Multiple sequence alignment - TraesCS7A01G107700

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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 TraesCS7A01G107700 chr7A 100.000 3494 0 0 1 3494 65155840 65152347 0.000000e+00 6453
1 TraesCS7A01G107700 chr7A 88.519 1080 118 6 1774 2850 65551802 65550726 0.000000e+00 1303
2 TraesCS7A01G107700 chr7A 82.084 1334 228 10 1138 2466 65441918 65443245 0.000000e+00 1129
3 TraesCS7A01G107700 chr7A 87.423 326 35 5 3170 3492 65545561 65545239 1.530000e-98 370
4 TraesCS7A01G107700 chr7A 93.117 247 17 0 296 542 171538419 171538665 2.560000e-96 363
5 TraesCS7A01G107700 chr7A 93.023 129 9 0 2853 2981 294405149 294405021 4.600000e-44 189
6 TraesCS7A01G107700 chr7D 97.550 2204 51 3 538 2739 61229392 61227190 0.000000e+00 3768
7 TraesCS7A01G107700 chr7D 88.769 1478 162 4 1024 2499 60705558 60704083 0.000000e+00 1807
8 TraesCS7A01G107700 chr7D 82.443 1367 222 17 1138 2495 62280164 62281521 0.000000e+00 1179
9 TraesCS7A01G107700 chr7D 81.764 1338 233 10 1138 2470 62122074 62123405 0.000000e+00 1109
10 TraesCS7A01G107700 chr7D 94.200 500 25 2 2977 3472 61226791 61226292 0.000000e+00 760
11 TraesCS7A01G107700 chr7D 96.591 264 8 1 1 263 61229652 61229389 1.490000e-118 436
12 TraesCS7A01G107700 chr7D 92.829 251 18 0 296 546 90452980 90452730 7.130000e-97 364
13 TraesCS7A01G107700 chr7D 94.815 135 4 1 2734 2865 61226922 61226788 1.270000e-49 207
14 TraesCS7A01G107700 chr7B 86.481 1472 197 2 1024 2494 3342531 3341061 0.000000e+00 1615
15 TraesCS7A01G107700 chr7B 85.411 1556 219 8 997 2548 3540080 3541631 0.000000e+00 1609
16 TraesCS7A01G107700 chr7B 87.471 1309 133 7 1340 2644 3507860 3506579 0.000000e+00 1480
17 TraesCS7A01G107700 chr7B 86.017 236 32 1 867 1101 3509786 3509551 5.790000e-63 252
18 TraesCS7A01G107700 chr7B 82.594 293 33 7 549 832 3510071 3509788 3.480000e-60 243
19 TraesCS7A01G107700 chr2B 82.677 1270 213 5 1200 2467 731536559 731535295 0.000000e+00 1120
20 TraesCS7A01G107700 chr2B 88.000 100 11 1 80 178 485340295 485340394 2.200000e-22 117
21 TraesCS7A01G107700 chrUn 93.117 247 17 0 296 542 262503060 262502814 2.560000e-96 363
22 TraesCS7A01G107700 chrUn 93.117 247 17 0 296 542 322126449 322126203 2.560000e-96 363
23 TraesCS7A01G107700 chr6B 92.800 250 18 0 292 541 682836285 682836534 2.560000e-96 363
24 TraesCS7A01G107700 chr4D 92.800 250 18 0 292 541 154797339 154797090 2.560000e-96 363
25 TraesCS7A01G107700 chr3D 93.117 247 17 0 292 538 6672550 6672796 2.560000e-96 363
26 TraesCS7A01G107700 chr3D 96.667 120 4 0 2863 2982 337959509 337959628 2.130000e-47 200
27 TraesCS7A01G107700 chr1D 92.771 249 18 0 292 540 203866450 203866202 9.220000e-96 361
28 TraesCS7A01G107700 chr6D 92.430 251 19 0 292 542 455101068 455100818 3.320000e-95 359
29 TraesCS7A01G107700 chr6D 92.958 142 7 3 2845 2986 348647322 348647460 1.640000e-48 204
30 TraesCS7A01G107700 chr5A 96.721 122 4 0 2858 2979 505594138 505594259 1.640000e-48 204
31 TraesCS7A01G107700 chr2A 97.458 118 3 0 2863 2980 175483356 175483473 5.910000e-48 202
32 TraesCS7A01G107700 chr2A 96.721 122 2 2 2859 2979 429716290 429716170 5.910000e-48 202
33 TraesCS7A01G107700 chr6A 96.667 120 2 2 2862 2980 448220909 448220791 7.650000e-47 198
34 TraesCS7A01G107700 chr6A 93.798 129 7 1 2856 2984 348784980 348784853 3.560000e-45 193
35 TraesCS7A01G107700 chr3B 93.893 131 5 3 2851 2979 504148793 504148922 9.900000e-46 195


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 TraesCS7A01G107700 chr7A 65152347 65155840 3493 True 6453.000000 6453 100.000000 1 3494 1 chr7A.!!$R1 3493
1 TraesCS7A01G107700 chr7A 65550726 65551802 1076 True 1303.000000 1303 88.519000 1774 2850 1 chr7A.!!$R3 1076
2 TraesCS7A01G107700 chr7A 65441918 65443245 1327 False 1129.000000 1129 82.084000 1138 2466 1 chr7A.!!$F1 1328
3 TraesCS7A01G107700 chr7D 60704083 60705558 1475 True 1807.000000 1807 88.769000 1024 2499 1 chr7D.!!$R1 1475
4 TraesCS7A01G107700 chr7D 61226292 61229652 3360 True 1292.750000 3768 95.789000 1 3472 4 chr7D.!!$R3 3471
5 TraesCS7A01G107700 chr7D 62280164 62281521 1357 False 1179.000000 1179 82.443000 1138 2495 1 chr7D.!!$F2 1357
6 TraesCS7A01G107700 chr7D 62122074 62123405 1331 False 1109.000000 1109 81.764000 1138 2470 1 chr7D.!!$F1 1332
7 TraesCS7A01G107700 chr7B 3341061 3342531 1470 True 1615.000000 1615 86.481000 1024 2494 1 chr7B.!!$R1 1470
8 TraesCS7A01G107700 chr7B 3540080 3541631 1551 False 1609.000000 1609 85.411000 997 2548 1 chr7B.!!$F1 1551
9 TraesCS7A01G107700 chr7B 3506579 3510071 3492 True 658.333333 1480 85.360667 549 2644 3 chr7B.!!$R2 2095
10 TraesCS7A01G107700 chr2B 731535295 731536559 1264 True 1120.000000 1120 82.677000 1200 2467 1 chr2B.!!$R1 1267

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
285 287 0.036952 ATTCACAGACTCACAGCGGG 60.037 55.0 0.00 0.00 0.0 6.13 F
850 862 0.232303 CGGTGTGCAGAGAAACGTTC 59.768 55.0 0.00 0.00 0.0 3.95 F
995 1007 0.748005 CCCTTACGGTTGCATCCTGG 60.748 60.0 11.96 8.21 0.0 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1848 3326 0.027455 TCGACAACAACTTTGCAGCG 59.973 50.000 0.0 0.0 0.00 5.18 R
2157 3635 2.091588 GCAGAAATGCTCAAATGCAACG 59.908 45.455 0.0 0.0 46.61 4.10 R
2963 4715 0.107508 TACGTACTCCCTCCGTCCAG 60.108 60.000 0.0 0.0 36.12 3.86 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
79 81 1.467342 CCATAGCATGCATCCGATGTG 59.533 52.381 21.98 6.30 0.00 3.21
116 118 2.101783 TGCACCATTTTCCCTATGCAG 58.898 47.619 0.00 0.00 38.11 4.41
147 149 2.996621 CACGAAGGAAGCAGTAAGAAGG 59.003 50.000 0.00 0.00 0.00 3.46
186 188 2.083774 TGATTTTCTGGAATCGCGCTT 58.916 42.857 5.56 0.00 38.57 4.68
242 244 0.804989 CCCGAAAAGTCACCATGAGC 59.195 55.000 0.00 0.00 0.00 4.26
259 261 1.563173 GCGAACGCGAGAAAACAGT 59.437 52.632 15.93 0.00 40.82 3.55
260 262 0.042448 GCGAACGCGAGAAAACAGTT 60.042 50.000 15.93 0.00 40.82 3.16
261 263 1.190763 GCGAACGCGAGAAAACAGTTA 59.809 47.619 15.93 0.00 40.82 2.24
262 264 2.717893 GCGAACGCGAGAAAACAGTTAG 60.718 50.000 15.93 0.00 40.82 2.34
263 265 2.722629 CGAACGCGAGAAAACAGTTAGA 59.277 45.455 15.93 0.00 40.82 2.10
264 266 3.420162 CGAACGCGAGAAAACAGTTAGAC 60.420 47.826 15.93 0.00 40.82 2.59
265 267 3.366440 ACGCGAGAAAACAGTTAGACT 57.634 42.857 15.93 0.00 0.00 3.24
266 268 4.494350 ACGCGAGAAAACAGTTAGACTA 57.506 40.909 15.93 0.00 0.00 2.59
267 269 5.056894 ACGCGAGAAAACAGTTAGACTAT 57.943 39.130 15.93 0.00 0.00 2.12
268 270 5.467705 ACGCGAGAAAACAGTTAGACTATT 58.532 37.500 15.93 0.00 0.00 1.73
269 271 5.572126 ACGCGAGAAAACAGTTAGACTATTC 59.428 40.000 15.93 0.00 0.00 1.75
270 272 5.571741 CGCGAGAAAACAGTTAGACTATTCA 59.428 40.000 0.00 0.00 0.00 2.57
271 273 6.452611 CGCGAGAAAACAGTTAGACTATTCAC 60.453 42.308 0.00 0.00 0.00 3.18
272 274 6.365247 GCGAGAAAACAGTTAGACTATTCACA 59.635 38.462 0.00 0.00 0.00 3.58
273 275 7.410942 GCGAGAAAACAGTTAGACTATTCACAG 60.411 40.741 0.00 0.00 0.00 3.66
274 276 7.808381 CGAGAAAACAGTTAGACTATTCACAGA 59.192 37.037 0.00 0.00 0.00 3.41
275 277 8.819643 AGAAAACAGTTAGACTATTCACAGAC 57.180 34.615 0.00 0.00 0.00 3.51
276 278 8.643324 AGAAAACAGTTAGACTATTCACAGACT 58.357 33.333 0.00 0.00 0.00 3.24
277 279 8.819643 AAAACAGTTAGACTATTCACAGACTC 57.180 34.615 0.00 0.00 0.00 3.36
278 280 7.526142 AACAGTTAGACTATTCACAGACTCA 57.474 36.000 0.00 0.00 0.00 3.41
279 281 6.915349 ACAGTTAGACTATTCACAGACTCAC 58.085 40.000 0.00 0.00 0.00 3.51
280 282 6.490381 ACAGTTAGACTATTCACAGACTCACA 59.510 38.462 0.00 0.00 0.00 3.58
281 283 7.026562 CAGTTAGACTATTCACAGACTCACAG 58.973 42.308 0.00 0.00 0.00 3.66
282 284 4.448537 AGACTATTCACAGACTCACAGC 57.551 45.455 0.00 0.00 0.00 4.40
283 285 3.119673 AGACTATTCACAGACTCACAGCG 60.120 47.826 0.00 0.00 0.00 5.18
284 286 2.094494 ACTATTCACAGACTCACAGCGG 60.094 50.000 0.00 0.00 0.00 5.52
285 287 0.036952 ATTCACAGACTCACAGCGGG 60.037 55.000 0.00 0.00 0.00 6.13
286 288 1.112916 TTCACAGACTCACAGCGGGA 61.113 55.000 0.00 0.00 0.00 5.14
287 289 1.112916 TCACAGACTCACAGCGGGAA 61.113 55.000 0.00 0.00 0.00 3.97
288 290 0.249868 CACAGACTCACAGCGGGAAA 60.250 55.000 0.00 0.00 0.00 3.13
289 291 0.687354 ACAGACTCACAGCGGGAAAT 59.313 50.000 0.00 0.00 0.00 2.17
290 292 1.899814 ACAGACTCACAGCGGGAAATA 59.100 47.619 0.00 0.00 0.00 1.40
291 293 2.301870 ACAGACTCACAGCGGGAAATAA 59.698 45.455 0.00 0.00 0.00 1.40
292 294 2.673368 CAGACTCACAGCGGGAAATAAC 59.327 50.000 0.00 0.00 0.00 1.89
293 295 2.567615 AGACTCACAGCGGGAAATAACT 59.432 45.455 0.00 0.00 0.00 2.24
294 296 3.008049 AGACTCACAGCGGGAAATAACTT 59.992 43.478 0.00 0.00 0.00 2.66
295 297 3.074412 ACTCACAGCGGGAAATAACTTG 58.926 45.455 0.00 0.00 0.00 3.16
296 298 3.074412 CTCACAGCGGGAAATAACTTGT 58.926 45.455 0.00 0.00 0.00 3.16
297 299 4.250464 CTCACAGCGGGAAATAACTTGTA 58.750 43.478 0.00 0.00 0.00 2.41
298 300 4.643463 TCACAGCGGGAAATAACTTGTAA 58.357 39.130 0.00 0.00 0.00 2.41
299 301 4.453136 TCACAGCGGGAAATAACTTGTAAC 59.547 41.667 0.00 0.00 0.00 2.50
300 302 4.214545 CACAGCGGGAAATAACTTGTAACA 59.785 41.667 0.00 0.00 0.00 2.41
301 303 5.007682 ACAGCGGGAAATAACTTGTAACAT 58.992 37.500 0.00 0.00 0.00 2.71
302 304 5.106317 ACAGCGGGAAATAACTTGTAACATG 60.106 40.000 0.00 0.00 0.00 3.21
303 305 5.123186 CAGCGGGAAATAACTTGTAACATGA 59.877 40.000 0.00 0.00 0.00 3.07
304 306 5.708230 AGCGGGAAATAACTTGTAACATGAA 59.292 36.000 0.00 0.00 0.00 2.57
305 307 6.377146 AGCGGGAAATAACTTGTAACATGAAT 59.623 34.615 0.00 0.00 0.00 2.57
306 308 7.554835 AGCGGGAAATAACTTGTAACATGAATA 59.445 33.333 0.00 0.00 0.00 1.75
307 309 8.349983 GCGGGAAATAACTTGTAACATGAATAT 58.650 33.333 0.00 0.00 0.00 1.28
308 310 9.663904 CGGGAAATAACTTGTAACATGAATATG 57.336 33.333 0.00 0.00 40.24 1.78
330 332 9.878737 ATATGTTACTAGTCTATGTTACCACCT 57.121 33.333 0.00 0.00 0.00 4.00
331 333 7.636150 TGTTACTAGTCTATGTTACCACCTC 57.364 40.000 0.00 0.00 0.00 3.85
332 334 6.604795 TGTTACTAGTCTATGTTACCACCTCC 59.395 42.308 0.00 0.00 0.00 4.30
333 335 5.202746 ACTAGTCTATGTTACCACCTCCA 57.797 43.478 0.00 0.00 0.00 3.86
334 336 4.954826 ACTAGTCTATGTTACCACCTCCAC 59.045 45.833 0.00 0.00 0.00 4.02
335 337 3.786553 AGTCTATGTTACCACCTCCACA 58.213 45.455 0.00 0.00 0.00 4.17
336 338 3.769844 AGTCTATGTTACCACCTCCACAG 59.230 47.826 0.00 0.00 0.00 3.66
337 339 3.514309 GTCTATGTTACCACCTCCACAGT 59.486 47.826 0.00 0.00 0.00 3.55
338 340 2.859165 ATGTTACCACCTCCACAGTG 57.141 50.000 0.00 0.00 34.91 3.66
354 356 6.816136 TCCACAGTGGATAGTAACATATGTG 58.184 40.000 19.21 13.65 42.67 3.21
355 357 6.382859 TCCACAGTGGATAGTAACATATGTGT 59.617 38.462 19.21 2.63 42.67 3.72
356 358 7.047891 CCACAGTGGATAGTAACATATGTGTT 58.952 38.462 15.35 12.73 44.97 3.32
357 359 7.011389 CCACAGTGGATAGTAACATATGTGTTG 59.989 40.741 15.35 0.62 43.67 3.33
367 369 5.648178 AACATATGTGTTGTGTCATGCAT 57.352 34.783 9.63 0.00 46.43 3.96
368 370 5.239359 ACATATGTGTTGTGTCATGCATC 57.761 39.130 7.78 0.00 34.01 3.91
369 371 4.701171 ACATATGTGTTGTGTCATGCATCA 59.299 37.500 7.78 0.00 34.01 3.07
370 372 3.564235 ATGTGTTGTGTCATGCATCAC 57.436 42.857 10.76 10.76 35.43 3.06
371 373 2.574450 TGTGTTGTGTCATGCATCACT 58.426 42.857 16.78 0.00 35.82 3.41
372 374 2.950975 TGTGTTGTGTCATGCATCACTT 59.049 40.909 16.78 0.00 35.82 3.16
373 375 3.003585 TGTGTTGTGTCATGCATCACTTC 59.996 43.478 16.78 11.17 35.82 3.01
374 376 3.003585 GTGTTGTGTCATGCATCACTTCA 59.996 43.478 16.78 13.00 35.82 3.02
375 377 3.822167 TGTTGTGTCATGCATCACTTCAT 59.178 39.130 16.78 0.00 35.82 2.57
376 378 4.278919 TGTTGTGTCATGCATCACTTCATT 59.721 37.500 16.78 0.00 35.82 2.57
377 379 5.221283 TGTTGTGTCATGCATCACTTCATTT 60.221 36.000 16.78 0.00 35.82 2.32
378 380 6.016443 TGTTGTGTCATGCATCACTTCATTTA 60.016 34.615 16.78 0.00 35.82 1.40
379 381 6.762702 TGTGTCATGCATCACTTCATTTAT 57.237 33.333 16.78 0.00 35.82 1.40
380 382 7.160547 TGTGTCATGCATCACTTCATTTATT 57.839 32.000 16.78 0.00 35.82 1.40
381 383 8.278729 TGTGTCATGCATCACTTCATTTATTA 57.721 30.769 16.78 0.00 35.82 0.98
382 384 8.905850 TGTGTCATGCATCACTTCATTTATTAT 58.094 29.630 16.78 0.00 35.82 1.28
383 385 9.177304 GTGTCATGCATCACTTCATTTATTATG 57.823 33.333 1.37 0.00 0.00 1.90
384 386 8.905850 TGTCATGCATCACTTCATTTATTATGT 58.094 29.630 1.37 0.00 0.00 2.29
385 387 9.740239 GTCATGCATCACTTCATTTATTATGTT 57.260 29.630 0.00 0.00 0.00 2.71
386 388 9.738832 TCATGCATCACTTCATTTATTATGTTG 57.261 29.630 0.00 0.00 0.00 3.33
387 389 9.524106 CATGCATCACTTCATTTATTATGTTGT 57.476 29.630 0.00 0.00 0.00 3.32
440 442 8.648698 TGTTACAGTAACTACCTATGTTACCA 57.351 34.615 21.56 0.00 46.31 3.25
441 443 8.522830 TGTTACAGTAACTACCTATGTTACCAC 58.477 37.037 21.56 6.27 46.31 4.16
442 444 8.522830 GTTACAGTAACTACCTATGTTACCACA 58.477 37.037 15.22 0.00 46.31 4.17
443 445 7.729124 ACAGTAACTACCTATGTTACCACAT 57.271 36.000 11.59 0.00 46.31 3.21
444 446 7.553334 ACAGTAACTACCTATGTTACCACATG 58.447 38.462 11.59 0.00 46.31 3.21
445 447 6.479001 CAGTAACTACCTATGTTACCACATGC 59.521 42.308 11.59 0.00 46.31 4.06
446 448 4.417426 ACTACCTATGTTACCACATGCC 57.583 45.455 0.00 0.00 43.92 4.40
447 449 4.037927 ACTACCTATGTTACCACATGCCT 58.962 43.478 0.00 0.00 43.92 4.75
448 450 3.560636 ACCTATGTTACCACATGCCTC 57.439 47.619 0.00 0.00 43.92 4.70
449 451 3.115390 ACCTATGTTACCACATGCCTCT 58.885 45.455 0.00 0.00 43.92 3.69
450 452 3.523564 ACCTATGTTACCACATGCCTCTT 59.476 43.478 0.00 0.00 43.92 2.85
451 453 4.018415 ACCTATGTTACCACATGCCTCTTT 60.018 41.667 0.00 0.00 43.92 2.52
452 454 4.949856 CCTATGTTACCACATGCCTCTTTT 59.050 41.667 0.00 0.00 43.92 2.27
453 455 5.418840 CCTATGTTACCACATGCCTCTTTTT 59.581 40.000 0.00 0.00 43.92 1.94
454 456 4.846779 TGTTACCACATGCCTCTTTTTC 57.153 40.909 0.00 0.00 0.00 2.29
455 457 4.469657 TGTTACCACATGCCTCTTTTTCT 58.530 39.130 0.00 0.00 0.00 2.52
456 458 4.892934 TGTTACCACATGCCTCTTTTTCTT 59.107 37.500 0.00 0.00 0.00 2.52
457 459 5.362430 TGTTACCACATGCCTCTTTTTCTTT 59.638 36.000 0.00 0.00 0.00 2.52
458 460 6.547880 TGTTACCACATGCCTCTTTTTCTTTA 59.452 34.615 0.00 0.00 0.00 1.85
459 461 7.232534 TGTTACCACATGCCTCTTTTTCTTTAT 59.767 33.333 0.00 0.00 0.00 1.40
460 462 6.670695 ACCACATGCCTCTTTTTCTTTATT 57.329 33.333 0.00 0.00 0.00 1.40
461 463 7.775053 ACCACATGCCTCTTTTTCTTTATTA 57.225 32.000 0.00 0.00 0.00 0.98
462 464 8.189119 ACCACATGCCTCTTTTTCTTTATTAA 57.811 30.769 0.00 0.00 0.00 1.40
463 465 8.815912 ACCACATGCCTCTTTTTCTTTATTAAT 58.184 29.630 0.00 0.00 0.00 1.40
464 466 9.657419 CCACATGCCTCTTTTTCTTTATTAATT 57.343 29.630 0.00 0.00 0.00 1.40
487 489 8.597662 ATTAAATGCCACATCATCTATTTTGC 57.402 30.769 0.00 0.00 0.00 3.68
488 490 4.595762 ATGCCACATCATCTATTTTGCC 57.404 40.909 0.00 0.00 0.00 4.52
489 491 3.634504 TGCCACATCATCTATTTTGCCT 58.365 40.909 0.00 0.00 0.00 4.75
490 492 4.790937 TGCCACATCATCTATTTTGCCTA 58.209 39.130 0.00 0.00 0.00 3.93
491 493 4.823442 TGCCACATCATCTATTTTGCCTAG 59.177 41.667 0.00 0.00 0.00 3.02
492 494 5.065914 GCCACATCATCTATTTTGCCTAGA 58.934 41.667 0.00 0.00 0.00 2.43
493 495 5.709164 GCCACATCATCTATTTTGCCTAGAT 59.291 40.000 0.00 0.00 36.58 1.98
494 496 6.881065 GCCACATCATCTATTTTGCCTAGATA 59.119 38.462 0.00 0.00 34.84 1.98
495 497 7.391554 GCCACATCATCTATTTTGCCTAGATAA 59.608 37.037 0.00 0.00 34.84 1.75
496 498 9.288576 CCACATCATCTATTTTGCCTAGATAAA 57.711 33.333 0.00 0.00 34.84 1.40
510 512 9.502091 TTGCCTAGATAAATATGATGTTACCAC 57.498 33.333 0.00 0.00 0.00 4.16
511 513 8.880244 TGCCTAGATAAATATGATGTTACCACT 58.120 33.333 0.00 0.00 0.00 4.00
512 514 9.726438 GCCTAGATAAATATGATGTTACCACTT 57.274 33.333 0.00 0.00 0.00 3.16
522 524 9.998106 ATATGATGTTACCACTTATGTTACTCC 57.002 33.333 0.00 0.00 0.00 3.85
523 525 6.646267 TGATGTTACCACTTATGTTACTCCC 58.354 40.000 0.00 0.00 0.00 4.30
524 526 6.213802 TGATGTTACCACTTATGTTACTCCCA 59.786 38.462 0.00 0.00 0.00 4.37
525 527 5.797051 TGTTACCACTTATGTTACTCCCAC 58.203 41.667 0.00 0.00 0.00 4.61
526 528 3.994931 ACCACTTATGTTACTCCCACC 57.005 47.619 0.00 0.00 0.00 4.61
527 529 2.235402 ACCACTTATGTTACTCCCACCG 59.765 50.000 0.00 0.00 0.00 4.94
528 530 2.235402 CCACTTATGTTACTCCCACCGT 59.765 50.000 0.00 0.00 0.00 4.83
529 531 3.259064 CACTTATGTTACTCCCACCGTG 58.741 50.000 0.00 0.00 0.00 4.94
530 532 2.235402 ACTTATGTTACTCCCACCGTGG 59.765 50.000 10.95 10.95 37.25 4.94
578 581 6.207417 TCAAAACCTCTTGTCCATCTTCAATC 59.793 38.462 0.00 0.00 0.00 2.67
583 586 6.881602 ACCTCTTGTCCATCTTCAATCTTTAC 59.118 38.462 0.00 0.00 0.00 2.01
653 665 5.510671 GTGATATGAAAAACATGGGCTACG 58.489 41.667 0.00 0.00 39.77 3.51
701 713 2.557490 GTGGAGTAGTTGAGAAGTCGGT 59.443 50.000 0.00 0.00 0.00 4.69
741 753 3.692576 AGTACAACTATCGTCGCACATC 58.307 45.455 0.00 0.00 0.00 3.06
761 773 8.186821 GCACATCTACTATTGCAGAATTCTTTT 58.813 33.333 4.86 0.00 34.97 2.27
834 846 5.943416 TGAATGTTGTTATGGAAGATTCGGT 59.057 36.000 0.00 0.00 36.40 4.69
850 862 0.232303 CGGTGTGCAGAGAAACGTTC 59.768 55.000 0.00 0.00 0.00 3.95
851 863 1.583054 GGTGTGCAGAGAAACGTTCT 58.417 50.000 0.00 0.00 44.21 3.01
899 911 1.134521 AGTTGACGCTTGGACAGTTGA 60.135 47.619 0.00 0.00 0.00 3.18
995 1007 0.748005 CCCTTACGGTTGCATCCTGG 60.748 60.000 11.96 8.21 0.00 4.45
1029 1042 2.080286 ACTACGCTACCAGCAACAAG 57.920 50.000 0.00 0.00 42.58 3.16
1084 1097 1.156736 GTTGTACAATCGCACTGCCT 58.843 50.000 12.26 0.00 0.00 4.75
1128 1427 1.961277 CACAACCACACTCGGAGCC 60.961 63.158 4.58 0.00 0.00 4.70
2157 3635 3.889538 GGCCATACATCCCTAACTTTTCC 59.110 47.826 0.00 0.00 0.00 3.13
2564 4043 4.202245 ACACTATTGCGTGTCCAATACT 57.798 40.909 0.00 0.00 44.32 2.12
2673 4152 9.788960 GAATGACTTTAAGGGTAATGATTTGAC 57.211 33.333 0.00 0.00 0.00 3.18
2745 4497 3.670627 CGCAAGGGAAAACTAAGATGCAC 60.671 47.826 0.00 0.00 33.00 4.57
2810 4562 2.299867 GGACAAATGCCTGACCAATTGT 59.700 45.455 4.43 0.00 40.48 2.71
2835 4587 5.808366 ACCTTACAGAACACAAGAGATCA 57.192 39.130 0.00 0.00 0.00 2.92
2871 4623 8.697507 AAAATGATTTATCATGTACTCCCTCC 57.302 34.615 6.01 0.00 46.22 4.30
2872 4624 7.392766 AATGATTTATCATGTACTCCCTCCA 57.607 36.000 6.01 0.00 46.22 3.86
2873 4625 7.579940 ATGATTTATCATGTACTCCCTCCAT 57.420 36.000 4.48 0.00 45.27 3.41
2874 4626 7.009179 TGATTTATCATGTACTCCCTCCATC 57.991 40.000 0.00 0.00 0.00 3.51
2875 4627 5.825593 TTTATCATGTACTCCCTCCATCC 57.174 43.478 0.00 0.00 0.00 3.51
2876 4628 1.704641 TCATGTACTCCCTCCATCCG 58.295 55.000 0.00 0.00 0.00 4.18
2877 4629 0.681733 CATGTACTCCCTCCATCCGG 59.318 60.000 0.00 0.00 0.00 5.14
2878 4630 0.561184 ATGTACTCCCTCCATCCGGA 59.439 55.000 6.61 6.61 39.79 5.14
2879 4631 0.337082 TGTACTCCCTCCATCCGGAA 59.663 55.000 9.01 0.00 42.21 4.30
2880 4632 1.273381 TGTACTCCCTCCATCCGGAAA 60.273 52.381 9.01 0.00 42.21 3.13
2881 4633 2.047830 GTACTCCCTCCATCCGGAAAT 58.952 52.381 9.01 0.00 42.21 2.17
2882 4634 2.489528 ACTCCCTCCATCCGGAAATA 57.510 50.000 9.01 0.00 42.21 1.40
2883 4635 2.047830 ACTCCCTCCATCCGGAAATAC 58.952 52.381 9.01 0.00 42.21 1.89
2884 4636 2.330216 CTCCCTCCATCCGGAAATACT 58.670 52.381 9.01 0.00 42.21 2.12
2885 4637 2.706190 CTCCCTCCATCCGGAAATACTT 59.294 50.000 9.01 0.00 42.21 2.24
2886 4638 2.438021 TCCCTCCATCCGGAAATACTTG 59.562 50.000 9.01 0.00 42.21 3.16
2887 4639 2.172717 CCCTCCATCCGGAAATACTTGT 59.827 50.000 9.01 0.00 42.21 3.16
2888 4640 3.467803 CCTCCATCCGGAAATACTTGTC 58.532 50.000 9.01 0.00 42.21 3.18
2889 4641 3.467803 CTCCATCCGGAAATACTTGTCC 58.532 50.000 9.01 0.00 42.21 4.02
2898 4650 3.877508 GGAAATACTTGTCCGAGGAATGG 59.122 47.826 0.00 0.00 0.00 3.16
2899 4651 4.383770 GGAAATACTTGTCCGAGGAATGGA 60.384 45.833 0.00 0.00 0.00 3.41
2900 4652 5.368989 GAAATACTTGTCCGAGGAATGGAT 58.631 41.667 0.00 0.00 37.93 3.41
2901 4653 2.698855 ACTTGTCCGAGGAATGGATG 57.301 50.000 0.00 0.00 37.93 3.51
2902 4654 1.909302 ACTTGTCCGAGGAATGGATGT 59.091 47.619 0.00 0.00 37.93 3.06
2903 4655 3.104512 ACTTGTCCGAGGAATGGATGTA 58.895 45.455 0.00 0.00 37.93 2.29
2904 4656 3.711704 ACTTGTCCGAGGAATGGATGTAT 59.288 43.478 0.00 0.00 37.93 2.29
2905 4657 4.202264 ACTTGTCCGAGGAATGGATGTATC 60.202 45.833 0.00 0.00 37.93 2.24
2906 4658 3.576861 TGTCCGAGGAATGGATGTATCT 58.423 45.455 0.00 0.00 37.93 1.98
2907 4659 4.736473 TGTCCGAGGAATGGATGTATCTA 58.264 43.478 0.00 0.00 37.93 1.98
2908 4660 4.767409 TGTCCGAGGAATGGATGTATCTAG 59.233 45.833 0.00 0.00 37.93 2.43
2909 4661 5.010933 GTCCGAGGAATGGATGTATCTAGA 58.989 45.833 0.00 0.00 37.93 2.43
2910 4662 5.654650 GTCCGAGGAATGGATGTATCTAGAT 59.345 44.000 10.73 10.73 37.93 1.98
2911 4663 5.654209 TCCGAGGAATGGATGTATCTAGATG 59.346 44.000 15.79 0.00 0.00 2.90
2912 4664 5.420421 CCGAGGAATGGATGTATCTAGATGT 59.580 44.000 15.79 1.25 0.00 3.06
2913 4665 6.603599 CCGAGGAATGGATGTATCTAGATGTA 59.396 42.308 15.79 4.44 0.00 2.29
2914 4666 7.286546 CCGAGGAATGGATGTATCTAGATGTAT 59.713 40.741 15.79 9.11 0.00 2.29
2915 4667 8.690884 CGAGGAATGGATGTATCTAGATGTATT 58.309 37.037 15.79 6.57 0.00 1.89
2967 4719 9.958180 TCAATTTCTATGACAAGTATTTCTGGA 57.042 29.630 0.00 0.00 0.00 3.86
2968 4720 9.994432 CAATTTCTATGACAAGTATTTCTGGAC 57.006 33.333 0.00 0.00 0.00 4.02
2969 4721 7.827819 TTTCTATGACAAGTATTTCTGGACG 57.172 36.000 0.00 0.00 0.00 4.79
2970 4722 5.902681 TCTATGACAAGTATTTCTGGACGG 58.097 41.667 0.00 0.00 0.00 4.79
2971 4723 4.819105 ATGACAAGTATTTCTGGACGGA 57.181 40.909 0.00 0.00 0.00 4.69
2972 4724 4.188247 TGACAAGTATTTCTGGACGGAG 57.812 45.455 0.00 0.00 0.00 4.63
2973 4725 3.056107 TGACAAGTATTTCTGGACGGAGG 60.056 47.826 0.00 0.00 0.00 4.30
2974 4726 2.236395 ACAAGTATTTCTGGACGGAGGG 59.764 50.000 0.00 0.00 0.00 4.30
2975 4727 2.500098 CAAGTATTTCTGGACGGAGGGA 59.500 50.000 0.00 0.00 0.00 4.20
2991 4743 3.370209 GGAGGGAGTACGTAAAATTGGCT 60.370 47.826 0.00 0.00 0.00 4.75
2996 4748 5.698089 GGGAGTACGTAAAATTGGCTATACC 59.302 44.000 0.00 0.00 39.84 2.73
3036 4788 8.684973 GGTAACTACACTGACAGTACATAAAG 57.315 38.462 8.02 2.67 0.00 1.85
3043 4795 6.479001 ACACTGACAGTACATAAAGTTGTCAC 59.521 38.462 8.02 0.00 40.97 3.67
3096 4848 1.202132 TGCGACAAACTTCACTTGTGC 60.202 47.619 0.00 0.00 37.14 4.57
3105 4858 7.816640 ACAAACTTCACTTGTGCGATATATTT 58.183 30.769 0.00 0.00 35.70 1.40
3129 4882 0.392863 CACATCATGCCAACGAGGGA 60.393 55.000 0.00 0.00 44.34 4.20
3231 4984 4.362677 TGGCCCTTCTCTACTTATCAAGT 58.637 43.478 0.00 0.00 45.40 3.16
3233 4986 4.123506 GCCCTTCTCTACTTATCAAGTGC 58.876 47.826 1.84 0.00 42.84 4.40
3234 4987 4.141824 GCCCTTCTCTACTTATCAAGTGCT 60.142 45.833 1.84 0.00 42.84 4.40
3270 5026 1.206523 GCGCGGTATAACCAAGAGAC 58.793 55.000 8.83 0.00 38.47 3.36
3339 5095 6.611613 TGAGTGGATCAGAAATTCAGTAGT 57.388 37.500 0.00 0.00 32.77 2.73
3344 5100 8.474025 AGTGGATCAGAAATTCAGTAGTAGAAG 58.526 37.037 0.00 0.00 0.00 2.85
3345 5101 8.254508 GTGGATCAGAAATTCAGTAGTAGAAGT 58.745 37.037 0.00 0.00 0.00 3.01
3353 5109 8.494016 AAATTCAGTAGTAGAAGTATGGTTGC 57.506 34.615 0.00 0.00 0.00 4.17
3399 5155 8.696175 GTTGGTAAATGAAATTTTAGGTGTTCG 58.304 33.333 0.00 0.00 46.10 3.95
3430 5186 1.335872 GGTGATTGTGTTTTGCTCCGG 60.336 52.381 0.00 0.00 0.00 5.14
3441 5197 4.095782 TGTTTTGCTCCGGTTATTAGCATC 59.904 41.667 14.81 9.56 45.09 3.91
3446 5202 3.804036 CTCCGGTTATTAGCATCAACCA 58.196 45.455 0.00 0.00 41.52 3.67
3472 5228 1.597854 TTGGCTCGCAGACAACTGG 60.598 57.895 0.88 0.00 38.55 4.00
3473 5229 2.038814 TTGGCTCGCAGACAACTGGA 62.039 55.000 0.88 0.00 38.55 3.86
3474 5230 1.301716 GGCTCGCAGACAACTGGAA 60.302 57.895 0.00 0.00 43.62 3.53
3475 5231 0.674895 GGCTCGCAGACAACTGGAAT 60.675 55.000 0.00 0.00 43.62 3.01
3476 5232 0.445436 GCTCGCAGACAACTGGAATG 59.555 55.000 0.00 0.00 43.62 2.67
3477 5233 0.445436 CTCGCAGACAACTGGAATGC 59.555 55.000 0.00 0.00 43.62 3.56
3478 5234 0.250252 TCGCAGACAACTGGAATGCA 60.250 50.000 0.00 0.00 43.62 3.96
3479 5235 0.592637 CGCAGACAACTGGAATGCAA 59.407 50.000 0.00 0.00 43.62 4.08
3480 5236 1.664016 CGCAGACAACTGGAATGCAAC 60.664 52.381 0.00 0.00 43.62 4.17
3481 5237 1.337703 GCAGACAACTGGAATGCAACA 59.662 47.619 0.00 0.00 43.62 3.33
3482 5238 2.223782 GCAGACAACTGGAATGCAACAA 60.224 45.455 0.00 0.00 43.62 2.83
3483 5239 3.374745 CAGACAACTGGAATGCAACAAC 58.625 45.455 0.00 0.00 40.14 3.32
3484 5240 2.033299 AGACAACTGGAATGCAACAACG 59.967 45.455 0.00 0.00 0.00 4.10
3485 5241 1.130955 CAACTGGAATGCAACAACGC 58.869 50.000 0.00 0.00 0.00 4.84
3487 5243 0.743688 ACTGGAATGCAACAACGCAA 59.256 45.000 0.00 0.00 46.87 4.85
3488 5244 1.269206 ACTGGAATGCAACAACGCAAG 60.269 47.619 0.00 0.00 46.87 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 6.973460 AGTACACAAAGGTCTAGTAACAGT 57.027 37.500 0.00 0.00 0.00 3.55
17 18 6.867293 GGAAGTACACAAAGGTCTAGTAACAG 59.133 42.308 0.00 0.00 0.00 3.16
79 81 1.081242 CATCTGGCAAACCGTGTGC 60.081 57.895 4.98 4.98 41.45 4.57
215 217 2.148768 GTGACTTTTCGGGTCGGAATT 58.851 47.619 0.00 0.00 36.58 2.17
242 244 2.722629 TCTAACTGTTTTCTCGCGTTCG 59.277 45.455 5.77 0.00 0.00 3.95
259 261 5.392057 CGCTGTGAGTCTGTGAATAGTCTAA 60.392 44.000 0.00 0.00 0.00 2.10
260 262 4.095036 CGCTGTGAGTCTGTGAATAGTCTA 59.905 45.833 0.00 0.00 0.00 2.59
261 263 3.119673 CGCTGTGAGTCTGTGAATAGTCT 60.120 47.826 0.00 0.00 0.00 3.24
262 264 3.175152 CGCTGTGAGTCTGTGAATAGTC 58.825 50.000 0.00 0.00 0.00 2.59
263 265 2.094494 CCGCTGTGAGTCTGTGAATAGT 60.094 50.000 0.00 0.00 0.00 2.12
264 266 2.534298 CCGCTGTGAGTCTGTGAATAG 58.466 52.381 0.00 0.00 0.00 1.73
265 267 1.204704 CCCGCTGTGAGTCTGTGAATA 59.795 52.381 0.00 0.00 0.00 1.75
266 268 0.036952 CCCGCTGTGAGTCTGTGAAT 60.037 55.000 0.00 0.00 0.00 2.57
267 269 1.112916 TCCCGCTGTGAGTCTGTGAA 61.113 55.000 0.00 0.00 0.00 3.18
268 270 1.112916 TTCCCGCTGTGAGTCTGTGA 61.113 55.000 0.00 0.00 0.00 3.58
269 271 0.249868 TTTCCCGCTGTGAGTCTGTG 60.250 55.000 0.00 0.00 0.00 3.66
270 272 0.687354 ATTTCCCGCTGTGAGTCTGT 59.313 50.000 0.00 0.00 0.00 3.41
271 273 2.672961 TATTTCCCGCTGTGAGTCTG 57.327 50.000 0.00 0.00 0.00 3.51
272 274 2.567615 AGTTATTTCCCGCTGTGAGTCT 59.432 45.455 0.00 0.00 0.00 3.24
273 275 2.973945 AGTTATTTCCCGCTGTGAGTC 58.026 47.619 0.00 0.00 0.00 3.36
274 276 3.074412 CAAGTTATTTCCCGCTGTGAGT 58.926 45.455 0.00 0.00 0.00 3.41
275 277 3.074412 ACAAGTTATTTCCCGCTGTGAG 58.926 45.455 0.00 0.00 0.00 3.51
276 278 3.134574 ACAAGTTATTTCCCGCTGTGA 57.865 42.857 0.00 0.00 0.00 3.58
277 279 4.214545 TGTTACAAGTTATTTCCCGCTGTG 59.785 41.667 0.00 0.00 0.00 3.66
278 280 4.391155 TGTTACAAGTTATTTCCCGCTGT 58.609 39.130 0.00 0.00 0.00 4.40
279 281 5.123186 TCATGTTACAAGTTATTTCCCGCTG 59.877 40.000 0.00 0.00 0.00 5.18
280 282 5.250200 TCATGTTACAAGTTATTTCCCGCT 58.750 37.500 0.00 0.00 0.00 5.52
281 283 5.554822 TCATGTTACAAGTTATTTCCCGC 57.445 39.130 0.00 0.00 0.00 6.13
282 284 9.663904 CATATTCATGTTACAAGTTATTTCCCG 57.336 33.333 0.00 0.00 0.00 5.14
315 317 7.586390 CCACTGTGGAGGTGGTAACATAGAC 62.586 52.000 22.33 0.00 46.31 2.59
316 318 5.601778 CCACTGTGGAGGTGGTAACATAGA 61.602 50.000 22.33 0.00 46.31 1.98
317 319 3.369471 CCACTGTGGAGGTGGTAACATAG 60.369 52.174 22.33 0.00 46.31 2.23
318 320 2.569853 CCACTGTGGAGGTGGTAACATA 59.430 50.000 22.33 0.00 46.31 2.29
319 321 1.351017 CCACTGTGGAGGTGGTAACAT 59.649 52.381 22.33 0.00 46.31 2.71
320 322 0.762418 CCACTGTGGAGGTGGTAACA 59.238 55.000 22.33 0.00 46.42 2.41
321 323 3.625745 CCACTGTGGAGGTGGTAAC 57.374 57.895 22.33 0.00 46.42 2.50
329 331 7.417911 ACACATATGTTACTATCCACTGTGGAG 60.418 40.741 30.99 21.78 43.22 3.86
330 332 6.382859 ACACATATGTTACTATCCACTGTGGA 59.617 38.462 30.08 30.08 43.85 4.02
331 333 6.582636 ACACATATGTTACTATCCACTGTGG 58.417 40.000 20.86 20.86 34.46 4.17
346 348 4.701171 TGATGCATGACACAACACATATGT 59.299 37.500 2.46 1.41 42.46 2.29
347 349 5.032220 GTGATGCATGACACAACACATATG 58.968 41.667 11.72 0.00 37.05 1.78
348 350 4.945543 AGTGATGCATGACACAACACATAT 59.054 37.500 18.76 0.00 39.18 1.78
349 351 4.325972 AGTGATGCATGACACAACACATA 58.674 39.130 18.76 0.00 39.18 2.29
350 352 3.151554 AGTGATGCATGACACAACACAT 58.848 40.909 18.76 0.00 39.18 3.21
351 353 2.574450 AGTGATGCATGACACAACACA 58.426 42.857 18.76 0.00 39.18 3.72
352 354 3.003585 TGAAGTGATGCATGACACAACAC 59.996 43.478 18.76 11.21 39.18 3.32
353 355 3.212685 TGAAGTGATGCATGACACAACA 58.787 40.909 18.76 13.99 39.18 3.33
354 356 3.902261 TGAAGTGATGCATGACACAAC 57.098 42.857 18.76 11.93 39.18 3.32
355 357 5.456548 AAATGAAGTGATGCATGACACAA 57.543 34.783 18.76 3.33 39.18 3.33
356 358 6.762702 ATAAATGAAGTGATGCATGACACA 57.237 33.333 18.76 16.77 39.18 3.72
357 359 9.177304 CATAATAAATGAAGTGATGCATGACAC 57.823 33.333 18.76 14.04 37.30 3.67
358 360 8.905850 ACATAATAAATGAAGTGATGCATGACA 58.094 29.630 18.76 1.11 0.00 3.58
359 361 9.740239 AACATAATAAATGAAGTGATGCATGAC 57.260 29.630 8.39 8.39 0.00 3.06
360 362 9.738832 CAACATAATAAATGAAGTGATGCATGA 57.261 29.630 2.46 0.00 0.00 3.07
361 363 9.524106 ACAACATAATAAATGAAGTGATGCATG 57.476 29.630 2.46 0.00 0.00 4.06
414 416 9.258629 TGGTAACATAGGTAGTTACTGTAACAT 57.741 33.333 27.12 16.67 46.49 2.71
415 417 8.648698 TGGTAACATAGGTAGTTACTGTAACA 57.351 34.615 27.12 13.79 46.49 2.41
434 436 5.453567 AAGAAAAAGAGGCATGTGGTAAC 57.546 39.130 0.00 0.00 0.00 2.50
435 437 7.775053 ATAAAGAAAAAGAGGCATGTGGTAA 57.225 32.000 0.00 0.00 0.00 2.85
436 438 7.775053 AATAAAGAAAAAGAGGCATGTGGTA 57.225 32.000 0.00 0.00 0.00 3.25
437 439 6.670695 AATAAAGAAAAAGAGGCATGTGGT 57.329 33.333 0.00 0.00 0.00 4.16
438 440 9.657419 AATTAATAAAGAAAAAGAGGCATGTGG 57.343 29.630 0.00 0.00 0.00 4.17
461 463 9.048446 GCAAAATAGATGATGTGGCATTTAATT 57.952 29.630 0.00 0.00 0.00 1.40
462 464 7.658575 GGCAAAATAGATGATGTGGCATTTAAT 59.341 33.333 0.00 0.00 32.18 1.40
463 465 6.985645 GGCAAAATAGATGATGTGGCATTTAA 59.014 34.615 0.00 0.00 32.18 1.52
464 466 6.324512 AGGCAAAATAGATGATGTGGCATTTA 59.675 34.615 0.00 0.00 33.54 1.40
465 467 5.129815 AGGCAAAATAGATGATGTGGCATTT 59.870 36.000 0.00 0.00 33.54 2.32
466 468 4.652421 AGGCAAAATAGATGATGTGGCATT 59.348 37.500 0.00 0.00 33.54 3.56
467 469 4.220724 AGGCAAAATAGATGATGTGGCAT 58.779 39.130 0.00 0.00 33.54 4.40
468 470 3.634504 AGGCAAAATAGATGATGTGGCA 58.365 40.909 0.00 0.00 33.54 4.92
469 471 5.065914 TCTAGGCAAAATAGATGATGTGGC 58.934 41.667 0.00 0.00 32.08 5.01
470 472 8.853077 TTATCTAGGCAAAATAGATGATGTGG 57.147 34.615 5.87 0.00 39.68 4.17
503 505 5.181009 GGTGGGAGTAACATAAGTGGTAAC 58.819 45.833 0.00 0.00 0.00 2.50
504 506 4.081531 CGGTGGGAGTAACATAAGTGGTAA 60.082 45.833 0.00 0.00 0.00 2.85
505 507 3.448301 CGGTGGGAGTAACATAAGTGGTA 59.552 47.826 0.00 0.00 0.00 3.25
506 508 2.235402 CGGTGGGAGTAACATAAGTGGT 59.765 50.000 0.00 0.00 0.00 4.16
507 509 2.235402 ACGGTGGGAGTAACATAAGTGG 59.765 50.000 0.00 0.00 0.00 4.00
508 510 3.259064 CACGGTGGGAGTAACATAAGTG 58.741 50.000 0.00 0.00 0.00 3.16
509 511 2.235402 CCACGGTGGGAGTAACATAAGT 59.765 50.000 19.63 0.00 32.67 2.24
510 512 2.901249 CCACGGTGGGAGTAACATAAG 58.099 52.381 19.63 0.00 32.67 1.73
522 524 1.553706 ACTAAGACTACCCACGGTGG 58.446 55.000 20.41 20.41 40.15 4.61
523 525 2.298163 ACAACTAAGACTACCCACGGTG 59.702 50.000 0.00 0.00 36.19 4.94
524 526 2.601905 ACAACTAAGACTACCCACGGT 58.398 47.619 0.00 0.00 40.16 4.83
525 527 3.672767 AACAACTAAGACTACCCACGG 57.327 47.619 0.00 0.00 0.00 4.94
526 528 6.470235 CGTAATAACAACTAAGACTACCCACG 59.530 42.308 0.00 0.00 0.00 4.94
527 529 7.315890 ACGTAATAACAACTAAGACTACCCAC 58.684 38.462 0.00 0.00 0.00 4.61
528 530 7.466746 ACGTAATAACAACTAAGACTACCCA 57.533 36.000 0.00 0.00 0.00 4.51
529 531 8.028938 TGAACGTAATAACAACTAAGACTACCC 58.971 37.037 0.00 0.00 0.00 3.69
530 532 8.970691 TGAACGTAATAACAACTAAGACTACC 57.029 34.615 0.00 0.00 0.00 3.18
534 536 9.373750 GGTTTTGAACGTAATAACAACTAAGAC 57.626 33.333 0.00 0.00 0.00 3.01
535 537 9.328845 AGGTTTTGAACGTAATAACAACTAAGA 57.671 29.630 0.00 0.00 0.00 2.10
536 538 9.590088 GAGGTTTTGAACGTAATAACAACTAAG 57.410 33.333 0.00 0.00 0.00 2.18
583 586 9.277783 CAGATTATTAAGGGGACATTAGAACAG 57.722 37.037 0.00 0.00 0.00 3.16
653 665 8.526147 AGAATATTATTCATGTTGCCCAATAGC 58.474 33.333 16.68 0.00 0.00 2.97
701 713 5.824097 TGTACTACGTATGAGACCTTGCATA 59.176 40.000 0.00 0.00 0.00 3.14
741 753 8.499162 CCGGATAAAAGAATTCTGCAATAGTAG 58.501 37.037 9.17 0.00 0.00 2.57
775 787 5.107065 GGAATATGCAACGTCATAGGCTAAC 60.107 44.000 0.00 0.00 32.99 2.34
834 846 3.266636 TCAAAGAACGTTTCTCTGCACA 58.733 40.909 0.46 0.00 39.61 4.57
850 862 5.073311 TGTCCTTCGACCTAATCTCAAAG 57.927 43.478 0.00 0.00 38.32 2.77
851 863 5.477607 TTGTCCTTCGACCTAATCTCAAA 57.522 39.130 0.00 0.00 38.32 2.69
891 903 9.665264 AATATTTTCGAAAAGTCTTCAACTGTC 57.335 29.630 25.87 0.00 38.58 3.51
995 1007 4.745649 AGCGTAGTTTACCTTCATGAGAC 58.254 43.478 0.00 0.00 0.00 3.36
1084 1097 3.071892 ACAATTGGAAGGACGAGGTTGTA 59.928 43.478 10.83 0.00 0.00 2.41
1588 3066 1.099295 GGTACCGGGCTAAATGCACC 61.099 60.000 6.32 0.00 43.53 5.01
1848 3326 0.027455 TCGACAACAACTTTGCAGCG 59.973 50.000 0.00 0.00 0.00 5.18
2157 3635 2.091588 GCAGAAATGCTCAAATGCAACG 59.908 45.455 0.00 0.00 46.61 4.10
2552 4031 4.307432 ACTCACAAGAAGTATTGGACACG 58.693 43.478 0.00 0.00 34.36 4.49
2647 4126 9.788960 GTCAAATCATTACCCTTAAAGTCATTC 57.211 33.333 0.00 0.00 0.00 2.67
2810 4562 5.607939 TCTCTTGTGTTCTGTAAGGTTCA 57.392 39.130 0.00 0.00 0.00 3.18
2850 4602 6.013379 GGATGGAGGGAGTACATGATAAATCA 60.013 42.308 0.00 0.00 41.70 2.57
2851 4603 6.410540 GGATGGAGGGAGTACATGATAAATC 58.589 44.000 0.00 0.00 0.00 2.17
2852 4604 5.046304 CGGATGGAGGGAGTACATGATAAAT 60.046 44.000 0.00 0.00 0.00 1.40
2854 4606 3.832490 CGGATGGAGGGAGTACATGATAA 59.168 47.826 0.00 0.00 0.00 1.75
2855 4607 3.431415 CGGATGGAGGGAGTACATGATA 58.569 50.000 0.00 0.00 0.00 2.15
2856 4608 2.251818 CGGATGGAGGGAGTACATGAT 58.748 52.381 0.00 0.00 0.00 2.45
2858 4610 0.681733 CCGGATGGAGGGAGTACATG 59.318 60.000 0.00 0.00 37.49 3.21
2859 4611 0.561184 TCCGGATGGAGGGAGTACAT 59.439 55.000 0.00 0.00 40.17 2.29
2869 4621 3.553828 GGACAAGTATTTCCGGATGGA 57.446 47.619 4.15 0.00 44.61 3.41
2876 4628 3.877508 CCATTCCTCGGACAAGTATTTCC 59.122 47.826 0.00 0.00 0.00 3.13
2877 4629 4.766375 TCCATTCCTCGGACAAGTATTTC 58.234 43.478 0.00 0.00 0.00 2.17
2878 4630 4.837093 TCCATTCCTCGGACAAGTATTT 57.163 40.909 0.00 0.00 0.00 1.40
2879 4631 4.164221 ACATCCATTCCTCGGACAAGTATT 59.836 41.667 0.00 0.00 34.69 1.89
2880 4632 3.711704 ACATCCATTCCTCGGACAAGTAT 59.288 43.478 0.00 0.00 34.69 2.12
2881 4633 3.104512 ACATCCATTCCTCGGACAAGTA 58.895 45.455 0.00 0.00 34.69 2.24
2882 4634 1.909302 ACATCCATTCCTCGGACAAGT 59.091 47.619 0.00 0.00 34.69 3.16
2883 4635 2.698855 ACATCCATTCCTCGGACAAG 57.301 50.000 0.00 0.00 34.69 3.16
2884 4636 3.967326 AGATACATCCATTCCTCGGACAA 59.033 43.478 0.00 0.00 34.69 3.18
2885 4637 3.576861 AGATACATCCATTCCTCGGACA 58.423 45.455 0.00 0.00 34.69 4.02
2886 4638 5.010933 TCTAGATACATCCATTCCTCGGAC 58.989 45.833 0.00 0.00 34.69 4.79
2887 4639 5.256806 TCTAGATACATCCATTCCTCGGA 57.743 43.478 0.00 0.00 36.84 4.55
2888 4640 5.420421 ACATCTAGATACATCCATTCCTCGG 59.580 44.000 4.54 0.00 0.00 4.63
2889 4641 6.522625 ACATCTAGATACATCCATTCCTCG 57.477 41.667 4.54 0.00 0.00 4.63
2941 4693 9.958180 TCCAGAAATACTTGTCATAGAAATTGA 57.042 29.630 0.00 0.00 0.00 2.57
2942 4694 9.994432 GTCCAGAAATACTTGTCATAGAAATTG 57.006 33.333 0.00 0.00 0.00 2.32
2943 4695 8.883731 CGTCCAGAAATACTTGTCATAGAAATT 58.116 33.333 0.00 0.00 0.00 1.82
2944 4696 7.495934 CCGTCCAGAAATACTTGTCATAGAAAT 59.504 37.037 0.00 0.00 0.00 2.17
2945 4697 6.816640 CCGTCCAGAAATACTTGTCATAGAAA 59.183 38.462 0.00 0.00 0.00 2.52
2946 4698 6.153851 TCCGTCCAGAAATACTTGTCATAGAA 59.846 38.462 0.00 0.00 0.00 2.10
2947 4699 5.655090 TCCGTCCAGAAATACTTGTCATAGA 59.345 40.000 0.00 0.00 0.00 1.98
2948 4700 5.902681 TCCGTCCAGAAATACTTGTCATAG 58.097 41.667 0.00 0.00 0.00 2.23
2949 4701 5.163447 CCTCCGTCCAGAAATACTTGTCATA 60.163 44.000 0.00 0.00 0.00 2.15
2950 4702 4.383118 CCTCCGTCCAGAAATACTTGTCAT 60.383 45.833 0.00 0.00 0.00 3.06
2951 4703 3.056107 CCTCCGTCCAGAAATACTTGTCA 60.056 47.826 0.00 0.00 0.00 3.58
2952 4704 3.522553 CCTCCGTCCAGAAATACTTGTC 58.477 50.000 0.00 0.00 0.00 3.18
2953 4705 2.236395 CCCTCCGTCCAGAAATACTTGT 59.764 50.000 0.00 0.00 0.00 3.16
2954 4706 2.500098 TCCCTCCGTCCAGAAATACTTG 59.500 50.000 0.00 0.00 0.00 3.16
2955 4707 2.766828 CTCCCTCCGTCCAGAAATACTT 59.233 50.000 0.00 0.00 0.00 2.24
2956 4708 2.292323 ACTCCCTCCGTCCAGAAATACT 60.292 50.000 0.00 0.00 0.00 2.12
2957 4709 2.108970 ACTCCCTCCGTCCAGAAATAC 58.891 52.381 0.00 0.00 0.00 1.89
2958 4710 2.544844 ACTCCCTCCGTCCAGAAATA 57.455 50.000 0.00 0.00 0.00 1.40
2959 4711 2.108970 GTACTCCCTCCGTCCAGAAAT 58.891 52.381 0.00 0.00 0.00 2.17
2960 4712 1.553706 GTACTCCCTCCGTCCAGAAA 58.446 55.000 0.00 0.00 0.00 2.52
2961 4713 0.679002 CGTACTCCCTCCGTCCAGAA 60.679 60.000 0.00 0.00 0.00 3.02
2962 4714 1.077930 CGTACTCCCTCCGTCCAGA 60.078 63.158 0.00 0.00 0.00 3.86
2963 4715 0.107508 TACGTACTCCCTCCGTCCAG 60.108 60.000 0.00 0.00 36.12 3.86
2964 4716 0.327924 TTACGTACTCCCTCCGTCCA 59.672 55.000 0.00 0.00 36.12 4.02
2965 4717 1.463674 TTTACGTACTCCCTCCGTCC 58.536 55.000 0.00 0.00 36.12 4.79
2966 4718 3.790152 ATTTTACGTACTCCCTCCGTC 57.210 47.619 0.00 0.00 36.12 4.79
2967 4719 3.368739 CCAATTTTACGTACTCCCTCCGT 60.369 47.826 0.00 0.00 38.53 4.69
2968 4720 3.192466 CCAATTTTACGTACTCCCTCCG 58.808 50.000 0.00 0.00 0.00 4.63
2969 4721 2.941064 GCCAATTTTACGTACTCCCTCC 59.059 50.000 0.00 0.00 0.00 4.30
2970 4722 3.870274 AGCCAATTTTACGTACTCCCTC 58.130 45.455 0.00 0.00 0.00 4.30
2971 4723 3.994931 AGCCAATTTTACGTACTCCCT 57.005 42.857 0.00 0.00 0.00 4.20
2972 4724 5.698089 GGTATAGCCAATTTTACGTACTCCC 59.302 44.000 0.00 0.00 37.17 4.30
2973 4725 6.282930 TGGTATAGCCAATTTTACGTACTCC 58.717 40.000 0.00 0.00 45.94 3.85
2996 4748 9.823647 AGTGTAGTTACCTGAAATGATAGATTG 57.176 33.333 0.00 0.00 0.00 2.67
3036 4788 3.963383 AAACTGAATCCACGTGACAAC 57.037 42.857 19.30 6.48 0.00 3.32
3043 4795 7.581476 AGTTGTTGTATTAAACTGAATCCACG 58.419 34.615 0.00 0.00 33.01 4.94
3105 4858 2.228582 CTCGTTGGCATGATGTGGAAAA 59.771 45.455 0.00 0.00 0.00 2.29
3109 4862 1.378882 CCCTCGTTGGCATGATGTGG 61.379 60.000 0.00 0.00 0.00 4.17
3129 4882 5.105228 CCAGTTGTTTTCATGCAGGGATTAT 60.105 40.000 0.00 0.00 0.00 1.28
3180 4933 5.656416 TGGCTAGGGTTGAAAATTTCCATAG 59.344 40.000 9.73 9.73 37.39 2.23
3182 4935 4.424842 TGGCTAGGGTTGAAAATTTCCAT 58.575 39.130 3.00 0.00 0.00 3.41
3184 4937 4.711846 AGATGGCTAGGGTTGAAAATTTCC 59.288 41.667 3.00 0.00 0.00 3.13
3221 4974 2.409948 GCCTCCAGCACTTGATAAGT 57.590 50.000 0.00 0.00 44.06 2.24
3243 4999 1.153147 TTATACCGCGCAATGGGCA 60.153 52.632 21.79 3.12 45.17 5.36
3270 5026 0.249120 TGGGTCTGCTATCCACGTTG 59.751 55.000 0.00 0.00 0.00 4.10
3315 5071 7.192852 ACTACTGAATTTCTGATCCACTCAT 57.807 36.000 9.92 0.00 32.10 2.90
3339 5095 6.041979 TGCTCATCTATGCAACCATACTTCTA 59.958 38.462 0.00 0.00 36.15 2.10
3344 5100 5.243981 AGATGCTCATCTATGCAACCATAC 58.756 41.667 10.42 0.00 45.69 2.39
3345 5101 5.494390 AGATGCTCATCTATGCAACCATA 57.506 39.130 10.42 0.00 45.69 2.74
3399 5155 1.181098 ACAATCACCAGCCAGCAACC 61.181 55.000 0.00 0.00 0.00 3.77
3430 5186 7.478520 ACGTTAGATGGTTGATGCTAATAAC 57.521 36.000 0.00 0.00 0.00 1.89
3441 5197 1.393539 CGAGCCAACGTTAGATGGTTG 59.606 52.381 0.00 0.00 41.78 3.77
3446 5202 0.530744 TCTGCGAGCCAACGTTAGAT 59.469 50.000 0.00 0.00 35.59 1.98
3472 5228 2.225491 TCCTACTTGCGTTGTTGCATTC 59.775 45.455 0.00 0.00 45.78 2.67
3473 5229 2.226330 TCCTACTTGCGTTGTTGCATT 58.774 42.857 0.00 0.00 45.78 3.56
3474 5230 1.890876 TCCTACTTGCGTTGTTGCAT 58.109 45.000 0.00 0.00 45.78 3.96
3475 5231 3.388272 TCCTACTTGCGTTGTTGCA 57.612 47.368 0.00 0.00 44.61 4.08


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

AutoCloner maintained by Alex Coulton.