Multiple sequence alignment - TraesCS6D01G217600

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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 TraesCS6D01G217600 chr6D 100.000 5482 0 0 1 5482 307123722 307118241 0.000000e+00 10124.0
1 TraesCS6D01G217600 chr6D 95.146 103 4 1 1707 1808 307121909 307121807 1.580000e-35 161.0
2 TraesCS6D01G217600 chr6D 95.146 103 4 1 1814 1916 307122016 307121915 1.580000e-35 161.0
3 TraesCS6D01G217600 chr6A 89.595 2220 140 39 2663 4847 443425107 443422944 0.000000e+00 2736.0
4 TraesCS6D01G217600 chr6A 93.101 1725 73 17 373 2087 443427871 443426183 0.000000e+00 2484.0
5 TraesCS6D01G217600 chr6A 91.535 508 27 7 4988 5482 443422869 443422365 0.000000e+00 686.0
6 TraesCS6D01G217600 chr6A 97.070 273 8 0 1 273 443428134 443427862 1.390000e-125 460.0
7 TraesCS6D01G217600 chr6A 85.986 421 25 13 2205 2617 443425877 443425483 2.360000e-113 420.0
8 TraesCS6D01G217600 chr6A 95.413 109 4 1 1814 1922 443426532 443426425 7.300000e-39 172.0
9 TraesCS6D01G217600 chr6A 94.318 88 5 0 4904 4991 93285701 93285788 9.580000e-28 135.0
10 TraesCS6D01G217600 chr6A 93.407 91 6 0 1707 1797 443426428 443426338 9.580000e-28 135.0
11 TraesCS6D01G217600 chr6A 100.000 33 0 0 4862 4894 609316392 609316360 1.650000e-05 62.1
12 TraesCS6D01G217600 chr6B 92.792 1540 88 13 3372 4908 474439359 474437840 0.000000e+00 2207.0
13 TraesCS6D01G217600 chr6B 92.918 1285 53 18 647 1918 474442483 474441224 0.000000e+00 1834.0
14 TraesCS6D01G217600 chr6B 90.851 1246 55 24 1712 2909 474441322 474440088 0.000000e+00 1615.0
15 TraesCS6D01G217600 chr6B 89.888 445 39 4 203 646 474442990 474442551 7.970000e-158 568.0
16 TraesCS6D01G217600 chr6B 86.056 502 32 16 4988 5482 474437843 474437373 6.340000e-139 505.0
17 TraesCS6D01G217600 chr6B 92.157 255 20 0 3020 3274 474439944 474439690 1.450000e-95 361.0
18 TraesCS6D01G217600 chr6B 96.000 100 3 1 1819 1918 474441429 474441331 1.580000e-35 161.0
19 TraesCS6D01G217600 chr6B 94.118 102 6 0 1707 1808 474441220 474441119 7.350000e-34 156.0
20 TraesCS6D01G217600 chr6B 93.258 89 6 0 4905 4993 359864721 359864633 1.240000e-26 132.0
21 TraesCS6D01G217600 chr6B 91.398 93 8 0 4899 4991 474189195 474189287 1.600000e-25 128.0
22 TraesCS6D01G217600 chr6B 83.146 89 11 3 793 880 688887642 688887557 1.640000e-10 78.7
23 TraesCS6D01G217600 chr6B 97.436 39 1 0 2977 3015 661856574 661856612 3.540000e-07 67.6
24 TraesCS6D01G217600 chr5A 77.922 385 72 12 183 560 316663924 316663546 1.540000e-55 228.0
25 TraesCS6D01G217600 chr5A 91.071 56 5 0 878 933 646567136 646567191 5.890000e-10 76.8
26 TraesCS6D01G217600 chr5A 95.238 42 1 1 2974 3015 78322019 78321979 1.270000e-06 65.8
27 TraesCS6D01G217600 chr5A 95.238 42 1 1 2974 3015 623553064 623553024 1.270000e-06 65.8
28 TraesCS6D01G217600 chr3D 94.382 89 5 0 4905 4993 436676898 436676986 2.660000e-28 137.0
29 TraesCS6D01G217600 chr3D 94.186 86 5 0 4906 4991 499945189 499945104 1.240000e-26 132.0
30 TraesCS6D01G217600 chr5B 94.186 86 5 0 4906 4991 62940322 62940407 1.240000e-26 132.0
31 TraesCS6D01G217600 chr5B 77.473 182 31 9 382 557 267431453 267431276 3.490000e-17 100.0
32 TraesCS6D01G217600 chr4B 93.182 88 6 0 4904 4991 673204471 673204558 4.460000e-26 130.0
33 TraesCS6D01G217600 chr2B 93.182 88 6 0 4905 4992 34360695 34360608 4.460000e-26 130.0
34 TraesCS6D01G217600 chr2B 93.878 49 2 1 793 840 250254169 250254217 7.620000e-09 73.1
35 TraesCS6D01G217600 chr4D 91.489 94 7 1 4900 4993 493742444 493742352 1.600000e-25 128.0
36 TraesCS6D01G217600 chr2D 90.000 70 5 2 793 862 194442278 194442345 7.560000e-14 89.8
37 TraesCS6D01G217600 chr2D 89.583 48 5 0 4849 4896 190575194 190575241 1.650000e-05 62.1
38 TraesCS6D01G217600 chr1B 81.373 102 15 4 1595 1694 327478915 327479014 4.550000e-11 80.5
39 TraesCS6D01G217600 chr3A 97.500 40 1 0 4850 4889 560107735 560107774 9.850000e-08 69.4
40 TraesCS6D01G217600 chr1A 95.238 42 1 1 2974 3015 97643769 97643729 1.270000e-06 65.8
41 TraesCS6D01G217600 chr1A 95.238 42 1 1 2974 3015 587384831 587384791 1.270000e-06 65.8


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 TraesCS6D01G217600 chr6D 307118241 307123722 5481 True 3482.000000 10124 96.7640 1 5482 3 chr6D.!!$R1 5481
1 TraesCS6D01G217600 chr6A 443422365 443428134 5769 True 1013.285714 2736 92.3010 1 5482 7 chr6A.!!$R2 5481
2 TraesCS6D01G217600 chr6B 474437373 474442990 5617 True 925.875000 2207 91.8475 203 5482 8 chr6B.!!$R3 5279

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
325 433 0.034896 GTGGCCTCGAAAGACTTGGA 59.965 55.0 3.32 0.00 35.39 3.53 F
326 434 0.321671 TGGCCTCGAAAGACTTGGAG 59.678 55.0 3.32 8.78 37.20 3.86 F
327 435 0.321996 GGCCTCGAAAGACTTGGAGT 59.678 55.0 12.86 0.00 36.06 3.85 F
346 454 0.470766 TACAAGACAAGGCAACCGGT 59.529 50.0 0.00 0.00 37.17 5.28 F
2150 2635 0.758685 CCCCAGCTGGAACCAACAAA 60.759 55.0 34.91 0.00 37.39 2.83 F
3412 4595 0.250858 TAACAGGCTGCACTGCACAT 60.251 50.0 15.89 0.00 42.21 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1808 1999 0.607620 GCAAGGGCAGGCAATTGTTA 59.392 50.000 7.40 0.00 40.72 2.41 R
2278 2798 0.912487 AACTCGGGGGCAGGAATGTA 60.912 55.000 0.00 0.00 0.00 2.29 R
2295 2815 2.356069 GGGAGATCAAGAAATGCCGAAC 59.644 50.000 0.00 0.00 0.00 3.95 R
2324 2845 8.400184 TCTTAATGATTGGATTATTCTGCAGG 57.600 34.615 15.13 0.00 0.00 4.85 R
3856 5041 0.694771 TGAGCAGCCTTCAACTGGAT 59.305 50.000 0.00 0.00 35.62 3.41 R
5318 6545 1.134367 TCTGTCATCGTAAGCTTCCCG 59.866 52.381 0.00 7.22 37.18 5.14 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
47 48 6.389091 GGAGATCAGCTATCTACATCAACAG 58.611 44.000 9.35 0.00 45.35 3.16
76 77 1.813513 AAGTGAGCTTCATGAACCGG 58.186 50.000 3.38 0.00 0.00 5.28
117 118 6.373216 TGATACTTGTGGGTTATTACTTGCAC 59.627 38.462 0.00 0.00 0.00 4.57
186 187 1.546476 AGACCAGTTCGAAGGCTACTG 59.454 52.381 0.00 7.96 39.13 2.74
267 375 0.108019 GGGCCCCTAGGTCGTTTATG 59.892 60.000 12.23 0.00 39.40 1.90
268 376 0.835276 GGCCCCTAGGTCGTTTATGT 59.165 55.000 8.29 0.00 34.57 2.29
269 377 1.202615 GGCCCCTAGGTCGTTTATGTC 60.203 57.143 8.29 0.00 34.57 3.06
270 378 1.483415 GCCCCTAGGTCGTTTATGTCA 59.517 52.381 8.29 0.00 34.57 3.58
271 379 2.104281 GCCCCTAGGTCGTTTATGTCAT 59.896 50.000 8.29 0.00 34.57 3.06
272 380 3.728845 CCCCTAGGTCGTTTATGTCATG 58.271 50.000 8.29 0.00 0.00 3.07
273 381 3.494398 CCCCTAGGTCGTTTATGTCATGG 60.494 52.174 8.29 0.00 0.00 3.66
274 382 3.494398 CCCTAGGTCGTTTATGTCATGGG 60.494 52.174 8.29 0.00 0.00 4.00
275 383 2.038387 AGGTCGTTTATGTCATGGGC 57.962 50.000 0.00 0.00 0.00 5.36
276 384 1.021968 GGTCGTTTATGTCATGGGCC 58.978 55.000 0.00 0.00 0.00 5.80
277 385 1.680555 GGTCGTTTATGTCATGGGCCA 60.681 52.381 9.61 9.61 0.00 5.36
278 386 2.088423 GTCGTTTATGTCATGGGCCAA 58.912 47.619 11.89 0.00 0.00 4.52
279 387 2.687935 GTCGTTTATGTCATGGGCCAAT 59.312 45.455 11.89 1.02 0.00 3.16
280 388 2.948979 TCGTTTATGTCATGGGCCAATC 59.051 45.455 11.89 4.54 0.00 2.67
281 389 2.687425 CGTTTATGTCATGGGCCAATCA 59.313 45.455 11.89 10.80 0.00 2.57
282 390 3.130164 CGTTTATGTCATGGGCCAATCAA 59.870 43.478 11.89 0.00 0.00 2.57
283 391 4.432712 GTTTATGTCATGGGCCAATCAAC 58.567 43.478 11.89 7.17 0.00 3.18
284 392 1.488390 ATGTCATGGGCCAATCAACC 58.512 50.000 11.89 0.00 0.00 3.77
286 394 1.001503 TCATGGGCCAATCAACCCC 59.998 57.895 11.89 0.00 46.43 4.95
287 395 2.065789 CATGGGCCAATCAACCCCC 61.066 63.158 11.89 0.00 46.43 5.40
301 409 4.430388 CCCCCTATGGCCCTACAA 57.570 61.111 0.00 0.00 0.00 2.41
302 410 1.844130 CCCCCTATGGCCCTACAAC 59.156 63.158 0.00 0.00 0.00 3.32
303 411 1.450211 CCCCTATGGCCCTACAACG 59.550 63.158 0.00 0.00 0.00 4.10
304 412 1.342672 CCCCTATGGCCCTACAACGT 61.343 60.000 0.00 0.00 0.00 3.99
305 413 0.179056 CCCTATGGCCCTACAACGTG 60.179 60.000 0.00 0.00 0.00 4.49
306 414 0.179056 CCTATGGCCCTACAACGTGG 60.179 60.000 0.00 0.00 0.00 4.94
307 415 0.539986 CTATGGCCCTACAACGTGGT 59.460 55.000 0.00 0.00 0.00 4.16
308 416 0.250793 TATGGCCCTACAACGTGGTG 59.749 55.000 5.64 0.00 0.00 4.17
309 417 2.359478 GGCCCTACAACGTGGTGG 60.359 66.667 5.64 1.76 0.00 4.61
310 418 3.053896 GCCCTACAACGTGGTGGC 61.054 66.667 5.64 7.31 0.00 5.01
311 419 2.359478 CCCTACAACGTGGTGGCC 60.359 66.667 5.64 0.00 0.00 5.36
312 420 2.747686 CCTACAACGTGGTGGCCT 59.252 61.111 5.64 0.00 0.00 5.19
313 421 1.375523 CCTACAACGTGGTGGCCTC 60.376 63.158 5.64 0.00 0.00 4.70
314 422 1.736645 CTACAACGTGGTGGCCTCG 60.737 63.158 5.64 6.48 44.64 4.63
315 423 2.149803 CTACAACGTGGTGGCCTCGA 62.150 60.000 5.64 0.00 42.19 4.04
316 424 1.746322 TACAACGTGGTGGCCTCGAA 61.746 55.000 5.64 0.00 42.19 3.71
317 425 1.890041 CAACGTGGTGGCCTCGAAA 60.890 57.895 15.14 0.00 42.19 3.46
318 426 1.597027 AACGTGGTGGCCTCGAAAG 60.597 57.895 15.14 0.00 42.19 2.62
319 427 2.035237 AACGTGGTGGCCTCGAAAGA 62.035 55.000 15.14 0.00 42.19 2.52
320 428 2.027625 CGTGGTGGCCTCGAAAGAC 61.028 63.158 3.32 0.00 42.19 3.01
321 429 1.371558 GTGGTGGCCTCGAAAGACT 59.628 57.895 3.32 0.00 35.39 3.24
322 430 0.250338 GTGGTGGCCTCGAAAGACTT 60.250 55.000 3.32 0.00 35.39 3.01
323 431 0.250295 TGGTGGCCTCGAAAGACTTG 60.250 55.000 3.32 0.00 35.39 3.16
324 432 0.955919 GGTGGCCTCGAAAGACTTGG 60.956 60.000 3.32 0.00 35.39 3.61
325 433 0.034896 GTGGCCTCGAAAGACTTGGA 59.965 55.000 3.32 0.00 35.39 3.53
326 434 0.321671 TGGCCTCGAAAGACTTGGAG 59.678 55.000 3.32 8.78 37.20 3.86
327 435 0.321996 GGCCTCGAAAGACTTGGAGT 59.678 55.000 12.86 0.00 36.06 3.85
328 436 1.549170 GGCCTCGAAAGACTTGGAGTA 59.451 52.381 12.86 0.00 36.06 2.59
329 437 2.608268 GCCTCGAAAGACTTGGAGTAC 58.392 52.381 12.86 0.00 36.06 2.73
330 438 2.029290 GCCTCGAAAGACTTGGAGTACA 60.029 50.000 12.86 0.00 36.06 2.90
331 439 3.554337 GCCTCGAAAGACTTGGAGTACAA 60.554 47.826 12.86 0.00 36.06 2.41
341 449 3.569194 TTGGAGTACAAGACAAGGCAA 57.431 42.857 0.00 0.00 33.18 4.52
342 450 2.846193 TGGAGTACAAGACAAGGCAAC 58.154 47.619 0.00 0.00 0.00 4.17
343 451 2.152016 GGAGTACAAGACAAGGCAACC 58.848 52.381 0.00 0.00 37.17 3.77
344 452 1.798813 GAGTACAAGACAAGGCAACCG 59.201 52.381 0.00 0.00 37.17 4.44
345 453 0.872388 GTACAAGACAAGGCAACCGG 59.128 55.000 0.00 0.00 37.17 5.28
346 454 0.470766 TACAAGACAAGGCAACCGGT 59.529 50.000 0.00 0.00 37.17 5.28
347 455 1.101049 ACAAGACAAGGCAACCGGTG 61.101 55.000 8.52 3.35 37.17 4.94
348 456 1.101049 CAAGACAAGGCAACCGGTGT 61.101 55.000 8.52 0.00 37.17 4.16
349 457 0.818040 AAGACAAGGCAACCGGTGTC 60.818 55.000 8.52 10.50 40.93 3.67
350 458 2.203294 ACAAGGCAACCGGTGTCC 60.203 61.111 8.52 13.06 29.16 4.02
373 481 3.837399 AGGACTCCTCCTTACTGACTT 57.163 47.619 0.00 0.00 45.77 3.01
374 482 4.949966 AGGACTCCTCCTTACTGACTTA 57.050 45.455 0.00 0.00 45.77 2.24
375 483 4.862371 AGGACTCCTCCTTACTGACTTAG 58.138 47.826 0.00 0.00 45.77 2.18
394 502 7.839705 TGACTTAGATCATGTAACCCTAGACTT 59.160 37.037 0.00 0.00 0.00 3.01
416 524 1.211212 GGTACCCATATATTCCGGGGC 59.789 57.143 0.00 4.10 44.96 5.80
520 628 2.287069 ACACGAGCATGAGTAGCGTATC 60.287 50.000 0.00 0.00 37.01 2.24
526 634 3.133003 AGCATGAGTAGCGTATCACCTTT 59.867 43.478 0.00 0.00 37.01 3.11
751 932 2.349590 TCACCTCGTCAAATGCATGAG 58.650 47.619 0.00 1.56 0.00 2.90
814 997 6.612306 AGAAGGATTTCGCTACAAATCAAAC 58.388 36.000 12.20 5.33 42.40 2.93
817 1000 5.048991 AGGATTTCGCTACAAATCAAACGTT 60.049 36.000 0.00 0.00 42.40 3.99
916 1099 2.743553 AGAAAATTGCCATCCTCAGGG 58.256 47.619 0.00 0.00 0.00 4.45
970 1158 2.396590 TGCTTAGACATTCCCGGAAC 57.603 50.000 0.73 0.00 0.00 3.62
976 1164 5.699097 TTAGACATTCCCGGAACAAAAAG 57.301 39.130 0.73 0.00 0.00 2.27
983 1171 3.674997 TCCCGGAACAAAAAGATCTCTG 58.325 45.455 0.73 0.00 0.00 3.35
985 1173 4.285003 TCCCGGAACAAAAAGATCTCTGTA 59.715 41.667 0.73 0.00 0.00 2.74
996 1187 7.995463 AAAAGATCTCTGTAAATCTAGCGAC 57.005 36.000 0.00 0.00 32.01 5.19
1030 1221 6.626488 CGAATTGAAGAAACATTCGCATCTAG 59.374 38.462 0.99 0.00 37.81 2.43
1032 1223 8.492673 AATTGAAGAAACATTCGCATCTAGTA 57.507 30.769 0.00 0.00 34.02 1.82
1033 1224 7.525688 TTGAAGAAACATTCGCATCTAGTAG 57.474 36.000 0.00 0.00 34.02 2.57
1034 1225 6.631016 TGAAGAAACATTCGCATCTAGTAGT 58.369 36.000 0.00 0.00 34.02 2.73
1035 1226 7.768240 TGAAGAAACATTCGCATCTAGTAGTA 58.232 34.615 0.00 0.00 34.02 1.82
1036 1227 7.701078 TGAAGAAACATTCGCATCTAGTAGTAC 59.299 37.037 0.00 0.00 34.02 2.73
1037 1228 7.336161 AGAAACATTCGCATCTAGTAGTACT 57.664 36.000 8.14 8.14 34.02 2.73
1038 1229 7.197017 AGAAACATTCGCATCTAGTAGTACTG 58.803 38.462 13.29 3.54 34.02 2.74
1091 1282 2.038033 CCTTTTCGTGTACCCTTCCTCA 59.962 50.000 0.00 0.00 0.00 3.86
1242 1433 1.151810 TCCCTCTCTGCCCCAAACT 60.152 57.895 0.00 0.00 0.00 2.66
1244 1435 1.204113 CCCTCTCTGCCCCAAACTCT 61.204 60.000 0.00 0.00 0.00 3.24
1797 1988 1.354705 GGTTCCACTTAGCTTCCCCTT 59.645 52.381 0.00 0.00 0.00 3.95
1808 1999 3.923648 AGCTTCCCCTTGGTTTTAGTTT 58.076 40.909 0.00 0.00 0.00 2.66
1809 2000 5.069518 AGCTTCCCCTTGGTTTTAGTTTA 57.930 39.130 0.00 0.00 0.00 2.01
1810 2001 5.460416 AGCTTCCCCTTGGTTTTAGTTTAA 58.540 37.500 0.00 0.00 0.00 1.52
1851 2152 2.069273 CCGTGTGCTTCTTTCCTAGTG 58.931 52.381 0.00 0.00 0.00 2.74
1874 2175 2.413765 GCATTGCATCCATACGATCTGC 60.414 50.000 3.15 0.00 0.00 4.26
1918 2219 3.335579 CTTCCCCTCGGTTTTAGTTCAG 58.664 50.000 0.00 0.00 0.00 3.02
1920 2221 2.707257 TCCCCTCGGTTTTAGTTCAGTT 59.293 45.455 0.00 0.00 0.00 3.16
1921 2222 2.812011 CCCCTCGGTTTTAGTTCAGTTG 59.188 50.000 0.00 0.00 0.00 3.16
1923 2224 4.131596 CCCTCGGTTTTAGTTCAGTTGAA 58.868 43.478 0.00 0.00 0.00 2.69
1969 2293 6.735130 ACCACAATGTCTTTACTTTACAAGC 58.265 36.000 0.00 0.00 0.00 4.01
1970 2294 6.546034 ACCACAATGTCTTTACTTTACAAGCT 59.454 34.615 0.00 0.00 0.00 3.74
1971 2295 7.717875 ACCACAATGTCTTTACTTTACAAGCTA 59.282 33.333 0.00 0.00 0.00 3.32
1972 2296 8.015658 CCACAATGTCTTTACTTTACAAGCTAC 58.984 37.037 0.00 0.00 0.00 3.58
1973 2297 8.556194 CACAATGTCTTTACTTTACAAGCTACA 58.444 33.333 0.00 0.00 0.00 2.74
2019 2351 6.039616 CGATAAGCTAAGATATCCAAGAGCC 58.960 44.000 0.00 0.00 0.00 4.70
2149 2634 1.152567 CCCCAGCTGGAACCAACAA 60.153 57.895 34.91 0.00 37.39 2.83
2150 2635 0.758685 CCCCAGCTGGAACCAACAAA 60.759 55.000 34.91 0.00 37.39 2.83
2278 2798 6.342338 ACACCTCATTTTCTAGTAGTTCGT 57.658 37.500 0.00 0.00 0.00 3.85
2295 2815 1.146263 GTACATTCCTGCCCCCGAG 59.854 63.158 0.00 0.00 0.00 4.63
2324 2845 5.866092 GCATTTCTTGATCTCCCTGTTTTTC 59.134 40.000 0.00 0.00 0.00 2.29
2467 2988 2.993471 GCAAACACCCCTGCCATCG 61.993 63.158 0.00 0.00 32.18 3.84
2495 3016 7.816031 CAGACATTTTTCATTAGAAGGTGCAAT 59.184 33.333 0.00 0.00 34.71 3.56
2576 3105 4.625324 GCCATACTTTATCTCCCACACACA 60.625 45.833 0.00 0.00 0.00 3.72
2617 3146 7.862372 TGTTCAATGCTTTCACTAACTTTGATC 59.138 33.333 0.00 0.00 0.00 2.92
2618 3147 6.602179 TCAATGCTTTCACTAACTTTGATCG 58.398 36.000 0.00 0.00 0.00 3.69
2775 3646 9.752228 ATGCATCTTCAGATAGAGAATACTAGA 57.248 33.333 0.00 0.00 32.63 2.43
2850 3721 1.604604 AACCAGAACAACCGTCATGG 58.395 50.000 0.00 0.00 46.41 3.66
2981 3931 8.431910 TCAACCTGGTTAGAATTTCTAGTACT 57.568 34.615 12.53 0.00 29.56 2.73
2991 3941 6.430007 AGAATTTCTAGTACTCCCTCCGTTA 58.570 40.000 0.00 0.00 0.00 3.18
3015 3965 7.972832 ACATAATTCTTGTCGTGGTTTTAGA 57.027 32.000 0.00 0.00 0.00 2.10
3016 3966 8.029642 ACATAATTCTTGTCGTGGTTTTAGAG 57.970 34.615 0.00 0.00 0.00 2.43
3017 3967 5.941948 AATTCTTGTCGTGGTTTTAGAGG 57.058 39.130 0.00 0.00 0.00 3.69
3018 3968 3.396260 TCTTGTCGTGGTTTTAGAGGG 57.604 47.619 0.00 0.00 0.00 4.30
3066 4016 5.586243 TGTATTTTCTGTGCAATCTAGAGGC 59.414 40.000 11.26 11.26 0.00 4.70
3074 4024 2.487762 TGCAATCTAGAGGCGGTTTTTG 59.512 45.455 12.84 4.79 0.00 2.44
3085 4035 4.765273 AGGCGGTTTTTGAATTGAAGTTT 58.235 34.783 0.00 0.00 0.00 2.66
3114 4064 7.940850 TCATATTAGACCTAAATTTTGCCAGC 58.059 34.615 0.00 0.00 0.00 4.85
3178 4128 1.399791 GCTCATGTCTGGTTTGCTAGC 59.600 52.381 8.10 8.10 0.00 3.42
3179 4129 2.938756 GCTCATGTCTGGTTTGCTAGCT 60.939 50.000 17.23 0.00 0.00 3.32
3202 4152 6.403636 GCTTACTCCAACATGTTCTACCATTG 60.404 42.308 8.48 0.00 0.00 2.82
3257 4207 2.301738 GGGGAGGGAGAGGTTGGTG 61.302 68.421 0.00 0.00 0.00 4.17
3310 4305 0.823356 TGTGAGTTCCAAAGCAGGCC 60.823 55.000 0.00 0.00 0.00 5.19
3329 4324 3.181450 GGCCTAAGCACCTCATTGTCTAT 60.181 47.826 0.00 0.00 42.56 1.98
3362 4357 2.419436 CCTGGCCCAGTTTTTCGTTTTT 60.419 45.455 10.47 0.00 0.00 1.94
3367 4362 3.305897 GCCCAGTTTTTCGTTTTTCTGTG 59.694 43.478 0.00 0.00 0.00 3.66
3368 4363 3.305897 CCCAGTTTTTCGTTTTTCTGTGC 59.694 43.478 0.00 0.00 0.00 4.57
3370 4365 4.201580 CCAGTTTTTCGTTTTTCTGTGCAC 60.202 41.667 10.75 10.75 0.00 4.57
3380 4563 3.969117 TTTCTGTGCACATGTGTCTTC 57.031 42.857 26.01 10.66 0.00 2.87
3381 4564 2.618442 TCTGTGCACATGTGTCTTCA 57.382 45.000 26.01 13.16 0.00 3.02
3412 4595 0.250858 TAACAGGCTGCACTGCACAT 60.251 50.000 15.89 0.00 42.21 3.21
3479 4662 7.500227 ACAAGATTGGTGTGATTATATGACTGG 59.500 37.037 0.00 0.00 0.00 4.00
3526 4709 4.670992 CGTCAGCATTCCATGAGAAAAGTG 60.671 45.833 0.00 0.00 38.21 3.16
3543 4726 5.948992 AAAGTGCTGGAGTATGTTTCTTC 57.051 39.130 0.00 0.00 0.00 2.87
3551 4734 6.404074 GCTGGAGTATGTTTCTTCTTGGATTG 60.404 42.308 0.00 0.00 0.00 2.67
3561 4744 5.138125 TCTTCTTGGATTGGCAAAACATC 57.862 39.130 3.01 0.00 0.00 3.06
3600 4783 7.709269 TCTTTGCCATACGCTATTAAAGTAG 57.291 36.000 0.00 0.00 38.78 2.57
3605 4788 5.047519 GCCATACGCTATTAAAGTAGGAGGA 60.048 44.000 0.00 0.00 0.00 3.71
3633 4816 1.743394 GTTCGTGGGCTTAGGGATTTG 59.257 52.381 0.00 0.00 0.00 2.32
3635 4818 1.065709 TCGTGGGCTTAGGGATTTGAC 60.066 52.381 0.00 0.00 0.00 3.18
3647 4830 2.418976 GGGATTTGACGTAAGGTTCTGC 59.581 50.000 0.00 0.00 46.39 4.26
3786 4971 0.911769 TGCAGGCTGCCTTGTACTAT 59.088 50.000 34.58 0.00 44.23 2.12
3820 5005 0.618458 TGCACTGGTTATCCCTCCAC 59.382 55.000 0.00 0.00 0.00 4.02
3856 5041 4.971939 TGAAAGATCATGGTTGTCTCACA 58.028 39.130 0.00 0.00 0.00 3.58
3954 5139 1.608542 GGCGAGGAGATAGCTCGACTA 60.609 57.143 0.00 0.00 44.37 2.59
3963 5148 4.270834 AGATAGCTCGACTACAGTTTGGA 58.729 43.478 0.00 0.00 32.32 3.53
3964 5149 4.336993 AGATAGCTCGACTACAGTTTGGAG 59.663 45.833 0.00 0.00 33.50 3.86
4026 5211 2.507886 TCCCGCTTCCCTTTATGATTCA 59.492 45.455 0.00 0.00 0.00 2.57
4149 5334 1.065199 CCCTTGCCATCAGCTTCACTA 60.065 52.381 0.00 0.00 44.23 2.74
4254 5439 1.612950 TGAAATGAAGCAATGGCACGT 59.387 42.857 0.00 0.00 44.61 4.49
4315 5500 5.412594 TGCAGCAGAGATTATCGAAAAAGTT 59.587 36.000 0.00 0.00 0.00 2.66
4396 5581 4.010349 GGACCATTCTAGTTGAACCTTGG 58.990 47.826 4.50 4.50 37.98 3.61
4441 5626 3.582647 TGCTGGAATCACTCAGGTTTCTA 59.417 43.478 0.00 0.00 0.00 2.10
4503 5688 3.441572 GTCAGCCATTTCAGTAAGCACAT 59.558 43.478 0.00 0.00 0.00 3.21
4511 5696 6.742718 CCATTTCAGTAAGCACATACTTTTCG 59.257 38.462 0.00 0.00 33.90 3.46
4659 5846 6.920758 TGTGTTTTGTTGCTGTGGATAATTAC 59.079 34.615 0.00 0.00 0.00 1.89
4739 5926 8.428186 TGTAGGAACAATTATACGAACCATTC 57.572 34.615 0.00 0.00 30.91 2.67
4759 5961 6.708054 CCATTCGGAGCTTACTGAATTTCTAT 59.292 38.462 6.72 0.00 41.93 1.98
4816 6018 9.579932 TTTTTAGAAATGCCAAAAATATTGGGT 57.420 25.926 9.12 0.00 39.90 4.51
4894 6114 2.471815 ACATGGATCGGAGGGAGTAA 57.528 50.000 0.00 0.00 0.00 2.24
4916 6136 2.833631 AAACACAAGTACTCCCTCCG 57.166 50.000 0.00 0.00 0.00 4.63
4917 6137 1.713297 AACACAAGTACTCCCTCCGT 58.287 50.000 0.00 0.00 0.00 4.69
4918 6138 2.592102 ACACAAGTACTCCCTCCGTA 57.408 50.000 0.00 0.00 0.00 4.02
4919 6139 2.880443 ACACAAGTACTCCCTCCGTAA 58.120 47.619 0.00 0.00 0.00 3.18
4920 6140 3.233507 ACACAAGTACTCCCTCCGTAAA 58.766 45.455 0.00 0.00 0.00 2.01
4921 6141 3.257624 ACACAAGTACTCCCTCCGTAAAG 59.742 47.826 0.00 0.00 0.00 1.85
4922 6142 3.257624 CACAAGTACTCCCTCCGTAAAGT 59.742 47.826 0.00 0.00 0.00 2.66
4923 6143 4.460382 CACAAGTACTCCCTCCGTAAAGTA 59.540 45.833 0.00 0.00 0.00 2.24
4924 6144 5.047802 CACAAGTACTCCCTCCGTAAAGTAA 60.048 44.000 0.00 0.00 0.00 2.24
4925 6145 5.718607 ACAAGTACTCCCTCCGTAAAGTAAT 59.281 40.000 0.00 0.00 0.00 1.89
4926 6146 6.891908 ACAAGTACTCCCTCCGTAAAGTAATA 59.108 38.462 0.00 0.00 0.00 0.98
4927 6147 7.562821 ACAAGTACTCCCTCCGTAAAGTAATAT 59.437 37.037 0.00 0.00 0.00 1.28
4928 6148 9.071276 CAAGTACTCCCTCCGTAAAGTAATATA 57.929 37.037 0.00 0.00 0.00 0.86
4929 6149 9.646522 AAGTACTCCCTCCGTAAAGTAATATAA 57.353 33.333 0.00 0.00 0.00 0.98
4930 6150 9.294614 AGTACTCCCTCCGTAAAGTAATATAAG 57.705 37.037 0.00 0.00 0.00 1.73
4931 6151 9.289782 GTACTCCCTCCGTAAAGTAATATAAGA 57.710 37.037 0.00 0.00 0.00 2.10
4932 6152 8.406730 ACTCCCTCCGTAAAGTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
4933 6153 7.039853 ACTCCCTCCGTAAAGTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
4934 6154 6.072286 TCCCTCCGTAAAGTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
4935 6155 6.294397 CCCTCCGTAAAGTAATATAAGAGCGT 60.294 42.308 0.00 0.00 0.00 5.07
4936 6156 7.144000 CCTCCGTAAAGTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
4937 6157 7.650903 CCTCCGTAAAGTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
4938 6158 9.669353 CTCCGTAAAGTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
4939 6159 9.669353 TCCGTAAAGTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 0.00 1.85
4940 6160 9.669353 CCGTAAAGTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 0.00 2.10
4954 6174 8.635877 AGAGCGTTTAGATGACTATTTTAGTG 57.364 34.615 0.00 0.00 39.59 2.74
4955 6175 8.467598 AGAGCGTTTAGATGACTATTTTAGTGA 58.532 33.333 0.00 0.00 39.59 3.41
4956 6176 9.250624 GAGCGTTTAGATGACTATTTTAGTGAT 57.749 33.333 0.00 0.00 39.59 3.06
4957 6177 9.250624 AGCGTTTAGATGACTATTTTAGTGATC 57.749 33.333 6.14 6.14 45.85 2.92
5062 6282 7.532682 TTTACAGCACTGGATTTTGTTTTTC 57.467 32.000 2.21 0.00 34.19 2.29
5065 6285 3.454082 AGCACTGGATTTTGTTTTTCCCA 59.546 39.130 0.00 0.00 0.00 4.37
5069 6290 5.928264 CACTGGATTTTGTTTTTCCCAGATC 59.072 40.000 12.54 0.00 42.69 2.75
5087 6308 8.058235 TCCCAGATCCAAAACATATGACATTTA 58.942 33.333 10.38 0.00 0.00 1.40
5152 6373 3.926527 TCAGAAGACACGAACATGTATGC 59.073 43.478 0.00 0.00 31.24 3.14
5254 6481 7.332678 AGGAATTTCACAATTCTTTGCTTATGC 59.667 33.333 7.45 0.00 45.45 3.14
5287 6514 5.289675 GTCTGTTGAGTATTTCGTGATCAGG 59.710 44.000 9.16 9.16 0.00 3.86
5318 6545 3.845781 TCTGAGATTGATAACAGCCCC 57.154 47.619 0.00 0.00 0.00 5.80
5384 6621 0.249657 GCCCGGATGCAACAAAAACA 60.250 50.000 0.73 0.00 0.00 2.83
5419 6656 2.288961 ATTACAGTACGCAACCCTCG 57.711 50.000 0.00 0.00 0.00 4.63
5445 6684 0.390340 GCACAATCCTCACTCGCTCA 60.390 55.000 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 6.398918 TCATGAAGCTCACTTAGTCCTAAAC 58.601 40.000 0.00 0.00 35.82 2.01
76 77 2.977405 ATCAGCAAGCTTGTCGAAAC 57.023 45.000 26.55 9.65 0.00 2.78
135 136 2.939261 GCTTCTTGGTCGGGGTCGA 61.939 63.158 0.00 0.00 43.86 4.20
267 375 1.329913 GGGGTTGATTGGCCCATGAC 61.330 60.000 0.00 0.00 46.59 3.06
268 376 1.001503 GGGGTTGATTGGCCCATGA 59.998 57.895 0.00 0.00 46.59 3.07
269 377 2.065789 GGGGGTTGATTGGCCCATG 61.066 63.158 0.00 0.00 46.59 3.66
270 378 2.368188 GGGGGTTGATTGGCCCAT 59.632 61.111 0.00 0.00 46.59 4.00
284 392 1.844130 GTTGTAGGGCCATAGGGGG 59.156 63.158 6.18 0.00 37.04 5.40
285 393 1.342672 ACGTTGTAGGGCCATAGGGG 61.343 60.000 6.18 0.00 40.85 4.79
286 394 0.179056 CACGTTGTAGGGCCATAGGG 60.179 60.000 6.18 0.00 37.18 3.53
287 395 0.179056 CCACGTTGTAGGGCCATAGG 60.179 60.000 6.18 0.00 0.00 2.57
288 396 0.539986 ACCACGTTGTAGGGCCATAG 59.460 55.000 6.18 0.00 0.00 2.23
289 397 0.250793 CACCACGTTGTAGGGCCATA 59.749 55.000 6.18 0.00 0.00 2.74
290 398 1.002624 CACCACGTTGTAGGGCCAT 60.003 57.895 6.18 0.00 0.00 4.40
291 399 2.428187 CACCACGTTGTAGGGCCA 59.572 61.111 6.18 0.00 0.00 5.36
292 400 2.359478 CCACCACGTTGTAGGGCC 60.359 66.667 0.00 0.00 0.00 5.80
293 401 3.053896 GCCACCACGTTGTAGGGC 61.054 66.667 5.52 5.52 0.00 5.19
294 402 2.359478 GGCCACCACGTTGTAGGG 60.359 66.667 0.00 2.12 0.00 3.53
295 403 1.375523 GAGGCCACCACGTTGTAGG 60.376 63.158 5.01 0.00 0.00 3.18
296 404 1.736645 CGAGGCCACCACGTTGTAG 60.737 63.158 5.01 0.00 33.22 2.74
297 405 1.746322 TTCGAGGCCACCACGTTGTA 61.746 55.000 5.01 0.00 38.64 2.41
298 406 2.596553 TTTCGAGGCCACCACGTTGT 62.597 55.000 5.01 0.00 38.64 3.32
299 407 1.841663 CTTTCGAGGCCACCACGTTG 61.842 60.000 5.01 0.00 38.64 4.10
300 408 1.597027 CTTTCGAGGCCACCACGTT 60.597 57.895 5.01 0.00 38.64 3.99
301 409 2.030562 CTTTCGAGGCCACCACGT 59.969 61.111 5.01 0.00 38.64 4.49
302 410 2.027625 GTCTTTCGAGGCCACCACG 61.028 63.158 5.01 5.35 38.87 4.94
303 411 0.250338 AAGTCTTTCGAGGCCACCAC 60.250 55.000 5.01 0.00 0.00 4.16
304 412 0.250295 CAAGTCTTTCGAGGCCACCA 60.250 55.000 5.01 0.00 0.00 4.17
305 413 0.955919 CCAAGTCTTTCGAGGCCACC 60.956 60.000 5.01 0.00 0.00 4.61
306 414 0.034896 TCCAAGTCTTTCGAGGCCAC 59.965 55.000 5.01 0.00 0.00 5.01
307 415 0.321671 CTCCAAGTCTTTCGAGGCCA 59.678 55.000 5.01 0.00 0.00 5.36
308 416 0.321996 ACTCCAAGTCTTTCGAGGCC 59.678 55.000 0.00 0.00 0.00 5.19
309 417 2.029290 TGTACTCCAAGTCTTTCGAGGC 60.029 50.000 10.02 4.78 0.00 4.70
310 418 3.936372 TGTACTCCAAGTCTTTCGAGG 57.064 47.619 10.02 0.00 0.00 4.63
321 429 3.211045 GTTGCCTTGTCTTGTACTCCAA 58.789 45.455 0.00 0.00 0.00 3.53
322 430 2.486548 GGTTGCCTTGTCTTGTACTCCA 60.487 50.000 0.00 0.00 0.00 3.86
323 431 2.152016 GGTTGCCTTGTCTTGTACTCC 58.848 52.381 0.00 0.00 0.00 3.85
324 432 1.798813 CGGTTGCCTTGTCTTGTACTC 59.201 52.381 0.00 0.00 0.00 2.59
325 433 1.542547 CCGGTTGCCTTGTCTTGTACT 60.543 52.381 0.00 0.00 0.00 2.73
326 434 0.872388 CCGGTTGCCTTGTCTTGTAC 59.128 55.000 0.00 0.00 0.00 2.90
327 435 0.470766 ACCGGTTGCCTTGTCTTGTA 59.529 50.000 0.00 0.00 0.00 2.41
328 436 1.101049 CACCGGTTGCCTTGTCTTGT 61.101 55.000 2.97 0.00 0.00 3.16
329 437 1.101049 ACACCGGTTGCCTTGTCTTG 61.101 55.000 2.97 0.00 0.00 3.02
330 438 0.818040 GACACCGGTTGCCTTGTCTT 60.818 55.000 2.97 0.00 33.86 3.01
331 439 1.227853 GACACCGGTTGCCTTGTCT 60.228 57.895 2.97 0.00 33.86 3.41
332 440 2.258726 GGACACCGGTTGCCTTGTC 61.259 63.158 2.97 8.39 35.06 3.18
333 441 2.203294 GGACACCGGTTGCCTTGT 60.203 61.111 2.97 0.00 0.00 3.16
334 442 3.353836 CGGACACCGGTTGCCTTG 61.354 66.667 17.83 3.63 44.15 3.61
354 462 4.857679 TCTAAGTCAGTAAGGAGGAGTCC 58.142 47.826 0.00 0.00 44.33 3.85
355 463 6.123651 TGATCTAAGTCAGTAAGGAGGAGTC 58.876 44.000 0.00 0.00 0.00 3.36
356 464 6.080969 TGATCTAAGTCAGTAAGGAGGAGT 57.919 41.667 0.00 0.00 0.00 3.85
357 465 6.549364 ACATGATCTAAGTCAGTAAGGAGGAG 59.451 42.308 0.00 0.00 0.00 3.69
358 466 6.436027 ACATGATCTAAGTCAGTAAGGAGGA 58.564 40.000 0.00 0.00 0.00 3.71
359 467 6.723298 ACATGATCTAAGTCAGTAAGGAGG 57.277 41.667 0.00 0.00 0.00 4.30
360 468 8.138712 GGTTACATGATCTAAGTCAGTAAGGAG 58.861 40.741 0.00 0.00 30.15 3.69
361 469 7.069578 GGGTTACATGATCTAAGTCAGTAAGGA 59.930 40.741 0.00 0.00 30.15 3.36
362 470 7.070074 AGGGTTACATGATCTAAGTCAGTAAGG 59.930 40.741 0.00 0.00 30.15 2.69
363 471 8.012957 AGGGTTACATGATCTAAGTCAGTAAG 57.987 38.462 0.00 0.00 30.15 2.34
364 472 7.973048 AGGGTTACATGATCTAAGTCAGTAA 57.027 36.000 0.00 0.00 0.00 2.24
365 473 8.500238 TCTAGGGTTACATGATCTAAGTCAGTA 58.500 37.037 0.00 0.00 0.00 2.74
366 474 7.285858 GTCTAGGGTTACATGATCTAAGTCAGT 59.714 40.741 0.00 0.00 0.00 3.41
367 475 7.504238 AGTCTAGGGTTACATGATCTAAGTCAG 59.496 40.741 0.00 0.00 0.00 3.51
368 476 7.355101 AGTCTAGGGTTACATGATCTAAGTCA 58.645 38.462 0.00 0.00 0.00 3.41
369 477 7.826918 AGTCTAGGGTTACATGATCTAAGTC 57.173 40.000 0.00 0.00 0.00 3.01
370 478 8.478877 CAAAGTCTAGGGTTACATGATCTAAGT 58.521 37.037 0.00 0.00 0.00 2.24
371 479 7.928706 CCAAAGTCTAGGGTTACATGATCTAAG 59.071 40.741 0.00 0.00 0.00 2.18
372 480 7.402071 ACCAAAGTCTAGGGTTACATGATCTAA 59.598 37.037 0.00 0.00 0.00 2.10
373 481 6.901300 ACCAAAGTCTAGGGTTACATGATCTA 59.099 38.462 0.00 0.00 0.00 1.98
374 482 5.726793 ACCAAAGTCTAGGGTTACATGATCT 59.273 40.000 0.00 0.00 0.00 2.75
375 483 5.990668 ACCAAAGTCTAGGGTTACATGATC 58.009 41.667 0.00 0.00 0.00 2.92
416 524 4.250464 TGTTGTTTATTCGACTAGGCTGG 58.750 43.478 0.00 0.00 0.00 4.85
520 628 4.272489 TCAGGCCATTGATAGAAAAGGTG 58.728 43.478 5.01 0.00 0.00 4.00
526 634 4.103153 CCTAGGTTCAGGCCATTGATAGAA 59.897 45.833 5.01 0.00 0.00 2.10
643 751 7.648112 GTGAGACAGTGTTAGCGATGATAATTA 59.352 37.037 0.00 0.00 0.00 1.40
751 932 7.435192 CCAAATAAACTTCAAACTGTCTTGGAC 59.565 37.037 0.00 0.00 32.03 4.02
806 989 5.814705 TGCTCAAAAATCCAACGTTTGATTT 59.185 32.000 26.21 26.21 39.74 2.17
814 997 3.899734 TGACATGCTCAAAAATCCAACG 58.100 40.909 0.00 0.00 0.00 4.10
916 1099 8.841444 ACGTTTCTTATGACAAATTATGATGC 57.159 30.769 0.00 0.00 0.00 3.91
970 1158 8.324567 GTCGCTAGATTTACAGAGATCTTTTTG 58.675 37.037 0.00 0.00 34.60 2.44
976 1164 4.915085 GCTGTCGCTAGATTTACAGAGATC 59.085 45.833 14.61 0.00 41.47 2.75
983 1171 5.005394 TCGAATTTGCTGTCGCTAGATTTAC 59.995 40.000 0.00 0.00 37.19 2.01
985 1173 3.932710 TCGAATTTGCTGTCGCTAGATTT 59.067 39.130 0.00 0.00 37.19 2.17
996 1187 6.752335 TGTTTCTTCAATTCGAATTTGCTG 57.248 33.333 20.56 10.66 31.69 4.41
1030 1221 3.325716 TCCCCAGGTTTTCACAGTACTAC 59.674 47.826 0.00 0.00 0.00 2.73
1032 1223 2.414612 TCCCCAGGTTTTCACAGTACT 58.585 47.619 0.00 0.00 0.00 2.73
1033 1224 2.943036 TCCCCAGGTTTTCACAGTAC 57.057 50.000 0.00 0.00 0.00 2.73
1034 1225 3.955524 TTTCCCCAGGTTTTCACAGTA 57.044 42.857 0.00 0.00 0.00 2.74
1035 1226 2.764010 GTTTTCCCCAGGTTTTCACAGT 59.236 45.455 0.00 0.00 0.00 3.55
1036 1227 3.031013 AGTTTTCCCCAGGTTTTCACAG 58.969 45.455 0.00 0.00 0.00 3.66
1037 1228 2.763448 CAGTTTTCCCCAGGTTTTCACA 59.237 45.455 0.00 0.00 0.00 3.58
1038 1229 3.028130 TCAGTTTTCCCCAGGTTTTCAC 58.972 45.455 0.00 0.00 0.00 3.18
1403 1594 3.718210 GACGGCGGCCTTCTCGAAT 62.718 63.158 18.34 0.00 0.00 3.34
1797 1988 5.755861 GCAGGCAATTGTTAAACTAAAACCA 59.244 36.000 7.40 0.00 0.00 3.67
1808 1999 0.607620 GCAAGGGCAGGCAATTGTTA 59.392 50.000 7.40 0.00 40.72 2.41
1809 2000 1.372307 GCAAGGGCAGGCAATTGTT 59.628 52.632 7.40 0.00 40.72 2.83
1810 2001 2.586293 GGCAAGGGCAGGCAATTGT 61.586 57.895 7.40 0.00 43.71 2.71
1851 2152 1.470098 GATCGTATGGATGCAATGCCC 59.530 52.381 1.53 0.00 34.82 5.36
1874 2175 4.567159 GCTAAGTGGAACCTAGAACAATCG 59.433 45.833 0.00 0.00 32.53 3.34
1918 2219 5.769162 ACGATATACTCCCTCCTAGTTCAAC 59.231 44.000 0.00 0.00 0.00 3.18
1920 2221 5.579753 ACGATATACTCCCTCCTAGTTCA 57.420 43.478 0.00 0.00 0.00 3.18
1921 2222 7.094420 GGTTTACGATATACTCCCTCCTAGTTC 60.094 44.444 0.00 0.00 0.00 3.01
1923 2224 6.183361 TGGTTTACGATATACTCCCTCCTAGT 60.183 42.308 0.00 0.00 0.00 2.57
1924 2225 6.150809 GTGGTTTACGATATACTCCCTCCTAG 59.849 46.154 0.00 0.00 0.00 3.02
1925 2226 6.006449 GTGGTTTACGATATACTCCCTCCTA 58.994 44.000 0.00 0.00 0.00 2.94
1961 2285 6.443934 TTGCTTTCTGTTGTAGCTTGTAAA 57.556 33.333 0.00 0.00 35.93 2.01
2019 2351 7.423199 CAAAGATCATGGAGTTTATCATGTGG 58.577 38.462 0.00 0.00 40.94 4.17
2149 2634 9.392259 AGCTGTTAGTAGTCTAGTTTTGTTTTT 57.608 29.630 0.00 0.00 0.00 1.94
2150 2635 8.827677 CAGCTGTTAGTAGTCTAGTTTTGTTTT 58.172 33.333 5.25 0.00 0.00 2.43
2278 2798 0.912487 AACTCGGGGGCAGGAATGTA 60.912 55.000 0.00 0.00 0.00 2.29
2295 2815 2.356069 GGGAGATCAAGAAATGCCGAAC 59.644 50.000 0.00 0.00 0.00 3.95
2324 2845 8.400184 TCTTAATGATTGGATTATTCTGCAGG 57.600 34.615 15.13 0.00 0.00 4.85
2356 2877 6.032956 TCACGTTCCTGTTAGTATGATTGT 57.967 37.500 0.00 0.00 0.00 2.71
2365 2886 3.775202 CTGATCCTCACGTTCCTGTTAG 58.225 50.000 0.00 0.00 0.00 2.34
2393 2914 9.733556 ATAGTGTGGTGTTTGACAATCTTATTA 57.266 29.630 0.00 0.00 0.00 0.98
2394 2915 6.959639 AGTGTGGTGTTTGACAATCTTATT 57.040 33.333 0.00 0.00 0.00 1.40
2395 2916 8.635765 AATAGTGTGGTGTTTGACAATCTTAT 57.364 30.769 0.00 0.00 0.00 1.73
2467 2988 6.803807 GCACCTTCTAATGAAAAATGTCTGAC 59.196 38.462 0.00 0.00 0.00 3.51
2495 3016 3.451178 GGATTAGCCTCACAACCTCTACA 59.549 47.826 0.00 0.00 0.00 2.74
2576 3105 5.754890 GCATTGAACAGAATCAAAACCTTGT 59.245 36.000 0.00 0.00 42.22 3.16
2617 3146 7.113124 CGTAAGGTGCTAGAGAACATTATAACG 59.887 40.741 0.00 0.00 33.09 3.18
2618 3147 8.133627 TCGTAAGGTGCTAGAGAACATTATAAC 58.866 37.037 0.00 0.00 33.09 1.89
2626 3472 4.499758 CGAATTCGTAAGGTGCTAGAGAAC 59.500 45.833 19.67 0.00 38.47 3.01
2707 3566 6.893958 AAATGATCTCAAAGCGTAGTACAG 57.106 37.500 0.38 0.00 0.00 2.74
2786 3657 7.767198 TCTTTCTCAACTTTCTTCGGACTTTAA 59.233 33.333 0.00 0.00 0.00 1.52
2850 3721 4.095483 CCTGAGACATGCAAGGTAACATTC 59.905 45.833 0.00 0.00 41.41 2.67
2937 3887 8.887717 CAGGTTGATTGGTTTGAACAAATTTAA 58.112 29.630 3.34 1.19 32.79 1.52
2938 3888 7.497249 CCAGGTTGATTGGTTTGAACAAATTTA 59.503 33.333 3.34 0.00 32.79 1.40
2939 3889 6.318396 CCAGGTTGATTGGTTTGAACAAATTT 59.682 34.615 3.34 0.00 32.79 1.82
2960 3910 6.612049 AGGGAGTACTAGAAATTCTAACCAGG 59.388 42.308 4.13 0.00 0.00 4.45
2968 3918 5.595257 AACGGAGGGAGTACTAGAAATTC 57.405 43.478 0.00 0.00 0.00 2.17
2981 3931 5.667466 GACAAGAATTATGTAACGGAGGGA 58.333 41.667 0.00 0.00 0.00 4.20
2991 3941 7.119262 CCTCTAAAACCACGACAAGAATTATGT 59.881 37.037 0.00 0.00 0.00 2.29
3015 3965 3.707102 GCTTCACCAATCTAGTACTCCCT 59.293 47.826 0.00 0.00 0.00 4.20
3016 3966 3.491104 CGCTTCACCAATCTAGTACTCCC 60.491 52.174 0.00 0.00 0.00 4.30
3017 3967 3.707793 CGCTTCACCAATCTAGTACTCC 58.292 50.000 0.00 0.00 0.00 3.85
3018 3968 3.117046 GCGCTTCACCAATCTAGTACTC 58.883 50.000 0.00 0.00 0.00 2.59
3066 4016 8.795786 TGATCTAAACTTCAATTCAAAAACCG 57.204 30.769 0.00 0.00 0.00 4.44
3107 4057 4.458989 CCAGAAACAGTTATAAGCTGGCAA 59.541 41.667 15.13 0.00 38.22 4.52
3114 4064 5.473504 AGTGGCAACCAGAAACAGTTATAAG 59.526 40.000 0.00 0.00 32.34 1.73
3178 4128 6.655003 ACAATGGTAGAACATGTTGGAGTAAG 59.345 38.462 17.58 2.39 0.00 2.34
3179 4129 6.429692 CACAATGGTAGAACATGTTGGAGTAA 59.570 38.462 17.58 0.00 0.00 2.24
3202 4152 2.408271 TGTGATCCTCATCAAGCCAC 57.592 50.000 0.00 0.00 40.90 5.01
3346 4341 3.305897 GCACAGAAAAACGAAAAACTGGG 59.694 43.478 0.00 0.00 32.79 4.45
3362 4357 2.618442 TGAAGACACATGTGCACAGA 57.382 45.000 25.84 1.79 0.00 3.41
3367 4362 3.397482 ACTCTCTTGAAGACACATGTGC 58.603 45.455 25.68 17.50 0.00 4.57
3368 4363 4.450419 GGAACTCTCTTGAAGACACATGTG 59.550 45.833 24.25 24.25 0.00 3.21
3370 4365 4.635223 TGGAACTCTCTTGAAGACACATG 58.365 43.478 0.00 0.00 0.00 3.21
3380 4563 3.937706 CAGCCTGTTATGGAACTCTCTTG 59.062 47.826 0.00 0.00 36.45 3.02
3381 4564 3.620966 GCAGCCTGTTATGGAACTCTCTT 60.621 47.826 0.00 0.00 36.45 2.85
3453 4636 7.500227 CCAGTCATATAATCACACCAATCTTGT 59.500 37.037 0.00 0.00 0.00 3.16
3475 4658 4.025360 TCATGCCAAAAATATCTGCCAGT 58.975 39.130 0.00 0.00 0.00 4.00
3479 4662 4.986659 GGACATCATGCCAAAAATATCTGC 59.013 41.667 0.00 0.00 0.00 4.26
3526 4709 4.579869 TCCAAGAAGAAACATACTCCAGC 58.420 43.478 0.00 0.00 0.00 4.85
3543 4726 3.574284 TCGATGTTTTGCCAATCCAAG 57.426 42.857 0.00 0.00 0.00 3.61
3551 4734 4.083324 TCTGATTCAGTTCGATGTTTTGCC 60.083 41.667 13.23 0.00 32.61 4.52
3561 4744 4.154737 TGGCAAAGATTCTGATTCAGTTCG 59.845 41.667 13.23 2.34 32.61 3.95
3600 4783 1.409427 CCACGAACCTACTGATCCTCC 59.591 57.143 0.00 0.00 0.00 4.30
3605 4788 1.276622 AAGCCCACGAACCTACTGAT 58.723 50.000 0.00 0.00 0.00 2.90
3633 4816 1.071605 CAGCAGCAGAACCTTACGTC 58.928 55.000 0.00 0.00 0.00 4.34
3635 4818 1.728971 CTTCAGCAGCAGAACCTTACG 59.271 52.381 0.00 0.00 0.00 3.18
3647 4830 4.978083 ATTATCTTTGCCACTTCAGCAG 57.022 40.909 0.00 0.00 42.17 4.24
3716 4901 9.491675 TGATGTCAAATATTTTCTGTGCATTTT 57.508 25.926 0.00 0.00 0.00 1.82
3820 5005 4.276678 TGATCTTTCAAAGTGGTTCTGCAG 59.723 41.667 7.63 7.63 0.00 4.41
3856 5041 0.694771 TGAGCAGCCTTCAACTGGAT 59.305 50.000 0.00 0.00 35.62 3.41
3921 5106 2.615912 CTCCTCGCCAATTTCCATCTTC 59.384 50.000 0.00 0.00 0.00 2.87
3954 5139 4.644685 ACAACTGCATTAACTCCAAACTGT 59.355 37.500 0.00 0.00 0.00 3.55
3963 5148 3.573538 TGGCATCAACAACTGCATTAACT 59.426 39.130 0.00 0.00 40.18 2.24
3964 5149 3.911868 TGGCATCAACAACTGCATTAAC 58.088 40.909 0.00 0.00 40.18 2.01
4026 5211 4.917906 ATCTTGTTCTAGCCTGGAAACT 57.082 40.909 0.00 0.00 0.00 2.66
4149 5334 0.832135 TCTTGGAAGCAGACCGGACT 60.832 55.000 9.46 3.68 0.00 3.85
4254 5439 1.745115 GCAACAGCGGCACAGGATA 60.745 57.895 1.45 0.00 0.00 2.59
4315 5500 6.142958 CACTAGATACACGACGACTATACGAA 59.857 42.308 0.00 0.00 37.03 3.85
4396 5581 1.839424 ACAGCCTACCAAGCATTTCC 58.161 50.000 0.00 0.00 0.00 3.13
4441 5626 3.350219 ACGGCACAAAAGGAGTATCAT 57.650 42.857 0.00 0.00 36.25 2.45
4503 5688 5.267776 GCTTGTGCTAAAACACGAAAAGTA 58.732 37.500 0.00 0.00 43.74 2.24
4857 6059 5.182190 TCCATGTTAATTGTCGCTGCTTTAA 59.818 36.000 0.00 0.00 0.00 1.52
4865 6085 2.869801 TCCGATCCATGTTAATTGTCGC 59.130 45.455 0.00 0.00 0.00 5.19
4903 6123 9.646522 TTATATTACTTTACGGAGGGAGTACTT 57.353 33.333 0.00 0.00 0.00 2.24
4904 6124 9.294614 CTTATATTACTTTACGGAGGGAGTACT 57.705 37.037 0.00 0.00 0.00 2.73
4905 6125 9.289782 TCTTATATTACTTTACGGAGGGAGTAC 57.710 37.037 0.00 0.00 0.00 2.73
4906 6126 9.512588 CTCTTATATTACTTTACGGAGGGAGTA 57.487 37.037 0.00 0.00 0.00 2.59
4907 6127 7.039853 GCTCTTATATTACTTTACGGAGGGAGT 60.040 40.741 0.00 0.00 0.00 3.85
4908 6128 7.314393 GCTCTTATATTACTTTACGGAGGGAG 58.686 42.308 0.00 0.00 0.00 4.30
4909 6129 6.072286 CGCTCTTATATTACTTTACGGAGGGA 60.072 42.308 0.00 0.00 34.63 4.20
4910 6130 6.091437 CGCTCTTATATTACTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
4911 6131 6.675987 ACGCTCTTATATTACTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
4912 6132 8.571461 AAACGCTCTTATATTACTTTACGGAG 57.429 34.615 0.00 0.00 0.00 4.63
4913 6133 9.669353 CTAAACGCTCTTATATTACTTTACGGA 57.331 33.333 0.00 0.00 0.00 4.69
4914 6134 9.669353 TCTAAACGCTCTTATATTACTTTACGG 57.331 33.333 0.00 0.00 0.00 4.02
4928 6148 9.088512 CACTAAAATAGTCATCTAAACGCTCTT 57.911 33.333 0.00 0.00 36.76 2.85
4929 6149 8.467598 TCACTAAAATAGTCATCTAAACGCTCT 58.532 33.333 0.00 0.00 36.76 4.09
4930 6150 8.630278 TCACTAAAATAGTCATCTAAACGCTC 57.370 34.615 0.00 0.00 36.76 5.03
4931 6151 9.250624 GATCACTAAAATAGTCATCTAAACGCT 57.749 33.333 0.00 0.00 34.00 5.07
4932 6152 9.250624 AGATCACTAAAATAGTCATCTAAACGC 57.749 33.333 2.55 0.00 43.56 4.84
4963 6183 9.495382 ACTCCCTCTGTAAAGAAATATAAGAGT 57.505 33.333 0.00 0.00 0.00 3.24
4969 6189 9.838339 CACAATACTCCCTCTGTAAAGAAATAT 57.162 33.333 0.00 0.00 0.00 1.28
4970 6190 9.042450 TCACAATACTCCCTCTGTAAAGAAATA 57.958 33.333 0.00 0.00 0.00 1.40
4971 6191 7.824779 GTCACAATACTCCCTCTGTAAAGAAAT 59.175 37.037 0.00 0.00 0.00 2.17
4972 6192 7.159372 GTCACAATACTCCCTCTGTAAAGAAA 58.841 38.462 0.00 0.00 0.00 2.52
4973 6193 6.295688 GGTCACAATACTCCCTCTGTAAAGAA 60.296 42.308 0.00 0.00 0.00 2.52
4974 6194 5.187186 GGTCACAATACTCCCTCTGTAAAGA 59.813 44.000 0.00 0.00 0.00 2.52
4975 6195 5.187967 AGGTCACAATACTCCCTCTGTAAAG 59.812 44.000 0.00 0.00 0.00 1.85
4976 6196 5.046591 CAGGTCACAATACTCCCTCTGTAAA 60.047 44.000 0.00 0.00 0.00 2.01
4977 6197 4.466370 CAGGTCACAATACTCCCTCTGTAA 59.534 45.833 0.00 0.00 0.00 2.41
4978 6198 4.023980 CAGGTCACAATACTCCCTCTGTA 58.976 47.826 0.00 0.00 0.00 2.74
4979 6199 2.834549 CAGGTCACAATACTCCCTCTGT 59.165 50.000 0.00 0.00 0.00 3.41
4980 6200 2.834549 ACAGGTCACAATACTCCCTCTG 59.165 50.000 0.00 0.00 0.00 3.35
4981 6201 2.834549 CACAGGTCACAATACTCCCTCT 59.165 50.000 0.00 0.00 0.00 3.69
4982 6202 2.678190 GCACAGGTCACAATACTCCCTC 60.678 54.545 0.00 0.00 0.00 4.30
4983 6203 1.279271 GCACAGGTCACAATACTCCCT 59.721 52.381 0.00 0.00 0.00 4.20
4984 6204 1.279271 AGCACAGGTCACAATACTCCC 59.721 52.381 0.00 0.00 0.00 4.30
4985 6205 2.770164 AGCACAGGTCACAATACTCC 57.230 50.000 0.00 0.00 0.00 3.85
4986 6206 5.073311 TCTTAGCACAGGTCACAATACTC 57.927 43.478 0.00 0.00 0.00 2.59
5062 6282 6.720112 AATGTCATATGTTTTGGATCTGGG 57.280 37.500 1.90 0.00 0.00 4.45
5069 6290 8.706492 AAGCACATAAATGTCATATGTTTTGG 57.294 30.769 1.90 2.80 40.96 3.28
5175 6396 7.439108 ACAGTAAAAGGAGCATAGGAAGTAT 57.561 36.000 0.00 0.00 0.00 2.12
5181 6402 5.940470 ACTCAAACAGTAAAAGGAGCATAGG 59.060 40.000 0.00 0.00 31.37 2.57
5182 6403 6.621596 GCACTCAAACAGTAAAAGGAGCATAG 60.622 42.308 0.00 0.00 32.21 2.23
5229 6456 7.458677 GCATAAGCAAAGAATTGTGAAATTCC 58.541 34.615 7.41 0.00 38.97 3.01
5254 6481 8.017373 ACGAAATACTCAACAGACAATGAAATG 58.983 33.333 0.00 0.00 0.00 2.32
5261 6488 6.220201 TGATCACGAAATACTCAACAGACAA 58.780 36.000 0.00 0.00 0.00 3.18
5262 6489 5.778862 TGATCACGAAATACTCAACAGACA 58.221 37.500 0.00 0.00 0.00 3.41
5287 6514 2.548057 TCAATCTCAGAAAACGGTGCAC 59.452 45.455 8.80 8.80 0.00 4.57
5318 6545 1.134367 TCTGTCATCGTAAGCTTCCCG 59.866 52.381 0.00 7.22 37.18 5.14
5384 6621 5.186198 ACTGTAATATTTCTGGCGCTTTCT 58.814 37.500 7.64 0.00 0.00 2.52
5445 6684 2.178106 AGAGGTGGAGGAACGGATAGAT 59.822 50.000 0.00 0.00 0.00 1.98


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

AutoCloner maintained by Alex Coulton.