Multiple sequence alignment - TraesCS2B01G357500

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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 TraesCS2B01G357500 chr2B 100.000 4421 0 0 1 4421 510584570 510588990 0.000000e+00 8165
1 TraesCS2B01G357500 chr2A 93.832 3810 141 29 516 4271 554744379 554740610 0.000000e+00 5648
2 TraesCS2B01G357500 chr2A 97.143 140 4 0 4260 4399 554740539 554740400 2.060000e-58 237
3 TraesCS2B01G357500 chr2D 93.688 3707 155 35 587 4268 431673892 431677544 0.000000e+00 5476
4 TraesCS2B01G357500 chr2D 96.503 143 5 0 4257 4399 431677615 431677757 2.060000e-58 237
5 TraesCS2B01G357500 chr2D 89.091 165 16 2 41 204 431672088 431672251 2.080000e-48 204
6 TraesCS2B01G357500 chr6D 79.070 258 45 3 2563 2811 44816096 44816353 7.600000e-38 169
7 TraesCS2B01G357500 chr5D 83.871 155 20 5 2600 2751 495076417 495076265 4.610000e-30 143
8 TraesCS2B01G357500 chr6A 75.581 258 45 6 2563 2811 514046095 514045847 1.300000e-20 111


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 TraesCS2B01G357500 chr2B 510584570 510588990 4420 False 8165.000000 8165 100.0000 1 4421 1 chr2B.!!$F1 4420
1 TraesCS2B01G357500 chr2A 554740400 554744379 3979 True 2942.500000 5648 95.4875 516 4399 2 chr2A.!!$R1 3883
2 TraesCS2B01G357500 chr2D 431672088 431677757 5669 False 1972.333333 5476 93.0940 41 4399 3 chr2D.!!$F1 4358

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
393 1803 0.028770 CGCGTTGTGGAGCTTCAAAA 59.971 50.000 0.00 0.0 0.00 2.44 F
754 2177 1.142778 GATCTCGTCGCAGTGCCTTC 61.143 60.000 10.11 0.0 0.00 3.46 F
825 2248 1.304617 CCCTCTTGAAGCCCTTCCC 59.695 63.158 5.64 0.0 38.77 3.97 F
2260 3742 0.792640 CACGGAGTCACTGACAATGC 59.207 55.000 11.80 0.0 41.61 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1910 3359 0.107643 TCAATGTCGTTGGTGGCTCA 59.892 50.0 4.95 0.00 38.39 4.26 R
2247 3729 0.384725 GTGCGTGCATTGTCAGTGAC 60.385 55.0 16.68 16.68 0.00 3.67 R
2821 4303 0.787183 GCAAGACGAACAGAGCAGAC 59.213 55.0 0.00 0.00 0.00 3.51 R
3940 5435 0.035630 ACAGCAGCCTCTGGAACATC 60.036 55.0 7.59 0.00 38.20 3.06 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
17 18 3.495729 TCCAAGTTGGGAGGGAGC 58.504 61.111 21.85 0.00 38.32 4.70
18 19 2.045926 CCAAGTTGGGAGGGAGCG 60.046 66.667 14.64 0.00 32.67 5.03
19 20 2.747855 CAAGTTGGGAGGGAGCGC 60.748 66.667 0.00 0.00 0.00 5.92
20 21 3.249189 AAGTTGGGAGGGAGCGCA 61.249 61.111 11.47 0.00 0.00 6.09
21 22 3.553095 AAGTTGGGAGGGAGCGCAC 62.553 63.158 11.47 1.97 0.00 5.34
25 26 4.115199 GGGAGGGAGCGCACCAAT 62.115 66.667 25.48 13.26 0.00 3.16
26 27 2.742116 GGGAGGGAGCGCACCAATA 61.742 63.158 25.48 0.00 0.00 1.90
27 28 1.451936 GGAGGGAGCGCACCAATAT 59.548 57.895 25.48 7.97 0.00 1.28
28 29 0.886490 GGAGGGAGCGCACCAATATG 60.886 60.000 25.48 0.00 0.00 1.78
29 30 0.886490 GAGGGAGCGCACCAATATGG 60.886 60.000 25.48 0.00 45.02 2.74
30 31 1.898574 GGGAGCGCACCAATATGGG 60.899 63.158 25.48 0.00 43.37 4.00
34 35 2.123939 CGCACCAATATGGGCCCA 60.124 61.111 30.92 30.92 43.37 5.36
35 36 1.531365 CGCACCAATATGGGCCCAT 60.531 57.895 38.67 38.67 43.37 4.00
36 37 1.808531 CGCACCAATATGGGCCCATG 61.809 60.000 42.19 29.28 43.37 3.66
37 38 0.469705 GCACCAATATGGGCCCATGA 60.470 55.000 42.19 27.22 43.37 3.07
38 39 1.624336 CACCAATATGGGCCCATGAG 58.376 55.000 42.19 30.07 43.37 2.90
39 40 0.484212 ACCAATATGGGCCCATGAGG 59.516 55.000 42.19 37.08 43.37 3.86
53 54 5.733620 CCCATGAGGCTGCATATAAATTT 57.266 39.130 0.50 0.00 0.00 1.82
62 63 5.244626 GGCTGCATATAAATTTGGAGTGGAT 59.755 40.000 0.50 0.00 34.19 3.41
65 66 7.275888 TGCATATAAATTTGGAGTGGATGTC 57.724 36.000 0.00 0.00 0.00 3.06
124 125 4.815846 ACAAAAATCCCAGTGAATTGCAAC 59.184 37.500 0.00 0.00 0.00 4.17
138 139 6.311200 GTGAATTGCAACCCTATGAATCAAAC 59.689 38.462 0.00 0.00 0.00 2.93
155 156 9.545105 TGAATCAAACAATGCAGTAAGAAAAAT 57.455 25.926 0.00 0.00 0.00 1.82
161 163 7.775053 ACAATGCAGTAAGAAAAATCCCTAA 57.225 32.000 0.00 0.00 0.00 2.69
197 199 6.669154 TCCTTTCAATTAAAGATGCCCTCAAT 59.331 34.615 0.00 0.00 46.44 2.57
199 201 7.364056 CCTTTCAATTAAAGATGCCCTCAATGA 60.364 37.037 0.00 0.00 46.44 2.57
203 205 8.542080 TCAATTAAAGATGCCCTCAATGATTTT 58.458 29.630 0.00 0.00 0.00 1.82
204 206 8.609176 CAATTAAAGATGCCCTCAATGATTTTG 58.391 33.333 0.00 0.00 0.00 2.44
208 210 5.205821 AGATGCCCTCAATGATTTTGATGA 58.794 37.500 0.00 0.00 0.00 2.92
209 211 5.839063 AGATGCCCTCAATGATTTTGATGAT 59.161 36.000 0.00 0.00 0.00 2.45
210 212 5.270893 TGCCCTCAATGATTTTGATGATG 57.729 39.130 0.00 0.00 0.00 3.07
212 214 5.188163 TGCCCTCAATGATTTTGATGATGTT 59.812 36.000 0.00 0.00 0.00 2.71
213 215 5.522460 GCCCTCAATGATTTTGATGATGTTG 59.478 40.000 0.00 0.00 0.00 3.33
214 216 6.046593 CCCTCAATGATTTTGATGATGTTGG 58.953 40.000 0.00 0.00 0.00 3.77
215 217 5.522460 CCTCAATGATTTTGATGATGTTGGC 59.478 40.000 0.00 0.00 0.00 4.52
216 218 6.038997 TCAATGATTTTGATGATGTTGGCA 57.961 33.333 0.00 0.00 0.00 4.92
217 219 5.870433 TCAATGATTTTGATGATGTTGGCAC 59.130 36.000 0.00 0.00 0.00 5.01
220 222 5.472148 TGATTTTGATGATGTTGGCACTTC 58.528 37.500 0.00 0.00 0.00 3.01
221 223 3.940209 TTTGATGATGTTGGCACTTCC 57.060 42.857 0.00 0.00 0.00 3.46
222 224 2.885135 TGATGATGTTGGCACTTCCT 57.115 45.000 0.00 0.00 35.26 3.36
224 226 4.299586 TGATGATGTTGGCACTTCCTAA 57.700 40.909 0.00 0.00 35.26 2.69
227 1637 2.754552 TGATGTTGGCACTTCCTAATGC 59.245 45.455 0.00 0.00 41.29 3.56
229 1639 1.885887 TGTTGGCACTTCCTAATGCAC 59.114 47.619 0.00 0.00 43.93 4.57
242 1652 4.655649 TCCTAATGCACTCACATATCACCT 59.344 41.667 0.00 0.00 0.00 4.00
246 1656 4.341366 TGCACTCACATATCACCTATGG 57.659 45.455 0.00 0.00 41.41 2.74
251 1661 6.219473 CACTCACATATCACCTATGGAAGAC 58.781 44.000 0.00 0.00 41.41 3.01
252 1662 5.305644 ACTCACATATCACCTATGGAAGACC 59.694 44.000 0.00 0.00 41.41 3.85
258 1668 1.000163 CACCTATGGAAGACCGGATCG 60.000 57.143 9.46 0.00 39.42 3.69
260 1670 2.171840 CCTATGGAAGACCGGATCGAT 58.828 52.381 9.46 8.84 39.42 3.59
261 1671 3.245158 ACCTATGGAAGACCGGATCGATA 60.245 47.826 9.46 9.53 39.42 2.92
263 1673 4.402793 CCTATGGAAGACCGGATCGATATT 59.597 45.833 9.46 0.00 39.42 1.28
266 1676 2.288825 GGAAGACCGGATCGATATTGCA 60.289 50.000 9.46 0.00 0.00 4.08
267 1677 2.732412 AGACCGGATCGATATTGCAG 57.268 50.000 9.46 0.00 0.00 4.41
268 1678 2.239400 AGACCGGATCGATATTGCAGA 58.761 47.619 9.46 0.00 0.00 4.26
269 1679 2.230025 AGACCGGATCGATATTGCAGAG 59.770 50.000 9.46 0.00 0.00 3.35
270 1680 1.337260 ACCGGATCGATATTGCAGAGC 60.337 52.381 9.46 0.00 0.00 4.09
271 1681 1.067283 CCGGATCGATATTGCAGAGCT 60.067 52.381 0.00 0.00 0.00 4.09
272 1682 2.611473 CCGGATCGATATTGCAGAGCTT 60.611 50.000 0.00 0.00 0.00 3.74
273 1683 2.665537 CGGATCGATATTGCAGAGCTTC 59.334 50.000 0.00 0.00 0.00 3.86
274 1684 2.665537 GGATCGATATTGCAGAGCTTCG 59.334 50.000 0.00 0.00 0.00 3.79
275 1685 2.140065 TCGATATTGCAGAGCTTCGG 57.860 50.000 0.80 0.00 0.00 4.30
276 1686 1.681264 TCGATATTGCAGAGCTTCGGA 59.319 47.619 0.80 0.00 0.00 4.55
277 1687 2.297315 TCGATATTGCAGAGCTTCGGAT 59.703 45.455 0.80 0.00 0.00 4.18
278 1688 2.411069 CGATATTGCAGAGCTTCGGATG 59.589 50.000 0.00 0.00 0.00 3.51
279 1689 2.988010 TATTGCAGAGCTTCGGATGT 57.012 45.000 0.00 0.00 0.00 3.06
280 1690 2.119801 ATTGCAGAGCTTCGGATGTT 57.880 45.000 0.00 0.00 0.00 2.71
281 1691 1.159285 TTGCAGAGCTTCGGATGTTG 58.841 50.000 0.00 0.00 0.00 3.33
282 1692 1.300971 TGCAGAGCTTCGGATGTTGC 61.301 55.000 0.00 8.87 0.00 4.17
283 1693 1.986575 GCAGAGCTTCGGATGTTGCC 61.987 60.000 0.00 0.00 0.00 4.52
284 1694 0.392193 CAGAGCTTCGGATGTTGCCT 60.392 55.000 0.00 0.00 0.00 4.75
285 1695 0.326264 AGAGCTTCGGATGTTGCCTT 59.674 50.000 0.00 0.00 0.00 4.35
286 1696 1.168714 GAGCTTCGGATGTTGCCTTT 58.831 50.000 0.00 0.00 0.00 3.11
287 1697 1.131315 GAGCTTCGGATGTTGCCTTTC 59.869 52.381 0.00 0.00 0.00 2.62
288 1698 0.881118 GCTTCGGATGTTGCCTTTCA 59.119 50.000 0.00 0.00 0.00 2.69
289 1699 1.474077 GCTTCGGATGTTGCCTTTCAT 59.526 47.619 0.00 0.00 0.00 2.57
290 1700 2.094545 GCTTCGGATGTTGCCTTTCATT 60.095 45.455 0.00 0.00 0.00 2.57
291 1701 3.614870 GCTTCGGATGTTGCCTTTCATTT 60.615 43.478 0.00 0.00 0.00 2.32
292 1702 4.380444 GCTTCGGATGTTGCCTTTCATTTA 60.380 41.667 0.00 0.00 0.00 1.40
293 1703 5.708948 CTTCGGATGTTGCCTTTCATTTAA 58.291 37.500 0.00 0.00 0.00 1.52
294 1704 5.713792 TCGGATGTTGCCTTTCATTTAAA 57.286 34.783 0.00 0.00 0.00 1.52
295 1705 6.090483 TCGGATGTTGCCTTTCATTTAAAA 57.910 33.333 0.00 0.00 0.00 1.52
296 1706 6.516718 TCGGATGTTGCCTTTCATTTAAAAA 58.483 32.000 0.00 0.00 0.00 1.94
321 1731 9.710900 AAATCCTTGTTAATAAGAAGCCAAAAG 57.289 29.630 13.07 0.00 30.91 2.27
322 1732 6.687604 TCCTTGTTAATAAGAAGCCAAAAGC 58.312 36.000 13.07 0.00 44.25 3.51
333 1743 1.559831 GCCAAAAGCACTGACAACAC 58.440 50.000 0.00 0.00 42.97 3.32
334 1744 1.802508 GCCAAAAGCACTGACAACACC 60.803 52.381 0.00 0.00 42.97 4.16
335 1745 1.476085 CCAAAAGCACTGACAACACCA 59.524 47.619 0.00 0.00 0.00 4.17
336 1746 2.529151 CAAAAGCACTGACAACACCAC 58.471 47.619 0.00 0.00 0.00 4.16
337 1747 1.832883 AAAGCACTGACAACACCACA 58.167 45.000 0.00 0.00 0.00 4.17
338 1748 1.094785 AAGCACTGACAACACCACAC 58.905 50.000 0.00 0.00 0.00 3.82
339 1749 0.035534 AGCACTGACAACACCACACA 60.036 50.000 0.00 0.00 0.00 3.72
340 1750 0.098728 GCACTGACAACACCACACAC 59.901 55.000 0.00 0.00 0.00 3.82
341 1751 1.447945 CACTGACAACACCACACACA 58.552 50.000 0.00 0.00 0.00 3.72
342 1752 2.016318 CACTGACAACACCACACACAT 58.984 47.619 0.00 0.00 0.00 3.21
343 1753 2.016318 ACTGACAACACCACACACATG 58.984 47.619 0.00 0.00 0.00 3.21
344 1754 0.737804 TGACAACACCACACACATGC 59.262 50.000 0.00 0.00 0.00 4.06
345 1755 0.737804 GACAACACCACACACATGCA 59.262 50.000 0.00 0.00 0.00 3.96
346 1756 0.455410 ACAACACCACACACATGCAC 59.545 50.000 0.00 0.00 0.00 4.57
347 1757 0.740149 CAACACCACACACATGCACT 59.260 50.000 0.00 0.00 0.00 4.40
348 1758 1.024271 AACACCACACACATGCACTC 58.976 50.000 0.00 0.00 0.00 3.51
349 1759 0.107263 ACACCACACACATGCACTCA 60.107 50.000 0.00 0.00 0.00 3.41
350 1760 0.308684 CACCACACACATGCACTCAC 59.691 55.000 0.00 0.00 0.00 3.51
351 1761 0.107263 ACCACACACATGCACTCACA 60.107 50.000 0.00 0.00 0.00 3.58
352 1762 1.241165 CCACACACATGCACTCACAT 58.759 50.000 0.00 0.00 0.00 3.21
353 1763 1.198408 CCACACACATGCACTCACATC 59.802 52.381 0.00 0.00 0.00 3.06
354 1764 2.148768 CACACACATGCACTCACATCT 58.851 47.619 0.00 0.00 0.00 2.90
355 1765 2.159037 CACACACATGCACTCACATCTC 59.841 50.000 0.00 0.00 0.00 2.75
356 1766 1.392510 CACACATGCACTCACATCTCG 59.607 52.381 0.00 0.00 0.00 4.04
357 1767 0.372679 CACATGCACTCACATCTCGC 59.627 55.000 0.00 0.00 0.00 5.03
358 1768 0.742281 ACATGCACTCACATCTCGCC 60.742 55.000 0.00 0.00 0.00 5.54
359 1769 0.461516 CATGCACTCACATCTCGCCT 60.462 55.000 0.00 0.00 0.00 5.52
360 1770 1.114627 ATGCACTCACATCTCGCCTA 58.885 50.000 0.00 0.00 0.00 3.93
361 1771 0.173481 TGCACTCACATCTCGCCTAC 59.827 55.000 0.00 0.00 0.00 3.18
362 1772 0.528684 GCACTCACATCTCGCCTACC 60.529 60.000 0.00 0.00 0.00 3.18
363 1773 0.248661 CACTCACATCTCGCCTACCG 60.249 60.000 0.00 0.00 38.61 4.02
364 1774 0.393944 ACTCACATCTCGCCTACCGA 60.394 55.000 0.00 0.00 45.15 4.69
365 1775 0.738975 CTCACATCTCGCCTACCGAA 59.261 55.000 0.00 0.00 46.81 4.30
366 1776 0.738975 TCACATCTCGCCTACCGAAG 59.261 55.000 0.00 0.00 46.81 3.79
367 1777 0.738975 CACATCTCGCCTACCGAAGA 59.261 55.000 0.00 0.00 46.81 2.87
368 1778 1.338337 CACATCTCGCCTACCGAAGAT 59.662 52.381 0.00 0.00 46.81 2.40
369 1779 1.609555 ACATCTCGCCTACCGAAGATC 59.390 52.381 0.00 0.00 46.81 2.75
370 1780 0.875728 ATCTCGCCTACCGAAGATCG 59.124 55.000 0.00 0.00 46.81 3.69
379 1789 4.303853 CGAAGATCGGATCGCGTT 57.696 55.556 20.50 0.00 36.00 4.84
380 1790 1.840061 CGAAGATCGGATCGCGTTG 59.160 57.895 20.50 9.10 36.00 4.10
381 1791 0.866061 CGAAGATCGGATCGCGTTGT 60.866 55.000 20.50 0.00 36.00 3.32
392 1802 0.812014 TCGCGTTGTGGAGCTTCAAA 60.812 50.000 5.77 0.00 0.00 2.69
393 1803 0.028770 CGCGTTGTGGAGCTTCAAAA 59.971 50.000 0.00 0.00 0.00 2.44
394 1804 1.477105 GCGTTGTGGAGCTTCAAAAC 58.523 50.000 17.14 17.14 32.89 2.43
399 1809 3.558931 TGTGGAGCTTCAAAACTGAGA 57.441 42.857 0.00 0.00 0.00 3.27
408 1818 4.096382 GCTTCAAAACTGAGAAAGTCACCA 59.904 41.667 0.00 0.00 38.56 4.17
411 1821 5.192927 TCAAAACTGAGAAAGTCACCACAT 58.807 37.500 0.00 0.00 38.56 3.21
413 1823 6.260050 TCAAAACTGAGAAAGTCACCACATAC 59.740 38.462 0.00 0.00 38.56 2.39
419 1829 3.646162 AGAAAGTCACCACATACACCTCA 59.354 43.478 0.00 0.00 0.00 3.86
420 1830 3.402628 AAGTCACCACATACACCTCAC 57.597 47.619 0.00 0.00 0.00 3.51
423 1833 4.157246 AGTCACCACATACACCTCACTAA 58.843 43.478 0.00 0.00 0.00 2.24
424 1834 4.220821 AGTCACCACATACACCTCACTAAG 59.779 45.833 0.00 0.00 0.00 2.18
433 1849 3.067106 ACACCTCACTAAGAATGTTGCG 58.933 45.455 0.00 0.00 0.00 4.85
436 1852 2.673368 CCTCACTAAGAATGTTGCGTCC 59.327 50.000 0.00 0.00 0.00 4.79
437 1853 2.673368 CTCACTAAGAATGTTGCGTCCC 59.327 50.000 0.00 0.00 0.00 4.46
439 1855 2.159627 CACTAAGAATGTTGCGTCCCAC 59.840 50.000 0.00 0.00 0.00 4.61
442 1858 2.386661 AGAATGTTGCGTCCCACTAG 57.613 50.000 0.00 0.00 0.00 2.57
445 1861 2.386661 ATGTTGCGTCCCACTAGAAG 57.613 50.000 0.00 0.00 0.00 2.85
454 1870 4.547532 CGTCCCACTAGAAGAATAATCCG 58.452 47.826 0.00 0.00 0.00 4.18
458 1874 4.692625 CCCACTAGAAGAATAATCCGCATG 59.307 45.833 0.00 0.00 0.00 4.06
462 1878 7.819415 CCACTAGAAGAATAATCCGCATGAATA 59.181 37.037 0.00 0.00 0.00 1.75
464 1880 9.209175 ACTAGAAGAATAATCCGCATGAATAAC 57.791 33.333 0.00 0.00 0.00 1.89
466 1882 8.450578 AGAAGAATAATCCGCATGAATAACAA 57.549 30.769 0.00 0.00 0.00 2.83
495 1911 2.609491 GCGTCAGTCATCCAACACTGTA 60.609 50.000 0.00 0.00 40.85 2.74
496 1912 3.849911 CGTCAGTCATCCAACACTGTAT 58.150 45.455 0.00 0.00 40.85 2.29
513 1929 7.976826 ACACTGTATGTTTTTCTTGACGTAAA 58.023 30.769 0.00 0.00 38.98 2.01
583 1999 1.808411 ACTGTCGGGCAAAGTACATG 58.192 50.000 0.00 0.00 0.00 3.21
588 2004 2.417586 GTCGGGCAAAGTACATGTTACC 59.582 50.000 2.30 0.00 0.00 2.85
589 2005 1.741145 CGGGCAAAGTACATGTTACCC 59.259 52.381 2.30 5.61 0.00 3.69
638 2057 6.868339 GGCATCCCAAAACATATATAAACTGC 59.132 38.462 0.00 0.00 0.00 4.40
641 2060 7.581213 TCCCAAAACATATATAAACTGCAGG 57.419 36.000 19.93 0.00 0.00 4.85
707 2130 4.819105 TCTTTATCTCCTTTTCAGCCGA 57.181 40.909 0.00 0.00 0.00 5.54
754 2177 1.142778 GATCTCGTCGCAGTGCCTTC 61.143 60.000 10.11 0.00 0.00 3.46
825 2248 1.304617 CCCTCTTGAAGCCCTTCCC 59.695 63.158 5.64 0.00 38.77 3.97
956 2389 4.565166 CGTGTGGCATTATATATACACCCG 59.435 45.833 8.07 5.56 36.09 5.28
959 2392 3.118186 TGGCATTATATATACACCCGCCC 60.118 47.826 11.60 0.00 36.15 6.13
1344 2777 2.617532 GCAGTCTTTCCAGAGGCTCAAT 60.618 50.000 18.26 0.00 30.86 2.57
1477 2914 4.440758 CGCTTAATTTGTGTTGGTGTCAAG 59.559 41.667 0.00 0.00 32.92 3.02
1591 3028 2.591715 GGTGGTGCTGCGACAACT 60.592 61.111 4.45 0.00 0.00 3.16
1761 3198 5.045215 TCAAACGACTGGTACAAGTAAGTG 58.955 41.667 1.89 0.04 38.70 3.16
1773 3214 6.368243 GGTACAAGTAAGTGCTTTTCTCCTAC 59.632 42.308 0.00 0.00 0.00 3.18
1807 3248 8.482128 AGATTGATCACTAAAACCAAACCAAAA 58.518 29.630 0.00 0.00 0.00 2.44
1808 3249 9.271828 GATTGATCACTAAAACCAAACCAAAAT 57.728 29.630 0.00 0.00 0.00 1.82
1809 3250 9.625747 ATTGATCACTAAAACCAAACCAAAATT 57.374 25.926 0.00 0.00 0.00 1.82
1910 3359 4.681643 CGTGTGGCAATGCGCGTT 62.682 61.111 9.57 9.57 43.84 4.84
1937 3387 4.023279 CCACCAACGACATTGAGATTTTGA 60.023 41.667 0.00 0.00 41.23 2.69
1955 3405 1.315690 GATCATGTGCATGTCCTGGG 58.684 55.000 11.38 0.00 39.72 4.45
1957 3407 2.043652 ATGTGCATGTCCTGGGCC 60.044 61.111 0.00 0.00 0.00 5.80
2081 3534 2.958818 AGTGATAGGATAGCCGTCCAA 58.041 47.619 7.64 0.00 40.90 3.53
2244 3726 2.320587 GCTGAGCTGGGTTGACACG 61.321 63.158 0.00 0.00 0.00 4.49
2247 3729 1.374758 GAGCTGGGTTGACACGGAG 60.375 63.158 0.00 0.00 0.00 4.63
2249 3731 1.668151 GCTGGGTTGACACGGAGTC 60.668 63.158 0.00 3.60 41.61 3.36
2257 3739 3.959478 GACACGGAGTCACTGACAA 57.041 52.632 11.80 0.00 46.77 3.18
2258 3740 2.440539 GACACGGAGTCACTGACAAT 57.559 50.000 11.80 0.00 46.77 2.71
2259 3741 2.061773 GACACGGAGTCACTGACAATG 58.938 52.381 11.80 6.27 46.77 2.82
2260 3742 0.792640 CACGGAGTCACTGACAATGC 59.207 55.000 11.80 0.00 41.61 3.56
2839 4321 1.423395 GGTCTGCTCTGTTCGTCTTG 58.577 55.000 0.00 0.00 0.00 3.02
2866 4349 1.079819 GCCTGTGAGCTTGCGACTA 60.080 57.895 0.00 0.00 0.00 2.59
2873 4356 3.186409 TGTGAGCTTGCGACTAATTTCAC 59.814 43.478 0.00 0.00 35.48 3.18
2875 4358 1.732259 AGCTTGCGACTAATTTCACGG 59.268 47.619 0.00 0.00 0.00 4.94
2884 4367 3.547746 ACTAATTTCACGGTGTTGGTGT 58.452 40.909 8.17 0.00 36.76 4.16
2886 4369 0.383949 ATTTCACGGTGTTGGTGTGC 59.616 50.000 8.17 0.00 36.76 4.57
3183 4666 3.112075 CTGCACGTCGCCGTCAAT 61.112 61.111 0.00 0.00 46.28 2.57
3204 4687 1.852351 GTCGTCTTCGTCGTCGTCG 60.852 63.158 5.50 5.50 38.33 5.12
3272 4755 2.047844 CCAGAGCGTGGTCACCAG 60.048 66.667 0.00 0.00 42.17 4.00
3395 4878 0.601311 GAGCTGCCTGTGAAACTCGT 60.601 55.000 0.00 0.00 38.04 4.18
3425 4908 0.460284 ATTCGCTCGCTTTGATCGGT 60.460 50.000 0.00 0.00 36.87 4.69
3426 4909 0.171679 TTCGCTCGCTTTGATCGGTA 59.828 50.000 0.00 0.00 36.87 4.02
3429 4912 1.480219 GCTCGCTTTGATCGGTACCG 61.480 60.000 28.66 28.66 41.35 4.02
3490 4980 4.386951 TAGCTGCAAAGGCGCCGA 62.387 61.111 23.20 2.69 45.35 5.54
3543 5033 7.739825 TGGAGTAATATCCTTCAGAATTCAGG 58.260 38.462 8.44 6.10 40.29 3.86
3586 5076 2.124151 GAGCACGATGGCCCCAAT 60.124 61.111 0.00 0.00 0.00 3.16
3611 5101 2.769376 CAAAATCCGTCCGTTCATTCG 58.231 47.619 0.00 0.00 0.00 3.34
3613 5103 1.636988 AATCCGTCCGTTCATTCGAC 58.363 50.000 0.00 0.00 0.00 4.20
3635 5125 9.443323 TCGACCAAATAATCTCATAAAAAGTGA 57.557 29.630 0.00 0.00 0.00 3.41
3700 5193 3.472652 ACAGCCATAACGACACAGAAAA 58.527 40.909 0.00 0.00 0.00 2.29
3701 5194 3.250040 ACAGCCATAACGACACAGAAAAC 59.750 43.478 0.00 0.00 0.00 2.43
3776 5271 1.757118 TCTAAATCCGGTGAGCAGAGG 59.243 52.381 0.00 0.00 0.00 3.69
3845 5340 4.753107 CGGTGTAAACATCAGTAGTTGGTT 59.247 41.667 0.00 0.00 0.00 3.67
3849 5344 6.261381 GTGTAAACATCAGTAGTTGGTTTCCA 59.739 38.462 0.00 0.00 0.00 3.53
3851 5346 6.976934 AAACATCAGTAGTTGGTTTCCAAT 57.023 33.333 4.51 0.00 45.80 3.16
3914 5409 2.303022 AGGTCACATACAGGTTCAGGTG 59.697 50.000 0.00 0.00 0.00 4.00
3988 5483 4.082665 TCCATCTGAGAGATCAAATGCC 57.917 45.455 0.00 0.00 31.32 4.40
4039 5534 1.736126 ACTTCATGCGCATCAACTCTG 59.264 47.619 22.51 9.50 0.00 3.35
4072 5567 0.685097 TAGCAGATGAATACGCCCCC 59.315 55.000 0.00 0.00 0.00 5.40
4114 5609 2.941453 TGATCTGAACTGTCGTAGCC 57.059 50.000 0.00 0.00 0.00 3.93
4186 5681 0.546122 TGTTGAGCAGTCCAAGTGGT 59.454 50.000 0.00 0.00 36.34 4.16
4228 5723 4.363999 CGTAAACCTGGTGCAAAAATGAA 58.636 39.130 0.00 0.00 0.00 2.57
4268 5763 3.990318 AGCAAACTAGGCTCAACAAAC 57.010 42.857 0.00 0.00 36.81 2.93
4271 5766 3.249080 GCAAACTAGGCTCAACAAACGTA 59.751 43.478 0.00 0.00 0.00 3.57
4272 5767 4.260866 GCAAACTAGGCTCAACAAACGTAA 60.261 41.667 0.00 0.00 0.00 3.18
4273 5768 8.156720 AGCAAACTAGGCTCAACAAACGTAAG 62.157 42.308 0.00 0.00 36.81 2.34
4274 5769 3.064931 ACTAGGCTCAACAAACGTAAGC 58.935 45.455 0.00 0.00 45.62 3.09
4275 5770 1.961793 AGGCTCAACAAACGTAAGCA 58.038 45.000 0.00 0.00 45.62 3.91
4285 5862 0.035439 AACGTAAGCATGGGGTGGAG 60.035 55.000 0.00 0.00 45.62 3.86
4345 5922 5.178061 TCACATGTCATAGTGACCAATGAC 58.822 41.667 17.15 17.15 46.40 3.06
4399 5976 6.738114 TGAAAGAGAACCTGCAATACAAAAG 58.262 36.000 0.00 0.00 0.00 2.27
4400 5977 6.321181 TGAAAGAGAACCTGCAATACAAAAGT 59.679 34.615 0.00 0.00 0.00 2.66
4401 5978 6.715347 AAGAGAACCTGCAATACAAAAGTT 57.285 33.333 0.00 0.00 0.00 2.66
4402 5979 7.817418 AAGAGAACCTGCAATACAAAAGTTA 57.183 32.000 0.00 0.00 0.00 2.24
4403 5980 7.817418 AGAGAACCTGCAATACAAAAGTTAA 57.183 32.000 0.00 0.00 0.00 2.01
4404 5981 7.649057 AGAGAACCTGCAATACAAAAGTTAAC 58.351 34.615 0.00 0.00 0.00 2.01
4405 5982 7.502561 AGAGAACCTGCAATACAAAAGTTAACT 59.497 33.333 1.12 1.12 0.00 2.24
4406 5983 8.685838 AGAACCTGCAATACAAAAGTTAACTA 57.314 30.769 8.92 0.00 0.00 2.24
4407 5984 9.297037 AGAACCTGCAATACAAAAGTTAACTAT 57.703 29.630 8.92 0.00 0.00 2.12
4408 5985 9.341899 GAACCTGCAATACAAAAGTTAACTATG 57.658 33.333 8.92 13.34 0.00 2.23
4409 5986 8.630054 ACCTGCAATACAAAAGTTAACTATGA 57.370 30.769 21.70 10.28 0.00 2.15
4410 5987 9.243105 ACCTGCAATACAAAAGTTAACTATGAT 57.757 29.630 21.70 11.59 0.00 2.45
4411 5988 9.507280 CCTGCAATACAAAAGTTAACTATGATG 57.493 33.333 21.70 17.59 0.00 3.07
4416 5993 9.855021 AATACAAAAGTTAACTATGATGTTGGC 57.145 29.630 21.70 0.00 0.00 4.52
4417 5994 7.524717 ACAAAAGTTAACTATGATGTTGGCT 57.475 32.000 21.70 0.00 0.00 4.75
4418 5995 7.370383 ACAAAAGTTAACTATGATGTTGGCTG 58.630 34.615 21.70 6.32 0.00 4.85
4419 5996 7.014230 ACAAAAGTTAACTATGATGTTGGCTGT 59.986 33.333 21.70 6.81 0.00 4.40
4420 5997 8.511321 CAAAAGTTAACTATGATGTTGGCTGTA 58.489 33.333 8.92 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.592993 CGCTCCCTCCCAACTTGGA 61.593 63.158 9.61 0.00 40.96 3.53
1 2 2.045926 CGCTCCCTCCCAACTTGG 60.046 66.667 0.12 0.12 37.25 3.61
2 3 2.747855 GCGCTCCCTCCCAACTTG 60.748 66.667 0.00 0.00 0.00 3.16
3 4 3.249189 TGCGCTCCCTCCCAACTT 61.249 61.111 9.73 0.00 0.00 2.66
4 5 4.021925 GTGCGCTCCCTCCCAACT 62.022 66.667 9.73 0.00 0.00 3.16
8 9 2.056906 ATATTGGTGCGCTCCCTCCC 62.057 60.000 24.73 7.80 0.00 4.30
9 10 0.886490 CATATTGGTGCGCTCCCTCC 60.886 60.000 24.73 11.72 0.00 4.30
10 11 0.886490 CCATATTGGTGCGCTCCCTC 60.886 60.000 24.73 1.65 31.35 4.30
11 12 1.149174 CCATATTGGTGCGCTCCCT 59.851 57.895 24.73 14.76 31.35 4.20
12 13 1.898574 CCCATATTGGTGCGCTCCC 60.899 63.158 24.73 16.95 35.17 4.30
13 14 2.555547 GCCCATATTGGTGCGCTCC 61.556 63.158 21.41 21.41 35.17 4.70
14 15 2.555547 GGCCCATATTGGTGCGCTC 61.556 63.158 9.73 4.47 35.45 5.03
15 16 2.519302 GGCCCATATTGGTGCGCT 60.519 61.111 9.73 0.00 35.45 5.92
16 17 3.605664 GGGCCCATATTGGTGCGC 61.606 66.667 19.95 0.00 38.60 6.09
17 18 1.531365 ATGGGCCCATATTGGTGCG 60.531 57.895 36.79 0.00 35.45 5.34
18 19 0.469705 TCATGGGCCCATATTGGTGC 60.470 55.000 36.95 0.00 35.17 5.01
19 20 1.624336 CTCATGGGCCCATATTGGTG 58.376 55.000 36.95 24.76 35.17 4.17
20 21 0.484212 CCTCATGGGCCCATATTGGT 59.516 55.000 36.95 13.00 35.17 3.67
21 22 3.369042 CCTCATGGGCCCATATTGG 57.631 57.895 36.95 30.30 37.25 3.16
31 32 5.475719 CAAATTTATATGCAGCCTCATGGG 58.524 41.667 0.00 0.00 38.36 4.00
32 33 5.244402 TCCAAATTTATATGCAGCCTCATGG 59.756 40.000 0.00 0.00 0.00 3.66
33 34 6.015688 ACTCCAAATTTATATGCAGCCTCATG 60.016 38.462 0.00 0.00 0.00 3.07
34 35 6.015688 CACTCCAAATTTATATGCAGCCTCAT 60.016 38.462 0.00 0.00 0.00 2.90
35 36 5.300034 CACTCCAAATTTATATGCAGCCTCA 59.700 40.000 0.00 0.00 0.00 3.86
36 37 5.278660 CCACTCCAAATTTATATGCAGCCTC 60.279 44.000 0.00 0.00 0.00 4.70
37 38 4.586001 CCACTCCAAATTTATATGCAGCCT 59.414 41.667 0.00 0.00 0.00 4.58
38 39 4.584325 TCCACTCCAAATTTATATGCAGCC 59.416 41.667 0.00 0.00 0.00 4.85
39 40 5.772825 TCCACTCCAAATTTATATGCAGC 57.227 39.130 0.00 0.00 0.00 5.25
42 43 7.275888 TGACATCCACTCCAAATTTATATGC 57.724 36.000 0.00 0.00 0.00 3.14
49 50 7.307131 AGAAAATTGACATCCACTCCAAATT 57.693 32.000 0.00 0.00 0.00 1.82
51 52 6.729690 AAGAAAATTGACATCCACTCCAAA 57.270 33.333 0.00 0.00 0.00 3.28
53 54 7.174413 TCATAAGAAAATTGACATCCACTCCA 58.826 34.615 0.00 0.00 0.00 3.86
111 112 5.125900 TGATTCATAGGGTTGCAATTCACTG 59.874 40.000 0.59 0.00 0.00 3.66
112 113 5.263599 TGATTCATAGGGTTGCAATTCACT 58.736 37.500 0.59 0.00 0.00 3.41
124 125 5.587388 ACTGCATTGTTTGATTCATAGGG 57.413 39.130 0.00 0.00 0.00 3.53
138 139 8.469200 TCATTAGGGATTTTTCTTACTGCATTG 58.531 33.333 0.00 0.00 0.00 2.82
178 180 8.609176 CAAAATCATTGAGGGCATCTTTAATTG 58.391 33.333 0.00 0.00 0.00 2.32
188 190 4.712829 ACATCATCAAAATCATTGAGGGCA 59.287 37.500 3.42 0.00 31.82 5.36
197 199 5.471556 AAGTGCCAACATCATCAAAATCA 57.528 34.783 0.00 0.00 0.00 2.57
199 201 4.529377 AGGAAGTGCCAACATCATCAAAAT 59.471 37.500 0.00 0.00 40.02 1.82
203 205 2.885135 AGGAAGTGCCAACATCATCA 57.115 45.000 0.00 0.00 40.02 3.07
204 206 4.498682 GCATTAGGAAGTGCCAACATCATC 60.499 45.833 0.00 0.00 40.02 2.92
208 210 2.493278 GTGCATTAGGAAGTGCCAACAT 59.507 45.455 0.00 0.00 40.56 2.71
209 211 1.885887 GTGCATTAGGAAGTGCCAACA 59.114 47.619 0.00 0.00 40.56 3.33
210 212 2.162408 GAGTGCATTAGGAAGTGCCAAC 59.838 50.000 0.00 0.00 40.56 3.77
212 214 1.350684 TGAGTGCATTAGGAAGTGCCA 59.649 47.619 0.00 0.00 40.56 4.92
213 215 1.740025 GTGAGTGCATTAGGAAGTGCC 59.260 52.381 0.00 0.00 40.56 5.01
214 216 2.426522 TGTGAGTGCATTAGGAAGTGC 58.573 47.619 0.00 0.00 41.61 4.40
215 217 6.018425 GTGATATGTGAGTGCATTAGGAAGTG 60.018 42.308 0.00 0.00 0.00 3.16
216 218 6.051717 GTGATATGTGAGTGCATTAGGAAGT 58.948 40.000 0.00 0.00 0.00 3.01
217 219 5.468072 GGTGATATGTGAGTGCATTAGGAAG 59.532 44.000 0.00 0.00 0.00 3.46
220 222 4.965814 AGGTGATATGTGAGTGCATTAGG 58.034 43.478 0.00 0.00 0.00 2.69
221 223 6.592994 CCATAGGTGATATGTGAGTGCATTAG 59.407 42.308 0.00 0.00 39.84 1.73
222 224 6.269769 TCCATAGGTGATATGTGAGTGCATTA 59.730 38.462 0.00 0.00 39.84 1.90
224 226 4.594491 TCCATAGGTGATATGTGAGTGCAT 59.406 41.667 0.00 0.00 39.84 3.96
227 1637 6.219473 GTCTTCCATAGGTGATATGTGAGTG 58.781 44.000 0.00 0.00 39.84 3.51
229 1639 5.565637 CGGTCTTCCATAGGTGATATGTGAG 60.566 48.000 0.00 0.00 39.84 3.51
242 1652 4.381612 GCAATATCGATCCGGTCTTCCATA 60.382 45.833 0.00 0.00 0.00 2.74
246 1656 2.989840 CTGCAATATCGATCCGGTCTTC 59.010 50.000 0.00 0.00 0.00 2.87
251 1661 1.067283 AGCTCTGCAATATCGATCCGG 60.067 52.381 0.00 0.00 0.00 5.14
252 1662 2.360553 AGCTCTGCAATATCGATCCG 57.639 50.000 0.00 0.00 0.00 4.18
258 1668 3.397482 ACATCCGAAGCTCTGCAATATC 58.603 45.455 0.00 0.00 0.00 1.63
260 1670 2.938451 CAACATCCGAAGCTCTGCAATA 59.062 45.455 0.00 0.00 0.00 1.90
261 1671 1.741706 CAACATCCGAAGCTCTGCAAT 59.258 47.619 0.00 0.00 0.00 3.56
263 1673 1.300971 GCAACATCCGAAGCTCTGCA 61.301 55.000 0.00 0.00 0.00 4.41
266 1676 0.326264 AAGGCAACATCCGAAGCTCT 59.674 50.000 0.00 0.00 41.41 4.09
267 1677 1.131315 GAAAGGCAACATCCGAAGCTC 59.869 52.381 0.00 0.00 41.41 4.09
268 1678 1.168714 GAAAGGCAACATCCGAAGCT 58.831 50.000 0.00 0.00 41.41 3.74
269 1679 0.881118 TGAAAGGCAACATCCGAAGC 59.119 50.000 0.00 0.00 41.41 3.86
270 1680 3.855689 AATGAAAGGCAACATCCGAAG 57.144 42.857 0.00 0.00 41.41 3.79
271 1681 5.713792 TTAAATGAAAGGCAACATCCGAA 57.286 34.783 0.00 0.00 41.41 4.30
272 1682 5.713792 TTTAAATGAAAGGCAACATCCGA 57.286 34.783 0.00 0.00 41.41 4.55
273 1683 6.777526 TTTTTAAATGAAAGGCAACATCCG 57.222 33.333 0.00 0.00 41.41 4.18
295 1705 9.710900 CTTTTGGCTTCTTATTAACAAGGATTT 57.289 29.630 0.00 0.00 0.00 2.17
296 1706 7.819415 GCTTTTGGCTTCTTATTAACAAGGATT 59.181 33.333 0.00 0.00 38.06 3.01
297 1707 7.039082 TGCTTTTGGCTTCTTATTAACAAGGAT 60.039 33.333 0.00 0.00 42.39 3.24
298 1708 6.266558 TGCTTTTGGCTTCTTATTAACAAGGA 59.733 34.615 0.00 0.00 42.39 3.36
299 1709 6.366061 GTGCTTTTGGCTTCTTATTAACAAGG 59.634 38.462 0.00 0.00 42.39 3.61
300 1710 7.115378 CAGTGCTTTTGGCTTCTTATTAACAAG 59.885 37.037 0.00 0.00 42.39 3.16
301 1711 6.922957 CAGTGCTTTTGGCTTCTTATTAACAA 59.077 34.615 0.00 0.00 42.39 2.83
302 1712 6.264292 TCAGTGCTTTTGGCTTCTTATTAACA 59.736 34.615 0.00 0.00 42.39 2.41
303 1713 6.582672 GTCAGTGCTTTTGGCTTCTTATTAAC 59.417 38.462 0.00 0.00 42.39 2.01
304 1714 6.264292 TGTCAGTGCTTTTGGCTTCTTATTAA 59.736 34.615 0.00 0.00 42.39 1.40
305 1715 5.767665 TGTCAGTGCTTTTGGCTTCTTATTA 59.232 36.000 0.00 0.00 42.39 0.98
306 1716 4.584325 TGTCAGTGCTTTTGGCTTCTTATT 59.416 37.500 0.00 0.00 42.39 1.40
307 1717 4.144297 TGTCAGTGCTTTTGGCTTCTTAT 58.856 39.130 0.00 0.00 42.39 1.73
308 1718 3.550820 TGTCAGTGCTTTTGGCTTCTTA 58.449 40.909 0.00 0.00 42.39 2.10
309 1719 2.378038 TGTCAGTGCTTTTGGCTTCTT 58.622 42.857 0.00 0.00 42.39 2.52
310 1720 2.057137 TGTCAGTGCTTTTGGCTTCT 57.943 45.000 0.00 0.00 42.39 2.85
311 1721 2.159254 TGTTGTCAGTGCTTTTGGCTTC 60.159 45.455 0.00 0.00 42.39 3.86
312 1722 1.824230 TGTTGTCAGTGCTTTTGGCTT 59.176 42.857 0.00 0.00 42.39 4.35
313 1723 1.134946 GTGTTGTCAGTGCTTTTGGCT 59.865 47.619 0.00 0.00 42.39 4.75
314 1724 1.559831 GTGTTGTCAGTGCTTTTGGC 58.440 50.000 0.00 0.00 42.22 4.52
315 1725 1.476085 TGGTGTTGTCAGTGCTTTTGG 59.524 47.619 0.00 0.00 0.00 3.28
316 1726 2.094803 TGTGGTGTTGTCAGTGCTTTTG 60.095 45.455 0.00 0.00 0.00 2.44
317 1727 2.094752 GTGTGGTGTTGTCAGTGCTTTT 60.095 45.455 0.00 0.00 0.00 2.27
318 1728 1.472480 GTGTGGTGTTGTCAGTGCTTT 59.528 47.619 0.00 0.00 0.00 3.51
319 1729 1.094785 GTGTGGTGTTGTCAGTGCTT 58.905 50.000 0.00 0.00 0.00 3.91
320 1730 0.035534 TGTGTGGTGTTGTCAGTGCT 60.036 50.000 0.00 0.00 0.00 4.40
321 1731 0.098728 GTGTGTGGTGTTGTCAGTGC 59.901 55.000 0.00 0.00 0.00 4.40
322 1732 1.447945 TGTGTGTGGTGTTGTCAGTG 58.552 50.000 0.00 0.00 0.00 3.66
323 1733 2.016318 CATGTGTGTGGTGTTGTCAGT 58.984 47.619 0.00 0.00 0.00 3.41
324 1734 1.268692 GCATGTGTGTGGTGTTGTCAG 60.269 52.381 0.00 0.00 0.00 3.51
325 1735 0.737804 GCATGTGTGTGGTGTTGTCA 59.262 50.000 0.00 0.00 0.00 3.58
326 1736 0.737804 TGCATGTGTGTGGTGTTGTC 59.262 50.000 0.00 0.00 0.00 3.18
327 1737 0.455410 GTGCATGTGTGTGGTGTTGT 59.545 50.000 0.00 0.00 0.00 3.32
328 1738 0.740149 AGTGCATGTGTGTGGTGTTG 59.260 50.000 0.00 0.00 0.00 3.33
329 1739 1.024271 GAGTGCATGTGTGTGGTGTT 58.976 50.000 0.00 0.00 0.00 3.32
330 1740 0.107263 TGAGTGCATGTGTGTGGTGT 60.107 50.000 0.00 0.00 0.00 4.16
331 1741 0.308684 GTGAGTGCATGTGTGTGGTG 59.691 55.000 0.00 0.00 0.00 4.17
332 1742 0.107263 TGTGAGTGCATGTGTGTGGT 60.107 50.000 0.00 0.00 0.00 4.16
333 1743 1.198408 GATGTGAGTGCATGTGTGTGG 59.802 52.381 0.00 0.00 0.00 4.17
334 1744 2.148768 AGATGTGAGTGCATGTGTGTG 58.851 47.619 0.00 0.00 0.00 3.82
335 1745 2.420642 GAGATGTGAGTGCATGTGTGT 58.579 47.619 0.00 0.00 0.00 3.72
336 1746 1.392510 CGAGATGTGAGTGCATGTGTG 59.607 52.381 0.00 0.00 0.00 3.82
337 1747 1.718396 CGAGATGTGAGTGCATGTGT 58.282 50.000 0.00 0.00 0.00 3.72
338 1748 0.372679 GCGAGATGTGAGTGCATGTG 59.627 55.000 0.00 0.00 0.00 3.21
339 1749 0.742281 GGCGAGATGTGAGTGCATGT 60.742 55.000 0.00 0.00 0.00 3.21
340 1750 0.461516 AGGCGAGATGTGAGTGCATG 60.462 55.000 0.00 0.00 0.00 4.06
341 1751 1.114627 TAGGCGAGATGTGAGTGCAT 58.885 50.000 0.00 0.00 0.00 3.96
342 1752 0.173481 GTAGGCGAGATGTGAGTGCA 59.827 55.000 0.00 0.00 0.00 4.57
343 1753 0.528684 GGTAGGCGAGATGTGAGTGC 60.529 60.000 0.00 0.00 0.00 4.40
344 1754 0.248661 CGGTAGGCGAGATGTGAGTG 60.249 60.000 0.00 0.00 0.00 3.51
345 1755 0.393944 TCGGTAGGCGAGATGTGAGT 60.394 55.000 0.00 0.00 0.00 3.41
346 1756 0.738975 TTCGGTAGGCGAGATGTGAG 59.261 55.000 0.00 0.00 0.00 3.51
347 1757 0.738975 CTTCGGTAGGCGAGATGTGA 59.261 55.000 0.00 0.00 0.00 3.58
348 1758 0.738975 TCTTCGGTAGGCGAGATGTG 59.261 55.000 0.00 0.00 0.00 3.21
349 1759 1.609555 GATCTTCGGTAGGCGAGATGT 59.390 52.381 0.00 0.00 0.00 3.06
350 1760 1.400371 CGATCTTCGGTAGGCGAGATG 60.400 57.143 0.00 0.00 36.00 2.90
351 1761 0.875728 CGATCTTCGGTAGGCGAGAT 59.124 55.000 0.00 0.00 36.00 2.75
352 1762 2.318224 CGATCTTCGGTAGGCGAGA 58.682 57.895 0.00 0.00 36.00 4.04
353 1763 4.924924 CGATCTTCGGTAGGCGAG 57.075 61.111 0.00 0.00 36.00 5.03
362 1772 0.866061 ACAACGCGATCCGATCTTCG 60.866 55.000 15.93 14.48 41.02 3.79
363 1773 0.572590 CACAACGCGATCCGATCTTC 59.427 55.000 15.93 0.00 41.02 2.87
364 1774 0.806102 CCACAACGCGATCCGATCTT 60.806 55.000 15.93 0.00 41.02 2.40
365 1775 1.226974 CCACAACGCGATCCGATCT 60.227 57.895 15.93 0.00 41.02 2.75
366 1776 1.209275 CTCCACAACGCGATCCGATC 61.209 60.000 15.93 0.00 41.02 3.69
367 1777 1.226974 CTCCACAACGCGATCCGAT 60.227 57.895 15.93 0.00 41.02 4.18
368 1778 2.180769 CTCCACAACGCGATCCGA 59.819 61.111 15.93 0.00 41.02 4.55
369 1779 3.554692 GCTCCACAACGCGATCCG 61.555 66.667 15.93 0.00 44.21 4.18
370 1780 1.696832 GAAGCTCCACAACGCGATCC 61.697 60.000 15.93 0.00 0.00 3.36
371 1781 1.014044 TGAAGCTCCACAACGCGATC 61.014 55.000 15.93 0.00 0.00 3.69
372 1782 0.602638 TTGAAGCTCCACAACGCGAT 60.603 50.000 15.93 0.00 0.00 4.58
373 1783 0.812014 TTTGAAGCTCCACAACGCGA 60.812 50.000 15.93 0.00 0.00 5.87
374 1784 0.028770 TTTTGAAGCTCCACAACGCG 59.971 50.000 3.53 3.53 0.00 6.01
375 1785 1.065551 AGTTTTGAAGCTCCACAACGC 59.934 47.619 0.00 0.00 33.36 4.84
376 1786 2.354510 TCAGTTTTGAAGCTCCACAACG 59.645 45.455 0.00 0.00 33.36 4.10
377 1787 3.627577 TCTCAGTTTTGAAGCTCCACAAC 59.372 43.478 0.00 0.00 31.69 3.32
378 1788 3.884895 TCTCAGTTTTGAAGCTCCACAA 58.115 40.909 0.00 0.00 31.69 3.33
379 1789 3.558931 TCTCAGTTTTGAAGCTCCACA 57.441 42.857 0.00 0.00 31.69 4.17
380 1790 4.336713 ACTTTCTCAGTTTTGAAGCTCCAC 59.663 41.667 0.00 0.00 31.69 4.02
381 1791 4.526970 ACTTTCTCAGTTTTGAAGCTCCA 58.473 39.130 0.00 0.00 31.69 3.86
392 1802 5.057149 GTGTATGTGGTGACTTTCTCAGTT 58.943 41.667 0.00 0.00 35.01 3.16
393 1803 4.503296 GGTGTATGTGGTGACTTTCTCAGT 60.503 45.833 0.00 0.00 39.07 3.41
394 1804 3.997021 GGTGTATGTGGTGACTTTCTCAG 59.003 47.826 0.00 0.00 0.00 3.35
399 1809 3.391296 AGTGAGGTGTATGTGGTGACTTT 59.609 43.478 0.00 0.00 0.00 2.66
408 1818 5.643777 GCAACATTCTTAGTGAGGTGTATGT 59.356 40.000 0.00 0.00 0.00 2.29
411 1821 4.242475 CGCAACATTCTTAGTGAGGTGTA 58.758 43.478 0.00 0.00 0.00 2.90
413 1823 3.067106 ACGCAACATTCTTAGTGAGGTG 58.933 45.455 0.00 0.00 0.00 4.00
419 1829 2.038557 AGTGGGACGCAACATTCTTAGT 59.961 45.455 0.00 0.00 44.14 2.24
420 1830 2.699954 AGTGGGACGCAACATTCTTAG 58.300 47.619 0.00 0.00 44.14 2.18
423 1833 1.899814 TCTAGTGGGACGCAACATTCT 59.100 47.619 0.00 0.00 44.14 2.40
424 1834 2.380084 TCTAGTGGGACGCAACATTC 57.620 50.000 0.00 0.00 44.14 2.67
433 1849 4.202223 TGCGGATTATTCTTCTAGTGGGAC 60.202 45.833 0.00 0.00 0.00 4.46
436 1852 5.541845 TCATGCGGATTATTCTTCTAGTGG 58.458 41.667 0.00 0.00 0.00 4.00
437 1853 7.664082 ATTCATGCGGATTATTCTTCTAGTG 57.336 36.000 0.00 0.00 0.00 2.74
439 1855 9.208022 TGTTATTCATGCGGATTATTCTTCTAG 57.792 33.333 0.00 0.00 0.00 2.43
442 1858 7.324616 GCTTGTTATTCATGCGGATTATTCTTC 59.675 37.037 0.00 0.00 37.44 2.87
445 1861 5.858581 GGCTTGTTATTCATGCGGATTATTC 59.141 40.000 0.00 0.00 44.70 1.75
454 1870 3.061161 CGCTTTTGGCTTGTTATTCATGC 59.939 43.478 0.00 0.00 43.57 4.06
458 1874 3.896122 TGACGCTTTTGGCTTGTTATTC 58.104 40.909 0.00 0.00 39.13 1.75
462 1878 1.065551 GACTGACGCTTTTGGCTTGTT 59.934 47.619 0.00 0.00 39.13 2.83
464 1880 0.662619 TGACTGACGCTTTTGGCTTG 59.337 50.000 0.00 0.00 39.13 4.01
466 1882 1.160137 GATGACTGACGCTTTTGGCT 58.840 50.000 0.00 0.00 39.13 4.75
502 1918 8.786826 AGGACATTTCATATTTTACGTCAAGA 57.213 30.769 0.00 0.00 0.00 3.02
503 1919 8.122952 GGAGGACATTTCATATTTTACGTCAAG 58.877 37.037 0.00 0.00 0.00 3.02
583 1999 1.562575 CGGTGCTTGTGTCGGGTAAC 61.563 60.000 0.00 0.00 0.00 2.50
588 2004 3.414700 GAGCGGTGCTTGTGTCGG 61.415 66.667 0.00 0.00 39.88 4.79
589 2005 3.767230 CGAGCGGTGCTTGTGTCG 61.767 66.667 0.00 0.00 39.88 4.35
638 2057 2.514458 AAATGGCCACCTAACTCCTG 57.486 50.000 8.16 0.00 0.00 3.86
641 2060 3.444034 GGAGAAAAATGGCCACCTAACTC 59.556 47.826 8.16 14.59 0.00 3.01
707 2130 2.770164 ACTGCTCCTAATTCGCAACT 57.230 45.000 0.00 0.00 32.66 3.16
754 2177 8.915871 ATGCAACAACTATTTTATAGTGCTTG 57.084 30.769 0.00 6.35 0.00 4.01
825 2248 1.270305 ACGGGTCTTGACATGTGTGAG 60.270 52.381 1.15 0.00 0.00 3.51
1001 2434 4.974438 AACGCCTCACCCTCCCCA 62.974 66.667 0.00 0.00 0.00 4.96
1477 2914 0.734942 GCCATGCACACATCAACAGC 60.735 55.000 0.00 0.00 32.87 4.40
1591 3028 4.668118 GAACCCGTTGCCGTCCGA 62.668 66.667 0.00 0.00 0.00 4.55
1761 3198 5.615925 TCTAATCAGGGTAGGAGAAAAGC 57.384 43.478 0.00 0.00 0.00 3.51
1773 3214 7.775093 TGGTTTTAGTGATCAATCTAATCAGGG 59.225 37.037 0.00 0.00 33.94 4.45
1872 3321 5.120674 CACGCACTTGAGACTTTTATCATCA 59.879 40.000 0.00 0.00 0.00 3.07
1873 3322 5.120830 ACACGCACTTGAGACTTTTATCATC 59.879 40.000 0.00 0.00 0.00 2.92
1874 3323 4.997395 ACACGCACTTGAGACTTTTATCAT 59.003 37.500 0.00 0.00 0.00 2.45
1910 3359 0.107643 TCAATGTCGTTGGTGGCTCA 59.892 50.000 4.95 0.00 38.39 4.26
1937 3387 0.754217 GCCCAGGACATGCACATGAT 60.754 55.000 17.19 1.91 41.20 2.45
1955 3405 2.436417 TGTTCAGGCTCATTTACTGGC 58.564 47.619 0.00 0.00 33.19 4.85
1957 3407 4.074970 AGGTTGTTCAGGCTCATTTACTG 58.925 43.478 0.00 0.00 0.00 2.74
2081 3534 3.070734 ACTGAAAGACTGATGCTGTCTGT 59.929 43.478 7.57 2.80 40.75 3.41
2197 3679 0.875908 CATGACACTATGACGGGGCG 60.876 60.000 0.00 0.00 0.00 6.13
2244 3726 0.792640 CGTGCATTGTCAGTGACTCC 59.207 55.000 23.29 9.77 33.15 3.85
2247 3729 0.384725 GTGCGTGCATTGTCAGTGAC 60.385 55.000 16.68 16.68 0.00 3.67
2248 3730 1.830368 CGTGCGTGCATTGTCAGTGA 61.830 55.000 0.00 0.00 0.00 3.41
2249 3731 1.439201 CGTGCGTGCATTGTCAGTG 60.439 57.895 0.00 0.00 0.00 3.66
2250 3732 2.938253 CGTGCGTGCATTGTCAGT 59.062 55.556 0.00 0.00 0.00 3.41
2251 3733 2.500369 GCGTGCGTGCATTGTCAG 60.500 61.111 0.00 0.00 34.15 3.51
2252 3734 4.367340 CGCGTGCGTGCATTGTCA 62.367 61.111 6.00 0.00 34.15 3.58
2821 4303 0.787183 GCAAGACGAACAGAGCAGAC 59.213 55.000 0.00 0.00 0.00 3.51
2866 4349 1.202359 GCACACCAACACCGTGAAATT 60.202 47.619 5.28 0.00 35.17 1.82
2873 4356 2.259875 AAACACGCACACCAACACCG 62.260 55.000 0.00 0.00 0.00 4.94
2875 4358 1.409982 GCAAACACGCACACCAACAC 61.410 55.000 0.00 0.00 0.00 3.32
2884 4367 4.892965 AGGCCCTGCAAACACGCA 62.893 61.111 0.00 0.00 40.32 5.24
2886 4369 3.673484 CCAGGCCCTGCAAACACG 61.673 66.667 4.81 0.00 0.00 4.49
2918 4401 0.600255 GAACAGCACTGTGTACGGCT 60.600 55.000 9.86 0.00 44.13 5.52
3057 4540 2.046988 CACATCAGCGGGCTGTCA 60.047 61.111 19.21 2.63 43.96 3.58
3390 4873 2.553079 GAATCTTCGAGCTCACGAGT 57.447 50.000 15.40 5.56 43.04 4.18
3444 4931 5.872617 GGATGCGTGCACCTATACAATTATA 59.127 40.000 12.15 0.00 0.00 0.98
3445 4932 4.695455 GGATGCGTGCACCTATACAATTAT 59.305 41.667 12.15 0.00 0.00 1.28
3446 4933 4.062293 GGATGCGTGCACCTATACAATTA 58.938 43.478 12.15 0.00 0.00 1.40
3447 4934 2.878406 GGATGCGTGCACCTATACAATT 59.122 45.455 12.15 0.00 0.00 2.32
3490 4980 0.459489 GCAGCTTCTCTCGTCCATCT 59.541 55.000 0.00 0.00 0.00 2.90
3543 5033 2.099756 GCCCCAGCATTCATTCAGTTAC 59.900 50.000 0.00 0.00 39.53 2.50
3573 5063 1.754234 GCAAGATTGGGGCCATCGT 60.754 57.895 4.39 0.00 0.00 3.73
3574 5064 1.321805 TTGCAAGATTGGGGCCATCG 61.322 55.000 4.39 0.00 0.00 3.84
3586 5076 1.533731 GAACGGACGGATTTTGCAAGA 59.466 47.619 0.00 0.00 0.00 3.02
3637 5127 9.823647 ACAACTCCACATTAGAGATTTATGTAG 57.176 33.333 0.00 0.00 35.27 2.74
3638 5128 9.599866 CACAACTCCACATTAGAGATTTATGTA 57.400 33.333 0.00 0.00 35.27 2.29
3639 5129 8.103305 ACACAACTCCACATTAGAGATTTATGT 58.897 33.333 0.00 0.00 35.27 2.29
3640 5130 8.498054 ACACAACTCCACATTAGAGATTTATG 57.502 34.615 0.00 0.00 35.27 1.90
3776 5271 4.037327 GCCTCCCAGCTTCAGAAATAATTC 59.963 45.833 0.00 0.00 35.70 2.17
3826 5321 6.870971 TGGAAACCAACTACTGATGTTTAC 57.129 37.500 0.00 0.00 0.00 2.01
3845 5340 3.698539 TCTGCGCCATTCATTTATTGGAA 59.301 39.130 4.18 0.00 31.32 3.53
3849 5344 2.689471 TGCTCTGCGCCATTCATTTATT 59.311 40.909 4.18 0.00 38.05 1.40
3851 5346 1.672363 CTGCTCTGCGCCATTCATTTA 59.328 47.619 4.18 0.00 38.05 1.40
3914 5409 2.171840 TCTCTACACAGCCTCCTGAAC 58.828 52.381 0.00 0.00 41.77 3.18
3940 5435 0.035630 ACAGCAGCCTCTGGAACATC 60.036 55.000 7.59 0.00 38.20 3.06
3988 5483 2.949644 TCATTCTGATGATGGCTTGCTG 59.050 45.455 0.00 0.00 37.37 4.41
4072 5567 2.742372 CGAGGGCCAGGACGTTTG 60.742 66.667 6.18 0.00 0.00 2.93
4114 5609 2.096069 CACAGGCACAGTTGATTCTTCG 60.096 50.000 0.00 0.00 0.00 3.79
4228 5723 9.846248 GTTTGCTTCATATTCTTACAGAAACAT 57.154 29.630 0.00 0.00 37.82 2.71
4250 5745 3.963383 ACGTTTGTTGAGCCTAGTTTG 57.037 42.857 0.00 0.00 0.00 2.93
4268 5763 0.179073 CTCTCCACCCCATGCTTACG 60.179 60.000 0.00 0.00 0.00 3.18
4271 5766 1.075601 TTTCTCTCCACCCCATGCTT 58.924 50.000 0.00 0.00 0.00 3.91
4272 5767 1.213926 GATTTCTCTCCACCCCATGCT 59.786 52.381 0.00 0.00 0.00 3.79
4273 5768 1.213926 AGATTTCTCTCCACCCCATGC 59.786 52.381 0.00 0.00 0.00 4.06
4274 5769 2.507058 TCAGATTTCTCTCCACCCCATG 59.493 50.000 0.00 0.00 0.00 3.66
4275 5770 2.507471 GTCAGATTTCTCTCCACCCCAT 59.493 50.000 0.00 0.00 0.00 4.00
4285 5862 4.098044 TCACCGATACAGGTCAGATTTCTC 59.902 45.833 0.00 0.00 43.89 2.87


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

AutoCloner maintained by Alex Coulton.