Multiple sequence alignment - TraesCS4D01G031300

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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 TraesCS4D01G031300 chr4D 100.000 3186 0 0 1 3186 14662101 14665286 0.000000e+00 5884.0
1 TraesCS4D01G031300 chr4D 88.071 964 49 24 1796 2728 14610656 14609728 0.000000e+00 1083.0
2 TraesCS4D01G031300 chr4D 87.379 927 44 31 746 1636 14611669 14610780 0.000000e+00 996.0
3 TraesCS4D01G031300 chr4D 94.659 337 15 1 2850 3186 14609474 14609141 1.310000e-143 520.0
4 TraesCS4D01G031300 chr4D 99.383 162 1 0 50 211 14657685 14657846 8.640000e-76 294.0
5 TraesCS4D01G031300 chr4A 89.221 1438 87 23 1796 3186 586737635 586736219 0.000000e+00 1735.0
6 TraesCS4D01G031300 chr4A 88.089 1444 102 33 210 1633 586739170 586737777 0.000000e+00 1650.0
7 TraesCS4D01G031300 chr4A 88.506 1305 83 25 1934 3186 574197879 574196590 0.000000e+00 1517.0
8 TraesCS4D01G031300 chr4A 88.975 907 47 17 747 1633 456489296 456488423 0.000000e+00 1072.0
9 TraesCS4D01G031300 chr4A 92.468 624 31 9 2140 2759 456485524 456484913 0.000000e+00 878.0
10 TraesCS4D01G031300 chr4A 87.788 565 43 11 1072 1633 574198878 574198337 3.470000e-179 638.0
11 TraesCS4D01G031300 chr4A 96.232 345 13 0 2842 3186 456484879 456484535 1.660000e-157 566.0
12 TraesCS4D01G031300 chr4A 84.593 344 20 18 747 1071 574207088 574206759 8.580000e-81 311.0
13 TraesCS4D01G031300 chr4A 92.453 212 6 1 1796 1997 456488281 456488070 8.640000e-76 294.0
14 TraesCS4D01G031300 chr4A 96.032 126 5 0 1872 1997 456486095 456485970 4.170000e-49 206.0
15 TraesCS4D01G031300 chr4A 95.238 126 6 0 1872 1997 456486900 456486775 1.940000e-47 200.0
16 TraesCS4D01G031300 chr4A 93.798 129 8 0 1796 1924 574198195 574198067 9.020000e-46 195.0
17 TraesCS4D01G031300 chr4A 91.270 126 3 2 1872 1997 456487687 456487570 7.070000e-37 165.0
18 TraesCS4D01G031300 chr4A 89.773 88 2 3 1631 1712 574198280 574198194 4.350000e-19 106.0
19 TraesCS4D01G031300 chr4A 94.286 70 2 2 1631 1699 586737720 586737652 4.350000e-19 106.0
20 TraesCS4D01G031300 chr4A 88.636 88 3 3 1631 1712 456488366 456488280 2.020000e-17 100.0
21 TraesCS4D01G031300 chr4B 91.507 989 60 9 1796 2764 24564079 24565063 0.000000e+00 1339.0
22 TraesCS4D01G031300 chr4B 86.731 927 49 34 746 1630 24563013 24563907 0.000000e+00 963.0
23 TraesCS4D01G031300 chr4B 92.483 439 15 4 2766 3186 24565330 24565768 2.100000e-171 612.0
24 TraesCS4D01G031300 chr4B 96.875 32 1 0 255 286 55326774 55326805 2.000000e-03 54.7
25 TraesCS4D01G031300 chr3B 87.863 964 72 18 1796 2741 452864430 452863494 0.000000e+00 1090.0
26 TraesCS4D01G031300 chr3B 90.437 847 34 20 812 1636 452865361 452864540 0.000000e+00 1072.0
27 TraesCS4D01G031300 chr3B 93.491 338 17 3 2850 3186 452863371 452863038 6.140000e-137 497.0
28 TraesCS4D01G031300 chr3B 98.864 88 0 1 1710 1797 793269202 793269116 4.260000e-34 156.0
29 TraesCS4D01G031300 chr3B 96.591 88 2 1 1710 1797 674477193 674477279 9.210000e-31 145.0
30 TraesCS4D01G031300 chr1D 98.571 210 2 1 1 210 15853171 15853379 1.400000e-98 370.0
31 TraesCS4D01G031300 chr1D 99.383 162 0 1 50 211 15848783 15848943 3.110000e-75 292.0
32 TraesCS4D01G031300 chr1D 80.658 243 37 8 401 638 439066249 439066486 2.520000e-41 180.0
33 TraesCS4D01G031300 chr3D 97.642 212 4 1 1 212 155718021 155718231 2.340000e-96 363.0
34 TraesCS4D01G031300 chr3D 99.383 162 1 0 50 211 155713605 155713766 8.640000e-76 294.0
35 TraesCS4D01G031300 chr3D 80.753 239 35 9 406 638 596656984 596657217 3.270000e-40 176.0
36 TraesCS4D01G031300 chr3D 80.162 247 37 8 402 642 16012466 16012706 1.170000e-39 174.0
37 TraesCS4D01G031300 chr3D 78.968 252 40 10 394 638 105464467 105464712 3.290000e-35 159.0
38 TraesCS4D01G031300 chr5A 97.143 210 5 1 1 210 53217852 53218060 1.410000e-93 353.0
39 TraesCS4D01G031300 chr5A 97.531 162 3 1 50 211 53211950 53212110 3.130000e-70 276.0
40 TraesCS4D01G031300 chr5A 97.531 162 3 1 50 211 53213304 53213464 3.130000e-70 276.0
41 TraesCS4D01G031300 chr5A 96.914 162 4 1 50 211 53201129 53201289 1.460000e-68 270.0
42 TraesCS4D01G031300 chr7D 81.481 243 34 8 402 638 164760648 164760411 4.200000e-44 189.0
43 TraesCS4D01G031300 chr2D 80.417 240 40 5 403 638 351375633 351375869 3.270000e-40 176.0
44 TraesCS4D01G031300 chr2D 78.195 266 40 15 364 622 81148259 81148005 1.530000e-33 154.0
45 TraesCS4D01G031300 chr5B 79.468 263 40 11 405 658 491226795 491227052 1.170000e-39 174.0
46 TraesCS4D01G031300 chr3A 79.920 249 39 9 396 638 569671588 569671345 4.230000e-39 172.0
47 TraesCS4D01G031300 chr3A 89.844 128 5 7 1674 1799 520438110 520437989 1.180000e-34 158.0
48 TraesCS4D01G031300 chr7A 79.528 254 41 8 398 645 712206453 712206701 1.520000e-38 171.0
49 TraesCS4D01G031300 chr7A 79.668 241 38 9 404 638 283158303 283158068 2.540000e-36 163.0
50 TraesCS4D01G031300 chr7A 78.161 261 46 9 404 658 729060748 729060493 4.260000e-34 156.0
51 TraesCS4D01G031300 chr7A 98.851 87 0 1 1711 1797 383342 383427 1.530000e-33 154.0
52 TraesCS4D01G031300 chr6D 79.087 263 44 9 404 658 17505891 17506150 1.520000e-38 171.0
53 TraesCS4D01G031300 chr6D 97.753 89 1 1 1709 1797 69585638 69585725 5.500000e-33 152.0
54 TraesCS4D01G031300 chr1A 79.447 253 41 8 399 645 425051467 425051714 5.470000e-38 169.0
55 TraesCS4D01G031300 chr1A 79.447 253 38 9 399 645 64511941 64512185 1.970000e-37 167.0
56 TraesCS4D01G031300 chr2A 78.656 253 42 9 399 645 58993189 58993435 1.180000e-34 158.0
57 TraesCS4D01G031300 chr2A 95.050 101 2 3 1699 1798 68248995 68249093 4.260000e-34 156.0
58 TraesCS4D01G031300 chr5D 94.059 101 4 2 1698 1797 51699405 51699306 5.500000e-33 152.0
59 TraesCS4D01G031300 chr2B 95.745 94 4 0 1709 1802 753788789 753788882 5.500000e-33 152.0
60 TraesCS4D01G031300 chr1B 97.753 89 1 1 1709 1797 479430025 479429938 5.500000e-33 152.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G031300 chr4D 14662101 14665286 3185 False 5884.000000 5884 100.000000 1 3186 1 chr4D.!!$F2 3185
1 TraesCS4D01G031300 chr4D 14609141 14611669 2528 True 866.333333 1083 90.036333 746 3186 3 chr4D.!!$R1 2440
2 TraesCS4D01G031300 chr4A 586736219 586739170 2951 True 1163.666667 1735 90.532000 210 3186 3 chr4A.!!$R4 2976
3 TraesCS4D01G031300 chr4A 574196590 574198878 2288 True 614.000000 1517 89.966250 1072 3186 4 chr4A.!!$R3 2114
4 TraesCS4D01G031300 chr4A 456484535 456489296 4761 True 435.125000 1072 92.663000 747 3186 8 chr4A.!!$R2 2439
5 TraesCS4D01G031300 chr4B 24563013 24565768 2755 False 971.333333 1339 90.240333 746 3186 3 chr4B.!!$F2 2440
6 TraesCS4D01G031300 chr3B 452863038 452865361 2323 True 886.333333 1090 90.597000 812 3186 3 chr3B.!!$R2 2374
7 TraesCS4D01G031300 chr5A 53211950 53213464 1514 False 276.000000 276 97.531000 50 211 2 chr5A.!!$F3 161

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
24 25 0.044855 AGAGGGGCAGTGGATTAGGT 59.955 55.0 0.0 0.0 0.0 3.08 F
25 26 0.181350 GAGGGGCAGTGGATTAGGTG 59.819 60.0 0.0 0.0 0.0 4.00 F
1726 2303 0.549950 ATCTACTCCCTCCGTTCCGA 59.450 55.0 0.0 0.0 0.0 4.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1841 2418 1.071699 CCAACCCAGAAACGGAAGAGA 59.928 52.381 0.00 0.0 0.00 3.10 R
1842 2419 1.071699 TCCAACCCAGAAACGGAAGAG 59.928 52.381 0.00 0.0 0.00 2.85 R
2822 6316 0.525311 TTGCATATGTGGCAACGTGG 59.475 50.000 4.29 0.0 45.57 4.94 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
17 18 3.086600 GAGGGAGAGGGGCAGTGG 61.087 72.222 0.00 0.00 0.00 4.00
18 19 3.615811 AGGGAGAGGGGCAGTGGA 61.616 66.667 0.00 0.00 0.00 4.02
19 20 2.367512 GGGAGAGGGGCAGTGGAT 60.368 66.667 0.00 0.00 0.00 3.41
20 21 2.003548 GGGAGAGGGGCAGTGGATT 61.004 63.158 0.00 0.00 0.00 3.01
21 22 0.694444 GGGAGAGGGGCAGTGGATTA 60.694 60.000 0.00 0.00 0.00 1.75
22 23 0.761802 GGAGAGGGGCAGTGGATTAG 59.238 60.000 0.00 0.00 0.00 1.73
23 24 0.761802 GAGAGGGGCAGTGGATTAGG 59.238 60.000 0.00 0.00 0.00 2.69
24 25 0.044855 AGAGGGGCAGTGGATTAGGT 59.955 55.000 0.00 0.00 0.00 3.08
25 26 0.181350 GAGGGGCAGTGGATTAGGTG 59.819 60.000 0.00 0.00 0.00 4.00
26 27 1.227383 GGGGCAGTGGATTAGGTGG 59.773 63.158 0.00 0.00 0.00 4.61
27 28 1.279025 GGGGCAGTGGATTAGGTGGA 61.279 60.000 0.00 0.00 0.00 4.02
28 29 0.846693 GGGCAGTGGATTAGGTGGAT 59.153 55.000 0.00 0.00 0.00 3.41
29 30 1.202818 GGGCAGTGGATTAGGTGGATC 60.203 57.143 0.00 0.00 0.00 3.36
30 31 1.771255 GGCAGTGGATTAGGTGGATCT 59.229 52.381 0.00 0.00 0.00 2.75
31 32 2.224402 GGCAGTGGATTAGGTGGATCTC 60.224 54.545 0.00 0.00 0.00 2.75
32 33 2.435805 GCAGTGGATTAGGTGGATCTCA 59.564 50.000 0.00 0.00 0.00 3.27
33 34 3.494048 GCAGTGGATTAGGTGGATCTCAG 60.494 52.174 0.00 0.00 0.00 3.35
34 35 3.963374 CAGTGGATTAGGTGGATCTCAGA 59.037 47.826 0.00 0.00 0.00 3.27
35 36 4.592351 CAGTGGATTAGGTGGATCTCAGAT 59.408 45.833 0.00 0.00 0.00 2.90
36 37 5.071519 CAGTGGATTAGGTGGATCTCAGATT 59.928 44.000 0.00 0.00 0.00 2.40
37 38 6.268617 CAGTGGATTAGGTGGATCTCAGATTA 59.731 42.308 0.00 0.00 0.00 1.75
38 39 6.496565 AGTGGATTAGGTGGATCTCAGATTAG 59.503 42.308 0.00 0.00 0.00 1.73
39 40 5.782331 TGGATTAGGTGGATCTCAGATTAGG 59.218 44.000 0.00 0.00 0.00 2.69
40 41 5.337975 GGATTAGGTGGATCTCAGATTAGGC 60.338 48.000 0.00 0.00 0.00 3.93
41 42 3.342926 AGGTGGATCTCAGATTAGGCT 57.657 47.619 0.00 0.00 0.00 4.58
42 43 2.971330 AGGTGGATCTCAGATTAGGCTG 59.029 50.000 0.00 0.00 37.24 4.85
43 44 2.968574 GGTGGATCTCAGATTAGGCTGA 59.031 50.000 0.00 0.00 42.31 4.26
44 45 3.582208 GGTGGATCTCAGATTAGGCTGAT 59.418 47.826 0.00 0.00 43.43 2.90
45 46 4.774726 GGTGGATCTCAGATTAGGCTGATA 59.225 45.833 0.00 0.00 43.43 2.15
46 47 5.337169 GGTGGATCTCAGATTAGGCTGATAC 60.337 48.000 0.00 0.00 43.43 2.24
47 48 4.774726 TGGATCTCAGATTAGGCTGATACC 59.225 45.833 0.00 0.00 43.43 2.73
48 49 4.774726 GGATCTCAGATTAGGCTGATACCA 59.225 45.833 0.00 0.00 43.43 3.25
84 85 2.100087 CGAGTAAGGAAAGAGAGAGGGC 59.900 54.545 0.00 0.00 0.00 5.19
135 136 6.256321 GTGGGGTTACACAGTTTATATACACG 59.744 42.308 0.00 0.00 40.99 4.49
205 206 5.407387 AGAATACATAAACACACGTTCGCTT 59.593 36.000 0.00 0.00 32.91 4.68
207 208 6.709145 ATACATAAACACACGTTCGCTTAA 57.291 33.333 0.00 0.00 32.91 1.85
208 209 4.764940 ACATAAACACACGTTCGCTTAAC 58.235 39.130 0.00 0.00 32.91 2.01
215 216 4.084745 ACACACGTTCGCTTAACACTATTG 60.085 41.667 0.00 0.00 38.03 1.90
295 296 4.404715 AGTGGAGCGAGTTTATAGCCTTAA 59.595 41.667 0.00 0.00 0.00 1.85
346 423 8.034215 CCATTTTACATGGTGAGCAAAGAATAA 58.966 33.333 0.00 0.00 34.56 1.40
358 435 8.613482 GTGAGCAAAGAATAAGAATTACCCTAC 58.387 37.037 0.00 0.00 30.46 3.18
402 479 6.276847 ACTGTATGAAGTAGCAGTAATCAGC 58.723 40.000 0.00 0.00 40.00 4.26
408 485 3.522553 AGTAGCAGTAATCAGCCGAAAC 58.477 45.455 0.00 0.00 0.00 2.78
459 536 2.025981 TGATTTCCACCTCCCATGTCAG 60.026 50.000 0.00 0.00 0.00 3.51
514 595 2.959030 GCAACCCAGGAGTTCTCTTTTT 59.041 45.455 0.00 0.00 0.00 1.94
583 784 9.445786 TTTGTCTAAATCTTGAATCGTTTTCAC 57.554 29.630 3.58 0.00 0.00 3.18
584 785 8.378172 TGTCTAAATCTTGAATCGTTTTCACT 57.622 30.769 3.58 0.00 0.00 3.41
589 790 6.618287 ATCTTGAATCGTTTTCACTGTTGA 57.382 33.333 3.58 0.00 0.00 3.18
597 798 6.429791 TCGTTTTCACTGTTGAATTCTTCA 57.570 33.333 7.05 5.15 41.50 3.02
607 808 4.621460 TGTTGAATTCTTCACGTCGAGATC 59.379 41.667 7.05 0.00 39.87 2.75
610 811 4.859245 TGAATTCTTCACGTCGAGATCTTG 59.141 41.667 7.05 3.24 34.08 3.02
625 826 7.952637 GTCGAGATCTTGAAAACTAAATCACAC 59.047 37.037 14.50 0.00 0.00 3.82
634 835 7.802738 TGAAAACTAAATCACACGTCAATAGG 58.197 34.615 0.00 0.00 0.00 2.57
640 841 6.737254 AAATCACACGTCAATAGGTTTAGG 57.263 37.500 0.00 0.00 0.00 2.69
645 846 4.822896 ACACGTCAATAGGTTTAGGCAAAA 59.177 37.500 0.00 0.00 0.00 2.44
685 1022 3.403057 GCTGAAAGACGCGTGCGA 61.403 61.111 20.70 0.00 43.21 5.10
690 1027 0.762504 GAAAGACGCGTGCGAAAAAC 59.237 50.000 20.70 0.00 42.83 2.43
696 1033 2.777305 GACGCGTGCGAAAAACTAAAAA 59.223 40.909 20.70 0.00 42.83 1.94
712 1049 3.692791 AAAAACCAAGTGACGCTCTTC 57.307 42.857 0.00 0.00 0.00 2.87
720 1057 2.435059 GACGCTCTTCCAGCCCAC 60.435 66.667 0.00 0.00 46.74 4.61
721 1058 3.959991 GACGCTCTTCCAGCCCACC 62.960 68.421 0.00 0.00 46.74 4.61
722 1059 4.785453 CGCTCTTCCAGCCCACCC 62.785 72.222 0.00 0.00 46.74 4.61
729 1066 4.684134 CCAGCCCACCCCCAAGTG 62.684 72.222 0.00 0.00 37.51 3.16
810 1166 3.562343 ACTCATAGCTGACTACTCCGA 57.438 47.619 0.00 0.00 0.00 4.55
1011 1402 0.760567 AGGCAGAGATGGTGGCGATA 60.761 55.000 0.00 0.00 44.93 2.92
1289 1686 3.883549 GGAGGAGGAGGGCCATGC 61.884 72.222 6.18 1.32 36.29 4.06
1319 1781 0.748367 CAGCAGCAGCATCATCAGGT 60.748 55.000 3.17 0.00 45.49 4.00
1386 1854 3.024782 GCAAGACGAGCAGCAGCAG 62.025 63.158 3.17 0.00 45.49 4.24
1387 1855 2.741598 AAGACGAGCAGCAGCAGC 60.742 61.111 3.17 0.46 45.49 5.25
1388 1856 3.526210 AAGACGAGCAGCAGCAGCA 62.526 57.895 12.92 0.00 45.49 4.41
1389 1857 3.046087 GACGAGCAGCAGCAGCAA 61.046 61.111 12.92 0.00 45.49 3.91
1390 1858 3.024782 GACGAGCAGCAGCAGCAAG 62.025 63.158 12.92 7.69 45.49 4.01
1391 1859 3.800863 CGAGCAGCAGCAGCAAGG 61.801 66.667 12.92 0.00 45.49 3.61
1392 1860 2.359602 GAGCAGCAGCAGCAAGGA 60.360 61.111 12.92 0.00 45.49 3.36
1393 1861 2.360100 AGCAGCAGCAGCAAGGAG 60.360 61.111 12.92 0.00 45.49 3.69
1394 1862 2.359602 GCAGCAGCAGCAAGGAGA 60.360 61.111 4.63 0.00 45.49 3.71
1395 1863 2.688794 GCAGCAGCAGCAAGGAGAC 61.689 63.158 4.63 0.00 45.49 3.36
1396 1864 2.047465 AGCAGCAGCAAGGAGACG 60.047 61.111 3.17 0.00 45.49 4.18
1397 1865 2.047844 GCAGCAGCAAGGAGACGA 60.048 61.111 0.00 0.00 41.58 4.20
1398 1866 2.099431 GCAGCAGCAAGGAGACGAG 61.099 63.158 0.00 0.00 41.58 4.18
1399 1867 1.447489 CAGCAGCAAGGAGACGAGG 60.447 63.158 0.00 0.00 0.00 4.63
1400 1868 2.125350 GCAGCAAGGAGACGAGGG 60.125 66.667 0.00 0.00 0.00 4.30
1401 1869 2.581354 CAGCAAGGAGACGAGGGG 59.419 66.667 0.00 0.00 0.00 4.79
1613 2084 7.056635 CCTGTTGATCTATGTGGGATTTTAGT 58.943 38.462 0.00 0.00 0.00 2.24
1715 2292 8.466617 TGTGGTTCTATCTTAGAATCTACTCC 57.533 38.462 8.55 2.22 45.63 3.85
1716 2293 7.506261 TGTGGTTCTATCTTAGAATCTACTCCC 59.494 40.741 8.55 1.66 45.63 4.30
1717 2294 7.726738 GTGGTTCTATCTTAGAATCTACTCCCT 59.273 40.741 8.55 0.00 45.63 4.20
1718 2295 7.945664 TGGTTCTATCTTAGAATCTACTCCCTC 59.054 40.741 8.55 0.00 45.63 4.30
1719 2296 7.395206 GGTTCTATCTTAGAATCTACTCCCTCC 59.605 44.444 0.69 0.00 45.63 4.30
1720 2297 6.713276 TCTATCTTAGAATCTACTCCCTCCG 58.287 44.000 0.00 0.00 0.00 4.63
1721 2298 4.792513 TCTTAGAATCTACTCCCTCCGT 57.207 45.455 0.00 0.00 0.00 4.69
1722 2299 5.126699 TCTTAGAATCTACTCCCTCCGTT 57.873 43.478 0.00 0.00 0.00 4.44
1723 2300 5.131784 TCTTAGAATCTACTCCCTCCGTTC 58.868 45.833 0.00 0.00 0.00 3.95
1724 2301 2.668625 AGAATCTACTCCCTCCGTTCC 58.331 52.381 0.00 0.00 0.00 3.62
1725 2302 1.337387 GAATCTACTCCCTCCGTTCCG 59.663 57.143 0.00 0.00 0.00 4.30
1726 2303 0.549950 ATCTACTCCCTCCGTTCCGA 59.450 55.000 0.00 0.00 0.00 4.55
1727 2304 0.549950 TCTACTCCCTCCGTTCCGAT 59.450 55.000 0.00 0.00 0.00 4.18
1728 2305 1.064166 TCTACTCCCTCCGTTCCGATT 60.064 52.381 0.00 0.00 0.00 3.34
1729 2306 1.755380 CTACTCCCTCCGTTCCGATTT 59.245 52.381 0.00 0.00 0.00 2.17
1730 2307 1.856629 ACTCCCTCCGTTCCGATTTA 58.143 50.000 0.00 0.00 0.00 1.40
1731 2308 1.479730 ACTCCCTCCGTTCCGATTTAC 59.520 52.381 0.00 0.00 0.00 2.01
1732 2309 1.755380 CTCCCTCCGTTCCGATTTACT 59.245 52.381 0.00 0.00 0.00 2.24
1733 2310 2.167900 CTCCCTCCGTTCCGATTTACTT 59.832 50.000 0.00 0.00 0.00 2.24
1734 2311 2.093869 TCCCTCCGTTCCGATTTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
1735 2312 2.354403 CCCTCCGTTCCGATTTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
1736 2313 2.928116 CCTCCGTTCCGATTTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
1737 2314 2.597305 CTCCGTTCCGATTTACTTGTCG 59.403 50.000 0.00 0.00 37.58 4.35
1738 2315 2.030007 TCCGTTCCGATTTACTTGTCGT 60.030 45.455 0.00 0.00 36.17 4.34
1739 2316 2.091588 CCGTTCCGATTTACTTGTCGTG 59.908 50.000 0.00 0.00 36.17 4.35
1740 2317 2.091588 CGTTCCGATTTACTTGTCGTGG 59.908 50.000 0.00 0.00 36.17 4.94
1741 2318 3.062042 GTTCCGATTTACTTGTCGTGGT 58.938 45.455 0.00 0.00 36.17 4.16
1742 2319 3.389925 TCCGATTTACTTGTCGTGGTT 57.610 42.857 0.00 0.00 36.17 3.67
1743 2320 3.731089 TCCGATTTACTTGTCGTGGTTT 58.269 40.909 0.00 0.00 36.17 3.27
1744 2321 4.128643 TCCGATTTACTTGTCGTGGTTTT 58.871 39.130 0.00 0.00 36.17 2.43
1745 2322 5.295950 TCCGATTTACTTGTCGTGGTTTTA 58.704 37.500 0.00 0.00 36.17 1.52
1746 2323 5.406175 TCCGATTTACTTGTCGTGGTTTTAG 59.594 40.000 0.00 0.00 36.17 1.85
1747 2324 5.178067 CCGATTTACTTGTCGTGGTTTTAGT 59.822 40.000 0.00 0.00 36.17 2.24
1748 2325 6.293027 CCGATTTACTTGTCGTGGTTTTAGTT 60.293 38.462 0.00 0.00 36.17 2.24
1749 2326 6.788930 CGATTTACTTGTCGTGGTTTTAGTTC 59.211 38.462 0.00 0.00 33.42 3.01
1750 2327 6.981762 TTTACTTGTCGTGGTTTTAGTTCA 57.018 33.333 0.00 0.00 0.00 3.18
1751 2328 6.981762 TTACTTGTCGTGGTTTTAGTTCAA 57.018 33.333 0.00 0.00 0.00 2.69
1752 2329 5.883503 ACTTGTCGTGGTTTTAGTTCAAA 57.116 34.783 0.00 0.00 0.00 2.69
1753 2330 6.445357 ACTTGTCGTGGTTTTAGTTCAAAT 57.555 33.333 0.00 0.00 0.00 2.32
1754 2331 6.859017 ACTTGTCGTGGTTTTAGTTCAAATT 58.141 32.000 0.00 0.00 0.00 1.82
1755 2332 7.317390 ACTTGTCGTGGTTTTAGTTCAAATTT 58.683 30.769 0.00 0.00 0.00 1.82
1756 2333 8.460428 ACTTGTCGTGGTTTTAGTTCAAATTTA 58.540 29.630 0.00 0.00 0.00 1.40
1757 2334 8.844441 TTGTCGTGGTTTTAGTTCAAATTTAG 57.156 30.769 0.00 0.00 0.00 1.85
1758 2335 8.211116 TGTCGTGGTTTTAGTTCAAATTTAGA 57.789 30.769 0.00 0.00 0.00 2.10
1759 2336 8.675504 TGTCGTGGTTTTAGTTCAAATTTAGAA 58.324 29.630 0.00 0.00 0.00 2.10
1760 2337 8.950961 GTCGTGGTTTTAGTTCAAATTTAGAAC 58.049 33.333 18.14 18.14 44.32 3.01
1772 2349 8.950961 GTTCAAATTTAGAACTAAAACCACGAC 58.049 33.333 18.36 3.90 41.56 4.34
1773 2350 7.346695 TCAAATTTAGAACTAAAACCACGACG 58.653 34.615 10.38 0.00 38.38 5.12
1774 2351 7.224362 TCAAATTTAGAACTAAAACCACGACGA 59.776 33.333 0.00 0.00 38.38 4.20
1775 2352 6.701432 ATTTAGAACTAAAACCACGACGAG 57.299 37.500 0.00 0.00 38.38 4.18
1776 2353 3.722728 AGAACTAAAACCACGACGAGT 57.277 42.857 0.00 0.00 0.00 4.18
1777 2354 4.836125 AGAACTAAAACCACGACGAGTA 57.164 40.909 0.00 0.00 0.00 2.59
1778 2355 5.186996 AGAACTAAAACCACGACGAGTAA 57.813 39.130 0.00 0.00 0.00 2.24
1779 2356 5.591099 AGAACTAAAACCACGACGAGTAAA 58.409 37.500 0.00 0.00 0.00 2.01
1780 2357 6.218746 AGAACTAAAACCACGACGAGTAAAT 58.781 36.000 0.00 0.00 0.00 1.40
1781 2358 6.364435 AGAACTAAAACCACGACGAGTAAATC 59.636 38.462 0.00 0.00 0.00 2.17
1782 2359 5.531634 ACTAAAACCACGACGAGTAAATCA 58.468 37.500 0.00 0.00 0.00 2.57
1783 2360 4.985044 AAAACCACGACGAGTAAATCAG 57.015 40.909 0.00 0.00 0.00 2.90
1784 2361 3.928727 AACCACGACGAGTAAATCAGA 57.071 42.857 0.00 0.00 0.00 3.27
1785 2362 3.928727 ACCACGACGAGTAAATCAGAA 57.071 42.857 0.00 0.00 0.00 3.02
1786 2363 3.572584 ACCACGACGAGTAAATCAGAAC 58.427 45.455 0.00 0.00 0.00 3.01
1787 2364 2.592897 CCACGACGAGTAAATCAGAACG 59.407 50.000 0.00 0.00 0.00 3.95
1788 2365 2.592897 CACGACGAGTAAATCAGAACGG 59.407 50.000 0.00 0.00 0.00 4.44
1789 2366 2.485426 ACGACGAGTAAATCAGAACGGA 59.515 45.455 0.00 0.00 0.00 4.69
1790 2367 3.099362 CGACGAGTAAATCAGAACGGAG 58.901 50.000 0.00 0.00 0.00 4.63
1791 2368 3.436496 GACGAGTAAATCAGAACGGAGG 58.564 50.000 0.00 0.00 0.00 4.30
1792 2369 2.165845 ACGAGTAAATCAGAACGGAGGG 59.834 50.000 0.00 0.00 0.00 4.30
1793 2370 2.426024 CGAGTAAATCAGAACGGAGGGA 59.574 50.000 0.00 0.00 0.00 4.20
1794 2371 3.489398 CGAGTAAATCAGAACGGAGGGAG 60.489 52.174 0.00 0.00 0.00 4.30
1795 2372 3.442076 AGTAAATCAGAACGGAGGGAGT 58.558 45.455 0.00 0.00 0.00 3.85
1796 2373 4.607239 AGTAAATCAGAACGGAGGGAGTA 58.393 43.478 0.00 0.00 0.00 2.59
1799 2376 2.893215 TCAGAACGGAGGGAGTAGAA 57.107 50.000 0.00 0.00 0.00 2.10
1841 2418 5.782925 AGTAGGATGAGATTCCTAGGTTGT 58.217 41.667 9.08 0.00 46.57 3.32
1842 2419 5.836358 AGTAGGATGAGATTCCTAGGTTGTC 59.164 44.000 9.08 6.67 46.57 3.18
1920 2512 6.296026 ACACCTACTCAACAATTAAGCTTCA 58.704 36.000 0.00 0.00 0.00 3.02
1961 4838 4.161377 AGTCAGCTCTTTCCTGAGAATACC 59.839 45.833 0.00 0.00 39.79 2.73
2023 4997 3.977427 AGTTTTTCACGGAGATTTTGCC 58.023 40.909 0.00 0.00 0.00 4.52
2024 4998 3.383185 AGTTTTTCACGGAGATTTTGCCA 59.617 39.130 0.00 0.00 0.00 4.92
2183 5385 5.312443 AGTCCTATTTCTGTTTAGGTGGGTT 59.688 40.000 0.00 0.00 37.00 4.11
2212 5414 4.357918 TGGAGTTGAAGAAAGGAAGAGG 57.642 45.455 0.00 0.00 0.00 3.69
2425 5630 4.819630 TGGTTGACAACTTCAGGTGATAAC 59.180 41.667 17.52 3.58 34.94 1.89
2463 5668 9.430623 TGACTGTTTTCATCATTAATCGAGTAA 57.569 29.630 7.89 7.89 0.00 2.24
2477 5682 6.642683 AATCGAGTAACCACTTGAAATACG 57.357 37.500 0.00 0.00 46.18 3.06
2502 5707 6.255670 GCTGGTTCGAATGAGTTTTTCTTTTT 59.744 34.615 0.00 0.00 0.00 1.94
2503 5708 7.515215 GCTGGTTCGAATGAGTTTTTCTTTTTC 60.515 37.037 0.00 0.00 0.00 2.29
2561 5769 5.416639 TCCCATCTGAATGTGAAACTGATTG 59.583 40.000 0.00 0.00 38.04 2.67
2564 5772 6.805271 CCATCTGAATGTGAAACTGATTGAAC 59.195 38.462 0.00 0.00 38.04 3.18
2657 5865 2.813754 CAAAGTTCGTCACCATGGACAT 59.186 45.455 21.47 0.00 37.66 3.06
2666 5877 4.620567 CGTCACCATGGACATGAAGAGTTA 60.621 45.833 21.47 0.00 41.20 2.24
2705 5916 7.062371 GGAGTTGCTTATATATGCTAACTGACG 59.938 40.741 25.42 0.00 33.89 4.35
2873 6485 7.645340 ACAGTTACACAGTAAGTACAAACGTAG 59.355 37.037 0.00 0.00 0.00 3.51
2923 6547 4.142609 ACAATTATCTGCGGTGATCACT 57.857 40.909 24.50 7.02 0.00 3.41
2924 6548 5.276461 ACAATTATCTGCGGTGATCACTA 57.724 39.130 24.50 11.05 0.00 2.74
2925 6549 5.858381 ACAATTATCTGCGGTGATCACTAT 58.142 37.500 24.50 12.80 0.00 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.905676 ATCCACTGCCCCTCTCCCTC 62.906 65.000 0.00 0.00 0.00 4.30
1 2 2.498820 AATCCACTGCCCCTCTCCCT 62.499 60.000 0.00 0.00 0.00 4.20
2 3 0.694444 TAATCCACTGCCCCTCTCCC 60.694 60.000 0.00 0.00 0.00 4.30
3 4 0.761802 CTAATCCACTGCCCCTCTCC 59.238 60.000 0.00 0.00 0.00 3.71
4 5 0.761802 CCTAATCCACTGCCCCTCTC 59.238 60.000 0.00 0.00 0.00 3.20
5 6 0.044855 ACCTAATCCACTGCCCCTCT 59.955 55.000 0.00 0.00 0.00 3.69
6 7 0.181350 CACCTAATCCACTGCCCCTC 59.819 60.000 0.00 0.00 0.00 4.30
7 8 1.281925 CCACCTAATCCACTGCCCCT 61.282 60.000 0.00 0.00 0.00 4.79
8 9 1.227383 CCACCTAATCCACTGCCCC 59.773 63.158 0.00 0.00 0.00 5.80
9 10 0.846693 ATCCACCTAATCCACTGCCC 59.153 55.000 0.00 0.00 0.00 5.36
10 11 1.771255 AGATCCACCTAATCCACTGCC 59.229 52.381 0.00 0.00 0.00 4.85
11 12 2.435805 TGAGATCCACCTAATCCACTGC 59.564 50.000 0.00 0.00 0.00 4.40
12 13 3.963374 TCTGAGATCCACCTAATCCACTG 59.037 47.826 0.00 0.00 0.00 3.66
13 14 4.271807 TCTGAGATCCACCTAATCCACT 57.728 45.455 0.00 0.00 0.00 4.00
14 15 5.559148 AATCTGAGATCCACCTAATCCAC 57.441 43.478 0.00 0.00 0.00 4.02
15 16 5.782331 CCTAATCTGAGATCCACCTAATCCA 59.218 44.000 0.00 0.00 0.00 3.41
16 17 5.337975 GCCTAATCTGAGATCCACCTAATCC 60.338 48.000 0.00 0.00 0.00 3.01
17 18 5.483583 AGCCTAATCTGAGATCCACCTAATC 59.516 44.000 0.00 0.00 0.00 1.75
18 19 5.248020 CAGCCTAATCTGAGATCCACCTAAT 59.752 44.000 0.00 0.00 36.19 1.73
19 20 4.590647 CAGCCTAATCTGAGATCCACCTAA 59.409 45.833 0.00 0.00 36.19 2.69
20 21 4.140924 TCAGCCTAATCTGAGATCCACCTA 60.141 45.833 0.00 0.00 38.11 3.08
21 22 2.971330 CAGCCTAATCTGAGATCCACCT 59.029 50.000 0.00 0.00 36.19 4.00
22 23 2.968574 TCAGCCTAATCTGAGATCCACC 59.031 50.000 0.00 0.00 38.11 4.61
23 24 4.888326 ATCAGCCTAATCTGAGATCCAC 57.112 45.455 0.00 0.00 45.22 4.02
24 25 4.774726 GGTATCAGCCTAATCTGAGATCCA 59.225 45.833 0.00 0.00 45.22 3.41
25 26 4.774726 TGGTATCAGCCTAATCTGAGATCC 59.225 45.833 0.00 0.00 45.22 3.36
26 27 5.991933 TGGTATCAGCCTAATCTGAGATC 57.008 43.478 0.00 0.00 45.22 2.75
27 28 8.484575 CAATATGGTATCAGCCTAATCTGAGAT 58.515 37.037 0.00 0.00 45.22 2.75
28 29 7.093156 CCAATATGGTATCAGCCTAATCTGAGA 60.093 40.741 0.00 0.00 38.38 3.27
29 30 7.046652 CCAATATGGTATCAGCCTAATCTGAG 58.953 42.308 0.00 0.00 38.38 3.35
30 31 6.730507 TCCAATATGGTATCAGCCTAATCTGA 59.269 38.462 0.00 0.00 41.75 3.27
31 32 6.950842 TCCAATATGGTATCAGCCTAATCTG 58.049 40.000 0.00 0.00 39.03 2.90
32 33 6.352565 GCTCCAATATGGTATCAGCCTAATCT 60.353 42.308 0.00 0.00 39.03 2.40
33 34 5.819901 GCTCCAATATGGTATCAGCCTAATC 59.180 44.000 0.00 0.00 39.03 1.75
34 35 5.339530 GGCTCCAATATGGTATCAGCCTAAT 60.340 44.000 15.81 0.00 45.37 1.73
35 36 4.019321 GGCTCCAATATGGTATCAGCCTAA 60.019 45.833 15.81 0.00 45.37 2.69
36 37 3.519510 GGCTCCAATATGGTATCAGCCTA 59.480 47.826 15.81 0.00 45.37 3.93
37 38 2.307098 GGCTCCAATATGGTATCAGCCT 59.693 50.000 15.81 0.00 45.37 4.58
38 39 2.716217 GGCTCCAATATGGTATCAGCC 58.284 52.381 10.10 10.10 43.61 4.85
39 40 3.008375 TCTGGCTCCAATATGGTATCAGC 59.992 47.826 0.00 0.00 39.03 4.26
40 41 4.829968 CTCTGGCTCCAATATGGTATCAG 58.170 47.826 0.00 3.52 39.03 2.90
41 42 3.008375 GCTCTGGCTCCAATATGGTATCA 59.992 47.826 0.00 0.00 39.03 2.15
42 43 3.604582 GCTCTGGCTCCAATATGGTATC 58.395 50.000 0.00 0.00 39.03 2.24
43 44 2.027745 CGCTCTGGCTCCAATATGGTAT 60.028 50.000 0.00 0.00 39.03 2.73
44 45 1.344438 CGCTCTGGCTCCAATATGGTA 59.656 52.381 0.00 0.00 39.03 3.25
45 46 0.107456 CGCTCTGGCTCCAATATGGT 59.893 55.000 0.00 0.00 39.03 3.55
46 47 0.394192 TCGCTCTGGCTCCAATATGG 59.606 55.000 0.00 0.00 39.43 2.74
47 48 1.069823 ACTCGCTCTGGCTCCAATATG 59.930 52.381 0.00 0.00 36.09 1.78
48 49 1.418334 ACTCGCTCTGGCTCCAATAT 58.582 50.000 0.00 0.00 36.09 1.28
84 85 2.811431 TCAATACAAGGAAGGTTGCACG 59.189 45.455 0.00 0.00 0.00 5.34
124 125 5.808540 GTGTCAGTTGAGCCGTGTATATAAA 59.191 40.000 0.00 0.00 0.00 1.40
135 136 1.599542 GTTGAGTGTGTCAGTTGAGCC 59.400 52.381 0.00 0.00 36.21 4.70
205 206 7.070696 AGCCACATATGTCTACCAATAGTGTTA 59.929 37.037 5.07 0.00 0.00 2.41
207 208 5.366768 AGCCACATATGTCTACCAATAGTGT 59.633 40.000 5.07 0.00 0.00 3.55
208 209 5.858381 AGCCACATATGTCTACCAATAGTG 58.142 41.667 5.07 0.00 0.00 2.74
215 216 4.960938 TGATTGAGCCACATATGTCTACC 58.039 43.478 5.07 0.00 0.00 3.18
295 296 4.777366 CCCTGTAATGGGGTTCATCTTTTT 59.223 41.667 0.00 0.00 43.45 1.94
318 388 1.824230 TGCTCACCATGTAAAATGGGC 59.176 47.619 9.10 3.73 43.32 5.36
346 423 0.179092 GCCGCACGTAGGGTAATTCT 60.179 55.000 10.71 0.00 0.00 2.40
358 435 4.270084 CAGTATAATATAATGGGCCGCACG 59.730 45.833 0.00 0.00 0.00 5.34
392 469 2.699954 AGTGGTTTCGGCTGATTACTG 58.300 47.619 0.00 0.00 0.00 2.74
402 479 7.603024 AGAGTTCTTCTTAATTAGTGGTTTCGG 59.397 37.037 0.00 0.00 29.61 4.30
432 509 5.044179 ACATGGGAGGTGGAAATCATCTTTA 60.044 40.000 0.00 0.00 36.86 1.85
443 520 0.909610 GTCCTGACATGGGAGGTGGA 60.910 60.000 11.06 1.25 33.04 4.02
459 536 2.126346 GCAATGCGCCACTTGTCC 60.126 61.111 4.18 0.00 32.94 4.02
552 753 9.778993 AACGATTCAAGATTTAGACAAATGATG 57.221 29.630 0.00 0.00 34.44 3.07
557 758 9.445786 GTGAAAACGATTCAAGATTTAGACAAA 57.554 29.630 9.38 0.00 0.00 2.83
560 761 8.283291 ACAGTGAAAACGATTCAAGATTTAGAC 58.717 33.333 9.38 0.00 0.00 2.59
561 762 8.378172 ACAGTGAAAACGATTCAAGATTTAGA 57.622 30.769 9.38 0.00 0.00 2.10
562 763 8.895845 CAACAGTGAAAACGATTCAAGATTTAG 58.104 33.333 9.38 0.58 0.00 1.85
563 764 8.616942 TCAACAGTGAAAACGATTCAAGATTTA 58.383 29.630 9.38 0.00 0.00 1.40
571 772 7.914537 AAGAATTCAACAGTGAAAACGATTC 57.085 32.000 8.44 0.00 46.66 2.52
589 790 5.060662 TCAAGATCTCGACGTGAAGAATT 57.939 39.130 3.45 0.00 0.00 2.17
597 798 6.866770 TGATTTAGTTTTCAAGATCTCGACGT 59.133 34.615 0.00 0.00 0.00 4.34
607 808 9.318041 CTATTGACGTGTGATTTAGTTTTCAAG 57.682 33.333 0.00 0.00 0.00 3.02
610 811 7.803724 ACCTATTGACGTGTGATTTAGTTTTC 58.196 34.615 0.00 0.00 0.00 2.29
652 989 7.432252 CGTCTTTCAGCTTTTTAGATGTTTTGT 59.568 33.333 0.00 0.00 0.00 2.83
653 990 7.565789 GCGTCTTTCAGCTTTTTAGATGTTTTG 60.566 37.037 0.00 0.00 0.00 2.44
654 991 6.417930 GCGTCTTTCAGCTTTTTAGATGTTTT 59.582 34.615 0.00 0.00 0.00 2.43
655 992 5.915196 GCGTCTTTCAGCTTTTTAGATGTTT 59.085 36.000 0.00 0.00 0.00 2.83
656 993 5.452777 GCGTCTTTCAGCTTTTTAGATGTT 58.547 37.500 0.00 0.00 0.00 2.71
685 1022 5.716094 AGCGTCACTTGGTTTTTAGTTTTT 58.284 33.333 0.00 0.00 0.00 1.94
690 1027 4.319549 GGAAGAGCGTCACTTGGTTTTTAG 60.320 45.833 0.00 0.00 0.00 1.85
696 1033 0.034059 CTGGAAGAGCGTCACTTGGT 59.966 55.000 0.00 0.00 34.07 3.67
712 1049 4.684134 CACTTGGGGGTGGGCTGG 62.684 72.222 0.00 0.00 33.95 4.85
729 1066 2.431419 GTTACTACTTCAGGAGCCTCCC 59.569 54.545 7.26 0.00 37.19 4.30
739 1076 6.817184 AGAACAGCTTTGAGTTACTACTTCA 58.183 36.000 0.00 0.00 33.84 3.02
787 1124 4.705507 TCGGAGTAGTCAGCTATGAGTTTT 59.294 41.667 0.00 0.00 39.81 2.43
788 1125 4.270834 TCGGAGTAGTCAGCTATGAGTTT 58.729 43.478 0.00 0.00 39.81 2.66
791 1128 3.252215 CCTTCGGAGTAGTCAGCTATGAG 59.748 52.174 0.00 0.00 35.66 2.90
792 1129 3.215151 CCTTCGGAGTAGTCAGCTATGA 58.785 50.000 0.00 0.00 0.00 2.15
807 1144 2.478335 TTAGTTGCTGGGCCCTTCGG 62.478 60.000 25.70 11.63 0.00 4.30
808 1164 0.394352 ATTAGTTGCTGGGCCCTTCG 60.394 55.000 25.70 12.70 0.00 3.79
810 1166 0.033109 GGATTAGTTGCTGGGCCCTT 60.033 55.000 25.70 4.04 0.00 3.95
855 1230 0.320374 TCCTTGTGGAATTCGTCGCT 59.680 50.000 0.00 0.00 39.87 4.93
1011 1402 1.881252 GTTGCCGCGGTACATCGAT 60.881 57.895 28.70 0.00 0.00 3.59
1243 1634 2.765356 CCTGATGCTGCTGCTGCTG 61.765 63.158 27.67 16.73 40.48 4.41
1319 1781 1.081092 CCCTGTCCCTCTTCCTCCA 59.919 63.158 0.00 0.00 0.00 3.86
1362 1830 3.997064 CTGCTCGTCTTGCCCCTCG 62.997 68.421 0.00 0.00 0.00 4.63
1399 1867 2.040359 CTCCCCCTCTTCTCCCCC 60.040 72.222 0.00 0.00 0.00 5.40
1400 1868 2.770475 GCTCCCCCTCTTCTCCCC 60.770 72.222 0.00 0.00 0.00 4.81
1401 1869 2.041265 TGCTCCCCCTCTTCTCCC 59.959 66.667 0.00 0.00 0.00 4.30
1613 2084 2.754552 GTCATTGTTAGCAGGATGGCAA 59.245 45.455 0.00 0.00 35.86 4.52
1666 2230 7.385205 ACATAATACCATGACGAGTAGCAATTC 59.615 37.037 0.00 0.00 0.00 2.17
1720 2297 3.062042 ACCACGACAAGTAAATCGGAAC 58.938 45.455 0.00 0.00 42.67 3.62
1721 2298 3.389925 ACCACGACAAGTAAATCGGAA 57.610 42.857 0.00 0.00 42.67 4.30
1722 2299 3.389925 AACCACGACAAGTAAATCGGA 57.610 42.857 0.00 0.00 42.67 4.55
1723 2300 4.477302 AAAACCACGACAAGTAAATCGG 57.523 40.909 0.00 0.00 42.67 4.18
1724 2301 6.219302 ACTAAAACCACGACAAGTAAATCG 57.781 37.500 0.00 0.00 43.97 3.34
1725 2302 7.632721 TGAACTAAAACCACGACAAGTAAATC 58.367 34.615 0.00 0.00 0.00 2.17
1726 2303 7.556733 TGAACTAAAACCACGACAAGTAAAT 57.443 32.000 0.00 0.00 0.00 1.40
1727 2304 6.981762 TGAACTAAAACCACGACAAGTAAA 57.018 33.333 0.00 0.00 0.00 2.01
1728 2305 6.981762 TTGAACTAAAACCACGACAAGTAA 57.018 33.333 0.00 0.00 0.00 2.24
1729 2306 6.981762 TTTGAACTAAAACCACGACAAGTA 57.018 33.333 0.00 0.00 0.00 2.24
1730 2307 5.883503 TTTGAACTAAAACCACGACAAGT 57.116 34.783 0.00 0.00 0.00 3.16
1731 2308 7.749539 AAATTTGAACTAAAACCACGACAAG 57.250 32.000 0.00 0.00 0.00 3.16
1732 2309 8.675504 TCTAAATTTGAACTAAAACCACGACAA 58.324 29.630 0.00 0.00 0.00 3.18
1733 2310 8.211116 TCTAAATTTGAACTAAAACCACGACA 57.789 30.769 0.00 0.00 0.00 4.35
1734 2311 8.950961 GTTCTAAATTTGAACTAAAACCACGAC 58.049 33.333 18.36 0.00 40.23 4.34
1746 2323 8.950961 GTCGTGGTTTTAGTTCTAAATTTGAAC 58.049 33.333 18.14 18.14 42.77 3.18
1747 2324 7.851963 CGTCGTGGTTTTAGTTCTAAATTTGAA 59.148 33.333 0.00 0.23 0.00 2.69
1748 2325 7.224362 TCGTCGTGGTTTTAGTTCTAAATTTGA 59.776 33.333 0.00 0.00 0.00 2.69
1749 2326 7.346695 TCGTCGTGGTTTTAGTTCTAAATTTG 58.653 34.615 0.00 0.00 0.00 2.32
1750 2327 7.225341 ACTCGTCGTGGTTTTAGTTCTAAATTT 59.775 33.333 5.95 0.00 0.00 1.82
1751 2328 6.703165 ACTCGTCGTGGTTTTAGTTCTAAATT 59.297 34.615 5.95 0.00 0.00 1.82
1752 2329 6.218746 ACTCGTCGTGGTTTTAGTTCTAAAT 58.781 36.000 5.95 0.00 0.00 1.40
1753 2330 5.591099 ACTCGTCGTGGTTTTAGTTCTAAA 58.409 37.500 1.47 1.47 0.00 1.85
1754 2331 5.186996 ACTCGTCGTGGTTTTAGTTCTAA 57.813 39.130 0.00 0.00 0.00 2.10
1755 2332 4.836125 ACTCGTCGTGGTTTTAGTTCTA 57.164 40.909 0.00 0.00 0.00 2.10
1756 2333 3.722728 ACTCGTCGTGGTTTTAGTTCT 57.277 42.857 0.00 0.00 0.00 3.01
1757 2334 5.888412 TTTACTCGTCGTGGTTTTAGTTC 57.112 39.130 0.00 0.00 0.00 3.01
1758 2335 5.984926 TGATTTACTCGTCGTGGTTTTAGTT 59.015 36.000 0.00 0.00 0.00 2.24
1759 2336 5.531634 TGATTTACTCGTCGTGGTTTTAGT 58.468 37.500 0.00 0.00 0.00 2.24
1760 2337 5.860182 TCTGATTTACTCGTCGTGGTTTTAG 59.140 40.000 0.00 0.00 0.00 1.85
1761 2338 5.771469 TCTGATTTACTCGTCGTGGTTTTA 58.229 37.500 0.00 0.00 0.00 1.52
1762 2339 4.624015 TCTGATTTACTCGTCGTGGTTTT 58.376 39.130 0.00 0.00 0.00 2.43
1763 2340 4.247267 TCTGATTTACTCGTCGTGGTTT 57.753 40.909 0.00 0.00 0.00 3.27
1764 2341 3.928727 TCTGATTTACTCGTCGTGGTT 57.071 42.857 0.00 0.00 0.00 3.67
1765 2342 3.572584 GTTCTGATTTACTCGTCGTGGT 58.427 45.455 0.00 0.00 0.00 4.16
1766 2343 2.592897 CGTTCTGATTTACTCGTCGTGG 59.407 50.000 0.00 0.00 0.00 4.94
1767 2344 2.592897 CCGTTCTGATTTACTCGTCGTG 59.407 50.000 0.00 0.00 0.00 4.35
1768 2345 2.485426 TCCGTTCTGATTTACTCGTCGT 59.515 45.455 0.00 0.00 0.00 4.34
1769 2346 3.099362 CTCCGTTCTGATTTACTCGTCG 58.901 50.000 0.00 0.00 0.00 5.12
1770 2347 3.436496 CCTCCGTTCTGATTTACTCGTC 58.564 50.000 0.00 0.00 0.00 4.20
1771 2348 2.165845 CCCTCCGTTCTGATTTACTCGT 59.834 50.000 0.00 0.00 0.00 4.18
1772 2349 2.426024 TCCCTCCGTTCTGATTTACTCG 59.574 50.000 0.00 0.00 0.00 4.18
1773 2350 3.447944 ACTCCCTCCGTTCTGATTTACTC 59.552 47.826 0.00 0.00 0.00 2.59
1774 2351 3.442076 ACTCCCTCCGTTCTGATTTACT 58.558 45.455 0.00 0.00 0.00 2.24
1775 2352 3.889520 ACTCCCTCCGTTCTGATTTAC 57.110 47.619 0.00 0.00 0.00 2.01
1776 2353 4.863548 TCTACTCCCTCCGTTCTGATTTA 58.136 43.478 0.00 0.00 0.00 1.40
1777 2354 3.709587 TCTACTCCCTCCGTTCTGATTT 58.290 45.455 0.00 0.00 0.00 2.17
1778 2355 3.383698 TCTACTCCCTCCGTTCTGATT 57.616 47.619 0.00 0.00 0.00 2.57
1779 2356 3.383698 TTCTACTCCCTCCGTTCTGAT 57.616 47.619 0.00 0.00 0.00 2.90
1780 2357 2.893215 TTCTACTCCCTCCGTTCTGA 57.107 50.000 0.00 0.00 0.00 3.27
1781 2358 4.473477 AAATTCTACTCCCTCCGTTCTG 57.527 45.455 0.00 0.00 0.00 3.02
1782 2359 5.395435 GCTAAAATTCTACTCCCTCCGTTCT 60.395 44.000 0.00 0.00 0.00 3.01
1783 2360 4.809958 GCTAAAATTCTACTCCCTCCGTTC 59.190 45.833 0.00 0.00 0.00 3.95
1784 2361 4.224370 TGCTAAAATTCTACTCCCTCCGTT 59.776 41.667 0.00 0.00 0.00 4.44
1785 2362 3.773119 TGCTAAAATTCTACTCCCTCCGT 59.227 43.478 0.00 0.00 0.00 4.69
1786 2363 4.120589 GTGCTAAAATTCTACTCCCTCCG 58.879 47.826 0.00 0.00 0.00 4.63
1787 2364 5.099042 TGTGCTAAAATTCTACTCCCTCC 57.901 43.478 0.00 0.00 0.00 4.30
1788 2365 6.599638 ACAATGTGCTAAAATTCTACTCCCTC 59.400 38.462 0.00 0.00 0.00 4.30
1789 2366 6.485171 ACAATGTGCTAAAATTCTACTCCCT 58.515 36.000 0.00 0.00 0.00 4.20
1790 2367 6.759497 ACAATGTGCTAAAATTCTACTCCC 57.241 37.500 0.00 0.00 0.00 4.30
1791 2368 7.029563 CCAACAATGTGCTAAAATTCTACTCC 58.970 38.462 0.00 0.00 0.00 3.85
1792 2369 7.816640 TCCAACAATGTGCTAAAATTCTACTC 58.183 34.615 0.00 0.00 0.00 2.59
1793 2370 7.759489 TCCAACAATGTGCTAAAATTCTACT 57.241 32.000 0.00 0.00 0.00 2.57
1794 2371 8.082242 ACTTCCAACAATGTGCTAAAATTCTAC 58.918 33.333 0.00 0.00 0.00 2.59
1795 2372 8.177119 ACTTCCAACAATGTGCTAAAATTCTA 57.823 30.769 0.00 0.00 0.00 2.10
1796 2373 7.054491 ACTTCCAACAATGTGCTAAAATTCT 57.946 32.000 0.00 0.00 0.00 2.40
1799 2376 6.719370 TCCTACTTCCAACAATGTGCTAAAAT 59.281 34.615 0.00 0.00 0.00 1.82
1841 2418 1.071699 CCAACCCAGAAACGGAAGAGA 59.928 52.381 0.00 0.00 0.00 3.10
1842 2419 1.071699 TCCAACCCAGAAACGGAAGAG 59.928 52.381 0.00 0.00 0.00 2.85
1920 2512 2.105006 CTGTTGTCCAGTGCAGCTAT 57.895 50.000 0.00 0.00 36.37 2.97
1961 4838 6.260714 TGTTCAGCAGCAACCAGTAATATATG 59.739 38.462 0.00 0.00 0.00 1.78
2023 4997 3.567164 ACTCAGGAATCACAAAGCACTTG 59.433 43.478 0.00 0.00 41.19 3.16
2024 4998 3.825328 ACTCAGGAATCACAAAGCACTT 58.175 40.909 0.00 0.00 0.00 3.16
2135 5132 7.122650 ACTCAGAGGTCTAGATGAAAAAGAGAG 59.877 40.741 1.53 0.00 0.00 3.20
2183 5385 5.309543 TCCTTTCTTCAACTCCATCAGGTTA 59.690 40.000 0.00 0.00 35.89 2.85
2212 5414 1.070758 TCCAGCTTGTCAGTCAACTCC 59.929 52.381 0.00 0.00 32.18 3.85
2284 5489 5.463061 CGGCAGTCAAAACAATGAGAAAATT 59.537 36.000 0.00 0.00 0.00 1.82
2285 5490 4.984161 CGGCAGTCAAAACAATGAGAAAAT 59.016 37.500 0.00 0.00 0.00 1.82
2286 5491 4.358851 CGGCAGTCAAAACAATGAGAAAA 58.641 39.130 0.00 0.00 0.00 2.29
2425 5630 3.691049 AAACAGTCAAATCCACACACG 57.309 42.857 0.00 0.00 0.00 4.49
2463 5668 2.561478 ACCAGCGTATTTCAAGTGGT 57.439 45.000 0.00 0.00 33.35 4.16
2477 5682 4.489679 AGAAAAACTCATTCGAACCAGC 57.510 40.909 0.00 0.00 32.04 4.85
2620 5828 8.918961 ACGAACTTTGTACAATTCAAAATTGA 57.081 26.923 17.71 0.00 34.96 2.57
2621 5829 8.802856 TGACGAACTTTGTACAATTCAAAATTG 58.197 29.630 17.71 10.13 34.96 2.32
2622 5830 8.803799 GTGACGAACTTTGTACAATTCAAAATT 58.196 29.630 17.71 0.00 34.96 1.82
2623 5831 7.434013 GGTGACGAACTTTGTACAATTCAAAAT 59.566 33.333 17.71 4.58 34.96 1.82
2624 5832 6.748198 GGTGACGAACTTTGTACAATTCAAAA 59.252 34.615 17.71 0.12 34.96 2.44
2657 5865 7.665559 ACTCCAATTACTTTGCATAACTCTTCA 59.334 33.333 0.00 0.00 33.73 3.02
2666 5877 5.473066 AAGCAACTCCAATTACTTTGCAT 57.527 34.783 12.91 2.19 44.06 3.96
2705 5916 3.151554 ACAAATTCCACCCGGTTCTTAC 58.848 45.455 0.00 0.00 0.00 2.34
2764 5975 8.507249 ACATGTTTGATAAAGAGAGTAACAAGC 58.493 33.333 0.00 0.00 0.00 4.01
2822 6316 0.525311 TTGCATATGTGGCAACGTGG 59.475 50.000 4.29 0.00 45.57 4.94
2848 6460 6.817270 ACGTTTGTACTTACTGTGTAACTG 57.183 37.500 0.00 0.00 42.04 3.16
2873 6485 2.947938 ATAGAGCATGCGGCCACCAC 62.948 60.000 13.01 0.00 46.50 4.16


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

AutoCloner maintained by Alex Coulton.