Multiple sequence alignment - TraesCS3B01G134300

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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 TraesCS3B01G134300 chr3B 100.000 5008 0 0 1 5008 116189399 116194406 0.000000e+00 9249.0
1 TraesCS3B01G134300 chr3B 87.247 1482 92 42 2338 3785 117553652 117552234 0.000000e+00 1600.0
2 TraesCS3B01G134300 chr3B 87.565 764 54 11 4275 5008 425683093 425682341 0.000000e+00 846.0
3 TraesCS3B01G134300 chr3B 85.974 770 62 18 4273 5008 52660100 52660857 0.000000e+00 782.0
4 TraesCS3B01G134300 chr3B 89.303 402 19 5 1899 2299 117554027 117553649 2.710000e-132 483.0
5 TraesCS3B01G134300 chr3B 94.624 93 5 0 1811 1903 62673279 62673187 1.450000e-30 145.0
6 TraesCS3B01G134300 chr3D 92.317 2369 94 32 1896 4207 70726154 70728491 0.000000e+00 3286.0
7 TraesCS3B01G134300 chr3D 92.737 1363 63 17 2430 3775 510300220 510301563 0.000000e+00 1936.0
8 TraesCS3B01G134300 chr3D 90.953 1437 71 20 1895 3282 71496614 71495188 0.000000e+00 1879.0
9 TraesCS3B01G134300 chr3D 89.039 1113 68 27 699 1775 70725047 70726141 0.000000e+00 1330.0
10 TraesCS3B01G134300 chr3D 90.805 609 41 10 1 603 70724347 70724946 0.000000e+00 800.0
11 TraesCS3B01G134300 chr3D 80.657 274 35 12 4342 4610 8723813 8724073 3.960000e-46 196.0
12 TraesCS3B01G134300 chr3D 93.939 99 1 5 4129 4224 19360295 19360199 1.450000e-30 145.0
13 TraesCS3B01G134300 chr3D 89.908 109 11 0 1794 1902 65607330 65607222 1.880000e-29 141.0
14 TraesCS3B01G134300 chr3D 94.624 93 2 2 4130 4222 71497055 71496966 1.880000e-29 141.0
15 TraesCS3B01G134300 chr3D 95.455 88 4 0 1810 1897 609371567 609371480 1.880000e-29 141.0
16 TraesCS3B01G134300 chr3A 93.520 1960 73 19 1896 3827 82440840 82442773 0.000000e+00 2867.0
17 TraesCS3B01G134300 chr3A 91.808 1294 58 16 1895 3148 83725423 83724138 0.000000e+00 1759.0
18 TraesCS3B01G134300 chr3A 87.265 1115 81 28 1 1090 82439008 82440086 0.000000e+00 1216.0
19 TraesCS3B01G134300 chr3A 84.235 1072 103 30 3988 5008 82442935 82443991 0.000000e+00 983.0
20 TraesCS3B01G134300 chr3A 86.908 718 64 13 1112 1814 82440150 82440852 0.000000e+00 778.0
21 TraesCS3B01G134300 chr3A 87.752 596 57 8 4275 4857 443172861 443172269 0.000000e+00 682.0
22 TraesCS3B01G134300 chr3A 95.604 91 3 1 4123 4213 83725882 83725793 1.450000e-30 145.0
23 TraesCS3B01G134300 chr3A 86.486 111 8 2 4870 4980 443123559 443123456 1.140000e-21 115.0
24 TraesCS3B01G134300 chr3A 87.671 73 8 1 1112 1183 726004810 726004738 3.210000e-12 84.2
25 TraesCS3B01G134300 chr4D 93.068 1356 61 16 2433 3775 497616139 497614804 0.000000e+00 1953.0
26 TraesCS3B01G134300 chr4D 89.878 573 45 7 4275 4836 16612987 16612417 0.000000e+00 725.0
27 TraesCS3B01G134300 chr4D 94.624 93 5 0 1804 1896 69190382 69190474 1.450000e-30 145.0
28 TraesCS3B01G134300 chr4D 98.649 74 1 0 4135 4208 6288122 6288049 1.130000e-26 132.0
29 TraesCS3B01G134300 chr1B 90.392 510 43 5 4277 4782 489241721 489241214 0.000000e+00 665.0
30 TraesCS3B01G134300 chr1B 88.034 117 10 4 4100 4214 665492987 665493101 8.750000e-28 135.0
31 TraesCS3B01G134300 chr4A 86.583 559 61 9 4286 4837 583918590 583919141 5.550000e-169 604.0
32 TraesCS3B01G134300 chrUn 86.654 532 43 13 4495 5008 16712740 16712219 9.410000e-157 564.0
33 TraesCS3B01G134300 chrUn 90.476 105 8 2 1801 1903 29307071 29306967 2.430000e-28 137.0
34 TraesCS3B01G134300 chr2D 81.232 341 44 14 1250 1576 6722813 6723147 1.790000e-64 257.0
35 TraesCS3B01G134300 chr2D 94.624 93 5 0 1811 1903 59723535 59723443 1.450000e-30 145.0
36 TraesCS3B01G134300 chr4B 78.107 338 56 11 1251 1576 579786559 579786890 1.100000e-46 198.0
37 TraesCS3B01G134300 chr4B 93.878 49 2 1 1111 1158 610797877 610797925 6.950000e-09 73.1
38 TraesCS3B01G134300 chr5A 96.667 90 3 0 1808 1897 243379858 243379947 3.120000e-32 150.0
39 TraesCS3B01G134300 chr5B 95.652 92 3 1 1810 1901 681345006 681345096 4.040000e-31 147.0
40 TraesCS3B01G134300 chr5D 94.681 94 4 1 1811 1903 252117315 252117408 1.450000e-30 145.0
41 TraesCS3B01G134300 chr6A 89.565 115 8 4 4108 4219 7983763 7983650 5.230000e-30 143.0
42 TraesCS3B01G134300 chr1D 97.468 79 2 0 4129 4207 478271243 478271321 8.750000e-28 135.0
43 TraesCS3B01G134300 chr7D 87.671 73 8 1 1112 1183 521640349 521640421 3.210000e-12 84.2
44 TraesCS3B01G134300 chr7D 93.878 49 2 1 1111 1158 205655530 205655482 6.950000e-09 73.1


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 TraesCS3B01G134300 chr3B 116189399 116194406 5007 False 9249.000000 9249 100.000000 1 5008 1 chr3B.!!$F2 5007
1 TraesCS3B01G134300 chr3B 117552234 117554027 1793 True 1041.500000 1600 88.275000 1899 3785 2 chr3B.!!$R3 1886
2 TraesCS3B01G134300 chr3B 425682341 425683093 752 True 846.000000 846 87.565000 4275 5008 1 chr3B.!!$R2 733
3 TraesCS3B01G134300 chr3B 52660100 52660857 757 False 782.000000 782 85.974000 4273 5008 1 chr3B.!!$F1 735
4 TraesCS3B01G134300 chr3D 510300220 510301563 1343 False 1936.000000 1936 92.737000 2430 3775 1 chr3D.!!$F2 1345
5 TraesCS3B01G134300 chr3D 70724347 70728491 4144 False 1805.333333 3286 90.720333 1 4207 3 chr3D.!!$F3 4206
6 TraesCS3B01G134300 chr3D 71495188 71497055 1867 True 1010.000000 1879 92.788500 1895 4222 2 chr3D.!!$R4 2327
7 TraesCS3B01G134300 chr3A 82439008 82443991 4983 False 1461.000000 2867 87.982000 1 5008 4 chr3A.!!$F1 5007
8 TraesCS3B01G134300 chr3A 83724138 83725882 1744 True 952.000000 1759 93.706000 1895 4213 2 chr3A.!!$R4 2318
9 TraesCS3B01G134300 chr3A 443172269 443172861 592 True 682.000000 682 87.752000 4275 4857 1 chr3A.!!$R2 582
10 TraesCS3B01G134300 chr4D 497614804 497616139 1335 True 1953.000000 1953 93.068000 2433 3775 1 chr4D.!!$R3 1342
11 TraesCS3B01G134300 chr4D 16612417 16612987 570 True 725.000000 725 89.878000 4275 4836 1 chr4D.!!$R2 561
12 TraesCS3B01G134300 chr1B 489241214 489241721 507 True 665.000000 665 90.392000 4277 4782 1 chr1B.!!$R1 505
13 TraesCS3B01G134300 chr4A 583918590 583919141 551 False 604.000000 604 86.583000 4286 4837 1 chr4A.!!$F1 551
14 TraesCS3B01G134300 chrUn 16712219 16712740 521 True 564.000000 564 86.654000 4495 5008 1 chrUn.!!$R1 513

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
377 385 0.179040 GGGTTCAAAGTGACCACCGA 60.179 55.0 0.0 0.0 29.98 4.69 F
1059 1106 0.107017 AGATTCAGTTGGCATCCGGG 60.107 55.0 0.0 0.0 0.00 5.73 F
1211 1300 0.179234 TAGGGTGTGTGTGTGTGTGG 59.821 55.0 0.0 0.0 0.00 4.17 F
1647 1750 0.181587 TGAAGACGGGGAAAAGTGCA 59.818 50.0 0.0 0.0 0.00 4.57 F
3300 3492 0.332972 GGAGGATTTTCTGGCTGGGT 59.667 55.0 0.0 0.0 0.00 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1453 1556 0.179116 CTCTGCACGAGATGGACAGG 60.179 60.0 7.22 0.0 42.62 4.00 R
1885 1992 0.453390 GGTAACACGTACTCCCTCGG 59.547 60.0 0.00 0.0 32.80 4.63 R
2159 2296 1.089112 CTGCAGCACGAATCCATCAA 58.911 50.0 0.00 0.0 0.00 2.57 R
3306 3498 1.138047 GCACGTCGATCCGGTAGTTG 61.138 60.0 0.00 0.0 0.00 3.16 R
4522 4836 0.249489 GGAGGTTGTCCGGATGATCG 60.249 60.0 7.81 0.0 34.84 3.69 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 2.975851 CAAGCAAATGAGAAAGTGACGC 59.024 45.455 0.00 0.00 0.00 5.19
32 33 0.249489 AGAAAGTGACGCGAACAGCT 60.249 50.000 15.93 9.72 45.59 4.24
57 58 5.126061 GCTAATCAAGAAGCAATTGAAGGGA 59.874 40.000 10.34 0.00 39.92 4.20
176 178 2.484770 GGTTTCAAACTTTCAAGGGGGC 60.485 50.000 0.00 0.00 0.00 5.80
342 350 7.622081 AGACAATGATATATCGGGTGGGTTATA 59.378 37.037 8.19 0.00 0.00 0.98
375 383 1.407618 GTTGGGTTCAAAGTGACCACC 59.592 52.381 0.00 0.00 34.28 4.61
376 384 0.464735 TGGGTTCAAAGTGACCACCG 60.465 55.000 0.00 0.00 29.98 4.94
377 385 0.179040 GGGTTCAAAGTGACCACCGA 60.179 55.000 0.00 0.00 29.98 4.69
381 389 3.139077 GTTCAAAGTGACCACCGAAGAT 58.861 45.455 0.00 0.00 0.00 2.40
399 407 5.606505 GAAGATGACCTACTTGATTCCCTC 58.393 45.833 0.00 0.00 0.00 4.30
457 466 5.293569 CCAACAAGAAGTACAGAAACGTCTT 59.706 40.000 0.00 0.30 45.24 3.01
468 477 3.610242 CAGAAACGTCTTCTCCGATCTTG 59.390 47.826 9.20 0.00 28.78 3.02
469 478 3.506455 AGAAACGTCTTCTCCGATCTTGA 59.494 43.478 7.04 0.00 0.00 3.02
478 487 3.550820 TCTCCGATCTTGAGAAGAGGAG 58.449 50.000 16.79 16.79 44.96 3.69
480 489 1.268999 CCGATCTTGAGAAGAGGAGCG 60.269 57.143 0.00 0.00 41.61 5.03
482 491 2.293122 CGATCTTGAGAAGAGGAGCGAT 59.707 50.000 0.00 0.00 41.61 4.58
489 498 3.195610 TGAGAAGAGGAGCGATAAAGCAA 59.804 43.478 0.00 0.00 40.15 3.91
536 547 5.006358 GTCAGTGAGTCAACAAACACGTAAT 59.994 40.000 0.00 0.00 38.15 1.89
580 591 4.082571 CCGCATCATTCTTAATCCCATTCC 60.083 45.833 0.00 0.00 0.00 3.01
622 651 1.065701 CTATCAGACACCGAACTCCCG 59.934 57.143 0.00 0.00 0.00 5.14
633 662 1.828979 GAACTCCCGGCCACAAAATA 58.171 50.000 2.24 0.00 0.00 1.40
641 670 2.297597 CCGGCCACAAAATAAACAGGAA 59.702 45.455 2.24 0.00 0.00 3.36
684 713 4.220602 ACACCACTCCAAAAATGAATAGGC 59.779 41.667 0.00 0.00 0.00 3.93
687 716 6.152661 CACCACTCCAAAAATGAATAGGCTAA 59.847 38.462 0.00 0.00 0.00 3.09
688 717 6.897413 ACCACTCCAAAAATGAATAGGCTAAT 59.103 34.615 0.00 0.00 0.00 1.73
689 718 7.068716 ACCACTCCAAAAATGAATAGGCTAATC 59.931 37.037 0.00 0.00 0.00 1.75
740 775 2.804986 TATTTCAGCAGACCATGGCA 57.195 45.000 13.04 0.00 0.00 4.92
851 886 1.642728 AAACAAGTACACACGCGTGA 58.357 45.000 42.94 20.79 46.80 4.35
855 894 2.018727 AAGTACACACGCGTGACCCA 62.019 55.000 42.94 22.31 46.80 4.51
875 914 2.188837 TCGATGGATTGAACGTCTCG 57.811 50.000 0.00 0.00 0.00 4.04
887 929 8.136165 GGATTGAACGTCTCGCCTATATATATT 58.864 37.037 0.00 0.00 0.00 1.28
891 933 6.045698 ACGTCTCGCCTATATATATTCACG 57.954 41.667 0.00 3.02 0.00 4.35
925 972 2.496817 CTGCTGTCTACTCGGCCC 59.503 66.667 0.00 0.00 38.77 5.80
1021 1068 1.228552 ACCAATCCACCACAGCACC 60.229 57.895 0.00 0.00 0.00 5.01
1023 1070 2.034066 AATCCACCACAGCACCGG 59.966 61.111 0.00 0.00 0.00 5.28
1024 1071 4.722700 ATCCACCACAGCACCGGC 62.723 66.667 0.00 0.00 41.61 6.13
1053 1100 2.487762 CGGCTTTTAGATTCAGTTGGCA 59.512 45.455 0.00 0.00 0.00 4.92
1054 1101 3.129287 CGGCTTTTAGATTCAGTTGGCAT 59.871 43.478 0.00 0.00 0.00 4.40
1055 1102 4.676546 GGCTTTTAGATTCAGTTGGCATC 58.323 43.478 0.00 0.00 0.00 3.91
1059 1106 0.107017 AGATTCAGTTGGCATCCGGG 60.107 55.000 0.00 0.00 0.00 5.73
1092 1139 3.750652 GCACAGGGAAGAAGAAGAAGAAG 59.249 47.826 0.00 0.00 0.00 2.85
1093 1140 4.745172 GCACAGGGAAGAAGAAGAAGAAGT 60.745 45.833 0.00 0.00 0.00 3.01
1098 1145 5.482526 AGGGAAGAAGAAGAAGAAGTAGGAC 59.517 44.000 0.00 0.00 0.00 3.85
1099 1146 5.337733 GGGAAGAAGAAGAAGAAGTAGGACC 60.338 48.000 0.00 0.00 0.00 4.46
1121 1210 3.016971 CTGGGGGAGATGGTGGCA 61.017 66.667 0.00 0.00 0.00 4.92
1198 1287 2.690173 GATCGATCGAGTGTAGGGTG 57.310 55.000 23.84 0.00 0.00 4.61
1199 1288 1.948145 GATCGATCGAGTGTAGGGTGT 59.052 52.381 23.84 1.76 0.00 4.16
1206 1295 1.865865 GAGTGTAGGGTGTGTGTGTG 58.134 55.000 0.00 0.00 0.00 3.82
1207 1296 1.138266 GAGTGTAGGGTGTGTGTGTGT 59.862 52.381 0.00 0.00 0.00 3.72
1208 1297 1.134521 AGTGTAGGGTGTGTGTGTGTG 60.135 52.381 0.00 0.00 0.00 3.82
1210 1299 1.295792 GTAGGGTGTGTGTGTGTGTG 58.704 55.000 0.00 0.00 0.00 3.82
1211 1300 0.179234 TAGGGTGTGTGTGTGTGTGG 59.821 55.000 0.00 0.00 0.00 4.17
1250 1339 2.123897 GGTGTGTTGTGGGCTGGT 60.124 61.111 0.00 0.00 0.00 4.00
1386 1482 0.461961 GGGTGCTAGCAAGATCGAGT 59.538 55.000 21.29 0.00 0.00 4.18
1401 1500 1.007336 CGAGTTCCCGGTTCGAGTTG 61.007 60.000 0.00 0.00 36.49 3.16
1429 1528 2.735772 GGGATCGCAGCCTCCTTCA 61.736 63.158 4.64 0.00 31.16 3.02
1443 1546 1.203428 TCCTTCATCCCCTTCTCACCA 60.203 52.381 0.00 0.00 0.00 4.17
1453 1556 3.306294 CCCCTTCTCACCATTTTTGCTTC 60.306 47.826 0.00 0.00 0.00 3.86
1460 1563 2.364970 CACCATTTTTGCTTCCTGTCCA 59.635 45.455 0.00 0.00 0.00 4.02
1477 1580 0.820226 CCATCTCGTGCAGAGGAGAA 59.180 55.000 14.02 1.70 44.27 2.87
1567 1670 5.624159 TCACATCTCAGTTTCACCTCATTT 58.376 37.500 0.00 0.00 0.00 2.32
1569 1672 6.547141 TCACATCTCAGTTTCACCTCATTTTT 59.453 34.615 0.00 0.00 0.00 1.94
1581 1684 9.672673 TTTCACCTCATTTTTATGTTTGGAAAA 57.327 25.926 0.00 0.00 0.00 2.29
1586 1689 9.065798 CCTCATTTTTATGTTTGGAAAATTGGT 57.934 29.630 0.00 0.00 32.35 3.67
1589 1692 8.966194 CATTTTTATGTTTGGAAAATTGGTTGC 58.034 29.630 0.00 0.00 32.35 4.17
1611 1714 1.958205 CTTCCGCGGATCCATGAGC 60.958 63.158 31.56 5.89 0.00 4.26
1647 1750 0.181587 TGAAGACGGGGAAAAGTGCA 59.818 50.000 0.00 0.00 0.00 4.57
1747 1854 5.520376 ACTTGATTTTGGTTGAGGACTTG 57.480 39.130 0.00 0.00 0.00 3.16
1774 1881 4.089780 TCGATTTTGCGCATTTTCACAATC 59.910 37.500 12.75 9.52 0.00 2.67
1778 1885 3.572604 TGCGCATTTTCACAATCATCA 57.427 38.095 5.66 0.00 0.00 3.07
1779 1886 3.503891 TGCGCATTTTCACAATCATCAG 58.496 40.909 5.66 0.00 0.00 2.90
1806 1913 1.338107 TCTGACCATCGAACACCTGT 58.662 50.000 0.00 0.00 0.00 4.00
1810 1917 2.631062 TGACCATCGAACACCTGTTACT 59.369 45.455 0.00 0.00 38.56 2.24
1811 1918 3.827876 TGACCATCGAACACCTGTTACTA 59.172 43.478 0.00 0.00 38.56 1.82
1812 1919 4.171754 GACCATCGAACACCTGTTACTAC 58.828 47.826 0.00 0.00 38.56 2.73
1813 1920 3.830755 ACCATCGAACACCTGTTACTACT 59.169 43.478 0.00 0.00 38.56 2.57
1814 1921 4.082354 ACCATCGAACACCTGTTACTACTC 60.082 45.833 0.00 0.00 38.56 2.59
1815 1922 4.421948 CATCGAACACCTGTTACTACTCC 58.578 47.826 0.00 0.00 38.56 3.85
1816 1923 2.821969 TCGAACACCTGTTACTACTCCC 59.178 50.000 0.00 0.00 38.56 4.30
1817 1924 2.824341 CGAACACCTGTTACTACTCCCT 59.176 50.000 0.00 0.00 38.56 4.20
1818 1925 3.119566 CGAACACCTGTTACTACTCCCTC 60.120 52.174 0.00 0.00 38.56 4.30
1819 1926 2.817665 ACACCTGTTACTACTCCCTCC 58.182 52.381 0.00 0.00 0.00 4.30
1820 1927 1.749634 CACCTGTTACTACTCCCTCCG 59.250 57.143 0.00 0.00 0.00 4.63
1821 1928 1.357079 ACCTGTTACTACTCCCTCCGT 59.643 52.381 0.00 0.00 0.00 4.69
1822 1929 2.225217 ACCTGTTACTACTCCCTCCGTT 60.225 50.000 0.00 0.00 0.00 4.44
1823 1930 2.426381 CCTGTTACTACTCCCTCCGTTC 59.574 54.545 0.00 0.00 0.00 3.95
1824 1931 2.426381 CTGTTACTACTCCCTCCGTTCC 59.574 54.545 0.00 0.00 0.00 3.62
1825 1932 2.225091 TGTTACTACTCCCTCCGTTCCA 60.225 50.000 0.00 0.00 0.00 3.53
1826 1933 2.827921 GTTACTACTCCCTCCGTTCCAA 59.172 50.000 0.00 0.00 0.00 3.53
1827 1934 2.019807 ACTACTCCCTCCGTTCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
1828 1935 2.547990 ACTACTCCCTCCGTTCCAAAT 58.452 47.619 0.00 0.00 0.00 2.32
1829 1936 2.910977 ACTACTCCCTCCGTTCCAAATT 59.089 45.455 0.00 0.00 0.00 1.82
1830 1937 4.098894 ACTACTCCCTCCGTTCCAAATTA 58.901 43.478 0.00 0.00 0.00 1.40
1831 1938 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
1832 1939 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
1833 1940 4.098894 ACTCCCTCCGTTCCAAATTACTA 58.901 43.478 0.00 0.00 0.00 1.82
1834 1941 4.161754 ACTCCCTCCGTTCCAAATTACTAG 59.838 45.833 0.00 0.00 0.00 2.57
1835 1942 4.098894 TCCCTCCGTTCCAAATTACTAGT 58.901 43.478 0.00 0.00 0.00 2.57
1836 1943 4.161001 TCCCTCCGTTCCAAATTACTAGTC 59.839 45.833 0.00 0.00 0.00 2.59
1837 1944 4.110482 CCTCCGTTCCAAATTACTAGTCG 58.890 47.826 0.00 0.00 0.00 4.18
1838 1945 4.381292 CCTCCGTTCCAAATTACTAGTCGT 60.381 45.833 0.00 0.00 0.00 4.34
1839 1946 4.487948 TCCGTTCCAAATTACTAGTCGTG 58.512 43.478 0.00 0.00 0.00 4.35
1840 1947 3.615496 CCGTTCCAAATTACTAGTCGTGG 59.385 47.826 0.00 3.15 0.00 4.94
1841 1948 4.240096 CGTTCCAAATTACTAGTCGTGGT 58.760 43.478 0.00 0.00 0.00 4.16
1842 1949 4.687483 CGTTCCAAATTACTAGTCGTGGTT 59.313 41.667 0.00 0.00 0.00 3.67
1843 1950 5.178067 CGTTCCAAATTACTAGTCGTGGTTT 59.822 40.000 0.00 0.00 0.00 3.27
1844 1951 6.596703 GTTCCAAATTACTAGTCGTGGTTTC 58.403 40.000 0.00 0.00 0.00 2.78
1845 1952 5.856156 TCCAAATTACTAGTCGTGGTTTCA 58.144 37.500 0.00 0.00 0.00 2.69
1846 1953 5.929992 TCCAAATTACTAGTCGTGGTTTCAG 59.070 40.000 0.00 0.00 0.00 3.02
1847 1954 5.699458 CCAAATTACTAGTCGTGGTTTCAGT 59.301 40.000 0.00 0.00 0.00 3.41
1848 1955 6.204108 CCAAATTACTAGTCGTGGTTTCAGTT 59.796 38.462 0.00 0.00 0.00 3.16
1849 1956 7.288672 CAAATTACTAGTCGTGGTTTCAGTTC 58.711 38.462 0.00 0.00 0.00 3.01
1850 1957 5.518848 TTACTAGTCGTGGTTTCAGTTCA 57.481 39.130 0.00 0.00 0.00 3.18
1851 1958 4.395959 ACTAGTCGTGGTTTCAGTTCAA 57.604 40.909 0.00 0.00 0.00 2.69
1852 1959 4.761975 ACTAGTCGTGGTTTCAGTTCAAA 58.238 39.130 0.00 0.00 0.00 2.69
1853 1960 5.365619 ACTAGTCGTGGTTTCAGTTCAAAT 58.634 37.500 0.00 0.00 0.00 2.32
1854 1961 5.820947 ACTAGTCGTGGTTTCAGTTCAAATT 59.179 36.000 0.00 0.00 0.00 1.82
1855 1962 5.576447 AGTCGTGGTTTCAGTTCAAATTT 57.424 34.783 0.00 0.00 0.00 1.82
1856 1963 6.687081 AGTCGTGGTTTCAGTTCAAATTTA 57.313 33.333 0.00 0.00 0.00 1.40
1857 1964 7.090953 AGTCGTGGTTTCAGTTCAAATTTAA 57.909 32.000 0.00 0.00 0.00 1.52
1858 1965 7.540299 AGTCGTGGTTTCAGTTCAAATTTAAA 58.460 30.769 0.00 0.00 0.00 1.52
1859 1966 7.486870 AGTCGTGGTTTCAGTTCAAATTTAAAC 59.513 33.333 0.00 0.00 0.00 2.01
1860 1967 7.486870 GTCGTGGTTTCAGTTCAAATTTAAACT 59.513 33.333 0.51 0.51 36.16 2.66
1861 1968 8.675504 TCGTGGTTTCAGTTCAAATTTAAACTA 58.324 29.630 6.40 0.86 34.05 2.24
1862 1969 9.291664 CGTGGTTTCAGTTCAAATTTAAACTAA 57.708 29.630 6.40 0.00 34.05 2.24
1869 1976 9.291664 TCAGTTCAAATTTAAACTAAAACCACG 57.708 29.630 6.40 0.00 34.05 4.94
1870 1977 9.291664 CAGTTCAAATTTAAACTAAAACCACGA 57.708 29.630 6.40 0.00 34.05 4.35
1871 1978 9.292846 AGTTCAAATTTAAACTAAAACCACGAC 57.707 29.630 4.83 0.00 34.05 4.34
1872 1979 7.895582 TCAAATTTAAACTAAAACCACGACG 57.104 32.000 0.00 0.00 0.00 5.12
1873 1980 7.692088 TCAAATTTAAACTAAAACCACGACGA 58.308 30.769 0.00 0.00 0.00 4.20
1874 1981 7.851963 TCAAATTTAAACTAAAACCACGACGAG 59.148 33.333 0.00 0.00 0.00 4.18
1875 1982 6.849588 ATTTAAACTAAAACCACGACGAGT 57.150 33.333 0.00 0.00 0.00 4.18
1876 1983 7.945033 ATTTAAACTAAAACCACGACGAGTA 57.055 32.000 0.00 0.00 0.00 2.59
1877 1984 7.763172 TTTAAACTAAAACCACGACGAGTAA 57.237 32.000 0.00 0.00 0.00 2.24
1878 1985 7.945033 TTAAACTAAAACCACGACGAGTAAT 57.055 32.000 0.00 0.00 0.00 1.89
1879 1986 6.849588 AAACTAAAACCACGACGAGTAATT 57.150 33.333 0.00 1.08 0.00 1.40
1880 1987 6.849588 AACTAAAACCACGACGAGTAATTT 57.150 33.333 0.00 0.34 0.00 1.82
1881 1988 6.219302 ACTAAAACCACGACGAGTAATTTG 57.781 37.500 0.00 2.39 0.00 2.32
1882 1989 4.477302 AAAACCACGACGAGTAATTTGG 57.523 40.909 0.00 0.00 0.00 3.28
1883 1990 3.389925 AACCACGACGAGTAATTTGGA 57.610 42.857 0.00 0.00 0.00 3.53
1884 1991 3.389925 ACCACGACGAGTAATTTGGAA 57.610 42.857 0.00 0.00 0.00 3.53
1885 1992 3.062042 ACCACGACGAGTAATTTGGAAC 58.938 45.455 0.00 0.00 0.00 3.62
1886 1993 2.414138 CCACGACGAGTAATTTGGAACC 59.586 50.000 0.00 0.00 0.00 3.62
1887 1994 2.091588 CACGACGAGTAATTTGGAACCG 59.908 50.000 0.00 0.00 0.00 4.44
1888 1995 2.030007 ACGACGAGTAATTTGGAACCGA 60.030 45.455 0.00 0.00 0.00 4.69
1889 1996 2.597305 CGACGAGTAATTTGGAACCGAG 59.403 50.000 0.00 0.00 0.00 4.63
1890 1997 2.928116 GACGAGTAATTTGGAACCGAGG 59.072 50.000 0.00 0.00 0.00 4.63
1891 1998 2.277084 CGAGTAATTTGGAACCGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
1892 1999 2.093869 CGAGTAATTTGGAACCGAGGGA 60.094 50.000 0.00 0.00 0.00 4.20
1893 2000 3.532542 GAGTAATTTGGAACCGAGGGAG 58.467 50.000 0.00 0.00 0.00 4.30
1894 2001 2.910977 AGTAATTTGGAACCGAGGGAGT 59.089 45.455 0.00 0.00 0.00 3.85
1895 2002 4.098894 AGTAATTTGGAACCGAGGGAGTA 58.901 43.478 0.00 0.00 0.00 2.59
1896 2003 3.345508 AATTTGGAACCGAGGGAGTAC 57.654 47.619 0.00 0.00 0.00 2.73
1897 2004 0.604578 TTTGGAACCGAGGGAGTACG 59.395 55.000 0.00 0.00 0.00 3.67
1909 2016 1.670967 GGGAGTACGTGTTACCACTGC 60.671 57.143 0.00 0.00 39.55 4.40
1932 2041 5.346822 GCCAAATTTGCATTCTGAACTACTG 59.653 40.000 12.92 0.00 0.00 2.74
1983 2099 1.308069 CCTCATGAACCGCCCTGTTG 61.308 60.000 0.00 0.00 0.00 3.33
2015 2131 0.831966 CTGCAGAAGAGAGCCTGGAT 59.168 55.000 8.42 0.00 30.53 3.41
2126 2262 4.633596 CACGATCGCGGCGCATTC 62.634 66.667 32.61 24.44 43.17 2.67
2155 2292 4.025401 CGGTTCTTGGCGTGGTGC 62.025 66.667 0.00 0.00 45.38 5.01
2158 2295 1.891919 GTTCTTGGCGTGGTGCTGA 60.892 57.895 0.00 0.00 45.43 4.26
2159 2296 1.073025 TTCTTGGCGTGGTGCTGAT 59.927 52.632 0.00 0.00 45.43 2.90
2299 2436 2.347490 GTGCTCGGCTTCCAGGAA 59.653 61.111 0.71 0.71 0.00 3.36
2423 2565 2.187163 GCTCGAGGCCCAAGTACC 59.813 66.667 15.58 0.00 34.27 3.34
2806 2978 2.365635 CCCGACCTGGACCTGGAT 60.366 66.667 23.36 8.15 42.00 3.41
2816 2988 2.362503 ACCTGGATCTCGACGGCA 60.363 61.111 0.00 0.00 0.00 5.69
3208 3391 1.521580 TCAACTGATCATGCACGCAA 58.478 45.000 0.00 0.00 0.00 4.85
3209 3392 1.197492 TCAACTGATCATGCACGCAAC 59.803 47.619 0.00 0.00 0.00 4.17
3210 3393 1.069091 CAACTGATCATGCACGCAACA 60.069 47.619 0.00 0.00 0.00 3.33
3211 3394 0.518636 ACTGATCATGCACGCAACAC 59.481 50.000 0.00 0.00 0.00 3.32
3212 3395 0.518195 CTGATCATGCACGCAACACA 59.482 50.000 0.00 0.00 0.00 3.72
3213 3396 1.131693 CTGATCATGCACGCAACACAT 59.868 47.619 0.00 0.00 0.00 3.21
3215 3398 1.399440 GATCATGCACGCAACACATCT 59.601 47.619 0.00 0.00 0.00 2.90
3254 3442 2.044053 ACCAATGCATCACCCCGG 60.044 61.111 0.00 0.00 0.00 5.73
3300 3492 0.332972 GGAGGATTTTCTGGCTGGGT 59.667 55.000 0.00 0.00 0.00 4.51
3306 3498 2.496899 TTTTCTGGCTGGGTGATCTC 57.503 50.000 0.00 0.00 0.00 2.75
3339 3531 4.148230 GTGCCGTACGACAGAGTG 57.852 61.111 18.76 0.00 0.00 3.51
3349 3541 4.320456 ACAGAGTGCACGGCCTGG 62.320 66.667 27.78 16.62 0.00 4.45
3351 3543 4.320456 AGAGTGCACGGCCTGGTG 62.320 66.667 12.01 3.38 40.89 4.17
3352 3544 4.626081 GAGTGCACGGCCTGGTGT 62.626 66.667 12.01 0.00 40.08 4.16
3400 3592 3.182967 GAGAAAGATCAGGTACGCAGTG 58.817 50.000 0.00 0.00 45.73 3.66
3407 3599 1.972223 AGGTACGCAGTGTCGCTCT 60.972 57.895 6.83 0.94 45.73 4.09
3416 3608 1.851053 CAGTGTCGCTCTTCATCATCG 59.149 52.381 0.00 0.00 0.00 3.84
3859 4124 1.300971 ACACGACATGGACATGCAGC 61.301 55.000 11.96 2.01 42.39 5.25
3953 4219 3.147132 TGACGGTGTCACTGGCAT 58.853 55.556 16.82 0.00 37.64 4.40
3954 4220 1.005037 TGACGGTGTCACTGGCATC 60.005 57.895 16.82 5.17 37.64 3.91
3955 4221 1.005037 GACGGTGTCACTGGCATCA 60.005 57.895 13.14 0.00 31.10 3.07
3956 4222 1.004560 ACGGTGTCACTGGCATCAG 60.005 57.895 16.20 0.00 46.10 2.90
3970 4236 2.277858 ATCAGTCGGTCTGGTGGTC 58.722 57.895 2.52 0.00 43.76 4.02
3971 4237 0.251832 ATCAGTCGGTCTGGTGGTCT 60.252 55.000 2.52 0.00 43.76 3.85
3995 4261 5.624344 AATCATCGGCAGATCAATGAATC 57.376 39.130 0.00 0.00 34.23 2.52
4054 4321 1.194781 TTCTCCCCTGTCAGGCTGTC 61.195 60.000 13.99 9.82 32.73 3.51
4055 4322 1.915266 CTCCCCTGTCAGGCTGTCA 60.915 63.158 13.99 14.36 32.73 3.58
4056 4323 1.897225 CTCCCCTGTCAGGCTGTCAG 61.897 65.000 27.76 27.76 34.16 3.51
4057 4324 2.219875 CCCCTGTCAGGCTGTCAGT 61.220 63.158 30.45 0.00 32.84 3.41
4058 4325 0.904865 CCCCTGTCAGGCTGTCAGTA 60.905 60.000 30.45 4.97 32.84 2.74
4067 4334 2.433604 CAGGCTGTCAGTATGGTGAGAT 59.566 50.000 6.28 0.00 36.16 2.75
4133 4430 8.510243 AAAAACAGAAAGAATGAGGCAAAAAT 57.490 26.923 0.00 0.00 0.00 1.82
4147 4444 1.476085 CAAAAATATGCACCAGCCGGA 59.524 47.619 5.05 0.00 41.13 5.14
4211 4508 3.195610 CACTAGACCACTGGTGCTTATGA 59.804 47.826 5.10 0.00 45.52 2.15
4214 4511 1.672881 GACCACTGGTGCTTATGATGC 59.327 52.381 5.10 0.00 35.25 3.91
4217 4514 3.054434 ACCACTGGTGCTTATGATGCTAA 60.054 43.478 0.00 0.00 32.98 3.09
4219 4516 4.214971 CCACTGGTGCTTATGATGCTAATC 59.785 45.833 0.00 0.00 0.00 1.75
4220 4517 4.818005 CACTGGTGCTTATGATGCTAATCA 59.182 41.667 0.00 0.00 46.71 2.57
4224 4521 6.798482 TGGTGCTTATGATGCTAATCAAAAG 58.202 36.000 0.00 0.00 45.81 2.27
4226 4523 6.039717 GGTGCTTATGATGCTAATCAAAAGGA 59.960 38.462 0.00 0.00 45.81 3.36
4229 4526 8.530311 TGCTTATGATGCTAATCAAAAGGAAAA 58.470 29.630 0.00 0.00 45.81 2.29
4327 4628 9.712305 TGCTTAAACAGGAGAATTATATAGAGC 57.288 33.333 0.00 0.00 0.00 4.09
4400 4701 0.179026 TACGATCCTCGCTAGCCTGT 60.179 55.000 9.66 0.07 45.12 4.00
4427 4741 1.942657 CATCTATGCTGTCCCGGTTTG 59.057 52.381 0.00 0.00 0.00 2.93
4433 4747 3.326889 CTGTCCCGGTTTGCATGCG 62.327 63.158 14.09 0.00 0.00 4.73
4438 4752 4.088762 CGGTTTGCATGCGCGAGT 62.089 61.111 12.10 0.00 42.97 4.18
4439 4753 2.255252 GGTTTGCATGCGCGAGTT 59.745 55.556 12.10 0.00 42.97 3.01
4468 4782 2.050144 TCAAAACTGGAGCTCACCTCT 58.950 47.619 17.19 0.00 40.57 3.69
4480 4794 2.501723 GCTCACCTCTTGGACCTCATAA 59.498 50.000 0.00 0.00 37.04 1.90
4522 4836 3.681417 GCCCTCTTGAAATTTGCAACATC 59.319 43.478 0.00 0.00 0.00 3.06
4600 4914 5.290493 AGATCCATTGCTAAACGGATACA 57.710 39.130 0.00 0.00 38.38 2.29
4702 5016 3.193267 CCATTGTGGTTTCGAATCACCAT 59.807 43.478 21.43 15.53 44.98 3.55
4826 5141 1.001406 CGGTGCTTCTTCACTCCTTCT 59.999 52.381 0.00 0.00 37.16 2.85
4854 5169 9.872721 ATGTAGCAAGATCATGAATAGTATCAG 57.127 33.333 0.00 0.00 31.76 2.90
4859 5174 7.041576 GCAAGATCATGAATAGTATCAGTTGCA 60.042 37.037 0.00 0.00 32.75 4.08
4888 5220 1.207089 GACATCGTTCCCCATGTCTCA 59.793 52.381 5.64 0.00 43.80 3.27
4903 5235 6.016527 CCCATGTCTCATATTGTTCCATTCTG 60.017 42.308 0.00 0.00 0.00 3.02
4910 5242 6.115446 TCATATTGTTCCATTCTGTCCAGAC 58.885 40.000 0.00 0.00 37.14 3.51
4911 5243 2.455674 TGTTCCATTCTGTCCAGACG 57.544 50.000 0.00 0.00 37.14 4.18
4912 5244 1.079503 GTTCCATTCTGTCCAGACGC 58.920 55.000 0.00 0.00 37.14 5.19
4913 5245 0.389817 TTCCATTCTGTCCAGACGCG 60.390 55.000 3.53 3.53 37.14 6.01
4915 5247 1.078759 CCATTCTGTCCAGACGCGTC 61.079 60.000 31.30 31.30 37.14 5.19
4916 5248 1.078759 CATTCTGTCCAGACGCGTCC 61.079 60.000 34.08 19.80 37.14 4.79
4917 5249 1.532604 ATTCTGTCCAGACGCGTCCA 61.533 55.000 34.08 23.15 37.14 4.02
4918 5250 2.126307 CTGTCCAGACGCGTCCAG 60.126 66.667 34.08 27.62 0.00 3.86
4957 5289 3.887716 AGATAATGGCAGCAAGTGATTCC 59.112 43.478 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 3.484886 GCTTCTTGATTAGCAGCTGTTCG 60.485 47.826 16.64 0.00 39.66 3.95
32 33 5.105635 CCCTTCAATTGCTTCTTGATTAGCA 60.106 40.000 0.00 0.00 45.06 3.49
51 52 8.765219 GCAATTAAGACTTTTCTTTTTCCCTTC 58.235 33.333 0.00 0.00 39.17 3.46
57 58 8.478066 ACAGAGGCAATTAAGACTTTTCTTTTT 58.522 29.630 0.00 0.00 39.17 1.94
75 76 0.613260 ATTACGGCTTGACAGAGGCA 59.387 50.000 10.30 0.00 41.92 4.75
176 178 1.375013 GTGGCAAGCAAAGCATGGG 60.375 57.895 0.00 0.00 0.00 4.00
228 233 5.334802 GGCACATTTTCCTGCATTTTAAACC 60.335 40.000 0.00 0.00 34.90 3.27
316 324 4.168101 ACCCACCCGATATATCATTGTCT 58.832 43.478 13.11 0.00 0.00 3.41
342 350 0.991920 ACCCAACCGAATCATGGAGT 59.008 50.000 0.00 0.00 36.27 3.85
375 383 4.100189 AGGGAATCAAGTAGGTCATCTTCG 59.900 45.833 0.00 0.00 0.00 3.79
376 384 5.454045 GGAGGGAATCAAGTAGGTCATCTTC 60.454 48.000 0.00 0.00 0.00 2.87
377 385 4.410555 GGAGGGAATCAAGTAGGTCATCTT 59.589 45.833 0.00 0.00 0.00 2.40
381 389 3.199442 TGGAGGGAATCAAGTAGGTCA 57.801 47.619 0.00 0.00 0.00 4.02
457 466 3.550820 CTCCTCTTCTCAAGATCGGAGA 58.449 50.000 13.94 13.94 45.78 3.71
468 477 3.444703 TGCTTTATCGCTCCTCTTCTC 57.555 47.619 0.00 0.00 0.00 2.87
469 478 3.895232 TTGCTTTATCGCTCCTCTTCT 57.105 42.857 0.00 0.00 0.00 2.85
580 591 1.543614 CAGACGACTTCAGCTGATCG 58.456 55.000 29.13 29.13 40.39 3.69
614 643 1.828979 TATTTTGTGGCCGGGAGTTC 58.171 50.000 2.18 0.00 0.00 3.01
622 651 4.698575 TGTTTCCTGTTTATTTTGTGGCC 58.301 39.130 0.00 0.00 0.00 5.36
633 662 7.893302 TCATGGTTATTATCCTGTTTCCTGTTT 59.107 33.333 0.00 0.00 0.00 2.83
641 670 6.951198 TGGTGTTTCATGGTTATTATCCTGTT 59.049 34.615 0.00 0.00 0.00 3.16
732 766 0.179037 CATCACGGAGATGCCATGGT 60.179 55.000 14.67 0.00 46.90 3.55
740 775 4.694760 TTTGATCCATCATCACGGAGAT 57.305 40.909 0.00 0.00 41.56 2.75
787 822 3.838795 GCACTTACGCTGACGCCG 61.839 66.667 0.00 0.00 45.53 6.46
799 834 2.398554 CGGCCATTACTGCGCACTT 61.399 57.895 5.66 0.00 0.00 3.16
855 894 2.732366 CGAGACGTTCAATCCATCGAT 58.268 47.619 0.00 0.00 0.00 3.59
865 904 7.470079 GTGAATATATATAGGCGAGACGTTCA 58.530 38.462 0.00 0.00 0.00 3.18
873 912 5.048921 GCTAGCCGTGAATATATATAGGCGA 60.049 44.000 2.29 14.48 46.83 5.54
874 913 5.048643 AGCTAGCCGTGAATATATATAGGCG 60.049 44.000 12.13 12.39 46.83 5.52
875 914 6.334102 AGCTAGCCGTGAATATATATAGGC 57.666 41.667 12.13 17.00 43.07 3.93
1023 1070 0.738412 TCTAAAAGCCGCCGTACAGC 60.738 55.000 0.00 0.00 0.00 4.40
1024 1071 1.935933 ATCTAAAAGCCGCCGTACAG 58.064 50.000 0.00 0.00 0.00 2.74
1025 1072 2.273557 GAATCTAAAAGCCGCCGTACA 58.726 47.619 0.00 0.00 0.00 2.90
1026 1073 2.273557 TGAATCTAAAAGCCGCCGTAC 58.726 47.619 0.00 0.00 0.00 3.67
1027 1074 2.093869 ACTGAATCTAAAAGCCGCCGTA 60.094 45.455 0.00 0.00 0.00 4.02
1028 1075 1.338769 ACTGAATCTAAAAGCCGCCGT 60.339 47.619 0.00 0.00 0.00 5.68
1029 1076 1.369625 ACTGAATCTAAAAGCCGCCG 58.630 50.000 0.00 0.00 0.00 6.46
1039 1086 1.140852 CCCGGATGCCAACTGAATCTA 59.859 52.381 0.73 0.00 0.00 1.98
1053 1100 3.790437 CTCTGCAGTGCCCCGGAT 61.790 66.667 14.67 0.00 0.00 4.18
1059 1106 3.054503 CCTGTGCTCTGCAGTGCC 61.055 66.667 31.61 23.80 40.08 5.01
1066 1113 2.301296 TCTTCTTCTTCCCTGTGCTCTG 59.699 50.000 0.00 0.00 0.00 3.35
1099 1146 1.692042 ACCATCTCCCCCAGCTCTG 60.692 63.158 0.00 0.00 0.00 3.35
1121 1210 1.513158 CGGCGTCCTCTGATTCTGT 59.487 57.895 0.00 0.00 0.00 3.41
1198 1287 0.878416 AACACACCACACACACACAC 59.122 50.000 0.00 0.00 0.00 3.82
1199 1288 1.160989 GAACACACCACACACACACA 58.839 50.000 0.00 0.00 0.00 3.72
1206 1295 1.745232 TCACCAAGAACACACCACAC 58.255 50.000 0.00 0.00 0.00 3.82
1207 1296 2.687425 CAATCACCAAGAACACACCACA 59.313 45.455 0.00 0.00 0.00 4.17
1208 1297 2.948979 TCAATCACCAAGAACACACCAC 59.051 45.455 0.00 0.00 0.00 4.16
1210 1299 4.853924 AATCAATCACCAAGAACACACC 57.146 40.909 0.00 0.00 0.00 4.16
1211 1300 4.984161 CCAAATCAATCACCAAGAACACAC 59.016 41.667 0.00 0.00 0.00 3.82
1250 1339 1.303561 GGCCAGAACACCTGCATCA 60.304 57.895 0.00 0.00 41.57 3.07
1386 1482 2.356553 CGCAACTCGAACCGGGAA 60.357 61.111 6.32 0.00 41.67 3.97
1429 1528 2.833943 GCAAAAATGGTGAGAAGGGGAT 59.166 45.455 0.00 0.00 0.00 3.85
1443 1546 3.441572 CGAGATGGACAGGAAGCAAAAAT 59.558 43.478 0.00 0.00 0.00 1.82
1453 1556 0.179116 CTCTGCACGAGATGGACAGG 60.179 60.000 7.22 0.00 42.62 4.00
1460 1563 1.476085 CAGTTCTCCTCTGCACGAGAT 59.524 52.381 12.91 0.00 42.62 2.75
1524 1627 2.125512 GAGCTCACCGGCGATGTT 60.126 61.111 9.30 0.00 37.29 2.71
1567 1670 5.817816 ACGCAACCAATTTTCCAAACATAAA 59.182 32.000 0.00 0.00 0.00 1.40
1569 1672 4.747108 CACGCAACCAATTTTCCAAACATA 59.253 37.500 0.00 0.00 0.00 2.29
1581 1684 2.953821 CGGAAGCACGCAACCAAT 59.046 55.556 0.00 0.00 0.00 3.16
1611 1714 5.285651 GTCTTCAGGATCGGATAAGAACAG 58.714 45.833 3.21 0.00 0.00 3.16
1647 1750 0.608308 GGGCTAAACGGTCCAAAGCT 60.608 55.000 0.00 0.00 33.67 3.74
1681 1785 1.490490 GGTGGGAATCTGGTATCAGCA 59.510 52.381 0.00 0.00 40.69 4.41
1747 1854 3.181377 TGAAAATGCGCAAAATCGACAAC 59.819 39.130 17.11 0.00 0.00 3.32
1774 1881 0.445436 GGTCAGAAGCAACGCTGATG 59.555 55.000 0.00 0.00 42.51 3.07
1778 1885 1.016130 CGATGGTCAGAAGCAACGCT 61.016 55.000 0.00 0.00 41.20 5.07
1779 1886 1.014044 TCGATGGTCAGAAGCAACGC 61.014 55.000 2.94 0.00 45.34 4.84
1806 1913 2.905415 TGGAACGGAGGGAGTAGTAA 57.095 50.000 0.00 0.00 0.00 2.24
1810 1917 4.098894 AGTAATTTGGAACGGAGGGAGTA 58.901 43.478 0.00 0.00 0.00 2.59
1811 1918 2.910977 AGTAATTTGGAACGGAGGGAGT 59.089 45.455 0.00 0.00 0.00 3.85
1812 1919 3.629142 AGTAATTTGGAACGGAGGGAG 57.371 47.619 0.00 0.00 0.00 4.30
1813 1920 4.098894 ACTAGTAATTTGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
1814 1921 4.439968 GACTAGTAATTTGGAACGGAGGG 58.560 47.826 0.00 0.00 0.00 4.30
1815 1922 4.110482 CGACTAGTAATTTGGAACGGAGG 58.890 47.826 0.00 0.00 0.00 4.30
1816 1923 4.561606 CACGACTAGTAATTTGGAACGGAG 59.438 45.833 0.00 0.00 0.00 4.63
1817 1924 4.487948 CACGACTAGTAATTTGGAACGGA 58.512 43.478 0.00 0.00 0.00 4.69
1818 1925 3.615496 CCACGACTAGTAATTTGGAACGG 59.385 47.826 0.00 0.00 0.00 4.44
1819 1926 4.240096 ACCACGACTAGTAATTTGGAACG 58.760 43.478 15.15 6.05 0.00 3.95
1820 1927 6.203338 TGAAACCACGACTAGTAATTTGGAAC 59.797 38.462 15.15 8.38 0.00 3.62
1821 1928 6.289834 TGAAACCACGACTAGTAATTTGGAA 58.710 36.000 15.15 0.55 0.00 3.53
1822 1929 5.856156 TGAAACCACGACTAGTAATTTGGA 58.144 37.500 15.15 0.00 0.00 3.53
1823 1930 5.699458 ACTGAAACCACGACTAGTAATTTGG 59.301 40.000 0.00 2.67 0.00 3.28
1824 1931 6.780706 ACTGAAACCACGACTAGTAATTTG 57.219 37.500 0.00 0.00 0.00 2.32
1825 1932 6.987992 TGAACTGAAACCACGACTAGTAATTT 59.012 34.615 0.00 0.00 0.00 1.82
1826 1933 6.518493 TGAACTGAAACCACGACTAGTAATT 58.482 36.000 0.00 0.00 0.00 1.40
1827 1934 6.092955 TGAACTGAAACCACGACTAGTAAT 57.907 37.500 0.00 0.00 0.00 1.89
1828 1935 5.518848 TGAACTGAAACCACGACTAGTAA 57.481 39.130 0.00 0.00 0.00 2.24
1829 1936 5.518848 TTGAACTGAAACCACGACTAGTA 57.481 39.130 0.00 0.00 0.00 1.82
1830 1937 4.395959 TTGAACTGAAACCACGACTAGT 57.604 40.909 0.00 0.00 0.00 2.57
1831 1938 5.924475 ATTTGAACTGAAACCACGACTAG 57.076 39.130 0.00 0.00 0.00 2.57
1832 1939 6.687081 AAATTTGAACTGAAACCACGACTA 57.313 33.333 0.00 0.00 0.00 2.59
1833 1940 5.576447 AAATTTGAACTGAAACCACGACT 57.424 34.783 0.00 0.00 0.00 4.18
1834 1941 7.486870 AGTTTAAATTTGAACTGAAACCACGAC 59.513 33.333 23.18 0.00 35.92 4.34
1835 1942 7.540299 AGTTTAAATTTGAACTGAAACCACGA 58.460 30.769 23.18 0.00 35.92 4.35
1836 1943 7.749539 AGTTTAAATTTGAACTGAAACCACG 57.250 32.000 23.18 0.00 35.92 4.94
1843 1950 9.291664 CGTGGTTTTAGTTTAAATTTGAACTGA 57.708 29.630 28.93 21.84 37.53 3.41
1844 1951 9.291664 TCGTGGTTTTAGTTTAAATTTGAACTG 57.708 29.630 28.93 15.18 37.53 3.16
1845 1952 9.292846 GTCGTGGTTTTAGTTTAAATTTGAACT 57.707 29.630 25.84 25.84 39.80 3.01
1846 1953 8.254470 CGTCGTGGTTTTAGTTTAAATTTGAAC 58.746 33.333 15.93 15.93 0.00 3.18
1847 1954 8.180267 TCGTCGTGGTTTTAGTTTAAATTTGAA 58.820 29.630 0.00 0.00 0.00 2.69
1848 1955 7.692088 TCGTCGTGGTTTTAGTTTAAATTTGA 58.308 30.769 0.00 0.00 0.00 2.69
1849 1956 7.641020 ACTCGTCGTGGTTTTAGTTTAAATTTG 59.359 33.333 0.00 0.00 0.00 2.32
1850 1957 7.696755 ACTCGTCGTGGTTTTAGTTTAAATTT 58.303 30.769 0.00 0.00 0.00 1.82
1851 1958 7.250445 ACTCGTCGTGGTTTTAGTTTAAATT 57.750 32.000 0.00 0.00 0.00 1.82
1852 1959 6.849588 ACTCGTCGTGGTTTTAGTTTAAAT 57.150 33.333 0.00 0.00 0.00 1.40
1853 1960 7.763172 TTACTCGTCGTGGTTTTAGTTTAAA 57.237 32.000 0.00 0.00 0.00 1.52
1854 1961 7.945033 ATTACTCGTCGTGGTTTTAGTTTAA 57.055 32.000 0.00 0.00 0.00 1.52
1855 1962 7.945033 AATTACTCGTCGTGGTTTTAGTTTA 57.055 32.000 0.00 0.00 0.00 2.01
1856 1963 6.849588 AATTACTCGTCGTGGTTTTAGTTT 57.150 33.333 0.00 0.00 0.00 2.66
1857 1964 6.293027 CCAAATTACTCGTCGTGGTTTTAGTT 60.293 38.462 0.00 0.00 0.00 2.24
1858 1965 5.178067 CCAAATTACTCGTCGTGGTTTTAGT 59.822 40.000 0.00 0.00 0.00 2.24
1859 1966 5.406175 TCCAAATTACTCGTCGTGGTTTTAG 59.594 40.000 0.00 0.00 0.00 1.85
1860 1967 5.295950 TCCAAATTACTCGTCGTGGTTTTA 58.704 37.500 0.00 0.00 0.00 1.52
1861 1968 4.128643 TCCAAATTACTCGTCGTGGTTTT 58.871 39.130 0.00 0.00 0.00 2.43
1862 1969 3.731089 TCCAAATTACTCGTCGTGGTTT 58.269 40.909 0.00 0.00 0.00 3.27
1863 1970 3.389925 TCCAAATTACTCGTCGTGGTT 57.610 42.857 0.00 0.00 0.00 3.67
1864 1971 3.062042 GTTCCAAATTACTCGTCGTGGT 58.938 45.455 0.00 0.00 0.00 4.16
1865 1972 2.414138 GGTTCCAAATTACTCGTCGTGG 59.586 50.000 0.00 0.00 0.00 4.94
1866 1973 2.091588 CGGTTCCAAATTACTCGTCGTG 59.908 50.000 0.00 0.00 0.00 4.35
1867 1974 2.030007 TCGGTTCCAAATTACTCGTCGT 60.030 45.455 0.00 0.00 0.00 4.34
1868 1975 2.597305 CTCGGTTCCAAATTACTCGTCG 59.403 50.000 0.00 0.00 0.00 5.12
1869 1976 2.928116 CCTCGGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
1870 1977 2.354403 CCCTCGGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
1871 1978 2.093869 TCCCTCGGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
1872 1979 3.055312 ACTCCCTCGGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
1873 1980 2.910977 ACTCCCTCGGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
1874 1981 3.345508 ACTCCCTCGGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
1875 1982 3.119029 CGTACTCCCTCGGTTCCAAATTA 60.119 47.826 0.00 0.00 0.00 1.40
1876 1983 2.354403 CGTACTCCCTCGGTTCCAAATT 60.354 50.000 0.00 0.00 0.00 1.82
1877 1984 1.206371 CGTACTCCCTCGGTTCCAAAT 59.794 52.381 0.00 0.00 0.00 2.32
1878 1985 0.604578 CGTACTCCCTCGGTTCCAAA 59.395 55.000 0.00 0.00 0.00 3.28
1879 1986 0.540365 ACGTACTCCCTCGGTTCCAA 60.540 55.000 0.00 0.00 0.00 3.53
1880 1987 1.075482 ACGTACTCCCTCGGTTCCA 59.925 57.895 0.00 0.00 0.00 3.53
1881 1988 1.246737 ACACGTACTCCCTCGGTTCC 61.247 60.000 0.00 0.00 0.00 3.62
1882 1989 0.600057 AACACGTACTCCCTCGGTTC 59.400 55.000 0.00 0.00 0.00 3.62
1883 1990 1.541588 GTAACACGTACTCCCTCGGTT 59.458 52.381 0.00 0.00 0.00 4.44
1884 1991 1.168714 GTAACACGTACTCCCTCGGT 58.831 55.000 0.00 0.00 0.00 4.69
1885 1992 0.453390 GGTAACACGTACTCCCTCGG 59.547 60.000 0.00 0.00 32.80 4.63
1886 1993 1.167851 TGGTAACACGTACTCCCTCG 58.832 55.000 0.00 0.00 46.17 4.63
1909 2016 5.865552 CCAGTAGTTCAGAATGCAAATTTGG 59.134 40.000 19.47 2.17 34.76 3.28
1932 2041 6.315393 TCTGAATTTTGCTTCCGATTAGTACC 59.685 38.462 0.00 0.00 0.00 3.34
1983 2099 3.990469 TCTTCTGCAGATCGTTCAAGAAC 59.010 43.478 19.04 2.89 37.92 3.01
2155 2292 2.286831 GCAGCACGAATCCATCAATCAG 60.287 50.000 0.00 0.00 0.00 2.90
2158 2295 1.674441 CTGCAGCACGAATCCATCAAT 59.326 47.619 0.00 0.00 0.00 2.57
2159 2296 1.089112 CTGCAGCACGAATCCATCAA 58.911 50.000 0.00 0.00 0.00 2.57
2299 2436 2.591715 GTGTTGAGCGGCACCACT 60.592 61.111 1.45 0.00 37.00 4.00
2494 2636 2.726912 GCGTCGTCGTCGGTTTCA 60.727 61.111 13.43 0.00 39.49 2.69
2669 2831 2.763215 GGTGGCCATCAGGTCCAA 59.237 61.111 12.38 0.00 40.96 3.53
2927 3102 1.194781 ATGTTCTGGACGCACCTCCT 61.195 55.000 1.15 0.00 39.86 3.69
3208 3391 7.094631 TGCAATTTCGTAGTAGTAAGATGTGT 58.905 34.615 0.00 0.00 0.00 3.72
3209 3392 7.520119 TGCAATTTCGTAGTAGTAAGATGTG 57.480 36.000 0.00 0.00 0.00 3.21
3210 3393 7.438459 GGATGCAATTTCGTAGTAGTAAGATGT 59.562 37.037 0.00 0.00 0.00 3.06
3211 3394 7.438160 TGGATGCAATTTCGTAGTAGTAAGATG 59.562 37.037 0.00 0.00 0.00 2.90
3212 3395 7.438459 GTGGATGCAATTTCGTAGTAGTAAGAT 59.562 37.037 0.00 0.00 0.00 2.40
3213 3396 6.755141 GTGGATGCAATTTCGTAGTAGTAAGA 59.245 38.462 0.00 0.00 0.00 2.10
3215 3398 5.813672 GGTGGATGCAATTTCGTAGTAGTAA 59.186 40.000 0.00 0.00 0.00 2.24
3254 3442 5.163913 CGGAAGAACATCTCTGTCAAATCAC 60.164 44.000 0.00 0.00 33.36 3.06
3259 3447 2.037121 TGCGGAAGAACATCTCTGTCAA 59.963 45.455 0.00 0.00 33.36 3.18
3300 3492 2.617308 GTCGATCCGGTAGTTGAGATCA 59.383 50.000 0.00 0.00 35.85 2.92
3306 3498 1.138047 GCACGTCGATCCGGTAGTTG 61.138 60.000 0.00 0.00 0.00 3.16
3400 3592 1.543941 CGGCGATGATGAAGAGCGAC 61.544 60.000 0.00 0.00 0.00 5.19
3407 3599 1.893335 CCATGGCGGCGATGATGAA 60.893 57.895 24.05 0.00 0.00 2.57
3416 3608 1.377202 TTCAGAGTTCCATGGCGGC 60.377 57.895 6.96 0.00 33.14 6.53
3527 3742 4.764336 TACGTGGGCGCGAACTCG 62.764 66.667 12.10 16.46 42.83 4.18
3539 3754 1.464687 CCGACCTCGTACTTGTACGTG 60.465 57.143 25.76 23.35 43.31 4.49
3659 3874 2.678934 AGCTCCGACCTGCCGTAA 60.679 61.111 0.00 0.00 0.00 3.18
3678 3893 3.414700 CTTGTGGTCCGACAGCGC 61.415 66.667 0.00 0.00 35.83 5.92
3859 4124 1.387084 GTCGACGCAGCTGAAAACTAG 59.613 52.381 20.43 1.16 0.00 2.57
3954 4220 1.254026 TAAGACCACCAGACCGACTG 58.746 55.000 3.25 3.25 45.36 3.51
3955 4221 2.005370 TTAAGACCACCAGACCGACT 57.995 50.000 0.00 0.00 0.00 4.18
3956 4222 2.232941 TGATTAAGACCACCAGACCGAC 59.767 50.000 0.00 0.00 0.00 4.79
3957 4223 2.531771 TGATTAAGACCACCAGACCGA 58.468 47.619 0.00 0.00 0.00 4.69
3970 4236 6.549912 TTCATTGATCTGCCGATGATTAAG 57.450 37.500 0.00 0.00 36.96 1.85
3971 4237 6.938596 AGATTCATTGATCTGCCGATGATTAA 59.061 34.615 0.00 0.00 36.96 1.40
4054 4321 4.142071 ACAGCACACTATCTCACCATACTG 60.142 45.833 0.00 0.00 0.00 2.74
4055 4322 4.026744 ACAGCACACTATCTCACCATACT 58.973 43.478 0.00 0.00 0.00 2.12
4056 4323 4.392921 ACAGCACACTATCTCACCATAC 57.607 45.455 0.00 0.00 0.00 2.39
4057 4324 5.046663 TCAAACAGCACACTATCTCACCATA 60.047 40.000 0.00 0.00 0.00 2.74
4058 4325 3.988976 AACAGCACACTATCTCACCAT 57.011 42.857 0.00 0.00 0.00 3.55
4089 4356 1.825090 TTATGCTTCTGTGCCACTGG 58.175 50.000 1.68 0.00 0.00 4.00
4115 4383 6.036408 GGTGCATATTTTTGCCTCATTCTTTC 59.964 38.462 0.00 0.00 42.06 2.62
4126 4394 1.280066 CGGCTGGTGCATATTTTTGC 58.720 50.000 0.00 0.00 43.07 3.68
4133 4430 0.813610 CGATTTCCGGCTGGTGCATA 60.814 55.000 12.43 0.00 41.91 3.14
4147 4444 1.066645 GTACAGACCCGGGTTCGATTT 60.067 52.381 30.89 11.77 39.00 2.17
4229 4526 5.897250 AGAACACAAACCAAGTAATCCCTTT 59.103 36.000 0.00 0.00 0.00 3.11
4231 4528 5.061721 AGAACACAAACCAAGTAATCCCT 57.938 39.130 0.00 0.00 0.00 4.20
4233 4530 7.708998 TGTTTAGAACACAAACCAAGTAATCC 58.291 34.615 0.00 0.00 36.25 3.01
4239 4536 6.677781 TCTCTGTTTAGAACACAAACCAAG 57.322 37.500 0.00 0.00 36.25 3.61
4282 4580 2.650608 CAGTAAAGCTTGTGTTTCGCC 58.349 47.619 0.00 0.00 0.00 5.54
4327 4628 8.940952 CCTCTTTTCTTCTAGGTTGTATTCAAG 58.059 37.037 0.00 0.00 33.97 3.02
4416 4717 3.361158 CGCATGCAAACCGGGACA 61.361 61.111 19.57 0.00 0.00 4.02
4417 4718 4.776647 GCGCATGCAAACCGGGAC 62.777 66.667 19.57 0.00 42.15 4.46
4427 4741 2.020559 CTTCGAACTCGCGCATGC 59.979 61.111 7.91 7.91 39.60 4.06
4433 4747 3.186613 AGTTTTGATTCCTTCGAACTCGC 59.813 43.478 0.00 0.00 39.60 5.03
4438 4752 3.502211 GCTCCAGTTTTGATTCCTTCGAA 59.498 43.478 0.00 0.00 0.00 3.71
4439 4753 3.074412 GCTCCAGTTTTGATTCCTTCGA 58.926 45.455 0.00 0.00 0.00 3.71
4468 4782 5.047377 GCTTCCATTTGTTTATGAGGTCCAA 60.047 40.000 0.00 0.00 0.00 3.53
4480 4794 3.181476 GGCGGATATTGCTTCCATTTGTT 60.181 43.478 1.56 0.00 32.45 2.83
4522 4836 0.249489 GGAGGTTGTCCGGATGATCG 60.249 60.000 7.81 0.00 34.84 3.69
4600 4914 2.037208 CCTTGGCAACCCGGGATT 59.963 61.111 32.02 15.41 0.00 3.01
4608 4922 0.968405 TTCATGGAAGCCTTGGCAAC 59.032 50.000 14.54 6.94 30.78 4.17
4610 4924 0.899717 GGTTCATGGAAGCCTTGGCA 60.900 55.000 14.54 0.00 34.45 4.92
4854 5169 2.241722 CGATGTCGTTCCATTTGCAAC 58.758 47.619 0.00 0.00 34.11 4.17
4888 5220 5.118990 CGTCTGGACAGAATGGAACAATAT 58.881 41.667 3.18 0.00 43.62 1.28
4903 5235 3.628280 GACCTGGACGCGTCTGGAC 62.628 68.421 38.00 31.95 0.00 4.02
4912 5244 4.394712 GGGTGCTGGACCTGGACG 62.395 72.222 18.16 0.00 45.33 4.79
4913 5245 2.829384 TTGGGTGCTGGACCTGGAC 61.829 63.158 18.16 13.71 45.33 4.02
4915 5247 1.488705 TAGTTGGGTGCTGGACCTGG 61.489 60.000 18.16 0.00 45.33 4.45
4916 5248 0.400213 TTAGTTGGGTGCTGGACCTG 59.600 55.000 18.16 0.00 45.33 4.00
4917 5249 0.693049 CTTAGTTGGGTGCTGGACCT 59.307 55.000 18.16 0.53 45.33 3.85
4918 5250 0.690762 TCTTAGTTGGGTGCTGGACC 59.309 55.000 10.21 10.21 45.28 4.46
4957 5289 4.349663 TGTTGACAACAAGGAAGTTTCG 57.650 40.909 18.56 0.00 38.72 3.46


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

AutoCloner maintained by Alex Coulton.