Multiple sequence alignment - TraesCS5B01G101100

Loading Multiple Alignment...

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 TraesCS5B01G101100 chr5B 100.000 2312 0 0 1 2312 134121836 134119525 0.000000e+00 4270
1 TraesCS5B01G101100 chr5B 96.212 1188 29 8 368 1554 134542822 134543994 0.000000e+00 1930
2 TraesCS5B01G101100 chr5B 81.818 319 55 3 999 1314 133893507 133893189 4.900000e-67 265
3 TraesCS5B01G101100 chr5B 81.058 359 24 19 1958 2281 134544114 134544463 1.770000e-61 246
4 TraesCS5B01G101100 chr5B 83.945 218 15 7 172 370 134542575 134542791 8.430000e-45 191
5 TraesCS5B01G101100 chr5B 96.364 110 4 0 1 110 134542091 134542200 5.070000e-42 182
6 TraesCS5B01G101100 chr5A 94.141 1280 45 14 368 1629 132092951 132091684 0.000000e+00 1921
7 TraesCS5B01G101100 chr5A 87.767 1030 58 17 146 1126 132970766 132971776 0.000000e+00 1142
8 TraesCS5B01G101100 chr5A 93.039 431 21 4 1124 1554 132975455 132975876 2.520000e-174 621
9 TraesCS5B01G101100 chr5A 86.967 422 18 10 1913 2312 132975976 132976382 7.580000e-120 440
10 TraesCS5B01G101100 chr5A 96.000 250 8 1 15 264 132093310 132093063 2.770000e-109 405
11 TraesCS5B01G101100 chr5A 90.759 303 7 5 1949 2230 132091668 132091366 3.600000e-103 385
12 TraesCS5B01G101100 chr5A 87.814 279 24 5 1631 1903 570517601 570517327 3.710000e-83 318
13 TraesCS5B01G101100 chr5A 75.472 318 75 3 1000 1316 40813296 40813611 3.980000e-33 152
14 TraesCS5B01G101100 chr5D 93.138 1195 52 14 368 1554 121295791 121296963 0.000000e+00 1725
15 TraesCS5B01G101100 chr5D 94.968 934 35 7 703 1629 121073087 121072159 0.000000e+00 1454
16 TraesCS5B01G101100 chr5D 94.236 347 14 4 368 711 121074628 121074285 2.030000e-145 525
17 TraesCS5B01G101100 chr5D 89.157 415 17 11 1908 2312 121072173 121071777 2.060000e-135 492
18 TraesCS5B01G101100 chr5D 83.117 231 19 8 148 370 121295542 121295760 2.340000e-45 193
19 TraesCS5B01G101100 chr5D 75.497 302 70 3 1000 1299 51637522 51637821 6.660000e-31 145
20 TraesCS5B01G101100 chr5D 75.161 310 71 5 1000 1306 51675302 51675608 8.610000e-30 141
21 TraesCS5B01G101100 chr5D 96.000 75 2 1 148 221 121074795 121074721 1.120000e-23 121
22 TraesCS5B01G101100 chr2D 89.818 275 26 2 1630 1903 572927986 572927713 3.650000e-93 351
23 TraesCS5B01G101100 chr4B 89.170 277 28 2 1629 1903 133583167 133583443 6.120000e-91 344
24 TraesCS5B01G101100 chr4B 88.214 280 29 3 1627 1903 504770281 504770559 4.760000e-87 331
25 TraesCS5B01G101100 chr3D 88.693 283 29 3 1629 1910 19783992 19784272 2.200000e-90 342
26 TraesCS5B01G101100 chr3A 89.377 273 22 4 1629 1900 432384051 432384317 1.020000e-88 337
27 TraesCS5B01G101100 chr3A 87.455 279 26 6 1629 1903 519270463 519270190 1.720000e-81 313
28 TraesCS5B01G101100 chr2A 87.857 280 26 7 1628 1903 94122202 94122477 2.870000e-84 322
29 TraesCS5B01G101100 chr1D 81.884 276 43 5 1630 1903 429018756 429018486 2.310000e-55 226


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 TraesCS5B01G101100 chr5B 134119525 134121836 2311 True 4270.000000 4270 100.000000 1 2312 1 chr5B.!!$R2 2311
1 TraesCS5B01G101100 chr5B 134542091 134544463 2372 False 637.250000 1930 89.394750 1 2281 4 chr5B.!!$F1 2280
2 TraesCS5B01G101100 chr5A 132091366 132093310 1944 True 903.666667 1921 93.633333 15 2230 3 chr5A.!!$R2 2215
3 TraesCS5B01G101100 chr5A 132970766 132976382 5616 False 734.333333 1142 89.257667 146 2312 3 chr5A.!!$F2 2166
4 TraesCS5B01G101100 chr5D 121295542 121296963 1421 False 959.000000 1725 88.127500 148 1554 2 chr5D.!!$F3 1406
5 TraesCS5B01G101100 chr5D 121071777 121074795 3018 True 648.000000 1454 93.590250 148 2312 4 chr5D.!!$R1 2164

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
943 2558 0.390492 ACTTCAAAGCAAAGCAGGCC 59.61 50.0 0.0 0.0 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1870 7212 0.039617 CGTTGCAAAGGCCATCGAAA 60.04 50.0 5.01 0.0 40.13 3.46 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
24 25 6.373186 AGCGCTCTTTGTTAAGTAAAAACT 57.627 33.333 2.64 0.00 32.98 2.66
119 120 7.282224 TCAAACGAGGAGAGAAATCTTGAAAAA 59.718 33.333 0.00 0.00 0.00 1.94
264 579 2.628178 TCCGGATTTCTACTCGATGCAT 59.372 45.455 0.00 0.00 0.00 3.96
265 580 2.733552 CCGGATTTCTACTCGATGCATG 59.266 50.000 2.46 0.00 0.00 4.06
312 644 5.048504 GTGCATTCTATCACCCATTACCATG 60.049 44.000 0.00 0.00 0.00 3.66
337 687 0.995024 AGATTGACCACCCCTTCCAG 59.005 55.000 0.00 0.00 0.00 3.86
419 806 5.241949 GGACCTCTCCATAGGCATATATACG 59.758 48.000 0.00 0.00 40.62 3.06
420 807 6.014771 ACCTCTCCATAGGCATATATACGA 57.985 41.667 0.00 0.00 40.62 3.43
472 863 9.155975 CTTAGAAAATCGATCGGATTATTCCAT 57.844 33.333 16.41 0.00 44.59 3.41
680 1081 5.731686 GCAATGTTAAAGATGGCTGCTAGAC 60.732 44.000 0.00 0.00 0.00 2.59
707 2314 1.602377 GGTCTGTTCCAAACACTTCCG 59.398 52.381 0.00 0.00 36.25 4.30
943 2558 0.390492 ACTTCAAAGCAAAGCAGGCC 59.610 50.000 0.00 0.00 0.00 5.19
1049 2665 0.534412 AGAGCGGTGGTGATCTTCAG 59.466 55.000 0.00 0.00 0.00 3.02
1142 6439 1.827399 GAGCTCGACCAAGACCCCAA 61.827 60.000 0.00 0.00 0.00 4.12
1334 6631 2.370459 AATGCAGGTGCCACTTGGGA 62.370 55.000 9.15 0.00 40.01 4.37
1375 6687 8.668353 TCAAAGAGTGTCAAGTATATGCATTTC 58.332 33.333 3.54 0.00 0.00 2.17
1407 6719 5.774102 ACTTAACTAATGGCCTGGTTAGT 57.226 39.130 17.49 17.49 41.54 2.24
1546 6879 5.179368 CACTCAGGTGTACAATCATCGTTTT 59.821 40.000 0.00 0.00 38.54 2.43
1559 6893 5.283060 TCATCGTTTTTCAAAGAGCTAGC 57.717 39.130 6.62 6.62 0.00 3.42
1613 6955 4.000988 ACATGCCGTCTTTAACCTACAAG 58.999 43.478 0.00 0.00 0.00 3.16
1616 6958 4.453751 TGCCGTCTTTAACCTACAAGTTT 58.546 39.130 0.00 0.00 0.00 2.66
1653 6995 3.492421 TTTGAAAGATCCAGCAATCGC 57.508 42.857 0.00 0.00 38.99 4.58
1664 7006 3.727419 GCAATCGCTGGCTTTTCAT 57.273 47.368 0.00 0.00 34.30 2.57
1665 7007 2.849880 GCAATCGCTGGCTTTTCATA 57.150 45.000 0.00 0.00 34.30 2.15
1666 7008 3.360249 GCAATCGCTGGCTTTTCATAT 57.640 42.857 0.00 0.00 34.30 1.78
1667 7009 3.303406 GCAATCGCTGGCTTTTCATATC 58.697 45.455 0.00 0.00 34.30 1.63
1668 7010 3.243168 GCAATCGCTGGCTTTTCATATCA 60.243 43.478 0.00 0.00 34.30 2.15
1669 7011 4.558095 GCAATCGCTGGCTTTTCATATCAT 60.558 41.667 0.00 0.00 34.30 2.45
1670 7012 5.526115 CAATCGCTGGCTTTTCATATCATT 58.474 37.500 0.00 0.00 0.00 2.57
1671 7013 6.671190 CAATCGCTGGCTTTTCATATCATTA 58.329 36.000 0.00 0.00 0.00 1.90
1672 7014 5.929697 TCGCTGGCTTTTCATATCATTAG 57.070 39.130 0.00 0.00 0.00 1.73
1673 7015 4.214119 TCGCTGGCTTTTCATATCATTAGC 59.786 41.667 0.00 0.00 0.00 3.09
1674 7016 4.023792 CGCTGGCTTTTCATATCATTAGCA 60.024 41.667 0.00 0.00 0.00 3.49
1675 7017 5.458891 GCTGGCTTTTCATATCATTAGCAG 58.541 41.667 0.00 0.00 0.00 4.24
1676 7018 5.240183 GCTGGCTTTTCATATCATTAGCAGA 59.760 40.000 0.00 0.00 0.00 4.26
1677 7019 6.238842 GCTGGCTTTTCATATCATTAGCAGAA 60.239 38.462 0.00 0.00 0.00 3.02
1678 7020 7.643569 TGGCTTTTCATATCATTAGCAGAAA 57.356 32.000 0.00 0.00 0.00 2.52
1679 7021 8.241497 TGGCTTTTCATATCATTAGCAGAAAT 57.759 30.769 0.00 0.00 0.00 2.17
1680 7022 8.355169 TGGCTTTTCATATCATTAGCAGAAATC 58.645 33.333 0.00 0.00 0.00 2.17
1681 7023 8.355169 GGCTTTTCATATCATTAGCAGAAATCA 58.645 33.333 0.00 0.00 0.00 2.57
1682 7024 9.740239 GCTTTTCATATCATTAGCAGAAATCAA 57.260 29.630 0.00 0.00 0.00 2.57
1686 7028 9.577222 TTCATATCATTAGCAGAAATCAATGGA 57.423 29.630 0.00 0.00 0.00 3.41
1687 7029 9.577222 TCATATCATTAGCAGAAATCAATGGAA 57.423 29.630 0.00 0.00 0.00 3.53
1691 7033 8.761575 TCATTAGCAGAAATCAATGGAAAAAC 57.238 30.769 0.00 0.00 0.00 2.43
1692 7034 8.366401 TCATTAGCAGAAATCAATGGAAAAACA 58.634 29.630 0.00 0.00 0.00 2.83
1693 7035 8.991026 CATTAGCAGAAATCAATGGAAAAACAA 58.009 29.630 0.00 0.00 0.00 2.83
1694 7036 8.592105 TTAGCAGAAATCAATGGAAAAACAAG 57.408 30.769 0.00 0.00 0.00 3.16
1695 7037 5.993441 AGCAGAAATCAATGGAAAAACAAGG 59.007 36.000 0.00 0.00 0.00 3.61
1696 7038 5.179929 GCAGAAATCAATGGAAAAACAAGGG 59.820 40.000 0.00 0.00 0.00 3.95
1697 7039 6.290605 CAGAAATCAATGGAAAAACAAGGGT 58.709 36.000 0.00 0.00 0.00 4.34
1698 7040 6.203338 CAGAAATCAATGGAAAAACAAGGGTG 59.797 38.462 0.00 0.00 0.00 4.61
1699 7041 3.467374 TCAATGGAAAAACAAGGGTGC 57.533 42.857 0.00 0.00 0.00 5.01
1700 7042 2.134346 CAATGGAAAAACAAGGGTGCG 58.866 47.619 0.00 0.00 0.00 5.34
1701 7043 1.408969 ATGGAAAAACAAGGGTGCGT 58.591 45.000 0.00 0.00 0.00 5.24
1702 7044 1.187087 TGGAAAAACAAGGGTGCGTT 58.813 45.000 0.00 0.00 0.00 4.84
1703 7045 1.134965 TGGAAAAACAAGGGTGCGTTG 60.135 47.619 0.00 0.00 35.67 4.10
1704 7046 1.566404 GAAAAACAAGGGTGCGTTGG 58.434 50.000 0.00 0.00 34.13 3.77
1705 7047 1.135333 GAAAAACAAGGGTGCGTTGGA 59.865 47.619 0.00 0.00 34.13 3.53
1706 7048 0.744281 AAAACAAGGGTGCGTTGGAG 59.256 50.000 0.00 0.00 34.13 3.86
1707 7049 1.106944 AAACAAGGGTGCGTTGGAGG 61.107 55.000 0.00 0.00 34.13 4.30
1708 7050 2.672996 CAAGGGTGCGTTGGAGGG 60.673 66.667 0.00 0.00 0.00 4.30
1709 7051 3.175710 AAGGGTGCGTTGGAGGGT 61.176 61.111 0.00 0.00 0.00 4.34
1710 7052 3.192103 AAGGGTGCGTTGGAGGGTC 62.192 63.158 0.00 0.00 0.00 4.46
1711 7053 4.717313 GGGTGCGTTGGAGGGTCC 62.717 72.222 0.00 0.00 36.96 4.46
1712 7054 3.637273 GGTGCGTTGGAGGGTCCT 61.637 66.667 0.00 0.00 37.46 3.85
1713 7055 2.288025 GGTGCGTTGGAGGGTCCTA 61.288 63.158 0.00 0.00 37.46 2.94
1714 7056 1.675219 GTGCGTTGGAGGGTCCTAA 59.325 57.895 0.00 0.00 37.46 2.69
1715 7057 0.391263 GTGCGTTGGAGGGTCCTAAG 60.391 60.000 0.00 0.00 37.46 2.18
1716 7058 0.543410 TGCGTTGGAGGGTCCTAAGA 60.543 55.000 0.00 0.00 37.46 2.10
1717 7059 0.108281 GCGTTGGAGGGTCCTAAGAC 60.108 60.000 0.00 0.00 42.73 3.01
1732 7074 6.756221 GTCCTAAGACCAGTACAGAAAAAGA 58.244 40.000 0.00 0.00 37.00 2.52
1733 7075 7.387643 GTCCTAAGACCAGTACAGAAAAAGAT 58.612 38.462 0.00 0.00 37.00 2.40
1734 7076 7.878644 GTCCTAAGACCAGTACAGAAAAAGATT 59.121 37.037 0.00 0.00 37.00 2.40
1735 7077 9.096823 TCCTAAGACCAGTACAGAAAAAGATTA 57.903 33.333 0.00 0.00 0.00 1.75
1736 7078 9.152595 CCTAAGACCAGTACAGAAAAAGATTAC 57.847 37.037 0.00 0.00 0.00 1.89
1737 7079 9.706691 CTAAGACCAGTACAGAAAAAGATTACA 57.293 33.333 0.00 0.00 0.00 2.41
1738 7080 8.974060 AAGACCAGTACAGAAAAAGATTACAA 57.026 30.769 0.00 0.00 0.00 2.41
1739 7081 8.379457 AGACCAGTACAGAAAAAGATTACAAC 57.621 34.615 0.00 0.00 0.00 3.32
1740 7082 7.170998 AGACCAGTACAGAAAAAGATTACAACG 59.829 37.037 0.00 0.00 0.00 4.10
1741 7083 6.987992 ACCAGTACAGAAAAAGATTACAACGA 59.012 34.615 0.00 0.00 0.00 3.85
1742 7084 7.042254 ACCAGTACAGAAAAAGATTACAACGAC 60.042 37.037 0.00 0.00 0.00 4.34
1743 7085 7.288672 CAGTACAGAAAAAGATTACAACGACC 58.711 38.462 0.00 0.00 0.00 4.79
1744 7086 7.170998 CAGTACAGAAAAAGATTACAACGACCT 59.829 37.037 0.00 0.00 0.00 3.85
1745 7087 6.937436 ACAGAAAAAGATTACAACGACCTT 57.063 33.333 0.00 0.00 0.00 3.50
1746 7088 6.725246 ACAGAAAAAGATTACAACGACCTTG 58.275 36.000 0.00 0.00 35.77 3.61
1747 7089 5.625311 CAGAAAAAGATTACAACGACCTTGC 59.375 40.000 0.00 0.00 32.41 4.01
1748 7090 5.531287 AGAAAAAGATTACAACGACCTTGCT 59.469 36.000 0.00 0.00 32.41 3.91
1749 7091 5.767816 AAAAGATTACAACGACCTTGCTT 57.232 34.783 0.00 0.00 32.41 3.91
1750 7092 5.358298 AAAGATTACAACGACCTTGCTTC 57.642 39.130 0.00 0.00 32.41 3.86
1751 7093 2.993899 AGATTACAACGACCTTGCTTCG 59.006 45.455 0.00 0.00 42.36 3.79
1752 7094 1.504359 TTACAACGACCTTGCTTCGG 58.496 50.000 0.00 0.00 40.92 4.30
1753 7095 0.947180 TACAACGACCTTGCTTCGGC 60.947 55.000 0.00 0.00 40.92 5.54
1754 7096 2.668550 AACGACCTTGCTTCGGCC 60.669 61.111 0.00 0.00 40.92 6.13
1755 7097 3.469863 AACGACCTTGCTTCGGCCA 62.470 57.895 2.24 0.00 40.92 5.36
1756 7098 2.668212 CGACCTTGCTTCGGCCAA 60.668 61.111 2.24 0.00 40.91 4.52
1757 7099 2.258013 CGACCTTGCTTCGGCCAAA 61.258 57.895 2.24 0.00 40.91 3.28
1758 7100 1.581447 GACCTTGCTTCGGCCAAAG 59.419 57.895 2.24 0.00 40.91 2.77
1763 7105 4.250080 GCTTCGGCCAAAGCTTTG 57.750 55.556 28.69 28.69 46.51 2.77
1764 7106 2.023771 GCTTCGGCCAAAGCTTTGC 61.024 57.895 29.93 23.94 46.51 3.68
1765 7107 1.662044 CTTCGGCCAAAGCTTTGCT 59.338 52.632 29.93 0.00 42.56 3.91
1766 7108 0.665369 CTTCGGCCAAAGCTTTGCTG 60.665 55.000 29.93 26.81 39.62 4.41
1767 7109 1.106351 TTCGGCCAAAGCTTTGCTGA 61.106 50.000 29.93 28.25 39.62 4.26
1768 7110 1.372128 CGGCCAAAGCTTTGCTGAC 60.372 57.895 29.93 19.89 39.62 3.51
1769 7111 1.005748 GGCCAAAGCTTTGCTGACC 60.006 57.895 29.93 22.85 39.62 4.02
1770 7112 1.372128 GCCAAAGCTTTGCTGACCG 60.372 57.895 29.93 17.69 39.62 4.79
1771 7113 1.795170 GCCAAAGCTTTGCTGACCGA 61.795 55.000 29.93 0.00 39.62 4.69
1772 7114 0.667993 CCAAAGCTTTGCTGACCGAA 59.332 50.000 29.93 0.00 39.62 4.30
1773 7115 1.335324 CCAAAGCTTTGCTGACCGAAG 60.335 52.381 29.93 11.91 39.62 3.79
1775 7117 1.754745 AGCTTTGCTGACCGAAGGA 59.245 52.632 0.00 0.00 46.20 3.36
1776 7118 0.108585 AGCTTTGCTGACCGAAGGAA 59.891 50.000 0.00 0.00 46.20 3.36
1777 7119 1.879796 AGCTTTGCTGACCGAAGGAAG 60.880 52.381 0.00 0.00 46.20 3.46
1778 7120 4.192422 AGCTTTGCTGACCGAAGGAAGA 62.192 50.000 0.00 0.00 46.20 2.87
1779 7121 5.976326 AGCTTTGCTGACCGAAGGAAGAG 62.976 52.174 0.00 0.00 46.20 2.85
1792 7134 6.111768 CGAAGGAAGAGTGGAATTACAATG 57.888 41.667 0.00 0.00 0.00 2.82
1793 7135 5.065218 CGAAGGAAGAGTGGAATTACAATGG 59.935 44.000 0.00 0.00 0.00 3.16
1794 7136 4.273318 AGGAAGAGTGGAATTACAATGGC 58.727 43.478 0.00 0.00 0.00 4.40
1795 7137 3.381590 GGAAGAGTGGAATTACAATGGCC 59.618 47.826 0.00 0.00 0.00 5.36
1796 7138 4.273318 GAAGAGTGGAATTACAATGGCCT 58.727 43.478 3.32 0.00 0.00 5.19
1797 7139 5.437060 GAAGAGTGGAATTACAATGGCCTA 58.563 41.667 3.32 0.00 0.00 3.93
1798 7140 5.653255 AGAGTGGAATTACAATGGCCTAT 57.347 39.130 3.32 0.00 0.00 2.57
1799 7141 6.763715 AGAGTGGAATTACAATGGCCTATA 57.236 37.500 3.32 0.00 0.00 1.31
1800 7142 7.335127 AGAGTGGAATTACAATGGCCTATAT 57.665 36.000 3.32 0.00 0.00 0.86
1801 7143 7.398024 AGAGTGGAATTACAATGGCCTATATC 58.602 38.462 3.32 0.00 0.00 1.63
1802 7144 7.238514 AGAGTGGAATTACAATGGCCTATATCT 59.761 37.037 3.32 0.00 0.00 1.98
1803 7145 7.398024 AGTGGAATTACAATGGCCTATATCTC 58.602 38.462 3.32 0.00 0.00 2.75
1804 7146 7.017551 AGTGGAATTACAATGGCCTATATCTCA 59.982 37.037 3.32 0.00 0.00 3.27
1805 7147 7.831193 GTGGAATTACAATGGCCTATATCTCAT 59.169 37.037 3.32 0.00 0.00 2.90
1806 7148 7.830697 TGGAATTACAATGGCCTATATCTCATG 59.169 37.037 3.32 0.00 0.00 3.07
1807 7149 7.284034 GGAATTACAATGGCCTATATCTCATGG 59.716 40.741 3.32 0.00 0.00 3.66
1808 7150 3.960571 ACAATGGCCTATATCTCATGGC 58.039 45.455 3.32 0.00 44.22 4.40
1809 7151 2.941064 CAATGGCCTATATCTCATGGCG 59.059 50.000 3.32 0.00 45.75 5.69
1810 7152 0.904649 TGGCCTATATCTCATGGCGG 59.095 55.000 3.32 0.00 45.75 6.13
1811 7153 1.195115 GGCCTATATCTCATGGCGGA 58.805 55.000 0.00 0.00 45.75 5.54
1812 7154 1.765314 GGCCTATATCTCATGGCGGAT 59.235 52.381 0.00 0.00 45.75 4.18
1813 7155 2.224161 GGCCTATATCTCATGGCGGATC 60.224 54.545 0.00 0.00 45.75 3.36
1814 7156 2.224161 GCCTATATCTCATGGCGGATCC 60.224 54.545 0.00 0.00 35.79 3.36
1815 7157 2.366916 CCTATATCTCATGGCGGATCCC 59.633 54.545 6.06 0.00 0.00 3.85
1816 7158 1.956869 ATATCTCATGGCGGATCCCA 58.043 50.000 6.06 0.00 39.65 4.37
1817 7159 1.269958 TATCTCATGGCGGATCCCAG 58.730 55.000 6.06 0.00 38.50 4.45
1818 7160 1.486997 ATCTCATGGCGGATCCCAGG 61.487 60.000 6.06 0.82 38.50 4.45
1819 7161 2.040988 TCATGGCGGATCCCAGGA 60.041 61.111 6.06 3.56 42.81 3.86
1820 7162 2.142761 TCATGGCGGATCCCAGGAG 61.143 63.158 6.06 0.00 40.43 3.69
1821 7163 2.851102 ATGGCGGATCCCAGGAGG 60.851 66.667 6.06 0.00 38.50 4.30
1836 7178 3.181526 GAGGGGCTCTCCAAACATG 57.818 57.895 1.89 0.00 36.52 3.21
1837 7179 0.620556 GAGGGGCTCTCCAAACATGA 59.379 55.000 1.89 0.00 36.52 3.07
1838 7180 1.213926 GAGGGGCTCTCCAAACATGAT 59.786 52.381 1.89 0.00 36.52 2.45
1839 7181 2.439507 GAGGGGCTCTCCAAACATGATA 59.560 50.000 1.89 0.00 36.52 2.15
1840 7182 2.173569 AGGGGCTCTCCAAACATGATAC 59.826 50.000 0.00 0.00 37.22 2.24
1841 7183 2.213499 GGGCTCTCCAAACATGATACG 58.787 52.381 0.00 0.00 35.00 3.06
1842 7184 1.599542 GGCTCTCCAAACATGATACGC 59.400 52.381 0.00 0.00 0.00 4.42
1843 7185 1.599542 GCTCTCCAAACATGATACGCC 59.400 52.381 0.00 0.00 0.00 5.68
1844 7186 2.213499 CTCTCCAAACATGATACGCCC 58.787 52.381 0.00 0.00 0.00 6.13
1845 7187 0.937304 CTCCAAACATGATACGCCCG 59.063 55.000 0.00 0.00 0.00 6.13
1846 7188 1.092921 TCCAAACATGATACGCCCGC 61.093 55.000 0.00 0.00 0.00 6.13
1847 7189 1.355210 CAAACATGATACGCCCGCC 59.645 57.895 0.00 0.00 0.00 6.13
1848 7190 1.095228 CAAACATGATACGCCCGCCT 61.095 55.000 0.00 0.00 0.00 5.52
1849 7191 1.095228 AAACATGATACGCCCGCCTG 61.095 55.000 0.00 0.00 0.00 4.85
1850 7192 3.349006 CATGATACGCCCGCCTGC 61.349 66.667 0.00 0.00 0.00 4.85
1851 7193 4.626081 ATGATACGCCCGCCTGCC 62.626 66.667 0.00 0.00 0.00 4.85
1861 7203 4.183686 CGCCTGCCGCCAAAGATG 62.184 66.667 0.00 0.00 0.00 2.90
1862 7204 4.503314 GCCTGCCGCCAAAGATGC 62.503 66.667 0.00 0.00 0.00 3.91
1863 7205 3.063704 CCTGCCGCCAAAGATGCA 61.064 61.111 0.00 0.00 0.00 3.96
1864 7206 2.180017 CTGCCGCCAAAGATGCAC 59.820 61.111 0.00 0.00 0.00 4.57
1865 7207 2.282391 TGCCGCCAAAGATGCACT 60.282 55.556 0.00 0.00 0.00 4.40
1866 7208 2.180017 GCCGCCAAAGATGCACTG 59.820 61.111 0.00 0.00 0.00 3.66
1867 7209 2.334946 GCCGCCAAAGATGCACTGA 61.335 57.895 0.00 0.00 0.00 3.41
1868 7210 1.865788 GCCGCCAAAGATGCACTGAA 61.866 55.000 0.00 0.00 0.00 3.02
1869 7211 0.813184 CCGCCAAAGATGCACTGAAT 59.187 50.000 0.00 0.00 0.00 2.57
1870 7212 1.203052 CCGCCAAAGATGCACTGAATT 59.797 47.619 0.00 0.00 0.00 2.17
1871 7213 2.353011 CCGCCAAAGATGCACTGAATTT 60.353 45.455 0.00 0.00 0.00 1.82
1872 7214 3.319755 CGCCAAAGATGCACTGAATTTT 58.680 40.909 0.00 0.00 0.00 1.82
1873 7215 3.365820 CGCCAAAGATGCACTGAATTTTC 59.634 43.478 0.00 0.00 0.00 2.29
1874 7216 3.365820 GCCAAAGATGCACTGAATTTTCG 59.634 43.478 0.00 0.00 0.00 3.46
1875 7217 4.797471 CCAAAGATGCACTGAATTTTCGA 58.203 39.130 0.00 0.00 0.00 3.71
1876 7218 5.404946 CCAAAGATGCACTGAATTTTCGAT 58.595 37.500 0.00 0.00 0.00 3.59
1877 7219 5.287752 CCAAAGATGCACTGAATTTTCGATG 59.712 40.000 0.00 0.00 0.00 3.84
1878 7220 4.627611 AGATGCACTGAATTTTCGATGG 57.372 40.909 0.00 0.00 0.00 3.51
1879 7221 2.634982 TGCACTGAATTTTCGATGGC 57.365 45.000 0.00 0.00 0.00 4.40
1880 7222 1.202114 TGCACTGAATTTTCGATGGCC 59.798 47.619 0.00 0.00 0.00 5.36
1881 7223 1.474077 GCACTGAATTTTCGATGGCCT 59.526 47.619 3.32 0.00 0.00 5.19
1882 7224 2.094545 GCACTGAATTTTCGATGGCCTT 60.095 45.455 3.32 0.00 0.00 4.35
1883 7225 3.614870 GCACTGAATTTTCGATGGCCTTT 60.615 43.478 3.32 0.00 0.00 3.11
1884 7226 3.922240 CACTGAATTTTCGATGGCCTTTG 59.078 43.478 3.32 0.86 0.00 2.77
1885 7227 2.925563 CTGAATTTTCGATGGCCTTTGC 59.074 45.455 3.32 0.00 0.00 3.68
1886 7228 2.298446 TGAATTTTCGATGGCCTTTGCA 59.702 40.909 3.32 0.00 40.13 4.08
1887 7229 3.244009 TGAATTTTCGATGGCCTTTGCAA 60.244 39.130 3.32 0.00 40.13 4.08
1888 7230 2.147436 TTTTCGATGGCCTTTGCAAC 57.853 45.000 3.32 0.00 40.13 4.17
1889 7231 0.039617 TTTCGATGGCCTTTGCAACG 60.040 50.000 3.32 0.00 40.13 4.10
1890 7232 1.169661 TTCGATGGCCTTTGCAACGT 61.170 50.000 3.32 0.00 40.13 3.99
1891 7233 1.154225 CGATGGCCTTTGCAACGTC 60.154 57.895 3.32 0.00 40.13 4.34
1892 7234 1.212751 GATGGCCTTTGCAACGTCC 59.787 57.895 3.32 0.00 40.13 4.79
1893 7235 2.212900 GATGGCCTTTGCAACGTCCC 62.213 60.000 3.32 0.51 40.13 4.46
1894 7236 2.597510 GGCCTTTGCAACGTCCCT 60.598 61.111 0.00 0.00 40.13 4.20
1895 7237 2.200337 GGCCTTTGCAACGTCCCTT 61.200 57.895 0.00 0.00 40.13 3.95
1896 7238 1.007387 GCCTTTGCAACGTCCCTTG 60.007 57.895 0.00 0.00 37.47 3.61
1897 7239 1.007387 CCTTTGCAACGTCCCTTGC 60.007 57.895 0.00 2.98 45.80 4.01
1898 7240 1.455383 CCTTTGCAACGTCCCTTGCT 61.455 55.000 10.97 0.00 45.79 3.91
1899 7241 0.318107 CTTTGCAACGTCCCTTGCTG 60.318 55.000 10.97 0.00 45.79 4.41
1900 7242 2.348605 TTTGCAACGTCCCTTGCTGC 62.349 55.000 10.97 5.42 45.79 5.25
1901 7243 4.043200 GCAACGTCCCTTGCTGCC 62.043 66.667 2.71 0.00 42.84 4.85
1902 7244 3.726517 CAACGTCCCTTGCTGCCG 61.727 66.667 0.00 0.00 0.00 5.69
1940 7282 7.080353 TGCATTGCATATTGATCATAGTAGC 57.920 36.000 7.38 0.00 31.71 3.58
1941 7283 6.882678 TGCATTGCATATTGATCATAGTAGCT 59.117 34.615 7.38 0.00 31.71 3.32
1942 7284 8.042515 TGCATTGCATATTGATCATAGTAGCTA 58.957 33.333 7.38 0.00 31.71 3.32
1943 7285 8.333908 GCATTGCATATTGATCATAGTAGCTAC 58.666 37.037 16.43 16.43 0.00 3.58
1944 7286 8.538039 CATTGCATATTGATCATAGTAGCTACG 58.462 37.037 17.99 4.63 0.00 3.51
1945 7287 7.158099 TGCATATTGATCATAGTAGCTACGT 57.842 36.000 17.99 8.50 0.00 3.57
1946 7288 8.276252 TGCATATTGATCATAGTAGCTACGTA 57.724 34.615 17.99 11.08 0.00 3.57
1947 7289 8.182227 TGCATATTGATCATAGTAGCTACGTAC 58.818 37.037 17.99 8.47 0.00 3.67
1948 7290 8.399425 GCATATTGATCATAGTAGCTACGTACT 58.601 37.037 17.99 5.14 37.09 2.73
2050 7416 2.343758 GGTCCAGCTGCTGTTCGA 59.656 61.111 26.41 14.88 0.00 3.71
2222 7612 2.126228 TCCCGTGATGACGTTCGC 60.126 61.111 3.53 0.00 44.54 4.70
2227 7617 1.134530 CGTGATGACGTTCGCCTCTC 61.135 60.000 0.00 0.00 40.91 3.20
2228 7618 0.802607 GTGATGACGTTCGCCTCTCC 60.803 60.000 0.00 0.00 0.00 3.71
2229 7619 1.586564 GATGACGTTCGCCTCTCCG 60.587 63.158 0.00 0.00 0.00 4.63
2230 7620 2.938539 GATGACGTTCGCCTCTCCGG 62.939 65.000 0.00 0.00 0.00 5.14
2289 7679 3.181493 GCTTTGATGATGTGGTGATGTCC 60.181 47.826 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 7.184106 TGTCAGTTTTTACTTAACAAAGAGCG 58.816 34.615 0.00 0.00 0.00 5.03
24 25 5.066375 CAGATGAACAACTTGGTCTTTGTCA 59.934 40.000 8.30 0.00 34.53 3.58
67 68 7.877612 AGTTTTCAAAAAGGAAAGCAGAAAAGA 59.122 29.630 0.00 0.00 39.53 2.52
129 130 4.440839 ACGAAATTCCAAGGCAGATTTC 57.559 40.909 0.00 10.04 0.00 2.17
264 579 1.484653 CCACAGATTACGATCCACCCA 59.515 52.381 0.00 0.00 32.44 4.51
265 580 1.810412 GCCACAGATTACGATCCACCC 60.810 57.143 0.00 0.00 32.44 4.61
274 605 1.755179 ATGCACAGGCCACAGATTAC 58.245 50.000 5.01 0.00 40.13 1.89
312 644 4.645136 GGAAGGGGTGGTCAATCTTAATTC 59.355 45.833 0.00 0.00 0.00 2.17
472 863 1.228003 ATGGACCCAAACACGCGAA 60.228 52.632 15.93 0.00 0.00 4.70
631 1032 7.171337 GCACAAAGAGCAATTTGGATTTTTCTA 59.829 33.333 15.47 0.00 43.10 2.10
632 1033 6.017687 GCACAAAGAGCAATTTGGATTTTTCT 60.018 34.615 15.47 0.00 43.10 2.52
680 1081 1.676006 GTTTGGAACAGACCAGTGTGG 59.324 52.381 0.00 0.00 42.00 4.17
707 2314 5.703130 GGAATATCCAGTGCAAGTAAGATCC 59.297 44.000 0.00 0.00 36.28 3.36
943 2558 1.669265 TGTACGTGCACGGATCTCTAG 59.331 52.381 39.21 12.35 44.95 2.43
1142 6439 2.959171 GCTCTCTCCATCTCCTTTCCCT 60.959 54.545 0.00 0.00 0.00 4.20
1308 6605 0.991146 TGGCACCTGCATTCCTCTAA 59.009 50.000 0.00 0.00 44.36 2.10
1375 6687 9.057089 CAGGCCATTAGTTAAGTTATTCTAAGG 57.943 37.037 5.01 10.80 0.00 2.69
1590 6930 3.331150 TGTAGGTTAAAGACGGCATGTG 58.669 45.455 0.00 0.00 0.00 3.21
1591 6931 3.688694 TGTAGGTTAAAGACGGCATGT 57.311 42.857 0.00 0.00 0.00 3.21
1592 6932 4.000988 ACTTGTAGGTTAAAGACGGCATG 58.999 43.478 0.00 0.00 0.00 4.06
1593 6933 4.281898 ACTTGTAGGTTAAAGACGGCAT 57.718 40.909 0.00 0.00 0.00 4.40
1594 6934 3.756933 ACTTGTAGGTTAAAGACGGCA 57.243 42.857 0.00 0.00 0.00 5.69
1595 6935 5.209977 CAAAACTTGTAGGTTAAAGACGGC 58.790 41.667 0.00 0.00 0.00 5.68
1596 6936 6.367686 ACAAAACTTGTAGGTTAAAGACGG 57.632 37.500 0.00 0.00 43.27 4.79
1631 6973 4.236935 GCGATTGCTGGATCTTTCAAAAA 58.763 39.130 0.00 0.00 38.39 1.94
1632 6974 3.836949 GCGATTGCTGGATCTTTCAAAA 58.163 40.909 0.00 0.00 38.39 2.44
1633 6975 3.492421 GCGATTGCTGGATCTTTCAAA 57.508 42.857 0.00 0.00 38.39 2.69
1646 6988 2.849880 TATGAAAAGCCAGCGATTGC 57.150 45.000 0.00 0.00 43.24 3.56
1647 6989 4.556942 TGATATGAAAAGCCAGCGATTG 57.443 40.909 0.00 0.00 0.00 2.67
1648 6990 5.779529 AATGATATGAAAAGCCAGCGATT 57.220 34.783 0.00 0.00 0.00 3.34
1649 6991 5.106396 GCTAATGATATGAAAAGCCAGCGAT 60.106 40.000 0.00 0.00 0.00 4.58
1650 6992 4.214119 GCTAATGATATGAAAAGCCAGCGA 59.786 41.667 0.00 0.00 0.00 4.93
1651 6993 4.023792 TGCTAATGATATGAAAAGCCAGCG 60.024 41.667 0.00 0.00 0.00 5.18
1652 6994 5.240183 TCTGCTAATGATATGAAAAGCCAGC 59.760 40.000 0.00 0.00 0.00 4.85
1653 6995 6.872628 TCTGCTAATGATATGAAAAGCCAG 57.127 37.500 0.00 0.00 0.00 4.85
1654 6996 7.643569 TTTCTGCTAATGATATGAAAAGCCA 57.356 32.000 0.00 0.00 0.00 4.75
1655 6997 8.355169 TGATTTCTGCTAATGATATGAAAAGCC 58.645 33.333 0.00 0.00 0.00 4.35
1656 6998 9.740239 TTGATTTCTGCTAATGATATGAAAAGC 57.260 29.630 0.00 0.00 0.00 3.51
1660 7002 9.577222 TCCATTGATTTCTGCTAATGATATGAA 57.423 29.630 0.00 0.00 33.50 2.57
1661 7003 9.577222 TTCCATTGATTTCTGCTAATGATATGA 57.423 29.630 0.00 0.00 33.50 2.15
1665 7007 9.374838 GTTTTTCCATTGATTTCTGCTAATGAT 57.625 29.630 0.00 0.00 33.50 2.45
1666 7008 8.366401 TGTTTTTCCATTGATTTCTGCTAATGA 58.634 29.630 0.00 0.00 33.50 2.57
1667 7009 8.537049 TGTTTTTCCATTGATTTCTGCTAATG 57.463 30.769 0.00 0.00 0.00 1.90
1668 7010 9.211485 CTTGTTTTTCCATTGATTTCTGCTAAT 57.789 29.630 0.00 0.00 0.00 1.73
1669 7011 7.656948 CCTTGTTTTTCCATTGATTTCTGCTAA 59.343 33.333 0.00 0.00 0.00 3.09
1670 7012 7.153985 CCTTGTTTTTCCATTGATTTCTGCTA 58.846 34.615 0.00 0.00 0.00 3.49
1671 7013 5.993441 CCTTGTTTTTCCATTGATTTCTGCT 59.007 36.000 0.00 0.00 0.00 4.24
1672 7014 5.179929 CCCTTGTTTTTCCATTGATTTCTGC 59.820 40.000 0.00 0.00 0.00 4.26
1673 7015 6.203338 CACCCTTGTTTTTCCATTGATTTCTG 59.797 38.462 0.00 0.00 0.00 3.02
1674 7016 6.290605 CACCCTTGTTTTTCCATTGATTTCT 58.709 36.000 0.00 0.00 0.00 2.52
1675 7017 5.049474 GCACCCTTGTTTTTCCATTGATTTC 60.049 40.000 0.00 0.00 0.00 2.17
1676 7018 4.821260 GCACCCTTGTTTTTCCATTGATTT 59.179 37.500 0.00 0.00 0.00 2.17
1677 7019 4.388485 GCACCCTTGTTTTTCCATTGATT 58.612 39.130 0.00 0.00 0.00 2.57
1678 7020 3.554752 CGCACCCTTGTTTTTCCATTGAT 60.555 43.478 0.00 0.00 0.00 2.57
1679 7021 2.223923 CGCACCCTTGTTTTTCCATTGA 60.224 45.455 0.00 0.00 0.00 2.57
1680 7022 2.134346 CGCACCCTTGTTTTTCCATTG 58.866 47.619 0.00 0.00 0.00 2.82
1681 7023 1.760029 ACGCACCCTTGTTTTTCCATT 59.240 42.857 0.00 0.00 0.00 3.16
1682 7024 1.408969 ACGCACCCTTGTTTTTCCAT 58.591 45.000 0.00 0.00 0.00 3.41
1683 7025 1.134965 CAACGCACCCTTGTTTTTCCA 60.135 47.619 0.00 0.00 0.00 3.53
1684 7026 1.566404 CAACGCACCCTTGTTTTTCC 58.434 50.000 0.00 0.00 0.00 3.13
1685 7027 1.135333 TCCAACGCACCCTTGTTTTTC 59.865 47.619 0.00 0.00 0.00 2.29
1686 7028 1.136110 CTCCAACGCACCCTTGTTTTT 59.864 47.619 0.00 0.00 0.00 1.94
1687 7029 0.744281 CTCCAACGCACCCTTGTTTT 59.256 50.000 0.00 0.00 0.00 2.43
1688 7030 1.106944 CCTCCAACGCACCCTTGTTT 61.107 55.000 0.00 0.00 0.00 2.83
1689 7031 1.528309 CCTCCAACGCACCCTTGTT 60.528 57.895 0.00 0.00 0.00 2.83
1690 7032 2.113139 CCTCCAACGCACCCTTGT 59.887 61.111 0.00 0.00 0.00 3.16
1691 7033 2.672996 CCCTCCAACGCACCCTTG 60.673 66.667 0.00 0.00 0.00 3.61
1692 7034 3.175710 ACCCTCCAACGCACCCTT 61.176 61.111 0.00 0.00 0.00 3.95
1693 7035 3.637273 GACCCTCCAACGCACCCT 61.637 66.667 0.00 0.00 0.00 4.34
1694 7036 4.717313 GGACCCTCCAACGCACCC 62.717 72.222 0.00 0.00 36.28 4.61
1695 7037 1.833787 TTAGGACCCTCCAACGCACC 61.834 60.000 0.00 0.00 39.61 5.01
1696 7038 0.391263 CTTAGGACCCTCCAACGCAC 60.391 60.000 0.00 0.00 39.61 5.34
1697 7039 0.543410 TCTTAGGACCCTCCAACGCA 60.543 55.000 0.00 0.00 39.61 5.24
1698 7040 0.108281 GTCTTAGGACCCTCCAACGC 60.108 60.000 0.00 0.00 39.61 4.84
1708 7050 6.756221 TCTTTTTCTGTACTGGTCTTAGGAC 58.244 40.000 0.00 0.00 41.43 3.85
1709 7051 6.989155 TCTTTTTCTGTACTGGTCTTAGGA 57.011 37.500 0.00 0.00 0.00 2.94
1710 7052 9.152595 GTAATCTTTTTCTGTACTGGTCTTAGG 57.847 37.037 0.00 0.00 0.00 2.69
1711 7053 9.706691 TGTAATCTTTTTCTGTACTGGTCTTAG 57.293 33.333 0.00 0.00 0.00 2.18
1713 7055 8.837389 GTTGTAATCTTTTTCTGTACTGGTCTT 58.163 33.333 0.00 0.00 0.00 3.01
1714 7056 7.170998 CGTTGTAATCTTTTTCTGTACTGGTCT 59.829 37.037 0.00 0.00 0.00 3.85
1715 7057 7.170320 TCGTTGTAATCTTTTTCTGTACTGGTC 59.830 37.037 0.00 0.00 0.00 4.02
1716 7058 6.987992 TCGTTGTAATCTTTTTCTGTACTGGT 59.012 34.615 0.00 0.00 0.00 4.00
1717 7059 7.288672 GTCGTTGTAATCTTTTTCTGTACTGG 58.711 38.462 0.00 0.00 0.00 4.00
1718 7060 7.170998 AGGTCGTTGTAATCTTTTTCTGTACTG 59.829 37.037 0.00 0.00 0.00 2.74
1719 7061 7.215085 AGGTCGTTGTAATCTTTTTCTGTACT 58.785 34.615 0.00 0.00 0.00 2.73
1720 7062 7.417496 AGGTCGTTGTAATCTTTTTCTGTAC 57.583 36.000 0.00 0.00 0.00 2.90
1721 7063 7.519328 GCAAGGTCGTTGTAATCTTTTTCTGTA 60.519 37.037 7.09 0.00 38.55 2.74
1722 7064 6.725246 CAAGGTCGTTGTAATCTTTTTCTGT 58.275 36.000 0.00 0.00 0.00 3.41
1723 7065 5.625311 GCAAGGTCGTTGTAATCTTTTTCTG 59.375 40.000 7.09 0.00 38.55 3.02
1724 7066 5.531287 AGCAAGGTCGTTGTAATCTTTTTCT 59.469 36.000 7.09 0.00 38.55 2.52
1725 7067 5.758924 AGCAAGGTCGTTGTAATCTTTTTC 58.241 37.500 7.09 0.00 38.55 2.29
1726 7068 5.767816 AGCAAGGTCGTTGTAATCTTTTT 57.232 34.783 7.09 0.00 38.55 1.94
1727 7069 5.560183 CGAAGCAAGGTCGTTGTAATCTTTT 60.560 40.000 7.09 0.00 38.55 2.27
1728 7070 4.084013 CGAAGCAAGGTCGTTGTAATCTTT 60.084 41.667 7.09 0.00 38.55 2.52
1729 7071 3.432252 CGAAGCAAGGTCGTTGTAATCTT 59.568 43.478 7.09 2.18 38.55 2.40
1730 7072 2.993899 CGAAGCAAGGTCGTTGTAATCT 59.006 45.455 7.09 0.00 38.55 2.40
1731 7073 2.093783 CCGAAGCAAGGTCGTTGTAATC 59.906 50.000 7.09 3.08 38.55 1.75
1732 7074 2.073816 CCGAAGCAAGGTCGTTGTAAT 58.926 47.619 7.09 0.00 38.55 1.89
1733 7075 1.504359 CCGAAGCAAGGTCGTTGTAA 58.496 50.000 7.09 0.00 38.55 2.41
1734 7076 0.947180 GCCGAAGCAAGGTCGTTGTA 60.947 55.000 7.09 0.00 38.55 2.41
1735 7077 2.251642 GCCGAAGCAAGGTCGTTGT 61.252 57.895 7.09 0.00 38.55 3.32
1736 7078 2.556287 GCCGAAGCAAGGTCGTTG 59.444 61.111 0.77 0.77 39.53 4.10
1737 7079 2.668550 GGCCGAAGCAAGGTCGTT 60.669 61.111 0.00 0.00 42.56 3.85
1738 7080 2.951475 TTTGGCCGAAGCAAGGTCGT 62.951 55.000 0.00 0.00 42.56 4.34
1739 7081 2.187599 CTTTGGCCGAAGCAAGGTCG 62.188 60.000 19.99 0.00 42.56 4.79
1740 7082 1.581447 CTTTGGCCGAAGCAAGGTC 59.419 57.895 19.99 0.00 42.56 3.85
1741 7083 3.763671 CTTTGGCCGAAGCAAGGT 58.236 55.556 19.99 0.00 42.56 3.50
1747 7089 0.665369 CAGCAAAGCTTTGGCCGAAG 60.665 55.000 34.02 26.33 36.40 3.79
1748 7090 1.106351 TCAGCAAAGCTTTGGCCGAA 61.106 50.000 34.02 15.20 36.40 4.30
1749 7091 1.528076 TCAGCAAAGCTTTGGCCGA 60.528 52.632 34.02 22.41 36.40 5.54
1750 7092 1.372128 GTCAGCAAAGCTTTGGCCG 60.372 57.895 34.02 20.84 36.40 6.13
1751 7093 1.005748 GGTCAGCAAAGCTTTGGCC 60.006 57.895 34.02 20.82 36.40 5.36
1752 7094 1.372128 CGGTCAGCAAAGCTTTGGC 60.372 57.895 34.02 26.28 36.40 4.52
1753 7095 0.667993 TTCGGTCAGCAAAGCTTTGG 59.332 50.000 34.02 21.52 36.40 3.28
1754 7096 1.335324 CCTTCGGTCAGCAAAGCTTTG 60.335 52.381 30.70 30.70 36.40 2.77
1755 7097 0.954452 CCTTCGGTCAGCAAAGCTTT 59.046 50.000 5.69 5.69 36.40 3.51
1756 7098 0.108585 TCCTTCGGTCAGCAAAGCTT 59.891 50.000 0.00 0.00 36.40 3.74
1757 7099 0.108585 TTCCTTCGGTCAGCAAAGCT 59.891 50.000 0.00 0.00 40.77 3.74
1758 7100 0.519077 CTTCCTTCGGTCAGCAAAGC 59.481 55.000 0.00 0.00 0.00 3.51
1759 7101 2.072298 CTCTTCCTTCGGTCAGCAAAG 58.928 52.381 0.00 0.00 0.00 2.77
1760 7102 1.416401 ACTCTTCCTTCGGTCAGCAAA 59.584 47.619 0.00 0.00 0.00 3.68
1761 7103 1.048601 ACTCTTCCTTCGGTCAGCAA 58.951 50.000 0.00 0.00 0.00 3.91
1762 7104 0.318441 CACTCTTCCTTCGGTCAGCA 59.682 55.000 0.00 0.00 0.00 4.41
1763 7105 0.390472 CCACTCTTCCTTCGGTCAGC 60.390 60.000 0.00 0.00 0.00 4.26
1764 7106 1.257743 TCCACTCTTCCTTCGGTCAG 58.742 55.000 0.00 0.00 0.00 3.51
1765 7107 1.712056 TTCCACTCTTCCTTCGGTCA 58.288 50.000 0.00 0.00 0.00 4.02
1766 7108 3.336138 AATTCCACTCTTCCTTCGGTC 57.664 47.619 0.00 0.00 0.00 4.79
1767 7109 3.581332 TGTAATTCCACTCTTCCTTCGGT 59.419 43.478 0.00 0.00 0.00 4.69
1768 7110 4.202245 TGTAATTCCACTCTTCCTTCGG 57.798 45.455 0.00 0.00 0.00 4.30
1769 7111 5.065218 CCATTGTAATTCCACTCTTCCTTCG 59.935 44.000 0.00 0.00 0.00 3.79
1770 7112 5.163612 GCCATTGTAATTCCACTCTTCCTTC 60.164 44.000 0.00 0.00 0.00 3.46
1771 7113 4.706962 GCCATTGTAATTCCACTCTTCCTT 59.293 41.667 0.00 0.00 0.00 3.36
1772 7114 4.273318 GCCATTGTAATTCCACTCTTCCT 58.727 43.478 0.00 0.00 0.00 3.36
1773 7115 3.381590 GGCCATTGTAATTCCACTCTTCC 59.618 47.826 0.00 0.00 0.00 3.46
1774 7116 4.273318 AGGCCATTGTAATTCCACTCTTC 58.727 43.478 5.01 0.00 0.00 2.87
1775 7117 4.322057 AGGCCATTGTAATTCCACTCTT 57.678 40.909 5.01 0.00 0.00 2.85
1776 7118 5.653255 ATAGGCCATTGTAATTCCACTCT 57.347 39.130 5.01 0.00 0.00 3.24
1777 7119 7.398024 AGATATAGGCCATTGTAATTCCACTC 58.602 38.462 5.01 0.00 0.00 3.51
1778 7120 7.017551 TGAGATATAGGCCATTGTAATTCCACT 59.982 37.037 5.01 0.00 0.00 4.00
1779 7121 7.168219 TGAGATATAGGCCATTGTAATTCCAC 58.832 38.462 5.01 0.00 0.00 4.02
1780 7122 7.328404 TGAGATATAGGCCATTGTAATTCCA 57.672 36.000 5.01 0.00 0.00 3.53
1781 7123 7.284034 CCATGAGATATAGGCCATTGTAATTCC 59.716 40.741 5.01 0.00 0.00 3.01
1782 7124 7.201767 GCCATGAGATATAGGCCATTGTAATTC 60.202 40.741 5.01 0.00 41.25 2.17
1783 7125 6.604795 GCCATGAGATATAGGCCATTGTAATT 59.395 38.462 5.01 0.00 41.25 1.40
1784 7126 6.125029 GCCATGAGATATAGGCCATTGTAAT 58.875 40.000 5.01 0.00 41.25 1.89
1785 7127 5.500234 GCCATGAGATATAGGCCATTGTAA 58.500 41.667 5.01 0.00 41.25 2.41
1786 7128 4.383010 CGCCATGAGATATAGGCCATTGTA 60.383 45.833 5.01 0.00 44.18 2.41
1787 7129 3.620719 CGCCATGAGATATAGGCCATTGT 60.621 47.826 5.01 0.00 44.18 2.71
1788 7130 2.941064 CGCCATGAGATATAGGCCATTG 59.059 50.000 5.01 0.00 44.18 2.82
1789 7131 2.092753 CCGCCATGAGATATAGGCCATT 60.093 50.000 5.01 0.00 44.18 3.16
1790 7132 1.487976 CCGCCATGAGATATAGGCCAT 59.512 52.381 5.01 0.00 44.18 4.40
1791 7133 0.904649 CCGCCATGAGATATAGGCCA 59.095 55.000 5.01 0.00 44.18 5.36
1792 7134 1.195115 TCCGCCATGAGATATAGGCC 58.805 55.000 0.00 0.00 44.18 5.19
1793 7135 2.224161 GGATCCGCCATGAGATATAGGC 60.224 54.545 0.00 0.00 43.61 3.93
1794 7136 2.366916 GGGATCCGCCATGAGATATAGG 59.633 54.545 5.45 0.00 38.95 2.57
1795 7137 3.033909 TGGGATCCGCCATGAGATATAG 58.966 50.000 5.45 0.00 38.95 1.31
1796 7138 3.033909 CTGGGATCCGCCATGAGATATA 58.966 50.000 5.45 0.00 38.95 0.86
1797 7139 1.836166 CTGGGATCCGCCATGAGATAT 59.164 52.381 5.45 0.00 38.95 1.63
1798 7140 1.269958 CTGGGATCCGCCATGAGATA 58.730 55.000 5.45 0.00 38.95 1.98
1799 7141 1.486997 CCTGGGATCCGCCATGAGAT 61.487 60.000 5.45 0.00 38.95 2.75
1800 7142 2.142761 CCTGGGATCCGCCATGAGA 61.143 63.158 5.45 0.00 38.95 3.27
1801 7143 2.109517 CTCCTGGGATCCGCCATGAG 62.110 65.000 5.45 7.22 38.95 2.90
1802 7144 2.040988 TCCTGGGATCCGCCATGA 60.041 61.111 5.45 0.00 38.95 3.07
1803 7145 2.429058 CTCCTGGGATCCGCCATG 59.571 66.667 5.45 0.00 38.95 3.66
1804 7146 2.851102 CCTCCTGGGATCCGCCAT 60.851 66.667 5.45 0.00 38.95 4.40
1818 7160 0.620556 TCATGTTTGGAGAGCCCCTC 59.379 55.000 0.00 0.00 41.22 4.30
1819 7161 1.302907 ATCATGTTTGGAGAGCCCCT 58.697 50.000 0.00 0.00 0.00 4.79
1820 7162 2.576615 GTATCATGTTTGGAGAGCCCC 58.423 52.381 0.00 0.00 0.00 5.80
1821 7163 2.213499 CGTATCATGTTTGGAGAGCCC 58.787 52.381 0.00 0.00 0.00 5.19
1822 7164 1.599542 GCGTATCATGTTTGGAGAGCC 59.400 52.381 0.00 0.00 0.00 4.70
1823 7165 1.599542 GGCGTATCATGTTTGGAGAGC 59.400 52.381 0.00 0.00 0.00 4.09
1824 7166 2.213499 GGGCGTATCATGTTTGGAGAG 58.787 52.381 0.00 0.00 0.00 3.20
1825 7167 1.472552 CGGGCGTATCATGTTTGGAGA 60.473 52.381 0.00 0.00 0.00 3.71
1826 7168 0.937304 CGGGCGTATCATGTTTGGAG 59.063 55.000 0.00 0.00 0.00 3.86
1827 7169 1.092921 GCGGGCGTATCATGTTTGGA 61.093 55.000 0.00 0.00 0.00 3.53
1828 7170 1.355210 GCGGGCGTATCATGTTTGG 59.645 57.895 0.00 0.00 0.00 3.28
1829 7171 1.095228 AGGCGGGCGTATCATGTTTG 61.095 55.000 0.00 0.00 0.00 2.93
1830 7172 1.095228 CAGGCGGGCGTATCATGTTT 61.095 55.000 0.00 0.00 0.00 2.83
1831 7173 1.523711 CAGGCGGGCGTATCATGTT 60.524 57.895 0.00 0.00 0.00 2.71
1832 7174 2.108976 CAGGCGGGCGTATCATGT 59.891 61.111 0.00 0.00 0.00 3.21
1833 7175 3.349006 GCAGGCGGGCGTATCATG 61.349 66.667 0.00 0.00 0.00 3.07
1834 7176 4.626081 GGCAGGCGGGCGTATCAT 62.626 66.667 0.00 0.00 33.57 2.45
1845 7187 4.503314 GCATCTTTGGCGGCAGGC 62.503 66.667 12.87 2.73 44.11 4.85
1846 7188 3.063704 TGCATCTTTGGCGGCAGG 61.064 61.111 12.87 9.70 0.00 4.85
1847 7189 2.180017 GTGCATCTTTGGCGGCAG 59.820 61.111 12.87 1.01 36.86 4.85
1848 7190 2.282391 AGTGCATCTTTGGCGGCA 60.282 55.556 7.97 7.97 0.00 5.69
1849 7191 1.865788 TTCAGTGCATCTTTGGCGGC 61.866 55.000 0.00 0.00 0.00 6.53
1850 7192 0.813184 ATTCAGTGCATCTTTGGCGG 59.187 50.000 0.00 0.00 0.00 6.13
1851 7193 2.642139 AATTCAGTGCATCTTTGGCG 57.358 45.000 0.00 0.00 0.00 5.69
1852 7194 3.365820 CGAAAATTCAGTGCATCTTTGGC 59.634 43.478 0.00 0.00 0.00 4.52
1853 7195 4.797471 TCGAAAATTCAGTGCATCTTTGG 58.203 39.130 0.00 0.00 0.00 3.28
1854 7196 5.287752 CCATCGAAAATTCAGTGCATCTTTG 59.712 40.000 0.00 0.00 0.00 2.77
1855 7197 5.404946 CCATCGAAAATTCAGTGCATCTTT 58.595 37.500 0.00 0.00 0.00 2.52
1856 7198 4.676196 GCCATCGAAAATTCAGTGCATCTT 60.676 41.667 0.00 0.00 0.00 2.40
1857 7199 3.181493 GCCATCGAAAATTCAGTGCATCT 60.181 43.478 0.00 0.00 0.00 2.90
1858 7200 3.111098 GCCATCGAAAATTCAGTGCATC 58.889 45.455 0.00 0.00 0.00 3.91
1859 7201 2.159198 GGCCATCGAAAATTCAGTGCAT 60.159 45.455 0.00 0.00 0.00 3.96
1860 7202 1.202114 GGCCATCGAAAATTCAGTGCA 59.798 47.619 0.00 0.00 0.00 4.57
1861 7203 1.474077 AGGCCATCGAAAATTCAGTGC 59.526 47.619 5.01 0.00 0.00 4.40
1862 7204 3.855689 AAGGCCATCGAAAATTCAGTG 57.144 42.857 5.01 0.00 0.00 3.66
1863 7205 3.614870 GCAAAGGCCATCGAAAATTCAGT 60.615 43.478 5.01 0.00 0.00 3.41
1864 7206 2.925563 GCAAAGGCCATCGAAAATTCAG 59.074 45.455 5.01 0.00 0.00 3.02
1865 7207 2.298446 TGCAAAGGCCATCGAAAATTCA 59.702 40.909 5.01 0.00 40.13 2.57
1866 7208 2.958213 TGCAAAGGCCATCGAAAATTC 58.042 42.857 5.01 0.00 40.13 2.17
1867 7209 3.066380 GTTGCAAAGGCCATCGAAAATT 58.934 40.909 5.01 0.00 40.13 1.82
1868 7210 2.687370 GTTGCAAAGGCCATCGAAAAT 58.313 42.857 5.01 0.00 40.13 1.82
1869 7211 1.601663 CGTTGCAAAGGCCATCGAAAA 60.602 47.619 5.01 0.00 40.13 2.29
1870 7212 0.039617 CGTTGCAAAGGCCATCGAAA 60.040 50.000 5.01 0.00 40.13 3.46
1871 7213 1.169661 ACGTTGCAAAGGCCATCGAA 61.170 50.000 16.80 0.00 40.13 3.71
1872 7214 1.573829 GACGTTGCAAAGGCCATCGA 61.574 55.000 16.80 0.00 40.13 3.59
1873 7215 1.154225 GACGTTGCAAAGGCCATCG 60.154 57.895 16.80 9.36 40.13 3.84
1874 7216 1.212751 GGACGTTGCAAAGGCCATC 59.787 57.895 29.76 11.65 40.13 3.51
1875 7217 2.275380 GGGACGTTGCAAAGGCCAT 61.275 57.895 33.96 6.26 40.13 4.40
1876 7218 2.909965 GGGACGTTGCAAAGGCCA 60.910 61.111 33.96 0.00 40.13 5.36
1877 7219 2.200337 AAGGGACGTTGCAAAGGCC 61.200 57.895 27.35 27.35 40.13 5.19
1878 7220 1.007387 CAAGGGACGTTGCAAAGGC 60.007 57.895 16.80 13.70 41.68 4.35
1885 7227 3.726517 CGGCAGCAAGGGACGTTG 61.727 66.667 0.00 0.69 0.00 4.10
1896 7238 1.210155 CTACAAAACTGGCGGCAGC 59.790 57.895 36.06 0.00 44.18 5.25
1897 7239 0.951558 AACTACAAAACTGGCGGCAG 59.048 50.000 34.75 34.75 0.00 4.85
1898 7240 0.665835 CAACTACAAAACTGGCGGCA 59.334 50.000 12.58 12.58 0.00 5.69
1899 7241 0.663269 GCAACTACAAAACTGGCGGC 60.663 55.000 0.00 0.00 0.00 6.53
1900 7242 0.665835 TGCAACTACAAAACTGGCGG 59.334 50.000 0.00 0.00 0.00 6.13
1901 7243 2.704725 ATGCAACTACAAAACTGGCG 57.295 45.000 0.00 0.00 0.00 5.69
1902 7244 2.476241 GCAATGCAACTACAAAACTGGC 59.524 45.455 0.00 0.00 0.00 4.85
1903 7245 3.715495 TGCAATGCAACTACAAAACTGG 58.285 40.909 5.01 0.00 34.76 4.00
1904 7246 7.328982 TCAATATGCAATGCAACTACAAAACTG 59.671 33.333 13.45 0.00 43.62 3.16
1905 7247 7.377398 TCAATATGCAATGCAACTACAAAACT 58.623 30.769 13.45 0.00 43.62 2.66
1906 7248 7.579589 TCAATATGCAATGCAACTACAAAAC 57.420 32.000 13.45 0.00 43.62 2.43
1993 7342 3.059884 GAGGTGCCGATGTATATGTGTG 58.940 50.000 0.00 0.00 0.00 3.82
1994 7343 2.037251 GGAGGTGCCGATGTATATGTGT 59.963 50.000 0.00 0.00 0.00 3.72
2050 7416 3.958860 AAGCCGTCAGCCAGCCTT 61.959 61.111 0.00 0.00 45.47 4.35
2192 7582 0.812412 CACGGGAGGTTCAACACGTT 60.812 55.000 0.00 0.00 43.66 3.99
2289 7679 3.328382 TGACATACAGGACCGGAAAAG 57.672 47.619 9.46 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.