Multiple sequence alignment - TraesCS3D01G458300

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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 TraesCS3D01G458300 chr3D 100.000 3236 0 0 1 3236 563681319 563684554 0.000000e+00 5976.0
1 TraesCS3D01G458300 chr3D 93.134 2141 116 13 1112 3236 559580909 559578784 0.000000e+00 3110.0
2 TraesCS3D01G458300 chr3D 84.793 868 93 15 97 946 563710889 563711735 0.000000e+00 835.0
3 TraesCS3D01G458300 chr3D 92.857 560 38 2 1338 1896 563723474 563724032 0.000000e+00 811.0
4 TraesCS3D01G458300 chr3D 91.327 392 26 1 952 1343 563714635 563715018 2.210000e-146 529.0
5 TraesCS3D01G458300 chr3D 79.800 500 90 6 1105 1593 577029032 577029531 1.430000e-93 353.0
6 TraesCS3D01G458300 chr3D 77.883 529 93 15 1946 2468 577029799 577030309 1.130000e-79 307.0
7 TraesCS3D01G458300 chr3D 77.255 510 91 16 1946 2438 563619374 563618873 3.180000e-70 276.0
8 TraesCS3D01G458300 chr3A 92.297 1389 88 10 1245 2623 628661249 628662628 0.000000e+00 1954.0
9 TraesCS3D01G458300 chr3A 93.234 872 46 6 1758 2623 695895105 695894241 0.000000e+00 1271.0
10 TraesCS3D01G458300 chr3A 91.932 880 51 5 1758 2623 628632758 628631885 0.000000e+00 1214.0
11 TraesCS3D01G458300 chr3A 82.688 1317 170 36 1341 2638 698704320 698703043 0.000000e+00 1116.0
12 TraesCS3D01G458300 chr3A 92.033 728 54 4 1112 1837 695895831 695895106 0.000000e+00 1020.0
13 TraesCS3D01G458300 chr3A 90.463 734 59 6 1112 1837 628633489 628632759 0.000000e+00 957.0
14 TraesCS3D01G458300 chr3A 90.484 641 44 6 2606 3236 695894176 695893543 0.000000e+00 830.0
15 TraesCS3D01G458300 chr3A 83.459 925 120 20 1639 2551 698515508 698516411 0.000000e+00 830.0
16 TraesCS3D01G458300 chr3A 89.952 627 48 4 2606 3224 628662692 628663311 0.000000e+00 795.0
17 TraesCS3D01G458300 chr3A 89.236 641 52 6 2606 3236 628631820 628631187 0.000000e+00 785.0
18 TraesCS3D01G458300 chr3A 74.210 791 137 42 1857 2618 698212463 698213215 5.320000e-68 268.0
19 TraesCS3D01G458300 chr3A 75.066 377 84 6 1126 1497 699418172 699418543 2.000000e-37 167.0
20 TraesCS3D01G458300 chr3A 86.047 129 14 2 2492 2617 698350038 698349911 5.630000e-28 135.0
21 TraesCS3D01G458300 chr3B 81.953 942 129 23 776 1687 751511628 751510698 0.000000e+00 760.0
22 TraesCS3D01G458300 chr3B 76.956 703 97 39 1946 2638 751506972 751506325 1.110000e-89 340.0
23 TraesCS3D01G458300 chr3B 77.667 403 77 8 1109 1503 752344301 752344698 1.940000e-57 233.0
24 TraesCS3D01G458300 chr3B 73.750 400 101 4 1109 1506 752274243 752274640 1.550000e-33 154.0
25 TraesCS3D01G458300 chr3B 75.063 397 60 17 797 1160 751159576 751159966 7.230000e-32 148.0
26 TraesCS3D01G458300 chr3B 88.571 70 7 1 2786 2855 751231279 751231347 2.070000e-12 84.2
27 TraesCS3D01G458300 chr3B 88.333 60 5 2 3079 3138 751509442 751509385 1.610000e-08 71.3
28 TraesCS3D01G458300 chr2D 78.529 503 93 11 1946 2442 439463529 439463036 1.870000e-82 316.0
29 TraesCS3D01G458300 chr5D 80.503 159 24 6 2385 2543 559475610 559475459 7.340000e-22 115.0
30 TraesCS3D01G458300 chrUn 80.892 157 18 8 2385 2540 339798160 339798305 2.640000e-21 113.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G458300 chr3D 563681319 563684554 3235 False 5976.000000 5976 100.000000 1 3236 1 chr3D.!!$F1 3235
1 TraesCS3D01G458300 chr3D 559578784 559580909 2125 True 3110.000000 3110 93.134000 1112 3236 1 chr3D.!!$R1 2124
2 TraesCS3D01G458300 chr3D 563723474 563724032 558 False 811.000000 811 92.857000 1338 1896 1 chr3D.!!$F2 558
3 TraesCS3D01G458300 chr3D 563710889 563715018 4129 False 682.000000 835 88.060000 97 1343 2 chr3D.!!$F3 1246
4 TraesCS3D01G458300 chr3D 577029032 577030309 1277 False 330.000000 353 78.841500 1105 2468 2 chr3D.!!$F4 1363
5 TraesCS3D01G458300 chr3D 563618873 563619374 501 True 276.000000 276 77.255000 1946 2438 1 chr3D.!!$R2 492
6 TraesCS3D01G458300 chr3A 628661249 628663311 2062 False 1374.500000 1954 91.124500 1245 3224 2 chr3A.!!$F4 1979
7 TraesCS3D01G458300 chr3A 698703043 698704320 1277 True 1116.000000 1116 82.688000 1341 2638 1 chr3A.!!$R2 1297
8 TraesCS3D01G458300 chr3A 695893543 695895831 2288 True 1040.333333 1271 91.917000 1112 3236 3 chr3A.!!$R4 2124
9 TraesCS3D01G458300 chr3A 628631187 628633489 2302 True 985.333333 1214 90.543667 1112 3236 3 chr3A.!!$R3 2124
10 TraesCS3D01G458300 chr3A 698515508 698516411 903 False 830.000000 830 83.459000 1639 2551 1 chr3A.!!$F2 912
11 TraesCS3D01G458300 chr3A 698212463 698213215 752 False 268.000000 268 74.210000 1857 2618 1 chr3A.!!$F1 761
12 TraesCS3D01G458300 chr3B 751506325 751511628 5303 True 390.433333 760 82.414000 776 3138 3 chr3B.!!$R1 2362

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
88 89 0.176680 AGATCACCGTGCTGGATCAC 59.823 55.0 2.38 0.00 42.00 3.06 F
739 755 0.179040 TTCGAAACGGAGGCACCTTT 60.179 50.0 0.00 0.00 36.31 3.11 F
1936 5051 0.392327 GCTCTGCCTTCTGAAGACCC 60.392 60.0 18.68 7.25 0.00 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1755 4701 0.396811 AGAAAACCTCGGTCACAGGG 59.603 55.000 0.00 0.0 35.01 4.45 R
2202 5329 1.074405 TGCAAGGCCAGTTGAGAATCT 59.926 47.619 5.01 0.0 34.92 2.40 R
3181 6681 0.467384 ATGGCGCTGCAGTTCTAGAT 59.533 50.000 16.64 0.0 0.00 1.98 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
18 19 3.935993 CCAACCTGTCCAAGACGAT 57.064 52.632 0.00 0.00 34.95 3.73
19 20 1.442769 CCAACCTGTCCAAGACGATG 58.557 55.000 0.00 0.00 34.95 3.84
20 21 0.798776 CAACCTGTCCAAGACGATGC 59.201 55.000 0.00 0.00 34.95 3.91
21 22 0.321653 AACCTGTCCAAGACGATGCC 60.322 55.000 0.00 0.00 34.95 4.40
22 23 1.296392 CCTGTCCAAGACGATGCCA 59.704 57.895 0.00 0.00 34.95 4.92
23 24 1.021390 CCTGTCCAAGACGATGCCAC 61.021 60.000 0.00 0.00 34.95 5.01
24 25 1.354337 CTGTCCAAGACGATGCCACG 61.354 60.000 0.00 0.00 34.95 4.94
25 26 1.080093 GTCCAAGACGATGCCACGA 60.080 57.895 6.64 0.00 37.03 4.35
26 27 1.080093 TCCAAGACGATGCCACGAC 60.080 57.895 6.64 0.88 37.03 4.34
27 28 1.374125 CCAAGACGATGCCACGACA 60.374 57.895 6.64 0.00 37.03 4.35
28 29 0.740868 CCAAGACGATGCCACGACAT 60.741 55.000 6.64 0.00 37.03 3.06
29 30 0.647410 CAAGACGATGCCACGACATC 59.353 55.000 6.64 0.00 42.52 3.06
30 31 0.460284 AAGACGATGCCACGACATCC 60.460 55.000 6.64 1.28 42.91 3.51
31 32 1.141881 GACGATGCCACGACATCCT 59.858 57.895 6.64 2.19 42.91 3.24
32 33 0.872021 GACGATGCCACGACATCCTC 60.872 60.000 6.64 6.65 42.91 3.71
33 34 1.323271 ACGATGCCACGACATCCTCT 61.323 55.000 6.64 0.00 42.91 3.69
34 35 0.179100 CGATGCCACGACATCCTCTT 60.179 55.000 10.64 0.00 42.91 2.85
35 36 1.576356 GATGCCACGACATCCTCTTC 58.424 55.000 0.00 0.00 40.52 2.87
36 37 1.137872 GATGCCACGACATCCTCTTCT 59.862 52.381 0.00 0.00 40.52 2.85
37 38 0.532573 TGCCACGACATCCTCTTCTC 59.467 55.000 0.00 0.00 0.00 2.87
38 39 0.820871 GCCACGACATCCTCTTCTCT 59.179 55.000 0.00 0.00 0.00 3.10
39 40 2.025155 GCCACGACATCCTCTTCTCTA 58.975 52.381 0.00 0.00 0.00 2.43
40 41 2.034053 GCCACGACATCCTCTTCTCTAG 59.966 54.545 0.00 0.00 0.00 2.43
41 42 3.283751 CCACGACATCCTCTTCTCTAGT 58.716 50.000 0.00 0.00 0.00 2.57
42 43 3.066064 CCACGACATCCTCTTCTCTAGTG 59.934 52.174 0.00 0.00 0.00 2.74
43 44 3.692101 CACGACATCCTCTTCTCTAGTGT 59.308 47.826 0.00 0.00 0.00 3.55
44 45 3.942748 ACGACATCCTCTTCTCTAGTGTC 59.057 47.826 0.00 0.00 33.15 3.67
45 46 3.314080 CGACATCCTCTTCTCTAGTGTCC 59.686 52.174 0.00 0.00 32.94 4.02
46 47 4.532834 GACATCCTCTTCTCTAGTGTCCT 58.467 47.826 0.00 0.00 0.00 3.85
47 48 4.277476 ACATCCTCTTCTCTAGTGTCCTG 58.723 47.826 0.00 0.00 0.00 3.86
48 49 3.374042 TCCTCTTCTCTAGTGTCCTGG 57.626 52.381 0.00 0.00 0.00 4.45
49 50 2.650322 TCCTCTTCTCTAGTGTCCTGGT 59.350 50.000 0.00 0.00 0.00 4.00
50 51 3.020984 CCTCTTCTCTAGTGTCCTGGTC 58.979 54.545 0.00 0.00 0.00 4.02
51 52 3.562393 CCTCTTCTCTAGTGTCCTGGTCA 60.562 52.174 0.00 0.00 0.00 4.02
52 53 3.691575 TCTTCTCTAGTGTCCTGGTCAG 58.308 50.000 0.00 0.00 0.00 3.51
71 72 4.697756 CCAGGCCGCCGTTGAAGA 62.698 66.667 3.05 0.00 0.00 2.87
72 73 2.436646 CAGGCCGCCGTTGAAGAT 60.437 61.111 3.05 0.00 0.00 2.40
73 74 2.125106 AGGCCGCCGTTGAAGATC 60.125 61.111 3.05 0.00 0.00 2.75
74 75 2.435938 GGCCGCCGTTGAAGATCA 60.436 61.111 0.00 0.00 0.00 2.92
75 76 2.750888 GGCCGCCGTTGAAGATCAC 61.751 63.158 0.00 0.00 0.00 3.06
76 77 2.750888 GCCGCCGTTGAAGATCACC 61.751 63.158 0.00 0.00 0.00 4.02
77 78 2.452813 CCGCCGTTGAAGATCACCG 61.453 63.158 0.00 0.00 31.85 4.94
78 79 1.736645 CGCCGTTGAAGATCACCGT 60.737 57.895 0.00 0.00 29.95 4.83
79 80 1.787847 GCCGTTGAAGATCACCGTG 59.212 57.895 0.00 0.00 29.95 4.94
80 81 1.787847 CCGTTGAAGATCACCGTGC 59.212 57.895 0.00 0.00 29.95 5.34
81 82 0.670546 CCGTTGAAGATCACCGTGCT 60.671 55.000 0.00 0.00 29.95 4.40
82 83 0.439985 CGTTGAAGATCACCGTGCTG 59.560 55.000 0.00 0.00 27.32 4.41
83 84 0.798776 GTTGAAGATCACCGTGCTGG 59.201 55.000 0.00 0.00 46.41 4.85
84 85 0.684535 TTGAAGATCACCGTGCTGGA 59.315 50.000 2.38 0.00 42.00 3.86
85 86 0.904649 TGAAGATCACCGTGCTGGAT 59.095 50.000 2.38 0.00 42.00 3.41
86 87 1.134699 TGAAGATCACCGTGCTGGATC 60.135 52.381 2.38 0.00 42.00 3.36
87 88 0.904649 AAGATCACCGTGCTGGATCA 59.095 50.000 2.38 0.00 42.00 2.92
88 89 0.176680 AGATCACCGTGCTGGATCAC 59.823 55.000 2.38 0.00 42.00 3.06
89 90 0.811616 GATCACCGTGCTGGATCACC 60.812 60.000 2.38 0.00 42.00 4.02
90 91 1.552799 ATCACCGTGCTGGATCACCA 61.553 55.000 2.38 0.00 44.76 4.17
91 92 1.302431 CACCGTGCTGGATCACCAA 60.302 57.895 2.38 0.00 46.32 3.67
92 93 1.302511 ACCGTGCTGGATCACCAAC 60.303 57.895 2.38 0.00 46.32 3.77
93 94 2.390599 CCGTGCTGGATCACCAACG 61.391 63.158 0.00 0.00 46.32 4.10
94 95 2.870372 GTGCTGGATCACCAACGC 59.130 61.111 0.00 0.00 46.32 4.84
95 96 2.359850 TGCTGGATCACCAACGCC 60.360 61.111 0.00 0.00 46.32 5.68
96 97 3.499737 GCTGGATCACCAACGCCG 61.500 66.667 0.00 0.00 46.32 6.46
97 98 3.499737 CTGGATCACCAACGCCGC 61.500 66.667 0.00 0.00 46.32 6.53
98 99 3.958147 CTGGATCACCAACGCCGCT 62.958 63.158 0.00 0.00 46.32 5.52
99 100 3.499737 GGATCACCAACGCCGCTG 61.500 66.667 0.00 0.00 35.97 5.18
100 101 2.742372 GATCACCAACGCCGCTGT 60.742 61.111 0.00 0.00 0.00 4.40
101 102 2.281484 ATCACCAACGCCGCTGTT 60.281 55.556 0.00 0.00 0.00 3.16
102 103 1.004320 ATCACCAACGCCGCTGTTA 60.004 52.632 1.24 0.00 0.00 2.41
103 104 1.019278 ATCACCAACGCCGCTGTTAG 61.019 55.000 1.24 0.00 0.00 2.34
104 105 2.358247 ACCAACGCCGCTGTTAGG 60.358 61.111 1.24 7.30 0.00 2.69
129 130 0.389166 CCTGTCGAGAGCCACAACTC 60.389 60.000 3.56 0.00 36.91 3.01
136 137 2.022129 GAGCCACAACTCGACCACG 61.022 63.158 0.00 0.00 41.26 4.94
138 139 3.403057 CCACAACTCGACCACGCG 61.403 66.667 3.53 3.53 39.58 6.01
149 150 3.698463 CCACGCGTCACCGTTGTC 61.698 66.667 9.86 0.00 39.83 3.18
156 157 1.066918 GTCACCGTTGTCGTCCTGT 59.933 57.895 0.00 0.00 35.01 4.00
157 158 0.529119 GTCACCGTTGTCGTCCTGTT 60.529 55.000 0.00 0.00 35.01 3.16
164 165 2.800544 CGTTGTCGTCCTGTTGAGAAAT 59.199 45.455 0.00 0.00 0.00 2.17
272 273 5.405935 AAGTTTTGCCTATGGTCCATTTC 57.594 39.130 10.33 0.39 0.00 2.17
274 275 4.463891 AGTTTTGCCTATGGTCCATTTCAG 59.536 41.667 10.33 1.11 0.00 3.02
279 280 3.370953 GCCTATGGTCCATTTCAGTCTGT 60.371 47.826 10.33 0.00 0.00 3.41
299 300 9.372369 AGTCTGTATATAAGTTTTGTCTGAAGC 57.628 33.333 0.00 0.00 0.00 3.86
302 303 8.492673 TGTATATAAGTTTTGTCTGAAGCCAG 57.507 34.615 0.00 0.00 41.74 4.85
319 320 6.098266 TGAAGCCAGACTTATATGCAGACTAA 59.902 38.462 0.00 0.00 39.29 2.24
323 324 7.443575 AGCCAGACTTATATGCAGACTAAAATG 59.556 37.037 0.00 0.00 0.00 2.32
324 325 7.308229 GCCAGACTTATATGCAGACTAAAATGG 60.308 40.741 0.00 0.00 0.00 3.16
326 327 7.443575 CAGACTTATATGCAGACTAAAATGGCT 59.556 37.037 0.00 0.00 0.00 4.75
327 328 7.443575 AGACTTATATGCAGACTAAAATGGCTG 59.556 37.037 0.00 0.00 0.00 4.85
329 330 7.227512 ACTTATATGCAGACTAAAATGGCTGAC 59.772 37.037 1.07 0.00 0.00 3.51
335 336 5.327091 CAGACTAAAATGGCTGACAAATCG 58.673 41.667 0.00 0.00 0.00 3.34
345 346 2.157668 GCTGACAAATCGTATATGCGGG 59.842 50.000 13.39 3.87 0.00 6.13
349 350 4.202233 TGACAAATCGTATATGCGGGGTAA 60.202 41.667 13.39 0.00 0.00 2.85
357 358 5.524646 TCGTATATGCGGGGTAAAAAGAAAG 59.475 40.000 13.39 0.00 0.00 2.62
362 363 4.653868 TGCGGGGTAAAAAGAAAGTCATA 58.346 39.130 0.00 0.00 0.00 2.15
408 409 7.501515 GGTAAATTGTTCAAGAAAAATGCTCG 58.498 34.615 0.00 0.00 29.19 5.03
432 433 5.003121 GTGCACGTTTCAGTTAGTTTTTCAC 59.997 40.000 0.00 0.00 0.00 3.18
434 435 5.741982 GCACGTTTCAGTTAGTTTTTCACAT 59.258 36.000 0.00 0.00 0.00 3.21
469 470 8.499403 AGCCTTTTGAGATTTTGTACTATCTC 57.501 34.615 18.37 18.37 44.48 2.75
475 476 7.028926 TGAGATTTTGTACTATCTCCGACTC 57.971 40.000 20.53 0.00 43.90 3.36
484 485 4.537751 ACTATCTCCGACTCATCCTTGAA 58.462 43.478 0.00 0.00 0.00 2.69
488 489 5.932619 TCTCCGACTCATCCTTGAAAATA 57.067 39.130 0.00 0.00 0.00 1.40
489 490 5.907207 TCTCCGACTCATCCTTGAAAATAG 58.093 41.667 0.00 0.00 0.00 1.73
495 499 6.521151 ACTCATCCTTGAAAATAGCTTTGG 57.479 37.500 0.00 0.00 0.00 3.28
497 501 4.160252 TCATCCTTGAAAATAGCTTTGGCC 59.840 41.667 0.00 0.00 39.73 5.36
507 511 6.618287 AAATAGCTTTGGCCTTTTTCAAAC 57.382 33.333 3.32 0.00 39.73 2.93
526 530 4.699522 GAAGGGTTGCGGCTCGGT 62.700 66.667 0.00 0.00 0.00 4.69
537 541 2.125106 GCTCGGTGGGGATGTGAC 60.125 66.667 0.00 0.00 0.00 3.67
587 591 1.092921 TGGCGTGCGTGAGTTTTTCT 61.093 50.000 0.00 0.00 0.00 2.52
589 593 1.136336 GGCGTGCGTGAGTTTTTCTAG 60.136 52.381 0.00 0.00 0.00 2.43
591 595 2.159960 GCGTGCGTGAGTTTTTCTAGAG 60.160 50.000 0.00 0.00 0.00 2.43
670 676 9.599322 CGTGAATTTATGCTCTAAAATATGTCC 57.401 33.333 0.00 0.00 0.00 4.02
680 686 8.432013 TGCTCTAAAATATGTCCACATACATCT 58.568 33.333 1.42 0.00 41.15 2.90
681 687 9.929180 GCTCTAAAATATGTCCACATACATCTA 57.071 33.333 1.42 0.00 41.15 1.98
689 695 7.997773 ATGTCCACATACATCTATACGTAGT 57.002 36.000 0.08 0.00 39.31 2.73
690 696 7.430992 TGTCCACATACATCTATACGTAGTC 57.569 40.000 0.08 0.00 43.93 2.59
691 697 6.429078 TGTCCACATACATCTATACGTAGTCC 59.571 42.308 0.08 0.00 43.93 3.85
693 699 7.120873 GTCCACATACATCTATACGTAGTCCAT 59.879 40.741 0.08 0.00 43.93 3.41
694 700 8.323567 TCCACATACATCTATACGTAGTCCATA 58.676 37.037 0.08 0.00 43.93 2.74
695 701 8.396390 CCACATACATCTATACGTAGTCCATAC 58.604 40.741 0.08 0.00 43.93 2.39
707 723 7.642082 ACGTAGTCCATACTGAAATCTTAGT 57.358 36.000 0.00 0.00 29.74 2.24
739 755 0.179040 TTCGAAACGGAGGCACCTTT 60.179 50.000 0.00 0.00 36.31 3.11
750 766 1.203063 AGGCACCTTTTTCTCCTTCCC 60.203 52.381 0.00 0.00 0.00 3.97
754 770 1.711375 ACCTTTTTCTCCTTCCCCCTC 59.289 52.381 0.00 0.00 0.00 4.30
756 772 2.025793 CCTTTTTCTCCTTCCCCCTCTC 60.026 54.545 0.00 0.00 0.00 3.20
767 783 1.571773 CCCCCTCTCCCGTTCCATTT 61.572 60.000 0.00 0.00 0.00 2.32
781 797 3.319137 TCCATTTGAACACTCTCCTCG 57.681 47.619 0.00 0.00 0.00 4.63
806 822 4.823364 TTACCTCATCTCATCTCCTCCT 57.177 45.455 0.00 0.00 0.00 3.69
808 824 3.575805 ACCTCATCTCATCTCCTCCTTC 58.424 50.000 0.00 0.00 0.00 3.46
835 853 1.294659 GCTCTTGCTGTGTTCCTCCG 61.295 60.000 0.00 0.00 36.03 4.63
836 854 1.294659 CTCTTGCTGTGTTCCTCCGC 61.295 60.000 0.00 0.00 0.00 5.54
899 927 5.710513 TCATTTCTTTATGCAGCTGTTGT 57.289 34.783 16.64 4.24 0.00 3.32
931 960 1.294659 CTCCTTCACGCTGCACCTTC 61.295 60.000 0.00 0.00 0.00 3.46
961 3884 5.772393 TTTTTACAGGCCATCTAGAAGGA 57.228 39.130 18.19 0.00 0.00 3.36
962 3885 5.359194 TTTTACAGGCCATCTAGAAGGAG 57.641 43.478 18.19 8.77 0.00 3.69
1105 4028 4.776322 CCATGGCGGCCGAAGACA 62.776 66.667 33.48 21.48 0.00 3.41
1168 4091 0.596577 CTCCTTCCTCGACGACAACA 59.403 55.000 0.00 0.00 0.00 3.33
1242 4171 2.893398 GACGACCCAAGGAGCGAT 59.107 61.111 7.40 0.00 0.00 4.58
1303 4233 1.344942 CGACGAGGTTTTCCAGAGCG 61.345 60.000 0.00 0.00 43.73 5.03
1305 4235 0.608640 ACGAGGTTTTCCAGAGCGAT 59.391 50.000 0.00 0.00 43.73 4.58
1381 4314 3.450115 AGCTCGGCGAGTACCACC 61.450 66.667 34.41 18.68 31.39 4.61
1416 4349 0.445436 TCGACGGCTACTTCGTTCTC 59.555 55.000 0.00 0.00 41.22 2.87
1533 4473 2.178580 GCTGATGTCATTTTCCCCCAA 58.821 47.619 0.00 0.00 0.00 4.12
1755 4701 4.983671 ATTTCTGCCGGTTAATCTTTCC 57.016 40.909 1.90 0.00 0.00 3.13
1898 5013 4.558226 TGGCTCTCTTTGCTCTTCAATA 57.442 40.909 0.00 0.00 34.12 1.90
1912 5027 5.400066 TCTTCAATATGACACCGAGACAA 57.600 39.130 0.00 0.00 0.00 3.18
1925 5040 1.203523 CGAGACAAGTAAGCTCTGCCT 59.796 52.381 0.00 0.00 0.00 4.75
1936 5051 0.392327 GCTCTGCCTTCTGAAGACCC 60.392 60.000 18.68 7.25 0.00 4.46
2109 5230 2.824961 GAGGATCTCTGGAGCTGCT 58.175 57.895 6.82 0.00 0.00 4.24
2115 5236 3.543665 GATCTCTGGAGCTGCTGATTTT 58.456 45.455 14.95 3.68 0.00 1.82
2178 5305 2.795231 ACACCATCATCCACCTTCTG 57.205 50.000 0.00 0.00 0.00 3.02
2202 5329 1.423541 AGCTACACCATCAACAACCCA 59.576 47.619 0.00 0.00 0.00 4.51
2315 5451 7.352079 AGGCTATGCATTTGCTAAGTAATTT 57.648 32.000 19.16 0.00 42.66 1.82
2343 5493 6.796705 TGTTTCCCTTCTAATCTTTCGTTC 57.203 37.500 0.00 0.00 0.00 3.95
2587 5775 8.889717 GTGCTTAATTTCTGGCAGTAGTAAATA 58.110 33.333 15.27 0.00 35.29 1.40
2622 5892 3.495331 TGGCAACTTCTGGATTTTGCTA 58.505 40.909 12.96 7.30 43.20 3.49
2640 5910 2.417933 GCTACTGCAGTGGAACAATCTG 59.582 50.000 31.87 9.00 41.43 2.90
2641 5911 1.901591 ACTGCAGTGGAACAATCTGG 58.098 50.000 20.97 0.00 44.16 3.86
2652 5922 3.953612 GGAACAATCTGGGCAATGTCATA 59.046 43.478 0.00 0.00 0.00 2.15
2654 5924 5.769662 GGAACAATCTGGGCAATGTCATATA 59.230 40.000 0.00 0.00 0.00 0.86
2659 5929 4.707105 TCTGGGCAATGTCATATACTGTG 58.293 43.478 0.00 0.00 0.00 3.66
2671 5941 6.658816 TGTCATATACTGTGCAAGAAATGGTT 59.341 34.615 0.00 0.00 0.00 3.67
2753 6023 6.981722 ACAGGTTATGAAAGGAATGTTTCAC 58.018 36.000 1.30 0.00 46.53 3.18
2778 6048 4.764679 TTTTTGTAATGCTCTGATGCGT 57.235 36.364 0.00 0.00 35.36 5.24
2779 6049 4.340894 TTTTGTAATGCTCTGATGCGTC 57.659 40.909 0.00 0.00 35.36 5.19
2780 6050 2.967599 TGTAATGCTCTGATGCGTCT 57.032 45.000 7.58 0.00 35.36 4.18
2781 6051 4.385358 TTGTAATGCTCTGATGCGTCTA 57.615 40.909 7.58 0.00 35.36 2.59
2782 6052 4.590850 TGTAATGCTCTGATGCGTCTAT 57.409 40.909 7.58 0.00 35.36 1.98
2783 6053 5.705609 TGTAATGCTCTGATGCGTCTATA 57.294 39.130 7.58 0.00 35.36 1.31
2784 6054 5.461526 TGTAATGCTCTGATGCGTCTATAC 58.538 41.667 7.58 1.52 35.36 1.47
2790 6060 6.407202 TGCTCTGATGCGTCTATACTCTATA 58.593 40.000 7.58 0.00 35.36 1.31
2846 6122 5.493133 TGTTCGTTGTATTTATGGGCATC 57.507 39.130 0.00 0.00 0.00 3.91
2850 6126 4.574421 TCGTTGTATTTATGGGCATCACTG 59.426 41.667 0.00 0.00 0.00 3.66
2855 6131 5.822519 TGTATTTATGGGCATCACTGAAGAC 59.177 40.000 0.00 0.00 0.00 3.01
2887 6163 5.463286 TGCAGCATGAATGTTGTTAAAGAG 58.537 37.500 8.63 0.00 40.55 2.85
2935 6211 4.846779 AAATATTTGTCACGCAGTTGGT 57.153 36.364 0.00 0.00 41.61 3.67
3027 6315 5.070446 TCCTGTTTAGAGAATGTGTGTGTCT 59.930 40.000 0.00 0.00 0.00 3.41
3075 6364 5.424895 AGACTATCAGGAGCTCAAAATGTCT 59.575 40.000 17.19 16.64 0.00 3.41
3076 6365 5.426504 ACTATCAGGAGCTCAAAATGTCTG 58.573 41.667 17.19 11.48 0.00 3.51
3152 6472 6.715280 AGTGGATGAACTACTGAAACATCAT 58.285 36.000 0.00 0.00 38.85 2.45
3213 6718 1.573829 GCGCCATCGGTTTGTTCTCA 61.574 55.000 0.00 0.00 35.95 3.27
3216 6721 1.464997 GCCATCGGTTTGTTCTCAGAC 59.535 52.381 0.00 0.00 0.00 3.51
3224 6729 4.044426 GGTTTGTTCTCAGACAACAATGC 58.956 43.478 4.97 2.50 42.04 3.56
3227 6732 3.723260 TGTTCTCAGACAACAATGCGTA 58.277 40.909 0.00 0.00 30.67 4.42
3228 6733 4.123506 TGTTCTCAGACAACAATGCGTAA 58.876 39.130 0.00 0.00 30.67 3.18
3229 6734 4.211164 TGTTCTCAGACAACAATGCGTAAG 59.789 41.667 0.00 0.00 30.67 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 0.321653 GGCATCGTCTTGGACAGGTT 60.322 55.000 0.00 0.00 32.09 3.50
5 6 1.354337 CGTGGCATCGTCTTGGACAG 61.354 60.000 0.00 0.00 32.09 3.51
8 9 1.080093 GTCGTGGCATCGTCTTGGA 60.080 57.895 8.80 0.00 0.00 3.53
11 12 0.460284 GGATGTCGTGGCATCGTCTT 60.460 55.000 8.24 3.19 44.47 3.01
14 15 1.141881 GAGGATGTCGTGGCATCGT 59.858 57.895 9.18 9.18 44.47 3.73
15 16 0.179100 AAGAGGATGTCGTGGCATCG 60.179 55.000 8.24 0.00 44.47 3.84
16 17 1.137872 AGAAGAGGATGTCGTGGCATC 59.862 52.381 5.90 5.90 43.22 3.91
17 18 1.137872 GAGAAGAGGATGTCGTGGCAT 59.862 52.381 0.00 0.00 0.00 4.40
18 19 0.532573 GAGAAGAGGATGTCGTGGCA 59.467 55.000 0.00 0.00 0.00 4.92
19 20 0.820871 AGAGAAGAGGATGTCGTGGC 59.179 55.000 0.00 0.00 0.00 5.01
20 21 3.066064 CACTAGAGAAGAGGATGTCGTGG 59.934 52.174 0.00 0.00 0.00 4.94
21 22 3.692101 ACACTAGAGAAGAGGATGTCGTG 59.308 47.826 0.00 0.00 0.00 4.35
22 23 3.942748 GACACTAGAGAAGAGGATGTCGT 59.057 47.826 0.00 0.00 0.00 4.34
23 24 3.314080 GGACACTAGAGAAGAGGATGTCG 59.686 52.174 0.00 0.00 36.65 4.35
24 25 4.338118 CAGGACACTAGAGAAGAGGATGTC 59.662 50.000 0.00 0.00 35.37 3.06
25 26 4.277476 CAGGACACTAGAGAAGAGGATGT 58.723 47.826 0.00 0.00 0.00 3.06
26 27 3.636300 CCAGGACACTAGAGAAGAGGATG 59.364 52.174 0.00 0.00 0.00 3.51
27 28 3.270960 ACCAGGACACTAGAGAAGAGGAT 59.729 47.826 0.00 0.00 0.00 3.24
28 29 2.650322 ACCAGGACACTAGAGAAGAGGA 59.350 50.000 0.00 0.00 0.00 3.71
29 30 3.020984 GACCAGGACACTAGAGAAGAGG 58.979 54.545 0.00 0.00 0.00 3.69
30 31 3.691575 TGACCAGGACACTAGAGAAGAG 58.308 50.000 0.00 0.00 0.00 2.85
31 32 3.691575 CTGACCAGGACACTAGAGAAGA 58.308 50.000 0.00 0.00 0.00 2.87
54 55 3.976701 ATCTTCAACGGCGGCCTGG 62.977 63.158 18.34 4.77 0.00 4.45
55 56 2.436646 ATCTTCAACGGCGGCCTG 60.437 61.111 18.34 13.03 0.00 4.85
56 57 2.125106 GATCTTCAACGGCGGCCT 60.125 61.111 18.34 0.89 0.00 5.19
57 58 2.435938 TGATCTTCAACGGCGGCC 60.436 61.111 13.24 9.54 0.00 6.13
58 59 2.750888 GGTGATCTTCAACGGCGGC 61.751 63.158 13.24 0.00 0.00 6.53
59 60 3.486263 GGTGATCTTCAACGGCGG 58.514 61.111 13.24 0.00 0.00 6.13
64 65 0.798776 CCAGCACGGTGATCTTCAAC 59.201 55.000 13.29 0.00 0.00 3.18
65 66 0.684535 TCCAGCACGGTGATCTTCAA 59.315 50.000 13.29 0.00 35.57 2.69
66 67 0.904649 ATCCAGCACGGTGATCTTCA 59.095 50.000 13.29 0.00 35.57 3.02
67 68 1.134699 TGATCCAGCACGGTGATCTTC 60.135 52.381 13.29 2.73 36.65 2.87
68 69 0.904649 TGATCCAGCACGGTGATCTT 59.095 50.000 13.29 0.00 36.65 2.40
69 70 0.176680 GTGATCCAGCACGGTGATCT 59.823 55.000 13.29 0.00 36.65 2.75
70 71 0.811616 GGTGATCCAGCACGGTGATC 60.812 60.000 13.29 6.46 39.66 2.92
71 72 1.221840 GGTGATCCAGCACGGTGAT 59.778 57.895 13.29 1.50 39.66 3.06
72 73 1.763546 TTGGTGATCCAGCACGGTGA 61.764 55.000 13.29 0.00 45.22 4.02
73 74 1.302431 TTGGTGATCCAGCACGGTG 60.302 57.895 3.15 3.15 45.22 4.94
74 75 1.302511 GTTGGTGATCCAGCACGGT 60.303 57.895 0.00 0.00 45.22 4.83
75 76 2.390599 CGTTGGTGATCCAGCACGG 61.391 63.158 0.00 0.00 45.22 4.94
76 77 3.027170 GCGTTGGTGATCCAGCACG 62.027 63.158 12.83 12.83 45.35 5.34
77 78 2.690778 GGCGTTGGTGATCCAGCAC 61.691 63.158 0.00 0.00 45.22 4.40
78 79 2.359850 GGCGTTGGTGATCCAGCA 60.360 61.111 0.00 0.00 45.22 4.41
79 80 3.499737 CGGCGTTGGTGATCCAGC 61.500 66.667 0.00 0.00 45.22 4.85
80 81 3.499737 GCGGCGTTGGTGATCCAG 61.500 66.667 9.37 0.00 45.22 3.86
81 82 4.015406 AGCGGCGTTGGTGATCCA 62.015 61.111 9.37 0.00 42.66 3.41
82 83 3.499737 CAGCGGCGTTGGTGATCC 61.500 66.667 16.38 0.00 39.68 3.36
83 84 1.017177 TAACAGCGGCGTTGGTGATC 61.017 55.000 24.73 0.00 39.68 2.92
84 85 1.004320 TAACAGCGGCGTTGGTGAT 60.004 52.632 24.73 11.12 39.68 3.06
85 86 1.666553 CTAACAGCGGCGTTGGTGA 60.667 57.895 24.73 9.23 39.68 4.02
86 87 2.677003 CCTAACAGCGGCGTTGGTG 61.677 63.158 24.73 13.52 42.86 4.17
87 88 2.358247 CCTAACAGCGGCGTTGGT 60.358 61.111 26.86 23.68 0.00 3.67
88 89 3.799755 GCCTAACAGCGGCGTTGG 61.800 66.667 26.86 10.93 37.87 3.77
93 94 3.415808 GGCAATGCCTAACAGCGGC 62.416 63.158 18.47 0.00 46.69 6.53
94 95 2.800736 GGCAATGCCTAACAGCGG 59.199 61.111 18.47 0.00 46.69 5.52
104 105 2.467826 GGCTCTCGACAGGCAATGC 61.468 63.158 9.41 0.00 38.83 3.56
105 106 1.078918 TGGCTCTCGACAGGCAATG 60.079 57.895 14.49 0.00 45.45 2.82
106 107 3.392228 TGGCTCTCGACAGGCAAT 58.608 55.556 14.49 0.00 45.45 3.56
138 139 0.529119 AACAGGACGACAACGGTGAC 60.529 55.000 7.88 0.00 44.46 3.67
149 150 5.168526 TCAACAAATTTCTCAACAGGACG 57.831 39.130 0.00 0.00 0.00 4.79
228 229 9.528018 AACTTATATAAATTTTTCCCACATGCG 57.472 29.630 0.00 0.00 0.00 4.73
248 249 6.667414 TGAAATGGACCATAGGCAAAACTTAT 59.333 34.615 7.59 0.00 0.00 1.73
261 262 8.938883 ACTTATATACAGACTGAAATGGACCAT 58.061 33.333 10.08 0.00 0.00 3.55
274 275 8.604890 GGCTTCAGACAAAACTTATATACAGAC 58.395 37.037 0.00 0.00 0.00 3.51
298 299 7.308229 CCATTTTAGTCTGCATATAAGTCTGGC 60.308 40.741 0.00 0.00 0.00 4.85
299 300 7.308229 GCCATTTTAGTCTGCATATAAGTCTGG 60.308 40.741 0.00 0.00 0.00 3.86
302 303 7.442364 TCAGCCATTTTAGTCTGCATATAAGTC 59.558 37.037 0.00 0.00 0.00 3.01
306 307 6.591001 TGTCAGCCATTTTAGTCTGCATATA 58.409 36.000 0.00 0.00 0.00 0.86
312 313 5.106555 ACGATTTGTCAGCCATTTTAGTCTG 60.107 40.000 0.00 0.00 0.00 3.51
319 320 5.560760 CGCATATACGATTTGTCAGCCATTT 60.561 40.000 0.00 0.00 34.06 2.32
323 324 2.157668 CCGCATATACGATTTGTCAGCC 59.842 50.000 0.00 0.00 34.06 4.85
324 325 2.157668 CCCGCATATACGATTTGTCAGC 59.842 50.000 0.00 0.00 34.06 4.26
326 327 2.103432 ACCCCGCATATACGATTTGTCA 59.897 45.455 0.00 0.00 34.06 3.58
327 328 2.762745 ACCCCGCATATACGATTTGTC 58.237 47.619 0.00 0.00 34.06 3.18
329 330 5.676532 TTTTACCCCGCATATACGATTTG 57.323 39.130 0.00 0.00 34.06 2.32
335 336 6.316890 TGACTTTCTTTTTACCCCGCATATAC 59.683 38.462 0.00 0.00 0.00 1.47
370 371 9.878667 TTGAACAATTTACCGATAGTTAGATCA 57.121 29.630 0.00 0.00 0.00 2.92
408 409 5.003121 GTGAAAAACTAACTGAAACGTGCAC 59.997 40.000 6.82 6.82 0.00 4.57
442 443 9.384764 AGATAGTACAAAATCTCAAAAGGCTAC 57.615 33.333 0.00 0.00 0.00 3.58
460 461 5.064558 TCAAGGATGAGTCGGAGATAGTAC 58.935 45.833 0.00 0.00 40.67 2.73
463 464 5.521906 TTTCAAGGATGAGTCGGAGATAG 57.478 43.478 0.00 0.00 40.67 2.08
469 470 4.446371 AGCTATTTTCAAGGATGAGTCGG 58.554 43.478 0.00 0.00 36.78 4.79
475 476 4.161001 AGGCCAAAGCTATTTTCAAGGATG 59.839 41.667 5.01 0.00 39.73 3.51
484 485 5.530915 GGTTTGAAAAAGGCCAAAGCTATTT 59.469 36.000 5.01 0.00 43.43 1.40
488 489 2.741553 CGGTTTGAAAAAGGCCAAAGCT 60.742 45.455 5.01 0.00 44.13 3.74
489 490 1.597195 CGGTTTGAAAAAGGCCAAAGC 59.403 47.619 5.01 4.18 43.37 3.51
495 499 1.411246 ACCCTTCGGTTTGAAAAAGGC 59.589 47.619 2.12 0.00 40.58 4.35
518 522 4.838152 CACATCCCCACCGAGCCG 62.838 72.222 0.00 0.00 0.00 5.52
519 523 3.399181 TCACATCCCCACCGAGCC 61.399 66.667 0.00 0.00 0.00 4.70
520 524 2.125106 GTCACATCCCCACCGAGC 60.125 66.667 0.00 0.00 0.00 5.03
521 525 2.184322 CGTCACATCCCCACCGAG 59.816 66.667 0.00 0.00 0.00 4.63
522 526 4.077184 GCGTCACATCCCCACCGA 62.077 66.667 0.00 0.00 0.00 4.69
524 528 4.388499 ACGCGTCACATCCCCACC 62.388 66.667 5.58 0.00 0.00 4.61
525 529 3.118454 CACGCGTCACATCCCCAC 61.118 66.667 9.86 0.00 0.00 4.61
527 531 4.760047 AGCACGCGTCACATCCCC 62.760 66.667 9.86 0.00 0.00 4.81
528 532 3.490759 CAGCACGCGTCACATCCC 61.491 66.667 9.86 0.00 0.00 3.85
529 533 4.152625 GCAGCACGCGTCACATCC 62.153 66.667 9.86 0.00 0.00 3.51
530 534 2.743752 ATGCAGCACGCGTCACATC 61.744 57.895 9.86 1.02 46.97 3.06
571 575 2.159960 GCTCTAGAAAAACTCACGCACG 60.160 50.000 0.00 0.00 0.00 5.34
576 580 3.403038 TGCCAGCTCTAGAAAAACTCAC 58.597 45.455 0.00 0.00 0.00 3.51
587 591 2.988010 AACGATGAATGCCAGCTCTA 57.012 45.000 0.00 0.00 0.00 2.43
589 593 2.541762 GAGTAACGATGAATGCCAGCTC 59.458 50.000 0.00 0.00 0.00 4.09
591 595 1.599542 GGAGTAACGATGAATGCCAGC 59.400 52.381 0.00 0.00 0.00 4.85
655 661 8.839310 AGATGTATGTGGACATATTTTAGAGC 57.161 34.615 2.88 0.00 40.18 4.09
670 676 9.163899 AGTATGGACTACGTATAGATGTATGTG 57.836 37.037 0.00 0.00 35.35 3.21
672 678 9.379791 TCAGTATGGACTACGTATAGATGTATG 57.620 37.037 0.00 0.00 36.16 2.39
681 687 9.352191 ACTAAGATTTCAGTATGGACTACGTAT 57.648 33.333 0.00 0.00 36.16 3.06
707 723 8.177013 GCCTCCGTTTCGAAATATAAGTTTTTA 58.823 33.333 14.69 0.00 0.00 1.52
723 739 1.954382 AGAAAAAGGTGCCTCCGTTTC 59.046 47.619 8.71 11.59 44.63 2.78
728 744 2.163509 GAAGGAGAAAAAGGTGCCTCC 58.836 52.381 0.00 0.00 44.14 4.30
739 755 0.253207 GGGAGAGGGGGAAGGAGAAA 60.253 60.000 0.00 0.00 0.00 2.52
750 766 0.618458 TCAAATGGAACGGGAGAGGG 59.382 55.000 0.00 0.00 0.00 4.30
767 783 3.194968 GGTAAATCCGAGGAGAGTGTTCA 59.805 47.826 0.00 0.00 0.00 3.18
781 797 5.046663 GGAGGAGATGAGATGAGGTAAATCC 60.047 48.000 0.00 0.00 0.00 3.01
899 927 4.024048 GCGTGAAGGAGACTGAAAATGAAA 60.024 41.667 0.00 0.00 42.68 2.69
946 975 1.761009 GCCTCTCCTTCTAGATGGCCT 60.761 57.143 17.90 0.00 35.49 5.19
947 976 0.684535 GCCTCTCCTTCTAGATGGCC 59.315 60.000 17.90 0.00 35.49 5.36
949 978 0.316841 GCGCCTCTCCTTCTAGATGG 59.683 60.000 16.84 16.84 0.00 3.51
961 3884 4.862092 CGACATGAGCGCGCCTCT 62.862 66.667 30.33 9.92 41.35 3.69
1105 4028 4.003788 CGGAAGCGTGGACCACCT 62.004 66.667 19.11 13.60 37.04 4.00
1168 4091 1.549170 GTCCATGTACCAGTCGAGGTT 59.451 52.381 1.16 0.00 43.08 3.50
1221 4144 2.572284 CTCCTTGGGTCGTCGGTC 59.428 66.667 0.00 0.00 0.00 4.79
1303 4233 2.092753 TCAACAGGAGCAGATTCCCATC 60.093 50.000 0.00 0.00 38.02 3.51
1305 4235 1.361204 TCAACAGGAGCAGATTCCCA 58.639 50.000 0.00 0.00 38.02 4.37
1442 4375 0.832135 AAGAGGGTTGAGGACGCAGA 60.832 55.000 0.00 0.00 43.23 4.26
1506 4446 3.378112 GGAAAATGACATCAGCGATTCCA 59.622 43.478 10.50 0.00 36.09 3.53
1755 4701 0.396811 AGAAAACCTCGGTCACAGGG 59.603 55.000 0.00 0.00 35.01 4.45
1898 5013 2.563179 AGCTTACTTGTCTCGGTGTCAT 59.437 45.455 0.00 0.00 0.00 3.06
1912 5027 3.056179 GTCTTCAGAAGGCAGAGCTTACT 60.056 47.826 10.07 0.00 32.07 2.24
1925 5040 2.398754 TCTGTCTGGGGTCTTCAGAA 57.601 50.000 0.00 0.00 42.13 3.02
1936 5051 4.347360 TGAAGATGGCATATCTGTCTGG 57.653 45.455 0.00 0.00 0.00 3.86
2102 5223 2.030540 TGCTTCACAAAATCAGCAGCTC 60.031 45.455 0.00 0.00 37.35 4.09
2109 5230 4.206375 TCTTGTCCTGCTTCACAAAATCA 58.794 39.130 0.00 0.00 32.16 2.57
2115 5236 3.281727 AACTTCTTGTCCTGCTTCACA 57.718 42.857 0.00 0.00 0.00 3.58
2178 5305 2.472695 TGTTGATGGTGTAGCTGACC 57.527 50.000 9.34 9.34 0.00 4.02
2180 5307 2.552155 GGGTTGTTGATGGTGTAGCTGA 60.552 50.000 0.00 0.00 0.00 4.26
2202 5329 1.074405 TGCAAGGCCAGTTGAGAATCT 59.926 47.619 5.01 0.00 34.92 2.40
2315 5451 7.501225 ACGAAAGATTAGAAGGGAAACAAGAAA 59.499 33.333 0.00 0.00 0.00 2.52
2343 5493 8.028938 GGCAAGGCATAATAACCATAATAACTG 58.971 37.037 0.00 0.00 0.00 3.16
2421 5589 5.772521 ACCAATTAAGACATCAAACTGCAC 58.227 37.500 0.00 0.00 0.00 4.57
2603 5791 4.479619 CAGTAGCAAAATCCAGAAGTTGC 58.520 43.478 9.49 9.49 45.29 4.17
2622 5892 1.546323 CCCAGATTGTTCCACTGCAGT 60.546 52.381 15.25 15.25 0.00 4.40
2635 5905 5.766670 CACAGTATATGACATTGCCCAGATT 59.233 40.000 0.00 0.00 0.00 2.40
2640 5910 3.213506 TGCACAGTATATGACATTGCCC 58.786 45.455 5.34 0.00 37.30 5.36
2641 5911 4.576053 TCTTGCACAGTATATGACATTGCC 59.424 41.667 5.34 0.00 37.30 4.52
2652 5922 7.759489 TCTAAAACCATTTCTTGCACAGTAT 57.241 32.000 0.00 0.00 0.00 2.12
2654 5924 6.655078 ATCTAAAACCATTTCTTGCACAGT 57.345 33.333 0.00 0.00 0.00 3.55
2659 5929 7.425577 AAGCAAATCTAAAACCATTTCTTGC 57.574 32.000 0.00 0.00 34.05 4.01
2671 5941 8.220755 ACAAACTGTCAGTAAGCAAATCTAAA 57.779 30.769 5.77 0.00 0.00 1.85
2753 6023 5.911280 CGCATCAGAGCATTACAAAAATAGG 59.089 40.000 0.00 0.00 0.00 2.57
2778 6048 6.721843 AGGGGCTCAAGTATAGAGTATAGA 57.278 41.667 0.00 0.00 35.55 1.98
2779 6049 6.948886 TCAAGGGGCTCAAGTATAGAGTATAG 59.051 42.308 0.00 0.00 35.55 1.31
2780 6050 6.860034 TCAAGGGGCTCAAGTATAGAGTATA 58.140 40.000 0.00 0.00 35.55 1.47
2781 6051 5.716979 TCAAGGGGCTCAAGTATAGAGTAT 58.283 41.667 0.00 0.00 35.55 2.12
2782 6052 5.138758 TCAAGGGGCTCAAGTATAGAGTA 57.861 43.478 0.00 0.00 35.55 2.59
2783 6053 3.995636 TCAAGGGGCTCAAGTATAGAGT 58.004 45.455 0.00 0.00 35.55 3.24
2784 6054 4.407296 AGTTCAAGGGGCTCAAGTATAGAG 59.593 45.833 0.00 0.00 36.21 2.43
2790 6060 2.339769 ACTAGTTCAAGGGGCTCAAGT 58.660 47.619 0.00 0.00 0.00 3.16
2846 6122 2.874086 TGCAGATTGTGTGTCTTCAGTG 59.126 45.455 0.00 0.00 0.00 3.66
2850 6126 1.875514 TGCTGCAGATTGTGTGTCTTC 59.124 47.619 20.43 0.00 0.00 2.87
2855 6131 3.179048 CATTCATGCTGCAGATTGTGTG 58.821 45.455 20.43 12.22 0.00 3.82
2887 6163 6.976636 AGCAGAGAACATCTTTAGTTTAGC 57.023 37.500 0.00 0.00 35.47 3.09
2905 6181 7.279981 ACTGCGTGACAAATATTTATAAGCAGA 59.720 33.333 29.94 11.28 46.84 4.26
2935 6211 2.158871 ACCCTTGTAGAAACAGCAACGA 60.159 45.455 0.00 0.00 36.83 3.85
3027 6315 2.981898 TCTCTCGTTCGTGATCAGGTA 58.018 47.619 14.67 2.93 0.00 3.08
3075 6364 2.900716 TACTGTTGCAGCAGTACACA 57.099 45.000 32.00 17.55 46.68 3.72
3181 6681 0.467384 ATGGCGCTGCAGTTCTAGAT 59.533 50.000 16.64 0.00 0.00 1.98
3213 6718 1.508632 ACGCTTACGCATTGTTGTCT 58.491 45.000 0.00 0.00 45.53 3.41


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

AutoCloner maintained by Alex Coulton.