Multiple sequence alignment - TraesCS1D01G260700

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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 TraesCS1D01G260700 chr1D 100.000 2464 0 0 1 2464 355087002 355089465 0.000000e+00 4551.0
1 TraesCS1D01G260700 chr1B 91.782 1302 48 22 329 1588 476919610 476920894 0.000000e+00 1757.0
2 TraesCS1D01G260700 chr1B 84.142 309 27 6 2060 2360 476924798 476925092 1.870000e-71 279.0
3 TraesCS1D01G260700 chr1B 89.683 126 7 2 1792 1917 476924653 476924772 3.280000e-34 156.0
4 TraesCS1D01G260700 chr1B 83.495 103 8 6 1707 1800 476922901 476923003 1.210000e-13 87.9
5 TraesCS1D01G260700 chr1B 90.909 44 4 0 1945 1988 476924730 476924773 2.650000e-05 60.2
6 TraesCS1D01G260700 chr1A 85.595 1680 95 56 322 1911 454532827 454534449 0.000000e+00 1626.0
7 TraesCS1D01G260700 chr1A 86.435 317 25 9 1 310 454529879 454530184 5.080000e-87 331.0
8 TraesCS1D01G260700 chr1A 82.609 322 13 16 2060 2360 454534468 454534767 6.810000e-61 244.0
9 TraesCS1D01G260700 chr2B 95.833 72 3 0 2393 2464 683763360 683763431 1.550000e-22 117.0
10 TraesCS1D01G260700 chr2B 95.833 72 3 0 2393 2464 683763793 683763864 1.550000e-22 117.0
11 TraesCS1D01G260700 chr5A 95.652 69 3 0 2396 2464 448573411 448573343 7.200000e-21 111.0
12 TraesCS1D01G260700 chr5A 79.787 94 15 2 64 157 455463510 455463599 5.690000e-07 65.8
13 TraesCS1D01G260700 chr3A 92.754 69 5 0 2396 2464 747398346 747398278 1.560000e-17 100.0
14 TraesCS1D01G260700 chr4B 90.000 60 6 0 2405 2464 96450914 96450855 7.310000e-11 78.7
15 TraesCS1D01G260700 chr3D 100.000 30 0 0 2432 2461 51790415 51790444 3.420000e-04 56.5


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 TraesCS1D01G260700 chr1D 355087002 355089465 2463 False 4551.000000 4551 100.000000 1 2464 1 chr1D.!!$F1 2463
1 TraesCS1D01G260700 chr1B 476919610 476925092 5482 False 468.020000 1757 88.002200 329 2360 5 chr1B.!!$F1 2031
2 TraesCS1D01G260700 chr1A 454529879 454534767 4888 False 733.666667 1626 84.879667 1 2360 3 chr1A.!!$F1 2359

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
210 216 0.110328 TCTCACGAGCGAAGAACGAC 60.11 55.0 0.0 0.0 45.77 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2000 8303 0.037975 TTTACCGGGTTGAGAGCGAC 60.038 55.0 4.31 0.0 0.0 5.19 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
56 62 4.744570 CGCCAAACAACTCTACTCTATCA 58.255 43.478 0.00 0.00 0.00 2.15
77 83 2.047274 CCGACAGCAACCCGACAT 60.047 61.111 0.00 0.00 0.00 3.06
81 87 1.470805 CGACAGCAACCCGACATGATA 60.471 52.381 0.00 0.00 0.00 2.15
90 96 2.880268 ACCCGACATGATATACGAACGA 59.120 45.455 0.00 0.00 0.00 3.85
126 132 6.016610 TCCAGAACATAGTTAAAACACAAGCC 60.017 38.462 0.00 0.00 0.00 4.35
131 137 5.243730 ACATAGTTAAAACACAAGCCAGCAT 59.756 36.000 0.00 0.00 0.00 3.79
133 139 5.376854 AGTTAAAACACAAGCCAGCATAG 57.623 39.130 0.00 0.00 0.00 2.23
197 203 7.545965 ACTTGATACAAAGGAGTTAATCTCACG 59.454 37.037 7.18 0.00 44.40 4.35
198 204 7.165460 TGATACAAAGGAGTTAATCTCACGA 57.835 36.000 0.00 0.00 44.40 4.35
200 206 4.246458 ACAAAGGAGTTAATCTCACGAGC 58.754 43.478 0.00 0.00 44.40 5.03
201 207 2.853731 AGGAGTTAATCTCACGAGCG 57.146 50.000 0.00 0.00 44.40 5.03
202 208 2.366533 AGGAGTTAATCTCACGAGCGA 58.633 47.619 0.00 0.00 44.40 4.93
203 209 2.753452 AGGAGTTAATCTCACGAGCGAA 59.247 45.455 0.00 0.00 44.40 4.70
204 210 3.109619 GGAGTTAATCTCACGAGCGAAG 58.890 50.000 0.00 0.00 44.40 3.79
205 211 3.181499 GGAGTTAATCTCACGAGCGAAGA 60.181 47.826 0.00 0.00 44.40 2.87
206 212 4.413087 GAGTTAATCTCACGAGCGAAGAA 58.587 43.478 0.00 0.00 42.34 2.52
207 213 4.167268 AGTTAATCTCACGAGCGAAGAAC 58.833 43.478 0.00 0.00 0.00 3.01
208 214 1.618861 AATCTCACGAGCGAAGAACG 58.381 50.000 0.00 0.00 45.66 3.95
209 215 0.803117 ATCTCACGAGCGAAGAACGA 59.197 50.000 0.00 0.00 45.77 3.85
210 216 0.110328 TCTCACGAGCGAAGAACGAC 60.110 55.000 0.00 0.00 45.77 4.34
240 248 5.454062 AGCCTCTAGTCTCTATCATGTGTT 58.546 41.667 0.00 0.00 0.00 3.32
257 265 2.028020 GTGTTCTGTAGTCCTTCCCTGG 60.028 54.545 0.00 0.00 0.00 4.45
268 276 3.009584 GTCCTTCCCTGGAACATTCTTCT 59.990 47.826 0.00 0.00 38.20 2.85
269 277 3.264450 TCCTTCCCTGGAACATTCTTCTC 59.736 47.826 0.00 0.00 38.20 2.87
274 282 4.019860 TCCCTGGAACATTCTTCTCTTCAG 60.020 45.833 0.00 0.00 38.20 3.02
278 286 5.555017 TGGAACATTCTTCTCTTCAGGAAG 58.445 41.667 2.60 2.60 40.85 3.46
283 291 2.877866 TCTTCTCTTCAGGAAGGACGT 58.122 47.619 9.03 0.00 40.17 4.34
285 293 1.257743 TCTCTTCAGGAAGGACGTGG 58.742 55.000 9.03 0.00 38.88 4.94
286 294 0.247736 CTCTTCAGGAAGGACGTGGG 59.752 60.000 9.03 0.00 38.88 4.61
288 296 0.905357 CTTCAGGAAGGACGTGGGAT 59.095 55.000 0.00 0.00 34.87 3.85
289 297 2.108168 CTTCAGGAAGGACGTGGGATA 58.892 52.381 0.00 0.00 34.87 2.59
292 300 2.434336 TCAGGAAGGACGTGGGATAATG 59.566 50.000 0.00 0.00 35.42 1.90
296 304 2.710096 AGGACGTGGGATAATGTTGG 57.290 50.000 0.00 0.00 0.00 3.77
303 311 4.080243 ACGTGGGATAATGTTGGGATACAA 60.080 41.667 0.00 0.00 36.54 2.41
317 2937 6.702449 TGGGATACAATATTAGCATCTGGT 57.298 37.500 0.00 0.00 39.74 4.00
318 2938 6.711277 TGGGATACAATATTAGCATCTGGTC 58.289 40.000 0.00 0.00 39.74 4.02
327 2947 3.077907 CATCTGGTCCCACCGGTT 58.922 61.111 2.97 0.00 45.01 4.44
328 2948 1.906105 GCATCTGGTCCCACCGGTTA 61.906 60.000 2.97 0.00 45.01 2.85
330 2950 0.252558 ATCTGGTCCCACCGGTTAGT 60.253 55.000 2.97 0.00 45.01 2.24
350 2988 5.836024 AGTATCTGTAACCCTTCAACCAA 57.164 39.130 0.00 0.00 0.00 3.67
351 2989 5.557866 AGTATCTGTAACCCTTCAACCAAC 58.442 41.667 0.00 0.00 0.00 3.77
352 2990 3.217681 TCTGTAACCCTTCAACCAACC 57.782 47.619 0.00 0.00 0.00 3.77
353 2991 2.510382 TCTGTAACCCTTCAACCAACCA 59.490 45.455 0.00 0.00 0.00 3.67
379 3017 2.293399 ACATTCTTTCTTTCCACCACGC 59.707 45.455 0.00 0.00 0.00 5.34
383 3021 2.054140 TTTCTTTCCACCACGCGCAC 62.054 55.000 5.73 0.00 0.00 5.34
391 3029 1.260561 CCACCACGCGCACTATATTTC 59.739 52.381 5.73 0.00 0.00 2.17
394 3032 0.111266 CACGCGCACTATATTTCCGC 60.111 55.000 5.73 0.00 41.10 5.54
441 3098 2.092158 AGCTAATCAAGGGGGAAGAAGC 60.092 50.000 0.00 0.00 0.00 3.86
520 3177 2.093447 ACCAATCCCAAGACGTCATCTC 60.093 50.000 19.50 0.00 36.27 2.75
603 3260 2.706339 AGAAGCCACAGCCATTAGAG 57.294 50.000 0.00 0.00 41.25 2.43
608 3265 1.009829 CCACAGCCATTAGAGAACGC 58.990 55.000 0.00 0.00 0.00 4.84
612 3269 3.246226 CACAGCCATTAGAGAACGCATAC 59.754 47.826 0.00 0.00 0.00 2.39
626 3283 1.122849 GCATACATTGCCAAATCGCG 58.877 50.000 0.00 0.00 46.15 5.87
654 3311 5.290158 TCATCGAACCGTAAAATAACTCAGC 59.710 40.000 0.00 0.00 0.00 4.26
711 3368 1.462378 CGCGATGTGTTGTGATGTGAC 60.462 52.381 0.00 0.00 0.00 3.67
784 3441 0.396435 TGGTTGTGAGAAGGCGACAT 59.604 50.000 0.00 0.00 0.00 3.06
821 3488 7.451732 AGGAGATCATTCATTCAGTATTCTGG 58.548 38.462 0.00 0.00 41.59 3.86
827 3496 8.055279 TCATTCATTCAGTATTCTGGGAAAAC 57.945 34.615 0.00 0.00 41.59 2.43
865 3534 3.426695 GGTCTTGATTGACGCAGAAATGG 60.427 47.826 0.00 0.00 37.81 3.16
870 3539 3.065233 TGATTGACGCAGAAATGGTATGC 59.935 43.478 0.00 0.00 36.60 3.14
910 3582 4.450419 CCGCCTGAATTGATGATCTTCTAC 59.550 45.833 9.75 0.82 0.00 2.59
911 3583 5.295950 CGCCTGAATTGATGATCTTCTACT 58.704 41.667 9.75 0.00 0.00 2.57
912 3584 5.757320 CGCCTGAATTGATGATCTTCTACTT 59.243 40.000 9.75 1.58 0.00 2.24
913 3585 6.925718 CGCCTGAATTGATGATCTTCTACTTA 59.074 38.462 9.75 0.00 0.00 2.24
929 3601 8.101419 TCTTCTACTTATTTCTTTCCCTCCAAC 58.899 37.037 0.00 0.00 0.00 3.77
940 3612 2.639286 CTCCAACTGGCGTGCAAC 59.361 61.111 0.00 0.00 34.44 4.17
941 3613 1.893808 CTCCAACTGGCGTGCAACT 60.894 57.895 0.00 0.00 34.44 3.16
1016 3731 2.422377 GGTCGGTATAAAATGGCCCACT 60.422 50.000 0.00 0.00 0.00 4.00
1031 3746 0.613260 CCACTCAACCAATCTCCCGA 59.387 55.000 0.00 0.00 0.00 5.14
1036 3751 1.229853 AACCAATCTCCCGACCCCT 60.230 57.895 0.00 0.00 0.00 4.79
1041 3756 0.188834 AATCTCCCGACCCCTAGAGG 59.811 60.000 0.00 0.00 0.00 3.69
1106 3832 1.773635 CCATTCCTCACCAACCCCA 59.226 57.895 0.00 0.00 0.00 4.96
1109 3835 0.776080 ATTCCTCACCAACCCCACCT 60.776 55.000 0.00 0.00 0.00 4.00
1114 3840 2.203182 ACCAACCCCACCTCTCGA 59.797 61.111 0.00 0.00 0.00 4.04
1118 3844 1.486211 CAACCCCACCTCTCGACTAT 58.514 55.000 0.00 0.00 0.00 2.12
1139 3865 1.267574 ACCTCACGATCATGGGCAGT 61.268 55.000 0.00 0.00 0.00 4.40
1526 4260 2.159282 AGTCCGGTAGATGCGTACTTTG 60.159 50.000 0.00 0.00 0.00 2.77
1554 4288 1.392589 CTTTGTGGGTCAAGTGCAGT 58.607 50.000 0.00 0.00 37.35 4.40
1604 4909 4.333372 TGCATACGTACGAGTGATTCAGTA 59.667 41.667 24.41 0.00 0.00 2.74
1605 4910 5.163733 TGCATACGTACGAGTGATTCAGTAA 60.164 40.000 24.41 0.00 0.00 2.24
1667 4976 9.450807 CATACTTCTCGTTTCAATTTTGTTTCT 57.549 29.630 0.00 0.00 0.00 2.52
1690 4999 6.757010 TCTCAAATCCTCGTGTTATTCTTAGC 59.243 38.462 0.00 0.00 0.00 3.09
1691 5000 6.403049 TCAAATCCTCGTGTTATTCTTAGCA 58.597 36.000 0.00 0.00 0.00 3.49
1701 5016 4.759693 TGTTATTCTTAGCACCACCACTTG 59.240 41.667 0.00 0.00 0.00 3.16
1727 6349 7.137426 GCTTGATATATTGCTGAGAAAGGTTG 58.863 38.462 0.00 0.00 0.00 3.77
1728 6350 6.624352 TGATATATTGCTGAGAAAGGTTGC 57.376 37.500 0.00 0.00 0.00 4.17
1729 6351 5.532406 TGATATATTGCTGAGAAAGGTTGCC 59.468 40.000 0.00 0.00 0.00 4.52
1730 6352 2.299326 ATTGCTGAGAAAGGTTGCCT 57.701 45.000 0.00 0.00 33.87 4.75
1731 6353 1.609208 TTGCTGAGAAAGGTTGCCTC 58.391 50.000 0.00 0.00 30.89 4.70
1732 6354 0.473755 TGCTGAGAAAGGTTGCCTCA 59.526 50.000 0.00 0.00 35.81 3.86
1734 6356 1.742268 GCTGAGAAAGGTTGCCTCATC 59.258 52.381 0.00 0.00 36.48 2.92
1735 6357 2.617532 GCTGAGAAAGGTTGCCTCATCT 60.618 50.000 0.00 3.94 36.48 2.90
1737 6359 3.679389 TGAGAAAGGTTGCCTCATCTTC 58.321 45.455 0.00 0.00 32.33 2.87
1740 6362 4.331108 AGAAAGGTTGCCTCATCTTCTTC 58.669 43.478 0.00 0.00 29.22 2.87
1741 6363 4.042684 AGAAAGGTTGCCTCATCTTCTTCT 59.957 41.667 0.00 0.00 29.22 2.85
1788 6419 4.640771 ACCAAGATATATTGCCGGATGT 57.359 40.909 5.05 0.00 0.00 3.06
1790 6421 4.761739 ACCAAGATATATTGCCGGATGTTG 59.238 41.667 5.05 3.33 0.00 3.33
1795 8085 0.814457 TATTGCCGGATGTTGTTGCC 59.186 50.000 5.05 0.00 0.00 4.52
1819 8109 9.674824 GCCTTTTCTTATGATGAAATCTATGTG 57.325 33.333 0.00 0.00 45.81 3.21
1911 8214 6.597672 TGATTAATTAGCTTCTTCTTCGGCAA 59.402 34.615 0.00 0.00 0.00 4.52
1912 8215 6.811253 TTAATTAGCTTCTTCTTCGGCAAA 57.189 33.333 0.00 0.00 0.00 3.68
1913 8216 5.705609 AATTAGCTTCTTCTTCGGCAAAA 57.294 34.783 0.00 0.00 0.00 2.44
1914 8217 5.705609 ATTAGCTTCTTCTTCGGCAAAAA 57.294 34.783 0.00 0.00 0.00 1.94
1917 8220 3.130340 AGCTTCTTCTTCGGCAAAAACAA 59.870 39.130 0.00 0.00 0.00 2.83
1918 8221 3.862845 GCTTCTTCTTCGGCAAAAACAAA 59.137 39.130 0.00 0.00 0.00 2.83
1920 8223 4.442375 TCTTCTTCGGCAAAAACAAACA 57.558 36.364 0.00 0.00 0.00 2.83
1922 8225 6.137794 TCTTCTTCGGCAAAAACAAACATA 57.862 33.333 0.00 0.00 0.00 2.29
1925 8228 7.708752 TCTTCTTCGGCAAAAACAAACATAATT 59.291 29.630 0.00 0.00 0.00 1.40
1926 8229 8.873215 TTCTTCGGCAAAAACAAACATAATTA 57.127 26.923 0.00 0.00 0.00 1.40
1928 8231 9.482627 TCTTCGGCAAAAACAAACATAATTATT 57.517 25.926 0.00 0.00 0.00 1.40
1930 8233 9.869844 TTCGGCAAAAACAAACATAATTATTTG 57.130 25.926 9.13 9.13 40.83 2.32
1957 8260 5.432885 TTTTTGCGGGAAAAACAAACAAA 57.567 30.435 14.93 0.00 38.38 2.83
1958 8261 5.432885 TTTTGCGGGAAAAACAAACAAAA 57.567 30.435 4.86 0.00 33.29 2.44
1959 8262 5.629079 TTTGCGGGAAAAACAAACAAAAT 57.371 30.435 0.00 0.00 0.00 1.82
1960 8263 5.629079 TTGCGGGAAAAACAAACAAAATT 57.371 30.435 0.00 0.00 0.00 1.82
1961 8264 6.737254 TTGCGGGAAAAACAAACAAAATTA 57.263 29.167 0.00 0.00 0.00 1.40
1962 8265 6.737254 TGCGGGAAAAACAAACAAAATTAA 57.263 29.167 0.00 0.00 0.00 1.40
1963 8266 7.321745 TGCGGGAAAAACAAACAAAATTAAT 57.678 28.000 0.00 0.00 0.00 1.40
1964 8267 7.762382 TGCGGGAAAAACAAACAAAATTAATT 58.238 26.923 0.00 0.00 0.00 1.40
1965 8268 8.889717 TGCGGGAAAAACAAACAAAATTAATTA 58.110 25.926 0.01 0.00 0.00 1.40
1966 8269 9.376171 GCGGGAAAAACAAACAAAATTAATTAG 57.624 29.630 0.01 0.25 0.00 1.73
1967 8270 9.376171 CGGGAAAAACAAACAAAATTAATTAGC 57.624 29.630 0.01 0.00 0.00 3.09
1978 8281 9.626045 AACAAAATTAATTAGCTTCTTCTTCGG 57.374 29.630 0.01 0.00 0.00 4.30
1979 8282 7.755373 ACAAAATTAATTAGCTTCTTCTTCGGC 59.245 33.333 0.01 0.00 0.00 5.54
1980 8283 6.378710 AATTAATTAGCTTCTTCTTCGGCC 57.621 37.500 0.00 0.00 0.00 6.13
1981 8284 3.350219 AATTAGCTTCTTCTTCGGCCA 57.650 42.857 2.24 0.00 0.00 5.36
1982 8285 2.851263 TTAGCTTCTTCTTCGGCCAA 57.149 45.000 2.24 0.00 0.00 4.52
1983 8286 2.851263 TAGCTTCTTCTTCGGCCAAA 57.149 45.000 2.24 0.00 0.00 3.28
1984 8287 1.981256 AGCTTCTTCTTCGGCCAAAA 58.019 45.000 2.24 0.00 0.00 2.44
1985 8288 1.609072 AGCTTCTTCTTCGGCCAAAAC 59.391 47.619 2.24 0.00 0.00 2.43
1986 8289 1.336755 GCTTCTTCTTCGGCCAAAACA 59.663 47.619 2.24 0.00 0.00 2.83
1987 8290 2.029918 GCTTCTTCTTCGGCCAAAACAT 60.030 45.455 2.24 0.00 0.00 2.71
1988 8291 3.568538 CTTCTTCTTCGGCCAAAACATG 58.431 45.455 2.24 0.00 0.00 3.21
1997 8300 2.566010 CAAAACATGGACGGCCCG 59.434 61.111 3.83 0.00 37.93 6.13
1998 8301 2.114411 AAAACATGGACGGCCCGT 59.886 55.556 9.43 9.43 45.10 5.28
1999 8302 1.529713 AAAACATGGACGGCCCGTT 60.530 52.632 11.54 5.39 41.37 4.44
2000 8303 1.801309 AAAACATGGACGGCCCGTTG 61.801 55.000 11.54 7.70 41.37 4.10
2001 8304 2.969300 AAACATGGACGGCCCGTTGT 62.969 55.000 11.54 8.48 41.37 3.32
2002 8305 3.124921 CATGGACGGCCCGTTGTC 61.125 66.667 11.54 4.13 41.37 3.18
2003 8306 4.752879 ATGGACGGCCCGTTGTCG 62.753 66.667 11.54 0.00 41.37 4.35
2009 8312 4.373116 GGCCCGTTGTCGCTCTCA 62.373 66.667 0.00 0.00 35.54 3.27
2010 8313 2.357034 GCCCGTTGTCGCTCTCAA 60.357 61.111 0.00 0.00 35.54 3.02
2011 8314 2.668280 GCCCGTTGTCGCTCTCAAC 61.668 63.158 0.00 0.00 40.89 3.18
2012 8315 2.027625 CCCGTTGTCGCTCTCAACC 61.028 63.158 8.94 0.00 41.13 3.77
2013 8316 2.027625 CCGTTGTCGCTCTCAACCC 61.028 63.158 8.94 0.00 41.13 4.11
2014 8317 2.372690 CGTTGTCGCTCTCAACCCG 61.373 63.158 8.94 0.00 41.13 5.28
2015 8318 2.027625 GTTGTCGCTCTCAACCCGG 61.028 63.158 0.00 0.00 39.13 5.73
2016 8319 2.504274 TTGTCGCTCTCAACCCGGT 61.504 57.895 0.00 0.00 0.00 5.28
2017 8320 1.180456 TTGTCGCTCTCAACCCGGTA 61.180 55.000 0.00 0.00 0.00 4.02
2018 8321 1.180456 TGTCGCTCTCAACCCGGTAA 61.180 55.000 0.00 0.00 0.00 2.85
2019 8322 0.037975 GTCGCTCTCAACCCGGTAAA 60.038 55.000 0.00 0.00 0.00 2.01
2020 8323 0.680618 TCGCTCTCAACCCGGTAAAA 59.319 50.000 0.00 0.00 0.00 1.52
2021 8324 1.076332 CGCTCTCAACCCGGTAAAAG 58.924 55.000 0.00 0.00 0.00 2.27
2022 8325 1.337447 CGCTCTCAACCCGGTAAAAGA 60.337 52.381 0.00 0.00 0.00 2.52
2023 8326 2.074576 GCTCTCAACCCGGTAAAAGAC 58.925 52.381 0.00 0.00 0.00 3.01
2024 8327 2.289506 GCTCTCAACCCGGTAAAAGACT 60.290 50.000 0.00 0.00 0.00 3.24
2025 8328 3.056322 GCTCTCAACCCGGTAAAAGACTA 60.056 47.826 0.00 0.00 0.00 2.59
2026 8329 4.745649 CTCTCAACCCGGTAAAAGACTAG 58.254 47.826 0.00 0.00 0.00 2.57
2027 8330 3.056322 TCTCAACCCGGTAAAAGACTAGC 60.056 47.826 0.00 0.00 0.00 3.42
2028 8331 2.027837 TCAACCCGGTAAAAGACTAGCC 60.028 50.000 0.00 0.00 0.00 3.93
2029 8332 0.533951 ACCCGGTAAAAGACTAGCCG 59.466 55.000 0.00 0.00 41.82 5.52
2030 8333 0.533951 CCCGGTAAAAGACTAGCCGT 59.466 55.000 0.00 0.00 40.70 5.68
2031 8334 1.750778 CCCGGTAAAAGACTAGCCGTA 59.249 52.381 0.00 0.00 40.70 4.02
2032 8335 2.166254 CCCGGTAAAAGACTAGCCGTAA 59.834 50.000 0.00 0.00 40.70 3.18
2033 8336 3.368323 CCCGGTAAAAGACTAGCCGTAAA 60.368 47.826 0.00 0.00 40.70 2.01
2034 8337 3.861689 CCGGTAAAAGACTAGCCGTAAAG 59.138 47.826 0.00 0.00 40.70 1.85
2035 8338 3.861689 CGGTAAAAGACTAGCCGTAAAGG 59.138 47.826 0.00 0.00 44.97 3.11
2036 8339 4.380867 CGGTAAAAGACTAGCCGTAAAGGA 60.381 45.833 0.00 0.00 45.00 3.36
2037 8340 5.482006 GGTAAAAGACTAGCCGTAAAGGAA 58.518 41.667 0.00 0.00 45.00 3.36
2038 8341 5.579904 GGTAAAAGACTAGCCGTAAAGGAAG 59.420 44.000 0.00 0.00 45.00 3.46
2039 8342 5.479124 AAAAGACTAGCCGTAAAGGAAGA 57.521 39.130 0.00 0.00 45.00 2.87
2040 8343 5.479124 AAAGACTAGCCGTAAAGGAAGAA 57.521 39.130 0.00 0.00 45.00 2.52
2041 8344 4.722361 AGACTAGCCGTAAAGGAAGAAG 57.278 45.455 0.00 0.00 45.00 2.85
2042 8345 4.342359 AGACTAGCCGTAAAGGAAGAAGA 58.658 43.478 0.00 0.00 45.00 2.87
2043 8346 4.771054 AGACTAGCCGTAAAGGAAGAAGAA 59.229 41.667 0.00 0.00 45.00 2.52
2044 8347 4.818642 ACTAGCCGTAAAGGAAGAAGAAC 58.181 43.478 0.00 0.00 45.00 3.01
2045 8348 3.764237 AGCCGTAAAGGAAGAAGAACA 57.236 42.857 0.00 0.00 45.00 3.18
2046 8349 4.287766 AGCCGTAAAGGAAGAAGAACAT 57.712 40.909 0.00 0.00 45.00 2.71
2047 8350 4.254492 AGCCGTAAAGGAAGAAGAACATC 58.746 43.478 0.00 0.00 45.00 3.06
2048 8351 4.000988 GCCGTAAAGGAAGAAGAACATCA 58.999 43.478 0.00 0.00 45.00 3.07
2049 8352 4.454504 GCCGTAAAGGAAGAAGAACATCAA 59.545 41.667 0.00 0.00 45.00 2.57
2050 8353 5.390991 GCCGTAAAGGAAGAAGAACATCAAG 60.391 44.000 0.00 0.00 45.00 3.02
2051 8354 5.390991 CCGTAAAGGAAGAAGAACATCAAGC 60.391 44.000 0.00 0.00 45.00 4.01
2052 8355 5.179368 CGTAAAGGAAGAAGAACATCAAGCA 59.821 40.000 0.00 0.00 0.00 3.91
2053 8356 6.128172 CGTAAAGGAAGAAGAACATCAAGCAT 60.128 38.462 0.00 0.00 0.00 3.79
2054 8357 5.893897 AAGGAAGAAGAACATCAAGCATC 57.106 39.130 0.00 0.00 0.00 3.91
2055 8358 5.176741 AGGAAGAAGAACATCAAGCATCT 57.823 39.130 0.00 0.00 0.00 2.90
2056 8359 4.942483 AGGAAGAAGAACATCAAGCATCTG 59.058 41.667 0.00 0.00 0.00 2.90
2057 8360 4.438472 GGAAGAAGAACATCAAGCATCTGC 60.438 45.833 0.00 0.00 42.49 4.26
2073 8376 1.870055 CTGCGCACAAGCCTGGATTT 61.870 55.000 5.66 0.00 37.52 2.17
2080 8383 3.681417 GCACAAGCCTGGATTTTGAATTC 59.319 43.478 14.52 0.00 33.58 2.17
2099 8402 4.604843 TTCATTCGTGTGATTCTCATGC 57.395 40.909 3.56 0.00 0.00 4.06
2118 8425 1.269621 GCAGTACGGATATTGCGAGGT 60.270 52.381 0.00 0.00 34.73 3.85
2371 8711 4.761975 CCTAACTAGGCAAATGTAACGGA 58.238 43.478 0.00 0.00 36.53 4.69
2372 8712 5.180271 CCTAACTAGGCAAATGTAACGGAA 58.820 41.667 0.00 0.00 36.53 4.30
2373 8713 5.644636 CCTAACTAGGCAAATGTAACGGAAA 59.355 40.000 0.00 0.00 36.53 3.13
2374 8714 6.149807 CCTAACTAGGCAAATGTAACGGAAAA 59.850 38.462 0.00 0.00 36.53 2.29
2375 8715 6.584185 AACTAGGCAAATGTAACGGAAAAT 57.416 33.333 0.00 0.00 0.00 1.82
2376 8716 5.949735 ACTAGGCAAATGTAACGGAAAATG 58.050 37.500 0.00 0.00 0.00 2.32
2377 8717 4.864704 AGGCAAATGTAACGGAAAATGT 57.135 36.364 0.00 0.00 0.00 2.71
2378 8718 5.968528 AGGCAAATGTAACGGAAAATGTA 57.031 34.783 0.00 0.00 0.00 2.29
2379 8719 5.949735 AGGCAAATGTAACGGAAAATGTAG 58.050 37.500 0.00 0.00 0.00 2.74
2380 8720 5.099575 GGCAAATGTAACGGAAAATGTAGG 58.900 41.667 0.00 0.00 0.00 3.18
2381 8721 5.099575 GCAAATGTAACGGAAAATGTAGGG 58.900 41.667 0.00 0.00 0.00 3.53
2382 8722 5.106078 GCAAATGTAACGGAAAATGTAGGGA 60.106 40.000 0.00 0.00 0.00 4.20
2383 8723 6.319399 CAAATGTAACGGAAAATGTAGGGAC 58.681 40.000 0.00 0.00 0.00 4.46
2384 8724 3.941573 TGTAACGGAAAATGTAGGGACC 58.058 45.455 0.00 0.00 0.00 4.46
2385 8725 3.583966 TGTAACGGAAAATGTAGGGACCT 59.416 43.478 0.00 0.00 0.00 3.85
2386 8726 4.776837 TGTAACGGAAAATGTAGGGACCTA 59.223 41.667 0.00 0.00 0.00 3.08
2387 8727 4.914177 AACGGAAAATGTAGGGACCTAA 57.086 40.909 0.00 0.00 0.00 2.69
2388 8728 4.212143 ACGGAAAATGTAGGGACCTAAC 57.788 45.455 0.00 0.00 0.00 2.34
2389 8729 3.842436 ACGGAAAATGTAGGGACCTAACT 59.158 43.478 0.00 0.00 0.00 2.24
2390 8730 5.025453 ACGGAAAATGTAGGGACCTAACTA 58.975 41.667 0.00 0.00 0.00 2.24
2391 8731 5.128335 ACGGAAAATGTAGGGACCTAACTAG 59.872 44.000 0.00 0.00 0.00 2.57
2403 8743 2.843701 CCTAACTAGGCAGCAGATTGG 58.156 52.381 0.00 0.00 36.53 3.16
2404 8744 2.216898 CTAACTAGGCAGCAGATTGGC 58.783 52.381 0.00 0.00 43.41 4.52
2410 8750 4.809496 CAGCAGATTGGCGGGGCT 62.809 66.667 0.00 0.00 39.27 5.19
2411 8751 4.052518 AGCAGATTGGCGGGGCTT 62.053 61.111 0.00 0.00 39.27 4.35
2412 8752 3.521796 GCAGATTGGCGGGGCTTC 61.522 66.667 0.00 0.00 0.00 3.86
2413 8753 3.204827 CAGATTGGCGGGGCTTCG 61.205 66.667 0.00 0.00 0.00 3.79
2422 8762 2.349755 GGGGCTTCGCACAGGTTA 59.650 61.111 0.00 0.00 30.93 2.85
2423 8763 1.745489 GGGGCTTCGCACAGGTTAG 60.745 63.158 0.00 0.00 30.93 2.34
2424 8764 1.745489 GGGCTTCGCACAGGTTAGG 60.745 63.158 0.00 0.00 0.00 2.69
2425 8765 2.399356 GGCTTCGCACAGGTTAGGC 61.399 63.158 0.00 0.00 0.00 3.93
2426 8766 1.376037 GCTTCGCACAGGTTAGGCT 60.376 57.895 0.00 0.00 0.00 4.58
2427 8767 0.955919 GCTTCGCACAGGTTAGGCTT 60.956 55.000 0.00 0.00 0.00 4.35
2428 8768 1.079503 CTTCGCACAGGTTAGGCTTC 58.920 55.000 0.00 0.00 0.00 3.86
2429 8769 0.669318 TTCGCACAGGTTAGGCTTCG 60.669 55.000 0.00 0.00 0.00 3.79
2430 8770 1.374252 CGCACAGGTTAGGCTTCGT 60.374 57.895 0.00 0.00 0.00 3.85
2431 8771 1.352156 CGCACAGGTTAGGCTTCGTC 61.352 60.000 0.00 0.00 0.00 4.20
2432 8772 0.037232 GCACAGGTTAGGCTTCGTCT 60.037 55.000 0.00 0.00 0.00 4.18
2433 8773 1.714794 CACAGGTTAGGCTTCGTCTG 58.285 55.000 0.00 0.00 0.00 3.51
2434 8774 0.608640 ACAGGTTAGGCTTCGTCTGG 59.391 55.000 0.00 0.00 0.00 3.86
2435 8775 0.108138 CAGGTTAGGCTTCGTCTGGG 60.108 60.000 0.00 0.00 0.00 4.45
2436 8776 1.449778 GGTTAGGCTTCGTCTGGGC 60.450 63.158 0.00 0.00 0.00 5.36
2437 8777 1.449778 GTTAGGCTTCGTCTGGGCC 60.450 63.158 0.00 0.00 45.57 5.80
2459 8799 4.694233 CACGCAGGAGCAGCCAGT 62.694 66.667 0.00 0.00 42.27 4.00
2460 8800 4.694233 ACGCAGGAGCAGCCAGTG 62.694 66.667 0.00 0.00 42.27 3.66
2462 8802 4.341783 GCAGGAGCAGCCAGTGGT 62.342 66.667 11.74 0.00 41.58 4.16
2463 8803 2.359602 CAGGAGCAGCCAGTGGTG 60.360 66.667 11.74 9.06 42.91 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 9.627395 TGGTTTAATTATACAATGTTTGAACCG 57.373 29.630 13.73 0.00 35.59 4.44
56 62 1.982395 TCGGGTTGCTGTCGGAGAT 60.982 57.895 0.00 0.00 40.67 2.75
102 108 6.149633 GGCTTGTGTTTTAACTATGTTCTGG 58.850 40.000 0.00 0.00 0.00 3.86
178 184 4.246458 GCTCGTGAGATTAACTCCTTTGT 58.754 43.478 0.00 0.00 44.34 2.83
183 189 2.846039 TCGCTCGTGAGATTAACTCC 57.154 50.000 0.00 0.00 44.34 3.85
200 206 0.362512 GCTAACAGCGTCGTTCTTCG 59.637 55.000 0.00 0.00 41.41 3.79
201 207 0.714439 GGCTAACAGCGTCGTTCTTC 59.286 55.000 0.00 0.00 43.62 2.87
202 208 0.317479 AGGCTAACAGCGTCGTTCTT 59.683 50.000 0.00 0.00 43.62 2.52
203 209 0.109226 GAGGCTAACAGCGTCGTTCT 60.109 55.000 5.24 0.00 44.62 3.01
204 210 2.360794 GAGGCTAACAGCGTCGTTC 58.639 57.895 5.24 0.00 44.62 3.95
205 211 4.573162 GAGGCTAACAGCGTCGTT 57.427 55.556 5.24 0.00 44.62 3.85
209 215 2.018515 GAGACTAGAGGCTAACAGCGT 58.981 52.381 0.00 0.00 43.62 5.07
210 216 2.294074 AGAGACTAGAGGCTAACAGCG 58.706 52.381 0.00 0.00 43.62 5.18
240 248 2.158219 TGTTCCAGGGAAGGACTACAGA 60.158 50.000 0.00 0.00 37.42 3.41
257 265 5.641636 GTCCTTCCTGAAGAGAAGAATGTTC 59.358 44.000 8.46 0.00 42.80 3.18
268 276 0.178944 TCCCACGTCCTTCCTGAAGA 60.179 55.000 8.46 0.00 40.79 2.87
269 277 0.905357 ATCCCACGTCCTTCCTGAAG 59.095 55.000 0.00 0.00 38.14 3.02
274 282 2.943033 CAACATTATCCCACGTCCTTCC 59.057 50.000 0.00 0.00 0.00 3.46
278 286 1.210967 TCCCAACATTATCCCACGTCC 59.789 52.381 0.00 0.00 0.00 4.79
283 291 9.973661 CTAATATTGTATCCCAACATTATCCCA 57.026 33.333 0.00 0.00 33.24 4.37
285 293 9.461312 TGCTAATATTGTATCCCAACATTATCC 57.539 33.333 0.00 0.00 33.24 2.59
289 297 9.017509 CAGATGCTAATATTGTATCCCAACATT 57.982 33.333 0.00 0.00 34.61 2.71
292 300 6.942576 ACCAGATGCTAATATTGTATCCCAAC 59.057 38.462 0.00 0.00 35.44 3.77
296 304 6.116126 GGGACCAGATGCTAATATTGTATCC 58.884 44.000 0.00 0.00 0.00 2.59
303 311 2.303022 CGGTGGGACCAGATGCTAATAT 59.697 50.000 0.00 0.00 38.47 1.28
317 2937 2.537633 ACAGATACTAACCGGTGGGA 57.462 50.000 8.52 0.30 36.97 4.37
318 2938 3.181472 GGTTACAGATACTAACCGGTGGG 60.181 52.174 8.52 6.70 35.13 4.61
327 2947 6.296030 GGTTGGTTGAAGGGTTACAGATACTA 60.296 42.308 0.00 0.00 0.00 1.82
328 2948 5.514310 GGTTGGTTGAAGGGTTACAGATACT 60.514 44.000 0.00 0.00 0.00 2.12
330 2950 4.351407 TGGTTGGTTGAAGGGTTACAGATA 59.649 41.667 0.00 0.00 0.00 1.98
350 2988 3.259123 GGAAAGAAAGAATGTGGCATGGT 59.741 43.478 0.00 0.00 0.00 3.55
351 2989 3.258872 TGGAAAGAAAGAATGTGGCATGG 59.741 43.478 0.00 0.00 0.00 3.66
352 2990 4.240096 GTGGAAAGAAAGAATGTGGCATG 58.760 43.478 0.00 0.00 0.00 4.06
353 2991 3.259123 GGTGGAAAGAAAGAATGTGGCAT 59.741 43.478 0.00 0.00 0.00 4.40
383 3021 1.001048 TGGTCGTCCGCGGAAATATAG 60.001 52.381 32.93 16.60 38.89 1.31
441 3098 1.571919 GCACTATAAGCTGTGACCCG 58.428 55.000 6.12 0.00 36.38 5.28
485 3142 2.354704 GGATTGGTCGAGAACATGTCCA 60.355 50.000 14.37 0.00 34.91 4.02
520 3177 0.940991 GCTGGGCGACTTTTGCTTTG 60.941 55.000 0.00 0.00 0.00 2.77
608 3265 2.223226 TGTCGCGATTTGGCAATGTATG 60.223 45.455 14.06 0.00 0.00 2.39
612 3269 1.202166 TGATGTCGCGATTTGGCAATG 60.202 47.619 14.06 0.00 0.00 2.82
626 3283 7.009815 TGAGTTATTTTACGGTTCGATGATGTC 59.990 37.037 0.00 0.00 0.00 3.06
711 3368 0.907837 CAGCGTTATCTGTCGTCACG 59.092 55.000 0.00 0.00 0.00 4.35
784 3441 6.345298 TGAATGATCTCCTAAAATACGCACA 58.655 36.000 0.00 0.00 0.00 4.57
821 3488 3.667960 CGTCAGTTGCATGCTAGTTTTCC 60.668 47.826 20.33 0.00 0.00 3.13
827 3496 1.002366 GACCGTCAGTTGCATGCTAG 58.998 55.000 20.33 6.10 0.00 3.42
865 3534 0.236711 GGCGCAGATCACATGCATAC 59.763 55.000 10.83 0.00 44.05 2.39
870 3539 2.528743 GGACGGCGCAGATCACATG 61.529 63.158 16.26 0.00 0.00 3.21
910 3582 4.158579 GCCAGTTGGAGGGAAAGAAATAAG 59.841 45.833 1.45 0.00 37.39 1.73
911 3583 4.086457 GCCAGTTGGAGGGAAAGAAATAA 58.914 43.478 1.45 0.00 37.39 1.40
912 3584 3.697166 GCCAGTTGGAGGGAAAGAAATA 58.303 45.455 1.45 0.00 37.39 1.40
913 3585 2.529632 GCCAGTTGGAGGGAAAGAAAT 58.470 47.619 1.45 0.00 37.39 2.17
929 3601 1.350193 CAGTAGTAGTTGCACGCCAG 58.650 55.000 0.00 0.00 0.00 4.85
940 3612 6.201044 CGGATTGAAATGGTAAGCAGTAGTAG 59.799 42.308 0.00 0.00 0.00 2.57
941 3613 6.046593 CGGATTGAAATGGTAAGCAGTAGTA 58.953 40.000 0.00 0.00 0.00 1.82
1016 3731 1.559065 GGGGTCGGGAGATTGGTTGA 61.559 60.000 0.00 0.00 43.27 3.18
1031 3746 2.604152 CCTCTCGCCTCTAGGGGT 59.396 66.667 11.24 0.00 46.93 4.95
1036 3751 0.179032 CTCTCAGCCTCTCGCCTCTA 60.179 60.000 0.00 0.00 38.78 2.43
1041 3756 1.599606 TTGACCTCTCAGCCTCTCGC 61.600 60.000 0.00 0.00 37.98 5.03
1106 3832 2.645802 GTGAGGTGATAGTCGAGAGGT 58.354 52.381 0.00 0.00 0.00 3.85
1109 3835 2.685850 TCGTGAGGTGATAGTCGAGA 57.314 50.000 0.00 0.00 0.00 4.04
1114 3840 2.630098 CCCATGATCGTGAGGTGATAGT 59.370 50.000 16.77 0.00 0.00 2.12
1118 3844 1.264045 TGCCCATGATCGTGAGGTGA 61.264 55.000 16.77 4.77 0.00 4.02
1139 3865 2.852075 AGGCCTTCCACCCGTGAA 60.852 61.111 0.00 0.00 33.74 3.18
1526 4260 2.170166 TGACCCACAAAGCATGAATCC 58.830 47.619 0.00 0.00 0.00 3.01
1554 4288 5.220970 GCTTCAACCAAAACTTGCACTACTA 60.221 40.000 0.00 0.00 0.00 1.82
1604 4909 7.761981 ATCTCCAACTCCTGCCATATATATT 57.238 36.000 0.00 0.00 0.00 1.28
1605 4910 7.183475 ACAATCTCCAACTCCTGCCATATATAT 59.817 37.037 0.00 0.00 0.00 0.86
1614 4923 3.440522 GGTTTACAATCTCCAACTCCTGC 59.559 47.826 0.00 0.00 0.00 4.85
1641 4950 9.450807 AGAAACAAAATTGAAACGAGAAGTATG 57.549 29.630 0.00 0.00 0.00 2.39
1667 4976 6.312918 GTGCTAAGAATAACACGAGGATTTGA 59.687 38.462 0.00 0.00 0.00 2.69
1701 5016 5.767168 ACCTTTCTCAGCAATATATCAAGCC 59.233 40.000 0.00 0.00 0.00 4.35
1782 6413 3.369546 AAGAAAAGGCAACAACATCCG 57.630 42.857 0.00 0.00 41.41 4.18
1788 6419 8.587608 AGATTTCATCATAAGAAAAGGCAACAA 58.412 29.630 0.00 0.00 38.36 2.83
1851 8141 3.308866 GCTTGTTATGTCATGGTCCGTAC 59.691 47.826 0.00 0.00 0.00 3.67
1935 8238 5.432885 TTTGTTTGTTTTTCCCGCAAAAA 57.567 30.435 0.00 0.46 40.93 1.94
1936 8239 5.432885 TTTTGTTTGTTTTTCCCGCAAAA 57.567 30.435 0.00 0.00 34.47 2.44
1937 8240 5.629079 ATTTTGTTTGTTTTTCCCGCAAA 57.371 30.435 0.00 0.00 0.00 3.68
1938 8241 5.629079 AATTTTGTTTGTTTTTCCCGCAA 57.371 30.435 0.00 0.00 0.00 4.85
1939 8242 6.737254 TTAATTTTGTTTGTTTTTCCCGCA 57.263 29.167 0.00 0.00 0.00 5.69
1940 8243 9.376171 CTAATTAATTTTGTTTGTTTTTCCCGC 57.624 29.630 5.91 0.00 0.00 6.13
1941 8244 9.376171 GCTAATTAATTTTGTTTGTTTTTCCCG 57.624 29.630 5.91 0.00 0.00 5.14
1952 8255 9.626045 CCGAAGAAGAAGCTAATTAATTTTGTT 57.374 29.630 5.91 0.00 0.00 2.83
1953 8256 7.755373 GCCGAAGAAGAAGCTAATTAATTTTGT 59.245 33.333 5.91 0.00 0.00 2.83
1954 8257 7.220875 GGCCGAAGAAGAAGCTAATTAATTTTG 59.779 37.037 5.91 1.60 0.00 2.44
1955 8258 7.093945 TGGCCGAAGAAGAAGCTAATTAATTTT 60.094 33.333 5.91 0.00 0.00 1.82
1956 8259 6.377146 TGGCCGAAGAAGAAGCTAATTAATTT 59.623 34.615 5.91 0.00 0.00 1.82
1957 8260 5.885912 TGGCCGAAGAAGAAGCTAATTAATT 59.114 36.000 5.89 5.89 0.00 1.40
1958 8261 5.437060 TGGCCGAAGAAGAAGCTAATTAAT 58.563 37.500 0.00 0.00 0.00 1.40
1959 8262 4.839121 TGGCCGAAGAAGAAGCTAATTAA 58.161 39.130 0.00 0.00 0.00 1.40
1960 8263 4.481368 TGGCCGAAGAAGAAGCTAATTA 57.519 40.909 0.00 0.00 0.00 1.40
1961 8264 3.350219 TGGCCGAAGAAGAAGCTAATT 57.650 42.857 0.00 0.00 0.00 1.40
1962 8265 3.350219 TTGGCCGAAGAAGAAGCTAAT 57.650 42.857 0.00 0.00 0.00 1.73
1963 8266 2.851263 TTGGCCGAAGAAGAAGCTAA 57.149 45.000 0.00 0.00 0.00 3.09
1964 8267 2.812011 GTTTTGGCCGAAGAAGAAGCTA 59.188 45.455 5.34 0.00 0.00 3.32
1965 8268 1.609072 GTTTTGGCCGAAGAAGAAGCT 59.391 47.619 5.34 0.00 0.00 3.74
1966 8269 1.336755 TGTTTTGGCCGAAGAAGAAGC 59.663 47.619 5.34 0.00 0.00 3.86
1967 8270 3.568538 CATGTTTTGGCCGAAGAAGAAG 58.431 45.455 5.34 0.00 0.00 2.85
1968 8271 2.295909 CCATGTTTTGGCCGAAGAAGAA 59.704 45.455 5.34 0.00 39.09 2.52
1969 8272 1.885887 CCATGTTTTGGCCGAAGAAGA 59.114 47.619 5.34 0.00 39.09 2.87
1970 8273 1.885887 TCCATGTTTTGGCCGAAGAAG 59.114 47.619 5.34 0.00 46.01 2.85
1971 8274 1.611491 GTCCATGTTTTGGCCGAAGAA 59.389 47.619 5.34 0.00 46.01 2.52
1972 8275 1.243902 GTCCATGTTTTGGCCGAAGA 58.756 50.000 5.34 0.00 46.01 2.87
1973 8276 3.792716 GTCCATGTTTTGGCCGAAG 57.207 52.632 5.34 0.00 46.01 3.79
1976 8279 2.566010 CCGTCCATGTTTTGGCCG 59.434 61.111 0.00 0.00 46.32 6.13
1977 8280 2.261361 GCCGTCCATGTTTTGGCC 59.739 61.111 0.00 0.00 46.01 5.36
1978 8281 2.261361 GGCCGTCCATGTTTTGGC 59.739 61.111 6.89 6.89 46.01 4.52
1980 8283 1.801309 AACGGGCCGTCCATGTTTTG 61.801 55.000 34.23 0.00 39.99 2.44
1981 8284 1.529713 AACGGGCCGTCCATGTTTT 60.530 52.632 34.23 11.46 39.99 2.43
1982 8285 2.114411 AACGGGCCGTCCATGTTT 59.886 55.556 34.23 12.35 39.99 2.83
1983 8286 2.671619 CAACGGGCCGTCCATGTT 60.672 61.111 34.23 13.23 39.99 2.71
1984 8287 3.894547 GACAACGGGCCGTCCATGT 62.895 63.158 34.23 31.31 39.99 3.21
1985 8288 3.124921 GACAACGGGCCGTCCATG 61.125 66.667 34.23 28.17 39.99 3.66
1986 8289 4.752879 CGACAACGGGCCGTCCAT 62.753 66.667 34.23 20.64 39.99 3.41
1992 8295 3.876589 TTGAGAGCGACAACGGGCC 62.877 63.158 0.00 0.00 40.15 5.80
1993 8296 2.357034 TTGAGAGCGACAACGGGC 60.357 61.111 0.00 0.00 40.15 6.13
1994 8297 2.027625 GGTTGAGAGCGACAACGGG 61.028 63.158 13.97 0.00 45.56 5.28
1995 8298 2.027625 GGGTTGAGAGCGACAACGG 61.028 63.158 13.97 0.00 45.56 4.44
1996 8299 2.372690 CGGGTTGAGAGCGACAACG 61.373 63.158 13.97 0.00 45.56 4.10
1997 8300 2.027625 CCGGGTTGAGAGCGACAAC 61.028 63.158 12.68 12.68 44.40 3.32
1998 8301 1.180456 TACCGGGTTGAGAGCGACAA 61.180 55.000 4.31 0.00 0.00 3.18
1999 8302 1.180456 TTACCGGGTTGAGAGCGACA 61.180 55.000 4.31 0.00 0.00 4.35
2000 8303 0.037975 TTTACCGGGTTGAGAGCGAC 60.038 55.000 4.31 0.00 0.00 5.19
2001 8304 0.680618 TTTTACCGGGTTGAGAGCGA 59.319 50.000 4.31 0.00 0.00 4.93
2002 8305 1.076332 CTTTTACCGGGTTGAGAGCG 58.924 55.000 4.31 0.00 0.00 5.03
2003 8306 2.074576 GTCTTTTACCGGGTTGAGAGC 58.925 52.381 4.31 0.00 0.00 4.09
2004 8307 3.679824 AGTCTTTTACCGGGTTGAGAG 57.320 47.619 4.31 0.00 0.00 3.20
2005 8308 3.056322 GCTAGTCTTTTACCGGGTTGAGA 60.056 47.826 4.31 3.84 0.00 3.27
2006 8309 3.259902 GCTAGTCTTTTACCGGGTTGAG 58.740 50.000 4.31 1.23 0.00 3.02
2007 8310 2.027837 GGCTAGTCTTTTACCGGGTTGA 60.028 50.000 4.31 0.00 0.00 3.18
2008 8311 2.353323 GGCTAGTCTTTTACCGGGTTG 58.647 52.381 4.31 0.00 0.00 3.77
2009 8312 1.066645 CGGCTAGTCTTTTACCGGGTT 60.067 52.381 4.31 0.00 40.18 4.11
2010 8313 0.533951 CGGCTAGTCTTTTACCGGGT 59.466 55.000 6.32 4.46 40.18 5.28
2011 8314 3.357504 CGGCTAGTCTTTTACCGGG 57.642 57.895 6.32 0.00 40.18 5.73
2014 8317 5.077134 TCCTTTACGGCTAGTCTTTTACC 57.923 43.478 0.00 0.00 0.00 2.85
2015 8318 6.393171 TCTTCCTTTACGGCTAGTCTTTTAC 58.607 40.000 0.00 0.00 0.00 2.01
2016 8319 6.594788 TCTTCCTTTACGGCTAGTCTTTTA 57.405 37.500 0.00 0.00 0.00 1.52
2017 8320 5.479124 TCTTCCTTTACGGCTAGTCTTTT 57.521 39.130 0.00 0.00 0.00 2.27
2018 8321 5.245526 TCTTCTTCCTTTACGGCTAGTCTTT 59.754 40.000 0.00 0.00 0.00 2.52
2019 8322 4.771054 TCTTCTTCCTTTACGGCTAGTCTT 59.229 41.667 0.00 0.00 0.00 3.01
2020 8323 4.342359 TCTTCTTCCTTTACGGCTAGTCT 58.658 43.478 0.00 0.00 0.00 3.24
2021 8324 4.715527 TCTTCTTCCTTTACGGCTAGTC 57.284 45.455 0.00 0.00 0.00 2.59
2022 8325 4.282703 TGTTCTTCTTCCTTTACGGCTAGT 59.717 41.667 0.00 0.00 0.00 2.57
2023 8326 4.817517 TGTTCTTCTTCCTTTACGGCTAG 58.182 43.478 0.00 0.00 0.00 3.42
2024 8327 4.877378 TGTTCTTCTTCCTTTACGGCTA 57.123 40.909 0.00 0.00 0.00 3.93
2025 8328 3.764237 TGTTCTTCTTCCTTTACGGCT 57.236 42.857 0.00 0.00 0.00 5.52
2026 8329 4.000988 TGATGTTCTTCTTCCTTTACGGC 58.999 43.478 0.00 0.00 0.00 5.68
2027 8330 5.390991 GCTTGATGTTCTTCTTCCTTTACGG 60.391 44.000 0.00 0.00 0.00 4.02
2028 8331 5.179368 TGCTTGATGTTCTTCTTCCTTTACG 59.821 40.000 0.00 0.00 0.00 3.18
2029 8332 6.560253 TGCTTGATGTTCTTCTTCCTTTAC 57.440 37.500 0.00 0.00 0.00 2.01
2030 8333 7.120285 CAGATGCTTGATGTTCTTCTTCCTTTA 59.880 37.037 0.00 0.00 0.00 1.85
2031 8334 6.008960 AGATGCTTGATGTTCTTCTTCCTTT 58.991 36.000 0.00 0.00 0.00 3.11
2032 8335 5.415077 CAGATGCTTGATGTTCTTCTTCCTT 59.585 40.000 0.00 0.00 0.00 3.36
2033 8336 4.942483 CAGATGCTTGATGTTCTTCTTCCT 59.058 41.667 0.00 0.00 0.00 3.36
2034 8337 4.438472 GCAGATGCTTGATGTTCTTCTTCC 60.438 45.833 0.00 0.00 38.21 3.46
2035 8338 4.660105 GCAGATGCTTGATGTTCTTCTTC 58.340 43.478 0.00 0.00 38.21 2.87
2036 8339 3.126514 CGCAGATGCTTGATGTTCTTCTT 59.873 43.478 2.95 0.00 39.32 2.52
2037 8340 2.676839 CGCAGATGCTTGATGTTCTTCT 59.323 45.455 2.95 0.00 39.32 2.85
2038 8341 2.790468 GCGCAGATGCTTGATGTTCTTC 60.790 50.000 0.30 0.00 39.32 2.87
2039 8342 1.131883 GCGCAGATGCTTGATGTTCTT 59.868 47.619 0.30 0.00 39.32 2.52
2040 8343 0.731417 GCGCAGATGCTTGATGTTCT 59.269 50.000 0.30 0.00 39.32 3.01
2041 8344 0.448990 TGCGCAGATGCTTGATGTTC 59.551 50.000 5.66 0.00 39.32 3.18
2042 8345 0.169672 GTGCGCAGATGCTTGATGTT 59.830 50.000 12.22 0.00 39.32 2.71
2043 8346 0.956902 TGTGCGCAGATGCTTGATGT 60.957 50.000 12.22 0.00 39.32 3.06
2044 8347 0.169451 TTGTGCGCAGATGCTTGATG 59.831 50.000 12.22 0.00 39.32 3.07
2045 8348 0.450583 CTTGTGCGCAGATGCTTGAT 59.549 50.000 12.22 0.00 39.32 2.57
2046 8349 1.871077 CTTGTGCGCAGATGCTTGA 59.129 52.632 12.22 0.00 39.32 3.02
2047 8350 1.800315 GCTTGTGCGCAGATGCTTG 60.800 57.895 30.30 11.51 39.32 4.01
2048 8351 2.564975 GCTTGTGCGCAGATGCTT 59.435 55.556 30.30 0.00 39.32 3.91
2049 8352 3.437795 GGCTTGTGCGCAGATGCT 61.438 61.111 33.82 0.00 40.82 3.79
2050 8353 3.437795 AGGCTTGTGCGCAGATGC 61.438 61.111 29.94 29.94 40.82 3.91
2051 8354 2.483745 CAGGCTTGTGCGCAGATG 59.516 61.111 12.22 14.03 40.82 2.90
2052 8355 2.547640 ATCCAGGCTTGTGCGCAGAT 62.548 55.000 12.22 4.20 40.82 2.90
2053 8356 2.753009 AATCCAGGCTTGTGCGCAGA 62.753 55.000 12.22 6.80 40.82 4.26
2054 8357 1.870055 AAATCCAGGCTTGTGCGCAG 61.870 55.000 12.22 0.00 40.82 5.18
2055 8358 1.462731 AAAATCCAGGCTTGTGCGCA 61.463 50.000 5.66 5.66 40.82 6.09
2056 8359 1.010419 CAAAATCCAGGCTTGTGCGC 61.010 55.000 0.00 0.00 40.82 6.09
2057 8360 0.597568 TCAAAATCCAGGCTTGTGCG 59.402 50.000 0.00 0.00 40.82 5.34
2058 8361 2.818130 TTCAAAATCCAGGCTTGTGC 57.182 45.000 0.00 0.00 38.76 4.57
2073 8376 6.799926 TGAGAATCACACGAATGAATTCAA 57.200 33.333 13.09 0.00 42.56 2.69
2099 8402 2.794910 CAACCTCGCAATATCCGTACTG 59.205 50.000 0.00 0.00 0.00 2.74
2290 8628 4.431131 CATGGGCTTGTCGGGGCT 62.431 66.667 0.00 0.00 0.00 5.19
2360 8700 5.416639 GGTCCCTACATTTTCCGTTACATTT 59.583 40.000 0.00 0.00 0.00 2.32
2361 8701 4.945543 GGTCCCTACATTTTCCGTTACATT 59.054 41.667 0.00 0.00 0.00 2.71
2362 8702 4.226620 AGGTCCCTACATTTTCCGTTACAT 59.773 41.667 0.00 0.00 0.00 2.29
2363 8703 3.583966 AGGTCCCTACATTTTCCGTTACA 59.416 43.478 0.00 0.00 0.00 2.41
2364 8704 4.212143 AGGTCCCTACATTTTCCGTTAC 57.788 45.455 0.00 0.00 0.00 2.50
2365 8705 5.484998 AGTTAGGTCCCTACATTTTCCGTTA 59.515 40.000 0.00 0.00 0.00 3.18
2366 8706 4.287845 AGTTAGGTCCCTACATTTTCCGTT 59.712 41.667 0.00 0.00 0.00 4.44
2367 8707 3.842436 AGTTAGGTCCCTACATTTTCCGT 59.158 43.478 0.00 0.00 0.00 4.69
2368 8708 4.482952 AGTTAGGTCCCTACATTTTCCG 57.517 45.455 0.00 0.00 0.00 4.30
2369 8709 5.686913 GCCTAGTTAGGTCCCTACATTTTCC 60.687 48.000 7.03 0.00 45.42 3.13
2370 8710 5.104652 TGCCTAGTTAGGTCCCTACATTTTC 60.105 44.000 7.03 0.00 45.42 2.29
2371 8711 4.786454 TGCCTAGTTAGGTCCCTACATTTT 59.214 41.667 7.03 0.00 45.42 1.82
2372 8712 4.368067 TGCCTAGTTAGGTCCCTACATTT 58.632 43.478 7.03 0.00 45.42 2.32
2373 8713 3.967987 CTGCCTAGTTAGGTCCCTACATT 59.032 47.826 7.03 0.00 45.42 2.71
2374 8714 3.577919 CTGCCTAGTTAGGTCCCTACAT 58.422 50.000 7.03 0.00 45.42 2.29
2375 8715 2.953620 GCTGCCTAGTTAGGTCCCTACA 60.954 54.545 7.03 0.00 45.42 2.74
2376 8716 1.687660 GCTGCCTAGTTAGGTCCCTAC 59.312 57.143 7.03 0.00 45.42 3.18
2377 8717 1.289830 TGCTGCCTAGTTAGGTCCCTA 59.710 52.381 7.03 0.00 45.42 3.53
2378 8718 0.042731 TGCTGCCTAGTTAGGTCCCT 59.957 55.000 7.03 0.00 45.42 4.20
2379 8719 0.466124 CTGCTGCCTAGTTAGGTCCC 59.534 60.000 7.03 0.00 45.42 4.46
2380 8720 1.486211 TCTGCTGCCTAGTTAGGTCC 58.514 55.000 7.03 0.00 45.42 4.46
2381 8721 3.462021 CAATCTGCTGCCTAGTTAGGTC 58.538 50.000 7.03 0.90 45.42 3.85
2382 8722 2.171448 CCAATCTGCTGCCTAGTTAGGT 59.829 50.000 7.03 0.00 45.42 3.08
2383 8723 2.843701 CCAATCTGCTGCCTAGTTAGG 58.156 52.381 0.00 0.63 46.42 2.69
2384 8724 2.216898 GCCAATCTGCTGCCTAGTTAG 58.783 52.381 0.00 0.00 0.00 2.34
2385 8725 1.473257 CGCCAATCTGCTGCCTAGTTA 60.473 52.381 0.00 0.00 0.00 2.24
2386 8726 0.745845 CGCCAATCTGCTGCCTAGTT 60.746 55.000 0.00 0.00 0.00 2.24
2387 8727 1.153289 CGCCAATCTGCTGCCTAGT 60.153 57.895 0.00 0.00 0.00 2.57
2388 8728 1.890979 CCGCCAATCTGCTGCCTAG 60.891 63.158 0.00 0.00 0.00 3.02
2389 8729 2.190313 CCGCCAATCTGCTGCCTA 59.810 61.111 0.00 0.00 0.00 3.93
2390 8730 4.809496 CCCGCCAATCTGCTGCCT 62.809 66.667 0.00 0.00 0.00 4.75
2393 8733 4.809496 AGCCCCGCCAATCTGCTG 62.809 66.667 0.00 0.00 0.00 4.41
2394 8734 4.052518 AAGCCCCGCCAATCTGCT 62.053 61.111 0.00 0.00 0.00 4.24
2395 8735 3.521796 GAAGCCCCGCCAATCTGC 61.522 66.667 0.00 0.00 0.00 4.26
2396 8736 3.204827 CGAAGCCCCGCCAATCTG 61.205 66.667 0.00 0.00 0.00 2.90
2409 8749 1.079503 GAAGCCTAACCTGTGCGAAG 58.920 55.000 0.00 0.00 0.00 3.79
2410 8750 0.669318 CGAAGCCTAACCTGTGCGAA 60.669 55.000 0.00 0.00 0.00 4.70
2411 8751 1.080093 CGAAGCCTAACCTGTGCGA 60.080 57.895 0.00 0.00 0.00 5.10
2412 8752 1.352156 GACGAAGCCTAACCTGTGCG 61.352 60.000 0.00 0.00 0.00 5.34
2413 8753 0.037232 AGACGAAGCCTAACCTGTGC 60.037 55.000 0.00 0.00 0.00 4.57
2414 8754 1.673033 CCAGACGAAGCCTAACCTGTG 60.673 57.143 0.00 0.00 0.00 3.66
2415 8755 0.608640 CCAGACGAAGCCTAACCTGT 59.391 55.000 0.00 0.00 0.00 4.00
2416 8756 0.108138 CCCAGACGAAGCCTAACCTG 60.108 60.000 0.00 0.00 0.00 4.00
2417 8757 1.900545 GCCCAGACGAAGCCTAACCT 61.901 60.000 0.00 0.00 0.00 3.50
2418 8758 1.449778 GCCCAGACGAAGCCTAACC 60.450 63.158 0.00 0.00 0.00 2.85
2419 8759 1.449778 GGCCCAGACGAAGCCTAAC 60.450 63.158 0.00 0.00 43.62 2.34
2420 8760 2.987125 GGCCCAGACGAAGCCTAA 59.013 61.111 0.00 0.00 43.62 2.69
2421 8761 3.458163 CGGCCCAGACGAAGCCTA 61.458 66.667 0.00 0.00 44.84 3.93
2442 8782 4.694233 ACTGGCTGCTCCTGCGTG 62.694 66.667 0.00 0.00 43.34 5.34
2443 8783 4.694233 CACTGGCTGCTCCTGCGT 62.694 66.667 0.00 0.00 43.34 5.24
2445 8785 4.341783 ACCACTGGCTGCTCCTGC 62.342 66.667 0.00 0.00 37.30 4.85
2446 8786 2.359602 CACCACTGGCTGCTCCTG 60.360 66.667 0.00 0.00 39.46 3.86


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

AutoCloner maintained by Alex Coulton.