Multiple sequence alignment - TraesCS5B01G297700

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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 TraesCS5B01G297700 chr5B 100.000 4845 0 0 1 4845 480295845 480291001 0.000000e+00 8948.0
1 TraesCS5B01G297700 chr5A 91.928 2775 135 49 15 2751 505614306 505611583 0.000000e+00 3801.0
2 TraesCS5B01G297700 chr5A 92.622 1613 68 16 2744 4346 505611301 505609730 0.000000e+00 2272.0
3 TraesCS5B01G297700 chr5A 95.600 250 10 1 4581 4829 505609597 505609348 2.720000e-107 399.0
4 TraesCS5B01G297700 chr5A 96.364 55 2 0 4528 4582 505609733 505609679 1.860000e-14 91.6
5 TraesCS5B01G297700 chr5D 96.090 2097 55 9 673 2748 400281926 400279836 0.000000e+00 3393.0
6 TraesCS5B01G297700 chr5D 96.244 1571 39 11 3273 4829 400278931 400277367 0.000000e+00 2556.0
7 TraesCS5B01G297700 chr5D 96.744 645 20 1 2744 3388 400279551 400278908 0.000000e+00 1074.0
8 TraesCS5B01G297700 chr5D 84.879 496 38 17 183 652 400282396 400281912 2.640000e-127 466.0
9 TraesCS5B01G297700 chr3D 96.204 764 22 2 971 1734 554063307 554064063 0.000000e+00 1243.0
10 TraesCS5B01G297700 chr3D 80.408 490 74 18 1228 1712 457018913 457019385 2.150000e-93 353.0
11 TraesCS5B01G297700 chr7D 95.331 771 29 2 964 1734 77074674 77075437 0.000000e+00 1218.0
12 TraesCS5B01G297700 chr7D 80.741 270 52 0 1579 1848 251374733 251374464 1.370000e-50 211.0
13 TraesCS5B01G297700 chr6B 95.652 552 22 2 974 1525 513612797 513612248 0.000000e+00 885.0
14 TraesCS5B01G297700 chr6B 83.784 185 28 2 1664 1847 717076325 717076142 1.790000e-39 174.0
15 TraesCS5B01G297700 chr3B 95.495 555 23 2 971 1525 576333409 576333961 0.000000e+00 885.0
16 TraesCS5B01G297700 chr3B 92.349 562 30 4 964 1525 82299965 82300513 0.000000e+00 787.0
17 TraesCS5B01G297700 chr3B 90.625 480 23 9 964 1443 464613634 464613177 6.890000e-173 617.0
18 TraesCS5B01G297700 chr2B 91.637 562 24 7 964 1525 698085635 698085097 0.000000e+00 756.0
19 TraesCS5B01G297700 chr2A 91.892 555 22 10 971 1525 66913738 66913207 0.000000e+00 754.0
20 TraesCS5B01G297700 chr3A 79.794 485 76 18 1228 1707 599861200 599861667 2.790000e-87 333.0
21 TraesCS5B01G297700 chr1D 79.412 476 74 16 1243 1712 388651032 388650575 1.010000e-81 315.0
22 TraesCS5B01G297700 chr1A 79.412 476 74 16 1243 1712 487741407 487740950 1.010000e-81 315.0
23 TraesCS5B01G297700 chr1B 79.202 476 75 18 1243 1712 522061084 522060627 4.710000e-80 309.0
24 TraesCS5B01G297700 chr7A 80.741 270 52 0 1579 1848 270042937 270043206 1.370000e-50 211.0
25 TraesCS5B01G297700 chr7B 80.370 270 53 0 1579 1848 228363472 228363203 6.360000e-49 206.0
26 TraesCS5B01G297700 chr6A 82.162 185 31 2 1664 1847 617657601 617657784 1.810000e-34 158.0
27 TraesCS5B01G297700 chr4D 90.654 107 10 0 1741 1847 12410790 12410896 5.050000e-30 143.0
28 TraesCS5B01G297700 chr6D 80.851 188 28 5 1664 1847 472358413 472358230 1.820000e-29 141.0


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 TraesCS5B01G297700 chr5B 480291001 480295845 4844 True 8948.00 8948 100.00000 1 4845 1 chr5B.!!$R1 4844
1 TraesCS5B01G297700 chr5A 505609348 505614306 4958 True 1640.90 3801 94.12850 15 4829 4 chr5A.!!$R1 4814
2 TraesCS5B01G297700 chr5D 400277367 400282396 5029 True 1872.25 3393 93.48925 183 4829 4 chr5D.!!$R1 4646
3 TraesCS5B01G297700 chr3D 554063307 554064063 756 False 1243.00 1243 96.20400 971 1734 1 chr3D.!!$F2 763
4 TraesCS5B01G297700 chr7D 77074674 77075437 763 False 1218.00 1218 95.33100 964 1734 1 chr7D.!!$F1 770
5 TraesCS5B01G297700 chr6B 513612248 513612797 549 True 885.00 885 95.65200 974 1525 1 chr6B.!!$R1 551
6 TraesCS5B01G297700 chr3B 576333409 576333961 552 False 885.00 885 95.49500 971 1525 1 chr3B.!!$F2 554
7 TraesCS5B01G297700 chr3B 82299965 82300513 548 False 787.00 787 92.34900 964 1525 1 chr3B.!!$F1 561
8 TraesCS5B01G297700 chr2B 698085097 698085635 538 True 756.00 756 91.63700 964 1525 1 chr2B.!!$R1 561
9 TraesCS5B01G297700 chr2A 66913207 66913738 531 True 754.00 754 91.89200 971 1525 1 chr2A.!!$R1 554

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
279 291 0.172803 AACAGAGTAACTAGGCCGCG 59.827 55.000 0.00 0.00 0.00 6.46 F
526 548 0.179225 GATGTTCGCGCGTGTGAAAT 60.179 50.000 30.98 19.20 45.53 2.17 F
527 549 0.237235 ATGTTCGCGCGTGTGAAATT 59.763 45.000 30.98 13.38 45.53 1.82 F
717 752 1.227380 GGCCTCTAGCATGACCGTG 60.227 63.158 0.00 0.00 46.50 4.94 F
2159 2229 0.320421 GGTGTAGTTTCCAGCTCGCA 60.320 55.000 0.00 0.00 0.00 5.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1987 2057 0.396811 CACCCCGGATTATGGACTCC 59.603 60.000 0.73 0.0 0.00 3.85 R
2143 2213 1.336887 TGTCTGCGAGCTGGAAACTAC 60.337 52.381 0.00 0.0 0.00 2.73 R
2159 2229 1.846007 TGTGTTTGTTTGGCCTGTCT 58.154 45.000 3.32 0.0 0.00 3.41 R
2222 2292 3.492102 TTGCAGGAGTAGCAAACTTCT 57.508 42.857 0.00 0.0 45.79 2.85 R
4004 4486 2.075338 CTGCTTCTGCTTCAGGAACTC 58.925 52.381 0.00 0.0 36.82 3.01 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
41 42 4.180946 CGCGACTGGTCCCTCTCG 62.181 72.222 0.00 0.00 0.00 4.04
64 65 0.803768 ACGATGTCGATGCAGTGAGC 60.804 55.000 9.67 0.00 43.02 4.26
73 74 2.745492 GCAGTGAGCTGTGGCCTC 60.745 66.667 3.32 0.00 44.32 4.70
112 113 2.729479 CGAGGCACTGGGAGAGCAT 61.729 63.158 0.00 0.00 41.55 3.79
115 116 2.202987 GCACTGGGAGAGCATCGG 60.203 66.667 0.00 0.00 42.67 4.18
138 139 1.643868 CGACCGCATTGCCTTGCTTA 61.644 55.000 2.41 0.00 40.54 3.09
151 152 3.529533 CCTTGCTTATGGTCAGTCTGAG 58.470 50.000 1.75 0.00 0.00 3.35
156 157 3.194542 GCTTATGGTCAGTCTGAGACAGT 59.805 47.826 15.86 0.00 37.74 3.55
181 182 9.255304 GTAAAATCACAAATTAGGTTGAAAGCA 57.745 29.630 0.00 0.00 32.59 3.91
187 188 8.081633 TCACAAATTAGGTTGAAAGCAATAGTG 58.918 33.333 0.00 0.00 36.22 2.74
205 206 1.161843 TGCATCACACATCAGCAGTG 58.838 50.000 0.00 0.00 42.56 3.66
209 210 1.601477 CACACATCAGCAGTGCCCA 60.601 57.895 12.58 0.00 40.59 5.36
246 249 6.303839 TCTAAAAAGACATTAACAGTGGCCT 58.696 36.000 3.32 0.00 0.00 5.19
247 250 7.455058 TCTAAAAAGACATTAACAGTGGCCTA 58.545 34.615 3.32 0.00 0.00 3.93
254 257 7.048512 AGACATTAACAGTGGCCTAAATAGAC 58.951 38.462 3.32 0.00 0.00 2.59
276 288 2.431419 GGGAGAACAGAGTAACTAGGCC 59.569 54.545 0.00 0.00 0.00 5.19
277 289 2.099427 GGAGAACAGAGTAACTAGGCCG 59.901 54.545 0.00 0.00 0.00 6.13
279 291 0.172803 AACAGAGTAACTAGGCCGCG 59.827 55.000 0.00 0.00 0.00 6.46
356 369 4.394300 AGCATCGGAAGACAAGATCAAAAG 59.606 41.667 0.00 0.00 46.97 2.27
387 400 0.236449 GGTTTTACCTGCGTCAACCG 59.764 55.000 0.00 0.00 34.73 4.44
388 401 1.219646 GTTTTACCTGCGTCAACCGA 58.780 50.000 0.00 0.00 39.56 4.69
389 402 1.070376 GTTTTACCTGCGTCAACCGAC 60.070 52.381 0.00 0.00 39.56 4.79
480 502 0.915364 ATCCAAGGAAGGAGGCAGTC 59.085 55.000 0.00 0.00 41.90 3.51
526 548 0.179225 GATGTTCGCGCGTGTGAAAT 60.179 50.000 30.98 19.20 45.53 2.17
527 549 0.237235 ATGTTCGCGCGTGTGAAATT 59.763 45.000 30.98 13.38 45.53 1.82
550 579 2.632377 TGCAGAAATGGACGAGAATCC 58.368 47.619 0.00 0.00 39.45 3.01
551 580 1.594862 GCAGAAATGGACGAGAATCCG 59.405 52.381 0.00 0.00 42.24 4.18
552 581 2.738643 GCAGAAATGGACGAGAATCCGA 60.739 50.000 0.00 0.00 42.24 4.55
553 582 3.119291 CAGAAATGGACGAGAATCCGAG 58.881 50.000 0.00 0.00 42.24 4.63
554 583 2.761208 AGAAATGGACGAGAATCCGAGT 59.239 45.455 0.00 0.00 42.24 4.18
555 584 2.873133 AATGGACGAGAATCCGAGTC 57.127 50.000 0.00 0.00 42.24 3.36
596 625 3.057245 CCGTTCTCTGACAGTCTGATTCA 60.057 47.826 6.91 0.00 0.00 2.57
599 628 5.160641 GTTCTCTGACAGTCTGATTCACTC 58.839 45.833 6.91 0.00 0.00 3.51
717 752 1.227380 GGCCTCTAGCATGACCGTG 60.227 63.158 0.00 0.00 46.50 4.94
764 805 4.715523 CGGCCGGGTTCCACACAT 62.716 66.667 20.10 0.00 0.00 3.21
771 812 2.672996 GTTCCACACATGCCGGCT 60.673 61.111 29.70 10.60 0.00 5.52
1149 1210 1.743252 CAGGAAGAAGCGCAGGTCC 60.743 63.158 11.47 10.83 37.06 4.46
1878 1939 3.305676 GCCTTTCTTCCTTGCTTCTTTCC 60.306 47.826 0.00 0.00 0.00 3.13
1879 1940 3.891366 CCTTTCTTCCTTGCTTCTTTCCA 59.109 43.478 0.00 0.00 0.00 3.53
1890 1951 3.214328 GCTTCTTTCCACACCTTCTTCA 58.786 45.455 0.00 0.00 0.00 3.02
1892 1953 4.455606 CTTCTTTCCACACCTTCTTCAGT 58.544 43.478 0.00 0.00 0.00 3.41
2159 2229 0.320421 GGTGTAGTTTCCAGCTCGCA 60.320 55.000 0.00 0.00 0.00 5.10
2180 2250 2.094234 AGACAGGCCAAACAAACACAAC 60.094 45.455 5.01 0.00 0.00 3.32
2236 2306 6.546972 AAACTTGCTAGAAGTTTGCTACTC 57.453 37.500 21.79 0.00 45.58 2.59
2237 2307 4.570930 ACTTGCTAGAAGTTTGCTACTCC 58.429 43.478 1.04 0.00 35.54 3.85
2238 2308 4.284746 ACTTGCTAGAAGTTTGCTACTCCT 59.715 41.667 1.04 0.00 35.54 3.69
2239 2309 4.193826 TGCTAGAAGTTTGCTACTCCTG 57.806 45.455 0.00 0.00 35.54 3.86
2240 2310 2.933260 GCTAGAAGTTTGCTACTCCTGC 59.067 50.000 0.00 0.00 35.54 4.85
2241 2311 3.617531 GCTAGAAGTTTGCTACTCCTGCA 60.618 47.826 0.00 0.00 35.54 4.41
2242 2312 3.492102 AGAAGTTTGCTACTCCTGCAA 57.508 42.857 0.00 0.00 46.90 4.08
2732 2831 2.072298 GCTGTTAGAAGCTGTGAGTGG 58.928 52.381 0.00 0.00 40.20 4.00
2802 3192 7.537306 TGAAAAATAAAGTTAGCAGCGTCATTC 59.463 33.333 0.00 0.00 0.00 2.67
2807 3197 2.996621 AGTTAGCAGCGTCATTCTGAAC 59.003 45.455 0.00 0.00 33.54 3.18
2817 3207 4.058124 CGTCATTCTGAACTGGAACTTCA 58.942 43.478 0.00 0.00 0.00 3.02
2826 3216 1.077663 ACTGGAACTTCATGGGGCATT 59.922 47.619 0.00 0.00 0.00 3.56
2874 3264 4.457257 GGCACATATCTAGCTTTCCCAATC 59.543 45.833 0.00 0.00 0.00 2.67
2940 3330 6.752351 ACGAGCTACATTATGTTCTAACACAG 59.248 38.462 2.23 0.00 42.51 3.66
3019 3409 7.497595 AGTTTGTGACAGTCTTACTTCACATA 58.502 34.615 17.59 13.36 41.31 2.29
3281 3671 5.535333 AGTTGACCTTGCTGATTTTGAATG 58.465 37.500 0.00 0.00 0.00 2.67
3313 3795 8.884323 ACTGTAGACACCATTTATCCATATCAT 58.116 33.333 0.00 0.00 0.00 2.45
3388 3870 9.014297 CCATTTTAAATCCTGAAACTGTAGACT 57.986 33.333 0.00 0.00 0.00 3.24
3417 3899 1.001378 CTGTTTCCAGTGAAAAGGGCG 60.001 52.381 0.00 0.00 41.92 6.13
3418 3900 0.313987 GTTTCCAGTGAAAAGGGCGG 59.686 55.000 0.00 0.00 41.92 6.13
3419 3901 1.460273 TTTCCAGTGAAAAGGGCGGC 61.460 55.000 0.00 0.00 37.53 6.53
3424 3906 0.037590 AGTGAAAAGGGCGGCACATA 59.962 50.000 12.47 0.00 33.85 2.29
3426 3908 0.250945 TGAAAAGGGCGGCACATACA 60.251 50.000 12.47 2.13 0.00 2.29
3500 3982 7.176589 TGACAAAAGGAAATTACAACACCTT 57.823 32.000 0.00 0.00 41.83 3.50
4004 4486 0.742281 CCCAGTTGCTCGGATGACAG 60.742 60.000 0.00 0.00 0.00 3.51
4103 4585 6.081872 ACATACTAATGTCTTAGGTACGGC 57.918 41.667 0.00 0.00 42.92 5.68
4255 4737 7.308830 GCATTCCAATTTCCATCCAGTATACTC 60.309 40.741 1.26 0.00 0.00 2.59
4358 4849 7.437713 AAGACAGATATAAATCAGGGTGACA 57.562 36.000 0.00 0.00 34.28 3.58
4359 4850 7.060383 AGACAGATATAAATCAGGGTGACAG 57.940 40.000 0.00 0.00 34.28 3.51
4360 4851 5.615289 ACAGATATAAATCAGGGTGACAGC 58.385 41.667 0.00 0.00 34.28 4.40
4361 4852 4.999950 CAGATATAAATCAGGGTGACAGCC 59.000 45.833 16.14 16.14 34.28 4.85
4363 4854 3.567478 ATAAATCAGGGTGACAGCCTC 57.433 47.619 23.36 0.00 43.92 4.70
4364 4855 0.329596 AAATCAGGGTGACAGCCTCC 59.670 55.000 23.36 0.00 43.92 4.30
4365 4856 0.842030 AATCAGGGTGACAGCCTCCA 60.842 55.000 23.36 13.24 43.92 3.86
4366 4857 0.622738 ATCAGGGTGACAGCCTCCAT 60.623 55.000 23.36 14.89 43.92 3.41
4367 4858 0.842030 TCAGGGTGACAGCCTCCATT 60.842 55.000 23.36 0.00 43.92 3.16
4368 4859 0.038744 CAGGGTGACAGCCTCCATTT 59.961 55.000 23.36 0.00 43.92 2.32
4369 4860 0.329596 AGGGTGACAGCCTCCATTTC 59.670 55.000 20.65 0.00 43.92 2.17
4370 4861 1.026718 GGGTGACAGCCTCCATTTCG 61.027 60.000 16.60 0.00 31.81 3.46
4371 4862 0.036388 GGTGACAGCCTCCATTTCGA 60.036 55.000 0.00 0.00 0.00 3.71
4372 4863 1.610624 GGTGACAGCCTCCATTTCGAA 60.611 52.381 0.00 0.00 0.00 3.71
4373 4864 2.151202 GTGACAGCCTCCATTTCGAAA 58.849 47.619 13.91 13.91 0.00 3.46
4374 4865 2.095718 GTGACAGCCTCCATTTCGAAAC 60.096 50.000 13.81 0.00 0.00 2.78
4375 4866 2.224523 TGACAGCCTCCATTTCGAAACT 60.225 45.455 13.81 1.41 0.00 2.66
4376 4867 3.007506 TGACAGCCTCCATTTCGAAACTA 59.992 43.478 13.81 0.57 0.00 2.24
4377 4868 4.000988 GACAGCCTCCATTTCGAAACTAA 58.999 43.478 13.81 0.23 0.00 2.24
4378 4869 4.003648 ACAGCCTCCATTTCGAAACTAAG 58.996 43.478 13.81 10.09 0.00 2.18
4379 4870 3.375299 CAGCCTCCATTTCGAAACTAAGG 59.625 47.826 21.45 21.45 0.00 2.69
4380 4871 3.009143 AGCCTCCATTTCGAAACTAAGGT 59.991 43.478 24.17 12.90 0.00 3.50
4381 4872 4.224370 AGCCTCCATTTCGAAACTAAGGTA 59.776 41.667 24.17 11.21 0.00 3.08
4382 4873 4.939439 GCCTCCATTTCGAAACTAAGGTAA 59.061 41.667 24.17 8.12 0.00 2.85
4383 4874 5.413523 GCCTCCATTTCGAAACTAAGGTAAA 59.586 40.000 24.17 7.63 0.00 2.01
4384 4875 6.095021 GCCTCCATTTCGAAACTAAGGTAAAT 59.905 38.462 24.17 2.78 0.00 1.40
4385 4876 7.362660 GCCTCCATTTCGAAACTAAGGTAAATT 60.363 37.037 24.17 2.35 0.00 1.82
4386 4877 7.968405 CCTCCATTTCGAAACTAAGGTAAATTG 59.032 37.037 13.81 2.81 0.00 2.32
4387 4878 8.398878 TCCATTTCGAAACTAAGGTAAATTGT 57.601 30.769 13.81 0.00 0.00 2.71
4388 4879 9.504708 TCCATTTCGAAACTAAGGTAAATTGTA 57.495 29.630 13.81 0.00 0.00 2.41
4418 4909 6.607004 GGCTATATAGGCCTCTGTCTAAAA 57.393 41.667 22.57 0.00 45.57 1.52
4419 4910 7.005709 GGCTATATAGGCCTCTGTCTAAAAA 57.994 40.000 22.57 0.00 45.57 1.94
4437 4928 4.955925 AAAAACATGACAACTGACACGA 57.044 36.364 0.00 0.00 0.00 4.35
4438 4929 4.955925 AAAACATGACAACTGACACGAA 57.044 36.364 0.00 0.00 0.00 3.85
4439 4930 5.499139 AAAACATGACAACTGACACGAAT 57.501 34.783 0.00 0.00 0.00 3.34
4440 4931 5.499139 AAACATGACAACTGACACGAATT 57.501 34.783 0.00 0.00 0.00 2.17
4441 4932 6.612247 AAACATGACAACTGACACGAATTA 57.388 33.333 0.00 0.00 0.00 1.40
4442 4933 5.591643 ACATGACAACTGACACGAATTAC 57.408 39.130 0.00 0.00 0.00 1.89
4443 4934 5.053811 ACATGACAACTGACACGAATTACA 58.946 37.500 0.00 0.00 0.00 2.41
4444 4935 5.700832 ACATGACAACTGACACGAATTACAT 59.299 36.000 0.00 0.00 0.00 2.29
4445 4936 6.204688 ACATGACAACTGACACGAATTACATT 59.795 34.615 0.00 0.00 0.00 2.71
4446 4937 7.386573 ACATGACAACTGACACGAATTACATTA 59.613 33.333 0.00 0.00 0.00 1.90
4447 4938 7.716768 TGACAACTGACACGAATTACATTAA 57.283 32.000 0.00 0.00 0.00 1.40
4448 4939 7.792925 TGACAACTGACACGAATTACATTAAG 58.207 34.615 0.00 0.00 0.00 1.85
4449 4940 7.439955 TGACAACTGACACGAATTACATTAAGT 59.560 33.333 0.00 0.00 0.00 2.24
4450 4941 7.793902 ACAACTGACACGAATTACATTAAGTC 58.206 34.615 0.00 0.00 0.00 3.01
4451 4942 7.439955 ACAACTGACACGAATTACATTAAGTCA 59.560 33.333 0.00 0.00 32.71 3.41
4452 4943 7.347508 ACTGACACGAATTACATTAAGTCAC 57.652 36.000 0.00 0.00 32.71 3.67
4453 4944 6.367969 ACTGACACGAATTACATTAAGTCACC 59.632 38.462 0.00 0.00 32.71 4.02
4454 4945 6.460781 TGACACGAATTACATTAAGTCACCT 58.539 36.000 0.00 0.00 32.71 4.00
4455 4946 6.932400 TGACACGAATTACATTAAGTCACCTT 59.068 34.615 0.00 0.00 32.71 3.50
4456 4947 7.117236 TGACACGAATTACATTAAGTCACCTTC 59.883 37.037 0.00 0.00 32.71 3.46
4457 4948 6.932400 ACACGAATTACATTAAGTCACCTTCA 59.068 34.615 0.00 0.00 32.71 3.02
4458 4949 7.442969 ACACGAATTACATTAAGTCACCTTCAA 59.557 33.333 0.00 0.00 32.71 2.69
4459 4950 8.286800 CACGAATTACATTAAGTCACCTTCAAA 58.713 33.333 0.00 0.00 32.71 2.69
4460 4951 8.504005 ACGAATTACATTAAGTCACCTTCAAAG 58.496 33.333 0.00 0.00 32.71 2.77
4461 4952 7.481798 CGAATTACATTAAGTCACCTTCAAAGC 59.518 37.037 0.00 0.00 32.71 3.51
4462 4953 8.409358 AATTACATTAAGTCACCTTCAAAGCT 57.591 30.769 0.00 0.00 31.89 3.74
4463 4954 9.515226 AATTACATTAAGTCACCTTCAAAGCTA 57.485 29.630 0.00 0.00 31.89 3.32
4464 4955 8.547967 TTACATTAAGTCACCTTCAAAGCTAG 57.452 34.615 0.00 0.00 31.89 3.42
4465 4956 5.412904 ACATTAAGTCACCTTCAAAGCTAGC 59.587 40.000 6.62 6.62 31.89 3.42
4466 4957 3.778954 AAGTCACCTTCAAAGCTAGCT 57.221 42.857 12.68 12.68 0.00 3.32
4467 4958 3.051081 AGTCACCTTCAAAGCTAGCTG 57.949 47.619 20.16 7.93 0.00 4.24
4468 4959 1.466558 GTCACCTTCAAAGCTAGCTGC 59.533 52.381 20.16 0.00 43.29 5.25
4469 4960 0.807496 CACCTTCAAAGCTAGCTGCC 59.193 55.000 20.16 0.00 44.23 4.85
4470 4961 0.401738 ACCTTCAAAGCTAGCTGCCA 59.598 50.000 20.16 1.36 44.23 4.92
4471 4962 1.202927 ACCTTCAAAGCTAGCTGCCAA 60.203 47.619 20.16 9.96 44.23 4.52
4472 4963 1.471684 CCTTCAAAGCTAGCTGCCAAG 59.528 52.381 20.16 18.31 44.23 3.61
4473 4964 1.471684 CTTCAAAGCTAGCTGCCAAGG 59.528 52.381 20.16 4.69 44.23 3.61
4474 4965 0.962356 TCAAAGCTAGCTGCCAAGGC 60.962 55.000 20.16 3.61 44.23 4.35
4475 4966 2.042831 AAAGCTAGCTGCCAAGGCG 61.043 57.895 20.16 2.74 45.51 5.52
4476 4967 2.754664 AAAGCTAGCTGCCAAGGCGT 62.755 55.000 20.16 0.00 45.51 5.68
4477 4968 3.503363 GCTAGCTGCCAAGGCGTG 61.503 66.667 7.70 3.17 45.51 5.34
4478 4969 2.265739 CTAGCTGCCAAGGCGTGA 59.734 61.111 6.60 0.00 45.51 4.35
4479 4970 1.375908 CTAGCTGCCAAGGCGTGAA 60.376 57.895 6.60 0.00 45.51 3.18
4480 4971 0.955428 CTAGCTGCCAAGGCGTGAAA 60.955 55.000 6.60 0.00 45.51 2.69
4481 4972 0.322456 TAGCTGCCAAGGCGTGAAAT 60.322 50.000 6.60 0.00 45.51 2.17
4482 4973 0.322456 AGCTGCCAAGGCGTGAAATA 60.322 50.000 6.60 0.00 45.51 1.40
4483 4974 0.740737 GCTGCCAAGGCGTGAAATAT 59.259 50.000 6.60 0.00 45.51 1.28
4484 4975 1.268743 GCTGCCAAGGCGTGAAATATC 60.269 52.381 6.60 0.00 45.51 1.63
4485 4976 2.016318 CTGCCAAGGCGTGAAATATCA 58.984 47.619 6.60 0.00 45.51 2.15
4486 4977 2.016318 TGCCAAGGCGTGAAATATCAG 58.984 47.619 6.60 0.00 45.51 2.90
4487 4978 2.017049 GCCAAGGCGTGAAATATCAGT 58.983 47.619 0.76 0.00 35.88 3.41
4488 4979 2.032178 GCCAAGGCGTGAAATATCAGTC 59.968 50.000 0.76 0.00 35.88 3.51
4489 4980 2.614057 CCAAGGCGTGAAATATCAGTCC 59.386 50.000 0.76 0.00 35.88 3.85
4490 4981 3.535561 CAAGGCGTGAAATATCAGTCCT 58.464 45.455 0.00 0.00 39.09 3.85
4491 4982 4.442893 CCAAGGCGTGAAATATCAGTCCTA 60.443 45.833 0.76 0.00 37.45 2.94
4492 4983 5.116180 CAAGGCGTGAAATATCAGTCCTAA 58.884 41.667 0.00 0.00 37.45 2.69
4493 4984 5.552870 AGGCGTGAAATATCAGTCCTAAT 57.447 39.130 0.00 0.00 36.96 1.73
4494 4985 5.930135 AGGCGTGAAATATCAGTCCTAATT 58.070 37.500 0.00 0.00 36.96 1.40
4495 4986 6.357367 AGGCGTGAAATATCAGTCCTAATTT 58.643 36.000 0.00 0.00 36.96 1.82
4496 4987 6.260936 AGGCGTGAAATATCAGTCCTAATTTG 59.739 38.462 0.00 0.00 36.96 2.32
4497 4988 6.430451 GCGTGAAATATCAGTCCTAATTTGG 58.570 40.000 0.00 0.00 35.88 3.28
4498 4989 6.513393 GCGTGAAATATCAGTCCTAATTTGGG 60.513 42.308 6.08 0.00 35.88 4.12
4499 4990 6.765989 CGTGAAATATCAGTCCTAATTTGGGA 59.234 38.462 6.08 0.00 35.88 4.37
4507 4998 4.718940 GTCCTAATTTGGGACCATGTTG 57.281 45.455 18.53 0.00 45.31 3.33
4508 4999 3.096092 TCCTAATTTGGGACCATGTTGC 58.904 45.455 6.08 0.00 0.00 4.17
4509 5000 2.830923 CCTAATTTGGGACCATGTTGCA 59.169 45.455 0.00 0.00 0.00 4.08
4510 5001 3.119029 CCTAATTTGGGACCATGTTGCAG 60.119 47.826 0.00 0.00 0.00 4.41
4511 5002 2.307496 ATTTGGGACCATGTTGCAGA 57.693 45.000 0.00 0.00 0.00 4.26
4512 5003 1.327303 TTTGGGACCATGTTGCAGAC 58.673 50.000 0.00 0.00 0.00 3.51
4513 5004 0.184692 TTGGGACCATGTTGCAGACA 59.815 50.000 0.00 4.56 43.71 3.41
4659 5418 5.192522 AGGGTCACCAAGAATCATATCTGTT 59.807 40.000 0.00 0.00 40.13 3.16
4766 5526 5.652452 AGCAGTAGAAATTTATCCCAACCAC 59.348 40.000 0.00 0.00 0.00 4.16
4781 5541 6.001460 TCCCAACCACTAAGAATGTGTAAAG 58.999 40.000 0.00 0.00 33.92 1.85
4835 5596 4.846779 AACTGTGTGTTGTTGACTTGTT 57.153 36.364 0.00 0.00 37.52 2.83
4836 5597 4.159377 ACTGTGTGTTGTTGACTTGTTG 57.841 40.909 0.00 0.00 0.00 3.33
4837 5598 3.568007 ACTGTGTGTTGTTGACTTGTTGT 59.432 39.130 0.00 0.00 0.00 3.32
4838 5599 4.037446 ACTGTGTGTTGTTGACTTGTTGTT 59.963 37.500 0.00 0.00 0.00 2.83
4839 5600 4.541779 TGTGTGTTGTTGACTTGTTGTTC 58.458 39.130 0.00 0.00 0.00 3.18
4840 5601 4.277174 TGTGTGTTGTTGACTTGTTGTTCT 59.723 37.500 0.00 0.00 0.00 3.01
4841 5602 5.470437 TGTGTGTTGTTGACTTGTTGTTCTA 59.530 36.000 0.00 0.00 0.00 2.10
4842 5603 6.150307 TGTGTGTTGTTGACTTGTTGTTCTAT 59.850 34.615 0.00 0.00 0.00 1.98
4843 5604 7.027161 GTGTGTTGTTGACTTGTTGTTCTATT 58.973 34.615 0.00 0.00 0.00 1.73
4844 5605 7.218204 GTGTGTTGTTGACTTGTTGTTCTATTC 59.782 37.037 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 2.404186 CGTCGAGACCGTCCCATCA 61.404 63.158 0.00 0.00 37.05 3.07
1 2 2.408022 CGTCGAGACCGTCCCATC 59.592 66.667 0.00 0.00 37.05 3.51
2 3 3.138798 CCGTCGAGACCGTCCCAT 61.139 66.667 0.00 0.00 37.05 4.00
5 6 4.477975 CTGCCGTCGAGACCGTCC 62.478 72.222 0.00 0.00 37.05 4.79
6 7 4.477975 CCTGCCGTCGAGACCGTC 62.478 72.222 0.00 0.00 37.05 4.79
41 42 2.511373 TGCATCGACATCGTGCCC 60.511 61.111 19.08 3.12 41.82 5.36
64 65 0.459237 GTCTCATGACGAGGCCACAG 60.459 60.000 5.01 0.00 40.77 3.66
73 74 1.550065 CGGCTTACTGTCTCATGACG 58.450 55.000 0.00 0.00 45.70 4.35
130 131 3.196469 TCTCAGACTGACCATAAGCAAGG 59.804 47.826 0.00 0.00 0.00 3.61
131 132 4.180057 GTCTCAGACTGACCATAAGCAAG 58.820 47.826 0.00 0.00 0.00 4.01
133 134 3.165071 TGTCTCAGACTGACCATAAGCA 58.835 45.455 6.33 0.00 33.15 3.91
138 139 5.808366 TTTTACTGTCTCAGACTGACCAT 57.192 39.130 17.96 0.00 35.84 3.55
151 152 9.959749 TTCAACCTAATTTGTGATTTTACTGTC 57.040 29.630 0.00 0.00 0.00 3.51
156 157 9.823647 TTGCTTTCAACCTAATTTGTGATTTTA 57.176 25.926 0.00 0.00 0.00 1.52
187 188 0.179171 GCACTGCTGATGTGTGATGC 60.179 55.000 0.00 0.00 37.70 3.91
192 193 0.251474 ATTGGGCACTGCTGATGTGT 60.251 50.000 0.00 0.00 37.70 3.72
242 245 2.433239 TGTTCTCCCGTCTATTTAGGCC 59.567 50.000 0.00 0.00 0.00 5.19
246 249 6.888632 AGTTACTCTGTTCTCCCGTCTATTTA 59.111 38.462 0.00 0.00 0.00 1.40
247 250 5.715753 AGTTACTCTGTTCTCCCGTCTATTT 59.284 40.000 0.00 0.00 0.00 1.40
254 257 2.099427 GCCTAGTTACTCTGTTCTCCCG 59.901 54.545 0.00 0.00 0.00 5.14
276 288 3.137637 GAAATGGGGATTGGGCGCG 62.138 63.158 0.00 0.00 0.00 6.86
277 289 1.402107 ATGAAATGGGGATTGGGCGC 61.402 55.000 0.00 0.00 0.00 6.53
279 291 1.792115 TCATGAAATGGGGATTGGGC 58.208 50.000 0.00 0.00 46.73 5.36
340 353 4.460731 CCCCTTCCTTTTGATCTTGTCTTC 59.539 45.833 0.00 0.00 0.00 2.87
380 393 0.716108 CAGATCTTGCGTCGGTTGAC 59.284 55.000 0.00 0.00 41.91 3.18
417 430 3.913573 CGTCCGGCGAGATTTGCG 61.914 66.667 9.30 0.06 44.77 4.85
418 431 4.223964 GCGTCCGGCGAGATTTGC 62.224 66.667 20.06 6.48 44.77 3.68
419 432 3.564027 GGCGTCCGGCGAGATTTG 61.564 66.667 20.06 0.04 44.92 2.32
439 452 3.431415 TCATTTTCTCTCCTCTCCGACA 58.569 45.455 0.00 0.00 0.00 4.35
450 463 6.144845 TCCTTCCTTGGATTCATTTTCTCT 57.855 37.500 0.00 0.00 0.00 3.10
526 548 3.333029 TCTCGTCCATTTCTGCATCAA 57.667 42.857 0.00 0.00 0.00 2.57
527 549 3.333029 TTCTCGTCCATTTCTGCATCA 57.667 42.857 0.00 0.00 0.00 3.07
550 579 3.898627 AACACAGCGCTCGGACTCG 62.899 63.158 7.13 0.00 37.82 4.18
551 580 2.049063 AACACAGCGCTCGGACTC 60.049 61.111 7.13 0.00 0.00 3.36
552 581 2.049063 GAACACAGCGCTCGGACT 60.049 61.111 7.13 0.00 0.00 3.85
553 582 3.470567 CGAACACAGCGCTCGGAC 61.471 66.667 7.13 2.09 0.00 4.79
554 583 3.891586 GACGAACACAGCGCTCGGA 62.892 63.158 18.41 0.00 36.90 4.55
555 584 3.470567 GACGAACACAGCGCTCGG 61.471 66.667 18.41 11.51 36.90 4.63
664 699 0.659957 GCAGTGGCATTCGATTCTCC 59.340 55.000 0.00 0.00 40.72 3.71
668 703 1.089920 GACAGCAGTGGCATTCGATT 58.910 50.000 0.00 0.00 44.61 3.34
669 704 0.251354 AGACAGCAGTGGCATTCGAT 59.749 50.000 0.00 0.00 44.61 3.59
670 705 0.671472 CAGACAGCAGTGGCATTCGA 60.671 55.000 0.00 0.00 44.61 3.71
671 706 0.671472 TCAGACAGCAGTGGCATTCG 60.671 55.000 0.00 0.00 44.61 3.34
672 707 1.400846 CATCAGACAGCAGTGGCATTC 59.599 52.381 0.00 0.00 44.61 2.67
673 708 1.460504 CATCAGACAGCAGTGGCATT 58.539 50.000 0.00 0.00 44.61 3.56
674 709 0.393944 CCATCAGACAGCAGTGGCAT 60.394 55.000 0.00 0.00 44.61 4.40
675 710 1.002990 CCATCAGACAGCAGTGGCA 60.003 57.895 0.00 0.00 44.61 4.92
1133 1194 2.035442 GTGGACCTGCGCTTCTTCC 61.035 63.158 9.73 9.89 0.00 3.46
1149 1210 1.374758 GCTCCGTCTCCACTTGGTG 60.375 63.158 0.00 0.00 36.34 4.17
1878 1939 6.457934 GCATTCATCATACTGAAGAAGGTGTG 60.458 42.308 8.07 0.99 37.92 3.82
1879 1940 5.587844 GCATTCATCATACTGAAGAAGGTGT 59.412 40.000 8.07 0.00 37.92 4.16
1890 1951 4.719026 ATGGACCTGCATTCATCATACT 57.281 40.909 0.00 0.00 0.00 2.12
1892 1953 4.105217 AGGAATGGACCTGCATTCATCATA 59.895 41.667 18.00 0.00 39.01 2.15
1897 1960 1.064463 GGAGGAATGGACCTGCATTCA 60.064 52.381 18.00 0.00 45.58 2.57
1987 2057 0.396811 CACCCCGGATTATGGACTCC 59.603 60.000 0.73 0.00 0.00 3.85
1993 2063 4.207165 ACTTGATTTCACCCCGGATTATG 58.793 43.478 0.73 0.00 0.00 1.90
2143 2213 1.336887 TGTCTGCGAGCTGGAAACTAC 60.337 52.381 0.00 0.00 0.00 2.73
2159 2229 1.846007 TGTGTTTGTTTGGCCTGTCT 58.154 45.000 3.32 0.00 0.00 3.41
2180 2250 4.548494 TGTAGCAAATTTGTGAGTGCATG 58.452 39.130 19.03 0.00 39.50 4.06
2221 2291 4.617253 TTGCAGGAGTAGCAAACTTCTA 57.383 40.909 0.01 0.00 42.70 2.10
2222 2292 3.492102 TTGCAGGAGTAGCAAACTTCT 57.508 42.857 0.00 0.00 45.79 2.85
2244 2314 9.206690 TCCCAATAATACCATGAAATAAGCAAA 57.793 29.630 0.00 0.00 0.00 3.68
2245 2315 8.774546 TCCCAATAATACCATGAAATAAGCAA 57.225 30.769 0.00 0.00 0.00 3.91
2246 2316 8.774546 TTCCCAATAATACCATGAAATAAGCA 57.225 30.769 0.00 0.00 0.00 3.91
2247 2317 9.476202 GTTTCCCAATAATACCATGAAATAAGC 57.524 33.333 0.00 0.00 0.00 3.09
2248 2318 9.981114 GGTTTCCCAATAATACCATGAAATAAG 57.019 33.333 0.00 0.00 0.00 1.73
2732 2831 6.301169 ACCCCTCTAAATGCATATAGTAGC 57.699 41.667 0.00 0.00 0.00 3.58
2802 3192 2.440409 CCCCATGAAGTTCCAGTTCAG 58.560 52.381 0.00 0.00 40.49 3.02
2807 3197 1.856629 AATGCCCCATGAAGTTCCAG 58.143 50.000 0.00 0.00 0.00 3.86
2817 3207 3.443052 TCAATTGTGAGAAATGCCCCAT 58.557 40.909 5.13 0.00 0.00 4.00
2826 3216 6.646653 CACTGCTAAGTACTCAATTGTGAGAA 59.353 38.462 14.16 0.00 43.84 2.87
2874 3264 1.009829 GCATTTAGACTCGTGCCAGG 58.990 55.000 0.00 0.00 0.00 4.45
3224 3614 9.793252 GATACAACAGCATTAAGTGATCAATTT 57.207 29.630 14.34 6.35 0.00 1.82
3225 3615 9.182214 AGATACAACAGCATTAAGTGATCAATT 57.818 29.630 13.58 13.58 0.00 2.32
3244 3634 6.017109 GCAAGGTCAACTTTCTTGAGATACAA 60.017 38.462 6.49 0.00 39.97 2.41
3281 3671 6.647067 GGATAAATGGTGTCTACAGTATCAGC 59.353 42.308 7.66 7.66 0.00 4.26
3313 3795 9.396022 CTAGCTTAAAATTTCCTTGGACTCATA 57.604 33.333 0.00 0.00 0.00 2.15
3417 3899 5.072040 AGCAGGTAATTTTTGTATGTGCC 57.928 39.130 0.00 0.00 0.00 5.01
3418 3900 6.090763 GGAAAGCAGGTAATTTTTGTATGTGC 59.909 38.462 0.00 0.00 0.00 4.57
3419 3901 6.589907 GGGAAAGCAGGTAATTTTTGTATGTG 59.410 38.462 0.00 0.00 0.00 3.21
3424 3906 3.326588 GGGGGAAAGCAGGTAATTTTTGT 59.673 43.478 0.00 0.00 0.00 2.83
3493 3975 5.298276 TGATTTACGCTTCTTTCAAGGTGTT 59.702 36.000 0.00 0.00 0.00 3.32
3500 3982 6.125327 TGTTGTTGATTTACGCTTCTTTCA 57.875 33.333 0.00 0.00 0.00 2.69
4004 4486 2.075338 CTGCTTCTGCTTCAGGAACTC 58.925 52.381 0.00 0.00 36.82 3.01
4091 4573 2.154567 ACATCTGGCCGTACCTAAGA 57.845 50.000 0.00 0.00 40.22 2.10
4103 4585 4.156739 GTGCTTTTCTTCCCTTACATCTGG 59.843 45.833 0.00 0.00 0.00 3.86
4255 4737 2.535534 CGCGTATCAGTTCATTGCACAG 60.536 50.000 0.00 0.00 0.00 3.66
4337 4828 5.455326 GGCTGTCACCCTGATTTATATCTGT 60.455 44.000 0.00 0.00 0.00 3.41
4342 4833 3.391296 GGAGGCTGTCACCCTGATTTATA 59.609 47.826 0.00 0.00 31.41 0.98
4343 4834 2.173569 GGAGGCTGTCACCCTGATTTAT 59.826 50.000 0.00 0.00 31.41 1.40
4344 4835 1.559682 GGAGGCTGTCACCCTGATTTA 59.440 52.381 0.00 0.00 31.41 1.40
4345 4836 0.329596 GGAGGCTGTCACCCTGATTT 59.670 55.000 0.00 0.00 31.41 2.17
4346 4837 0.842030 TGGAGGCTGTCACCCTGATT 60.842 55.000 0.00 0.00 31.41 2.57
4347 4838 0.622738 ATGGAGGCTGTCACCCTGAT 60.623 55.000 0.00 0.00 31.41 2.90
4348 4839 0.842030 AATGGAGGCTGTCACCCTGA 60.842 55.000 0.00 0.00 31.41 3.86
4349 4840 0.038744 AAATGGAGGCTGTCACCCTG 59.961 55.000 0.00 0.00 31.41 4.45
4350 4841 0.329596 GAAATGGAGGCTGTCACCCT 59.670 55.000 0.00 0.00 34.77 4.34
4351 4842 1.026718 CGAAATGGAGGCTGTCACCC 61.027 60.000 0.00 0.00 0.00 4.61
4352 4843 0.036388 TCGAAATGGAGGCTGTCACC 60.036 55.000 0.00 0.00 0.00 4.02
4353 4844 1.808411 TTCGAAATGGAGGCTGTCAC 58.192 50.000 0.00 0.00 0.00 3.67
4354 4845 2.151202 GTTTCGAAATGGAGGCTGTCA 58.849 47.619 14.69 0.00 0.00 3.58
4355 4846 2.427506 AGTTTCGAAATGGAGGCTGTC 58.572 47.619 14.69 0.00 0.00 3.51
4356 4847 2.568623 AGTTTCGAAATGGAGGCTGT 57.431 45.000 14.69 0.00 0.00 4.40
4357 4848 3.375299 CCTTAGTTTCGAAATGGAGGCTG 59.625 47.826 14.69 0.20 0.00 4.85
4358 4849 3.009143 ACCTTAGTTTCGAAATGGAGGCT 59.991 43.478 24.41 15.20 0.00 4.58
4359 4850 3.344515 ACCTTAGTTTCGAAATGGAGGC 58.655 45.455 24.41 9.94 0.00 4.70
4360 4851 7.625828 ATTTACCTTAGTTTCGAAATGGAGG 57.374 36.000 23.54 23.54 0.00 4.30
4361 4852 8.512138 ACAATTTACCTTAGTTTCGAAATGGAG 58.488 33.333 14.69 11.30 0.00 3.86
4362 4853 8.398878 ACAATTTACCTTAGTTTCGAAATGGA 57.601 30.769 14.69 0.00 0.00 3.41
4416 4907 4.955925 TCGTGTCAGTTGTCATGTTTTT 57.044 36.364 0.00 0.00 0.00 1.94
4417 4908 4.955925 TTCGTGTCAGTTGTCATGTTTT 57.044 36.364 0.00 0.00 0.00 2.43
4418 4909 5.499139 AATTCGTGTCAGTTGTCATGTTT 57.501 34.783 0.00 0.00 0.00 2.83
4419 4910 5.525745 TGTAATTCGTGTCAGTTGTCATGTT 59.474 36.000 0.00 0.00 0.00 2.71
4420 4911 5.053811 TGTAATTCGTGTCAGTTGTCATGT 58.946 37.500 0.00 0.00 0.00 3.21
4421 4912 5.590104 TGTAATTCGTGTCAGTTGTCATG 57.410 39.130 0.00 0.00 0.00 3.07
4422 4913 6.801539 AATGTAATTCGTGTCAGTTGTCAT 57.198 33.333 0.00 0.00 0.00 3.06
4423 4914 7.439955 ACTTAATGTAATTCGTGTCAGTTGTCA 59.560 33.333 0.00 0.00 37.87 3.58
4424 4915 7.793902 ACTTAATGTAATTCGTGTCAGTTGTC 58.206 34.615 0.00 0.00 37.87 3.18
4425 4916 7.439955 TGACTTAATGTAATTCGTGTCAGTTGT 59.560 33.333 0.00 0.00 37.87 3.32
4426 4917 7.740346 GTGACTTAATGTAATTCGTGTCAGTTG 59.260 37.037 0.00 0.00 39.08 3.16
4427 4918 7.095355 GGTGACTTAATGTAATTCGTGTCAGTT 60.095 37.037 0.00 0.00 39.08 3.16
4428 4919 6.367969 GGTGACTTAATGTAATTCGTGTCAGT 59.632 38.462 0.00 0.00 39.08 3.41
4429 4920 6.590292 AGGTGACTTAATGTAATTCGTGTCAG 59.410 38.462 0.00 0.00 39.08 3.51
4430 4921 6.460781 AGGTGACTTAATGTAATTCGTGTCA 58.539 36.000 0.00 0.00 37.44 3.58
4431 4922 6.963049 AGGTGACTTAATGTAATTCGTGTC 57.037 37.500 0.00 0.00 37.44 3.67
4442 4933 9.679721 GCAGCTAGCTTTGAAGGTGACTTAATG 62.680 44.444 16.46 0.00 46.25 1.90
4443 4934 7.789386 GCAGCTAGCTTTGAAGGTGACTTAAT 61.789 42.308 16.46 0.00 46.25 1.40
4444 4935 6.540982 GCAGCTAGCTTTGAAGGTGACTTAA 61.541 44.000 16.46 0.00 46.25 1.85
4445 4936 5.098178 GCAGCTAGCTTTGAAGGTGACTTA 61.098 45.833 16.46 0.00 46.25 2.24
4447 4938 2.873649 GCAGCTAGCTTTGAAGGTGACT 60.874 50.000 16.46 0.71 42.45 3.41
4448 4939 1.466558 GCAGCTAGCTTTGAAGGTGAC 59.533 52.381 16.46 5.23 42.45 3.67
4449 4940 1.611673 GGCAGCTAGCTTTGAAGGTGA 60.612 52.381 16.46 0.00 42.45 4.02
4450 4941 0.807496 GGCAGCTAGCTTTGAAGGTG 59.193 55.000 16.46 8.71 44.79 4.00
4451 4942 0.401738 TGGCAGCTAGCTTTGAAGGT 59.598 50.000 16.46 0.80 44.79 3.50
4452 4943 1.471684 CTTGGCAGCTAGCTTTGAAGG 59.528 52.381 16.46 3.53 44.79 3.46
4453 4944 1.471684 CCTTGGCAGCTAGCTTTGAAG 59.528 52.381 16.46 15.63 44.79 3.02
4454 4945 1.538047 CCTTGGCAGCTAGCTTTGAA 58.462 50.000 16.46 6.70 44.79 2.69
4455 4946 0.962356 GCCTTGGCAGCTAGCTTTGA 60.962 55.000 16.46 0.00 44.79 2.69
4456 4947 1.509923 GCCTTGGCAGCTAGCTTTG 59.490 57.895 16.46 7.10 44.79 2.77
4457 4948 2.042831 CGCCTTGGCAGCTAGCTTT 61.043 57.895 16.46 0.00 44.79 3.51
4458 4949 2.437359 CGCCTTGGCAGCTAGCTT 60.437 61.111 16.46 0.00 44.79 3.74
4459 4950 3.710722 ACGCCTTGGCAGCTAGCT 61.711 61.111 12.68 12.68 44.79 3.32
4460 4951 3.503363 CACGCCTTGGCAGCTAGC 61.503 66.667 6.62 6.62 44.65 3.42
4461 4952 0.955428 TTTCACGCCTTGGCAGCTAG 60.955 55.000 12.45 0.00 0.00 3.42
4462 4953 0.322456 ATTTCACGCCTTGGCAGCTA 60.322 50.000 12.45 0.00 0.00 3.32
4463 4954 0.322456 TATTTCACGCCTTGGCAGCT 60.322 50.000 12.45 0.00 0.00 4.24
4464 4955 0.740737 ATATTTCACGCCTTGGCAGC 59.259 50.000 12.45 0.00 0.00 5.25
4465 4956 2.016318 TGATATTTCACGCCTTGGCAG 58.984 47.619 12.45 7.13 0.00 4.85
4466 4957 2.016318 CTGATATTTCACGCCTTGGCA 58.984 47.619 12.45 0.00 0.00 4.92
4467 4958 2.017049 ACTGATATTTCACGCCTTGGC 58.983 47.619 0.75 0.75 0.00 4.52
4468 4959 2.614057 GGACTGATATTTCACGCCTTGG 59.386 50.000 0.00 0.00 0.00 3.61
4469 4960 3.535561 AGGACTGATATTTCACGCCTTG 58.464 45.455 0.00 0.00 0.00 3.61
4470 4961 3.914426 AGGACTGATATTTCACGCCTT 57.086 42.857 0.00 0.00 0.00 4.35
4471 4962 5.552870 ATTAGGACTGATATTTCACGCCT 57.447 39.130 7.08 7.08 0.00 5.52
4472 4963 6.430451 CAAATTAGGACTGATATTTCACGCC 58.570 40.000 0.00 0.00 0.00 5.68
4473 4964 6.430451 CCAAATTAGGACTGATATTTCACGC 58.570 40.000 0.00 0.00 0.00 5.34
4474 4965 6.765989 TCCCAAATTAGGACTGATATTTCACG 59.234 38.462 0.00 0.00 0.00 4.35
4487 4978 3.096092 GCAACATGGTCCCAAATTAGGA 58.904 45.455 0.00 0.00 0.00 2.94
4488 4979 2.830923 TGCAACATGGTCCCAAATTAGG 59.169 45.455 0.00 0.00 0.00 2.69
4489 4980 3.763360 TCTGCAACATGGTCCCAAATTAG 59.237 43.478 0.00 0.00 0.00 1.73
4490 4981 3.509575 GTCTGCAACATGGTCCCAAATTA 59.490 43.478 0.00 0.00 0.00 1.40
4491 4982 2.299867 GTCTGCAACATGGTCCCAAATT 59.700 45.455 0.00 0.00 0.00 1.82
4492 4983 1.895131 GTCTGCAACATGGTCCCAAAT 59.105 47.619 0.00 0.00 0.00 2.32
4493 4984 1.327303 GTCTGCAACATGGTCCCAAA 58.673 50.000 0.00 0.00 0.00 3.28
4494 4985 0.184692 TGTCTGCAACATGGTCCCAA 59.815 50.000 0.00 0.00 31.20 4.12
4495 4986 0.405198 ATGTCTGCAACATGGTCCCA 59.595 50.000 11.96 0.00 47.00 4.37
4496 4987 3.271250 ATGTCTGCAACATGGTCCC 57.729 52.632 11.96 0.00 47.00 4.46
4519 5010 8.796475 GCTGGTATGGTTCAATATAATGACATT 58.204 33.333 5.87 5.87 0.00 2.71
4520 5011 7.944000 TGCTGGTATGGTTCAATATAATGACAT 59.056 33.333 0.00 0.00 0.00 3.06
4521 5012 7.286313 TGCTGGTATGGTTCAATATAATGACA 58.714 34.615 0.00 0.00 0.00 3.58
4522 5013 7.744087 TGCTGGTATGGTTCAATATAATGAC 57.256 36.000 0.00 0.00 0.00 3.06
4523 5014 8.938801 ATTGCTGGTATGGTTCAATATAATGA 57.061 30.769 0.00 0.00 0.00 2.57
4524 5015 9.985730 AAATTGCTGGTATGGTTCAATATAATG 57.014 29.630 0.00 0.00 0.00 1.90
4659 5418 3.181479 CGCTAGGTACTGCTGAAATGGTA 60.181 47.826 0.00 0.00 41.52 3.25
4766 5526 9.155975 ACAGTTATGAGCTTTACACATTCTTAG 57.844 33.333 0.00 0.00 31.51 2.18
4781 5541 6.270815 TGGTCGACTAAATACAGTTATGAGC 58.729 40.000 16.46 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.