Multiple sequence alignment - TraesCS3B01G090800

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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 TraesCS3B01G090800 chr3B 100.000 7567 0 0 1 7567 59748640 59756206 0.000000e+00 13974.0
1 TraesCS3B01G090800 chr3B 91.014 2081 110 34 2452 4502 59997207 59995174 0.000000e+00 2736.0
2 TraesCS3B01G090800 chr3B 94.238 1024 44 3 4682 5701 59968849 59967837 0.000000e+00 1550.0
3 TraesCS3B01G090800 chr3B 86.002 1043 109 21 5700 6737 59962210 59961200 0.000000e+00 1083.0
4 TraesCS3B01G090800 chr3B 96.147 597 21 2 6972 7567 200177357 200176762 0.000000e+00 974.0
5 TraesCS3B01G090800 chr3A 93.454 6370 298 40 580 6866 47551499 47557832 0.000000e+00 9343.0
6 TraesCS3B01G090800 chr3A 93.617 4042 196 20 2873 6872 47526122 47530143 0.000000e+00 5978.0
7 TraesCS3B01G090800 chr3A 93.345 3922 183 33 29 3893 47579455 47583355 0.000000e+00 5725.0
8 TraesCS3B01G090800 chr3A 93.644 3021 142 23 3886 6874 47583521 47586523 0.000000e+00 4470.0
9 TraesCS3B01G090800 chr3A 89.690 1678 119 15 394 2035 47523714 47525373 0.000000e+00 2091.0
10 TraesCS3B01G090800 chr3A 93.026 760 47 2 2073 2832 47525371 47526124 0.000000e+00 1105.0
11 TraesCS3B01G090800 chr3A 97.643 594 14 0 6974 7567 750714282 750713689 0.000000e+00 1020.0
12 TraesCS3B01G090800 chr3A 91.625 597 37 6 1 590 47544679 47545269 0.000000e+00 813.0
13 TraesCS3B01G090800 chr3A 90.709 409 27 7 6471 6874 47557831 47558233 1.120000e-147 534.0
14 TraesCS3B01G090800 chr3A 94.366 71 1 1 6903 6970 47530207 47530277 1.040000e-18 106.0
15 TraesCS3B01G090800 chr3D 93.152 4629 240 40 2393 6972 37267922 37272522 0.000000e+00 6721.0
16 TraesCS3B01G090800 chr3D 93.792 4011 166 25 1265 5204 37285912 37289910 0.000000e+00 5951.0
17 TraesCS3B01G090800 chr3D 93.287 3620 180 27 2393 5979 37453568 37449979 0.000000e+00 5280.0
18 TraesCS3B01G090800 chr3D 91.277 3554 197 36 394 3886 37243370 37246871 0.000000e+00 4741.0
19 TraesCS3B01G090800 chr3D 93.361 3133 157 26 3873 6972 37246892 37250006 0.000000e+00 4586.0
20 TraesCS3B01G090800 chr3D 92.741 2576 124 25 2393 4937 37546660 37544117 0.000000e+00 3663.0
21 TraesCS3B01G090800 chr3D 90.546 2401 152 24 37 2398 37455895 37453531 0.000000e+00 3107.0
22 TraesCS3B01G090800 chr3D 89.985 2037 129 24 394 2398 37265966 37267959 0.000000e+00 2562.0
23 TraesCS3B01G090800 chr3D 92.658 1689 106 12 5195 6874 37442307 37440628 0.000000e+00 2416.0
24 TraesCS3B01G090800 chr3D 90.065 1681 103 19 753 2398 37548274 37546623 0.000000e+00 2121.0
25 TraesCS3B01G090800 chr3D 89.780 1683 106 30 753 2398 37534706 37533053 0.000000e+00 2095.0
26 TraesCS3B01G090800 chr3D 89.314 1151 115 7 5592 6737 37526991 37525844 0.000000e+00 1437.0
27 TraesCS3B01G090800 chr3D 89.314 1151 115 7 5592 6737 37540860 37539713 0.000000e+00 1437.0
28 TraesCS3B01G090800 chr3D 87.743 824 76 11 437 1249 37285116 37285925 0.000000e+00 939.0
29 TraesCS3B01G090800 chr3D 93.939 594 26 1 5003 5596 37532843 37532260 0.000000e+00 889.0
30 TraesCS3B01G090800 chr3D 86.145 729 58 16 37 764 37550321 37549635 0.000000e+00 747.0
31 TraesCS3B01G090800 chr3D 85.597 729 62 16 37 764 38107704 38107018 0.000000e+00 725.0
32 TraesCS3B01G090800 chr3D 86.080 352 37 5 1 351 37243029 37243369 1.200000e-97 368.0
33 TraesCS3B01G090800 chr3D 97.842 139 3 0 4880 5018 37532995 37532857 2.730000e-59 241.0
34 TraesCS3B01G090800 chr3D 96.040 101 4 0 2393 2493 37533090 37532990 1.690000e-36 165.0
35 TraesCS3B01G090800 chr3D 97.368 38 1 0 2361 2398 37245360 37245397 1.760000e-06 65.8
36 TraesCS3B01G090800 chr3D 91.111 45 4 0 1 45 37553590 37553546 2.280000e-05 62.1
37 TraesCS3B01G090800 chr3D 88.235 51 5 1 339 388 116553881 116553831 8.200000e-05 60.2
38 TraesCS3B01G090800 chr5A 98.154 596 11 0 6972 7567 573624059 573623464 0.000000e+00 1040.0
39 TraesCS3B01G090800 chr1B 98.157 597 10 1 6972 7567 563704503 563703907 0.000000e+00 1040.0
40 TraesCS3B01G090800 chr6B 97.980 594 12 0 6974 7567 57581840 57581247 0.000000e+00 1031.0
41 TraesCS3B01G090800 chr6B 97.647 595 14 0 6973 7567 715202105 715202699 0.000000e+00 1022.0
42 TraesCS3B01G090800 chr4A 97.647 595 13 1 6973 7567 77446227 77446820 0.000000e+00 1020.0
43 TraesCS3B01G090800 chr4A 100.000 28 0 0 2156 2183 271160973 271161000 1.400000e-02 52.8
44 TraesCS3B01G090800 chr2B 97.138 594 17 0 6974 7567 453226320 453226913 0.000000e+00 1003.0
45 TraesCS3B01G090800 chr1A 96.477 596 17 3 6973 7567 23425806 23425214 0.000000e+00 981.0
46 TraesCS3B01G090800 chr2A 100.000 28 0 0 339 366 745124679 745124706 1.400000e-02 52.8


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 TraesCS3B01G090800 chr3B 59748640 59756206 7566 False 13974.00 13974 100.00000 1 7567 1 chr3B.!!$F1 7566
1 TraesCS3B01G090800 chr3B 59995174 59997207 2033 True 2736.00 2736 91.01400 2452 4502 1 chr3B.!!$R3 2050
2 TraesCS3B01G090800 chr3B 59967837 59968849 1012 True 1550.00 1550 94.23800 4682 5701 1 chr3B.!!$R2 1019
3 TraesCS3B01G090800 chr3B 59961200 59962210 1010 True 1083.00 1083 86.00200 5700 6737 1 chr3B.!!$R1 1037
4 TraesCS3B01G090800 chr3B 200176762 200177357 595 True 974.00 974 96.14700 6972 7567 1 chr3B.!!$R4 595
5 TraesCS3B01G090800 chr3A 47579455 47586523 7068 False 5097.50 5725 93.49450 29 6874 2 chr3A.!!$F4 6845
6 TraesCS3B01G090800 chr3A 47551499 47558233 6734 False 4938.50 9343 92.08150 580 6874 2 chr3A.!!$F3 6294
7 TraesCS3B01G090800 chr3A 47523714 47530277 6563 False 2320.00 5978 92.67475 394 6970 4 chr3A.!!$F2 6576
8 TraesCS3B01G090800 chr3A 750713689 750714282 593 True 1020.00 1020 97.64300 6974 7567 1 chr3A.!!$R1 593
9 TraesCS3B01G090800 chr3A 47544679 47545269 590 False 813.00 813 91.62500 1 590 1 chr3A.!!$F1 589
10 TraesCS3B01G090800 chr3D 37265966 37272522 6556 False 4641.50 6721 91.56850 394 6972 2 chr3D.!!$F2 6578
11 TraesCS3B01G090800 chr3D 37449979 37455895 5916 True 4193.50 5280 91.91650 37 5979 2 chr3D.!!$R5 5942
12 TraesCS3B01G090800 chr3D 37285116 37289910 4794 False 3445.00 5951 90.76750 437 5204 2 chr3D.!!$F3 4767
13 TraesCS3B01G090800 chr3D 37243029 37250006 6977 False 2440.20 4741 92.02150 1 6972 4 chr3D.!!$F1 6971
14 TraesCS3B01G090800 chr3D 37440628 37442307 1679 True 2416.00 2416 92.65800 5195 6874 1 chr3D.!!$R1 1679
15 TraesCS3B01G090800 chr3D 37539713 37553590 13877 True 1606.02 3663 89.87520 1 6737 5 chr3D.!!$R7 6736
16 TraesCS3B01G090800 chr3D 37525844 37526991 1147 True 1437.00 1437 89.31400 5592 6737 1 chr3D.!!$R2 1145
17 TraesCS3B01G090800 chr3D 37532260 37534706 2446 True 847.50 2095 94.40025 753 5596 4 chr3D.!!$R6 4843
18 TraesCS3B01G090800 chr3D 38107018 38107704 686 True 725.00 725 85.59700 37 764 1 chr3D.!!$R3 727
19 TraesCS3B01G090800 chr5A 573623464 573624059 595 True 1040.00 1040 98.15400 6972 7567 1 chr5A.!!$R1 595
20 TraesCS3B01G090800 chr1B 563703907 563704503 596 True 1040.00 1040 98.15700 6972 7567 1 chr1B.!!$R1 595
21 TraesCS3B01G090800 chr6B 57581247 57581840 593 True 1031.00 1031 97.98000 6974 7567 1 chr6B.!!$R1 593
22 TraesCS3B01G090800 chr6B 715202105 715202699 594 False 1022.00 1022 97.64700 6973 7567 1 chr6B.!!$F1 594
23 TraesCS3B01G090800 chr4A 77446227 77446820 593 False 1020.00 1020 97.64700 6973 7567 1 chr4A.!!$F1 594
24 TraesCS3B01G090800 chr2B 453226320 453226913 593 False 1003.00 1003 97.13800 6974 7567 1 chr2B.!!$F1 593
25 TraesCS3B01G090800 chr1A 23425214 23425806 592 True 981.00 981 96.47700 6973 7567 1 chr1A.!!$R1 594

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
201 3439 0.172803 CGAGGACTAGTTTCCCGTGG 59.827 60.000 0.00 0.00 36.12 4.94 F
1243 5878 0.250338 GGACGGTGAGTTTGCCTTCT 60.250 55.000 0.00 0.00 0.00 2.85 F
1340 5984 0.238289 CTTACAAGGCTGCGTGGTTG 59.762 55.000 7.77 4.62 0.00 3.77 F
1453 6100 1.272490 TGTTCTAGTCAACTGAGGCGG 59.728 52.381 0.00 0.00 0.00 6.13 F
2907 7659 1.202359 CGGGGAAAATAATGTTGCCGG 60.202 52.381 0.00 0.00 37.35 6.13 F
4015 9028 2.460757 ATGTGATTGTTTTGCAGCCC 57.539 45.000 0.00 0.00 0.00 5.19 F
5168 11398 1.211457 AGGTGCCTTCTGCTGATAAGG 59.789 52.381 6.91 6.91 44.32 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1318 5962 0.951558 CCACGCAGCCTTGTAAGTTT 59.048 50.000 0.00 0.00 0.00 2.66 R
2421 7136 1.804151 TCGGCAACATGTTCTACAAGC 59.196 47.619 8.48 7.94 0.00 4.01 R
2674 7426 1.999735 TCGCTGACGATTCAATCCAAC 59.000 47.619 0.00 0.00 45.12 3.77 R
3157 7920 2.374184 TCTTAATTCCCGGGTGCAATG 58.626 47.619 22.86 8.60 0.00 2.82 R
4516 9566 0.379669 GCAGCACATTCTGATTCCCG 59.620 55.000 0.00 0.00 36.19 5.14 R
5625 13278 1.743958 CTGGACCGACGTAGAACTGAT 59.256 52.381 0.00 0.00 0.00 2.90 R
6899 14975 0.034089 GCCCCTGTTTAGCATCAGGT 60.034 55.000 9.79 0.00 46.79 4.00 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
45 3279 5.603596 GCATGAATTGCCTGGATAATTTGA 58.396 37.500 0.00 0.00 46.15 2.69
91 3325 1.054406 AACATCGATCGGTGGGGGAT 61.054 55.000 30.41 7.98 0.00 3.85
98 3332 3.470888 CGGTGGGGGATTCGAGCT 61.471 66.667 0.00 0.00 0.00 4.09
118 3352 2.561419 CTCCTCGAACCACTTGGACTTA 59.439 50.000 1.14 0.00 38.94 2.24
121 3355 3.244112 CCTCGAACCACTTGGACTTAACT 60.244 47.826 1.14 0.00 38.94 2.24
198 3436 1.141234 GCCGAGGACTAGTTTCCCG 59.859 63.158 0.00 1.09 36.12 5.14
199 3437 1.602327 GCCGAGGACTAGTTTCCCGT 61.602 60.000 0.00 0.00 36.12 5.28
201 3439 0.172803 CGAGGACTAGTTTCCCGTGG 59.827 60.000 0.00 0.00 36.12 4.94
233 3471 1.207791 GACATGATCTGACCAGGGGT 58.792 55.000 0.00 0.00 39.44 4.95
238 3476 2.543067 GATCTGACCAGGGGTGGTGC 62.543 65.000 0.72 0.00 43.24 5.01
239 3477 4.351054 CTGACCAGGGGTGGTGCC 62.351 72.222 0.72 0.00 43.24 5.01
241 3479 4.351054 GACCAGGGGTGGTGCCAG 62.351 72.222 0.72 0.00 43.24 4.85
371 3609 0.465705 CAGCTGACCCCACATCGTAT 59.534 55.000 8.42 0.00 0.00 3.06
597 3839 0.313987 TCAGCACACACACTCTACGG 59.686 55.000 0.00 0.00 0.00 4.02
622 3876 6.476053 GTCGATCCAGTTTAGTATCTCAAACC 59.524 42.308 0.00 0.00 35.66 3.27
640 3894 9.832445 TCTCAAACCTTAAATGGTAGTGATATC 57.168 33.333 0.00 0.00 39.83 1.63
658 3912 1.075601 TCTGGCCCTGGAAACTGATT 58.924 50.000 0.00 0.00 0.00 2.57
666 3920 3.189287 CCCTGGAAACTGATTGAACGAAG 59.811 47.826 0.00 0.00 0.00 3.79
712 3966 1.202336 CCCAAAATCAATCTCCAGCGC 60.202 52.381 0.00 0.00 0.00 5.92
773 5399 4.099419 CCCCAAAGTTAATGCCCAATACTC 59.901 45.833 0.00 0.00 0.00 2.59
874 5501 3.187700 AGAGCGTTCACCTATAAAAGCG 58.812 45.455 1.01 0.00 35.44 4.68
875 5502 3.119245 AGAGCGTTCACCTATAAAAGCGA 60.119 43.478 1.01 0.00 35.44 4.93
997 5632 0.323302 TGGTTGGCGAGCATCTTACA 59.677 50.000 1.65 0.00 0.00 2.41
1238 5873 1.671379 GGGAGGACGGTGAGTTTGC 60.671 63.158 0.00 0.00 0.00 3.68
1243 5878 0.250338 GGACGGTGAGTTTGCCTTCT 60.250 55.000 0.00 0.00 0.00 2.85
1318 5962 2.164338 GCTTGGATCGGGGTTACAAAA 58.836 47.619 0.00 0.00 0.00 2.44
1340 5984 0.238289 CTTACAAGGCTGCGTGGTTG 59.762 55.000 7.77 4.62 0.00 3.77
1382 6029 9.646427 GTGAAGTCTGTGATTTACTAGATTTCT 57.354 33.333 0.00 0.00 36.01 2.52
1453 6100 1.272490 TGTTCTAGTCAACTGAGGCGG 59.728 52.381 0.00 0.00 0.00 6.13
1567 6214 2.739913 CGTTTCGGGTTTGCAGAATCTA 59.260 45.455 0.00 0.00 0.00 1.98
1760 6416 6.932901 TGAGAATTGAATCGCAAATTGAAC 57.067 33.333 0.00 0.00 40.48 3.18
1855 6512 2.568956 AGGCTTCATAGACTGCTTGTGA 59.431 45.455 0.00 0.00 38.73 3.58
1975 6657 1.981256 ACCGGATGTATGATTTGGGC 58.019 50.000 9.46 0.00 0.00 5.36
2067 6749 8.820628 AAACGAAATGACATGTTCATATTACG 57.179 30.769 0.00 10.68 44.86 3.18
2184 6866 4.836125 TTTCAAGTCAGCCAAGATTGAC 57.164 40.909 0.00 0.00 43.08 3.18
2187 6869 2.886523 CAAGTCAGCCAAGATTGACCAA 59.113 45.455 1.34 0.00 43.64 3.67
2237 6919 4.044426 GATTGCATTTGGCGATTAGGAAC 58.956 43.478 0.00 0.00 46.90 3.62
2391 7106 4.018597 AGGAAGAGAATGGAATCAGCAGTT 60.019 41.667 0.00 0.00 0.00 3.16
2392 7107 4.704057 GGAAGAGAATGGAATCAGCAGTTT 59.296 41.667 0.00 0.00 0.00 2.66
2393 7108 5.392811 GGAAGAGAATGGAATCAGCAGTTTG 60.393 44.000 0.00 0.00 0.00 2.93
2394 7109 4.660168 AGAGAATGGAATCAGCAGTTTGT 58.340 39.130 0.00 0.00 0.00 2.83
2395 7110 5.809001 AGAGAATGGAATCAGCAGTTTGTA 58.191 37.500 0.00 0.00 0.00 2.41
2396 7111 5.879223 AGAGAATGGAATCAGCAGTTTGTAG 59.121 40.000 0.00 0.00 0.00 2.74
2397 7112 5.809001 AGAATGGAATCAGCAGTTTGTAGA 58.191 37.500 0.00 0.00 0.00 2.59
2398 7113 6.421485 AGAATGGAATCAGCAGTTTGTAGAT 58.579 36.000 0.00 0.00 0.00 1.98
2399 7114 6.888632 AGAATGGAATCAGCAGTTTGTAGATT 59.111 34.615 0.00 0.00 0.00 2.40
2400 7115 5.885230 TGGAATCAGCAGTTTGTAGATTG 57.115 39.130 0.00 0.00 0.00 2.67
2401 7116 4.701651 TGGAATCAGCAGTTTGTAGATTGG 59.298 41.667 0.00 0.00 0.00 3.16
2402 7117 4.096984 GGAATCAGCAGTTTGTAGATTGGG 59.903 45.833 0.00 0.00 0.00 4.12
2403 7118 4.574674 ATCAGCAGTTTGTAGATTGGGA 57.425 40.909 0.00 0.00 0.00 4.37
2404 7119 4.365514 TCAGCAGTTTGTAGATTGGGAA 57.634 40.909 0.00 0.00 0.00 3.97
2405 7120 4.326826 TCAGCAGTTTGTAGATTGGGAAG 58.673 43.478 0.00 0.00 0.00 3.46
2406 7121 4.041567 TCAGCAGTTTGTAGATTGGGAAGA 59.958 41.667 0.00 0.00 0.00 2.87
2407 7122 4.394300 CAGCAGTTTGTAGATTGGGAAGAG 59.606 45.833 0.00 0.00 0.00 2.85
2408 7123 4.287067 AGCAGTTTGTAGATTGGGAAGAGA 59.713 41.667 0.00 0.00 0.00 3.10
2409 7124 5.003804 GCAGTTTGTAGATTGGGAAGAGAA 58.996 41.667 0.00 0.00 0.00 2.87
2410 7125 5.649831 GCAGTTTGTAGATTGGGAAGAGAAT 59.350 40.000 0.00 0.00 0.00 2.40
2411 7126 6.404074 GCAGTTTGTAGATTGGGAAGAGAATG 60.404 42.308 0.00 0.00 0.00 2.67
2412 7127 6.094603 CAGTTTGTAGATTGGGAAGAGAATGG 59.905 42.308 0.00 0.00 0.00 3.16
2413 7128 6.012508 AGTTTGTAGATTGGGAAGAGAATGGA 60.013 38.462 0.00 0.00 0.00 3.41
2414 7129 6.387192 TTGTAGATTGGGAAGAGAATGGAA 57.613 37.500 0.00 0.00 0.00 3.53
2415 7130 6.581388 TGTAGATTGGGAAGAGAATGGAAT 57.419 37.500 0.00 0.00 0.00 3.01
2416 7131 6.595682 TGTAGATTGGGAAGAGAATGGAATC 58.404 40.000 0.00 0.00 0.00 2.52
2417 7132 5.722172 AGATTGGGAAGAGAATGGAATCA 57.278 39.130 0.00 0.00 0.00 2.57
2418 7133 5.692928 AGATTGGGAAGAGAATGGAATCAG 58.307 41.667 0.00 0.00 0.00 2.90
2419 7134 3.287867 TGGGAAGAGAATGGAATCAGC 57.712 47.619 0.00 0.00 0.00 4.26
2420 7135 2.577563 TGGGAAGAGAATGGAATCAGCA 59.422 45.455 0.00 0.00 0.00 4.41
2421 7136 3.212685 GGGAAGAGAATGGAATCAGCAG 58.787 50.000 0.00 0.00 0.00 4.24
2422 7137 2.617774 GGAAGAGAATGGAATCAGCAGC 59.382 50.000 0.00 0.00 0.00 5.25
2508 7258 6.151691 CGATATGGCAAAATATCTTTGTGGG 58.848 40.000 0.00 0.00 37.38 4.61
2571 7321 3.040147 TCGGAAAAGTCAAGTAGGCAG 57.960 47.619 0.00 0.00 0.00 4.85
2674 7426 6.072838 TGTCTATCTTACTTCCGCCGTAATAG 60.073 42.308 0.00 0.00 0.00 1.73
2707 7459 2.159366 CGTCAGCGAGAGGAATTGTAGT 60.159 50.000 0.00 0.00 41.33 2.73
2708 7460 3.673594 CGTCAGCGAGAGGAATTGTAGTT 60.674 47.826 0.00 0.00 41.33 2.24
2709 7461 4.246458 GTCAGCGAGAGGAATTGTAGTTT 58.754 43.478 0.00 0.00 0.00 2.66
2710 7462 4.691216 GTCAGCGAGAGGAATTGTAGTTTT 59.309 41.667 0.00 0.00 0.00 2.43
2752 7504 7.659799 GGGTTGGTTTGTTTCAAATTAGCTAAT 59.340 33.333 13.37 13.37 0.00 1.73
2808 7560 8.897752 GCTTCATAGATTTCTTTTGGTCACTAT 58.102 33.333 0.00 0.00 0.00 2.12
2889 7641 2.745281 ACCATGGTGTAAAATTCGACGG 59.255 45.455 18.99 0.00 0.00 4.79
2907 7659 1.202359 CGGGGAAAATAATGTTGCCGG 60.202 52.381 0.00 0.00 37.35 6.13
3069 7827 5.163854 GGCGTCGTTACTTACAGTCTAACTA 60.164 44.000 0.00 0.00 0.00 2.24
3087 7845 8.044908 GTCTAACTATTGGGAGTTGAATTGGTA 58.955 37.037 0.00 0.00 39.96 3.25
3088 7846 8.265055 TCTAACTATTGGGAGTTGAATTGGTAG 58.735 37.037 0.00 0.00 39.96 3.18
3138 7901 5.533528 GGGCCACACGGTTTATTTATAAGAT 59.466 40.000 4.39 0.00 33.28 2.40
3139 7902 6.711645 GGGCCACACGGTTTATTTATAAGATA 59.288 38.462 4.39 0.00 33.28 1.98
3140 7903 7.094933 GGGCCACACGGTTTATTTATAAGATAG 60.095 40.741 4.39 0.00 33.28 2.08
3141 7904 7.295930 GCCACACGGTTTATTTATAAGATAGC 58.704 38.462 0.00 0.00 33.28 2.97
3165 7928 3.056607 AGCCAAGATTTGTACATTGCACC 60.057 43.478 0.00 0.00 0.00 5.01
3207 7987 8.729805 AAGAGAATGGAAGTAGAGCTTAAATG 57.270 34.615 0.00 0.00 37.59 2.32
3417 8213 7.867305 TGTTTCTGTTATTGGTGTTGTCTAA 57.133 32.000 0.00 0.00 0.00 2.10
3597 8394 4.407365 AGGGAACTGAATGTGGGTTAAAG 58.593 43.478 0.00 0.00 41.13 1.85
3609 8408 7.611213 ATGTGGGTTAAAGATTCGTTAAGAG 57.389 36.000 5.22 0.00 0.00 2.85
3631 8430 6.096846 AGAGTTTTTCTAGTTTGTGCACCATT 59.903 34.615 15.69 0.03 33.23 3.16
3712 8512 9.444600 TGGATTTCATAGTTAACCTAGTCAAAC 57.555 33.333 0.88 0.00 0.00 2.93
3773 8573 6.846350 AGTGAAGAGCAAAATTGTACATAGC 58.154 36.000 0.00 0.00 0.00 2.97
3824 8624 5.116180 GGACATCCGATAATTGTCTGTTCA 58.884 41.667 0.46 0.00 39.70 3.18
4015 9028 2.460757 ATGTGATTGTTTTGCAGCCC 57.539 45.000 0.00 0.00 0.00 5.19
4425 9475 5.123027 GGAATTCACTCACAATGACCTTCTC 59.877 44.000 7.93 0.00 0.00 2.87
4478 9528 5.058149 AGCGCTGTAATCATGAGAGATAG 57.942 43.478 10.39 0.00 0.00 2.08
4516 9566 6.526566 AATGCTTCGGATTCGTTAACTATC 57.473 37.500 3.71 6.54 37.69 2.08
4557 9607 5.208503 GCAGAAGCTGTGAAAAGTCTTAAC 58.791 41.667 0.43 0.00 37.91 2.01
4618 9668 6.352516 AGAGCTCAGAAAAAGTCAGAAAGAA 58.647 36.000 17.77 0.00 0.00 2.52
4624 9674 7.601856 TCAGAAAAAGTCAGAAAGAAAAGCAA 58.398 30.769 0.00 0.00 0.00 3.91
4646 9696 6.128580 GCAAAACTGAAAGAAAACTTTGAGCA 60.129 34.615 8.55 0.00 37.43 4.26
4695 9745 5.353394 TTGAAGGGCTCAATCTATACGTT 57.647 39.130 0.00 0.00 39.20 3.99
4826 9876 8.484214 TTCTGGTTCTTAGTATCATAGCTCAT 57.516 34.615 0.00 0.00 0.00 2.90
4953 10004 8.802267 AGTAACATGGTTTAGTTGTATGCAAAT 58.198 29.630 1.40 1.40 36.22 2.32
5042 11272 3.384789 CGGGATGAACAGGAAGATAGTCA 59.615 47.826 0.00 0.00 0.00 3.41
5168 11398 1.211457 AGGTGCCTTCTGCTGATAAGG 59.789 52.381 6.91 6.91 44.32 2.69
5185 11415 7.598759 TGATAAGGGATAAGTAGTGACTTCC 57.401 40.000 0.00 0.00 42.50 3.46
5235 12232 6.030228 GTGCTGTTTGAGTTCTAATATTGCC 58.970 40.000 0.00 0.00 0.00 4.52
5625 13278 2.122768 ACCACAAAATTTTGCTCCCCA 58.877 42.857 26.94 0.00 41.79 4.96
5759 13413 6.287107 GCATGACGCCATATACATATAACC 57.713 41.667 0.00 0.00 32.94 2.85
5910 13565 1.973281 AAAGTGCATCCAGCCGTGG 60.973 57.895 0.00 0.00 46.63 4.94
5921 13576 4.120331 GCCGTGGCCATGTTCAGC 62.120 66.667 23.39 15.38 34.56 4.26
5969 13625 6.261381 ACCTGACTTTTCGTGCTTTTACAATA 59.739 34.615 0.00 0.00 0.00 1.90
5999 13655 0.763986 ACCCAAATGCCAACCAAGCT 60.764 50.000 0.00 0.00 0.00 3.74
6020 13676 5.047164 AGCTTTCACATACATGCCAAATTCA 60.047 36.000 0.00 0.00 0.00 2.57
6034 13690 6.231951 TGCCAAATTCAATGAATGTGAATGT 58.768 32.000 23.77 0.00 43.32 2.71
6070 13726 2.111043 CCCGGGCTTCGCACATAT 59.889 61.111 8.08 0.00 37.59 1.78
6143 13800 3.173151 TGCTGTAGATTCTTCTGACCCA 58.827 45.455 0.00 0.00 33.17 4.51
6166 13824 6.102663 CAGAGAAACAACATCTCGTAAGGAT 58.897 40.000 0.00 0.00 46.31 3.24
6312 13974 1.806542 TGCAGATTCAAGGCGAGAAAC 59.193 47.619 0.00 0.00 0.00 2.78
6330 13992 1.448540 CTGTACCCGCTGGCTGAAG 60.449 63.158 0.00 0.00 33.59 3.02
6336 13998 1.219124 CCGCTGGCTGAAGAGCTTA 59.781 57.895 0.00 0.00 45.44 3.09
6389 14051 0.899717 TGGGTGAAGCAATGGAAGCC 60.900 55.000 0.00 0.00 0.00 4.35
6396 14058 1.079612 GCAATGGAAGCCCTGCAAC 60.080 57.895 0.00 0.00 33.34 4.17
6413 14075 2.814336 GCAACGAAGGAAAGTGGAAGAT 59.186 45.455 0.00 0.00 0.00 2.40
6449 14111 2.025727 CTCGCGTCCGTACCATCC 59.974 66.667 5.77 0.00 35.54 3.51
6450 14112 2.751036 TCGCGTCCGTACCATCCA 60.751 61.111 5.77 0.00 35.54 3.41
6524 14186 1.140589 CTCGAGTGCTTCCGCTGAT 59.859 57.895 3.62 0.00 36.97 2.90
6567 14629 1.202348 CGTCATCCTCGAGTGCTTGAT 60.202 52.381 12.31 3.45 0.00 2.57
6572 14634 1.824852 TCCTCGAGTGCTTGATTGCTA 59.175 47.619 12.31 0.00 0.00 3.49
6669 14734 5.755375 GCTTCATGATATTTTCGGTCAGAGA 59.245 40.000 0.00 0.00 0.00 3.10
6740 14812 9.807921 TTCCCCAATATTTAGGATAACTTCATC 57.192 33.333 4.42 0.00 0.00 2.92
6741 14813 8.954729 TCCCCAATATTTAGGATAACTTCATCA 58.045 33.333 3.25 0.00 0.00 3.07
6789 14864 2.024941 CCTTTGGCAGGGATCCTAGTTT 60.025 50.000 12.58 0.00 39.39 2.66
6803 14879 6.260271 GGATCCTAGTTTCTTCCAATTTACGG 59.740 42.308 3.84 0.00 0.00 4.02
6805 14881 6.168389 TCCTAGTTTCTTCCAATTTACGGAC 58.832 40.000 0.00 0.00 30.29 4.79
6872 14948 3.233578 CTCACAAAACACACACACACAC 58.766 45.455 0.00 0.00 0.00 3.82
6875 14951 2.359214 ACAAAACACACACACACACACA 59.641 40.909 0.00 0.00 0.00 3.72
6876 14952 2.697431 AAACACACACACACACACAC 57.303 45.000 0.00 0.00 0.00 3.82
6879 14955 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
6880 14956 1.136000 CACACACACACACACACACAG 60.136 52.381 0.00 0.00 0.00 3.66
6882 14958 1.128507 CACACACACACACACACAGAC 59.871 52.381 0.00 0.00 0.00 3.51
6884 14960 1.128507 CACACACACACACACAGACAC 59.871 52.381 0.00 0.00 0.00 3.67
6885 14961 1.270571 ACACACACACACACAGACACA 60.271 47.619 0.00 0.00 0.00 3.72
6886 14962 1.128507 CACACACACACACAGACACAC 59.871 52.381 0.00 0.00 0.00 3.82
6887 14963 1.270571 ACACACACACACAGACACACA 60.271 47.619 0.00 0.00 0.00 3.72
6888 14964 1.128507 CACACACACACAGACACACAC 59.871 52.381 0.00 0.00 0.00 3.82
6890 14966 1.394572 CACACACACAGACACACACAG 59.605 52.381 0.00 0.00 0.00 3.66
6891 14967 1.275010 ACACACACAGACACACACAGA 59.725 47.619 0.00 0.00 0.00 3.41
6892 14968 1.660607 CACACACAGACACACACAGAC 59.339 52.381 0.00 0.00 0.00 3.51
6893 14969 1.275010 ACACACAGACACACACAGACA 59.725 47.619 0.00 0.00 0.00 3.41
6894 14970 1.660607 CACACAGACACACACAGACAC 59.339 52.381 0.00 0.00 0.00 3.67
6895 14971 1.275010 ACACAGACACACACAGACACA 59.725 47.619 0.00 0.00 0.00 3.72
6896 14972 1.660607 CACAGACACACACAGACACAC 59.339 52.381 0.00 0.00 0.00 3.82
6897 14973 1.290203 CAGACACACACAGACACACC 58.710 55.000 0.00 0.00 0.00 4.16
6898 14974 0.901827 AGACACACACAGACACACCA 59.098 50.000 0.00 0.00 0.00 4.17
6899 14975 1.277842 AGACACACACAGACACACCAA 59.722 47.619 0.00 0.00 0.00 3.67
6900 14976 1.396996 GACACACACAGACACACCAAC 59.603 52.381 0.00 0.00 0.00 3.77
6901 14977 0.732571 CACACACAGACACACCAACC 59.267 55.000 0.00 0.00 0.00 3.77
7127 15240 5.682659 TCTGTCGCTACTCCTATCTAACTT 58.317 41.667 0.00 0.00 0.00 2.66
7200 15313 5.338708 CCAAACCTAACATCTGAGACCTGAT 60.339 44.000 0.00 0.00 0.00 2.90
7290 15403 4.849310 GGTATGAGGCCGCCGCAA 62.849 66.667 20.38 6.90 36.81 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 3279 6.538742 GTGTTATACACTTGGCATCACTGTAT 59.461 38.462 2.82 10.08 45.27 2.29
72 3306 1.054406 ATCCCCCACCGATCGATGTT 61.054 55.000 18.66 0.00 0.00 2.71
98 3332 1.420430 AAGTCCAAGTGGTTCGAGGA 58.580 50.000 0.00 0.00 36.34 3.71
175 3413 3.959329 AACTAGTCCTCGGCCGCCT 62.959 63.158 23.51 15.47 0.00 5.52
198 3436 0.106918 TGTCCCCTTGTTGTCACCAC 60.107 55.000 0.00 0.00 0.00 4.16
199 3437 0.850100 ATGTCCCCTTGTTGTCACCA 59.150 50.000 0.00 0.00 0.00 4.17
201 3439 2.270352 TCATGTCCCCTTGTTGTCAC 57.730 50.000 0.00 0.00 0.00 3.67
238 3476 3.914579 CTCCTGGTGCTGGTGCTGG 62.915 68.421 0.00 0.00 40.48 4.85
239 3477 2.359602 CTCCTGGTGCTGGTGCTG 60.360 66.667 0.00 0.00 40.48 4.41
240 3478 3.644606 CCTCCTGGTGCTGGTGCT 61.645 66.667 0.00 0.00 40.48 4.40
242 3480 3.644606 AGCCTCCTGGTGCTGGTG 61.645 66.667 11.65 0.00 36.23 4.17
289 3527 9.982291 TCGTATTTATGCAAGAAAATAAGACAC 57.018 29.630 16.62 7.57 33.82 3.67
336 3574 3.073798 TCAGCTGACCCCATAACTTTTCA 59.926 43.478 13.74 0.00 0.00 2.69
371 3609 3.511540 CAGATCCAGGGCGATTCTACATA 59.488 47.826 0.00 0.00 0.00 2.29
539 3781 2.295349 AGTTGTCTGCTCAGCATTTTGG 59.705 45.455 0.00 0.00 38.13 3.28
573 3815 1.580845 GAGTGTGTGTGCTGATGGCC 61.581 60.000 0.00 0.00 40.92 5.36
597 3839 6.476053 GGTTTGAGATACTAAACTGGATCGAC 59.524 42.308 0.00 0.00 37.07 4.20
622 3876 5.940470 GGGCCAGATATCACTACCATTTAAG 59.060 44.000 4.39 0.00 0.00 1.85
640 3894 1.180029 CAATCAGTTTCCAGGGCCAG 58.820 55.000 6.18 0.00 0.00 4.85
712 3966 7.492669 AGTGTGTTTTTGATGGAGATATCTACG 59.507 37.037 10.45 0.00 0.00 3.51
805 5431 8.253810 CCTATCCTCGCTTCTCATTAATTGATA 58.746 37.037 0.00 0.00 32.72 2.15
1260 5904 1.792949 CAAAGAGACGAAGACAACCCG 59.207 52.381 0.00 0.00 0.00 5.28
1318 5962 0.951558 CCACGCAGCCTTGTAAGTTT 59.048 50.000 0.00 0.00 0.00 2.66
1340 5984 5.992217 AGACTTCACAACCAAACAGATCTAC 59.008 40.000 0.00 0.00 0.00 2.59
1382 6029 2.039613 TGGTGTGCCACATCTTGTATGA 59.960 45.455 9.89 0.00 40.46 2.15
1453 6100 2.094026 GCATGTTCCATCAAAAGACCCC 60.094 50.000 0.00 0.00 0.00 4.95
1471 6118 4.391830 CAGGTCAACACACTATTTACGCAT 59.608 41.667 0.00 0.00 0.00 4.73
1478 6125 3.492102 ACTGCAGGTCAACACACTATT 57.508 42.857 19.93 0.00 0.00 1.73
1560 6207 5.419155 TCCGATTCCGATAGCATTAGATTCT 59.581 40.000 0.00 0.00 38.22 2.40
1567 6214 2.351835 CGAGTCCGATTCCGATAGCATT 60.352 50.000 0.00 0.00 38.22 3.56
1760 6416 6.445357 ACCCAACTTAACAACAAACTACAG 57.555 37.500 0.00 0.00 0.00 2.74
1975 6657 9.515020 AACAATTGTGTGTGTCTACTTATTTTG 57.485 29.630 12.82 0.00 38.27 2.44
2019 6701 2.346803 GGCATAACTCAGCGAACAGAA 58.653 47.619 0.00 0.00 0.00 3.02
2067 6749 7.228706 CACCATAAATAAGATAGACAACCACCC 59.771 40.741 0.00 0.00 0.00 4.61
2187 6869 6.524018 TGAAGTCATTCCCTCATTGGTAACAT 60.524 38.462 0.00 0.00 39.93 2.71
2237 6919 7.912250 CCGAGATTTAGTCAAAATTCCATTCTG 59.088 37.037 0.00 0.00 37.93 3.02
2279 6961 5.697082 ATGGAATGTGCATAAACCCAATT 57.303 34.783 6.06 0.00 0.00 2.32
2337 7020 8.409358 ACAGTGCCTTGAACTTATATTTCTTT 57.591 30.769 0.00 0.00 0.00 2.52
2349 7032 5.086104 TCCTAATCTACAGTGCCTTGAAC 57.914 43.478 0.00 0.00 0.00 3.18
2391 7106 6.387192 TTCCATTCTCTTCCCAATCTACAA 57.613 37.500 0.00 0.00 0.00 2.41
2392 7107 6.158520 TGATTCCATTCTCTTCCCAATCTACA 59.841 38.462 0.00 0.00 0.00 2.74
2393 7108 6.595682 TGATTCCATTCTCTTCCCAATCTAC 58.404 40.000 0.00 0.00 0.00 2.59
2394 7109 6.689946 GCTGATTCCATTCTCTTCCCAATCTA 60.690 42.308 0.00 0.00 0.00 1.98
2395 7110 5.692928 CTGATTCCATTCTCTTCCCAATCT 58.307 41.667 0.00 0.00 0.00 2.40
2396 7111 4.277921 GCTGATTCCATTCTCTTCCCAATC 59.722 45.833 0.00 0.00 0.00 2.67
2397 7112 4.213513 GCTGATTCCATTCTCTTCCCAAT 58.786 43.478 0.00 0.00 0.00 3.16
2398 7113 3.010472 TGCTGATTCCATTCTCTTCCCAA 59.990 43.478 0.00 0.00 0.00 4.12
2399 7114 2.577563 TGCTGATTCCATTCTCTTCCCA 59.422 45.455 0.00 0.00 0.00 4.37
2400 7115 3.212685 CTGCTGATTCCATTCTCTTCCC 58.787 50.000 0.00 0.00 0.00 3.97
2401 7116 2.617774 GCTGCTGATTCCATTCTCTTCC 59.382 50.000 0.00 0.00 0.00 3.46
2402 7117 3.543665 AGCTGCTGATTCCATTCTCTTC 58.456 45.455 0.00 0.00 0.00 2.87
2403 7118 3.648507 AGCTGCTGATTCCATTCTCTT 57.351 42.857 0.00 0.00 0.00 2.85
2404 7119 3.280295 CAAGCTGCTGATTCCATTCTCT 58.720 45.455 1.35 0.00 0.00 3.10
2405 7120 3.015327 ACAAGCTGCTGATTCCATTCTC 58.985 45.455 1.35 0.00 0.00 2.87
2406 7121 3.083122 ACAAGCTGCTGATTCCATTCT 57.917 42.857 1.35 0.00 0.00 2.40
2407 7122 4.194640 TCTACAAGCTGCTGATTCCATTC 58.805 43.478 1.35 0.00 0.00 2.67
2408 7123 4.226427 TCTACAAGCTGCTGATTCCATT 57.774 40.909 1.35 0.00 0.00 3.16
2409 7124 3.920231 TCTACAAGCTGCTGATTCCAT 57.080 42.857 1.35 0.00 0.00 3.41
2410 7125 3.244526 TGTTCTACAAGCTGCTGATTCCA 60.245 43.478 1.35 0.00 0.00 3.53
2411 7126 3.338249 TGTTCTACAAGCTGCTGATTCC 58.662 45.455 1.35 0.00 0.00 3.01
2412 7127 4.394300 ACATGTTCTACAAGCTGCTGATTC 59.606 41.667 1.35 0.00 0.00 2.52
2413 7128 4.330250 ACATGTTCTACAAGCTGCTGATT 58.670 39.130 1.35 0.00 0.00 2.57
2414 7129 3.947868 ACATGTTCTACAAGCTGCTGAT 58.052 40.909 1.35 0.00 0.00 2.90
2415 7130 3.407424 ACATGTTCTACAAGCTGCTGA 57.593 42.857 1.35 0.00 0.00 4.26
2416 7131 3.818387 CAACATGTTCTACAAGCTGCTG 58.182 45.455 8.48 0.00 0.00 4.41
2417 7132 2.227388 GCAACATGTTCTACAAGCTGCT 59.773 45.455 8.48 0.00 31.35 4.24
2418 7133 2.589014 GCAACATGTTCTACAAGCTGC 58.411 47.619 8.48 2.62 0.00 5.25
2419 7134 2.413239 CGGCAACATGTTCTACAAGCTG 60.413 50.000 8.48 9.32 0.00 4.24
2420 7135 1.806542 CGGCAACATGTTCTACAAGCT 59.193 47.619 8.48 0.00 0.00 3.74
2421 7136 1.804151 TCGGCAACATGTTCTACAAGC 59.196 47.619 8.48 7.94 0.00 4.01
2422 7137 2.159653 GCTCGGCAACATGTTCTACAAG 60.160 50.000 8.48 4.34 0.00 3.16
2508 7258 3.369756 TCGTATTCCGACAGCATTTGTTC 59.630 43.478 0.00 0.00 41.60 3.18
2571 7321 6.966021 ACACATTAATTACAACTGGTGTGTC 58.034 36.000 8.96 0.00 43.66 3.67
2663 7415 2.828877 TCAATCCAACTATTACGGCGG 58.171 47.619 13.24 0.00 0.00 6.13
2674 7426 1.999735 TCGCTGACGATTCAATCCAAC 59.000 47.619 0.00 0.00 45.12 3.77
2724 7476 5.236263 GCTAATTTGAAACAAACCAACCCAG 59.764 40.000 0.00 0.00 0.00 4.45
2832 7584 9.832445 ACGCAGAAATCTTAATAGGATCTTAAA 57.168 29.630 0.00 0.00 0.00 1.52
2889 7641 5.010617 ACATATCCGGCAACATTATTTTCCC 59.989 40.000 0.00 0.00 0.00 3.97
2907 7659 7.358765 CGATTTTGAGTCGGATTCTGACATATC 60.359 40.741 24.02 14.85 38.83 1.63
2954 7706 4.701956 ATAATTGTGTGTGCCTACTTGC 57.298 40.909 0.00 0.00 0.00 4.01
3069 7827 3.596046 TCCCTACCAATTCAACTCCCAAT 59.404 43.478 0.00 0.00 0.00 3.16
3138 7901 5.296780 GCAATGTACAAATCTTGGCTAGCTA 59.703 40.000 15.72 5.44 34.12 3.32
3139 7902 4.096984 GCAATGTACAAATCTTGGCTAGCT 59.903 41.667 15.72 0.00 34.12 3.32
3140 7903 4.142403 TGCAATGTACAAATCTTGGCTAGC 60.142 41.667 6.04 6.04 34.12 3.42
3141 7904 5.335127 GTGCAATGTACAAATCTTGGCTAG 58.665 41.667 0.00 0.00 34.12 3.42
3157 7920 2.374184 TCTTAATTCCCGGGTGCAATG 58.626 47.619 22.86 8.60 0.00 2.82
3165 7928 7.041098 CCATTCTCTTATGTTCTTAATTCCCGG 60.041 40.741 0.00 0.00 0.00 5.73
3207 7987 8.116753 CACAATCTACAATGAAATCGTAAGGAC 58.883 37.037 0.00 0.00 38.47 3.85
3609 8408 5.810074 ACAATGGTGCACAAACTAGAAAAAC 59.190 36.000 20.43 0.00 0.00 2.43
3631 8430 4.571176 TGTAATGTAGCACGTTTCAACACA 59.429 37.500 0.00 0.00 0.00 3.72
3712 8512 6.971184 GTGGAGCATGAATAAACTGATGAAAG 59.029 38.462 0.00 0.00 0.00 2.62
3929 8935 4.148838 AGTAGGGCAAGCAAACATACAAA 58.851 39.130 0.00 0.00 0.00 2.83
4015 9028 8.728088 AAATTTAAAGAGTCTAATGCACGTTG 57.272 30.769 0.00 0.00 0.00 4.10
4437 9487 3.739300 CGCTAGTAATTGTACCGAATGGG 59.261 47.826 0.00 0.00 40.75 4.00
4516 9566 0.379669 GCAGCACATTCTGATTCCCG 59.620 55.000 0.00 0.00 36.19 5.14
4557 9607 7.986085 AATTGTATCCTTAATCATCTTCCCG 57.014 36.000 0.00 0.00 0.00 5.14
4618 9668 8.376889 TCAAAGTTTTCTTTCAGTTTTGCTTT 57.623 26.923 0.00 0.00 46.89 3.51
4624 9674 6.036408 GCATGCTCAAAGTTTTCTTTCAGTTT 59.964 34.615 11.37 0.00 46.89 2.66
4646 9696 7.869429 ACTTTTTGAATTTCTCATTTCTCGCAT 59.131 29.630 0.00 0.00 32.78 4.73
4792 9842 9.642343 TGATACTAAGAACCAGAATTAGCTAGA 57.358 33.333 0.00 0.00 31.12 2.43
5042 11272 4.202346 ACCAACATACAATGGCTTTTTGCT 60.202 37.500 0.00 0.00 40.51 3.91
5625 13278 1.743958 CTGGACCGACGTAGAACTGAT 59.256 52.381 0.00 0.00 0.00 2.90
5793 13447 5.505286 GGTGTAGATTGATTTCTTGATGCG 58.495 41.667 0.00 0.00 0.00 4.73
5910 13565 2.749076 TGTGACATAAGCTGAACATGGC 59.251 45.455 0.00 0.00 0.00 4.40
5921 13576 7.604164 AGGTGAATTGACTACTTGTGACATAAG 59.396 37.037 10.14 10.14 0.00 1.73
5954 13610 5.121611 CACCATCTGTATTGTAAAAGCACGA 59.878 40.000 0.00 0.00 0.00 4.35
5999 13655 7.384477 TCATTGAATTTGGCATGTATGTGAAA 58.616 30.769 0.00 0.00 0.00 2.69
6020 13676 6.487668 TCACAGAGTTGACATTCACATTCATT 59.512 34.615 0.00 0.00 0.00 2.57
6068 13724 9.727859 GATGGAGTAGAGACAGTACTATCAATA 57.272 37.037 3.57 0.00 30.60 1.90
6070 13726 7.717436 CAGATGGAGTAGAGACAGTACTATCAA 59.283 40.741 3.57 0.00 30.60 2.57
6143 13800 5.723672 TCCTTACGAGATGTTGTTTCTCT 57.276 39.130 0.00 0.00 37.96 3.10
6255 13916 6.877611 ATACGACCAAACTGAAAATTCACT 57.122 33.333 0.00 0.00 32.90 3.41
6265 13927 8.508875 AGGTAAACAAAATATACGACCAAACTG 58.491 33.333 0.00 0.00 0.00 3.16
6312 13974 1.448540 CTTCAGCCAGCGGGTACAG 60.449 63.158 4.36 0.00 36.17 2.74
6330 13992 4.384940 CCTCCTAATTCTGGCTTAAGCTC 58.615 47.826 25.88 16.52 41.70 4.09
6336 13998 2.511637 CCTTCCCTCCTAATTCTGGCTT 59.488 50.000 0.00 0.00 0.00 4.35
6389 14051 0.593128 CCACTTTCCTTCGTTGCAGG 59.407 55.000 0.00 0.00 0.00 4.85
6396 14058 1.740025 GGCATCTTCCACTTTCCTTCG 59.260 52.381 0.00 0.00 0.00 3.79
6449 14111 0.888619 TAGCACTCAAGGTCGAGGTG 59.111 55.000 0.00 0.00 37.34 4.00
6450 14112 1.178276 CTAGCACTCAAGGTCGAGGT 58.822 55.000 0.00 0.00 37.34 3.85
6572 14634 9.661954 TTCAGGTTGATAGAGATATTAGGAACT 57.338 33.333 0.00 0.00 46.37 3.01
6823 14899 8.685427 CCATCATGAATTGTTAAACAGATACCA 58.315 33.333 0.00 0.00 0.00 3.25
6872 14948 1.660607 GTCTGTGTGTGTCTGTGTGTG 59.339 52.381 0.00 0.00 0.00 3.82
6875 14951 1.275010 TGTGTCTGTGTGTGTCTGTGT 59.725 47.619 0.00 0.00 0.00 3.72
6876 14952 1.660607 GTGTGTCTGTGTGTGTCTGTG 59.339 52.381 0.00 0.00 0.00 3.66
6879 14955 0.901827 TGGTGTGTCTGTGTGTGTCT 59.098 50.000 0.00 0.00 0.00 3.41
6880 14956 1.396996 GTTGGTGTGTCTGTGTGTGTC 59.603 52.381 0.00 0.00 0.00 3.67
6882 14958 0.732571 GGTTGGTGTGTCTGTGTGTG 59.267 55.000 0.00 0.00 0.00 3.82
6884 14960 1.016627 CAGGTTGGTGTGTCTGTGTG 58.983 55.000 0.00 0.00 0.00 3.82
6885 14961 0.908910 TCAGGTTGGTGTGTCTGTGT 59.091 50.000 0.00 0.00 0.00 3.72
6886 14962 1.875514 CATCAGGTTGGTGTGTCTGTG 59.124 52.381 0.00 0.00 0.00 3.66
6887 14963 1.815408 GCATCAGGTTGGTGTGTCTGT 60.815 52.381 0.00 0.00 29.39 3.41
6888 14964 0.877071 GCATCAGGTTGGTGTGTCTG 59.123 55.000 0.00 0.00 29.39 3.51
6890 14966 2.472695 TAGCATCAGGTTGGTGTGTC 57.527 50.000 0.00 0.00 29.39 3.67
6891 14967 2.884639 GTTTAGCATCAGGTTGGTGTGT 59.115 45.455 0.00 0.00 29.39 3.72
6892 14968 2.884012 TGTTTAGCATCAGGTTGGTGTG 59.116 45.455 0.00 0.00 29.39 3.82
6893 14969 3.149196 CTGTTTAGCATCAGGTTGGTGT 58.851 45.455 0.00 0.00 29.39 4.16
6894 14970 2.489329 CCTGTTTAGCATCAGGTTGGTG 59.511 50.000 3.38 0.00 44.19 4.17
6895 14971 2.555227 CCCTGTTTAGCATCAGGTTGGT 60.555 50.000 9.79 0.00 46.79 3.67
6896 14972 2.094675 CCCTGTTTAGCATCAGGTTGG 58.905 52.381 9.79 0.00 46.79 3.77
6897 14973 2.094675 CCCCTGTTTAGCATCAGGTTG 58.905 52.381 9.79 0.00 46.79 3.77
6898 14974 1.616994 GCCCCTGTTTAGCATCAGGTT 60.617 52.381 9.79 0.00 46.79 3.50
6899 14975 0.034089 GCCCCTGTTTAGCATCAGGT 60.034 55.000 9.79 0.00 46.79 4.00
6901 14977 2.134789 AAGCCCCTGTTTAGCATCAG 57.865 50.000 0.00 0.00 0.00 2.90
7027 15139 7.946381 TGTGTTATAATCAATAAAGTGGCCA 57.054 32.000 0.00 0.00 31.82 5.36
7127 15240 0.546122 ACCATCAGCGCCCTTTCATA 59.454 50.000 2.29 0.00 0.00 2.15
7203 15316 1.192146 CGGAAGGAGTCCTGGTTGGA 61.192 60.000 13.89 0.00 45.36 3.53
7290 15403 2.771943 AGATGGATTGATGGTACGTGGT 59.228 45.455 0.00 0.00 0.00 4.16
7484 15597 0.041982 GAGGGGACAAGAGGAGGAGT 59.958 60.000 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.