Multiple sequence alignment - TraesCS2D01G339400

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 TraesCS2D01G339400 chr2D 100.000 7836 0 0 1 7836 433502068 433509903 0.000000e+00 14471.0
1 TraesCS2D01G339400 chr2D 99.301 143 1 0 4263 4405 433506187 433506329 7.800000e-65 259.0
2 TraesCS2D01G339400 chr2D 99.301 143 1 0 4120 4262 433506330 433506472 7.800000e-65 259.0
3 TraesCS2D01G339400 chr2D 76.993 439 63 27 7353 7770 22786670 22786249 4.760000e-52 217.0
4 TraesCS2D01G339400 chr2A 97.312 4279 88 15 4 4262 553491320 553487049 0.000000e+00 7239.0
5 TraesCS2D01G339400 chr2A 95.494 2796 58 23 4263 7002 553487193 553484410 0.000000e+00 4403.0
6 TraesCS2D01G339400 chr2A 94.526 749 23 8 7089 7836 553484240 553483509 0.000000e+00 1140.0
7 TraesCS2D01G339400 chr2A 79.646 452 80 11 7351 7796 203002932 203002487 1.640000e-81 315.0
8 TraesCS2D01G339400 chr2A 90.909 165 12 2 5138 5302 537476548 537476709 1.320000e-52 219.0
9 TraesCS2D01G339400 chr2A 76.077 418 80 17 7350 7757 24181040 24181447 4.800000e-47 200.0
10 TraesCS2D01G339400 chr2A 75.610 410 78 18 7350 7747 24276749 24277148 4.830000e-42 183.0
11 TraesCS2D01G339400 chr2B 92.006 3928 191 51 1 3878 511272033 511275887 0.000000e+00 5400.0
12 TraesCS2D01G339400 chr2B 93.892 2767 85 23 4263 7002 511276210 511278919 0.000000e+00 4096.0
13 TraesCS2D01G339400 chr2B 97.394 729 19 0 7106 7834 511278919 511279647 0.000000e+00 1242.0
14 TraesCS2D01G339400 chr2B 95.103 388 14 4 3877 4262 511275969 511276353 2.420000e-169 606.0
15 TraesCS2D01G339400 chr2B 79.646 452 80 11 7351 7796 245006914 245006469 1.640000e-81 315.0
16 TraesCS2D01G339400 chr2B 76.415 424 74 20 7353 7760 39158066 39158479 1.030000e-48 206.0
17 TraesCS2D01G339400 chrUn 100.000 418 0 0 1436 1853 477061841 477062258 0.000000e+00 773.0
18 TraesCS2D01G339400 chr4D 86.521 549 66 7 4365 4910 94260260 94259717 1.460000e-166 597.0
19 TraesCS2D01G339400 chr4D 81.886 668 101 16 4365 5025 93845533 93844879 5.350000e-151 545.0
20 TraesCS2D01G339400 chr4D 78.121 713 111 28 5860 6560 94259223 94258544 2.040000e-110 411.0
21 TraesCS2D01G339400 chr4D 83.278 299 42 6 3827 4121 93845965 93845671 1.300000e-67 268.0
22 TraesCS2D01G339400 chr4D 87.440 207 23 2 3917 4121 94260673 94260468 1.310000e-57 235.0
23 TraesCS2D01G339400 chr4D 79.503 322 41 15 3125 3441 94261233 94260932 1.030000e-48 206.0
24 TraesCS2D01G339400 chr4B 86.521 549 66 8 4365 4910 132854601 132854058 1.460000e-166 597.0
25 TraesCS2D01G339400 chr4B 80.514 662 104 22 1347 1995 132338509 132337860 1.180000e-132 484.0
26 TraesCS2D01G339400 chr4B 78.641 721 93 29 5860 6560 132853543 132852864 9.400000e-114 422.0
27 TraesCS2D01G339400 chr4B 86.246 349 38 7 1348 1694 132856353 132856013 3.450000e-98 370.0
28 TraesCS2D01G339400 chr4B 81.667 300 46 7 3826 4121 132336278 132335984 2.830000e-59 241.0
29 TraesCS2D01G339400 chr4B 86.957 207 24 2 3917 4121 132855015 132854810 6.120000e-56 230.0
30 TraesCS2D01G339400 chr4B 78.510 349 62 12 3019 3358 132855687 132855343 4.760000e-52 217.0
31 TraesCS2D01G339400 chr4A 88.706 487 50 5 4365 4848 486641667 486642151 2.440000e-164 590.0
32 TraesCS2D01G339400 chr4A 82.212 669 98 17 4365 5025 487864724 487865379 2.470000e-154 556.0
33 TraesCS2D01G339400 chr4A 79.909 662 108 22 1347 1995 487862057 487862706 5.540000e-126 462.0
34 TraesCS2D01G339400 chr4A 82.008 528 55 18 5857 6370 486642715 486643216 5.660000e-111 412.0
35 TraesCS2D01G339400 chr4A 82.609 299 45 5 3826 4121 487864299 487864593 2.810000e-64 257.0
36 TraesCS2D01G339400 chr4A 86.538 208 23 3 3918 4121 486641243 486641449 2.850000e-54 224.0
37 TraesCS2D01G339400 chr4A 76.380 453 81 21 2928 3358 486640461 486640909 3.680000e-53 220.0
38 TraesCS2D01G339400 chr7A 82.308 390 68 1 7353 7742 136284013 136283625 3.500000e-88 337.0
39 TraesCS2D01G339400 chr7A 89.412 170 17 1 5144 5312 692336895 692337064 6.160000e-51 213.0
40 TraesCS2D01G339400 chr7A 88.824 170 16 3 5144 5311 670531681 670531513 1.030000e-48 206.0
41 TraesCS2D01G339400 chr5B 77.925 453 83 9 4382 4819 172628249 172627799 4.660000e-67 267.0
42 TraesCS2D01G339400 chr5D 77.193 456 87 9 4379 4819 175761857 175762310 4.690000e-62 250.0
43 TraesCS2D01G339400 chr6A 90.741 162 14 1 5144 5304 7988618 7988457 1.710000e-51 215.0
44 TraesCS2D01G339400 chr6A 90.683 161 14 1 5144 5303 603917572 603917732 6.160000e-51 213.0
45 TraesCS2D01G339400 chr1D 89.941 169 14 3 5144 5311 493673664 493673830 1.710000e-51 215.0
46 TraesCS2D01G339400 chr1D 89.017 173 16 3 5144 5315 443741826 443741656 2.220000e-50 211.0
47 TraesCS2D01G339400 chr5A 89.820 167 16 1 5144 5309 345670718 345670552 6.160000e-51 213.0
48 TraesCS2D01G339400 chr6D 88.889 54 3 1 5324 5377 62197653 62197603 6.560000e-06 63.9


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 TraesCS2D01G339400 chr2D 433502068 433509903 7835 False 4996.333333 14471 99.534000 1 7836 3 chr2D.!!$F1 7835
1 TraesCS2D01G339400 chr2A 553483509 553491320 7811 True 4260.666667 7239 95.777333 4 7836 3 chr2A.!!$R2 7832
2 TraesCS2D01G339400 chr2B 511272033 511279647 7614 False 2836.000000 5400 94.598750 1 7834 4 chr2B.!!$F2 7833
3 TraesCS2D01G339400 chr4D 93844879 93845965 1086 True 406.500000 545 82.582000 3827 5025 2 chr4D.!!$R1 1198
4 TraesCS2D01G339400 chr4D 94258544 94261233 2689 True 362.250000 597 82.896250 3125 6560 4 chr4D.!!$R2 3435
5 TraesCS2D01G339400 chr4B 132852864 132856353 3489 True 367.200000 597 83.375000 1348 6560 5 chr4B.!!$R2 5212
6 TraesCS2D01G339400 chr4B 132335984 132338509 2525 True 362.500000 484 81.090500 1347 4121 2 chr4B.!!$R1 2774
7 TraesCS2D01G339400 chr4A 487862057 487865379 3322 False 425.000000 556 81.576667 1347 5025 3 chr4A.!!$F2 3678
8 TraesCS2D01G339400 chr4A 486640461 486643216 2755 False 361.500000 590 83.408000 2928 6370 4 chr4A.!!$F1 3442

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
763 788 0.906756 CCTCCAGCTCCCAACTCTGA 60.907 60.000 0.00 0.00 0.00 3.27 F
1035 1062 0.619255 TCTCCCGCCAATACCCTGAA 60.619 55.000 0.00 0.00 0.00 3.02 F
2053 2138 1.717194 TAGTTGGAAGCGTTAAGGCG 58.283 50.000 14.02 0.00 38.18 5.52 F
2483 2732 2.092592 ACCCGTCCAGTTTTTCTTCTGT 60.093 45.455 0.00 0.00 0.00 3.41 F
3547 4035 3.252974 AGACATGCAGGCTAACACTAC 57.747 47.619 0.00 0.00 29.36 2.73 F
4186 4820 0.037232 GCAACTCTTCTGTAGCCGGT 60.037 55.000 1.90 0.00 0.00 5.28 F
4190 4824 0.176680 CTCTTCTGTAGCCGGTGCAT 59.823 55.000 1.90 0.00 41.13 3.96 F
5034 5818 0.605589 GAGGTGCACAGAGTACTGCT 59.394 55.000 20.43 2.34 46.95 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2053 2138 4.691216 CACTTGCCTAACTAGGTCAAACTC 59.309 45.833 4.72 0.00 45.42 3.01 R
2913 3197 3.117436 GGGGTAAGGGCCAATATGTTACA 60.117 47.826 6.18 0.00 0.00 2.41 R
3141 3454 3.256704 ACTATCAACCCACCCAAGAGAA 58.743 45.455 0.00 0.00 0.00 2.87 R
4167 4801 0.037232 ACCGGCTACAGAAGAGTTGC 60.037 55.000 0.00 0.00 39.10 4.17 R
4348 5097 2.706890 ACAAACCGTTCTTGTCACAGT 58.293 42.857 0.00 0.00 31.29 3.55 R
5661 6499 0.795085 CAGTCTGCTGCTTAGTGTGC 59.205 55.000 0.00 0.00 35.77 4.57 R
5985 6856 2.686835 GGCAGGAGGCTCCTCAGT 60.687 66.667 33.04 10.45 45.66 3.41 R
7011 7891 0.511221 CGTCGCCGTCACTTTCAAAT 59.489 50.000 0.00 0.00 0.00 2.32 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
434 459 5.760253 CACACTTGTAAACTGAACTCTCCAT 59.240 40.000 0.00 0.00 0.00 3.41
583 608 5.221263 ACCGTGGTTATTGCATTTTGTTACA 60.221 36.000 0.00 0.00 0.00 2.41
640 665 9.973450 TTGCAGTATTTATTGCTTTTGAAGTTA 57.027 25.926 6.63 0.00 39.36 2.24
763 788 0.906756 CCTCCAGCTCCCAACTCTGA 60.907 60.000 0.00 0.00 0.00 3.27
791 817 2.350895 CATGGACTGCCCCGAACA 59.649 61.111 0.00 0.00 0.00 3.18
869 895 1.428869 CGAGGGATTCCAGGATTCCT 58.571 55.000 24.06 15.40 33.91 3.36
904 930 4.081420 ACGATGAGTTGCTCAGAATTACCT 60.081 41.667 5.09 0.00 44.08 3.08
1028 1055 1.451504 CCAGCATCTCCCGCCAATA 59.548 57.895 0.00 0.00 0.00 1.90
1035 1062 0.619255 TCTCCCGCCAATACCCTGAA 60.619 55.000 0.00 0.00 0.00 3.02
1116 1143 4.201783 CGCTGTAATTAAGAAACCCCTTCG 60.202 45.833 0.00 0.00 39.22 3.79
1145 1173 8.735315 TCGTTATATTCCACATGTCACAAATTT 58.265 29.630 0.00 0.00 0.00 1.82
1853 1892 8.552083 AGCAGTTTTTGTTTCTTTCTCATTTT 57.448 26.923 0.00 0.00 0.00 1.82
2053 2138 1.717194 TAGTTGGAAGCGTTAAGGCG 58.283 50.000 14.02 0.00 38.18 5.52
2343 2591 6.079712 AGTGCTAGTTTAATCATTTCCCCT 57.920 37.500 0.00 0.00 0.00 4.79
2465 2714 7.962964 TTGATAATTATCTGATCGTTGACCC 57.037 36.000 22.77 0.00 33.88 4.46
2483 2732 2.092592 ACCCGTCCAGTTTTTCTTCTGT 60.093 45.455 0.00 0.00 0.00 3.41
2611 2888 8.897752 GTGAATAATTTGATGGTAAAGCTCTCT 58.102 33.333 0.00 0.00 0.00 3.10
3141 3454 7.315142 CCTTTGTATTACTGCATGAATTGTGT 58.685 34.615 0.00 0.00 0.00 3.72
3152 3465 4.801891 CATGAATTGTGTTCTCTTGGGTG 58.198 43.478 0.00 0.00 0.00 4.61
3547 4035 3.252974 AGACATGCAGGCTAACACTAC 57.747 47.619 0.00 0.00 29.36 2.73
3721 4209 7.074653 ACATCTACTCCAACCTCTTGTTAAA 57.925 36.000 0.00 0.00 34.69 1.52
3784 4272 9.683069 CACTCTATTGCTGTGTTTTTCTTATTT 57.317 29.630 0.00 0.00 0.00 1.40
4159 4793 8.740123 TTTTTATACTTGTTCTCCTCACAACA 57.260 30.769 0.00 0.00 30.83 3.33
4160 4794 8.918202 TTTTATACTTGTTCTCCTCACAACAT 57.082 30.769 0.00 0.00 32.60 2.71
4164 4798 6.867662 ACTTGTTCTCCTCACAACATAAAG 57.132 37.500 0.00 0.00 32.60 1.85
4165 4799 5.239525 ACTTGTTCTCCTCACAACATAAAGC 59.760 40.000 0.00 0.00 32.60 3.51
4166 4800 4.973168 TGTTCTCCTCACAACATAAAGCT 58.027 39.130 0.00 0.00 0.00 3.74
4167 4801 4.756642 TGTTCTCCTCACAACATAAAGCTG 59.243 41.667 0.00 0.00 0.00 4.24
4168 4802 3.338249 TCTCCTCACAACATAAAGCTGC 58.662 45.455 0.00 0.00 0.00 5.25
4169 4803 3.076621 CTCCTCACAACATAAAGCTGCA 58.923 45.455 1.02 0.00 0.00 4.41
4170 4804 3.485394 TCCTCACAACATAAAGCTGCAA 58.515 40.909 1.02 0.00 0.00 4.08
4171 4805 3.253188 TCCTCACAACATAAAGCTGCAAC 59.747 43.478 1.02 0.00 0.00 4.17
4172 4806 3.254166 CCTCACAACATAAAGCTGCAACT 59.746 43.478 1.02 0.00 0.00 3.16
4173 4807 4.470462 CTCACAACATAAAGCTGCAACTC 58.530 43.478 1.02 0.00 0.00 3.01
4174 4808 4.136796 TCACAACATAAAGCTGCAACTCT 58.863 39.130 1.02 0.00 0.00 3.24
4175 4809 4.580167 TCACAACATAAAGCTGCAACTCTT 59.420 37.500 1.02 0.00 0.00 2.85
4176 4810 4.913924 CACAACATAAAGCTGCAACTCTTC 59.086 41.667 1.02 0.00 0.00 2.87
4177 4811 4.823989 ACAACATAAAGCTGCAACTCTTCT 59.176 37.500 1.02 0.00 0.00 2.85
4178 4812 5.152097 CAACATAAAGCTGCAACTCTTCTG 58.848 41.667 1.02 0.00 0.00 3.02
4179 4813 4.392940 ACATAAAGCTGCAACTCTTCTGT 58.607 39.130 1.02 0.00 0.00 3.41
4180 4814 5.551233 ACATAAAGCTGCAACTCTTCTGTA 58.449 37.500 1.02 0.00 0.00 2.74
4181 4815 5.641209 ACATAAAGCTGCAACTCTTCTGTAG 59.359 40.000 1.02 0.00 0.00 2.74
4183 4817 1.082690 GCTGCAACTCTTCTGTAGCC 58.917 55.000 0.00 0.00 44.07 3.93
4184 4818 1.354040 CTGCAACTCTTCTGTAGCCG 58.646 55.000 0.00 0.00 0.00 5.52
4185 4819 0.037326 TGCAACTCTTCTGTAGCCGG 60.037 55.000 0.00 0.00 0.00 6.13
4186 4820 0.037232 GCAACTCTTCTGTAGCCGGT 60.037 55.000 1.90 0.00 0.00 5.28
4187 4821 1.714794 CAACTCTTCTGTAGCCGGTG 58.285 55.000 1.90 0.00 0.00 4.94
4188 4822 0.037232 AACTCTTCTGTAGCCGGTGC 60.037 55.000 1.90 0.00 37.95 5.01
4189 4823 1.185618 ACTCTTCTGTAGCCGGTGCA 61.186 55.000 1.90 0.00 41.13 4.57
4190 4824 0.176680 CTCTTCTGTAGCCGGTGCAT 59.823 55.000 1.90 0.00 41.13 3.96
4191 4825 0.613260 TCTTCTGTAGCCGGTGCATT 59.387 50.000 1.90 0.00 41.13 3.56
4192 4826 1.003118 TCTTCTGTAGCCGGTGCATTT 59.997 47.619 1.90 0.00 41.13 2.32
4193 4827 1.812571 CTTCTGTAGCCGGTGCATTTT 59.187 47.619 1.90 0.00 41.13 1.82
4194 4828 1.904287 TCTGTAGCCGGTGCATTTTT 58.096 45.000 1.90 0.00 41.13 1.94
4195 4829 3.060736 TCTGTAGCCGGTGCATTTTTA 57.939 42.857 1.90 0.00 41.13 1.52
4196 4830 3.616219 TCTGTAGCCGGTGCATTTTTAT 58.384 40.909 1.90 0.00 41.13 1.40
4197 4831 4.013728 TCTGTAGCCGGTGCATTTTTATT 58.986 39.130 1.90 0.00 41.13 1.40
4198 4832 4.461081 TCTGTAGCCGGTGCATTTTTATTT 59.539 37.500 1.90 0.00 41.13 1.40
4199 4833 4.739195 TGTAGCCGGTGCATTTTTATTTC 58.261 39.130 1.90 0.00 41.13 2.17
4200 4834 3.245518 AGCCGGTGCATTTTTATTTCC 57.754 42.857 1.90 0.00 41.13 3.13
4201 4835 2.831526 AGCCGGTGCATTTTTATTTCCT 59.168 40.909 1.90 0.00 41.13 3.36
4202 4836 4.020543 AGCCGGTGCATTTTTATTTCCTA 58.979 39.130 1.90 0.00 41.13 2.94
4203 4837 4.097892 AGCCGGTGCATTTTTATTTCCTAG 59.902 41.667 1.90 0.00 41.13 3.02
4204 4838 4.142249 GCCGGTGCATTTTTATTTCCTAGT 60.142 41.667 1.90 0.00 37.47 2.57
4205 4839 5.066764 GCCGGTGCATTTTTATTTCCTAGTA 59.933 40.000 1.90 0.00 37.47 1.82
4206 4840 6.492254 CCGGTGCATTTTTATTTCCTAGTAC 58.508 40.000 0.00 0.00 0.00 2.73
4207 4841 6.317893 CCGGTGCATTTTTATTTCCTAGTACT 59.682 38.462 0.00 0.00 0.00 2.73
4208 4842 7.186804 CGGTGCATTTTTATTTCCTAGTACTG 58.813 38.462 5.39 0.00 0.00 2.74
4209 4843 7.148306 CGGTGCATTTTTATTTCCTAGTACTGT 60.148 37.037 5.39 0.00 0.00 3.55
4210 4844 7.968405 GGTGCATTTTTATTTCCTAGTACTGTG 59.032 37.037 5.39 0.00 0.00 3.66
4211 4845 8.726988 GTGCATTTTTATTTCCTAGTACTGTGA 58.273 33.333 5.39 0.00 0.00 3.58
4212 4846 8.726988 TGCATTTTTATTTCCTAGTACTGTGAC 58.273 33.333 5.39 0.00 0.00 3.67
4213 4847 8.726988 GCATTTTTATTTCCTAGTACTGTGACA 58.273 33.333 5.39 0.00 0.00 3.58
4218 4852 9.485206 TTTATTTCCTAGTACTGTGACAAGAAC 57.515 33.333 5.39 0.00 0.00 3.01
4219 4853 4.761235 TCCTAGTACTGTGACAAGAACG 57.239 45.455 5.39 0.00 0.00 3.95
4220 4854 3.504906 TCCTAGTACTGTGACAAGAACGG 59.495 47.826 5.39 0.00 0.00 4.44
4221 4855 3.255149 CCTAGTACTGTGACAAGAACGGT 59.745 47.826 5.39 0.00 40.27 4.83
4222 4856 3.814005 AGTACTGTGACAAGAACGGTT 57.186 42.857 0.00 0.00 38.16 4.44
4223 4857 4.133013 AGTACTGTGACAAGAACGGTTT 57.867 40.909 0.00 0.00 38.16 3.27
4224 4858 3.869246 AGTACTGTGACAAGAACGGTTTG 59.131 43.478 0.00 0.00 38.16 2.93
4225 4859 2.706890 ACTGTGACAAGAACGGTTTGT 58.293 42.857 0.00 0.00 41.21 2.83
4226 4860 3.864243 ACTGTGACAAGAACGGTTTGTA 58.136 40.909 0.00 0.00 38.78 2.41
4227 4861 4.448210 ACTGTGACAAGAACGGTTTGTAT 58.552 39.130 0.00 0.00 38.78 2.29
4228 4862 4.879545 ACTGTGACAAGAACGGTTTGTATT 59.120 37.500 0.00 0.00 38.78 1.89
4229 4863 5.163302 TGTGACAAGAACGGTTTGTATTG 57.837 39.130 0.00 1.74 38.78 1.90
4230 4864 4.636648 TGTGACAAGAACGGTTTGTATTGT 59.363 37.500 11.77 11.77 41.03 2.71
4231 4865 5.124138 TGTGACAAGAACGGTTTGTATTGTT 59.876 36.000 12.64 0.00 39.43 2.83
4232 4866 5.454232 GTGACAAGAACGGTTTGTATTGTTG 59.546 40.000 12.64 0.00 39.43 3.33
4233 4867 5.124138 TGACAAGAACGGTTTGTATTGTTGT 59.876 36.000 12.64 0.00 39.43 3.32
4234 4868 5.336744 ACAAGAACGGTTTGTATTGTTGTG 58.663 37.500 0.00 0.00 37.34 3.33
4235 4869 5.106078 ACAAGAACGGTTTGTATTGTTGTGT 60.106 36.000 0.00 0.00 37.34 3.72
4236 4870 4.915704 AGAACGGTTTGTATTGTTGTGTG 58.084 39.130 0.00 0.00 0.00 3.82
4237 4871 4.396790 AGAACGGTTTGTATTGTTGTGTGT 59.603 37.500 0.00 0.00 0.00 3.72
4238 4872 5.585445 AGAACGGTTTGTATTGTTGTGTGTA 59.415 36.000 0.00 0.00 0.00 2.90
4239 4873 5.412526 ACGGTTTGTATTGTTGTGTGTAG 57.587 39.130 0.00 0.00 0.00 2.74
4240 4874 4.273969 ACGGTTTGTATTGTTGTGTGTAGG 59.726 41.667 0.00 0.00 0.00 3.18
4241 4875 4.512198 CGGTTTGTATTGTTGTGTGTAGGA 59.488 41.667 0.00 0.00 0.00 2.94
4242 4876 5.007823 CGGTTTGTATTGTTGTGTGTAGGAA 59.992 40.000 0.00 0.00 0.00 3.36
4243 4877 6.435428 GGTTTGTATTGTTGTGTGTAGGAAG 58.565 40.000 0.00 0.00 0.00 3.46
4244 4878 6.038936 GGTTTGTATTGTTGTGTGTAGGAAGT 59.961 38.462 0.00 0.00 0.00 3.01
4245 4879 6.612247 TTGTATTGTTGTGTGTAGGAAGTG 57.388 37.500 0.00 0.00 0.00 3.16
4246 4880 5.676552 TGTATTGTTGTGTGTAGGAAGTGT 58.323 37.500 0.00 0.00 0.00 3.55
4247 4881 6.818233 TGTATTGTTGTGTGTAGGAAGTGTA 58.182 36.000 0.00 0.00 0.00 2.90
4248 4882 7.446769 TGTATTGTTGTGTGTAGGAAGTGTAT 58.553 34.615 0.00 0.00 0.00 2.29
4249 4883 6.801539 ATTGTTGTGTGTAGGAAGTGTATG 57.198 37.500 0.00 0.00 0.00 2.39
4250 4884 5.538849 TGTTGTGTGTAGGAAGTGTATGA 57.461 39.130 0.00 0.00 0.00 2.15
4251 4885 5.919755 TGTTGTGTGTAGGAAGTGTATGAA 58.080 37.500 0.00 0.00 0.00 2.57
4252 4886 5.756347 TGTTGTGTGTAGGAAGTGTATGAAC 59.244 40.000 0.00 0.00 0.00 3.18
4253 4887 5.538849 TGTGTGTAGGAAGTGTATGAACA 57.461 39.130 0.00 0.00 0.00 3.18
4254 4888 5.919755 TGTGTGTAGGAAGTGTATGAACAA 58.080 37.500 0.00 0.00 37.36 2.83
4255 4889 5.756347 TGTGTGTAGGAAGTGTATGAACAAC 59.244 40.000 0.00 0.00 37.36 3.32
4256 4890 5.756347 GTGTGTAGGAAGTGTATGAACAACA 59.244 40.000 0.00 0.00 37.36 3.33
4257 4891 5.989168 TGTGTAGGAAGTGTATGAACAACAG 59.011 40.000 0.00 0.00 37.36 3.16
4258 4892 6.183360 TGTGTAGGAAGTGTATGAACAACAGA 60.183 38.462 0.00 0.00 37.36 3.41
4259 4893 6.704493 GTGTAGGAAGTGTATGAACAACAGAA 59.296 38.462 0.00 0.00 37.36 3.02
4260 4894 6.929049 TGTAGGAAGTGTATGAACAACAGAAG 59.071 38.462 0.00 0.00 37.36 2.85
4261 4895 5.308825 AGGAAGTGTATGAACAACAGAAGG 58.691 41.667 0.00 0.00 37.36 3.46
4262 4896 5.063880 GGAAGTGTATGAACAACAGAAGGT 58.936 41.667 0.00 0.00 37.36 3.50
4263 4897 6.042781 AGGAAGTGTATGAACAACAGAAGGTA 59.957 38.462 0.00 0.00 37.36 3.08
4264 4898 6.369065 GGAAGTGTATGAACAACAGAAGGTAG 59.631 42.308 0.00 0.00 37.36 3.18
4265 4899 5.238583 AGTGTATGAACAACAGAAGGTAGC 58.761 41.667 0.00 0.00 37.36 3.58
4266 4900 4.994852 GTGTATGAACAACAGAAGGTAGCA 59.005 41.667 0.00 0.00 37.36 3.49
4267 4901 4.994852 TGTATGAACAACAGAAGGTAGCAC 59.005 41.667 0.00 0.00 30.91 4.40
4268 4902 3.552132 TGAACAACAGAAGGTAGCACA 57.448 42.857 0.00 0.00 0.00 4.57
4269 4903 3.202906 TGAACAACAGAAGGTAGCACAC 58.797 45.455 0.00 0.00 0.00 3.82
4270 4904 3.202906 GAACAACAGAAGGTAGCACACA 58.797 45.455 0.00 0.00 0.00 3.72
4271 4905 3.492102 ACAACAGAAGGTAGCACACAT 57.508 42.857 0.00 0.00 0.00 3.21
4272 4906 4.617253 ACAACAGAAGGTAGCACACATA 57.383 40.909 0.00 0.00 0.00 2.29
4273 4907 4.968259 ACAACAGAAGGTAGCACACATAA 58.032 39.130 0.00 0.00 0.00 1.90
4274 4908 5.560724 ACAACAGAAGGTAGCACACATAAT 58.439 37.500 0.00 0.00 0.00 1.28
4275 4909 5.643777 ACAACAGAAGGTAGCACACATAATC 59.356 40.000 0.00 0.00 0.00 1.75
4276 4910 5.683876 ACAGAAGGTAGCACACATAATCT 57.316 39.130 0.00 0.00 0.00 2.40
4277 4911 6.054860 ACAGAAGGTAGCACACATAATCTT 57.945 37.500 0.00 0.00 0.00 2.40
4278 4912 6.476378 ACAGAAGGTAGCACACATAATCTTT 58.524 36.000 0.00 0.00 0.00 2.52
4279 4913 6.942576 ACAGAAGGTAGCACACATAATCTTTT 59.057 34.615 0.00 0.00 0.00 2.27
4280 4914 7.448469 ACAGAAGGTAGCACACATAATCTTTTT 59.552 33.333 0.00 0.00 0.00 1.94
4326 5065 3.467374 AGCTGCAACTCTTCTATAGCC 57.533 47.619 1.02 0.00 0.00 3.93
4345 5087 4.020543 AGCCGGTGCATTTTTATTTCCTA 58.979 39.130 1.90 0.00 41.13 2.94
4346 5088 4.097892 AGCCGGTGCATTTTTATTTCCTAG 59.902 41.667 1.90 0.00 41.13 3.02
4348 5097 5.066764 GCCGGTGCATTTTTATTTCCTAGTA 59.933 40.000 1.90 0.00 37.47 1.82
4369 5133 3.864243 ACTGTGACAAGAACGGTTTGTA 58.136 40.909 0.00 0.00 38.78 2.41
5032 5816 2.071688 GTGAGGTGCACAGAGTACTG 57.928 55.000 20.43 0.00 46.91 2.74
5034 5818 0.605589 GAGGTGCACAGAGTACTGCT 59.394 55.000 20.43 2.34 46.95 4.24
5042 5826 4.202315 TGCACAGAGTACTGCTTCCTTTTA 60.202 41.667 0.00 0.00 46.95 1.52
5271 6085 9.982651 GATAGGACTTAGATGTGCAATACTTAA 57.017 33.333 0.00 0.00 0.00 1.85
5274 6088 6.017852 GGACTTAGATGTGCAATACTTAAGGC 60.018 42.308 7.53 0.84 31.49 4.35
5579 6411 7.667043 TGTCTGTTGTCATTTCTGTTATACC 57.333 36.000 0.00 0.00 0.00 2.73
5661 6499 4.828296 GCATGTGGGGCCTGGGAG 62.828 72.222 0.84 0.00 0.00 4.30
5817 6673 5.695851 ATGCTCTTTGTTGTGAAGTAAGG 57.304 39.130 0.00 0.00 0.00 2.69
5985 6856 0.179059 TCAGCGTGCTCCTGTGAAAA 60.179 50.000 0.00 0.00 0.00 2.29
6393 7264 0.321653 GGATCACCAGAACACGGCTT 60.322 55.000 0.00 0.00 35.97 4.35
6535 7412 2.023673 CGAGAGAGACATCAAGAGGCT 58.976 52.381 0.00 0.00 0.00 4.58
6585 7463 2.202932 CCCTGGCGAAGGTGATCG 60.203 66.667 3.60 0.00 45.78 3.69
6593 7471 1.144057 GAAGGTGATCGGCGGTGAT 59.856 57.895 7.21 0.00 0.00 3.06
6622 7500 1.034838 ACTGGTGTTTTGAGCGCCAA 61.035 50.000 2.29 5.36 44.67 4.52
6678 7556 0.890683 AGGTGCTTGTTTGCCTATGC 59.109 50.000 0.00 0.00 38.26 3.14
6972 7852 5.184287 TGGTACTGTCAATCATCGTCAGTTA 59.816 40.000 0.00 0.00 39.54 2.24
6995 7875 2.959516 TGGTGTGAGAAGCGAGTAATG 58.040 47.619 0.00 0.00 0.00 1.90
7002 7882 3.109619 GAGAAGCGAGTAATGAACGAGG 58.890 50.000 0.00 0.00 0.00 4.63
7003 7883 2.159226 AGAAGCGAGTAATGAACGAGGG 60.159 50.000 0.00 0.00 0.00 4.30
7007 7887 1.202382 CGAGTAATGAACGAGGGACCC 60.202 57.143 0.59 0.59 0.00 4.46
7009 7889 2.101082 GAGTAATGAACGAGGGACCCTC 59.899 54.545 28.50 28.50 46.44 4.30
7020 7900 4.846168 GAGGGACCCTCTATTTGAAAGT 57.154 45.455 30.51 0.00 46.41 2.66
7021 7901 4.518249 GAGGGACCCTCTATTTGAAAGTG 58.482 47.826 30.51 0.00 46.41 3.16
7024 7904 3.933332 GGACCCTCTATTTGAAAGTGACG 59.067 47.826 0.00 0.00 0.00 4.35
7025 7905 3.933332 GACCCTCTATTTGAAAGTGACGG 59.067 47.826 0.00 0.00 0.00 4.79
7027 7907 2.348666 CCTCTATTTGAAAGTGACGGCG 59.651 50.000 4.80 4.80 0.00 6.46
7028 7908 3.250744 CTCTATTTGAAAGTGACGGCGA 58.749 45.455 16.62 0.00 0.00 5.54
7045 7925 4.295119 ACGAACGGCCGTCAGCTT 62.295 61.111 34.29 16.62 43.05 3.74
7046 7926 3.777925 CGAACGGCCGTCAGCTTG 61.778 66.667 34.29 16.36 43.05 4.01
7047 7927 2.357034 GAACGGCCGTCAGCTTGA 60.357 61.111 34.29 0.00 43.05 3.02
7055 7935 3.414700 GTCAGCTTGACGCCACCG 61.415 66.667 0.00 0.00 37.67 4.94
7086 7966 4.230002 CCCTCGGGCGGCGATTAA 62.230 66.667 12.98 0.00 0.00 1.40
7087 7967 2.030562 CCTCGGGCGGCGATTAAT 59.969 61.111 12.98 0.00 0.00 1.40
7093 8056 0.872388 GGGCGGCGATTAATAACCAG 59.128 55.000 12.98 2.07 0.00 4.00
7099 8062 4.000988 CGGCGATTAATAACCAGGCTATT 58.999 43.478 0.00 0.69 0.00 1.73
7130 8093 8.554528 TGTTTCGGTACATTTTCGTAACAAATA 58.445 29.630 9.82 0.00 39.71 1.40
7331 8294 1.078848 GGCGATCACCAGCTTGTCT 60.079 57.895 0.00 0.00 0.00 3.41
7493 8456 3.490759 CCGTGCAGCGCGAAGAAT 61.491 61.111 29.62 0.00 39.94 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
434 459 3.136260 AGGTAACCCAACGTGAAACCTAA 59.864 43.478 0.00 0.00 33.36 2.69
583 608 1.134670 GCTCCTGCCAAATACGAGACT 60.135 52.381 0.00 0.00 0.00 3.24
707 732 5.086621 GCCTTAATCACCCCATAAATCCAT 58.913 41.667 0.00 0.00 0.00 3.41
709 734 3.832490 GGCCTTAATCACCCCATAAATCC 59.168 47.826 0.00 0.00 0.00 3.01
763 788 1.610673 AGTCCATGTGCTCCGTCCT 60.611 57.895 0.00 0.00 0.00 3.85
791 817 7.341805 ACCAATTCAGCTCACAGAGTTATATT 58.658 34.615 0.00 0.00 31.39 1.28
869 895 4.183865 CAACTCATCGTTTGGCTAGATCA 58.816 43.478 0.00 0.00 32.27 2.92
904 930 2.875672 GCTGAGTCCAGTGGTATTTGCA 60.876 50.000 9.54 0.00 42.35 4.08
1028 1055 3.637273 GCGTCAGGGGTTCAGGGT 61.637 66.667 0.00 0.00 0.00 4.34
1035 1062 3.850098 CTTGGCTTGCGTCAGGGGT 62.850 63.158 0.00 0.00 0.00 4.95
1116 1143 5.583061 TGTGACATGTGGAATATAACGAACC 59.417 40.000 1.15 0.00 0.00 3.62
1145 1173 3.838565 TGGAAGCCCAGTAATTCAAACA 58.161 40.909 0.00 0.00 37.58 2.83
1237 1265 9.461312 GGCATCAAACTATATTCCCAATACATA 57.539 33.333 0.00 0.00 0.00 2.29
1434 1472 6.870895 AGTCTGCATGATATCCATCTATGT 57.129 37.500 0.00 0.00 31.94 2.29
1979 2022 8.969267 GTTATAGAACATAGTCATGCACAGTAC 58.031 37.037 0.00 0.00 35.39 2.73
2053 2138 4.691216 CACTTGCCTAACTAGGTCAAACTC 59.309 45.833 4.72 0.00 45.42 3.01
2343 2591 5.659440 AAAGCAGACAAGTTTTTCTGGAA 57.341 34.783 11.56 0.00 39.81 3.53
2465 2714 5.333416 GCTTAGACAGAAGAAAAACTGGACG 60.333 44.000 0.00 0.00 38.30 4.79
2483 2732 7.276218 GCACATAAATGCTCAAAAATGCTTAGA 59.724 33.333 0.00 0.00 42.62 2.10
2913 3197 3.117436 GGGGTAAGGGCCAATATGTTACA 60.117 47.826 6.18 0.00 0.00 2.41
3075 3384 4.460948 ACATTCATGGAGCAAATGTTCC 57.539 40.909 9.14 9.14 44.52 3.62
3141 3454 3.256704 ACTATCAACCCACCCAAGAGAA 58.743 45.455 0.00 0.00 0.00 2.87
3152 3465 9.797556 GAAAATACCATAAACAACTATCAACCC 57.202 33.333 0.00 0.00 0.00 4.11
3361 3682 7.308589 GCCTACCATGCATAGAAAACGATTTAT 60.309 37.037 0.00 0.00 0.00 1.40
3547 4035 5.333299 TCATTTGAATCAAAGATGCCCTG 57.667 39.130 14.10 5.84 36.76 4.45
3657 4145 5.517924 TCTAATGCAAATGGATCAAGGGAA 58.482 37.500 0.00 0.00 0.00 3.97
3721 4209 5.669798 ATACCCCAAAAGCATAGGATTCT 57.330 39.130 0.00 0.00 0.00 2.40
3784 4272 7.448161 TGATTCACAGGATTTCTAAAGCAAAGA 59.552 33.333 0.00 0.00 0.00 2.52
3833 4322 6.433093 TGCTCTATATTGTACGCTATCCAAGA 59.567 38.462 0.00 0.00 0.00 3.02
4151 4785 4.214971 AGAGTTGCAGCTTTATGTTGTGAG 59.785 41.667 3.97 0.00 0.00 3.51
4152 4786 4.136796 AGAGTTGCAGCTTTATGTTGTGA 58.863 39.130 3.97 0.00 0.00 3.58
4153 4787 4.494350 AGAGTTGCAGCTTTATGTTGTG 57.506 40.909 3.97 0.00 0.00 3.33
4154 4788 4.823989 AGAAGAGTTGCAGCTTTATGTTGT 59.176 37.500 3.97 0.00 0.00 3.32
4155 4789 5.152097 CAGAAGAGTTGCAGCTTTATGTTG 58.848 41.667 3.97 0.00 0.00 3.33
4156 4790 4.823989 ACAGAAGAGTTGCAGCTTTATGTT 59.176 37.500 3.97 0.00 0.00 2.71
4157 4791 4.392940 ACAGAAGAGTTGCAGCTTTATGT 58.607 39.130 3.97 11.27 0.00 2.29
4158 4792 5.447010 GCTACAGAAGAGTTGCAGCTTTATG 60.447 44.000 3.97 10.69 39.51 1.90
4159 4793 4.633565 GCTACAGAAGAGTTGCAGCTTTAT 59.366 41.667 3.97 0.00 39.51 1.40
4160 4794 3.997021 GCTACAGAAGAGTTGCAGCTTTA 59.003 43.478 3.97 0.00 39.51 1.85
4161 4795 2.810852 GCTACAGAAGAGTTGCAGCTTT 59.189 45.455 3.97 0.00 39.51 3.51
4162 4796 2.421619 GCTACAGAAGAGTTGCAGCTT 58.578 47.619 3.97 1.10 39.51 3.74
4163 4797 1.338579 GGCTACAGAAGAGTTGCAGCT 60.339 52.381 1.30 1.30 41.09 4.24
4164 4798 1.082690 GGCTACAGAAGAGTTGCAGC 58.917 55.000 0.00 0.00 41.09 5.25
4165 4799 1.354040 CGGCTACAGAAGAGTTGCAG 58.646 55.000 0.00 0.00 41.09 4.41
4166 4800 0.037326 CCGGCTACAGAAGAGTTGCA 60.037 55.000 0.00 0.00 41.09 4.08
4167 4801 0.037232 ACCGGCTACAGAAGAGTTGC 60.037 55.000 0.00 0.00 39.10 4.17
4168 4802 1.714794 CACCGGCTACAGAAGAGTTG 58.285 55.000 0.00 0.00 0.00 3.16
4169 4803 0.037232 GCACCGGCTACAGAAGAGTT 60.037 55.000 0.00 0.00 36.96 3.01
4170 4804 1.185618 TGCACCGGCTACAGAAGAGT 61.186 55.000 0.00 0.00 41.91 3.24
4171 4805 0.176680 ATGCACCGGCTACAGAAGAG 59.823 55.000 0.00 0.00 41.91 2.85
4172 4806 0.613260 AATGCACCGGCTACAGAAGA 59.387 50.000 0.00 0.00 41.91 2.87
4173 4807 1.453155 AAATGCACCGGCTACAGAAG 58.547 50.000 0.00 0.00 41.91 2.85
4174 4808 1.904287 AAAATGCACCGGCTACAGAA 58.096 45.000 0.00 0.00 41.91 3.02
4175 4809 1.904287 AAAAATGCACCGGCTACAGA 58.096 45.000 0.00 0.00 41.91 3.41
4176 4810 4.370364 AATAAAAATGCACCGGCTACAG 57.630 40.909 0.00 0.00 41.91 2.74
4177 4811 4.381079 GGAAATAAAAATGCACCGGCTACA 60.381 41.667 0.00 0.00 41.91 2.74
4178 4812 4.109766 GGAAATAAAAATGCACCGGCTAC 58.890 43.478 0.00 0.00 41.91 3.58
4179 4813 4.020543 AGGAAATAAAAATGCACCGGCTA 58.979 39.130 0.00 0.00 41.91 3.93
4180 4814 2.831526 AGGAAATAAAAATGCACCGGCT 59.168 40.909 0.00 0.00 41.91 5.52
4181 4815 3.245518 AGGAAATAAAAATGCACCGGC 57.754 42.857 0.00 0.00 41.68 6.13
4182 4816 5.576447 ACTAGGAAATAAAAATGCACCGG 57.424 39.130 0.00 0.00 0.00 5.28
4183 4817 7.148306 ACAGTACTAGGAAATAAAAATGCACCG 60.148 37.037 0.00 0.00 0.00 4.94
4184 4818 7.968405 CACAGTACTAGGAAATAAAAATGCACC 59.032 37.037 0.00 0.00 0.00 5.01
4185 4819 8.726988 TCACAGTACTAGGAAATAAAAATGCAC 58.273 33.333 0.00 0.00 0.00 4.57
4186 4820 8.726988 GTCACAGTACTAGGAAATAAAAATGCA 58.273 33.333 0.00 0.00 0.00 3.96
4187 4821 8.726988 TGTCACAGTACTAGGAAATAAAAATGC 58.273 33.333 0.00 0.00 0.00 3.56
4192 4826 9.485206 GTTCTTGTCACAGTACTAGGAAATAAA 57.515 33.333 0.00 0.00 0.00 1.40
4193 4827 7.811236 CGTTCTTGTCACAGTACTAGGAAATAA 59.189 37.037 0.00 0.00 0.00 1.40
4194 4828 7.310664 CGTTCTTGTCACAGTACTAGGAAATA 58.689 38.462 0.00 0.00 0.00 1.40
4195 4829 6.157211 CGTTCTTGTCACAGTACTAGGAAAT 58.843 40.000 0.00 0.00 0.00 2.17
4196 4830 5.508489 CCGTTCTTGTCACAGTACTAGGAAA 60.508 44.000 0.00 0.00 0.00 3.13
4197 4831 4.022589 CCGTTCTTGTCACAGTACTAGGAA 60.023 45.833 0.00 0.00 0.00 3.36
4198 4832 3.504906 CCGTTCTTGTCACAGTACTAGGA 59.495 47.826 0.00 0.00 0.00 2.94
4199 4833 3.255149 ACCGTTCTTGTCACAGTACTAGG 59.745 47.826 0.00 0.00 0.00 3.02
4200 4834 4.500603 ACCGTTCTTGTCACAGTACTAG 57.499 45.455 0.00 0.00 0.00 2.57
4201 4835 4.924305 AACCGTTCTTGTCACAGTACTA 57.076 40.909 0.00 0.00 0.00 1.82
4202 4836 3.814005 AACCGTTCTTGTCACAGTACT 57.186 42.857 0.00 0.00 0.00 2.73
4203 4837 3.619929 ACAAACCGTTCTTGTCACAGTAC 59.380 43.478 0.00 0.00 31.29 2.73
4204 4838 3.864243 ACAAACCGTTCTTGTCACAGTA 58.136 40.909 0.00 0.00 31.29 2.74
4205 4839 2.706890 ACAAACCGTTCTTGTCACAGT 58.293 42.857 0.00 0.00 31.29 3.55
4206 4840 5.204833 CAATACAAACCGTTCTTGTCACAG 58.795 41.667 0.00 0.00 38.05 3.66
4207 4841 4.636648 ACAATACAAACCGTTCTTGTCACA 59.363 37.500 0.00 0.00 38.05 3.58
4208 4842 5.164606 ACAATACAAACCGTTCTTGTCAC 57.835 39.130 0.00 0.00 38.05 3.67
4209 4843 5.124138 ACAACAATACAAACCGTTCTTGTCA 59.876 36.000 0.00 0.00 38.05 3.58
4210 4844 5.454232 CACAACAATACAAACCGTTCTTGTC 59.546 40.000 0.00 0.00 38.05 3.18
4211 4845 5.106078 ACACAACAATACAAACCGTTCTTGT 60.106 36.000 0.00 0.00 40.13 3.16
4212 4846 5.229052 CACACAACAATACAAACCGTTCTTG 59.771 40.000 0.00 0.00 0.00 3.02
4213 4847 5.106078 ACACACAACAATACAAACCGTTCTT 60.106 36.000 0.00 0.00 0.00 2.52
4214 4848 4.396790 ACACACAACAATACAAACCGTTCT 59.603 37.500 0.00 0.00 0.00 3.01
4215 4849 4.664188 ACACACAACAATACAAACCGTTC 58.336 39.130 0.00 0.00 0.00 3.95
4216 4850 4.705337 ACACACAACAATACAAACCGTT 57.295 36.364 0.00 0.00 0.00 4.44
4217 4851 4.273969 CCTACACACAACAATACAAACCGT 59.726 41.667 0.00 0.00 0.00 4.83
4218 4852 4.512198 TCCTACACACAACAATACAAACCG 59.488 41.667 0.00 0.00 0.00 4.44
4219 4853 6.038936 ACTTCCTACACACAACAATACAAACC 59.961 38.462 0.00 0.00 0.00 3.27
4220 4854 6.910433 CACTTCCTACACACAACAATACAAAC 59.090 38.462 0.00 0.00 0.00 2.93
4221 4855 6.600032 ACACTTCCTACACACAACAATACAAA 59.400 34.615 0.00 0.00 0.00 2.83
4222 4856 6.116806 ACACTTCCTACACACAACAATACAA 58.883 36.000 0.00 0.00 0.00 2.41
4223 4857 5.676552 ACACTTCCTACACACAACAATACA 58.323 37.500 0.00 0.00 0.00 2.29
4224 4858 7.601130 TCATACACTTCCTACACACAACAATAC 59.399 37.037 0.00 0.00 0.00 1.89
4225 4859 7.672240 TCATACACTTCCTACACACAACAATA 58.328 34.615 0.00 0.00 0.00 1.90
4226 4860 6.530120 TCATACACTTCCTACACACAACAAT 58.470 36.000 0.00 0.00 0.00 2.71
4227 4861 5.919755 TCATACACTTCCTACACACAACAA 58.080 37.500 0.00 0.00 0.00 2.83
4228 4862 5.538849 TCATACACTTCCTACACACAACA 57.461 39.130 0.00 0.00 0.00 3.33
4229 4863 5.756347 TGTTCATACACTTCCTACACACAAC 59.244 40.000 0.00 0.00 0.00 3.32
4230 4864 5.919755 TGTTCATACACTTCCTACACACAA 58.080 37.500 0.00 0.00 0.00 3.33
4231 4865 5.538849 TGTTCATACACTTCCTACACACA 57.461 39.130 0.00 0.00 0.00 3.72
4232 4866 5.756347 TGTTGTTCATACACTTCCTACACAC 59.244 40.000 0.00 0.00 32.98 3.82
4233 4867 5.919755 TGTTGTTCATACACTTCCTACACA 58.080 37.500 0.00 0.00 32.98 3.72
4234 4868 6.220930 TCTGTTGTTCATACACTTCCTACAC 58.779 40.000 0.00 0.00 32.98 2.90
4235 4869 6.413783 TCTGTTGTTCATACACTTCCTACA 57.586 37.500 0.00 0.00 32.98 2.74
4236 4870 6.369065 CCTTCTGTTGTTCATACACTTCCTAC 59.631 42.308 0.00 0.00 32.98 3.18
4237 4871 6.042781 ACCTTCTGTTGTTCATACACTTCCTA 59.957 38.462 0.00 0.00 32.98 2.94
4238 4872 5.163195 ACCTTCTGTTGTTCATACACTTCCT 60.163 40.000 0.00 0.00 32.98 3.36
4239 4873 5.063880 ACCTTCTGTTGTTCATACACTTCC 58.936 41.667 0.00 0.00 32.98 3.46
4240 4874 6.128526 GCTACCTTCTGTTGTTCATACACTTC 60.129 42.308 0.00 0.00 32.98 3.01
4241 4875 5.701290 GCTACCTTCTGTTGTTCATACACTT 59.299 40.000 0.00 0.00 32.98 3.16
4242 4876 5.221641 TGCTACCTTCTGTTGTTCATACACT 60.222 40.000 0.00 0.00 32.98 3.55
4243 4877 4.994852 TGCTACCTTCTGTTGTTCATACAC 59.005 41.667 0.00 0.00 32.98 2.90
4244 4878 4.994852 GTGCTACCTTCTGTTGTTCATACA 59.005 41.667 0.00 0.00 0.00 2.29
4245 4879 4.994852 TGTGCTACCTTCTGTTGTTCATAC 59.005 41.667 0.00 0.00 0.00 2.39
4246 4880 4.994852 GTGTGCTACCTTCTGTTGTTCATA 59.005 41.667 0.00 0.00 0.00 2.15
4247 4881 3.815401 GTGTGCTACCTTCTGTTGTTCAT 59.185 43.478 0.00 0.00 0.00 2.57
4248 4882 3.202906 GTGTGCTACCTTCTGTTGTTCA 58.797 45.455 0.00 0.00 0.00 3.18
4249 4883 3.202906 TGTGTGCTACCTTCTGTTGTTC 58.797 45.455 0.00 0.00 0.00 3.18
4250 4884 3.275617 TGTGTGCTACCTTCTGTTGTT 57.724 42.857 0.00 0.00 0.00 2.83
4251 4885 3.492102 ATGTGTGCTACCTTCTGTTGT 57.508 42.857 0.00 0.00 0.00 3.32
4252 4886 5.877012 AGATTATGTGTGCTACCTTCTGTTG 59.123 40.000 0.00 0.00 0.00 3.33
4253 4887 6.054860 AGATTATGTGTGCTACCTTCTGTT 57.945 37.500 0.00 0.00 0.00 3.16
4254 4888 5.683876 AGATTATGTGTGCTACCTTCTGT 57.316 39.130 0.00 0.00 0.00 3.41
4255 4889 6.992063 AAAGATTATGTGTGCTACCTTCTG 57.008 37.500 0.00 0.00 0.00 3.02
4277 4911 8.740123 TGTTGTGAGGAGAACAAGTATAAAAA 57.260 30.769 0.00 0.00 38.17 1.94
4278 4912 8.918202 ATGTTGTGAGGAGAACAAGTATAAAA 57.082 30.769 0.00 0.00 38.72 1.52
4281 4915 9.653287 CTTTATGTTGTGAGGAGAACAAGTATA 57.347 33.333 0.00 0.00 38.72 1.47
4282 4916 7.119846 GCTTTATGTTGTGAGGAGAACAAGTAT 59.880 37.037 0.00 0.00 38.72 2.12
4283 4917 6.426937 GCTTTATGTTGTGAGGAGAACAAGTA 59.573 38.462 0.00 0.00 38.72 2.24
4284 4918 5.239525 GCTTTATGTTGTGAGGAGAACAAGT 59.760 40.000 0.00 0.00 38.72 3.16
4285 4919 5.471456 AGCTTTATGTTGTGAGGAGAACAAG 59.529 40.000 0.00 0.00 38.72 3.16
4286 4920 5.239306 CAGCTTTATGTTGTGAGGAGAACAA 59.761 40.000 0.00 0.00 38.72 2.83
4287 4921 4.756642 CAGCTTTATGTTGTGAGGAGAACA 59.243 41.667 0.00 0.00 39.50 3.18
4288 4922 4.378874 GCAGCTTTATGTTGTGAGGAGAAC 60.379 45.833 0.00 0.00 0.00 3.01
4289 4923 3.753272 GCAGCTTTATGTTGTGAGGAGAA 59.247 43.478 0.00 0.00 0.00 2.87
4290 4924 3.244526 TGCAGCTTTATGTTGTGAGGAGA 60.245 43.478 0.00 0.00 0.00 3.71
4291 4925 3.076621 TGCAGCTTTATGTTGTGAGGAG 58.923 45.455 0.00 0.00 0.00 3.69
4292 4926 3.138884 TGCAGCTTTATGTTGTGAGGA 57.861 42.857 0.00 0.00 0.00 3.71
4326 5065 7.148306 ACAGTACTAGGAAATAAAAATGCACCG 60.148 37.037 0.00 0.00 0.00 4.94
4345 5087 3.814005 AACCGTTCTTGTCACAGTACT 57.186 42.857 0.00 0.00 0.00 2.73
4346 5088 3.619929 ACAAACCGTTCTTGTCACAGTAC 59.380 43.478 0.00 0.00 31.29 2.73
4348 5097 2.706890 ACAAACCGTTCTTGTCACAGT 58.293 42.857 0.00 0.00 31.29 3.55
4369 5133 6.530120 TCATACACTTCCTACACACAACAAT 58.470 36.000 0.00 0.00 0.00 2.71
5032 5816 7.679144 GCTTGCTCAAATTATTAAAAGGAAGC 58.321 34.615 17.32 17.32 46.01 3.86
5034 5818 9.206870 CAAGCTTGCTCAAATTATTAAAAGGAA 57.793 29.630 14.65 0.00 0.00 3.36
5042 5826 8.115490 ACTAAGACAAGCTTGCTCAAATTATT 57.885 30.769 26.27 10.74 37.42 1.40
5661 6499 0.795085 CAGTCTGCTGCTTAGTGTGC 59.205 55.000 0.00 0.00 35.77 4.57
5985 6856 2.686835 GGCAGGAGGCTCCTCAGT 60.687 66.667 33.04 10.45 45.66 3.41
6393 7264 2.281484 GGTGTTCTCCGCCTTGCA 60.281 61.111 0.00 0.00 40.81 4.08
6535 7412 4.409901 TGAATACTTCATCTCATGGCCTCA 59.590 41.667 3.32 0.00 34.08 3.86
6577 7455 2.501128 CATCACCGCCGATCACCT 59.499 61.111 0.00 0.00 0.00 4.00
6585 7463 0.741221 GTTCTCAGTCCATCACCGCC 60.741 60.000 0.00 0.00 0.00 6.13
6593 7471 3.054728 TCAAAACACCAGTTCTCAGTCCA 60.055 43.478 0.00 0.00 36.84 4.02
6622 7500 2.486592 GCAAAAACTAGGTACCACGCAT 59.513 45.455 15.94 0.00 0.00 4.73
6629 7507 2.222953 CCGCGATGCAAAAACTAGGTAC 60.223 50.000 8.23 0.00 0.00 3.34
6678 7556 7.065085 CAGTACAGTACATTTCAAATCTCCCAG 59.935 40.741 13.37 0.00 0.00 4.45
6760 7638 1.292061 TCGTTCCTCAACACCAAACG 58.708 50.000 0.00 0.00 42.87 3.60
6824 7702 7.495279 TGCTTGGAATCCATGTATTTAAAATGC 59.505 33.333 15.35 0.00 31.53 3.56
6845 7723 3.899052 ATGTCCCAATCCAAATGCTTG 57.101 42.857 0.00 0.00 0.00 4.01
6890 7770 3.763360 CACCAGCATAGAAATGTCCCAAA 59.237 43.478 0.00 0.00 35.38 3.28
6972 7852 2.550830 ACTCGCTTCTCACACCAATT 57.449 45.000 0.00 0.00 0.00 2.32
7002 7882 3.933332 CGTCACTTTCAAATAGAGGGTCC 59.067 47.826 0.00 0.00 0.00 4.46
7003 7883 3.933332 CCGTCACTTTCAAATAGAGGGTC 59.067 47.826 0.00 0.00 31.52 4.46
7007 7887 3.060895 GTCGCCGTCACTTTCAAATAGAG 59.939 47.826 0.00 0.00 0.00 2.43
7009 7889 2.222508 CGTCGCCGTCACTTTCAAATAG 60.223 50.000 0.00 0.00 0.00 1.73
7010 7890 1.722464 CGTCGCCGTCACTTTCAAATA 59.278 47.619 0.00 0.00 0.00 1.40
7011 7891 0.511221 CGTCGCCGTCACTTTCAAAT 59.489 50.000 0.00 0.00 0.00 2.32
7012 7892 0.528033 TCGTCGCCGTCACTTTCAAA 60.528 50.000 0.00 0.00 35.01 2.69
7013 7893 0.528033 TTCGTCGCCGTCACTTTCAA 60.528 50.000 0.00 0.00 35.01 2.69
7014 7894 1.066093 TTCGTCGCCGTCACTTTCA 59.934 52.632 0.00 0.00 35.01 2.69
7015 7895 1.485943 GTTCGTCGCCGTCACTTTC 59.514 57.895 0.00 0.00 35.01 2.62
7028 7908 4.295119 AAGCTGACGGCCGTTCGT 62.295 61.111 34.65 19.24 46.83 3.85
7030 7910 2.357034 TCAAGCTGACGGCCGTTC 60.357 61.111 34.65 24.51 43.05 3.95
7031 7911 2.665185 GTCAAGCTGACGGCCGTT 60.665 61.111 34.65 14.40 43.05 4.44
7073 7953 0.881159 TGGTTATTAATCGCCGCCCG 60.881 55.000 0.00 0.00 38.61 6.13
7074 7954 0.872388 CTGGTTATTAATCGCCGCCC 59.128 55.000 0.00 0.00 0.00 6.13
7075 7955 0.872388 CCTGGTTATTAATCGCCGCC 59.128 55.000 0.00 0.00 0.00 6.13
7076 7956 0.237498 GCCTGGTTATTAATCGCCGC 59.763 55.000 0.00 0.00 0.00 6.53
7077 7957 1.878953 AGCCTGGTTATTAATCGCCG 58.121 50.000 0.00 0.00 0.00 6.46
7079 7959 6.743575 ATCAATAGCCTGGTTATTAATCGC 57.256 37.500 14.39 0.00 0.00 4.58
7080 7960 8.567948 ACAAATCAATAGCCTGGTTATTAATCG 58.432 33.333 14.39 5.27 0.00 3.34
7085 7965 7.257722 CGAAACAAATCAATAGCCTGGTTATT 58.742 34.615 9.70 9.70 0.00 1.40
7086 7966 6.183360 CCGAAACAAATCAATAGCCTGGTTAT 60.183 38.462 0.00 0.00 0.00 1.89
7087 7967 5.124776 CCGAAACAAATCAATAGCCTGGTTA 59.875 40.000 0.00 0.00 0.00 2.85
7093 8056 5.554822 TGTACCGAAACAAATCAATAGCC 57.445 39.130 0.00 0.00 0.00 3.93
7099 8062 6.062434 ACGAAAATGTACCGAAACAAATCA 57.938 33.333 0.00 0.00 32.02 2.57
7808 8771 0.826256 ACCAGTACGTCCTGCTCACA 60.826 55.000 2.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.