Multiple sequence alignment - TraesCS2A01G456300

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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 TraesCS2A01G456300 chr2A 100.000 4244 0 0 1 4244 705067342 705071585 0.000000e+00 7838.0
1 TraesCS2A01G456300 chr2B 92.523 2394 136 25 1880 4244 675515119 675517498 0.000000e+00 3389.0
2 TraesCS2A01G456300 chr2B 93.362 1401 59 19 1 1380 675513398 675514785 0.000000e+00 2041.0
3 TraesCS2A01G456300 chr2B 90.260 154 10 5 1499 1649 783655430 783655581 3.350000e-46 196.0
4 TraesCS2A01G456300 chr2B 88.820 161 11 6 1501 1657 646471748 646471905 1.560000e-44 191.0
5 TraesCS2A01G456300 chr2B 90.071 141 9 2 1365 1504 675514801 675514937 1.210000e-40 178.0
6 TraesCS2A01G456300 chr2D 91.503 2448 162 26 1818 4242 564384798 564387222 0.000000e+00 3326.0
7 TraesCS2A01G456300 chr2D 95.394 1346 45 13 71 1408 564382939 564384275 0.000000e+00 2126.0
8 TraesCS2A01G456300 chr2D 96.104 77 2 1 1631 1706 564384476 564384552 1.600000e-24 124.0
9 TraesCS2A01G456300 chr2D 100.000 29 0 0 1 29 564382897 564382925 2.000000e-03 54.7
10 TraesCS2A01G456300 chr3B 92.308 143 9 2 1492 1632 520452793 520452935 7.200000e-48 202.0
11 TraesCS2A01G456300 chr3B 85.542 83 10 2 1234 1315 823029116 823029197 7.560000e-13 86.1
12 TraesCS2A01G456300 chr5D 88.272 162 11 8 1501 1657 95238901 95239059 2.010000e-43 187.0
13 TraesCS2A01G456300 chr5D 88.272 162 11 7 1501 1657 391135410 391135568 2.010000e-43 187.0
14 TraesCS2A01G456300 chr4D 88.272 162 11 7 1501 1657 238379219 238379377 2.010000e-43 187.0
15 TraesCS2A01G456300 chr4D 88.272 162 11 7 1501 1657 344231840 344231998 2.010000e-43 187.0
16 TraesCS2A01G456300 chr4D 88.272 162 11 7 1501 1657 349491922 349492080 2.010000e-43 187.0
17 TraesCS2A01G456300 chr4D 77.778 180 30 9 1114 1288 423429856 423429682 7.510000e-18 102.0
18 TraesCS2A01G456300 chr3A 88.535 157 14 4 1471 1625 739559884 739560038 2.010000e-43 187.0
19 TraesCS2A01G456300 chr3A 76.471 187 21 15 1124 1288 749469722 749469907 3.520000e-11 80.5
20 TraesCS2A01G456300 chr4B 79.121 182 28 9 1112 1288 519824622 519824446 2.680000e-22 117.0
21 TraesCS2A01G456300 chr5A 79.762 168 26 7 1125 1288 592638861 592638698 9.640000e-22 115.0
22 TraesCS2A01G456300 chr5B 80.645 155 22 7 1138 1288 580366684 580366534 3.470000e-21 113.0
23 TraesCS2A01G456300 chr4A 77.778 180 30 9 1114 1288 40860220 40860394 7.510000e-18 102.0


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 TraesCS2A01G456300 chr2A 705067342 705071585 4243 False 7838.000000 7838 100.000000 1 4244 1 chr2A.!!$F1 4243
1 TraesCS2A01G456300 chr2B 675513398 675517498 4100 False 1869.333333 3389 91.985333 1 4244 3 chr2B.!!$F3 4243
2 TraesCS2A01G456300 chr2D 564382897 564387222 4325 False 1407.675000 3326 95.750250 1 4242 4 chr2D.!!$F1 4241

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
538 549 0.314578 CGCTGCAATCTCGCTTTACG 60.315 55.0 0.0 0.0 45.62 3.18 F
1341 1362 0.535797 CGTACTGTCCCCTTCCTTCC 59.464 60.0 0.0 0.0 0.00 3.46 F
1627 1791 0.036952 TTCGGACGGAGAGAGTACGT 60.037 55.0 0.0 0.0 45.42 3.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1608 1772 0.036952 ACGTACTCTCTCCGTCCGAA 60.037 55.0 0.00 0.0 0.00 4.30 R
2799 3127 0.672711 GGTTCGTAAGGTGCTCCCAC 60.673 60.0 0.00 0.0 41.32 4.61 R
3439 3783 0.457337 GAACGTCGTCGGGCTAACAT 60.457 55.0 7.05 0.0 41.85 2.71 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
29 30 0.621082 TCTCTCCTCTTCTCTCGGCA 59.379 55.000 0.00 0.00 0.00 5.69
33 34 2.581953 CTCTTCTCTCGGCAGCGC 60.582 66.667 0.00 0.00 0.00 5.92
137 142 0.547075 AGCGCCTCCACTAGACTAGA 59.453 55.000 16.55 0.00 0.00 2.43
222 227 3.482783 GCGCCAACTGCTCGACTC 61.483 66.667 0.00 0.00 38.05 3.36
223 228 3.175240 CGCCAACTGCTCGACTCG 61.175 66.667 0.00 0.00 38.05 4.18
224 229 2.258591 GCCAACTGCTCGACTCGA 59.741 61.111 0.29 0.29 36.87 4.04
282 287 0.591170 TTCTCCCGCGCTTTTTCTTG 59.409 50.000 5.56 0.00 0.00 3.02
289 294 0.848305 GCGCTTTTTCTTGCACACAG 59.152 50.000 0.00 0.00 0.00 3.66
363 374 4.741342 ACTTATAACAGTACAGTGCGTCC 58.259 43.478 0.00 0.00 0.00 4.79
495 506 2.125391 GTCCGGCGACCCCTTTAC 60.125 66.667 9.30 0.00 32.40 2.01
538 549 0.314578 CGCTGCAATCTCGCTTTACG 60.315 55.000 0.00 0.00 45.62 3.18
539 550 0.721718 GCTGCAATCTCGCTTTACGT 59.278 50.000 0.00 0.00 44.19 3.57
540 551 1.924524 GCTGCAATCTCGCTTTACGTA 59.075 47.619 0.00 0.00 44.19 3.57
541 552 2.285084 GCTGCAATCTCGCTTTACGTAC 60.285 50.000 0.00 0.00 44.19 3.67
669 684 3.821033 GCAAGTACCTGAAAACCATCACT 59.179 43.478 0.00 0.00 0.00 3.41
871 886 4.926207 GGTACGTAGGCACAAGGG 57.074 61.111 0.00 0.00 0.00 3.95
872 887 2.279842 GGTACGTAGGCACAAGGGA 58.720 57.895 0.00 0.00 0.00 4.20
873 888 0.609662 GGTACGTAGGCACAAGGGAA 59.390 55.000 0.00 0.00 0.00 3.97
875 890 0.899720 TACGTAGGCACAAGGGAAGG 59.100 55.000 0.00 0.00 0.00 3.46
876 891 1.078426 CGTAGGCACAAGGGAAGGG 60.078 63.158 0.00 0.00 0.00 3.95
877 892 1.303282 GTAGGCACAAGGGAAGGGG 59.697 63.158 0.00 0.00 0.00 4.79
878 893 1.151677 TAGGCACAAGGGAAGGGGT 60.152 57.895 0.00 0.00 0.00 4.95
1207 1228 1.534235 AACGAGGTGCTGGAGGACT 60.534 57.895 0.00 0.00 36.56 3.85
1290 1311 2.498941 CGAGGCCTCCCGCTTCATA 61.499 63.158 27.20 0.00 43.65 2.15
1302 1323 2.213499 CGCTTCATATCCAACCACCTC 58.787 52.381 0.00 0.00 0.00 3.85
1341 1362 0.535797 CGTACTGTCCCCTTCCTTCC 59.464 60.000 0.00 0.00 0.00 3.46
1369 1424 7.201635 CCCCATTTATTTCAGCTATGTTTTTGC 60.202 37.037 0.00 0.00 0.00 3.68
1418 1576 6.143919 GCTTACAAATTGGTAGCAGTTGTTTC 59.856 38.462 23.00 13.19 34.43 2.78
1469 1633 4.466828 CACTATGCAGTAACACAACTTGC 58.533 43.478 0.00 0.00 32.21 4.01
1507 1671 8.119062 AGGATTTTCCTTGATTTATACTCCCT 57.881 34.615 0.00 0.00 46.91 4.20
1508 1672 8.221251 AGGATTTTCCTTGATTTATACTCCCTC 58.779 37.037 0.00 0.00 46.91 4.30
1509 1673 7.448777 GGATTTTCCTTGATTTATACTCCCTCC 59.551 40.741 0.00 0.00 32.53 4.30
1510 1674 5.546621 TTCCTTGATTTATACTCCCTCCG 57.453 43.478 0.00 0.00 0.00 4.63
1511 1675 4.553678 TCCTTGATTTATACTCCCTCCGT 58.446 43.478 0.00 0.00 0.00 4.69
1512 1676 4.587684 TCCTTGATTTATACTCCCTCCGTC 59.412 45.833 0.00 0.00 0.00 4.79
1513 1677 4.262506 CCTTGATTTATACTCCCTCCGTCC 60.263 50.000 0.00 0.00 0.00 4.79
1514 1678 2.889045 TGATTTATACTCCCTCCGTCCG 59.111 50.000 0.00 0.00 0.00 4.79
1515 1679 2.734755 TTTATACTCCCTCCGTCCGA 57.265 50.000 0.00 0.00 0.00 4.55
1516 1680 2.734755 TTATACTCCCTCCGTCCGAA 57.265 50.000 0.00 0.00 0.00 4.30
1517 1681 2.734755 TATACTCCCTCCGTCCGAAA 57.265 50.000 0.00 0.00 0.00 3.46
1518 1682 1.856629 ATACTCCCTCCGTCCGAAAA 58.143 50.000 0.00 0.00 0.00 2.29
1519 1683 1.856629 TACTCCCTCCGTCCGAAAAT 58.143 50.000 0.00 0.00 0.00 1.82
1520 1684 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
1521 1685 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
1522 1686 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
1523 1687 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
1524 1688 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
1525 1689 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
1526 1690 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
1527 1691 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
1528 1692 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
1529 1693 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
1530 1694 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
1531 1695 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
1532 1696 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
1533 1697 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
1534 1698 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
1535 1699 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
1536 1700 7.273381 GTCCGAAAATACTTGTCATCAAAATGG 59.727 37.037 0.00 0.00 33.42 3.16
1537 1701 7.175816 TCCGAAAATACTTGTCATCAAAATGGA 59.824 33.333 0.00 0.00 33.42 3.41
1538 1702 7.273381 CCGAAAATACTTGTCATCAAAATGGAC 59.727 37.037 0.00 0.00 33.42 4.02
1539 1703 7.807433 CGAAAATACTTGTCATCAAAATGGACA 59.193 33.333 0.00 0.00 33.42 4.02
1540 1704 9.474920 GAAAATACTTGTCATCAAAATGGACAA 57.525 29.630 0.00 0.00 34.59 3.18
1541 1705 9.829507 AAAATACTTGTCATCAAAATGGACAAA 57.170 25.926 7.70 0.00 34.98 2.83
1542 1706 9.829507 AAATACTTGTCATCAAAATGGACAAAA 57.170 25.926 7.70 0.84 34.98 2.44
1543 1707 9.829507 AATACTTGTCATCAAAATGGACAAAAA 57.170 25.926 7.70 0.55 34.98 1.94
1545 1709 8.145316 ACTTGTCATCAAAATGGACAAAAATG 57.855 30.769 7.70 0.11 34.98 2.32
1546 1710 7.986320 ACTTGTCATCAAAATGGACAAAAATGA 59.014 29.630 7.70 0.00 34.98 2.57
1547 1711 7.949903 TGTCATCAAAATGGACAAAAATGAG 57.050 32.000 0.00 0.00 33.42 2.90
1548 1712 7.499292 TGTCATCAAAATGGACAAAAATGAGT 58.501 30.769 0.00 0.00 33.42 3.41
1549 1713 7.438757 TGTCATCAAAATGGACAAAAATGAGTG 59.561 33.333 0.00 0.00 33.42 3.51
1550 1714 7.439056 GTCATCAAAATGGACAAAAATGAGTGT 59.561 33.333 0.00 0.00 33.42 3.55
1551 1715 8.637099 TCATCAAAATGGACAAAAATGAGTGTA 58.363 29.630 0.00 0.00 33.42 2.90
1552 1716 9.426837 CATCAAAATGGACAAAAATGAGTGTAT 57.573 29.630 0.00 0.00 0.00 2.29
1553 1717 9.643693 ATCAAAATGGACAAAAATGAGTGTATC 57.356 29.630 0.00 0.00 0.00 2.24
1554 1718 8.859090 TCAAAATGGACAAAAATGAGTGTATCT 58.141 29.630 0.00 0.00 0.00 1.98
1560 1724 9.349713 TGGACAAAAATGAGTGTATCTAAAACT 57.650 29.630 0.00 0.00 0.00 2.66
1614 1778 9.834628 TTATTTTGATGACAAGTATTTTCGGAC 57.165 29.630 0.00 0.00 37.32 4.79
1615 1779 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
1616 1780 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
1617 1781 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
1618 1782 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
1619 1783 3.256383 TGACAAGTATTTTCGGACGGAGA 59.744 43.478 0.00 0.00 0.00 3.71
1620 1784 3.846360 ACAAGTATTTTCGGACGGAGAG 58.154 45.455 0.00 0.00 0.00 3.20
1621 1785 3.508793 ACAAGTATTTTCGGACGGAGAGA 59.491 43.478 0.00 0.00 0.00 3.10
1622 1786 4.106197 CAAGTATTTTCGGACGGAGAGAG 58.894 47.826 0.00 0.00 0.00 3.20
1623 1787 3.354467 AGTATTTTCGGACGGAGAGAGT 58.646 45.455 0.00 0.00 0.00 3.24
1624 1788 4.521146 AGTATTTTCGGACGGAGAGAGTA 58.479 43.478 0.00 0.00 0.00 2.59
1625 1789 3.779271 ATTTTCGGACGGAGAGAGTAC 57.221 47.619 0.00 0.00 0.00 2.73
1626 1790 1.081892 TTTCGGACGGAGAGAGTACG 58.918 55.000 0.00 0.00 46.50 3.67
1627 1791 0.036952 TTCGGACGGAGAGAGTACGT 60.037 55.000 0.00 0.00 45.42 3.57
1628 1792 0.817654 TCGGACGGAGAGAGTACGTA 59.182 55.000 0.82 0.00 45.42 3.57
1629 1793 0.926846 CGGACGGAGAGAGTACGTAC 59.073 60.000 18.10 18.10 40.75 3.67
1630 1794 1.470632 CGGACGGAGAGAGTACGTACT 60.471 57.143 27.71 27.71 40.75 2.73
1631 1795 2.223595 CGGACGGAGAGAGTACGTACTA 60.224 54.545 27.44 0.00 40.75 1.82
1632 1796 3.120041 GGACGGAGAGAGTACGTACTAC 58.880 54.545 27.44 22.26 41.40 2.73
1633 1797 3.181480 GGACGGAGAGAGTACGTACTACT 60.181 52.174 27.44 25.96 41.40 2.57
1636 1800 3.980775 CGGAGAGAGTACGTACTACTAGC 59.019 52.174 27.44 14.85 35.66 3.42
1743 1988 7.393234 AGCTATTTTTATCTGTGCCACTGTAAA 59.607 33.333 0.00 1.71 0.00 2.01
1752 1997 2.159627 GTGCCACTGTAAAGACGAATGG 59.840 50.000 0.00 0.00 0.00 3.16
1755 2000 3.689649 GCCACTGTAAAGACGAATGGAAT 59.310 43.478 0.00 0.00 29.83 3.01
1756 2001 4.156008 GCCACTGTAAAGACGAATGGAATT 59.844 41.667 0.00 0.00 40.93 2.17
1768 2013 8.066612 AGACGAATGGAATTTTGAAATACCAT 57.933 30.769 0.00 0.00 36.07 3.55
1769 2014 8.531146 AGACGAATGGAATTTTGAAATACCATT 58.469 29.630 17.12 17.12 46.31 3.16
1770 2015 9.150348 GACGAATGGAATTTTGAAATACCATTT 57.850 29.630 17.72 8.82 44.55 2.32
1780 2063 5.720371 TGAAATACCATTTGTCCAACTGG 57.280 39.130 13.16 13.16 44.05 4.00
1785 2068 2.698274 ACCATTTGTCCAACTGGGTTTC 59.302 45.455 17.49 0.00 43.13 2.78
1789 2072 2.818751 TGTCCAACTGGGTTTCACTT 57.181 45.000 0.00 0.00 38.11 3.16
1792 2075 4.601084 TGTCCAACTGGGTTTCACTTTTA 58.399 39.130 0.00 0.00 38.11 1.52
1793 2076 5.205056 TGTCCAACTGGGTTTCACTTTTAT 58.795 37.500 0.00 0.00 38.11 1.40
1794 2077 5.300792 TGTCCAACTGGGTTTCACTTTTATC 59.699 40.000 0.00 0.00 38.11 1.75
1816 2099 6.748333 TCTTACTTCCTTTGATGATTGCTG 57.252 37.500 0.00 0.00 0.00 4.41
1827 2126 2.785540 TGATTGCTGCACCTCACATA 57.214 45.000 0.00 0.00 0.00 2.29
1829 2128 3.208594 TGATTGCTGCACCTCACATATC 58.791 45.455 0.00 0.44 0.00 1.63
1838 2137 3.812053 GCACCTCACATATCCTGATTCAC 59.188 47.826 0.00 0.00 0.00 3.18
1841 2140 4.723789 ACCTCACATATCCTGATTCACCTT 59.276 41.667 0.00 0.00 0.00 3.50
1848 2147 2.907892 TCCTGATTCACCTTCCTGACT 58.092 47.619 0.00 0.00 0.00 3.41
1852 2151 6.202331 TCCTGATTCACCTTCCTGACTATTA 58.798 40.000 0.00 0.00 0.00 0.98
1855 2154 8.651389 CCTGATTCACCTTCCTGACTATTATTA 58.349 37.037 0.00 0.00 0.00 0.98
1856 2155 9.703892 CTGATTCACCTTCCTGACTATTATTAG 57.296 37.037 0.00 0.00 0.00 1.73
1859 2158 7.973048 TCACCTTCCTGACTATTATTAGTGT 57.027 36.000 2.07 0.00 38.81 3.55
1931 2256 8.487028 TGTTTACCCATTTTTAATGGAAACTGT 58.513 29.630 22.65 14.49 41.64 3.55
2025 2350 1.003233 GGAAGGCTTCCTGTCGCTT 60.003 57.895 33.93 0.00 46.57 4.68
2109 2434 5.473162 TGGTGTCATATGGAGAAAAACACTG 59.527 40.000 16.55 0.00 36.62 3.66
2244 2569 4.165758 AGGCAGGAGCTTAAATCTCTTCAT 59.834 41.667 0.00 0.00 41.70 2.57
2268 2593 5.645067 TCCTGATGATTCACAGATTGTTGTC 59.355 40.000 14.14 0.00 36.38 3.18
2333 2658 8.975439 GGTATACAATACAGACCTTTTATCACG 58.025 37.037 5.01 0.00 0.00 4.35
2338 2663 2.280628 CAGACCTTTTATCACGAGCCC 58.719 52.381 0.00 0.00 0.00 5.19
2353 2681 2.808543 CGAGCCCTGTATTTATGAAGCC 59.191 50.000 0.00 0.00 0.00 4.35
2364 2692 7.122715 TGTATTTATGAAGCCTGGGTAAACAT 58.877 34.615 0.00 8.37 0.00 2.71
2365 2693 8.275758 TGTATTTATGAAGCCTGGGTAAACATA 58.724 33.333 0.00 7.43 0.00 2.29
2366 2694 7.582667 ATTTATGAAGCCTGGGTAAACATAC 57.417 36.000 14.93 0.00 0.00 2.39
2368 2696 3.950397 TGAAGCCTGGGTAAACATACAG 58.050 45.455 0.00 0.00 0.00 2.74
2506 2834 1.194781 AGGTGGTCACTAGGTGCAGG 61.195 60.000 0.00 0.00 32.98 4.85
2614 2942 1.327764 GGAACATTCGTCTGATTCGCC 59.672 52.381 0.00 0.00 0.00 5.54
2745 3073 3.914426 ACTTCCGAGCCATCAATAAGT 57.086 42.857 0.00 0.00 0.00 2.24
2787 3115 7.271223 CCACAAGATAGTTTTGTTATCTTTGCG 59.729 37.037 5.10 0.00 42.36 4.85
2799 3127 1.368641 TCTTTGCGTCGGATGGATTG 58.631 50.000 0.00 0.00 0.00 2.67
2814 3142 1.369625 GATTGTGGGAGCACCTTACG 58.630 55.000 0.00 0.00 41.11 3.18
2848 3176 3.296628 GTCGAAATCGTGCACAACAATT 58.703 40.909 18.64 7.71 40.80 2.32
2860 3188 3.966218 GCACAACAATTCACGTGAAGTAC 59.034 43.478 32.19 17.13 37.48 2.73
2902 3230 3.822735 TCTGTCTTTGCTTTTCTGGATGG 59.177 43.478 0.00 0.00 0.00 3.51
3012 3346 2.225467 GGTATTGCAAGGAGGCTGATC 58.775 52.381 4.94 0.00 34.04 2.92
3341 3675 6.471233 TCTGTTATTGCATAGCAGAGTACT 57.529 37.500 14.23 0.00 44.62 2.73
3342 3676 7.582667 TCTGTTATTGCATAGCAGAGTACTA 57.417 36.000 14.23 0.00 44.62 1.82
3414 3756 0.108138 ATGTCCGGCTACAGTGCTTC 60.108 55.000 0.00 0.00 31.70 3.86
3439 3783 9.197306 TCTCTACTGTCCTATAACAATAAGCAA 57.803 33.333 0.00 0.00 0.00 3.91
3507 3856 7.936301 AGATATGGTATTTTTGAGCTCTTCTCC 59.064 37.037 16.19 8.71 41.18 3.71
3510 3859 4.637977 GGTATTTTTGAGCTCTTCTCCTGG 59.362 45.833 16.19 0.00 41.18 4.45
3511 3860 4.647564 ATTTTTGAGCTCTTCTCCTGGA 57.352 40.909 16.19 0.00 41.18 3.86
3519 3868 2.290577 GCTCTTCTCCTGGAATGTGGTT 60.291 50.000 0.00 0.00 33.01 3.67
3522 3871 3.138283 TCTTCTCCTGGAATGTGGTTTGT 59.862 43.478 0.00 0.00 33.01 2.83
3623 3973 3.389329 TGGGCCTTGATAAAACTTTGCAA 59.611 39.130 4.53 0.00 0.00 4.08
3649 3999 4.422073 TGTCACTCCTTTGTTCACTCAT 57.578 40.909 0.00 0.00 0.00 2.90
3685 4035 7.566760 TTTCTTGCTTCAGTTGAGTGAAATA 57.433 32.000 3.15 0.00 36.01 1.40
3777 4129 6.496565 ACAAATTGTTCATTGGGGTTGAGATA 59.503 34.615 0.00 0.00 0.00 1.98
3778 4130 7.016072 ACAAATTGTTCATTGGGGTTGAGATAA 59.984 33.333 0.00 0.00 0.00 1.75
3779 4131 7.738437 AATTGTTCATTGGGGTTGAGATAAT 57.262 32.000 0.00 0.00 0.00 1.28
3780 4132 7.738437 ATTGTTCATTGGGGTTGAGATAATT 57.262 32.000 0.00 0.00 0.00 1.40
3781 4133 7.552050 TTGTTCATTGGGGTTGAGATAATTT 57.448 32.000 0.00 0.00 0.00 1.82
3782 4134 7.552050 TGTTCATTGGGGTTGAGATAATTTT 57.448 32.000 0.00 0.00 0.00 1.82
3783 4135 7.972301 TGTTCATTGGGGTTGAGATAATTTTT 58.028 30.769 0.00 0.00 0.00 1.94
3864 4216 6.067350 GGATGCTATTCAGGAAAAGGAGAAT 58.933 40.000 0.00 0.00 35.17 2.40
3869 4221 6.183360 GCTATTCAGGAAAAGGAGAATTGACC 60.183 42.308 0.00 0.00 33.22 4.02
3870 4222 4.722526 TCAGGAAAAGGAGAATTGACCA 57.277 40.909 0.00 0.00 0.00 4.02
3871 4223 5.261040 TCAGGAAAAGGAGAATTGACCAT 57.739 39.130 0.00 0.00 0.00 3.55
3873 4225 4.768968 CAGGAAAAGGAGAATTGACCATGT 59.231 41.667 0.00 0.00 0.00 3.21
3877 4229 7.675619 AGGAAAAGGAGAATTGACCATGTAAAT 59.324 33.333 0.00 0.00 0.00 1.40
3883 4235 8.428063 AGGAGAATTGACCATGTAAATAGAGAG 58.572 37.037 0.00 0.00 0.00 3.20
3915 4267 6.747414 AGCTGTGAATCTTGGTGGTATATA 57.253 37.500 0.00 0.00 0.00 0.86
3916 4268 6.525629 AGCTGTGAATCTTGGTGGTATATAC 58.474 40.000 4.14 4.14 0.00 1.47
3929 4281 2.606308 GGTATATACGGGTGCACGACTG 60.606 54.545 11.45 5.54 37.61 3.51
3931 4283 1.748950 TATACGGGTGCACGACTGTA 58.251 50.000 11.45 13.39 37.61 2.74
3943 4295 1.201647 ACGACTGTAGATCCACCAACG 59.798 52.381 0.00 0.00 0.00 4.10
3947 4299 4.171754 GACTGTAGATCCACCAACGTTAC 58.828 47.826 0.00 0.00 0.00 2.50
3978 4330 2.238646 TCTCAACCACTGTGTTTCCACT 59.761 45.455 7.08 0.00 42.34 4.00
3993 4345 0.543749 CCACTGGTTCCCCTCATCTC 59.456 60.000 0.00 0.00 0.00 2.75
4000 4352 1.630878 GTTCCCCTCATCTCTGGTTGT 59.369 52.381 0.00 0.00 0.00 3.32
4001 4353 2.040412 GTTCCCCTCATCTCTGGTTGTT 59.960 50.000 0.00 0.00 0.00 2.83
4008 4360 4.020751 CCTCATCTCTGGTTGTTTCTCTGA 60.021 45.833 0.00 0.00 0.00 3.27
4011 4363 4.963318 TCTCTGGTTGTTTCTCTGACAT 57.037 40.909 0.00 0.00 0.00 3.06
4097 4449 2.278013 GGCGACGACATCTCGACC 60.278 66.667 0.00 0.00 43.06 4.79
4106 4458 3.442625 ACGACATCTCGACCATAAAGACA 59.557 43.478 0.00 0.00 43.06 3.41
4107 4459 4.098044 ACGACATCTCGACCATAAAGACAT 59.902 41.667 0.00 0.00 43.06 3.06
4113 4466 4.391830 TCTCGACCATAAAGACATTGTTGC 59.608 41.667 0.00 0.00 0.00 4.17
4114 4467 4.068599 TCGACCATAAAGACATTGTTGCA 58.931 39.130 0.00 0.00 0.00 4.08
4132 4485 1.683385 GCATGGAATAAAGGCTCCACC 59.317 52.381 0.00 0.00 44.42 4.61
4138 4491 3.118519 GGAATAAAGGCTCCACCGTTCTA 60.119 47.826 0.00 0.00 46.52 2.10
4140 4493 1.349067 AAAGGCTCCACCGTTCTACT 58.651 50.000 0.00 0.00 46.52 2.57
4153 4506 2.689646 GTTCTACTCCAGTTCTGGTGC 58.310 52.381 17.00 0.56 0.00 5.01
4192 4546 2.341452 CGATACCGGAGAGGATGCA 58.659 57.895 9.46 0.00 45.00 3.96
4199 4553 1.207089 CCGGAGAGGATGCAGTGTTTA 59.793 52.381 0.00 0.00 45.00 2.01
4202 4556 3.274288 GGAGAGGATGCAGTGTTTAAGG 58.726 50.000 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 1.065572 CATGATACGTATCGCGCGCT 61.066 55.000 30.48 19.99 46.11 5.92
137 142 2.675423 TGTACGCCGGTCAGAGCT 60.675 61.111 1.90 0.00 0.00 4.09
178 183 3.041940 GGAACCTGTGACACCGCG 61.042 66.667 0.00 0.00 0.00 6.46
223 228 0.591236 GATGAGTCGAGCGAGCACTC 60.591 60.000 6.99 6.99 37.63 3.51
224 229 1.029408 AGATGAGTCGAGCGAGCACT 61.029 55.000 0.00 0.00 0.00 4.40
289 294 1.005340 CAGATCAGAAAGCGCACTCC 58.995 55.000 11.47 0.00 0.00 3.85
339 347 6.501781 GGACGCACTGTACTGTTATAAGTAT 58.498 40.000 2.16 0.00 35.20 2.12
363 374 0.387112 AATGACCAAATGCACGCACG 60.387 50.000 0.00 0.00 0.00 5.34
447 458 3.959975 CAACCCAACCGTGCACCG 61.960 66.667 12.15 7.55 0.00 4.94
692 707 2.330231 TCATGGAAAAAGCGCGAAAG 57.670 45.000 12.10 0.00 0.00 2.62
809 824 1.251527 ACTACCAGAGTGCACTCCGG 61.252 60.000 36.89 36.89 44.29 5.14
822 837 4.347000 GGGAGCAGTGGAATATTACTACCA 59.653 45.833 0.00 0.00 0.00 3.25
824 839 5.298347 GTGGGAGCAGTGGAATATTACTAC 58.702 45.833 0.00 0.00 0.00 2.73
871 886 0.895559 CAAAGCCAGGTCACCCCTTC 60.896 60.000 0.00 0.00 42.73 3.46
872 887 1.153756 CAAAGCCAGGTCACCCCTT 59.846 57.895 0.00 0.00 42.73 3.95
875 890 0.251341 ATCACAAAGCCAGGTCACCC 60.251 55.000 0.00 0.00 0.00 4.61
876 891 1.168714 GATCACAAAGCCAGGTCACC 58.831 55.000 0.00 0.00 0.00 4.02
877 892 1.808945 CAGATCACAAAGCCAGGTCAC 59.191 52.381 0.00 0.00 0.00 3.67
878 893 1.421268 ACAGATCACAAAGCCAGGTCA 59.579 47.619 0.00 0.00 0.00 4.02
887 902 1.075212 TGCCCCATCACAGATCACAAA 59.925 47.619 0.00 0.00 0.00 2.83
1290 1311 2.990479 GCGGAGAGGTGGTTGGAT 59.010 61.111 0.00 0.00 0.00 3.41
1341 1362 6.469782 AACATAGCTGAAATAAATGGGGTG 57.530 37.500 0.00 0.00 0.00 4.61
1369 1424 1.526887 CGAACAGCACAAGTACAGTGG 59.473 52.381 16.93 6.82 37.46 4.00
1504 1668 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
1505 1669 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
1506 1670 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
1507 1671 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
1508 1672 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
1509 1673 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
1510 1674 7.273381 CCATTTTGATGACAAGTATTTTCGGAC 59.727 37.037 0.00 0.00 37.32 4.79
1511 1675 7.175816 TCCATTTTGATGACAAGTATTTTCGGA 59.824 33.333 0.00 0.00 37.32 4.55
1512 1676 7.273381 GTCCATTTTGATGACAAGTATTTTCGG 59.727 37.037 0.00 0.00 37.32 4.30
1513 1677 7.807433 TGTCCATTTTGATGACAAGTATTTTCG 59.193 33.333 0.00 0.00 37.32 3.46
1514 1678 9.474920 TTGTCCATTTTGATGACAAGTATTTTC 57.525 29.630 0.00 0.00 37.32 2.29
1515 1679 9.829507 TTTGTCCATTTTGATGACAAGTATTTT 57.170 25.926 0.00 0.00 37.13 1.82
1516 1680 9.829507 TTTTGTCCATTTTGATGACAAGTATTT 57.170 25.926 0.00 0.00 37.13 1.40
1517 1681 9.829507 TTTTTGTCCATTTTGATGACAAGTATT 57.170 25.926 0.00 0.00 37.13 1.89
1519 1683 9.258826 CATTTTTGTCCATTTTGATGACAAGTA 57.741 29.630 0.00 0.00 37.13 2.24
1520 1684 7.986320 TCATTTTTGTCCATTTTGATGACAAGT 59.014 29.630 0.00 0.00 37.13 3.16
1521 1685 8.367943 TCATTTTTGTCCATTTTGATGACAAG 57.632 30.769 0.00 0.00 37.13 3.16
1522 1686 7.986320 ACTCATTTTTGTCCATTTTGATGACAA 59.014 29.630 0.00 0.00 34.47 3.18
1523 1687 7.438757 CACTCATTTTTGTCCATTTTGATGACA 59.561 33.333 0.00 0.00 0.00 3.58
1524 1688 7.439056 ACACTCATTTTTGTCCATTTTGATGAC 59.561 33.333 0.00 0.00 0.00 3.06
1525 1689 7.499292 ACACTCATTTTTGTCCATTTTGATGA 58.501 30.769 0.00 0.00 0.00 2.92
1526 1690 7.718272 ACACTCATTTTTGTCCATTTTGATG 57.282 32.000 0.00 0.00 0.00 3.07
1527 1691 9.643693 GATACACTCATTTTTGTCCATTTTGAT 57.356 29.630 0.00 0.00 0.00 2.57
1528 1692 8.859090 AGATACACTCATTTTTGTCCATTTTGA 58.141 29.630 0.00 0.00 0.00 2.69
1534 1698 9.349713 AGTTTTAGATACACTCATTTTTGTCCA 57.650 29.630 0.00 0.00 0.00 4.02
1588 1752 9.834628 GTCCGAAAATACTTGTCATCAAAATAA 57.165 29.630 0.00 0.00 32.87 1.40
1589 1753 8.172484 CGTCCGAAAATACTTGTCATCAAAATA 58.828 33.333 0.00 0.00 32.87 1.40
1590 1754 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
1591 1755 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
1592 1756 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
1593 1757 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
1594 1758 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
1595 1759 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
1596 1760 4.081862 TCTCCGTCCGAAAATACTTGTCAT 60.082 41.667 0.00 0.00 0.00 3.06
1597 1761 3.256383 TCTCCGTCCGAAAATACTTGTCA 59.744 43.478 0.00 0.00 0.00 3.58
1598 1762 3.841643 TCTCCGTCCGAAAATACTTGTC 58.158 45.455 0.00 0.00 0.00 3.18
1599 1763 3.508793 TCTCTCCGTCCGAAAATACTTGT 59.491 43.478 0.00 0.00 0.00 3.16
1600 1764 4.106029 TCTCTCCGTCCGAAAATACTTG 57.894 45.455 0.00 0.00 0.00 3.16
1601 1765 3.762823 ACTCTCTCCGTCCGAAAATACTT 59.237 43.478 0.00 0.00 0.00 2.24
1602 1766 3.354467 ACTCTCTCCGTCCGAAAATACT 58.646 45.455 0.00 0.00 0.00 2.12
1603 1767 3.779271 ACTCTCTCCGTCCGAAAATAC 57.221 47.619 0.00 0.00 0.00 1.89
1604 1768 3.310774 CGTACTCTCTCCGTCCGAAAATA 59.689 47.826 0.00 0.00 0.00 1.40
1605 1769 2.097142 CGTACTCTCTCCGTCCGAAAAT 59.903 50.000 0.00 0.00 0.00 1.82
1606 1770 1.466167 CGTACTCTCTCCGTCCGAAAA 59.534 52.381 0.00 0.00 0.00 2.29
1607 1771 1.081892 CGTACTCTCTCCGTCCGAAA 58.918 55.000 0.00 0.00 0.00 3.46
1608 1772 0.036952 ACGTACTCTCTCCGTCCGAA 60.037 55.000 0.00 0.00 0.00 4.30
1609 1773 0.817654 TACGTACTCTCTCCGTCCGA 59.182 55.000 0.00 0.00 36.12 4.55
1610 1774 0.926846 GTACGTACTCTCTCCGTCCG 59.073 60.000 18.47 0.00 36.12 4.79
1611 1775 2.307934 AGTACGTACTCTCTCCGTCC 57.692 55.000 22.45 0.00 36.12 4.79
1612 1776 4.040445 AGTAGTACGTACTCTCTCCGTC 57.960 50.000 30.53 12.07 37.41 4.79
1613 1777 4.499019 GCTAGTAGTACGTACTCTCTCCGT 60.499 50.000 30.53 8.23 41.42 4.69
1614 1778 3.980775 GCTAGTAGTACGTACTCTCTCCG 59.019 52.174 30.53 21.38 41.42 4.63
1615 1779 4.984161 CAGCTAGTAGTACGTACTCTCTCC 59.016 50.000 30.53 20.74 41.42 3.71
1616 1780 4.445385 GCAGCTAGTAGTACGTACTCTCTC 59.555 50.000 30.53 18.48 41.42 3.20
1617 1781 4.370917 GCAGCTAGTAGTACGTACTCTCT 58.629 47.826 30.53 27.48 41.42 3.10
1618 1782 3.494251 GGCAGCTAGTAGTACGTACTCTC 59.506 52.174 30.53 22.91 41.42 3.20
1619 1783 3.118482 TGGCAGCTAGTAGTACGTACTCT 60.118 47.826 30.53 25.62 41.42 3.24
1620 1784 3.201290 TGGCAGCTAGTAGTACGTACTC 58.799 50.000 30.53 20.84 41.42 2.59
1621 1785 3.204526 CTGGCAGCTAGTAGTACGTACT 58.795 50.000 29.62 29.62 44.69 2.73
1622 1786 2.941720 ACTGGCAGCTAGTAGTACGTAC 59.058 50.000 18.10 18.10 0.00 3.67
1623 1787 3.272574 ACTGGCAGCTAGTAGTACGTA 57.727 47.619 15.89 0.00 0.00 3.57
1624 1788 2.125773 ACTGGCAGCTAGTAGTACGT 57.874 50.000 15.89 0.00 0.00 3.57
1625 1789 2.031857 GCTACTGGCAGCTAGTAGTACG 60.032 54.545 34.18 18.75 45.91 3.67
1626 1790 3.629438 GCTACTGGCAGCTAGTAGTAC 57.371 52.381 34.18 21.52 45.91 2.73
1636 1800 3.064545 GCAGACAAAATAGCTACTGGCAG 59.935 47.826 14.16 14.16 44.79 4.85
1645 1809 2.002586 TCTGCTCGCAGACAAAATAGC 58.997 47.619 17.01 0.00 46.80 2.97
1729 1974 2.148916 TCGTCTTTACAGTGGCACAG 57.851 50.000 21.41 15.03 41.80 3.66
1743 1988 7.461182 TGGTATTTCAAAATTCCATTCGTCT 57.539 32.000 9.08 0.00 39.81 4.18
1752 1997 9.271828 AGTTGGACAAATGGTATTTCAAAATTC 57.728 29.630 0.00 0.00 0.00 2.17
1768 2013 3.094484 AGTGAAACCCAGTTGGACAAA 57.906 42.857 0.00 0.00 37.80 2.83
1769 2014 2.818751 AGTGAAACCCAGTTGGACAA 57.181 45.000 0.00 0.00 37.80 3.18
1770 2015 2.818751 AAGTGAAACCCAGTTGGACA 57.181 45.000 0.00 0.00 37.06 4.02
1773 2056 6.405278 AAGATAAAAGTGAAACCCAGTTGG 57.595 37.500 0.00 0.00 38.38 3.77
1780 2063 9.678941 CAAAGGAAGTAAGATAAAAGTGAAACC 57.321 33.333 0.00 0.00 37.80 3.27
1789 2072 9.466497 AGCAATCATCAAAGGAAGTAAGATAAA 57.534 29.630 0.00 0.00 0.00 1.40
1792 2075 6.183360 GCAGCAATCATCAAAGGAAGTAAGAT 60.183 38.462 0.00 0.00 0.00 2.40
1793 2076 5.124457 GCAGCAATCATCAAAGGAAGTAAGA 59.876 40.000 0.00 0.00 0.00 2.10
1794 2077 5.106038 TGCAGCAATCATCAAAGGAAGTAAG 60.106 40.000 0.00 0.00 0.00 2.34
1811 2094 1.561076 AGGATATGTGAGGTGCAGCAA 59.439 47.619 19.63 2.56 0.00 3.91
1816 2099 3.812053 GTGAATCAGGATATGTGAGGTGC 59.188 47.826 0.00 0.00 0.00 5.01
1827 2126 3.458831 AGTCAGGAAGGTGAATCAGGAT 58.541 45.455 0.00 0.00 0.00 3.24
1829 2128 5.365021 AATAGTCAGGAAGGTGAATCAGG 57.635 43.478 0.00 0.00 0.00 3.86
1906 2227 8.896320 ACAGTTTCCATTAAAAATGGGTAAAC 57.104 30.769 18.88 18.88 38.25 2.01
1911 2232 7.800155 AACAACAGTTTCCATTAAAAATGGG 57.200 32.000 16.58 4.99 38.25 4.00
1931 2256 4.374689 TGGGCAAGACCTGTAATAACAA 57.625 40.909 0.00 0.00 39.10 2.83
2041 2366 6.291377 TGGCAGCTATAGAAGGTTTTATCAG 58.709 40.000 3.21 0.00 32.16 2.90
2148 2473 8.137437 ACAATCTTGTTTGATCCAACTAAACAG 58.863 33.333 10.69 5.44 42.92 3.16
2244 2569 5.563592 ACAACAATCTGTGAATCATCAGGA 58.436 37.500 11.07 0.00 35.88 3.86
2268 2593 1.068333 CGCCAGACACCATTTTTCAGG 60.068 52.381 0.00 0.00 0.00 3.86
2333 2658 3.817647 CAGGCTTCATAAATACAGGGCTC 59.182 47.826 0.00 0.00 0.00 4.70
2338 2663 6.601613 TGTTTACCCAGGCTTCATAAATACAG 59.398 38.462 0.00 0.00 0.00 2.74
2353 2681 5.934402 AGTACTCCTGTATGTTTACCCAG 57.066 43.478 0.00 0.00 0.00 4.45
2480 2808 2.104281 ACCTAGTGACCACCTGTTTGTC 59.896 50.000 0.00 0.00 0.00 3.18
2506 2834 5.488341 ACACCTGAACATAGTGATACAACC 58.512 41.667 10.56 0.00 35.47 3.77
2787 3115 0.815615 GCTCCCACAATCCATCCGAC 60.816 60.000 0.00 0.00 0.00 4.79
2799 3127 0.672711 GGTTCGTAAGGTGCTCCCAC 60.673 60.000 0.00 0.00 41.32 4.61
2814 3142 1.503818 TTTCGACGGCTTGCTGGTTC 61.504 55.000 6.39 0.00 0.00 3.62
2860 3188 4.093998 CAGAGGGTGAAATGATGAAGAACG 59.906 45.833 0.00 0.00 0.00 3.95
2864 3192 4.841422 AGACAGAGGGTGAAATGATGAAG 58.159 43.478 0.00 0.00 0.00 3.02
2902 3230 9.197306 AGTTTCCCCAAAATAATATTACAGGTC 57.803 33.333 0.00 0.00 0.00 3.85
3189 3523 2.421619 GAGCCTCCTGACTCAACAAAG 58.578 52.381 0.00 0.00 32.98 2.77
3305 3639 5.221422 TGCAATAACAGAACCAAAAGAAGGG 60.221 40.000 0.00 0.00 0.00 3.95
3362 3704 3.108144 GCACGACAATTCCAATATGTGC 58.892 45.455 0.00 0.00 43.66 4.57
3379 3721 3.429085 GGACATTGCTAAGAATTGCACG 58.571 45.455 0.00 0.00 39.05 5.34
3414 3756 9.988815 ATTGCTTATTGTTATAGGACAGTAGAG 57.011 33.333 0.00 0.00 0.00 2.43
3439 3783 0.457337 GAACGTCGTCGGGCTAACAT 60.457 55.000 7.05 0.00 41.85 2.71
3498 3847 1.280421 ACCACATTCCAGGAGAAGAGC 59.720 52.381 0.00 0.00 38.07 4.09
3507 3856 4.605640 ATTCCAACAAACCACATTCCAG 57.394 40.909 0.00 0.00 0.00 3.86
3510 3859 4.511082 CACCAATTCCAACAAACCACATTC 59.489 41.667 0.00 0.00 0.00 2.67
3511 3860 4.450053 CACCAATTCCAACAAACCACATT 58.550 39.130 0.00 0.00 0.00 2.71
3519 3868 7.841282 TTAGATAAACCACCAATTCCAACAA 57.159 32.000 0.00 0.00 0.00 2.83
3522 3871 7.578571 GCACATTAGATAAACCACCAATTCCAA 60.579 37.037 0.00 0.00 0.00 3.53
3623 3973 4.080863 AGTGAACAAAGGAGTGACAAGAGT 60.081 41.667 0.00 0.00 0.00 3.24
3649 3999 9.816354 AACTGAAGCAAGAAAATTAAGCTAAAA 57.184 25.926 0.00 0.00 34.66 1.52
3701 4051 7.937394 AGTACCACCACATATAGAAAAATAGCC 59.063 37.037 0.00 0.00 0.00 3.93
3780 4132 6.405731 CCACACATCCAAGTCAGAAAGAAAAA 60.406 38.462 0.00 0.00 0.00 1.94
3781 4133 5.067674 CCACACATCCAAGTCAGAAAGAAAA 59.932 40.000 0.00 0.00 0.00 2.29
3782 4134 4.580167 CCACACATCCAAGTCAGAAAGAAA 59.420 41.667 0.00 0.00 0.00 2.52
3783 4135 4.136796 CCACACATCCAAGTCAGAAAGAA 58.863 43.478 0.00 0.00 0.00 2.52
3784 4136 3.390967 TCCACACATCCAAGTCAGAAAGA 59.609 43.478 0.00 0.00 0.00 2.52
3785 4137 3.743521 TCCACACATCCAAGTCAGAAAG 58.256 45.455 0.00 0.00 0.00 2.62
3786 4138 3.855255 TCCACACATCCAAGTCAGAAA 57.145 42.857 0.00 0.00 0.00 2.52
3787 4139 3.855255 TTCCACACATCCAAGTCAGAA 57.145 42.857 0.00 0.00 0.00 3.02
3877 4229 8.922237 AGATTCACAGCTAATTTCATCTCTCTA 58.078 33.333 0.00 0.00 0.00 2.43
3883 4235 6.971184 CACCAAGATTCACAGCTAATTTCATC 59.029 38.462 0.00 0.00 0.00 2.92
3888 4240 4.666512 ACCACCAAGATTCACAGCTAATT 58.333 39.130 0.00 0.00 0.00 1.40
3915 4267 1.248785 ATCTACAGTCGTGCACCCGT 61.249 55.000 12.15 5.82 0.00 5.28
3916 4268 0.525668 GATCTACAGTCGTGCACCCG 60.526 60.000 12.15 0.00 0.00 5.28
3929 4281 3.492421 TCGTAACGTTGGTGGATCTAC 57.508 47.619 11.99 0.00 0.00 2.59
3931 4283 2.418197 CCATCGTAACGTTGGTGGATCT 60.418 50.000 11.99 0.00 40.53 2.75
3943 4295 3.119245 TGGTTGAGAGCTACCATCGTAAC 60.119 47.826 1.76 0.00 43.45 2.50
4008 4360 1.550976 GTTCCCCTCGTCTTCTGATGT 59.449 52.381 0.00 0.00 0.00 3.06
4011 4363 0.178944 TGGTTCCCCTCGTCTTCTGA 60.179 55.000 0.00 0.00 0.00 3.27
4083 4435 4.036352 GTCTTTATGGTCGAGATGTCGTC 58.964 47.826 12.41 6.55 46.85 4.20
4097 4449 8.929827 TTATTCCATGCAACAATGTCTTTATG 57.070 30.769 0.00 0.00 0.00 1.90
4106 4458 4.141869 GGAGCCTTTATTCCATGCAACAAT 60.142 41.667 0.00 0.00 33.55 2.71
4107 4459 3.195396 GGAGCCTTTATTCCATGCAACAA 59.805 43.478 0.00 0.00 33.55 2.83
4113 4466 1.949525 CGGTGGAGCCTTTATTCCATG 59.050 52.381 0.00 0.00 44.74 3.66
4114 4467 1.564348 ACGGTGGAGCCTTTATTCCAT 59.436 47.619 0.00 0.00 44.74 3.41
4153 4506 3.431055 TTGTCAGCCACAAAGCCG 58.569 55.556 0.00 0.00 42.35 5.52
4182 4536 2.680339 GCCTTAAACACTGCATCCTCTC 59.320 50.000 0.00 0.00 0.00 3.20
4184 4538 1.745653 GGCCTTAAACACTGCATCCTC 59.254 52.381 0.00 0.00 0.00 3.71
4191 4545 2.686816 CCGCGGGCCTTAAACACTG 61.687 63.158 20.10 0.00 0.00 3.66
4192 4546 2.193087 ATCCGCGGGCCTTAAACACT 62.193 55.000 27.83 0.00 0.00 3.55
4199 4553 0.110486 ATCATTAATCCGCGGGCCTT 59.890 50.000 27.83 18.42 0.00 4.35
4202 4556 1.464997 GAGAATCATTAATCCGCGGGC 59.535 52.381 27.83 2.08 33.17 6.13


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

AutoCloner maintained by Alex Coulton.