Multiple sequence alignment - TraesCS6A01G117200

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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 TraesCS6A01G117200 chr6A 100.000 2468 0 0 1 2468 87654743 87652276 0.000000e+00 4558.0
1 TraesCS6A01G117200 chr6A 82.372 1214 130 47 779 1943 87906664 87907842 0.000000e+00 979.0
2 TraesCS6A01G117200 chr6A 83.624 861 105 23 807 1648 180625858 180625015 0.000000e+00 776.0
3 TraesCS6A01G117200 chr6B 90.659 1638 98 23 352 1978 144921358 144919765 0.000000e+00 2126.0
4 TraesCS6A01G117200 chr6B 83.917 1200 132 34 779 1943 145043425 145044598 0.000000e+00 1090.0
5 TraesCS6A01G117200 chr6B 83.333 870 101 31 948 1790 237416948 237416096 0.000000e+00 763.0
6 TraesCS6A01G117200 chr6B 92.381 210 11 5 2093 2300 144919323 144919117 6.670000e-76 294.0
7 TraesCS6A01G117200 chr6B 94.253 87 5 0 2382 2468 144919112 144919026 1.540000e-27 134.0
8 TraesCS6A01G117200 chr6B 87.302 63 3 1 1914 1976 144896197 144896140 1.580000e-07 67.6
9 TraesCS6A01G117200 chr6B 97.059 34 1 0 2435 2468 144893309 144893276 9.530000e-05 58.4
10 TraesCS6A01G117200 chr6D 88.605 1641 109 33 352 1976 69933408 69931830 0.000000e+00 1923.0
11 TraesCS6A01G117200 chr6D 85.238 1050 93 34 779 1799 70634103 70635119 0.000000e+00 1024.0
12 TraesCS6A01G117200 chr6D 85.965 228 30 1 4 229 69935124 69934897 2.450000e-60 243.0
13 TraesCS6A01G117200 chr6D 96.094 128 5 0 226 353 379557281 379557154 2.490000e-50 209.0
14 TraesCS6A01G117200 chr6D 90.789 152 10 1 353 500 69934898 69934747 1.500000e-47 200.0
15 TraesCS6A01G117200 chr2B 87.819 862 51 18 691 1537 756674726 756673904 0.000000e+00 961.0
16 TraesCS6A01G117200 chr2B 88.066 243 23 3 429 667 756696715 756696475 1.440000e-72 283.0
17 TraesCS6A01G117200 chr2B 85.034 147 19 2 1833 1976 756673773 756673627 1.980000e-31 147.0
18 TraesCS6A01G117200 chr2B 92.000 75 6 0 1982 2056 756673578 756673504 3.360000e-19 106.0
19 TraesCS6A01G117200 chr5D 91.083 471 36 3 994 1464 358798379 358798843 1.250000e-177 632.0
20 TraesCS6A01G117200 chr5D 96.094 128 5 0 227 354 460650530 460650657 2.490000e-50 209.0
21 TraesCS6A01G117200 chr5D 95.420 131 5 1 224 353 460652890 460652760 8.950000e-50 207.0
22 TraesCS6A01G117200 chr7B 96.063 127 5 0 227 353 537460997 537460871 8.950000e-50 207.0
23 TraesCS6A01G117200 chr7A 96.063 127 5 0 227 353 140764077 140763951 8.950000e-50 207.0
24 TraesCS6A01G117200 chr7A 96.063 127 5 0 227 353 141052968 141052842 8.950000e-50 207.0
25 TraesCS6A01G117200 chr7A 96.063 127 5 0 227 353 141307755 141307629 8.950000e-50 207.0
26 TraesCS6A01G117200 chr7A 96.063 127 5 0 227 353 141647746 141647620 8.950000e-50 207.0
27 TraesCS6A01G117200 chr5A 96.063 127 5 0 227 353 279670422 279670548 8.950000e-50 207.0


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 TraesCS6A01G117200 chr6A 87652276 87654743 2467 True 4558.000000 4558 100.000000 1 2468 1 chr6A.!!$R1 2467
1 TraesCS6A01G117200 chr6A 87906664 87907842 1178 False 979.000000 979 82.372000 779 1943 1 chr6A.!!$F1 1164
2 TraesCS6A01G117200 chr6A 180625015 180625858 843 True 776.000000 776 83.624000 807 1648 1 chr6A.!!$R2 841
3 TraesCS6A01G117200 chr6B 145043425 145044598 1173 False 1090.000000 1090 83.917000 779 1943 1 chr6B.!!$F1 1164
4 TraesCS6A01G117200 chr6B 144919026 144921358 2332 True 851.333333 2126 92.431000 352 2468 3 chr6B.!!$R3 2116
5 TraesCS6A01G117200 chr6B 237416096 237416948 852 True 763.000000 763 83.333000 948 1790 1 chr6B.!!$R1 842
6 TraesCS6A01G117200 chr6D 70634103 70635119 1016 False 1024.000000 1024 85.238000 779 1799 1 chr6D.!!$F1 1020
7 TraesCS6A01G117200 chr6D 69931830 69935124 3294 True 788.666667 1923 88.453000 4 1976 3 chr6D.!!$R2 1972
8 TraesCS6A01G117200 chr2B 756673504 756674726 1222 True 404.666667 961 88.284333 691 2056 3 chr2B.!!$R2 1365

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
245 1739 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.0 5.23 0.0 44.66 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1705 3285 0.242825 CTACCTTCGCAACTGACCGA 59.757 55.0 0.0 0.0 0.0 4.69 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
32 33 2.490903 GTGGGCAGCATATCCATCATTC 59.509 50.000 0.00 0.00 32.71 2.67
37 38 3.750130 GCAGCATATCCATCATTCGAAGT 59.250 43.478 3.35 0.00 0.00 3.01
38 39 4.142945 GCAGCATATCCATCATTCGAAGTC 60.143 45.833 3.35 0.00 0.00 3.01
42 43 0.534873 TCCATCATTCGAAGTCGGCA 59.465 50.000 3.35 0.00 40.29 5.69
61 62 1.478510 CATCGAAGCCTCTACCACACT 59.521 52.381 0.00 0.00 0.00 3.55
69 70 0.532573 CTCTACCACACTGACGCCAT 59.467 55.000 0.00 0.00 0.00 4.40
100 1592 8.063200 ACTGAAACTACCATATATATGCGCTA 57.937 34.615 16.08 0.00 32.40 4.26
106 1598 3.181465 ACCATATATATGCGCTAGTGGCC 60.181 47.826 16.08 0.00 37.74 5.36
167 1661 1.338136 CGAAGGTGGCTAGGGTCCAT 61.338 60.000 0.00 0.00 35.81 3.41
170 1664 0.983378 AGGTGGCTAGGGTCCATGAC 60.983 60.000 0.00 0.00 35.81 3.06
200 1694 1.707427 AGGAGGTGAAGATTTGTGGCT 59.293 47.619 0.00 0.00 0.00 4.75
212 1706 0.537143 TTGTGGCTTCGCTCATTGGT 60.537 50.000 0.00 0.00 0.00 3.67
226 1720 1.480137 CATTGGTCGCCTCTCTCTTCT 59.520 52.381 0.00 0.00 0.00 2.85
227 1721 2.509166 TTGGTCGCCTCTCTCTTCTA 57.491 50.000 0.00 0.00 0.00 2.10
228 1722 1.752683 TGGTCGCCTCTCTCTTCTAC 58.247 55.000 0.00 0.00 0.00 2.59
229 1723 1.282447 TGGTCGCCTCTCTCTTCTACT 59.718 52.381 0.00 0.00 0.00 2.57
230 1724 1.944709 GGTCGCCTCTCTCTTCTACTC 59.055 57.143 0.00 0.00 0.00 2.59
231 1725 1.944709 GTCGCCTCTCTCTTCTACTCC 59.055 57.143 0.00 0.00 0.00 3.85
232 1726 1.134037 TCGCCTCTCTCTTCTACTCCC 60.134 57.143 0.00 0.00 0.00 4.30
233 1727 1.133915 CGCCTCTCTCTTCTACTCCCT 60.134 57.143 0.00 0.00 0.00 4.20
234 1728 2.583143 GCCTCTCTCTTCTACTCCCTC 58.417 57.143 0.00 0.00 0.00 4.30
235 1729 2.751816 GCCTCTCTCTTCTACTCCCTCC 60.752 59.091 0.00 0.00 0.00 4.30
236 1730 2.486548 CCTCTCTCTTCTACTCCCTCCG 60.487 59.091 0.00 0.00 0.00 4.63
237 1731 2.171870 CTCTCTCTTCTACTCCCTCCGT 59.828 54.545 0.00 0.00 0.00 4.69
238 1732 2.171027 TCTCTCTTCTACTCCCTCCGTC 59.829 54.545 0.00 0.00 0.00 4.79
239 1733 1.212441 TCTCTTCTACTCCCTCCGTCC 59.788 57.143 0.00 0.00 0.00 4.79
240 1734 0.107312 TCTTCTACTCCCTCCGTCCG 60.107 60.000 0.00 0.00 0.00 4.79
241 1735 1.077212 TTCTACTCCCTCCGTCCGG 60.077 63.158 0.00 0.00 0.00 5.14
242 1736 1.565390 TTCTACTCCCTCCGTCCGGA 61.565 60.000 0.00 0.00 42.90 5.14
243 1737 1.077212 CTACTCCCTCCGTCCGGAA 60.077 63.158 5.23 0.00 44.66 4.30
244 1738 0.682209 CTACTCCCTCCGTCCGGAAA 60.682 60.000 5.23 0.00 44.66 3.13
245 1739 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
246 1740 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
247 1741 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
248 1742 1.044790 TCCCTCCGTCCGGAAATACC 61.045 60.000 5.23 0.00 44.66 2.73
249 1743 1.047034 CCCTCCGTCCGGAAATACCT 61.047 60.000 5.23 0.00 44.66 3.08
250 1744 0.104304 CCTCCGTCCGGAAATACCTG 59.896 60.000 5.23 0.00 44.66 4.00
251 1745 0.822164 CTCCGTCCGGAAATACCTGT 59.178 55.000 5.23 0.00 44.66 4.00
252 1746 0.819582 TCCGTCCGGAAATACCTGTC 59.180 55.000 5.23 0.00 42.05 3.51
253 1747 0.533491 CCGTCCGGAAATACCTGTCA 59.467 55.000 5.23 0.00 37.50 3.58
254 1748 1.138266 CCGTCCGGAAATACCTGTCAT 59.862 52.381 5.23 0.00 37.50 3.06
255 1749 2.470821 CGTCCGGAAATACCTGTCATC 58.529 52.381 5.23 0.00 36.31 2.92
256 1750 2.470821 GTCCGGAAATACCTGTCATCG 58.529 52.381 5.23 0.00 36.31 3.84
257 1751 2.100252 GTCCGGAAATACCTGTCATCGA 59.900 50.000 5.23 0.00 36.31 3.59
258 1752 2.761767 TCCGGAAATACCTGTCATCGAA 59.238 45.455 0.00 0.00 36.31 3.71
259 1753 3.196039 TCCGGAAATACCTGTCATCGAAA 59.804 43.478 0.00 0.00 36.31 3.46
260 1754 4.127171 CCGGAAATACCTGTCATCGAAAT 58.873 43.478 0.00 0.00 36.31 2.17
261 1755 4.024893 CCGGAAATACCTGTCATCGAAATG 60.025 45.833 0.00 0.00 36.31 2.32
262 1756 4.024893 CGGAAATACCTGTCATCGAAATGG 60.025 45.833 0.00 0.00 36.31 3.16
263 1757 5.123227 GGAAATACCTGTCATCGAAATGGA 58.877 41.667 0.00 0.00 32.97 3.41
264 1758 5.765182 GGAAATACCTGTCATCGAAATGGAT 59.235 40.000 0.00 0.00 32.97 3.41
265 1759 6.934645 GGAAATACCTGTCATCGAAATGGATA 59.065 38.462 0.00 0.00 32.97 2.59
266 1760 7.444183 GGAAATACCTGTCATCGAAATGGATAA 59.556 37.037 0.00 0.00 32.97 1.75
267 1761 8.746052 AAATACCTGTCATCGAAATGGATAAA 57.254 30.769 0.00 0.00 33.42 1.40
268 1762 8.746052 AATACCTGTCATCGAAATGGATAAAA 57.254 30.769 0.00 0.00 33.42 1.52
269 1763 8.746052 ATACCTGTCATCGAAATGGATAAAAA 57.254 30.769 0.00 0.00 33.42 1.94
270 1764 7.088589 ACCTGTCATCGAAATGGATAAAAAG 57.911 36.000 0.00 0.00 33.42 2.27
271 1765 6.095440 ACCTGTCATCGAAATGGATAAAAAGG 59.905 38.462 0.00 0.00 33.42 3.11
272 1766 6.449635 TGTCATCGAAATGGATAAAAAGGG 57.550 37.500 0.00 0.00 33.42 3.95
273 1767 5.359576 TGTCATCGAAATGGATAAAAAGGGG 59.640 40.000 0.00 0.00 33.42 4.79
274 1768 5.359860 GTCATCGAAATGGATAAAAAGGGGT 59.640 40.000 0.00 0.00 33.42 4.95
275 1769 5.359576 TCATCGAAATGGATAAAAAGGGGTG 59.640 40.000 0.00 0.00 33.42 4.61
276 1770 4.668636 TCGAAATGGATAAAAAGGGGTGT 58.331 39.130 0.00 0.00 0.00 4.16
277 1771 5.817784 TCGAAATGGATAAAAAGGGGTGTA 58.182 37.500 0.00 0.00 0.00 2.90
278 1772 6.428295 TCGAAATGGATAAAAAGGGGTGTAT 58.572 36.000 0.00 0.00 0.00 2.29
279 1773 6.544564 TCGAAATGGATAAAAAGGGGTGTATC 59.455 38.462 0.00 0.00 0.00 2.24
280 1774 6.546034 CGAAATGGATAAAAAGGGGTGTATCT 59.454 38.462 0.00 0.00 0.00 1.98
281 1775 7.717875 CGAAATGGATAAAAAGGGGTGTATCTA 59.282 37.037 0.00 0.00 0.00 1.98
282 1776 8.996651 AAATGGATAAAAAGGGGTGTATCTAG 57.003 34.615 0.00 0.00 0.00 2.43
283 1777 7.947782 ATGGATAAAAAGGGGTGTATCTAGA 57.052 36.000 0.00 0.00 0.00 2.43
284 1778 7.758820 TGGATAAAAAGGGGTGTATCTAGAA 57.241 36.000 0.00 0.00 0.00 2.10
285 1779 7.571025 TGGATAAAAAGGGGTGTATCTAGAAC 58.429 38.462 0.00 0.00 0.00 3.01
286 1780 7.404980 TGGATAAAAAGGGGTGTATCTAGAACT 59.595 37.037 0.00 0.00 0.00 3.01
287 1781 8.931568 GGATAAAAAGGGGTGTATCTAGAACTA 58.068 37.037 0.00 0.00 0.00 2.24
294 1788 8.849543 AGGGGTGTATCTAGAACTAAAATACA 57.150 34.615 0.00 0.00 32.07 2.29
295 1789 9.448587 AGGGGTGTATCTAGAACTAAAATACAT 57.551 33.333 0.00 3.35 35.81 2.29
327 1821 8.827832 ACATCCCTTTTTATTCATCTTGATGA 57.172 30.769 9.02 9.02 32.39 2.92
328 1822 8.689972 ACATCCCTTTTTATTCATCTTGATGAC 58.310 33.333 12.28 0.00 32.39 3.06
329 1823 8.689061 CATCCCTTTTTATTCATCTTGATGACA 58.311 33.333 12.28 5.64 0.00 3.58
330 1824 8.648698 TCCCTTTTTATTCATCTTGATGACAA 57.351 30.769 12.28 7.53 34.65 3.18
342 1836 5.470845 CTTGATGACAAGTATTTCCGGAC 57.529 43.478 1.83 0.00 45.73 4.79
343 1837 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
344 1838 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
345 1839 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
346 1840 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
347 1841 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
348 1842 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
349 1843 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
350 1844 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
365 1859 3.532542 GAGGGAGTACAACATAGCCAAC 58.467 50.000 0.00 0.00 0.00 3.77
374 1868 8.534954 AGTACAACATAGCCAACTTAGATCTA 57.465 34.615 0.00 0.00 0.00 1.98
394 1888 0.687354 ATTGGCCTATGTCCGGCTAG 59.313 55.000 3.32 0.00 46.73 3.42
399 1893 1.254954 CCTATGTCCGGCTAGGTACC 58.745 60.000 2.73 2.73 41.99 3.34
529 2024 3.635373 GACACCCTCAAGTACATCGGATA 59.365 47.826 0.00 0.00 0.00 2.59
559 2054 6.105333 GCTACATGGCAATTTTCACCATAAA 58.895 36.000 0.00 0.00 42.31 1.40
563 2058 6.997476 ACATGGCAATTTTCACCATAAAAACT 59.003 30.769 0.00 0.00 42.31 2.66
576 2071 6.589907 CACCATAAAAACTTGGCAAATCCTAC 59.410 38.462 0.00 0.00 36.41 3.18
591 2086 7.416664 GGCAAATCCTACACACAAATATGACAT 60.417 37.037 0.00 0.00 0.00 3.06
592 2087 7.975616 GCAAATCCTACACACAAATATGACATT 59.024 33.333 0.00 0.00 0.00 2.71
646 2141 9.092876 TGGTTGTCAGATTTTAAACATTTTCAC 57.907 29.630 0.00 0.00 0.00 3.18
666 2161 6.954487 TCACTACATAGACCATCGTTGTAT 57.046 37.500 0.00 0.00 0.00 2.29
667 2162 8.454570 TTCACTACATAGACCATCGTTGTATA 57.545 34.615 0.00 0.00 0.00 1.47
668 2163 8.631480 TCACTACATAGACCATCGTTGTATAT 57.369 34.615 0.00 0.00 0.00 0.86
669 2164 9.074576 TCACTACATAGACCATCGTTGTATATT 57.925 33.333 0.00 0.00 0.00 1.28
670 2165 9.692749 CACTACATAGACCATCGTTGTATATTT 57.307 33.333 0.00 0.00 0.00 1.40
708 2209 2.536365 TCATCGTCCATGAAACTACGC 58.464 47.619 0.00 0.00 38.68 4.42
720 2221 6.293407 CCATGAAACTACGCCAATATTCGAAT 60.293 38.462 16.15 16.15 0.00 3.34
733 2234 4.090066 AATATTCGAATATCTGCGTGTCGC 59.910 41.667 26.59 7.20 40.64 5.19
756 2257 1.205485 CTCGCGCATAGCTCTGTCAC 61.205 60.000 8.75 0.00 45.59 3.67
954 2479 1.475280 CAAGCAATCCCCACACATCTG 59.525 52.381 0.00 0.00 0.00 2.90
976 2502 0.397816 CACTCCCCGAATCCTCTCCT 60.398 60.000 0.00 0.00 0.00 3.69
1383 2912 1.677633 CCCCAACATCAACCCGGTC 60.678 63.158 0.00 0.00 0.00 4.79
1471 3000 1.550130 CCCCAAGAAGGCGTAGGTGA 61.550 60.000 0.00 0.00 35.39 4.02
1618 3193 2.166459 TGATGTTTTGTTCGTTTGCCCA 59.834 40.909 0.00 0.00 0.00 5.36
1630 3205 2.294791 CGTTTGCCCATTGTTGTTCCTA 59.705 45.455 0.00 0.00 0.00 2.94
1690 3270 4.945543 TCATGTCCTGTGAATTTCATCCAG 59.054 41.667 1.78 6.25 0.00 3.86
1691 3271 4.639078 TGTCCTGTGAATTTCATCCAGA 57.361 40.909 15.14 3.85 0.00 3.86
1705 3285 2.311854 CCAGATCCAGGGGCTTGGT 61.312 63.158 8.13 0.00 39.35 3.67
1734 3323 0.529992 GCGAAGGTAGGTGGGAATCG 60.530 60.000 0.00 0.00 0.00 3.34
1737 3326 1.138464 GAAGGTAGGTGGGAATCGACC 59.862 57.143 0.00 0.00 41.41 4.79
1769 3359 5.977129 CGGGTGTTTGAAATATTTGGCTATC 59.023 40.000 5.17 0.00 0.00 2.08
1840 3443 5.569059 GCAAAATTTCATAATATCCCGCTCG 59.431 40.000 0.00 0.00 0.00 5.03
1847 3450 6.335471 TCATAATATCCCGCTCGAGTTTTA 57.665 37.500 15.13 0.17 0.00 1.52
1851 3458 0.319083 TCCCGCTCGAGTTTTAAGCA 59.681 50.000 15.13 0.00 35.76 3.91
1852 3459 0.721718 CCCGCTCGAGTTTTAAGCAG 59.278 55.000 15.13 0.00 35.76 4.24
1943 3565 3.733960 GGCGGGCGACTGAAAACC 61.734 66.667 0.00 0.00 39.98 3.27
1944 3566 2.668550 GCGGGCGACTGAAAACCT 60.669 61.111 0.00 0.00 39.98 3.50
2056 3756 5.653507 TGCATAAATGGCAGATGAAAGAAC 58.346 37.500 10.12 0.00 36.11 3.01
2057 3757 4.736793 GCATAAATGGCAGATGAAAGAACG 59.263 41.667 10.12 0.00 0.00 3.95
2061 3761 3.071874 TGGCAGATGAAAGAACGGAAT 57.928 42.857 0.00 0.00 0.00 3.01
2062 3762 3.420893 TGGCAGATGAAAGAACGGAATT 58.579 40.909 0.00 0.00 0.00 2.17
2063 3763 3.191162 TGGCAGATGAAAGAACGGAATTG 59.809 43.478 0.00 0.00 0.00 2.32
2064 3764 3.191371 GGCAGATGAAAGAACGGAATTGT 59.809 43.478 0.00 0.00 0.00 2.71
2065 3765 4.406943 GCAGATGAAAGAACGGAATTGTC 58.593 43.478 0.00 0.00 0.00 3.18
2066 3766 4.154918 GCAGATGAAAGAACGGAATTGTCT 59.845 41.667 0.00 0.00 0.00 3.41
2067 3767 5.351465 GCAGATGAAAGAACGGAATTGTCTA 59.649 40.000 0.00 0.00 0.00 2.59
2068 3768 6.128282 GCAGATGAAAGAACGGAATTGTCTAA 60.128 38.462 0.00 0.00 0.00 2.10
2069 3769 7.573096 GCAGATGAAAGAACGGAATTGTCTAAA 60.573 37.037 0.00 0.00 0.00 1.85
2070 3770 8.289618 CAGATGAAAGAACGGAATTGTCTAAAA 58.710 33.333 0.00 0.00 0.00 1.52
2071 3771 8.846211 AGATGAAAGAACGGAATTGTCTAAAAA 58.154 29.630 0.00 0.00 0.00 1.94
2105 4056 6.357367 AGAACGGAAGATGCTTTGGTATATT 58.643 36.000 0.00 0.00 0.00 1.28
2110 4061 5.067674 GGAAGATGCTTTGGTATATTGTGCA 59.932 40.000 0.00 0.00 0.00 4.57
2165 4116 0.538057 AGCTGCAGGCAAGCTACAAA 60.538 50.000 17.12 0.00 44.79 2.83
2178 4129 5.230726 GCAAGCTACAAATCATAACACATGC 59.769 40.000 0.00 0.00 0.00 4.06
2180 4131 6.513806 AGCTACAAATCATAACACATGCAA 57.486 33.333 0.00 0.00 0.00 4.08
2188 4139 9.142515 CAAATCATAACACATGCAATACAAGTT 57.857 29.630 0.00 0.00 0.00 2.66
2237 4188 2.289382 TGACACGGCTGCTCTATTTCAA 60.289 45.455 0.00 0.00 0.00 2.69
2258 4210 7.730364 TCAATTCTGAAGTTACTTCTGGTTC 57.270 36.000 24.60 2.88 40.73 3.62
2264 4216 4.202326 TGAAGTTACTTCTGGTTCCTGGAC 60.202 45.833 23.27 0.00 40.73 4.02
2270 4222 0.471780 TCTGGTTCCTGGACAGAGCA 60.472 55.000 11.76 5.88 36.41 4.26
2300 4253 5.010516 TCCAAAATCGATTCAGCCAAAAAGA 59.989 36.000 11.83 0.00 0.00 2.52
2301 4254 5.119125 CCAAAATCGATTCAGCCAAAAAGAC 59.881 40.000 11.83 0.00 0.00 3.01
2304 4257 6.817765 AATCGATTCAGCCAAAAAGACTAA 57.182 33.333 4.39 0.00 0.00 2.24
2305 4258 6.817765 ATCGATTCAGCCAAAAAGACTAAA 57.182 33.333 0.00 0.00 0.00 1.85
2306 4259 5.997385 TCGATTCAGCCAAAAAGACTAAAC 58.003 37.500 0.00 0.00 0.00 2.01
2307 4260 5.048991 TCGATTCAGCCAAAAAGACTAAACC 60.049 40.000 0.00 0.00 0.00 3.27
2308 4261 4.561735 TTCAGCCAAAAAGACTAAACCG 57.438 40.909 0.00 0.00 0.00 4.44
2309 4262 3.811083 TCAGCCAAAAAGACTAAACCGA 58.189 40.909 0.00 0.00 0.00 4.69
2310 4263 4.394729 TCAGCCAAAAAGACTAAACCGAT 58.605 39.130 0.00 0.00 0.00 4.18
2311 4264 4.215399 TCAGCCAAAAAGACTAAACCGATG 59.785 41.667 0.00 0.00 0.00 3.84
2312 4265 4.215399 CAGCCAAAAAGACTAAACCGATGA 59.785 41.667 0.00 0.00 0.00 2.92
2313 4266 5.010282 AGCCAAAAAGACTAAACCGATGAT 58.990 37.500 0.00 0.00 0.00 2.45
2314 4267 5.095490 GCCAAAAAGACTAAACCGATGATG 58.905 41.667 0.00 0.00 0.00 3.07
2315 4268 5.640732 CCAAAAAGACTAAACCGATGATGG 58.359 41.667 0.00 0.00 0.00 3.51
2316 4269 5.183140 CCAAAAAGACTAAACCGATGATGGT 59.817 40.000 0.00 0.00 46.67 3.55
2317 4270 6.314784 CAAAAAGACTAAACCGATGATGGTC 58.685 40.000 0.00 0.00 42.89 4.02
2318 4271 4.819105 AAGACTAAACCGATGATGGTCA 57.181 40.909 0.00 0.00 42.89 4.02
2319 4272 4.124851 AGACTAAACCGATGATGGTCAC 57.875 45.455 0.00 0.00 42.89 3.67
2320 4273 2.858344 GACTAAACCGATGATGGTCACG 59.142 50.000 0.00 0.00 42.89 4.35
2321 4274 1.593006 CTAAACCGATGATGGTCACGC 59.407 52.381 0.00 0.00 42.89 5.34
2322 4275 0.321210 AAACCGATGATGGTCACGCA 60.321 50.000 0.00 0.00 42.89 5.24
2323 4276 0.321210 AACCGATGATGGTCACGCAA 60.321 50.000 0.00 0.00 42.89 4.85
2324 4277 0.107703 ACCGATGATGGTCACGCAAT 60.108 50.000 0.00 0.00 37.91 3.56
2325 4278 0.305617 CCGATGATGGTCACGCAATG 59.694 55.000 0.00 0.00 0.00 2.82
2326 4279 0.316442 CGATGATGGTCACGCAATGC 60.316 55.000 0.00 0.00 0.00 3.56
2327 4280 0.734309 GATGATGGTCACGCAATGCA 59.266 50.000 5.91 0.00 0.00 3.96
2328 4281 0.452987 ATGATGGTCACGCAATGCAC 59.547 50.000 5.91 0.00 0.00 4.57
2329 4282 0.606130 TGATGGTCACGCAATGCACT 60.606 50.000 5.91 0.00 0.00 4.40
2330 4283 1.338579 TGATGGTCACGCAATGCACTA 60.339 47.619 5.91 0.00 0.00 2.74
2331 4284 1.942657 GATGGTCACGCAATGCACTAT 59.057 47.619 5.91 0.00 0.00 2.12
2332 4285 1.819928 TGGTCACGCAATGCACTATT 58.180 45.000 5.91 0.00 0.00 1.73
2344 4297 2.179949 GCACTATTGCGCCTTTCTTC 57.820 50.000 4.18 0.00 39.50 2.87
2345 4298 1.468520 GCACTATTGCGCCTTTCTTCA 59.531 47.619 4.18 0.00 39.50 3.02
2346 4299 2.098117 GCACTATTGCGCCTTTCTTCAT 59.902 45.455 4.18 0.00 39.50 2.57
2347 4300 3.790123 GCACTATTGCGCCTTTCTTCATC 60.790 47.826 4.18 0.00 39.50 2.92
2348 4301 3.374988 CACTATTGCGCCTTTCTTCATCA 59.625 43.478 4.18 0.00 0.00 3.07
2349 4302 2.927553 ATTGCGCCTTTCTTCATCAC 57.072 45.000 4.18 0.00 0.00 3.06
2350 4303 1.603456 TTGCGCCTTTCTTCATCACA 58.397 45.000 4.18 0.00 0.00 3.58
2351 4304 1.159285 TGCGCCTTTCTTCATCACAG 58.841 50.000 4.18 0.00 0.00 3.66
2352 4305 1.160137 GCGCCTTTCTTCATCACAGT 58.840 50.000 0.00 0.00 0.00 3.55
2353 4306 1.537202 GCGCCTTTCTTCATCACAGTT 59.463 47.619 0.00 0.00 0.00 3.16
2354 4307 2.030805 GCGCCTTTCTTCATCACAGTTT 60.031 45.455 0.00 0.00 0.00 2.66
2355 4308 3.814945 CGCCTTTCTTCATCACAGTTTC 58.185 45.455 0.00 0.00 0.00 2.78
2356 4309 3.250762 CGCCTTTCTTCATCACAGTTTCA 59.749 43.478 0.00 0.00 0.00 2.69
2357 4310 4.540824 GCCTTTCTTCATCACAGTTTCAC 58.459 43.478 0.00 0.00 0.00 3.18
2358 4311 4.776743 CCTTTCTTCATCACAGTTTCACG 58.223 43.478 0.00 0.00 0.00 4.35
2359 4312 4.319766 CCTTTCTTCATCACAGTTTCACGG 60.320 45.833 0.00 0.00 0.00 4.94
2360 4313 2.766313 TCTTCATCACAGTTTCACGGG 58.234 47.619 0.00 0.00 0.00 5.28
2361 4314 1.806542 CTTCATCACAGTTTCACGGGG 59.193 52.381 0.00 0.00 0.00 5.73
2362 4315 0.605319 TCATCACAGTTTCACGGGGC 60.605 55.000 0.00 0.00 0.00 5.80
2363 4316 0.888736 CATCACAGTTTCACGGGGCA 60.889 55.000 0.00 0.00 0.00 5.36
2364 4317 0.889186 ATCACAGTTTCACGGGGCAC 60.889 55.000 0.00 0.00 0.00 5.01
2378 4331 3.921257 GGCACCCTACTACGTTTGT 57.079 52.632 0.00 0.00 0.00 2.83
2379 4332 2.174363 GGCACCCTACTACGTTTGTT 57.826 50.000 0.00 0.00 0.00 2.83
2380 4333 2.071540 GGCACCCTACTACGTTTGTTC 58.928 52.381 0.00 0.00 0.00 3.18
2394 4347 3.695816 GTTTGTTCCAGTTTCAGTCAGC 58.304 45.455 0.00 0.00 0.00 4.26
2396 4349 2.564771 TGTTCCAGTTTCAGTCAGCAG 58.435 47.619 0.00 0.00 0.00 4.24
2418 4371 1.978097 CGTGTGGACAATTCAATTGCG 59.022 47.619 10.21 0.87 43.98 4.85
2448 4401 6.764308 AGCACAAAAGCATATATGAAGTGT 57.236 33.333 17.10 10.59 36.85 3.55
2464 4417 2.755650 AGTGTCCACTGAAATGACGTC 58.244 47.619 9.11 9.11 40.75 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.086600 CTGCCCACCCTCCTCCTC 61.087 72.222 0.00 0.00 0.00 3.71
32 33 2.517450 GGCTTCGATGCCGACTTCG 61.517 63.158 24.65 0.47 45.50 3.79
42 43 1.478510 CAGTGTGGTAGAGGCTTCGAT 59.521 52.381 0.00 0.00 0.00 3.59
53 54 2.356992 TGATGGCGTCAGTGTGGTA 58.643 52.632 5.03 0.00 31.80 3.25
61 62 2.542020 TTCAGTTTCTGATGGCGTCA 57.458 45.000 9.42 9.42 40.39 4.35
73 74 7.878127 AGCGCATATATATGGTAGTTTCAGTTT 59.122 33.333 21.50 0.00 34.32 2.66
78 79 7.435488 CCACTAGCGCATATATATGGTAGTTTC 59.565 40.741 21.50 4.90 34.32 2.78
106 1598 3.537874 GGGGTGTCCCGATCCTCG 61.538 72.222 0.00 0.00 46.66 4.63
123 1615 1.411246 TCGATTCGGTGGTTAGATGGG 59.589 52.381 6.18 0.00 0.00 4.00
126 1618 3.518590 GTTGTCGATTCGGTGGTTAGAT 58.481 45.455 6.18 0.00 0.00 1.98
127 1619 2.353011 GGTTGTCGATTCGGTGGTTAGA 60.353 50.000 6.18 0.00 0.00 2.10
128 1620 1.997606 GGTTGTCGATTCGGTGGTTAG 59.002 52.381 6.18 0.00 0.00 2.34
130 1622 0.947180 CGGTTGTCGATTCGGTGGTT 60.947 55.000 6.18 0.00 42.43 3.67
131 1623 1.373748 CGGTTGTCGATTCGGTGGT 60.374 57.895 6.18 0.00 42.43 4.16
132 1624 1.080366 TCGGTTGTCGATTCGGTGG 60.080 57.895 6.18 0.00 43.74 4.61
133 1625 4.563630 TCGGTTGTCGATTCGGTG 57.436 55.556 6.18 0.00 43.74 4.94
162 1656 1.611673 CCTGTTGGTGAGGTCATGGAC 60.612 57.143 0.00 0.00 0.00 4.02
167 1661 2.452116 CCTCCTGTTGGTGAGGTCA 58.548 57.895 0.00 0.00 42.67 4.02
177 1671 3.490348 CCACAAATCTTCACCTCCTGTT 58.510 45.455 0.00 0.00 0.00 3.16
178 1672 2.815589 GCCACAAATCTTCACCTCCTGT 60.816 50.000 0.00 0.00 0.00 4.00
180 1674 1.707427 AGCCACAAATCTTCACCTCCT 59.293 47.619 0.00 0.00 0.00 3.69
200 1694 1.447838 GAGGCGACCAATGAGCGAA 60.448 57.895 0.00 0.00 0.00 4.70
212 1706 1.134037 GGGAGTAGAAGAGAGAGGCGA 60.134 57.143 0.00 0.00 0.00 5.54
226 1720 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
227 1721 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
228 1722 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
229 1723 1.044790 GGTATTTCCGGACGGAGGGA 61.045 60.000 13.64 4.95 46.06 4.20
230 1724 1.047034 AGGTATTTCCGGACGGAGGG 61.047 60.000 13.64 0.00 46.06 4.30
231 1725 0.104304 CAGGTATTTCCGGACGGAGG 59.896 60.000 13.64 0.00 46.06 4.30
232 1726 0.822164 ACAGGTATTTCCGGACGGAG 59.178 55.000 13.64 3.15 46.06 4.63
233 1727 0.819582 GACAGGTATTTCCGGACGGA 59.180 55.000 1.83 9.76 43.52 4.69
234 1728 0.533491 TGACAGGTATTTCCGGACGG 59.467 55.000 1.83 3.96 41.99 4.79
235 1729 2.470821 GATGACAGGTATTTCCGGACG 58.529 52.381 1.83 0.00 41.99 4.79
236 1730 2.100252 TCGATGACAGGTATTTCCGGAC 59.900 50.000 1.83 0.00 41.99 4.79
237 1731 2.380941 TCGATGACAGGTATTTCCGGA 58.619 47.619 0.00 0.00 41.99 5.14
238 1732 2.882927 TCGATGACAGGTATTTCCGG 57.117 50.000 0.00 0.00 41.99 5.14
239 1733 4.024893 CCATTTCGATGACAGGTATTTCCG 60.025 45.833 0.00 0.00 41.99 4.30
240 1734 5.123227 TCCATTTCGATGACAGGTATTTCC 58.877 41.667 0.00 0.00 0.00 3.13
241 1735 6.867662 ATCCATTTCGATGACAGGTATTTC 57.132 37.500 0.00 0.00 0.00 2.17
242 1736 8.746052 TTTATCCATTTCGATGACAGGTATTT 57.254 30.769 0.00 0.00 0.00 1.40
243 1737 8.746052 TTTTATCCATTTCGATGACAGGTATT 57.254 30.769 0.00 0.00 0.00 1.89
244 1738 8.746052 TTTTTATCCATTTCGATGACAGGTAT 57.254 30.769 0.00 0.00 0.00 2.73
245 1739 7.282224 CCTTTTTATCCATTTCGATGACAGGTA 59.718 37.037 0.00 0.00 0.00 3.08
246 1740 6.095440 CCTTTTTATCCATTTCGATGACAGGT 59.905 38.462 0.00 0.00 0.00 4.00
247 1741 6.460123 CCCTTTTTATCCATTTCGATGACAGG 60.460 42.308 0.00 0.00 0.00 4.00
248 1742 6.460123 CCCCTTTTTATCCATTTCGATGACAG 60.460 42.308 0.00 0.00 0.00 3.51
249 1743 5.359576 CCCCTTTTTATCCATTTCGATGACA 59.640 40.000 0.00 0.00 0.00 3.58
250 1744 5.359860 ACCCCTTTTTATCCATTTCGATGAC 59.640 40.000 0.00 0.00 0.00 3.06
251 1745 5.359576 CACCCCTTTTTATCCATTTCGATGA 59.640 40.000 0.00 0.00 0.00 2.92
252 1746 5.127031 ACACCCCTTTTTATCCATTTCGATG 59.873 40.000 0.00 0.00 0.00 3.84
253 1747 5.269189 ACACCCCTTTTTATCCATTTCGAT 58.731 37.500 0.00 0.00 0.00 3.59
254 1748 4.668636 ACACCCCTTTTTATCCATTTCGA 58.331 39.130 0.00 0.00 0.00 3.71
255 1749 6.546034 AGATACACCCCTTTTTATCCATTTCG 59.454 38.462 0.00 0.00 0.00 3.46
256 1750 7.898014 AGATACACCCCTTTTTATCCATTTC 57.102 36.000 0.00 0.00 0.00 2.17
257 1751 8.787818 TCTAGATACACCCCTTTTTATCCATTT 58.212 33.333 0.00 0.00 0.00 2.32
258 1752 8.344939 TCTAGATACACCCCTTTTTATCCATT 57.655 34.615 0.00 0.00 0.00 3.16
259 1753 7.947782 TCTAGATACACCCCTTTTTATCCAT 57.052 36.000 0.00 0.00 0.00 3.41
260 1754 7.404980 AGTTCTAGATACACCCCTTTTTATCCA 59.595 37.037 0.00 0.00 0.00 3.41
261 1755 7.803131 AGTTCTAGATACACCCCTTTTTATCC 58.197 38.462 0.00 0.00 0.00 2.59
268 1762 9.275572 TGTATTTTAGTTCTAGATACACCCCTT 57.724 33.333 0.00 0.00 30.60 3.95
269 1763 8.849543 TGTATTTTAGTTCTAGATACACCCCT 57.150 34.615 0.00 0.00 30.60 4.79
301 1795 9.919416 TCATCAAGATGAATAAAAAGGGATGTA 57.081 29.630 10.16 0.00 44.14 2.29
302 1796 8.827832 TCATCAAGATGAATAAAAAGGGATGT 57.172 30.769 10.16 0.00 44.14 3.06
319 1813 8.994207 CCGTCCGGAAATACTTGTCATCAAGA 62.994 46.154 5.23 0.31 44.37 3.02
320 1814 6.918800 CCGTCCGGAAATACTTGTCATCAAG 61.919 48.000 5.23 6.44 45.65 3.02
321 1815 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
322 1816 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
323 1817 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
324 1818 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
325 1819 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
326 1820 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
327 1821 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
328 1822 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
329 1823 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
330 1824 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
331 1825 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
332 1826 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
333 1827 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
334 1828 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
335 1829 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
336 1830 2.141011 TTGTACTCCCTCCGTCCGGA 62.141 60.000 0.00 0.00 42.90 5.14
337 1831 1.679977 TTGTACTCCCTCCGTCCGG 60.680 63.158 0.00 0.00 0.00 5.14
338 1832 1.246056 TGTTGTACTCCCTCCGTCCG 61.246 60.000 0.00 0.00 0.00 4.79
339 1833 1.192428 ATGTTGTACTCCCTCCGTCC 58.808 55.000 0.00 0.00 0.00 4.79
340 1834 2.223758 GCTATGTTGTACTCCCTCCGTC 60.224 54.545 0.00 0.00 0.00 4.79
341 1835 1.755380 GCTATGTTGTACTCCCTCCGT 59.245 52.381 0.00 0.00 0.00 4.69
342 1836 1.068741 GGCTATGTTGTACTCCCTCCG 59.931 57.143 0.00 0.00 0.00 4.63
343 1837 2.116238 TGGCTATGTTGTACTCCCTCC 58.884 52.381 0.00 0.00 0.00 4.30
344 1838 3.197983 AGTTGGCTATGTTGTACTCCCTC 59.802 47.826 0.00 0.00 0.00 4.30
345 1839 3.182152 AGTTGGCTATGTTGTACTCCCT 58.818 45.455 0.00 0.00 0.00 4.20
346 1840 3.629142 AGTTGGCTATGTTGTACTCCC 57.371 47.619 0.00 0.00 0.00 4.30
347 1841 5.974108 TCTAAGTTGGCTATGTTGTACTCC 58.026 41.667 0.00 0.00 0.00 3.85
348 1842 7.493367 AGATCTAAGTTGGCTATGTTGTACTC 58.507 38.462 0.00 0.00 0.00 2.59
349 1843 7.425224 AGATCTAAGTTGGCTATGTTGTACT 57.575 36.000 0.00 0.00 0.00 2.73
350 1844 9.765795 ATTAGATCTAAGTTGGCTATGTTGTAC 57.234 33.333 19.51 0.00 0.00 2.90
365 1859 6.102663 CGGACATAGGCCAATTAGATCTAAG 58.897 44.000 19.51 8.32 0.00 2.18
394 1888 8.899427 AGAAACTTAACTTCAAGTTAGGTACC 57.101 34.615 21.72 16.48 46.13 3.34
399 1893 9.922305 CACAAGAGAAACTTAACTTCAAGTTAG 57.078 33.333 9.93 7.45 45.68 2.34
442 1937 8.100164 TGAAGTCCATGTGTAAGTGAAATATGA 58.900 33.333 0.00 0.00 0.00 2.15
449 1944 9.952030 TTTATATTGAAGTCCATGTGTAAGTGA 57.048 29.630 0.00 0.00 0.00 3.41
477 1972 8.650143 TTTTAGCCCTAAAAATCTGACTTCAT 57.350 30.769 10.00 0.00 40.74 2.57
504 1999 3.190079 CGATGTACTTGAGGGTGTCATG 58.810 50.000 0.00 0.00 34.17 3.07
529 2024 5.804979 GTGAAAATTGCCATGTAGCGTAAAT 59.195 36.000 0.00 0.00 34.65 1.40
559 2054 3.957497 TGTGTGTAGGATTTGCCAAGTTT 59.043 39.130 0.00 0.00 40.02 2.66
563 2058 6.435591 TCATATTTGTGTGTAGGATTTGCCAA 59.564 34.615 0.00 0.00 40.02 4.52
643 2138 6.954487 ATACAACGATGGTCTATGTAGTGA 57.046 37.500 0.00 0.00 30.76 3.41
668 2163 9.675464 ACGATGATTGTTCCCTAAATAAGTAAA 57.325 29.630 0.00 0.00 0.00 2.01
669 2164 9.321562 GACGATGATTGTTCCCTAAATAAGTAA 57.678 33.333 0.00 0.00 0.00 2.24
670 2165 7.929785 GGACGATGATTGTTCCCTAAATAAGTA 59.070 37.037 0.00 0.00 0.00 2.24
672 2167 6.765989 TGGACGATGATTGTTCCCTAAATAAG 59.234 38.462 0.00 0.00 0.00 1.73
673 2168 6.654959 TGGACGATGATTGTTCCCTAAATAA 58.345 36.000 0.00 0.00 0.00 1.40
686 2181 3.555956 GCGTAGTTTCATGGACGATGATT 59.444 43.478 0.58 0.00 40.92 2.57
708 2209 5.443301 CGACACGCAGATATTCGAATATTGG 60.443 44.000 27.00 22.16 31.96 3.16
737 2238 1.064783 TGACAGAGCTATGCGCGAG 59.935 57.895 12.10 3.43 45.59 5.03
738 2239 1.226688 GTGACAGAGCTATGCGCGA 60.227 57.895 12.10 0.00 45.59 5.87
739 2240 0.873312 ATGTGACAGAGCTATGCGCG 60.873 55.000 8.60 0.00 45.59 6.86
740 2241 0.580578 CATGTGACAGAGCTATGCGC 59.419 55.000 8.60 0.00 39.57 6.09
741 2242 1.857217 GACATGTGACAGAGCTATGCG 59.143 52.381 8.60 0.00 0.00 4.73
742 2243 2.864946 CAGACATGTGACAGAGCTATGC 59.135 50.000 8.60 1.93 0.00 3.14
743 2244 4.120792 ACAGACATGTGACAGAGCTATG 57.879 45.455 1.15 6.84 38.57 2.23
744 2245 4.815533 AACAGACATGTGACAGAGCTAT 57.184 40.909 1.15 0.00 40.39 2.97
756 2257 1.467734 GCAGCAGGAGAAACAGACATG 59.532 52.381 0.00 0.00 0.00 3.21
863 2371 0.104620 TTATACAGGAGGGGGAGGGC 60.105 60.000 0.00 0.00 0.00 5.19
954 2479 0.688087 AGAGGATTCGGGGAGTGGAC 60.688 60.000 0.00 0.00 0.00 4.02
976 2502 4.994471 CTGCTGCGCTGGTGGTGA 62.994 66.667 16.47 0.00 0.00 4.02
1383 2912 1.301293 GGTCTTCTTGGGGAGCAGG 59.699 63.158 0.00 0.00 0.00 4.85
1471 3000 4.081087 ACTCCGACATAACTAAGCAATGGT 60.081 41.667 0.00 0.00 0.00 3.55
1601 3149 2.933260 ACAATGGGCAAACGAACAAAAC 59.067 40.909 0.00 0.00 0.00 2.43
1618 3193 6.626623 GCAAATCTGAGCATAGGAACAACAAT 60.627 38.462 0.00 0.00 0.00 2.71
1690 3270 2.190578 CGACCAAGCCCCTGGATC 59.809 66.667 0.00 0.00 38.96 3.36
1691 3271 3.411517 CCGACCAAGCCCCTGGAT 61.412 66.667 0.00 0.00 38.96 3.41
1705 3285 0.242825 CTACCTTCGCAACTGACCGA 59.757 55.000 0.00 0.00 0.00 4.69
1734 3323 2.692273 AAACACCCGCCAAGGAGGTC 62.692 60.000 8.11 0.00 45.00 3.85
1737 3326 0.821711 TTCAAACACCCGCCAAGGAG 60.822 55.000 0.00 0.00 45.00 3.69
1840 3443 6.912051 CCAAAATTTTTGGCTGCTTAAAACTC 59.088 34.615 24.03 0.00 32.18 3.01
1847 3450 2.871633 CGTCCAAAATTTTTGGCTGCTT 59.128 40.909 28.57 0.00 39.38 3.91
1851 3458 6.510960 CGAAATTTCGTCCAAAATTTTTGGCT 60.511 34.615 28.57 11.82 44.66 4.75
1852 3459 5.619202 CGAAATTTCGTCCAAAATTTTTGGC 59.381 36.000 28.57 22.70 44.66 4.52
1878 3486 1.445410 GGGAAATTTCGCCGCCAAC 60.445 57.895 21.33 1.69 34.41 3.77
1933 3555 1.531578 GCGAGGACAAGGTTTTCAGTC 59.468 52.381 0.00 0.00 0.00 3.51
2070 3770 6.015940 AGCATCTTCCGTTCTTTCATCTTTTT 60.016 34.615 0.00 0.00 0.00 1.94
2071 3771 5.474876 AGCATCTTCCGTTCTTTCATCTTTT 59.525 36.000 0.00 0.00 0.00 2.27
2074 3774 4.213564 AGCATCTTCCGTTCTTTCATCT 57.786 40.909 0.00 0.00 0.00 2.90
2075 3775 4.954092 AAGCATCTTCCGTTCTTTCATC 57.046 40.909 0.00 0.00 0.00 2.92
2077 3777 3.253188 CCAAAGCATCTTCCGTTCTTTCA 59.747 43.478 0.00 0.00 0.00 2.69
2078 3778 3.253432 ACCAAAGCATCTTCCGTTCTTTC 59.747 43.478 0.00 0.00 0.00 2.62
2079 3779 3.222603 ACCAAAGCATCTTCCGTTCTTT 58.777 40.909 0.00 0.00 0.00 2.52
2080 3780 2.863809 ACCAAAGCATCTTCCGTTCTT 58.136 42.857 0.00 0.00 0.00 2.52
2081 3781 2.568623 ACCAAAGCATCTTCCGTTCT 57.431 45.000 0.00 0.00 0.00 3.01
2082 3782 6.038271 ACAATATACCAAAGCATCTTCCGTTC 59.962 38.462 0.00 0.00 0.00 3.95
2084 3784 5.296780 CACAATATACCAAAGCATCTTCCGT 59.703 40.000 0.00 0.00 0.00 4.69
2085 3785 5.751680 CACAATATACCAAAGCATCTTCCG 58.248 41.667 0.00 0.00 0.00 4.30
2086 3786 5.067674 TGCACAATATACCAAAGCATCTTCC 59.932 40.000 0.00 0.00 0.00 3.46
2087 3787 5.973565 GTGCACAATATACCAAAGCATCTTC 59.026 40.000 13.17 0.00 32.75 2.87
2088 3788 5.449041 CGTGCACAATATACCAAAGCATCTT 60.449 40.000 18.64 0.00 32.75 2.40
2089 3789 4.035558 CGTGCACAATATACCAAAGCATCT 59.964 41.667 18.64 0.00 32.75 2.90
2090 3790 4.201910 ACGTGCACAATATACCAAAGCATC 60.202 41.667 18.64 0.00 32.75 3.91
2091 3791 3.694072 ACGTGCACAATATACCAAAGCAT 59.306 39.130 18.64 0.00 32.75 3.79
2110 4061 1.515521 GCTGGGCTTAGCACAAACGT 61.516 55.000 11.34 0.00 43.23 3.99
2205 4156 2.425312 CAGCCGTGTCAGATTAGAGTCT 59.575 50.000 0.00 0.00 0.00 3.24
2206 4157 2.803451 CAGCCGTGTCAGATTAGAGTC 58.197 52.381 0.00 0.00 0.00 3.36
2207 4158 1.134965 GCAGCCGTGTCAGATTAGAGT 60.135 52.381 0.00 0.00 0.00 3.24
2237 4188 6.234177 CAGGAACCAGAAGTAACTTCAGAAT 58.766 40.000 0.00 0.00 42.37 2.40
2258 4210 0.747283 GAAGGCATGCTCTGTCCAGG 60.747 60.000 18.92 0.00 0.00 4.45
2264 4216 2.479049 CGATTTTGGAAGGCATGCTCTG 60.479 50.000 18.92 0.00 0.00 3.35
2270 4222 3.181483 GCTGAATCGATTTTGGAAGGCAT 60.181 43.478 12.81 0.00 0.00 4.40
2300 4253 2.888594 CGTGACCATCATCGGTTTAGT 58.111 47.619 0.00 0.00 40.22 2.24
2301 4254 1.593006 GCGTGACCATCATCGGTTTAG 59.407 52.381 0.00 0.00 40.22 1.85
2304 4257 0.321210 TTGCGTGACCATCATCGGTT 60.321 50.000 0.00 0.00 40.22 4.44
2305 4258 0.107703 ATTGCGTGACCATCATCGGT 60.108 50.000 0.00 0.00 43.91 4.69
2306 4259 0.305617 CATTGCGTGACCATCATCGG 59.694 55.000 0.00 0.00 0.00 4.18
2307 4260 0.316442 GCATTGCGTGACCATCATCG 60.316 55.000 0.00 0.00 0.00 3.84
2308 4261 0.734309 TGCATTGCGTGACCATCATC 59.266 50.000 3.84 0.00 0.00 2.92
2309 4262 0.452987 GTGCATTGCGTGACCATCAT 59.547 50.000 3.84 0.00 0.00 2.45
2310 4263 0.606130 AGTGCATTGCGTGACCATCA 60.606 50.000 3.84 0.00 0.00 3.07
2311 4264 1.368641 TAGTGCATTGCGTGACCATC 58.631 50.000 3.84 0.00 0.00 3.51
2312 4265 2.042686 ATAGTGCATTGCGTGACCAT 57.957 45.000 3.84 0.00 0.00 3.55
2313 4266 1.468127 CAATAGTGCATTGCGTGACCA 59.532 47.619 3.84 0.00 37.80 4.02
2314 4267 2.178474 CAATAGTGCATTGCGTGACC 57.822 50.000 3.84 0.00 37.80 4.02
2326 4279 3.374988 TGATGAAGAAAGGCGCAATAGTG 59.625 43.478 10.83 0.00 0.00 2.74
2327 4280 3.375299 GTGATGAAGAAAGGCGCAATAGT 59.625 43.478 10.83 0.00 0.00 2.12
2328 4281 3.374988 TGTGATGAAGAAAGGCGCAATAG 59.625 43.478 10.83 0.00 0.00 1.73
2329 4282 3.342719 TGTGATGAAGAAAGGCGCAATA 58.657 40.909 10.83 0.00 0.00 1.90
2330 4283 2.161855 TGTGATGAAGAAAGGCGCAAT 58.838 42.857 10.83 0.00 0.00 3.56
2331 4284 1.536766 CTGTGATGAAGAAAGGCGCAA 59.463 47.619 10.83 0.00 0.00 4.85
2332 4285 1.159285 CTGTGATGAAGAAAGGCGCA 58.841 50.000 10.83 0.00 0.00 6.09
2333 4286 1.160137 ACTGTGATGAAGAAAGGCGC 58.840 50.000 0.00 0.00 0.00 6.53
2334 4287 3.250762 TGAAACTGTGATGAAGAAAGGCG 59.749 43.478 0.00 0.00 0.00 5.52
2335 4288 4.540824 GTGAAACTGTGATGAAGAAAGGC 58.459 43.478 0.00 0.00 0.00 4.35
2336 4289 4.319766 CCGTGAAACTGTGATGAAGAAAGG 60.320 45.833 0.00 0.00 31.75 3.11
2337 4290 4.319766 CCCGTGAAACTGTGATGAAGAAAG 60.320 45.833 0.00 0.00 31.75 2.62
2338 4291 3.563808 CCCGTGAAACTGTGATGAAGAAA 59.436 43.478 0.00 0.00 31.75 2.52
2339 4292 3.138304 CCCGTGAAACTGTGATGAAGAA 58.862 45.455 0.00 0.00 31.75 2.52
2340 4293 2.549992 CCCCGTGAAACTGTGATGAAGA 60.550 50.000 0.00 0.00 31.75 2.87
2341 4294 1.806542 CCCCGTGAAACTGTGATGAAG 59.193 52.381 0.00 0.00 31.75 3.02
2342 4295 1.890876 CCCCGTGAAACTGTGATGAA 58.109 50.000 0.00 0.00 31.75 2.57
2343 4296 0.605319 GCCCCGTGAAACTGTGATGA 60.605 55.000 0.00 0.00 31.75 2.92
2344 4297 0.888736 TGCCCCGTGAAACTGTGATG 60.889 55.000 0.00 0.00 31.75 3.07
2345 4298 0.889186 GTGCCCCGTGAAACTGTGAT 60.889 55.000 0.00 0.00 31.75 3.06
2346 4299 1.525077 GTGCCCCGTGAAACTGTGA 60.525 57.895 0.00 0.00 31.75 3.58
2347 4300 2.551912 GGTGCCCCGTGAAACTGTG 61.552 63.158 0.00 0.00 31.75 3.66
2348 4301 2.203294 GGTGCCCCGTGAAACTGT 60.203 61.111 0.00 0.00 31.75 3.55
2349 4302 2.983592 GGGTGCCCCGTGAAACTG 60.984 66.667 0.00 0.00 32.13 3.16
2357 4310 1.891722 AAACGTAGTAGGGTGCCCCG 61.892 60.000 3.17 2.58 46.94 5.73
2358 4311 0.392060 CAAACGTAGTAGGGTGCCCC 60.392 60.000 3.17 2.16 45.00 5.80
2359 4312 0.322648 ACAAACGTAGTAGGGTGCCC 59.677 55.000 0.00 0.00 45.00 5.36
2360 4313 2.071540 GAACAAACGTAGTAGGGTGCC 58.928 52.381 0.00 0.00 45.00 5.01
2361 4314 2.071540 GGAACAAACGTAGTAGGGTGC 58.928 52.381 0.00 0.00 45.00 5.01
2362 4315 3.243975 ACTGGAACAAACGTAGTAGGGTG 60.244 47.826 0.00 0.00 45.00 4.61
2363 4316 2.967887 ACTGGAACAAACGTAGTAGGGT 59.032 45.455 0.00 0.00 45.00 4.34
2364 4317 3.672767 ACTGGAACAAACGTAGTAGGG 57.327 47.619 0.00 0.00 45.00 3.53
2365 4318 5.051816 TGAAACTGGAACAAACGTAGTAGG 58.948 41.667 0.00 0.00 45.00 3.18
2366 4319 5.751990 ACTGAAACTGGAACAAACGTAGTAG 59.248 40.000 0.00 0.00 45.00 2.57
2367 4320 5.663456 ACTGAAACTGGAACAAACGTAGTA 58.337 37.500 0.00 0.00 45.00 1.82
2369 4322 4.569162 TGACTGAAACTGGAACAAACGTAG 59.431 41.667 0.00 0.00 38.70 3.51
2370 4323 4.505808 TGACTGAAACTGGAACAAACGTA 58.494 39.130 0.00 0.00 38.70 3.57
2371 4324 3.340034 TGACTGAAACTGGAACAAACGT 58.660 40.909 0.00 0.00 38.70 3.99
2372 4325 3.788797 GCTGACTGAAACTGGAACAAACG 60.789 47.826 0.00 0.00 38.70 3.60
2373 4326 3.128589 TGCTGACTGAAACTGGAACAAAC 59.871 43.478 0.00 0.00 38.70 2.93
2374 4327 3.351740 TGCTGACTGAAACTGGAACAAA 58.648 40.909 0.00 0.00 38.70 2.83
2375 4328 2.945008 CTGCTGACTGAAACTGGAACAA 59.055 45.455 0.00 0.00 38.70 2.83
2376 4329 2.170397 TCTGCTGACTGAAACTGGAACA 59.830 45.455 0.00 0.00 0.00 3.18
2377 4330 2.545946 GTCTGCTGACTGAAACTGGAAC 59.454 50.000 15.81 0.00 39.94 3.62
2378 4331 2.803133 CGTCTGCTGACTGAAACTGGAA 60.803 50.000 19.86 0.00 40.86 3.53
2379 4332 1.269778 CGTCTGCTGACTGAAACTGGA 60.270 52.381 19.86 0.00 40.86 3.86
2380 4333 1.143305 CGTCTGCTGACTGAAACTGG 58.857 55.000 19.86 0.14 40.86 4.00
2394 4347 4.221342 CAATTGAATTGTCCACACGTCTG 58.779 43.478 9.67 0.00 35.57 3.51
2396 4349 2.979813 GCAATTGAATTGTCCACACGTC 59.020 45.455 18.12 0.00 42.20 4.34
2418 4371 9.787532 TTCATATATGCTTTTGTGCTTTAAGAC 57.212 29.630 7.92 0.00 0.00 3.01
2448 4401 0.669318 GCGGACGTCATTTCAGTGGA 60.669 55.000 18.91 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.