Multiple sequence alignment - TraesCS5B01G222100

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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 TraesCS5B01G222100 chr5B 100.000 6215 0 0 1 6215 396622388 396628602 0.000000e+00 11478
1 TraesCS5B01G222100 chr5B 94.337 830 34 3 4408 5228 396834639 396835464 0.000000e+00 1260
2 TraesCS5B01G222100 chr5B 88.310 787 42 16 5463 6215 396835906 396836676 0.000000e+00 898
3 TraesCS5B01G222100 chr5B 84.465 766 63 26 3435 4188 396879069 396879790 0.000000e+00 704
4 TraesCS5B01G222100 chr5B 84.687 751 62 22 3435 4175 396827172 396827879 0.000000e+00 701
5 TraesCS5B01G222100 chr5B 94.659 337 9 5 5882 6215 396838711 396839041 1.190000e-141 514
6 TraesCS5B01G222100 chr5B 94.659 337 9 5 5882 6215 396841375 396841705 1.190000e-141 514
7 TraesCS5B01G222100 chr5B 94.659 337 9 5 5882 6215 396846543 396846873 1.190000e-141 514
8 TraesCS5B01G222100 chr5B 96.667 60 2 0 1396 1455 396623731 396623790 3.960000e-17 100
9 TraesCS5B01G222100 chr5B 96.667 60 2 0 1344 1403 396623783 396623842 3.960000e-17 100
10 TraesCS5B01G222100 chr5A 91.886 2588 153 29 1598 4164 438920747 438923298 0.000000e+00 3563
11 TraesCS5B01G222100 chr5A 93.071 1169 56 6 4068 5215 438923168 438924332 0.000000e+00 1687
12 TraesCS5B01G222100 chr5A 87.719 798 60 21 5229 6010 438924505 438925280 0.000000e+00 896
13 TraesCS5B01G222100 chr5A 95.872 533 17 4 233 765 438919373 438919900 0.000000e+00 857
14 TraesCS5B01G222100 chr5A 89.279 513 22 6 918 1402 438920139 438920646 4.120000e-171 612
15 TraesCS5B01G222100 chr5A 78.686 746 154 5 2778 3519 438922017 438922761 5.600000e-135 492
16 TraesCS5B01G222100 chr5A 78.165 774 150 14 2848 3610 438921895 438922660 5.640000e-130 475
17 TraesCS5B01G222100 chr5A 95.531 179 8 0 1 179 438918871 438919049 2.840000e-73 287
18 TraesCS5B01G222100 chr5A 91.954 174 12 1 1397 1570 438920589 438920760 6.220000e-60 243
19 TraesCS5B01G222100 chr5A 90.441 136 3 4 789 924 438919985 438920110 2.980000e-38 171
20 TraesCS5B01G222100 chr5D 92.528 2409 132 22 1599 3988 337700863 337703242 0.000000e+00 3408
21 TraesCS5B01G222100 chr5D 96.209 765 27 1 1 765 337699186 337699948 0.000000e+00 1251
22 TraesCS5B01G222100 chr5D 88.112 1001 86 12 4044 5022 337703323 337704312 0.000000e+00 1158
23 TraesCS5B01G222100 chr5D 87.481 655 29 14 5347 5967 337704815 337705450 0.000000e+00 706
24 TraesCS5B01G222100 chr5D 89.784 509 22 7 917 1402 337700260 337700761 5.290000e-175 625
25 TraesCS5B01G222100 chr5D 93.143 175 10 1 1396 1570 337700703 337700875 8.000000e-64 255
26 TraesCS5B01G222100 chr5D 86.335 161 4 8 781 924 337700069 337700228 6.450000e-35 159
27 TraesCS5B01G222100 chrUn 94.659 337 9 5 5882 6215 371429551 371429221 1.190000e-141 514


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 TraesCS5B01G222100 chr5B 396622388 396628602 6214 False 11478.000000 11478 100.000000 1 6215 1 chr5B.!!$F1 6214
1 TraesCS5B01G222100 chr5B 396834639 396841705 7066 False 796.500000 1260 92.991250 4408 6215 4 chr5B.!!$F6 1807
2 TraesCS5B01G222100 chr5B 396879069 396879790 721 False 704.000000 704 84.465000 3435 4188 1 chr5B.!!$F4 753
3 TraesCS5B01G222100 chr5B 396827172 396827879 707 False 701.000000 701 84.687000 3435 4175 1 chr5B.!!$F2 740
4 TraesCS5B01G222100 chr5A 438918871 438925280 6409 False 928.300000 3563 89.260400 1 6010 10 chr5A.!!$F1 6009
5 TraesCS5B01G222100 chr5D 337699186 337705450 6264 False 1080.285714 3408 90.513143 1 5967 7 chr5D.!!$F1 5966

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
32 33 0.179000 GCATCAACCGATCCTCCTGT 59.821 55.0 0.00 0.0 0.00 4.00 F
1320 1779 0.603707 CGTCCCTGACTGCACATTGT 60.604 55.0 0.00 0.0 0.00 2.71 F
2216 2684 0.110238 CGTTCTGTCATTGGCAACGG 60.110 55.0 0.00 0.0 36.93 4.44 F
2696 3164 0.036164 TACCTGCTGCGACCAATGTT 59.964 50.0 0.00 0.0 0.00 2.71 F
3377 3845 0.322975 AAGCGAAGGACAGTCATGCT 59.677 50.0 2.17 0.0 0.00 3.79 F
3430 3898 0.598065 GAGCAACCCAAGCGTGAAAT 59.402 50.0 0.00 0.0 37.01 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1913 2378 0.682209 GGCAGAGCATTGTGGGTGAT 60.682 55.000 0.00 0.00 0.00 3.06 R
2389 2857 0.038166 AGTCATCAACGGCAACCCAT 59.962 50.000 0.00 0.00 0.00 4.00 R
3523 3991 0.107263 TGCTTCACACTGCTGACCAA 60.107 50.000 0.00 0.00 0.00 3.67 R
4632 5244 0.329261 CTTTGAGATGGTGGCTCCCA 59.671 55.000 2.66 0.68 39.27 4.37 R
4983 5610 2.669569 GTGCAGCCACCGACATGT 60.670 61.111 0.00 0.00 35.92 3.21 R
5234 6285 5.164320 CCGACATTTCAAACGAAATCGAAAC 60.164 40.000 10.16 0.00 40.38 2.78 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 0.179000 GCATCAACCGATCCTCCTGT 59.821 55.000 0.00 0.00 0.00 4.00
78 79 4.529219 TACGCCAGCGCCATCCTG 62.529 66.667 12.72 0.00 44.19 3.86
513 784 2.027024 TCGCACGACGCTGACTTT 59.973 55.556 0.00 0.00 43.23 2.66
657 928 0.902984 TGGCGAGGTTCAAGGAGCTA 60.903 55.000 0.00 0.00 0.00 3.32
690 961 2.202987 GCCGCCATGGAGTGAGAG 60.203 66.667 18.40 0.00 42.00 3.20
691 962 2.202987 CCGCCATGGAGTGAGAGC 60.203 66.667 18.40 0.00 42.00 4.09
693 964 2.729479 CGCCATGGAGTGAGAGCCT 61.729 63.158 18.40 0.00 0.00 4.58
695 966 1.440893 CCATGGAGTGAGAGCCTCG 59.559 63.158 5.56 0.00 32.35 4.63
696 967 1.227205 CATGGAGTGAGAGCCTCGC 60.227 63.158 7.45 7.45 40.84 5.03
697 968 2.430610 ATGGAGTGAGAGCCTCGCC 61.431 63.158 10.86 6.80 41.38 5.54
698 969 4.200283 GGAGTGAGAGCCTCGCCG 62.200 72.222 10.86 0.00 41.38 6.46
699 970 3.134792 GAGTGAGAGCCTCGCCGA 61.135 66.667 10.86 0.00 41.38 5.54
754 1025 4.582240 TGTAATGTGAAATGTGCAGGTGAA 59.418 37.500 0.00 0.00 0.00 3.18
765 1036 8.807948 AAATGTGCAGGTGAAAGTATATAGTT 57.192 30.769 0.00 0.00 0.00 2.24
766 1037 7.792374 ATGTGCAGGTGAAAGTATATAGTTG 57.208 36.000 3.54 0.00 0.00 3.16
769 1040 7.979537 TGTGCAGGTGAAAGTATATAGTTGTAG 59.020 37.037 3.54 0.00 0.00 2.74
818 1198 8.011673 CGTGTATAATCAGAATTTCATGCGAAT 58.988 33.333 0.00 0.00 0.00 3.34
830 1210 9.252962 GAATTTCATGCGAATAAAGGATCAAAT 57.747 29.630 0.00 0.00 0.00 2.32
958 1394 2.127496 CAGTTGCGCTGCGAGTTG 60.127 61.111 28.07 13.43 38.52 3.16
995 1431 2.831742 AACGCGCTATCGGAGGGA 60.832 61.111 5.73 0.00 40.59 4.20
1205 1643 2.895372 CCGCACGGTAATGAGGCC 60.895 66.667 0.00 0.00 32.46 5.19
1320 1779 0.603707 CGTCCCTGACTGCACATTGT 60.604 55.000 0.00 0.00 0.00 2.71
1352 1816 4.617875 CGAATCGCAAGGGAGGTT 57.382 55.556 0.00 0.00 38.47 3.50
1353 1817 2.384203 CGAATCGCAAGGGAGGTTC 58.616 57.895 0.00 0.00 38.47 3.62
1354 1818 1.421410 CGAATCGCAAGGGAGGTTCG 61.421 60.000 7.97 7.97 38.47 3.95
1355 1819 1.078426 AATCGCAAGGGAGGTTCGG 60.078 57.895 0.00 0.00 38.47 4.30
1356 1820 2.536997 AATCGCAAGGGAGGTTCGGG 62.537 60.000 0.00 0.00 38.47 5.14
1357 1821 4.778143 CGCAAGGGAGGTTCGGGG 62.778 72.222 0.00 0.00 0.00 5.73
1358 1822 3.327404 GCAAGGGAGGTTCGGGGA 61.327 66.667 0.00 0.00 0.00 4.81
1359 1823 2.680370 GCAAGGGAGGTTCGGGGAT 61.680 63.158 0.00 0.00 0.00 3.85
1360 1824 1.999346 CAAGGGAGGTTCGGGGATT 59.001 57.895 0.00 0.00 0.00 3.01
1361 1825 1.209621 CAAGGGAGGTTCGGGGATTA 58.790 55.000 0.00 0.00 0.00 1.75
1362 1826 1.141053 CAAGGGAGGTTCGGGGATTAG 59.859 57.143 0.00 0.00 0.00 1.73
1363 1827 1.054978 AGGGAGGTTCGGGGATTAGC 61.055 60.000 0.00 0.00 0.00 3.09
1364 1828 1.069258 GGAGGTTCGGGGATTAGCG 59.931 63.158 0.00 0.00 0.00 4.26
1365 1829 1.683418 GGAGGTTCGGGGATTAGCGT 61.683 60.000 0.00 0.00 0.00 5.07
1366 1830 1.035139 GAGGTTCGGGGATTAGCGTA 58.965 55.000 0.00 0.00 0.00 4.42
1367 1831 1.410153 GAGGTTCGGGGATTAGCGTAA 59.590 52.381 0.00 0.00 0.00 3.18
1368 1832 1.411612 AGGTTCGGGGATTAGCGTAAG 59.588 52.381 0.00 0.00 43.44 2.34
1369 1833 1.410153 GGTTCGGGGATTAGCGTAAGA 59.590 52.381 0.00 0.00 43.02 2.10
1370 1834 2.036862 GGTTCGGGGATTAGCGTAAGAT 59.963 50.000 0.00 0.00 43.02 2.40
1371 1835 3.493873 GGTTCGGGGATTAGCGTAAGATT 60.494 47.826 0.00 0.00 43.02 2.40
1372 1836 3.380479 TCGGGGATTAGCGTAAGATTG 57.620 47.619 0.00 0.00 43.02 2.67
1373 1837 2.696707 TCGGGGATTAGCGTAAGATTGT 59.303 45.455 0.00 0.00 43.02 2.71
1374 1838 3.133362 TCGGGGATTAGCGTAAGATTGTT 59.867 43.478 0.00 0.00 43.02 2.83
1375 1839 3.875134 CGGGGATTAGCGTAAGATTGTTT 59.125 43.478 0.00 0.00 43.02 2.83
1376 1840 4.334481 CGGGGATTAGCGTAAGATTGTTTT 59.666 41.667 0.00 0.00 43.02 2.43
1377 1841 5.578776 GGGGATTAGCGTAAGATTGTTTTG 58.421 41.667 0.00 0.00 43.02 2.44
1378 1842 5.449999 GGGGATTAGCGTAAGATTGTTTTGG 60.450 44.000 0.00 0.00 43.02 3.28
1379 1843 5.124936 GGGATTAGCGTAAGATTGTTTTGGT 59.875 40.000 0.00 0.00 43.02 3.67
1380 1844 6.316890 GGGATTAGCGTAAGATTGTTTTGGTA 59.683 38.462 0.00 0.00 43.02 3.25
1381 1845 7.407337 GGATTAGCGTAAGATTGTTTTGGTAG 58.593 38.462 0.00 0.00 43.02 3.18
1382 1846 7.279313 GGATTAGCGTAAGATTGTTTTGGTAGA 59.721 37.037 0.00 0.00 43.02 2.59
1383 1847 7.591006 TTAGCGTAAGATTGTTTTGGTAGAG 57.409 36.000 0.00 0.00 43.02 2.43
1384 1848 5.548406 AGCGTAAGATTGTTTTGGTAGAGT 58.452 37.500 0.00 0.00 43.02 3.24
1385 1849 5.408604 AGCGTAAGATTGTTTTGGTAGAGTG 59.591 40.000 0.00 0.00 43.02 3.51
1386 1850 5.178809 GCGTAAGATTGTTTTGGTAGAGTGT 59.821 40.000 0.00 0.00 43.02 3.55
1387 1851 6.366877 GCGTAAGATTGTTTTGGTAGAGTGTA 59.633 38.462 0.00 0.00 43.02 2.90
1388 1852 7.620806 GCGTAAGATTGTTTTGGTAGAGTGTAC 60.621 40.741 0.00 0.00 43.02 2.90
1389 1853 7.383029 CGTAAGATTGTTTTGGTAGAGTGTACA 59.617 37.037 0.00 0.00 43.02 2.90
1390 1854 9.048446 GTAAGATTGTTTTGGTAGAGTGTACAA 57.952 33.333 0.00 0.00 0.00 2.41
1391 1855 8.514330 AAGATTGTTTTGGTAGAGTGTACAAA 57.486 30.769 0.00 0.00 0.00 2.83
1392 1856 8.691661 AGATTGTTTTGGTAGAGTGTACAAAT 57.308 30.769 0.00 0.00 33.40 2.32
1393 1857 8.784043 AGATTGTTTTGGTAGAGTGTACAAATC 58.216 33.333 0.00 0.00 33.40 2.17
1394 1858 8.691661 ATTGTTTTGGTAGAGTGTACAAATCT 57.308 30.769 14.43 14.43 33.40 2.40
1395 1859 9.787435 ATTGTTTTGGTAGAGTGTACAAATCTA 57.213 29.630 12.77 12.77 33.40 1.98
1454 1918 7.339721 TGGTAGAGTGTACAAATCTAAGAGAGG 59.660 40.741 16.67 0.00 0.00 3.69
1467 1931 6.744175 TCTAAGAGAGGCAGATGATCATTT 57.256 37.500 10.14 0.28 0.00 2.32
1480 1944 8.559536 GCAGATGATCATTTTCCGATTTAGTTA 58.440 33.333 10.14 0.00 0.00 2.24
1501 1965 7.918076 AGTTATTGTTCACCCTAATTCTCAGA 58.082 34.615 0.00 0.00 0.00 3.27
1565 2029 8.628630 TTCACTGTGATGTAATAATTGGTTCA 57.371 30.769 11.86 0.00 0.00 3.18
1566 2030 8.806429 TCACTGTGATGTAATAATTGGTTCAT 57.194 30.769 6.36 0.00 0.00 2.57
1567 2031 8.892723 TCACTGTGATGTAATAATTGGTTCATC 58.107 33.333 6.36 0.00 34.28 2.92
1568 2032 8.131100 CACTGTGATGTAATAATTGGTTCATCC 58.869 37.037 0.32 0.00 33.20 3.51
1569 2033 8.055181 ACTGTGATGTAATAATTGGTTCATCCT 58.945 33.333 0.00 0.00 37.07 3.24
1570 2034 8.821686 TGTGATGTAATAATTGGTTCATCCTT 57.178 30.769 0.00 0.00 37.07 3.36
1571 2035 9.913310 TGTGATGTAATAATTGGTTCATCCTTA 57.087 29.630 0.00 0.00 37.07 2.69
1573 2037 9.349713 TGATGTAATAATTGGTTCATCCTTACC 57.650 33.333 0.00 0.00 37.07 2.85
1574 2038 8.706322 ATGTAATAATTGGTTCATCCTTACCC 57.294 34.615 0.00 0.00 37.07 3.69
1575 2039 6.768861 TGTAATAATTGGTTCATCCTTACCCG 59.231 38.462 0.00 0.00 37.07 5.28
1576 2040 2.052782 ATTGGTTCATCCTTACCCGC 57.947 50.000 0.00 0.00 37.07 6.13
1577 2041 0.693622 TTGGTTCATCCTTACCCGCA 59.306 50.000 0.00 0.00 37.07 5.69
1578 2042 0.693622 TGGTTCATCCTTACCCGCAA 59.306 50.000 0.00 0.00 37.07 4.85
1579 2043 1.074084 TGGTTCATCCTTACCCGCAAA 59.926 47.619 0.00 0.00 37.07 3.68
1580 2044 2.164338 GGTTCATCCTTACCCGCAAAA 58.836 47.619 0.00 0.00 0.00 2.44
1581 2045 2.758423 GGTTCATCCTTACCCGCAAAAT 59.242 45.455 0.00 0.00 0.00 1.82
1582 2046 3.949113 GGTTCATCCTTACCCGCAAAATA 59.051 43.478 0.00 0.00 0.00 1.40
1583 2047 4.399934 GGTTCATCCTTACCCGCAAAATAA 59.600 41.667 0.00 0.00 0.00 1.40
1584 2048 5.105675 GGTTCATCCTTACCCGCAAAATAAA 60.106 40.000 0.00 0.00 0.00 1.40
1585 2049 6.391537 GTTCATCCTTACCCGCAAAATAAAA 58.608 36.000 0.00 0.00 0.00 1.52
1586 2050 6.591750 TCATCCTTACCCGCAAAATAAAAA 57.408 33.333 0.00 0.00 0.00 1.94
1587 2051 7.176589 TCATCCTTACCCGCAAAATAAAAAT 57.823 32.000 0.00 0.00 0.00 1.82
1588 2052 8.294954 TCATCCTTACCCGCAAAATAAAAATA 57.705 30.769 0.00 0.00 0.00 1.40
1589 2053 8.750298 TCATCCTTACCCGCAAAATAAAAATAA 58.250 29.630 0.00 0.00 0.00 1.40
1590 2054 9.372369 CATCCTTACCCGCAAAATAAAAATAAA 57.628 29.630 0.00 0.00 0.00 1.40
1591 2055 9.945904 ATCCTTACCCGCAAAATAAAAATAAAA 57.054 25.926 0.00 0.00 0.00 1.52
1592 2056 9.774413 TCCTTACCCGCAAAATAAAAATAAAAA 57.226 25.926 0.00 0.00 0.00 1.94
1647 2111 8.660373 GGAATGTAGTATTTGTTCTCAGAGTTG 58.340 37.037 0.00 0.00 0.00 3.16
1706 2170 2.851104 GACGGTTTTCGGCGTCTG 59.149 61.111 6.85 4.25 44.45 3.51
1707 2171 1.662446 GACGGTTTTCGGCGTCTGA 60.662 57.895 6.85 0.00 44.45 3.27
1708 2172 1.216941 GACGGTTTTCGGCGTCTGAA 61.217 55.000 6.85 0.00 44.45 3.02
1737 2201 5.721232 ACTAAGAAATTCTCCGACGAATGT 58.279 37.500 0.00 0.00 34.07 2.71
1750 2214 4.260212 CCGACGAATGTGAATTAGCGAAAT 60.260 41.667 0.00 0.00 0.00 2.17
1792 2256 1.862201 TCGCTAAACGTTTGTGTCTGG 59.138 47.619 23.46 5.87 44.19 3.86
1855 2319 7.661437 TGAATAGGCTATTATTTACCACTGCAG 59.339 37.037 19.27 13.48 0.00 4.41
1878 2342 0.958382 TGCACGCCATGTCCCTAAAC 60.958 55.000 0.00 0.00 0.00 2.01
1882 2347 1.073284 ACGCCATGTCCCTAAACACTT 59.927 47.619 0.00 0.00 30.55 3.16
1913 2378 2.704065 GGCAGTGATACCTTAAGCCCTA 59.296 50.000 0.00 0.00 34.71 3.53
1935 2400 2.036098 CCACAATGCTCTGCCCCA 59.964 61.111 0.00 0.00 0.00 4.96
1983 2450 8.696175 CGTGTTCATTTTTGGGATTAAAAGTAC 58.304 33.333 0.00 0.00 31.80 2.73
1984 2451 9.758651 GTGTTCATTTTTGGGATTAAAAGTACT 57.241 29.630 0.00 0.00 31.80 2.73
2029 2496 3.347077 AAGAGTGGCAGATCCTTCAAG 57.653 47.619 0.00 0.00 35.26 3.02
2046 2513 9.612879 ATCCTTCAAGAGATATCTCCAGAAATA 57.387 33.333 25.88 18.89 43.88 1.40
2047 2514 9.439461 TCCTTCAAGAGATATCTCCAGAAATAA 57.561 33.333 25.88 15.07 43.88 1.40
2146 2613 5.232463 ACATGTGATGCCATGAAAAAGAAC 58.768 37.500 0.00 0.00 43.99 3.01
2216 2684 0.110238 CGTTCTGTCATTGGCAACGG 60.110 55.000 0.00 0.00 36.93 4.44
2438 2906 1.004320 GGTGATGTACCGCACACCA 60.004 57.895 17.01 0.00 42.97 4.17
2474 2942 1.946283 GCTTCTTGGTGGTACAGGAGC 60.946 57.143 0.00 0.00 41.80 4.70
2585 3053 3.793144 CAAGAACGCGGCAGCTCC 61.793 66.667 12.47 0.00 42.32 4.70
2590 3058 3.358076 AACGCGGCAGCTCCTCTAC 62.358 63.158 12.47 0.00 42.32 2.59
2686 3154 0.523519 GAAGCTTTGGTACCTGCTGC 59.476 55.000 21.81 18.11 35.79 5.25
2696 3164 0.036164 TACCTGCTGCGACCAATGTT 59.964 50.000 0.00 0.00 0.00 2.71
2952 3420 4.635765 GTCAACAGCTAAATCATGTAGCCA 59.364 41.667 2.89 0.00 44.22 4.75
3031 3499 7.012799 GGAGAGTGGAATTCAGATAAATGAACC 59.987 40.741 7.93 0.00 41.76 3.62
3090 3558 1.901591 AGTGAAGGACAACCATGCAG 58.098 50.000 0.00 0.00 38.94 4.41
3113 3581 2.295885 CAGCTGATGGGAAGTGGAATC 58.704 52.381 8.42 0.00 0.00 2.52
3318 3786 4.026475 CGAGTGGAATTCAGATAAGCGAAC 60.026 45.833 7.93 0.00 0.00 3.95
3338 3806 1.211709 GCTAAATTGTGCGGCCGTT 59.788 52.632 28.70 14.47 0.00 4.44
3352 3820 1.671054 CCGTTGGTCAGGAACGCAT 60.671 57.895 0.00 0.00 43.83 4.73
3371 3839 4.683432 GCAGAAGCGAAGGACAGT 57.317 55.556 0.00 0.00 0.00 3.55
3376 3844 0.723981 GAAGCGAAGGACAGTCATGC 59.276 55.000 2.17 0.00 0.00 4.06
3377 3845 0.322975 AAGCGAAGGACAGTCATGCT 59.677 50.000 2.17 0.00 0.00 3.79
3413 3881 8.936864 ACGGAAAATAAAATACAGAGAAGTGAG 58.063 33.333 0.00 0.00 0.00 3.51
3419 3887 3.618690 ATACAGAGAAGTGAGCAACCC 57.381 47.619 0.00 0.00 0.00 4.11
3430 3898 0.598065 GAGCAACCCAAGCGTGAAAT 59.402 50.000 0.00 0.00 37.01 2.17
3519 3987 2.551459 CAGAGAAGTGAACAGCCAAAGG 59.449 50.000 0.00 0.00 0.00 3.11
3520 3988 2.173569 AGAGAAGTGAACAGCCAAAGGT 59.826 45.455 0.00 0.00 0.00 3.50
3521 3989 2.550180 GAGAAGTGAACAGCCAAAGGTC 59.450 50.000 0.00 0.00 0.00 3.85
3522 3990 2.173569 AGAAGTGAACAGCCAAAGGTCT 59.826 45.455 0.00 0.00 0.00 3.85
3523 3991 2.736670 AGTGAACAGCCAAAGGTCTT 57.263 45.000 0.00 0.00 0.00 3.01
3534 4002 2.301346 CAAAGGTCTTTGGTCAGCAGT 58.699 47.619 13.89 0.00 44.47 4.40
3552 4029 3.625938 CAGTGTGAAGCAGAAGAAAAGC 58.374 45.455 0.00 0.00 0.00 3.51
3610 4087 0.954452 CAGGGAAGTGAACAGCCAAC 59.046 55.000 0.00 0.00 0.00 3.77
3624 4101 2.256461 CAACGCCTGCAAAGCCTC 59.744 61.111 2.96 0.00 0.00 4.70
3723 4200 1.809209 GAGCAGAAGAGACCAGCGC 60.809 63.158 0.00 0.00 0.00 5.92
3740 4217 3.114558 GCTCAACGAGGTGAGTGAG 57.885 57.895 18.13 4.94 45.75 3.51
3742 4219 1.540267 GCTCAACGAGGTGAGTGAGTA 59.460 52.381 18.13 0.00 45.75 2.59
3822 4316 7.412891 GCCAATATTTAAGTTTCGCAATTGCTT 60.413 33.333 26.86 16.45 39.32 3.91
3846 4340 6.036470 TGCTTCACTAATATCTTCAGTGACG 58.964 40.000 3.27 3.56 46.17 4.35
3859 4353 2.226200 TCAGTGACGAACATGGCAAATG 59.774 45.455 0.00 0.00 0.00 2.32
3860 4354 2.030893 CAGTGACGAACATGGCAAATGT 60.031 45.455 0.00 0.00 0.00 2.71
3887 4381 8.924511 TTTCTCTTGGTCTTAATGAAACTGAT 57.075 30.769 0.00 0.00 0.00 2.90
3913 4407 2.561478 TCCTGGTAGCCACTTTGAAC 57.439 50.000 0.00 0.00 0.00 3.18
3914 4408 2.054799 TCCTGGTAGCCACTTTGAACT 58.945 47.619 0.00 0.00 0.00 3.01
3915 4409 3.244582 TCCTGGTAGCCACTTTGAACTA 58.755 45.455 0.00 0.00 0.00 2.24
3916 4410 3.007614 TCCTGGTAGCCACTTTGAACTAC 59.992 47.826 0.00 0.00 35.36 2.73
3919 4413 2.039348 GGTAGCCACTTTGAACTACCCA 59.961 50.000 6.77 0.00 45.91 4.51
3920 4414 3.497227 GGTAGCCACTTTGAACTACCCAA 60.497 47.826 6.77 0.00 45.91 4.12
3921 4415 3.525800 AGCCACTTTGAACTACCCAAT 57.474 42.857 0.00 0.00 0.00 3.16
3922 4416 3.157087 AGCCACTTTGAACTACCCAATG 58.843 45.455 0.00 0.00 0.00 2.82
3923 4417 2.231235 GCCACTTTGAACTACCCAATGG 59.769 50.000 0.00 0.00 37.80 3.16
3924 4418 3.761897 CCACTTTGAACTACCCAATGGA 58.238 45.455 0.00 0.00 34.81 3.41
3925 4419 4.148838 CCACTTTGAACTACCCAATGGAA 58.851 43.478 0.00 0.00 34.81 3.53
3926 4420 4.772100 CCACTTTGAACTACCCAATGGAAT 59.228 41.667 0.00 0.00 34.81 3.01
3927 4421 5.336690 CCACTTTGAACTACCCAATGGAATG 60.337 44.000 0.00 0.00 34.81 2.67
3928 4422 5.243730 CACTTTGAACTACCCAATGGAATGT 59.756 40.000 0.00 0.00 34.81 2.71
3929 4423 5.838521 ACTTTGAACTACCCAATGGAATGTT 59.161 36.000 0.00 2.03 34.81 2.71
3930 4424 5.975693 TTGAACTACCCAATGGAATGTTC 57.024 39.130 17.50 17.50 38.18 3.18
3997 4574 8.677300 TGAAACAGAAATGATACCAAATAGCTC 58.323 33.333 0.00 0.00 0.00 4.09
4001 4578 8.486210 ACAGAAATGATACCAAATAGCTCACTA 58.514 33.333 0.00 0.00 0.00 2.74
4058 4635 8.814038 ATAGAAATGATACCAAAAAGCTCACT 57.186 30.769 0.00 0.00 0.00 3.41
4059 4636 6.917533 AGAAATGATACCAAAAAGCTCACTG 58.082 36.000 0.00 0.00 0.00 3.66
4060 4637 6.716628 AGAAATGATACCAAAAAGCTCACTGA 59.283 34.615 0.00 0.00 0.00 3.41
4061 4638 7.395489 AGAAATGATACCAAAAAGCTCACTGAT 59.605 33.333 0.00 0.00 0.00 2.90
4062 4639 6.690194 ATGATACCAAAAAGCTCACTGATC 57.310 37.500 0.00 0.00 0.00 2.92
4063 4640 4.943705 TGATACCAAAAAGCTCACTGATCC 59.056 41.667 0.00 0.00 0.00 3.36
4064 4641 2.519013 ACCAAAAAGCTCACTGATCCC 58.481 47.619 0.00 0.00 0.00 3.85
4077 4657 6.105397 TCACTGATCCCGTTACTTTAGTTT 57.895 37.500 0.00 0.00 0.00 2.66
4119 4715 5.048991 TGCAACTTACTTTAGTTAGGCAAGC 60.049 40.000 0.00 0.00 35.43 4.01
4128 4724 1.066787 AGTTAGGCAAGCTCTTCGGAC 60.067 52.381 0.00 0.00 0.00 4.79
4164 4760 9.959721 TTTAGTTAGGCAAGTTCTTCAGATATT 57.040 29.630 0.00 0.00 0.00 1.28
4165 4761 7.856145 AGTTAGGCAAGTTCTTCAGATATTG 57.144 36.000 0.00 0.00 0.00 1.90
4194 4791 7.497925 ACTTTAGTTAGGCAAGTTCTTCAAG 57.502 36.000 0.00 0.00 0.00 3.02
4294 4906 3.636153 ACCTGAGATTACCTTCCTTGC 57.364 47.619 0.00 0.00 0.00 4.01
4305 4917 4.048970 ACCTTCCTTGCTCACTAGTCTA 57.951 45.455 0.00 0.00 0.00 2.59
4473 5085 2.127708 ACCCTCTGTCAAGTGAACCTT 58.872 47.619 0.00 0.00 0.00 3.50
4566 5178 7.850819 GTCCAGGCAGAAAGCATTTGGATTC 62.851 48.000 9.36 0.00 45.33 2.52
5082 5748 8.215050 CCATCCAGGTGTACATATTAGGTTTTA 58.785 37.037 0.00 0.00 0.00 1.52
5133 5816 1.607148 GGAGTGGTTCCCTTTTTCACG 59.393 52.381 0.00 0.00 40.37 4.35
5135 5818 3.469739 GAGTGGTTCCCTTTTTCACGTA 58.530 45.455 0.00 0.00 33.98 3.57
5141 5824 4.393990 GGTTCCCTTTTTCACGTATTCGAT 59.606 41.667 0.00 0.00 40.62 3.59
5227 5920 9.220767 GTAATTGAAGAAGAATCTACCTTGTGT 57.779 33.333 3.17 0.00 33.77 3.72
5234 6285 8.567285 AGAAGAATCTACCTTGTGTAATTTGG 57.433 34.615 0.00 0.00 32.88 3.28
5297 6349 6.318628 CCCGTGATTTTATTCGACAATTTGA 58.681 36.000 2.79 0.00 0.00 2.69
5461 6520 0.541863 ACCTGCAGGAAATAGGACGG 59.458 55.000 39.19 9.37 38.94 4.79
5510 6569 2.092211 CCAAGTTTGTCTACGACGCATC 59.908 50.000 0.00 0.00 34.95 3.91
5524 6583 1.431488 CGCATCCATCCTCACCGTTG 61.431 60.000 0.00 0.00 0.00 4.10
5628 6690 0.455815 GTGATCGGGACCAATTTGCC 59.544 55.000 0.00 0.00 0.00 4.52
5673 6735 2.743928 CGCCCACTGCTGTTCTCC 60.744 66.667 0.00 0.00 38.05 3.71
5676 6738 1.835927 GCCCACTGCTGTTCTCCTCT 61.836 60.000 0.00 0.00 36.87 3.69
5719 6781 4.475135 GGCTCGGCCTCAGGTTCC 62.475 72.222 0.00 0.00 46.69 3.62
5728 6796 3.708220 CTCAGGTTCCTCTCGCCGC 62.708 68.421 0.00 0.00 0.00 6.53
5749 6817 3.376935 CTGCTCTGCTACCACCGGG 62.377 68.421 6.32 0.00 41.29 5.73
5827 6914 4.697756 CGGCCAACGCTTCCCTGA 62.698 66.667 2.24 0.00 34.82 3.86
5828 6915 3.056328 GGCCAACGCTTCCCTGAC 61.056 66.667 0.00 0.00 34.44 3.51
5851 6938 2.435234 GCCGCATGGTAACCGTCA 60.435 61.111 0.00 0.00 37.67 4.35
5866 6953 1.399572 CGTCAAGTCACTGTCACTCG 58.600 55.000 0.00 0.00 0.00 4.18
5880 6967 0.733729 CACTCGTACCTTCTCCTCGG 59.266 60.000 0.00 0.00 0.00 4.63
5975 12126 4.864334 CCGCTGGGAGTGGGATGC 62.864 72.222 0.00 0.00 42.09 3.91
5976 12127 4.864334 CGCTGGGAGTGGGATGCC 62.864 72.222 0.00 0.00 0.00 4.40
5977 12128 3.415087 GCTGGGAGTGGGATGCCT 61.415 66.667 4.35 0.00 0.00 4.75
5978 12129 2.988839 GCTGGGAGTGGGATGCCTT 61.989 63.158 4.35 0.00 0.00 4.35
5979 12130 1.693640 CTGGGAGTGGGATGCCTTT 59.306 57.895 4.35 0.00 0.00 3.11
5980 12131 0.394899 CTGGGAGTGGGATGCCTTTC 60.395 60.000 4.35 1.80 0.00 2.62
5981 12132 0.846427 TGGGAGTGGGATGCCTTTCT 60.846 55.000 4.35 0.11 0.00 2.52
5982 12133 0.106967 GGGAGTGGGATGCCTTTCTC 60.107 60.000 4.35 9.59 0.00 2.87
6113 12267 6.237901 TGCAAATGTAGTACAACTCTTCCAT 58.762 36.000 7.16 0.00 0.00 3.41
6116 12270 4.713824 TGTAGTACAACTCTTCCATCGG 57.286 45.455 0.00 0.00 0.00 4.18
6158 12312 2.740826 GTGCAAAGGGACGCGCTA 60.741 61.111 5.73 0.00 35.76 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
507 778 3.172106 TCGCCCCACCCAAAGTCA 61.172 61.111 0.00 0.00 0.00 3.41
657 928 0.390860 CGGCCATCTCCTCGAAGAAT 59.609 55.000 2.24 0.00 34.09 2.40
690 961 4.838152 TCATGGCTTCGGCGAGGC 62.838 66.667 32.49 32.49 42.91 4.70
691 962 1.958205 GATCATGGCTTCGGCGAGG 60.958 63.158 15.27 15.27 42.91 4.63
693 964 2.279451 CGATCATGGCTTCGGCGA 60.279 61.111 4.99 4.99 42.91 5.54
695 966 3.017323 CACGATCATGGCTTCGGC 58.983 61.111 14.89 0.00 39.61 5.54
696 967 0.249447 TAGCACGATCATGGCTTCGG 60.249 55.000 14.89 7.62 39.61 4.30
697 968 0.855349 GTAGCACGATCATGGCTTCG 59.145 55.000 7.90 10.66 39.01 3.79
698 969 0.855349 CGTAGCACGATCATGGCTTC 59.145 55.000 7.90 3.18 46.05 3.86
699 970 0.175760 ACGTAGCACGATCATGGCTT 59.824 50.000 14.18 0.00 46.05 4.35
740 1011 8.677300 CAACTATATACTTTCACCTGCACATTT 58.323 33.333 0.00 0.00 0.00 2.32
830 1210 4.340666 TCTGGCAGTTCTTTTGCATGTAAA 59.659 37.500 15.27 4.71 43.28 2.01
877 1268 4.616143 CGGATCACGTTTTCTCTCTCAGAA 60.616 45.833 0.00 0.00 37.28 3.02
879 1270 3.119814 TCGGATCACGTTTTCTCTCTCAG 60.120 47.826 0.00 0.00 44.69 3.35
880 1271 2.817844 TCGGATCACGTTTTCTCTCTCA 59.182 45.455 0.00 0.00 44.69 3.27
881 1272 3.489180 TCGGATCACGTTTTCTCTCTC 57.511 47.619 0.00 0.00 44.69 3.20
958 1394 1.134694 GTTCGCGAGATTGGTTGCC 59.865 57.895 9.59 0.00 41.60 4.52
995 1431 4.698625 AGGGGAAGGCGGACTCGT 62.699 66.667 0.00 0.00 38.89 4.18
1214 1652 2.271497 GTCCCGGACGAGAGAGGA 59.729 66.667 0.73 0.00 0.00 3.71
1290 1749 1.734465 GTCAGGGACGAATTTCAGCAG 59.266 52.381 0.00 0.00 0.00 4.24
1293 1752 1.734465 GCAGTCAGGGACGAATTTCAG 59.266 52.381 0.00 0.00 37.67 3.02
1344 1808 1.054978 GCTAATCCCCGAACCTCCCT 61.055 60.000 0.00 0.00 0.00 4.20
1345 1809 1.450642 GCTAATCCCCGAACCTCCC 59.549 63.158 0.00 0.00 0.00 4.30
1346 1810 1.069258 CGCTAATCCCCGAACCTCC 59.931 63.158 0.00 0.00 0.00 4.30
1347 1811 1.035139 TACGCTAATCCCCGAACCTC 58.965 55.000 0.00 0.00 0.00 3.85
1348 1812 1.411612 CTTACGCTAATCCCCGAACCT 59.588 52.381 0.00 0.00 0.00 3.50
1349 1813 1.410153 TCTTACGCTAATCCCCGAACC 59.590 52.381 0.00 0.00 0.00 3.62
1350 1814 2.877043 TCTTACGCTAATCCCCGAAC 57.123 50.000 0.00 0.00 0.00 3.95
1351 1815 3.133362 ACAATCTTACGCTAATCCCCGAA 59.867 43.478 0.00 0.00 0.00 4.30
1352 1816 2.696707 ACAATCTTACGCTAATCCCCGA 59.303 45.455 0.00 0.00 0.00 5.14
1353 1817 3.107642 ACAATCTTACGCTAATCCCCG 57.892 47.619 0.00 0.00 0.00 5.73
1354 1818 5.449999 CCAAAACAATCTTACGCTAATCCCC 60.450 44.000 0.00 0.00 0.00 4.81
1355 1819 5.124936 ACCAAAACAATCTTACGCTAATCCC 59.875 40.000 0.00 0.00 0.00 3.85
1356 1820 6.190954 ACCAAAACAATCTTACGCTAATCC 57.809 37.500 0.00 0.00 0.00 3.01
1357 1821 8.193250 TCTACCAAAACAATCTTACGCTAATC 57.807 34.615 0.00 0.00 0.00 1.75
1358 1822 7.822822 ACTCTACCAAAACAATCTTACGCTAAT 59.177 33.333 0.00 0.00 0.00 1.73
1359 1823 7.117236 CACTCTACCAAAACAATCTTACGCTAA 59.883 37.037 0.00 0.00 0.00 3.09
1360 1824 6.588756 CACTCTACCAAAACAATCTTACGCTA 59.411 38.462 0.00 0.00 0.00 4.26
1361 1825 5.408604 CACTCTACCAAAACAATCTTACGCT 59.591 40.000 0.00 0.00 0.00 5.07
1362 1826 5.178809 ACACTCTACCAAAACAATCTTACGC 59.821 40.000 0.00 0.00 0.00 4.42
1363 1827 6.780706 ACACTCTACCAAAACAATCTTACG 57.219 37.500 0.00 0.00 0.00 3.18
1364 1828 8.597662 TGTACACTCTACCAAAACAATCTTAC 57.402 34.615 0.00 0.00 0.00 2.34
1365 1829 9.616156 TTTGTACACTCTACCAAAACAATCTTA 57.384 29.630 0.00 0.00 0.00 2.10
1366 1830 8.514330 TTTGTACACTCTACCAAAACAATCTT 57.486 30.769 0.00 0.00 0.00 2.40
1367 1831 8.691661 ATTTGTACACTCTACCAAAACAATCT 57.308 30.769 0.00 0.00 0.00 2.40
1368 1832 8.784043 AGATTTGTACACTCTACCAAAACAATC 58.216 33.333 0.00 0.00 0.00 2.67
1369 1833 8.691661 AGATTTGTACACTCTACCAAAACAAT 57.308 30.769 0.00 0.00 0.00 2.71
1370 1834 9.616156 TTAGATTTGTACACTCTACCAAAACAA 57.384 29.630 11.96 0.00 0.00 2.83
1371 1835 9.268268 CTTAGATTTGTACACTCTACCAAAACA 57.732 33.333 11.96 0.00 0.00 2.83
1372 1836 9.485206 TCTTAGATTTGTACACTCTACCAAAAC 57.515 33.333 11.96 0.00 0.00 2.43
1373 1837 9.706691 CTCTTAGATTTGTACACTCTACCAAAA 57.293 33.333 11.96 2.03 0.00 2.44
1374 1838 9.085645 TCTCTTAGATTTGTACACTCTACCAAA 57.914 33.333 11.96 0.00 0.00 3.28
1375 1839 8.645814 TCTCTTAGATTTGTACACTCTACCAA 57.354 34.615 11.96 0.00 0.00 3.67
1376 1840 7.339721 CCTCTCTTAGATTTGTACACTCTACCA 59.660 40.741 11.96 3.94 0.00 3.25
1377 1841 7.339976 ACCTCTCTTAGATTTGTACACTCTACC 59.660 40.741 11.96 0.00 0.00 3.18
1378 1842 8.283699 ACCTCTCTTAGATTTGTACACTCTAC 57.716 38.462 11.96 0.00 0.00 2.59
1379 1843 8.880991 AACCTCTCTTAGATTTGTACACTCTA 57.119 34.615 9.33 9.33 0.00 2.43
1380 1844 7.362229 CGAACCTCTCTTAGATTTGTACACTCT 60.362 40.741 10.97 10.97 0.00 3.24
1381 1845 6.748198 CGAACCTCTCTTAGATTTGTACACTC 59.252 42.308 0.00 0.00 0.00 3.51
1382 1846 6.350277 CCGAACCTCTCTTAGATTTGTACACT 60.350 42.308 0.00 0.00 0.00 3.55
1383 1847 5.805994 CCGAACCTCTCTTAGATTTGTACAC 59.194 44.000 0.00 0.00 0.00 2.90
1384 1848 5.105473 CCCGAACCTCTCTTAGATTTGTACA 60.105 44.000 0.00 0.00 0.00 2.90
1385 1849 5.349809 CCCGAACCTCTCTTAGATTTGTAC 58.650 45.833 0.00 0.00 0.00 2.90
1386 1850 4.404715 CCCCGAACCTCTCTTAGATTTGTA 59.595 45.833 0.00 0.00 0.00 2.41
1387 1851 3.197983 CCCCGAACCTCTCTTAGATTTGT 59.802 47.826 0.00 0.00 0.00 2.83
1388 1852 3.451178 TCCCCGAACCTCTCTTAGATTTG 59.549 47.826 0.00 0.00 0.00 2.32
1389 1853 3.721021 TCCCCGAACCTCTCTTAGATTT 58.279 45.455 0.00 0.00 0.00 2.17
1390 1854 3.399952 TCCCCGAACCTCTCTTAGATT 57.600 47.619 0.00 0.00 0.00 2.40
1391 1855 3.621682 ATCCCCGAACCTCTCTTAGAT 57.378 47.619 0.00 0.00 0.00 1.98
1392 1856 3.399952 AATCCCCGAACCTCTCTTAGA 57.600 47.619 0.00 0.00 0.00 2.10
1393 1857 3.006003 GCTAATCCCCGAACCTCTCTTAG 59.994 52.174 0.00 0.00 0.00 2.18
1394 1858 2.963782 GCTAATCCCCGAACCTCTCTTA 59.036 50.000 0.00 0.00 0.00 2.10
1395 1859 1.763545 GCTAATCCCCGAACCTCTCTT 59.236 52.381 0.00 0.00 0.00 2.85
1454 1918 6.963796 ACTAAATCGGAAAATGATCATCTGC 58.036 36.000 9.06 4.03 0.00 4.26
1467 1931 6.478129 AGGGTGAACAATAACTAAATCGGAA 58.522 36.000 0.00 0.00 0.00 4.30
1480 1944 6.962182 TCATCTGAGAATTAGGGTGAACAAT 58.038 36.000 0.00 0.00 0.00 2.71
1556 2020 2.291282 TGCGGGTAAGGATGAACCAATT 60.291 45.455 0.00 0.00 42.04 2.32
1557 2021 1.283613 TGCGGGTAAGGATGAACCAAT 59.716 47.619 0.00 0.00 42.04 3.16
1558 2022 0.693622 TGCGGGTAAGGATGAACCAA 59.306 50.000 0.00 0.00 42.04 3.67
1559 2023 0.693622 TTGCGGGTAAGGATGAACCA 59.306 50.000 0.00 0.00 42.04 3.67
1560 2024 1.828979 TTTGCGGGTAAGGATGAACC 58.171 50.000 0.00 0.00 39.35 3.62
1561 2025 5.570234 TTATTTTGCGGGTAAGGATGAAC 57.430 39.130 0.00 0.00 0.00 3.18
1562 2026 6.591750 TTTTATTTTGCGGGTAAGGATGAA 57.408 33.333 0.00 0.00 0.00 2.57
1563 2027 6.591750 TTTTTATTTTGCGGGTAAGGATGA 57.408 33.333 0.00 0.00 0.00 2.92
1564 2028 8.934507 TTATTTTTATTTTGCGGGTAAGGATG 57.065 30.769 0.00 0.00 0.00 3.51
1565 2029 9.945904 TTTTATTTTTATTTTGCGGGTAAGGAT 57.054 25.926 0.00 0.00 0.00 3.24
1566 2030 9.774413 TTTTTATTTTTATTTTGCGGGTAAGGA 57.226 25.926 0.00 0.00 0.00 3.36
1587 2051 9.732130 CCCAGGATGAACCAATTTTTATTTTTA 57.268 29.630 0.00 0.00 39.69 1.52
1588 2052 7.176515 GCCCAGGATGAACCAATTTTTATTTTT 59.823 33.333 0.00 0.00 39.69 1.94
1589 2053 6.658816 GCCCAGGATGAACCAATTTTTATTTT 59.341 34.615 0.00 0.00 39.69 1.82
1590 2054 6.179756 GCCCAGGATGAACCAATTTTTATTT 58.820 36.000 0.00 0.00 39.69 1.40
1591 2055 5.250313 TGCCCAGGATGAACCAATTTTTATT 59.750 36.000 0.00 0.00 39.69 1.40
1592 2056 4.782156 TGCCCAGGATGAACCAATTTTTAT 59.218 37.500 0.00 0.00 39.69 1.40
1593 2057 4.163427 TGCCCAGGATGAACCAATTTTTA 58.837 39.130 0.00 0.00 39.69 1.52
1594 2058 2.978278 TGCCCAGGATGAACCAATTTTT 59.022 40.909 0.00 0.00 39.69 1.94
1595 2059 2.618794 TGCCCAGGATGAACCAATTTT 58.381 42.857 0.00 0.00 39.69 1.82
1596 2060 2.323999 TGCCCAGGATGAACCAATTT 57.676 45.000 0.00 0.00 39.69 1.82
1705 2169 7.117812 GTCGGAGAATTTCTTAGTTCACATTCA 59.882 37.037 0.00 0.00 39.69 2.57
1706 2170 7.457060 GTCGGAGAATTTCTTAGTTCACATTC 58.543 38.462 0.00 0.00 39.69 2.67
1707 2171 6.090898 CGTCGGAGAATTTCTTAGTTCACATT 59.909 38.462 0.00 0.00 39.69 2.71
1708 2172 5.577164 CGTCGGAGAATTTCTTAGTTCACAT 59.423 40.000 0.00 0.00 39.69 3.21
1772 2236 1.862201 CCAGACACAAACGTTTAGCGA 59.138 47.619 14.20 0.00 44.77 4.93
1780 2244 7.539712 AGATTTATATGTCCAGACACAAACG 57.460 36.000 1.88 0.00 45.05 3.60
1878 2342 2.664851 TGCCGACGGAGCAAAGTG 60.665 61.111 20.50 0.00 37.28 3.16
1882 2347 1.600511 TATCACTGCCGACGGAGCAA 61.601 55.000 20.50 4.61 40.35 3.91
1913 2378 0.682209 GGCAGAGCATTGTGGGTGAT 60.682 55.000 0.00 0.00 0.00 3.06
2231 2699 1.373497 GTCTGCCTGTGGTGAGTCG 60.373 63.158 0.00 0.00 0.00 4.18
2389 2857 0.038166 AGTCATCAACGGCAACCCAT 59.962 50.000 0.00 0.00 0.00 4.00
2435 2903 0.393077 CTTCCTCACTTGACCGTGGT 59.607 55.000 0.00 0.00 35.63 4.16
2438 2906 0.759346 AAGCTTCCTCACTTGACCGT 59.241 50.000 0.00 0.00 0.00 4.83
2444 2912 2.487986 CCACCAAGAAGCTTCCTCACTT 60.488 50.000 22.81 7.44 0.00 3.16
2585 3053 1.993370 GTTGCTACAACTGGCGTAGAG 59.007 52.381 9.21 0.00 38.94 2.43
2590 3058 0.320771 AGGAGTTGCTACAACTGGCG 60.321 55.000 17.11 0.00 0.00 5.69
2836 3304 0.110192 GGCTGCACGCTTTAACTGTC 60.110 55.000 0.50 0.00 39.13 3.51
2905 3373 3.808466 TCTGAATTCCACTCTCCATCG 57.192 47.619 2.27 0.00 0.00 3.84
2952 3420 2.298163 CTGCTTTGCTTCCTTGACCAAT 59.702 45.455 0.00 0.00 0.00 3.16
3090 3558 1.310933 CCACTTCCCATCAGCTGCAC 61.311 60.000 9.47 0.00 0.00 4.57
3103 3571 3.238108 TGCTTCTCTCGATTCCACTTC 57.762 47.619 0.00 0.00 0.00 3.01
3104 3572 3.685139 TTGCTTCTCTCGATTCCACTT 57.315 42.857 0.00 0.00 0.00 3.16
3157 3625 2.575532 TGTCCTTCACTTCTGCTTTGG 58.424 47.619 0.00 0.00 0.00 3.28
3318 3786 1.226379 CGGCCGCACAATTTAGCTG 60.226 57.895 14.67 0.00 0.00 4.24
3326 3794 4.858680 TGACCAACGGCCGCACAA 62.859 61.111 28.58 2.92 0.00 3.33
3332 3800 3.047877 CGTTCCTGACCAACGGCC 61.048 66.667 0.00 0.00 42.36 6.13
3338 3806 0.108186 CTGCTATGCGTTCCTGACCA 60.108 55.000 0.00 0.00 0.00 4.02
3352 3820 1.202582 GACTGTCCTTCGCTTCTGCTA 59.797 52.381 0.00 0.00 36.97 3.49
3376 3844 0.877071 ATTTTCCGTCAGCTGCACAG 59.123 50.000 9.47 1.06 0.00 3.66
3377 3845 2.177394 TATTTTCCGTCAGCTGCACA 57.823 45.000 9.47 0.00 0.00 4.57
3379 3847 4.782019 ATTTTATTTTCCGTCAGCTGCA 57.218 36.364 9.47 0.00 0.00 4.41
3388 3856 7.905493 GCTCACTTCTCTGTATTTTATTTTCCG 59.095 37.037 0.00 0.00 0.00 4.30
3392 3860 8.515414 GGTTGCTCACTTCTCTGTATTTTATTT 58.485 33.333 0.00 0.00 0.00 1.40
3413 3881 1.864565 AAATTTCACGCTTGGGTTGC 58.135 45.000 0.00 0.00 0.00 4.17
3416 3884 2.169561 ACCAAAAATTTCACGCTTGGGT 59.830 40.909 18.37 1.87 40.74 4.51
3419 3887 3.490526 CCTGACCAAAAATTTCACGCTTG 59.509 43.478 0.00 0.00 0.00 4.01
3430 3898 2.098443 GCTTCACGTTCCTGACCAAAAA 59.902 45.455 0.00 0.00 0.00 1.94
3519 3987 1.953559 TCACACTGCTGACCAAAGAC 58.046 50.000 0.00 0.00 0.00 3.01
3520 3988 2.564771 CTTCACACTGCTGACCAAAGA 58.435 47.619 0.00 0.00 0.00 2.52
3521 3989 1.002033 GCTTCACACTGCTGACCAAAG 60.002 52.381 0.00 0.00 0.00 2.77
3522 3990 1.024271 GCTTCACACTGCTGACCAAA 58.976 50.000 0.00 0.00 0.00 3.28
3523 3991 0.107263 TGCTTCACACTGCTGACCAA 60.107 50.000 0.00 0.00 0.00 3.67
3526 3994 1.530293 CTTCTGCTTCACACTGCTGAC 59.470 52.381 0.00 0.00 37.00 3.51
3527 3995 1.413812 TCTTCTGCTTCACACTGCTGA 59.586 47.619 0.00 0.00 35.83 4.26
3528 3996 1.875009 TCTTCTGCTTCACACTGCTG 58.125 50.000 0.00 0.00 0.00 4.41
3529 3997 2.627515 TTCTTCTGCTTCACACTGCT 57.372 45.000 0.00 0.00 0.00 4.24
3530 3998 3.625938 CTTTTCTTCTGCTTCACACTGC 58.374 45.455 0.00 0.00 0.00 4.40
3531 3999 3.065786 TGCTTTTCTTCTGCTTCACACTG 59.934 43.478 0.00 0.00 0.00 3.66
3532 4000 3.282021 TGCTTTTCTTCTGCTTCACACT 58.718 40.909 0.00 0.00 0.00 3.55
3533 4001 3.698029 TGCTTTTCTTCTGCTTCACAC 57.302 42.857 0.00 0.00 0.00 3.82
3534 4002 5.180117 GTCTATGCTTTTCTTCTGCTTCACA 59.820 40.000 0.00 0.00 0.00 3.58
3569 4046 3.181456 GGATTCCACTCTCCTCCATCAAG 60.181 52.174 0.00 0.00 0.00 3.02
3624 4101 5.390673 GCTCATCGATGCAATCTTTCATAGG 60.391 44.000 20.81 0.00 42.58 2.57
3740 4217 9.244799 CAAACAAGGACAAATTAAAAGGTCTAC 57.755 33.333 0.00 0.00 0.00 2.59
3742 4219 7.847096 ACAAACAAGGACAAATTAAAAGGTCT 58.153 30.769 0.00 0.00 0.00 3.85
3829 4323 6.074088 GCCATGTTCGTCACTGAAGATATTAG 60.074 42.308 0.00 0.00 31.35 1.73
3846 4340 6.293027 CCAAGAGAAAAACATTTGCCATGTTC 60.293 38.462 10.85 1.36 40.94 3.18
3859 4353 9.237846 CAGTTTCATTAAGACCAAGAGAAAAAC 57.762 33.333 0.00 0.00 0.00 2.43
3860 4354 9.184523 TCAGTTTCATTAAGACCAAGAGAAAAA 57.815 29.630 0.00 0.00 0.00 1.94
3887 4381 2.546899 AGTGGCTACCAGGATTGTGTA 58.453 47.619 0.00 0.00 32.34 2.90
3922 4416 1.070038 TAACGAACGCGGAACATTCC 58.930 50.000 12.47 0.09 44.05 3.01
3923 4417 2.859870 TTAACGAACGCGGAACATTC 57.140 45.000 12.47 3.38 43.17 2.67
3924 4418 2.737783 TGATTAACGAACGCGGAACATT 59.262 40.909 12.47 0.00 43.17 2.71
3925 4419 2.339418 TGATTAACGAACGCGGAACAT 58.661 42.857 12.47 0.00 43.17 2.71
3926 4420 1.780806 TGATTAACGAACGCGGAACA 58.219 45.000 12.47 0.00 43.17 3.18
3927 4421 2.096811 TGTTGATTAACGAACGCGGAAC 60.097 45.455 12.47 0.00 43.17 3.62
3928 4422 2.133553 TGTTGATTAACGAACGCGGAA 58.866 42.857 12.47 0.00 43.17 4.30
3929 4423 1.780806 TGTTGATTAACGAACGCGGA 58.219 45.000 12.47 0.00 43.17 5.54
3930 4424 2.159761 ACATGTTGATTAACGAACGCGG 60.160 45.455 12.47 0.00 43.17 6.46
3931 4425 3.098381 ACATGTTGATTAACGAACGCG 57.902 42.857 3.53 3.53 39.71 6.01
3932 4426 5.447846 CACATACATGTTGATTAACGAACGC 59.552 40.000 2.30 0.00 39.39 4.84
3933 4427 5.447846 GCACATACATGTTGATTAACGAACG 59.552 40.000 2.30 0.00 39.39 3.95
3934 4428 6.542852 AGCACATACATGTTGATTAACGAAC 58.457 36.000 2.30 0.00 39.39 3.95
3935 4429 6.735678 AGCACATACATGTTGATTAACGAA 57.264 33.333 2.30 0.00 39.39 3.85
3936 4430 9.705290 ATATAGCACATACATGTTGATTAACGA 57.295 29.630 2.30 0.00 39.39 3.85
3997 4574 8.980143 ACATTTTTATTGAAACGGGATTAGTG 57.020 30.769 0.00 0.00 0.00 2.74
4001 4578 7.666623 ACTGACATTTTTATTGAAACGGGATT 58.333 30.769 0.00 0.00 0.00 3.01
4035 4612 6.716628 TCAGTGAGCTTTTTGGTATCATTTCT 59.283 34.615 0.00 0.00 0.00 2.52
4039 4616 5.591877 GGATCAGTGAGCTTTTTGGTATCAT 59.408 40.000 8.52 0.00 0.00 2.45
4042 4619 4.273318 GGGATCAGTGAGCTTTTTGGTAT 58.727 43.478 8.52 0.00 0.00 2.73
4044 4621 2.519013 GGGATCAGTGAGCTTTTTGGT 58.481 47.619 8.52 0.00 0.00 3.67
4045 4622 1.470098 CGGGATCAGTGAGCTTTTTGG 59.530 52.381 8.52 0.00 0.00 3.28
4046 4623 2.154462 ACGGGATCAGTGAGCTTTTTG 58.846 47.619 8.52 0.00 0.00 2.44
4047 4624 2.568623 ACGGGATCAGTGAGCTTTTT 57.431 45.000 8.52 0.00 0.00 1.94
4048 4625 2.568623 AACGGGATCAGTGAGCTTTT 57.431 45.000 8.52 0.00 0.00 2.27
4049 4626 2.567615 AGTAACGGGATCAGTGAGCTTT 59.432 45.455 8.52 2.41 0.00 3.51
4050 4627 2.180276 AGTAACGGGATCAGTGAGCTT 58.820 47.619 8.52 0.00 0.00 3.74
4051 4628 1.853963 AGTAACGGGATCAGTGAGCT 58.146 50.000 8.52 0.00 0.00 4.09
4052 4629 2.674796 AAGTAACGGGATCAGTGAGC 57.325 50.000 0.00 0.00 0.00 4.26
4053 4630 5.326200 ACTAAAGTAACGGGATCAGTGAG 57.674 43.478 0.00 0.00 0.00 3.51
4054 4631 5.733620 AACTAAAGTAACGGGATCAGTGA 57.266 39.130 0.00 0.00 0.00 3.41
4055 4632 5.121768 CCAAACTAAAGTAACGGGATCAGTG 59.878 44.000 0.00 0.00 0.00 3.66
4056 4633 5.243207 CCAAACTAAAGTAACGGGATCAGT 58.757 41.667 0.00 0.00 0.00 3.41
4057 4634 4.094442 GCCAAACTAAAGTAACGGGATCAG 59.906 45.833 0.00 0.00 0.00 2.90
4058 4635 4.004982 GCCAAACTAAAGTAACGGGATCA 58.995 43.478 0.00 0.00 0.00 2.92
4059 4636 4.004982 TGCCAAACTAAAGTAACGGGATC 58.995 43.478 0.00 0.00 0.00 3.36
4060 4637 4.023726 TGCCAAACTAAAGTAACGGGAT 57.976 40.909 0.00 0.00 0.00 3.85
4061 4638 3.488778 TGCCAAACTAAAGTAACGGGA 57.511 42.857 0.00 0.00 0.00 5.14
4062 4639 4.571372 TTTGCCAAACTAAAGTAACGGG 57.429 40.909 0.00 0.00 0.00 5.28
4063 4640 6.443792 AGAATTTGCCAAACTAAAGTAACGG 58.556 36.000 0.00 0.00 0.00 4.44
4064 4641 7.924103 AAGAATTTGCCAAACTAAAGTAACG 57.076 32.000 0.00 0.00 0.00 3.18
4119 4715 3.904136 AAAGTTTGCATGTCCGAAGAG 57.096 42.857 0.00 0.00 0.00 2.85
4128 4724 6.215845 ACTTGCCTAACTAAAAGTTTGCATG 58.784 36.000 18.06 18.06 41.26 4.06
4164 4760 7.732996 AGAACTTGCCTAACTAAAGTAGTTCA 58.267 34.615 17.22 0.00 45.38 3.18
4165 4761 8.604640 AAGAACTTGCCTAACTAAAGTAGTTC 57.395 34.615 3.99 10.94 45.38 3.01
4281 4893 5.026790 AGACTAGTGAGCAAGGAAGGTAAT 58.973 41.667 0.00 0.00 0.00 1.89
4352 4964 4.057224 CACTAGGCGTGGTTTGCA 57.943 55.556 0.00 0.00 40.02 4.08
4371 4983 3.292492 AAAACCGGTCTCCTTTTCACT 57.708 42.857 8.04 0.00 0.00 3.41
4473 5085 3.616560 GCATCAAGTCTTCTTCACGGGTA 60.617 47.826 0.00 0.00 0.00 3.69
4557 5169 1.164411 TGCGCAAGTCGAATCCAAAT 58.836 45.000 8.16 0.00 41.67 2.32
4566 5178 1.291184 TGAGATGGTTGCGCAAGTCG 61.291 55.000 25.78 0.00 42.12 4.18
4632 5244 0.329261 CTTTGAGATGGTGGCTCCCA 59.671 55.000 2.66 0.68 39.27 4.37
4983 5610 2.669569 GTGCAGCCACCGACATGT 60.670 61.111 0.00 0.00 35.92 3.21
5131 5814 5.950758 AATCAGCTCTCTATCGAATACGT 57.049 39.130 0.00 0.00 40.69 3.57
5133 5816 7.027161 GGAGAAATCAGCTCTCTATCGAATAC 58.973 42.308 0.00 0.00 39.48 1.89
5135 5818 5.335583 CGGAGAAATCAGCTCTCTATCGAAT 60.336 44.000 0.00 0.00 39.48 3.34
5141 5824 5.221342 GGAAATCGGAGAAATCAGCTCTCTA 60.221 44.000 0.55 0.00 43.58 2.43
5216 5909 6.289834 TCGAAACCAAATTACACAAGGTAGA 58.710 36.000 0.00 0.00 32.49 2.59
5227 5920 8.630278 TTTCAAACGAAATCGAAACCAAATTA 57.370 26.923 10.16 0.00 43.02 1.40
5234 6285 5.164320 CCGACATTTCAAACGAAATCGAAAC 60.164 40.000 10.16 0.00 40.38 2.78
5461 6520 3.064207 TGAGATCTTGTTTACACGGCAC 58.936 45.455 0.00 0.00 0.00 5.01
5510 6569 2.076863 GAGTTTCAACGGTGAGGATGG 58.923 52.381 2.09 0.00 34.49 3.51
5524 6583 1.786928 CGAAATGCCGAAGCGAGTTTC 60.787 52.381 0.00 0.00 44.31 2.78
5628 6690 2.096218 CGAGGAAAAGGAGCGTGAAAAG 60.096 50.000 0.00 0.00 0.00 2.27
5661 6723 1.254284 CGGGAGAGGAGAACAGCAGT 61.254 60.000 0.00 0.00 0.00 4.40
5705 6767 1.682684 GAGAGGAACCTGAGGCCGA 60.683 63.158 0.00 0.00 0.00 5.54
5728 6796 2.510238 GTGGTAGCAGAGCAGCCG 60.510 66.667 0.00 0.00 35.85 5.52
5729 6797 2.124942 GGTGGTAGCAGAGCAGCC 60.125 66.667 8.38 0.00 46.12 4.85
5828 6915 4.169696 TTACCATGCGGCGGAGGG 62.170 66.667 30.01 30.01 34.57 4.30
5840 6927 1.758280 ACAGTGACTTGACGGTTACCA 59.242 47.619 1.13 0.00 0.00 3.25
5851 6938 2.584236 AGGTACGAGTGACAGTGACTT 58.416 47.619 0.00 0.00 0.00 3.01
5866 6953 2.038164 ACCAAAACCGAGGAGAAGGTAC 59.962 50.000 0.00 0.00 40.37 3.34
5967 12118 3.350219 TTGTAGAGAAAGGCATCCCAC 57.650 47.619 0.00 0.00 0.00 4.61
5968 12119 4.591321 AATTGTAGAGAAAGGCATCCCA 57.409 40.909 0.00 0.00 0.00 4.37
5969 12120 7.939588 AGTATAAATTGTAGAGAAAGGCATCCC 59.060 37.037 0.00 0.00 0.00 3.85
5970 12121 8.910351 AGTATAAATTGTAGAGAAAGGCATCC 57.090 34.615 0.00 0.00 0.00 3.51
6011 12162 2.936919 TGTGCCTCACAAACAGATCT 57.063 45.000 0.00 0.00 41.69 2.75
6113 12267 4.559502 GCTCTACAACATATGATCTGCCGA 60.560 45.833 10.38 3.57 0.00 5.54
6116 12270 3.677121 CCGCTCTACAACATATGATCTGC 59.323 47.826 10.38 3.64 0.00 4.26
6158 12312 3.990469 CAGCGTGACAAGAATTCTACACT 59.010 43.478 24.26 12.13 0.00 3.55


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

AutoCloner maintained by Alex Coulton.