Multiple sequence alignment - TraesCS1B01G324500

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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 TraesCS1B01G324500 chr1B 100.000 2381 0 0 1 2381 549890232 549892612 0.000000e+00 4397
1 TraesCS1B01G324500 chr1B 88.274 307 31 5 1662 1964 550033916 550034221 1.740000e-96 363
2 TraesCS1B01G324500 chr1A 89.461 1689 113 36 1 1659 504631425 504633078 0.000000e+00 2073
3 TraesCS1B01G324500 chr1A 89.963 269 25 2 1662 1929 504641550 504641817 1.750000e-91 346
4 TraesCS1B01G324500 chr1D 92.577 943 60 7 718 1659 408534559 408535492 0.000000e+00 1345
5 TraesCS1B01G324500 chr1D 92.927 919 49 7 519 1421 408556946 408557864 0.000000e+00 1323
6 TraesCS1B01G324500 chr1D 88.906 658 63 4 1003 1659 408631290 408631938 0.000000e+00 802
7 TraesCS1B01G324500 chr1D 85.277 686 61 23 1 677 408533901 408534555 0.000000e+00 671
8 TraesCS1B01G324500 chr1D 85.639 571 68 10 1662 2219 408567607 408568176 2.640000e-164 588
9 TraesCS1B01G324500 chr1D 77.119 826 130 41 420 1227 408769351 408770135 7.870000e-115 424
10 TraesCS1B01G324500 chr1D 78.333 660 90 26 445 1084 408816503 408817129 6.210000e-101 377
11 TraesCS1B01G324500 chr1D 90.661 257 22 1 1670 1924 408536010 408536266 8.150000e-90 340
12 TraesCS1B01G324500 chr1D 90.514 253 17 4 1413 1659 408566160 408566411 6.350000e-86 327
13 TraesCS1B01G324500 chr1D 79.325 474 45 26 170 631 408711334 408711766 1.390000e-72 283
14 TraesCS1B01G324500 chr1D 90.521 211 20 0 1662 1872 408713470 408713680 1.800000e-71 279
15 TraesCS1B01G324500 chr1D 87.444 223 27 1 1663 1885 408632924 408633145 3.040000e-64 255
16 TraesCS1B01G324500 chr1D 92.222 90 5 2 389 477 408556857 408556945 2.480000e-25 126


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 TraesCS1B01G324500 chr1B 549890232 549892612 2380 False 4397.000000 4397 100.0000 1 2381 1 chr1B.!!$F1 2380
1 TraesCS1B01G324500 chr1A 504631425 504633078 1653 False 2073.000000 2073 89.4610 1 1659 1 chr1A.!!$F1 1658
2 TraesCS1B01G324500 chr1D 408533901 408536266 2365 False 785.333333 1345 89.5050 1 1924 3 chr1D.!!$F3 1923
3 TraesCS1B01G324500 chr1D 408556857 408557864 1007 False 724.500000 1323 92.5745 389 1421 2 chr1D.!!$F4 1032
4 TraesCS1B01G324500 chr1D 408631290 408633145 1855 False 528.500000 802 88.1750 1003 1885 2 chr1D.!!$F6 882
5 TraesCS1B01G324500 chr1D 408566160 408568176 2016 False 457.500000 588 88.0765 1413 2219 2 chr1D.!!$F5 806
6 TraesCS1B01G324500 chr1D 408769351 408770135 784 False 424.000000 424 77.1190 420 1227 1 chr1D.!!$F1 807
7 TraesCS1B01G324500 chr1D 408816503 408817129 626 False 377.000000 377 78.3330 445 1084 1 chr1D.!!$F2 639
8 TraesCS1B01G324500 chr1D 408711334 408713680 2346 False 281.000000 283 84.9230 170 1872 2 chr1D.!!$F7 1702

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
104 106 0.036164 CGGTGATCCAACCCAAGTCA 59.964 55.0 0.0 0.0 36.84 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1983 3946 0.182061 ATGAGCGCATCTGATGGGTT 59.818 50.0 28.27 24.77 44.22 4.11 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 6.979701 AAATAAACAAAAGCCTAACGAACG 57.020 33.333 0.00 0.00 0.00 3.95
25 26 5.678132 ATAAACAAAAGCCTAACGAACGT 57.322 34.783 0.00 0.00 0.00 3.99
26 27 3.597377 AACAAAAGCCTAACGAACGTC 57.403 42.857 0.00 0.00 0.00 4.34
28 29 1.868498 CAAAAGCCTAACGAACGTCCA 59.132 47.619 0.00 0.00 0.00 4.02
29 30 2.467566 AAAGCCTAACGAACGTCCAT 57.532 45.000 0.00 0.00 0.00 3.41
30 31 2.467566 AAGCCTAACGAACGTCCATT 57.532 45.000 0.00 0.00 0.00 3.16
31 32 2.005971 AGCCTAACGAACGTCCATTC 57.994 50.000 0.00 0.00 0.00 2.67
44 46 1.304879 CCATTCGGCCCAAAAGGGA 60.305 57.895 4.37 0.00 40.01 4.20
45 47 0.902516 CCATTCGGCCCAAAAGGGAA 60.903 55.000 4.37 0.00 40.01 3.97
48 50 0.753867 TTCGGCCCAAAAGGGAAAAC 59.246 50.000 4.37 0.00 40.01 2.43
50 52 1.369692 GGCCCAAAAGGGAAAACCG 59.630 57.895 4.37 0.00 46.96 4.44
85 87 0.110644 CCTTCTTTCGCTGAACACGC 60.111 55.000 0.00 0.00 0.00 5.34
100 102 2.359354 CGCGGTGATCCAACCCAA 60.359 61.111 0.00 0.00 36.84 4.12
101 103 2.398554 CGCGGTGATCCAACCCAAG 61.399 63.158 0.00 0.00 36.84 3.61
102 104 1.303317 GCGGTGATCCAACCCAAGT 60.303 57.895 0.00 0.00 36.84 3.16
103 105 1.305930 GCGGTGATCCAACCCAAGTC 61.306 60.000 0.00 0.00 36.84 3.01
104 106 0.036164 CGGTGATCCAACCCAAGTCA 59.964 55.000 0.00 0.00 36.84 3.41
105 107 1.826385 GGTGATCCAACCCAAGTCAG 58.174 55.000 0.00 0.00 33.79 3.51
115 117 0.036577 CCCAAGTCAGGAGAGCACTG 60.037 60.000 0.00 0.00 37.30 3.66
118 120 1.345741 CAAGTCAGGAGAGCACTGGAA 59.654 52.381 0.00 0.00 36.62 3.53
119 121 0.972883 AGTCAGGAGAGCACTGGAAC 59.027 55.000 0.00 0.00 36.62 3.62
138 145 1.139058 ACAGAAGTGAACTGGCGAAGT 59.861 47.619 0.00 0.00 42.60 3.01
174 191 4.380550 GGATTGCCTCGGTAAAAAGAAAGG 60.381 45.833 0.00 0.00 0.00 3.11
178 195 4.830600 TGCCTCGGTAAAAAGAAAGGATTT 59.169 37.500 0.00 0.00 43.98 2.17
249 276 2.959071 GCCGACTCGATCTGCAGC 60.959 66.667 9.47 0.00 37.49 5.25
258 285 1.812922 GATCTGCAGCCGGTGAGTG 60.813 63.158 9.47 0.00 0.00 3.51
259 286 3.965539 ATCTGCAGCCGGTGAGTGC 62.966 63.158 9.47 8.31 37.73 4.40
296 323 3.452474 CTGGTTAATCTCTTCCGCTCTG 58.548 50.000 0.00 0.00 0.00 3.35
298 327 3.260884 TGGTTAATCTCTTCCGCTCTGTT 59.739 43.478 0.00 0.00 0.00 3.16
322 352 2.291346 TGATCTGTTACTCCCCGTCTCA 60.291 50.000 0.00 0.00 0.00 3.27
404 458 2.100605 GGAATCTGTTTCCGCAGTCT 57.899 50.000 1.95 0.00 44.46 3.24
504 561 5.311265 TGATTTGTGCTCTGTTCTGAGATT 58.689 37.500 10.14 0.00 36.23 2.40
515 572 6.476378 TCTGTTCTGAGATTAAGAAAAGGGG 58.524 40.000 4.05 0.00 38.86 4.79
517 574 5.074515 TGTTCTGAGATTAAGAAAAGGGGGT 59.925 40.000 0.00 0.00 35.50 4.95
573 631 4.889409 AGTTCTGCTGAAAGTTTTGATGGA 59.111 37.500 7.68 0.00 35.30 3.41
577 636 6.819284 TCTGCTGAAAGTTTTGATGGAAAAT 58.181 32.000 0.00 0.00 35.96 1.82
582 641 9.815936 GCTGAAAGTTTTGATGGAAAATTTATG 57.184 29.630 0.00 0.00 37.05 1.90
708 781 0.239347 ATTTCTGTCGCTGCAACTGC 59.761 50.000 0.00 0.00 42.50 4.40
920 1037 9.429359 CTGATTAGATATCGTAAAGCAGGAAAT 57.571 33.333 18.27 0.94 0.00 2.17
931 1048 6.251376 CGTAAAGCAGGAAATCATTTAAGCAC 59.749 38.462 4.36 0.00 0.00 4.40
1105 1229 1.417517 ACACTGCAGATTCTCACACCA 59.582 47.619 23.35 0.00 0.00 4.17
1227 1355 2.202987 GACATCGGCAGCCTCCTG 60.203 66.667 10.54 6.54 42.13 3.86
1358 1486 2.203195 TGACACCGCAAGCAAGCT 60.203 55.556 0.00 0.00 0.00 3.74
1452 1581 4.278170 CCATGTTTCTGTAGTTTTCCAGCA 59.722 41.667 0.00 0.00 0.00 4.41
1542 1675 3.128349 ACACACGAGTTATGCGAAAGTT 58.872 40.909 0.00 0.00 0.00 2.66
1625 1762 5.576774 GGTCAGAACTCAACCTTTTGTTTTG 59.423 40.000 0.00 0.00 34.00 2.44
1627 1764 6.866248 GTCAGAACTCAACCTTTTGTTTTGAA 59.134 34.615 0.00 0.00 36.04 2.69
1659 1800 5.994668 GGATTCTCCAGCCTAGACAAATAAG 59.005 44.000 0.00 0.00 36.28 1.73
1660 1801 4.408182 TCTCCAGCCTAGACAAATAAGC 57.592 45.455 0.00 0.00 0.00 3.09
1668 3618 7.147976 CAGCCTAGACAAATAAGCAAGTTTTT 58.852 34.615 0.00 0.00 0.00 1.94
1675 3625 9.869757 AGACAAATAAGCAAGTTTTTAGTGTTT 57.130 25.926 0.00 0.00 0.00 2.83
1692 3642 8.997621 TTAGTGTTTACCTTATAAGCTCACTG 57.002 34.615 21.76 8.55 35.66 3.66
1762 3712 7.070946 TGGGCCATGTGTTATTGATTTCATTAT 59.929 33.333 0.00 0.00 0.00 1.28
1841 3795 6.347725 GCTACCACTTCCAGCGATATATTTTG 60.348 42.308 0.00 0.00 0.00 2.44
1928 3891 6.484308 CCTGCACATGATAACAATGACTGATA 59.516 38.462 0.00 0.00 0.00 2.15
1930 3893 8.454570 TGCACATGATAACAATGACTGATATT 57.545 30.769 0.00 0.00 0.00 1.28
1932 3895 9.740239 GCACATGATAACAATGACTGATATTTT 57.260 29.630 0.00 0.00 0.00 1.82
1942 3905 9.897744 ACAATGACTGATATTTTTGTGTAGTTG 57.102 29.630 0.00 0.00 0.00 3.16
1991 3954 9.747898 ACTATTTACAACTATGAAAACCCATCA 57.252 29.630 0.00 0.00 0.00 3.07
1997 3960 3.879295 ACTATGAAAACCCATCAGATGCG 59.121 43.478 4.68 0.00 0.00 4.73
2000 3963 1.064654 GAAAACCCATCAGATGCGCTC 59.935 52.381 9.73 3.60 0.00 5.03
2002 3965 0.182061 AACCCATCAGATGCGCTCAT 59.818 50.000 9.73 0.00 35.17 2.90
2005 3968 2.158769 ACCCATCAGATGCGCTCATAAA 60.159 45.455 9.73 0.00 31.96 1.40
2007 3970 2.096565 CCATCAGATGCGCTCATAAACG 60.097 50.000 9.73 0.00 31.96 3.60
2023 3986 8.342634 GCTCATAAACGGTTGTGATATGTTTAT 58.657 33.333 13.34 3.53 43.01 1.40
2052 4016 6.156256 AGTTATGGTCATTTGTCAGCTACCTA 59.844 38.462 0.09 0.00 0.00 3.08
2063 4027 7.997107 TTGTCAGCTACCTAACAATTATACG 57.003 36.000 0.00 0.00 0.00 3.06
2101 4065 8.476657 TGTACATGCAAATTTATTGATTGTGG 57.523 30.769 0.00 0.00 0.00 4.17
2109 4073 9.503427 GCAAATTTATTGATTGTGGTCTAGTAC 57.497 33.333 0.00 0.00 0.00 2.73
2110 4074 9.702726 CAAATTTATTGATTGTGGTCTAGTACG 57.297 33.333 0.00 0.00 0.00 3.67
2115 4079 7.596749 ATTGATTGTGGTCTAGTACGAAAAG 57.403 36.000 0.00 0.00 0.00 2.27
2126 4090 7.203910 GTCTAGTACGAAAAGATGTCCATCAT 58.796 38.462 9.76 0.00 40.22 2.45
2127 4091 8.350722 GTCTAGTACGAAAAGATGTCCATCATA 58.649 37.037 9.76 0.00 40.22 2.15
2150 4116 9.098355 CATATTGATGGGGTGTTATAATCGTAG 57.902 37.037 0.00 0.00 0.00 3.51
2159 4125 8.146412 GGGGTGTTATAATCGTAGTATGAACTT 58.854 37.037 0.00 0.00 37.15 2.66
2163 4129 9.589111 TGTTATAATCGTAGTATGAACTTGCAA 57.411 29.630 0.00 0.00 37.15 4.08
2171 4137 7.333423 TCGTAGTATGAACTTGCAATAGCTTTT 59.667 33.333 0.00 0.00 38.23 2.27
2186 4152 3.033909 AGCTTTTCTTGCACTTTCCCTT 58.966 40.909 0.00 0.00 0.00 3.95
2190 4156 3.799281 TTCTTGCACTTTCCCTTGTTG 57.201 42.857 0.00 0.00 0.00 3.33
2197 4163 3.243401 GCACTTTCCCTTGTTGTAAGTGG 60.243 47.826 13.27 0.00 43.53 4.00
2201 4167 1.422402 TCCCTTGTTGTAAGTGGTCCC 59.578 52.381 0.00 0.00 0.00 4.46
2202 4168 1.144093 CCCTTGTTGTAAGTGGTCCCA 59.856 52.381 0.00 0.00 0.00 4.37
2215 4181 3.844211 AGTGGTCCCAAACTAATGCTCTA 59.156 43.478 0.00 0.00 0.00 2.43
2219 4185 6.152831 GTGGTCCCAAACTAATGCTCTATTTT 59.847 38.462 0.00 0.00 0.00 1.82
2220 4186 6.377146 TGGTCCCAAACTAATGCTCTATTTTC 59.623 38.462 0.00 0.00 0.00 2.29
2221 4187 6.603599 GGTCCCAAACTAATGCTCTATTTTCT 59.396 38.462 0.00 0.00 0.00 2.52
2222 4188 7.122799 GGTCCCAAACTAATGCTCTATTTTCTT 59.877 37.037 0.00 0.00 0.00 2.52
2223 4189 7.970614 GTCCCAAACTAATGCTCTATTTTCTTG 59.029 37.037 0.00 0.00 0.00 3.02
2224 4190 7.122650 TCCCAAACTAATGCTCTATTTTCTTGG 59.877 37.037 0.00 0.00 33.47 3.61
2225 4191 7.122650 CCCAAACTAATGCTCTATTTTCTTGGA 59.877 37.037 0.00 0.00 34.47 3.53
2226 4192 8.522830 CCAAACTAATGCTCTATTTTCTTGGAA 58.477 33.333 0.00 0.00 34.47 3.53
2227 4193 9.912634 CAAACTAATGCTCTATTTTCTTGGAAA 57.087 29.630 0.00 0.00 0.00 3.13
2230 4196 8.743714 ACTAATGCTCTATTTTCTTGGAAAAGG 58.256 33.333 10.47 6.80 0.00 3.11
2231 4197 7.781324 AATGCTCTATTTTCTTGGAAAAGGA 57.219 32.000 10.47 9.72 0.00 3.36
2232 4198 6.824305 TGCTCTATTTTCTTGGAAAAGGAG 57.176 37.500 20.53 20.53 0.00 3.69
2233 4199 5.711976 TGCTCTATTTTCTTGGAAAAGGAGG 59.288 40.000 23.02 13.81 0.00 4.30
2234 4200 5.946377 GCTCTATTTTCTTGGAAAAGGAGGA 59.054 40.000 23.02 13.63 0.00 3.71
2235 4201 6.605194 GCTCTATTTTCTTGGAAAAGGAGGAT 59.395 38.462 23.02 8.69 0.00 3.24
2236 4202 7.416101 GCTCTATTTTCTTGGAAAAGGAGGATG 60.416 40.741 23.02 13.64 0.00 3.51
2237 4203 7.698912 TCTATTTTCTTGGAAAAGGAGGATGA 58.301 34.615 10.47 1.01 0.00 2.92
2238 4204 6.596309 ATTTTCTTGGAAAAGGAGGATGAC 57.404 37.500 10.47 0.00 0.00 3.06
2239 4205 5.324832 TTTCTTGGAAAAGGAGGATGACT 57.675 39.130 0.00 0.00 0.00 3.41
2240 4206 4.292186 TCTTGGAAAAGGAGGATGACTG 57.708 45.455 0.00 0.00 0.00 3.51
2241 4207 2.496899 TGGAAAAGGAGGATGACTGC 57.503 50.000 0.00 0.00 37.90 4.40
2249 4215 4.686191 AGGAGGATGACTGCTCTATTTG 57.314 45.455 0.00 0.00 45.79 2.32
2250 4216 3.137533 GGAGGATGACTGCTCTATTTGC 58.862 50.000 0.00 0.00 39.63 3.68
2251 4217 3.432749 GGAGGATGACTGCTCTATTTGCA 60.433 47.826 0.00 0.00 39.63 4.08
2252 4218 4.194640 GAGGATGACTGCTCTATTTGCAA 58.805 43.478 0.00 0.00 40.13 4.08
2253 4219 4.789807 AGGATGACTGCTCTATTTGCAAT 58.210 39.130 0.00 0.00 40.13 3.56
2254 4220 5.933617 AGGATGACTGCTCTATTTGCAATA 58.066 37.500 0.00 0.00 40.13 1.90
2255 4221 6.359804 AGGATGACTGCTCTATTTGCAATAA 58.640 36.000 0.00 0.00 40.13 1.40
2256 4222 6.830324 AGGATGACTGCTCTATTTGCAATAAA 59.170 34.615 0.00 0.00 40.13 1.40
2257 4223 7.340232 AGGATGACTGCTCTATTTGCAATAAAA 59.660 33.333 0.00 0.00 40.13 1.52
2258 4224 7.646922 GGATGACTGCTCTATTTGCAATAAAAG 59.353 37.037 0.00 0.00 40.13 2.27
2259 4225 7.686438 TGACTGCTCTATTTGCAATAAAAGA 57.314 32.000 0.00 0.26 40.13 2.52
2260 4226 7.755591 TGACTGCTCTATTTGCAATAAAAGAG 58.244 34.615 17.13 17.13 40.13 2.85
2261 4227 7.607607 TGACTGCTCTATTTGCAATAAAAGAGA 59.392 33.333 22.14 10.94 40.13 3.10
2267 4233 9.376075 CTCTATTTGCAATAAAAGAGAGTCAGA 57.624 33.333 16.75 0.00 44.69 3.27
2268 4234 9.896645 TCTATTTGCAATAAAAGAGAGTCAGAT 57.103 29.630 0.00 0.00 33.60 2.90
2274 4240 9.896645 TGCAATAAAAGAGAGTCAGATTAATCT 57.103 29.630 12.37 12.37 37.72 2.40
2277 4243 9.757227 AATAAAAGAGAGTCAGATTAATCTCCG 57.243 33.333 15.24 5.78 39.19 4.63
2278 4244 6.783708 AAAGAGAGTCAGATTAATCTCCGT 57.216 37.500 15.24 2.55 39.19 4.69
2279 4245 5.766150 AGAGAGTCAGATTAATCTCCGTG 57.234 43.478 15.24 5.61 39.19 4.94
2280 4246 4.037446 AGAGAGTCAGATTAATCTCCGTGC 59.963 45.833 15.24 4.69 39.19 5.34
2281 4247 3.957497 AGAGTCAGATTAATCTCCGTGCT 59.043 43.478 15.24 8.77 34.22 4.40
2282 4248 4.047822 GAGTCAGATTAATCTCCGTGCTG 58.952 47.826 15.24 3.84 34.22 4.41
2283 4249 3.126831 GTCAGATTAATCTCCGTGCTGG 58.873 50.000 15.24 2.22 34.22 4.85
2284 4250 1.869767 CAGATTAATCTCCGTGCTGGC 59.130 52.381 15.24 0.00 37.80 4.85
2285 4251 1.486310 AGATTAATCTCCGTGCTGGCA 59.514 47.619 12.37 0.00 37.80 4.92
2286 4252 1.869767 GATTAATCTCCGTGCTGGCAG 59.130 52.381 10.94 10.94 37.80 4.85
2287 4253 0.901827 TTAATCTCCGTGCTGGCAGA 59.098 50.000 20.86 0.00 37.80 4.26
2288 4254 0.901827 TAATCTCCGTGCTGGCAGAA 59.098 50.000 20.86 4.21 37.80 3.02
2289 4255 0.392193 AATCTCCGTGCTGGCAGAAG 60.392 55.000 20.86 8.00 37.80 2.85
2290 4256 1.548357 ATCTCCGTGCTGGCAGAAGT 61.548 55.000 20.86 0.00 37.80 3.01
2291 4257 0.898326 TCTCCGTGCTGGCAGAAGTA 60.898 55.000 20.86 0.00 37.80 2.24
2292 4258 0.459237 CTCCGTGCTGGCAGAAGTAG 60.459 60.000 20.86 1.13 37.80 2.57
2293 4259 1.448540 CCGTGCTGGCAGAAGTAGG 60.449 63.158 20.86 7.98 0.00 3.18
2294 4260 1.448540 CGTGCTGGCAGAAGTAGGG 60.449 63.158 20.86 0.00 0.00 3.53
2295 4261 1.888436 CGTGCTGGCAGAAGTAGGGA 61.888 60.000 20.86 0.00 0.00 4.20
2296 4262 0.107945 GTGCTGGCAGAAGTAGGGAG 60.108 60.000 20.86 0.00 0.00 4.30
2297 4263 0.545309 TGCTGGCAGAAGTAGGGAGT 60.545 55.000 20.86 0.00 0.00 3.85
2298 4264 0.615850 GCTGGCAGAAGTAGGGAGTT 59.384 55.000 20.86 0.00 0.00 3.01
2299 4265 1.003696 GCTGGCAGAAGTAGGGAGTTT 59.996 52.381 20.86 0.00 0.00 2.66
2300 4266 2.553247 GCTGGCAGAAGTAGGGAGTTTT 60.553 50.000 20.86 0.00 0.00 2.43
2301 4267 3.077359 CTGGCAGAAGTAGGGAGTTTTG 58.923 50.000 9.42 0.00 0.00 2.44
2302 4268 2.224769 TGGCAGAAGTAGGGAGTTTTGG 60.225 50.000 0.00 0.00 0.00 3.28
2303 4269 2.224793 GGCAGAAGTAGGGAGTTTTGGT 60.225 50.000 0.00 0.00 0.00 3.67
2304 4270 2.814336 GCAGAAGTAGGGAGTTTTGGTG 59.186 50.000 0.00 0.00 0.00 4.17
2305 4271 3.496160 GCAGAAGTAGGGAGTTTTGGTGA 60.496 47.826 0.00 0.00 0.00 4.02
2306 4272 4.714632 CAGAAGTAGGGAGTTTTGGTGAA 58.285 43.478 0.00 0.00 0.00 3.18
2307 4273 5.130350 CAGAAGTAGGGAGTTTTGGTGAAA 58.870 41.667 0.00 0.00 0.00 2.69
2308 4274 5.239525 CAGAAGTAGGGAGTTTTGGTGAAAG 59.760 44.000 0.00 0.00 0.00 2.62
2309 4275 5.132144 AGAAGTAGGGAGTTTTGGTGAAAGA 59.868 40.000 0.00 0.00 0.00 2.52
2310 4276 5.584551 AGTAGGGAGTTTTGGTGAAAGAT 57.415 39.130 0.00 0.00 0.00 2.40
2311 4277 5.316987 AGTAGGGAGTTTTGGTGAAAGATG 58.683 41.667 0.00 0.00 0.00 2.90
2312 4278 2.893489 AGGGAGTTTTGGTGAAAGATGC 59.107 45.455 0.00 0.00 0.00 3.91
2313 4279 2.627699 GGGAGTTTTGGTGAAAGATGCA 59.372 45.455 0.00 0.00 0.00 3.96
2314 4280 3.069443 GGGAGTTTTGGTGAAAGATGCAA 59.931 43.478 0.00 0.00 0.00 4.08
2315 4281 4.051237 GGAGTTTTGGTGAAAGATGCAAC 58.949 43.478 0.00 0.00 0.00 4.17
2316 4282 4.202151 GGAGTTTTGGTGAAAGATGCAACT 60.202 41.667 0.00 0.00 0.00 3.16
2317 4283 4.685924 AGTTTTGGTGAAAGATGCAACTG 58.314 39.130 0.00 0.00 0.00 3.16
2318 4284 4.402155 AGTTTTGGTGAAAGATGCAACTGA 59.598 37.500 0.00 0.00 0.00 3.41
2319 4285 4.998671 TTTGGTGAAAGATGCAACTGAA 57.001 36.364 0.00 0.00 0.00 3.02
2320 4286 4.998671 TTGGTGAAAGATGCAACTGAAA 57.001 36.364 0.00 0.00 0.00 2.69
2321 4287 4.998671 TGGTGAAAGATGCAACTGAAAA 57.001 36.364 0.00 0.00 0.00 2.29
2322 4288 5.336150 TGGTGAAAGATGCAACTGAAAAA 57.664 34.783 0.00 0.00 0.00 1.94
2323 4289 5.916318 TGGTGAAAGATGCAACTGAAAAAT 58.084 33.333 0.00 0.00 0.00 1.82
2324 4290 6.347696 TGGTGAAAGATGCAACTGAAAAATT 58.652 32.000 0.00 0.00 0.00 1.82
2325 4291 7.495901 TGGTGAAAGATGCAACTGAAAAATTA 58.504 30.769 0.00 0.00 0.00 1.40
2326 4292 8.149647 TGGTGAAAGATGCAACTGAAAAATTAT 58.850 29.630 0.00 0.00 0.00 1.28
2327 4293 9.638239 GGTGAAAGATGCAACTGAAAAATTATA 57.362 29.630 0.00 0.00 0.00 0.98
2331 4297 8.707938 AAGATGCAACTGAAAAATTATAAGGC 57.292 30.769 0.00 0.00 0.00 4.35
2332 4298 8.071177 AGATGCAACTGAAAAATTATAAGGCT 57.929 30.769 0.00 0.00 0.00 4.58
2333 4299 8.193438 AGATGCAACTGAAAAATTATAAGGCTC 58.807 33.333 0.00 0.00 0.00 4.70
2334 4300 6.321717 TGCAACTGAAAAATTATAAGGCTCG 58.678 36.000 0.00 0.00 0.00 5.03
2335 4301 6.150307 TGCAACTGAAAAATTATAAGGCTCGA 59.850 34.615 0.00 0.00 0.00 4.04
2336 4302 7.148086 TGCAACTGAAAAATTATAAGGCTCGAT 60.148 33.333 0.00 0.00 0.00 3.59
2337 4303 7.702348 GCAACTGAAAAATTATAAGGCTCGATT 59.298 33.333 0.00 0.00 0.00 3.34
2338 4304 9.226345 CAACTGAAAAATTATAAGGCTCGATTC 57.774 33.333 0.00 0.00 0.00 2.52
2339 4305 7.931275 ACTGAAAAATTATAAGGCTCGATTCC 58.069 34.615 0.00 0.00 0.00 3.01
2340 4306 7.775561 ACTGAAAAATTATAAGGCTCGATTCCT 59.224 33.333 0.88 0.88 34.90 3.36
2341 4307 9.273016 CTGAAAAATTATAAGGCTCGATTCCTA 57.727 33.333 6.78 0.00 32.65 2.94
2342 4308 9.273016 TGAAAAATTATAAGGCTCGATTCCTAG 57.727 33.333 6.78 0.00 32.65 3.02
2343 4309 7.674471 AAAATTATAAGGCTCGATTCCTAGC 57.326 36.000 6.78 0.00 38.03 3.42
2344 4310 6.360370 AATTATAAGGCTCGATTCCTAGCA 57.640 37.500 6.78 0.00 40.61 3.49
2345 4311 5.801531 TTATAAGGCTCGATTCCTAGCAA 57.198 39.130 6.78 0.21 40.61 3.91
2346 4312 4.899352 ATAAGGCTCGATTCCTAGCAAT 57.101 40.909 6.78 0.00 40.61 3.56
2347 4313 3.567478 AAGGCTCGATTCCTAGCAATT 57.433 42.857 6.78 0.84 40.61 2.32
2348 4314 3.567478 AGGCTCGATTCCTAGCAATTT 57.433 42.857 4.71 0.00 40.61 1.82
2349 4315 3.471680 AGGCTCGATTCCTAGCAATTTC 58.528 45.455 4.71 0.00 40.61 2.17
2350 4316 3.118261 AGGCTCGATTCCTAGCAATTTCA 60.118 43.478 4.71 0.00 40.61 2.69
2351 4317 3.817647 GGCTCGATTCCTAGCAATTTCAT 59.182 43.478 7.68 0.00 40.61 2.57
2352 4318 4.997395 GGCTCGATTCCTAGCAATTTCATA 59.003 41.667 7.68 0.00 40.61 2.15
2353 4319 5.645497 GGCTCGATTCCTAGCAATTTCATAT 59.355 40.000 7.68 0.00 40.61 1.78
2354 4320 6.150140 GGCTCGATTCCTAGCAATTTCATATT 59.850 38.462 7.68 0.00 40.61 1.28
2355 4321 7.308830 GGCTCGATTCCTAGCAATTTCATATTT 60.309 37.037 7.68 0.00 40.61 1.40
2356 4322 8.721478 GCTCGATTCCTAGCAATTTCATATTTA 58.279 33.333 0.00 0.00 38.63 1.40
2359 4325 9.994432 CGATTCCTAGCAATTTCATATTTATCC 57.006 33.333 0.00 0.00 0.00 2.59
2362 4328 9.639563 TTCCTAGCAATTTCATATTTATCCACA 57.360 29.630 0.00 0.00 0.00 4.17
2363 4329 9.066892 TCCTAGCAATTTCATATTTATCCACAC 57.933 33.333 0.00 0.00 0.00 3.82
2364 4330 8.849168 CCTAGCAATTTCATATTTATCCACACA 58.151 33.333 0.00 0.00 0.00 3.72
2365 4331 9.669353 CTAGCAATTTCATATTTATCCACACAC 57.331 33.333 0.00 0.00 0.00 3.82
2366 4332 8.065473 AGCAATTTCATATTTATCCACACACA 57.935 30.769 0.00 0.00 0.00 3.72
2367 4333 8.192774 AGCAATTTCATATTTATCCACACACAG 58.807 33.333 0.00 0.00 0.00 3.66
2368 4334 7.436080 GCAATTTCATATTTATCCACACACAGG 59.564 37.037 0.00 0.00 0.00 4.00
2369 4335 6.449635 TTTCATATTTATCCACACACAGGC 57.550 37.500 0.00 0.00 0.00 4.85
2370 4336 4.126437 TCATATTTATCCACACACAGGCG 58.874 43.478 0.00 0.00 0.00 5.52
2371 4337 1.094785 ATTTATCCACACACAGGCGC 58.905 50.000 0.00 0.00 0.00 6.53
2372 4338 0.250510 TTTATCCACACACAGGCGCA 60.251 50.000 10.83 0.00 0.00 6.09
2373 4339 0.953471 TTATCCACACACAGGCGCAC 60.953 55.000 10.83 0.00 0.00 5.34
2376 4342 3.043713 CACACACAGGCGCACGAT 61.044 61.111 10.83 0.00 0.00 3.73
2377 4343 2.280797 ACACACAGGCGCACGATT 60.281 55.556 10.83 0.00 0.00 3.34
2378 4344 1.891919 ACACACAGGCGCACGATTT 60.892 52.632 10.83 0.00 0.00 2.17
2379 4345 1.154413 CACACAGGCGCACGATTTC 60.154 57.895 10.83 0.00 0.00 2.17
2380 4346 1.301716 ACACAGGCGCACGATTTCT 60.302 52.632 10.83 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 1.890174 CCTTTTGGGCCGAATGGAC 59.110 57.895 27.07 0.00 45.75 4.02
25 26 4.432601 CCTTTTGGGCCGAATGGA 57.567 55.556 27.07 4.53 36.79 3.41
44 46 1.096386 TAACGTGGCACTGCGGTTTT 61.096 50.000 16.72 2.47 0.00 2.43
45 47 1.524165 TAACGTGGCACTGCGGTTT 60.524 52.632 16.72 2.80 0.00 3.27
48 50 3.419759 GGTAACGTGGCACTGCGG 61.420 66.667 16.72 2.12 0.00 5.69
50 52 3.053896 GGGGTAACGTGGCACTGC 61.054 66.667 16.72 0.92 37.60 4.40
85 87 0.036164 TGACTTGGGTTGGATCACCG 59.964 55.000 0.00 0.00 37.76 4.94
100 102 0.972883 GTTCCAGTGCTCTCCTGACT 59.027 55.000 0.00 0.00 31.38 3.41
101 103 0.681733 TGTTCCAGTGCTCTCCTGAC 59.318 55.000 0.00 0.00 31.38 3.51
102 104 0.972134 CTGTTCCAGTGCTCTCCTGA 59.028 55.000 0.00 0.00 31.38 3.86
103 105 0.972134 TCTGTTCCAGTGCTCTCCTG 59.028 55.000 0.00 0.00 32.61 3.86
104 106 1.622811 CTTCTGTTCCAGTGCTCTCCT 59.377 52.381 0.00 0.00 32.61 3.69
105 107 1.346068 ACTTCTGTTCCAGTGCTCTCC 59.654 52.381 0.00 0.00 32.61 3.71
115 117 0.868406 CGCCAGTTCACTTCTGTTCC 59.132 55.000 0.00 0.00 0.00 3.62
118 120 1.139058 ACTTCGCCAGTTCACTTCTGT 59.861 47.619 0.00 0.00 27.32 3.41
119 121 1.528586 CACTTCGCCAGTTCACTTCTG 59.471 52.381 0.00 0.00 30.92 3.02
122 124 2.158957 TCTTCACTTCGCCAGTTCACTT 60.159 45.455 0.00 0.00 30.92 3.16
138 145 1.063717 GGCAATCCAATCCCCTCTTCA 60.064 52.381 0.00 0.00 0.00 3.02
174 191 1.909700 TCCACACAGCCAAGGAAATC 58.090 50.000 0.00 0.00 0.00 2.17
178 195 1.059584 TCCTTCCACACAGCCAAGGA 61.060 55.000 0.00 0.00 41.79 3.36
179 196 0.607489 CTCCTTCCACACAGCCAAGG 60.607 60.000 0.00 0.00 37.36 3.61
188 205 1.599606 GAGAGCTCGCTCCTTCCACA 61.600 60.000 14.83 0.00 43.70 4.17
263 290 1.234615 TTAACCAGCTGCAAGGCGAC 61.235 55.000 8.66 0.00 37.29 5.19
266 293 1.403323 GAGATTAACCAGCTGCAAGGC 59.597 52.381 8.66 0.00 0.00 4.35
273 300 1.834263 AGCGGAAGAGATTAACCAGCT 59.166 47.619 0.00 0.00 0.00 4.24
275 302 3.118956 ACAGAGCGGAAGAGATTAACCAG 60.119 47.826 0.00 0.00 0.00 4.00
296 323 3.056035 ACGGGGAGTAACAGATCAAGAAC 60.056 47.826 0.00 0.00 0.00 3.01
298 327 2.758979 GACGGGGAGTAACAGATCAAGA 59.241 50.000 0.00 0.00 0.00 3.02
322 352 4.932200 CGAAGCTACAAAGAACCAGAAGAT 59.068 41.667 0.00 0.00 0.00 2.40
397 451 1.095228 ACCAAACCACACAGACTGCG 61.095 55.000 1.25 0.00 0.00 5.18
404 458 3.367498 GCAACTACAAACCAAACCACACA 60.367 43.478 0.00 0.00 0.00 3.72
504 561 8.966155 AGATTAATTTGAACCCCCTTTTCTTA 57.034 30.769 0.00 0.00 0.00 2.10
515 572 4.110036 AGCGCCAAGATTAATTTGAACC 57.890 40.909 2.29 0.00 0.00 3.62
517 574 7.045416 TCTACTAGCGCCAAGATTAATTTGAA 58.955 34.615 13.83 0.00 0.00 2.69
564 621 9.087871 TCTCACCTCATAAATTTTCCATCAAAA 57.912 29.630 0.00 0.00 38.38 2.44
568 625 8.566260 CAGATCTCACCTCATAAATTTTCCATC 58.434 37.037 0.00 0.00 0.00 3.51
573 631 8.049117 TGCTACAGATCTCACCTCATAAATTTT 58.951 33.333 0.00 0.00 0.00 1.82
577 636 6.515696 CGATGCTACAGATCTCACCTCATAAA 60.516 42.308 0.00 0.00 0.00 1.40
582 641 2.621055 ACGATGCTACAGATCTCACCTC 59.379 50.000 0.00 0.00 0.00 3.85
708 781 0.392998 ATTACTCCAGCCGTGCCTTG 60.393 55.000 0.00 0.00 0.00 3.61
909 1010 5.048083 TCGTGCTTAAATGATTTCCTGCTTT 60.048 36.000 0.00 0.00 0.00 3.51
912 1013 4.355543 TCGTGCTTAAATGATTTCCTGC 57.644 40.909 0.00 0.00 0.00 4.85
920 1037 5.699001 ACACAGTAACATCGTGCTTAAATGA 59.301 36.000 0.00 0.00 33.89 2.57
931 1048 6.509517 GCACCACATTATACACAGTAACATCG 60.510 42.308 0.00 0.00 0.00 3.84
1105 1229 4.256920 CCATTCACTGAAGTCGGATTTCT 58.743 43.478 13.42 0.00 0.00 2.52
1227 1355 2.109126 GGAGTCCATCGCTGTTGGC 61.109 63.158 3.60 0.00 34.06 4.52
1452 1581 2.936202 ACCAACTGAAGCACAACAGAT 58.064 42.857 0.00 0.00 37.54 2.90
1542 1675 5.122396 GCAACACAACACCAAATAAAACCAA 59.878 36.000 0.00 0.00 0.00 3.67
1668 3618 7.398047 TCCAGTGAGCTTATAAGGTAAACACTA 59.602 37.037 25.14 15.10 37.15 2.74
1675 3625 7.563924 ACATAGTTCCAGTGAGCTTATAAGGTA 59.436 37.037 16.84 3.89 36.78 3.08
1684 3634 3.957497 CCTCTACATAGTTCCAGTGAGCT 59.043 47.826 0.00 0.00 35.98 4.09
1692 3642 5.428253 TCATTTGCACCTCTACATAGTTCC 58.572 41.667 0.00 0.00 0.00 3.62
1762 3712 0.545071 TGGACAGATGGCTGGTGAGA 60.545 55.000 0.00 0.00 46.60 3.27
1823 3777 9.817365 CATCTAAACAAAATATATCGCTGGAAG 57.183 33.333 0.00 0.00 0.00 3.46
1841 3795 4.802876 GCACCATGCTAGACATCTAAAC 57.197 45.455 0.00 0.00 40.96 2.01
1865 3819 8.475331 AAGTTCATAACTACACCTTGATTACG 57.525 34.615 0.00 0.00 41.91 3.18
1965 3928 9.747898 TGATGGGTTTTCATAGTTGTAAATAGT 57.252 29.630 0.00 0.00 0.00 2.12
1969 3932 8.739039 CATCTGATGGGTTTTCATAGTTGTAAA 58.261 33.333 9.82 0.00 0.00 2.01
1983 3946 0.182061 ATGAGCGCATCTGATGGGTT 59.818 50.000 28.27 24.77 44.22 4.11
1985 3948 2.174363 TTATGAGCGCATCTGATGGG 57.826 50.000 25.26 25.26 45.06 4.00
1987 3950 2.096565 CCGTTTATGAGCGCATCTGATG 60.097 50.000 11.47 13.26 35.94 3.07
1991 3954 1.665679 CAACCGTTTATGAGCGCATCT 59.334 47.619 11.47 0.00 35.94 2.90
1997 3960 5.734855 ACATATCACAACCGTTTATGAGC 57.265 39.130 7.41 0.00 0.00 4.26
2023 3986 9.542462 GTAGCTGACAAATGACCATAACTAATA 57.458 33.333 0.00 0.00 0.00 0.98
2072 4036 8.657729 CAATCAATAAATTTGCATGTACAAGCA 58.342 29.630 21.06 21.06 39.32 3.91
2101 4065 6.561614 TGATGGACATCTTTTCGTACTAGAC 58.438 40.000 12.97 0.00 38.60 2.59
2126 4090 8.197592 ACTACGATTATAACACCCCATCAATA 57.802 34.615 0.00 0.00 0.00 1.90
2127 4091 7.074653 ACTACGATTATAACACCCCATCAAT 57.925 36.000 0.00 0.00 0.00 2.57
2136 4102 9.027129 TGCAAGTTCATACTACGATTATAACAC 57.973 33.333 0.00 0.00 33.17 3.32
2150 4116 7.201384 GCAAGAAAAGCTATTGCAAGTTCATAC 60.201 37.037 16.50 0.00 46.64 2.39
2163 4129 4.411013 AGGGAAAGTGCAAGAAAAGCTAT 58.589 39.130 0.00 0.00 0.00 2.97
2165 4131 2.670939 AGGGAAAGTGCAAGAAAAGCT 58.329 42.857 0.00 0.00 0.00 3.74
2171 4137 2.733956 ACAACAAGGGAAAGTGCAAGA 58.266 42.857 0.00 0.00 0.00 3.02
2186 4152 3.655615 AGTTTGGGACCACTTACAACA 57.344 42.857 0.00 0.00 0.00 3.33
2190 4156 4.332828 AGCATTAGTTTGGGACCACTTAC 58.667 43.478 0.00 0.00 0.00 2.34
2197 4163 7.631717 AGAAAATAGAGCATTAGTTTGGGAC 57.368 36.000 0.00 0.00 0.00 4.46
2201 4167 9.912634 TTTCCAAGAAAATAGAGCATTAGTTTG 57.087 29.630 0.00 0.00 0.00 2.93
2215 4181 6.210185 CAGTCATCCTCCTTTTCCAAGAAAAT 59.790 38.462 3.17 0.00 30.57 1.82
2219 4185 3.560025 GCAGTCATCCTCCTTTTCCAAGA 60.560 47.826 0.00 0.00 30.57 3.02
2220 4186 2.751806 GCAGTCATCCTCCTTTTCCAAG 59.248 50.000 0.00 0.00 0.00 3.61
2221 4187 2.376518 AGCAGTCATCCTCCTTTTCCAA 59.623 45.455 0.00 0.00 0.00 3.53
2222 4188 1.988107 AGCAGTCATCCTCCTTTTCCA 59.012 47.619 0.00 0.00 0.00 3.53
2223 4189 2.238395 AGAGCAGTCATCCTCCTTTTCC 59.762 50.000 0.00 0.00 0.00 3.13
2224 4190 3.625649 AGAGCAGTCATCCTCCTTTTC 57.374 47.619 0.00 0.00 0.00 2.29
2225 4191 5.707066 AATAGAGCAGTCATCCTCCTTTT 57.293 39.130 0.00 0.00 0.00 2.27
2226 4192 5.435291 CAAATAGAGCAGTCATCCTCCTTT 58.565 41.667 0.00 0.00 0.00 3.11
2227 4193 4.685575 GCAAATAGAGCAGTCATCCTCCTT 60.686 45.833 0.00 0.00 0.00 3.36
2228 4194 3.181456 GCAAATAGAGCAGTCATCCTCCT 60.181 47.826 0.00 0.00 0.00 3.69
2229 4195 3.137533 GCAAATAGAGCAGTCATCCTCC 58.862 50.000 0.00 0.00 0.00 4.30
2230 4196 3.801698 TGCAAATAGAGCAGTCATCCTC 58.198 45.455 0.00 0.00 37.02 3.71
2231 4197 3.920231 TGCAAATAGAGCAGTCATCCT 57.080 42.857 0.00 0.00 37.02 3.24
2232 4198 6.624352 TTATTGCAAATAGAGCAGTCATCC 57.376 37.500 1.71 0.00 43.75 3.51
2233 4199 8.400947 TCTTTTATTGCAAATAGAGCAGTCATC 58.599 33.333 1.71 0.00 43.75 2.92
2234 4200 8.284945 TCTTTTATTGCAAATAGAGCAGTCAT 57.715 30.769 1.71 0.00 43.75 3.06
2235 4201 7.607607 TCTCTTTTATTGCAAATAGAGCAGTCA 59.392 33.333 18.23 5.69 43.75 3.41
2236 4202 7.978982 TCTCTTTTATTGCAAATAGAGCAGTC 58.021 34.615 18.23 0.00 43.75 3.51
2237 4203 7.609532 ACTCTCTTTTATTGCAAATAGAGCAGT 59.390 33.333 18.23 17.77 43.75 4.40
2238 4204 7.983307 ACTCTCTTTTATTGCAAATAGAGCAG 58.017 34.615 18.23 17.38 43.75 4.24
2239 4205 7.607607 TGACTCTCTTTTATTGCAAATAGAGCA 59.392 33.333 18.23 14.48 39.16 4.26
2240 4206 7.978982 TGACTCTCTTTTATTGCAAATAGAGC 58.021 34.615 18.23 12.98 39.16 4.09
2241 4207 9.376075 TCTGACTCTCTTTTATTGCAAATAGAG 57.624 33.333 1.71 12.76 40.40 2.43
2242 4208 9.896645 ATCTGACTCTCTTTTATTGCAAATAGA 57.103 29.630 1.71 3.24 0.00 1.98
2248 4214 9.896645 AGATTAATCTGACTCTCTTTTATTGCA 57.103 29.630 17.26 0.00 35.42 4.08
2251 4217 9.757227 CGGAGATTAATCTGACTCTCTTTTATT 57.243 33.333 22.61 0.00 37.25 1.40
2252 4218 8.919145 ACGGAGATTAATCTGACTCTCTTTTAT 58.081 33.333 22.61 0.00 37.25 1.40
2253 4219 8.191446 CACGGAGATTAATCTGACTCTCTTTTA 58.809 37.037 22.61 0.00 37.25 1.52
2254 4220 7.038659 CACGGAGATTAATCTGACTCTCTTTT 58.961 38.462 22.61 0.00 37.25 2.27
2255 4221 6.568869 CACGGAGATTAATCTGACTCTCTTT 58.431 40.000 22.61 0.00 37.25 2.52
2256 4222 5.451242 GCACGGAGATTAATCTGACTCTCTT 60.451 44.000 22.61 0.00 37.25 2.85
2257 4223 4.037446 GCACGGAGATTAATCTGACTCTCT 59.963 45.833 22.61 0.00 37.25 3.10
2258 4224 4.037446 AGCACGGAGATTAATCTGACTCTC 59.963 45.833 22.61 7.76 37.25 3.20
2259 4225 3.957497 AGCACGGAGATTAATCTGACTCT 59.043 43.478 22.61 9.69 37.25 3.24
2260 4226 4.047822 CAGCACGGAGATTAATCTGACTC 58.952 47.826 22.61 8.17 37.25 3.36
2261 4227 3.181471 CCAGCACGGAGATTAATCTGACT 60.181 47.826 22.61 9.10 37.25 3.41
2262 4228 3.126831 CCAGCACGGAGATTAATCTGAC 58.873 50.000 22.61 13.50 37.25 3.51
2263 4229 2.483714 GCCAGCACGGAGATTAATCTGA 60.484 50.000 22.61 0.00 37.25 3.27
2264 4230 1.869767 GCCAGCACGGAGATTAATCTG 59.130 52.381 22.61 11.50 37.25 2.90
2265 4231 1.486310 TGCCAGCACGGAGATTAATCT 59.514 47.619 17.96 17.96 40.50 2.40
2266 4232 1.869767 CTGCCAGCACGGAGATTAATC 59.130 52.381 7.41 7.41 36.56 1.75
2267 4233 1.486310 TCTGCCAGCACGGAGATTAAT 59.514 47.619 0.00 0.00 36.56 1.40
2268 4234 0.901827 TCTGCCAGCACGGAGATTAA 59.098 50.000 0.00 0.00 36.56 1.40
2269 4235 0.901827 TTCTGCCAGCACGGAGATTA 59.098 50.000 0.00 0.00 36.56 1.75
2270 4236 0.392193 CTTCTGCCAGCACGGAGATT 60.392 55.000 0.00 0.00 36.56 2.40
2271 4237 1.220206 CTTCTGCCAGCACGGAGAT 59.780 57.895 0.00 0.00 36.56 2.75
2272 4238 0.898326 TACTTCTGCCAGCACGGAGA 60.898 55.000 0.00 0.00 36.56 3.71
2273 4239 0.459237 CTACTTCTGCCAGCACGGAG 60.459 60.000 0.00 0.00 36.56 4.63
2274 4240 1.591703 CTACTTCTGCCAGCACGGA 59.408 57.895 0.00 0.00 36.56 4.69
2275 4241 1.448540 CCTACTTCTGCCAGCACGG 60.449 63.158 0.00 0.00 38.11 4.94
2276 4242 1.448540 CCCTACTTCTGCCAGCACG 60.449 63.158 0.00 0.00 0.00 5.34
2277 4243 0.107945 CTCCCTACTTCTGCCAGCAC 60.108 60.000 0.00 0.00 0.00 4.40
2278 4244 0.545309 ACTCCCTACTTCTGCCAGCA 60.545 55.000 0.00 0.00 0.00 4.41
2279 4245 0.615850 AACTCCCTACTTCTGCCAGC 59.384 55.000 0.00 0.00 0.00 4.85
2280 4246 3.077359 CAAAACTCCCTACTTCTGCCAG 58.923 50.000 0.00 0.00 0.00 4.85
2281 4247 2.224769 CCAAAACTCCCTACTTCTGCCA 60.225 50.000 0.00 0.00 0.00 4.92
2282 4248 2.224793 ACCAAAACTCCCTACTTCTGCC 60.225 50.000 0.00 0.00 0.00 4.85
2283 4249 2.814336 CACCAAAACTCCCTACTTCTGC 59.186 50.000 0.00 0.00 0.00 4.26
2284 4250 4.351874 TCACCAAAACTCCCTACTTCTG 57.648 45.455 0.00 0.00 0.00 3.02
2285 4251 5.132144 TCTTTCACCAAAACTCCCTACTTCT 59.868 40.000 0.00 0.00 0.00 2.85
2286 4252 5.374071 TCTTTCACCAAAACTCCCTACTTC 58.626 41.667 0.00 0.00 0.00 3.01
2287 4253 5.382664 TCTTTCACCAAAACTCCCTACTT 57.617 39.130 0.00 0.00 0.00 2.24
2288 4254 5.316987 CATCTTTCACCAAAACTCCCTACT 58.683 41.667 0.00 0.00 0.00 2.57
2289 4255 4.082733 GCATCTTTCACCAAAACTCCCTAC 60.083 45.833 0.00 0.00 0.00 3.18
2290 4256 4.079253 GCATCTTTCACCAAAACTCCCTA 58.921 43.478 0.00 0.00 0.00 3.53
2291 4257 2.893489 GCATCTTTCACCAAAACTCCCT 59.107 45.455 0.00 0.00 0.00 4.20
2292 4258 2.627699 TGCATCTTTCACCAAAACTCCC 59.372 45.455 0.00 0.00 0.00 4.30
2293 4259 4.051237 GTTGCATCTTTCACCAAAACTCC 58.949 43.478 0.00 0.00 0.00 3.85
2294 4260 4.741676 CAGTTGCATCTTTCACCAAAACTC 59.258 41.667 0.00 0.00 0.00 3.01
2295 4261 4.402155 TCAGTTGCATCTTTCACCAAAACT 59.598 37.500 0.00 0.00 0.00 2.66
2296 4262 4.681744 TCAGTTGCATCTTTCACCAAAAC 58.318 39.130 0.00 0.00 0.00 2.43
2297 4263 4.998671 TCAGTTGCATCTTTCACCAAAA 57.001 36.364 0.00 0.00 0.00 2.44
2298 4264 4.998671 TTCAGTTGCATCTTTCACCAAA 57.001 36.364 0.00 0.00 0.00 3.28
2299 4265 4.998671 TTTCAGTTGCATCTTTCACCAA 57.001 36.364 0.00 0.00 0.00 3.67
2300 4266 4.998671 TTTTCAGTTGCATCTTTCACCA 57.001 36.364 0.00 0.00 0.00 4.17
2301 4267 6.849588 AATTTTTCAGTTGCATCTTTCACC 57.150 33.333 0.00 0.00 0.00 4.02
2305 4271 9.154847 GCCTTATAATTTTTCAGTTGCATCTTT 57.845 29.630 0.00 0.00 0.00 2.52
2306 4272 8.534496 AGCCTTATAATTTTTCAGTTGCATCTT 58.466 29.630 0.00 0.00 0.00 2.40
2307 4273 8.071177 AGCCTTATAATTTTTCAGTTGCATCT 57.929 30.769 0.00 0.00 0.00 2.90
2308 4274 7.166473 CGAGCCTTATAATTTTTCAGTTGCATC 59.834 37.037 0.00 0.00 0.00 3.91
2309 4275 6.974622 CGAGCCTTATAATTTTTCAGTTGCAT 59.025 34.615 0.00 0.00 0.00 3.96
2310 4276 6.150307 TCGAGCCTTATAATTTTTCAGTTGCA 59.850 34.615 0.00 0.00 0.00 4.08
2311 4277 6.551736 TCGAGCCTTATAATTTTTCAGTTGC 58.448 36.000 0.00 0.00 0.00 4.17
2312 4278 9.226345 GAATCGAGCCTTATAATTTTTCAGTTG 57.774 33.333 0.00 0.00 0.00 3.16
2313 4279 8.406297 GGAATCGAGCCTTATAATTTTTCAGTT 58.594 33.333 0.00 0.00 0.00 3.16
2314 4280 7.775561 AGGAATCGAGCCTTATAATTTTTCAGT 59.224 33.333 3.89 0.00 29.44 3.41
2315 4281 8.159344 AGGAATCGAGCCTTATAATTTTTCAG 57.841 34.615 3.89 0.00 29.44 3.02
2316 4282 9.273016 CTAGGAATCGAGCCTTATAATTTTTCA 57.727 33.333 14.08 0.00 36.96 2.69
2317 4283 8.231161 GCTAGGAATCGAGCCTTATAATTTTTC 58.769 37.037 14.08 0.00 35.92 2.29
2318 4284 7.719633 TGCTAGGAATCGAGCCTTATAATTTTT 59.280 33.333 14.08 0.00 40.28 1.94
2319 4285 7.224297 TGCTAGGAATCGAGCCTTATAATTTT 58.776 34.615 14.08 0.00 40.28 1.82
2320 4286 6.769512 TGCTAGGAATCGAGCCTTATAATTT 58.230 36.000 14.08 0.00 40.28 1.82
2321 4287 6.360370 TGCTAGGAATCGAGCCTTATAATT 57.640 37.500 14.08 0.00 40.28 1.40
2322 4288 6.360370 TTGCTAGGAATCGAGCCTTATAAT 57.640 37.500 14.08 0.00 40.28 1.28
2323 4289 5.801531 TTGCTAGGAATCGAGCCTTATAA 57.198 39.130 14.08 5.56 40.28 0.98
2324 4290 6.360370 AATTGCTAGGAATCGAGCCTTATA 57.640 37.500 10.17 0.00 40.28 0.98
2325 4291 4.899352 ATTGCTAGGAATCGAGCCTTAT 57.101 40.909 14.08 2.64 40.28 1.73
2326 4292 4.689612 AATTGCTAGGAATCGAGCCTTA 57.310 40.909 10.17 0.00 40.28 2.69
2327 4293 3.567478 AATTGCTAGGAATCGAGCCTT 57.433 42.857 10.17 0.00 40.28 4.35
2328 4294 3.118261 TGAAATTGCTAGGAATCGAGCCT 60.118 43.478 10.17 13.46 40.28 4.58
2329 4295 3.206150 TGAAATTGCTAGGAATCGAGCC 58.794 45.455 10.17 0.00 40.28 4.70
2330 4296 6.734104 ATATGAAATTGCTAGGAATCGAGC 57.266 37.500 10.17 1.40 41.19 5.03
2333 4299 9.994432 GGATAAATATGAAATTGCTAGGAATCG 57.006 33.333 10.17 0.00 0.00 3.34
2336 4302 9.639563 TGTGGATAAATATGAAATTGCTAGGAA 57.360 29.630 0.00 0.00 0.00 3.36
2337 4303 9.066892 GTGTGGATAAATATGAAATTGCTAGGA 57.933 33.333 0.00 0.00 0.00 2.94
2338 4304 8.849168 TGTGTGGATAAATATGAAATTGCTAGG 58.151 33.333 0.00 0.00 0.00 3.02
2339 4305 9.669353 GTGTGTGGATAAATATGAAATTGCTAG 57.331 33.333 0.00 0.00 0.00 3.42
2340 4306 9.183368 TGTGTGTGGATAAATATGAAATTGCTA 57.817 29.630 0.00 0.00 0.00 3.49
2341 4307 8.065473 TGTGTGTGGATAAATATGAAATTGCT 57.935 30.769 0.00 0.00 0.00 3.91
2342 4308 7.436080 CCTGTGTGTGGATAAATATGAAATTGC 59.564 37.037 0.00 0.00 0.00 3.56
2343 4309 7.436080 GCCTGTGTGTGGATAAATATGAAATTG 59.564 37.037 0.00 0.00 0.00 2.32
2344 4310 7.491682 GCCTGTGTGTGGATAAATATGAAATT 58.508 34.615 0.00 0.00 0.00 1.82
2345 4311 6.238731 CGCCTGTGTGTGGATAAATATGAAAT 60.239 38.462 0.00 0.00 0.00 2.17
2346 4312 5.065859 CGCCTGTGTGTGGATAAATATGAAA 59.934 40.000 0.00 0.00 0.00 2.69
2347 4313 4.574421 CGCCTGTGTGTGGATAAATATGAA 59.426 41.667 0.00 0.00 0.00 2.57
2348 4314 4.126437 CGCCTGTGTGTGGATAAATATGA 58.874 43.478 0.00 0.00 0.00 2.15
2349 4315 3.303990 GCGCCTGTGTGTGGATAAATATG 60.304 47.826 0.00 0.00 0.00 1.78
2350 4316 2.878406 GCGCCTGTGTGTGGATAAATAT 59.122 45.455 0.00 0.00 0.00 1.28
2351 4317 2.285083 GCGCCTGTGTGTGGATAAATA 58.715 47.619 0.00 0.00 0.00 1.40
2352 4318 1.094785 GCGCCTGTGTGTGGATAAAT 58.905 50.000 0.00 0.00 0.00 1.40
2353 4319 0.250510 TGCGCCTGTGTGTGGATAAA 60.251 50.000 4.18 0.00 0.00 1.40
2354 4320 0.953471 GTGCGCCTGTGTGTGGATAA 60.953 55.000 4.18 0.00 0.00 1.75
2355 4321 1.375396 GTGCGCCTGTGTGTGGATA 60.375 57.895 4.18 0.00 0.00 2.59
2356 4322 2.669569 GTGCGCCTGTGTGTGGAT 60.670 61.111 4.18 0.00 0.00 3.41
2359 4325 2.116736 AAATCGTGCGCCTGTGTGTG 62.117 55.000 4.18 0.00 0.00 3.82
2360 4326 1.841663 GAAATCGTGCGCCTGTGTGT 61.842 55.000 4.18 0.00 0.00 3.72
2361 4327 1.154413 GAAATCGTGCGCCTGTGTG 60.154 57.895 4.18 0.00 0.00 3.82
2362 4328 1.301716 AGAAATCGTGCGCCTGTGT 60.302 52.632 4.18 0.00 0.00 3.72
2363 4329 3.566261 AGAAATCGTGCGCCTGTG 58.434 55.556 4.18 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.