985 8660 1.069978 GCCTCCCATGCTCTACTCTTC 59.930 57.143 0.00 0.00 0.00 2.87
4986 8661 1.691434 CCTCCCATGCTCTACTCTTCC 59.309 57.143 0.00 0.00 0.00 3.46
4987 8662 2.676748 CTCCCATGCTCTACTCTTCCT 58.323 52.381 0.00 0.00 0.00 3.36
4988 8663 3.437198 CCTCCCATGCTCTACTCTTCCTA 60.437 52.174 0.00 0.00 0.00 2.94
4989 8664 4.219115 CTCCCATGCTCTACTCTTCCTAA 58.781 47.826 0.00 0.00 0.00 2.69
4990 8665 3.961408 TCCCATGCTCTACTCTTCCTAAC 59.039 47.826 0.00 0.00 0.00 2.34
4991 8666 3.964031 CCCATGCTCTACTCTTCCTAACT 59.036 47.826 0.00 0.00 0.00 2.24
4992 8667 4.202202 CCCATGCTCTACTCTTCCTAACTG 60.202 50.000 0.00 0.00 0.00 3.16
4993 8668 4.404073 CCATGCTCTACTCTTCCTAACTGT 59.596 45.833 0.00 0.00 0.00 3.55
4994 8669 5.451242 CCATGCTCTACTCTTCCTAACTGTC 60.451 48.000 0.00 0.00 0.00 3.51
4995 8670 3.690139 TGCTCTACTCTTCCTAACTGTCG 59.310 47.826 0.00 0.00 0.00 4.35
4996 8671 3.065648 GCTCTACTCTTCCTAACTGTCGG 59.934 52.174 0.00 0.00 0.00 4.79
4997 8672 3.015327 TCTACTCTTCCTAACTGTCGGC 58.985 50.000 0.00 0.00 0.00 5.54
4998 8673 0.526662 ACTCTTCCTAACTGTCGGCG 59.473 55.000 0.00 0.00 0.00 6.46
4999 8674 0.179134 CTCTTCCTAACTGTCGGCGG 60.179 60.000 7.21 0.00 0.00 6.13
5000 8675 0.896940 TCTTCCTAACTGTCGGCGGT 60.897 55.000 7.21 0.00 35.32 5.68
5001 8676 0.736325 CTTCCTAACTGTCGGCGGTG 60.736 60.000 0.17 0.00 33.83 4.94
5002 8677 2.775032 TTCCTAACTGTCGGCGGTGC 62.775 60.000 0.17 0.00 33.83 5.01
5003 8678 2.813908 CTAACTGTCGGCGGTGCC 60.814 66.667 0.17 0.00 46.75 5.01
5024 8699 2.741211 GGACGTGCCGGTTTCCTC 60.741 66.667 1.90 0.00 0.00 3.71
5025 8700 3.110178 GACGTGCCGGTTTCCTCG 61.110 66.667 1.90 1.12 0.00 4.63
5026 8701 3.853597 GACGTGCCGGTTTCCTCGT 62.854 63.158 1.90 4.84 0.00 4.18
5027 8702 3.110178 CGTGCCGGTTTCCTCGTC 61.110 66.667 1.90 0.00 0.00 4.20
5028 8703 3.110178 GTGCCGGTTTCCTCGTCG 61.110 66.667 1.90 0.00 0.00 5.12
5029 8704 3.608662 TGCCGGTTTCCTCGTCGT 61.609 61.111 1.90 0.00 0.00 4.34
5030 8705 3.110178 GCCGGTTTCCTCGTCGTG 61.110 66.667 1.90 0.00 0.00 4.35
5031 8706 2.431942 CCGGTTTCCTCGTCGTGG 60.432 66.667 7.02 7.02 0.00 4.94
5032 8707 3.110178 CGGTTTCCTCGTCGTGGC 61.110 66.667 8.49 0.00 0.00 5.01
5033 8708 2.029964 GGTTTCCTCGTCGTGGCA 59.970 61.111 8.49 0.00 0.00 4.92
5034 8709 1.375523 GGTTTCCTCGTCGTGGCAT 60.376 57.895 8.49 0.00 0.00 4.40
5035 8710 1.359459 GGTTTCCTCGTCGTGGCATC 61.359 60.000 8.49 0.00 0.00 3.91
5036 8711 1.445410 TTTCCTCGTCGTGGCATCG 60.445 57.895 8.49 0.00 0.00 3.84
5037 8712 2.829043 TTTCCTCGTCGTGGCATCGG 62.829 60.000 8.49 0.00 0.00 4.18
5038 8713 4.873129 CCTCGTCGTGGCATCGGG 62.873 72.222 0.00 6.20 0.00 5.14
5039 8714 4.873129 CTCGTCGTGGCATCGGGG 62.873 72.222 9.05 3.19 0.00 5.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 4.394920 GCACTAATTCACTGGATCGGAAAA 59.605 41.667 0.00 0.00 0.00 2.29
65 66 0.603707 CGGCAGCCAGACTCTTTTGA 60.604 55.000 13.30 0.00 0.00 2.69
72 73 4.335647 CAACCCGGCAGCCAGACT 62.336 66.667 13.30 0.00 0.00 3.24
98 99 3.724732 AATAACCCTCCGGCAAAAGTA 57.275 42.857 0.00 0.00 0.00 2.24
116 117 5.551233 CATCGAATCCCACACCACTATAAT 58.449 41.667 0.00 0.00 0.00 1.28
129 130 2.069273 CCTATCGTTGCATCGAATCCC 58.931 52.381 22.45 0.00 42.99 3.85
212 213 0.771127 TCCCAAGAAACACAGGGGAG 59.229 55.000 0.00 0.00 42.75 4.30
217 219 4.401925 AGGAAATCTCCCAAGAAACACAG 58.598 43.478 0.00 0.00 43.64 3.66
238 240 7.246674 TGCACTTCTACAACAGTAAAGAAAG 57.753 36.000 0.00 0.00 0.00 2.62
242 244 8.745837 CATTTTTGCACTTCTACAACAGTAAAG 58.254 33.333 0.00 0.00 0.00 1.85
245 247 7.282224 AGACATTTTTGCACTTCTACAACAGTA 59.718 33.333 0.00 0.00 0.00 2.74
246 248 6.095440 AGACATTTTTGCACTTCTACAACAGT 59.905 34.615 0.00 0.00 0.00 3.55
252 274 5.748592 ACGAAGACATTTTTGCACTTCTAC 58.251 37.500 8.72 0.00 36.04 2.59
260 282 6.900299 GCTAGTACATACGAAGACATTTTTGC 59.100 38.462 0.00 0.00 0.00 3.68
263 285 8.464404 TGTAGCTAGTACATACGAAGACATTTT 58.536 33.333 0.00 0.00 36.67 1.82
290 312 7.821359 CCATTGTACGAGCTACTACTACCTATA 59.179 40.741 0.00 0.00 0.00 1.31
299 321 5.653769 ACTAAACCCATTGTACGAGCTACTA 59.346 40.000 0.00 0.00 0.00 1.82
300 322 3.975168 AAACCCATTGTACGAGCTACT 57.025 42.857 0.00 0.00 0.00 2.57
301 323 4.752146 ACTAAACCCATTGTACGAGCTAC 58.248 43.478 0.00 0.00 0.00 3.58
302 324 5.887598 TCTACTAAACCCATTGTACGAGCTA 59.112 40.000 0.00 0.00 0.00 3.32
324 346 2.294233 GCACATGACAATGGTGTGTTCT 59.706 45.455 0.00 0.00 43.80 3.01
346 368 4.350368 TCATCTCAAAGTGCAGGTAACA 57.650 40.909 0.00 0.00 41.41 2.41
365 387 9.378551 GTCATAAGTAGTTCAAATACCACATCA 57.621 33.333 0.00 0.00 0.00 3.07
375 397 9.692749 CAAGTCTACTGTCATAAGTAGTTCAAA 57.307 33.333 10.33 0.00 46.53 2.69
384 406 4.744795 AGGCCAAGTCTACTGTCATAAG 57.255 45.455 5.01 0.00 0.00 1.73
415 437 2.172293 ACCCAACAAAACGTACCCACTA 59.828 45.455 0.00 0.00 0.00 2.74
541 584 5.689383 ATAGCCGCAATTTTGGTAGTATG 57.311 39.130 0.00 0.00 0.00 2.39
592 636 3.108289 CACGTGCTCCGCTGACTG 61.108 66.667 0.82 0.00 41.42 3.51
659 718 4.988716 TCACGGCGGAGGACCACT 62.989 66.667 13.24 0.00 35.59 4.00
709 768 4.742649 AGCGTGAGAGGCCCGAGA 62.743 66.667 0.00 0.00 0.00 4.04
733 792 3.465871 ACTACTACTGCTACTACCGCTC 58.534 50.000 0.00 0.00 0.00 5.03
775 834 0.756903 GGGCTTGATTCGGCTACCTA 59.243 55.000 2.38 0.00 0.00 3.08
776 835 1.527370 GGGCTTGATTCGGCTACCT 59.473 57.895 2.38 0.00 0.00 3.08
778 837 1.526225 GGGGGCTTGATTCGGCTAC 60.526 63.158 2.38 0.00 0.00 3.58
779 838 2.915869 GGGGGCTTGATTCGGCTA 59.084 61.111 2.38 0.00 0.00 3.93
780 839 4.489771 CGGGGGCTTGATTCGGCT 62.490 66.667 2.38 0.00 0.00 5.52
793 852 4.785453 GAACAGGAGCAGCCGGGG 62.785 72.222 2.18 0.00 43.43 5.73
794 853 3.672295 GAGAACAGGAGCAGCCGGG 62.672 68.421 2.18 0.00 43.43 5.73
795 854 2.125350 GAGAACAGGAGCAGCCGG 60.125 66.667 0.00 0.00 43.43 6.13
796 855 2.507992 CGAGAACAGGAGCAGCCG 60.508 66.667 0.00 0.00 43.43 5.52
810 909 2.458006 GAAGGTTTGGTTGCGGCGAG 62.458 60.000 12.98 0.00 0.00 5.03
908 3749 0.545309 TCAGAGGTCTGGGTTCTGGG 60.545 60.000 7.14 0.00 43.91 4.45
989 3871 2.718073 GCCTCCATGCTTGGCCTTG 61.718 63.158 13.75 0.00 43.29 3.61
990 3872 2.363406 GCCTCCATGCTTGGCCTT 60.363 61.111 13.75 0.00 43.29 4.35
1331 4223 0.322546 AAACGAGAAGGTGGATGGGC 60.323 55.000 0.00 0.00 0.00 5.36
1336 4232 1.673920 GCAAACAAACGAGAAGGTGGA 59.326 47.619 0.00 0.00 0.00 4.02
1342 4238 4.034626 TCAAATCGAGCAAACAAACGAGAA 59.965 37.500 0.00 0.00 38.12 2.87
1343 4239 3.558006 TCAAATCGAGCAAACAAACGAGA 59.442 39.130 0.00 0.00 38.12 4.04
1345 4241 3.953874 TCAAATCGAGCAAACAAACGA 57.046 38.095 0.00 0.00 39.01 3.85
1348 4244 4.022935 AGCAGATCAAATCGAGCAAACAAA 60.023 37.500 0.00 0.00 37.56 2.83
1349 4245 3.503363 AGCAGATCAAATCGAGCAAACAA 59.497 39.130 0.00 0.00 37.56 2.83
1350 4246 3.076621 AGCAGATCAAATCGAGCAAACA 58.923 40.909 0.00 0.00 37.56 2.83
1351 4247 3.486542 GGAGCAGATCAAATCGAGCAAAC 60.487 47.826 0.00 2.68 37.56 2.93
1352 4248 2.679837 GGAGCAGATCAAATCGAGCAAA 59.320 45.455 0.00 0.00 37.56 3.68
1354 4250 1.483827 AGGAGCAGATCAAATCGAGCA 59.516 47.619 0.00 0.00 37.56 4.26
1421 4330 2.740714 GCATCAAGCGACCGACCAC 61.741 63.158 0.00 0.00 0.00 4.16
1454 4363 2.034878 TCCCATGAATCTCTGGAGTCG 58.965 52.381 0.00 0.00 39.15 4.18
1464 4456 3.004734 CGCCCACTAAATTCCCATGAATC 59.995 47.826 0.00 0.00 40.34 2.52
1469 4461 0.033601 TGCGCCCACTAAATTCCCAT 60.034 50.000 4.18 0.00 0.00 4.00
1504 4496 2.737252 GAGAAGCAAACTACAGGAACCG 59.263 50.000 0.00 0.00 0.00 4.44
1513 4505 8.161425 AGGGTAAACAATTAGAGAAGCAAACTA 58.839 33.333 0.00 0.00 0.00 2.24
1516 4508 7.174946 CAGAGGGTAAACAATTAGAGAAGCAAA 59.825 37.037 0.00 0.00 0.00 3.68
1577 4603 1.080839 CCAAATGCGTTTGTCCGGG 60.081 57.895 25.66 9.95 42.50 5.73
1598 4624 1.940613 GCAGTAGAAAAGGTATGCCGG 59.059 52.381 0.00 0.00 40.50 6.13
1599 4625 2.609459 CTGCAGTAGAAAAGGTATGCCG 59.391 50.000 5.25 0.00 40.50 5.69
1606 4632 7.283329 AGGTATTAATCCTGCAGTAGAAAAGG 58.717 38.462 13.81 0.00 33.62 3.11
1669 4695 5.602628 AGAACAACTAGACAAGAGTGAACC 58.397 41.667 0.00 0.00 0.00 3.62
1704 4733 2.546778 TCGAGGACAACAGTGAACAAC 58.453 47.619 0.00 0.00 0.00 3.32
1705 4734 2.971660 TCGAGGACAACAGTGAACAA 57.028 45.000 0.00 0.00 0.00 2.83
1706 4735 2.971660 TTCGAGGACAACAGTGAACA 57.028 45.000 0.00 0.00 0.00 3.18
1707 4736 3.869246 TCTTTTCGAGGACAACAGTGAAC 59.131 43.478 0.00 0.00 0.00 3.18
1728 4757 5.659971 TCCTAGTTGGATACCTACTTGGTTC 59.340 44.000 22.30 0.00 45.76 3.62
1735 4764 4.216708 ACAGCTCCTAGTTGGATACCTAC 58.783 47.826 0.00 0.00 45.16 3.18
1736 4765 4.537945 ACAGCTCCTAGTTGGATACCTA 57.462 45.455 0.00 0.00 45.16 3.08
1737 4766 3.406512 ACAGCTCCTAGTTGGATACCT 57.593 47.619 0.00 0.00 45.16 3.08
1738 4767 4.894114 TCTAACAGCTCCTAGTTGGATACC 59.106 45.833 0.00 0.00 45.16 2.73
1817 4847 4.619160 CGACTCAGACAGGTGAAATCATGA 60.619 45.833 0.00 0.00 0.00 3.07
1879 4909 3.580895 TGGTCAATCTAGTGTTAGTGCCA 59.419 43.478 0.00 0.00 0.00 4.92
1882 4912 8.035394 ACAAGTATGGTCAATCTAGTGTTAGTG 58.965 37.037 0.00 0.00 0.00 2.74
1916 4983 9.431887 CCTAAGTTGCAGAACATTAAACTACTA 57.568 33.333 0.00 0.00 34.17 1.82
1917 4984 7.094762 GCCTAAGTTGCAGAACATTAAACTACT 60.095 37.037 0.00 0.00 34.17 2.57
1918 4985 7.021790 GCCTAAGTTGCAGAACATTAAACTAC 58.978 38.462 0.00 0.00 34.17 2.73
2002 5071 6.127619 CCTGAAAGTGGAACAGAAGAAAAGTT 60.128 38.462 0.00 0.00 41.80 2.66
2045 5114 8.919145 ACCAAATAATTGACCACTGACTTTAAA 58.081 29.630 0.00 0.00 38.94 1.52
2447 5911 5.220739 GGCATAACTGAAAGCATACAGACAG 60.221 44.000 10.16 0.00 37.60 3.51
2534 5998 8.998277 TGCACTCTACTCTCCTAGTATTATTT 57.002 34.615 0.00 0.00 39.96 1.40
2586 6050 4.023107 CGTCACTCTTCTGACAAGAGGTAA 60.023 45.833 14.36 0.00 46.05 2.85
2650 6115 7.775053 TTATCAAATGGAAAAGGTAGCTTGT 57.225 32.000 8.16 1.61 0.00 3.16
2809 6275 6.635755 ACAGCCTCTCTTATCAAAAGACTAC 58.364 40.000 0.00 0.00 0.00 2.73
2826 6292 2.772287 GGGATATGCAACTACAGCCTC 58.228 52.381 0.00 0.00 0.00 4.70
2868 6334 8.593492 AAAATAAAGTTTCAGTGAATCCAAGC 57.407 30.769 6.36 0.00 0.00 4.01
2902 6369 5.020795 TGTATGTCAGGCTTACTTCCACTA 58.979 41.667 0.00 0.00 0.00 2.74
3082 6574 2.868583 CGAGAAATCACCTGGTGCATAG 59.131 50.000 22.02 5.65 32.98 2.23
3200 6692 1.906574 GGAGACAAGTACATGGACCCA 59.093 52.381 3.84 0.00 0.00 4.51
3205 6697 3.961480 TGTGAGGAGACAAGTACATGG 57.039 47.619 2.78 0.00 0.00 3.66
3245 6739 6.710278 TGGTCATGTGTTCTTGATAAGATGA 58.290 36.000 0.00 0.00 37.38 2.92
3298 6951 6.054295 AGCCATCATTCTGATTCTCTGTAAC 58.946 40.000 0.00 0.00 34.28 2.50
3505 7158 8.802856 CAGTAATCGTTGATCACTTCTCTTTAG 58.197 37.037 0.00 0.00 0.00 1.85
3523 7176 5.120208 CACCAACCTGAAAGTACAGTAATCG 59.880 44.000 0.00 0.00 36.30 3.34
3531 7184 2.616842 CACCACACCAACCTGAAAGTAC 59.383 50.000 0.00 0.00 0.00 2.73
3534 7187 2.051334 TCACCACACCAACCTGAAAG 57.949 50.000 0.00 0.00 0.00 2.62
3688 7341 8.420374 ACATTCGAAAGCTATTAATCGAGAAA 57.580 30.769 0.00 0.00 44.11 2.52
3778 7431 9.357161 TCAACTAAATAAAATTGGTACAGTGGT 57.643 29.630 0.00 0.00 42.39 4.16
3828 7487 4.342092 ACAAGAAGAAGGTTGGTTCAATGG 59.658 41.667 0.00 0.00 0.00 3.16
3882 7543 4.771114 AAGCCTATACCATGCAGTTACA 57.229 40.909 0.00 0.00 0.00 2.41
4054 7715 7.880695 GCAGAATGAATCGCAAAGCTGTGAT 62.881 44.000 8.49 1.66 45.19 3.06
4066 7727 3.066342 AGCTTCCATTGCAGAATGAATCG 59.934 43.478 0.00 0.00 41.49 3.34
4317 7980 8.067189 GCAAGAGAAAACAAGACAAAACAAAAA 58.933 29.630 0.00 0.00 0.00 1.94
4318 7981 7.225538 TGCAAGAGAAAACAAGACAAAACAAAA 59.774 29.630 0.00 0.00 0.00 2.44
4319 7982 6.703607 TGCAAGAGAAAACAAGACAAAACAAA 59.296 30.769 0.00 0.00 0.00 2.83
4329 7992 3.705043 AGTGCTGCAAGAGAAAACAAG 57.295 42.857 2.77 0.00 34.07 3.16
4351 8014 5.183713 TGGTGTTGCCTATTCAAAAGATCTG 59.816 40.000 0.00 0.00 38.35 2.90
4525 8188 4.552355 TCAAGATGCAAAATGTGAAGCTG 58.448 39.130 0.00 0.00 29.28 4.24
4597 8261 3.262405 ACGTTGGAGATGCCCTAAGTTTA 59.738 43.478 0.00 0.00 34.97 2.01
4619 8283 2.676750 CGATGTCCGATTTGAGGGTCAA 60.677 50.000 0.00 0.00 41.76 3.18
4633 8297 1.228063 ATGGCCAGATGCGATGTCC 60.228 57.895 13.05 0.00 42.61 4.02
4638 8302 1.451927 GTTGGATGGCCAGATGCGA 60.452 57.895 13.05 0.00 46.91 5.10
4645 8309 0.975135 CCAAACATGTTGGATGGCCA 59.025 50.000 14.90 8.56 44.17 5.36
4661 8336 5.238868 TCAATTCCGTTCGAAATGTAACCAA 59.761 36.000 0.00 0.00 33.72 3.67
4834 8509 2.270352 ATTTCACTTTCCGTGGCTCA 57.730 45.000 0.00 0.00 43.94 4.26
4842 8517 1.472878 GGAGGCGGAATTTCACTTTCC 59.527 52.381 0.00 0.00 39.44 3.13
4853 8528 4.329545 AGCTTTGCGGAGGCGGAA 62.330 61.111 0.00 0.00 44.10 4.30
4870 8545 2.359850 CTGGTTAGCCGCTTGCCA 60.360 61.111 13.02 13.02 42.71 4.92
4884 8559 2.353889 CAGTTTCTTCATCATCGGCTGG 59.646 50.000 0.00 0.00 0.00 4.85
4886 8561 2.012673 GCAGTTTCTTCATCATCGGCT 58.987 47.619 0.00 0.00 0.00 5.52
4888 8563 2.358957 TGGCAGTTTCTTCATCATCGG 58.641 47.619 0.00 0.00 0.00 4.18
4894 8569 2.299326 AGGCTTGGCAGTTTCTTCAT 57.701 45.000 0.00 0.00 0.00 2.57
4895 8570 2.783135 CTAGGCTTGGCAGTTTCTTCA 58.217 47.619 0.00 0.00 0.00 3.02
4896 8571 1.470494 GCTAGGCTTGGCAGTTTCTTC 59.530 52.381 0.00 0.00 0.00 2.87
4897 8572 1.074566 AGCTAGGCTTGGCAGTTTCTT 59.925 47.619 6.99 0.00 33.89 2.52
4898 8573 0.695347 AGCTAGGCTTGGCAGTTTCT 59.305 50.000 6.99 0.00 33.89 2.52
4899 8574 3.256281 AGCTAGGCTTGGCAGTTTC 57.744 52.632 6.99 0.00 33.89 2.78
4909 8584 0.179000 CATCCCGTTGAAGCTAGGCT 59.821 55.000 0.00 0.00 42.56 4.58
4910 8585 0.815615 CCATCCCGTTGAAGCTAGGC 60.816 60.000 0.00 0.00 0.00 3.93
4911 8586 0.179045 CCCATCCCGTTGAAGCTAGG 60.179 60.000 0.00 0.00 0.00 3.02
4912 8587 0.179045 CCCCATCCCGTTGAAGCTAG 60.179 60.000 0.00 0.00 0.00 3.42
4913 8588 0.619255 TCCCCATCCCGTTGAAGCTA 60.619 55.000 0.00 0.00 0.00 3.32
4914 8589 1.915078 CTCCCCATCCCGTTGAAGCT 61.915 60.000 0.00 0.00 0.00 3.74
4915 8590 1.452108 CTCCCCATCCCGTTGAAGC 60.452 63.158 0.00 0.00 0.00 3.86
4916 8591 0.392998 CACTCCCCATCCCGTTGAAG 60.393 60.000 0.00 0.00 0.00 3.02
4917 8592 1.682849 CACTCCCCATCCCGTTGAA 59.317 57.895 0.00 0.00 0.00 2.69
4918 8593 2.297895 CCACTCCCCATCCCGTTGA 61.298 63.158 0.00 0.00 0.00 3.18
4919 8594 2.272146 CCACTCCCCATCCCGTTG 59.728 66.667 0.00 0.00 0.00 4.10
4920 8595 2.204090 ACCACTCCCCATCCCGTT 60.204 61.111 0.00 0.00 0.00 4.44
4921 8596 3.009115 CACCACTCCCCATCCCGT 61.009 66.667 0.00 0.00 0.00 5.28
4922 8597 3.797353 CCACCACTCCCCATCCCG 61.797 72.222 0.00 0.00 0.00 5.14
4923 8598 4.129148 GCCACCACTCCCCATCCC 62.129 72.222 0.00 0.00 0.00 3.85
4924 8599 4.129148 GGCCACCACTCCCCATCC 62.129 72.222 0.00 0.00 0.00 3.51
4925 8600 2.155197 AAAGGCCACCACTCCCCATC 62.155 60.000 5.01 0.00 0.00 3.51
4926 8601 2.169810 AAAGGCCACCACTCCCCAT 61.170 57.895 5.01 0.00 0.00 4.00
4927 8602 2.780924 AAAGGCCACCACTCCCCA 60.781 61.111 5.01 0.00 0.00 4.96
4928 8603 2.283173 CAAAGGCCACCACTCCCC 60.283 66.667 5.01 0.00 0.00 4.81
4929 8604 1.903404 CACAAAGGCCACCACTCCC 60.903 63.158 5.01 0.00 0.00 4.30
4930 8605 1.903404 CCACAAAGGCCACCACTCC 60.903 63.158 5.01 0.00 0.00 3.85
4931 8606 1.903404 CCCACAAAGGCCACCACTC 60.903 63.158 5.01 0.00 35.39 3.51
4932 8607 2.198426 CCCACAAAGGCCACCACT 59.802 61.111 5.01 0.00 35.39 4.00
4933 8608 2.197324 TCCCACAAAGGCCACCAC 59.803 61.111 5.01 0.00 35.39 4.16
4934 8609 2.197324 GTCCCACAAAGGCCACCA 59.803 61.111 5.01 0.00 35.39 4.17
4935 8610 2.600470 GGTCCCACAAAGGCCACC 60.600 66.667 5.01 0.00 35.39 4.61
4936 8611 2.600470 GGGTCCCACAAAGGCCAC 60.600 66.667 5.01 0.00 35.39 5.01
4937 8612 2.655077 CTTGGGTCCCACAAAGGCCA 62.655 60.000 11.24 0.00 35.39 5.36
4938 8613 1.908299 CTTGGGTCCCACAAAGGCC 60.908 63.158 11.24 0.00 35.39 5.19
4939 8614 0.111639 TACTTGGGTCCCACAAAGGC 59.888 55.000 11.24 0.00 35.39 4.35
4940 8615 2.723273 GATACTTGGGTCCCACAAAGG 58.277 52.381 11.24 1.36 30.78 3.11
4941 8616 2.356135 CGATACTTGGGTCCCACAAAG 58.644 52.381 11.24 8.46 30.78 2.77
4942 8617 1.003812 CCGATACTTGGGTCCCACAAA 59.996 52.381 11.24 0.00 30.78 2.83
4943 8618 0.616371 CCGATACTTGGGTCCCACAA 59.384 55.000 11.24 0.00 30.78 3.33
4944 8619 1.906105 GCCGATACTTGGGTCCCACA 61.906 60.000 11.24 0.00 30.78 4.17
4945 8620 1.153229 GCCGATACTTGGGTCCCAC 60.153 63.158 11.24 0.00 30.78 4.61
4946 8621 2.727392 CGCCGATACTTGGGTCCCA 61.727 63.158 6.47 6.47 0.00 4.37
4947 8622 2.108362 CGCCGATACTTGGGTCCC 59.892 66.667 0.00 0.00 0.00 4.46
4948 8623 2.108362 CCGCCGATACTTGGGTCC 59.892 66.667 0.00 0.00 0.00 4.46
4949 8624 2.588034 GCCGCCGATACTTGGGTC 60.588 66.667 0.00 0.00 0.00 4.46
4950 8625 4.171103 GGCCGCCGATACTTGGGT 62.171 66.667 0.00 0.00 0.00 4.51
4951 8626 3.809374 GAGGCCGCCGATACTTGGG 62.809 68.421 3.05 0.00 0.00 4.12
4952 8627 2.280186 GAGGCCGCCGATACTTGG 60.280 66.667 3.05 0.00 0.00 3.61
4953 8628 2.280186 GGAGGCCGCCGATACTTG 60.280 66.667 10.77 0.00 0.00 3.16
4954 8629 3.547513 GGGAGGCCGCCGATACTT 61.548 66.667 20.27 0.00 0.00 2.24
4955 8630 4.853142 TGGGAGGCCGCCGATACT 62.853 66.667 20.27 0.00 0.00 2.12
4956 8631 3.626924 ATGGGAGGCCGCCGATAC 61.627 66.667 21.39 6.90 0.00 2.24
4957 8632 3.625897 CATGGGAGGCCGCCGATA 61.626 66.667 22.19 10.30 0.00 2.92
4962 8637 3.550431 TAGAGCATGGGAGGCCGC 61.550 66.667 0.00 0.00 0.00 6.53
4963 8638 2.093537 GAGTAGAGCATGGGAGGCCG 62.094 65.000 0.00 0.00 0.00 6.13
4964 8639 0.762461 AGAGTAGAGCATGGGAGGCC 60.762 60.000 0.00 0.00 0.00 5.19
4965 8640 1.069978 GAAGAGTAGAGCATGGGAGGC 59.930 57.143 0.00 0.00 0.00 4.70
4966 8641 1.691434 GGAAGAGTAGAGCATGGGAGG 59.309 57.143 0.00 0.00 0.00 4.30
4967 8642 2.676748 AGGAAGAGTAGAGCATGGGAG 58.323 52.381 0.00 0.00 0.00 4.30
4968 8643 2.856760 AGGAAGAGTAGAGCATGGGA 57.143 50.000 0.00 0.00 0.00 4.37
4969 8644 3.964031 AGTTAGGAAGAGTAGAGCATGGG 59.036 47.826 0.00 0.00 0.00 4.00
4970 8645 4.404073 ACAGTTAGGAAGAGTAGAGCATGG 59.596 45.833 0.00 0.00 0.00 3.66
4971 8646 5.587289 GACAGTTAGGAAGAGTAGAGCATG 58.413 45.833 0.00 0.00 0.00 4.06
4972 8647 4.336993 CGACAGTTAGGAAGAGTAGAGCAT 59.663 45.833 0.00 0.00 0.00 3.79
4973 8648 3.690139 CGACAGTTAGGAAGAGTAGAGCA 59.310 47.826 0.00 0.00 0.00 4.26
4974 8649 3.065648 CCGACAGTTAGGAAGAGTAGAGC 59.934 52.174 0.00 0.00 0.00 4.09
4975 8650 3.065648 GCCGACAGTTAGGAAGAGTAGAG 59.934 52.174 0.52 0.00 0.00 2.43
4976 8651 3.015327 GCCGACAGTTAGGAAGAGTAGA 58.985 50.000 0.52 0.00 0.00 2.59
4977 8652 2.223294 CGCCGACAGTTAGGAAGAGTAG 60.223 54.545 0.52 0.00 0.00 2.57
4978 8653 1.741706 CGCCGACAGTTAGGAAGAGTA 59.258 52.381 0.52 0.00 0.00 2.59
4979 8654 0.526662 CGCCGACAGTTAGGAAGAGT 59.473 55.000 0.52 0.00 0.00 3.24
4980 8655 0.179134 CCGCCGACAGTTAGGAAGAG 60.179 60.000 0.52 0.00 0.00 2.85
4981 8656 0.896940 ACCGCCGACAGTTAGGAAGA 60.897 55.000 0.52 0.00 0.00 2.87
4982 8657 0.736325 CACCGCCGACAGTTAGGAAG 60.736 60.000 0.52 0.00 0.00 3.46
4983 8658 1.290955 CACCGCCGACAGTTAGGAA 59.709 57.895 0.52 0.00 0.00 3.36
4984 8659 2.967397 CACCGCCGACAGTTAGGA 59.033 61.111 0.52 0.00 0.00 2.94
4985 8660 2.813908 GCACCGCCGACAGTTAGG 60.814 66.667 0.00 0.00 0.00 2.69
4986 8661 2.813908 GGCACCGCCGACAGTTAG 60.814 66.667 0.00 0.00 39.62 2.34
5011 8686 3.110178 CGACGAGGAAACCGGCAC 61.110 66.667 0.00 0.00 34.04 5.01
5012 8687 3.608662 ACGACGAGGAAACCGGCA 61.609 61.111 0.00 0.00 34.04 5.69
5013 8688 3.110178 CACGACGAGGAAACCGGC 61.110 66.667 0.00 0.00 0.00 6.13
5014 8689 2.431942 CCACGACGAGGAAACCGG 60.432 66.667 5.25 0.00 0.00 5.28
5015 8690 3.110178 GCCACGACGAGGAAACCG 61.110 66.667 15.98 0.00 0.00 4.44
5016 8691 1.359459 GATGCCACGACGAGGAAACC 61.359 60.000 15.98 0.00 0.00 3.27
5017 8692 1.683790 CGATGCCACGACGAGGAAAC 61.684 60.000 15.98 2.22 35.09 2.78
5018 8693 1.445410 CGATGCCACGACGAGGAAA 60.445 57.895 15.98 2.55 35.09 3.13
5019 8694 2.180769 CGATGCCACGACGAGGAA 59.819 61.111 15.98 4.70 35.09 3.36
5020 8695 3.822192 CCGATGCCACGACGAGGA 61.822 66.667 15.98 0.63 35.09 3.71
5021 8696 4.873129 CCCGATGCCACGACGAGG 62.873 72.222 6.99 6.99 35.09 4.63
5022 8697 4.873129 CCCCGATGCCACGACGAG 62.873 72.222 0.00 0.00 35.09 4.18


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

AutoCloner maintained by Alex Coulton.