Multiple sequence alignment - TraesCS6D01G348300

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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 TraesCS6D01G348300 chr6D 100.000 2432 0 0 1 2432 446482281 446484712 0.000000e+00 4492.0
1 TraesCS6D01G348300 chr6D 84.226 691 83 12 489 1155 446476720 446477408 0.000000e+00 649.0
2 TraesCS6D01G348300 chrUn 89.182 1137 71 21 334 1449 79254124 79255229 0.000000e+00 1371.0
3 TraesCS6D01G348300 chrUn 88.742 1137 76 26 334 1449 79285050 79286155 0.000000e+00 1343.0
4 TraesCS6D01G348300 chrUn 87.150 1144 83 28 335 1449 79313806 79314914 0.000000e+00 1240.0
5 TraesCS6D01G348300 chrUn 90.486 925 56 12 335 1234 79282126 79283043 0.000000e+00 1192.0
6 TraesCS6D01G348300 chrUn 85.944 996 74 20 490 1449 79267947 79268912 0.000000e+00 1003.0
7 TraesCS6D01G348300 chrUn 85.643 996 76 24 490 1449 79299274 79300238 0.000000e+00 985.0
8 TraesCS6D01G348300 chrUn 93.120 407 23 5 1442 1848 79316533 79316934 2.080000e-165 592.0
9 TraesCS6D01G348300 chrUn 84.353 556 39 18 893 1445 366253257 366253767 3.610000e-138 501.0
10 TraesCS6D01G348300 chrUn 84.201 557 38 18 893 1445 372783090 372783600 1.680000e-136 496.0
11 TraesCS6D01G348300 chrUn 91.205 307 23 2 1 305 79313515 79313819 4.840000e-112 414.0
12 TraesCS6D01G348300 chrUn 90.228 307 26 2 1 305 79281835 79282139 4.870000e-107 398.0
13 TraesCS6D01G348300 chrUn 93.939 198 10 1 1 198 79251397 79251592 5.080000e-77 298.0
14 TraesCS6D01G348300 chrUn 97.500 160 4 0 2099 2258 79329073 79329232 8.570000e-70 274.0
15 TraesCS6D01G348300 chrUn 93.701 127 4 1 1977 2103 79316985 79317107 1.150000e-43 187.0
16 TraesCS6D01G348300 chrUn 76.774 310 43 17 1140 1449 79271643 79271923 1.950000e-31 147.0
17 TraesCS6D01G348300 chrUn 76.452 310 44 17 1140 1449 79303324 79303604 9.070000e-30 141.0
18 TraesCS6D01G348300 chrUn 89.130 92 6 2 2003 2094 79292801 79292888 7.110000e-21 111.0
19 TraesCS6D01G348300 chrUn 93.333 75 3 1 124 198 372782206 372782278 2.560000e-20 110.0
20 TraesCS6D01G348300 chrUn 97.917 48 0 1 1837 1884 79316946 79316992 5.570000e-12 82.4
21 TraesCS6D01G348300 chr6A 87.511 1145 83 25 336 1451 593299436 593300549 0.000000e+00 1267.0
22 TraesCS6D01G348300 chr6A 95.455 792 28 4 1438 2227 593302502 593303287 0.000000e+00 1256.0
23 TraesCS6D01G348300 chr6A 87.060 1136 92 28 333 1449 593277972 593279071 0.000000e+00 1232.0
24 TraesCS6D01G348300 chr6A 85.920 973 98 17 505 1449 593297060 593298021 0.000000e+00 1002.0
25 TraesCS6D01G348300 chr6A 84.840 686 78 11 489 1151 593284115 593284797 0.000000e+00 667.0
26 TraesCS6D01G348300 chr6A 87.302 315 29 4 1 305 593277674 593277987 1.380000e-92 350.0
27 TraesCS6D01G348300 chr6B 87.715 1107 73 25 354 1445 674918361 674919419 0.000000e+00 1232.0
28 TraesCS6D01G348300 chr1B 86.111 72 9 1 1828 1899 22270437 22270507 2.590000e-10 76.8
29 TraesCS6D01G348300 chr5A 84.932 73 8 3 1828 1899 36310945 36311015 1.210000e-08 71.3


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 TraesCS6D01G348300 chr6D 446482281 446484712 2431 False 4492.000000 4492 100.000000 1 2432 1 chr6D.!!$F2 2431
1 TraesCS6D01G348300 chr6D 446476720 446477408 688 False 649.000000 649 84.226000 489 1155 1 chr6D.!!$F1 666
2 TraesCS6D01G348300 chrUn 79281835 79286155 4320 False 977.666667 1343 89.818667 1 1449 3 chrUn.!!$F6 1448
3 TraesCS6D01G348300 chrUn 79251397 79255229 3832 False 834.500000 1371 91.560500 1 1449 2 chrUn.!!$F4 1448
4 TraesCS6D01G348300 chrUn 79267947 79271923 3976 False 575.000000 1003 81.359000 490 1449 2 chrUn.!!$F5 959
5 TraesCS6D01G348300 chrUn 79299274 79303604 4330 False 563.000000 985 81.047500 490 1449 2 chrUn.!!$F7 959
6 TraesCS6D01G348300 chrUn 79313515 79317107 3592 False 503.080000 1240 92.618600 1 2103 5 chrUn.!!$F8 2102
7 TraesCS6D01G348300 chrUn 366253257 366253767 510 False 501.000000 501 84.353000 893 1445 1 chrUn.!!$F3 552
8 TraesCS6D01G348300 chrUn 372782206 372783600 1394 False 303.000000 496 88.767000 124 1445 2 chrUn.!!$F9 1321
9 TraesCS6D01G348300 chr6A 593297060 593303287 6227 False 1175.000000 1267 89.628667 336 2227 3 chr6A.!!$F3 1891
10 TraesCS6D01G348300 chr6A 593277674 593279071 1397 False 791.000000 1232 87.181000 1 1449 2 chr6A.!!$F2 1448
11 TraesCS6D01G348300 chr6A 593284115 593284797 682 False 667.000000 667 84.840000 489 1151 1 chr6A.!!$F1 662
12 TraesCS6D01G348300 chr6B 674918361 674919419 1058 False 1232.000000 1232 87.715000 354 1445 1 chr6B.!!$F1 1091

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
158 167 0.770499 TTGATGAGAGTTGGTGGCCA 59.230 50.000 0.0 0.0 0.00 5.36 F
1160 6650 1.796151 TGCTCAATGTAAGCAGCGC 59.204 52.632 0.0 0.0 44.51 5.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1285 6779 0.107654 CCGGAACCCTTGACCAGATC 60.108 60.0 0.00 0.00 0.0 2.75 R
2365 12934 0.105039 CCAGTAGCCTCCGGATGAAC 59.895 60.0 11.34 7.63 0.0 3.18 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
70 79 2.365293 GCCAACAGTTCCATTTTCAGGT 59.635 45.455 0.00 0.00 0.00 4.00
158 167 0.770499 TTGATGAGAGTTGGTGGCCA 59.230 50.000 0.00 0.00 0.00 5.36
201 2647 5.593095 GTGGGGAACTTTTGAGACTTAACTT 59.407 40.000 0.00 0.00 0.00 2.66
202 2648 5.592688 TGGGGAACTTTTGAGACTTAACTTG 59.407 40.000 0.00 0.00 0.00 3.16
227 2673 5.654650 TGAGTTAACCTTTTGAGCCTTTGAA 59.345 36.000 0.88 0.00 0.00 2.69
231 2677 7.505923 AGTTAACCTTTTGAGCCTTTGAATAGT 59.494 33.333 0.88 0.00 0.00 2.12
243 2689 5.010282 CCTTTGAATAGTTGTGGCTTACCT 58.990 41.667 0.00 0.00 36.63 3.08
244 2690 5.123979 CCTTTGAATAGTTGTGGCTTACCTC 59.876 44.000 0.00 0.00 36.63 3.85
300 2746 6.963049 TTTTTAGAGTTCGGTTAGAGATGC 57.037 37.500 0.00 0.00 0.00 3.91
301 2747 5.916661 TTTAGAGTTCGGTTAGAGATGCT 57.083 39.130 0.00 0.00 0.00 3.79
302 2748 5.502153 TTAGAGTTCGGTTAGAGATGCTC 57.498 43.478 0.00 0.00 0.00 4.26
303 2749 3.626930 AGAGTTCGGTTAGAGATGCTCT 58.373 45.455 2.22 2.22 43.83 4.09
304 2750 4.020543 AGAGTTCGGTTAGAGATGCTCTT 58.979 43.478 1.88 0.00 41.50 2.85
305 2751 4.464597 AGAGTTCGGTTAGAGATGCTCTTT 59.535 41.667 1.88 0.00 41.50 2.52
306 2752 5.046950 AGAGTTCGGTTAGAGATGCTCTTTT 60.047 40.000 1.88 0.00 41.50 2.27
307 2753 5.552178 AGTTCGGTTAGAGATGCTCTTTTT 58.448 37.500 1.88 0.00 41.50 1.94
338 2784 3.395630 GGTTCGCCCCAGGTTAGA 58.604 61.111 0.00 0.00 0.00 2.10
423 2869 8.917088 CCTCCACATCATTAAATCCAACTTATT 58.083 33.333 0.00 0.00 0.00 1.40
424 2870 9.740239 CTCCACATCATTAAATCCAACTTATTG 57.260 33.333 0.00 0.00 35.40 1.90
440 2886 6.454223 ACTTATTGATAGCCCCACATGTAT 57.546 37.500 0.00 0.00 0.00 2.29
451 2897 4.202050 GCCCCACATGTATTAGAAGCTTTG 60.202 45.833 0.00 0.00 0.00 2.77
623 3095 7.820872 AGCAGCTAATTTAAAGTGATGCATTTT 59.179 29.630 21.20 0.00 33.69 1.82
956 6421 5.183140 ACTCTCTTCTTAGCTGAAGACTGAC 59.817 44.000 11.44 0.00 45.00 3.51
1012 6496 5.068855 TCAATCTCTGACATGATGAGGAGTC 59.931 44.000 0.00 0.00 0.00 3.36
1022 6506 3.125656 TGATGAGGAGTCCCATTTCCAT 58.874 45.455 5.25 0.26 35.88 3.41
1109 6596 2.052690 GGCTAGACGCAGAGACCCA 61.053 63.158 0.00 0.00 41.67 4.51
1160 6650 1.796151 TGCTCAATGTAAGCAGCGC 59.204 52.632 0.00 0.00 44.51 5.92
1178 6668 2.275318 CGCTTCTCATCTTCTGTTCCC 58.725 52.381 0.00 0.00 0.00 3.97
1205 6698 6.950041 TGTCTGAATCTTTGGATGATCCTTTT 59.050 34.615 13.44 0.00 37.46 2.27
1283 6777 2.874664 CGGTCAAGGGTTCCGGTGA 61.875 63.158 0.00 0.00 40.49 4.02
1284 6778 1.683441 GGTCAAGGGTTCCGGTGAT 59.317 57.895 0.00 0.00 0.00 3.06
1285 6779 0.676782 GGTCAAGGGTTCCGGTGATG 60.677 60.000 0.00 0.00 0.00 3.07
1286 6780 0.323629 GTCAAGGGTTCCGGTGATGA 59.676 55.000 0.00 0.00 0.00 2.92
1287 6781 1.065418 GTCAAGGGTTCCGGTGATGAT 60.065 52.381 0.00 0.00 0.00 2.45
1288 6782 1.209504 TCAAGGGTTCCGGTGATGATC 59.790 52.381 0.00 0.00 0.00 2.92
1289 6783 1.210478 CAAGGGTTCCGGTGATGATCT 59.790 52.381 0.00 0.00 0.00 2.75
1290 6784 0.833287 AGGGTTCCGGTGATGATCTG 59.167 55.000 0.00 0.00 0.00 2.90
1291 6785 0.179045 GGGTTCCGGTGATGATCTGG 60.179 60.000 0.00 0.00 0.00 3.86
1292 6786 0.541863 GGTTCCGGTGATGATCTGGT 59.458 55.000 0.00 0.00 33.44 4.00
1293 6787 1.473434 GGTTCCGGTGATGATCTGGTC 60.473 57.143 0.00 0.00 33.44 4.02
1294 6788 1.207089 GTTCCGGTGATGATCTGGTCA 59.793 52.381 0.00 0.00 42.06 4.02
1295 6789 1.567357 TCCGGTGATGATCTGGTCAA 58.433 50.000 0.00 0.00 40.97 3.18
1296 6790 1.482182 TCCGGTGATGATCTGGTCAAG 59.518 52.381 0.00 0.00 40.97 3.02
1297 6791 1.473965 CCGGTGATGATCTGGTCAAGG 60.474 57.143 0.00 0.53 40.97 3.61
1298 6792 1.473965 CGGTGATGATCTGGTCAAGGG 60.474 57.143 0.00 0.00 40.97 3.95
1299 6793 1.561542 GGTGATGATCTGGTCAAGGGT 59.438 52.381 0.00 0.00 40.97 4.34
1300 6794 2.025887 GGTGATGATCTGGTCAAGGGTT 60.026 50.000 0.00 0.00 40.97 4.11
1301 6795 3.274288 GTGATGATCTGGTCAAGGGTTC 58.726 50.000 0.00 0.00 40.97 3.62
1302 6796 2.239654 TGATGATCTGGTCAAGGGTTCC 59.760 50.000 0.00 0.00 40.97 3.62
1303 6797 0.613260 TGATCTGGTCAAGGGTTCCG 59.387 55.000 0.00 0.00 32.78 4.30
1304 6798 0.107654 GATCTGGTCAAGGGTTCCGG 60.108 60.000 0.00 0.00 0.00 5.14
1305 6799 0.840722 ATCTGGTCAAGGGTTCCGGT 60.841 55.000 0.00 0.00 0.00 5.28
1306 6800 1.302511 CTGGTCAAGGGTTCCGGTG 60.303 63.158 0.00 0.00 0.00 4.94
1321 6815 4.933064 GTGGATCGGCGAGCGAGG 62.933 72.222 19.61 0.00 0.00 4.63
1342 6836 1.000019 ACAGGGAGCGCTGGTACTA 60.000 57.895 18.48 0.00 0.00 1.82
1404 6902 5.531122 TCCAGGAAGACTATTATGTTCCG 57.469 43.478 0.00 0.00 44.79 4.30
1502 11947 7.338449 ACACATAGTGTCGGCCTATTTTTATTT 59.662 33.333 0.00 0.00 43.92 1.40
1572 12017 2.698855 TGGCTTTGAGGATCTGCTAC 57.301 50.000 0.00 0.00 34.92 3.58
1627 12072 1.302832 AAGGGTTGCAGGAAGCTCG 60.303 57.895 3.69 0.00 45.94 5.03
1674 12119 7.474398 AAACCTACTCGAACTTAACTTGAAC 57.526 36.000 0.00 0.00 0.00 3.18
1880 12448 2.553086 CAATGTTGGCAAAACAGTGCT 58.447 42.857 15.83 0.00 44.31 4.40
1881 12449 2.228138 ATGTTGGCAAAACAGTGCTG 57.772 45.000 0.00 0.00 44.31 4.41
1882 12450 0.175302 TGTTGGCAAAACAGTGCTGG 59.825 50.000 0.00 0.00 44.31 4.85
1883 12451 0.459489 GTTGGCAAAACAGTGCTGGA 59.541 50.000 0.00 0.00 44.31 3.86
1884 12452 1.134848 GTTGGCAAAACAGTGCTGGAA 60.135 47.619 0.00 0.00 44.31 3.53
1885 12453 0.746063 TGGCAAAACAGTGCTGGAAG 59.254 50.000 4.11 0.00 44.31 3.46
1902 12470 5.734720 CTGGAAGCTAAATGAGTAACCAGA 58.265 41.667 0.00 0.00 40.08 3.86
1903 12471 6.313519 TGGAAGCTAAATGAGTAACCAGAT 57.686 37.500 0.00 0.00 0.00 2.90
1904 12472 6.721318 TGGAAGCTAAATGAGTAACCAGATT 58.279 36.000 0.00 0.00 0.00 2.40
1905 12473 6.823689 TGGAAGCTAAATGAGTAACCAGATTC 59.176 38.462 0.00 0.00 0.00 2.52
1906 12474 6.261158 GGAAGCTAAATGAGTAACCAGATTCC 59.739 42.308 1.18 1.18 40.23 3.01
1907 12475 5.685728 AGCTAAATGAGTAACCAGATTCCC 58.314 41.667 0.00 0.00 0.00 3.97
1908 12476 5.430089 AGCTAAATGAGTAACCAGATTCCCT 59.570 40.000 0.00 0.00 0.00 4.20
1909 12477 6.069381 AGCTAAATGAGTAACCAGATTCCCTT 60.069 38.462 0.00 0.00 0.00 3.95
1910 12478 6.603599 GCTAAATGAGTAACCAGATTCCCTTT 59.396 38.462 0.00 0.00 0.00 3.11
1911 12479 6.840780 AAATGAGTAACCAGATTCCCTTTG 57.159 37.500 0.00 0.00 0.00 2.77
1912 12480 3.686016 TGAGTAACCAGATTCCCTTTGC 58.314 45.455 0.00 0.00 0.00 3.68
1913 12481 2.678336 GAGTAACCAGATTCCCTTTGCG 59.322 50.000 0.00 0.00 0.00 4.85
1914 12482 2.039879 AGTAACCAGATTCCCTTTGCGT 59.960 45.455 0.00 0.00 0.00 5.24
1915 12483 1.534729 AACCAGATTCCCTTTGCGTC 58.465 50.000 0.00 0.00 0.00 5.19
1916 12484 0.400213 ACCAGATTCCCTTTGCGTCA 59.600 50.000 0.00 0.00 0.00 4.35
1917 12485 1.004745 ACCAGATTCCCTTTGCGTCAT 59.995 47.619 0.00 0.00 0.00 3.06
1918 12486 2.094675 CCAGATTCCCTTTGCGTCATT 58.905 47.619 0.00 0.00 0.00 2.57
1919 12487 2.159338 CCAGATTCCCTTTGCGTCATTG 60.159 50.000 0.00 0.00 0.00 2.82
1920 12488 2.489329 CAGATTCCCTTTGCGTCATTGT 59.511 45.455 0.00 0.00 0.00 2.71
1921 12489 2.489329 AGATTCCCTTTGCGTCATTGTG 59.511 45.455 0.00 0.00 0.00 3.33
1922 12490 0.313672 TTCCCTTTGCGTCATTGTGC 59.686 50.000 0.00 0.00 0.00 4.57
1923 12491 0.537143 TCCCTTTGCGTCATTGTGCT 60.537 50.000 5.51 0.00 0.00 4.40
1924 12492 0.314935 CCCTTTGCGTCATTGTGCTT 59.685 50.000 5.51 0.00 0.00 3.91
1925 12493 1.539388 CCCTTTGCGTCATTGTGCTTA 59.461 47.619 5.51 0.00 0.00 3.09
1926 12494 2.414559 CCCTTTGCGTCATTGTGCTTAG 60.415 50.000 5.51 3.40 0.00 2.18
1927 12495 2.483877 CCTTTGCGTCATTGTGCTTAGA 59.516 45.455 5.51 0.00 0.00 2.10
1928 12496 3.425359 CCTTTGCGTCATTGTGCTTAGAG 60.425 47.826 5.51 0.00 0.00 2.43
1929 12497 1.078709 TGCGTCATTGTGCTTAGAGC 58.921 50.000 5.51 0.00 42.82 4.09
1947 12515 8.457261 GCTTAGAGCAAAATATTATCCAGATGG 58.543 37.037 0.00 0.00 41.89 3.51
1962 12530 5.879763 TCCAGATGGAAATTTCTTGACAGA 58.120 37.500 17.42 6.32 42.18 3.41
1963 12531 6.306199 TCCAGATGGAAATTTCTTGACAGAA 58.694 36.000 17.42 0.00 42.18 3.02
1964 12532 6.777091 TCCAGATGGAAATTTCTTGACAGAAA 59.223 34.615 17.42 0.04 45.63 2.52
1965 12533 7.287466 TCCAGATGGAAATTTCTTGACAGAAAA 59.713 33.333 17.42 0.00 45.18 2.29
1966 12534 7.927629 CCAGATGGAAATTTCTTGACAGAAAAA 59.072 33.333 17.42 0.00 43.84 1.94
2033 12601 6.299141 TGTCAGGTTTAGAAGCTTTCAAGAT 58.701 36.000 0.00 0.00 37.06 2.40
2048 12616 6.688922 GCTTTCAAGATGGGGTATATCTGACA 60.689 42.308 0.00 0.00 35.20 3.58
2069 12638 5.690865 ACAAGTAGGTGATGGAACTCAAAA 58.309 37.500 0.00 0.00 0.00 2.44
2071 12640 6.207417 ACAAGTAGGTGATGGAACTCAAAATG 59.793 38.462 0.00 0.00 0.00 2.32
2103 12672 3.007506 TGGTGCGATAATTGGATACCGAT 59.992 43.478 0.00 0.00 0.00 4.18
2194 12763 1.543429 CCAGTTTCAGGTGAGTGGGAC 60.543 57.143 0.00 0.00 0.00 4.46
2227 12796 3.426615 TCCGTCTATGTTTTGGCCAATT 58.573 40.909 21.26 7.47 0.00 2.32
2228 12797 3.192422 TCCGTCTATGTTTTGGCCAATTG 59.808 43.478 21.26 5.41 0.00 2.32
2229 12798 3.192422 CCGTCTATGTTTTGGCCAATTGA 59.808 43.478 21.26 7.96 0.00 2.57
2230 12799 4.165779 CGTCTATGTTTTGGCCAATTGAC 58.834 43.478 21.26 18.32 0.00 3.18
2231 12800 4.165779 GTCTATGTTTTGGCCAATTGACG 58.834 43.478 21.26 6.91 0.00 4.35
2233 12802 0.749649 TGTTTTGGCCAATTGACGCT 59.250 45.000 21.26 0.00 0.00 5.07
2235 12804 1.035923 TTTTGGCCAATTGACGCTGA 58.964 45.000 21.26 0.00 0.00 4.26
2236 12805 1.035923 TTTGGCCAATTGACGCTGAA 58.964 45.000 21.26 0.00 0.00 3.02
2237 12806 0.597568 TTGGCCAATTGACGCTGAAG 59.402 50.000 16.05 0.00 0.00 3.02
2238 12807 1.153958 GGCCAATTGACGCTGAAGC 60.154 57.895 7.12 0.00 37.78 3.86
2239 12808 1.580942 GCCAATTGACGCTGAAGCA 59.419 52.632 7.12 0.00 42.21 3.91
2240 12809 0.039256 GCCAATTGACGCTGAAGCAA 60.039 50.000 7.12 0.00 42.21 3.91
2241 12810 1.403249 GCCAATTGACGCTGAAGCAAT 60.403 47.619 7.12 0.00 42.21 3.56
2243 12812 3.489738 GCCAATTGACGCTGAAGCAATAT 60.490 43.478 7.12 0.00 42.21 1.28
2244 12813 4.675510 CCAATTGACGCTGAAGCAATATT 58.324 39.130 7.12 0.00 42.21 1.28
2245 12814 5.733091 GCCAATTGACGCTGAAGCAATATTA 60.733 40.000 7.12 0.00 42.21 0.98
2246 12815 5.682862 CCAATTGACGCTGAAGCAATATTAC 59.317 40.000 7.12 0.00 42.21 1.89
2247 12816 4.875544 TTGACGCTGAAGCAATATTACC 57.124 40.909 2.79 0.00 42.21 2.85
2248 12817 3.867857 TGACGCTGAAGCAATATTACCA 58.132 40.909 2.79 0.00 42.21 3.25
2249 12818 4.257731 TGACGCTGAAGCAATATTACCAA 58.742 39.130 2.79 0.00 42.21 3.67
2251 12820 5.007626 TGACGCTGAAGCAATATTACCAATC 59.992 40.000 2.79 0.00 42.21 2.67
2252 12821 4.275936 ACGCTGAAGCAATATTACCAATCC 59.724 41.667 2.79 0.00 42.21 3.01
2253 12822 4.516698 CGCTGAAGCAATATTACCAATCCT 59.483 41.667 2.79 0.00 42.21 3.24
2254 12823 5.334414 CGCTGAAGCAATATTACCAATCCTC 60.334 44.000 2.79 0.00 42.21 3.71
2255 12824 5.767168 GCTGAAGCAATATTACCAATCCTCT 59.233 40.000 0.00 0.00 41.59 3.69
2256 12825 6.936900 GCTGAAGCAATATTACCAATCCTCTA 59.063 38.462 0.00 0.00 41.59 2.43
2258 12827 6.936900 TGAAGCAATATTACCAATCCTCTAGC 59.063 38.462 0.00 0.00 0.00 3.42
2261 12830 5.178797 CAATATTACCAATCCTCTAGCGGG 58.821 45.833 0.00 0.00 0.00 6.13
2262 12831 2.170012 TTACCAATCCTCTAGCGGGT 57.830 50.000 0.00 0.00 0.00 5.28
2263 12832 1.410004 TACCAATCCTCTAGCGGGTG 58.590 55.000 0.00 0.00 0.00 4.61
2264 12833 1.338136 ACCAATCCTCTAGCGGGTGG 61.338 60.000 16.57 16.57 36.37 4.61
2265 12834 1.227674 CAATCCTCTAGCGGGTGGC 60.228 63.158 0.00 0.00 44.05 5.01
2266 12835 2.444256 AATCCTCTAGCGGGTGGCC 61.444 63.158 0.00 0.00 45.17 5.36
2267 12836 2.898472 AATCCTCTAGCGGGTGGCCT 62.898 60.000 3.32 0.00 45.17 5.19
2269 12838 3.854669 CTCTAGCGGGTGGCCTGG 61.855 72.222 3.32 0.00 45.17 4.45
2270 12839 4.392166 TCTAGCGGGTGGCCTGGA 62.392 66.667 3.32 0.00 45.17 3.86
2271 12840 3.399181 CTAGCGGGTGGCCTGGAA 61.399 66.667 3.32 0.00 45.17 3.53
2272 12841 3.391665 CTAGCGGGTGGCCTGGAAG 62.392 68.421 3.32 0.00 45.17 3.46
2273 12842 3.916438 TAGCGGGTGGCCTGGAAGA 62.916 63.158 3.32 0.00 45.17 2.87
2274 12843 4.115199 GCGGGTGGCCTGGAAGAT 62.115 66.667 3.32 0.00 34.07 2.40
2275 12844 2.677228 CGGGTGGCCTGGAAGATT 59.323 61.111 3.32 0.00 34.07 2.40
2276 12845 1.000896 CGGGTGGCCTGGAAGATTT 60.001 57.895 3.32 0.00 34.07 2.17
2277 12846 0.611896 CGGGTGGCCTGGAAGATTTT 60.612 55.000 3.32 0.00 34.07 1.82
2278 12847 0.897621 GGGTGGCCTGGAAGATTTTG 59.102 55.000 3.32 0.00 34.07 2.44
2280 12849 1.273327 GGTGGCCTGGAAGATTTTGTG 59.727 52.381 3.32 0.00 34.07 3.33
2281 12850 1.273327 GTGGCCTGGAAGATTTTGTGG 59.727 52.381 3.32 0.00 34.07 4.17
2283 12852 2.109128 TGGCCTGGAAGATTTTGTGGTA 59.891 45.455 3.32 0.00 34.07 3.25
2284 12853 3.245586 TGGCCTGGAAGATTTTGTGGTAT 60.246 43.478 3.32 0.00 34.07 2.73
2285 12854 3.131046 GGCCTGGAAGATTTTGTGGTATG 59.869 47.826 0.00 0.00 34.07 2.39
2286 12855 3.131046 GCCTGGAAGATTTTGTGGTATGG 59.869 47.826 0.00 0.00 34.07 2.74
2287 12856 3.131046 CCTGGAAGATTTTGTGGTATGGC 59.869 47.826 0.00 0.00 34.07 4.40
2289 12858 4.352009 TGGAAGATTTTGTGGTATGGCAT 58.648 39.130 4.88 4.88 0.00 4.40
2290 12859 5.514169 TGGAAGATTTTGTGGTATGGCATA 58.486 37.500 2.32 2.32 0.00 3.14
2292 12861 6.127479 TGGAAGATTTTGTGGTATGGCATAAC 60.127 38.462 15.67 15.67 0.00 1.89
2294 12863 6.699575 AGATTTTGTGGTATGGCATAACTC 57.300 37.500 22.25 18.91 0.00 3.01
2295 12864 6.186957 AGATTTTGTGGTATGGCATAACTCA 58.813 36.000 22.25 21.15 0.00 3.41
2296 12865 6.663093 AGATTTTGTGGTATGGCATAACTCAA 59.337 34.615 27.29 27.29 35.02 3.02
2297 12866 6.656632 TTTTGTGGTATGGCATAACTCAAA 57.343 33.333 32.70 32.70 41.45 2.69
2298 12867 6.656632 TTTGTGGTATGGCATAACTCAAAA 57.343 33.333 33.55 22.80 40.72 2.44
2299 12868 6.656632 TTGTGGTATGGCATAACTCAAAAA 57.343 33.333 28.29 13.36 34.22 1.94
2300 12869 6.019779 TGTGGTATGGCATAACTCAAAAAC 57.980 37.500 21.38 11.93 0.00 2.43
2301 12870 5.092781 GTGGTATGGCATAACTCAAAAACG 58.907 41.667 22.25 0.00 0.00 3.60
2302 12871 4.156922 TGGTATGGCATAACTCAAAAACGG 59.843 41.667 22.25 0.00 0.00 4.44
2303 12872 4.396790 GGTATGGCATAACTCAAAAACGGA 59.603 41.667 15.28 0.00 0.00 4.69
2304 12873 5.106078 GGTATGGCATAACTCAAAAACGGAA 60.106 40.000 15.28 0.00 0.00 4.30
2325 12894 9.698309 ACGGAAGTATTATCTATCAAATCAGTG 57.302 33.333 0.00 0.00 46.88 3.66
2336 12905 8.996651 TCTATCAAATCAGTGTACTATGGAGA 57.003 34.615 0.00 0.00 0.00 3.71
2337 12906 9.072375 TCTATCAAATCAGTGTACTATGGAGAG 57.928 37.037 0.00 0.00 0.00 3.20
2338 12907 7.667575 ATCAAATCAGTGTACTATGGAGAGT 57.332 36.000 0.00 0.00 0.00 3.24
2340 12909 8.226819 TCAAATCAGTGTACTATGGAGAGTAG 57.773 38.462 0.00 0.00 32.56 2.57
2341 12910 7.834681 TCAAATCAGTGTACTATGGAGAGTAGT 59.165 37.037 0.00 0.00 36.44 2.73
2342 12911 7.811117 AATCAGTGTACTATGGAGAGTAGTC 57.189 40.000 0.00 0.00 34.43 2.59
2343 12912 6.563037 TCAGTGTACTATGGAGAGTAGTCT 57.437 41.667 0.00 0.00 34.43 3.24
2358 12927 7.954788 AGAGTAGTCTCACAAATTCAGAAAC 57.045 36.000 0.00 0.00 42.66 2.78
2359 12928 7.500992 AGAGTAGTCTCACAAATTCAGAAACA 58.499 34.615 0.00 0.00 42.66 2.83
2360 12929 7.987458 AGAGTAGTCTCACAAATTCAGAAACAA 59.013 33.333 0.00 0.00 42.66 2.83
2361 12930 8.682936 AGTAGTCTCACAAATTCAGAAACAAT 57.317 30.769 0.00 0.00 0.00 2.71
2362 12931 9.778741 AGTAGTCTCACAAATTCAGAAACAATA 57.221 29.630 0.00 0.00 0.00 1.90
2365 12934 9.903682 AGTCTCACAAATTCAGAAACAATATTG 57.096 29.630 14.01 14.01 0.00 1.90
2366 12935 9.683069 GTCTCACAAATTCAGAAACAATATTGT 57.317 29.630 15.47 15.47 44.72 2.71
2378 12947 3.214328 ACAATATTGTTCATCCGGAGGC 58.786 45.455 15.47 0.00 44.10 4.70
2379 12948 3.117888 ACAATATTGTTCATCCGGAGGCT 60.118 43.478 15.47 0.00 44.10 4.58
2380 12949 4.102524 ACAATATTGTTCATCCGGAGGCTA 59.897 41.667 15.47 0.00 44.10 3.93
2381 12950 5.973077 ACAATATTGTTCATCCGGAGGCTAC 60.973 44.000 15.47 12.36 44.10 3.58
2382 12951 8.100366 ACAATATTGTTCATCCGGAGGCTACT 62.100 42.308 15.47 0.21 44.10 2.57
2383 12952 9.990885 ACAATATTGTTCATCCGGAGGCTACTG 62.991 44.444 15.47 2.16 44.10 2.74
2388 12957 2.363795 CCGGAGGCTACTGGTGGA 60.364 66.667 0.00 0.00 46.14 4.02
2389 12958 1.762460 CCGGAGGCTACTGGTGGAT 60.762 63.158 0.00 0.00 46.14 3.41
2390 12959 1.742768 CGGAGGCTACTGGTGGATC 59.257 63.158 0.00 0.00 0.00 3.36
2391 12960 1.742768 GGAGGCTACTGGTGGATCG 59.257 63.158 0.00 0.00 0.00 3.69
2392 12961 0.755698 GGAGGCTACTGGTGGATCGA 60.756 60.000 0.00 0.00 0.00 3.59
2393 12962 0.386113 GAGGCTACTGGTGGATCGAC 59.614 60.000 0.00 0.00 0.00 4.20
2394 12963 0.324368 AGGCTACTGGTGGATCGACA 60.324 55.000 10.22 0.00 0.00 4.35
2395 12964 0.535335 GGCTACTGGTGGATCGACAA 59.465 55.000 10.22 0.00 0.00 3.18
2396 12965 1.066430 GGCTACTGGTGGATCGACAAA 60.066 52.381 10.22 0.00 0.00 2.83
2397 12966 2.000447 GCTACTGGTGGATCGACAAAC 59.000 52.381 10.22 0.00 0.00 2.93
2398 12967 2.611971 GCTACTGGTGGATCGACAAACA 60.612 50.000 10.22 0.00 0.00 2.83
2399 12968 2.631160 ACTGGTGGATCGACAAACAA 57.369 45.000 10.22 0.00 0.00 2.83
2400 12969 3.140325 ACTGGTGGATCGACAAACAAT 57.860 42.857 10.22 0.00 0.00 2.71
2401 12970 2.813754 ACTGGTGGATCGACAAACAATG 59.186 45.455 10.22 0.00 0.00 2.82
2403 12972 2.551887 TGGTGGATCGACAAACAATGTG 59.448 45.455 10.22 0.00 44.12 3.21
2404 12973 2.095263 GGTGGATCGACAAACAATGTGG 60.095 50.000 10.22 0.00 44.12 4.17
2405 12974 2.552315 GTGGATCGACAAACAATGTGGT 59.448 45.455 2.59 0.00 44.12 4.16
2406 12975 3.004315 GTGGATCGACAAACAATGTGGTT 59.996 43.478 2.59 0.00 44.12 3.67
2407 12976 3.634448 TGGATCGACAAACAATGTGGTTT 59.366 39.130 0.00 0.00 44.12 3.27
2413 12982 2.618442 AAACAATGTGGTTTGGGCTG 57.382 45.000 0.00 0.00 39.40 4.85
2414 12983 1.494960 AACAATGTGGTTTGGGCTGT 58.505 45.000 0.00 0.00 0.00 4.40
2415 12984 1.494960 ACAATGTGGTTTGGGCTGTT 58.505 45.000 0.00 0.00 0.00 3.16
2416 12985 2.672098 ACAATGTGGTTTGGGCTGTTA 58.328 42.857 0.00 0.00 0.00 2.41
2417 12986 3.238597 ACAATGTGGTTTGGGCTGTTAT 58.761 40.909 0.00 0.00 0.00 1.89
2418 12987 4.411927 ACAATGTGGTTTGGGCTGTTATA 58.588 39.130 0.00 0.00 0.00 0.98
2419 12988 5.022787 ACAATGTGGTTTGGGCTGTTATAT 58.977 37.500 0.00 0.00 0.00 0.86
2420 12989 5.105392 ACAATGTGGTTTGGGCTGTTATATG 60.105 40.000 0.00 0.00 0.00 1.78
2421 12990 3.360867 TGTGGTTTGGGCTGTTATATGG 58.639 45.455 0.00 0.00 0.00 2.74
2422 12991 3.010696 TGTGGTTTGGGCTGTTATATGGA 59.989 43.478 0.00 0.00 0.00 3.41
2423 12992 4.020543 GTGGTTTGGGCTGTTATATGGAA 58.979 43.478 0.00 0.00 0.00 3.53
2424 12993 4.464597 GTGGTTTGGGCTGTTATATGGAAA 59.535 41.667 0.00 0.00 0.00 3.13
2425 12994 5.128663 GTGGTTTGGGCTGTTATATGGAAAT 59.871 40.000 0.00 0.00 0.00 2.17
2426 12995 5.362430 TGGTTTGGGCTGTTATATGGAAATC 59.638 40.000 0.00 0.00 0.00 2.17
2427 12996 5.362430 GGTTTGGGCTGTTATATGGAAATCA 59.638 40.000 0.00 0.00 0.00 2.57
2428 12997 6.127196 GGTTTGGGCTGTTATATGGAAATCAA 60.127 38.462 0.00 0.00 0.00 2.57
2429 12998 7.327214 GTTTGGGCTGTTATATGGAAATCAAA 58.673 34.615 0.00 0.00 0.00 2.69
2430 12999 6.463995 TGGGCTGTTATATGGAAATCAAAC 57.536 37.500 0.00 0.00 0.00 2.93
2431 13000 5.954752 TGGGCTGTTATATGGAAATCAAACA 59.045 36.000 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 79 1.594833 CGCTACAACCACCAGGCTA 59.405 57.895 0.00 0.00 39.06 3.93
97 106 3.746949 CTCACATGGCGCCTCTCCC 62.747 68.421 29.70 0.00 0.00 4.30
158 167 4.081198 CCCACTCTCTCTATTTTGAGCAGT 60.081 45.833 0.00 0.00 34.29 4.40
201 2647 4.164843 AGGCTCAAAAGGTTAACTCACA 57.835 40.909 5.42 0.00 0.00 3.58
202 2648 5.067283 TCAAAGGCTCAAAAGGTTAACTCAC 59.933 40.000 5.42 0.00 0.00 3.51
227 2673 3.450904 TGAGGAGGTAAGCCACAACTAT 58.549 45.455 0.00 0.00 37.19 2.12
231 2677 3.586470 TTTTGAGGAGGTAAGCCACAA 57.414 42.857 0.00 0.00 34.82 3.33
321 2767 1.221021 CTCTAACCTGGGGCGAACC 59.779 63.158 0.00 0.00 39.11 3.62
322 2768 0.831307 ATCTCTAACCTGGGGCGAAC 59.169 55.000 0.00 0.00 0.00 3.95
323 2769 0.830648 CATCTCTAACCTGGGGCGAA 59.169 55.000 0.00 0.00 0.00 4.70
324 2770 1.686325 GCATCTCTAACCTGGGGCGA 61.686 60.000 0.00 0.00 0.00 5.54
325 2771 1.227674 GCATCTCTAACCTGGGGCG 60.228 63.158 0.00 0.00 0.00 6.13
326 2772 0.107643 GAGCATCTCTAACCTGGGGC 59.892 60.000 0.00 0.00 0.00 5.80
379 2825 3.892588 GGAGGGTTTCAATGTGTTTACCA 59.107 43.478 0.00 0.00 0.00 3.25
423 2869 5.513094 GCTTCTAATACATGTGGGGCTATCA 60.513 44.000 9.11 0.00 0.00 2.15
424 2870 4.938226 GCTTCTAATACATGTGGGGCTATC 59.062 45.833 9.11 0.00 0.00 2.08
440 2886 4.263068 CCTGGGTCTTCTCAAAGCTTCTAA 60.263 45.833 0.00 0.00 32.18 2.10
500 2948 2.873472 CCGGTGTGTCTAGTCTAGCTAG 59.127 54.545 15.01 15.01 46.59 3.42
516 2964 2.561037 GGAAAGTTGGGTGCCGGTG 61.561 63.158 1.90 0.00 0.00 4.94
803 6251 4.898320 TGCACTTATGTCTGTCATGAGTT 58.102 39.130 9.02 0.00 46.51 3.01
879 6328 1.938577 AGCTGAAGCATGCATCTAACG 59.061 47.619 22.26 10.16 45.16 3.18
956 6421 7.446769 TGACTAGCTAGGAGAGTATACTTCAG 58.553 42.308 24.35 1.96 0.00 3.02
1012 6496 4.156556 CAGTGACAAGTACATGGAAATGGG 59.843 45.833 2.78 0.00 0.00 4.00
1022 6506 0.467804 TGCAGCCAGTGACAAGTACA 59.532 50.000 0.00 0.00 0.00 2.90
1109 6596 2.729479 CCGCTGCTGATGGACTCCT 61.729 63.158 0.00 0.00 0.00 3.69
1158 6648 2.093764 AGGGAACAGAAGATGAGAAGCG 60.094 50.000 0.00 0.00 0.00 4.68
1160 6650 4.904241 ACAAGGGAACAGAAGATGAGAAG 58.096 43.478 0.00 0.00 0.00 2.85
1178 6668 6.120905 AGGATCATCCAAAGATTCAGACAAG 58.879 40.000 6.42 0.00 39.61 3.16
1205 6698 1.742831 CAGGTTAATTAGCGCCTGCAA 59.257 47.619 2.29 0.00 46.23 4.08
1243 6737 4.212004 CGCATCATCGATTGGTTTCTACAT 59.788 41.667 0.00 0.00 0.00 2.29
1246 6740 3.130633 CCGCATCATCGATTGGTTTCTA 58.869 45.455 0.00 0.00 0.00 2.10
1283 6777 1.210478 CGGAACCCTTGACCAGATCAT 59.790 52.381 0.00 0.00 37.11 2.45
1284 6778 0.613260 CGGAACCCTTGACCAGATCA 59.387 55.000 0.00 0.00 34.65 2.92
1285 6779 0.107654 CCGGAACCCTTGACCAGATC 60.108 60.000 0.00 0.00 0.00 2.75
1286 6780 0.840722 ACCGGAACCCTTGACCAGAT 60.841 55.000 9.46 0.00 0.00 2.90
1287 6781 1.460689 ACCGGAACCCTTGACCAGA 60.461 57.895 9.46 0.00 0.00 3.86
1288 6782 1.302511 CACCGGAACCCTTGACCAG 60.303 63.158 9.46 0.00 0.00 4.00
1289 6783 2.824880 CCACCGGAACCCTTGACCA 61.825 63.158 9.46 0.00 0.00 4.02
1290 6784 1.848886 ATCCACCGGAACCCTTGACC 61.849 60.000 9.46 0.00 34.34 4.02
1291 6785 0.392595 GATCCACCGGAACCCTTGAC 60.393 60.000 9.46 0.00 34.34 3.18
1292 6786 1.895020 CGATCCACCGGAACCCTTGA 61.895 60.000 9.46 0.00 34.34 3.02
1293 6787 1.449601 CGATCCACCGGAACCCTTG 60.450 63.158 9.46 0.00 34.34 3.61
1294 6788 2.987125 CGATCCACCGGAACCCTT 59.013 61.111 9.46 0.00 34.34 3.95
1303 6797 4.933064 CTCGCTCGCCGATCCACC 62.933 72.222 0.00 0.00 46.31 4.61
1304 6798 4.933064 CCTCGCTCGCCGATCCAC 62.933 72.222 0.00 0.00 46.31 4.02
1342 6836 1.215647 CTGCCCTAACTTCGCTCGT 59.784 57.895 0.00 0.00 0.00 4.18
1404 6902 0.391793 GCCTAGGGCTGTGAACACTC 60.392 60.000 11.72 0.00 46.69 3.51
1502 11947 7.872993 GTGGATTAAGCACTAGTTAGCATATCA 59.127 37.037 7.83 0.00 0.00 2.15
1627 12072 0.321653 CCTAGGCTTGGGTGTGTGTC 60.322 60.000 7.14 0.00 0.00 3.67
1785 12231 2.355756 CGAAGTTTCCACCATGCCATAG 59.644 50.000 0.00 0.00 0.00 2.23
1828 12274 0.323451 AATGAAGGTCCCGAAAGCCC 60.323 55.000 0.00 0.00 0.00 5.19
1879 12447 5.734720 TCTGGTTACTCATTTAGCTTCCAG 58.265 41.667 0.00 0.00 39.07 3.86
1880 12448 5.755409 TCTGGTTACTCATTTAGCTTCCA 57.245 39.130 0.00 0.00 0.00 3.53
1881 12449 6.261158 GGAATCTGGTTACTCATTTAGCTTCC 59.739 42.308 0.00 0.00 0.00 3.46
1882 12450 6.261158 GGGAATCTGGTTACTCATTTAGCTTC 59.739 42.308 0.00 0.00 0.00 3.86
1883 12451 6.069381 AGGGAATCTGGTTACTCATTTAGCTT 60.069 38.462 0.00 0.00 0.00 3.74
1884 12452 5.430089 AGGGAATCTGGTTACTCATTTAGCT 59.570 40.000 0.00 0.00 0.00 3.32
1885 12453 5.685728 AGGGAATCTGGTTACTCATTTAGC 58.314 41.667 0.00 0.00 0.00 3.09
1886 12454 7.415653 GCAAAGGGAATCTGGTTACTCATTTAG 60.416 40.741 0.00 0.00 0.00 1.85
1887 12455 6.377146 GCAAAGGGAATCTGGTTACTCATTTA 59.623 38.462 0.00 0.00 0.00 1.40
1888 12456 5.185828 GCAAAGGGAATCTGGTTACTCATTT 59.814 40.000 0.00 0.00 0.00 2.32
1889 12457 4.706962 GCAAAGGGAATCTGGTTACTCATT 59.293 41.667 0.00 0.00 0.00 2.57
1890 12458 4.273318 GCAAAGGGAATCTGGTTACTCAT 58.727 43.478 0.00 0.00 0.00 2.90
1891 12459 3.686016 GCAAAGGGAATCTGGTTACTCA 58.314 45.455 0.00 0.00 0.00 3.41
1892 12460 2.678336 CGCAAAGGGAATCTGGTTACTC 59.322 50.000 0.00 0.00 0.00 2.59
1893 12461 2.039879 ACGCAAAGGGAATCTGGTTACT 59.960 45.455 0.00 0.00 0.00 2.24
1894 12462 2.418976 GACGCAAAGGGAATCTGGTTAC 59.581 50.000 0.00 0.00 0.00 2.50
1895 12463 2.039216 TGACGCAAAGGGAATCTGGTTA 59.961 45.455 0.00 0.00 0.00 2.85
1896 12464 1.202879 TGACGCAAAGGGAATCTGGTT 60.203 47.619 0.00 0.00 0.00 3.67
1897 12465 0.400213 TGACGCAAAGGGAATCTGGT 59.600 50.000 0.00 0.00 0.00 4.00
1898 12466 1.755179 ATGACGCAAAGGGAATCTGG 58.245 50.000 0.00 0.00 0.00 3.86
1899 12467 2.489329 ACAATGACGCAAAGGGAATCTG 59.511 45.455 0.00 0.00 0.00 2.90
1900 12468 2.489329 CACAATGACGCAAAGGGAATCT 59.511 45.455 0.00 0.00 0.00 2.40
1901 12469 2.867429 CACAATGACGCAAAGGGAATC 58.133 47.619 0.00 0.00 0.00 2.52
1902 12470 1.067635 GCACAATGACGCAAAGGGAAT 60.068 47.619 0.00 0.00 0.00 3.01
1903 12471 0.313672 GCACAATGACGCAAAGGGAA 59.686 50.000 0.00 0.00 0.00 3.97
1904 12472 0.537143 AGCACAATGACGCAAAGGGA 60.537 50.000 2.74 0.00 0.00 4.20
1905 12473 0.314935 AAGCACAATGACGCAAAGGG 59.685 50.000 2.74 0.00 0.00 3.95
1906 12474 2.483877 TCTAAGCACAATGACGCAAAGG 59.516 45.455 2.74 0.00 0.00 3.11
1907 12475 3.740590 CTCTAAGCACAATGACGCAAAG 58.259 45.455 2.74 0.29 0.00 2.77
1908 12476 2.095768 GCTCTAAGCACAATGACGCAAA 60.096 45.455 2.74 0.00 41.89 3.68
1909 12477 1.464608 GCTCTAAGCACAATGACGCAA 59.535 47.619 2.74 0.00 41.89 4.85
1910 12478 1.078709 GCTCTAAGCACAATGACGCA 58.921 50.000 2.74 0.00 41.89 5.24
1911 12479 3.885777 GCTCTAAGCACAATGACGC 57.114 52.632 0.00 0.00 41.89 5.19
1921 12489 8.457261 CCATCTGGATAATATTTTGCTCTAAGC 58.543 37.037 0.00 0.00 38.61 3.09
1922 12490 9.730705 TCCATCTGGATAATATTTTGCTCTAAG 57.269 33.333 0.00 0.00 39.78 2.18
1925 12493 9.597681 ATTTCCATCTGGATAATATTTTGCTCT 57.402 29.630 0.00 0.00 44.98 4.09
1934 12502 9.919416 TGTCAAGAAATTTCCATCTGGATAATA 57.081 29.630 14.61 0.00 44.98 0.98
1935 12503 8.827832 TGTCAAGAAATTTCCATCTGGATAAT 57.172 30.769 14.61 1.14 44.98 1.28
1936 12504 8.108999 TCTGTCAAGAAATTTCCATCTGGATAA 58.891 33.333 14.61 0.00 44.98 1.75
1937 12505 7.632861 TCTGTCAAGAAATTTCCATCTGGATA 58.367 34.615 14.61 0.00 44.98 2.59
1938 12506 6.487828 TCTGTCAAGAAATTTCCATCTGGAT 58.512 36.000 14.61 0.00 44.98 3.41
1939 12507 5.879763 TCTGTCAAGAAATTTCCATCTGGA 58.120 37.500 14.61 0.00 43.73 3.86
1940 12508 6.579666 TTCTGTCAAGAAATTTCCATCTGG 57.420 37.500 14.61 2.59 39.52 3.86
1966 12534 3.922171 TGCCCCACACTTCAAATTTTT 57.078 38.095 0.00 0.00 0.00 1.94
1967 12535 3.390639 TGATGCCCCACACTTCAAATTTT 59.609 39.130 0.00 0.00 0.00 1.82
1968 12536 2.971330 TGATGCCCCACACTTCAAATTT 59.029 40.909 0.00 0.00 0.00 1.82
1969 12537 2.607499 TGATGCCCCACACTTCAAATT 58.393 42.857 0.00 0.00 0.00 1.82
1970 12538 2.307496 TGATGCCCCACACTTCAAAT 57.693 45.000 0.00 0.00 0.00 2.32
1971 12539 2.307496 ATGATGCCCCACACTTCAAA 57.693 45.000 0.00 0.00 0.00 2.69
1972 12540 2.307496 AATGATGCCCCACACTTCAA 57.693 45.000 0.00 0.00 0.00 2.69
1973 12541 2.307496 AAATGATGCCCCACACTTCA 57.693 45.000 0.00 0.00 0.00 3.02
1974 12542 3.356290 AGTAAATGATGCCCCACACTTC 58.644 45.455 0.00 0.00 0.00 3.01
1975 12543 3.456380 AGTAAATGATGCCCCACACTT 57.544 42.857 0.00 0.00 0.00 3.16
1976 12544 3.091545 CAAGTAAATGATGCCCCACACT 58.908 45.455 0.00 0.00 0.00 3.55
1977 12545 2.166254 CCAAGTAAATGATGCCCCACAC 59.834 50.000 0.00 0.00 0.00 3.82
1978 12546 2.455557 CCAAGTAAATGATGCCCCACA 58.544 47.619 0.00 0.00 0.00 4.17
1979 12547 1.136891 GCCAAGTAAATGATGCCCCAC 59.863 52.381 0.00 0.00 0.00 4.61
1983 12551 4.192429 AGTTTGCCAAGTAAATGATGCC 57.808 40.909 0.00 0.00 0.00 4.40
2033 12601 4.899457 CACCTACTTGTCAGATATACCCCA 59.101 45.833 0.00 0.00 0.00 4.96
2048 12616 5.183904 GCATTTTGAGTTCCATCACCTACTT 59.816 40.000 0.00 0.00 0.00 2.24
2069 12638 1.175654 TCGCACCAAATGACATGCAT 58.824 45.000 0.00 0.00 37.97 3.96
2071 12640 3.419264 TTATCGCACCAAATGACATGC 57.581 42.857 0.00 0.00 34.66 4.06
2103 12672 5.279006 GCAAGGACACGATGATAAGGATAGA 60.279 44.000 0.00 0.00 0.00 1.98
2114 12683 1.522668 TTTGGAGCAAGGACACGATG 58.477 50.000 0.00 0.00 0.00 3.84
2194 12763 3.066900 ACATAGACGGAACAAGATCCTCG 59.933 47.826 0.00 0.00 37.34 4.63
2227 12796 3.867857 TGGTAATATTGCTTCAGCGTCA 58.132 40.909 3.46 0.00 45.83 4.35
2228 12797 4.875544 TTGGTAATATTGCTTCAGCGTC 57.124 40.909 3.46 0.00 45.83 5.19
2229 12798 4.275936 GGATTGGTAATATTGCTTCAGCGT 59.724 41.667 3.46 0.00 45.83 5.07
2230 12799 4.516698 AGGATTGGTAATATTGCTTCAGCG 59.483 41.667 3.46 0.00 45.83 5.18
2231 12800 5.767168 AGAGGATTGGTAATATTGCTTCAGC 59.233 40.000 3.46 0.00 42.50 4.26
2233 12802 6.936900 GCTAGAGGATTGGTAATATTGCTTCA 59.063 38.462 3.46 0.00 0.00 3.02
2235 12804 5.934625 CGCTAGAGGATTGGTAATATTGCTT 59.065 40.000 3.46 0.00 0.00 3.91
2236 12805 5.482908 CGCTAGAGGATTGGTAATATTGCT 58.517 41.667 3.46 0.00 0.00 3.91
2237 12806 4.631813 CCGCTAGAGGATTGGTAATATTGC 59.368 45.833 6.69 0.00 0.00 3.56
2238 12807 5.178797 CCCGCTAGAGGATTGGTAATATTG 58.821 45.833 14.97 0.00 0.00 1.90
2239 12808 4.844655 ACCCGCTAGAGGATTGGTAATATT 59.155 41.667 14.97 0.00 0.00 1.28
2240 12809 4.223032 CACCCGCTAGAGGATTGGTAATAT 59.777 45.833 14.97 0.00 0.00 1.28
2241 12810 3.576982 CACCCGCTAGAGGATTGGTAATA 59.423 47.826 14.97 0.00 0.00 0.98
2243 12812 1.760613 CACCCGCTAGAGGATTGGTAA 59.239 52.381 14.97 0.00 0.00 2.85
2244 12813 1.410004 CACCCGCTAGAGGATTGGTA 58.590 55.000 14.97 0.00 0.00 3.25
2245 12814 1.338136 CCACCCGCTAGAGGATTGGT 61.338 60.000 14.97 0.00 32.63 3.67
2246 12815 1.447643 CCACCCGCTAGAGGATTGG 59.552 63.158 14.97 15.31 0.00 3.16
2247 12816 1.227674 GCCACCCGCTAGAGGATTG 60.228 63.158 14.97 10.26 0.00 2.67
2248 12817 2.444256 GGCCACCCGCTAGAGGATT 61.444 63.158 14.97 0.00 37.74 3.01
2249 12818 2.844839 GGCCACCCGCTAGAGGAT 60.845 66.667 14.97 0.00 37.74 3.24
2251 12820 3.854669 CAGGCCACCCGCTAGAGG 61.855 72.222 5.01 5.36 37.74 3.69
2252 12821 3.854669 CCAGGCCACCCGCTAGAG 61.855 72.222 5.01 0.00 37.74 2.43
2253 12822 3.916438 TTCCAGGCCACCCGCTAGA 62.916 63.158 5.01 0.00 37.74 2.43
2254 12823 3.391665 CTTCCAGGCCACCCGCTAG 62.392 68.421 5.01 0.00 37.74 3.42
2255 12824 3.399181 CTTCCAGGCCACCCGCTA 61.399 66.667 5.01 0.00 37.74 4.26
2258 12827 0.611896 AAAATCTTCCAGGCCACCCG 60.612 55.000 5.01 0.00 35.76 5.28
2261 12830 1.273327 CCACAAAATCTTCCAGGCCAC 59.727 52.381 5.01 0.00 0.00 5.01
2262 12831 1.133199 ACCACAAAATCTTCCAGGCCA 60.133 47.619 5.01 0.00 0.00 5.36
2263 12832 1.632589 ACCACAAAATCTTCCAGGCC 58.367 50.000 0.00 0.00 0.00 5.19
2264 12833 3.131046 CCATACCACAAAATCTTCCAGGC 59.869 47.826 0.00 0.00 0.00 4.85
2265 12834 3.131046 GCCATACCACAAAATCTTCCAGG 59.869 47.826 0.00 0.00 0.00 4.45
2266 12835 3.763360 TGCCATACCACAAAATCTTCCAG 59.237 43.478 0.00 0.00 0.00 3.86
2267 12836 3.772387 TGCCATACCACAAAATCTTCCA 58.228 40.909 0.00 0.00 0.00 3.53
2269 12838 7.100458 AGTTATGCCATACCACAAAATCTTC 57.900 36.000 0.00 0.00 0.00 2.87
2270 12839 6.663093 TGAGTTATGCCATACCACAAAATCTT 59.337 34.615 0.00 0.00 0.00 2.40
2271 12840 6.186957 TGAGTTATGCCATACCACAAAATCT 58.813 36.000 0.00 0.00 0.00 2.40
2272 12841 6.449635 TGAGTTATGCCATACCACAAAATC 57.550 37.500 0.00 0.00 0.00 2.17
2273 12842 6.849085 TTGAGTTATGCCATACCACAAAAT 57.151 33.333 0.00 0.00 0.00 1.82
2274 12843 6.656632 TTTGAGTTATGCCATACCACAAAA 57.343 33.333 3.14 0.00 0.00 2.44
2275 12844 6.656632 TTTTGAGTTATGCCATACCACAAA 57.343 33.333 1.77 1.77 0.00 2.83
2276 12845 6.451393 GTTTTTGAGTTATGCCATACCACAA 58.549 36.000 0.00 0.00 0.00 3.33
2277 12846 5.335269 CGTTTTTGAGTTATGCCATACCACA 60.335 40.000 0.00 0.00 0.00 4.17
2278 12847 5.092781 CGTTTTTGAGTTATGCCATACCAC 58.907 41.667 0.00 0.00 0.00 4.16
2280 12849 4.396790 TCCGTTTTTGAGTTATGCCATACC 59.603 41.667 0.00 0.00 0.00 2.73
2281 12850 5.554822 TCCGTTTTTGAGTTATGCCATAC 57.445 39.130 0.00 0.00 0.00 2.39
2283 12852 4.522789 ACTTCCGTTTTTGAGTTATGCCAT 59.477 37.500 0.00 0.00 0.00 4.40
2284 12853 3.886505 ACTTCCGTTTTTGAGTTATGCCA 59.113 39.130 0.00 0.00 0.00 4.92
2285 12854 4.499037 ACTTCCGTTTTTGAGTTATGCC 57.501 40.909 0.00 0.00 0.00 4.40
2286 12855 9.434559 GATAATACTTCCGTTTTTGAGTTATGC 57.565 33.333 0.00 0.00 0.00 3.14
2299 12868 9.698309 CACTGATTTGATAGATAATACTTCCGT 57.302 33.333 0.00 0.00 0.00 4.69
2300 12869 9.698309 ACACTGATTTGATAGATAATACTTCCG 57.302 33.333 0.00 0.00 0.00 4.30
2310 12879 9.593565 TCTCCATAGTACACTGATTTGATAGAT 57.406 33.333 0.00 0.00 0.00 1.98
2311 12880 8.996651 TCTCCATAGTACACTGATTTGATAGA 57.003 34.615 0.00 0.00 0.00 1.98
2312 12881 8.855110 ACTCTCCATAGTACACTGATTTGATAG 58.145 37.037 0.00 0.00 0.00 2.08
2313 12882 8.768501 ACTCTCCATAGTACACTGATTTGATA 57.231 34.615 0.00 0.00 0.00 2.15
2314 12883 7.667575 ACTCTCCATAGTACACTGATTTGAT 57.332 36.000 0.00 0.00 0.00 2.57
2315 12884 7.834681 ACTACTCTCCATAGTACACTGATTTGA 59.165 37.037 0.00 0.00 30.94 2.69
2316 12885 8.001881 ACTACTCTCCATAGTACACTGATTTG 57.998 38.462 0.00 0.00 30.94 2.32
2318 12887 7.579105 AGACTACTCTCCATAGTACACTGATT 58.421 38.462 0.00 0.00 32.93 2.57
2319 12888 7.144234 AGACTACTCTCCATAGTACACTGAT 57.856 40.000 0.00 0.00 32.93 2.90
2320 12889 6.156429 TGAGACTACTCTCCATAGTACACTGA 59.844 42.308 0.00 0.00 42.30 3.41
2321 12890 6.259167 GTGAGACTACTCTCCATAGTACACTG 59.741 46.154 0.00 0.00 42.30 3.66
2322 12891 6.070136 TGTGAGACTACTCTCCATAGTACACT 60.070 42.308 15.90 0.00 42.30 3.55
2323 12892 6.114089 TGTGAGACTACTCTCCATAGTACAC 58.886 44.000 0.00 11.58 42.30 2.90
2324 12893 6.309389 TGTGAGACTACTCTCCATAGTACA 57.691 41.667 0.00 0.00 42.30 2.90
2325 12894 7.627298 TTTGTGAGACTACTCTCCATAGTAC 57.373 40.000 0.00 0.00 42.30 2.73
2327 12896 7.397476 TGAATTTGTGAGACTACTCTCCATAGT 59.603 37.037 0.00 0.00 42.30 2.12
2328 12897 7.776107 TGAATTTGTGAGACTACTCTCCATAG 58.224 38.462 0.00 0.00 42.30 2.23
2329 12898 7.615757 TCTGAATTTGTGAGACTACTCTCCATA 59.384 37.037 0.00 0.00 42.30 2.74
2331 12900 5.775195 TCTGAATTTGTGAGACTACTCTCCA 59.225 40.000 0.00 0.00 42.30 3.86
2332 12901 6.274157 TCTGAATTTGTGAGACTACTCTCC 57.726 41.667 0.00 0.00 42.30 3.71
2333 12902 7.653713 TGTTTCTGAATTTGTGAGACTACTCTC 59.346 37.037 0.00 0.00 43.17 3.20
2335 12904 7.715265 TGTTTCTGAATTTGTGAGACTACTC 57.285 36.000 0.00 0.00 42.88 2.59
2336 12905 8.682936 ATTGTTTCTGAATTTGTGAGACTACT 57.317 30.769 0.00 0.00 0.00 2.57
2340 12909 9.683069 ACAATATTGTTTCTGAATTTGTGAGAC 57.317 29.630 15.47 0.00 38.47 3.36
2357 12926 3.117888 AGCCTCCGGATGAACAATATTGT 60.118 43.478 15.47 15.47 44.72 2.71
2358 12927 3.480470 AGCCTCCGGATGAACAATATTG 58.520 45.455 14.01 14.01 0.00 1.90
2359 12928 3.864789 AGCCTCCGGATGAACAATATT 57.135 42.857 11.34 0.00 0.00 1.28
2360 12929 3.904339 AGTAGCCTCCGGATGAACAATAT 59.096 43.478 11.34 0.00 0.00 1.28
2361 12930 3.069586 CAGTAGCCTCCGGATGAACAATA 59.930 47.826 11.34 0.00 0.00 1.90
2362 12931 2.119495 AGTAGCCTCCGGATGAACAAT 58.881 47.619 11.34 0.00 0.00 2.71
2363 12932 1.207089 CAGTAGCCTCCGGATGAACAA 59.793 52.381 11.34 0.00 0.00 2.83
2364 12933 0.824109 CAGTAGCCTCCGGATGAACA 59.176 55.000 11.34 0.00 0.00 3.18
2365 12934 0.105039 CCAGTAGCCTCCGGATGAAC 59.895 60.000 11.34 7.63 0.00 3.18
2366 12935 0.325296 ACCAGTAGCCTCCGGATGAA 60.325 55.000 11.34 0.00 0.00 2.57
2367 12936 1.043116 CACCAGTAGCCTCCGGATGA 61.043 60.000 11.34 0.00 0.00 2.92
2368 12937 1.443407 CACCAGTAGCCTCCGGATG 59.557 63.158 3.57 2.55 0.00 3.51
2369 12938 1.762460 CCACCAGTAGCCTCCGGAT 60.762 63.158 3.57 0.00 0.00 4.18
2370 12939 2.238319 ATCCACCAGTAGCCTCCGGA 62.238 60.000 2.93 2.93 0.00 5.14
2371 12940 1.749334 GATCCACCAGTAGCCTCCGG 61.749 65.000 0.00 0.00 0.00 5.14
2372 12941 1.742768 GATCCACCAGTAGCCTCCG 59.257 63.158 0.00 0.00 0.00 4.63
2373 12942 0.755698 TCGATCCACCAGTAGCCTCC 60.756 60.000 0.00 0.00 0.00 4.30
2374 12943 0.386113 GTCGATCCACCAGTAGCCTC 59.614 60.000 0.00 0.00 0.00 4.70
2375 12944 0.324368 TGTCGATCCACCAGTAGCCT 60.324 55.000 0.00 0.00 0.00 4.58
2376 12945 0.535335 TTGTCGATCCACCAGTAGCC 59.465 55.000 0.00 0.00 0.00 3.93
2377 12946 2.000447 GTTTGTCGATCCACCAGTAGC 59.000 52.381 0.00 0.00 0.00 3.58
2378 12947 3.313012 TGTTTGTCGATCCACCAGTAG 57.687 47.619 0.00 0.00 0.00 2.57
2379 12948 3.755112 TTGTTTGTCGATCCACCAGTA 57.245 42.857 0.00 0.00 0.00 2.74
2380 12949 2.631160 TTGTTTGTCGATCCACCAGT 57.369 45.000 0.00 0.00 0.00 4.00
2381 12950 2.813754 ACATTGTTTGTCGATCCACCAG 59.186 45.455 0.00 0.00 30.89 4.00
2382 12951 2.551887 CACATTGTTTGTCGATCCACCA 59.448 45.455 0.00 0.00 36.00 4.17
2383 12952 2.095263 CCACATTGTTTGTCGATCCACC 60.095 50.000 0.00 0.00 36.00 4.61
2384 12953 2.552315 ACCACATTGTTTGTCGATCCAC 59.448 45.455 0.00 0.00 36.00 4.02
2385 12954 2.857483 ACCACATTGTTTGTCGATCCA 58.143 42.857 0.00 0.00 36.00 3.41
2386 12955 3.915437 AACCACATTGTTTGTCGATCC 57.085 42.857 0.00 0.00 36.00 3.36
2394 12963 1.836802 ACAGCCCAAACCACATTGTTT 59.163 42.857 0.00 0.00 38.95 2.83
2395 12964 1.494960 ACAGCCCAAACCACATTGTT 58.505 45.000 0.00 0.00 0.00 2.83
2396 12965 1.494960 AACAGCCCAAACCACATTGT 58.505 45.000 0.00 0.00 0.00 2.71
2397 12966 3.959535 ATAACAGCCCAAACCACATTG 57.040 42.857 0.00 0.00 0.00 2.82
2398 12967 4.405358 CCATATAACAGCCCAAACCACATT 59.595 41.667 0.00 0.00 0.00 2.71
2399 12968 3.960102 CCATATAACAGCCCAAACCACAT 59.040 43.478 0.00 0.00 0.00 3.21
2400 12969 3.010696 TCCATATAACAGCCCAAACCACA 59.989 43.478 0.00 0.00 0.00 4.17
2401 12970 3.626930 TCCATATAACAGCCCAAACCAC 58.373 45.455 0.00 0.00 0.00 4.16
2402 12971 4.323569 TTCCATATAACAGCCCAAACCA 57.676 40.909 0.00 0.00 0.00 3.67
2403 12972 5.362430 TGATTTCCATATAACAGCCCAAACC 59.638 40.000 0.00 0.00 0.00 3.27
2404 12973 6.463995 TGATTTCCATATAACAGCCCAAAC 57.536 37.500 0.00 0.00 0.00 2.93
2405 12974 7.038729 TGTTTGATTTCCATATAACAGCCCAAA 60.039 33.333 0.00 0.00 0.00 3.28
2406 12975 6.438741 TGTTTGATTTCCATATAACAGCCCAA 59.561 34.615 0.00 0.00 0.00 4.12
2407 12976 5.954752 TGTTTGATTTCCATATAACAGCCCA 59.045 36.000 0.00 0.00 0.00 5.36
2408 12977 6.463995 TGTTTGATTTCCATATAACAGCCC 57.536 37.500 0.00 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.