Multiple sequence alignment - TraesCS1B01G444000

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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 TraesCS1B01G444000 chr1B 100.000 2462 0 0 1 2462 664977831 664975370 0.000000e+00 4547
1 TraesCS1B01G444000 chr1B 91.740 569 23 9 1 547 572832988 572832422 0.000000e+00 769
2 TraesCS1B01G444000 chr1B 92.166 217 8 2 598 806 667675449 667675234 5.150000e-77 298
3 TraesCS1B01G444000 chr1D 90.652 1487 86 26 579 2047 477281377 477279926 0.000000e+00 1927
4 TraesCS1B01G444000 chr1A 90.990 1465 77 14 572 2026 573638012 573636593 0.000000e+00 1923
5 TraesCS1B01G444000 chr1A 86.553 528 40 14 1174 1697 485018304 485017804 9.950000e-154 553
6 TraesCS1B01G444000 chr1A 86.528 527 40 14 1175 1697 577043147 577042648 3.580000e-153 551
7 TraesCS1B01G444000 chr6B 96.161 547 18 2 1 544 293099531 293100077 0.000000e+00 891
8 TraesCS1B01G444000 chr6B 94.805 539 26 1 1 539 116212656 116213192 0.000000e+00 839
9 TraesCS1B01G444000 chr6B 94.681 376 15 3 1 372 165300802 165301176 1.640000e-161 579
10 TraesCS1B01G444000 chr4A 95.037 544 25 1 1 544 652190409 652190950 0.000000e+00 854
11 TraesCS1B01G444000 chr4A 92.049 566 22 3 1 544 663371534 663370970 0.000000e+00 774
12 TraesCS1B01G444000 chr2B 94.698 547 25 2 1 544 507805207 507805752 0.000000e+00 846
13 TraesCS1B01G444000 chr7B 95.429 525 22 1 1 525 700436957 700436435 0.000000e+00 835
14 TraesCS1B01G444000 chr7B 87.560 418 28 7 1174 1591 467713108 467713501 1.720000e-126 462
15 TraesCS1B01G444000 chr7B 91.250 80 6 1 2383 2462 251770001 251770079 9.310000e-20 108
16 TraesCS1B01G444000 chr5B 93.784 547 30 2 1 544 578999348 578999893 0.000000e+00 819
17 TraesCS1B01G444000 chr3B 98.123 373 6 1 2091 2462 50350452 50350824 0.000000e+00 649
18 TraesCS1B01G444000 chr3D 88.994 527 43 7 1174 1697 189003533 189003019 2.670000e-179 638
19 TraesCS1B01G444000 chr2D 88.722 532 39 12 1174 1697 468361639 468361121 4.470000e-177 630
20 TraesCS1B01G444000 chr2D 86.782 522 40 8 1174 1691 57319650 57320146 2.770000e-154 555
21 TraesCS1B01G444000 chr2D 89.189 444 27 8 1256 1691 152092128 152092558 3.600000e-148 534
22 TraesCS1B01G444000 chr2D 87.526 481 36 12 1225 1697 607668338 607667874 3.600000e-148 534
23 TraesCS1B01G444000 chr5A 88.697 522 39 12 1174 1691 599255255 599255760 9.670000e-174 619
24 TraesCS1B01G444000 chr5A 91.954 87 5 2 2378 2462 544798355 544798441 1.200000e-23 121
25 TraesCS1B01G444000 chr4B 95.584 385 14 1 163 544 449507789 449507405 4.500000e-172 614
26 TraesCS1B01G444000 chr4D 87.146 529 44 14 1174 1694 414509186 414508674 1.640000e-161 579
27 TraesCS1B01G444000 chr5D 95.977 348 11 3 1 347 255683880 255684225 1.650000e-156 562
28 TraesCS1B01G444000 chr5D 88.347 472 34 11 1234 1697 160881154 160880696 4.630000e-152 547
29 TraesCS1B01G444000 chr5D 95.294 85 3 1 2378 2462 55071528 55071445 1.540000e-27 134
30 TraesCS1B01G444000 chr6D 88.478 460 32 10 1240 1691 392885733 392886179 1.000000e-148 536
31 TraesCS1B01G444000 chrUn 90.970 299 16 2 2091 2381 67414374 67414669 2.300000e-105 392
32 TraesCS1B01G444000 chr2A 96.250 80 3 0 2383 2462 678711805 678711726 5.520000e-27 132
33 TraesCS1B01G444000 chr2A 94.186 86 4 1 2378 2462 39733054 39732969 1.990000e-26 130
34 TraesCS1B01G444000 chr7A 93.671 79 4 1 2384 2462 732715704 732715627 1.550000e-22 117
35 TraesCS1B01G444000 chr7A 93.590 78 4 1 2385 2462 734146447 734146371 5.560000e-22 115
36 TraesCS1B01G444000 chr7D 95.522 67 3 0 2396 2462 151832653 151832719 9.310000e-20 108


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 TraesCS1B01G444000 chr1B 664975370 664977831 2461 True 4547 4547 100.000 1 2462 1 chr1B.!!$R2 2461
1 TraesCS1B01G444000 chr1B 572832422 572832988 566 True 769 769 91.740 1 547 1 chr1B.!!$R1 546
2 TraesCS1B01G444000 chr1D 477279926 477281377 1451 True 1927 1927 90.652 579 2047 1 chr1D.!!$R1 1468
3 TraesCS1B01G444000 chr1A 573636593 573638012 1419 True 1923 1923 90.990 572 2026 1 chr1A.!!$R2 1454
4 TraesCS1B01G444000 chr1A 485017804 485018304 500 True 553 553 86.553 1174 1697 1 chr1A.!!$R1 523
5 TraesCS1B01G444000 chr6B 293099531 293100077 546 False 891 891 96.161 1 544 1 chr6B.!!$F3 543
6 TraesCS1B01G444000 chr6B 116212656 116213192 536 False 839 839 94.805 1 539 1 chr6B.!!$F1 538
7 TraesCS1B01G444000 chr4A 652190409 652190950 541 False 854 854 95.037 1 544 1 chr4A.!!$F1 543
8 TraesCS1B01G444000 chr4A 663370970 663371534 564 True 774 774 92.049 1 544 1 chr4A.!!$R1 543
9 TraesCS1B01G444000 chr2B 507805207 507805752 545 False 846 846 94.698 1 544 1 chr2B.!!$F1 543
10 TraesCS1B01G444000 chr7B 700436435 700436957 522 True 835 835 95.429 1 525 1 chr7B.!!$R1 524
11 TraesCS1B01G444000 chr5B 578999348 578999893 545 False 819 819 93.784 1 544 1 chr5B.!!$F1 543
12 TraesCS1B01G444000 chr3D 189003019 189003533 514 True 638 638 88.994 1174 1697 1 chr3D.!!$R1 523
13 TraesCS1B01G444000 chr2D 468361121 468361639 518 True 630 630 88.722 1174 1697 1 chr2D.!!$R1 523
14 TraesCS1B01G444000 chr5A 599255255 599255760 505 False 619 619 88.697 1174 1691 1 chr5A.!!$F2 517
15 TraesCS1B01G444000 chr4D 414508674 414509186 512 True 579 579 87.146 1174 1694 1 chr4D.!!$R1 520

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
980 1047 0.736053 AGATCTCGGAGCAAGTCGAC 59.264 55.0 7.7 7.7 0.0 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2210 2324 0.028902 AAGCGACAAAAAGCACCGTC 59.971 50.0 0.0 0.0 35.48 4.79 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
235 237 4.228567 TGGCAGTGTGTCGGCGAA 62.229 61.111 12.92 0.00 38.10 4.70
456 502 0.888736 CCACCGCATTTCAGGACACA 60.889 55.000 0.00 0.00 0.00 3.72
528 574 2.968156 CGTTCGTTTGGGGTCGCA 60.968 61.111 0.00 0.00 0.00 5.10
547 593 2.583441 CGGTGGAGTTGGCCTCAGA 61.583 63.158 3.32 0.00 42.40 3.27
548 594 1.003233 GGTGGAGTTGGCCTCAGAC 60.003 63.158 3.32 0.00 42.40 3.51
549 595 1.003233 GTGGAGTTGGCCTCAGACC 60.003 63.158 3.32 1.79 42.40 3.85
550 596 1.461268 TGGAGTTGGCCTCAGACCA 60.461 57.895 3.32 4.68 42.40 4.02
551 597 1.003233 GGAGTTGGCCTCAGACCAC 60.003 63.158 3.32 0.00 42.40 4.16
552 598 1.374758 GAGTTGGCCTCAGACCACG 60.375 63.158 3.32 0.00 40.17 4.94
553 599 2.358737 GTTGGCCTCAGACCACGG 60.359 66.667 3.32 0.00 36.76 4.94
554 600 3.636231 TTGGCCTCAGACCACGGG 61.636 66.667 3.32 0.00 36.76 5.28
568 614 2.828095 CGGGCCCGATGCATTTCA 60.828 61.111 41.82 0.00 43.89 2.69
569 615 2.807622 GGGCCCGATGCATTTCAC 59.192 61.111 5.69 0.00 43.89 3.18
570 616 2.051518 GGGCCCGATGCATTTCACA 61.052 57.895 5.69 0.00 43.89 3.58
594 640 1.227823 TGAAACTCCACAGGCCACG 60.228 57.895 5.01 0.00 0.00 4.94
656 709 3.795342 GTAAACCGCGCACGCCAT 61.795 61.111 8.75 0.00 38.22 4.40
850 908 1.228003 ACGTCCAAATCAACGGCCA 60.228 52.632 2.24 0.00 42.99 5.36
956 1023 2.808543 CCTATAAGAATCCGCAAGCACC 59.191 50.000 0.00 0.00 0.00 5.01
961 1028 2.852495 GAATCCGCAAGCACCCGAGA 62.852 60.000 0.00 0.00 0.00 4.04
980 1047 0.736053 AGATCTCGGAGCAAGTCGAC 59.264 55.000 7.70 7.70 0.00 4.20
984 1051 2.490217 CGGAGCAAGTCGACCGAT 59.510 61.111 13.01 1.79 46.94 4.18
985 1052 1.586564 CGGAGCAAGTCGACCGATC 60.587 63.158 13.01 12.01 46.94 3.69
1023 1090 0.885150 CGATGATCAGCTGCTGCCAT 60.885 55.000 25.98 25.98 40.80 4.40
1042 1109 1.447489 CAGCTCAAGCCTCCGTCTG 60.447 63.158 0.00 0.00 43.38 3.51
1064 1131 4.785453 CCTTCACCTCCAGCCGGC 62.785 72.222 21.89 21.89 0.00 6.13
1065 1132 4.785453 CTTCACCTCCAGCCGGCC 62.785 72.222 26.15 5.07 0.00 6.13
1479 1579 6.495181 CCCTCTGAATTAATCTAGCTAGGTGA 59.505 42.308 20.58 3.52 0.00 4.02
1490 1590 8.668510 AATCTAGCTAGGTGATGTAAATTGTG 57.331 34.615 20.58 0.00 0.00 3.33
1504 1604 7.209471 TGTAAATTGTGATTAAGTGGGTGAC 57.791 36.000 0.00 0.00 0.00 3.67
1533 1633 8.600449 ACTAGCAGATTAATTAGCTTAGCTTG 57.400 34.615 13.44 2.75 40.44 4.01
1602 1707 8.780846 ACGACCAACATATTGTTTTATCTGTA 57.219 30.769 0.00 0.00 38.77 2.74
1647 1752 9.731519 GTATTTTCAATTCATTGCTCGAAAAAG 57.268 29.630 0.00 0.00 37.68 2.27
1648 1753 8.592105 ATTTTCAATTCATTGCTCGAAAAAGA 57.408 26.923 0.00 0.00 37.68 2.52
1649 1754 7.627585 TTTCAATTCATTGCTCGAAAAAGAG 57.372 32.000 0.00 0.00 41.03 2.85
1687 1797 7.838079 TTATATATCTGGCATTTTGTTGGCT 57.162 32.000 0.00 0.00 42.34 4.75
1691 1801 2.295909 TCTGGCATTTTGTTGGCTACAC 59.704 45.455 0.07 0.00 42.34 2.90
1723 1833 0.388649 GGTGTCTGATCACGTCGCTT 60.389 55.000 0.00 0.00 39.00 4.68
1728 1838 3.102276 GTCTGATCACGTCGCTTTCTAG 58.898 50.000 0.00 0.00 0.00 2.43
1737 1847 2.412089 CGTCGCTTTCTAGGGAAAAGTG 59.588 50.000 8.83 8.83 43.95 3.16
1745 1855 1.210722 CTAGGGAAAAGTGGGAGGAGC 59.789 57.143 0.00 0.00 0.00 4.70
1746 1856 0.772124 AGGGAAAAGTGGGAGGAGCA 60.772 55.000 0.00 0.00 0.00 4.26
1747 1857 0.112412 GGGAAAAGTGGGAGGAGCAA 59.888 55.000 0.00 0.00 0.00 3.91
1749 1859 0.884514 GAAAAGTGGGAGGAGCAAGC 59.115 55.000 0.00 0.00 0.00 4.01
1886 2000 2.664851 TCAGCCGGTGTTCGCTTG 60.665 61.111 1.90 0.00 37.59 4.01
1915 2029 3.693578 AGCTTCAGGTTCGTAGTAGTACC 59.306 47.826 2.06 0.00 0.00 3.34
1921 2035 4.775236 AGGTTCGTAGTAGTACCTGGTAG 58.225 47.826 6.84 0.00 39.47 3.18
1933 2047 3.713826 ACCTGGTAGTACAATGGGTTG 57.286 47.619 0.00 0.00 41.20 3.77
1990 2104 5.362717 ACAATGACTCGAGGTATATGTGGAA 59.637 40.000 18.41 0.00 0.00 3.53
2009 2123 1.704641 AGAAGAAACTGCCCAAACCC 58.295 50.000 0.00 0.00 0.00 4.11
2043 2157 9.848710 ACATTGAGATTTCTATGAATGACTCAT 57.151 29.630 13.28 0.00 46.86 2.90
2047 2161 9.755804 TGAGATTTCTATGAATGACTCATGTAC 57.244 33.333 0.00 0.00 44.84 2.90
2048 2162 9.979578 GAGATTTCTATGAATGACTCATGTACT 57.020 33.333 0.00 0.00 44.84 2.73
2062 2176 9.871238 TGACTCATGTACTAGAAATAGAAAACC 57.129 33.333 0.00 0.00 0.00 3.27
2065 2179 9.535878 CTCATGTACTAGAAATAGAAAACCTCC 57.464 37.037 0.00 0.00 0.00 4.30
2066 2180 8.483758 TCATGTACTAGAAATAGAAAACCTCCC 58.516 37.037 0.00 0.00 0.00 4.30
2067 2181 8.487028 CATGTACTAGAAATAGAAAACCTCCCT 58.513 37.037 0.00 0.00 0.00 4.20
2068 2182 8.075761 TGTACTAGAAATAGAAAACCTCCCTC 57.924 38.462 0.00 0.00 0.00 4.30
2069 2183 7.676893 TGTACTAGAAATAGAAAACCTCCCTCA 59.323 37.037 0.00 0.00 0.00 3.86
2070 2184 7.569599 ACTAGAAATAGAAAACCTCCCTCAA 57.430 36.000 0.00 0.00 0.00 3.02
2071 2185 7.985589 ACTAGAAATAGAAAACCTCCCTCAAA 58.014 34.615 0.00 0.00 0.00 2.69
2072 2186 8.445588 ACTAGAAATAGAAAACCTCCCTCAAAA 58.554 33.333 0.00 0.00 0.00 2.44
2073 2187 9.297037 CTAGAAATAGAAAACCTCCCTCAAAAA 57.703 33.333 0.00 0.00 0.00 1.94
2101 2215 9.710900 AAAAGAAATAGAAAACCTAAATGCTGG 57.289 29.630 0.00 0.00 0.00 4.85
2102 2216 7.410120 AGAAATAGAAAACCTAAATGCTGGG 57.590 36.000 0.00 0.00 0.00 4.45
2103 2217 6.954102 AGAAATAGAAAACCTAAATGCTGGGT 59.046 34.615 0.00 0.00 34.47 4.51
2104 2218 6.530019 AATAGAAAACCTAAATGCTGGGTG 57.470 37.500 0.00 0.00 33.20 4.61
2105 2219 4.112634 AGAAAACCTAAATGCTGGGTGA 57.887 40.909 0.00 0.00 33.20 4.02
2106 2220 3.826729 AGAAAACCTAAATGCTGGGTGAC 59.173 43.478 0.00 0.00 33.20 3.67
2107 2221 1.821216 AACCTAAATGCTGGGTGACG 58.179 50.000 0.00 0.00 33.20 4.35
2108 2222 0.676782 ACCTAAATGCTGGGTGACGC 60.677 55.000 0.00 0.00 31.48 5.19
2109 2223 1.705337 CCTAAATGCTGGGTGACGCG 61.705 60.000 3.53 3.53 0.00 6.01
2110 2224 2.309764 CTAAATGCTGGGTGACGCGC 62.310 60.000 5.73 0.00 0.00 6.86
2155 2269 3.966215 CGCAGGACAACCGTTCAT 58.034 55.556 0.00 0.00 41.83 2.57
2156 2270 1.787847 CGCAGGACAACCGTTCATC 59.212 57.895 0.00 0.00 41.83 2.92
2157 2271 0.670546 CGCAGGACAACCGTTCATCT 60.671 55.000 0.00 0.00 41.83 2.90
2158 2272 0.798776 GCAGGACAACCGTTCATCTG 59.201 55.000 0.00 0.00 41.83 2.90
2159 2273 1.442769 CAGGACAACCGTTCATCTGG 58.557 55.000 0.00 0.00 41.83 3.86
2160 2274 0.321653 AGGACAACCGTTCATCTGGC 60.322 55.000 0.00 0.00 41.83 4.85
2161 2275 0.605319 GGACAACCGTTCATCTGGCA 60.605 55.000 0.00 0.00 0.00 4.92
2162 2276 0.517316 GACAACCGTTCATCTGGCAC 59.483 55.000 0.00 0.00 0.00 5.01
2163 2277 1.227999 ACAACCGTTCATCTGGCACG 61.228 55.000 0.00 0.00 0.00 5.34
2164 2278 0.948623 CAACCGTTCATCTGGCACGA 60.949 55.000 0.00 0.00 35.93 4.35
2165 2279 0.670546 AACCGTTCATCTGGCACGAG 60.671 55.000 0.00 0.00 35.93 4.18
2166 2280 1.215382 CCGTTCATCTGGCACGAGA 59.785 57.895 0.00 0.00 35.93 4.04
2167 2281 0.179100 CCGTTCATCTGGCACGAGAT 60.179 55.000 0.00 0.00 35.93 2.75
2168 2282 1.067060 CCGTTCATCTGGCACGAGATA 59.933 52.381 0.00 0.00 35.93 1.98
2169 2283 2.389059 CGTTCATCTGGCACGAGATAG 58.611 52.381 0.00 0.00 35.93 2.08
2170 2284 2.131183 GTTCATCTGGCACGAGATAGC 58.869 52.381 0.00 0.00 31.14 2.97
2171 2285 0.312102 TCATCTGGCACGAGATAGCG 59.688 55.000 0.00 0.00 31.14 4.26
2172 2286 0.312102 CATCTGGCACGAGATAGCGA 59.688 55.000 0.00 0.00 31.14 4.93
2173 2287 0.312416 ATCTGGCACGAGATAGCGAC 59.688 55.000 0.00 0.00 30.50 5.19
2174 2288 1.029947 TCTGGCACGAGATAGCGACA 61.030 55.000 0.00 0.00 34.83 4.35
2175 2289 0.867753 CTGGCACGAGATAGCGACAC 60.868 60.000 0.00 0.00 34.83 3.67
2176 2290 1.939785 GGCACGAGATAGCGACACG 60.940 63.158 0.00 0.00 34.83 4.49
2177 2291 1.226323 GCACGAGATAGCGACACGT 60.226 57.895 0.00 0.00 37.68 4.49
2178 2292 2.555770 CACGAGATAGCGACACGTG 58.444 57.895 15.48 15.48 45.46 4.49
2179 2293 0.861866 CACGAGATAGCGACACGTGG 60.862 60.000 21.57 3.72 46.43 4.94
2180 2294 1.303799 ACGAGATAGCGACACGTGGT 61.304 55.000 21.57 5.35 35.91 4.16
2181 2295 0.861866 CGAGATAGCGACACGTGGTG 60.862 60.000 21.57 12.68 39.75 4.17
2182 2296 0.525668 GAGATAGCGACACGTGGTGG 60.526 60.000 21.57 9.40 37.94 4.61
2183 2297 1.518572 GATAGCGACACGTGGTGGG 60.519 63.158 21.57 6.77 37.94 4.61
2184 2298 2.221906 GATAGCGACACGTGGTGGGT 62.222 60.000 21.57 15.49 37.94 4.51
2185 2299 1.823169 ATAGCGACACGTGGTGGGTT 61.823 55.000 21.57 6.27 37.94 4.11
2186 2300 2.702751 TAGCGACACGTGGTGGGTTG 62.703 60.000 21.57 3.11 37.94 3.77
2187 2301 2.107343 CGACACGTGGTGGGTTGA 59.893 61.111 21.57 0.00 37.94 3.18
2188 2302 2.241880 CGACACGTGGTGGGTTGAC 61.242 63.158 21.57 0.00 37.94 3.18
2189 2303 1.890510 GACACGTGGTGGGTTGACC 60.891 63.158 21.57 0.00 37.94 4.02
2190 2304 2.970324 CACGTGGTGGGTTGACCG 60.970 66.667 7.95 0.00 44.64 4.79
2191 2305 3.155861 ACGTGGTGGGTTGACCGA 61.156 61.111 0.00 0.00 44.64 4.69
2192 2306 2.663852 CGTGGTGGGTTGACCGAC 60.664 66.667 6.76 6.76 44.64 4.79
2196 2310 2.032071 GTGGGTTGACCGACCAGG 59.968 66.667 8.57 0.00 44.64 4.45
2205 2319 3.550974 CCGACCAGGTGGGATAGG 58.449 66.667 15.73 0.00 41.15 2.57
2206 2320 2.808206 CCGACCAGGTGGGATAGGC 61.808 68.421 15.73 0.00 41.15 3.93
2207 2321 2.063979 CGACCAGGTGGGATAGGCA 61.064 63.158 0.00 0.00 41.15 4.75
2208 2322 1.832912 GACCAGGTGGGATAGGCAG 59.167 63.158 0.00 0.00 41.15 4.85
2209 2323 0.691078 GACCAGGTGGGATAGGCAGA 60.691 60.000 0.00 0.00 41.15 4.26
2210 2324 0.692419 ACCAGGTGGGATAGGCAGAG 60.692 60.000 0.04 0.00 41.15 3.35
2211 2325 0.399091 CCAGGTGGGATAGGCAGAGA 60.399 60.000 0.00 0.00 40.01 3.10
2212 2326 0.755686 CAGGTGGGATAGGCAGAGAC 59.244 60.000 0.00 0.00 0.00 3.36
2213 2327 0.757188 AGGTGGGATAGGCAGAGACG 60.757 60.000 0.00 0.00 0.00 4.18
2214 2328 1.742768 GTGGGATAGGCAGAGACGG 59.257 63.158 0.00 0.00 0.00 4.79
2215 2329 1.043673 GTGGGATAGGCAGAGACGGT 61.044 60.000 0.00 0.00 0.00 4.83
2216 2330 1.043116 TGGGATAGGCAGAGACGGTG 61.043 60.000 0.00 0.00 0.00 4.94
2217 2331 1.068250 GGATAGGCAGAGACGGTGC 59.932 63.158 0.00 0.00 40.42 5.01
2218 2332 1.395826 GGATAGGCAGAGACGGTGCT 61.396 60.000 2.61 0.00 40.97 4.40
2219 2333 0.461961 GATAGGCAGAGACGGTGCTT 59.538 55.000 2.61 0.00 40.97 3.91
2220 2334 0.905357 ATAGGCAGAGACGGTGCTTT 59.095 50.000 2.61 0.00 40.97 3.51
2221 2335 0.685097 TAGGCAGAGACGGTGCTTTT 59.315 50.000 2.61 0.00 40.97 2.27
2222 2336 0.179018 AGGCAGAGACGGTGCTTTTT 60.179 50.000 2.61 0.00 40.97 1.94
2223 2337 0.040067 GGCAGAGACGGTGCTTTTTG 60.040 55.000 2.61 0.00 40.97 2.44
2224 2338 0.663153 GCAGAGACGGTGCTTTTTGT 59.337 50.000 0.00 0.00 37.96 2.83
2225 2339 1.334149 GCAGAGACGGTGCTTTTTGTC 60.334 52.381 0.00 0.00 37.96 3.18
2226 2340 1.070577 CAGAGACGGTGCTTTTTGTCG 60.071 52.381 0.00 0.00 36.49 4.35
2227 2341 0.384353 GAGACGGTGCTTTTTGTCGC 60.384 55.000 0.00 0.00 36.49 5.19
2228 2342 0.814010 AGACGGTGCTTTTTGTCGCT 60.814 50.000 0.00 0.00 36.49 4.93
2229 2343 0.028902 GACGGTGCTTTTTGTCGCTT 59.971 50.000 0.00 0.00 0.00 4.68
2230 2344 0.028902 ACGGTGCTTTTTGTCGCTTC 59.971 50.000 0.00 0.00 0.00 3.86
2231 2345 0.660300 CGGTGCTTTTTGTCGCTTCC 60.660 55.000 0.00 0.00 0.00 3.46
2232 2346 0.318699 GGTGCTTTTTGTCGCTTCCC 60.319 55.000 0.00 0.00 0.00 3.97
2233 2347 0.318699 GTGCTTTTTGTCGCTTCCCC 60.319 55.000 0.00 0.00 0.00 4.81
2234 2348 1.081442 GCTTTTTGTCGCTTCCCCG 60.081 57.895 0.00 0.00 0.00 5.73
2235 2349 1.792118 GCTTTTTGTCGCTTCCCCGT 61.792 55.000 0.00 0.00 0.00 5.28
2236 2350 0.666374 CTTTTTGTCGCTTCCCCGTT 59.334 50.000 0.00 0.00 0.00 4.44
2237 2351 0.664224 TTTTTGTCGCTTCCCCGTTC 59.336 50.000 0.00 0.00 0.00 3.95
2238 2352 1.167781 TTTTGTCGCTTCCCCGTTCC 61.168 55.000 0.00 0.00 0.00 3.62
2239 2353 3.540367 TTGTCGCTTCCCCGTTCCC 62.540 63.158 0.00 0.00 0.00 3.97
2240 2354 4.772687 GTCGCTTCCCCGTTCCCC 62.773 72.222 0.00 0.00 0.00 4.81
2242 2356 4.468689 CGCTTCCCCGTTCCCCTC 62.469 72.222 0.00 0.00 0.00 4.30
2243 2357 4.111053 GCTTCCCCGTTCCCCTCC 62.111 72.222 0.00 0.00 0.00 4.30
2244 2358 3.408853 CTTCCCCGTTCCCCTCCC 61.409 72.222 0.00 0.00 0.00 4.30
2245 2359 3.945064 CTTCCCCGTTCCCCTCCCT 62.945 68.421 0.00 0.00 0.00 4.20
2246 2360 3.510432 TTCCCCGTTCCCCTCCCTT 62.510 63.158 0.00 0.00 0.00 3.95
2247 2361 3.408853 CCCCGTTCCCCTCCCTTC 61.409 72.222 0.00 0.00 0.00 3.46
2248 2362 3.408853 CCCGTTCCCCTCCCTTCC 61.409 72.222 0.00 0.00 0.00 3.46
2249 2363 2.285442 CCGTTCCCCTCCCTTCCT 60.285 66.667 0.00 0.00 0.00 3.36
2250 2364 2.368011 CCGTTCCCCTCCCTTCCTC 61.368 68.421 0.00 0.00 0.00 3.71
2251 2365 1.306226 CGTTCCCCTCCCTTCCTCT 60.306 63.158 0.00 0.00 0.00 3.69
2252 2366 1.331399 CGTTCCCCTCCCTTCCTCTC 61.331 65.000 0.00 0.00 0.00 3.20
2253 2367 0.983905 GTTCCCCTCCCTTCCTCTCC 60.984 65.000 0.00 0.00 0.00 3.71
2254 2368 1.162951 TTCCCCTCCCTTCCTCTCCT 61.163 60.000 0.00 0.00 0.00 3.69
2255 2369 1.074850 CCCCTCCCTTCCTCTCCTC 60.075 68.421 0.00 0.00 0.00 3.71
2256 2370 1.074850 CCCTCCCTTCCTCTCCTCC 60.075 68.421 0.00 0.00 0.00 4.30
2257 2371 1.074850 CCTCCCTTCCTCTCCTCCC 60.075 68.421 0.00 0.00 0.00 4.30
2258 2372 1.456705 CTCCCTTCCTCTCCTCCCG 60.457 68.421 0.00 0.00 0.00 5.14
2259 2373 3.157949 CCCTTCCTCTCCTCCCGC 61.158 72.222 0.00 0.00 0.00 6.13
2260 2374 2.364317 CCTTCCTCTCCTCCCGCA 60.364 66.667 0.00 0.00 0.00 5.69
2261 2375 2.726351 CCTTCCTCTCCTCCCGCAC 61.726 68.421 0.00 0.00 0.00 5.34
2262 2376 3.068691 TTCCTCTCCTCCCGCACG 61.069 66.667 0.00 0.00 0.00 5.34
2279 2393 2.812499 GGCGACAGGGCGAGATAA 59.188 61.111 0.00 0.00 0.00 1.75
2280 2394 1.143183 GGCGACAGGGCGAGATAAA 59.857 57.895 0.00 0.00 0.00 1.40
2281 2395 0.249911 GGCGACAGGGCGAGATAAAT 60.250 55.000 0.00 0.00 0.00 1.40
2282 2396 1.140816 GCGACAGGGCGAGATAAATC 58.859 55.000 0.00 0.00 0.00 2.17
2283 2397 1.409412 CGACAGGGCGAGATAAATCG 58.591 55.000 0.00 0.00 45.48 3.34
2284 2398 1.001706 CGACAGGGCGAGATAAATCGA 60.002 52.381 0.00 0.00 45.56 3.59
2285 2399 2.351835 CGACAGGGCGAGATAAATCGAT 60.352 50.000 0.00 0.00 45.56 3.59
2286 2400 3.654414 GACAGGGCGAGATAAATCGATT 58.346 45.455 4.39 4.39 45.56 3.34
2287 2401 3.654414 ACAGGGCGAGATAAATCGATTC 58.346 45.455 11.83 0.00 45.56 2.52
2288 2402 2.663602 CAGGGCGAGATAAATCGATTCG 59.336 50.000 11.83 11.45 45.56 3.34
2289 2403 2.296471 AGGGCGAGATAAATCGATTCGT 59.704 45.455 11.83 2.88 45.56 3.85
2290 2404 3.504906 AGGGCGAGATAAATCGATTCGTA 59.495 43.478 11.83 1.25 45.56 3.43
2291 2405 4.158025 AGGGCGAGATAAATCGATTCGTAT 59.842 41.667 11.83 6.58 45.56 3.06
2292 2406 4.265556 GGGCGAGATAAATCGATTCGTATG 59.734 45.833 11.83 1.80 45.56 2.39
2293 2407 4.259451 GGCGAGATAAATCGATTCGTATGC 60.259 45.833 11.83 11.17 45.56 3.14
2294 2408 4.544586 GCGAGATAAATCGATTCGTATGCG 60.545 45.833 11.83 12.40 45.56 4.73
2295 2409 4.786575 CGAGATAAATCGATTCGTATGCGA 59.213 41.667 11.83 0.30 45.56 5.10
2296 2410 5.053610 CGAGATAAATCGATTCGTATGCGAG 60.054 44.000 11.83 0.00 45.68 5.03
2297 2411 8.362703 CGAGATAAATCGATTCGTATGCGAGC 62.363 46.154 11.83 2.19 45.68 5.03
2348 2462 3.918220 CGAAGCGAGCGCCACATC 61.918 66.667 11.66 4.61 43.17 3.06
2349 2463 2.815211 GAAGCGAGCGCCACATCA 60.815 61.111 11.66 0.00 43.17 3.07
2350 2464 2.806856 GAAGCGAGCGCCACATCAG 61.807 63.158 11.66 0.00 43.17 2.90
2351 2465 4.827087 AGCGAGCGCCACATCAGG 62.827 66.667 11.66 0.00 43.17 3.86
2354 2468 3.785859 GAGCGCCACATCAGGGGA 61.786 66.667 2.29 0.00 43.81 4.81
2355 2469 3.329542 GAGCGCCACATCAGGGGAA 62.330 63.158 2.29 0.00 43.81 3.97
2356 2470 2.825836 GCGCCACATCAGGGGAAG 60.826 66.667 0.00 0.00 43.81 3.46
2357 2471 2.124570 CGCCACATCAGGGGAAGG 60.125 66.667 0.00 0.00 43.81 3.46
2358 2472 2.971598 CGCCACATCAGGGGAAGGT 61.972 63.158 0.00 0.00 43.81 3.50
2359 2473 1.379044 GCCACATCAGGGGAAGGTG 60.379 63.158 0.00 0.00 34.18 4.00
2360 2474 1.304282 CCACATCAGGGGAAGGTGG 59.696 63.158 0.00 0.00 42.44 4.61
2361 2475 1.500783 CCACATCAGGGGAAGGTGGT 61.501 60.000 0.00 0.00 42.81 4.16
2362 2476 0.035056 CACATCAGGGGAAGGTGGTC 60.035 60.000 0.00 0.00 32.08 4.02
2363 2477 0.475632 ACATCAGGGGAAGGTGGTCA 60.476 55.000 0.00 0.00 0.00 4.02
2364 2478 0.035056 CATCAGGGGAAGGTGGTCAC 60.035 60.000 0.00 0.00 0.00 3.67
2374 2488 4.065110 GTGGTCACCAGCAAGTCC 57.935 61.111 0.00 0.00 32.34 3.85
2375 2489 1.148273 GTGGTCACCAGCAAGTCCA 59.852 57.895 0.00 0.00 32.34 4.02
2376 2490 1.148273 TGGTCACCAGCAAGTCCAC 59.852 57.895 0.00 0.00 0.00 4.02
2377 2491 1.961277 GGTCACCAGCAAGTCCACG 60.961 63.158 0.00 0.00 0.00 4.94
2378 2492 1.961277 GTCACCAGCAAGTCCACGG 60.961 63.158 0.00 0.00 0.00 4.94
2379 2493 2.669569 CACCAGCAAGTCCACGGG 60.670 66.667 0.00 0.00 0.00 5.28
2380 2494 3.953775 ACCAGCAAGTCCACGGGG 61.954 66.667 0.00 0.00 0.00 5.73
2400 2514 3.966543 GGGGGTGGGTGTGGTGAG 61.967 72.222 0.00 0.00 0.00 3.51
2401 2515 3.175710 GGGGTGGGTGTGGTGAGT 61.176 66.667 0.00 0.00 0.00 3.41
2402 2516 2.763645 GGGGTGGGTGTGGTGAGTT 61.764 63.158 0.00 0.00 0.00 3.01
2403 2517 1.528309 GGGTGGGTGTGGTGAGTTG 60.528 63.158 0.00 0.00 0.00 3.16
2404 2518 2.193536 GGTGGGTGTGGTGAGTTGC 61.194 63.158 0.00 0.00 0.00 4.17
2405 2519 1.152963 GTGGGTGTGGTGAGTTGCT 60.153 57.895 0.00 0.00 0.00 3.91
2406 2520 0.751643 GTGGGTGTGGTGAGTTGCTT 60.752 55.000 0.00 0.00 0.00 3.91
2407 2521 0.751277 TGGGTGTGGTGAGTTGCTTG 60.751 55.000 0.00 0.00 0.00 4.01
2408 2522 1.360192 GGTGTGGTGAGTTGCTTGC 59.640 57.895 0.00 0.00 0.00 4.01
2409 2523 1.009675 GTGTGGTGAGTTGCTTGCG 60.010 57.895 0.00 0.00 0.00 4.85
2410 2524 2.050985 GTGGTGAGTTGCTTGCGC 60.051 61.111 0.00 0.00 0.00 6.09
2411 2525 3.648982 TGGTGAGTTGCTTGCGCG 61.649 61.111 0.00 0.00 39.65 6.86
2428 2542 3.760035 GCGCGACCAGGGAGAAGA 61.760 66.667 12.10 0.00 34.27 2.87
2429 2543 2.492090 CGCGACCAGGGAGAAGAG 59.508 66.667 0.00 0.00 34.27 2.85
2430 2544 2.896443 GCGACCAGGGAGAAGAGG 59.104 66.667 0.00 0.00 0.00 3.69
2431 2545 2.726351 GCGACCAGGGAGAAGAGGG 61.726 68.421 0.00 0.00 0.00 4.30
2432 2546 1.000486 CGACCAGGGAGAAGAGGGA 60.000 63.158 0.00 0.00 0.00 4.20
2433 2547 1.040339 CGACCAGGGAGAAGAGGGAG 61.040 65.000 0.00 0.00 0.00 4.30
2434 2548 0.041982 GACCAGGGAGAAGAGGGAGT 59.958 60.000 0.00 0.00 0.00 3.85
2435 2549 0.494095 ACCAGGGAGAAGAGGGAGTT 59.506 55.000 0.00 0.00 0.00 3.01
2436 2550 0.908198 CCAGGGAGAAGAGGGAGTTG 59.092 60.000 0.00 0.00 0.00 3.16
2437 2551 0.908198 CAGGGAGAAGAGGGAGTTGG 59.092 60.000 0.00 0.00 0.00 3.77
2438 2552 0.252927 AGGGAGAAGAGGGAGTTGGG 60.253 60.000 0.00 0.00 0.00 4.12
2439 2553 1.604915 GGAGAAGAGGGAGTTGGGC 59.395 63.158 0.00 0.00 0.00 5.36
2440 2554 1.219393 GAGAAGAGGGAGTTGGGCG 59.781 63.158 0.00 0.00 0.00 6.13
2441 2555 1.536662 AGAAGAGGGAGTTGGGCGT 60.537 57.895 0.00 0.00 0.00 5.68
2442 2556 1.376037 GAAGAGGGAGTTGGGCGTG 60.376 63.158 0.00 0.00 0.00 5.34
2443 2557 2.804828 GAAGAGGGAGTTGGGCGTGG 62.805 65.000 0.00 0.00 0.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
235 237 4.064388 CGGCCTCCAAAATGAATGTTTTT 58.936 39.130 0.00 0.00 0.00 1.94
514 560 4.973055 CCGTGCGACCCCAAACGA 62.973 66.667 0.00 0.00 38.27 3.85
528 574 2.847234 TGAGGCCAACTCCACCGT 60.847 61.111 5.01 0.00 46.01 4.83
549 595 3.124798 GAAATGCATCGGGCCCGTG 62.125 63.158 41.57 35.21 43.89 4.94
550 596 2.828549 GAAATGCATCGGGCCCGT 60.829 61.111 41.57 26.88 43.89 5.28
551 597 2.828095 TGAAATGCATCGGGCCCG 60.828 61.111 39.13 39.13 43.89 6.13
552 598 2.051518 TGTGAAATGCATCGGGCCC 61.052 57.895 13.57 13.57 43.89 5.80
553 599 1.139520 GTGTGAAATGCATCGGGCC 59.860 57.895 0.00 0.00 43.89 5.80
554 600 1.226379 CGTGTGAAATGCATCGGGC 60.226 57.895 0.00 0.00 45.13 6.13
555 601 0.179192 CACGTGTGAAATGCATCGGG 60.179 55.000 7.58 0.00 33.36 5.14
556 602 0.179192 CCACGTGTGAAATGCATCGG 60.179 55.000 15.65 0.00 33.36 4.18
557 603 0.516877 ACCACGTGTGAAATGCATCG 59.483 50.000 15.65 0.00 34.55 3.84
567 613 0.655733 GTGGAGTTTCACCACGTGTG 59.344 55.000 15.65 12.72 46.15 3.82
568 614 3.074594 GTGGAGTTTCACCACGTGT 57.925 52.632 15.65 0.00 46.15 4.49
594 640 2.539338 TTGGCAACTGTTCCGTCGC 61.539 57.895 0.00 0.00 37.61 5.19
656 709 3.599412 GCCGGTAGATATTTGGCGA 57.401 52.632 1.90 0.00 35.77 5.54
734 787 4.133373 CCTCTCCCCGTCCCGGTA 62.133 72.222 0.00 0.00 46.80 4.02
813 871 0.393808 TGGACGCTGGATTTTAGCCC 60.394 55.000 0.00 0.00 37.90 5.19
865 923 0.605589 AGAGGAGTCTGTTCTTGGCG 59.394 55.000 0.00 0.00 0.00 5.69
868 926 1.552792 GGGGAGAGGAGTCTGTTCTTG 59.447 57.143 0.00 0.00 30.97 3.02
870 928 0.041982 GGGGGAGAGGAGTCTGTTCT 59.958 60.000 0.00 0.00 30.97 3.01
872 930 4.899243 GGGGGAGAGGAGTCTGTT 57.101 61.111 0.00 0.00 30.97 3.16
929 990 2.289072 TGCGGATTCTTATAGGCTCTGC 60.289 50.000 0.00 9.65 38.44 4.26
961 1028 0.736053 GTCGACTTGCTCCGAGATCT 59.264 55.000 8.70 0.00 35.31 2.75
980 1047 1.941734 GTCGCTGAGCTTCGATCGG 60.942 63.158 16.41 0.48 37.06 4.18
984 1051 1.153765 CATGGTCGCTGAGCTTCGA 60.154 57.895 1.78 0.00 0.00 3.71
985 1052 2.806856 GCATGGTCGCTGAGCTTCG 61.807 63.158 1.78 0.00 0.00 3.79
1023 1090 1.607756 AGACGGAGGCTTGAGCTGA 60.608 57.895 0.00 0.00 41.70 4.26
1042 1109 4.785453 CTGGAGGTGAAGGGGCGC 62.785 72.222 0.00 0.00 0.00 6.53
1479 1579 7.669722 AGTCACCCACTTAATCACAATTTACAT 59.330 33.333 0.00 0.00 26.56 2.29
1490 1590 5.360144 TGCTAGTCTAGTCACCCACTTAATC 59.640 44.000 8.68 0.00 36.43 1.75
1504 1604 9.567848 GCTAAGCTAATTAATCTGCTAGTCTAG 57.432 37.037 13.30 2.18 35.09 2.43
1533 1633 9.771534 ACCAATATGAGAGCTTATTTCTTCTAC 57.228 33.333 0.00 0.00 0.00 2.59
1625 1730 7.627585 CTCTTTTTCGAGCAATGAATTGAAA 57.372 32.000 7.21 0.00 40.14 2.69
1667 1777 4.955450 TGTAGCCAACAAAATGCCAGATAT 59.045 37.500 0.00 0.00 34.29 1.63
1676 1786 3.132925 ACGTACGTGTAGCCAACAAAAT 58.867 40.909 22.14 0.00 40.63 1.82
1678 1788 2.222007 ACGTACGTGTAGCCAACAAA 57.778 45.000 22.14 0.00 40.63 2.83
1681 1791 1.453148 GACAACGTACGTGTAGCCAAC 59.547 52.381 23.57 5.67 0.00 3.77
1687 1797 2.034432 ACACCATGACAACGTACGTGTA 59.966 45.455 23.57 9.06 30.86 2.90
1691 1801 1.719246 CAGACACCATGACAACGTACG 59.281 52.381 15.01 15.01 0.00 3.67
1723 1833 3.182152 CTCCTCCCACTTTTCCCTAGAA 58.818 50.000 0.00 0.00 0.00 2.10
1728 1838 0.112412 TTGCTCCTCCCACTTTTCCC 59.888 55.000 0.00 0.00 0.00 3.97
1737 1847 1.302511 TGTTTCGCTTGCTCCTCCC 60.303 57.895 0.00 0.00 0.00 4.30
1745 1855 1.730176 CTTGTCGTGTGTTTCGCTTG 58.270 50.000 0.00 0.00 0.00 4.01
1746 1856 0.027586 GCTTGTCGTGTGTTTCGCTT 59.972 50.000 0.00 0.00 0.00 4.68
1747 1857 1.087202 TGCTTGTCGTGTGTTTCGCT 61.087 50.000 0.00 0.00 0.00 4.93
1749 1859 0.650512 AGTGCTTGTCGTGTGTTTCG 59.349 50.000 0.00 0.00 0.00 3.46
1848 1958 6.533819 TGACCTTTACGTTCATTTGTACTG 57.466 37.500 0.00 0.00 0.00 2.74
1886 2000 0.951040 CGAACCTGAAGCTGTGACCC 60.951 60.000 0.00 0.00 0.00 4.46
1915 2029 2.356741 CCCCAACCCATTGTACTACCAG 60.357 54.545 0.00 0.00 33.60 4.00
1921 2035 0.406361 TCCACCCCAACCCATTGTAC 59.594 55.000 0.00 0.00 33.60 2.90
1933 2047 2.267961 CGGCTTGTACTCCACCCC 59.732 66.667 0.00 0.00 0.00 4.95
1990 2104 1.704641 GGGTTTGGGCAGTTTCTTCT 58.295 50.000 0.00 0.00 0.00 2.85
2043 2157 7.676893 TGAGGGAGGTTTTCTATTTCTAGTACA 59.323 37.037 0.00 0.00 0.00 2.90
2047 2161 8.863872 TTTTGAGGGAGGTTTTCTATTTCTAG 57.136 34.615 0.00 0.00 0.00 2.43
2075 2189 9.710900 CCAGCATTTAGGTTTTCTATTTCTTTT 57.289 29.630 0.00 0.00 0.00 2.27
2076 2190 8.314021 CCCAGCATTTAGGTTTTCTATTTCTTT 58.686 33.333 0.00 0.00 0.00 2.52
2077 2191 7.454694 ACCCAGCATTTAGGTTTTCTATTTCTT 59.545 33.333 0.00 0.00 0.00 2.52
2078 2192 6.954102 ACCCAGCATTTAGGTTTTCTATTTCT 59.046 34.615 0.00 0.00 0.00 2.52
2079 2193 7.035612 CACCCAGCATTTAGGTTTTCTATTTC 58.964 38.462 0.00 0.00 0.00 2.17
2080 2194 6.723977 TCACCCAGCATTTAGGTTTTCTATTT 59.276 34.615 0.00 0.00 0.00 1.40
2081 2195 6.152831 GTCACCCAGCATTTAGGTTTTCTATT 59.847 38.462 0.00 0.00 0.00 1.73
2082 2196 5.652452 GTCACCCAGCATTTAGGTTTTCTAT 59.348 40.000 0.00 0.00 0.00 1.98
2083 2197 5.007682 GTCACCCAGCATTTAGGTTTTCTA 58.992 41.667 0.00 0.00 0.00 2.10
2084 2198 3.826729 GTCACCCAGCATTTAGGTTTTCT 59.173 43.478 0.00 0.00 0.00 2.52
2085 2199 3.365969 CGTCACCCAGCATTTAGGTTTTC 60.366 47.826 0.00 0.00 0.00 2.29
2086 2200 2.556622 CGTCACCCAGCATTTAGGTTTT 59.443 45.455 0.00 0.00 0.00 2.43
2087 2201 2.159382 CGTCACCCAGCATTTAGGTTT 58.841 47.619 0.00 0.00 0.00 3.27
2088 2202 1.821216 CGTCACCCAGCATTTAGGTT 58.179 50.000 0.00 0.00 0.00 3.50
2089 2203 0.676782 GCGTCACCCAGCATTTAGGT 60.677 55.000 0.00 0.00 0.00 3.08
2090 2204 1.705337 CGCGTCACCCAGCATTTAGG 61.705 60.000 0.00 0.00 0.00 2.69
2091 2205 1.715585 CGCGTCACCCAGCATTTAG 59.284 57.895 0.00 0.00 0.00 1.85
2092 2206 2.395360 GCGCGTCACCCAGCATTTA 61.395 57.895 8.43 0.00 0.00 1.40
2093 2207 3.737172 GCGCGTCACCCAGCATTT 61.737 61.111 8.43 0.00 0.00 2.32
2136 2250 3.723348 GAACGGTTGTCCTGCGGC 61.723 66.667 0.00 0.00 0.00 6.53
2137 2251 1.635663 GATGAACGGTTGTCCTGCGG 61.636 60.000 0.00 0.00 0.00 5.69
2138 2252 0.670546 AGATGAACGGTTGTCCTGCG 60.671 55.000 0.00 0.00 0.00 5.18
2139 2253 0.798776 CAGATGAACGGTTGTCCTGC 59.201 55.000 0.00 0.00 0.00 4.85
2140 2254 1.442769 CCAGATGAACGGTTGTCCTG 58.557 55.000 0.00 2.35 0.00 3.86
2141 2255 0.321653 GCCAGATGAACGGTTGTCCT 60.322 55.000 0.00 0.00 0.00 3.85
2142 2256 0.605319 TGCCAGATGAACGGTTGTCC 60.605 55.000 0.00 0.00 0.00 4.02
2143 2257 0.517316 GTGCCAGATGAACGGTTGTC 59.483 55.000 0.00 0.00 0.00 3.18
2144 2258 1.227999 CGTGCCAGATGAACGGTTGT 61.228 55.000 0.00 0.00 33.77 3.32
2145 2259 0.948623 TCGTGCCAGATGAACGGTTG 60.949 55.000 0.00 0.00 37.87 3.77
2146 2260 0.670546 CTCGTGCCAGATGAACGGTT 60.671 55.000 0.00 0.00 37.87 4.44
2147 2261 1.079819 CTCGTGCCAGATGAACGGT 60.080 57.895 7.76 0.00 37.87 4.83
2148 2262 0.179100 ATCTCGTGCCAGATGAACGG 60.179 55.000 7.76 0.00 37.87 4.44
2149 2263 2.389059 CTATCTCGTGCCAGATGAACG 58.611 52.381 1.15 2.73 34.75 3.95
2150 2264 2.131183 GCTATCTCGTGCCAGATGAAC 58.869 52.381 1.15 0.00 34.75 3.18
2151 2265 1.269257 CGCTATCTCGTGCCAGATGAA 60.269 52.381 1.15 0.00 34.75 2.57
2152 2266 0.312102 CGCTATCTCGTGCCAGATGA 59.688 55.000 1.15 0.00 34.75 2.92
2153 2267 0.312102 TCGCTATCTCGTGCCAGATG 59.688 55.000 1.15 0.00 34.75 2.90
2154 2268 0.312416 GTCGCTATCTCGTGCCAGAT 59.688 55.000 0.00 0.00 36.97 2.90
2155 2269 1.029947 TGTCGCTATCTCGTGCCAGA 61.030 55.000 0.00 0.00 0.00 3.86
2156 2270 0.867753 GTGTCGCTATCTCGTGCCAG 60.868 60.000 0.00 0.00 0.00 4.85
2157 2271 1.138883 GTGTCGCTATCTCGTGCCA 59.861 57.895 0.00 0.00 0.00 4.92
2158 2272 1.939785 CGTGTCGCTATCTCGTGCC 60.940 63.158 0.00 0.00 0.00 5.01
2159 2273 1.226323 ACGTGTCGCTATCTCGTGC 60.226 57.895 0.00 0.00 34.58 5.34
2160 2274 0.861866 CCACGTGTCGCTATCTCGTG 60.862 60.000 15.65 15.03 45.70 4.35
2161 2275 1.303799 ACCACGTGTCGCTATCTCGT 61.304 55.000 15.65 0.00 35.87 4.18
2162 2276 0.861866 CACCACGTGTCGCTATCTCG 60.862 60.000 15.65 0.00 0.00 4.04
2163 2277 0.525668 CCACCACGTGTCGCTATCTC 60.526 60.000 15.65 0.00 0.00 2.75
2164 2278 1.511305 CCACCACGTGTCGCTATCT 59.489 57.895 15.65 0.00 0.00 1.98
2165 2279 1.518572 CCCACCACGTGTCGCTATC 60.519 63.158 15.65 0.00 0.00 2.08
2166 2280 1.823169 AACCCACCACGTGTCGCTAT 61.823 55.000 15.65 0.00 0.00 2.97
2167 2281 2.500714 AACCCACCACGTGTCGCTA 61.501 57.895 15.65 0.00 0.00 4.26
2168 2282 3.857038 AACCCACCACGTGTCGCT 61.857 61.111 15.65 0.00 0.00 4.93
2169 2283 3.645975 CAACCCACCACGTGTCGC 61.646 66.667 15.65 0.00 0.00 5.19
2170 2284 2.107343 TCAACCCACCACGTGTCG 59.893 61.111 15.65 4.56 0.00 4.35
2171 2285 1.890510 GGTCAACCCACCACGTGTC 60.891 63.158 15.65 0.00 36.32 3.67
2172 2286 2.191109 GGTCAACCCACCACGTGT 59.809 61.111 15.65 0.00 36.32 4.49
2173 2287 2.970324 CGGTCAACCCACCACGTG 60.970 66.667 9.08 9.08 36.01 4.49
2174 2288 3.155861 TCGGTCAACCCACCACGT 61.156 61.111 0.00 0.00 36.01 4.49
2175 2289 2.663852 GTCGGTCAACCCACCACG 60.664 66.667 0.00 0.00 36.01 4.94
2176 2290 2.281276 GGTCGGTCAACCCACCAC 60.281 66.667 10.70 0.00 36.01 4.16
2177 2291 2.768769 TGGTCGGTCAACCCACCA 60.769 61.111 13.87 13.87 40.16 4.17
2178 2292 2.032071 CTGGTCGGTCAACCCACC 59.968 66.667 8.86 8.86 38.65 4.61
2179 2293 2.032071 CCTGGTCGGTCAACCCAC 59.968 66.667 0.00 0.00 38.65 4.61
2180 2294 2.446994 ACCTGGTCGGTCAACCCA 60.447 61.111 0.00 0.00 44.93 4.51
2181 2295 2.032071 CACCTGGTCGGTCAACCC 59.968 66.667 0.00 0.00 44.93 4.11
2182 2296 2.032071 CCACCTGGTCGGTCAACC 59.968 66.667 0.00 0.00 44.93 3.77
2183 2297 1.838073 ATCCCACCTGGTCGGTCAAC 61.838 60.000 10.42 0.00 44.93 3.18
2184 2298 0.252330 TATCCCACCTGGTCGGTCAA 60.252 55.000 10.42 0.00 44.93 3.18
2185 2299 0.686441 CTATCCCACCTGGTCGGTCA 60.686 60.000 10.42 0.00 44.93 4.02
2186 2300 1.400530 CCTATCCCACCTGGTCGGTC 61.401 65.000 10.42 0.00 44.93 4.79
2188 2302 2.808206 GCCTATCCCACCTGGTCGG 61.808 68.421 3.81 3.81 39.35 4.79
2189 2303 2.032860 CTGCCTATCCCACCTGGTCG 62.033 65.000 0.00 0.00 34.77 4.79
2190 2304 0.691078 TCTGCCTATCCCACCTGGTC 60.691 60.000 0.00 0.00 34.77 4.02
2191 2305 0.692419 CTCTGCCTATCCCACCTGGT 60.692 60.000 0.00 0.00 34.77 4.00
2192 2306 0.399091 TCTCTGCCTATCCCACCTGG 60.399 60.000 0.00 0.00 0.00 4.45
2193 2307 0.755686 GTCTCTGCCTATCCCACCTG 59.244 60.000 0.00 0.00 0.00 4.00
2194 2308 0.757188 CGTCTCTGCCTATCCCACCT 60.757 60.000 0.00 0.00 0.00 4.00
2195 2309 1.742768 CGTCTCTGCCTATCCCACC 59.257 63.158 0.00 0.00 0.00 4.61
2196 2310 1.043673 ACCGTCTCTGCCTATCCCAC 61.044 60.000 0.00 0.00 0.00 4.61
2197 2311 1.043116 CACCGTCTCTGCCTATCCCA 61.043 60.000 0.00 0.00 0.00 4.37
2198 2312 1.742768 CACCGTCTCTGCCTATCCC 59.257 63.158 0.00 0.00 0.00 3.85
2199 2313 1.068250 GCACCGTCTCTGCCTATCC 59.932 63.158 0.00 0.00 0.00 2.59
2200 2314 0.461961 AAGCACCGTCTCTGCCTATC 59.538 55.000 0.00 0.00 35.01 2.08
2201 2315 0.905357 AAAGCACCGTCTCTGCCTAT 59.095 50.000 0.00 0.00 35.01 2.57
2202 2316 0.685097 AAAAGCACCGTCTCTGCCTA 59.315 50.000 0.00 0.00 35.01 3.93
2203 2317 0.179018 AAAAAGCACCGTCTCTGCCT 60.179 50.000 0.00 0.00 35.01 4.75
2204 2318 0.040067 CAAAAAGCACCGTCTCTGCC 60.040 55.000 0.00 0.00 35.01 4.85
2205 2319 0.663153 ACAAAAAGCACCGTCTCTGC 59.337 50.000 0.00 0.00 34.63 4.26
2206 2320 1.070577 CGACAAAAAGCACCGTCTCTG 60.071 52.381 0.00 0.00 0.00 3.35
2207 2321 1.217882 CGACAAAAAGCACCGTCTCT 58.782 50.000 0.00 0.00 0.00 3.10
2208 2322 0.384353 GCGACAAAAAGCACCGTCTC 60.384 55.000 0.00 0.00 0.00 3.36
2209 2323 0.814010 AGCGACAAAAAGCACCGTCT 60.814 50.000 0.00 0.00 35.48 4.18
2210 2324 0.028902 AAGCGACAAAAAGCACCGTC 59.971 50.000 0.00 0.00 35.48 4.79
2211 2325 0.028902 GAAGCGACAAAAAGCACCGT 59.971 50.000 0.00 0.00 35.48 4.83
2212 2326 0.660300 GGAAGCGACAAAAAGCACCG 60.660 55.000 0.00 0.00 35.48 4.94
2213 2327 0.318699 GGGAAGCGACAAAAAGCACC 60.319 55.000 0.00 0.00 35.48 5.01
2214 2328 0.318699 GGGGAAGCGACAAAAAGCAC 60.319 55.000 0.00 0.00 35.48 4.40
2215 2329 1.791103 CGGGGAAGCGACAAAAAGCA 61.791 55.000 0.00 0.00 35.48 3.91
2216 2330 1.081442 CGGGGAAGCGACAAAAAGC 60.081 57.895 0.00 0.00 0.00 3.51
2217 2331 0.666374 AACGGGGAAGCGACAAAAAG 59.334 50.000 0.00 0.00 0.00 2.27
2218 2332 0.664224 GAACGGGGAAGCGACAAAAA 59.336 50.000 0.00 0.00 0.00 1.94
2219 2333 1.167781 GGAACGGGGAAGCGACAAAA 61.168 55.000 0.00 0.00 0.00 2.44
2220 2334 1.598685 GGAACGGGGAAGCGACAAA 60.599 57.895 0.00 0.00 0.00 2.83
2221 2335 2.031465 GGAACGGGGAAGCGACAA 59.969 61.111 0.00 0.00 0.00 3.18
2222 2336 4.011517 GGGAACGGGGAAGCGACA 62.012 66.667 0.00 0.00 0.00 4.35
2223 2337 4.772687 GGGGAACGGGGAAGCGAC 62.773 72.222 0.00 0.00 0.00 5.19
2225 2339 4.468689 GAGGGGAACGGGGAAGCG 62.469 72.222 0.00 0.00 0.00 4.68
2226 2340 4.111053 GGAGGGGAACGGGGAAGC 62.111 72.222 0.00 0.00 0.00 3.86
2227 2341 3.408853 GGGAGGGGAACGGGGAAG 61.409 72.222 0.00 0.00 0.00 3.46
2228 2342 3.510432 AAGGGAGGGGAACGGGGAA 62.510 63.158 0.00 0.00 0.00 3.97
2229 2343 3.937372 GAAGGGAGGGGAACGGGGA 62.937 68.421 0.00 0.00 0.00 4.81
2230 2344 3.408853 GAAGGGAGGGGAACGGGG 61.409 72.222 0.00 0.00 0.00 5.73
2231 2345 3.408853 GGAAGGGAGGGGAACGGG 61.409 72.222 0.00 0.00 0.00 5.28
2232 2346 2.285442 AGGAAGGGAGGGGAACGG 60.285 66.667 0.00 0.00 0.00 4.44
2233 2347 1.306226 AGAGGAAGGGAGGGGAACG 60.306 63.158 0.00 0.00 0.00 3.95
2234 2348 0.983905 GGAGAGGAAGGGAGGGGAAC 60.984 65.000 0.00 0.00 0.00 3.62
2235 2349 1.162951 AGGAGAGGAAGGGAGGGGAA 61.163 60.000 0.00 0.00 0.00 3.97
2236 2350 1.550374 AGGAGAGGAAGGGAGGGGA 60.550 63.158 0.00 0.00 0.00 4.81
2237 2351 1.074850 GAGGAGAGGAAGGGAGGGG 60.075 68.421 0.00 0.00 0.00 4.79
2238 2352 1.074850 GGAGGAGAGGAAGGGAGGG 60.075 68.421 0.00 0.00 0.00 4.30
2239 2353 1.074850 GGGAGGAGAGGAAGGGAGG 60.075 68.421 0.00 0.00 0.00 4.30
2240 2354 1.456705 CGGGAGGAGAGGAAGGGAG 60.457 68.421 0.00 0.00 0.00 4.30
2241 2355 2.690452 CGGGAGGAGAGGAAGGGA 59.310 66.667 0.00 0.00 0.00 4.20
2242 2356 3.157949 GCGGGAGGAGAGGAAGGG 61.158 72.222 0.00 0.00 0.00 3.95
2243 2357 2.364317 TGCGGGAGGAGAGGAAGG 60.364 66.667 0.00 0.00 0.00 3.46
2244 2358 2.896443 GTGCGGGAGGAGAGGAAG 59.104 66.667 0.00 0.00 0.00 3.46
2245 2359 3.068691 CGTGCGGGAGGAGAGGAA 61.069 66.667 0.00 0.00 0.00 3.36
2261 2375 2.622903 TTTATCTCGCCCTGTCGCCG 62.623 60.000 0.00 0.00 0.00 6.46
2262 2376 0.249911 ATTTATCTCGCCCTGTCGCC 60.250 55.000 0.00 0.00 0.00 5.54
2263 2377 1.140816 GATTTATCTCGCCCTGTCGC 58.859 55.000 0.00 0.00 0.00 5.19
2264 2378 1.001706 TCGATTTATCTCGCCCTGTCG 60.002 52.381 0.00 0.00 38.52 4.35
2265 2379 2.795175 TCGATTTATCTCGCCCTGTC 57.205 50.000 0.00 0.00 38.52 3.51
2266 2380 3.654414 GAATCGATTTATCTCGCCCTGT 58.346 45.455 12.81 0.00 38.52 4.00
2267 2381 2.663602 CGAATCGATTTATCTCGCCCTG 59.336 50.000 12.81 0.00 38.52 4.45
2268 2382 2.296471 ACGAATCGATTTATCTCGCCCT 59.704 45.455 12.81 0.00 38.52 5.19
2269 2383 2.673833 ACGAATCGATTTATCTCGCCC 58.326 47.619 12.81 0.00 38.52 6.13
2270 2384 4.259451 GCATACGAATCGATTTATCTCGCC 60.259 45.833 12.81 0.00 38.52 5.54
2271 2385 4.544586 CGCATACGAATCGATTTATCTCGC 60.545 45.833 12.81 10.11 43.93 5.03
2272 2386 5.030693 CGCATACGAATCGATTTATCTCG 57.969 43.478 12.81 13.15 43.93 4.04
2331 2445 3.918220 GATGTGGCGCTCGCTTCG 61.918 66.667 7.64 0.00 41.60 3.79
2332 2446 2.806856 CTGATGTGGCGCTCGCTTC 61.807 63.158 7.64 12.13 41.60 3.86
2333 2447 2.816958 CTGATGTGGCGCTCGCTT 60.817 61.111 7.64 2.26 41.60 4.68
2334 2448 4.827087 CCTGATGTGGCGCTCGCT 62.827 66.667 7.64 0.00 41.60 4.93
2337 2451 3.329542 TTCCCCTGATGTGGCGCTC 62.330 63.158 7.64 1.21 0.00 5.03
2338 2452 3.329889 TTCCCCTGATGTGGCGCT 61.330 61.111 7.64 0.00 0.00 5.92
2339 2453 2.825836 CTTCCCCTGATGTGGCGC 60.826 66.667 0.00 0.00 0.00 6.53
2340 2454 2.124570 CCTTCCCCTGATGTGGCG 60.125 66.667 0.00 0.00 0.00 5.69
2341 2455 1.379044 CACCTTCCCCTGATGTGGC 60.379 63.158 0.00 0.00 0.00 5.01
2342 2456 1.304282 CCACCTTCCCCTGATGTGG 59.696 63.158 0.00 0.00 37.40 4.17
2343 2457 0.035056 GACCACCTTCCCCTGATGTG 60.035 60.000 0.00 0.00 0.00 3.21
2344 2458 0.475632 TGACCACCTTCCCCTGATGT 60.476 55.000 0.00 0.00 0.00 3.06
2345 2459 0.035056 GTGACCACCTTCCCCTGATG 60.035 60.000 0.00 0.00 0.00 3.07
2346 2460 2.387952 GTGACCACCTTCCCCTGAT 58.612 57.895 0.00 0.00 0.00 2.90
2347 2461 3.900888 GTGACCACCTTCCCCTGA 58.099 61.111 0.00 0.00 0.00 3.86
2357 2471 1.148273 TGGACTTGCTGGTGACCAC 59.852 57.895 0.00 0.00 0.00 4.16
2358 2472 1.148273 GTGGACTTGCTGGTGACCA 59.852 57.895 3.40 3.40 0.00 4.02
2359 2473 1.961277 CGTGGACTTGCTGGTGACC 60.961 63.158 0.00 0.00 0.00 4.02
2360 2474 1.961277 CCGTGGACTTGCTGGTGAC 60.961 63.158 0.00 0.00 0.00 3.67
2361 2475 2.425592 CCGTGGACTTGCTGGTGA 59.574 61.111 0.00 0.00 0.00 4.02
2362 2476 2.669569 CCCGTGGACTTGCTGGTG 60.670 66.667 0.00 0.00 0.00 4.17
2363 2477 3.953775 CCCCGTGGACTTGCTGGT 61.954 66.667 0.00 0.00 0.00 4.00
2383 2497 3.966543 CTCACCACACCCACCCCC 61.967 72.222 0.00 0.00 0.00 5.40
2384 2498 2.763645 AACTCACCACACCCACCCC 61.764 63.158 0.00 0.00 0.00 4.95
2385 2499 1.528309 CAACTCACCACACCCACCC 60.528 63.158 0.00 0.00 0.00 4.61
2386 2500 2.193536 GCAACTCACCACACCCACC 61.194 63.158 0.00 0.00 0.00 4.61
2387 2501 0.751643 AAGCAACTCACCACACCCAC 60.752 55.000 0.00 0.00 0.00 4.61
2388 2502 0.751277 CAAGCAACTCACCACACCCA 60.751 55.000 0.00 0.00 0.00 4.51
2389 2503 2.032981 CAAGCAACTCACCACACCC 58.967 57.895 0.00 0.00 0.00 4.61
2390 2504 1.360192 GCAAGCAACTCACCACACC 59.640 57.895 0.00 0.00 0.00 4.16
2391 2505 1.009675 CGCAAGCAACTCACCACAC 60.010 57.895 0.00 0.00 0.00 3.82
2392 2506 3.419828 CGCAAGCAACTCACCACA 58.580 55.556 0.00 0.00 0.00 4.17
2411 2525 3.708220 CTCTTCTCCCTGGTCGCGC 62.708 68.421 0.00 0.00 0.00 6.86
2412 2526 2.492090 CTCTTCTCCCTGGTCGCG 59.508 66.667 0.00 0.00 0.00 5.87
2413 2527 2.726351 CCCTCTTCTCCCTGGTCGC 61.726 68.421 0.00 0.00 0.00 5.19
2414 2528 1.000486 TCCCTCTTCTCCCTGGTCG 60.000 63.158 0.00 0.00 0.00 4.79
2415 2529 0.041982 ACTCCCTCTTCTCCCTGGTC 59.958 60.000 0.00 0.00 0.00 4.02
2416 2530 0.494095 AACTCCCTCTTCTCCCTGGT 59.506 55.000 0.00 0.00 0.00 4.00
2417 2531 0.908198 CAACTCCCTCTTCTCCCTGG 59.092 60.000 0.00 0.00 0.00 4.45
2418 2532 0.908198 CCAACTCCCTCTTCTCCCTG 59.092 60.000 0.00 0.00 0.00 4.45
2419 2533 0.252927 CCCAACTCCCTCTTCTCCCT 60.253 60.000 0.00 0.00 0.00 4.20
2420 2534 1.916206 GCCCAACTCCCTCTTCTCCC 61.916 65.000 0.00 0.00 0.00 4.30
2421 2535 1.604915 GCCCAACTCCCTCTTCTCC 59.395 63.158 0.00 0.00 0.00 3.71
2422 2536 1.219393 CGCCCAACTCCCTCTTCTC 59.781 63.158 0.00 0.00 0.00 2.87
2423 2537 1.536662 ACGCCCAACTCCCTCTTCT 60.537 57.895 0.00 0.00 0.00 2.85
2424 2538 1.376037 CACGCCCAACTCCCTCTTC 60.376 63.158 0.00 0.00 0.00 2.87
2425 2539 2.750350 CACGCCCAACTCCCTCTT 59.250 61.111 0.00 0.00 0.00 2.85
2426 2540 3.322466 CCACGCCCAACTCCCTCT 61.322 66.667 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.