Multiple sequence alignment - TraesCS6A01G135600

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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 TraesCS6A01G135600 chr6A 100.000 4646 0 0 1 4646 107213458 107218103 0.000000e+00 8580.0
1 TraesCS6A01G135600 chr6A 79.992 2664 486 38 993 3624 107681397 107684045 0.000000e+00 1923.0
2 TraesCS6A01G135600 chr6A 78.971 2701 502 44 995 3649 107243379 107246059 0.000000e+00 1781.0
3 TraesCS6A01G135600 chr6A 80.338 1658 298 22 2010 3649 107270618 107272265 0.000000e+00 1230.0
4 TraesCS6A01G135600 chr6A 79.661 1062 199 12 1063 2114 107269524 107270578 0.000000e+00 749.0
5 TraesCS6A01G135600 chr6B 95.107 3127 139 7 808 3921 171028995 171032120 0.000000e+00 4915.0
6 TraesCS6A01G135600 chr6B 79.867 2548 473 32 993 3511 171700041 171702577 0.000000e+00 1827.0
7 TraesCS6A01G135600 chr6B 79.245 2703 487 48 995 3649 171182709 171185385 0.000000e+00 1816.0
8 TraesCS6A01G135600 chr6B 80.109 1654 301 21 2010 3649 171206070 171207709 0.000000e+00 1206.0
9 TraesCS6A01G135600 chr6B 88.727 754 51 7 3920 4643 171032577 171033326 0.000000e+00 891.0
10 TraesCS6A01G135600 chr6B 80.669 1076 189 14 1000 2064 171204913 171205980 0.000000e+00 817.0
11 TraesCS6A01G135600 chr6B 85.897 78 8 1 3847 3921 171031956 171032033 3.850000e-11 80.5
12 TraesCS6A01G135600 chr6D 94.792 2976 131 11 400 3365 89067859 89070820 0.000000e+00 4615.0
13 TraesCS6A01G135600 chr6D 80.727 2449 437 31 1218 3649 89166897 89169327 0.000000e+00 1875.0
14 TraesCS6A01G135600 chr6D 79.458 1587 308 16 1529 3106 89301360 89302937 0.000000e+00 1109.0
15 TraesCS6A01G135600 chr6D 81.023 606 91 13 3008 3592 89305997 89306599 1.180000e-125 460.0
16 TraesCS6A01G135600 chr6D 90.233 215 18 2 5 217 89067527 89067740 1.270000e-70 278.0
17 TraesCS6A01G135600 chr7A 78.805 1991 372 27 1669 3619 732158018 732156038 0.000000e+00 1293.0
18 TraesCS6A01G135600 chrUn 79.158 1828 355 23 1292 3106 325921085 325919271 0.000000e+00 1242.0
19 TraesCS6A01G135600 chrUn 79.502 1766 344 16 993 2749 335904613 335906369 0.000000e+00 1240.0
20 TraesCS6A01G135600 chrUn 79.502 1766 344 16 993 2749 335907295 335909051 0.000000e+00 1240.0
21 TraesCS6A01G135600 chrUn 79.456 1470 284 16 1289 2749 394420116 394421576 0.000000e+00 1026.0


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 TraesCS6A01G135600 chr6A 107213458 107218103 4645 False 8580.000000 8580 100.000000 1 4646 1 chr6A.!!$F1 4645
1 TraesCS6A01G135600 chr6A 107681397 107684045 2648 False 1923.000000 1923 79.992000 993 3624 1 chr6A.!!$F3 2631
2 TraesCS6A01G135600 chr6A 107243379 107246059 2680 False 1781.000000 1781 78.971000 995 3649 1 chr6A.!!$F2 2654
3 TraesCS6A01G135600 chr6A 107269524 107272265 2741 False 989.500000 1230 79.999500 1063 3649 2 chr6A.!!$F4 2586
4 TraesCS6A01G135600 chr6B 171028995 171033326 4331 False 1962.166667 4915 89.910333 808 4643 3 chr6B.!!$F3 3835
5 TraesCS6A01G135600 chr6B 171700041 171702577 2536 False 1827.000000 1827 79.867000 993 3511 1 chr6B.!!$F2 2518
6 TraesCS6A01G135600 chr6B 171182709 171185385 2676 False 1816.000000 1816 79.245000 995 3649 1 chr6B.!!$F1 2654
7 TraesCS6A01G135600 chr6B 171204913 171207709 2796 False 1011.500000 1206 80.389000 1000 3649 2 chr6B.!!$F4 2649
8 TraesCS6A01G135600 chr6D 89067527 89070820 3293 False 2446.500000 4615 92.512500 5 3365 2 chr6D.!!$F2 3360
9 TraesCS6A01G135600 chr6D 89166897 89169327 2430 False 1875.000000 1875 80.727000 1218 3649 1 chr6D.!!$F1 2431
10 TraesCS6A01G135600 chr6D 89301360 89306599 5239 False 784.500000 1109 80.240500 1529 3592 2 chr6D.!!$F3 2063
11 TraesCS6A01G135600 chr7A 732156038 732158018 1980 True 1293.000000 1293 78.805000 1669 3619 1 chr7A.!!$R1 1950
12 TraesCS6A01G135600 chrUn 325919271 325921085 1814 True 1242.000000 1242 79.158000 1292 3106 1 chrUn.!!$R1 1814
13 TraesCS6A01G135600 chrUn 335904613 335909051 4438 False 1240.000000 1240 79.502000 993 2749 2 chrUn.!!$F2 1756
14 TraesCS6A01G135600 chrUn 394420116 394421576 1460 False 1026.000000 1026 79.456000 1289 2749 1 chrUn.!!$F1 1460


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
899 931 0.034896 CATATACCCCGCCCAGTGAC 59.965 60.000 0.00 0.0 0.00 3.67 F
1086 1130 1.338200 CCGGAAGCAGAAGCACTACTT 60.338 52.381 0.00 0.0 45.49 2.24 F
1215 1262 2.346803 GAGCTCCAACTTCATAACGCA 58.653 47.619 0.87 0.0 0.00 5.24 F
2444 2792 1.168714 GCAGTTCTTAAGGTGGCTGG 58.831 55.000 1.85 0.0 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1825 1872 0.768221 TGAAGCTCCCCAAGTGAGGT 60.768 55.000 0.00 0.0 42.05 3.85 R
2318 2654 2.512515 CTGCAGTAAGCTCGCCCC 60.513 66.667 5.25 0.0 45.94 5.80 R
2461 2827 2.957402 AAGGCAGACAATGGTTCTGA 57.043 45.000 5.21 0.0 33.65 3.27 R
3767 9380 0.036765 TGAGACATGCACCGTTACCC 60.037 55.000 0.00 0.0 0.00 3.69 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
36 37 4.946157 GGATCAGGCTTTGATTCTCTGAAA 59.054 41.667 5.86 0.00 46.51 2.69
42 43 7.066645 TCAGGCTTTGATTCTCTGAAATATGTG 59.933 37.037 0.00 0.00 32.36 3.21
71 72 6.620678 ACAGTTATGTATGTTTCATGGTTGC 58.379 36.000 0.00 0.00 38.09 4.17
102 105 2.989422 TTTTCGAGCTTTGCTTAGGC 57.011 45.000 0.00 0.00 39.88 3.93
105 108 0.528924 TCGAGCTTTGCTTAGGCGTA 59.471 50.000 0.00 0.00 39.88 4.42
119 122 5.766222 CTTAGGCGTATTTGTATAGTCGGT 58.234 41.667 0.00 0.00 0.00 4.69
130 133 3.951680 TGTATAGTCGGTCATGAGCTCAA 59.048 43.478 22.50 1.31 0.00 3.02
132 135 0.969149 AGTCGGTCATGAGCTCAACA 59.031 50.000 22.50 7.23 0.00 3.33
140 143 2.093288 TCATGAGCTCAACACCATCCTC 60.093 50.000 22.50 0.00 0.00 3.71
146 149 1.484240 CTCAACACCATCCTCCTCTCC 59.516 57.143 0.00 0.00 0.00 3.71
164 167 2.045926 GGCAGCCAGACCATCGTT 60.046 61.111 6.55 0.00 0.00 3.85
172 175 2.656002 CCAGACCATCGTTCTCTCCTA 58.344 52.381 0.00 0.00 0.00 2.94
191 194 0.694771 ATGAGGCTGTGACCACATGT 59.305 50.000 3.06 0.00 39.24 3.21
225 250 2.415010 CTGCCGGAGACCTCATCG 59.585 66.667 5.05 0.00 0.00 3.84
232 257 1.330655 GGAGACCTCATCGCCCTCAA 61.331 60.000 0.00 0.00 41.31 3.02
243 271 1.746615 GCCCTCAAGCTGCGATCAA 60.747 57.895 0.00 0.00 0.00 2.57
267 295 0.868186 GAGGATCCTAAGGAGGGGGA 59.132 60.000 16.16 0.00 43.94 4.81
277 305 1.019650 AGGAGGGGGAGTAGATGTGT 58.980 55.000 0.00 0.00 0.00 3.72
278 306 1.366435 AGGAGGGGGAGTAGATGTGTT 59.634 52.381 0.00 0.00 0.00 3.32
279 307 2.197465 GGAGGGGGAGTAGATGTGTTT 58.803 52.381 0.00 0.00 0.00 2.83
280 308 2.092914 GGAGGGGGAGTAGATGTGTTTG 60.093 54.545 0.00 0.00 0.00 2.93
281 309 2.572104 GAGGGGGAGTAGATGTGTTTGT 59.428 50.000 0.00 0.00 0.00 2.83
284 312 4.141018 AGGGGGAGTAGATGTGTTTGTTTT 60.141 41.667 0.00 0.00 0.00 2.43
285 313 4.587262 GGGGGAGTAGATGTGTTTGTTTTT 59.413 41.667 0.00 0.00 0.00 1.94
287 315 5.300792 GGGGAGTAGATGTGTTTGTTTTTCA 59.699 40.000 0.00 0.00 0.00 2.69
288 316 6.015434 GGGGAGTAGATGTGTTTGTTTTTCAT 60.015 38.462 0.00 0.00 0.00 2.57
289 317 7.084486 GGGAGTAGATGTGTTTGTTTTTCATC 58.916 38.462 0.00 0.00 36.25 2.92
290 318 7.084486 GGAGTAGATGTGTTTGTTTTTCATCC 58.916 38.462 0.00 0.00 36.54 3.51
292 320 6.777580 AGTAGATGTGTTTGTTTTTCATCCCT 59.222 34.615 0.00 0.00 36.54 4.20
293 321 6.484364 AGATGTGTTTGTTTTTCATCCCTT 57.516 33.333 0.00 0.00 36.54 3.95
295 323 6.986231 AGATGTGTTTGTTTTTCATCCCTTTC 59.014 34.615 0.00 0.00 36.54 2.62
296 324 6.293004 TGTGTTTGTTTTTCATCCCTTTCT 57.707 33.333 0.00 0.00 0.00 2.52
297 325 6.105333 TGTGTTTGTTTTTCATCCCTTTCTG 58.895 36.000 0.00 0.00 0.00 3.02
299 327 5.115480 GTTTGTTTTTCATCCCTTTCTGCA 58.885 37.500 0.00 0.00 0.00 4.41
300 328 4.589216 TGTTTTTCATCCCTTTCTGCAG 57.411 40.909 7.63 7.63 0.00 4.41
301 329 4.214310 TGTTTTTCATCCCTTTCTGCAGA 58.786 39.130 13.74 13.74 0.00 4.26
302 330 4.834496 TGTTTTTCATCCCTTTCTGCAGAT 59.166 37.500 19.04 0.00 0.00 2.90
303 331 5.305128 TGTTTTTCATCCCTTTCTGCAGATT 59.695 36.000 19.04 0.00 0.00 2.40
304 332 6.183360 TGTTTTTCATCCCTTTCTGCAGATTT 60.183 34.615 19.04 0.00 0.00 2.17
305 333 6.423776 TTTTCATCCCTTTCTGCAGATTTT 57.576 33.333 19.04 0.00 0.00 1.82
308 336 4.219070 TCATCCCTTTCTGCAGATTTTGTG 59.781 41.667 19.04 12.37 0.00 3.33
310 338 3.960102 TCCCTTTCTGCAGATTTTGTGTT 59.040 39.130 19.04 0.00 0.00 3.32
311 339 4.405358 TCCCTTTCTGCAGATTTTGTGTTT 59.595 37.500 19.04 0.00 0.00 2.83
312 340 4.508861 CCCTTTCTGCAGATTTTGTGTTTG 59.491 41.667 19.04 0.00 0.00 2.93
313 341 4.508861 CCTTTCTGCAGATTTTGTGTTTGG 59.491 41.667 19.04 4.25 0.00 3.28
314 342 4.734398 TTCTGCAGATTTTGTGTTTGGT 57.266 36.364 19.04 0.00 0.00 3.67
315 343 4.734398 TCTGCAGATTTTGTGTTTGGTT 57.266 36.364 13.74 0.00 0.00 3.67
316 344 5.083533 TCTGCAGATTTTGTGTTTGGTTT 57.916 34.783 13.74 0.00 0.00 3.27
317 345 5.486526 TCTGCAGATTTTGTGTTTGGTTTT 58.513 33.333 13.74 0.00 0.00 2.43
318 346 5.580297 TCTGCAGATTTTGTGTTTGGTTTTC 59.420 36.000 13.74 0.00 0.00 2.29
319 347 5.240891 TGCAGATTTTGTGTTTGGTTTTCA 58.759 33.333 0.00 0.00 0.00 2.69
320 348 5.702670 TGCAGATTTTGTGTTTGGTTTTCAA 59.297 32.000 0.00 0.00 0.00 2.69
321 349 6.205464 TGCAGATTTTGTGTTTGGTTTTCAAA 59.795 30.769 0.00 0.00 42.50 2.69
322 350 7.080724 GCAGATTTTGTGTTTGGTTTTCAAAA 58.919 30.769 0.00 0.00 45.74 2.44
323 351 7.592903 GCAGATTTTGTGTTTGGTTTTCAAAAA 59.407 29.630 0.00 0.00 45.74 1.94
324 352 9.623350 CAGATTTTGTGTTTGGTTTTCAAAAAT 57.377 25.926 0.00 0.00 45.74 1.82
357 385 6.808008 AGTTAATGGTCAGTTGACAATCTG 57.192 37.500 13.73 9.98 46.47 2.90
358 386 6.533730 AGTTAATGGTCAGTTGACAATCTGA 58.466 36.000 13.73 13.22 46.47 3.27
359 387 6.998074 AGTTAATGGTCAGTTGACAATCTGAA 59.002 34.615 16.81 7.75 46.47 3.02
360 388 5.954296 AATGGTCAGTTGACAATCTGAAG 57.046 39.130 16.81 0.00 46.47 3.02
361 389 3.743521 TGGTCAGTTGACAATCTGAAGG 58.256 45.455 16.81 0.00 46.47 3.46
362 390 3.136443 TGGTCAGTTGACAATCTGAAGGT 59.864 43.478 16.81 0.00 46.47 3.50
363 391 4.137543 GGTCAGTTGACAATCTGAAGGTT 58.862 43.478 16.81 0.00 46.47 3.50
364 392 4.023707 GGTCAGTTGACAATCTGAAGGTTG 60.024 45.833 16.81 1.70 46.47 3.77
365 393 3.565482 TCAGTTGACAATCTGAAGGTTGC 59.435 43.478 14.28 0.00 37.69 4.17
366 394 3.567164 CAGTTGACAATCTGAAGGTTGCT 59.433 43.478 3.18 0.00 34.02 3.91
367 395 4.756642 CAGTTGACAATCTGAAGGTTGCTA 59.243 41.667 3.18 0.00 34.02 3.49
368 396 4.757149 AGTTGACAATCTGAAGGTTGCTAC 59.243 41.667 3.18 4.37 0.00 3.58
369 397 4.350368 TGACAATCTGAAGGTTGCTACA 57.650 40.909 3.18 0.00 0.00 2.74
370 398 4.713553 TGACAATCTGAAGGTTGCTACAA 58.286 39.130 3.18 0.00 0.00 2.41
371 399 4.756642 TGACAATCTGAAGGTTGCTACAAG 59.243 41.667 3.18 0.00 0.00 3.16
372 400 4.973168 ACAATCTGAAGGTTGCTACAAGA 58.027 39.130 3.18 0.00 0.00 3.02
373 401 5.564550 ACAATCTGAAGGTTGCTACAAGAT 58.435 37.500 3.18 0.69 0.00 2.40
374 402 5.413833 ACAATCTGAAGGTTGCTACAAGATG 59.586 40.000 3.18 2.22 0.00 2.90
375 403 3.338249 TCTGAAGGTTGCTACAAGATGC 58.662 45.455 0.00 0.00 0.00 3.91
376 404 2.421424 CTGAAGGTTGCTACAAGATGCC 59.579 50.000 0.00 0.00 0.00 4.40
377 405 1.398390 GAAGGTTGCTACAAGATGCCG 59.602 52.381 0.00 0.00 0.00 5.69
378 406 0.324943 AGGTTGCTACAAGATGCCGT 59.675 50.000 0.00 0.00 0.00 5.68
379 407 0.727398 GGTTGCTACAAGATGCCGTC 59.273 55.000 0.00 0.00 0.00 4.79
380 408 1.438651 GTTGCTACAAGATGCCGTCA 58.561 50.000 0.00 0.00 0.00 4.35
381 409 1.394917 GTTGCTACAAGATGCCGTCAG 59.605 52.381 0.00 0.00 0.00 3.51
382 410 0.608130 TGCTACAAGATGCCGTCAGT 59.392 50.000 0.00 0.00 0.00 3.41
383 411 1.822371 TGCTACAAGATGCCGTCAGTA 59.178 47.619 0.00 0.00 0.00 2.74
384 412 2.159240 TGCTACAAGATGCCGTCAGTAG 60.159 50.000 10.49 10.49 39.11 2.57
385 413 2.799917 GCTACAAGATGCCGTCAGTAGG 60.800 54.545 14.48 2.43 37.79 3.18
386 414 0.537188 ACAAGATGCCGTCAGTAGGG 59.463 55.000 0.00 0.00 0.00 3.53
387 415 0.824109 CAAGATGCCGTCAGTAGGGA 59.176 55.000 0.00 0.00 31.98 4.20
388 416 1.207089 CAAGATGCCGTCAGTAGGGAA 59.793 52.381 0.00 0.00 31.98 3.97
389 417 1.115467 AGATGCCGTCAGTAGGGAAG 58.885 55.000 0.00 0.00 31.98 3.46
390 418 0.530870 GATGCCGTCAGTAGGGAAGC 60.531 60.000 0.00 0.00 31.98 3.86
391 419 2.202756 GCCGTCAGTAGGGAAGCG 60.203 66.667 0.00 0.00 31.98 4.68
392 420 2.707849 GCCGTCAGTAGGGAAGCGA 61.708 63.158 0.00 0.00 31.98 4.93
393 421 1.433879 CCGTCAGTAGGGAAGCGAG 59.566 63.158 0.00 0.00 31.98 5.03
394 422 1.226717 CGTCAGTAGGGAAGCGAGC 60.227 63.158 0.00 0.00 0.00 5.03
395 423 1.890894 GTCAGTAGGGAAGCGAGCA 59.109 57.895 0.00 0.00 0.00 4.26
396 424 0.246635 GTCAGTAGGGAAGCGAGCAA 59.753 55.000 0.00 0.00 0.00 3.91
397 425 0.532573 TCAGTAGGGAAGCGAGCAAG 59.467 55.000 0.00 0.00 0.00 4.01
398 426 1.086634 CAGTAGGGAAGCGAGCAAGC 61.087 60.000 0.00 0.00 37.41 4.01
402 430 2.359230 GGAAGCGAGCAAGCCTGT 60.359 61.111 0.00 0.00 38.01 4.00
415 443 1.080298 GCCTGTTGTTGCATCTGGC 60.080 57.895 10.70 10.70 39.58 4.85
427 455 3.971453 ATCTGGCACGACGCACGAG 62.971 63.158 9.43 2.98 45.17 4.18
430 458 3.764049 GGCACGACGCACGAGTTC 61.764 66.667 9.43 0.00 45.17 3.01
464 492 1.694696 CCCCCTCTAGATACAGTTGGC 59.305 57.143 0.00 0.00 0.00 4.52
466 494 3.438078 CCCCCTCTAGATACAGTTGGCTA 60.438 52.174 0.00 0.00 0.00 3.93
487 515 3.262420 ACCAGTGCTAGTGAAATAAGCG 58.738 45.455 0.00 0.00 39.14 4.68
497 525 7.710907 TGCTAGTGAAATAAGCGTCTGAATTAT 59.289 33.333 0.00 0.00 39.14 1.28
502 530 8.282592 GTGAAATAAGCGTCTGAATTATATGCA 58.717 33.333 0.00 0.00 0.00 3.96
503 531 9.002600 TGAAATAAGCGTCTGAATTATATGCAT 57.997 29.630 3.79 3.79 0.00 3.96
535 563 5.738619 TGATTTAGGTACAGAAGCTCACA 57.261 39.130 0.00 0.00 37.13 3.58
536 564 5.724328 TGATTTAGGTACAGAAGCTCACAG 58.276 41.667 0.00 0.00 37.13 3.66
543 571 1.625315 ACAGAAGCTCACAGCCACATA 59.375 47.619 0.00 0.00 43.77 2.29
544 572 2.038952 ACAGAAGCTCACAGCCACATAA 59.961 45.455 0.00 0.00 43.77 1.90
545 573 3.276857 CAGAAGCTCACAGCCACATAAT 58.723 45.455 0.00 0.00 43.77 1.28
546 574 3.693085 CAGAAGCTCACAGCCACATAATT 59.307 43.478 0.00 0.00 43.77 1.40
617 645 5.690865 TGTAGACTTTTGAAGGTTCCATGT 58.309 37.500 0.00 0.00 0.00 3.21
618 646 5.530915 TGTAGACTTTTGAAGGTTCCATGTG 59.469 40.000 0.00 0.00 0.00 3.21
661 693 2.414994 AGACATGGACTGGCTGATTG 57.585 50.000 0.00 0.00 43.63 2.67
663 695 0.994247 ACATGGACTGGCTGATTGGA 59.006 50.000 0.00 0.00 0.00 3.53
666 698 1.817099 GGACTGGCTGATTGGAGCG 60.817 63.158 0.00 0.00 40.13 5.03
669 701 0.957395 ACTGGCTGATTGGAGCGTTG 60.957 55.000 0.00 0.00 40.13 4.10
675 707 2.154462 CTGATTGGAGCGTTGGACTTT 58.846 47.619 0.00 0.00 0.00 2.66
680 712 1.202710 TGGAGCGTTGGACTTTAGCAA 60.203 47.619 0.00 0.00 0.00 3.91
681 713 2.084546 GGAGCGTTGGACTTTAGCAAT 58.915 47.619 0.00 0.00 0.00 3.56
769 801 2.161855 CAGCCATGACTTTACCTGCAA 58.838 47.619 0.00 0.00 0.00 4.08
773 805 3.428045 GCCATGACTTTACCTGCAATCAC 60.428 47.826 0.00 0.00 0.00 3.06
774 806 3.758023 CCATGACTTTACCTGCAATCACA 59.242 43.478 0.00 0.00 0.00 3.58
775 807 4.379813 CCATGACTTTACCTGCAATCACAC 60.380 45.833 0.00 0.00 0.00 3.82
776 808 3.146066 TGACTTTACCTGCAATCACACC 58.854 45.455 0.00 0.00 0.00 4.16
777 809 2.488153 GACTTTACCTGCAATCACACCC 59.512 50.000 0.00 0.00 0.00 4.61
778 810 1.818674 CTTTACCTGCAATCACACCCC 59.181 52.381 0.00 0.00 0.00 4.95
779 811 1.072266 TTACCTGCAATCACACCCCT 58.928 50.000 0.00 0.00 0.00 4.79
854 886 7.410174 AGGTTTGATATTTTCCTCACATGGTA 58.590 34.615 0.00 0.00 0.00 3.25
896 928 0.763035 GAACATATACCCCGCCCAGT 59.237 55.000 0.00 0.00 0.00 4.00
899 931 0.034896 CATATACCCCGCCCAGTGAC 59.965 60.000 0.00 0.00 0.00 3.67
907 939 2.280797 GCCCAGTGACTGCGACAA 60.281 61.111 7.16 0.00 0.00 3.18
909 941 2.310233 CCCAGTGACTGCGACAACG 61.310 63.158 7.16 0.00 42.93 4.10
925 957 6.274001 CGACAACGCTGAAATATATTCACT 57.726 37.500 0.00 0.00 0.00 3.41
931 963 8.798153 CAACGCTGAAATATATTCACTTTTTCC 58.202 33.333 0.00 0.00 0.00 3.13
933 965 7.122055 ACGCTGAAATATATTCACTTTTTCCCA 59.878 33.333 0.00 0.00 0.00 4.37
991 1035 3.765511 AGGCAATGCATACAACATTCTGT 59.234 39.130 7.79 0.00 35.58 3.41
1086 1130 1.338200 CCGGAAGCAGAAGCACTACTT 60.338 52.381 0.00 0.00 45.49 2.24
1162 1209 4.318332 CAACTCTACATGCTCTTGGTTCA 58.682 43.478 0.00 0.00 0.00 3.18
1215 1262 2.346803 GAGCTCCAACTTCATAACGCA 58.653 47.619 0.87 0.00 0.00 5.24
1405 1452 5.420409 CCTACCAACTTAGTAAGCTTCCAG 58.580 45.833 0.00 0.00 0.00 3.86
1636 1683 3.875369 GCCTGAGATGGTTCCAAGATTGT 60.875 47.826 0.00 0.00 0.00 2.71
1677 1724 3.922171 AGTGGATTCTCTGGTTCCATC 57.078 47.619 0.00 0.00 41.37 3.51
1773 1820 2.918712 AGGAGCTTGGGATGATAACG 57.081 50.000 0.00 0.00 0.00 3.18
1785 1832 5.546110 TGGGATGATAACGGGATTGAGAATA 59.454 40.000 0.00 0.00 0.00 1.75
1791 1838 6.700081 TGATAACGGGATTGAGAATACTTTCG 59.300 38.462 0.00 0.00 36.93 3.46
1882 1929 6.922957 GCTTAACATTGGAAACACTGATTTGA 59.077 34.615 0.00 0.00 43.19 2.69
1889 1936 9.350357 CATTGGAAACACTGATTTGATTTCTAG 57.650 33.333 0.00 0.00 43.19 2.43
2318 2654 3.087031 ACATCAGCTTCAACCATCTTGG 58.913 45.455 0.00 0.00 45.02 3.61
2329 2665 1.526887 CATCTTGGGGGCGAGCTTA 59.473 57.895 0.00 0.00 0.00 3.09
2341 2677 1.485838 CGAGCTTACTGCAGCCATCG 61.486 60.000 15.27 12.80 45.94 3.84
2364 2700 4.439776 GCGTTGTTGGTAAATCTTGTTGTC 59.560 41.667 0.00 0.00 0.00 3.18
2444 2792 1.168714 GCAGTTCTTAAGGTGGCTGG 58.831 55.000 1.85 0.00 0.00 4.85
2461 2827 2.943199 GCTGGGAATAGCAGCTTCTTGT 60.943 50.000 0.00 0.00 43.17 3.16
2783 3152 2.421388 CGTGGATAGGGGAAAGCAATCA 60.421 50.000 0.00 0.00 0.00 2.57
2909 4364 1.784358 TTCGTAGGGACCATACCAGG 58.216 55.000 10.62 0.00 0.00 4.45
3382 8976 6.372937 TGATCCGTCAATTTATAGCAACAACA 59.627 34.615 0.00 0.00 0.00 3.33
3433 9045 9.173021 ACATTTCATGTAAAAATGACTCGGATA 57.827 29.630 19.64 0.00 43.60 2.59
3440 9052 5.388599 AAAAATGACTCGGATAGGGGAAT 57.611 39.130 0.00 0.00 0.00 3.01
3498 9110 1.800805 ACTCAGTGATTGCTGGAACG 58.199 50.000 0.00 0.00 37.12 3.95
3573 9185 4.553323 GATGTGCTTTCTTGAGTTGCATT 58.447 39.130 0.00 0.00 36.04 3.56
3679 9291 9.301153 AGTTGACTTGACATATTTTGTTTCAAC 57.699 29.630 0.00 0.00 40.28 3.18
3687 9299 7.433719 TGACATATTTTGTTTCAACGTTCAAGG 59.566 33.333 0.00 0.00 39.18 3.61
3719 9331 4.878439 CATGTATTGGCATGGGATTTCTG 58.122 43.478 0.00 0.00 41.70 3.02
3726 9338 2.694628 GGCATGGGATTTCTGTTATGCA 59.305 45.455 0.00 0.00 41.84 3.96
3727 9339 3.243636 GGCATGGGATTTCTGTTATGCAG 60.244 47.826 0.00 0.00 46.34 4.41
3767 9380 7.907214 AGTTTGTTATACAGCTTTAGTCAGG 57.093 36.000 0.00 0.00 0.00 3.86
3773 9386 3.697619 ACAGCTTTAGTCAGGGGTAAC 57.302 47.619 0.00 0.00 0.00 2.50
3797 9410 4.261741 GGTGCATGTCTCACTCATGTTTTT 60.262 41.667 0.00 0.00 42.94 1.94
3824 9437 7.849804 AAGCGTCTGTTGTAATAAATCTCAT 57.150 32.000 0.00 0.00 0.00 2.90
3875 9488 3.084039 CAGTGGTAATGGTGCATGTCTT 58.916 45.455 0.00 0.00 0.00 3.01
3904 9517 6.164408 TGTTTTCATATGCGTCTGTTGTAG 57.836 37.500 0.00 0.00 0.00 2.74
3973 10044 5.634859 GCTGTAAGTTGCTAAAAATGTGCAT 59.365 36.000 0.00 0.00 36.55 3.96
3992 10063 4.858140 TGCATCATTTTTGTTAGCATCGTG 59.142 37.500 0.00 0.00 0.00 4.35
3996 10067 7.220683 GCATCATTTTTGTTAGCATCGTGTTAT 59.779 33.333 0.00 0.00 0.00 1.89
4012 10083 7.079182 TCGTGTTATGGTTATTTGTGGATTC 57.921 36.000 0.00 0.00 0.00 2.52
4021 10092 3.575965 ATTTGTGGATTCGGAAAGTGC 57.424 42.857 0.00 0.00 0.00 4.40
4062 10133 6.697019 GCAACAGTGTTGTTTTCATTCACTAT 59.303 34.615 31.12 0.00 45.01 2.12
4063 10134 7.306167 GCAACAGTGTTGTTTTCATTCACTATG 60.306 37.037 31.12 6.57 45.01 2.23
4064 10135 7.566760 ACAGTGTTGTTTTCATTCACTATGA 57.433 32.000 0.00 0.00 40.44 2.15
4065 10136 7.642669 ACAGTGTTGTTTTCATTCACTATGAG 58.357 34.615 0.00 0.00 38.23 2.90
4085 10156 2.560105 AGGAGTCAAAAGAATGCAAGGC 59.440 45.455 0.00 0.00 0.00 4.35
4101 10172 4.141937 TGCAAGGCTAAGGTGAGTACTATG 60.142 45.833 0.00 0.00 0.00 2.23
4180 10251 0.901124 GCCTCACTGACTGGAGATGT 59.099 55.000 0.00 0.00 32.87 3.06
4224 10295 2.040544 CCGCTGTTGTCATCACCCC 61.041 63.158 0.00 0.00 0.00 4.95
4227 10298 0.539438 GCTGTTGTCATCACCCCCAA 60.539 55.000 0.00 0.00 0.00 4.12
4230 10301 1.303236 TTGTCATCACCCCCAAGCG 60.303 57.895 0.00 0.00 0.00 4.68
4231 10302 2.063015 TTGTCATCACCCCCAAGCGT 62.063 55.000 0.00 0.00 0.00 5.07
4258 10329 1.212935 GGTAGACACCATGAGGCCATT 59.787 52.381 5.01 0.00 45.04 3.16
4304 10375 8.080417 CACAATCCCATGCTTATAGATGAAAAG 58.920 37.037 0.00 0.00 0.00 2.27
4321 10392 5.819991 TGAAAAGTCCAGAAGGCAGATTAT 58.180 37.500 0.00 0.00 33.74 1.28
4322 10393 6.248433 TGAAAAGTCCAGAAGGCAGATTATT 58.752 36.000 0.00 0.00 33.74 1.40
4335 10406 9.727627 GAAGGCAGATTATTTTCATACAGAAAG 57.272 33.333 0.00 0.00 46.24 2.62
4348 10419 8.574251 TTCATACAGAAAGGCTAAGCAAAATA 57.426 30.769 0.00 0.00 32.05 1.40
4352 10423 6.624423 ACAGAAAGGCTAAGCAAAATACATG 58.376 36.000 0.00 0.00 0.00 3.21
4359 10430 8.940397 AGGCTAAGCAAAATACATGGTAATAT 57.060 30.769 0.00 0.00 0.00 1.28
4360 10431 9.367160 AGGCTAAGCAAAATACATGGTAATATT 57.633 29.630 0.00 0.00 0.00 1.28
4361 10432 9.981114 GGCTAAGCAAAATACATGGTAATATTT 57.019 29.630 0.00 0.00 33.40 1.40
4403 10476 2.919228 ACATCGGCCTTAAATCTCCAC 58.081 47.619 0.00 0.00 0.00 4.02
4404 10477 2.222027 CATCGGCCTTAAATCTCCACC 58.778 52.381 0.00 0.00 0.00 4.61
4406 10479 0.254747 CGGCCTTAAATCTCCACCCA 59.745 55.000 0.00 0.00 0.00 4.51
4407 10480 1.133792 CGGCCTTAAATCTCCACCCAT 60.134 52.381 0.00 0.00 0.00 4.00
4408 10481 2.310538 GGCCTTAAATCTCCACCCATG 58.689 52.381 0.00 0.00 0.00 3.66
4427 10508 2.653726 TGGTCTGTTGTTCATGCAAGT 58.346 42.857 0.00 0.00 0.00 3.16
4477 10578 6.349197 CCCATATTATGTGACGCAATATGCAA 60.349 38.462 17.02 0.00 45.36 4.08
4480 10581 9.131416 CATATTATGTGACGCAATATGCAAATT 57.869 29.630 12.85 0.00 45.36 1.82
4488 10589 4.805192 ACGCAATATGCAAATTCATGGTTC 59.195 37.500 2.99 0.00 45.36 3.62
4502 10603 8.837099 AATTCATGGTTCCTAATTACATCCAA 57.163 30.769 0.00 0.00 0.00 3.53
4529 10630 1.338337 ACGGGATACTCAAGCATCGAG 59.662 52.381 0.00 0.00 36.53 4.04
4531 10632 2.605823 CGGGATACTCAAGCATCGAGTC 60.606 54.545 6.03 0.00 42.69 3.36
4533 10634 3.006323 GGGATACTCAAGCATCGAGTCAT 59.994 47.826 6.03 0.81 42.69 3.06
4539 10640 5.482908 ACTCAAGCATCGAGTCATTAACTT 58.517 37.500 0.00 0.00 39.56 2.66
4544 10645 4.872691 AGCATCGAGTCATTAACTTCTTGG 59.127 41.667 0.00 0.00 38.74 3.61
4565 10666 3.118542 GGGCAAACTATAGTACCGAACG 58.881 50.000 5.65 0.00 0.00 3.95
4601 10702 4.026744 CAGTTCTCAGGTCTCCATTCCTA 58.973 47.826 0.00 0.00 32.26 2.94
4628 10729 4.969484 ACCTAAGTGAAAAGGTCGTCAAT 58.031 39.130 0.00 0.00 42.60 2.57
4637 10738 3.915437 AAGGTCGTCAATCGCAAAAAT 57.085 38.095 0.00 0.00 39.67 1.82
4643 10744 4.841841 GTCGTCAATCGCAAAAATCGTTTA 59.158 37.500 0.00 0.00 39.67 2.01
4644 10745 5.506832 GTCGTCAATCGCAAAAATCGTTTAT 59.493 36.000 0.00 0.00 39.67 1.40
4645 10746 5.506485 TCGTCAATCGCAAAAATCGTTTATG 59.494 36.000 0.00 0.00 39.67 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.374058 AGCCTGATCCAAATTACGTTTCG 59.626 43.478 0.00 0.00 0.00 3.46
1 2 4.965119 AGCCTGATCCAAATTACGTTTC 57.035 40.909 0.00 0.00 0.00 2.78
3 4 4.764823 TCAAAGCCTGATCCAAATTACGTT 59.235 37.500 0.00 0.00 0.00 3.99
5 6 4.963276 TCAAAGCCTGATCCAAATTACG 57.037 40.909 0.00 0.00 0.00 3.18
6 7 7.067981 AGAGAATCAAAGCCTGATCCAAATTAC 59.932 37.037 0.00 0.00 44.43 1.89
7 8 7.067859 CAGAGAATCAAAGCCTGATCCAAATTA 59.932 37.037 0.00 0.00 44.43 1.40
8 9 5.956563 AGAGAATCAAAGCCTGATCCAAATT 59.043 36.000 0.00 0.00 44.43 1.82
9 10 5.360144 CAGAGAATCAAAGCCTGATCCAAAT 59.640 40.000 0.00 0.00 44.43 2.32
10 11 4.703575 CAGAGAATCAAAGCCTGATCCAAA 59.296 41.667 0.00 0.00 44.43 3.28
14 15 6.696441 ATTTCAGAGAATCAAAGCCTGATC 57.304 37.500 0.00 0.00 44.43 2.92
16 17 7.066645 CACATATTTCAGAGAATCAAAGCCTGA 59.933 37.037 0.00 0.00 37.82 3.86
42 43 9.162764 ACCATGAAACATACATAACTGTAACTC 57.837 33.333 0.00 0.00 41.09 3.01
96 99 5.766222 ACCGACTATACAAATACGCCTAAG 58.234 41.667 0.00 0.00 0.00 2.18
102 105 5.342525 GCTCATGACCGACTATACAAATACG 59.657 44.000 0.00 0.00 0.00 3.06
105 108 5.069119 TGAGCTCATGACCGACTATACAAAT 59.931 40.000 13.74 0.00 0.00 2.32
119 122 1.911357 AGGATGGTGTTGAGCTCATGA 59.089 47.619 19.04 3.95 0.00 3.07
130 133 1.381872 CCGGAGAGGAGGATGGTGT 60.382 63.158 0.00 0.00 45.00 4.16
132 135 2.444895 GCCGGAGAGGAGGATGGT 60.445 66.667 5.05 0.00 45.00 3.55
140 143 4.154347 GTCTGGCTGCCGGAGAGG 62.154 72.222 29.84 7.72 39.90 3.69
146 149 3.958147 AACGATGGTCTGGCTGCCG 62.958 63.158 14.98 9.13 0.00 5.69
164 167 2.660572 GTCACAGCCTCATAGGAGAGA 58.339 52.381 5.84 0.00 44.26 3.10
172 175 0.694771 ACATGTGGTCACAGCCTCAT 59.305 50.000 9.72 0.00 45.48 2.90
201 204 3.834799 GTCTCCGGCAGGGGTACG 61.835 72.222 1.56 0.00 39.67 3.67
217 220 1.992277 AGCTTGAGGGCGATGAGGT 60.992 57.895 0.00 0.00 37.29 3.85
225 250 1.712977 CTTGATCGCAGCTTGAGGGC 61.713 60.000 0.00 0.00 0.00 5.19
243 271 2.668144 CTCCTTAGGATCCTCCGACT 57.332 55.000 20.22 0.00 42.75 4.18
256 284 2.590611 ACACATCTACTCCCCCTCCTTA 59.409 50.000 0.00 0.00 0.00 2.69
257 285 1.366435 ACACATCTACTCCCCCTCCTT 59.634 52.381 0.00 0.00 0.00 3.36
267 295 6.777580 AGGGATGAAAAACAAACACATCTACT 59.222 34.615 0.00 0.00 37.87 2.57
277 305 5.128499 TCTGCAGAAAGGGATGAAAAACAAA 59.872 36.000 15.67 0.00 0.00 2.83
278 306 4.648762 TCTGCAGAAAGGGATGAAAAACAA 59.351 37.500 15.67 0.00 0.00 2.83
279 307 4.214310 TCTGCAGAAAGGGATGAAAAACA 58.786 39.130 15.67 0.00 0.00 2.83
280 308 4.853924 TCTGCAGAAAGGGATGAAAAAC 57.146 40.909 15.67 0.00 0.00 2.43
281 309 6.423776 AAATCTGCAGAAAGGGATGAAAAA 57.576 33.333 22.50 0.00 0.00 1.94
284 312 4.834496 ACAAAATCTGCAGAAAGGGATGAA 59.166 37.500 22.50 0.00 0.00 2.57
285 313 4.219070 CACAAAATCTGCAGAAAGGGATGA 59.781 41.667 22.50 0.00 0.00 2.92
287 315 4.154942 ACACAAAATCTGCAGAAAGGGAT 58.845 39.130 22.50 0.00 0.00 3.85
288 316 3.565307 ACACAAAATCTGCAGAAAGGGA 58.435 40.909 22.50 0.00 0.00 4.20
289 317 4.326504 AACACAAAATCTGCAGAAAGGG 57.673 40.909 22.50 13.99 0.00 3.95
290 318 4.508861 CCAAACACAAAATCTGCAGAAAGG 59.491 41.667 22.50 12.97 0.00 3.11
292 320 5.083533 ACCAAACACAAAATCTGCAGAAA 57.916 34.783 22.50 0.00 0.00 2.52
293 321 4.734398 ACCAAACACAAAATCTGCAGAA 57.266 36.364 22.50 4.23 0.00 3.02
295 323 5.350914 TGAAAACCAAACACAAAATCTGCAG 59.649 36.000 7.63 7.63 0.00 4.41
296 324 5.240891 TGAAAACCAAACACAAAATCTGCA 58.759 33.333 0.00 0.00 0.00 4.41
297 325 5.793026 TGAAAACCAAACACAAAATCTGC 57.207 34.783 0.00 0.00 0.00 4.26
331 359 8.950210 CAGATTGTCAACTGACCATTAACTTAT 58.050 33.333 7.37 0.00 44.15 1.73
332 360 8.154203 TCAGATTGTCAACTGACCATTAACTTA 58.846 33.333 7.37 0.00 44.15 2.24
333 361 6.998074 TCAGATTGTCAACTGACCATTAACTT 59.002 34.615 7.37 0.00 44.15 2.66
334 362 6.533730 TCAGATTGTCAACTGACCATTAACT 58.466 36.000 7.37 0.00 44.15 2.24
335 363 6.801539 TCAGATTGTCAACTGACCATTAAC 57.198 37.500 7.37 0.00 44.15 2.01
336 364 6.430925 CCTTCAGATTGTCAACTGACCATTAA 59.569 38.462 13.88 0.00 44.15 1.40
337 365 5.939883 CCTTCAGATTGTCAACTGACCATTA 59.060 40.000 13.88 3.46 44.15 1.90
338 366 4.763793 CCTTCAGATTGTCAACTGACCATT 59.236 41.667 13.88 0.00 44.15 3.16
339 367 4.202503 ACCTTCAGATTGTCAACTGACCAT 60.203 41.667 13.88 1.88 44.15 3.55
340 368 3.136443 ACCTTCAGATTGTCAACTGACCA 59.864 43.478 13.88 0.00 44.15 4.02
341 369 3.744660 ACCTTCAGATTGTCAACTGACC 58.255 45.455 13.88 0.00 44.15 4.02
342 370 4.555511 GCAACCTTCAGATTGTCAACTGAC 60.556 45.833 13.88 2.78 41.82 3.51
343 371 3.565482 GCAACCTTCAGATTGTCAACTGA 59.435 43.478 11.49 11.49 40.66 3.41
344 372 3.567164 AGCAACCTTCAGATTGTCAACTG 59.433 43.478 8.17 8.17 35.72 3.16
345 373 3.825328 AGCAACCTTCAGATTGTCAACT 58.175 40.909 0.00 0.00 0.00 3.16
346 374 4.515191 TGTAGCAACCTTCAGATTGTCAAC 59.485 41.667 0.00 0.00 0.00 3.18
347 375 4.713553 TGTAGCAACCTTCAGATTGTCAA 58.286 39.130 0.00 0.00 0.00 3.18
348 376 4.350368 TGTAGCAACCTTCAGATTGTCA 57.650 40.909 0.00 0.00 0.00 3.58
349 377 4.997395 TCTTGTAGCAACCTTCAGATTGTC 59.003 41.667 0.00 0.00 0.00 3.18
350 378 4.973168 TCTTGTAGCAACCTTCAGATTGT 58.027 39.130 0.00 0.00 0.00 2.71
351 379 5.675575 GCATCTTGTAGCAACCTTCAGATTG 60.676 44.000 0.00 0.00 0.00 2.67
352 380 4.397417 GCATCTTGTAGCAACCTTCAGATT 59.603 41.667 0.00 0.00 0.00 2.40
353 381 3.944015 GCATCTTGTAGCAACCTTCAGAT 59.056 43.478 0.00 0.00 0.00 2.90
354 382 3.338249 GCATCTTGTAGCAACCTTCAGA 58.662 45.455 0.00 0.00 0.00 3.27
355 383 2.421424 GGCATCTTGTAGCAACCTTCAG 59.579 50.000 0.00 0.00 0.00 3.02
356 384 2.436417 GGCATCTTGTAGCAACCTTCA 58.564 47.619 0.00 0.00 0.00 3.02
357 385 1.398390 CGGCATCTTGTAGCAACCTTC 59.602 52.381 0.00 0.00 0.00 3.46
358 386 1.271379 ACGGCATCTTGTAGCAACCTT 60.271 47.619 0.00 0.00 0.00 3.50
359 387 0.324943 ACGGCATCTTGTAGCAACCT 59.675 50.000 0.00 0.00 0.00 3.50
360 388 0.727398 GACGGCATCTTGTAGCAACC 59.273 55.000 0.00 0.00 0.00 3.77
361 389 1.394917 CTGACGGCATCTTGTAGCAAC 59.605 52.381 0.00 0.00 0.00 4.17
362 390 1.001974 ACTGACGGCATCTTGTAGCAA 59.998 47.619 0.00 0.00 0.00 3.91
363 391 0.608130 ACTGACGGCATCTTGTAGCA 59.392 50.000 0.00 0.00 0.00 3.49
364 392 2.464865 CTACTGACGGCATCTTGTAGC 58.535 52.381 0.00 0.00 32.50 3.58
365 393 2.223829 CCCTACTGACGGCATCTTGTAG 60.224 54.545 8.14 8.14 36.10 2.74
366 394 1.754803 CCCTACTGACGGCATCTTGTA 59.245 52.381 0.00 0.00 0.00 2.41
367 395 0.537188 CCCTACTGACGGCATCTTGT 59.463 55.000 0.00 0.00 0.00 3.16
368 396 0.824109 TCCCTACTGACGGCATCTTG 59.176 55.000 0.00 0.00 0.00 3.02
369 397 1.482593 CTTCCCTACTGACGGCATCTT 59.517 52.381 0.00 0.00 0.00 2.40
370 398 1.115467 CTTCCCTACTGACGGCATCT 58.885 55.000 0.00 0.00 0.00 2.90
371 399 0.530870 GCTTCCCTACTGACGGCATC 60.531 60.000 0.00 0.00 0.00 3.91
372 400 1.522569 GCTTCCCTACTGACGGCAT 59.477 57.895 0.00 0.00 0.00 4.40
373 401 2.978824 GCTTCCCTACTGACGGCA 59.021 61.111 0.00 0.00 0.00 5.69
374 402 2.202756 CGCTTCCCTACTGACGGC 60.203 66.667 0.00 0.00 0.00 5.68
375 403 1.433879 CTCGCTTCCCTACTGACGG 59.566 63.158 0.00 0.00 0.00 4.79
376 404 1.226717 GCTCGCTTCCCTACTGACG 60.227 63.158 0.00 0.00 0.00 4.35
377 405 0.246635 TTGCTCGCTTCCCTACTGAC 59.753 55.000 0.00 0.00 0.00 3.51
378 406 0.532573 CTTGCTCGCTTCCCTACTGA 59.467 55.000 0.00 0.00 0.00 3.41
379 407 1.086634 GCTTGCTCGCTTCCCTACTG 61.087 60.000 0.00 0.00 0.00 2.74
380 408 1.219393 GCTTGCTCGCTTCCCTACT 59.781 57.895 0.00 0.00 0.00 2.57
381 409 1.815840 GGCTTGCTCGCTTCCCTAC 60.816 63.158 0.00 0.00 0.00 3.18
382 410 1.990060 AGGCTTGCTCGCTTCCCTA 60.990 57.895 0.00 0.00 0.00 3.53
383 411 3.325753 AGGCTTGCTCGCTTCCCT 61.326 61.111 0.00 0.00 0.00 4.20
384 412 3.130160 CAGGCTTGCTCGCTTCCC 61.130 66.667 0.00 0.00 0.00 3.97
385 413 1.968540 AACAGGCTTGCTCGCTTCC 60.969 57.895 0.00 0.00 0.00 3.46
386 414 1.208614 CAACAGGCTTGCTCGCTTC 59.791 57.895 0.00 0.00 0.00 3.86
387 415 1.103398 AACAACAGGCTTGCTCGCTT 61.103 50.000 0.00 0.00 0.00 4.68
388 416 1.526917 AACAACAGGCTTGCTCGCT 60.527 52.632 0.00 0.00 0.00 4.93
389 417 1.370900 CAACAACAGGCTTGCTCGC 60.371 57.895 0.00 0.00 0.00 5.03
390 418 1.370900 GCAACAACAGGCTTGCTCG 60.371 57.895 0.00 0.00 39.79 5.03
391 419 0.316204 ATGCAACAACAGGCTTGCTC 59.684 50.000 9.32 0.00 42.77 4.26
392 420 0.316204 GATGCAACAACAGGCTTGCT 59.684 50.000 9.32 0.00 42.77 3.91
393 421 0.316204 AGATGCAACAACAGGCTTGC 59.684 50.000 0.00 1.19 42.67 4.01
394 422 1.336517 CCAGATGCAACAACAGGCTTG 60.337 52.381 0.00 0.00 0.00 4.01
395 423 0.963962 CCAGATGCAACAACAGGCTT 59.036 50.000 0.00 0.00 0.00 4.35
396 424 1.530013 GCCAGATGCAACAACAGGCT 61.530 55.000 10.85 0.00 40.77 4.58
397 425 1.080298 GCCAGATGCAACAACAGGC 60.080 57.895 0.00 0.00 40.77 4.85
427 455 2.681344 GGGGGATGACAAATACACGAAC 59.319 50.000 0.00 0.00 0.00 3.95
430 458 2.170607 AGAGGGGGATGACAAATACACG 59.829 50.000 0.00 0.00 0.00 4.49
433 461 6.497259 TGTATCTAGAGGGGGATGACAAATAC 59.503 42.308 0.00 0.00 0.00 1.89
440 468 4.483950 CAACTGTATCTAGAGGGGGATGA 58.516 47.826 0.00 0.00 0.00 2.92
464 492 4.504461 CGCTTATTTCACTAGCACTGGTAG 59.496 45.833 12.79 12.79 39.25 3.18
466 494 3.262420 CGCTTATTTCACTAGCACTGGT 58.738 45.455 0.00 0.00 34.62 4.00
535 563 4.081406 TCAGTTCAAGCAATTATGTGGCT 58.919 39.130 0.00 0.00 40.14 4.75
536 564 4.439305 TCAGTTCAAGCAATTATGTGGC 57.561 40.909 0.00 0.00 0.00 5.01
543 571 5.596836 TCTTTGGTTCAGTTCAAGCAATT 57.403 34.783 0.00 0.00 41.95 2.32
544 572 5.510179 CCATCTTTGGTTCAGTTCAAGCAAT 60.510 40.000 0.00 0.00 41.95 3.56
545 573 4.202141 CCATCTTTGGTTCAGTTCAAGCAA 60.202 41.667 0.00 0.00 40.98 3.91
546 574 3.318839 CCATCTTTGGTTCAGTTCAAGCA 59.681 43.478 0.00 0.00 38.30 3.91
587 615 7.391833 GGAACCTTCAAAAGTCTACAATGAGAT 59.608 37.037 0.00 0.00 0.00 2.75
589 617 6.486657 TGGAACCTTCAAAAGTCTACAATGAG 59.513 38.462 0.00 0.00 0.00 2.90
595 623 5.048713 CCACATGGAACCTTCAAAAGTCTAC 60.049 44.000 0.00 0.00 37.39 2.59
606 634 0.482446 TCTTGCCCACATGGAACCTT 59.518 50.000 0.00 0.00 37.39 3.50
617 645 1.642112 TGAATGCCAATTCTTGCCCA 58.358 45.000 0.63 0.00 42.40 5.36
618 646 2.766345 TTGAATGCCAATTCTTGCCC 57.234 45.000 0.63 0.00 42.40 5.36
661 693 1.519408 TTGCTAAAGTCCAACGCTCC 58.481 50.000 0.00 0.00 0.00 4.70
663 695 1.200020 GCATTGCTAAAGTCCAACGCT 59.800 47.619 0.16 0.00 28.60 5.07
666 698 2.229784 AGCTGCATTGCTAAAGTCCAAC 59.770 45.455 10.49 0.00 42.10 3.77
669 701 1.133790 CCAGCTGCATTGCTAAAGTCC 59.866 52.381 8.66 0.00 41.98 3.85
675 707 1.597797 GCCAACCAGCTGCATTGCTA 61.598 55.000 18.72 0.00 41.98 3.49
680 712 1.117142 ACAAAGCCAACCAGCTGCAT 61.117 50.000 8.66 0.00 44.11 3.96
681 713 1.757731 ACAAAGCCAACCAGCTGCA 60.758 52.632 8.66 0.00 44.11 4.41
733 765 1.471327 GGCTGATGACTGAGACTGCTC 60.471 57.143 0.00 0.00 41.67 4.26
751 783 2.754552 TGATTGCAGGTAAAGTCATGGC 59.245 45.455 0.00 0.00 0.00 4.40
777 809 0.106519 CCAATTCCTAGCCCCACAGG 60.107 60.000 0.00 0.00 39.47 4.00
778 810 0.106519 CCCAATTCCTAGCCCCACAG 60.107 60.000 0.00 0.00 0.00 3.66
779 811 0.551377 TCCCAATTCCTAGCCCCACA 60.551 55.000 0.00 0.00 0.00 4.17
854 886 8.314021 GTTCATAAAGAAATCAGATTTGGGGTT 58.686 33.333 13.38 4.59 38.13 4.11
869 901 5.310451 GGCGGGGTATATGTTCATAAAGAA 58.690 41.667 0.00 0.00 0.00 2.52
907 939 7.122055 TGGGAAAAAGTGAATATATTTCAGCGT 59.878 33.333 0.00 0.00 32.91 5.07
925 957 9.548631 TGGACCAAAGTTATTATATGGGAAAAA 57.451 29.630 0.00 0.00 35.44 1.94
931 963 7.014134 TGCACATGGACCAAAGTTATTATATGG 59.986 37.037 0.00 0.00 37.19 2.74
933 965 7.255590 GCTGCACATGGACCAAAGTTATTATAT 60.256 37.037 0.00 0.00 0.00 0.86
941 973 0.178981 AGCTGCACATGGACCAAAGT 60.179 50.000 0.00 0.00 0.00 2.66
947 986 2.393271 AGAAGTAGCTGCACATGGAC 57.607 50.000 4.12 0.00 0.00 4.02
950 989 3.064545 GCCTTTAGAAGTAGCTGCACATG 59.935 47.826 4.12 0.00 0.00 3.21
1162 1209 2.046892 GGCATCACAGGTGACGCT 60.047 61.111 18.32 0.00 46.67 5.07
1179 1226 1.876714 CTCGGTAACATGTCCGGCG 60.877 63.158 21.82 12.05 45.79 6.46
1215 1262 0.107654 GAAGCGTACCATGGAGCCTT 60.108 55.000 21.47 14.28 0.00 4.35
1405 1452 6.817765 TCCCAAATCTAACTCAACAATCAC 57.182 37.500 0.00 0.00 0.00 3.06
1636 1683 8.010697 TCCACTAGAGGATAAATTCAGATACCA 58.989 37.037 4.58 0.00 31.23 3.25
1658 1705 2.422093 GGGATGGAACCAGAGAATCCAC 60.422 54.545 11.10 0.42 45.47 4.02
1677 1724 1.515020 CCTTGAGAGTGAGCGAGGG 59.485 63.158 0.00 0.00 32.92 4.30
1752 1799 3.071023 CCGTTATCATCCCAAGCTCCTTA 59.929 47.826 0.00 0.00 0.00 2.69
1773 1820 4.192317 ACAGCGAAAGTATTCTCAATCCC 58.808 43.478 0.00 0.00 33.17 3.85
1785 1832 3.308866 GTGAGTTGTTGTACAGCGAAAGT 59.691 43.478 0.59 0.00 34.34 2.66
1791 1838 2.943033 ACCAAGTGAGTTGTTGTACAGC 59.057 45.455 2.25 2.25 33.87 4.40
1825 1872 0.768221 TGAAGCTCCCCAAGTGAGGT 60.768 55.000 0.00 0.00 42.05 3.85
1882 1929 1.409427 CTCGGGCGGAAGACTAGAAAT 59.591 52.381 0.00 0.00 40.87 2.17
1889 1936 4.821589 CCAGCTCGGGCGGAAGAC 62.822 72.222 9.70 0.00 44.37 3.01
2318 2654 2.512515 CTGCAGTAAGCTCGCCCC 60.513 66.667 5.25 0.00 45.94 5.80
2329 2665 3.425713 CAACGCGATGGCTGCAGT 61.426 61.111 15.93 0.00 36.88 4.40
2341 2677 4.356289 ACAACAAGATTTACCAACAACGC 58.644 39.130 0.00 0.00 0.00 4.84
2444 2792 3.866651 TCTGACAAGAAGCTGCTATTCC 58.133 45.455 0.90 0.00 0.00 3.01
2461 2827 2.957402 AAGGCAGACAATGGTTCTGA 57.043 45.000 5.21 0.00 33.65 3.27
2783 3152 3.896888 CAGTCTAAGGATCCTCAGCAGAT 59.103 47.826 16.52 0.00 0.00 2.90
2909 4364 9.206870 TCATTGAAGGAAAATATGCAAAACTTC 57.793 29.630 0.00 0.00 35.05 3.01
3382 8976 1.004044 CAGAGAGCCACAAAGTCCCAT 59.996 52.381 0.00 0.00 0.00 4.00
3426 9020 2.047061 TGTTCCATTCCCCTATCCGAG 58.953 52.381 0.00 0.00 0.00 4.63
3433 9045 3.075882 TCTTCATGTTGTTCCATTCCCCT 59.924 43.478 0.00 0.00 0.00 4.79
3440 9052 6.329496 GTTTCAAGTTCTTCATGTTGTTCCA 58.671 36.000 0.00 0.00 0.00 3.53
3498 9110 4.771903 ACCATAACCACAAACCAAAAACC 58.228 39.130 0.00 0.00 0.00 3.27
3573 9185 1.693062 ACCTTTTGTTGCATGGCATCA 59.307 42.857 0.00 0.00 38.76 3.07
3670 9282 3.057174 ACTTGCCTTGAACGTTGAAACAA 60.057 39.130 5.00 10.24 0.00 2.83
3751 9364 4.142004 CGTTACCCCTGACTAAAGCTGTAT 60.142 45.833 0.00 0.00 0.00 2.29
3754 9367 2.618053 CGTTACCCCTGACTAAAGCTG 58.382 52.381 0.00 0.00 0.00 4.24
3761 9374 1.198759 ATGCACCGTTACCCCTGACT 61.199 55.000 0.00 0.00 0.00 3.41
3767 9380 0.036765 TGAGACATGCACCGTTACCC 60.037 55.000 0.00 0.00 0.00 3.69
3773 9386 1.004595 CATGAGTGAGACATGCACCG 58.995 55.000 0.00 0.00 38.58 4.94
3797 9410 7.815549 TGAGATTTATTACAACAGACGCTTACA 59.184 33.333 0.00 0.00 0.00 2.41
3837 9450 2.421424 CACTGACCAAAGCAGAATAGGC 59.579 50.000 0.00 0.00 36.86 3.93
3844 9457 2.489329 CCATTACCACTGACCAAAGCAG 59.511 50.000 0.00 0.00 39.26 4.24
3854 9467 2.715046 AGACATGCACCATTACCACTG 58.285 47.619 0.00 0.00 0.00 3.66
3875 9488 5.353956 ACAGACGCATATGAAAACATAAGCA 59.646 36.000 6.97 0.00 33.01 3.91
3879 9492 6.735678 ACAACAGACGCATATGAAAACATA 57.264 33.333 6.97 0.00 0.00 2.29
3886 9499 5.774498 AGATCTACAACAGACGCATATGA 57.226 39.130 6.97 0.00 35.62 2.15
3887 9500 9.626045 TTATAAGATCTACAACAGACGCATATG 57.374 33.333 0.00 0.00 35.62 1.78
3926 9997 5.811100 GCCAAGTCTGTCCACTATAACTTAC 59.189 44.000 0.00 0.00 0.00 2.34
3933 10004 2.260822 ACAGCCAAGTCTGTCCACTAT 58.739 47.619 0.00 0.00 43.28 2.12
3973 10044 7.026562 CCATAACACGATGCTAACAAAAATGA 58.973 34.615 0.00 0.00 0.00 2.57
3992 10063 6.687081 TCCGAATCCACAAATAACCATAAC 57.313 37.500 0.00 0.00 0.00 1.89
3996 10067 5.048364 CACTTTCCGAATCCACAAATAACCA 60.048 40.000 0.00 0.00 0.00 3.67
4037 10108 4.864247 AGTGAATGAAAACAACACTGTTGC 59.136 37.500 19.86 6.15 45.25 4.17
4062 10133 3.822735 CCTTGCATTCTTTTGACTCCTCA 59.177 43.478 0.00 0.00 0.00 3.86
4063 10134 3.366781 GCCTTGCATTCTTTTGACTCCTC 60.367 47.826 0.00 0.00 0.00 3.71
4064 10135 2.560105 GCCTTGCATTCTTTTGACTCCT 59.440 45.455 0.00 0.00 0.00 3.69
4065 10136 2.560105 AGCCTTGCATTCTTTTGACTCC 59.440 45.455 0.00 0.00 0.00 3.85
4085 10156 5.972382 GCGAAGTTCATAGTACTCACCTTAG 59.028 44.000 0.00 0.00 0.00 2.18
4101 10172 3.308530 CCAATCTTTTGGTGCGAAGTTC 58.691 45.455 0.00 0.00 46.27 3.01
4169 10240 0.107945 GCCCTCACACATCTCCAGTC 60.108 60.000 0.00 0.00 0.00 3.51
4180 10251 4.007644 CGAGCACCTGCCCTCACA 62.008 66.667 0.00 0.00 43.38 3.58
4206 10277 2.040544 GGGGTGATGACAACAGCGG 61.041 63.158 8.56 0.00 35.07 5.52
4224 10295 0.669318 TCTACCGCTCAAACGCTTGG 60.669 55.000 0.00 0.00 33.01 3.61
4227 10298 0.666577 GTGTCTACCGCTCAAACGCT 60.667 55.000 0.00 0.00 0.00 5.07
4258 10329 1.342819 GCACATGTTTGTTGCCCCTTA 59.657 47.619 0.00 0.00 32.34 2.69
4304 10375 6.705863 ATGAAAATAATCTGCCTTCTGGAC 57.294 37.500 0.00 0.00 34.57 4.02
4321 10392 6.892658 TTGCTTAGCCTTTCTGTATGAAAA 57.107 33.333 0.29 0.00 43.25 2.29
4322 10393 6.892658 TTTGCTTAGCCTTTCTGTATGAAA 57.107 33.333 0.29 0.00 41.85 2.69
4335 10406 9.981114 AAATATTACCATGTATTTTGCTTAGCC 57.019 29.630 0.29 0.00 28.78 3.93
4366 10439 6.145696 GGCCGATGTTATTTATGTAGTCACTC 59.854 42.308 0.00 0.00 0.00 3.51
4368 10441 5.989777 AGGCCGATGTTATTTATGTAGTCAC 59.010 40.000 0.00 0.00 0.00 3.67
4388 10461 2.310538 CATGGGTGGAGATTTAAGGCC 58.689 52.381 0.00 0.00 0.00 5.19
4403 10476 1.203052 GCATGAACAACAGACCATGGG 59.797 52.381 18.09 0.00 37.46 4.00
4404 10477 1.887854 TGCATGAACAACAGACCATGG 59.112 47.619 11.19 11.19 37.46 3.66
4406 10479 3.005050 CACTTGCATGAACAACAGACCAT 59.995 43.478 6.60 0.00 0.00 3.55
4407 10480 2.358582 CACTTGCATGAACAACAGACCA 59.641 45.455 6.60 0.00 0.00 4.02
4408 10481 2.618241 TCACTTGCATGAACAACAGACC 59.382 45.455 6.60 0.00 0.00 3.85
4409 10482 3.969117 TCACTTGCATGAACAACAGAC 57.031 42.857 6.60 0.00 0.00 3.51
4477 10578 8.837099 TTGGATGTAATTAGGAACCATGAATT 57.163 30.769 0.00 0.00 0.00 2.17
4480 10581 8.694540 CATTTTGGATGTAATTAGGAACCATGA 58.305 33.333 0.00 0.00 0.00 3.07
4488 10589 5.280945 CGTGGCATTTTGGATGTAATTAGG 58.719 41.667 0.00 0.00 0.00 2.69
4502 10603 2.643551 CTTGAGTATCCCGTGGCATTT 58.356 47.619 0.00 0.00 0.00 2.32
4529 10630 4.280929 AGTTTGCCCCAAGAAGTTAATGAC 59.719 41.667 0.00 0.00 0.00 3.06
4531 10632 4.871933 AGTTTGCCCCAAGAAGTTAATG 57.128 40.909 0.00 0.00 0.00 1.90
4533 10634 6.786122 ACTATAGTTTGCCCCAAGAAGTTAA 58.214 36.000 0.00 0.00 0.00 2.01
4539 10640 3.133362 CGGTACTATAGTTTGCCCCAAGA 59.867 47.826 11.40 0.00 0.00 3.02
4544 10645 3.118542 CGTTCGGTACTATAGTTTGCCC 58.881 50.000 11.40 5.71 0.00 5.36
4584 10685 5.186797 GGTATGATAGGAATGGAGACCTGAG 59.813 48.000 0.00 0.00 37.68 3.35
4601 10702 6.070995 TGACGACCTTTTCACTTAGGTATGAT 60.071 38.462 0.00 0.00 44.65 2.45



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

AutoCloner maintained by Alex Coulton.