Multiple sequence alignment - TraesCS4B01G172800

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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 TraesCS4B01G172800 chr4B 100.000 6351 0 0 1 6351 377786045 377792395 0.000000e+00 11729.0
1 TraesCS4B01G172800 chr4D 95.604 6164 151 39 1 6092 303061870 303067985 0.000000e+00 9771.0
2 TraesCS4B01G172800 chr4D 100.000 28 0 0 708 735 503522037 503522064 1.200000e-02 52.8
3 TraesCS4B01G172800 chr4A 94.857 6164 185 52 1 6087 176601934 176595826 0.000000e+00 9505.0
4 TraesCS4B01G172800 chr2D 78.122 1001 204 14 3855 4848 39828337 39829329 6.990000e-174 621.0
5 TraesCS4B01G172800 chr2D 77.667 1003 205 15 3855 4848 55371373 55370381 1.520000e-165 593.0
6 TraesCS4B01G172800 chr2B 78.010 1005 198 19 3855 4848 87845084 87844092 1.510000e-170 610.0
7 TraesCS4B01G172800 chr2A 77.888 1004 201 16 3855 4848 56920461 56919469 7.040000e-169 604.0


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 TraesCS4B01G172800 chr4B 377786045 377792395 6350 False 11729 11729 100.000 1 6351 1 chr4B.!!$F1 6350
1 TraesCS4B01G172800 chr4D 303061870 303067985 6115 False 9771 9771 95.604 1 6092 1 chr4D.!!$F1 6091
2 TraesCS4B01G172800 chr4A 176595826 176601934 6108 True 9505 9505 94.857 1 6087 1 chr4A.!!$R1 6086
3 TraesCS4B01G172800 chr2D 39828337 39829329 992 False 621 621 78.122 3855 4848 1 chr2D.!!$F1 993
4 TraesCS4B01G172800 chr2D 55370381 55371373 992 True 593 593 77.667 3855 4848 1 chr2D.!!$R1 993
5 TraesCS4B01G172800 chr2B 87844092 87845084 992 True 610 610 78.010 3855 4848 1 chr2B.!!$R1 993
6 TraesCS4B01G172800 chr2A 56919469 56920461 992 True 604 604 77.888 3855 4848 1 chr2A.!!$R1 993

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
183 185 1.734465 GTCACAAGGAGAAATGCCTCG 59.266 52.381 0.00 0.0 33.76 4.63 F
383 385 1.896220 AATTCGAAGTGCTGCAAGGA 58.104 45.000 2.77 0.0 0.00 3.36 F
1590 1637 0.315251 TGTGAACGCAGAGACAGAGG 59.685 55.000 0.00 0.0 0.00 3.69 F
1591 1638 0.315568 GTGAACGCAGAGACAGAGGT 59.684 55.000 0.00 0.0 0.00 3.85 F
1788 1843 0.391263 GCCTACTAGCACGCCTTGTT 60.391 55.000 0.00 0.0 31.89 2.83 F
1965 2020 2.005451 CATTTCTGCCACTCTTCCTCG 58.995 52.381 0.00 0.0 0.00 4.63 F
3850 3921 2.498167 ACTGAATGACACTTGACCTGC 58.502 47.619 0.00 0.0 0.00 4.85 F
4931 5004 6.037940 CCAATATTTCCAGCTATCATCATCCG 59.962 42.308 0.00 0.0 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1129 1162 0.614134 GTAGGGGACAAGAGGGACGT 60.614 60.000 0.00 0.0 0.00 4.34 R
1593 1640 1.142870 TGCAAAGCCACTAACCTGAGT 59.857 47.619 0.00 0.0 0.00 3.41 R
2893 2957 2.620115 ACACACCAGCATTTGTTCAGAG 59.380 45.455 0.00 0.0 0.00 3.35 R
3036 3100 2.684001 CCAATTAGTGGGTCAGCGTA 57.316 50.000 0.00 0.0 44.64 4.42 R
3638 3705 2.802719 ACCATGAAATGCTAAACGGGT 58.197 42.857 0.00 0.0 44.97 5.28 R
4232 4303 7.934855 AGATGTTCAATCAGCAAAAGAGTAT 57.065 32.000 0.00 0.0 0.00 2.12 R
5080 5154 0.309302 CTCGTAGTGAGGCCTCATCG 59.691 60.000 37.07 34.2 42.18 3.84 R
6296 6398 0.107897 TGCGTGCCTATTGTCCGAAT 60.108 50.000 0.00 0.0 0.00 3.34 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
59 60 2.314215 TAGCTCGGAGGTGGGAGGA 61.314 63.158 19.35 0.00 0.00 3.71
115 116 2.750637 GGTCGTCGCTCCTGGAGA 60.751 66.667 27.53 4.58 0.00 3.71
141 143 2.440147 CCCCACACCATCAGGCAA 59.560 61.111 0.00 0.00 39.06 4.52
172 174 2.333926 CTCGCATTAACGTCACAAGGA 58.666 47.619 0.00 0.00 0.00 3.36
183 185 1.734465 GTCACAAGGAGAAATGCCTCG 59.266 52.381 0.00 0.00 33.76 4.63
208 210 4.451150 CTTCCCTAGGCGCGCACA 62.451 66.667 34.42 18.66 0.00 4.57
242 244 2.985282 CCTCTGGCAGCGGCAAAA 60.985 61.111 11.12 0.00 43.71 2.44
312 314 3.526931 TGTCTCTCATCGGAAATGACC 57.473 47.619 0.00 0.00 0.00 4.02
383 385 1.896220 AATTCGAAGTGCTGCAAGGA 58.104 45.000 2.77 0.00 0.00 3.36
433 435 6.367983 AGCACCACTGATATCCATTACAATT 58.632 36.000 0.00 0.00 0.00 2.32
468 470 4.634012 TCCCTCCGTCCCATATTAATTG 57.366 45.455 0.00 0.00 0.00 2.32
471 473 4.003648 CCTCCGTCCCATATTAATTGAGC 58.996 47.826 0.00 0.00 0.00 4.26
477 479 4.457257 GTCCCATATTAATTGAGCCTGAGC 59.543 45.833 0.00 0.00 40.32 4.26
511 514 4.817517 AGACGTCAATTAATATAGGGCGG 58.182 43.478 19.50 0.00 0.00 6.13
514 517 5.801380 ACGTCAATTAATATAGGGCGGAAT 58.199 37.500 7.80 0.00 0.00 3.01
735 763 2.232452 CTCTTTCTCTTTCTCCCTGCGA 59.768 50.000 0.00 0.00 0.00 5.10
1129 1162 2.342279 CCGCCGGTGAGTTCTTCA 59.658 61.111 18.79 0.00 0.00 3.02
1146 1179 1.913762 CACGTCCCTCTTGTCCCCT 60.914 63.158 0.00 0.00 0.00 4.79
1279 1323 2.743636 TGTCCTTCTTACTTGAGCCG 57.256 50.000 0.00 0.00 0.00 5.52
1315 1359 1.403679 TGGTTGTTTGCTGCAGTGTAC 59.596 47.619 16.64 10.97 0.00 2.90
1545 1592 6.981559 GGTAGAAAGAGACAGGATTGTACATC 59.018 42.308 0.00 0.00 37.76 3.06
1588 1635 1.889170 AGATGTGAACGCAGAGACAGA 59.111 47.619 0.00 0.00 0.00 3.41
1589 1636 2.094803 AGATGTGAACGCAGAGACAGAG 60.095 50.000 0.00 0.00 0.00 3.35
1590 1637 0.315251 TGTGAACGCAGAGACAGAGG 59.685 55.000 0.00 0.00 0.00 3.69
1591 1638 0.315568 GTGAACGCAGAGACAGAGGT 59.684 55.000 0.00 0.00 0.00 3.85
1592 1639 1.040646 TGAACGCAGAGACAGAGGTT 58.959 50.000 0.00 0.00 0.00 3.50
1593 1640 2.030185 GTGAACGCAGAGACAGAGGTTA 60.030 50.000 0.00 0.00 0.00 2.85
1594 1641 2.030185 TGAACGCAGAGACAGAGGTTAC 60.030 50.000 0.00 0.00 0.00 2.50
1595 1642 1.912417 ACGCAGAGACAGAGGTTACT 58.088 50.000 0.00 0.00 0.00 2.24
1596 1643 1.813786 ACGCAGAGACAGAGGTTACTC 59.186 52.381 0.00 0.00 44.31 2.59
1788 1843 0.391263 GCCTACTAGCACGCCTTGTT 60.391 55.000 0.00 0.00 31.89 2.83
1941 1996 3.242549 TGCTTGCTCTACTCTCACATG 57.757 47.619 0.00 0.00 0.00 3.21
1965 2020 2.005451 CATTTCTGCCACTCTTCCTCG 58.995 52.381 0.00 0.00 0.00 4.63
2154 2210 4.206375 TGAAGCAGACCAAATTGAGTTGA 58.794 39.130 0.00 0.00 0.00 3.18
2161 2217 4.949856 AGACCAAATTGAGTTGAACAGTGT 59.050 37.500 0.00 0.00 0.00 3.55
2162 2218 5.418840 AGACCAAATTGAGTTGAACAGTGTT 59.581 36.000 8.61 8.61 0.00 3.32
2163 2219 6.036577 ACCAAATTGAGTTGAACAGTGTTT 57.963 33.333 10.45 0.00 0.00 2.83
2164 2220 6.463360 ACCAAATTGAGTTGAACAGTGTTTT 58.537 32.000 10.45 0.00 0.00 2.43
2281 2337 5.911280 CGCATACAGAAATAATTCAAGCCAG 59.089 40.000 0.00 0.00 38.06 4.85
2499 2555 7.967854 CGTTACAGCTTTGGATAATTTGAATCA 59.032 33.333 0.00 0.00 0.00 2.57
2521 2577 8.682936 ATCATTGATGTGTTATCCTTTACTCC 57.317 34.615 0.00 0.00 0.00 3.85
2537 2593 6.717084 CCTTTACTCCTTTTTCTTCAGGATGT 59.283 38.462 0.00 0.00 38.58 3.06
2985 3049 4.078363 GCAATGTATGCGTTTGTAGTGT 57.922 40.909 0.00 0.00 46.87 3.55
2986 3050 3.845775 GCAATGTATGCGTTTGTAGTGTG 59.154 43.478 0.00 0.00 46.87 3.82
2998 3062 5.228665 GTTTGTAGTGTGTCTTCTCTACCC 58.771 45.833 0.00 0.00 35.11 3.69
3036 3100 6.061441 TGATGTACTCATGTTTCAGTTGGTT 58.939 36.000 0.00 0.00 34.06 3.67
3038 3102 6.854496 TGTACTCATGTTTCAGTTGGTTAC 57.146 37.500 0.00 0.00 0.00 2.50
3557 3624 6.885918 TGAAGCAGAATATCCAAGAACATGAA 59.114 34.615 0.00 0.00 0.00 2.57
3638 3705 4.142622 CGGCATGCTTGTTATTCTTCTTGA 60.143 41.667 18.92 0.00 0.00 3.02
3850 3921 2.498167 ACTGAATGACACTTGACCTGC 58.502 47.619 0.00 0.00 0.00 4.85
4432 4505 8.594881 AACTACGAGCATATTATTTTGGAGAG 57.405 34.615 0.00 0.00 0.00 3.20
4442 4515 8.636213 CATATTATTTTGGAGAGTTTGCCAGAT 58.364 33.333 0.00 0.00 35.23 2.90
4903 4976 9.320406 CTAAAGCATGCATTGTATTTTGTTTTG 57.680 29.630 21.98 4.29 0.00 2.44
4921 4994 7.531857 TGTTTTGTTCCAATATTTCCAGCTA 57.468 32.000 0.00 0.00 0.00 3.32
4922 4995 8.133024 TGTTTTGTTCCAATATTTCCAGCTAT 57.867 30.769 0.00 0.00 0.00 2.97
4931 5004 6.037940 CCAATATTTCCAGCTATCATCATCCG 59.962 42.308 0.00 0.00 0.00 4.18
4958 5031 8.151141 ACTTGATATAGTGAGCAATTGTGATG 57.849 34.615 7.40 0.00 0.00 3.07
5038 5112 8.284945 TCTTGCATGAAGTGATTAGCTTATTT 57.715 30.769 0.00 0.00 32.90 1.40
5039 5113 9.394767 TCTTGCATGAAGTGATTAGCTTATTTA 57.605 29.630 0.00 0.00 32.90 1.40
5040 5114 9.661187 CTTGCATGAAGTGATTAGCTTATTTAG 57.339 33.333 0.00 0.00 0.00 1.85
5080 5154 6.103997 TCTATTACAGTTCCGGAACAATGAC 58.896 40.000 40.66 20.43 43.47 3.06
5179 5253 3.589288 AGAGGTTGACTTTATCTGGGCTT 59.411 43.478 0.00 0.00 0.00 4.35
5360 5434 7.012327 GCAATGTAAGTCCATAGCATACTTTGA 59.988 37.037 11.62 0.00 35.40 2.69
5361 5435 8.892723 CAATGTAAGTCCATAGCATACTTTGAA 58.107 33.333 0.00 0.00 35.40 2.69
5362 5436 7.843490 TGTAAGTCCATAGCATACTTTGAAC 57.157 36.000 0.00 0.00 35.23 3.18
5363 5437 6.821665 TGTAAGTCCATAGCATACTTTGAACC 59.178 38.462 0.00 0.00 35.23 3.62
5364 5438 5.700402 AGTCCATAGCATACTTTGAACCT 57.300 39.130 0.00 0.00 0.00 3.50
5365 5439 5.431765 AGTCCATAGCATACTTTGAACCTG 58.568 41.667 0.00 0.00 0.00 4.00
5397 5471 5.407407 AGATTTGACTGACGGTAGATTGT 57.593 39.130 0.00 0.00 0.00 2.71
5430 5504 6.611785 ACTGCTGTACTATATACCAAGAGGA 58.388 40.000 0.00 0.00 38.69 3.71
5434 5508 7.014326 TGCTGTACTATATACCAAGAGGACAAG 59.986 40.741 0.00 0.00 38.69 3.16
5435 5509 7.286215 TGTACTATATACCAAGAGGACAAGC 57.714 40.000 0.00 0.00 38.69 4.01
5436 5510 6.837048 TGTACTATATACCAAGAGGACAAGCA 59.163 38.462 0.00 0.00 38.69 3.91
5437 5511 6.163135 ACTATATACCAAGAGGACAAGCAC 57.837 41.667 0.00 0.00 38.69 4.40
5438 5512 5.900123 ACTATATACCAAGAGGACAAGCACT 59.100 40.000 0.00 0.00 38.69 4.40
5440 5514 1.972872 ACCAAGAGGACAAGCACTTG 58.027 50.000 8.82 8.82 41.43 3.16
5536 5611 5.692115 TGAATTAGTGAGCTTGATGGGTA 57.308 39.130 0.00 0.00 0.00 3.69
5663 5739 4.767928 GTCATCTAGATTACGGGACAGGAT 59.232 45.833 1.33 0.00 0.00 3.24
5664 5740 5.244178 GTCATCTAGATTACGGGACAGGATT 59.756 44.000 1.33 0.00 0.00 3.01
5665 5741 5.243954 TCATCTAGATTACGGGACAGGATTG 59.756 44.000 1.33 0.00 0.00 2.67
5666 5742 4.543689 TCTAGATTACGGGACAGGATTGT 58.456 43.478 0.00 0.00 41.18 2.71
5852 5928 2.234300 TGTCAGAAACTTGTCGGTCC 57.766 50.000 0.00 0.00 0.00 4.46
5921 6019 4.853924 AATGTGAAATGGGTGTGTTCTC 57.146 40.909 0.00 0.00 0.00 2.87
6045 6146 3.241963 CGTTGGTACACGATGTGCTAATG 60.242 47.826 0.00 8.35 36.11 1.90
6092 6194 5.064834 TGCCGAAATATTTACATGTACGCAA 59.935 36.000 4.68 0.00 0.00 4.85
6093 6195 6.140110 GCCGAAATATTTACATGTACGCAAT 58.860 36.000 4.68 5.83 0.00 3.56
6094 6196 7.041984 TGCCGAAATATTTACATGTACGCAATA 60.042 33.333 4.68 7.89 0.00 1.90
6095 6197 7.267600 GCCGAAATATTTACATGTACGCAATAC 59.732 37.037 4.68 0.00 0.00 1.89
6113 6215 8.609478 CGCAATACGGTATTTGAAAATAAAGT 57.391 30.769 10.59 4.12 38.44 2.66
6114 6216 9.705471 CGCAATACGGTATTTGAAAATAAAGTA 57.295 29.630 10.59 11.03 38.44 2.24
6119 6221 7.967178 ACGGTATTTGAAAATAAAGTAGTCGG 58.033 34.615 0.00 0.00 33.05 4.79
6120 6222 7.603784 ACGGTATTTGAAAATAAAGTAGTCGGT 59.396 33.333 0.00 0.00 33.05 4.69
6121 6223 7.901377 CGGTATTTGAAAATAAAGTAGTCGGTG 59.099 37.037 0.00 0.00 33.05 4.94
6122 6224 8.938906 GGTATTTGAAAATAAAGTAGTCGGTGA 58.061 33.333 0.00 0.00 33.05 4.02
6125 6227 8.842358 TTTGAAAATAAAGTAGTCGGTGATCT 57.158 30.769 0.00 0.00 0.00 2.75
6126 6228 7.827819 TGAAAATAAAGTAGTCGGTGATCTG 57.172 36.000 0.00 0.00 0.00 2.90
6127 6229 6.816640 TGAAAATAAAGTAGTCGGTGATCTGG 59.183 38.462 0.00 0.00 0.00 3.86
6128 6230 2.674796 AAAGTAGTCGGTGATCTGGC 57.325 50.000 0.00 0.00 0.00 4.85
6129 6231 0.456221 AAGTAGTCGGTGATCTGGCG 59.544 55.000 0.00 0.00 0.00 5.69
6130 6232 1.065928 GTAGTCGGTGATCTGGCGG 59.934 63.158 0.00 0.00 0.00 6.13
6131 6233 1.077285 TAGTCGGTGATCTGGCGGA 60.077 57.895 0.00 0.00 0.00 5.54
6132 6234 1.381928 TAGTCGGTGATCTGGCGGAC 61.382 60.000 0.00 11.92 35.89 4.79
6133 6235 2.678580 TCGGTGATCTGGCGGACA 60.679 61.111 0.00 0.00 0.00 4.02
6134 6236 2.058001 TCGGTGATCTGGCGGACAT 61.058 57.895 0.00 0.00 0.00 3.06
6135 6237 1.884464 CGGTGATCTGGCGGACATG 60.884 63.158 0.00 0.00 0.00 3.21
6136 6238 1.221840 GGTGATCTGGCGGACATGT 59.778 57.895 0.00 0.00 0.00 3.21
6137 6239 0.392998 GGTGATCTGGCGGACATGTT 60.393 55.000 0.00 0.00 0.00 2.71
6138 6240 1.134521 GGTGATCTGGCGGACATGTTA 60.135 52.381 0.00 0.00 0.00 2.41
6139 6241 1.933853 GTGATCTGGCGGACATGTTAC 59.066 52.381 0.00 0.00 0.00 2.50
6140 6242 1.209128 GATCTGGCGGACATGTTACG 58.791 55.000 16.57 16.57 0.00 3.18
6146 6248 3.116073 CGGACATGTTACGCACTGA 57.884 52.632 0.00 0.00 0.00 3.41
6147 6249 0.713883 CGGACATGTTACGCACTGAC 59.286 55.000 0.00 0.00 0.00 3.51
6148 6250 1.790755 GGACATGTTACGCACTGACA 58.209 50.000 0.00 0.00 0.00 3.58
6149 6251 1.459592 GGACATGTTACGCACTGACAC 59.540 52.381 0.00 0.00 0.00 3.67
6150 6252 1.459592 GACATGTTACGCACTGACACC 59.540 52.381 0.00 0.00 0.00 4.16
6151 6253 0.796312 CATGTTACGCACTGACACCC 59.204 55.000 0.00 0.00 0.00 4.61
6152 6254 0.394938 ATGTTACGCACTGACACCCA 59.605 50.000 0.00 0.00 0.00 4.51
6153 6255 0.178301 TGTTACGCACTGACACCCAA 59.822 50.000 0.00 0.00 0.00 4.12
6154 6256 1.301423 GTTACGCACTGACACCCAAA 58.699 50.000 0.00 0.00 0.00 3.28
6155 6257 1.263217 GTTACGCACTGACACCCAAAG 59.737 52.381 0.00 0.00 0.00 2.77
6156 6258 0.250124 TACGCACTGACACCCAAAGG 60.250 55.000 0.00 0.00 40.04 3.11
6157 6259 2.908073 CGCACTGACACCCAAAGGC 61.908 63.158 0.00 0.00 36.11 4.35
6158 6260 2.564721 GCACTGACACCCAAAGGCC 61.565 63.158 0.00 0.00 36.11 5.19
6159 6261 1.903404 CACTGACACCCAAAGGCCC 60.903 63.158 0.00 0.00 36.11 5.80
6160 6262 2.672996 CTGACACCCAAAGGCCCG 60.673 66.667 0.00 0.00 36.11 6.13
6161 6263 4.278513 TGACACCCAAAGGCCCGG 62.279 66.667 0.00 0.00 36.11 5.73
6175 6277 4.113815 CCGGCAGGGCATCCTCAA 62.114 66.667 0.00 0.00 42.67 3.02
6176 6278 2.515523 CGGCAGGGCATCCTCAAG 60.516 66.667 0.00 0.00 42.67 3.02
6177 6279 2.123982 GGCAGGGCATCCTCAAGG 60.124 66.667 0.00 0.00 42.67 3.61
6178 6280 2.832201 GCAGGGCATCCTCAAGGC 60.832 66.667 0.00 0.00 42.67 4.35
6179 6281 2.515523 CAGGGCATCCTCAAGGCG 60.516 66.667 0.00 0.00 42.67 5.52
6180 6282 3.801997 AGGGCATCCTCAAGGCGG 61.802 66.667 0.00 0.00 39.80 6.13
6181 6283 3.797353 GGGCATCCTCAAGGCGGA 61.797 66.667 0.00 0.00 34.44 5.54
6182 6284 2.512896 GGCATCCTCAAGGCGGAT 59.487 61.111 0.00 0.00 41.88 4.18
6183 6285 1.599240 GGCATCCTCAAGGCGGATC 60.599 63.158 0.00 0.00 39.20 3.36
6184 6286 1.599240 GCATCCTCAAGGCGGATCC 60.599 63.158 0.00 0.00 39.20 3.36
6185 6287 1.072159 CATCCTCAAGGCGGATCCC 59.928 63.158 6.06 0.00 39.20 3.85
6199 6301 4.579454 CGGATCCCGTAAATTAGAGACA 57.421 45.455 6.06 0.00 42.73 3.41
6200 6302 4.940463 CGGATCCCGTAAATTAGAGACAA 58.060 43.478 6.06 0.00 42.73 3.18
6201 6303 4.982916 CGGATCCCGTAAATTAGAGACAAG 59.017 45.833 6.06 0.00 42.73 3.16
6202 6304 5.451520 CGGATCCCGTAAATTAGAGACAAGT 60.452 44.000 6.06 0.00 42.73 3.16
6203 6305 6.238842 CGGATCCCGTAAATTAGAGACAAGTA 60.239 42.308 6.06 0.00 42.73 2.24
6204 6306 7.523380 CGGATCCCGTAAATTAGAGACAAGTAT 60.523 40.741 6.06 0.00 42.73 2.12
6205 6307 8.800332 GGATCCCGTAAATTAGAGACAAGTATA 58.200 37.037 0.00 0.00 0.00 1.47
6208 6310 8.636213 TCCCGTAAATTAGAGACAAGTATAAGG 58.364 37.037 0.00 0.00 0.00 2.69
6209 6311 8.636213 CCCGTAAATTAGAGACAAGTATAAGGA 58.364 37.037 0.00 0.00 0.00 3.36
6210 6312 9.680315 CCGTAAATTAGAGACAAGTATAAGGAG 57.320 37.037 0.00 0.00 0.00 3.69
6211 6313 9.182933 CGTAAATTAGAGACAAGTATAAGGAGC 57.817 37.037 0.00 0.00 0.00 4.70
6217 6319 7.114866 AGAGACAAGTATAAGGAGCTTTACC 57.885 40.000 0.00 0.00 0.00 2.85
6218 6320 5.903810 AGACAAGTATAAGGAGCTTTACCG 58.096 41.667 0.00 0.00 0.00 4.02
6219 6321 5.421374 AGACAAGTATAAGGAGCTTTACCGT 59.579 40.000 0.00 0.00 0.00 4.83
6220 6322 6.604795 AGACAAGTATAAGGAGCTTTACCGTA 59.395 38.462 0.00 0.00 0.00 4.02
6221 6323 7.123247 AGACAAGTATAAGGAGCTTTACCGTAA 59.877 37.037 0.00 0.00 0.00 3.18
6222 6324 7.789026 ACAAGTATAAGGAGCTTTACCGTAAT 58.211 34.615 0.00 0.00 0.00 1.89
6223 6325 7.924947 ACAAGTATAAGGAGCTTTACCGTAATC 59.075 37.037 0.00 0.00 0.00 1.75
6224 6326 6.990798 AGTATAAGGAGCTTTACCGTAATCC 58.009 40.000 0.00 2.34 0.00 3.01
6225 6327 2.884894 AGGAGCTTTACCGTAATCCG 57.115 50.000 0.00 0.00 31.97 4.18
6238 6340 3.040795 CGTAATCCGGACAATAGACACG 58.959 50.000 6.12 3.94 0.00 4.49
6239 6341 1.935933 AATCCGGACAATAGACACGC 58.064 50.000 6.12 0.00 0.00 5.34
6240 6342 0.821517 ATCCGGACAATAGACACGCA 59.178 50.000 6.12 0.00 0.00 5.24
6241 6343 0.172578 TCCGGACAATAGACACGCAG 59.827 55.000 0.00 0.00 0.00 5.18
6242 6344 0.172578 CCGGACAATAGACACGCAGA 59.827 55.000 0.00 0.00 0.00 4.26
6243 6345 1.202417 CCGGACAATAGACACGCAGAT 60.202 52.381 0.00 0.00 0.00 2.90
6244 6346 2.120232 CGGACAATAGACACGCAGATC 58.880 52.381 0.00 0.00 0.00 2.75
6245 6347 2.223595 CGGACAATAGACACGCAGATCT 60.224 50.000 0.00 0.00 0.00 2.75
6246 6348 3.376540 GGACAATAGACACGCAGATCTC 58.623 50.000 0.00 0.00 0.00 2.75
6247 6349 3.039405 GACAATAGACACGCAGATCTCG 58.961 50.000 11.44 11.44 0.00 4.04
6248 6350 2.423892 ACAATAGACACGCAGATCTCGT 59.576 45.455 12.51 12.51 41.28 4.18
6249 6351 3.626217 ACAATAGACACGCAGATCTCGTA 59.374 43.478 16.31 5.52 38.19 3.43
6250 6352 4.095932 ACAATAGACACGCAGATCTCGTAA 59.904 41.667 16.31 6.73 38.19 3.18
6251 6353 4.895224 ATAGACACGCAGATCTCGTAAA 57.105 40.909 16.31 6.48 38.19 2.01
6252 6354 2.864968 AGACACGCAGATCTCGTAAAC 58.135 47.619 16.31 11.78 38.19 2.01
6253 6355 2.488545 AGACACGCAGATCTCGTAAACT 59.511 45.455 16.31 13.20 38.19 2.66
6254 6356 3.688185 AGACACGCAGATCTCGTAAACTA 59.312 43.478 16.31 0.00 38.19 2.24
6255 6357 4.017380 ACACGCAGATCTCGTAAACTAG 57.983 45.455 16.31 8.52 38.19 2.57
6256 6358 3.688185 ACACGCAGATCTCGTAAACTAGA 59.312 43.478 16.31 0.00 38.19 2.43
6257 6359 4.201832 ACACGCAGATCTCGTAAACTAGAG 60.202 45.833 16.31 7.47 38.19 2.43
6258 6360 4.034163 CACGCAGATCTCGTAAACTAGAGA 59.966 45.833 16.31 0.00 46.09 3.10
6259 6361 4.034279 ACGCAGATCTCGTAAACTAGAGAC 59.966 45.833 15.52 0.00 45.03 3.36
6260 6362 4.034163 CGCAGATCTCGTAAACTAGAGACA 59.966 45.833 0.00 0.00 45.03 3.41
6261 6363 5.447413 CGCAGATCTCGTAAACTAGAGACAA 60.447 44.000 0.00 0.00 45.03 3.18
6262 6364 6.323266 GCAGATCTCGTAAACTAGAGACAAA 58.677 40.000 0.00 0.00 45.03 2.83
6263 6365 6.975772 GCAGATCTCGTAAACTAGAGACAAAT 59.024 38.462 0.00 0.00 45.03 2.32
6264 6366 8.129840 GCAGATCTCGTAAACTAGAGACAAATA 58.870 37.037 0.00 0.00 45.03 1.40
6269 6371 9.064706 TCTCGTAAACTAGAGACAAATATAGGG 57.935 37.037 0.00 0.00 38.46 3.53
6270 6372 8.985315 TCGTAAACTAGAGACAAATATAGGGA 57.015 34.615 0.00 0.00 0.00 4.20
6271 6373 9.064706 TCGTAAACTAGAGACAAATATAGGGAG 57.935 37.037 0.00 0.00 0.00 4.30
6272 6374 9.064706 CGTAAACTAGAGACAAATATAGGGAGA 57.935 37.037 0.00 0.00 0.00 3.71
6274 6376 8.840200 AAACTAGAGACAAATATAGGGAGACA 57.160 34.615 0.00 0.00 0.00 3.41
6275 6377 8.840200 AACTAGAGACAAATATAGGGAGACAA 57.160 34.615 0.00 0.00 0.00 3.18
6276 6378 8.840200 ACTAGAGACAAATATAGGGAGACAAA 57.160 34.615 0.00 0.00 0.00 2.83
6277 6379 9.440761 ACTAGAGACAAATATAGGGAGACAAAT 57.559 33.333 0.00 0.00 0.00 2.32
6289 6391 8.743636 ATAGGGAGACAAATATAGGTAGCTTT 57.256 34.615 0.00 0.00 0.00 3.51
6290 6392 9.839185 ATAGGGAGACAAATATAGGTAGCTTTA 57.161 33.333 0.00 0.00 0.00 1.85
6291 6393 7.964624 AGGGAGACAAATATAGGTAGCTTTAC 58.035 38.462 0.00 0.00 0.00 2.01
6292 6394 6.867293 GGGAGACAAATATAGGTAGCTTTACG 59.133 42.308 0.00 0.00 0.00 3.18
6293 6395 6.867293 GGAGACAAATATAGGTAGCTTTACGG 59.133 42.308 0.00 0.00 0.00 4.02
6294 6396 6.756221 AGACAAATATAGGTAGCTTTACGGG 58.244 40.000 0.00 0.00 0.00 5.28
6295 6397 6.552350 AGACAAATATAGGTAGCTTTACGGGA 59.448 38.462 0.00 0.00 0.00 5.14
6296 6398 7.070322 AGACAAATATAGGTAGCTTTACGGGAA 59.930 37.037 0.00 0.00 0.00 3.97
6297 6399 7.742767 ACAAATATAGGTAGCTTTACGGGAAT 58.257 34.615 0.00 0.00 0.00 3.01
6298 6400 8.215736 ACAAATATAGGTAGCTTTACGGGAATT 58.784 33.333 0.00 0.00 0.00 2.17
6299 6401 8.718734 CAAATATAGGTAGCTTTACGGGAATTC 58.281 37.037 0.00 0.00 0.00 2.17
6300 6402 3.175109 AGGTAGCTTTACGGGAATTCG 57.825 47.619 0.00 0.00 0.00 3.34
6301 6403 2.159000 AGGTAGCTTTACGGGAATTCGG 60.159 50.000 0.00 0.00 0.00 4.30
6302 6404 2.159057 GGTAGCTTTACGGGAATTCGGA 60.159 50.000 0.00 0.00 0.00 4.55
6303 6405 2.019948 AGCTTTACGGGAATTCGGAC 57.980 50.000 0.00 0.00 0.00 4.79
6304 6406 1.276989 AGCTTTACGGGAATTCGGACA 59.723 47.619 0.00 0.00 0.00 4.02
6305 6407 2.078392 GCTTTACGGGAATTCGGACAA 58.922 47.619 0.00 0.00 0.00 3.18
6306 6408 2.681344 GCTTTACGGGAATTCGGACAAT 59.319 45.455 0.00 0.00 0.00 2.71
6307 6409 3.872771 GCTTTACGGGAATTCGGACAATA 59.127 43.478 0.00 0.00 0.00 1.90
6308 6410 4.025145 GCTTTACGGGAATTCGGACAATAG 60.025 45.833 0.00 0.00 0.00 1.73
6309 6411 2.614829 ACGGGAATTCGGACAATAGG 57.385 50.000 0.00 0.00 0.00 2.57
6310 6412 1.226746 CGGGAATTCGGACAATAGGC 58.773 55.000 0.00 0.00 0.00 3.93
6311 6413 1.474320 CGGGAATTCGGACAATAGGCA 60.474 52.381 0.00 0.00 0.00 4.75
6312 6414 1.947456 GGGAATTCGGACAATAGGCAC 59.053 52.381 0.00 0.00 0.00 5.01
6313 6415 1.597663 GGAATTCGGACAATAGGCACG 59.402 52.381 0.00 0.00 0.00 5.34
6314 6416 1.003866 GAATTCGGACAATAGGCACGC 60.004 52.381 0.00 0.00 0.00 5.34
6315 6417 0.107897 ATTCGGACAATAGGCACGCA 60.108 50.000 0.00 0.00 0.00 5.24
6316 6418 0.739462 TTCGGACAATAGGCACGCAG 60.739 55.000 0.00 0.00 0.00 5.18
6317 6419 2.173669 CGGACAATAGGCACGCAGG 61.174 63.158 0.00 0.00 0.00 4.85
6318 6420 1.220749 GGACAATAGGCACGCAGGA 59.779 57.895 0.00 0.00 0.00 3.86
6319 6421 1.090052 GGACAATAGGCACGCAGGAC 61.090 60.000 0.00 0.00 0.00 3.85
6320 6422 0.108138 GACAATAGGCACGCAGGACT 60.108 55.000 0.00 0.00 0.00 3.85
6321 6423 0.108138 ACAATAGGCACGCAGGACTC 60.108 55.000 0.00 0.00 0.00 3.36
6322 6424 0.811616 CAATAGGCACGCAGGACTCC 60.812 60.000 0.00 0.00 0.00 3.85
6323 6425 2.298158 AATAGGCACGCAGGACTCCG 62.298 60.000 0.00 0.00 0.00 4.63
6324 6426 3.931190 TAGGCACGCAGGACTCCGA 62.931 63.158 0.00 0.00 0.00 4.55
6325 6427 4.148825 GGCACGCAGGACTCCGAT 62.149 66.667 0.00 0.00 0.00 4.18
6326 6428 2.782222 GGCACGCAGGACTCCGATA 61.782 63.158 0.00 0.00 0.00 2.92
6327 6429 1.589196 GCACGCAGGACTCCGATAC 60.589 63.158 0.00 0.00 0.00 2.24
6328 6430 1.065928 CACGCAGGACTCCGATACC 59.934 63.158 0.00 0.00 0.00 2.73
6329 6431 2.125961 ACGCAGGACTCCGATACCC 61.126 63.158 0.00 0.00 0.00 3.69
6330 6432 1.828660 CGCAGGACTCCGATACCCT 60.829 63.158 0.00 0.00 0.00 4.34
6331 6433 1.742768 GCAGGACTCCGATACCCTG 59.257 63.158 0.00 0.00 46.67 4.45
6332 6434 1.749334 GCAGGACTCCGATACCCTGG 61.749 65.000 0.00 0.00 44.70 4.45
6333 6435 0.397254 CAGGACTCCGATACCCTGGT 60.397 60.000 0.00 0.00 41.76 4.00
6334 6436 0.338814 AGGACTCCGATACCCTGGTT 59.661 55.000 0.00 0.00 0.00 3.67
6335 6437 0.751452 GGACTCCGATACCCTGGTTC 59.249 60.000 0.00 0.00 0.00 3.62
6336 6438 1.481871 GACTCCGATACCCTGGTTCA 58.518 55.000 0.00 0.00 0.00 3.18
6337 6439 1.136500 GACTCCGATACCCTGGTTCAC 59.864 57.143 0.00 0.00 0.00 3.18
6338 6440 0.464452 CTCCGATACCCTGGTTCACC 59.536 60.000 0.00 0.00 0.00 4.02
6339 6441 0.979187 TCCGATACCCTGGTTCACCC 60.979 60.000 0.00 0.00 34.29 4.61
6340 6442 1.268992 CCGATACCCTGGTTCACCCA 61.269 60.000 0.00 0.00 42.51 4.51
6341 6443 0.616371 CGATACCCTGGTTCACCCAA 59.384 55.000 0.00 0.00 44.65 4.12
6342 6444 1.003812 CGATACCCTGGTTCACCCAAA 59.996 52.381 0.00 0.00 44.65 3.28
6343 6445 2.553466 CGATACCCTGGTTCACCCAAAA 60.553 50.000 0.00 0.00 44.65 2.44
6344 6446 3.502356 GATACCCTGGTTCACCCAAAAA 58.498 45.455 0.00 0.00 44.65 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.199946 GGTGACAACTATGGGAGGATGAA 59.800 47.826 0.00 0.00 0.00 2.57
20 21 1.762957 CGGTGACAACTATGGGAGGAT 59.237 52.381 0.00 0.00 0.00 3.24
59 60 2.987547 TCCTCGTCTCCGGCGTTT 60.988 61.111 6.01 0.00 33.95 3.60
96 97 4.361971 TCCAGGAGCGACGACCCT 62.362 66.667 0.00 0.07 0.00 4.34
115 116 3.809013 GGTGTGGGGCGGGATCAT 61.809 66.667 0.00 0.00 0.00 2.45
172 174 1.675641 GTGGTGGCGAGGCATTTCT 60.676 57.895 1.94 0.00 0.00 2.52
183 185 2.998949 CCTAGGGAAGGTGGTGGC 59.001 66.667 0.00 0.00 40.94 5.01
208 210 1.301479 GGGAACAACGACGAAGGCT 60.301 57.895 0.00 0.00 0.00 4.58
219 221 2.032528 CGCTGCCAGAGGGAACAA 59.967 61.111 0.00 0.00 36.74 2.83
239 241 1.855451 ACCCCAGATCCCCCGTTTT 60.855 57.895 0.00 0.00 0.00 2.43
241 243 2.691252 GACCCCAGATCCCCCGTT 60.691 66.667 0.00 0.00 0.00 4.44
242 244 4.019513 TGACCCCAGATCCCCCGT 62.020 66.667 0.00 0.00 0.00 5.28
249 251 3.402681 CCGCCAGTGACCCCAGAT 61.403 66.667 0.00 0.00 0.00 2.90
312 314 6.986231 AGAAATTTAAAACTCTTTGGGTGCAG 59.014 34.615 0.00 0.00 0.00 4.41
343 345 8.450964 CGAATTAGTTCCAGCATCTTTCTTTTA 58.549 33.333 0.00 0.00 0.00 1.52
356 358 3.181516 GCAGCACTTCGAATTAGTTCCAG 60.182 47.826 0.00 0.00 0.00 3.86
368 370 0.725686 CTCATCCTTGCAGCACTTCG 59.274 55.000 0.00 0.00 0.00 3.79
427 429 7.553760 GGAGGGAATAAAACTTACCGAATTGTA 59.446 37.037 0.00 0.00 33.98 2.41
433 435 3.515104 ACGGAGGGAATAAAACTTACCGA 59.485 43.478 0.00 0.00 40.78 4.69
471 473 3.190327 CGTCTAGATACATCCAGCTCAGG 59.810 52.174 0.00 0.00 0.00 3.86
514 517 9.929722 CGATTTTGCTATGCTGTTTATTACTTA 57.070 29.630 0.00 0.00 0.00 2.24
1129 1162 0.614134 GTAGGGGACAAGAGGGACGT 60.614 60.000 0.00 0.00 0.00 4.34
1279 1323 7.408910 CAAACAACCAAACCAATCAGAAAATC 58.591 34.615 0.00 0.00 0.00 2.17
1588 1635 2.903926 AGCCACTAACCTGAGTAACCT 58.096 47.619 0.00 0.00 0.00 3.50
1589 1636 3.697619 AAGCCACTAACCTGAGTAACC 57.302 47.619 0.00 0.00 0.00 2.85
1590 1637 3.188667 GCAAAGCCACTAACCTGAGTAAC 59.811 47.826 0.00 0.00 0.00 2.50
1591 1638 3.181449 TGCAAAGCCACTAACCTGAGTAA 60.181 43.478 0.00 0.00 0.00 2.24
1592 1639 2.370519 TGCAAAGCCACTAACCTGAGTA 59.629 45.455 0.00 0.00 0.00 2.59
1593 1640 1.142870 TGCAAAGCCACTAACCTGAGT 59.857 47.619 0.00 0.00 0.00 3.41
1594 1641 1.896220 TGCAAAGCCACTAACCTGAG 58.104 50.000 0.00 0.00 0.00 3.35
1595 1642 2.584835 ATGCAAAGCCACTAACCTGA 57.415 45.000 0.00 0.00 0.00 3.86
1596 1643 3.665745 AAATGCAAAGCCACTAACCTG 57.334 42.857 0.00 0.00 0.00 4.00
1633 1685 6.524734 AGATGCGGTTATATGAGTTCATCAA 58.475 36.000 0.00 0.00 42.53 2.57
1780 1832 6.963049 ACTGTATCTTTTAGTAACAAGGCG 57.037 37.500 5.53 0.00 0.00 5.52
1941 1996 3.006247 GGAAGAGTGGCAGAAATGACTC 58.994 50.000 0.00 0.00 35.97 3.36
1965 2020 7.493971 AGTCTGAAACATGCTGATAGACAATAC 59.506 37.037 15.52 0.00 36.45 1.89
2026 2081 5.775701 CCTTTTAGCATAGGCCTAGACTAGA 59.224 44.000 19.33 13.61 42.56 2.43
2032 2087 6.547510 ACAATTTCCTTTTAGCATAGGCCTAG 59.452 38.462 19.33 11.31 42.56 3.02
2098 2153 7.309194 CCATATACTTCATGATACAGTCGGTCA 60.309 40.741 1.79 0.00 0.00 4.02
2102 2157 6.071334 ACCCCATATACTTCATGATACAGTCG 60.071 42.308 1.79 0.00 0.00 4.18
2171 2227 4.798574 CACCATGTTTCTTTAAGCTGACC 58.201 43.478 0.00 0.00 0.00 4.02
2281 2337 4.367450 TGGTTTGTAGCTGTTTGAATTGC 58.633 39.130 0.00 0.00 0.00 3.56
2499 2555 9.533831 AAAAGGAGTAAAGGATAACACATCAAT 57.466 29.630 0.00 0.00 0.00 2.57
2521 2577 3.558505 CGTGCACATCCTGAAGAAAAAG 58.441 45.455 18.64 0.00 0.00 2.27
2616 2672 6.935741 AACTTTATGTAACAGTGTTGCAGA 57.064 33.333 27.06 21.93 0.00 4.26
2893 2957 2.620115 ACACACCAGCATTTGTTCAGAG 59.380 45.455 0.00 0.00 0.00 3.35
2985 3049 4.237976 AGAGAATCGGGTAGAGAAGACA 57.762 45.455 0.00 0.00 42.67 3.41
2986 3050 4.885325 AGAAGAGAATCGGGTAGAGAAGAC 59.115 45.833 0.00 0.00 42.67 3.01
2998 3062 6.733145 TGAGTACATCATGAGAAGAGAATCG 58.267 40.000 0.09 0.00 34.05 3.34
3036 3100 2.684001 CCAATTAGTGGGTCAGCGTA 57.316 50.000 0.00 0.00 44.64 4.42
3282 3346 6.716628 TCCTGGCATCAATATATTCTCCAAAC 59.283 38.462 0.00 0.00 0.00 2.93
3557 3624 5.892348 ACAATGGATTCACTTAGAACCCTT 58.108 37.500 0.00 0.00 40.98 3.95
3638 3705 2.802719 ACCATGAAATGCTAAACGGGT 58.197 42.857 0.00 0.00 44.97 5.28
4232 4303 7.934855 AGATGTTCAATCAGCAAAAGAGTAT 57.065 32.000 0.00 0.00 0.00 2.12
4432 4505 1.997606 GCATGCTGAAATCTGGCAAAC 59.002 47.619 11.37 0.00 39.46 2.93
4442 4515 1.034356 ACAACTGCTGCATGCTGAAA 58.966 45.000 26.71 13.32 42.27 2.69
4848 4921 4.510038 AATAAAAGCAGGCTGACAACAG 57.490 40.909 20.86 0.00 45.91 3.16
4903 4976 7.750229 TGATGATAGCTGGAAATATTGGAAC 57.250 36.000 0.00 0.00 0.00 3.62
4918 4991 8.625651 ACTATATCAAGTACGGATGATGATAGC 58.374 37.037 16.97 0.00 36.68 2.97
4921 4994 8.581253 TCACTATATCAAGTACGGATGATGAT 57.419 34.615 16.97 10.41 36.93 2.45
4922 4995 7.362142 GCTCACTATATCAAGTACGGATGATGA 60.362 40.741 16.97 11.56 36.93 2.92
4931 5004 8.648557 TCACAATTGCTCACTATATCAAGTAC 57.351 34.615 5.05 0.00 0.00 2.73
5080 5154 0.309302 CTCGTAGTGAGGCCTCATCG 59.691 60.000 37.07 34.20 42.18 3.84
5179 5253 4.404394 TCTTCAATTCCGTACTGATAGCCA 59.596 41.667 0.00 0.00 0.00 4.75
5233 5307 7.617723 AGCCAAGGTTTCATATTACCATTGTAA 59.382 33.333 0.00 0.00 41.03 2.41
5364 5438 4.821805 GTCAGTCAAATCTTCTGGTTTCCA 59.178 41.667 0.00 0.00 0.00 3.53
5365 5439 4.083802 CGTCAGTCAAATCTTCTGGTTTCC 60.084 45.833 0.00 0.00 0.00 3.13
5397 5471 8.562892 GGTATATAGTACAGCAGTAGACGAAAA 58.437 37.037 0.00 0.00 0.00 2.29
5436 5510 3.555966 CTGGTCTTTTTCACTCCCAAGT 58.444 45.455 0.00 0.00 35.60 3.16
5437 5511 2.887152 CCTGGTCTTTTTCACTCCCAAG 59.113 50.000 0.00 0.00 0.00 3.61
5438 5512 2.512056 TCCTGGTCTTTTTCACTCCCAA 59.488 45.455 0.00 0.00 0.00 4.12
5440 5514 2.951229 TCCTGGTCTTTTTCACTCCC 57.049 50.000 0.00 0.00 0.00 4.30
5447 5521 3.631250 TGACTGCTTTCCTGGTCTTTTT 58.369 40.909 0.00 0.00 0.00 1.94
5536 5611 9.343539 ACTAATTTCTCTAACTGCAGAAAAACT 57.656 29.630 23.35 3.93 40.99 2.66
5640 5716 4.142790 TCCTGTCCCGTAATCTAGATGAC 58.857 47.826 9.95 9.95 0.00 3.06
5663 5739 2.094494 ACAACGCATCACCAACAAACAA 60.094 40.909 0.00 0.00 0.00 2.83
5664 5740 1.474478 ACAACGCATCACCAACAAACA 59.526 42.857 0.00 0.00 0.00 2.83
5665 5741 1.851666 CACAACGCATCACCAACAAAC 59.148 47.619 0.00 0.00 0.00 2.93
5666 5742 1.202348 CCACAACGCATCACCAACAAA 60.202 47.619 0.00 0.00 0.00 2.83
5852 5928 3.214328 AGCTGTCAACCTTGTTAGTTGG 58.786 45.455 4.00 0.00 43.83 3.77
6045 6146 0.820871 AGTCTCGGGATCTCAGCAAC 59.179 55.000 0.00 0.00 0.00 4.17
6093 6195 9.086336 CCGACTACTTTATTTTCAAATACCGTA 57.914 33.333 0.00 0.00 31.03 4.02
6094 6196 7.603784 ACCGACTACTTTATTTTCAAATACCGT 59.396 33.333 0.00 0.00 31.03 4.83
6095 6197 7.901377 CACCGACTACTTTATTTTCAAATACCG 59.099 37.037 0.00 0.00 31.03 4.02
6096 6198 8.938906 TCACCGACTACTTTATTTTCAAATACC 58.061 33.333 0.00 0.00 31.03 2.73
6099 6201 9.449719 AGATCACCGACTACTTTATTTTCAAAT 57.550 29.630 0.00 0.00 0.00 2.32
6100 6202 8.717821 CAGATCACCGACTACTTTATTTTCAAA 58.282 33.333 0.00 0.00 0.00 2.69
6101 6203 7.333423 CCAGATCACCGACTACTTTATTTTCAA 59.667 37.037 0.00 0.00 0.00 2.69
6102 6204 6.816640 CCAGATCACCGACTACTTTATTTTCA 59.183 38.462 0.00 0.00 0.00 2.69
6103 6205 6.238130 GCCAGATCACCGACTACTTTATTTTC 60.238 42.308 0.00 0.00 0.00 2.29
6104 6206 5.585047 GCCAGATCACCGACTACTTTATTTT 59.415 40.000 0.00 0.00 0.00 1.82
6105 6207 5.116882 GCCAGATCACCGACTACTTTATTT 58.883 41.667 0.00 0.00 0.00 1.40
6106 6208 4.694339 GCCAGATCACCGACTACTTTATT 58.306 43.478 0.00 0.00 0.00 1.40
6107 6209 3.243434 CGCCAGATCACCGACTACTTTAT 60.243 47.826 0.00 0.00 0.00 1.40
6108 6210 2.098607 CGCCAGATCACCGACTACTTTA 59.901 50.000 0.00 0.00 0.00 1.85
6109 6211 1.135083 CGCCAGATCACCGACTACTTT 60.135 52.381 0.00 0.00 0.00 2.66
6110 6212 0.456221 CGCCAGATCACCGACTACTT 59.544 55.000 0.00 0.00 0.00 2.24
6111 6213 1.384989 CCGCCAGATCACCGACTACT 61.385 60.000 0.00 0.00 0.00 2.57
6112 6214 1.065928 CCGCCAGATCACCGACTAC 59.934 63.158 0.00 0.00 0.00 2.73
6113 6215 1.077285 TCCGCCAGATCACCGACTA 60.077 57.895 0.00 0.00 0.00 2.59
6114 6216 2.362503 TCCGCCAGATCACCGACT 60.363 61.111 0.00 0.00 0.00 4.18
6115 6217 2.202756 GTCCGCCAGATCACCGAC 60.203 66.667 0.00 0.00 0.00 4.79
6116 6218 2.058001 ATGTCCGCCAGATCACCGA 61.058 57.895 0.00 0.00 0.00 4.69
6117 6219 1.884464 CATGTCCGCCAGATCACCG 60.884 63.158 0.00 0.00 0.00 4.94
6118 6220 0.392998 AACATGTCCGCCAGATCACC 60.393 55.000 0.00 0.00 0.00 4.02
6119 6221 1.933853 GTAACATGTCCGCCAGATCAC 59.066 52.381 0.00 0.00 0.00 3.06
6120 6222 1.470805 CGTAACATGTCCGCCAGATCA 60.471 52.381 0.00 0.00 0.00 2.92
6121 6223 1.209128 CGTAACATGTCCGCCAGATC 58.791 55.000 0.00 0.00 0.00 2.75
6122 6224 0.810031 GCGTAACATGTCCGCCAGAT 60.810 55.000 24.48 0.15 41.50 2.90
6123 6225 1.447140 GCGTAACATGTCCGCCAGA 60.447 57.895 24.48 0.00 41.50 3.86
6124 6226 1.739929 TGCGTAACATGTCCGCCAG 60.740 57.895 28.92 9.07 46.44 4.85
6125 6227 2.030401 GTGCGTAACATGTCCGCCA 61.030 57.895 28.92 18.90 46.44 5.69
6126 6228 1.740296 AGTGCGTAACATGTCCGCC 60.740 57.895 28.92 22.27 46.44 6.13
6128 6230 0.713883 GTCAGTGCGTAACATGTCCG 59.286 55.000 12.17 12.17 0.00 4.79
6129 6231 1.459592 GTGTCAGTGCGTAACATGTCC 59.540 52.381 0.00 0.00 0.00 4.02
6130 6232 1.459592 GGTGTCAGTGCGTAACATGTC 59.540 52.381 0.00 0.00 0.00 3.06
6131 6233 1.508632 GGTGTCAGTGCGTAACATGT 58.491 50.000 0.00 0.00 0.00 3.21
6132 6234 0.796312 GGGTGTCAGTGCGTAACATG 59.204 55.000 0.00 0.00 0.00 3.21
6133 6235 0.394938 TGGGTGTCAGTGCGTAACAT 59.605 50.000 0.00 0.00 0.00 2.71
6134 6236 0.178301 TTGGGTGTCAGTGCGTAACA 59.822 50.000 0.00 0.00 0.00 2.41
6135 6237 1.263217 CTTTGGGTGTCAGTGCGTAAC 59.737 52.381 0.00 0.00 0.00 2.50
6136 6238 1.588674 CTTTGGGTGTCAGTGCGTAA 58.411 50.000 0.00 0.00 0.00 3.18
6137 6239 0.250124 CCTTTGGGTGTCAGTGCGTA 60.250 55.000 0.00 0.00 0.00 4.42
6138 6240 1.525995 CCTTTGGGTGTCAGTGCGT 60.526 57.895 0.00 0.00 0.00 5.24
6139 6241 2.908073 GCCTTTGGGTGTCAGTGCG 61.908 63.158 0.00 0.00 34.45 5.34
6140 6242 2.564721 GGCCTTTGGGTGTCAGTGC 61.565 63.158 0.00 0.00 34.45 4.40
6141 6243 1.903404 GGGCCTTTGGGTGTCAGTG 60.903 63.158 0.84 0.00 34.45 3.66
6142 6244 2.520968 GGGCCTTTGGGTGTCAGT 59.479 61.111 0.84 0.00 34.45 3.41
6143 6245 2.672996 CGGGCCTTTGGGTGTCAG 60.673 66.667 0.84 0.00 34.45 3.51
6144 6246 4.278513 CCGGGCCTTTGGGTGTCA 62.279 66.667 0.84 0.00 34.45 3.58
6158 6260 4.113815 TTGAGGATGCCCTGCCGG 62.114 66.667 0.00 0.00 44.53 6.13
6159 6261 2.515523 CTTGAGGATGCCCTGCCG 60.516 66.667 0.00 0.00 44.53 5.69
6160 6262 2.123982 CCTTGAGGATGCCCTGCC 60.124 66.667 0.00 0.00 44.53 4.85
6161 6263 2.832201 GCCTTGAGGATGCCCTGC 60.832 66.667 0.06 0.00 44.53 4.85
6162 6264 2.515523 CGCCTTGAGGATGCCCTG 60.516 66.667 0.06 0.00 44.53 4.45
6164 6266 3.125376 ATCCGCCTTGAGGATGCCC 62.125 63.158 0.06 0.00 46.01 5.36
6165 6267 2.512896 ATCCGCCTTGAGGATGCC 59.487 61.111 0.06 0.00 46.01 4.40
6169 6271 3.154473 CGGGATCCGCCTTGAGGA 61.154 66.667 5.45 0.00 41.17 3.71
6179 6281 5.915175 ACTTGTCTCTAATTTACGGGATCC 58.085 41.667 1.92 1.92 0.00 3.36
6182 6284 8.636213 CCTTATACTTGTCTCTAATTTACGGGA 58.364 37.037 0.00 0.00 0.00 5.14
6183 6285 8.636213 TCCTTATACTTGTCTCTAATTTACGGG 58.364 37.037 0.00 0.00 0.00 5.28
6184 6286 9.680315 CTCCTTATACTTGTCTCTAATTTACGG 57.320 37.037 0.00 0.00 0.00 4.02
6185 6287 9.182933 GCTCCTTATACTTGTCTCTAATTTACG 57.817 37.037 0.00 0.00 0.00 3.18
6191 6293 8.693625 GGTAAAGCTCCTTATACTTGTCTCTAA 58.306 37.037 0.00 0.00 0.00 2.10
6192 6294 7.013083 CGGTAAAGCTCCTTATACTTGTCTCTA 59.987 40.741 0.00 0.00 0.00 2.43
6193 6295 6.183360 CGGTAAAGCTCCTTATACTTGTCTCT 60.183 42.308 0.00 0.00 0.00 3.10
6194 6296 5.978322 CGGTAAAGCTCCTTATACTTGTCTC 59.022 44.000 0.00 0.00 0.00 3.36
6195 6297 5.421374 ACGGTAAAGCTCCTTATACTTGTCT 59.579 40.000 0.00 0.00 0.00 3.41
6196 6298 5.658468 ACGGTAAAGCTCCTTATACTTGTC 58.342 41.667 0.00 0.00 0.00 3.18
6197 6299 5.672421 ACGGTAAAGCTCCTTATACTTGT 57.328 39.130 0.00 0.00 0.00 3.16
6198 6300 7.384387 GGATTACGGTAAAGCTCCTTATACTTG 59.616 40.741 4.47 0.00 0.00 3.16
6199 6301 7.440198 GGATTACGGTAAAGCTCCTTATACTT 58.560 38.462 4.47 0.00 0.00 2.24
6200 6302 6.294397 CGGATTACGGTAAAGCTCCTTATACT 60.294 42.308 14.07 0.00 39.42 2.12
6201 6303 5.860716 CGGATTACGGTAAAGCTCCTTATAC 59.139 44.000 14.07 0.00 39.42 1.47
6202 6304 6.017400 CGGATTACGGTAAAGCTCCTTATA 57.983 41.667 14.07 0.00 39.42 0.98
6203 6305 4.879598 CGGATTACGGTAAAGCTCCTTAT 58.120 43.478 14.07 0.00 39.42 1.73
6204 6306 4.311816 CGGATTACGGTAAAGCTCCTTA 57.688 45.455 14.07 0.00 39.42 2.69
6205 6307 3.175109 CGGATTACGGTAAAGCTCCTT 57.825 47.619 14.07 0.00 39.42 3.36
6206 6308 2.884894 CGGATTACGGTAAAGCTCCT 57.115 50.000 14.07 0.00 39.42 3.69
6217 6319 3.040795 CGTGTCTATTGTCCGGATTACG 58.959 50.000 7.81 6.41 43.80 3.18
6218 6320 2.793232 GCGTGTCTATTGTCCGGATTAC 59.207 50.000 7.81 0.00 0.00 1.89
6219 6321 2.427812 TGCGTGTCTATTGTCCGGATTA 59.572 45.455 7.81 0.00 0.00 1.75
6220 6322 1.206132 TGCGTGTCTATTGTCCGGATT 59.794 47.619 7.81 0.00 0.00 3.01
6221 6323 0.821517 TGCGTGTCTATTGTCCGGAT 59.178 50.000 7.81 0.00 0.00 4.18
6222 6324 0.172578 CTGCGTGTCTATTGTCCGGA 59.827 55.000 0.00 0.00 0.00 5.14
6223 6325 0.172578 TCTGCGTGTCTATTGTCCGG 59.827 55.000 0.00 0.00 0.00 5.14
6224 6326 2.120232 GATCTGCGTGTCTATTGTCCG 58.880 52.381 0.00 0.00 0.00 4.79
6225 6327 3.376540 GAGATCTGCGTGTCTATTGTCC 58.623 50.000 0.00 0.00 0.00 4.02
6226 6328 3.039405 CGAGATCTGCGTGTCTATTGTC 58.961 50.000 0.00 0.00 0.00 3.18
6227 6329 2.423892 ACGAGATCTGCGTGTCTATTGT 59.576 45.455 16.09 0.00 40.94 2.71
6228 6330 3.071786 ACGAGATCTGCGTGTCTATTG 57.928 47.619 16.09 0.00 40.94 1.90
6229 6331 4.895224 TTACGAGATCTGCGTGTCTATT 57.105 40.909 22.31 4.54 42.62 1.73
6230 6332 4.335874 AGTTTACGAGATCTGCGTGTCTAT 59.664 41.667 22.31 8.43 42.62 1.98
6231 6333 3.688185 AGTTTACGAGATCTGCGTGTCTA 59.312 43.478 22.31 6.98 42.62 2.59
6232 6334 2.488545 AGTTTACGAGATCTGCGTGTCT 59.511 45.455 22.31 16.14 42.62 3.41
6233 6335 2.864968 AGTTTACGAGATCTGCGTGTC 58.135 47.619 22.31 14.83 42.62 3.67
6234 6336 3.688185 TCTAGTTTACGAGATCTGCGTGT 59.312 43.478 22.31 9.93 42.62 4.49
6235 6337 4.034163 TCTCTAGTTTACGAGATCTGCGTG 59.966 45.833 22.31 10.36 42.62 5.34
6236 6338 4.034279 GTCTCTAGTTTACGAGATCTGCGT 59.966 45.833 19.26 19.26 45.01 5.24
6237 6339 4.034163 TGTCTCTAGTTTACGAGATCTGCG 59.966 45.833 0.00 6.49 38.43 5.18
6238 6340 5.487153 TGTCTCTAGTTTACGAGATCTGC 57.513 43.478 0.00 0.00 38.43 4.26
6243 6345 9.064706 CCCTATATTTGTCTCTAGTTTACGAGA 57.935 37.037 0.00 0.00 34.12 4.04
6244 6346 9.064706 TCCCTATATTTGTCTCTAGTTTACGAG 57.935 37.037 0.00 0.00 0.00 4.18
6245 6347 8.985315 TCCCTATATTTGTCTCTAGTTTACGA 57.015 34.615 0.00 0.00 0.00 3.43
6246 6348 9.064706 TCTCCCTATATTTGTCTCTAGTTTACG 57.935 37.037 0.00 0.00 0.00 3.18
6248 6350 9.931698 TGTCTCCCTATATTTGTCTCTAGTTTA 57.068 33.333 0.00 0.00 0.00 2.01
6249 6351 8.840200 TGTCTCCCTATATTTGTCTCTAGTTT 57.160 34.615 0.00 0.00 0.00 2.66
6250 6352 8.840200 TTGTCTCCCTATATTTGTCTCTAGTT 57.160 34.615 0.00 0.00 0.00 2.24
6251 6353 8.840200 TTTGTCTCCCTATATTTGTCTCTAGT 57.160 34.615 0.00 0.00 0.00 2.57
6263 6365 9.839185 AAAGCTACCTATATTTGTCTCCCTATA 57.161 33.333 0.00 0.00 0.00 1.31
6264 6366 8.743636 AAAGCTACCTATATTTGTCTCCCTAT 57.256 34.615 0.00 0.00 0.00 2.57
6265 6367 9.086758 GTAAAGCTACCTATATTTGTCTCCCTA 57.913 37.037 0.00 0.00 0.00 3.53
6266 6368 7.255871 CGTAAAGCTACCTATATTTGTCTCCCT 60.256 40.741 0.00 0.00 0.00 4.20
6267 6369 6.867293 CGTAAAGCTACCTATATTTGTCTCCC 59.133 42.308 0.00 0.00 0.00 4.30
6268 6370 6.867293 CCGTAAAGCTACCTATATTTGTCTCC 59.133 42.308 0.00 0.00 0.00 3.71
6269 6371 6.867293 CCCGTAAAGCTACCTATATTTGTCTC 59.133 42.308 0.00 0.00 0.00 3.36
6270 6372 6.552350 TCCCGTAAAGCTACCTATATTTGTCT 59.448 38.462 0.00 0.00 0.00 3.41
6271 6373 6.752168 TCCCGTAAAGCTACCTATATTTGTC 58.248 40.000 0.00 0.00 0.00 3.18
6272 6374 6.736110 TCCCGTAAAGCTACCTATATTTGT 57.264 37.500 0.00 0.00 0.00 2.83
6273 6375 8.617290 AATTCCCGTAAAGCTACCTATATTTG 57.383 34.615 0.00 0.00 0.00 2.32
6274 6376 7.601508 CGAATTCCCGTAAAGCTACCTATATTT 59.398 37.037 0.00 0.00 0.00 1.40
6275 6377 7.095270 CGAATTCCCGTAAAGCTACCTATATT 58.905 38.462 0.00 0.00 0.00 1.28
6276 6378 6.350780 CCGAATTCCCGTAAAGCTACCTATAT 60.351 42.308 0.00 0.00 0.00 0.86
6277 6379 5.047802 CCGAATTCCCGTAAAGCTACCTATA 60.048 44.000 0.00 0.00 0.00 1.31
6278 6380 4.262335 CCGAATTCCCGTAAAGCTACCTAT 60.262 45.833 0.00 0.00 0.00 2.57
6279 6381 3.068590 CCGAATTCCCGTAAAGCTACCTA 59.931 47.826 0.00 0.00 0.00 3.08
6280 6382 2.159000 CCGAATTCCCGTAAAGCTACCT 60.159 50.000 0.00 0.00 0.00 3.08
6281 6383 2.159057 TCCGAATTCCCGTAAAGCTACC 60.159 50.000 0.00 0.00 0.00 3.18
6282 6384 2.862536 GTCCGAATTCCCGTAAAGCTAC 59.137 50.000 0.00 0.00 0.00 3.58
6283 6385 2.496871 TGTCCGAATTCCCGTAAAGCTA 59.503 45.455 0.00 0.00 0.00 3.32
6284 6386 1.276989 TGTCCGAATTCCCGTAAAGCT 59.723 47.619 0.00 0.00 0.00 3.74
6285 6387 1.729284 TGTCCGAATTCCCGTAAAGC 58.271 50.000 0.00 0.00 0.00 3.51
6286 6388 4.510340 CCTATTGTCCGAATTCCCGTAAAG 59.490 45.833 0.00 0.00 0.00 1.85
6287 6389 4.444536 CCTATTGTCCGAATTCCCGTAAA 58.555 43.478 0.00 0.00 0.00 2.01
6288 6390 3.742013 GCCTATTGTCCGAATTCCCGTAA 60.742 47.826 0.00 0.00 0.00 3.18
6289 6391 2.224113 GCCTATTGTCCGAATTCCCGTA 60.224 50.000 0.00 0.00 0.00 4.02
6290 6392 1.474498 GCCTATTGTCCGAATTCCCGT 60.474 52.381 0.00 0.00 0.00 5.28
6291 6393 1.226746 GCCTATTGTCCGAATTCCCG 58.773 55.000 0.00 0.00 0.00 5.14
6292 6394 1.947456 GTGCCTATTGTCCGAATTCCC 59.053 52.381 0.00 0.00 0.00 3.97
6293 6395 1.597663 CGTGCCTATTGTCCGAATTCC 59.402 52.381 0.00 0.00 0.00 3.01
6294 6396 1.003866 GCGTGCCTATTGTCCGAATTC 60.004 52.381 0.00 0.00 0.00 2.17
6295 6397 1.014352 GCGTGCCTATTGTCCGAATT 58.986 50.000 0.00 0.00 0.00 2.17
6296 6398 0.107897 TGCGTGCCTATTGTCCGAAT 60.108 50.000 0.00 0.00 0.00 3.34
6297 6399 0.739462 CTGCGTGCCTATTGTCCGAA 60.739 55.000 0.00 0.00 0.00 4.30
6298 6400 1.153647 CTGCGTGCCTATTGTCCGA 60.154 57.895 0.00 0.00 0.00 4.55
6299 6401 2.173669 CCTGCGTGCCTATTGTCCG 61.174 63.158 0.00 0.00 0.00 4.79
6300 6402 1.090052 GTCCTGCGTGCCTATTGTCC 61.090 60.000 0.00 0.00 0.00 4.02
6301 6403 0.108138 AGTCCTGCGTGCCTATTGTC 60.108 55.000 0.00 0.00 0.00 3.18
6302 6404 0.108138 GAGTCCTGCGTGCCTATTGT 60.108 55.000 0.00 0.00 0.00 2.71
6303 6405 0.811616 GGAGTCCTGCGTGCCTATTG 60.812 60.000 0.41 0.00 0.00 1.90
6304 6406 1.522569 GGAGTCCTGCGTGCCTATT 59.477 57.895 0.41 0.00 0.00 1.73
6305 6407 2.786495 CGGAGTCCTGCGTGCCTAT 61.786 63.158 7.77 0.00 39.61 2.57
6306 6408 3.449227 CGGAGTCCTGCGTGCCTA 61.449 66.667 7.77 0.00 39.61 3.93
6308 6410 2.782222 TATCGGAGTCCTGCGTGCC 61.782 63.158 7.77 0.00 44.84 5.01
6309 6411 1.589196 GTATCGGAGTCCTGCGTGC 60.589 63.158 7.77 0.00 44.84 5.34
6310 6412 1.065928 GGTATCGGAGTCCTGCGTG 59.934 63.158 7.77 0.00 44.84 5.34
6311 6413 2.125961 GGGTATCGGAGTCCTGCGT 61.126 63.158 7.77 0.00 44.84 5.24
6312 6414 1.828660 AGGGTATCGGAGTCCTGCG 60.829 63.158 7.77 1.44 45.95 5.18
6313 6415 1.742768 CAGGGTATCGGAGTCCTGC 59.257 63.158 7.77 0.00 40.04 4.85
6314 6416 0.397254 ACCAGGGTATCGGAGTCCTG 60.397 60.000 7.77 13.71 44.60 3.86
6315 6417 0.338814 AACCAGGGTATCGGAGTCCT 59.661 55.000 7.77 0.00 0.00 3.85
6316 6418 0.751452 GAACCAGGGTATCGGAGTCC 59.249 60.000 0.00 0.00 0.00 3.85
6317 6419 1.136500 GTGAACCAGGGTATCGGAGTC 59.864 57.143 0.00 0.00 0.00 3.36
6318 6420 1.192428 GTGAACCAGGGTATCGGAGT 58.808 55.000 0.00 0.00 0.00 3.85
6319 6421 0.464452 GGTGAACCAGGGTATCGGAG 59.536 60.000 0.00 0.00 35.64 4.63
6320 6422 0.979187 GGGTGAACCAGGGTATCGGA 60.979 60.000 1.16 0.00 39.85 4.55
6321 6423 1.268992 TGGGTGAACCAGGGTATCGG 61.269 60.000 1.16 0.00 46.80 4.18
6322 6424 2.292866 TGGGTGAACCAGGGTATCG 58.707 57.895 1.16 0.00 46.80 2.92


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

AutoCloner maintained by Alex Coulton.