Multiple sequence alignment - TraesCS6A01G209900

Loading Multiple Alignment...

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 TraesCS6A01G209900 chr6A 100.000 2894 0 0 1 2894 380363127 380360234 0.000000e+00 5345.0
1 TraesCS6A01G209900 chr6A 96.421 503 18 0 1419 1921 381026133 381025631 0.000000e+00 830.0
2 TraesCS6A01G209900 chr6A 91.971 137 11 0 1017 1153 381026350 381026214 2.940000e-45 193.0
3 TraesCS6A01G209900 chr6D 93.985 1596 59 13 520 2089 267238220 267236636 0.000000e+00 2381.0
4 TraesCS6A01G209900 chr6D 96.680 512 16 1 1410 1921 267515199 267514689 0.000000e+00 850.0
5 TraesCS6A01G209900 chr6D 90.998 511 20 9 2158 2654 267235133 267234635 0.000000e+00 665.0
6 TraesCS6A01G209900 chr6D 96.667 240 6 1 2655 2894 267234597 267234360 5.810000e-107 398.0
7 TraesCS6A01G209900 chr6D 91.852 135 11 0 1017 1151 267515402 267515268 3.810000e-44 189.0
8 TraesCS6A01G209900 chr6D 98.077 52 1 0 2110 2161 267235206 267235155 1.100000e-14 91.6
9 TraesCS6A01G209900 chr6D 100.000 32 0 0 2087 2118 267236608 267236577 3.110000e-05 60.2
10 TraesCS6A01G209900 chr6B 91.375 1542 53 20 571 2089 415790344 415788860 0.000000e+00 2037.0
11 TraesCS6A01G209900 chr6B 95.898 512 20 1 1410 1921 415864166 415863656 0.000000e+00 828.0
12 TraesCS6A01G209900 chr6B 96.047 430 12 2 2161 2589 415786936 415786511 0.000000e+00 695.0
13 TraesCS6A01G209900 chr6B 93.040 273 10 4 2628 2894 415786211 415785942 9.720000e-105 390.0
14 TraesCS6A01G209900 chr6B 94.531 128 7 0 1024 1151 415864360 415864233 6.330000e-47 198.0
15 TraesCS6A01G209900 chr6B 98.529 68 1 0 2092 2159 415787030 415786963 1.410000e-23 121.0
16 TraesCS6A01G209900 chr6B 95.918 49 2 0 536 584 415790406 415790358 2.390000e-11 80.5
17 TraesCS6A01G209900 chr4A 92.813 487 31 3 1410 1893 640232597 640233082 0.000000e+00 702.0
18 TraesCS6A01G209900 chr4A 86.965 537 51 13 1 522 352509391 352509923 1.160000e-163 586.0
19 TraesCS6A01G209900 chr4A 100.000 29 0 0 874 902 640232283 640232311 1.000000e-03 54.7
20 TraesCS6A01G209900 chr5D 92.857 476 31 2 1421 1893 531971707 531971232 0.000000e+00 688.0
21 TraesCS6A01G209900 chr5D 90.661 439 37 3 80 516 481940437 481940873 5.380000e-162 580.0
22 TraesCS6A01G209900 chr5D 85.581 534 60 13 1 520 6367672 6368202 7.050000e-151 544.0
23 TraesCS6A01G209900 chr5D 86.081 467 44 11 1422 1870 531901300 531900837 1.560000e-132 483.0
24 TraesCS6A01G209900 chr5D 91.241 137 12 0 1017 1153 531902146 531902010 1.370000e-43 187.0
25 TraesCS6A01G209900 chr5D 89.781 137 14 0 1017 1153 531971915 531971779 2.960000e-40 176.0
26 TraesCS6A01G209900 chr5D 100.000 30 0 0 873 902 531903675 531903646 4.030000e-04 56.5
27 TraesCS6A01G209900 chr5B 92.324 469 33 2 1431 1896 671188131 671187663 0.000000e+00 664.0
28 TraesCS6A01G209900 chr5B 91.971 137 11 0 1017 1153 671138053 671137917 2.940000e-45 193.0
29 TraesCS6A01G209900 chr5B 91.111 135 12 0 1019 1153 671188342 671188208 1.770000e-42 183.0
30 TraesCS6A01G209900 chr5B 94.595 37 2 0 874 910 671138165 671138129 1.120000e-04 58.4
31 TraesCS6A01G209900 chr7D 88.235 527 55 4 1 521 106975691 106976216 8.810000e-175 623.0
32 TraesCS6A01G209900 chr1A 87.594 532 54 7 3 527 53849496 53850022 8.870000e-170 606.0
33 TraesCS6A01G209900 chr4B 87.218 532 61 5 1 525 563643186 563643717 1.480000e-167 599.0
34 TraesCS6A01G209900 chr2D 87.266 534 57 7 1 525 629662981 629662450 1.480000e-167 599.0
35 TraesCS6A01G209900 chr3B 87.194 531 53 9 1 524 584529590 584530112 8.930000e-165 590.0
36 TraesCS6A01G209900 chr2A 85.311 531 65 8 1 521 417097757 417098284 1.180000e-148 536.0
37 TraesCS6A01G209900 chr2A 74.708 257 62 2 3 258 608598321 608598575 8.480000e-21 111.0


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 TraesCS6A01G209900 chr6A 380360234 380363127 2893 True 5345.000000 5345 100.000000 1 2894 1 chr6A.!!$R1 2893
1 TraesCS6A01G209900 chr6A 381025631 381026350 719 True 511.500000 830 94.196000 1017 1921 2 chr6A.!!$R2 904
2 TraesCS6A01G209900 chr6D 267234360 267238220 3860 True 719.160000 2381 95.945400 520 2894 5 chr6D.!!$R1 2374
3 TraesCS6A01G209900 chr6D 267514689 267515402 713 True 519.500000 850 94.266000 1017 1921 2 chr6D.!!$R2 904
4 TraesCS6A01G209900 chr6B 415785942 415790406 4464 True 664.700000 2037 94.981800 536 2894 5 chr6B.!!$R1 2358
5 TraesCS6A01G209900 chr6B 415863656 415864360 704 True 513.000000 828 95.214500 1024 1921 2 chr6B.!!$R2 897
6 TraesCS6A01G209900 chr4A 352509391 352509923 532 False 586.000000 586 86.965000 1 522 1 chr4A.!!$F1 521
7 TraesCS6A01G209900 chr4A 640232283 640233082 799 False 378.350000 702 96.406500 874 1893 2 chr4A.!!$F2 1019
8 TraesCS6A01G209900 chr5D 6367672 6368202 530 False 544.000000 544 85.581000 1 520 1 chr5D.!!$F1 519
9 TraesCS6A01G209900 chr5D 531971232 531971915 683 True 432.000000 688 91.319000 1017 1893 2 chr5D.!!$R2 876
10 TraesCS6A01G209900 chr5D 531900837 531903675 2838 True 242.166667 483 92.440667 873 1870 3 chr5D.!!$R1 997
11 TraesCS6A01G209900 chr5B 671187663 671188342 679 True 423.500000 664 91.717500 1019 1896 2 chr5B.!!$R2 877
12 TraesCS6A01G209900 chr7D 106975691 106976216 525 False 623.000000 623 88.235000 1 521 1 chr7D.!!$F1 520
13 TraesCS6A01G209900 chr1A 53849496 53850022 526 False 606.000000 606 87.594000 3 527 1 chr1A.!!$F1 524
14 TraesCS6A01G209900 chr4B 563643186 563643717 531 False 599.000000 599 87.218000 1 525 1 chr4B.!!$F1 524
15 TraesCS6A01G209900 chr2D 629662450 629662981 531 True 599.000000 599 87.266000 1 525 1 chr2D.!!$R1 524
16 TraesCS6A01G209900 chr3B 584529590 584530112 522 False 590.000000 590 87.194000 1 524 1 chr3B.!!$F1 523
17 TraesCS6A01G209900 chr2A 417097757 417098284 527 False 536.000000 536 85.311000 1 521 1 chr2A.!!$F1 520

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
268 273 0.038166 TCATCAACACCCTCCTTGCC 59.962 55.0 0.0 0.0 0.0 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2007 4105 0.10576 TGCACCCCAACATTTGTCCT 60.106 50.0 0.0 0.0 0.0 3.85 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 1.003718 CACCAACTTCCCCGACCTC 60.004 63.158 0.00 0.00 0.00 3.85
50 51 0.616679 CCAACTTCCCCGACCTCCTA 60.617 60.000 0.00 0.00 0.00 2.94
68 69 0.395724 TAGCTGAGATCCACGCCTCA 60.396 55.000 0.00 0.00 37.77 3.86
95 100 2.504367 GTTGCCGCCATATTAGATGGT 58.496 47.619 7.74 0.00 41.17 3.55
127 132 2.048222 CTCGCCTGGACGCTTTGA 60.048 61.111 0.00 0.00 0.00 2.69
130 135 1.207593 CGCCTGGACGCTTTGAAAG 59.792 57.895 0.00 0.00 0.00 2.62
170 175 3.685139 TTCAGAAAGTGCCTCTTCGAT 57.315 42.857 0.00 0.00 35.02 3.59
172 177 2.005451 CAGAAAGTGCCTCTTCGATGG 58.995 52.381 0.00 0.00 35.02 3.51
216 221 2.684374 TGTGTGGCTATTTGCAGCTATG 59.316 45.455 0.00 0.00 45.15 2.23
217 222 2.033801 GTGTGGCTATTTGCAGCTATGG 59.966 50.000 0.00 0.00 45.15 2.74
218 223 1.000938 GTGGCTATTTGCAGCTATGGC 60.001 52.381 0.00 0.00 45.15 4.40
219 224 0.239347 GGCTATTTGCAGCTATGGCG 59.761 55.000 0.00 0.00 45.15 5.69
220 225 0.239347 GCTATTTGCAGCTATGGCGG 59.761 55.000 0.00 0.00 44.37 6.13
227 232 3.546543 AGCTATGGCGGCCGCTTA 61.547 61.111 45.23 34.66 44.37 3.09
228 233 3.044305 GCTATGGCGGCCGCTTAG 61.044 66.667 45.23 39.47 41.60 2.18
229 234 3.044305 CTATGGCGGCCGCTTAGC 61.044 66.667 45.23 30.71 41.60 3.09
238 243 4.899239 CCGCTTAGCCGCCCTCAG 62.899 72.222 0.00 0.00 0.00 3.35
239 244 4.899239 CGCTTAGCCGCCCTCAGG 62.899 72.222 0.00 0.00 0.00 3.86
240 245 3.470888 GCTTAGCCGCCCTCAGGA 61.471 66.667 0.00 0.00 33.47 3.86
241 246 2.501610 CTTAGCCGCCCTCAGGAC 59.498 66.667 0.00 0.00 33.47 3.85
242 247 3.081409 TTAGCCGCCCTCAGGACC 61.081 66.667 0.00 0.00 33.47 4.46
260 265 4.296265 GGGACGTCATCAACACCC 57.704 61.111 18.91 3.08 37.10 4.61
261 266 1.677552 GGGACGTCATCAACACCCT 59.322 57.895 18.91 0.00 39.58 4.34
262 267 0.391263 GGGACGTCATCAACACCCTC 60.391 60.000 18.91 0.00 39.58 4.30
263 268 0.391263 GGACGTCATCAACACCCTCC 60.391 60.000 18.91 0.00 0.00 4.30
264 269 0.608640 GACGTCATCAACACCCTCCT 59.391 55.000 11.55 0.00 0.00 3.69
265 270 1.002087 GACGTCATCAACACCCTCCTT 59.998 52.381 11.55 0.00 0.00 3.36
266 271 1.270839 ACGTCATCAACACCCTCCTTG 60.271 52.381 0.00 0.00 0.00 3.61
267 272 1.168714 GTCATCAACACCCTCCTTGC 58.831 55.000 0.00 0.00 0.00 4.01
268 273 0.038166 TCATCAACACCCTCCTTGCC 59.962 55.000 0.00 0.00 0.00 4.52
269 274 1.002134 ATCAACACCCTCCTTGCCG 60.002 57.895 0.00 0.00 0.00 5.69
270 275 1.488705 ATCAACACCCTCCTTGCCGA 61.489 55.000 0.00 0.00 0.00 5.54
271 276 1.966451 CAACACCCTCCTTGCCGAC 60.966 63.158 0.00 0.00 0.00 4.79
272 277 3.192103 AACACCCTCCTTGCCGACC 62.192 63.158 0.00 0.00 0.00 4.79
273 278 3.322466 CACCCTCCTTGCCGACCT 61.322 66.667 0.00 0.00 0.00 3.85
274 279 2.529389 ACCCTCCTTGCCGACCTT 60.529 61.111 0.00 0.00 0.00 3.50
275 280 2.269241 CCCTCCTTGCCGACCTTC 59.731 66.667 0.00 0.00 0.00 3.46
276 281 2.125512 CCTCCTTGCCGACCTTCG 60.126 66.667 0.00 0.00 40.07 3.79
277 282 2.646175 CCTCCTTGCCGACCTTCGA 61.646 63.158 0.00 0.00 43.74 3.71
278 283 1.517832 CTCCTTGCCGACCTTCGAT 59.482 57.895 0.00 0.00 43.74 3.59
279 284 0.528684 CTCCTTGCCGACCTTCGATC 60.529 60.000 0.00 0.00 43.74 3.69
280 285 1.878522 CCTTGCCGACCTTCGATCG 60.879 63.158 9.36 9.36 43.74 3.69
281 286 1.138883 CTTGCCGACCTTCGATCGA 59.861 57.895 15.15 15.15 43.74 3.59
282 287 0.249073 CTTGCCGACCTTCGATCGAT 60.249 55.000 20.18 3.58 43.74 3.59
283 288 0.527600 TTGCCGACCTTCGATCGATG 60.528 55.000 20.18 20.53 43.74 3.84
284 289 1.661821 GCCGACCTTCGATCGATGG 60.662 63.158 35.69 35.69 43.74 3.51
285 290 1.661821 CCGACCTTCGATCGATGGC 60.662 63.158 36.68 29.12 43.74 4.40
286 291 1.661821 CGACCTTCGATCGATGGCC 60.662 63.158 36.68 29.48 43.74 5.36
287 292 1.742768 GACCTTCGATCGATGGCCT 59.257 57.895 36.68 24.85 41.49 5.19
288 293 0.105039 GACCTTCGATCGATGGCCTT 59.895 55.000 36.68 24.26 41.49 4.35
289 294 0.105039 ACCTTCGATCGATGGCCTTC 59.895 55.000 36.68 6.40 41.49 3.46
290 295 0.601311 CCTTCGATCGATGGCCTTCC 60.601 60.000 30.13 0.00 33.63 3.46
291 296 0.941463 CTTCGATCGATGGCCTTCCG 60.941 60.000 20.18 10.56 34.14 4.30
292 297 2.971428 TTCGATCGATGGCCTTCCGC 62.971 60.000 20.18 2.16 34.14 5.54
293 298 3.038417 GATCGATGGCCTTCCGCG 61.038 66.667 12.77 0.00 38.94 6.46
294 299 3.792053 GATCGATGGCCTTCCGCGT 62.792 63.158 12.77 2.09 38.94 6.01
295 300 4.812476 TCGATGGCCTTCCGCGTG 62.812 66.667 12.77 0.00 38.94 5.34
314 319 4.821589 CACCTCCGCTTCCGCCTC 62.822 72.222 0.00 0.00 0.00 4.70
317 322 4.214327 CTCCGCTTCCGCCTCCTC 62.214 72.222 0.00 0.00 0.00 3.71
332 337 4.292178 CTCCGCCGGAGCCTGATC 62.292 72.222 21.84 0.00 43.29 2.92
334 339 4.598894 CCGCCGGAGCCTGATCAG 62.599 72.222 16.24 16.24 34.57 2.90
349 354 4.996976 CAGGCTTACTGCTCGTGT 57.003 55.556 0.00 0.00 40.97 4.49
350 355 3.217242 CAGGCTTACTGCTCGTGTT 57.783 52.632 0.00 0.00 40.97 3.32
351 356 0.792640 CAGGCTTACTGCTCGTGTTG 59.207 55.000 0.00 0.00 40.97 3.33
352 357 0.951040 AGGCTTACTGCTCGTGTTGC 60.951 55.000 0.00 0.00 42.39 4.17
353 358 1.130613 GCTTACTGCTCGTGTTGCG 59.869 57.895 0.00 0.00 43.01 4.85
354 359 1.781555 CTTACTGCTCGTGTTGCGG 59.218 57.895 0.00 0.00 41.72 5.69
356 361 2.967076 ACTGCTCGTGTTGCGGTG 60.967 61.111 0.00 0.00 46.81 4.94
357 362 2.967076 CTGCTCGTGTTGCGGTGT 60.967 61.111 0.00 0.00 41.72 4.16
358 363 2.943345 CTGCTCGTGTTGCGGTGTC 61.943 63.158 0.00 0.00 41.72 3.67
359 364 2.661866 GCTCGTGTTGCGGTGTCT 60.662 61.111 0.00 0.00 41.72 3.41
360 365 2.943345 GCTCGTGTTGCGGTGTCTG 61.943 63.158 0.00 0.00 41.72 3.51
361 366 1.591594 CTCGTGTTGCGGTGTCTGT 60.592 57.895 0.00 0.00 41.72 3.41
362 367 1.821241 CTCGTGTTGCGGTGTCTGTG 61.821 60.000 0.00 0.00 41.72 3.66
363 368 2.171079 CGTGTTGCGGTGTCTGTGT 61.171 57.895 0.00 0.00 36.85 3.72
364 369 1.351707 GTGTTGCGGTGTCTGTGTG 59.648 57.895 0.00 0.00 0.00 3.82
365 370 1.078778 TGTTGCGGTGTCTGTGTGT 60.079 52.632 0.00 0.00 0.00 3.72
366 371 1.351707 GTTGCGGTGTCTGTGTGTG 59.648 57.895 0.00 0.00 0.00 3.82
367 372 1.078778 TTGCGGTGTCTGTGTGTGT 60.079 52.632 0.00 0.00 0.00 3.72
368 373 0.675208 TTGCGGTGTCTGTGTGTGTT 60.675 50.000 0.00 0.00 0.00 3.32
369 374 1.087202 TGCGGTGTCTGTGTGTGTTC 61.087 55.000 0.00 0.00 0.00 3.18
370 375 0.810031 GCGGTGTCTGTGTGTGTTCT 60.810 55.000 0.00 0.00 0.00 3.01
371 376 1.651987 CGGTGTCTGTGTGTGTTCTT 58.348 50.000 0.00 0.00 0.00 2.52
372 377 2.006888 CGGTGTCTGTGTGTGTTCTTT 58.993 47.619 0.00 0.00 0.00 2.52
373 378 3.191669 CGGTGTCTGTGTGTGTTCTTTA 58.808 45.455 0.00 0.00 0.00 1.85
374 379 3.807622 CGGTGTCTGTGTGTGTTCTTTAT 59.192 43.478 0.00 0.00 0.00 1.40
375 380 4.272504 CGGTGTCTGTGTGTGTTCTTTATT 59.727 41.667 0.00 0.00 0.00 1.40
376 381 5.220777 CGGTGTCTGTGTGTGTTCTTTATTT 60.221 40.000 0.00 0.00 0.00 1.40
377 382 6.560711 GGTGTCTGTGTGTGTTCTTTATTTT 58.439 36.000 0.00 0.00 0.00 1.82
378 383 7.033185 GGTGTCTGTGTGTGTTCTTTATTTTT 58.967 34.615 0.00 0.00 0.00 1.94
379 384 8.185505 GGTGTCTGTGTGTGTTCTTTATTTTTA 58.814 33.333 0.00 0.00 0.00 1.52
380 385 9.221775 GTGTCTGTGTGTGTTCTTTATTTTTAG 57.778 33.333 0.00 0.00 0.00 1.85
381 386 8.402472 TGTCTGTGTGTGTTCTTTATTTTTAGG 58.598 33.333 0.00 0.00 0.00 2.69
382 387 7.860872 GTCTGTGTGTGTTCTTTATTTTTAGGG 59.139 37.037 0.00 0.00 0.00 3.53
383 388 6.508777 TGTGTGTGTTCTTTATTTTTAGGGC 58.491 36.000 0.00 0.00 0.00 5.19
384 389 6.322712 TGTGTGTGTTCTTTATTTTTAGGGCT 59.677 34.615 0.00 0.00 0.00 5.19
385 390 7.147811 TGTGTGTGTTCTTTATTTTTAGGGCTT 60.148 33.333 0.00 0.00 0.00 4.35
386 391 7.169140 GTGTGTGTTCTTTATTTTTAGGGCTTG 59.831 37.037 0.00 0.00 0.00 4.01
387 392 7.147811 TGTGTGTTCTTTATTTTTAGGGCTTGT 60.148 33.333 0.00 0.00 0.00 3.16
388 393 7.709182 GTGTGTTCTTTATTTTTAGGGCTTGTT 59.291 33.333 0.00 0.00 0.00 2.83
389 394 7.708752 TGTGTTCTTTATTTTTAGGGCTTGTTG 59.291 33.333 0.00 0.00 0.00 3.33
390 395 7.923878 GTGTTCTTTATTTTTAGGGCTTGTTGA 59.076 33.333 0.00 0.00 0.00 3.18
391 396 8.141268 TGTTCTTTATTTTTAGGGCTTGTTGAG 58.859 33.333 0.00 0.00 0.00 3.02
400 405 4.488790 CTTGTTGAGCTGTGCCCT 57.511 55.556 0.00 0.00 0.00 5.19
401 406 2.251600 CTTGTTGAGCTGTGCCCTC 58.748 57.895 0.00 0.00 0.00 4.30
402 407 0.535780 CTTGTTGAGCTGTGCCCTCA 60.536 55.000 0.00 0.00 37.54 3.86
403 408 0.535780 TTGTTGAGCTGTGCCCTCAG 60.536 55.000 0.00 0.00 40.16 3.35
414 419 3.102090 GCCCTCAGCATTAACCCTC 57.898 57.895 0.00 0.00 42.97 4.30
415 420 0.548510 GCCCTCAGCATTAACCCTCT 59.451 55.000 0.00 0.00 42.97 3.69
416 421 1.064389 GCCCTCAGCATTAACCCTCTT 60.064 52.381 0.00 0.00 42.97 2.85
417 422 2.648059 CCCTCAGCATTAACCCTCTTG 58.352 52.381 0.00 0.00 0.00 3.02
418 423 2.025887 CCCTCAGCATTAACCCTCTTGT 60.026 50.000 0.00 0.00 0.00 3.16
419 424 3.199946 CCCTCAGCATTAACCCTCTTGTA 59.800 47.826 0.00 0.00 0.00 2.41
420 425 4.192317 CCTCAGCATTAACCCTCTTGTAC 58.808 47.826 0.00 0.00 0.00 2.90
421 426 4.080863 CCTCAGCATTAACCCTCTTGTACT 60.081 45.833 0.00 0.00 0.00 2.73
422 427 5.491982 CTCAGCATTAACCCTCTTGTACTT 58.508 41.667 0.00 0.00 0.00 2.24
423 428 5.876357 TCAGCATTAACCCTCTTGTACTTT 58.124 37.500 0.00 0.00 0.00 2.66
424 429 7.011499 TCAGCATTAACCCTCTTGTACTTTA 57.989 36.000 0.00 0.00 0.00 1.85
425 430 7.630082 TCAGCATTAACCCTCTTGTACTTTAT 58.370 34.615 0.00 0.00 0.00 1.40
426 431 8.107095 TCAGCATTAACCCTCTTGTACTTTATT 58.893 33.333 0.00 0.00 0.00 1.40
427 432 8.739972 CAGCATTAACCCTCTTGTACTTTATTT 58.260 33.333 0.00 0.00 0.00 1.40
428 433 8.739972 AGCATTAACCCTCTTGTACTTTATTTG 58.260 33.333 0.00 0.00 0.00 2.32
429 434 8.520351 GCATTAACCCTCTTGTACTTTATTTGT 58.480 33.333 0.00 0.00 0.00 2.83
430 435 9.840427 CATTAACCCTCTTGTACTTTATTTGTG 57.160 33.333 0.00 0.00 0.00 3.33
431 436 8.983702 TTAACCCTCTTGTACTTTATTTGTGT 57.016 30.769 0.00 0.00 0.00 3.72
432 437 6.877611 ACCCTCTTGTACTTTATTTGTGTG 57.122 37.500 0.00 0.00 0.00 3.82
433 438 6.362248 ACCCTCTTGTACTTTATTTGTGTGT 58.638 36.000 0.00 0.00 0.00 3.72
434 439 6.262273 ACCCTCTTGTACTTTATTTGTGTGTG 59.738 38.462 0.00 0.00 0.00 3.82
435 440 6.485313 CCCTCTTGTACTTTATTTGTGTGTGA 59.515 38.462 0.00 0.00 0.00 3.58
436 441 7.307989 CCCTCTTGTACTTTATTTGTGTGTGAG 60.308 40.741 0.00 0.00 0.00 3.51
437 442 7.441157 CCTCTTGTACTTTATTTGTGTGTGAGA 59.559 37.037 0.00 0.00 0.00 3.27
438 443 8.138365 TCTTGTACTTTATTTGTGTGTGAGAC 57.862 34.615 0.00 0.00 0.00 3.36
439 444 7.985184 TCTTGTACTTTATTTGTGTGTGAGACT 59.015 33.333 0.00 0.00 0.00 3.24
440 445 8.500753 TTGTACTTTATTTGTGTGTGAGACTT 57.499 30.769 0.00 0.00 0.00 3.01
441 446 9.602568 TTGTACTTTATTTGTGTGTGAGACTTA 57.397 29.630 0.00 0.00 0.00 2.24
442 447 9.772973 TGTACTTTATTTGTGTGTGAGACTTAT 57.227 29.630 0.00 0.00 0.00 1.73
444 449 8.677148 ACTTTATTTGTGTGTGAGACTTATGT 57.323 30.769 0.00 0.00 0.00 2.29
445 450 8.559536 ACTTTATTTGTGTGTGAGACTTATGTG 58.440 33.333 0.00 0.00 0.00 3.21
446 451 8.445275 TTTATTTGTGTGTGAGACTTATGTGT 57.555 30.769 0.00 0.00 0.00 3.72
447 452 5.733226 TTTGTGTGTGAGACTTATGTGTG 57.267 39.130 0.00 0.00 0.00 3.82
448 453 4.400529 TGTGTGTGAGACTTATGTGTGT 57.599 40.909 0.00 0.00 0.00 3.72
449 454 4.119136 TGTGTGTGAGACTTATGTGTGTG 58.881 43.478 0.00 0.00 0.00 3.82
450 455 4.142049 TGTGTGTGAGACTTATGTGTGTGA 60.142 41.667 0.00 0.00 0.00 3.58
451 456 4.808895 GTGTGTGAGACTTATGTGTGTGAA 59.191 41.667 0.00 0.00 0.00 3.18
452 457 4.808895 TGTGTGAGACTTATGTGTGTGAAC 59.191 41.667 0.00 0.00 0.00 3.18
453 458 4.211374 GTGTGAGACTTATGTGTGTGAACC 59.789 45.833 0.00 0.00 0.00 3.62
454 459 4.100963 TGTGAGACTTATGTGTGTGAACCT 59.899 41.667 0.00 0.00 0.00 3.50
455 460 5.057149 GTGAGACTTATGTGTGTGAACCTT 58.943 41.667 0.00 0.00 0.00 3.50
456 461 5.050091 GTGAGACTTATGTGTGTGAACCTTG 60.050 44.000 0.00 0.00 0.00 3.61
457 462 5.036117 AGACTTATGTGTGTGAACCTTGT 57.964 39.130 0.00 0.00 0.00 3.16
458 463 5.437060 AGACTTATGTGTGTGAACCTTGTT 58.563 37.500 0.00 0.00 0.00 2.83
459 464 5.296780 AGACTTATGTGTGTGAACCTTGTTG 59.703 40.000 0.00 0.00 0.00 3.33
460 465 4.338118 ACTTATGTGTGTGAACCTTGTTGG 59.662 41.667 0.00 0.00 42.93 3.77
461 466 2.498644 TGTGTGTGAACCTTGTTGGA 57.501 45.000 0.00 0.00 39.71 3.53
462 467 3.011566 TGTGTGTGAACCTTGTTGGAT 57.988 42.857 0.00 0.00 39.71 3.41
463 468 2.687425 TGTGTGTGAACCTTGTTGGATG 59.313 45.455 0.00 0.00 39.71 3.51
464 469 2.687935 GTGTGTGAACCTTGTTGGATGT 59.312 45.455 0.00 0.00 39.71 3.06
465 470 3.130340 GTGTGTGAACCTTGTTGGATGTT 59.870 43.478 0.00 0.00 39.71 2.71
466 471 3.766591 TGTGTGAACCTTGTTGGATGTTT 59.233 39.130 0.00 0.00 39.71 2.83
467 472 4.111916 GTGTGAACCTTGTTGGATGTTTG 58.888 43.478 0.00 0.00 39.71 2.93
468 473 3.131933 TGTGAACCTTGTTGGATGTTTGG 59.868 43.478 0.00 0.00 39.71 3.28
469 474 2.102252 TGAACCTTGTTGGATGTTTGGC 59.898 45.455 0.00 0.00 39.71 4.52
470 475 2.086610 ACCTTGTTGGATGTTTGGCT 57.913 45.000 0.00 0.00 39.71 4.75
471 476 1.963515 ACCTTGTTGGATGTTTGGCTC 59.036 47.619 0.00 0.00 39.71 4.70
472 477 1.068333 CCTTGTTGGATGTTTGGCTCG 60.068 52.381 0.00 0.00 38.35 5.03
473 478 0.958091 TTGTTGGATGTTTGGCTCGG 59.042 50.000 0.00 0.00 0.00 4.63
474 479 0.893270 TGTTGGATGTTTGGCTCGGG 60.893 55.000 0.00 0.00 0.00 5.14
475 480 1.976474 TTGGATGTTTGGCTCGGGC 60.976 57.895 0.00 0.00 37.82 6.13
476 481 3.508840 GGATGTTTGGCTCGGGCG 61.509 66.667 0.00 0.00 39.81 6.13
477 482 3.508840 GATGTTTGGCTCGGGCGG 61.509 66.667 0.00 0.00 39.81 6.13
478 483 4.344865 ATGTTTGGCTCGGGCGGT 62.345 61.111 0.00 0.00 39.81 5.68
479 484 3.860930 ATGTTTGGCTCGGGCGGTT 62.861 57.895 0.00 0.00 39.81 4.44
480 485 3.292159 GTTTGGCTCGGGCGGTTT 61.292 61.111 0.00 0.00 39.81 3.27
481 486 3.291383 TTTGGCTCGGGCGGTTTG 61.291 61.111 0.00 0.00 39.81 2.93
485 490 3.670377 GCTCGGGCGGTTTGCTTT 61.670 61.111 0.00 0.00 45.43 3.51
486 491 2.329614 GCTCGGGCGGTTTGCTTTA 61.330 57.895 0.00 0.00 45.43 1.85
487 492 1.654023 GCTCGGGCGGTTTGCTTTAT 61.654 55.000 0.00 0.00 45.43 1.40
488 493 1.658994 CTCGGGCGGTTTGCTTTATA 58.341 50.000 0.00 0.00 45.43 0.98
489 494 2.011222 CTCGGGCGGTTTGCTTTATAA 58.989 47.619 0.00 0.00 45.43 0.98
490 495 2.616842 CTCGGGCGGTTTGCTTTATAAT 59.383 45.455 0.00 0.00 45.43 1.28
491 496 3.806380 TCGGGCGGTTTGCTTTATAATA 58.194 40.909 0.00 0.00 45.43 0.98
492 497 4.391155 TCGGGCGGTTTGCTTTATAATAT 58.609 39.130 0.00 0.00 45.43 1.28
493 498 5.549347 TCGGGCGGTTTGCTTTATAATATA 58.451 37.500 0.00 0.00 45.43 0.86
494 499 5.996513 TCGGGCGGTTTGCTTTATAATATAA 59.003 36.000 0.00 0.00 45.43 0.98
495 500 6.485984 TCGGGCGGTTTGCTTTATAATATAAA 59.514 34.615 5.46 5.46 45.43 1.40
496 501 6.799925 CGGGCGGTTTGCTTTATAATATAAAG 59.200 38.462 22.11 22.11 45.43 1.85
503 508 4.905269 GCTTTATAATATAAAGCGGGGCG 58.095 43.478 30.20 10.34 46.31 6.13
504 509 4.632688 GCTTTATAATATAAAGCGGGGCGA 59.367 41.667 30.20 0.05 46.31 5.54
505 510 5.122711 GCTTTATAATATAAAGCGGGGCGAA 59.877 40.000 30.20 0.00 46.31 4.70
506 511 6.348704 GCTTTATAATATAAAGCGGGGCGAAA 60.349 38.462 30.20 0.57 46.31 3.46
507 512 6.730960 TTATAATATAAAGCGGGGCGAAAG 57.269 37.500 0.00 0.00 0.00 2.62
669 706 2.370281 TGAGCAAATCAGACGAGGAC 57.630 50.000 0.00 0.00 32.77 3.85
759 796 1.153429 GCTTAATCGGACGGGCACT 60.153 57.895 0.00 0.00 0.00 4.40
1104 2571 3.535629 CTCCAAGCTGCCGGTGACA 62.536 63.158 1.90 0.00 0.00 3.58
1107 2574 1.893808 CAAGCTGCCGGTGACACTT 60.894 57.895 1.90 0.00 0.00 3.16
1179 2647 3.627577 CGTATATGCTTCCTTGTTTGGCT 59.372 43.478 0.00 0.00 0.00 4.75
1258 2947 9.616634 CATATCCATGTATGCAACAAGTTAATC 57.383 33.333 0.00 0.00 42.70 1.75
1259 2948 6.117911 TCCATGTATGCAACAAGTTAATCG 57.882 37.500 0.00 0.00 42.70 3.34
1298 2987 2.025037 TCCAAATATGCCAAGGTCAGCT 60.025 45.455 0.00 0.00 0.00 4.24
1386 3076 3.380142 GAATTTTGTTTGCGCCTCTTCA 58.620 40.909 4.18 0.00 0.00 3.02
1390 3080 2.704725 TGTTTGCGCCTCTTCATTTC 57.295 45.000 4.18 0.00 0.00 2.17
1407 3196 8.289618 TCTTCATTTCCTTCATCGTAACAAAAG 58.710 33.333 0.00 0.00 0.00 2.27
1416 3468 7.170998 CCTTCATCGTAACAAAAGTGACTAACT 59.829 37.037 0.00 0.00 42.60 2.24
1566 3630 2.659610 GTGAGCCAGAAGGAGCGT 59.340 61.111 0.00 0.00 36.89 5.07
1906 3990 1.132643 ACAACTAGACGTGGAGATCGC 59.867 52.381 0.00 0.00 0.00 4.58
1948 4032 3.869473 TTCTCCGGCCGGTCGTTTG 62.869 63.158 41.57 24.25 36.47 2.93
1949 4033 4.675029 CTCCGGCCGGTCGTTTGT 62.675 66.667 41.57 0.00 36.47 2.83
1954 4038 2.322830 GGCCGGTCGTTTGTTCTCC 61.323 63.158 1.90 0.00 0.00 3.71
1956 4040 0.953960 GCCGGTCGTTTGTTCTCCAT 60.954 55.000 1.90 0.00 0.00 3.41
1964 4048 5.640357 GGTCGTTTGTTCTCCATATGTAACA 59.360 40.000 1.24 6.68 0.00 2.41
1965 4049 6.148150 GGTCGTTTGTTCTCCATATGTAACAA 59.852 38.462 17.52 17.52 39.39 2.83
1980 4064 9.524106 CATATGTAACAAAGTATCAGTACGGAA 57.476 33.333 0.00 0.00 35.92 4.30
2004 4102 2.800096 CGTACGTACGGCACAAACT 58.200 52.632 34.54 0.00 45.30 2.66
2005 4103 0.431984 CGTACGTACGGCACAAACTG 59.568 55.000 34.54 7.76 45.30 3.16
2006 4104 1.490621 GTACGTACGGCACAAACTGT 58.509 50.000 21.06 0.00 0.00 3.55
2007 4105 2.660490 GTACGTACGGCACAAACTGTA 58.340 47.619 21.06 0.00 0.00 2.74
2011 4114 2.064014 GTACGGCACAAACTGTAGGAC 58.936 52.381 0.00 0.00 32.11 3.85
2179 7549 9.883142 CTTTCATGGGATAGGAATAGAATAGTC 57.117 37.037 0.00 0.00 34.37 2.59
2185 7555 2.240279 AGGAATAGAATAGTCGCGGCT 58.760 47.619 20.79 20.79 36.34 5.52
2192 7562 2.796483 AATAGTCGCGGCTGGTGCAA 62.796 55.000 26.08 1.13 41.91 4.08
2193 7563 2.593468 ATAGTCGCGGCTGGTGCAAT 62.593 55.000 26.08 4.17 41.91 3.56
2194 7564 4.166011 GTCGCGGCTGGTGCAATC 62.166 66.667 1.90 0.00 41.91 2.67
2195 7565 4.695993 TCGCGGCTGGTGCAATCA 62.696 61.111 6.13 0.00 41.91 2.57
2196 7566 4.465512 CGCGGCTGGTGCAATCAC 62.466 66.667 0.00 0.00 41.91 3.06
2326 7702 0.110419 TTCGGCGCTCATTTCAAACG 60.110 50.000 7.64 0.00 0.00 3.60
2389 7765 5.500645 AAGTTGGAGTCGGAAAAAGAAAG 57.499 39.130 0.00 0.00 0.00 2.62
2390 7766 4.777463 AGTTGGAGTCGGAAAAAGAAAGA 58.223 39.130 0.00 0.00 0.00 2.52
2391 7767 4.816925 AGTTGGAGTCGGAAAAAGAAAGAG 59.183 41.667 0.00 0.00 0.00 2.85
2392 7768 4.682778 TGGAGTCGGAAAAAGAAAGAGA 57.317 40.909 0.00 0.00 0.00 3.10
2423 7799 7.307042 CCAATATTCTTCGTTAGATGCTCACTG 60.307 40.741 0.00 0.00 31.54 3.66
2573 7956 1.160137 GACCAAATGCACTCTTCGCT 58.840 50.000 0.00 0.00 0.00 4.93
2592 7975 4.740205 TCGCTACGAAAATCTGATCATCAC 59.260 41.667 0.00 0.00 31.06 3.06
2598 7981 3.589951 AAATCTGATCATCACAGGGGG 57.410 47.619 0.00 0.00 36.22 5.40
2619 8007 3.317149 GGGGAGTTGGTTTGAGTTTACAC 59.683 47.826 0.00 0.00 0.00 2.90
2620 8008 3.949113 GGGAGTTGGTTTGAGTTTACACA 59.051 43.478 0.00 0.00 0.00 3.72
2626 8014 3.181491 TGGTTTGAGTTTACACAGCAAGC 60.181 43.478 0.00 0.00 0.00 4.01
2653 8336 9.703892 ATGACAGCAACAAGTATCTATCTAATC 57.296 33.333 0.00 0.00 0.00 1.75
2828 8515 6.690194 ATTTATTCAGCTTCACATGGAGAC 57.310 37.500 0.00 0.00 0.00 3.36
2832 8519 0.534412 AGCTTCACATGGAGACGGAG 59.466 55.000 0.00 0.00 0.00 4.63
2833 8520 0.460987 GCTTCACATGGAGACGGAGG 60.461 60.000 0.00 0.00 0.00 4.30
2871 8560 5.278660 GGCTGAATGAACAATGTCAACTCTT 60.279 40.000 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.182284 CATTGTCCGCCGACCGTA 59.818 61.111 2.66 0.00 38.32 4.02
47 48 1.112315 AGGCGTGGATCTCAGCTAGG 61.112 60.000 0.00 0.00 0.00 3.02
50 51 1.683707 TGAGGCGTGGATCTCAGCT 60.684 57.895 0.00 0.00 35.37 4.24
95 100 1.303236 CGAGGACCCCAATGCACAA 60.303 57.895 0.00 0.00 0.00 3.33
221 226 4.899239 CTGAGGGCGGCTAAGCGG 62.899 72.222 9.56 0.00 38.18 5.52
222 227 4.899239 CCTGAGGGCGGCTAAGCG 62.899 72.222 9.56 0.00 38.18 4.68
223 228 3.470888 TCCTGAGGGCGGCTAAGC 61.471 66.667 9.56 0.00 0.00 3.09
224 229 2.501610 GTCCTGAGGGCGGCTAAG 59.498 66.667 9.56 4.00 0.00 2.18
225 230 3.081409 GGTCCTGAGGGCGGCTAA 61.081 66.667 9.56 0.00 0.00 3.09
233 238 3.450115 GACGTCCCGGTCCTGAGG 61.450 72.222 3.51 0.00 0.00 3.86
234 239 2.005960 GATGACGTCCCGGTCCTGAG 62.006 65.000 14.12 0.00 36.07 3.35
235 240 2.036731 ATGACGTCCCGGTCCTGA 59.963 61.111 14.12 0.00 36.07 3.86
236 241 1.884075 TTGATGACGTCCCGGTCCTG 61.884 60.000 14.12 0.00 36.07 3.86
237 242 1.608336 TTGATGACGTCCCGGTCCT 60.608 57.895 14.12 0.00 36.07 3.85
238 243 1.447314 GTTGATGACGTCCCGGTCC 60.447 63.158 14.12 0.00 36.07 4.46
239 244 1.012486 GTGTTGATGACGTCCCGGTC 61.012 60.000 14.12 6.74 37.45 4.79
240 245 1.005394 GTGTTGATGACGTCCCGGT 60.005 57.895 14.12 0.00 0.00 5.28
241 246 1.740296 GGTGTTGATGACGTCCCGG 60.740 63.158 14.12 0.00 0.00 5.73
242 247 1.740296 GGGTGTTGATGACGTCCCG 60.740 63.158 14.12 0.00 36.05 5.14
243 248 0.391263 GAGGGTGTTGATGACGTCCC 60.391 60.000 14.12 4.69 42.03 4.46
244 249 0.391263 GGAGGGTGTTGATGACGTCC 60.391 60.000 14.12 0.00 0.00 4.79
245 250 0.608640 AGGAGGGTGTTGATGACGTC 59.391 55.000 9.11 9.11 0.00 4.34
246 251 1.056660 AAGGAGGGTGTTGATGACGT 58.943 50.000 0.00 0.00 0.00 4.34
247 252 1.442769 CAAGGAGGGTGTTGATGACG 58.557 55.000 0.00 0.00 0.00 4.35
248 253 1.168714 GCAAGGAGGGTGTTGATGAC 58.831 55.000 0.00 0.00 0.00 3.06
249 254 0.038166 GGCAAGGAGGGTGTTGATGA 59.962 55.000 0.00 0.00 0.00 2.92
250 255 1.308069 CGGCAAGGAGGGTGTTGATG 61.308 60.000 0.00 0.00 0.00 3.07
251 256 1.002134 CGGCAAGGAGGGTGTTGAT 60.002 57.895 0.00 0.00 0.00 2.57
252 257 2.144078 TCGGCAAGGAGGGTGTTGA 61.144 57.895 0.00 0.00 0.00 3.18
253 258 1.966451 GTCGGCAAGGAGGGTGTTG 60.966 63.158 0.00 0.00 0.00 3.33
254 259 2.430367 GTCGGCAAGGAGGGTGTT 59.570 61.111 0.00 0.00 0.00 3.32
255 260 3.637273 GGTCGGCAAGGAGGGTGT 61.637 66.667 0.00 0.00 0.00 4.16
256 261 2.804828 GAAGGTCGGCAAGGAGGGTG 62.805 65.000 0.00 0.00 0.00 4.61
257 262 2.529389 AAGGTCGGCAAGGAGGGT 60.529 61.111 0.00 0.00 0.00 4.34
258 263 2.269241 GAAGGTCGGCAAGGAGGG 59.731 66.667 0.00 0.00 0.00 4.30
259 264 1.961180 ATCGAAGGTCGGCAAGGAGG 61.961 60.000 0.00 0.00 40.88 4.30
260 265 0.528684 GATCGAAGGTCGGCAAGGAG 60.529 60.000 0.00 0.00 40.88 3.69
261 266 1.515954 GATCGAAGGTCGGCAAGGA 59.484 57.895 0.00 0.00 40.88 3.36
262 267 1.878522 CGATCGAAGGTCGGCAAGG 60.879 63.158 10.26 0.00 40.88 3.61
263 268 0.249073 ATCGATCGAAGGTCGGCAAG 60.249 55.000 23.50 0.00 40.88 4.01
264 269 0.527600 CATCGATCGAAGGTCGGCAA 60.528 55.000 23.50 0.00 40.88 4.52
265 270 1.065764 CATCGATCGAAGGTCGGCA 59.934 57.895 23.50 0.00 40.88 5.69
266 271 1.661821 CCATCGATCGAAGGTCGGC 60.662 63.158 27.08 0.00 40.88 5.54
267 272 1.661821 GCCATCGATCGAAGGTCGG 60.662 63.158 32.83 22.64 40.88 4.79
268 273 1.661821 GGCCATCGATCGAAGGTCG 60.662 63.158 32.83 14.27 42.10 4.79
269 274 0.105039 AAGGCCATCGATCGAAGGTC 59.895 55.000 31.04 31.04 37.82 3.85
270 275 0.105039 GAAGGCCATCGATCGAAGGT 59.895 55.000 32.83 18.58 35.61 3.50
271 276 0.601311 GGAAGGCCATCGATCGAAGG 60.601 60.000 30.09 30.09 36.20 3.46
272 277 0.941463 CGGAAGGCCATCGATCGAAG 60.941 60.000 23.50 18.04 0.00 3.79
273 278 1.067416 CGGAAGGCCATCGATCGAA 59.933 57.895 23.50 5.77 0.00 3.71
274 279 2.728180 CGGAAGGCCATCGATCGA 59.272 61.111 21.86 21.86 0.00 3.59
275 280 3.038417 GCGGAAGGCCATCGATCG 61.038 66.667 9.36 9.36 34.80 3.69
276 281 3.038417 CGCGGAAGGCCATCGATC 61.038 66.667 5.01 0.00 38.94 3.69
277 282 3.849951 ACGCGGAAGGCCATCGAT 61.850 61.111 12.47 0.00 38.94 3.59
278 283 4.812476 CACGCGGAAGGCCATCGA 62.812 66.667 12.47 0.00 38.94 3.59
317 322 4.598894 CTGATCAGGCTCCGGCGG 62.599 72.222 22.51 22.51 39.81 6.13
318 323 4.598894 CCTGATCAGGCTCCGGCG 62.599 72.222 28.45 0.00 42.44 6.46
345 350 2.171079 ACACAGACACCGCAACACG 61.171 57.895 0.00 0.00 43.15 4.49
346 351 1.351707 CACACAGACACCGCAACAC 59.648 57.895 0.00 0.00 0.00 3.32
347 352 1.078778 ACACACAGACACCGCAACA 60.079 52.632 0.00 0.00 0.00 3.33
348 353 1.351707 CACACACAGACACCGCAAC 59.648 57.895 0.00 0.00 0.00 4.17
349 354 0.675208 AACACACACAGACACCGCAA 60.675 50.000 0.00 0.00 0.00 4.85
350 355 1.078778 AACACACACAGACACCGCA 60.079 52.632 0.00 0.00 0.00 5.69
351 356 0.810031 AGAACACACACAGACACCGC 60.810 55.000 0.00 0.00 0.00 5.68
352 357 1.651987 AAGAACACACACAGACACCG 58.348 50.000 0.00 0.00 0.00 4.94
353 358 5.751243 AATAAAGAACACACACAGACACC 57.249 39.130 0.00 0.00 0.00 4.16
354 359 9.221775 CTAAAAATAAAGAACACACACAGACAC 57.778 33.333 0.00 0.00 0.00 3.67
355 360 8.402472 CCTAAAAATAAAGAACACACACAGACA 58.598 33.333 0.00 0.00 0.00 3.41
356 361 7.860872 CCCTAAAAATAAAGAACACACACAGAC 59.139 37.037 0.00 0.00 0.00 3.51
357 362 7.469456 GCCCTAAAAATAAAGAACACACACAGA 60.469 37.037 0.00 0.00 0.00 3.41
358 363 6.640907 GCCCTAAAAATAAAGAACACACACAG 59.359 38.462 0.00 0.00 0.00 3.66
359 364 6.322712 AGCCCTAAAAATAAAGAACACACACA 59.677 34.615 0.00 0.00 0.00 3.72
360 365 6.745116 AGCCCTAAAAATAAAGAACACACAC 58.255 36.000 0.00 0.00 0.00 3.82
361 366 6.969993 AGCCCTAAAAATAAAGAACACACA 57.030 33.333 0.00 0.00 0.00 3.72
362 367 7.207383 ACAAGCCCTAAAAATAAAGAACACAC 58.793 34.615 0.00 0.00 0.00 3.82
363 368 7.354751 ACAAGCCCTAAAAATAAAGAACACA 57.645 32.000 0.00 0.00 0.00 3.72
364 369 7.923878 TCAACAAGCCCTAAAAATAAAGAACAC 59.076 33.333 0.00 0.00 0.00 3.32
365 370 8.012957 TCAACAAGCCCTAAAAATAAAGAACA 57.987 30.769 0.00 0.00 0.00 3.18
366 371 7.116376 GCTCAACAAGCCCTAAAAATAAAGAAC 59.884 37.037 0.00 0.00 45.92 3.01
367 372 7.151976 GCTCAACAAGCCCTAAAAATAAAGAA 58.848 34.615 0.00 0.00 45.92 2.52
368 373 6.687604 GCTCAACAAGCCCTAAAAATAAAGA 58.312 36.000 0.00 0.00 45.92 2.52
369 374 6.951256 GCTCAACAAGCCCTAAAAATAAAG 57.049 37.500 0.00 0.00 45.92 1.85
383 388 0.535780 TGAGGGCACAGCTCAACAAG 60.536 55.000 0.00 0.00 0.00 3.16
384 389 0.535780 CTGAGGGCACAGCTCAACAA 60.536 55.000 0.00 0.00 0.00 2.83
385 390 1.071987 CTGAGGGCACAGCTCAACA 59.928 57.895 0.00 0.00 0.00 3.33
386 391 3.978272 CTGAGGGCACAGCTCAAC 58.022 61.111 0.00 0.00 0.00 3.18
396 401 0.548510 AGAGGGTTAATGCTGAGGGC 59.451 55.000 0.00 0.00 42.22 5.19
397 402 2.025887 ACAAGAGGGTTAATGCTGAGGG 60.026 50.000 0.00 0.00 0.00 4.30
398 403 3.356529 ACAAGAGGGTTAATGCTGAGG 57.643 47.619 0.00 0.00 0.00 3.86
399 404 5.091261 AGTACAAGAGGGTTAATGCTGAG 57.909 43.478 0.00 0.00 0.00 3.35
400 405 5.499004 AAGTACAAGAGGGTTAATGCTGA 57.501 39.130 0.00 0.00 0.00 4.26
401 406 7.865706 ATAAAGTACAAGAGGGTTAATGCTG 57.134 36.000 0.00 0.00 0.00 4.41
402 407 8.739972 CAAATAAAGTACAAGAGGGTTAATGCT 58.260 33.333 0.00 0.00 0.00 3.79
403 408 8.520351 ACAAATAAAGTACAAGAGGGTTAATGC 58.480 33.333 0.00 0.00 0.00 3.56
404 409 9.840427 CACAAATAAAGTACAAGAGGGTTAATG 57.160 33.333 0.00 0.00 0.00 1.90
405 410 9.582648 ACACAAATAAAGTACAAGAGGGTTAAT 57.417 29.630 0.00 0.00 0.00 1.40
406 411 8.842280 CACACAAATAAAGTACAAGAGGGTTAA 58.158 33.333 0.00 0.00 0.00 2.01
407 412 7.994334 ACACACAAATAAAGTACAAGAGGGTTA 59.006 33.333 0.00 0.00 0.00 2.85
408 413 6.831868 ACACACAAATAAAGTACAAGAGGGTT 59.168 34.615 0.00 0.00 0.00 4.11
409 414 6.262273 CACACACAAATAAAGTACAAGAGGGT 59.738 38.462 0.00 0.00 0.00 4.34
410 415 6.485313 TCACACACAAATAAAGTACAAGAGGG 59.515 38.462 0.00 0.00 0.00 4.30
411 416 7.441157 TCTCACACACAAATAAAGTACAAGAGG 59.559 37.037 0.00 0.00 0.00 3.69
412 417 8.276325 GTCTCACACACAAATAAAGTACAAGAG 58.724 37.037 0.00 0.00 0.00 2.85
413 418 7.985184 AGTCTCACACACAAATAAAGTACAAGA 59.015 33.333 0.00 0.00 0.00 3.02
414 419 8.142994 AGTCTCACACACAAATAAAGTACAAG 57.857 34.615 0.00 0.00 0.00 3.16
415 420 8.500753 AAGTCTCACACACAAATAAAGTACAA 57.499 30.769 0.00 0.00 0.00 2.41
416 421 9.772973 ATAAGTCTCACACACAAATAAAGTACA 57.227 29.630 0.00 0.00 0.00 2.90
418 423 9.772973 ACATAAGTCTCACACACAAATAAAGTA 57.227 29.630 0.00 0.00 0.00 2.24
419 424 8.559536 CACATAAGTCTCACACACAAATAAAGT 58.440 33.333 0.00 0.00 0.00 2.66
420 425 8.559536 ACACATAAGTCTCACACACAAATAAAG 58.440 33.333 0.00 0.00 0.00 1.85
421 426 8.341903 CACACATAAGTCTCACACACAAATAAA 58.658 33.333 0.00 0.00 0.00 1.40
422 427 7.497579 ACACACATAAGTCTCACACACAAATAA 59.502 33.333 0.00 0.00 0.00 1.40
423 428 6.989759 ACACACATAAGTCTCACACACAAATA 59.010 34.615 0.00 0.00 0.00 1.40
424 429 5.822519 ACACACATAAGTCTCACACACAAAT 59.177 36.000 0.00 0.00 0.00 2.32
425 430 5.064579 CACACACATAAGTCTCACACACAAA 59.935 40.000 0.00 0.00 0.00 2.83
426 431 4.570369 CACACACATAAGTCTCACACACAA 59.430 41.667 0.00 0.00 0.00 3.33
427 432 4.119136 CACACACATAAGTCTCACACACA 58.881 43.478 0.00 0.00 0.00 3.72
428 433 4.368315 TCACACACATAAGTCTCACACAC 58.632 43.478 0.00 0.00 0.00 3.82
429 434 4.664150 TCACACACATAAGTCTCACACA 57.336 40.909 0.00 0.00 0.00 3.72
430 435 4.211374 GGTTCACACACATAAGTCTCACAC 59.789 45.833 0.00 0.00 0.00 3.82
431 436 4.100963 AGGTTCACACACATAAGTCTCACA 59.899 41.667 0.00 0.00 0.00 3.58
432 437 4.632153 AGGTTCACACACATAAGTCTCAC 58.368 43.478 0.00 0.00 0.00 3.51
433 438 4.955811 AGGTTCACACACATAAGTCTCA 57.044 40.909 0.00 0.00 0.00 3.27
434 439 5.057149 ACAAGGTTCACACACATAAGTCTC 58.943 41.667 0.00 0.00 0.00 3.36
435 440 5.036117 ACAAGGTTCACACACATAAGTCT 57.964 39.130 0.00 0.00 0.00 3.24
436 441 5.505654 CCAACAAGGTTCACACACATAAGTC 60.506 44.000 0.00 0.00 0.00 3.01
437 442 4.338118 CCAACAAGGTTCACACACATAAGT 59.662 41.667 0.00 0.00 0.00 2.24
438 443 4.578516 TCCAACAAGGTTCACACACATAAG 59.421 41.667 0.00 0.00 39.02 1.73
439 444 4.527944 TCCAACAAGGTTCACACACATAA 58.472 39.130 0.00 0.00 39.02 1.90
440 445 4.157849 TCCAACAAGGTTCACACACATA 57.842 40.909 0.00 0.00 39.02 2.29
441 446 3.011566 TCCAACAAGGTTCACACACAT 57.988 42.857 0.00 0.00 39.02 3.21
442 447 2.498644 TCCAACAAGGTTCACACACA 57.501 45.000 0.00 0.00 39.02 3.72
443 448 2.687935 ACATCCAACAAGGTTCACACAC 59.312 45.455 0.00 0.00 39.02 3.82
444 449 3.011566 ACATCCAACAAGGTTCACACA 57.988 42.857 0.00 0.00 39.02 3.72
445 450 4.111916 CAAACATCCAACAAGGTTCACAC 58.888 43.478 0.00 0.00 39.02 3.82
446 451 3.131933 CCAAACATCCAACAAGGTTCACA 59.868 43.478 0.00 0.00 39.02 3.58
447 452 3.716601 CCAAACATCCAACAAGGTTCAC 58.283 45.455 0.00 0.00 39.02 3.18
448 453 2.102252 GCCAAACATCCAACAAGGTTCA 59.898 45.455 0.00 0.00 39.02 3.18
449 454 2.365293 AGCCAAACATCCAACAAGGTTC 59.635 45.455 0.00 0.00 39.02 3.62
450 455 2.365293 GAGCCAAACATCCAACAAGGTT 59.635 45.455 0.00 0.00 39.02 3.50
451 456 1.963515 GAGCCAAACATCCAACAAGGT 59.036 47.619 0.00 0.00 39.02 3.50
452 457 1.068333 CGAGCCAAACATCCAACAAGG 60.068 52.381 0.00 0.00 39.47 3.61
453 458 1.068333 CCGAGCCAAACATCCAACAAG 60.068 52.381 0.00 0.00 0.00 3.16
454 459 0.958091 CCGAGCCAAACATCCAACAA 59.042 50.000 0.00 0.00 0.00 2.83
455 460 0.893270 CCCGAGCCAAACATCCAACA 60.893 55.000 0.00 0.00 0.00 3.33
456 461 1.883021 CCCGAGCCAAACATCCAAC 59.117 57.895 0.00 0.00 0.00 3.77
457 462 1.976474 GCCCGAGCCAAACATCCAA 60.976 57.895 0.00 0.00 0.00 3.53
458 463 2.361104 GCCCGAGCCAAACATCCA 60.361 61.111 0.00 0.00 0.00 3.41
459 464 3.508840 CGCCCGAGCCAAACATCC 61.509 66.667 0.00 0.00 34.57 3.51
460 465 3.508840 CCGCCCGAGCCAAACATC 61.509 66.667 0.00 0.00 34.57 3.06
461 466 3.860930 AACCGCCCGAGCCAAACAT 62.861 57.895 0.00 0.00 34.57 2.71
462 467 4.572571 AACCGCCCGAGCCAAACA 62.573 61.111 0.00 0.00 34.57 2.83
463 468 3.292159 AAACCGCCCGAGCCAAAC 61.292 61.111 0.00 0.00 34.57 2.93
464 469 3.291383 CAAACCGCCCGAGCCAAA 61.291 61.111 0.00 0.00 34.57 3.28
468 473 1.654023 ATAAAGCAAACCGCCCGAGC 61.654 55.000 0.00 0.00 44.04 5.03
469 474 1.658994 TATAAAGCAAACCGCCCGAG 58.341 50.000 0.00 0.00 44.04 4.63
470 475 2.110901 TTATAAAGCAAACCGCCCGA 57.889 45.000 0.00 0.00 44.04 5.14
471 476 4.759516 ATATTATAAAGCAAACCGCCCG 57.240 40.909 0.00 0.00 44.04 6.13
482 487 6.730960 TTCGCCCCGCTTTATATTATAAAG 57.269 37.500 23.28 23.28 37.53 1.85
483 488 6.348704 GCTTTCGCCCCGCTTTATATTATAAA 60.349 38.462 8.26 8.26 0.00 1.40
484 489 5.122711 GCTTTCGCCCCGCTTTATATTATAA 59.877 40.000 0.00 0.00 0.00 0.98
485 490 4.632688 GCTTTCGCCCCGCTTTATATTATA 59.367 41.667 0.00 0.00 0.00 0.98
486 491 3.439129 GCTTTCGCCCCGCTTTATATTAT 59.561 43.478 0.00 0.00 0.00 1.28
487 492 2.809696 GCTTTCGCCCCGCTTTATATTA 59.190 45.455 0.00 0.00 0.00 0.98
488 493 1.607148 GCTTTCGCCCCGCTTTATATT 59.393 47.619 0.00 0.00 0.00 1.28
489 494 1.235724 GCTTTCGCCCCGCTTTATAT 58.764 50.000 0.00 0.00 0.00 0.86
490 495 2.697819 GCTTTCGCCCCGCTTTATA 58.302 52.632 0.00 0.00 0.00 0.98
491 496 3.509659 GCTTTCGCCCCGCTTTAT 58.490 55.556 0.00 0.00 0.00 1.40
499 504 6.807607 TTTTACCGAAAAAGGCTTTCGCCC 62.808 45.833 13.76 2.28 46.89 6.13
500 505 3.796165 TTTTACCGAAAAAGGCTTTCGCC 60.796 43.478 13.76 0.00 46.89 5.54
501 506 2.691984 TTACCGAAAAAGGCTTTCGC 57.308 45.000 13.76 7.41 46.89 4.70
503 508 7.342194 GTTTGATTTTACCGAAAAAGGCTTTC 58.658 34.615 13.76 0.41 40.32 2.62
504 509 6.019398 CGTTTGATTTTACCGAAAAAGGCTTT 60.019 34.615 6.68 6.68 40.32 3.51
505 510 5.460748 CGTTTGATTTTACCGAAAAAGGCTT 59.539 36.000 0.00 0.00 40.32 4.35
506 511 4.979815 CGTTTGATTTTACCGAAAAAGGCT 59.020 37.500 0.00 0.00 40.32 4.58
507 512 4.375606 GCGTTTGATTTTACCGAAAAAGGC 60.376 41.667 0.00 0.00 40.32 4.35
508 513 4.979815 AGCGTTTGATTTTACCGAAAAAGG 59.020 37.500 0.00 0.00 40.32 3.11
509 514 5.116528 GGAGCGTTTGATTTTACCGAAAAAG 59.883 40.000 0.00 0.00 40.32 2.27
510 515 4.977347 GGAGCGTTTGATTTTACCGAAAAA 59.023 37.500 0.00 0.00 41.21 1.94
511 516 4.538917 GGAGCGTTTGATTTTACCGAAAA 58.461 39.130 0.00 0.00 38.87 2.29
512 517 3.058085 GGGAGCGTTTGATTTTACCGAAA 60.058 43.478 0.00 0.00 0.00 3.46
513 518 2.485038 GGGAGCGTTTGATTTTACCGAA 59.515 45.455 0.00 0.00 0.00 4.30
514 519 2.078392 GGGAGCGTTTGATTTTACCGA 58.922 47.619 0.00 0.00 0.00 4.69
515 520 2.081462 AGGGAGCGTTTGATTTTACCG 58.919 47.619 0.00 0.00 0.00 4.02
516 521 4.004982 TGTAGGGAGCGTTTGATTTTACC 58.995 43.478 0.00 0.00 0.00 2.85
517 522 5.813080 ATGTAGGGAGCGTTTGATTTTAC 57.187 39.130 0.00 0.00 0.00 2.01
518 523 6.827586 AAATGTAGGGAGCGTTTGATTTTA 57.172 33.333 0.00 0.00 0.00 1.52
586 623 1.462731 AATCAAACTGCAAGCGCCCA 61.463 50.000 2.29 0.00 37.60 5.36
669 706 2.081425 CTCTCCGAATCCCAGCCTCG 62.081 65.000 0.00 0.00 0.00 4.63
736 773 1.602416 GCCCGTCCGATTAAGCTACTC 60.602 57.143 0.00 0.00 0.00 2.59
806 843 0.319727 GCAGATGAGATCAGCGGGAG 60.320 60.000 0.00 0.00 37.34 4.30
807 844 1.744639 GCAGATGAGATCAGCGGGA 59.255 57.895 0.00 0.00 37.34 5.14
808 845 1.301558 GGCAGATGAGATCAGCGGG 60.302 63.158 0.00 0.00 42.05 6.13
809 846 0.319727 GAGGCAGATGAGATCAGCGG 60.320 60.000 0.00 0.00 42.05 5.52
941 990 1.135139 CGATCGGAGAAGGCAAGAGAA 59.865 52.381 7.38 0.00 43.58 2.87
1155 2623 4.275936 GCCAAACAAGGAAGCATATACGAT 59.724 41.667 0.00 0.00 0.00 3.73
1179 2647 3.057596 GGAAACATTTTCTCACATGCGGA 60.058 43.478 0.00 0.00 0.00 5.54
1259 2948 2.618312 GAATGGCATGCGACAAGGCC 62.618 60.000 12.44 14.48 46.58 5.19
1302 2991 0.618458 ATTCTTCTACTGGCCGGCAA 59.382 50.000 30.85 18.34 0.00 4.52
1386 3076 7.228706 AGTCACTTTTGTTACGATGAAGGAAAT 59.771 33.333 0.00 0.00 32.20 2.17
1390 3080 5.924475 AGTCACTTTTGTTACGATGAAGG 57.076 39.130 0.00 0.00 32.20 3.46
1407 3196 7.117956 GGTCAAGGATCAGTTAAAGTTAGTCAC 59.882 40.741 0.00 0.00 0.00 3.67
1545 3597 2.203788 TCCTTCTGGCTCACCGGT 60.204 61.111 0.00 0.00 43.58 5.28
1566 3630 3.555324 TGGGTCTTGCGCCACTCA 61.555 61.111 4.18 1.61 0.00 3.41
1906 3990 1.592081 CAACAAACATTGCCACGGTTG 59.408 47.619 0.00 0.00 0.00 3.77
1948 4032 9.601217 ACTGATACTTTGTTACATATGGAGAAC 57.399 33.333 7.80 8.75 0.00 3.01
1954 4038 9.524106 TTCCGTACTGATACTTTGTTACATATG 57.476 33.333 0.00 0.00 0.00 1.78
1964 4048 5.163581 ACGTGCTATTCCGTACTGATACTTT 60.164 40.000 0.00 0.00 35.16 2.66
1965 4049 4.337555 ACGTGCTATTCCGTACTGATACTT 59.662 41.667 0.00 0.00 35.16 2.24
1996 4094 4.568152 ACATTTGTCCTACAGTTTGTGC 57.432 40.909 0.00 0.00 0.00 4.57
1997 4095 5.280945 CCAACATTTGTCCTACAGTTTGTG 58.719 41.667 0.00 0.00 0.00 3.33
1998 4096 4.340950 CCCAACATTTGTCCTACAGTTTGT 59.659 41.667 0.00 0.00 0.00 2.83
2000 4098 3.895041 CCCCAACATTTGTCCTACAGTTT 59.105 43.478 0.00 0.00 0.00 2.66
2001 4099 3.117284 ACCCCAACATTTGTCCTACAGTT 60.117 43.478 0.00 0.00 0.00 3.16
2002 4100 2.445525 ACCCCAACATTTGTCCTACAGT 59.554 45.455 0.00 0.00 0.00 3.55
2004 4102 2.870175 CACCCCAACATTTGTCCTACA 58.130 47.619 0.00 0.00 0.00 2.74
2005 4103 1.544246 GCACCCCAACATTTGTCCTAC 59.456 52.381 0.00 0.00 0.00 3.18
2006 4104 1.145945 TGCACCCCAACATTTGTCCTA 59.854 47.619 0.00 0.00 0.00 2.94
2007 4105 0.105760 TGCACCCCAACATTTGTCCT 60.106 50.000 0.00 0.00 0.00 3.85
2011 4114 2.671130 GGTATGCACCCCAACATTTG 57.329 50.000 0.00 0.00 39.11 2.32
2083 4186 4.396166 ACCAAGTTGCTTCATATGTACAGC 59.604 41.667 0.33 13.92 0.00 4.40
2085 4188 5.767665 ACAACCAAGTTGCTTCATATGTACA 59.232 36.000 7.36 0.00 46.20 2.90
2179 7549 4.465512 GTGATTGCACCAGCCGCG 62.466 66.667 0.00 0.00 41.13 6.46
2185 7555 0.890542 GTGAGCCTGTGATTGCACCA 60.891 55.000 0.00 0.00 44.51 4.17
2192 7562 0.910338 ATCAGCTGTGAGCCTGTGAT 59.090 50.000 14.67 0.00 43.77 3.06
2193 7563 1.560505 TATCAGCTGTGAGCCTGTGA 58.439 50.000 14.67 0.00 43.77 3.58
2194 7564 2.616634 ATATCAGCTGTGAGCCTGTG 57.383 50.000 14.67 0.00 43.77 3.66
2195 7565 4.760530 TTTATATCAGCTGTGAGCCTGT 57.239 40.909 14.67 0.00 43.77 4.00
2196 7566 5.048921 CCATTTTATATCAGCTGTGAGCCTG 60.049 44.000 14.67 3.63 43.77 4.85
2389 7765 7.434492 TCTAACGAAGAATATTGGATGGTCTC 58.566 38.462 0.00 0.00 0.00 3.36
2390 7766 7.361457 TCTAACGAAGAATATTGGATGGTCT 57.639 36.000 0.00 0.00 0.00 3.85
2391 7767 7.360438 GCATCTAACGAAGAATATTGGATGGTC 60.360 40.741 10.35 0.00 40.04 4.02
2392 7768 6.428159 GCATCTAACGAAGAATATTGGATGGT 59.572 38.462 10.35 0.00 40.04 3.55
2423 7799 3.431233 GCCGACCAACTTAAGTCTTGTAC 59.569 47.826 8.95 0.67 0.00 2.90
2573 7956 5.359756 CCCTGTGATGATCAGATTTTCGTA 58.640 41.667 0.09 0.00 35.20 3.43
2598 7981 3.949113 TGTGTAAACTCAAACCAACTCCC 59.051 43.478 0.00 0.00 0.00 4.30
2619 8007 0.312729 TGTTGCTGTCATGCTTGCTG 59.687 50.000 0.00 0.00 0.00 4.41
2620 8008 1.000607 CTTGTTGCTGTCATGCTTGCT 60.001 47.619 0.00 0.00 0.00 3.91
2626 8014 8.877808 TTAGATAGATACTTGTTGCTGTCATG 57.122 34.615 0.00 0.00 0.00 3.07
2653 8336 8.031864 ACAAAGTTGACTCTGAGATGTATACAG 58.968 37.037 12.44 0.00 0.00 2.74
2713 8396 1.738099 CTTCCGTGACGCCTGAAGG 60.738 63.158 12.57 0.00 32.49 3.46
2871 8560 2.991190 GTTTAGAGCGACACAATTCCGA 59.009 45.455 0.00 0.00 0.00 4.55


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

AutoCloner maintained by Alex Coulton.