Multiple sequence alignment - TraesCS2B01G621700

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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 TraesCS2B01G621700 chr2B 100.000 3857 0 0 1 3857 795979352 795983208 0.000000e+00 7123.0
1 TraesCS2B01G621700 chr2B 83.417 398 62 4 497 892 796598903 796599298 2.190000e-97 366.0
2 TraesCS2B01G621700 chr2B 78.588 439 73 6 3157 3574 796599320 796599758 1.770000e-68 270.0
3 TraesCS2B01G621700 chr2B 75.000 444 79 11 3160 3572 789260810 789260368 3.960000e-40 176.0
4 TraesCS2B01G621700 chr2B 77.820 266 55 4 1700 1963 704118625 704118888 1.110000e-35 161.0
5 TraesCS2B01G621700 chr5B 100.000 2251 0 0 906 3156 419520518 419522768 0.000000e+00 4157.0
6 TraesCS2B01G621700 chr5B 99.023 2251 12 4 906 3156 491849012 491851252 0.000000e+00 4026.0
7 TraesCS2B01G621700 chr5B 88.406 138 12 4 264 399 230778763 230778898 3.080000e-36 163.0
8 TraesCS2B01G621700 chr5B 91.964 112 8 1 267 378 434616115 434616005 5.160000e-34 156.0
9 TraesCS2B01G621700 chr2D 100.000 2251 0 0 906 3156 617965245 617967495 0.000000e+00 4157.0
10 TraesCS2B01G621700 chr2D 89.073 723 79 0 906 1628 101557302 101558024 0.000000e+00 898.0
11 TraesCS2B01G621700 chr2D 83.005 406 65 3 497 900 637903261 637902858 7.870000e-97 364.0
12 TraesCS2B01G621700 chr2D 80.714 420 67 10 487 902 640025355 640024946 8.040000e-82 315.0
13 TraesCS2B01G621700 chr2D 78.539 438 72 7 3160 3576 637902841 637902405 6.350000e-68 268.0
14 TraesCS2B01G621700 chr2D 83.182 220 26 7 3604 3814 640024392 640024175 1.410000e-44 191.0
15 TraesCS2B01G621700 chr2D 95.370 108 5 0 271 378 617338703 617338810 5.120000e-39 172.0
16 TraesCS2B01G621700 chr2D 78.222 225 43 6 3351 3572 646421098 646421319 5.200000e-29 139.0
17 TraesCS2B01G621700 chr3A 94.936 1955 85 7 909 2862 34994399 34992458 0.000000e+00 3049.0
18 TraesCS2B01G621700 chr5A 95.334 1586 74 0 1277 2862 138081798 138080213 0.000000e+00 2519.0
19 TraesCS2B01G621700 chr5A 90.575 1496 130 4 1662 3153 469664647 469666135 0.000000e+00 1971.0
20 TraesCS2B01G621700 chr5A 94.175 309 18 0 909 1217 138082094 138081786 4.510000e-129 472.0
21 TraesCS2B01G621700 chr5A 91.358 162 14 0 909 1070 554564851 554565012 5.020000e-54 222.0
22 TraesCS2B01G621700 chr5A 91.818 110 7 2 270 378 512233468 512233576 6.670000e-33 152.0
23 TraesCS2B01G621700 chr5D 90.790 1531 132 9 1628 3156 467262774 467264297 0.000000e+00 2037.0
24 TraesCS2B01G621700 chr5D 88.579 394 37 2 1235 1628 467262338 467262723 4.510000e-129 472.0
25 TraesCS2B01G621700 chr7B 89.142 1538 150 10 1621 3156 664079270 664077748 0.000000e+00 1899.0
26 TraesCS2B01G621700 chr7B 84.915 590 55 6 1039 1628 664079868 664079313 2.010000e-157 566.0
27 TraesCS2B01G621700 chr7B 85.788 387 34 10 1242 1628 59646491 59646126 1.300000e-104 390.0
28 TraesCS2B01G621700 chr7B 76.098 205 35 10 937 1139 687852257 687852065 1.140000e-15 95.3
29 TraesCS2B01G621700 chr7A 91.009 1368 118 2 1798 3161 727382174 727380808 0.000000e+00 1840.0
30 TraesCS2B01G621700 chr7A 89.140 221 22 2 1481 1701 727383508 727383290 1.370000e-69 274.0
31 TraesCS2B01G621700 chrUn 96.829 473 14 1 2688 3160 8840144 8839673 0.000000e+00 789.0
32 TraesCS2B01G621700 chrUn 91.620 179 12 1 1 179 22436925 22436750 1.070000e-60 244.0
33 TraesCS2B01G621700 chrUn 84.579 214 27 5 3604 3814 22435448 22435238 1.400000e-49 207.0
34 TraesCS2B01G621700 chr2A 91.619 525 44 0 381 905 761897655 761898179 0.000000e+00 726.0
35 TraesCS2B01G621700 chr2A 86.087 460 39 9 3169 3607 761898185 761898640 4.510000e-129 472.0
36 TraesCS2B01G621700 chr2A 91.304 276 15 7 1 269 761897372 761897645 6.090000e-98 368.0
37 TraesCS2B01G621700 chr2A 83.005 406 65 4 497 900 761306363 761305960 7.870000e-97 364.0
38 TraesCS2B01G621700 chr2A 82.426 404 71 0 497 900 761856046 761856449 1.700000e-93 353.0
39 TraesCS2B01G621700 chr2A 78.112 466 81 6 3160 3604 761305943 761305478 3.800000e-70 276.0
40 TraesCS2B01G621700 chr2A 80.793 328 61 2 559 884 761521260 761520933 4.940000e-64 255.0
41 TraesCS2B01G621700 chr2A 82.710 214 30 7 3604 3814 761856996 761857205 2.370000e-42 183.0
42 TraesCS2B01G621700 chr1D 79.551 401 60 11 497 889 6541353 6541739 2.280000e-67 267.0
43 TraesCS2B01G621700 chr1D 77.778 405 67 9 3175 3557 6541782 6542185 1.080000e-55 228.0
44 TraesCS2B01G621700 chr1A 78.164 403 65 12 497 889 7812019 7811630 6.440000e-58 235.0
45 TraesCS2B01G621700 chr6A 89.344 122 9 4 262 381 419681189 419681308 2.400000e-32 150.0
46 TraesCS2B01G621700 chr7D 89.655 116 12 0 263 378 144501154 144501269 8.630000e-32 148.0
47 TraesCS2B01G621700 chr7D 88.800 125 8 4 263 386 426778557 426778676 8.630000e-32 148.0
48 TraesCS2B01G621700 chr3B 90.265 113 11 0 266 378 78608743 78608631 8.630000e-32 148.0
49 TraesCS2B01G621700 chr3B 76.585 205 34 10 937 1139 734746614 734746422 2.450000e-17 100.0
50 TraesCS2B01G621700 chr4B 89.076 119 9 4 270 387 600375812 600375697 1.120000e-30 145.0
51 TraesCS2B01G621700 chr6D 85.437 103 11 3 3475 3574 456098576 456098677 1.900000e-18 104.0
52 TraesCS2B01G621700 chr1B 80.374 107 13 4 3475 3574 676255614 676255509 1.490000e-09 75.0


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 TraesCS2B01G621700 chr2B 795979352 795983208 3856 False 7123.0 7123 100.0000 1 3857 1 chr2B.!!$F2 3856
1 TraesCS2B01G621700 chr2B 796598903 796599758 855 False 318.0 366 81.0025 497 3574 2 chr2B.!!$F3 3077
2 TraesCS2B01G621700 chr5B 419520518 419522768 2250 False 4157.0 4157 100.0000 906 3156 1 chr5B.!!$F2 2250
3 TraesCS2B01G621700 chr5B 491849012 491851252 2240 False 4026.0 4026 99.0230 906 3156 1 chr5B.!!$F3 2250
4 TraesCS2B01G621700 chr2D 617965245 617967495 2250 False 4157.0 4157 100.0000 906 3156 1 chr2D.!!$F3 2250
5 TraesCS2B01G621700 chr2D 101557302 101558024 722 False 898.0 898 89.0730 906 1628 1 chr2D.!!$F1 722
6 TraesCS2B01G621700 chr2D 637902405 637903261 856 True 316.0 364 80.7720 497 3576 2 chr2D.!!$R1 3079
7 TraesCS2B01G621700 chr2D 640024175 640025355 1180 True 253.0 315 81.9480 487 3814 2 chr2D.!!$R2 3327
8 TraesCS2B01G621700 chr3A 34992458 34994399 1941 True 3049.0 3049 94.9360 909 2862 1 chr3A.!!$R1 1953
9 TraesCS2B01G621700 chr5A 469664647 469666135 1488 False 1971.0 1971 90.5750 1662 3153 1 chr5A.!!$F1 1491
10 TraesCS2B01G621700 chr5A 138080213 138082094 1881 True 1495.5 2519 94.7545 909 2862 2 chr5A.!!$R1 1953
11 TraesCS2B01G621700 chr5D 467262338 467264297 1959 False 1254.5 2037 89.6845 1235 3156 2 chr5D.!!$F1 1921
12 TraesCS2B01G621700 chr7B 664077748 664079868 2120 True 1232.5 1899 87.0285 1039 3156 2 chr7B.!!$R3 2117
13 TraesCS2B01G621700 chr7A 727380808 727383508 2700 True 1057.0 1840 90.0745 1481 3161 2 chr7A.!!$R1 1680
14 TraesCS2B01G621700 chrUn 22435238 22436925 1687 True 225.5 244 88.0995 1 3814 2 chrUn.!!$R2 3813
15 TraesCS2B01G621700 chr2A 761897372 761898640 1268 False 522.0 726 89.6700 1 3607 3 chr2A.!!$F2 3606
16 TraesCS2B01G621700 chr2A 761305478 761306363 885 True 320.0 364 80.5585 497 3604 2 chr2A.!!$R2 3107
17 TraesCS2B01G621700 chr2A 761856046 761857205 1159 False 268.0 353 82.5680 497 3814 2 chr2A.!!$F1 3317
18 TraesCS2B01G621700 chr1D 6541353 6542185 832 False 247.5 267 78.6645 497 3557 2 chr1D.!!$F1 3060

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
257 308 0.596082 ACTTCCGTGCAAATTTCCGG 59.404 50.0 12.16 12.16 41.75 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3165 4558 0.456628 GACGAGGCCTTACTGGAGAC 59.543 60.0 6.77 0.0 38.35 3.36 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
27 28 1.672356 GGTGTGCTGCTCGTTCCAT 60.672 57.895 0.00 0.00 0.00 3.41
73 74 3.660111 GTGTGCGCACCCACTTCC 61.660 66.667 35.72 10.84 39.61 3.46
139 140 3.499737 CACGTGCGCCCAGAATCC 61.500 66.667 4.18 0.00 0.00 3.01
199 213 9.361712 GTTTCTTCAACAAGTATACGTGTTAAC 57.638 33.333 28.79 24.38 44.46 2.01
222 236 8.537728 AACATATTGATTATGAAAAGGCAGGA 57.462 30.769 1.73 0.00 40.22 3.86
230 278 9.246670 TGATTATGAAAAGGCAGGAATATATGG 57.753 33.333 0.00 0.00 0.00 2.74
256 307 2.723618 CGTACTTCCGTGCAAATTTCCG 60.724 50.000 0.00 0.00 0.00 4.30
257 308 0.596082 ACTTCCGTGCAAATTTCCGG 59.404 50.000 12.16 12.16 41.75 5.14
269 320 4.260334 GCAAATTTCCGGCTTCAAATATGC 60.260 41.667 0.00 0.00 0.00 3.14
272 323 4.893424 TTTCCGGCTTCAAATATGCTAC 57.107 40.909 0.00 0.00 0.00 3.58
273 324 3.838244 TCCGGCTTCAAATATGCTACT 57.162 42.857 0.00 0.00 0.00 2.57
274 325 3.728845 TCCGGCTTCAAATATGCTACTC 58.271 45.455 0.00 0.00 0.00 2.59
275 326 2.808543 CCGGCTTCAAATATGCTACTCC 59.191 50.000 0.00 0.00 0.00 3.85
277 328 3.495100 CGGCTTCAAATATGCTACTCCCT 60.495 47.826 0.00 0.00 0.00 4.20
278 329 4.068599 GGCTTCAAATATGCTACTCCCTC 58.931 47.826 0.00 0.00 0.00 4.30
281 332 6.296145 GGCTTCAAATATGCTACTCCCTCTAT 60.296 42.308 0.00 0.00 0.00 1.98
284 335 7.855784 TCAAATATGCTACTCCCTCTATTCA 57.144 36.000 0.00 0.00 0.00 2.57
286 337 7.510685 TCAAATATGCTACTCCCTCTATTCACT 59.489 37.037 0.00 0.00 0.00 3.41
287 338 7.863901 AATATGCTACTCCCTCTATTCACTT 57.136 36.000 0.00 0.00 0.00 3.16
288 339 7.863901 ATATGCTACTCCCTCTATTCACTTT 57.136 36.000 0.00 0.00 0.00 2.66
289 340 6.567602 ATGCTACTCCCTCTATTCACTTTT 57.432 37.500 0.00 0.00 0.00 2.27
291 342 7.676683 TGCTACTCCCTCTATTCACTTTTAT 57.323 36.000 0.00 0.00 0.00 1.40
294 345 9.699703 GCTACTCCCTCTATTCACTTTTATAAG 57.300 37.037 0.00 0.00 37.40 1.73
297 348 8.706521 ACTCCCTCTATTCACTTTTATAAGACC 58.293 37.037 0.00 0.00 35.30 3.85
300 351 9.907229 CCCTCTATTCACTTTTATAAGACCTTT 57.093 33.333 0.00 0.00 35.30 3.11
310 361 9.220767 ACTTTTATAAGACCTTTTAGACAGCAG 57.779 33.333 0.00 0.00 35.30 4.24
312 363 9.787435 TTTTATAAGACCTTTTAGACAGCAGAA 57.213 29.630 0.00 0.00 0.00 3.02
315 366 8.870075 ATAAGACCTTTTAGACAGCAGAAATT 57.130 30.769 0.00 0.00 0.00 1.82
316 367 6.566197 AGACCTTTTAGACAGCAGAAATTG 57.434 37.500 0.00 0.00 0.00 2.32
318 369 6.772716 AGACCTTTTAGACAGCAGAAATTGAA 59.227 34.615 0.00 0.00 0.00 2.69
319 370 6.739112 ACCTTTTAGACAGCAGAAATTGAAC 58.261 36.000 0.00 0.00 0.00 3.18
320 371 6.547510 ACCTTTTAGACAGCAGAAATTGAACT 59.452 34.615 0.00 0.00 0.00 3.01
321 372 6.860023 CCTTTTAGACAGCAGAAATTGAACTG 59.140 38.462 0.00 0.00 37.22 3.16
322 373 6.942532 TTTAGACAGCAGAAATTGAACTGT 57.057 33.333 0.00 0.00 43.93 3.55
323 374 6.942532 TTAGACAGCAGAAATTGAACTGTT 57.057 33.333 0.00 0.00 41.45 3.16
324 375 5.841957 AGACAGCAGAAATTGAACTGTTT 57.158 34.783 0.00 0.00 41.45 2.83
325 376 6.212888 AGACAGCAGAAATTGAACTGTTTT 57.787 33.333 0.00 0.00 41.45 2.43
327 378 7.420800 AGACAGCAGAAATTGAACTGTTTTAG 58.579 34.615 0.00 0.00 41.45 1.85
329 380 6.096846 ACAGCAGAAATTGAACTGTTTTAGGT 59.903 34.615 0.00 0.00 38.38 3.08
330 381 6.418819 CAGCAGAAATTGAACTGTTTTAGGTG 59.581 38.462 0.00 0.00 36.62 4.00
331 382 6.096846 AGCAGAAATTGAACTGTTTTAGGTGT 59.903 34.615 0.00 0.00 36.62 4.16
332 383 6.756542 GCAGAAATTGAACTGTTTTAGGTGTT 59.243 34.615 0.00 0.00 36.62 3.32
333 384 7.254084 GCAGAAATTGAACTGTTTTAGGTGTTG 60.254 37.037 0.00 0.00 36.62 3.33
334 385 7.759433 CAGAAATTGAACTGTTTTAGGTGTTGT 59.241 33.333 0.00 0.00 0.00 3.32
335 386 7.973944 AGAAATTGAACTGTTTTAGGTGTTGTC 59.026 33.333 0.00 0.00 0.00 3.18
336 387 7.404671 AATTGAACTGTTTTAGGTGTTGTCT 57.595 32.000 0.00 0.00 0.00 3.41
337 388 6.827586 TTGAACTGTTTTAGGTGTTGTCTT 57.172 33.333 0.00 0.00 0.00 3.01
338 389 7.925043 TTGAACTGTTTTAGGTGTTGTCTTA 57.075 32.000 0.00 0.00 0.00 2.10
339 390 7.925043 TGAACTGTTTTAGGTGTTGTCTTAA 57.075 32.000 0.00 0.00 0.00 1.85
340 391 8.338072 TGAACTGTTTTAGGTGTTGTCTTAAA 57.662 30.769 0.00 0.00 0.00 1.52
341 392 8.962679 TGAACTGTTTTAGGTGTTGTCTTAAAT 58.037 29.630 0.00 0.00 0.00 1.40
342 393 9.233232 GAACTGTTTTAGGTGTTGTCTTAAATG 57.767 33.333 0.00 0.00 0.00 2.32
343 394 8.288689 ACTGTTTTAGGTGTTGTCTTAAATGT 57.711 30.769 0.00 0.00 0.00 2.71
344 395 8.403236 ACTGTTTTAGGTGTTGTCTTAAATGTC 58.597 33.333 0.00 0.00 0.00 3.06
345 396 8.514330 TGTTTTAGGTGTTGTCTTAAATGTCT 57.486 30.769 0.00 0.00 0.00 3.41
346 397 9.616156 TGTTTTAGGTGTTGTCTTAAATGTCTA 57.384 29.630 0.00 0.00 0.00 2.59
350 401 7.186021 AGGTGTTGTCTTAAATGTCTAAACG 57.814 36.000 0.00 0.00 0.00 3.60
351 402 6.987992 AGGTGTTGTCTTAAATGTCTAAACGA 59.012 34.615 0.00 0.00 0.00 3.85
352 403 7.660208 AGGTGTTGTCTTAAATGTCTAAACGAT 59.340 33.333 0.00 0.00 0.00 3.73
353 404 7.955864 GGTGTTGTCTTAAATGTCTAAACGATC 59.044 37.037 0.00 0.00 0.00 3.69
354 405 8.709646 GTGTTGTCTTAAATGTCTAAACGATCT 58.290 33.333 0.00 0.00 0.00 2.75
355 406 9.268268 TGTTGTCTTAAATGTCTAAACGATCTT 57.732 29.630 0.00 0.00 0.00 2.40
358 409 9.917129 TGTCTTAAATGTCTAAACGATCTTACA 57.083 29.630 0.00 0.00 0.00 2.41
367 418 9.872757 TGTCTAAACGATCTTACAAAAATGAAC 57.127 29.630 0.00 0.00 0.00 3.18
368 419 9.037417 GTCTAAACGATCTTACAAAAATGAACG 57.963 33.333 0.00 0.00 0.00 3.95
369 420 8.767085 TCTAAACGATCTTACAAAAATGAACGT 58.233 29.630 0.00 0.00 39.03 3.99
371 422 8.928844 AAACGATCTTACAAAAATGAACGTAG 57.071 30.769 0.00 0.00 37.05 3.51
372 423 7.057149 ACGATCTTACAAAAATGAACGTAGG 57.943 36.000 0.00 0.00 36.48 3.18
373 424 6.091713 ACGATCTTACAAAAATGAACGTAGGG 59.908 38.462 0.00 0.00 36.48 3.53
374 425 6.311935 CGATCTTACAAAAATGAACGTAGGGA 59.688 38.462 0.00 0.00 0.00 4.20
375 426 7.464178 CGATCTTACAAAAATGAACGTAGGGAG 60.464 40.741 0.00 0.00 0.00 4.30
376 427 6.527423 TCTTACAAAAATGAACGTAGGGAGT 58.473 36.000 0.00 0.00 0.00 3.85
377 428 7.669427 TCTTACAAAAATGAACGTAGGGAGTA 58.331 34.615 0.00 0.00 0.00 2.59
378 429 8.316214 TCTTACAAAAATGAACGTAGGGAGTAT 58.684 33.333 0.00 0.00 0.00 2.12
379 430 8.851541 TTACAAAAATGAACGTAGGGAGTATT 57.148 30.769 0.00 0.00 0.00 1.89
380 431 7.141100 ACAAAAATGAACGTAGGGAGTATTG 57.859 36.000 0.00 0.00 0.00 1.90
381 432 6.713450 ACAAAAATGAACGTAGGGAGTATTGT 59.287 34.615 0.00 0.00 0.00 2.71
402 453 7.996465 TTGTAATTAATAGTGTCAAAACGCG 57.004 32.000 3.53 3.53 40.92 6.01
425 476 2.887568 CGGATGCAGGTCGCTCAC 60.888 66.667 0.00 0.00 43.06 3.51
450 501 4.980805 GGCCGCTCGTCCAACACA 62.981 66.667 0.00 0.00 0.00 3.72
468 519 1.980232 ATGGTACGCCGTGTCCAGA 60.980 57.895 17.74 0.51 37.67 3.86
530 644 1.070786 GGCTGAACCACTTGGACGA 59.929 57.895 1.14 0.00 38.86 4.20
554 668 2.833533 GCACAAGCAGGTCGTTGCA 61.834 57.895 10.81 0.00 46.47 4.08
563 677 2.594962 GGTCGTTGCACTCCACGTG 61.595 63.158 9.08 9.08 46.58 4.49
613 727 3.674050 ATGGGCTCGTACCTCCCGT 62.674 63.158 7.10 4.48 42.98 5.28
614 728 3.834799 GGGCTCGTACCTCCCGTG 61.835 72.222 0.00 0.00 0.00 4.94
672 786 1.005037 AAATGGCTCGCTGACGACA 60.005 52.632 0.00 0.00 45.12 4.35
772 886 2.202892 GGATCTTGGCGACGGTCC 60.203 66.667 1.91 0.00 0.00 4.46
773 887 2.577059 GATCTTGGCGACGGTCCA 59.423 61.111 1.91 0.00 0.00 4.02
792 912 0.763035 ACGCTAGTGGTTGGTCCTTT 59.237 50.000 8.42 0.00 37.07 3.11
817 937 2.605607 CCCATGAGGTCCTGTGCCA 61.606 63.158 0.00 0.00 0.00 4.92
865 985 1.201424 CTTGGGGGAGTAGTACACCC 58.799 60.000 23.71 23.71 46.71 4.61
884 1004 2.742372 GGAGCGCGTGTTGGTGAT 60.742 61.111 8.43 0.00 0.00 3.06
3170 4563 0.521735 AAAAAGAATGCCGCGTCTCC 59.478 50.000 4.92 0.00 0.00 3.71
3171 4564 0.605319 AAAAGAATGCCGCGTCTCCA 60.605 50.000 4.92 0.00 0.00 3.86
3172 4565 1.021390 AAAGAATGCCGCGTCTCCAG 61.021 55.000 4.92 0.00 0.00 3.86
3173 4566 2.125512 GAATGCCGCGTCTCCAGT 60.126 61.111 4.92 0.00 0.00 4.00
3174 4567 1.141019 GAATGCCGCGTCTCCAGTA 59.859 57.895 4.92 0.00 0.00 2.74
3175 4568 0.459585 GAATGCCGCGTCTCCAGTAA 60.460 55.000 4.92 0.00 0.00 2.24
3176 4569 0.460284 AATGCCGCGTCTCCAGTAAG 60.460 55.000 4.92 0.00 0.00 2.34
3177 4570 2.202756 GCCGCGTCTCCAGTAAGG 60.203 66.667 4.92 0.00 39.47 2.69
3178 4571 2.202756 CCGCGTCTCCAGTAAGGC 60.203 66.667 4.92 0.00 37.29 4.35
3179 4572 2.202756 CGCGTCTCCAGTAAGGCC 60.203 66.667 0.00 0.00 37.29 5.19
3180 4573 2.711922 CGCGTCTCCAGTAAGGCCT 61.712 63.158 0.00 0.00 37.29 5.19
3181 4574 1.142097 GCGTCTCCAGTAAGGCCTC 59.858 63.158 5.23 0.00 37.29 4.70
3182 4575 1.433879 CGTCTCCAGTAAGGCCTCG 59.566 63.158 5.23 0.00 37.29 4.63
3183 4576 1.313812 CGTCTCCAGTAAGGCCTCGT 61.314 60.000 5.23 0.00 37.29 4.18
3184 4577 0.456628 GTCTCCAGTAAGGCCTCGTC 59.543 60.000 5.23 0.00 37.29 4.20
3185 4578 1.030488 TCTCCAGTAAGGCCTCGTCG 61.030 60.000 5.23 0.00 37.29 5.12
3186 4579 2.005960 CTCCAGTAAGGCCTCGTCGG 62.006 65.000 5.23 5.16 37.29 4.79
3205 4598 4.389576 CTGCGTGCCGAGCCAAAC 62.390 66.667 0.00 0.00 0.00 2.93
3216 4609 3.353836 GCCAAACGGCGAGCAAGA 61.354 61.111 16.62 0.00 40.49 3.02
3217 4610 2.690778 GCCAAACGGCGAGCAAGAT 61.691 57.895 16.62 0.00 40.49 2.40
3218 4611 1.425428 CCAAACGGCGAGCAAGATC 59.575 57.895 16.62 0.00 0.00 2.75
3219 4612 1.021390 CCAAACGGCGAGCAAGATCT 61.021 55.000 16.62 0.00 0.00 2.75
3220 4613 0.371645 CAAACGGCGAGCAAGATCTC 59.628 55.000 16.62 0.00 0.00 2.75
3226 4619 4.317529 GAGCAAGATCTCGCCGAG 57.682 61.111 8.05 8.05 0.00 4.63
3227 4620 1.299773 GAGCAAGATCTCGCCGAGG 60.300 63.158 15.08 0.00 0.00 4.63
3228 4621 2.964389 GCAAGATCTCGCCGAGGC 60.964 66.667 15.08 5.37 37.85 4.70
3229 4622 2.811101 CAAGATCTCGCCGAGGCT 59.189 61.111 15.08 9.33 39.32 4.58
3230 4623 2.033793 CAAGATCTCGCCGAGGCTA 58.966 57.895 15.08 0.00 39.32 3.93
3231 4624 0.600557 CAAGATCTCGCCGAGGCTAT 59.399 55.000 15.08 0.00 39.32 2.97
3232 4625 0.600557 AAGATCTCGCCGAGGCTATG 59.399 55.000 15.08 2.40 39.32 2.23
3233 4626 1.214062 GATCTCGCCGAGGCTATGG 59.786 63.158 15.08 0.94 39.32 2.74
3239 4632 4.445699 CCGAGGCTATGGCTGTTC 57.554 61.111 0.00 0.00 38.98 3.18
3240 4633 1.826024 CCGAGGCTATGGCTGTTCT 59.174 57.895 0.00 0.00 38.98 3.01
3241 4634 0.249657 CCGAGGCTATGGCTGTTCTC 60.250 60.000 0.00 0.00 38.98 2.87
3242 4635 0.596083 CGAGGCTATGGCTGTTCTCG 60.596 60.000 11.67 11.67 38.98 4.04
3243 4636 0.878086 GAGGCTATGGCTGTTCTCGC 60.878 60.000 0.00 0.00 38.98 5.03
3250 4643 4.719369 GCTGTTCTCGCCGTCGGT 62.719 66.667 13.94 0.00 36.13 4.69
3251 4644 2.872557 CTGTTCTCGCCGTCGGTA 59.127 61.111 13.94 0.39 36.13 4.02
3252 4645 1.432251 CTGTTCTCGCCGTCGGTAT 59.568 57.895 13.94 0.00 36.13 2.73
3253 4646 0.591741 CTGTTCTCGCCGTCGGTATC 60.592 60.000 13.94 0.00 36.13 2.24
3254 4647 1.653533 GTTCTCGCCGTCGGTATCG 60.654 63.158 13.94 8.31 36.13 2.92
3262 4655 2.953669 CGTCGGTATCGGAAAGGTG 58.046 57.895 0.00 0.00 36.95 4.00
3263 4656 0.526954 CGTCGGTATCGGAAAGGTGG 60.527 60.000 0.00 0.00 36.95 4.61
3264 4657 0.533951 GTCGGTATCGGAAAGGTGGT 59.466 55.000 0.00 0.00 36.95 4.16
3265 4658 1.750778 GTCGGTATCGGAAAGGTGGTA 59.249 52.381 0.00 0.00 36.95 3.25
3266 4659 1.750778 TCGGTATCGGAAAGGTGGTAC 59.249 52.381 0.00 0.00 36.95 3.34
3267 4660 1.202452 CGGTATCGGAAAGGTGGTACC 60.202 57.143 4.43 4.43 38.99 3.34
3268 4661 1.832998 GGTATCGGAAAGGTGGTACCA 59.167 52.381 11.60 11.60 41.95 3.25
3269 4662 2.419159 GGTATCGGAAAGGTGGTACCAC 60.419 54.545 33.15 33.15 41.95 4.16
3270 4663 1.652947 ATCGGAAAGGTGGTACCACT 58.347 50.000 37.24 22.78 45.52 4.00
3271 4664 0.682852 TCGGAAAGGTGGTACCACTG 59.317 55.000 37.24 20.70 45.52 3.66
3272 4665 0.953960 CGGAAAGGTGGTACCACTGC 60.954 60.000 37.24 24.80 45.52 4.40
3273 4666 0.953960 GGAAAGGTGGTACCACTGCG 60.954 60.000 37.24 0.00 45.52 5.18
3274 4667 0.953960 GAAAGGTGGTACCACTGCGG 60.954 60.000 37.24 0.00 45.52 5.69
3289 4682 4.393155 CGGTGCCAGCCAGCTGTA 62.393 66.667 17.86 4.49 42.15 2.74
3290 4683 2.034066 GGTGCCAGCCAGCTGTAA 59.966 61.111 17.86 3.36 42.15 2.41
3291 4684 2.042831 GGTGCCAGCCAGCTGTAAG 61.043 63.158 17.86 4.63 42.15 2.34
3292 4685 2.042831 GTGCCAGCCAGCTGTAAGG 61.043 63.158 17.86 11.76 42.15 2.69
3297 4690 2.579201 GCCAGCTGTAAGGCGAGA 59.421 61.111 13.81 0.00 41.70 4.04
3298 4691 1.520342 GCCAGCTGTAAGGCGAGAG 60.520 63.158 13.81 0.00 41.70 3.20
3299 4692 1.142748 CCAGCTGTAAGGCGAGAGG 59.857 63.158 13.81 0.00 37.29 3.69
3310 4703 2.835431 CGAGAGGCGTCTGGGGAT 60.835 66.667 14.78 0.00 30.97 3.85
3311 4704 2.818132 GAGAGGCGTCTGGGGATG 59.182 66.667 14.78 0.00 30.97 3.51
3312 4705 2.039624 AGAGGCGTCTGGGGATGT 59.960 61.111 8.40 0.00 0.00 3.06
3313 4706 2.022240 GAGAGGCGTCTGGGGATGTC 62.022 65.000 14.78 0.00 30.97 3.06
3314 4707 3.432051 GAGGCGTCTGGGGATGTCG 62.432 68.421 0.00 0.00 38.06 4.35
3315 4708 4.530857 GGCGTCTGGGGATGTCGG 62.531 72.222 0.00 0.00 0.00 4.79
3316 4709 3.458163 GCGTCTGGGGATGTCGGA 61.458 66.667 0.00 0.00 0.00 4.55
3317 4710 2.494918 CGTCTGGGGATGTCGGAC 59.505 66.667 0.00 0.00 37.21 4.79
3318 4711 2.348104 CGTCTGGGGATGTCGGACA 61.348 63.158 14.01 14.01 39.73 4.02
3319 4712 1.218316 GTCTGGGGATGTCGGACAC 59.782 63.158 13.92 7.50 39.58 3.67
3320 4713 2.184322 CTGGGGATGTCGGACACG 59.816 66.667 13.92 0.00 42.74 4.49
3321 4714 2.602267 TGGGGATGTCGGACACGT 60.602 61.111 13.92 0.00 41.85 4.49
3322 4715 2.183555 GGGGATGTCGGACACGTC 59.816 66.667 13.92 8.07 41.85 4.34
3323 4716 2.642254 GGGGATGTCGGACACGTCA 61.642 63.158 13.92 0.00 42.27 4.35
3324 4717 1.290955 GGGATGTCGGACACGTCAA 59.709 57.895 13.92 0.00 42.27 3.18
3325 4718 0.320073 GGGATGTCGGACACGTCAAA 60.320 55.000 13.92 0.00 42.27 2.69
3326 4719 1.068474 GGATGTCGGACACGTCAAAG 58.932 55.000 13.92 0.00 42.27 2.77
3327 4720 1.604693 GGATGTCGGACACGTCAAAGT 60.605 52.381 13.92 0.00 42.27 2.66
3328 4721 1.719780 GATGTCGGACACGTCAAAGTC 59.280 52.381 13.92 0.53 41.12 3.01
3329 4722 0.593008 TGTCGGACACGTCAAAGTCG 60.593 55.000 6.76 0.00 41.85 4.18
3330 4723 0.317269 GTCGGACACGTCAAAGTCGA 60.317 55.000 2.62 0.00 41.85 4.20
3331 4724 0.317269 TCGGACACGTCAAAGTCGAC 60.317 55.000 7.70 7.70 41.85 4.20
3337 4730 3.774702 GTCAAAGTCGACGCGGCC 61.775 66.667 12.47 0.00 28.67 6.13
3389 4782 2.282040 AGCTGGTTGGACTGCAGC 60.282 61.111 15.27 6.61 37.72 5.25
3395 4788 3.573229 TTGGACTGCAGCTGGGCT 61.573 61.111 17.12 0.00 40.77 5.19
3396 4789 3.137385 TTGGACTGCAGCTGGGCTT 62.137 57.895 17.12 0.00 36.40 4.35
3397 4790 3.060615 GGACTGCAGCTGGGCTTG 61.061 66.667 17.12 2.22 36.40 4.01
3398 4791 3.060615 GACTGCAGCTGGGCTTGG 61.061 66.667 17.12 0.00 36.40 3.61
3445 4838 1.235281 GGGTTGGCGTTCTTCTCCAC 61.235 60.000 0.00 0.00 29.89 4.02
3452 4845 1.006571 GTTCTTCTCCACGTGCCGA 60.007 57.895 10.91 5.42 0.00 5.54
3560 4953 0.528466 CCACGCTCACGCACAGATAT 60.528 55.000 0.00 0.00 45.53 1.63
3576 4969 3.739810 CAGATATGACATCTGCTCCAACG 59.260 47.826 1.58 0.00 39.03 4.10
3630 5098 3.003027 TGAGCCAGCTCAGGAGAAT 57.997 52.632 18.14 0.00 46.80 2.40
3645 5113 9.004717 GCTCAGGAGAATAGTAAAATATTTCCC 57.995 37.037 0.10 0.00 30.60 3.97
3689 5157 5.273170 TCACTTTTGCTATTATTCATGCGC 58.727 37.500 0.00 0.00 0.00 6.09
3737 5205 3.473367 CTCGAGCACAAAAGTGAATTCG 58.527 45.455 0.00 5.72 0.00 3.34
3745 5214 7.973601 AGCACAAAAGTGAATTCGAAAAATTT 58.026 26.923 0.00 0.17 0.00 1.82
3814 5290 5.428184 TTTTTCCCAAACCTTCACACATT 57.572 34.783 0.00 0.00 0.00 2.71
3815 5291 5.428184 TTTTCCCAAACCTTCACACATTT 57.572 34.783 0.00 0.00 0.00 2.32
3816 5292 5.428184 TTTCCCAAACCTTCACACATTTT 57.572 34.783 0.00 0.00 0.00 1.82
3817 5293 4.664150 TCCCAAACCTTCACACATTTTC 57.336 40.909 0.00 0.00 0.00 2.29
3818 5294 3.067461 TCCCAAACCTTCACACATTTTCG 59.933 43.478 0.00 0.00 0.00 3.46
3819 5295 3.181480 CCCAAACCTTCACACATTTTCGT 60.181 43.478 0.00 0.00 0.00 3.85
3820 5296 4.429108 CCAAACCTTCACACATTTTCGTT 58.571 39.130 0.00 0.00 0.00 3.85
3821 5297 5.450688 CCCAAACCTTCACACATTTTCGTTA 60.451 40.000 0.00 0.00 0.00 3.18
3822 5298 6.037098 CCAAACCTTCACACATTTTCGTTAA 58.963 36.000 0.00 0.00 0.00 2.01
3823 5299 6.531948 CCAAACCTTCACACATTTTCGTTAAA 59.468 34.615 0.00 0.00 0.00 1.52
3824 5300 7.253950 CCAAACCTTCACACATTTTCGTTAAAG 60.254 37.037 0.00 0.00 0.00 1.85
3825 5301 6.687081 ACCTTCACACATTTTCGTTAAAGA 57.313 33.333 0.00 0.00 0.00 2.52
3826 5302 6.725246 ACCTTCACACATTTTCGTTAAAGAG 58.275 36.000 0.00 0.00 0.00 2.85
3827 5303 5.625311 CCTTCACACATTTTCGTTAAAGAGC 59.375 40.000 0.00 0.00 0.00 4.09
3828 5304 4.768145 TCACACATTTTCGTTAAAGAGCG 58.232 39.130 0.00 0.00 0.00 5.03
3829 5305 4.271533 TCACACATTTTCGTTAAAGAGCGT 59.728 37.500 0.00 0.00 0.00 5.07
3830 5306 4.607235 CACACATTTTCGTTAAAGAGCGTC 59.393 41.667 0.00 0.00 0.00 5.19
3831 5307 4.510340 ACACATTTTCGTTAAAGAGCGTCT 59.490 37.500 0.00 0.00 0.00 4.18
3832 5308 5.007332 ACACATTTTCGTTAAAGAGCGTCTT 59.993 36.000 0.00 0.00 38.59 3.01
3834 5310 6.413818 CACATTTTCGTTAAAGAGCGTCTTTT 59.586 34.615 15.04 2.83 43.62 2.27
3835 5311 7.584847 CACATTTTCGTTAAAGAGCGTCTTTTA 59.415 33.333 15.04 6.67 43.62 1.52
3836 5312 8.287503 ACATTTTCGTTAAAGAGCGTCTTTTAT 58.712 29.630 15.04 0.00 43.62 1.40
3837 5313 9.113876 CATTTTCGTTAAAGAGCGTCTTTTATT 57.886 29.630 15.04 0.00 43.62 1.40
3840 5316 9.962759 TTTCGTTAAAGAGCGTCTTTTATTATC 57.037 29.630 15.04 1.29 43.62 1.75
3841 5317 8.922058 TCGTTAAAGAGCGTCTTTTATTATCT 57.078 30.769 15.04 0.00 43.62 1.98
3842 5318 9.017669 TCGTTAAAGAGCGTCTTTTATTATCTC 57.982 33.333 15.04 0.00 43.62 2.75
3843 5319 8.804743 CGTTAAAGAGCGTCTTTTATTATCTCA 58.195 33.333 15.04 0.00 43.62 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
135 136 1.649271 GCATCCTGGAGGTGGGGATT 61.649 60.000 10.38 0.00 37.72 3.01
139 140 1.941403 ATTGGCATCCTGGAGGTGGG 61.941 60.000 10.38 0.00 36.34 4.61
215 229 6.668283 AGTACGATTACCATATATTCCTGCCT 59.332 38.462 0.00 0.00 0.00 4.75
256 307 4.068599 GAGGGAGTAGCATATTTGAAGCC 58.931 47.826 0.00 0.00 0.00 4.35
257 308 4.967036 AGAGGGAGTAGCATATTTGAAGC 58.033 43.478 0.00 0.00 0.00 3.86
272 323 8.929487 AGGTCTTATAAAAGTGAATAGAGGGAG 58.071 37.037 0.00 0.00 34.13 4.30
273 324 8.855804 AGGTCTTATAAAAGTGAATAGAGGGA 57.144 34.615 0.00 0.00 34.13 4.20
274 325 9.907229 AAAGGTCTTATAAAAGTGAATAGAGGG 57.093 33.333 0.00 0.00 34.13 4.30
284 335 9.220767 CTGCTGTCTAAAAGGTCTTATAAAAGT 57.779 33.333 0.00 0.00 34.13 2.66
286 337 9.787435 TTCTGCTGTCTAAAAGGTCTTATAAAA 57.213 29.630 0.00 0.00 0.00 1.52
287 338 9.787435 TTTCTGCTGTCTAAAAGGTCTTATAAA 57.213 29.630 0.00 0.00 0.00 1.40
288 339 9.959721 ATTTCTGCTGTCTAAAAGGTCTTATAA 57.040 29.630 0.00 0.00 0.00 0.98
289 340 9.959721 AATTTCTGCTGTCTAAAAGGTCTTATA 57.040 29.630 0.00 0.00 0.00 0.98
291 342 7.936847 TCAATTTCTGCTGTCTAAAAGGTCTTA 59.063 33.333 0.00 0.00 0.00 2.10
294 345 6.560253 TCAATTTCTGCTGTCTAAAAGGTC 57.440 37.500 0.00 0.00 0.00 3.85
295 346 6.547510 AGTTCAATTTCTGCTGTCTAAAAGGT 59.452 34.615 0.00 0.00 0.00 3.50
296 347 6.860023 CAGTTCAATTTCTGCTGTCTAAAAGG 59.140 38.462 0.00 0.00 0.00 3.11
297 348 7.420800 ACAGTTCAATTTCTGCTGTCTAAAAG 58.579 34.615 0.00 0.00 35.78 2.27
300 351 6.942532 AACAGTTCAATTTCTGCTGTCTAA 57.057 33.333 0.00 0.00 39.19 2.10
302 353 5.841957 AAACAGTTCAATTTCTGCTGTCT 57.158 34.783 0.00 0.00 39.19 3.41
303 354 6.638468 CCTAAAACAGTTCAATTTCTGCTGTC 59.362 38.462 0.00 0.00 39.19 3.51
304 355 6.096846 ACCTAAAACAGTTCAATTTCTGCTGT 59.903 34.615 0.00 0.00 41.51 4.40
305 356 6.418819 CACCTAAAACAGTTCAATTTCTGCTG 59.581 38.462 0.00 0.00 35.37 4.41
306 357 6.096846 ACACCTAAAACAGTTCAATTTCTGCT 59.903 34.615 0.00 0.00 35.37 4.24
307 358 6.273071 ACACCTAAAACAGTTCAATTTCTGC 58.727 36.000 0.00 0.00 35.37 4.26
310 361 7.973944 AGACAACACCTAAAACAGTTCAATTTC 59.026 33.333 0.00 0.00 0.00 2.17
312 363 7.404671 AGACAACACCTAAAACAGTTCAATT 57.595 32.000 0.00 0.00 0.00 2.32
315 366 7.925043 TTAAGACAACACCTAAAACAGTTCA 57.075 32.000 0.00 0.00 0.00 3.18
316 367 9.233232 CATTTAAGACAACACCTAAAACAGTTC 57.767 33.333 0.00 0.00 0.00 3.01
318 369 8.288689 ACATTTAAGACAACACCTAAAACAGT 57.711 30.769 0.00 0.00 0.00 3.55
319 370 8.621286 AGACATTTAAGACAACACCTAAAACAG 58.379 33.333 0.00 0.00 0.00 3.16
320 371 8.514330 AGACATTTAAGACAACACCTAAAACA 57.486 30.769 0.00 0.00 0.00 2.83
324 375 8.767085 CGTTTAGACATTTAAGACAACACCTAA 58.233 33.333 0.00 0.00 0.00 2.69
325 376 8.143193 TCGTTTAGACATTTAAGACAACACCTA 58.857 33.333 0.00 0.00 0.00 3.08
327 378 7.181143 TCGTTTAGACATTTAAGACAACACC 57.819 36.000 0.00 0.00 0.00 4.16
329 380 8.827177 AGATCGTTTAGACATTTAAGACAACA 57.173 30.769 0.00 0.00 0.00 3.33
332 383 9.917129 TGTAAGATCGTTTAGACATTTAAGACA 57.083 29.630 0.00 0.00 0.00 3.41
341 392 9.872757 GTTCATTTTTGTAAGATCGTTTAGACA 57.127 29.630 0.00 0.00 0.00 3.41
342 393 9.037417 CGTTCATTTTTGTAAGATCGTTTAGAC 57.963 33.333 0.00 0.00 0.00 2.59
343 394 8.767085 ACGTTCATTTTTGTAAGATCGTTTAGA 58.233 29.630 0.00 0.00 34.04 2.10
344 395 8.928844 ACGTTCATTTTTGTAAGATCGTTTAG 57.071 30.769 0.00 0.00 34.04 1.85
346 397 8.013378 CCTACGTTCATTTTTGTAAGATCGTTT 58.987 33.333 0.00 0.00 37.52 3.60
347 398 7.360607 CCCTACGTTCATTTTTGTAAGATCGTT 60.361 37.037 0.00 0.00 37.52 3.85
348 399 6.091713 CCCTACGTTCATTTTTGTAAGATCGT 59.908 38.462 0.00 0.00 39.10 3.73
349 400 6.311935 TCCCTACGTTCATTTTTGTAAGATCG 59.688 38.462 0.00 0.00 0.00 3.69
350 401 7.333672 ACTCCCTACGTTCATTTTTGTAAGATC 59.666 37.037 0.00 0.00 0.00 2.75
351 402 7.166167 ACTCCCTACGTTCATTTTTGTAAGAT 58.834 34.615 0.00 0.00 0.00 2.40
352 403 6.527423 ACTCCCTACGTTCATTTTTGTAAGA 58.473 36.000 0.00 0.00 0.00 2.10
353 404 6.796705 ACTCCCTACGTTCATTTTTGTAAG 57.203 37.500 0.00 0.00 0.00 2.34
354 405 8.723311 CAATACTCCCTACGTTCATTTTTGTAA 58.277 33.333 0.00 0.00 0.00 2.41
355 406 7.879160 ACAATACTCCCTACGTTCATTTTTGTA 59.121 33.333 0.00 0.00 0.00 2.41
356 407 6.713450 ACAATACTCCCTACGTTCATTTTTGT 59.287 34.615 0.00 0.00 0.00 2.83
357 408 7.141100 ACAATACTCCCTACGTTCATTTTTG 57.859 36.000 0.00 0.00 0.00 2.44
358 409 8.851541 TTACAATACTCCCTACGTTCATTTTT 57.148 30.769 0.00 0.00 0.00 1.94
359 410 9.457436 AATTACAATACTCCCTACGTTCATTTT 57.543 29.630 0.00 0.00 0.00 1.82
376 427 9.691795 CGCGTTTTGACACTATTAATTACAATA 57.308 29.630 0.00 0.00 0.00 1.90
377 428 7.694784 CCGCGTTTTGACACTATTAATTACAAT 59.305 33.333 4.92 0.00 0.00 2.71
378 429 7.016466 CCGCGTTTTGACACTATTAATTACAA 58.984 34.615 4.92 0.00 0.00 2.41
379 430 6.535811 CCGCGTTTTGACACTATTAATTACA 58.464 36.000 4.92 0.00 0.00 2.41
380 431 5.450066 GCCGCGTTTTGACACTATTAATTAC 59.550 40.000 4.92 0.00 0.00 1.89
381 432 5.447548 GGCCGCGTTTTGACACTATTAATTA 60.448 40.000 4.92 0.00 0.00 1.40
446 497 1.373748 GACACGGCGTACCATGTGT 60.374 57.895 14.22 4.09 41.54 3.72
450 501 1.980232 TCTGGACACGGCGTACCAT 60.980 57.895 28.59 10.96 34.57 3.55
539 653 1.571460 GAGTGCAACGACCTGCTTG 59.429 57.895 9.58 0.00 45.86 4.01
542 656 2.280797 TGGAGTGCAACGACCTGC 60.281 61.111 0.00 0.00 45.86 4.85
570 684 2.589540 GTCATCATCCCCGTGGCA 59.410 61.111 0.00 0.00 0.00 4.92
614 728 2.764128 TGGAGGAGATGGTCGGCC 60.764 66.667 0.00 0.00 0.00 6.13
622 736 2.052690 CGGTGACCGTGGAGGAGAT 61.053 63.158 17.28 0.00 45.00 2.75
640 754 0.529378 CCATTTGAGGACCAGCTTGC 59.471 55.000 0.00 0.00 0.00 4.01
672 786 3.403038 CTGGAACGAGGACTTCATGTTT 58.597 45.455 0.00 0.00 0.00 2.83
772 886 0.034896 AAGGACCAACCACTAGCGTG 59.965 55.000 0.00 0.00 42.04 5.34
773 887 0.763035 AAAGGACCAACCACTAGCGT 59.237 50.000 0.00 0.00 42.04 5.07
817 937 4.129737 CAGGGTCGCCGTCATCGT 62.130 66.667 0.00 0.00 35.01 3.73
865 985 3.716006 CACCAACACGCGCTCCAG 61.716 66.667 5.73 0.00 0.00 3.86
3161 4554 2.202756 GCCTTACTGGAGACGCGG 60.203 66.667 12.47 0.00 38.35 6.46
3162 4555 2.202756 GGCCTTACTGGAGACGCG 60.203 66.667 3.53 3.53 38.35 6.01
3163 4556 1.142097 GAGGCCTTACTGGAGACGC 59.858 63.158 6.77 0.00 38.35 5.19
3164 4557 1.313812 ACGAGGCCTTACTGGAGACG 61.314 60.000 6.77 4.69 38.35 4.18
3165 4558 0.456628 GACGAGGCCTTACTGGAGAC 59.543 60.000 6.77 0.00 38.35 3.36
3166 4559 1.030488 CGACGAGGCCTTACTGGAGA 61.030 60.000 6.77 0.00 38.35 3.71
3167 4560 1.433879 CGACGAGGCCTTACTGGAG 59.566 63.158 6.77 0.00 38.35 3.86
3168 4561 2.050350 CCGACGAGGCCTTACTGGA 61.050 63.158 6.77 0.00 38.35 3.86
3169 4562 2.494918 CCGACGAGGCCTTACTGG 59.505 66.667 6.77 3.31 39.35 4.00
3200 4593 1.021390 AGATCTTGCTCGCCGTTTGG 61.021 55.000 0.00 0.00 38.77 3.28
3201 4594 0.371645 GAGATCTTGCTCGCCGTTTG 59.628 55.000 0.00 0.00 0.00 2.93
3202 4595 2.755929 GAGATCTTGCTCGCCGTTT 58.244 52.632 0.00 0.00 0.00 3.60
3203 4596 4.504132 GAGATCTTGCTCGCCGTT 57.496 55.556 0.00 0.00 0.00 4.44
3209 4602 1.299773 CCTCGGCGAGATCTTGCTC 60.300 63.158 36.47 20.01 39.87 4.26
3210 4603 2.811101 CCTCGGCGAGATCTTGCT 59.189 61.111 36.47 0.00 39.87 3.91
3211 4604 2.964389 GCCTCGGCGAGATCTTGC 60.964 66.667 36.47 25.97 39.25 4.01
3222 4615 0.249657 GAGAACAGCCATAGCCTCGG 60.250 60.000 0.00 0.00 41.25 4.63
3223 4616 0.596083 CGAGAACAGCCATAGCCTCG 60.596 60.000 0.00 0.00 39.52 4.63
3224 4617 0.878086 GCGAGAACAGCCATAGCCTC 60.878 60.000 0.00 0.00 41.25 4.70
3225 4618 1.144936 GCGAGAACAGCCATAGCCT 59.855 57.895 0.00 0.00 41.25 4.58
3226 4619 3.724494 GCGAGAACAGCCATAGCC 58.276 61.111 0.00 0.00 41.25 3.93
3233 4626 2.609183 ATACCGACGGCGAGAACAGC 62.609 60.000 15.16 0.00 40.82 4.40
3234 4627 0.591741 GATACCGACGGCGAGAACAG 60.592 60.000 15.16 0.00 40.82 3.16
3235 4628 1.430632 GATACCGACGGCGAGAACA 59.569 57.895 15.16 0.00 40.82 3.18
3236 4629 1.653533 CGATACCGACGGCGAGAAC 60.654 63.158 15.16 0.00 40.82 3.01
3237 4630 2.711311 CGATACCGACGGCGAGAA 59.289 61.111 15.16 0.00 40.82 2.87
3238 4631 3.274586 CCGATACCGACGGCGAGA 61.275 66.667 15.16 0.00 43.74 4.04
3244 4637 0.526954 CCACCTTTCCGATACCGACG 60.527 60.000 0.00 0.00 38.22 5.12
3245 4638 0.533951 ACCACCTTTCCGATACCGAC 59.466 55.000 0.00 0.00 38.22 4.79
3246 4639 1.750778 GTACCACCTTTCCGATACCGA 59.249 52.381 0.00 0.00 38.22 4.69
3247 4640 1.202452 GGTACCACCTTTCCGATACCG 60.202 57.143 7.15 0.00 34.73 4.02
3248 4641 1.832998 TGGTACCACCTTTCCGATACC 59.167 52.381 11.60 0.00 39.58 2.73
3249 4642 2.897436 GTGGTACCACCTTTCCGATAC 58.103 52.381 31.39 4.38 39.58 2.24
3278 4671 1.812922 CTCGCCTTACAGCTGGCTG 60.813 63.158 19.93 19.42 46.42 4.85
3279 4672 1.954362 CTCTCGCCTTACAGCTGGCT 61.954 60.000 19.93 0.00 46.42 4.75
3280 4673 1.520342 CTCTCGCCTTACAGCTGGC 60.520 63.158 19.93 10.93 45.25 4.85
3281 4674 1.142748 CCTCTCGCCTTACAGCTGG 59.857 63.158 19.93 0.08 0.00 4.85
3282 4675 1.520342 GCCTCTCGCCTTACAGCTG 60.520 63.158 13.48 13.48 0.00 4.24
3283 4676 2.896443 GCCTCTCGCCTTACAGCT 59.104 61.111 0.00 0.00 0.00 4.24
3284 4677 2.583593 CGCCTCTCGCCTTACAGC 60.584 66.667 0.00 0.00 0.00 4.40
3285 4678 1.226717 GACGCCTCTCGCCTTACAG 60.227 63.158 0.00 0.00 43.23 2.74
3286 4679 1.677966 AGACGCCTCTCGCCTTACA 60.678 57.895 0.00 0.00 43.23 2.41
3287 4680 1.226717 CAGACGCCTCTCGCCTTAC 60.227 63.158 0.00 0.00 43.23 2.34
3288 4681 2.415608 CCAGACGCCTCTCGCCTTA 61.416 63.158 0.00 0.00 43.23 2.69
3289 4682 3.764466 CCAGACGCCTCTCGCCTT 61.764 66.667 0.00 0.00 43.23 4.35
3293 4686 2.835431 ATCCCCAGACGCCTCTCG 60.835 66.667 0.00 0.00 45.38 4.04
3294 4687 2.022240 GACATCCCCAGACGCCTCTC 62.022 65.000 0.00 0.00 0.00 3.20
3295 4688 2.039624 ACATCCCCAGACGCCTCT 59.960 61.111 0.00 0.00 0.00 3.69
3296 4689 2.501610 GACATCCCCAGACGCCTC 59.498 66.667 0.00 0.00 0.00 4.70
3297 4690 3.461773 CGACATCCCCAGACGCCT 61.462 66.667 0.00 0.00 0.00 5.52
3298 4691 4.530857 CCGACATCCCCAGACGCC 62.531 72.222 0.00 0.00 0.00 5.68
3299 4692 3.458163 TCCGACATCCCCAGACGC 61.458 66.667 0.00 0.00 0.00 5.19
3300 4693 2.348104 TGTCCGACATCCCCAGACG 61.348 63.158 0.00 0.00 0.00 4.18
3301 4694 1.218316 GTGTCCGACATCCCCAGAC 59.782 63.158 4.13 0.00 0.00 3.51
3302 4695 2.348104 CGTGTCCGACATCCCCAGA 61.348 63.158 4.13 0.00 35.63 3.86
3303 4696 2.184322 CGTGTCCGACATCCCCAG 59.816 66.667 4.13 0.00 35.63 4.45
3304 4697 2.602267 ACGTGTCCGACATCCCCA 60.602 61.111 4.13 0.00 37.88 4.96
3305 4698 2.162338 TTGACGTGTCCGACATCCCC 62.162 60.000 4.13 0.00 38.46 4.81
3306 4699 0.320073 TTTGACGTGTCCGACATCCC 60.320 55.000 4.13 0.00 38.46 3.85
3307 4700 1.068474 CTTTGACGTGTCCGACATCC 58.932 55.000 4.13 0.00 38.46 3.51
3308 4701 1.719780 GACTTTGACGTGTCCGACATC 59.280 52.381 4.13 0.00 38.46 3.06
3309 4702 1.779569 GACTTTGACGTGTCCGACAT 58.220 50.000 4.13 0.00 38.46 3.06
3310 4703 0.593008 CGACTTTGACGTGTCCGACA 60.593 55.000 0.00 0.00 36.99 4.35
3311 4704 0.317269 TCGACTTTGACGTGTCCGAC 60.317 55.000 0.00 0.00 37.88 4.79
3312 4705 0.317269 GTCGACTTTGACGTGTCCGA 60.317 55.000 8.70 0.00 37.88 4.55
3313 4706 2.130711 GTCGACTTTGACGTGTCCG 58.869 57.895 8.70 0.00 40.83 4.79
3320 4713 3.774702 GGCCGCGTCGACTTTGAC 61.775 66.667 14.70 0.00 35.49 3.18
3329 4722 3.910104 GATTTCGTCGGCCGCGTC 61.910 66.667 30.84 21.60 36.19 5.19
3338 4731 1.134694 GCACAAGGCCGATTTCGTC 59.865 57.895 0.00 0.00 37.74 4.20
3339 4732 0.889186 AAGCACAAGGCCGATTTCGT 60.889 50.000 0.00 0.00 46.50 3.85
3340 4733 0.454957 CAAGCACAAGGCCGATTTCG 60.455 55.000 0.00 0.00 46.50 3.46
3341 4734 0.881118 TCAAGCACAAGGCCGATTTC 59.119 50.000 0.00 0.00 46.50 2.17
3342 4735 0.598065 GTCAAGCACAAGGCCGATTT 59.402 50.000 0.00 0.00 46.50 2.17
3343 4736 1.577328 CGTCAAGCACAAGGCCGATT 61.577 55.000 0.00 0.00 46.50 3.34
3344 4737 2.034879 CGTCAAGCACAAGGCCGAT 61.035 57.895 0.00 0.00 46.50 4.18
3345 4738 2.449031 ATCGTCAAGCACAAGGCCGA 62.449 55.000 0.00 0.00 46.50 5.54
3346 4739 0.739462 TATCGTCAAGCACAAGGCCG 60.739 55.000 0.00 0.00 46.50 6.13
3347 4740 1.448985 TTATCGTCAAGCACAAGGCC 58.551 50.000 0.00 0.00 46.50 5.19
3348 4741 2.939103 AGATTATCGTCAAGCACAAGGC 59.061 45.455 0.00 0.00 45.30 4.35
3389 4782 1.001641 CACCTTCTCCCAAGCCCAG 60.002 63.158 0.00 0.00 0.00 4.45
3395 4788 2.553028 GCAGATGTTCACCTTCTCCCAA 60.553 50.000 0.00 0.00 0.00 4.12
3396 4789 1.003580 GCAGATGTTCACCTTCTCCCA 59.996 52.381 0.00 0.00 0.00 4.37
3397 4790 1.680249 GGCAGATGTTCACCTTCTCCC 60.680 57.143 0.00 0.00 0.00 4.30
3398 4791 1.743996 GGCAGATGTTCACCTTCTCC 58.256 55.000 0.00 0.00 0.00 3.71
3452 4845 0.674534 GTGACCTCAAGGACGTGACT 59.325 55.000 2.30 0.00 38.94 3.41
3459 4852 2.180276 GAAGCTAGGTGACCTCAAGGA 58.820 52.381 7.77 0.00 38.94 3.36
3513 4906 2.757124 GGGACCTGCCTACCATGGG 61.757 68.421 18.09 0.00 36.66 4.00
3560 4953 2.479560 CGATACGTTGGAGCAGATGTCA 60.480 50.000 0.00 0.00 0.00 3.58
3576 4969 1.252015 GATGACGTCAACGCACGATAC 59.748 52.381 24.13 0.86 42.69 2.24
3587 4980 2.483745 GCGACCGAGATGACGTCA 59.516 61.111 22.48 22.48 0.00 4.35
3618 5086 9.785982 GGAAATATTTTACTATTCTCCTGAGCT 57.214 33.333 1.43 0.00 0.00 4.09
3630 5098 6.381707 GGCTGGTTTGGGGAAATATTTTACTA 59.618 38.462 1.43 0.00 0.00 1.82
3645 5113 4.202305 TGAATTTTTGTAGGGCTGGTTTGG 60.202 41.667 0.00 0.00 0.00 3.28
3689 5157 6.446318 TCGAATTGAATTTTCTGTTTCCAGG 58.554 36.000 0.00 0.00 39.31 4.45
3797 5273 3.181480 ACGAAAATGTGTGAAGGTTTGGG 60.181 43.478 0.00 0.00 0.00 4.12
3806 5282 4.271533 ACGCTCTTTAACGAAAATGTGTGA 59.728 37.500 0.00 0.00 0.00 3.58
3814 5290 9.962759 GATAATAAAAGACGCTCTTTAACGAAA 57.037 29.630 11.62 0.00 45.19 3.46
3815 5291 9.362539 AGATAATAAAAGACGCTCTTTAACGAA 57.637 29.630 11.62 1.63 45.19 3.85
3816 5292 8.922058 AGATAATAAAAGACGCTCTTTAACGA 57.078 30.769 11.62 0.00 45.19 3.85
3817 5293 8.804743 TGAGATAATAAAAGACGCTCTTTAACG 58.195 33.333 11.62 0.00 45.19 3.18


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

AutoCloner maintained by Alex Coulton.