Multiple sequence alignment - TraesCS3A01G273700

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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 TraesCS3A01G273700 chr3A 100.000 5161 0 0 1 5161 502509884 502504724 0.000000e+00 9531.0
1 TraesCS3A01G273700 chr3A 97.561 205 4 1 4957 5161 648371255 648371458 2.960000e-92 350.0
2 TraesCS3A01G273700 chr3B 94.416 1988 65 17 2774 4722 493651062 493649082 0.000000e+00 3014.0
3 TraesCS3A01G273700 chr3B 92.095 1594 85 19 1 1560 493654075 493652489 0.000000e+00 2207.0
4 TraesCS3A01G273700 chr3B 93.404 1410 60 12 1373 2777 493652496 493651115 0.000000e+00 2058.0
5 TraesCS3A01G273700 chr3B 96.517 201 6 1 4962 5161 416805560 416805360 1.070000e-86 331.0
6 TraesCS3A01G273700 chr3D 96.831 1483 32 5 2774 4248 378574272 378572797 0.000000e+00 2464.0
7 TraesCS3A01G273700 chr3D 96.375 1407 43 6 1373 2777 378575718 378574318 0.000000e+00 2309.0
8 TraesCS3A01G273700 chr3D 91.980 1596 75 19 1 1560 378577289 378575711 0.000000e+00 2189.0
9 TraesCS3A01G273700 chr3D 95.753 730 26 3 4241 4966 378572717 378571989 0.000000e+00 1171.0
10 TraesCS3A01G273700 chr7A 98.515 202 3 0 4960 5161 193116743 193116944 1.770000e-94 357.0
11 TraesCS3A01G273700 chr7A 98.492 199 3 0 4963 5161 513204228 513204426 8.220000e-93 351.0
12 TraesCS3A01G273700 chr7A 97.990 199 4 0 4963 5161 669735884 669735686 3.830000e-91 346.0
13 TraesCS3A01G273700 chr1A 96.714 213 6 1 4950 5161 543651855 543651643 2.290000e-93 353.0
14 TraesCS3A01G273700 chr1A 80.851 188 31 4 2592 2777 157084257 157084073 5.390000e-30 143.0
15 TraesCS3A01G273700 chr4A 98.020 202 4 0 4960 5161 629494607 629494808 8.220000e-93 351.0
16 TraesCS3A01G273700 chr4A 97.500 200 5 0 4962 5161 62547534 62547335 4.950000e-90 342.0
17 TraesCS3A01G273700 chr5A 97.462 197 5 0 4965 5161 677761588 677761784 2.300000e-88 337.0
18 TraesCS3A01G273700 chr7B 81.988 161 21 8 2592 2748 501557645 501557801 4.190000e-26 130.0
19 TraesCS3A01G273700 chr7B 82.524 103 16 2 2592 2694 501559146 501559246 7.120000e-14 89.8


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 TraesCS3A01G273700 chr3A 502504724 502509884 5160 True 9531.000000 9531 100.00000 1 5161 1 chr3A.!!$R1 5160
1 TraesCS3A01G273700 chr3B 493649082 493654075 4993 True 2426.333333 3014 93.30500 1 4722 3 chr3B.!!$R2 4721
2 TraesCS3A01G273700 chr3D 378571989 378577289 5300 True 2033.250000 2464 95.23475 1 4966 4 chr3D.!!$R1 4965

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
866 867 0.833949 TGCAACACCAGTACACTCCA 59.166 50.000 0.00 0.00 0.00 3.86 F
1417 1631 0.464036 TAGTGCGGATACTTGGCCTG 59.536 55.000 3.32 0.00 32.19 4.85 F
1422 1636 0.527817 CGGATACTTGGCCTGTCGAC 60.528 60.000 9.11 9.11 0.00 4.20 F
2713 2933 0.579156 GCCAATTTTTCGTTTGCGCA 59.421 45.000 5.66 5.66 38.14 6.09 F
2738 2958 2.292267 GGATGTGCATACTCCCACTTG 58.708 52.381 0.00 0.00 33.26 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2728 2948 1.003580 CATAGGCACACAAGTGGGAGT 59.996 52.381 6.64 0.00 45.98 3.85 R
2762 2982 6.396450 TCAGCATGTAATATCTCAGATCTGC 58.604 40.000 18.36 2.20 37.40 4.26 R
2895 3171 8.090214 CAGATTTGGGTCAAAACTCACAAATAT 58.910 33.333 5.55 0.76 34.93 1.28 R
3724 4006 1.271597 ACTGGTGGAATGCCTCTCAAC 60.272 52.381 0.00 0.00 34.31 3.18 R
4533 4920 2.872245 TGTGTAAGCAACTGAGCACTTC 59.128 45.455 0.00 0.00 36.85 3.01 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
596 597 1.682684 GAAGAGGAGGCGGAGGTCA 60.683 63.158 0.00 0.00 0.00 4.02
866 867 0.833949 TGCAACACCAGTACACTCCA 59.166 50.000 0.00 0.00 0.00 3.86
907 908 2.182614 GACGGCACAACACAATCCCG 62.183 60.000 0.00 0.00 41.31 5.14
967 969 2.093606 ACATCACATCACAGAGGCTCAG 60.094 50.000 18.26 11.76 0.00 3.35
1049 1051 4.135153 CCGGCGACTCCTCCACTG 62.135 72.222 9.30 0.00 0.00 3.66
1158 1160 4.159321 TCTGATTGAGCTGTCTGTCTAAGG 59.841 45.833 0.00 0.00 0.00 2.69
1164 1166 1.731720 CTGTCTGTCTAAGGCTTGGC 58.268 55.000 10.69 4.11 0.00 4.52
1323 1334 8.801299 TCTAGCACATTTGTATTTTCCATTGAA 58.199 29.630 0.00 0.00 0.00 2.69
1325 1336 6.650390 AGCACATTTGTATTTTCCATTGAACC 59.350 34.615 0.00 0.00 0.00 3.62
1358 1369 4.146100 GTCTAGTTCGACGTGAAACAGTTC 59.854 45.833 11.11 0.00 38.60 3.01
1360 1371 4.297299 AGTTCGACGTGAAACAGTTCTA 57.703 40.909 11.11 0.00 38.60 2.10
1363 1374 5.175126 AGTTCGACGTGAAACAGTTCTATTG 59.825 40.000 11.11 0.00 38.60 1.90
1364 1375 4.862350 TCGACGTGAAACAGTTCTATTGA 58.138 39.130 0.00 0.00 35.74 2.57
1365 1376 4.678287 TCGACGTGAAACAGTTCTATTGAC 59.322 41.667 0.00 0.00 35.74 3.18
1366 1377 4.680110 CGACGTGAAACAGTTCTATTGACT 59.320 41.667 0.00 0.00 35.74 3.41
1367 1378 5.387444 CGACGTGAAACAGTTCTATTGACTG 60.387 44.000 0.00 2.93 35.74 3.51
1368 1379 4.211374 ACGTGAAACAGTTCTATTGACTGC 59.789 41.667 4.30 0.00 35.74 4.40
1369 1380 4.377431 CGTGAAACAGTTCTATTGACTGCC 60.377 45.833 4.30 0.00 35.74 4.85
1370 1381 4.072131 TGAAACAGTTCTATTGACTGCCC 58.928 43.478 4.30 0.00 35.08 5.36
1371 1382 2.789409 ACAGTTCTATTGACTGCCCC 57.211 50.000 4.30 0.00 35.08 5.80
1417 1631 0.464036 TAGTGCGGATACTTGGCCTG 59.536 55.000 3.32 0.00 32.19 4.85
1422 1636 0.527817 CGGATACTTGGCCTGTCGAC 60.528 60.000 9.11 9.11 0.00 4.20
1445 1659 2.795329 ACTGTGCCTCGATGGAATTTT 58.205 42.857 5.24 0.00 38.35 1.82
1477 1691 2.877168 CCACTATTCATGAGCTTCAGGC 59.123 50.000 0.00 0.00 42.19 4.85
1599 1813 8.897872 ATTGAAGCATGAAGAAAAAGTCAATT 57.102 26.923 0.00 0.00 31.00 2.32
1660 1876 5.185454 TCATATTGACTGGTGCCTTTGTAG 58.815 41.667 0.00 0.00 0.00 2.74
1685 1901 7.123397 AGGAAGAGAATAAAATTGCTTCTTCCC 59.877 37.037 20.72 8.41 46.96 3.97
1709 1925 2.789409 ATACCAAGTGGCAGGAGTTC 57.211 50.000 0.00 0.00 39.32 3.01
1759 1978 5.104259 AGCTGTAGGGAGGAAATACAAAG 57.896 43.478 0.00 0.00 0.00 2.77
1795 2014 6.976934 TCCTATAGTGTCACATGATGCTTA 57.023 37.500 5.62 0.00 0.00 3.09
1796 2015 6.986250 TCCTATAGTGTCACATGATGCTTAG 58.014 40.000 5.62 0.00 0.00 2.18
1797 2016 6.551227 TCCTATAGTGTCACATGATGCTTAGT 59.449 38.462 5.62 0.00 0.00 2.24
1798 2017 7.724061 TCCTATAGTGTCACATGATGCTTAGTA 59.276 37.037 5.62 0.00 0.00 1.82
1799 2018 8.026026 CCTATAGTGTCACATGATGCTTAGTAG 58.974 40.741 5.62 0.00 0.00 2.57
1887 2106 7.381408 GCTTTTCAGTAAATTTGTTCCAGTACC 59.619 37.037 0.00 0.00 0.00 3.34
1895 2114 7.662604 AAATTTGTTCCAGTACCGTAGTTAG 57.337 36.000 0.00 0.00 0.00 2.34
2379 2599 7.822334 CCACCACTATCTGTTATGTAAACTGAA 59.178 37.037 2.30 0.00 33.06 3.02
2439 2659 2.025887 GGAACCCTGTTCTCATGGTGAT 60.026 50.000 6.89 0.00 40.69 3.06
2570 2790 9.196552 CCAGTTTTTCTTTTTCCATCTTATCAC 57.803 33.333 0.00 0.00 0.00 3.06
2577 2797 8.648698 TCTTTTTCCATCTTATCACCATTTGA 57.351 30.769 0.00 0.00 39.11 2.69
2579 2799 6.455360 TTTCCATCTTATCACCATTTGAGC 57.545 37.500 0.00 0.00 37.77 4.26
2713 2933 0.579156 GCCAATTTTTCGTTTGCGCA 59.421 45.000 5.66 5.66 38.14 6.09
2728 2948 2.396700 CGCAAGCTGGATGTGCATA 58.603 52.632 8.00 0.00 38.19 3.14
2738 2958 2.292267 GGATGTGCATACTCCCACTTG 58.708 52.381 0.00 0.00 33.26 3.16
2762 2982 8.846943 TGTGTGCCTATGTTTATATAATGGAG 57.153 34.615 0.00 0.00 0.00 3.86
2959 3235 4.141959 CCCCATGAACTTTGACTGTTGTTT 60.142 41.667 0.00 0.00 0.00 2.83
3129 3405 5.451659 CCAAGGTTTGTTTCACATGTCATCA 60.452 40.000 0.00 0.00 0.00 3.07
3154 3430 9.881649 CATGGATCTTAGTGTATATACTGCATT 57.118 33.333 12.05 0.00 32.19 3.56
3199 3475 6.533730 TGATGTAATACCCTGGAATAAGCTG 58.466 40.000 0.00 0.00 0.00 4.24
3334 3616 4.890158 TCAGGTATGAACTTTGAGCTGA 57.110 40.909 0.00 0.00 42.46 4.26
3639 3921 9.415544 GTCTTTTTGAATAAATGCTTGATGAGT 57.584 29.630 0.00 0.00 0.00 3.41
3652 3934 5.873712 TGCTTGATGAGTCTTGAATTCTCTC 59.126 40.000 7.05 9.54 0.00 3.20
3700 3982 5.920903 TGTTACTGTTGCACCTAGTTTACT 58.079 37.500 2.46 0.00 0.00 2.24
3957 4242 8.607441 TGTTGATATATGCTGACAATTACTCC 57.393 34.615 0.00 0.00 0.00 3.85
3993 4278 8.571336 GCATTATATGATATGCAGAAATACCCC 58.429 37.037 11.94 0.00 44.99 4.95
4043 4328 8.586879 TGCATGCTACTAGAGATGTCTAATAT 57.413 34.615 20.33 0.00 34.73 1.28
4297 4674 6.688637 TTTCGCTCTGCTTAGTACAGTATA 57.311 37.500 0.00 0.00 36.50 1.47
4489 4876 5.777732 TGTGTGCTTACCCTATTTTGGATTT 59.222 36.000 0.00 0.00 0.00 2.17
4533 4920 2.785477 CACTTTGCTTTCAGAGTTTGCG 59.215 45.455 0.00 0.00 35.71 4.85
4742 5146 9.722056 CTTATAGTTGCAAGTCCATATGTTTTC 57.278 33.333 10.78 0.00 0.00 2.29
4744 5148 6.017400 AGTTGCAAGTCCATATGTTTTCAG 57.983 37.500 0.00 0.00 0.00 3.02
4820 5228 4.774200 ACATAGGCTTGGAAAATCTGCTTT 59.226 37.500 0.00 0.00 0.00 3.51
4829 5237 6.653526 TGGAAAATCTGCTTTCTTTCATCA 57.346 33.333 0.00 0.00 35.91 3.07
4830 5238 7.235935 TGGAAAATCTGCTTTCTTTCATCAT 57.764 32.000 0.00 0.00 35.91 2.45
4886 5294 8.040716 AGTCTTTTTGGTATTTTGTAGGATCG 57.959 34.615 0.00 0.00 0.00 3.69
4892 5300 5.667466 TGGTATTTTGTAGGATCGAAGTCC 58.333 41.667 0.00 0.00 38.62 3.85
4945 5353 1.618343 TCTGCTTTAGGGCAAAAAGGC 59.382 47.619 11.34 3.64 41.94 4.35
4961 5369 7.411480 GGCAAAAAGGCGAACAAAAAGTATATC 60.411 37.037 0.00 0.00 33.57 1.63
4989 5397 6.976636 TTTTTGAAACGAAGGCAAAAGATT 57.023 29.167 0.00 0.00 41.02 2.40
4990 5398 6.976636 TTTTGAAACGAAGGCAAAAGATTT 57.023 29.167 0.00 0.00 36.80 2.17
4991 5399 5.964887 TTGAAACGAAGGCAAAAGATTTG 57.035 34.783 0.00 0.00 0.00 2.32
4992 5400 3.801594 TGAAACGAAGGCAAAAGATTTGC 59.198 39.130 17.18 17.18 44.22 3.68
5000 5408 3.598019 GCAAAAGATTTGCCTCATCCA 57.402 42.857 15.12 0.00 39.38 3.41
5001 5409 4.133013 GCAAAAGATTTGCCTCATCCAT 57.867 40.909 15.12 0.00 39.38 3.41
5002 5410 4.510571 GCAAAAGATTTGCCTCATCCATT 58.489 39.130 15.12 0.00 39.38 3.16
5003 5411 5.663456 GCAAAAGATTTGCCTCATCCATTA 58.337 37.500 15.12 0.00 39.38 1.90
5004 5412 6.108015 GCAAAAGATTTGCCTCATCCATTAA 58.892 36.000 15.12 0.00 39.38 1.40
5005 5413 6.594937 GCAAAAGATTTGCCTCATCCATTAAA 59.405 34.615 15.12 0.00 39.38 1.52
5006 5414 7.281549 GCAAAAGATTTGCCTCATCCATTAAAT 59.718 33.333 15.12 0.00 39.38 1.40
5007 5415 9.820725 CAAAAGATTTGCCTCATCCATTAAATA 57.179 29.630 0.00 0.00 0.00 1.40
5010 5418 9.425248 AAGATTTGCCTCATCCATTAAATAAGA 57.575 29.630 0.00 0.00 0.00 2.10
5011 5419 9.075678 AGATTTGCCTCATCCATTAAATAAGAG 57.924 33.333 0.00 0.00 0.00 2.85
5012 5420 7.587037 TTTGCCTCATCCATTAAATAAGAGG 57.413 36.000 0.00 0.00 43.04 3.69
5013 5421 6.514012 TGCCTCATCCATTAAATAAGAGGA 57.486 37.500 9.57 5.13 42.87 3.71
5014 5422 6.537355 TGCCTCATCCATTAAATAAGAGGAG 58.463 40.000 9.57 9.14 42.87 3.69
5015 5423 6.329986 TGCCTCATCCATTAAATAAGAGGAGA 59.670 38.462 9.57 0.00 42.87 3.71
5016 5424 7.147320 TGCCTCATCCATTAAATAAGAGGAGAA 60.147 37.037 9.57 1.85 42.87 2.87
5017 5425 7.887495 GCCTCATCCATTAAATAAGAGGAGAAT 59.113 37.037 9.57 0.00 42.87 2.40
5040 5448 9.742552 GAATAGAGTTTAGAGTTTTTACAAGCG 57.257 33.333 0.00 0.00 0.00 4.68
5041 5449 5.986936 AGAGTTTAGAGTTTTTACAAGCGC 58.013 37.500 0.00 0.00 0.00 5.92
5042 5450 5.049612 AGAGTTTAGAGTTTTTACAAGCGCC 60.050 40.000 2.29 0.00 0.00 6.53
5043 5451 4.023450 AGTTTAGAGTTTTTACAAGCGCCC 60.023 41.667 2.29 0.00 0.00 6.13
5044 5452 2.271944 AGAGTTTTTACAAGCGCCCT 57.728 45.000 2.29 0.00 0.00 5.19
5045 5453 2.583143 AGAGTTTTTACAAGCGCCCTT 58.417 42.857 2.29 0.00 0.00 3.95
5052 5460 2.355009 CAAGCGCCCTTGCAACAC 60.355 61.111 2.29 0.00 41.72 3.32
5053 5461 3.964875 AAGCGCCCTTGCAACACG 61.965 61.111 2.29 0.32 37.32 4.49
5057 5465 3.683937 GCCCTTGCAACACGGCAT 61.684 61.111 18.26 0.00 44.48 4.40
5058 5466 2.259204 CCCTTGCAACACGGCATG 59.741 61.111 0.00 0.00 44.48 4.06
5060 5468 2.431260 CTTGCAACACGGCATGGC 60.431 61.111 9.69 9.69 44.48 4.40
5061 5469 3.210223 CTTGCAACACGGCATGGCA 62.210 57.895 20.37 3.09 44.48 4.92
5062 5470 2.696409 CTTGCAACACGGCATGGCAA 62.696 55.000 20.37 11.13 44.48 4.52
5063 5471 2.097201 TTGCAACACGGCATGGCAAT 62.097 50.000 20.37 3.38 44.48 3.56
5064 5472 1.374505 GCAACACGGCATGGCAATT 60.375 52.632 20.37 6.94 0.00 2.32
5065 5473 0.108898 GCAACACGGCATGGCAATTA 60.109 50.000 20.37 0.00 0.00 1.40
5066 5474 1.627879 CAACACGGCATGGCAATTAC 58.372 50.000 20.37 0.00 0.00 1.89
5067 5475 1.202114 CAACACGGCATGGCAATTACT 59.798 47.619 20.37 0.00 0.00 2.24
5068 5476 1.094785 ACACGGCATGGCAATTACTC 58.905 50.000 20.37 0.00 0.00 2.59
5069 5477 1.340017 ACACGGCATGGCAATTACTCT 60.340 47.619 20.37 0.00 0.00 3.24
5070 5478 1.331756 CACGGCATGGCAATTACTCTC 59.668 52.381 20.37 0.00 0.00 3.20
5071 5479 0.583438 CGGCATGGCAATTACTCTCG 59.417 55.000 20.37 0.00 0.00 4.04
5072 5480 1.668419 GGCATGGCAATTACTCTCGT 58.332 50.000 15.47 0.00 0.00 4.18
5073 5481 2.801699 CGGCATGGCAATTACTCTCGTA 60.802 50.000 20.37 0.00 0.00 3.43
5074 5482 2.544267 GGCATGGCAATTACTCTCGTAC 59.456 50.000 15.47 0.00 0.00 3.67
5075 5483 3.194861 GCATGGCAATTACTCTCGTACA 58.805 45.455 0.00 0.00 0.00 2.90
5076 5484 3.621268 GCATGGCAATTACTCTCGTACAA 59.379 43.478 0.00 0.00 0.00 2.41
5077 5485 4.494199 GCATGGCAATTACTCTCGTACAAC 60.494 45.833 0.00 0.00 0.00 3.32
5078 5486 4.260139 TGGCAATTACTCTCGTACAACA 57.740 40.909 0.00 0.00 0.00 3.33
5079 5487 4.633175 TGGCAATTACTCTCGTACAACAA 58.367 39.130 0.00 0.00 0.00 2.83
5080 5488 5.057819 TGGCAATTACTCTCGTACAACAAA 58.942 37.500 0.00 0.00 0.00 2.83
5081 5489 5.527951 TGGCAATTACTCTCGTACAACAAAA 59.472 36.000 0.00 0.00 0.00 2.44
5082 5490 5.849604 GGCAATTACTCTCGTACAACAAAAC 59.150 40.000 0.00 0.00 0.00 2.43
5083 5491 6.423862 GCAATTACTCTCGTACAACAAAACA 58.576 36.000 0.00 0.00 0.00 2.83
5084 5492 6.356190 GCAATTACTCTCGTACAACAAAACAC 59.644 38.462 0.00 0.00 0.00 3.32
5085 5493 5.971895 TTACTCTCGTACAACAAAACACC 57.028 39.130 0.00 0.00 0.00 4.16
5086 5494 3.200483 ACTCTCGTACAACAAAACACCC 58.800 45.455 0.00 0.00 0.00 4.61
5087 5495 3.118519 ACTCTCGTACAACAAAACACCCT 60.119 43.478 0.00 0.00 0.00 4.34
5088 5496 4.099881 ACTCTCGTACAACAAAACACCCTA 59.900 41.667 0.00 0.00 0.00 3.53
5089 5497 4.624015 TCTCGTACAACAAAACACCCTAG 58.376 43.478 0.00 0.00 0.00 3.02
5090 5498 4.099881 TCTCGTACAACAAAACACCCTAGT 59.900 41.667 0.00 0.00 0.00 2.57
5091 5499 4.768583 TCGTACAACAAAACACCCTAGTT 58.231 39.130 0.00 0.00 0.00 2.24
5092 5500 5.184711 TCGTACAACAAAACACCCTAGTTT 58.815 37.500 0.00 0.00 43.13 2.66
5093 5501 5.294060 TCGTACAACAAAACACCCTAGTTTC 59.706 40.000 0.00 0.00 40.60 2.78
5094 5502 5.295045 CGTACAACAAAACACCCTAGTTTCT 59.705 40.000 0.00 0.00 40.60 2.52
5095 5503 6.183360 CGTACAACAAAACACCCTAGTTTCTT 60.183 38.462 0.00 0.00 40.60 2.52
5096 5504 7.011295 CGTACAACAAAACACCCTAGTTTCTTA 59.989 37.037 0.00 0.00 40.60 2.10
5097 5505 7.329588 ACAACAAAACACCCTAGTTTCTTAG 57.670 36.000 0.00 0.00 40.60 2.18
5098 5506 6.183360 ACAACAAAACACCCTAGTTTCTTAGC 60.183 38.462 0.00 0.00 40.60 3.09
5099 5507 5.442391 ACAAAACACCCTAGTTTCTTAGCA 58.558 37.500 0.00 0.00 40.60 3.49
5100 5508 5.298527 ACAAAACACCCTAGTTTCTTAGCAC 59.701 40.000 0.00 0.00 40.60 4.40
5101 5509 3.697619 ACACCCTAGTTTCTTAGCACC 57.302 47.619 0.00 0.00 0.00 5.01
5102 5510 3.248888 ACACCCTAGTTTCTTAGCACCT 58.751 45.455 0.00 0.00 0.00 4.00
5103 5511 3.008049 ACACCCTAGTTTCTTAGCACCTG 59.992 47.826 0.00 0.00 0.00 4.00
5104 5512 2.027100 ACCCTAGTTTCTTAGCACCTGC 60.027 50.000 0.00 0.00 42.49 4.85
5105 5513 2.633488 CCTAGTTTCTTAGCACCTGCC 58.367 52.381 0.00 0.00 43.38 4.85
5106 5514 2.271800 CTAGTTTCTTAGCACCTGCCG 58.728 52.381 0.00 0.00 43.38 5.69
5107 5515 0.396811 AGTTTCTTAGCACCTGCCGT 59.603 50.000 0.00 0.00 43.38 5.68
5108 5516 1.621814 AGTTTCTTAGCACCTGCCGTA 59.378 47.619 0.00 0.00 43.38 4.02
5109 5517 2.038033 AGTTTCTTAGCACCTGCCGTAA 59.962 45.455 0.00 0.00 43.38 3.18
5110 5518 2.088950 TTCTTAGCACCTGCCGTAAC 57.911 50.000 0.00 0.00 43.38 2.50
5111 5519 0.248289 TCTTAGCACCTGCCGTAACC 59.752 55.000 0.00 0.00 43.38 2.85
5112 5520 0.743345 CTTAGCACCTGCCGTAACCC 60.743 60.000 0.00 0.00 43.38 4.11
5113 5521 1.481901 TTAGCACCTGCCGTAACCCA 61.482 55.000 0.00 0.00 43.38 4.51
5114 5522 1.268992 TAGCACCTGCCGTAACCCAT 61.269 55.000 0.00 0.00 43.38 4.00
5115 5523 1.222387 GCACCTGCCGTAACCCATA 59.778 57.895 0.00 0.00 34.31 2.74
5116 5524 0.393267 GCACCTGCCGTAACCCATAA 60.393 55.000 0.00 0.00 34.31 1.90
5117 5525 1.749286 GCACCTGCCGTAACCCATAAT 60.749 52.381 0.00 0.00 34.31 1.28
5118 5526 2.650322 CACCTGCCGTAACCCATAATT 58.350 47.619 0.00 0.00 0.00 1.40
5119 5527 3.020984 CACCTGCCGTAACCCATAATTT 58.979 45.455 0.00 0.00 0.00 1.82
5120 5528 3.445805 CACCTGCCGTAACCCATAATTTT 59.554 43.478 0.00 0.00 0.00 1.82
5121 5529 3.445805 ACCTGCCGTAACCCATAATTTTG 59.554 43.478 0.00 0.00 0.00 2.44
5122 5530 3.443976 CTGCCGTAACCCATAATTTTGC 58.556 45.455 0.00 0.00 0.00 3.68
5123 5531 2.166664 TGCCGTAACCCATAATTTTGCC 59.833 45.455 0.00 0.00 0.00 4.52
5124 5532 2.429250 GCCGTAACCCATAATTTTGCCT 59.571 45.455 0.00 0.00 0.00 4.75
5125 5533 3.490249 GCCGTAACCCATAATTTTGCCTC 60.490 47.826 0.00 0.00 0.00 4.70
5126 5534 3.697045 CCGTAACCCATAATTTTGCCTCA 59.303 43.478 0.00 0.00 0.00 3.86
5127 5535 4.158764 CCGTAACCCATAATTTTGCCTCAA 59.841 41.667 0.00 0.00 0.00 3.02
5128 5536 5.339990 CGTAACCCATAATTTTGCCTCAAG 58.660 41.667 0.00 0.00 0.00 3.02
5129 5537 3.893326 ACCCATAATTTTGCCTCAAGC 57.107 42.857 0.00 0.00 44.14 4.01
5141 5549 3.070429 GCCTCAAGCACGATATTTTGG 57.930 47.619 0.00 0.00 42.97 3.28
5142 5550 2.682856 GCCTCAAGCACGATATTTTGGA 59.317 45.455 0.00 0.00 42.97 3.53
5143 5551 3.242870 GCCTCAAGCACGATATTTTGGAG 60.243 47.826 0.00 0.00 42.97 3.86
5144 5552 3.242870 CCTCAAGCACGATATTTTGGAGC 60.243 47.826 0.00 0.00 0.00 4.70
5145 5553 3.342719 TCAAGCACGATATTTTGGAGCA 58.657 40.909 0.00 0.00 0.00 4.26
5146 5554 3.374988 TCAAGCACGATATTTTGGAGCAG 59.625 43.478 0.00 0.00 0.00 4.24
5147 5555 2.292267 AGCACGATATTTTGGAGCAGG 58.708 47.619 0.00 0.00 0.00 4.85
5148 5556 2.092968 AGCACGATATTTTGGAGCAGGA 60.093 45.455 0.00 0.00 0.00 3.86
5149 5557 2.880890 GCACGATATTTTGGAGCAGGAT 59.119 45.455 0.00 0.00 0.00 3.24
5150 5558 4.065088 GCACGATATTTTGGAGCAGGATA 58.935 43.478 0.00 0.00 0.00 2.59
5151 5559 4.153117 GCACGATATTTTGGAGCAGGATAG 59.847 45.833 0.00 0.00 0.00 2.08
5152 5560 4.692625 CACGATATTTTGGAGCAGGATAGG 59.307 45.833 0.00 0.00 0.00 2.57
5153 5561 3.686726 CGATATTTTGGAGCAGGATAGGC 59.313 47.826 0.00 0.00 0.00 3.93
5154 5562 1.972872 ATTTTGGAGCAGGATAGGCG 58.027 50.000 0.00 0.00 36.08 5.52
5155 5563 0.107214 TTTTGGAGCAGGATAGGCGG 60.107 55.000 0.00 0.00 36.08 6.13
5156 5564 2.608970 TTTGGAGCAGGATAGGCGGC 62.609 60.000 0.00 0.00 36.08 6.53
5157 5565 4.671569 GGAGCAGGATAGGCGGCG 62.672 72.222 0.51 0.51 36.08 6.46
5158 5566 4.671569 GAGCAGGATAGGCGGCGG 62.672 72.222 9.78 0.00 36.08 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
187 188 3.160047 AGATGCTGGAGGAGGGCG 61.160 66.667 0.00 0.00 0.00 6.13
281 282 2.126618 TACCACGCGCTCTTCACG 60.127 61.111 5.73 0.00 0.00 4.35
596 597 3.670629 CTCCCTCGCCTCCACCTCT 62.671 68.421 0.00 0.00 0.00 3.69
740 741 4.148825 CTCCCCTTCGCCACCTCG 62.149 72.222 0.00 0.00 0.00 4.63
803 804 3.781770 GATGAGCACGCTCCTCCGG 62.782 68.421 16.12 0.00 42.09 5.14
838 839 0.744414 CTGGTGTTGCAGTATCCCCG 60.744 60.000 0.00 0.00 0.00 5.73
839 840 0.328258 ACTGGTGTTGCAGTATCCCC 59.672 55.000 0.00 0.00 0.00 4.81
840 841 2.027561 TGTACTGGTGTTGCAGTATCCC 60.028 50.000 0.00 0.00 36.46 3.85
862 863 1.956477 CCTTTTGTGGGTTCTGTGGAG 59.044 52.381 0.00 0.00 0.00 3.86
866 867 0.032615 TGGCCTTTTGTGGGTTCTGT 60.033 50.000 3.32 0.00 0.00 3.41
895 896 2.961768 GGGTGCGGGATTGTGTTG 59.038 61.111 0.00 0.00 0.00 3.33
907 908 3.060000 GGTTGCCTAACCGGGTGC 61.060 66.667 0.00 0.00 46.30 5.01
938 939 0.095935 GTGATGTGATGTGAGCGTGC 59.904 55.000 0.00 0.00 0.00 5.34
982 984 0.678048 ATCCTTTCTGCAAGCCGACC 60.678 55.000 0.00 0.00 0.00 4.79
1077 1079 3.491652 GCGAAGAAGCGGAGTGGC 61.492 66.667 0.00 0.00 0.00 5.01
1323 1334 2.713877 GAACTAGACTCTGACGGAGGT 58.286 52.381 15.76 5.10 45.83 3.85
1325 1336 2.349275 GTCGAACTAGACTCTGACGGAG 59.651 54.545 9.88 9.88 46.87 4.63
1358 1369 2.936498 CAGTAAACGGGGCAGTCAATAG 59.064 50.000 0.00 0.00 0.00 1.73
1360 1371 1.349688 TCAGTAAACGGGGCAGTCAAT 59.650 47.619 0.00 0.00 0.00 2.57
1363 1374 0.606604 TCTCAGTAAACGGGGCAGTC 59.393 55.000 0.00 0.00 0.00 3.51
1364 1375 1.276622 ATCTCAGTAAACGGGGCAGT 58.723 50.000 0.00 0.00 0.00 4.40
1365 1376 2.403252 AATCTCAGTAAACGGGGCAG 57.597 50.000 0.00 0.00 0.00 4.85
1366 1377 3.101437 TCTAATCTCAGTAAACGGGGCA 58.899 45.455 0.00 0.00 0.00 5.36
1367 1378 3.814005 TCTAATCTCAGTAAACGGGGC 57.186 47.619 0.00 0.00 0.00 5.80
1368 1379 4.101119 ACCATCTAATCTCAGTAAACGGGG 59.899 45.833 0.00 0.00 0.00 5.73
1369 1380 5.277857 ACCATCTAATCTCAGTAAACGGG 57.722 43.478 0.00 0.00 0.00 5.28
1370 1381 6.338146 TCAACCATCTAATCTCAGTAAACGG 58.662 40.000 0.00 0.00 0.00 4.44
1371 1382 7.706607 TCATCAACCATCTAATCTCAGTAAACG 59.293 37.037 0.00 0.00 0.00 3.60
1417 1631 2.081212 CGAGGCACAGTTCGTCGAC 61.081 63.158 9.34 5.18 42.33 4.20
1422 1636 0.389817 TTCCATCGAGGCACAGTTCG 60.390 55.000 0.00 0.00 37.29 3.95
1445 1659 6.183360 GCTCATGAATAGTGGGAAGAAGTCTA 60.183 42.308 0.00 0.00 0.00 2.59
1477 1691 4.701765 AGCATCAGCCTATTAGAACACAG 58.298 43.478 0.00 0.00 43.56 3.66
1533 1747 4.803329 AGCACATCTCATTTCCCCTAAT 57.197 40.909 0.00 0.00 0.00 1.73
1599 1813 6.471233 TTTCACACACCAAATGGACAATTA 57.529 33.333 6.42 0.00 38.94 1.40
1660 1876 7.093771 TGGGAAGAAGCAATTTTATTCTCTTCC 60.094 37.037 16.21 16.21 45.77 3.46
1685 1901 1.837439 TCCTGCCACTTGGTATACCTG 59.163 52.381 22.41 16.60 37.57 4.00
1709 1925 7.658261 TCCGTACATCTATTCACCAATTCTAG 58.342 38.462 0.00 0.00 0.00 2.43
1759 1978 8.247562 GTGACACTATAGGATATCAGGATCAAC 58.752 40.741 4.83 0.00 0.00 3.18
1795 2014 9.326413 GGCAGTTATGTTATGTTATGTTCTACT 57.674 33.333 0.00 0.00 0.00 2.57
1796 2015 9.326413 AGGCAGTTATGTTATGTTATGTTCTAC 57.674 33.333 0.00 0.00 0.00 2.59
1797 2016 9.899661 AAGGCAGTTATGTTATGTTATGTTCTA 57.100 29.630 0.00 0.00 0.00 2.10
1798 2017 8.807948 AAGGCAGTTATGTTATGTTATGTTCT 57.192 30.769 0.00 0.00 0.00 3.01
1799 2018 9.855021 AAAAGGCAGTTATGTTATGTTATGTTC 57.145 29.630 0.00 0.00 0.00 3.18
1855 2074 7.307337 GGAACAAATTTACTGAAAAGCCATGTG 60.307 37.037 0.00 0.00 0.00 3.21
1887 2106 5.962433 TCTCTTGGAAATGGACTAACTACG 58.038 41.667 0.00 0.00 0.00 3.51
1895 2114 2.795329 TGCCTTCTCTTGGAAATGGAC 58.205 47.619 0.00 0.00 33.07 4.02
1977 2197 8.394971 TGATGTCAGTACAAATTCATGAACTT 57.605 30.769 11.07 2.62 39.58 2.66
2346 2566 4.844349 AACAGATAGTGGTGGCTACAAT 57.156 40.909 1.52 0.00 0.00 2.71
2347 2567 5.188948 ACATAACAGATAGTGGTGGCTACAA 59.811 40.000 1.52 0.00 0.00 2.41
2379 2599 5.187772 GGAGATGCTGGGAAAGGTTTAAAAT 59.812 40.000 0.00 0.00 0.00 1.82
2439 2659 3.343617 CCCAAGAATAGCACCGAGAAAA 58.656 45.455 0.00 0.00 0.00 2.29
2570 2790 2.818432 AGCAAAGAGACAGCTCAAATGG 59.182 45.455 0.00 0.00 43.81 3.16
2577 2797 3.549794 ACAGAAAAGCAAAGAGACAGCT 58.450 40.909 0.00 0.00 41.03 4.24
2579 2799 5.049129 CCCTAACAGAAAAGCAAAGAGACAG 60.049 44.000 0.00 0.00 0.00 3.51
2713 2933 1.133976 GGGAGTATGCACATCCAGCTT 60.134 52.381 13.91 0.00 34.62 3.74
2728 2948 1.003580 CATAGGCACACAAGTGGGAGT 59.996 52.381 6.64 0.00 45.98 3.85
2738 2958 7.390440 TGCTCCATTATATAAACATAGGCACAC 59.610 37.037 0.00 0.00 0.00 3.82
2762 2982 6.396450 TCAGCATGTAATATCTCAGATCTGC 58.604 40.000 18.36 2.20 37.40 4.26
2889 3165 8.364142 TGGGTCAAAACTCACAAATATAAAAGG 58.636 33.333 0.00 0.00 28.22 3.11
2895 3171 8.090214 CAGATTTGGGTCAAAACTCACAAATAT 58.910 33.333 5.55 0.76 34.93 1.28
3022 3298 9.520204 CCACCTGTTCAATAAAATATCATTCAC 57.480 33.333 0.00 0.00 0.00 3.18
3154 3430 9.725019 ACATCATAAGTTGTTGTGATCTTAAGA 57.275 29.630 7.82 7.82 41.25 2.10
3639 3921 6.536582 CCTAATTTGCTCGAGAGAATTCAAGA 59.463 38.462 18.75 5.49 41.32 3.02
3700 3982 5.010922 CCACCAGAAAAATTGTTCCATCAGA 59.989 40.000 4.66 0.00 0.00 3.27
3724 4006 1.271597 ACTGGTGGAATGCCTCTCAAC 60.272 52.381 0.00 0.00 34.31 3.18
3993 4278 9.043079 CATACATCTTCCATAGCATGCTATAAG 57.957 37.037 33.97 31.12 37.16 1.73
4477 4863 9.883142 AGAGTAGAAGAGTGAAATCCAAAATAG 57.117 33.333 0.00 0.00 0.00 1.73
4489 4876 5.535030 TGCACAGTAAAGAGTAGAAGAGTGA 59.465 40.000 0.00 0.00 0.00 3.41
4533 4920 2.872245 TGTGTAAGCAACTGAGCACTTC 59.128 45.455 0.00 0.00 36.85 3.01
4617 5021 3.933861 ACTGTCCACTTGTCCTTTTCT 57.066 42.857 0.00 0.00 0.00 2.52
4754 5160 8.684520 GCGTATATGATACTCCTACCATTTACT 58.315 37.037 0.00 0.00 0.00 2.24
4778 5184 1.026182 TGCAGCTACCCATCTTTGCG 61.026 55.000 0.00 0.00 34.44 4.85
4820 5228 6.317140 GCCACATGAAGAACTATGATGAAAGA 59.683 38.462 0.00 0.00 0.00 2.52
4829 5237 3.641434 AGCTGCCACATGAAGAACTAT 57.359 42.857 0.00 0.00 0.00 2.12
4830 5238 3.369471 GGTAGCTGCCACATGAAGAACTA 60.369 47.826 16.95 0.00 0.00 2.24
4886 5294 1.971357 TGGAGTTCACAGAGGGACTTC 59.029 52.381 0.00 0.00 41.55 3.01
4892 5300 1.341531 ACGAGTTGGAGTTCACAGAGG 59.658 52.381 0.00 0.00 0.00 3.69
4923 5331 3.306989 GCCTTTTTGCCCTAAAGCAGATT 60.307 43.478 0.00 0.00 45.13 2.40
4966 5374 6.976636 AATCTTTTGCCTTCGTTTCAAAAA 57.023 29.167 0.00 0.00 38.65 1.94
4967 5375 6.674278 GCAAATCTTTTGCCTTCGTTTCAAAA 60.674 34.615 12.74 0.00 39.38 2.44
4968 5376 5.220567 GCAAATCTTTTGCCTTCGTTTCAAA 60.221 36.000 12.74 0.00 39.38 2.69
4969 5377 4.269844 GCAAATCTTTTGCCTTCGTTTCAA 59.730 37.500 12.74 0.00 39.38 2.69
4970 5378 3.801594 GCAAATCTTTTGCCTTCGTTTCA 59.198 39.130 12.74 0.00 39.38 2.69
4971 5379 4.374990 GCAAATCTTTTGCCTTCGTTTC 57.625 40.909 12.74 0.00 39.38 2.78
4980 5388 3.598019 TGGATGAGGCAAATCTTTTGC 57.402 42.857 14.88 14.88 44.22 3.68
4981 5389 8.726870 ATTTAATGGATGAGGCAAATCTTTTG 57.273 30.769 0.00 0.00 0.00 2.44
4984 5392 9.425248 TCTTATTTAATGGATGAGGCAAATCTT 57.575 29.630 0.00 0.00 0.00 2.40
4985 5393 9.075678 CTCTTATTTAATGGATGAGGCAAATCT 57.924 33.333 0.00 0.00 0.00 2.40
4986 5394 8.302438 CCTCTTATTTAATGGATGAGGCAAATC 58.698 37.037 0.00 0.00 34.16 2.17
4987 5395 8.006564 TCCTCTTATTTAATGGATGAGGCAAAT 58.993 33.333 0.00 0.00 39.36 2.32
4988 5396 7.353525 TCCTCTTATTTAATGGATGAGGCAAA 58.646 34.615 0.00 0.00 39.36 3.68
4989 5397 6.910191 TCCTCTTATTTAATGGATGAGGCAA 58.090 36.000 0.00 0.00 39.36 4.52
4990 5398 6.329986 TCTCCTCTTATTTAATGGATGAGGCA 59.670 38.462 0.00 0.00 39.36 4.75
4991 5399 6.773638 TCTCCTCTTATTTAATGGATGAGGC 58.226 40.000 0.00 0.00 39.36 4.70
5014 5422 9.742552 CGCTTGTAAAAACTCTAAACTCTATTC 57.257 33.333 0.00 0.00 0.00 1.75
5015 5423 8.228464 GCGCTTGTAAAAACTCTAAACTCTATT 58.772 33.333 0.00 0.00 0.00 1.73
5016 5424 7.148457 GGCGCTTGTAAAAACTCTAAACTCTAT 60.148 37.037 7.64 0.00 0.00 1.98
5017 5425 6.146673 GGCGCTTGTAAAAACTCTAAACTCTA 59.853 38.462 7.64 0.00 0.00 2.43
5018 5426 5.049612 GGCGCTTGTAAAAACTCTAAACTCT 60.050 40.000 7.64 0.00 0.00 3.24
5019 5427 5.145059 GGCGCTTGTAAAAACTCTAAACTC 58.855 41.667 7.64 0.00 0.00 3.01
5020 5428 4.023450 GGGCGCTTGTAAAAACTCTAAACT 60.023 41.667 7.64 0.00 0.00 2.66
5021 5429 4.023450 AGGGCGCTTGTAAAAACTCTAAAC 60.023 41.667 7.64 0.00 0.00 2.01
5022 5430 4.139038 AGGGCGCTTGTAAAAACTCTAAA 58.861 39.130 7.64 0.00 0.00 1.85
5023 5431 3.746940 AGGGCGCTTGTAAAAACTCTAA 58.253 40.909 7.64 0.00 0.00 2.10
5024 5432 3.412237 AGGGCGCTTGTAAAAACTCTA 57.588 42.857 7.64 0.00 0.00 2.43
5025 5433 2.271944 AGGGCGCTTGTAAAAACTCT 57.728 45.000 7.64 0.00 0.00 3.24
5026 5434 2.661594 CAAGGGCGCTTGTAAAAACTC 58.338 47.619 29.80 0.00 0.00 3.01
5027 5435 1.269569 GCAAGGGCGCTTGTAAAAACT 60.270 47.619 35.16 2.76 36.74 2.66
5028 5436 1.136690 GCAAGGGCGCTTGTAAAAAC 58.863 50.000 35.16 19.35 36.74 2.43
5029 5437 0.747255 TGCAAGGGCGCTTGTAAAAA 59.253 45.000 35.16 18.53 45.35 1.94
5030 5438 0.747255 TTGCAAGGGCGCTTGTAAAA 59.253 45.000 33.78 25.38 45.35 1.52
5031 5439 0.031449 GTTGCAAGGGCGCTTGTAAA 59.969 50.000 36.08 28.48 45.35 2.01
5032 5440 1.103987 TGTTGCAAGGGCGCTTGTAA 61.104 50.000 32.79 32.79 45.35 2.41
5033 5441 1.527148 TGTTGCAAGGGCGCTTGTA 60.527 52.632 35.16 31.05 45.35 2.41
5034 5442 2.832661 TGTTGCAAGGGCGCTTGT 60.833 55.556 35.16 7.26 45.35 3.16
5035 5443 2.355009 GTGTTGCAAGGGCGCTTG 60.355 61.111 32.71 32.71 45.35 4.01
5036 5444 3.964875 CGTGTTGCAAGGGCGCTT 61.965 61.111 10.73 10.73 45.35 4.68
5040 5448 3.683937 ATGCCGTGTTGCAAGGGC 61.684 61.111 22.74 22.74 45.84 5.19
5041 5449 2.259204 CATGCCGTGTTGCAAGGG 59.741 61.111 0.00 2.72 45.84 3.95
5042 5450 2.259204 CCATGCCGTGTTGCAAGG 59.741 61.111 0.00 0.00 45.84 3.61
5043 5451 2.431260 GCCATGCCGTGTTGCAAG 60.431 61.111 0.00 0.00 45.84 4.01
5044 5452 2.097201 ATTGCCATGCCGTGTTGCAA 62.097 50.000 0.00 0.00 45.84 4.08
5045 5453 2.097201 AATTGCCATGCCGTGTTGCA 62.097 50.000 0.00 0.00 46.94 4.08
5046 5454 0.108898 TAATTGCCATGCCGTGTTGC 60.109 50.000 0.00 0.00 0.00 4.17
5047 5455 1.202114 AGTAATTGCCATGCCGTGTTG 59.798 47.619 0.00 0.00 0.00 3.33
5048 5456 1.472480 GAGTAATTGCCATGCCGTGTT 59.528 47.619 0.00 0.00 0.00 3.32
5049 5457 1.094785 GAGTAATTGCCATGCCGTGT 58.905 50.000 0.00 0.00 0.00 4.49
5050 5458 1.331756 GAGAGTAATTGCCATGCCGTG 59.668 52.381 0.00 0.00 0.00 4.94
5051 5459 1.668419 GAGAGTAATTGCCATGCCGT 58.332 50.000 0.00 0.00 0.00 5.68
5052 5460 0.583438 CGAGAGTAATTGCCATGCCG 59.417 55.000 0.00 0.00 0.00 5.69
5053 5461 1.668419 ACGAGAGTAATTGCCATGCC 58.332 50.000 0.00 0.00 46.88 4.40
5064 5472 4.099881 AGGGTGTTTTGTTGTACGAGAGTA 59.900 41.667 0.00 0.00 46.88 2.59
5066 5474 3.463944 AGGGTGTTTTGTTGTACGAGAG 58.536 45.455 0.00 0.00 0.00 3.20
5067 5475 3.547054 AGGGTGTTTTGTTGTACGAGA 57.453 42.857 0.00 0.00 0.00 4.04
5068 5476 4.374399 ACTAGGGTGTTTTGTTGTACGAG 58.626 43.478 0.00 0.00 0.00 4.18
5069 5477 4.405116 ACTAGGGTGTTTTGTTGTACGA 57.595 40.909 0.00 0.00 0.00 3.43
5070 5478 5.295045 AGAAACTAGGGTGTTTTGTTGTACG 59.705 40.000 0.00 0.00 39.86 3.67
5071 5479 6.688637 AGAAACTAGGGTGTTTTGTTGTAC 57.311 37.500 0.00 0.00 39.86 2.90
5072 5480 7.012610 GCTAAGAAACTAGGGTGTTTTGTTGTA 59.987 37.037 0.00 0.00 39.86 2.41
5073 5481 6.183360 GCTAAGAAACTAGGGTGTTTTGTTGT 60.183 38.462 0.00 0.00 39.86 3.32
5074 5482 6.183360 TGCTAAGAAACTAGGGTGTTTTGTTG 60.183 38.462 0.00 0.00 39.86 3.33
5075 5483 5.889289 TGCTAAGAAACTAGGGTGTTTTGTT 59.111 36.000 0.00 0.00 39.86 2.83
5076 5484 5.298527 GTGCTAAGAAACTAGGGTGTTTTGT 59.701 40.000 0.00 0.00 39.86 2.83
5077 5485 5.278315 GGTGCTAAGAAACTAGGGTGTTTTG 60.278 44.000 0.00 0.00 39.86 2.44
5078 5486 4.825634 GGTGCTAAGAAACTAGGGTGTTTT 59.174 41.667 0.00 0.00 39.86 2.43
5079 5487 4.104261 AGGTGCTAAGAAACTAGGGTGTTT 59.896 41.667 0.00 0.00 42.11 2.83
5080 5488 3.651423 AGGTGCTAAGAAACTAGGGTGTT 59.349 43.478 0.00 0.00 0.00 3.32
5081 5489 3.008049 CAGGTGCTAAGAAACTAGGGTGT 59.992 47.826 0.00 0.00 0.00 4.16
5082 5490 3.600388 CAGGTGCTAAGAAACTAGGGTG 58.400 50.000 0.00 0.00 0.00 4.61
5083 5491 2.027100 GCAGGTGCTAAGAAACTAGGGT 60.027 50.000 0.00 0.00 38.21 4.34
5084 5492 2.633488 GCAGGTGCTAAGAAACTAGGG 58.367 52.381 0.00 0.00 38.21 3.53
5085 5493 2.633488 GGCAGGTGCTAAGAAACTAGG 58.367 52.381 1.26 0.00 41.70 3.02
5086 5494 2.271800 CGGCAGGTGCTAAGAAACTAG 58.728 52.381 1.26 0.00 41.70 2.57
5087 5495 1.621814 ACGGCAGGTGCTAAGAAACTA 59.378 47.619 1.26 0.00 41.70 2.24
5088 5496 0.396811 ACGGCAGGTGCTAAGAAACT 59.603 50.000 1.26 0.00 41.70 2.66
5089 5497 2.088950 TACGGCAGGTGCTAAGAAAC 57.911 50.000 1.26 0.00 41.70 2.78
5090 5498 2.419667 GTTACGGCAGGTGCTAAGAAA 58.580 47.619 1.26 0.00 41.70 2.52
5091 5499 1.338389 GGTTACGGCAGGTGCTAAGAA 60.338 52.381 1.26 0.00 41.70 2.52
5092 5500 0.248289 GGTTACGGCAGGTGCTAAGA 59.752 55.000 1.26 0.00 41.70 2.10
5093 5501 0.743345 GGGTTACGGCAGGTGCTAAG 60.743 60.000 1.26 0.00 41.70 2.18
5094 5502 1.297364 GGGTTACGGCAGGTGCTAA 59.703 57.895 1.26 0.00 41.70 3.09
5095 5503 1.268992 ATGGGTTACGGCAGGTGCTA 61.269 55.000 1.26 0.00 41.70 3.49
5096 5504 1.268992 TATGGGTTACGGCAGGTGCT 61.269 55.000 1.26 0.00 41.70 4.40
5097 5505 0.393267 TTATGGGTTACGGCAGGTGC 60.393 55.000 0.00 0.00 41.14 5.01
5098 5506 2.341846 ATTATGGGTTACGGCAGGTG 57.658 50.000 0.00 0.00 0.00 4.00
5099 5507 3.375647 AAATTATGGGTTACGGCAGGT 57.624 42.857 0.00 0.00 0.00 4.00
5100 5508 3.736740 GCAAAATTATGGGTTACGGCAGG 60.737 47.826 0.00 0.00 0.00 4.85
5101 5509 3.443976 GCAAAATTATGGGTTACGGCAG 58.556 45.455 0.00 0.00 0.00 4.85
5102 5510 2.166664 GGCAAAATTATGGGTTACGGCA 59.833 45.455 0.00 0.00 0.00 5.69
5103 5511 2.429250 AGGCAAAATTATGGGTTACGGC 59.571 45.455 0.00 0.00 0.00 5.68
5104 5512 3.697045 TGAGGCAAAATTATGGGTTACGG 59.303 43.478 0.00 0.00 0.00 4.02
5105 5513 4.974368 TGAGGCAAAATTATGGGTTACG 57.026 40.909 0.00 0.00 0.00 3.18
5106 5514 5.109210 GCTTGAGGCAAAATTATGGGTTAC 58.891 41.667 0.00 0.00 41.35 2.50
5107 5515 5.337578 GCTTGAGGCAAAATTATGGGTTA 57.662 39.130 0.00 0.00 41.35 2.85
5108 5516 4.206477 GCTTGAGGCAAAATTATGGGTT 57.794 40.909 0.00 0.00 41.35 4.11
5109 5517 3.893326 GCTTGAGGCAAAATTATGGGT 57.107 42.857 0.00 0.00 41.35 4.51
5121 5529 2.682856 TCCAAAATATCGTGCTTGAGGC 59.317 45.455 0.00 0.00 42.22 4.70
5122 5530 3.242870 GCTCCAAAATATCGTGCTTGAGG 60.243 47.826 0.00 0.00 0.00 3.86
5123 5531 3.374988 TGCTCCAAAATATCGTGCTTGAG 59.625 43.478 0.00 0.00 0.00 3.02
5124 5532 3.342719 TGCTCCAAAATATCGTGCTTGA 58.657 40.909 0.00 0.00 0.00 3.02
5125 5533 3.488047 CCTGCTCCAAAATATCGTGCTTG 60.488 47.826 0.00 0.00 0.00 4.01
5126 5534 2.684881 CCTGCTCCAAAATATCGTGCTT 59.315 45.455 0.00 0.00 0.00 3.91
5127 5535 2.092968 TCCTGCTCCAAAATATCGTGCT 60.093 45.455 0.00 0.00 0.00 4.40
5128 5536 2.288666 TCCTGCTCCAAAATATCGTGC 58.711 47.619 0.00 0.00 0.00 5.34
5129 5537 4.692625 CCTATCCTGCTCCAAAATATCGTG 59.307 45.833 0.00 0.00 0.00 4.35
5130 5538 4.804261 GCCTATCCTGCTCCAAAATATCGT 60.804 45.833 0.00 0.00 0.00 3.73
5131 5539 3.686726 GCCTATCCTGCTCCAAAATATCG 59.313 47.826 0.00 0.00 0.00 2.92
5132 5540 3.686726 CGCCTATCCTGCTCCAAAATATC 59.313 47.826 0.00 0.00 0.00 1.63
5133 5541 3.560025 CCGCCTATCCTGCTCCAAAATAT 60.560 47.826 0.00 0.00 0.00 1.28
5134 5542 2.224523 CCGCCTATCCTGCTCCAAAATA 60.225 50.000 0.00 0.00 0.00 1.40
5135 5543 1.477558 CCGCCTATCCTGCTCCAAAAT 60.478 52.381 0.00 0.00 0.00 1.82
5136 5544 0.107214 CCGCCTATCCTGCTCCAAAA 60.107 55.000 0.00 0.00 0.00 2.44
5137 5545 1.526887 CCGCCTATCCTGCTCCAAA 59.473 57.895 0.00 0.00 0.00 3.28
5138 5546 3.106986 GCCGCCTATCCTGCTCCAA 62.107 63.158 0.00 0.00 0.00 3.53
5139 5547 3.550431 GCCGCCTATCCTGCTCCA 61.550 66.667 0.00 0.00 0.00 3.86
5140 5548 4.671569 CGCCGCCTATCCTGCTCC 62.672 72.222 0.00 0.00 0.00 4.70
5141 5549 4.671569 CCGCCGCCTATCCTGCTC 62.672 72.222 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.