Multiple sequence alignment - TraesCS6B01G468400

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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 TraesCS6B01G468400 chr6B 100.000 3047 0 0 1 3047 717905489 717902443 0.000000e+00 5627.0
1 TraesCS6B01G468400 chr6B 89.551 1158 108 6 966 2113 717953491 717954645 0.000000e+00 1456.0
2 TraesCS6B01G468400 chr6B 84.507 426 57 7 2559 2978 717956061 717956483 2.190000e-111 412.0
3 TraesCS6B01G468400 chr6B 95.429 175 8 0 2130 2304 95349579 95349405 2.310000e-71 279.0
4 TraesCS6B01G468400 chr6B 79.602 402 71 7 1001 1392 713176654 713177054 8.320000e-71 278.0
5 TraesCS6B01G468400 chr6B 78.973 409 73 9 1001 1398 713788515 713788109 1.800000e-67 267.0
6 TraesCS6B01G468400 chr6B 92.647 68 4 1 820 886 718911463 718911530 2.500000e-16 97.1
7 TraesCS6B01G468400 chr6D 96.719 1524 42 2 617 2137 472755486 472753968 0.000000e+00 2531.0
8 TraesCS6B01G468400 chr6D 86.754 838 83 10 1280 2111 472828070 472828885 0.000000e+00 907.0
9 TraesCS6B01G468400 chr6D 98.718 468 6 0 2559 3026 472753677 472753210 0.000000e+00 832.0
10 TraesCS6B01G468400 chr6D 96.691 272 4 3 2296 2566 472753971 472753704 5.990000e-122 448.0
11 TraesCS6B01G468400 chr6D 92.857 196 4 2 392 577 472756038 472755843 2.990000e-70 276.0
12 TraesCS6B01G468400 chr6D 91.160 181 7 2 1 173 472756259 472756080 1.410000e-58 237.0
13 TraesCS6B01G468400 chr6D 96.939 98 3 0 2950 3047 472753238 472753141 6.760000e-37 165.0
14 TraesCS6B01G468400 chr7D 90.087 1150 99 8 970 2111 20941948 20940806 0.000000e+00 1478.0
15 TraesCS6B01G468400 chr7D 96.970 165 5 0 2134 2298 193241975 193241811 8.320000e-71 278.0
16 TraesCS6B01G468400 chr1A 78.558 541 107 6 1500 2037 10490268 10489734 6.250000e-92 348.0
17 TraesCS6B01G468400 chr1A 95.161 62 3 0 292 353 497187237 497187176 6.950000e-17 99.0
18 TraesCS6B01G468400 chr5B 79.851 402 67 9 1001 1392 25335795 25335398 6.430000e-72 281.0
19 TraesCS6B01G468400 chr5B 74.146 410 87 13 1001 1396 97459593 97459997 5.260000e-33 152.0
20 TraesCS6B01G468400 chr5B 78.641 206 38 4 2744 2949 25332736 25332537 6.850000e-27 132.0
21 TraesCS6B01G468400 chr5D 96.988 166 5 0 2132 2297 198477386 198477551 2.310000e-71 279.0
22 TraesCS6B01G468400 chr5D 75.184 407 80 15 1001 1392 92110357 92110757 4.040000e-39 172.0
23 TraesCS6B01G468400 chr5D 95.161 62 3 0 292 353 526868053 526867992 6.950000e-17 99.0
24 TraesCS6B01G468400 chr3B 94.382 178 10 0 2134 2311 523154373 523154196 1.080000e-69 274.0
25 TraesCS6B01G468400 chr3B 95.161 62 3 0 292 353 829944396 829944457 6.950000e-17 99.0
26 TraesCS6B01G468400 chr3B 95.161 62 3 0 292 353 829966125 829966186 6.950000e-17 99.0
27 TraesCS6B01G468400 chr3B 95.161 62 3 0 292 353 830063616 830063677 6.950000e-17 99.0
28 TraesCS6B01G468400 chr7B 93.889 180 11 0 2134 2313 588875583 588875762 3.870000e-69 272.0
29 TraesCS6B01G468400 chr7B 80.645 155 22 7 2747 2897 750609835 750609685 2.480000e-21 113.0
30 TraesCS6B01G468400 chr7B 79.114 158 25 7 2744 2897 750411542 750411695 5.370000e-18 102.0
31 TraesCS6B01G468400 chr2B 94.857 175 8 1 2131 2304 540428258 540428432 3.870000e-69 272.0
32 TraesCS6B01G468400 chr5A 95.322 171 7 1 2134 2303 44602736 44602566 1.390000e-68 270.0
33 TraesCS6B01G468400 chr5A 75.366 410 82 14 1001 1396 85780179 85780583 2.410000e-41 180.0
34 TraesCS6B01G468400 chr3A 94.828 174 8 1 2124 2297 103676391 103676219 1.390000e-68 270.0
35 TraesCS6B01G468400 chr4B 93.370 181 11 1 2133 2312 117279292 117279112 1.800000e-67 267.0
36 TraesCS6B01G468400 chr1B 76.715 481 105 4 1559 2037 13390964 13390489 8.380000e-66 261.0
37 TraesCS6B01G468400 chr1B 76.507 481 106 4 1559 2037 13416676 13416201 3.900000e-64 255.0
38 TraesCS6B01G468400 chrUn 76.299 481 107 4 1559 2037 439715375 439714900 1.810000e-62 250.0
39 TraesCS6B01G468400 chr1D 75.565 487 103 15 1555 2035 9090819 9090343 3.060000e-55 226.0
40 TraesCS6B01G468400 chr7A 95.161 62 3 0 292 353 700332356 700332417 6.950000e-17 99.0
41 TraesCS6B01G468400 chr7A 95.161 62 3 0 292 353 726506793 726506854 6.950000e-17 99.0
42 TraesCS6B01G468400 chr3D 95.161 62 3 0 292 353 47491307 47491246 6.950000e-17 99.0
43 TraesCS6B01G468400 chr2D 95.161 62 3 0 292 353 586154926 586154865 6.950000e-17 99.0


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 TraesCS6B01G468400 chr6B 717902443 717905489 3046 True 5627.000000 5627 100.000 1 3047 1 chr6B.!!$R3 3046
1 TraesCS6B01G468400 chr6B 717953491 717956483 2992 False 934.000000 1456 87.029 966 2978 2 chr6B.!!$F3 2012
2 TraesCS6B01G468400 chr6D 472828070 472828885 815 False 907.000000 907 86.754 1280 2111 1 chr6D.!!$F1 831
3 TraesCS6B01G468400 chr6D 472753141 472756259 3118 True 748.166667 2531 95.514 1 3047 6 chr6D.!!$R1 3046
4 TraesCS6B01G468400 chr7D 20940806 20941948 1142 True 1478.000000 1478 90.087 970 2111 1 chr7D.!!$R1 1141
5 TraesCS6B01G468400 chr1A 10489734 10490268 534 True 348.000000 348 78.558 1500 2037 1 chr1A.!!$R1 537
6 TraesCS6B01G468400 chr5B 25332537 25335795 3258 True 206.500000 281 79.246 1001 2949 2 chr5B.!!$R1 1948

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
366 375 0.036022 AGCACTGAGGGACAAGCTTC 59.964 55.0 0.00 0.00 36.85 3.86 F
367 376 0.250467 GCACTGAGGGACAAGCTTCA 60.250 55.0 0.00 0.00 0.00 3.02 F
385 394 0.517316 CAAGCTTTTTCGGACCGAGG 59.483 55.0 17.51 9.83 37.14 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1865 3157 1.173043 GCACATTTTGACCCGATCCA 58.827 50.000 0.0 0.0 0.0 3.41 R
1880 3172 1.895798 TGTTGTTGTTTGGGAAGCACA 59.104 42.857 0.0 0.0 0.0 4.57 R
2233 3601 2.823747 ACAAGTGACTACATACGGAGCA 59.176 45.455 0.0 0.0 0.0 4.26 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
55 56 7.945134 AGGATAAAACCAGATATTGCATGTTC 58.055 34.615 0.00 0.00 0.00 3.18
102 103 4.935205 GGACTAGATTGTATGCAACACACA 59.065 41.667 0.00 0.00 38.00 3.72
115 116 2.490328 ACACACAAACATTTCCGCTG 57.510 45.000 0.00 0.00 0.00 5.18
174 183 3.506096 CTGTACGCCGCCTCGAGA 61.506 66.667 15.71 0.00 0.00 4.04
175 184 3.047718 CTGTACGCCGCCTCGAGAA 62.048 63.158 15.71 0.00 0.00 2.87
176 185 2.180017 GTACGCCGCCTCGAGAAA 59.820 61.111 15.71 0.00 0.00 2.52
177 186 1.444895 GTACGCCGCCTCGAGAAAA 60.445 57.895 15.71 0.00 0.00 2.29
178 187 1.010419 GTACGCCGCCTCGAGAAAAA 61.010 55.000 15.71 0.00 0.00 1.94
240 249 2.430921 CGACTGACTCGCACCACC 60.431 66.667 0.00 0.00 35.06 4.61
241 250 2.920645 CGACTGACTCGCACCACCT 61.921 63.158 0.00 0.00 35.06 4.00
242 251 1.080434 GACTGACTCGCACCACCTC 60.080 63.158 0.00 0.00 0.00 3.85
243 252 2.262915 CTGACTCGCACCACCTCC 59.737 66.667 0.00 0.00 0.00 4.30
244 253 2.203640 TGACTCGCACCACCTCCT 60.204 61.111 0.00 0.00 0.00 3.69
245 254 2.219325 CTGACTCGCACCACCTCCTC 62.219 65.000 0.00 0.00 0.00 3.71
246 255 2.997897 ACTCGCACCACCTCCTCC 60.998 66.667 0.00 0.00 0.00 4.30
247 256 3.775654 CTCGCACCACCTCCTCCC 61.776 72.222 0.00 0.00 0.00 4.30
248 257 4.631740 TCGCACCACCTCCTCCCA 62.632 66.667 0.00 0.00 0.00 4.37
249 258 3.636231 CGCACCACCTCCTCCCAA 61.636 66.667 0.00 0.00 0.00 4.12
250 259 2.352805 GCACCACCTCCTCCCAAG 59.647 66.667 0.00 0.00 0.00 3.61
251 260 2.352805 CACCACCTCCTCCCAAGC 59.647 66.667 0.00 0.00 0.00 4.01
252 261 2.936032 ACCACCTCCTCCCAAGCC 60.936 66.667 0.00 0.00 0.00 4.35
253 262 4.101448 CCACCTCCTCCCAAGCCG 62.101 72.222 0.00 0.00 0.00 5.52
254 263 4.101448 CACCTCCTCCCAAGCCGG 62.101 72.222 0.00 0.00 0.00 6.13
273 282 3.400599 ATTGCACCGACCCCCGATC 62.401 63.158 0.00 0.00 41.76 3.69
279 288 3.209318 CGACCCCCGATCGGTAAA 58.791 61.111 31.22 0.00 41.76 2.01
294 303 8.027771 CCGATCGGTAAATAATAAGCTCTTACT 58.972 37.037 26.35 0.00 0.00 2.24
295 304 9.063739 CGATCGGTAAATAATAAGCTCTTACTC 57.936 37.037 7.38 0.00 0.00 2.59
296 305 9.356433 GATCGGTAAATAATAAGCTCTTACTCC 57.644 37.037 0.00 0.00 0.00 3.85
297 306 7.664758 TCGGTAAATAATAAGCTCTTACTCCC 58.335 38.462 0.00 0.00 0.00 4.30
298 307 7.508296 TCGGTAAATAATAAGCTCTTACTCCCT 59.492 37.037 0.00 0.00 0.00 4.20
299 308 7.813627 CGGTAAATAATAAGCTCTTACTCCCTC 59.186 40.741 0.00 0.00 0.00 4.30
300 309 8.095792 GGTAAATAATAAGCTCTTACTCCCTCC 58.904 40.741 0.00 0.00 0.00 4.30
301 310 7.691993 AAATAATAAGCTCTTACTCCCTCCA 57.308 36.000 0.00 0.00 0.00 3.86
302 311 7.880265 AATAATAAGCTCTTACTCCCTCCAT 57.120 36.000 0.00 0.00 0.00 3.41
303 312 5.816955 AATAAGCTCTTACTCCCTCCATC 57.183 43.478 0.00 0.00 0.00 3.51
304 313 2.095604 AGCTCTTACTCCCTCCATCC 57.904 55.000 0.00 0.00 0.00 3.51
305 314 0.676736 GCTCTTACTCCCTCCATCCG 59.323 60.000 0.00 0.00 0.00 4.18
306 315 1.754555 GCTCTTACTCCCTCCATCCGA 60.755 57.143 0.00 0.00 0.00 4.55
307 316 2.667470 CTCTTACTCCCTCCATCCGAA 58.333 52.381 0.00 0.00 0.00 4.30
308 317 3.031736 CTCTTACTCCCTCCATCCGAAA 58.968 50.000 0.00 0.00 0.00 3.46
309 318 3.446968 TCTTACTCCCTCCATCCGAAAA 58.553 45.455 0.00 0.00 0.00 2.29
310 319 3.841845 TCTTACTCCCTCCATCCGAAAAA 59.158 43.478 0.00 0.00 0.00 1.94
328 337 4.655762 AAAAACTTGTCCCAAGCTTCTC 57.344 40.909 0.00 0.00 0.00 2.87
329 338 3.584733 AAACTTGTCCCAAGCTTCTCT 57.415 42.857 0.00 0.00 0.00 3.10
330 339 2.849294 ACTTGTCCCAAGCTTCTCTC 57.151 50.000 0.00 0.00 0.00 3.20
331 340 2.334023 ACTTGTCCCAAGCTTCTCTCT 58.666 47.619 0.00 0.00 0.00 3.10
332 341 2.301583 ACTTGTCCCAAGCTTCTCTCTC 59.698 50.000 0.00 0.00 0.00 3.20
333 342 2.015456 TGTCCCAAGCTTCTCTCTCA 57.985 50.000 0.00 0.00 0.00 3.27
334 343 2.329267 TGTCCCAAGCTTCTCTCTCAA 58.671 47.619 0.00 0.00 0.00 3.02
335 344 2.705658 TGTCCCAAGCTTCTCTCTCAAA 59.294 45.455 0.00 0.00 0.00 2.69
336 345 3.328931 TGTCCCAAGCTTCTCTCTCAAAT 59.671 43.478 0.00 0.00 0.00 2.32
337 346 3.688673 GTCCCAAGCTTCTCTCTCAAATG 59.311 47.826 0.00 0.00 0.00 2.32
338 347 3.015327 CCCAAGCTTCTCTCTCAAATGG 58.985 50.000 0.00 0.00 0.00 3.16
339 348 3.307975 CCCAAGCTTCTCTCTCAAATGGA 60.308 47.826 0.00 0.00 0.00 3.41
340 349 4.525024 CCAAGCTTCTCTCTCAAATGGAT 58.475 43.478 0.00 0.00 0.00 3.41
341 350 4.335874 CCAAGCTTCTCTCTCAAATGGATG 59.664 45.833 0.00 0.00 0.00 3.51
342 351 4.840716 AGCTTCTCTCTCAAATGGATGT 57.159 40.909 0.00 0.00 0.00 3.06
343 352 5.946942 AGCTTCTCTCTCAAATGGATGTA 57.053 39.130 0.00 0.00 0.00 2.29
344 353 6.497624 AGCTTCTCTCTCAAATGGATGTAT 57.502 37.500 0.00 0.00 0.00 2.29
345 354 6.523840 AGCTTCTCTCTCAAATGGATGTATC 58.476 40.000 0.00 0.00 0.00 2.24
346 355 6.327104 AGCTTCTCTCTCAAATGGATGTATCT 59.673 38.462 0.00 0.00 0.00 1.98
347 356 7.508636 AGCTTCTCTCTCAAATGGATGTATCTA 59.491 37.037 0.00 0.00 0.00 1.98
348 357 7.814107 GCTTCTCTCTCAAATGGATGTATCTAG 59.186 40.741 0.00 0.00 0.00 2.43
349 358 7.225784 TCTCTCTCAAATGGATGTATCTAGC 57.774 40.000 0.00 0.00 0.00 3.42
350 359 6.779539 TCTCTCTCAAATGGATGTATCTAGCA 59.220 38.462 0.00 0.00 0.00 3.49
351 360 6.753180 TCTCTCAAATGGATGTATCTAGCAC 58.247 40.000 0.00 0.00 0.00 4.40
352 361 6.552725 TCTCTCAAATGGATGTATCTAGCACT 59.447 38.462 0.00 0.00 0.00 4.40
353 362 6.519382 TCTCAAATGGATGTATCTAGCACTG 58.481 40.000 0.00 0.00 0.00 3.66
354 363 6.324770 TCTCAAATGGATGTATCTAGCACTGA 59.675 38.462 0.00 0.00 0.00 3.41
355 364 6.519382 TCAAATGGATGTATCTAGCACTGAG 58.481 40.000 0.00 0.00 0.00 3.35
356 365 5.480642 AATGGATGTATCTAGCACTGAGG 57.519 43.478 0.00 0.00 0.00 3.86
357 366 3.234353 TGGATGTATCTAGCACTGAGGG 58.766 50.000 0.00 0.00 0.00 4.30
358 367 3.117131 TGGATGTATCTAGCACTGAGGGA 60.117 47.826 0.00 0.00 0.00 4.20
359 368 3.257127 GGATGTATCTAGCACTGAGGGAC 59.743 52.174 0.00 0.00 0.00 4.46
360 369 3.382083 TGTATCTAGCACTGAGGGACA 57.618 47.619 0.00 0.00 0.00 4.02
361 370 3.708451 TGTATCTAGCACTGAGGGACAA 58.292 45.455 0.00 0.00 0.00 3.18
362 371 3.701542 TGTATCTAGCACTGAGGGACAAG 59.298 47.826 0.00 0.00 0.00 3.16
363 372 0.898320 TCTAGCACTGAGGGACAAGC 59.102 55.000 0.00 0.00 0.00 4.01
364 373 0.901124 CTAGCACTGAGGGACAAGCT 59.099 55.000 0.00 0.00 40.94 3.74
365 374 1.277557 CTAGCACTGAGGGACAAGCTT 59.722 52.381 0.00 0.00 39.48 3.74
366 375 0.036022 AGCACTGAGGGACAAGCTTC 59.964 55.000 0.00 0.00 36.85 3.86
367 376 0.250467 GCACTGAGGGACAAGCTTCA 60.250 55.000 0.00 0.00 0.00 3.02
368 377 1.815408 GCACTGAGGGACAAGCTTCAA 60.815 52.381 0.00 0.00 0.00 2.69
369 378 2.149578 CACTGAGGGACAAGCTTCAAG 58.850 52.381 0.00 0.00 0.00 3.02
370 379 1.163554 CTGAGGGACAAGCTTCAAGC 58.836 55.000 0.00 0.00 42.84 4.01
381 390 2.051879 GCTTCAAGCTTTTTCGGACC 57.948 50.000 0.71 0.00 38.45 4.46
382 391 1.663161 GCTTCAAGCTTTTTCGGACCG 60.663 52.381 7.84 7.84 38.45 4.79
383 392 1.871039 CTTCAAGCTTTTTCGGACCGA 59.129 47.619 13.88 13.88 0.00 4.69
384 393 1.508632 TCAAGCTTTTTCGGACCGAG 58.491 50.000 17.51 6.59 37.14 4.63
385 394 0.517316 CAAGCTTTTTCGGACCGAGG 59.483 55.000 17.51 9.83 37.14 4.63
386 395 0.605589 AAGCTTTTTCGGACCGAGGG 60.606 55.000 17.51 9.49 37.14 4.30
387 396 1.004200 GCTTTTTCGGACCGAGGGA 60.004 57.895 17.51 4.65 37.14 4.20
388 397 0.604511 GCTTTTTCGGACCGAGGGAA 60.605 55.000 17.51 10.60 37.14 3.97
389 398 1.949079 GCTTTTTCGGACCGAGGGAAT 60.949 52.381 17.51 0.00 37.14 3.01
390 399 2.678769 GCTTTTTCGGACCGAGGGAATA 60.679 50.000 17.51 3.42 37.14 1.75
475 484 6.433404 GGATCTGCCACAATCTATCAATCAAT 59.567 38.462 0.00 0.00 36.34 2.57
564 582 5.049954 TGCAAATGTTTACTCCAGTTCGTAC 60.050 40.000 0.00 0.00 0.00 3.67
571 841 1.073216 CTCCAGTTCGTACGCTGCTG 61.073 60.000 11.24 16.59 0.00 4.41
574 844 1.202256 CCAGTTCGTACGCTGCTGATA 60.202 52.381 24.46 0.87 0.00 2.15
576 846 2.531912 CAGTTCGTACGCTGCTGATAAG 59.468 50.000 20.77 2.28 0.00 1.73
580 850 1.927174 CGTACGCTGCTGATAAGCTTT 59.073 47.619 3.20 0.00 38.57 3.51
585 855 6.074516 CGTACGCTGCTGATAAGCTTTATTTA 60.075 38.462 3.20 0.00 38.57 1.40
586 856 6.867662 ACGCTGCTGATAAGCTTTATTTAT 57.132 33.333 3.20 0.00 38.57 1.40
587 857 7.264373 ACGCTGCTGATAAGCTTTATTTATT 57.736 32.000 3.20 0.00 38.57 1.40
589 859 8.190784 ACGCTGCTGATAAGCTTTATTTATTTT 58.809 29.630 3.20 0.00 38.57 1.82
593 863 9.097257 TGCTGATAAGCTTTATTTATTTTTGCC 57.903 29.630 3.20 0.00 35.49 4.52
594 864 9.097257 GCTGATAAGCTTTATTTATTTTTGCCA 57.903 29.630 3.20 0.00 0.00 4.92
599 869 7.075674 AGCTTTATTTATTTTTGCCATGTGC 57.924 32.000 0.00 0.00 41.77 4.57
748 1084 3.567585 TCAATTGATGTTTGCCTCGACAA 59.432 39.130 3.38 0.00 0.00 3.18
749 1085 3.837213 ATTGATGTTTGCCTCGACAAG 57.163 42.857 0.00 0.00 0.00 3.16
856 1192 6.405731 GGCAACATGAGGAATAAAGCAACATA 60.406 38.462 0.00 0.00 0.00 2.29
927 1263 3.362399 ATCTCCTCTGCACGCACCG 62.362 63.158 0.00 0.00 0.00 4.94
951 1287 4.275838 CCTCGTAGGTTACTCTCTTTCG 57.724 50.000 0.00 0.00 0.00 3.46
968 1304 0.685097 TCGCTATTATCCCCCACAGC 59.315 55.000 0.00 0.00 0.00 4.40
1465 2737 1.374343 ATCTGCAGCAGCGTCAATGG 61.374 55.000 18.43 0.00 46.23 3.16
1468 2740 0.605050 TGCAGCAGCGTCAATGGTTA 60.605 50.000 0.00 0.00 46.23 2.85
1865 3157 2.320781 CCTATCCACCATCGAGGAGTT 58.679 52.381 0.00 0.00 41.22 3.01
1880 3172 2.308866 AGGAGTTGGATCGGGTCAAAAT 59.691 45.455 0.00 0.00 0.00 1.82
2148 3516 4.701651 AAAATATACTCCCTCCGTTCCC 57.298 45.455 0.00 0.00 0.00 3.97
2150 3518 2.077687 TATACTCCCTCCGTTCCCAC 57.922 55.000 0.00 0.00 0.00 4.61
2154 3522 1.344087 ACTCCCTCCGTTCCCACATAT 60.344 52.381 0.00 0.00 0.00 1.78
2155 3523 1.768870 CTCCCTCCGTTCCCACATATT 59.231 52.381 0.00 0.00 0.00 1.28
2158 3526 2.356741 CCCTCCGTTCCCACATATTTGT 60.357 50.000 0.00 0.00 36.15 2.83
2160 3528 3.370527 CCTCCGTTCCCACATATTTGTCT 60.371 47.826 0.00 0.00 32.34 3.41
2161 3529 4.261801 CTCCGTTCCCACATATTTGTCTT 58.738 43.478 0.00 0.00 32.34 3.01
2162 3530 4.658063 TCCGTTCCCACATATTTGTCTTT 58.342 39.130 0.00 0.00 32.34 2.52
2163 3531 4.698304 TCCGTTCCCACATATTTGTCTTTC 59.302 41.667 0.00 0.00 32.34 2.62
2164 3532 4.700213 CCGTTCCCACATATTTGTCTTTCT 59.300 41.667 0.00 0.00 32.34 2.52
2165 3533 5.878116 CCGTTCCCACATATTTGTCTTTCTA 59.122 40.000 0.00 0.00 32.34 2.10
2166 3534 6.037172 CCGTTCCCACATATTTGTCTTTCTAG 59.963 42.308 0.00 0.00 32.34 2.43
2167 3535 6.037172 CGTTCCCACATATTTGTCTTTCTAGG 59.963 42.308 0.00 0.00 32.34 3.02
2168 3536 5.437060 TCCCACATATTTGTCTTTCTAGGC 58.563 41.667 0.00 0.00 32.34 3.93
2169 3537 5.045213 TCCCACATATTTGTCTTTCTAGGCA 60.045 40.000 0.00 0.00 33.22 4.75
2170 3538 5.829924 CCCACATATTTGTCTTTCTAGGCAT 59.170 40.000 0.00 0.00 35.56 4.40
2171 3539 6.322201 CCCACATATTTGTCTTTCTAGGCATT 59.678 38.462 0.00 0.00 35.56 3.56
2173 3541 7.917505 CCACATATTTGTCTTTCTAGGCATTTC 59.082 37.037 0.00 0.00 35.56 2.17
2178 3546 8.767478 ATTTGTCTTTCTAGGCATTTCAAATG 57.233 30.769 5.68 5.68 35.56 2.32
2179 3547 6.271488 TGTCTTTCTAGGCATTTCAAATGG 57.729 37.500 12.14 0.00 29.10 3.16
2180 3548 6.009589 TGTCTTTCTAGGCATTTCAAATGGA 58.990 36.000 12.14 0.00 29.10 3.41
2181 3549 6.071952 TGTCTTTCTAGGCATTTCAAATGGAC 60.072 38.462 12.14 8.23 29.10 4.02
2186 3554 3.993920 AGGCATTTCAAATGGACACAAC 58.006 40.909 12.14 0.00 0.00 3.32
2187 3555 3.387374 AGGCATTTCAAATGGACACAACA 59.613 39.130 12.14 0.00 0.00 3.33
2189 3557 5.245751 AGGCATTTCAAATGGACACAACATA 59.754 36.000 12.14 0.00 0.00 2.29
2190 3558 5.348451 GGCATTTCAAATGGACACAACATAC 59.652 40.000 12.14 0.00 0.00 2.39
2191 3559 5.060816 GCATTTCAAATGGACACAACATACG 59.939 40.000 12.14 0.00 0.00 3.06
2192 3560 4.757799 TTCAAATGGACACAACATACGG 57.242 40.909 0.00 0.00 0.00 4.02
2193 3561 4.009370 TCAAATGGACACAACATACGGA 57.991 40.909 0.00 0.00 0.00 4.69
2194 3562 4.584874 TCAAATGGACACAACATACGGAT 58.415 39.130 0.00 0.00 0.00 4.18
2195 3563 4.394610 TCAAATGGACACAACATACGGATG 59.605 41.667 5.94 5.94 39.16 3.51
2197 3565 4.746535 ATGGACACAACATACGGATGTA 57.253 40.909 15.10 0.00 45.93 2.29
2198 3566 4.746535 TGGACACAACATACGGATGTAT 57.253 40.909 15.10 2.23 45.93 2.29
2215 3583 9.909644 ACGGATGTATGTAGACATATTTTAGAC 57.090 33.333 5.69 0.00 40.18 2.59
2235 3603 6.734104 AGACTGTAGATTCACTCATTTTGC 57.266 37.500 0.00 0.00 0.00 3.68
2236 3604 6.471146 AGACTGTAGATTCACTCATTTTGCT 58.529 36.000 0.00 0.00 0.00 3.91
2237 3605 6.593382 AGACTGTAGATTCACTCATTTTGCTC 59.407 38.462 0.00 0.00 0.00 4.26
2238 3606 5.645497 ACTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 0.00 4.70
2239 3607 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
2240 3608 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
2241 3609 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
2242 3610 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
2243 3611 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
2244 3612 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
2245 3613 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
2246 3614 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
2247 3615 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
2248 3616 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
2249 3617 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
2250 3618 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
2251 3619 4.530710 TTTTGCTCCGTATGTAGTCACT 57.469 40.909 0.00 0.00 0.00 3.41
2252 3620 4.530710 TTTGCTCCGTATGTAGTCACTT 57.469 40.909 0.00 0.00 0.00 3.16
2253 3621 3.503827 TGCTCCGTATGTAGTCACTTG 57.496 47.619 0.00 0.00 0.00 3.16
2254 3622 2.823747 TGCTCCGTATGTAGTCACTTGT 59.176 45.455 0.00 0.00 0.00 3.16
2255 3623 3.257375 TGCTCCGTATGTAGTCACTTGTT 59.743 43.478 0.00 0.00 0.00 2.83
2256 3624 3.612860 GCTCCGTATGTAGTCACTTGTTG 59.387 47.826 0.00 0.00 0.00 3.33
2257 3625 4.617530 GCTCCGTATGTAGTCACTTGTTGA 60.618 45.833 0.00 0.00 0.00 3.18
2258 3626 5.456548 TCCGTATGTAGTCACTTGTTGAA 57.543 39.130 0.00 0.00 35.39 2.69
2259 3627 5.845103 TCCGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
2260 3628 6.460781 TCCGTATGTAGTCACTTGTTGAAAT 58.539 36.000 0.00 0.00 35.39 2.17
2261 3629 6.588756 TCCGTATGTAGTCACTTGTTGAAATC 59.411 38.462 0.00 0.00 35.39 2.17
2262 3630 6.590292 CCGTATGTAGTCACTTGTTGAAATCT 59.410 38.462 0.00 0.00 35.39 2.40
2263 3631 7.201444 CCGTATGTAGTCACTTGTTGAAATCTC 60.201 40.741 0.00 0.00 35.39 2.75
2264 3632 7.542477 CGTATGTAGTCACTTGTTGAAATCTCT 59.458 37.037 0.00 0.00 35.39 3.10
2265 3633 9.856488 GTATGTAGTCACTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 35.39 2.43
2266 3634 8.994429 ATGTAGTCACTTGTTGAAATCTCTAG 57.006 34.615 0.00 0.00 35.39 2.43
2267 3635 8.178313 TGTAGTCACTTGTTGAAATCTCTAGA 57.822 34.615 0.00 0.00 35.39 2.43
2268 3636 8.638873 TGTAGTCACTTGTTGAAATCTCTAGAA 58.361 33.333 0.00 0.00 35.39 2.10
2271 3639 8.424918 AGTCACTTGTTGAAATCTCTAGAAAGA 58.575 33.333 0.00 0.00 35.39 2.52
2274 3642 8.830580 CACTTGTTGAAATCTCTAGAAAGACAA 58.169 33.333 0.00 0.00 0.00 3.18
2275 3643 9.396022 ACTTGTTGAAATCTCTAGAAAGACAAA 57.604 29.630 0.00 0.00 0.00 2.83
2298 3666 7.698163 AATATTTGAGAATGGAGGGAGTACT 57.302 36.000 0.00 0.00 0.00 2.73
2468 4856 2.792878 TGGAATGTGATGTGCATGTCA 58.207 42.857 0.00 0.00 0.00 3.58
2487 4875 6.582677 TGTCATACATAAACCCCTGTTTTG 57.417 37.500 0.00 0.00 41.92 2.44
2498 4886 6.487299 AACCCCTGTTTTGCAAGTTAATTA 57.513 33.333 0.00 0.00 0.00 1.40
2499 4887 5.849510 ACCCCTGTTTTGCAAGTTAATTAC 58.150 37.500 0.00 0.00 0.00 1.89
3005 5649 4.087892 GCTCTCGCCCCTGCAAGA 62.088 66.667 0.00 0.00 37.32 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 69 9.579768 GCATACAATCTAGTCCATATTACAGAG 57.420 37.037 0.00 0.00 0.00 3.35
102 103 7.657336 CCATATTATTACCAGCGGAAATGTTT 58.343 34.615 1.50 0.00 0.00 2.83
115 116 5.137551 AGTGTGGGTTGCCATATTATTACC 58.862 41.667 0.00 0.00 0.00 2.85
157 166 2.537792 TTTCTCGAGGCGGCGTACAG 62.538 60.000 13.56 0.00 0.00 2.74
175 184 0.958876 GACTCCGGCCGGTCATTTTT 60.959 55.000 41.57 19.59 36.47 1.94
176 185 1.376812 GACTCCGGCCGGTCATTTT 60.377 57.895 41.57 21.00 36.47 1.82
177 186 2.267961 GACTCCGGCCGGTCATTT 59.732 61.111 41.57 22.79 36.47 2.32
178 187 2.683933 AGACTCCGGCCGGTCATT 60.684 61.111 41.57 24.61 35.18 2.57
179 188 3.461773 CAGACTCCGGCCGGTCAT 61.462 66.667 41.57 28.21 35.18 3.06
224 233 1.080434 GAGGTGGTGCGAGTCAGTC 60.080 63.158 0.00 0.00 0.00 3.51
225 234 2.574955 GGAGGTGGTGCGAGTCAGT 61.575 63.158 0.00 0.00 0.00 3.41
226 235 2.219325 GAGGAGGTGGTGCGAGTCAG 62.219 65.000 0.00 0.00 0.00 3.51
227 236 2.203640 AGGAGGTGGTGCGAGTCA 60.204 61.111 0.00 0.00 0.00 3.41
228 237 2.574399 GAGGAGGTGGTGCGAGTC 59.426 66.667 0.00 0.00 0.00 3.36
229 238 2.997897 GGAGGAGGTGGTGCGAGT 60.998 66.667 0.00 0.00 0.00 4.18
230 239 3.775654 GGGAGGAGGTGGTGCGAG 61.776 72.222 0.00 0.00 0.00 5.03
231 240 4.631740 TGGGAGGAGGTGGTGCGA 62.632 66.667 0.00 0.00 0.00 5.10
232 241 3.612247 CTTGGGAGGAGGTGGTGCG 62.612 68.421 0.00 0.00 0.00 5.34
233 242 2.352805 CTTGGGAGGAGGTGGTGC 59.647 66.667 0.00 0.00 0.00 5.01
234 243 2.352805 GCTTGGGAGGAGGTGGTG 59.647 66.667 0.00 0.00 0.00 4.17
235 244 2.936032 GGCTTGGGAGGAGGTGGT 60.936 66.667 0.00 0.00 0.00 4.16
236 245 4.101448 CGGCTTGGGAGGAGGTGG 62.101 72.222 0.00 0.00 0.00 4.61
237 246 4.101448 CCGGCTTGGGAGGAGGTG 62.101 72.222 0.00 0.00 0.00 4.00
238 247 3.642741 ATCCGGCTTGGGAGGAGGT 62.643 63.158 0.00 0.00 40.02 3.85
239 248 2.378634 AATCCGGCTTGGGAGGAGG 61.379 63.158 0.00 0.00 40.02 4.30
240 249 1.153086 CAATCCGGCTTGGGAGGAG 60.153 63.158 10.25 0.00 40.02 3.69
241 250 2.998097 CAATCCGGCTTGGGAGGA 59.002 61.111 10.25 0.00 40.02 3.71
242 251 2.830370 GCAATCCGGCTTGGGAGG 60.830 66.667 19.07 0.00 40.02 4.30
243 252 2.045045 TGCAATCCGGCTTGGGAG 60.045 61.111 19.07 0.00 40.02 4.30
244 253 2.361104 GTGCAATCCGGCTTGGGA 60.361 61.111 19.07 0.00 41.17 4.37
245 254 3.451894 GGTGCAATCCGGCTTGGG 61.452 66.667 19.07 0.00 38.76 4.12
246 255 3.814268 CGGTGCAATCCGGCTTGG 61.814 66.667 19.07 0.00 45.88 3.61
254 263 3.400599 ATCGGGGGTCGGTGCAATC 62.401 63.158 0.00 0.00 39.77 2.67
270 279 9.356433 GGAGTAAGAGCTTATTATTTACCGATC 57.644 37.037 0.00 0.00 0.00 3.69
273 282 7.668492 AGGGAGTAAGAGCTTATTATTTACCG 58.332 38.462 0.00 0.00 0.00 4.02
279 288 6.442244 GGATGGAGGGAGTAAGAGCTTATTAT 59.558 42.308 0.00 0.00 0.00 1.28
314 323 2.015456 TGAGAGAGAAGCTTGGGACA 57.985 50.000 2.10 0.00 0.00 4.02
315 324 3.409026 TTTGAGAGAGAAGCTTGGGAC 57.591 47.619 2.10 0.00 0.00 4.46
316 325 3.307975 CCATTTGAGAGAGAAGCTTGGGA 60.308 47.826 2.10 0.00 0.00 4.37
317 326 3.015327 CCATTTGAGAGAGAAGCTTGGG 58.985 50.000 2.10 0.00 0.00 4.12
318 327 3.947868 TCCATTTGAGAGAGAAGCTTGG 58.052 45.455 2.10 0.00 0.00 3.61
319 328 4.942483 ACATCCATTTGAGAGAGAAGCTTG 59.058 41.667 2.10 0.00 0.00 4.01
320 329 5.176741 ACATCCATTTGAGAGAGAAGCTT 57.823 39.130 0.00 0.00 0.00 3.74
321 330 4.840716 ACATCCATTTGAGAGAGAAGCT 57.159 40.909 0.00 0.00 0.00 3.74
322 331 6.523840 AGATACATCCATTTGAGAGAGAAGC 58.476 40.000 0.00 0.00 0.00 3.86
323 332 7.814107 GCTAGATACATCCATTTGAGAGAGAAG 59.186 40.741 0.00 0.00 0.00 2.85
324 333 7.288621 TGCTAGATACATCCATTTGAGAGAGAA 59.711 37.037 0.00 0.00 0.00 2.87
325 334 6.779539 TGCTAGATACATCCATTTGAGAGAGA 59.220 38.462 0.00 0.00 0.00 3.10
326 335 6.867816 GTGCTAGATACATCCATTTGAGAGAG 59.132 42.308 0.00 0.00 0.00 3.20
327 336 6.552725 AGTGCTAGATACATCCATTTGAGAGA 59.447 38.462 0.00 0.00 0.00 3.10
328 337 6.645827 CAGTGCTAGATACATCCATTTGAGAG 59.354 42.308 0.00 0.00 0.00 3.20
329 338 6.324770 TCAGTGCTAGATACATCCATTTGAGA 59.675 38.462 0.00 0.00 0.00 3.27
330 339 6.519382 TCAGTGCTAGATACATCCATTTGAG 58.481 40.000 0.00 0.00 0.00 3.02
331 340 6.463472 CCTCAGTGCTAGATACATCCATTTGA 60.463 42.308 0.00 0.00 0.00 2.69
332 341 5.699915 CCTCAGTGCTAGATACATCCATTTG 59.300 44.000 0.00 0.00 0.00 2.32
333 342 5.221803 CCCTCAGTGCTAGATACATCCATTT 60.222 44.000 0.00 0.00 0.00 2.32
334 343 4.285517 CCCTCAGTGCTAGATACATCCATT 59.714 45.833 0.00 0.00 0.00 3.16
335 344 3.837146 CCCTCAGTGCTAGATACATCCAT 59.163 47.826 0.00 0.00 0.00 3.41
336 345 3.117131 TCCCTCAGTGCTAGATACATCCA 60.117 47.826 0.00 0.00 0.00 3.41
337 346 3.257127 GTCCCTCAGTGCTAGATACATCC 59.743 52.174 0.00 0.00 0.00 3.51
338 347 3.891977 TGTCCCTCAGTGCTAGATACATC 59.108 47.826 0.00 0.00 0.00 3.06
339 348 3.916035 TGTCCCTCAGTGCTAGATACAT 58.084 45.455 0.00 0.00 0.00 2.29
340 349 3.382083 TGTCCCTCAGTGCTAGATACA 57.618 47.619 0.00 0.00 0.00 2.29
341 350 3.491792 GCTTGTCCCTCAGTGCTAGATAC 60.492 52.174 0.00 0.00 0.00 2.24
342 351 2.695666 GCTTGTCCCTCAGTGCTAGATA 59.304 50.000 0.00 0.00 0.00 1.98
343 352 1.484240 GCTTGTCCCTCAGTGCTAGAT 59.516 52.381 0.00 0.00 0.00 1.98
344 353 0.898320 GCTTGTCCCTCAGTGCTAGA 59.102 55.000 0.00 0.00 0.00 2.43
345 354 0.901124 AGCTTGTCCCTCAGTGCTAG 59.099 55.000 0.00 0.00 36.49 3.42
346 355 1.276421 GAAGCTTGTCCCTCAGTGCTA 59.724 52.381 2.10 0.00 36.95 3.49
347 356 0.036022 GAAGCTTGTCCCTCAGTGCT 59.964 55.000 2.10 0.00 38.54 4.40
348 357 0.250467 TGAAGCTTGTCCCTCAGTGC 60.250 55.000 2.10 0.00 0.00 4.40
349 358 2.149578 CTTGAAGCTTGTCCCTCAGTG 58.850 52.381 2.10 0.00 0.00 3.66
350 359 1.544314 GCTTGAAGCTTGTCCCTCAGT 60.544 52.381 10.44 0.00 38.45 3.41
351 360 1.163554 GCTTGAAGCTTGTCCCTCAG 58.836 55.000 10.44 0.00 38.45 3.35
352 361 3.329300 GCTTGAAGCTTGTCCCTCA 57.671 52.632 10.44 0.00 38.45 3.86
362 371 1.663161 CGGTCCGAAAAAGCTTGAAGC 60.663 52.381 9.59 9.59 42.84 3.86
363 372 1.871039 TCGGTCCGAAAAAGCTTGAAG 59.129 47.619 12.68 0.00 31.06 3.02
364 373 1.871039 CTCGGTCCGAAAAAGCTTGAA 59.129 47.619 16.23 0.00 34.74 2.69
365 374 1.508632 CTCGGTCCGAAAAAGCTTGA 58.491 50.000 16.23 0.00 34.74 3.02
366 375 0.517316 CCTCGGTCCGAAAAAGCTTG 59.483 55.000 16.23 0.47 34.74 4.01
367 376 0.605589 CCCTCGGTCCGAAAAAGCTT 60.606 55.000 16.23 0.00 34.74 3.74
368 377 1.003718 CCCTCGGTCCGAAAAAGCT 60.004 57.895 16.23 0.00 34.74 3.74
369 378 0.604511 TTCCCTCGGTCCGAAAAAGC 60.605 55.000 16.23 0.00 34.74 3.51
370 379 2.109425 ATTCCCTCGGTCCGAAAAAG 57.891 50.000 16.23 3.20 34.74 2.27
371 380 3.918294 ATATTCCCTCGGTCCGAAAAA 57.082 42.857 16.23 9.95 34.74 1.94
372 381 3.918294 AATATTCCCTCGGTCCGAAAA 57.082 42.857 16.23 10.31 34.74 2.29
373 382 3.918294 AAATATTCCCTCGGTCCGAAA 57.082 42.857 16.23 7.41 34.74 3.46
374 383 3.918294 AAAATATTCCCTCGGTCCGAA 57.082 42.857 16.23 0.00 34.74 4.30
375 384 3.918294 AAAAATATTCCCTCGGTCCGA 57.082 42.857 14.54 14.54 0.00 4.55
438 447 0.103208 GCAGATCCTGGAGTACACCG 59.897 60.000 1.52 0.13 31.21 4.94
475 484 3.440228 GCGTTGCCTTTGTTTTGAACTA 58.560 40.909 0.00 0.00 0.00 2.24
511 520 2.234908 AGGAAAATCTGTCTGTCTCCGG 59.765 50.000 0.00 0.00 0.00 5.14
574 844 7.529158 GCACATGGCAAAAATAAATAAAGCTT 58.471 30.769 0.00 0.00 43.97 3.74
591 861 2.433664 GCTGCCTTTGCACATGGC 60.434 61.111 14.70 14.70 44.23 4.40
592 862 1.080093 CTGCTGCCTTTGCACATGG 60.080 57.895 0.00 0.00 44.23 3.66
593 863 0.530744 ATCTGCTGCCTTTGCACATG 59.469 50.000 0.00 0.00 44.23 3.21
594 864 2.133281 TATCTGCTGCCTTTGCACAT 57.867 45.000 0.00 0.00 44.23 3.21
595 865 2.133281 ATATCTGCTGCCTTTGCACA 57.867 45.000 0.00 0.00 44.23 4.57
598 868 5.048504 TGCTTTATATATCTGCTGCCTTTGC 60.049 40.000 0.00 0.00 38.26 3.68
599 869 6.564709 TGCTTTATATATCTGCTGCCTTTG 57.435 37.500 0.00 0.00 0.00 2.77
600 870 6.547141 TGTTGCTTTATATATCTGCTGCCTTT 59.453 34.615 0.00 0.00 0.00 3.11
601 871 6.064060 TGTTGCTTTATATATCTGCTGCCTT 58.936 36.000 0.00 0.00 0.00 4.35
602 872 5.624159 TGTTGCTTTATATATCTGCTGCCT 58.376 37.500 0.00 0.00 0.00 4.75
603 873 5.947228 TGTTGCTTTATATATCTGCTGCC 57.053 39.130 0.00 0.00 0.00 4.85
604 874 6.728200 TGTTGTTGCTTTATATATCTGCTGC 58.272 36.000 0.00 0.00 0.00 5.25
605 875 7.012704 ACCTGTTGTTGCTTTATATATCTGCTG 59.987 37.037 0.00 0.00 0.00 4.41
606 876 7.056635 ACCTGTTGTTGCTTTATATATCTGCT 58.943 34.615 0.00 0.00 0.00 4.24
607 877 7.264373 ACCTGTTGTTGCTTTATATATCTGC 57.736 36.000 0.00 0.00 0.00 4.26
611 881 9.184523 TGCTTTACCTGTTGTTGCTTTATATAT 57.815 29.630 0.00 0.00 0.00 0.86
612 882 8.568676 TGCTTTACCTGTTGTTGCTTTATATA 57.431 30.769 0.00 0.00 0.00 0.86
613 883 7.461182 TGCTTTACCTGTTGTTGCTTTATAT 57.539 32.000 0.00 0.00 0.00 0.86
614 884 6.885952 TGCTTTACCTGTTGTTGCTTTATA 57.114 33.333 0.00 0.00 0.00 0.98
615 885 5.782893 TGCTTTACCTGTTGTTGCTTTAT 57.217 34.783 0.00 0.00 0.00 1.40
748 1084 2.611224 CGTGGTTAACGCCTTTACCTCT 60.611 50.000 0.00 0.00 46.99 3.69
749 1085 1.728425 CGTGGTTAACGCCTTTACCTC 59.272 52.381 0.00 1.68 46.99 3.85
856 1192 2.457813 TTGGCTTGGGCATCATATGT 57.542 45.000 1.90 0.00 38.08 2.29
889 1225 7.823310 AGGAGATGTTGATCTTGATATGTATGC 59.177 37.037 0.00 0.00 39.19 3.14
930 1266 3.487209 GCGAAAGAGAGTAACCTACGAGG 60.487 52.174 0.00 0.00 42.49 4.63
931 1267 3.374678 AGCGAAAGAGAGTAACCTACGAG 59.625 47.826 0.00 0.00 0.00 4.18
947 1283 2.486548 GCTGTGGGGGATAATAGCGAAA 60.487 50.000 0.00 0.00 0.00 3.46
948 1284 1.071699 GCTGTGGGGGATAATAGCGAA 59.928 52.381 0.00 0.00 0.00 4.70
949 1285 0.685097 GCTGTGGGGGATAATAGCGA 59.315 55.000 0.00 0.00 0.00 4.93
951 1287 0.038310 GGGCTGTGGGGGATAATAGC 59.962 60.000 0.00 0.00 0.00 2.97
968 1304 1.613437 GAGTTGTGGATTGGTTGTGGG 59.387 52.381 0.00 0.00 0.00 4.61
1110 1450 2.669133 CCCCGTGATGAAGGCCTGA 61.669 63.158 5.69 0.00 0.00 3.86
1314 1663 3.428589 GCTCTTTCATCTGATTTGCCACC 60.429 47.826 0.00 0.00 0.00 4.61
1465 2737 1.510480 GAGGCGCCATGGATGCTAAC 61.510 60.000 31.54 13.90 0.00 2.34
1468 2740 4.575973 GGAGGCGCCATGGATGCT 62.576 66.667 31.54 4.27 36.34 3.79
1793 3083 3.644966 TCACATACCCATCAAACTCCC 57.355 47.619 0.00 0.00 0.00 4.30
1865 3157 1.173043 GCACATTTTGACCCGATCCA 58.827 50.000 0.00 0.00 0.00 3.41
1880 3172 1.895798 TGTTGTTGTTTGGGAAGCACA 59.104 42.857 0.00 0.00 0.00 4.57
2148 3516 8.461222 TGAAATGCCTAGAAAGACAAATATGTG 58.539 33.333 0.00 0.00 40.74 3.21
2150 3518 9.859427 TTTGAAATGCCTAGAAAGACAAATATG 57.141 29.630 0.00 0.00 0.00 1.78
2154 3522 7.015098 TCCATTTGAAATGCCTAGAAAGACAAA 59.985 33.333 12.26 0.00 0.00 2.83
2155 3523 6.493115 TCCATTTGAAATGCCTAGAAAGACAA 59.507 34.615 12.26 0.00 0.00 3.18
2158 3526 6.009589 TGTCCATTTGAAATGCCTAGAAAGA 58.990 36.000 12.26 0.00 0.00 2.52
2160 3528 5.538053 TGTGTCCATTTGAAATGCCTAGAAA 59.462 36.000 12.26 0.00 0.00 2.52
2161 3529 5.076182 TGTGTCCATTTGAAATGCCTAGAA 58.924 37.500 12.26 0.00 0.00 2.10
2162 3530 4.661222 TGTGTCCATTTGAAATGCCTAGA 58.339 39.130 12.26 1.83 0.00 2.43
2163 3531 5.163513 GTTGTGTCCATTTGAAATGCCTAG 58.836 41.667 12.26 0.00 0.00 3.02
2164 3532 4.586421 TGTTGTGTCCATTTGAAATGCCTA 59.414 37.500 12.26 0.00 0.00 3.93
2165 3533 3.387374 TGTTGTGTCCATTTGAAATGCCT 59.613 39.130 12.26 0.00 0.00 4.75
2166 3534 3.726607 TGTTGTGTCCATTTGAAATGCC 58.273 40.909 12.26 5.75 0.00 4.40
2167 3535 5.060816 CGTATGTTGTGTCCATTTGAAATGC 59.939 40.000 12.26 0.87 0.00 3.56
2168 3536 5.572511 CCGTATGTTGTGTCCATTTGAAATG 59.427 40.000 10.84 10.84 0.00 2.32
2169 3537 5.475220 TCCGTATGTTGTGTCCATTTGAAAT 59.525 36.000 0.00 0.00 0.00 2.17
2170 3538 4.822350 TCCGTATGTTGTGTCCATTTGAAA 59.178 37.500 0.00 0.00 0.00 2.69
2171 3539 4.390264 TCCGTATGTTGTGTCCATTTGAA 58.610 39.130 0.00 0.00 0.00 2.69
2173 3541 4.155826 ACATCCGTATGTTGTGTCCATTTG 59.844 41.667 0.00 0.00 44.07 2.32
2189 3557 9.909644 GTCTAAAATATGTCTACATACATCCGT 57.090 33.333 4.98 0.00 41.15 4.69
2209 3577 8.721478 GCAAAATGAGTGAATCTACAGTCTAAA 58.279 33.333 0.00 0.00 39.91 1.85
2210 3578 8.097038 AGCAAAATGAGTGAATCTACAGTCTAA 58.903 33.333 0.00 0.00 39.91 2.10
2211 3579 7.615403 AGCAAAATGAGTGAATCTACAGTCTA 58.385 34.615 0.00 0.00 39.91 2.59
2212 3580 6.471146 AGCAAAATGAGTGAATCTACAGTCT 58.529 36.000 0.00 0.00 39.91 3.24
2213 3581 6.183360 GGAGCAAAATGAGTGAATCTACAGTC 60.183 42.308 0.00 0.00 39.73 3.51
2214 3582 5.645497 GGAGCAAAATGAGTGAATCTACAGT 59.355 40.000 0.00 0.00 0.00 3.55
2215 3583 5.220548 CGGAGCAAAATGAGTGAATCTACAG 60.221 44.000 0.00 0.00 0.00 2.74
2216 3584 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
2217 3585 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
2218 3586 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
2219 3587 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
2220 3588 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
2221 3589 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
2222 3590 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
2223 3591 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
2224 3592 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
2225 3593 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
2226 3594 5.005779 GTGACTACATACGGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
2227 3595 4.868171 GTGACTACATACGGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
2228 3596 4.870426 AGTGACTACATACGGAGCAAAATG 59.130 41.667 0.00 0.00 0.00 2.32
2229 3597 5.086104 AGTGACTACATACGGAGCAAAAT 57.914 39.130 0.00 0.00 0.00 1.82
2230 3598 4.530710 AGTGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
2231 3599 4.242475 CAAGTGACTACATACGGAGCAAA 58.758 43.478 0.00 0.00 0.00 3.68
2232 3600 3.257375 ACAAGTGACTACATACGGAGCAA 59.743 43.478 0.00 0.00 0.00 3.91
2233 3601 2.823747 ACAAGTGACTACATACGGAGCA 59.176 45.455 0.00 0.00 0.00 4.26
2234 3602 3.505464 ACAAGTGACTACATACGGAGC 57.495 47.619 0.00 0.00 0.00 4.70
2235 3603 5.055642 TCAACAAGTGACTACATACGGAG 57.944 43.478 0.00 0.00 0.00 4.63
2236 3604 5.456548 TTCAACAAGTGACTACATACGGA 57.543 39.130 0.00 0.00 35.39 4.69
2237 3605 6.590292 AGATTTCAACAAGTGACTACATACGG 59.410 38.462 0.00 0.00 35.39 4.02
2238 3606 7.542477 AGAGATTTCAACAAGTGACTACATACG 59.458 37.037 0.00 0.00 35.39 3.06
2239 3607 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
2241 3609 8.807118 TCTAGAGATTTCAACAAGTGACTACAT 58.193 33.333 0.00 0.00 35.39 2.29
2242 3610 8.178313 TCTAGAGATTTCAACAAGTGACTACA 57.822 34.615 0.00 0.00 35.39 2.74
2243 3611 9.477484 TTTCTAGAGATTTCAACAAGTGACTAC 57.523 33.333 0.00 0.00 35.39 2.73
2244 3612 9.698309 CTTTCTAGAGATTTCAACAAGTGACTA 57.302 33.333 0.00 0.00 35.39 2.59
2245 3613 8.424918 TCTTTCTAGAGATTTCAACAAGTGACT 58.575 33.333 0.00 0.00 35.39 3.41
2246 3614 8.491950 GTCTTTCTAGAGATTTCAACAAGTGAC 58.508 37.037 0.00 0.00 35.39 3.67
2247 3615 8.204160 TGTCTTTCTAGAGATTTCAACAAGTGA 58.796 33.333 0.00 0.00 0.00 3.41
2248 3616 8.370493 TGTCTTTCTAGAGATTTCAACAAGTG 57.630 34.615 0.00 0.00 0.00 3.16
2249 3617 8.964476 TTGTCTTTCTAGAGATTTCAACAAGT 57.036 30.769 0.00 0.00 0.00 3.16
2265 3633 8.964772 CCTCCATTCTCAAATATTTGTCTTTCT 58.035 33.333 23.95 6.52 39.18 2.52
2266 3634 8.193438 CCCTCCATTCTCAAATATTTGTCTTTC 58.807 37.037 23.95 0.00 39.18 2.62
2267 3635 7.895429 TCCCTCCATTCTCAAATATTTGTCTTT 59.105 33.333 23.95 8.74 39.18 2.52
2268 3636 7.413446 TCCCTCCATTCTCAAATATTTGTCTT 58.587 34.615 23.95 8.43 39.18 3.01
2271 3639 6.735556 ACTCCCTCCATTCTCAAATATTTGT 58.264 36.000 23.95 5.75 39.18 2.83
2274 3642 7.698163 AGTACTCCCTCCATTCTCAAATATT 57.302 36.000 0.00 0.00 0.00 1.28
2275 3643 7.570607 AGAAGTACTCCCTCCATTCTCAAATAT 59.429 37.037 0.00 0.00 0.00 1.28
2281 3649 5.894964 ACTAAGAAGTACTCCCTCCATTCTC 59.105 44.000 0.00 0.00 32.84 2.87
2282 3650 5.844601 ACTAAGAAGTACTCCCTCCATTCT 58.155 41.667 0.00 0.00 32.84 2.40
2468 4856 5.542251 ACTTGCAAAACAGGGGTTTATGTAT 59.458 36.000 0.00 0.00 46.20 2.29
2831 5475 1.335324 GCACAAGCACGCTTCTCAAAT 60.335 47.619 0.16 0.00 41.58 2.32


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

AutoCloner maintained by Alex Coulton.