Multiple sequence alignment - TraesCS5B01G183300

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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 TraesCS5B01G183300 chr5B 100.000 6498 0 0 1 6498 333257747 333251250 0.000000e+00 12000.0
1 TraesCS5B01G183300 chr5D 90.015 3385 177 59 2909 6246 292697984 292694714 0.000000e+00 4229.0
2 TraesCS5B01G183300 chr5D 94.742 1959 82 13 1 1948 292699918 292697970 0.000000e+00 3027.0
3 TraesCS5B01G183300 chr5D 85.714 168 18 6 1949 2114 447775335 447775172 8.660000e-39 172.0
4 TraesCS5B01G183300 chr5D 100.000 29 0 0 1968 1996 548104582 548104554 3.000000e-03 54.7
5 TraesCS5B01G183300 chr5A 92.517 1911 93 23 21 1910 385399704 385397823 0.000000e+00 2691.0
6 TraesCS5B01G183300 chr5A 82.624 1410 159 43 3228 4589 385397422 385396051 0.000000e+00 1168.0
7 TraesCS5B01G183300 chr5A 89.269 643 44 11 5863 6498 385395345 385394721 0.000000e+00 782.0
8 TraesCS5B01G183300 chr5A 93.254 504 32 1 5112 5615 385395847 385395346 0.000000e+00 741.0
9 TraesCS5B01G183300 chr5A 84.000 425 53 12 4659 5075 579918682 579919099 1.700000e-105 394.0
10 TraesCS5B01G183300 chr5A 83.841 427 50 14 4659 5075 579869394 579869811 7.900000e-104 388.0
11 TraesCS5B01G183300 chr5A 83.255 424 58 11 4659 5075 579855478 579855895 1.710000e-100 377.0
12 TraesCS5B01G183300 chr5A 86.103 331 24 12 2913 3222 385397823 385397494 2.900000e-88 337.0
13 TraesCS5B01G183300 chr2B 91.520 967 68 11 1949 2913 613221721 613222675 0.000000e+00 1319.0
14 TraesCS5B01G183300 chr2B 86.159 578 61 9 2346 2918 765789971 765790534 2.000000e-169 606.0
15 TraesCS5B01G183300 chr2B 87.218 266 32 2 1614 1877 548651208 548651473 1.060000e-77 302.0
16 TraesCS5B01G183300 chr2B 81.579 342 60 1 5160 5498 548651498 548651839 4.960000e-71 279.0
17 TraesCS5B01G183300 chr2B 85.200 250 37 0 1275 1524 548650866 548651115 2.320000e-64 257.0
18 TraesCS5B01G183300 chr1B 83.486 654 78 11 2273 2921 478575458 478574830 3.380000e-162 582.0
19 TraesCS5B01G183300 chr1B 84.706 425 47 13 4662 5078 38888174 38888588 6.060000e-110 409.0
20 TraesCS5B01G183300 chr1B 89.058 329 30 4 4754 5079 263981352 263981677 2.820000e-108 403.0
21 TraesCS5B01G183300 chr2A 81.759 614 95 15 1275 1877 611310539 611311146 1.260000e-136 497.0
22 TraesCS5B01G183300 chr2A 82.507 343 55 3 5160 5498 611311171 611311512 4.930000e-76 296.0
23 TraesCS5B01G183300 chr2D 81.433 614 97 13 1275 1877 470000146 470000753 2.720000e-133 486.0
24 TraesCS5B01G183300 chr2D 82.799 343 54 3 5160 5498 470000778 470001119 1.060000e-77 302.0
25 TraesCS5B01G183300 chr2D 87.805 164 19 1 2106 2269 624048408 624048570 2.390000e-44 191.0
26 TraesCS5B01G183300 chr1D 86.111 432 43 13 4657 5074 58568130 58567702 3.570000e-122 449.0
27 TraesCS5B01G183300 chr1D 78.497 386 64 17 2541 2917 452494662 452494287 1.090000e-57 235.0
28 TraesCS5B01G183300 chr1D 82.609 230 31 8 2302 2530 477432828 477432607 1.850000e-45 195.0
29 TraesCS5B01G183300 chr1D 75.538 372 63 15 2551 2916 471437421 471437770 2.430000e-34 158.0
30 TraesCS5B01G183300 chr1D 86.525 141 16 2 2106 2245 477432592 477432454 1.130000e-32 152.0
31 TraesCS5B01G183300 chr7D 84.742 426 52 10 4661 5079 631955945 631956364 1.300000e-111 414.0
32 TraesCS5B01G183300 chr7D 86.704 361 39 7 2566 2923 619102275 619101921 6.110000e-105 392.0
33 TraesCS5B01G183300 chr7D 100.000 29 0 0 1968 1996 139002415 139002387 3.000000e-03 54.7
34 TraesCS5B01G183300 chr3A 83.063 431 54 15 4661 5079 408023651 408023228 2.210000e-99 374.0
35 TraesCS5B01G183300 chr1A 82.381 420 56 11 4661 5074 497340311 497339904 3.730000e-92 350.0
36 TraesCS5B01G183300 chr6D 85.223 291 39 3 2630 2920 389593771 389594057 4.930000e-76 296.0
37 TraesCS5B01G183300 chr3B 84.615 182 26 2 2734 2914 670204057 670203877 5.180000e-41 180.0
38 TraesCS5B01G183300 chr3B 76.527 311 55 14 2615 2916 255983564 255983263 3.140000e-33 154.0
39 TraesCS5B01G183300 chr4A 80.147 136 22 5 2779 2911 710795652 710795785 5.360000e-16 97.1
40 TraesCS5B01G183300 chr6B 100.000 48 0 0 2 49 1275926 1275973 8.970000e-14 89.8
41 TraesCS5B01G183300 chr6A 96.875 32 1 0 1969 2000 12014955 12014986 3.000000e-03 54.7


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 TraesCS5B01G183300 chr5B 333251250 333257747 6497 True 12000.000000 12000 100.000000 1 6498 1 chr5B.!!$R1 6497
1 TraesCS5B01G183300 chr5D 292694714 292699918 5204 True 3628.000000 4229 92.378500 1 6246 2 chr5D.!!$R3 6245
2 TraesCS5B01G183300 chr5A 385394721 385399704 4983 True 1143.800000 2691 88.753400 21 6498 5 chr5A.!!$R1 6477
3 TraesCS5B01G183300 chr2B 613221721 613222675 954 False 1319.000000 1319 91.520000 1949 2913 1 chr2B.!!$F1 964
4 TraesCS5B01G183300 chr2B 765789971 765790534 563 False 606.000000 606 86.159000 2346 2918 1 chr2B.!!$F2 572
5 TraesCS5B01G183300 chr2B 548650866 548651839 973 False 279.333333 302 84.665667 1275 5498 3 chr2B.!!$F3 4223
6 TraesCS5B01G183300 chr1B 478574830 478575458 628 True 582.000000 582 83.486000 2273 2921 1 chr1B.!!$R1 648
7 TraesCS5B01G183300 chr2A 611310539 611311512 973 False 396.500000 497 82.133000 1275 5498 2 chr2A.!!$F1 4223
8 TraesCS5B01G183300 chr2D 470000146 470001119 973 False 394.000000 486 82.116000 1275 5498 2 chr2D.!!$F2 4223

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
116 124 0.041576 GGTTCGCCTCACGTTTTCAC 60.042 55.0 0.00 0.00 44.19 3.18 F
194 202 0.693049 GTTCGCCCATATCCATCCCT 59.307 55.0 0.00 0.00 0.00 4.20 F
1178 1206 0.734942 GATTCCTTCGTTGTCGGCGA 60.735 55.0 4.99 4.99 37.69 5.54 F
2182 2285 0.112412 AGTGGGCACAAAGGGGTTAG 59.888 55.0 0.00 0.00 0.00 2.34 F
2815 2924 0.459489 GTTGCAGAAAGTGGGCACAA 59.541 50.0 0.00 0.00 37.26 3.33 F
4035 4262 0.551131 AGGAAAGACCAGGGGCAGAT 60.551 55.0 0.00 0.00 42.04 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1183 1211 0.250234 TCGATGGTCTTCTGCCCTTG 59.750 55.0 0.00 0.00 0.00 3.61 R
1207 1235 0.333993 AGGACCAATGGCATCTGCTT 59.666 50.0 0.00 0.00 41.70 3.91 R
2549 2652 0.322098 ACGTTTGGCCGATGGATTGA 60.322 50.0 0.00 0.00 0.00 2.57 R
4035 4262 0.534877 ACTCAAATGCGCACACTGGA 60.535 50.0 14.90 5.51 0.00 3.86 R
4393 4624 0.664761 TTGCTGAAGCTGCACACTTC 59.335 50.0 14.98 14.98 43.15 3.01 R
5663 5928 0.030705 AGCCAGAGGGAGCTCCAATA 60.031 55.0 33.29 0.00 32.71 1.90 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
101 109 4.453136 TGCTAGTTTTACATCCAACGGTTC 59.547 41.667 0.00 0.00 0.00 3.62
107 115 1.375396 CATCCAACGGTTCGCCTCA 60.375 57.895 0.00 0.00 34.30 3.86
116 124 0.041576 GGTTCGCCTCACGTTTTCAC 60.042 55.000 0.00 0.00 44.19 3.18
194 202 0.693049 GTTCGCCCATATCCATCCCT 59.307 55.000 0.00 0.00 0.00 4.20
235 243 3.686726 CACCTGCAAAATCCAGAGTAGAC 59.313 47.826 0.00 0.00 32.03 2.59
264 272 3.907221 AGCCATCTTGCTCCAAATACAT 58.093 40.909 0.00 0.00 36.75 2.29
345 356 4.319766 CCAATTAAGCTATGATGACACGGC 60.320 45.833 0.00 0.00 0.00 5.68
350 361 1.215244 CTATGATGACACGGCAGCAG 58.785 55.000 0.00 0.00 37.62 4.24
398 409 7.665974 GCCAAGGTAGAACCAAATAGCTAATAT 59.334 37.037 0.00 0.00 41.95 1.28
597 612 5.707764 AGGCTCCTTCACTGAAAATTAAGTC 59.292 40.000 0.00 0.00 0.00 3.01
618 633 6.074648 AGTCATGGTTTTTAGATGGTTCCAA 58.925 36.000 0.00 0.00 0.00 3.53
619 634 6.553100 AGTCATGGTTTTTAGATGGTTCCAAA 59.447 34.615 0.00 0.00 0.00 3.28
790 815 4.829064 TTTTCGTTTGAAGGGATCACTG 57.171 40.909 0.00 0.00 37.92 3.66
799 824 5.102953 TGAAGGGATCACTGATAAGTTGG 57.897 43.478 0.00 0.00 31.50 3.77
852 877 2.289257 GGAACTACCGTACAGCCTTGTT 60.289 50.000 0.00 0.00 38.76 2.83
885 910 4.442893 GGCTTTATAAACCAGCATTTCCCC 60.443 45.833 9.30 0.00 35.05 4.81
1178 1206 0.734942 GATTCCTTCGTTGTCGGCGA 60.735 55.000 4.99 4.99 37.69 5.54
1256 1284 4.388499 GGAAGGTGCGGGCGAAGA 62.388 66.667 0.00 0.00 0.00 2.87
1329 1357 0.915364 AATGGCTGGAGGAGAAGGTC 59.085 55.000 0.00 0.00 0.00 3.85
1549 1648 0.546122 GAGCCCACACATACATCCCA 59.454 55.000 0.00 0.00 0.00 4.37
1568 1667 0.469144 ATGCCATGCCATGATCTGCA 60.469 50.000 6.18 7.53 42.52 4.41
1599 1698 1.675641 GCCGGCCTTGTGAAGTGAT 60.676 57.895 18.11 0.00 0.00 3.06
1604 1703 2.285220 CGGCCTTGTGAAGTGATTATCG 59.715 50.000 0.00 0.00 0.00 2.92
1636 1736 7.158021 GGGTTTTGTTTGGATCAATTGATGTA 58.842 34.615 25.37 10.95 34.37 2.29
1922 2023 3.359523 TCAGCTTGCTGGCTTGCG 61.360 61.111 20.62 0.00 41.00 4.85
1947 2049 3.867857 ACCACGATTTGCCTTTGTTTTT 58.132 36.364 0.00 0.00 0.00 1.94
1964 2066 1.812686 TTTGGGACTGCTACGCGTCT 61.813 55.000 18.63 0.00 34.47 4.18
2000 2102 2.852495 GAAAGATCCGCCGGCTCACA 62.852 60.000 26.68 5.30 0.00 3.58
2034 2136 2.890311 TGAAACAATCGGTCAGCCAAAT 59.110 40.909 0.00 0.00 34.09 2.32
2041 2144 5.221342 ACAATCGGTCAGCCAAATGTTTTAA 60.221 36.000 0.00 0.00 34.09 1.52
2055 2158 7.221067 CCAAATGTTTTAACTACTTCGCAACAA 59.779 33.333 0.00 0.00 0.00 2.83
2057 2160 7.908193 ATGTTTTAACTACTTCGCAACAAAG 57.092 32.000 0.00 0.00 0.00 2.77
2058 2161 7.074507 TGTTTTAACTACTTCGCAACAAAGA 57.925 32.000 0.00 0.00 0.00 2.52
2063 2166 5.156804 ACTACTTCGCAACAAAGAACTTG 57.843 39.130 0.00 0.00 41.19 3.16
2078 2181 8.692676 ACAAAGAACTTGTTGCGGAAACATTTT 61.693 33.333 1.60 0.00 46.49 1.82
2086 2189 6.100004 TGTTGCGGAAACATTTTAAACAAGA 58.900 32.000 0.00 0.00 43.96 3.02
2138 2241 4.013050 AGGCTAGTTGCAGAATTCCTTTC 58.987 43.478 0.65 0.00 45.15 2.62
2150 2253 6.350629 AGAATTCCTTTCTGAAACAATGGG 57.649 37.500 0.65 0.00 43.21 4.00
2160 2263 3.991773 CTGAAACAATGGGTCAATTGCAG 59.008 43.478 0.00 0.00 40.54 4.41
2166 2269 3.947910 ATGGGTCAATTGCAGAAAGTG 57.052 42.857 0.00 0.00 35.15 3.16
2178 2281 0.469892 AGAAAGTGGGCACAAAGGGG 60.470 55.000 0.00 0.00 0.00 4.79
2180 2283 0.326143 AAAGTGGGCACAAAGGGGTT 60.326 50.000 0.00 0.00 0.00 4.11
2181 2284 0.558712 AAGTGGGCACAAAGGGGTTA 59.441 50.000 0.00 0.00 0.00 2.85
2182 2285 0.112412 AGTGGGCACAAAGGGGTTAG 59.888 55.000 0.00 0.00 0.00 2.34
2230 2333 1.399855 CCGACAGACATATAGACGGCG 60.400 57.143 4.80 4.80 33.03 6.46
2247 2350 2.074942 CGGACGCTCGCACAAATTA 58.925 52.632 0.00 0.00 0.00 1.40
2252 2355 1.588404 ACGCTCGCACAAATTAGATCG 59.412 47.619 0.00 0.00 0.00 3.69
2253 2356 1.588404 CGCTCGCACAAATTAGATCGT 59.412 47.619 0.00 0.00 0.00 3.73
2261 2364 5.095490 GCACAAATTAGATCGTTTCAAGGG 58.905 41.667 0.00 0.00 0.00 3.95
2280 2383 1.657822 GAATCTTTCTCGGGACTGCC 58.342 55.000 0.00 0.00 0.00 4.85
2313 2416 3.871594 CGGCGGATGTTTCTAAAAGATCT 59.128 43.478 0.00 0.00 0.00 2.75
2316 2419 5.447818 GGCGGATGTTTCTAAAAGATCTGTG 60.448 44.000 15.60 6.50 0.00 3.66
2342 2445 2.872245 CACGAGCCGTTGGATTTGATAT 59.128 45.455 0.00 0.00 38.32 1.63
2396 2499 1.981256 ACAAAGGACTTGTTGCGGAT 58.019 45.000 0.00 0.00 46.49 4.18
2422 2525 6.416455 ACATTTGTAACAAGTGTTATGTTGCG 59.584 34.615 7.14 0.00 43.55 4.85
2423 2526 4.475763 TGTAACAAGTGTTATGTTGCGG 57.524 40.909 7.14 0.00 43.55 5.69
2424 2527 3.251245 TGTAACAAGTGTTATGTTGCGGG 59.749 43.478 7.14 0.00 43.55 6.13
2458 2561 3.505464 ACATAGGTTGTAGTGCGAGAC 57.495 47.619 0.00 0.00 36.57 3.36
2459 2562 2.159421 ACATAGGTTGTAGTGCGAGACG 60.159 50.000 0.00 0.00 36.57 4.18
2549 2652 7.011763 CAGTATCGTGAGTCATTGGATTTGATT 59.988 37.037 0.00 0.00 0.00 2.57
2559 2662 6.639686 GTCATTGGATTTGATTCAATCCATCG 59.360 38.462 21.12 17.06 42.16 3.84
2583 2686 4.272748 GCCAAACGTCTTTCTCTACTTTGT 59.727 41.667 0.00 0.00 0.00 2.83
2666 2771 6.072728 GCAACATAGATTGTATTGCGGGATTA 60.073 38.462 0.00 0.00 37.68 1.75
2775 2884 1.289160 AGGGGCTAGTTGCAGAATCA 58.711 50.000 0.00 0.00 45.15 2.57
2815 2924 0.459489 GTTGCAGAAAGTGGGCACAA 59.541 50.000 0.00 0.00 37.26 3.33
2820 2929 0.555769 AGAAAGTGGGCACAAAGGGA 59.444 50.000 0.00 0.00 0.00 4.20
2888 2997 1.731613 CGGACGCTCGCACAAAGTA 60.732 57.895 0.00 0.00 0.00 2.24
2980 3089 6.316440 TCGATGAAGATCTTCTCATCTCTG 57.684 41.667 30.45 16.57 40.14 3.35
2992 3101 8.359875 TCTTCTCATCTCTGTACAGAATCTTT 57.640 34.615 25.14 6.90 36.94 2.52
2999 3108 9.179552 CATCTCTGTACAGAATCTTTAATCTCG 57.820 37.037 25.14 9.81 36.94 4.04
3058 3181 4.391830 TCAGTCGCCTAAAAAGTAGCAATG 59.608 41.667 0.00 0.00 0.00 2.82
3330 3526 6.358118 TGAATTTCGGATTGCATAGTACAC 57.642 37.500 0.00 0.00 0.00 2.90
3457 3669 7.826918 ACAAAGCCACCTACTATTGTTTTAA 57.173 32.000 0.00 0.00 0.00 1.52
3658 3876 7.520451 AAGGACTACAATTGTTTCTTTACCC 57.480 36.000 17.78 7.24 0.00 3.69
3690 3908 2.104111 CCACTCCAATGATTAGCGGGTA 59.896 50.000 0.00 0.00 0.00 3.69
3815 4039 1.366111 GCCGATACAACCGCACACAT 61.366 55.000 0.00 0.00 0.00 3.21
3825 4049 4.941263 ACAACCGCACACATGATAGTTTAT 59.059 37.500 0.00 0.00 0.00 1.40
3826 4050 5.414454 ACAACCGCACACATGATAGTTTATT 59.586 36.000 0.00 0.00 0.00 1.40
3945 4170 6.014156 GGAACCTAGTCTATTGTCCATGCTAT 60.014 42.308 0.00 0.00 0.00 2.97
3986 4213 6.248433 CAACCCACCCAAGCTATTCATATAT 58.752 40.000 0.00 0.00 0.00 0.86
4035 4262 0.551131 AGGAAAGACCAGGGGCAGAT 60.551 55.000 0.00 0.00 42.04 2.90
4259 4490 9.911788 ACTGAAGGATAAGTGAAATATTGTGAT 57.088 29.630 0.00 0.00 0.00 3.06
4362 4593 8.669055 TGATAAACCCTAGTCACCTAAAACTA 57.331 34.615 0.00 0.00 0.00 2.24
4387 4618 7.402862 ACACATAAATAGAGCCTAACCTTGTT 58.597 34.615 0.00 0.00 0.00 2.83
4393 4624 2.569404 AGAGCCTAACCTTGTTCTCCAG 59.431 50.000 0.00 0.00 0.00 3.86
4423 4666 4.689345 GCAGCTTCAGCAAAAATCAGATTT 59.311 37.500 2.20 2.20 45.16 2.17
4524 4769 8.593492 AAAGGCACAAGCTTAAAAATAGAAAG 57.407 30.769 0.00 0.00 41.70 2.62
4566 4811 7.766219 AGCAATATCATCAAATTTTGTGCTC 57.234 32.000 12.66 0.00 33.54 4.26
4569 4814 3.574284 TCATCAAATTTTGTGCTCCGG 57.426 42.857 8.89 0.00 0.00 5.14
4779 5029 5.133221 ACAAGTAAACAAAGATGTGAGGCT 58.867 37.500 0.00 0.00 40.46 4.58
4818 5068 3.682858 CAGGATGAAATACGTTGAACCGT 59.317 43.478 0.00 0.00 41.37 4.83
4819 5069 3.682858 AGGATGAAATACGTTGAACCGTG 59.317 43.478 0.00 0.00 41.92 4.94
4866 5121 9.249053 TCATGGTCTAAGAGGATGAATAGTATC 57.751 37.037 0.00 0.00 0.00 2.24
4892 5147 5.994668 TGTGTTAAAATGCCCCAGATTTTTC 59.005 36.000 0.00 0.00 35.25 2.29
4893 5148 5.120053 GTGTTAAAATGCCCCAGATTTTTCG 59.880 40.000 0.00 0.00 35.25 3.46
4894 5149 5.221541 TGTTAAAATGCCCCAGATTTTTCGT 60.222 36.000 0.00 0.00 35.25 3.85
4895 5150 4.350368 AAAATGCCCCAGATTTTTCGTT 57.650 36.364 0.00 0.00 30.45 3.85
4897 5152 4.350368 AATGCCCCAGATTTTTCGTTTT 57.650 36.364 0.00 0.00 0.00 2.43
4898 5153 3.828875 TGCCCCAGATTTTTCGTTTTT 57.171 38.095 0.00 0.00 0.00 1.94
4899 5154 3.462021 TGCCCCAGATTTTTCGTTTTTG 58.538 40.909 0.00 0.00 0.00 2.44
4900 5155 2.223144 GCCCCAGATTTTTCGTTTTTGC 59.777 45.455 0.00 0.00 0.00 3.68
4901 5156 3.462021 CCCCAGATTTTTCGTTTTTGCA 58.538 40.909 0.00 0.00 0.00 4.08
4902 5157 3.247411 CCCCAGATTTTTCGTTTTTGCAC 59.753 43.478 0.00 0.00 0.00 4.57
4903 5158 3.868077 CCCAGATTTTTCGTTTTTGCACA 59.132 39.130 0.00 0.00 0.00 4.57
4904 5159 4.331168 CCCAGATTTTTCGTTTTTGCACAA 59.669 37.500 0.00 0.00 0.00 3.33
4905 5160 5.254842 CCAGATTTTTCGTTTTTGCACAAC 58.745 37.500 0.00 0.00 0.00 3.32
4906 5161 5.254842 CAGATTTTTCGTTTTTGCACAACC 58.745 37.500 0.00 0.00 0.00 3.77
4907 5162 4.331443 AGATTTTTCGTTTTTGCACAACCC 59.669 37.500 0.00 0.00 0.00 4.11
4908 5163 3.320673 TTTTCGTTTTTGCACAACCCT 57.679 38.095 0.00 0.00 0.00 4.34
4909 5164 2.570442 TTCGTTTTTGCACAACCCTC 57.430 45.000 0.00 0.00 0.00 4.30
4910 5165 1.464734 TCGTTTTTGCACAACCCTCA 58.535 45.000 0.00 0.00 0.00 3.86
4914 5169 3.245048 CGTTTTTGCACAACCCTCATTTC 59.755 43.478 0.00 0.00 0.00 2.17
4916 5171 1.974265 TTGCACAACCCTCATTTCGA 58.026 45.000 0.00 0.00 0.00 3.71
4917 5172 1.234821 TGCACAACCCTCATTTCGAC 58.765 50.000 0.00 0.00 0.00 4.20
4969 5224 4.091220 GTGCGCTATGCTTTCATCTATCTC 59.909 45.833 9.73 0.00 46.63 2.75
5050 5306 5.419239 TTTTTATTTGGAGGCCTTCATGG 57.581 39.130 16.58 0.00 39.35 3.66
5101 5357 7.119699 TGGTTGTATATGTTCTCAAAGAGCAAG 59.880 37.037 0.00 0.00 38.90 4.01
5102 5358 6.668541 TGTATATGTTCTCAAAGAGCAAGC 57.331 37.500 0.00 0.00 38.90 4.01
5103 5359 5.586243 TGTATATGTTCTCAAAGAGCAAGCC 59.414 40.000 0.00 0.00 38.90 4.35
5105 5361 2.498167 TGTTCTCAAAGAGCAAGCCTC 58.502 47.619 0.00 0.00 41.07 4.70
5299 5562 3.134127 GGGATGCACGGCAAGGAC 61.134 66.667 2.68 0.00 43.62 3.85
5443 5706 1.447838 CAACCTCGCCACGCTACAT 60.448 57.895 0.00 0.00 0.00 2.29
5499 5762 0.376852 GTCGCAACTTGCAAGTGACA 59.623 50.000 31.73 13.90 45.36 3.58
5540 5805 7.786178 TTATTTATTGATCAGAACTCCCACG 57.214 36.000 0.00 0.00 0.00 4.94
5544 5809 7.591421 TTATTGATCAGAACTCCCACGTATA 57.409 36.000 0.00 0.00 0.00 1.47
5572 5837 4.203226 TGGCGCATCCAATAGTTTATCAA 58.797 39.130 10.83 0.00 43.21 2.57
5577 5842 6.510478 GCGCATCCAATAGTTTATCAACGTAA 60.510 38.462 0.30 0.00 38.03 3.18
5615 5880 3.949113 ACAACACAATTTAACTGGGTCGT 59.051 39.130 0.00 0.00 27.62 4.34
5659 5924 0.465460 AGCGCAGTTGAACCTTTCCA 60.465 50.000 11.47 0.00 0.00 3.53
5663 5928 2.034558 CGCAGTTGAACCTTTCCAACAT 59.965 45.455 0.00 0.00 43.60 2.71
5666 5931 5.564651 CGCAGTTGAACCTTTCCAACATATT 60.565 40.000 0.00 0.00 43.60 1.28
5679 5944 3.474600 CAACATATTGGAGCTCCCTCTG 58.525 50.000 29.95 21.79 38.21 3.35
5681 5946 1.063183 ATATTGGAGCTCCCTCTGGC 58.937 55.000 29.95 3.46 38.21 4.85
5692 5957 1.277580 CCCTCTGGCTGAACCCTCAT 61.278 60.000 0.00 0.00 37.83 2.90
5694 5959 0.747283 CTCTGGCTGAACCCTCATGC 60.747 60.000 0.00 0.00 37.83 4.06
5696 5961 2.356278 GGCTGAACCCTCATGCCA 59.644 61.111 0.00 0.00 41.64 4.92
5698 5963 2.048603 GCTGAACCCTCATGCCACC 61.049 63.158 0.00 0.00 0.00 4.61
5699 5964 1.379916 CTGAACCCTCATGCCACCA 59.620 57.895 0.00 0.00 0.00 4.17
5701 5966 1.379044 GAACCCTCATGCCACCAGG 60.379 63.158 0.00 0.00 38.23 4.45
5702 5967 1.852157 AACCCTCATGCCACCAGGA 60.852 57.895 0.00 0.00 36.89 3.86
5703 5968 1.217057 AACCCTCATGCCACCAGGAT 61.217 55.000 0.00 0.00 36.89 3.24
5705 5970 1.638679 CCCTCATGCCACCAGGATCA 61.639 60.000 0.00 0.00 36.89 2.92
5706 5971 0.256752 CCTCATGCCACCAGGATCAA 59.743 55.000 0.00 0.00 36.89 2.57
5718 5996 4.093998 CACCAGGATCAAATCGACAAGAAG 59.906 45.833 0.00 0.00 0.00 2.85
5720 5998 4.937620 CCAGGATCAAATCGACAAGAAGAA 59.062 41.667 0.00 0.00 0.00 2.52
5722 6000 6.094603 CCAGGATCAAATCGACAAGAAGAATT 59.905 38.462 0.00 0.00 0.00 2.17
5749 6027 6.309712 TCAGATGAAAAAGAGCTTGAACTG 57.690 37.500 0.00 0.00 0.00 3.16
5750 6028 5.824624 TCAGATGAAAAAGAGCTTGAACTGT 59.175 36.000 0.00 0.00 0.00 3.55
5751 6029 6.017605 TCAGATGAAAAAGAGCTTGAACTGTC 60.018 38.462 0.00 0.00 0.00 3.51
5754 6032 4.704540 TGAAAAAGAGCTTGAACTGTCCAA 59.295 37.500 0.00 0.00 0.00 3.53
5765 6043 1.229428 ACTGTCCAACATGAAGCACG 58.771 50.000 0.00 0.00 0.00 5.34
5773 6051 4.218200 TCCAACATGAAGCACGAATTTCAT 59.782 37.500 0.00 0.00 42.98 2.57
5774 6052 4.560035 CCAACATGAAGCACGAATTTCATC 59.440 41.667 0.00 0.00 40.93 2.92
5786 6064 3.547468 CGAATTTCATCGTCCAATTTGGC 59.453 43.478 10.76 5.31 38.01 4.52
5787 6065 2.627863 TTTCATCGTCCAATTTGGCG 57.372 45.000 19.59 19.59 37.47 5.69
5788 6066 1.529226 TTCATCGTCCAATTTGGCGT 58.471 45.000 22.59 12.92 37.47 5.68
5789 6067 1.529226 TCATCGTCCAATTTGGCGTT 58.471 45.000 22.59 15.93 37.47 4.84
5790 6068 1.198867 TCATCGTCCAATTTGGCGTTG 59.801 47.619 22.99 22.99 37.47 4.10
5791 6069 0.109319 ATCGTCCAATTTGGCGTTGC 60.109 50.000 22.59 7.51 37.47 4.17
5792 6070 1.007964 CGTCCAATTTGGCGTTGCA 60.008 52.632 18.22 0.00 37.47 4.08
5793 6071 0.596083 CGTCCAATTTGGCGTTGCAA 60.596 50.000 18.22 0.00 37.47 4.08
5794 6072 1.576356 GTCCAATTTGGCGTTGCAAA 58.424 45.000 10.76 0.00 37.47 3.68
5795 6073 1.260297 GTCCAATTTGGCGTTGCAAAC 59.740 47.619 10.76 0.00 38.98 2.93
5808 6086 0.521291 TGCAAACCTATGTTGCGCTC 59.479 50.000 9.73 2.14 35.67 5.03
5819 6097 1.134936 TGTTGCGCTCGGCTAGAATTA 60.135 47.619 9.73 0.00 44.05 1.40
5823 6101 2.035961 TGCGCTCGGCTAGAATTATCTT 59.964 45.455 9.73 0.00 44.05 2.40
5826 6104 4.090210 GCGCTCGGCTAGAATTATCTTAAC 59.910 45.833 0.00 0.00 39.11 2.01
5870 6148 1.637553 AGATGTTGCCAACCTCATCCT 59.362 47.619 14.08 0.00 37.84 3.24
5887 6165 3.448093 TCCTATTGTTGTCATTGGCCA 57.552 42.857 0.00 0.00 0.00 5.36
5904 6182 2.014068 GCCACAGGTACCTTGATCTGC 61.014 57.143 13.15 9.01 0.00 4.26
5906 6184 1.066858 CACAGGTACCTTGATCTGCGT 60.067 52.381 13.15 0.97 0.00 5.24
6248 6546 3.118775 TCATGGATGTTCTTACTGGTCCG 60.119 47.826 0.00 0.00 0.00 4.79
6255 6553 2.527123 TTACTGGTCCGTGGCCCA 60.527 61.111 0.00 0.00 0.00 5.36
6270 6568 1.880027 GGCCCACTTCACAAACACTAG 59.120 52.381 0.00 0.00 0.00 2.57
6295 6593 2.611518 GAGCGCTAAGGGCATGTATAG 58.388 52.381 11.50 0.00 44.06 1.31
6296 6594 1.971357 AGCGCTAAGGGCATGTATAGT 59.029 47.619 8.99 0.00 44.06 2.12
6305 6603 7.278868 GCTAAGGGCATGTATAGTGATTGATAC 59.721 40.741 0.00 0.00 41.35 2.24
6309 6607 6.818644 GGGCATGTATAGTGATTGATACGAAT 59.181 38.462 0.00 0.00 32.22 3.34
6329 6627 7.311408 ACGAATAGAGTTATCTTAATACCGCC 58.689 38.462 0.00 0.00 36.96 6.13
6330 6628 7.040201 ACGAATAGAGTTATCTTAATACCGCCA 60.040 37.037 0.00 0.00 36.96 5.69
6331 6629 7.974501 CGAATAGAGTTATCTTAATACCGCCAT 59.025 37.037 0.00 0.00 36.96 4.40
6486 6784 4.531854 TGTGTGGTTTCTCTTTCATCCAA 58.468 39.130 0.00 0.00 0.00 3.53
6491 6789 5.299279 GTGGTTTCTCTTTCATCCAACTCAA 59.701 40.000 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 1.742761 ATGGCCACACTTCTGAATCG 58.257 50.000 8.16 0.00 0.00 3.34
77 85 4.585879 ACCGTTGGATGTAAAACTAGCAT 58.414 39.130 0.00 0.00 0.00 3.79
130 138 4.181010 CCCATCTGTGCTCCCCGG 62.181 72.222 0.00 0.00 0.00 5.73
194 202 0.035152 GATGACATGTGGTGGCTCCA 60.035 55.000 1.15 3.73 45.01 3.86
235 243 0.962356 AGCAAGATGGCTCGTTTGGG 60.962 55.000 0.00 0.00 41.05 4.12
345 356 3.259064 CAAAATCAGATTTGGCCTGCTG 58.741 45.455 9.24 6.35 36.79 4.41
350 361 6.110543 GCAAATACAAAATCAGATTTGGCC 57.889 37.500 9.24 0.00 43.10 5.36
493 504 4.699735 TCGCTATCATTGGCTTGAAAGAAA 59.300 37.500 0.00 0.00 0.00 2.52
618 633 4.223659 GACATTACACGCGGTTTGATTTT 58.776 39.130 12.47 0.00 0.00 1.82
619 634 3.365565 GGACATTACACGCGGTTTGATTT 60.366 43.478 12.47 0.00 0.00 2.17
790 815 5.191059 CGTACGTACGTACTCCAACTTATC 58.809 45.833 40.05 20.37 46.22 1.75
852 877 3.942748 GGTTTATAAAGCCGTCATGGTCA 59.057 43.478 15.09 0.00 41.21 4.02
885 910 6.293244 CGTACTTTTAAACTGGGGACTTCAAG 60.293 42.308 0.00 0.00 0.00 3.02
978 1005 6.210584 CCATGGTGGTTCCTTACAAAATTACT 59.789 38.462 2.57 0.00 37.07 2.24
1038 1066 4.493747 GCTTCGTAGTCGCCGGCT 62.494 66.667 26.68 8.66 36.96 5.52
1077 1105 0.595095 CTTCCAGCAGTTGCCTGTTC 59.405 55.000 0.00 0.00 43.38 3.18
1183 1211 0.250234 TCGATGGTCTTCTGCCCTTG 59.750 55.000 0.00 0.00 0.00 3.61
1207 1235 0.333993 AGGACCAATGGCATCTGCTT 59.666 50.000 0.00 0.00 41.70 3.91
1309 1337 0.622665 ACCTTCTCCTCCAGCCATTG 59.377 55.000 0.00 0.00 0.00 2.82
1407 1435 4.489771 CTGATGTCCGGCCACCCC 62.490 72.222 2.24 0.00 0.00 4.95
1549 1648 0.469144 TGCAGATCATGGCATGGCAT 60.469 50.000 27.75 27.75 34.58 4.40
1568 1667 2.040544 GCCGGCATGCTGTACTGTT 61.041 57.895 24.80 0.00 0.00 3.16
1599 1698 5.048364 CCAAACAAAACCCAGACATCGATAA 60.048 40.000 0.00 0.00 0.00 1.75
1604 1703 4.280677 TGATCCAAACAAAACCCAGACATC 59.719 41.667 0.00 0.00 0.00 3.06
1636 1736 0.905357 CCGGGAACTCCTTGATCTGT 59.095 55.000 0.00 0.00 35.95 3.41
1922 2023 1.135402 CAAAGGCAAATCGTGGTAGCC 60.135 52.381 0.00 0.00 45.54 3.93
1928 2030 3.002144 CCCAAAAACAAAGGCAAATCGTG 59.998 43.478 0.00 0.00 0.00 4.35
1964 2066 3.056393 TCTTTCTAAAAGATCCGCCGACA 60.056 43.478 0.00 0.00 0.00 4.35
1975 2077 1.330829 GCCGGCGGATCTTTCTAAAAG 59.669 52.381 33.44 0.00 0.00 2.27
2000 2102 3.810310 TTGTTTCAAATCCAACGGCTT 57.190 38.095 0.00 0.00 0.00 4.35
2034 2136 7.074507 TCTTTGTTGCGAAGTAGTTAAAACA 57.925 32.000 0.00 2.39 0.00 2.83
2041 2144 5.156804 CAAGTTCTTTGTTGCGAAGTAGT 57.843 39.130 0.00 0.00 31.92 2.73
2063 2166 6.576551 TCTTGTTTAAAATGTTTCCGCAAC 57.423 33.333 0.00 0.00 35.71 4.17
2112 2215 3.376546 GGAATTCTGCAACTAGCCTCTTG 59.623 47.826 5.23 0.00 44.83 3.02
2116 2219 3.728385 AAGGAATTCTGCAACTAGCCT 57.272 42.857 5.23 0.00 44.83 4.58
2138 2241 3.991773 CTGCAATTGACCCATTGTTTCAG 59.008 43.478 10.34 0.00 0.00 3.02
2150 2253 1.340889 TGCCCACTTTCTGCAATTGAC 59.659 47.619 10.34 1.02 30.85 3.18
2160 2263 0.759060 ACCCCTTTGTGCCCACTTTC 60.759 55.000 0.00 0.00 0.00 2.62
2166 2269 1.982395 GCCTAACCCCTTTGTGCCC 60.982 63.158 0.00 0.00 0.00 5.36
2178 2281 3.538634 ATCAACGGTAAGGAGCCTAAC 57.461 47.619 0.00 0.00 0.00 2.34
2180 2283 4.957954 TCTTAATCAACGGTAAGGAGCCTA 59.042 41.667 0.00 0.00 0.00 3.93
2181 2284 3.773119 TCTTAATCAACGGTAAGGAGCCT 59.227 43.478 0.00 0.00 0.00 4.58
2182 2285 4.120589 CTCTTAATCAACGGTAAGGAGCC 58.879 47.826 0.00 0.00 0.00 4.70
2192 2295 3.797256 GTCGGATGGACTCTTAATCAACG 59.203 47.826 0.00 0.00 42.62 4.10
2230 2333 1.355971 TCTAATTTGTGCGAGCGTCC 58.644 50.000 0.00 0.00 0.00 4.79
2238 2341 5.095490 CCCTTGAAACGATCTAATTTGTGC 58.905 41.667 0.00 0.00 0.00 4.57
2247 2350 5.810095 AGAAAGATTCCCTTGAAACGATCT 58.190 37.500 0.00 0.00 34.79 2.75
2252 2355 3.440522 CCCGAGAAAGATTCCCTTGAAAC 59.559 47.826 0.00 0.00 34.79 2.78
2253 2356 3.329520 TCCCGAGAAAGATTCCCTTGAAA 59.670 43.478 0.00 0.00 34.79 2.69
2261 2364 1.066143 TGGCAGTCCCGAGAAAGATTC 60.066 52.381 0.00 0.00 35.87 2.52
2342 2445 1.274167 AGACGTTTGGCTGACCGATTA 59.726 47.619 0.00 0.00 39.70 1.75
2396 2499 7.588123 CGCAACATAACACTTGTTACAAATGTA 59.412 33.333 12.55 2.62 42.55 2.29
2479 2582 5.163874 GCACATTTTCTTTCTGCAACACAAA 60.164 36.000 0.00 0.00 0.00 2.83
2549 2652 0.322098 ACGTTTGGCCGATGGATTGA 60.322 50.000 0.00 0.00 0.00 2.57
2559 2662 3.041508 AGTAGAGAAAGACGTTTGGCC 57.958 47.619 0.00 0.00 0.00 5.36
2583 2686 1.202710 TCCGCAACAAGACCTTTGCTA 60.203 47.619 4.91 0.00 44.94 3.49
2638 2742 5.181056 CCCGCAATACAATCTATGTTGCATA 59.819 40.000 8.79 0.00 43.09 3.14
2639 2743 4.022935 CCCGCAATACAATCTATGTTGCAT 60.023 41.667 8.79 0.00 43.09 3.96
2686 2793 4.141869 GGAGGGCAATATTTTCTGCAACAT 60.142 41.667 0.00 0.00 40.46 2.71
2775 2884 4.536765 ACTGGTCCATTGTTTCAGAAAGT 58.463 39.130 0.00 0.00 0.00 2.66
2820 2929 3.914426 AATCAACGGTGAGGAGCTAAT 57.086 42.857 9.97 0.00 37.14 1.73
2886 2995 4.674281 AGATTCCCTTCAACCGATCTAC 57.326 45.455 0.00 0.00 0.00 2.59
2888 2997 4.576330 AAAGATTCCCTTCAACCGATCT 57.424 40.909 0.00 0.00 33.02 2.75
2980 3089 5.279384 TCGCCGAGATTAAAGATTCTGTAC 58.721 41.667 0.00 0.00 0.00 2.90
2999 3108 6.804770 TCTACTAGTATTTGATCTCTCGCC 57.195 41.667 2.33 0.00 0.00 5.54
3050 3173 9.805966 GTTTTGTAAATTAAAAGGCATTGCTAC 57.194 29.630 8.82 0.70 0.00 3.58
3265 3461 6.101332 CACACCTCCACATTATTGAAAATGG 58.899 40.000 2.05 0.00 40.48 3.16
3267 3463 6.916360 ACACACCTCCACATTATTGAAAAT 57.084 33.333 0.00 0.00 0.00 1.82
3279 3475 2.633481 AGAAGGTAGAACACACCTCCAC 59.367 50.000 0.00 0.00 45.90 4.02
3330 3526 8.065407 TCGTGTAGTTAAATACAAGCACAAAAG 58.935 33.333 19.69 5.00 37.41 2.27
3338 3534 8.928270 AGGAAGATCGTGTAGTTAAATACAAG 57.072 34.615 16.67 17.84 37.41 3.16
3426 3623 4.772886 AGTAGGTGGCTTTGTATAAGGG 57.227 45.455 0.00 0.00 0.00 3.95
3658 3876 4.378774 TCATTGGAGTGGCAAAACAATTG 58.621 39.130 3.24 3.24 30.00 2.32
3690 3908 3.377253 AGGATTTCTCACCATGCATGT 57.623 42.857 24.58 10.59 0.00 3.21
3781 4005 8.995220 GGTTGTATCGGCTTAATGTTATGATAA 58.005 33.333 0.00 0.00 0.00 1.75
3782 4006 7.329962 CGGTTGTATCGGCTTAATGTTATGATA 59.670 37.037 0.00 0.00 0.00 2.15
3783 4007 6.147164 CGGTTGTATCGGCTTAATGTTATGAT 59.853 38.462 0.00 0.00 0.00 2.45
3784 4008 5.464057 CGGTTGTATCGGCTTAATGTTATGA 59.536 40.000 0.00 0.00 0.00 2.15
3788 4012 2.353579 GCGGTTGTATCGGCTTAATGTT 59.646 45.455 0.00 0.00 0.00 2.71
3792 4016 1.337917 TGTGCGGTTGTATCGGCTTAA 60.338 47.619 0.00 0.00 35.27 1.85
3825 4049 9.309516 GTATTTGATTGTATGTAGAACCGAGAA 57.690 33.333 0.00 0.00 0.00 2.87
3826 4050 7.646526 CGTATTTGATTGTATGTAGAACCGAGA 59.353 37.037 0.00 0.00 0.00 4.04
3934 4159 7.149202 AGGAGGTATTTTTATAGCATGGACA 57.851 36.000 0.00 0.00 0.00 4.02
3945 4170 4.090819 GGGTTGCCAAGGAGGTATTTTTA 58.909 43.478 0.00 0.00 40.61 1.52
3986 4213 1.941209 GCAGCGAGATTGGTGACTTGA 60.941 52.381 3.45 0.00 39.68 3.02
4035 4262 0.534877 ACTCAAATGCGCACACTGGA 60.535 50.000 14.90 5.51 0.00 3.86
4127 4358 8.647143 ATGTTTATTAACTATGCATGGTTTGC 57.353 30.769 30.01 15.43 42.15 3.68
4362 4593 6.958767 ACAAGGTTAGGCTCTATTTATGTGT 58.041 36.000 0.00 0.00 0.00 3.72
4387 4618 0.761187 AAGCTGCACACTTCTGGAGA 59.239 50.000 1.02 0.00 31.42 3.71
4393 4624 0.664761 TTGCTGAAGCTGCACACTTC 59.335 50.000 14.98 14.98 43.15 3.01
4566 4811 3.769739 TGGATATCCATTTCTCACCGG 57.230 47.619 20.98 0.00 42.01 5.28
4665 4911 2.903547 GCCGAGAGCAAAAACGCCA 61.904 57.895 0.00 0.00 42.97 5.69
4666 4912 2.126850 GCCGAGAGCAAAAACGCC 60.127 61.111 0.00 0.00 42.97 5.68
4768 5018 3.988976 ACACACATAAGCCTCACATCT 57.011 42.857 0.00 0.00 0.00 2.90
4833 5088 7.405292 TCATCCTCTTAGACCATGAATTTGTT 58.595 34.615 0.00 0.00 0.00 2.83
4841 5096 9.029368 TGATACTATTCATCCTCTTAGACCATG 57.971 37.037 0.00 0.00 0.00 3.66
4845 5100 9.853555 CACATGATACTATTCATCCTCTTAGAC 57.146 37.037 0.00 0.00 34.09 2.59
4866 5121 4.741321 ATCTGGGGCATTTTAACACATG 57.259 40.909 0.00 0.00 0.00 3.21
4892 5147 2.507339 ATGAGGGTTGTGCAAAAACG 57.493 45.000 0.00 0.00 33.84 3.60
4893 5148 3.245048 CGAAATGAGGGTTGTGCAAAAAC 59.755 43.478 0.00 0.00 31.60 2.43
4894 5149 3.131223 TCGAAATGAGGGTTGTGCAAAAA 59.869 39.130 0.00 0.00 0.00 1.94
4895 5150 2.690497 TCGAAATGAGGGTTGTGCAAAA 59.310 40.909 0.00 0.00 0.00 2.44
4897 5152 1.606668 GTCGAAATGAGGGTTGTGCAA 59.393 47.619 0.00 0.00 0.00 4.08
4898 5153 1.234821 GTCGAAATGAGGGTTGTGCA 58.765 50.000 0.00 0.00 0.00 4.57
4899 5154 0.165944 CGTCGAAATGAGGGTTGTGC 59.834 55.000 0.00 0.00 0.00 4.57
4900 5155 1.508632 ACGTCGAAATGAGGGTTGTG 58.491 50.000 0.00 0.00 36.79 3.33
4901 5156 3.604875 ATACGTCGAAATGAGGGTTGT 57.395 42.857 0.00 0.00 36.79 3.32
4902 5157 4.491924 CGAAATACGTCGAAATGAGGGTTG 60.492 45.833 0.00 0.00 43.86 3.77
4903 5158 3.615496 CGAAATACGTCGAAATGAGGGTT 59.385 43.478 0.00 0.00 43.86 4.11
4904 5159 3.184541 CGAAATACGTCGAAATGAGGGT 58.815 45.455 0.00 0.00 43.86 4.34
4905 5160 3.836229 CGAAATACGTCGAAATGAGGG 57.164 47.619 0.00 0.00 43.86 4.30
4917 5172 7.267600 GTGTGTAAATTTTCAGGACGAAATACG 59.732 37.037 0.00 0.00 43.12 3.06
5018 5273 9.161629 AGGCCTCCAAATAAAAATTAAAATTCG 57.838 29.630 0.00 0.00 0.00 3.34
5027 5282 5.725822 TCCATGAAGGCCTCCAAATAAAAAT 59.274 36.000 5.23 0.00 37.29 1.82
5032 5287 2.423373 GCTCCATGAAGGCCTCCAAATA 60.423 50.000 5.23 0.00 37.29 1.40
5037 5293 0.750911 CAAGCTCCATGAAGGCCTCC 60.751 60.000 5.23 0.00 37.29 4.30
5045 5301 0.405198 TTGAAGGCCAAGCTCCATGA 59.595 50.000 5.01 0.00 0.00 3.07
5050 5306 0.675633 TGCTTTTGAAGGCCAAGCTC 59.324 50.000 21.43 6.74 42.91 4.09
5131 5391 0.755686 TGCAAACATCCCAAACCACC 59.244 50.000 0.00 0.00 0.00 4.61
5327 5590 3.532155 GCTCGCTGGGATCTCGGT 61.532 66.667 2.68 0.00 0.00 4.69
5338 5601 3.406361 CGTTGCACGAAGCTCGCT 61.406 61.111 3.04 0.00 46.05 4.93
5499 5762 9.840427 CAATAAATAAAAAGAACTCATCGGTGT 57.160 29.630 0.00 0.00 0.00 4.16
5540 5805 1.156736 GGATGCGCCACATGGTATAC 58.843 55.000 4.18 0.00 39.84 1.47
5572 5837 3.247006 ACTGATTCGAATGCCTTACGT 57.753 42.857 16.96 0.00 0.00 3.57
5577 5842 3.684788 GTGTTGTACTGATTCGAATGCCT 59.315 43.478 16.96 0.00 0.00 4.75
5615 5880 2.239400 CATGGGGCGAGATACTAGACA 58.761 52.381 0.00 0.00 0.00 3.41
5659 5924 2.441001 CCAGAGGGAGCTCCAATATGTT 59.559 50.000 33.29 9.74 38.24 2.71
5663 5928 0.030705 AGCCAGAGGGAGCTCCAATA 60.031 55.000 33.29 0.00 32.71 1.90
5666 5931 2.686470 CAGCCAGAGGGAGCTCCA 60.686 66.667 33.29 0.00 37.18 3.86
5676 5941 1.300963 GCATGAGGGTTCAGCCAGA 59.699 57.895 0.00 0.00 39.65 3.86
5679 5944 2.048603 GTGGCATGAGGGTTCAGCC 61.049 63.158 0.00 0.00 42.77 4.85
5681 5946 0.679002 CTGGTGGCATGAGGGTTCAG 60.679 60.000 0.00 0.00 36.61 3.02
5692 5957 0.617935 TCGATTTGATCCTGGTGGCA 59.382 50.000 0.00 0.00 0.00 4.92
5694 5959 2.401583 TGTCGATTTGATCCTGGTGG 57.598 50.000 0.00 0.00 0.00 4.61
5696 5961 3.981071 TCTTGTCGATTTGATCCTGGT 57.019 42.857 0.00 0.00 0.00 4.00
5698 5963 6.674694 ATTCTTCTTGTCGATTTGATCCTG 57.325 37.500 0.00 0.00 0.00 3.86
5699 5964 7.108847 AGAATTCTTCTTGTCGATTTGATCCT 58.891 34.615 0.88 0.00 36.36 3.24
5723 6001 7.378995 CAGTTCAAGCTCTTTTTCATCTGAAAG 59.621 37.037 5.58 0.00 43.90 2.62
5735 6013 3.620488 TGTTGGACAGTTCAAGCTCTTT 58.380 40.909 0.00 0.00 0.00 2.52
5749 6027 3.559238 AATTCGTGCTTCATGTTGGAC 57.441 42.857 0.00 0.00 0.00 4.02
5750 6028 3.567585 TGAAATTCGTGCTTCATGTTGGA 59.432 39.130 0.00 0.00 0.00 3.53
5751 6029 3.899734 TGAAATTCGTGCTTCATGTTGG 58.100 40.909 0.00 0.00 0.00 3.77
5754 6032 4.007282 CGATGAAATTCGTGCTTCATGT 57.993 40.909 11.48 0.00 34.62 3.21
5765 6043 3.547468 CGCCAAATTGGACGATGAAATTC 59.453 43.478 17.47 0.00 40.96 2.17
5773 6051 1.284408 GCAACGCCAAATTGGACGA 59.716 52.632 26.53 0.00 40.96 4.20
5774 6052 0.596083 TTGCAACGCCAAATTGGACG 60.596 50.000 17.47 19.67 40.96 4.79
5777 6055 0.585838 GGTTTGCAACGCCAAATTGG 59.414 50.000 7.84 7.84 41.55 3.16
5779 6057 3.244044 ACATAGGTTTGCAACGCCAAATT 60.244 39.130 18.22 3.78 37.09 1.82
5780 6058 2.298729 ACATAGGTTTGCAACGCCAAAT 59.701 40.909 18.22 10.21 37.09 2.32
5781 6059 1.683917 ACATAGGTTTGCAACGCCAAA 59.316 42.857 18.22 8.68 32.66 3.28
5782 6060 1.323412 ACATAGGTTTGCAACGCCAA 58.677 45.000 18.22 0.00 0.00 4.52
5783 6061 1.000827 CAACATAGGTTTGCAACGCCA 60.001 47.619 18.22 7.56 34.21 5.69
5785 6063 1.059942 GCAACATAGGTTTGCAACGC 58.940 50.000 0.00 0.00 34.21 4.84
5786 6064 1.326576 CGCAACATAGGTTTGCAACG 58.673 50.000 0.00 0.00 34.21 4.10
5787 6065 1.059942 GCGCAACATAGGTTTGCAAC 58.940 50.000 0.30 0.00 36.38 4.17
5788 6066 0.958091 AGCGCAACATAGGTTTGCAA 59.042 45.000 11.47 0.00 37.95 4.08
5789 6067 0.521291 GAGCGCAACATAGGTTTGCA 59.479 50.000 11.47 0.00 37.95 4.08
5790 6068 0.521242 CGAGCGCAACATAGGTTTGC 60.521 55.000 11.47 6.21 36.53 3.68
5791 6069 0.096976 CCGAGCGCAACATAGGTTTG 59.903 55.000 11.47 0.00 34.21 2.93
5792 6070 1.644786 GCCGAGCGCAACATAGGTTT 61.645 55.000 11.47 0.00 34.21 3.27
5793 6071 2.106683 GCCGAGCGCAACATAGGTT 61.107 57.895 11.47 0.00 37.87 3.50
5794 6072 1.672854 TAGCCGAGCGCAACATAGGT 61.673 55.000 11.47 0.00 41.38 3.08
5795 6073 0.941463 CTAGCCGAGCGCAACATAGG 60.941 60.000 11.47 4.22 41.38 2.57
5808 6086 9.692749 TGTGATTAGTTAAGATAATTCTAGCCG 57.307 33.333 0.00 0.00 0.00 5.52
5858 6136 4.588899 TGACAACAATAGGATGAGGTTGG 58.411 43.478 0.00 0.00 42.23 3.77
5870 6148 2.824936 CCTGTGGCCAATGACAACAATA 59.175 45.455 7.24 0.00 0.00 1.90
5887 6165 1.267121 ACGCAGATCAAGGTACCTGT 58.733 50.000 17.14 4.65 0.00 4.00
5906 6184 1.448893 GGTTCACGGCAGCGGATAA 60.449 57.895 7.02 0.00 0.00 1.75
5916 6194 1.803334 TTCCTTGATTCGGTTCACGG 58.197 50.000 5.15 5.15 44.45 4.94
6033 6329 8.764524 TTTTCGTTTTTCTTTCCTTTTGATCA 57.235 26.923 0.00 0.00 0.00 2.92
6034 6330 9.083080 TCTTTTCGTTTTTCTTTCCTTTTGATC 57.917 29.630 0.00 0.00 0.00 2.92
6114 6410 4.996344 TGTCCCGTTTCTTTTTGGTTTAC 58.004 39.130 0.00 0.00 0.00 2.01
6223 6521 5.888161 GGACCAGTAAGAACATCCATGAAAT 59.112 40.000 0.00 0.00 0.00 2.17
6248 6546 0.102300 GTGTTTGTGAAGTGGGCCAC 59.898 55.000 29.32 29.32 34.10 5.01
6255 6553 2.364324 TCGCCTCTAGTGTTTGTGAAGT 59.636 45.455 0.00 0.00 0.00 3.01
6305 6603 7.310664 TGGCGGTATTAAGATAACTCTATTCG 58.689 38.462 0.00 0.00 0.00 3.34
6321 6619 9.601217 GTCATCTCTAAATTATATGGCGGTATT 57.399 33.333 0.00 0.00 0.00 1.89
6322 6620 8.758829 TGTCATCTCTAAATTATATGGCGGTAT 58.241 33.333 0.00 0.00 0.00 2.73
6323 6621 8.129496 TGTCATCTCTAAATTATATGGCGGTA 57.871 34.615 0.00 0.00 0.00 4.02
6324 6622 7.004555 TGTCATCTCTAAATTATATGGCGGT 57.995 36.000 0.00 0.00 0.00 5.68
6325 6623 7.905604 TTGTCATCTCTAAATTATATGGCGG 57.094 36.000 0.00 0.00 0.00 6.13
6365 6663 8.880991 TCTAGTTACTAGAGAGACAACCAATT 57.119 34.615 17.19 0.00 38.06 2.32
6406 6704 8.922237 TGATCTCTTAGCAATAAATCTCTCACT 58.078 33.333 0.00 0.00 0.00 3.41
6465 6763 4.580580 AGTTGGATGAAAGAGAAACCACAC 59.419 41.667 0.00 0.00 0.00 3.82


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

AutoCloner maintained by Alex Coulton.